Citrus Sinensis ID: 022768

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290--
Protein Sequence
MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE
Secondary Structure (PSIPRED)
ccHHHHHHccccccccccEEEEEEcccccccccccccHHHHHHHHHHHHcccccHHHHHHcccccccEEEEEcccccHHHHHHHHHHHHcccEEEEEEHHHHHHHHHccHHHHHHHHHHHHHHccccEEEEEccccccccccccccccHHHHHHHHHHHHHHcccccccccEEEEEEccccccccccccccccccEEEccccccHHHHHHHHHHHHccccccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHccccccHHcHHHcccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHccccccHHHHEEEEEccccccHcHcccHHHHHHHHHHHHccccccHHHHHHHccccccEEEEEcccccHHHHHHHHHHHHccccEEEEEcHHHHHHHHcHHHHHHHHHHHHHHHccccEEEEEcHHHHccccccccccccHHHHHHHHHHHHHHccccccccEEEEEEccccccccHHHcccccccEEEEEccccHHHHHHHHHHHHccccccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHcccccHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MTTLTIMralprevdpvvynmlhedpgnvsysavgGLSDQIRELRESielplmnpelflrvgikppkgvllygppgtgkTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGyardhqpciifMDEIDaiggrrfsegtsaDREIQRTLMELLNQLDGFDQLGKVKMImatnrpdvldpallrpgrldrkieiplpneqSRMEILKIHAAGIAKHGEIDYEAVVKLAEgfngadlrNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKklessahynadfgke
Flexible Loop (DISEMBL)
mttltimralprevDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMatnrpdvldpallrpgrldrkieiplpneqsRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNeakklessahynadfgke
Low Complexity Region (SEG)
MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE
Disordered region (IsUnstruct)
*****IMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG***DREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPL*****RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR*********************
Disordered Region (DISOPRED)
*TTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIG***************RTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKL********SAHYNADFG**
Disordered Region (DISEMBL)
MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE
Disordered Region (DISPRO)
*TTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRF***TSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFG**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	292	2.2.26 [Sep-21-2011]
Q9MAK9	399	26S protease regulatory s	yes	no	1.0	0.731	0.962	1e-165
Q9SEI3	399	26S protease regulatory s	yes	no	1.0	0.731	0.962	1e-165
O17071	406	Probable 26S protease reg	yes	no	0.976	0.701	0.828	1e-141
P62335	389	26S protease regulatory s	N/A	no	0.979	0.735	0.832	1e-140
P62334	389	26S protease regulatory s	yes	no	0.979	0.735	0.832	1e-140
P62333	389	26S protease regulatory s	yes	no	0.979	0.735	0.832	1e-140
Q2KIW6	389	26S protease regulatory s	yes	no	0.979	0.735	0.828	1e-139
Q54PJ1	393	26S protease regulatory s	yes	no	0.955	0.709	0.820	1e-136
O74445	388	Probable 26S protease sub	yes	no	0.979	0.737	0.779	1e-132
P53549	437	26S protease subunit RPT4	yes	no	0.979	0.654	0.706	1e-121

>sp|Q9MAK9|PS10B_ARATH 26S protease regulatory subunit S10B homolog B OS=Arabidopsis thaliana GN=RPT4B PE=2 SV=1

 Score =  582 bits (1500), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 281/292 (96%), Positives = 288/292 (98%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGN+SYSAVGGL DQIRELRESIELPLMNPELFLR
Sbjct: 108 MTTLTIMRALPREVDPVVYNMLHEDPGNISYSAVGGLGDQIRELRESIELPLMNPELFLR 167

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMF Y
Sbjct: 168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFNY 227

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           AR+HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 228 AREHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 287

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHA+GIAKHGEIDYEA+VKL EGFNGA
Sbjct: 288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHASGIAKHGEIDYEAIVKLGEGFNGA 347

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRN+CTEAGM AIRAERDYVIHEDFMKAVRKL+EAKKLESS+HYNADFGKE
Sbjct: 348 DLRNICTEAGMFAIRAERDYVIHEDFMKAVRKLSEAKKLESSSHYNADFGKE 399

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.
Arabidopsis thaliana (taxid: 3702)

>sp|Q9SEI3|PS10A_ARATH 26S protease regulatory subunit 10B homolog A OS=Arabidopsis thaliana GN=RPT4A PE=2 SV=1

 Score =  582 bits (1500), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 281/292 (96%), Positives = 288/292 (98%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGN+SYSAVGGL DQIRELRESIELPLMNPELFLR
Sbjct: 108 MTTLTIMRALPREVDPVVYNMLHEDPGNISYSAVGGLGDQIRELRESIELPLMNPELFLR 167

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMF Y
Sbjct: 168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFNY 227

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           AR+HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD LGKVKMIMATNR
Sbjct: 228 AREHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDNLGKVKMIMATNR 287

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRM+ILKIHAAGIAKHGEIDYEA+VKLAEGFNGA
Sbjct: 288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMDILKIHAAGIAKHGEIDYEAIVKLAEGFNGA 347

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRN+CTEAGM AIRAERDYVIHEDFMKAVRKL+EAKKLESS+HYNADFGKE
Sbjct: 348 DLRNICTEAGMFAIRAERDYVIHEDFMKAVRKLSEAKKLESSSHYNADFGKE 399

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Arabidopsis thaliana (taxid: 3702)

>sp|O17071|PRS10_CAEEL Probable 26S protease regulatory subunit 10B OS=Caenorhabditis elegans GN=rpt-4 PE=1 SV=2

 Score =  499 bits (1286), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 236/285 (82%), Positives = 261/285 (91%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMR LPREVDP+VY M HEDPGN+SYS VGGL++QIRELRE +ELPL+NPELF R
Sbjct: 119 MTTLTIMRQLPREVDPLVYKMSHEDPGNISYSDVGGLAEQIRELREVVELPLINPELFKR 178

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGI PPKG LL+GPPGTGKTLLARA+AS +D NFLKVVSSAI+DKYIGESAR+IREMF Y
Sbjct: 179 VGITPPKGCLLFGPPGTGKTLLARAVASQLDCNFLKVVSSAIVDKYIGESARMIREMFNY 238

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCI+FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD LGKVK+IMATNR
Sbjct: 239 ARDHQPCIVFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDSLGKVKVIMATNR 298

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRKIEI LPNEQSR+EILKIH+  I KHGEID+EAVVKL++GF+ A
Sbjct: 299 PDTLDPALLRPGRLDRKIEIGLPNEQSRLEILKIHSNKITKHGEIDFEAVVKLSDGFSAA 358

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
           DLRNVCTEAGM AIRAER++VI EDFMKAVRK+ +AK+LE+   Y
Sbjct: 359 DLRNVCTEAGMFAIRAEREFVIDEDFMKAVRKVGDAKRLETKLDY 403

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Caenorhabditis elegans (taxid: 6239)

>sp|P62335|PRS10_SPETR 26S protease regulatory subunit 10B OS=Spermophilus tridecemlineatus GN=PSMC6 PE=2 SV=1

 Score =  499 bits (1284), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 238/286 (83%), Positives = 259/286 (90%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct: 102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct: 162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct: 222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct: 282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y 
Sbjct: 342 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYK 387

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Spermophilus tridecemlineatus (taxid: 43179)

>sp|P62334|PRS10_MOUSE 26S protease regulatory subunit 10B OS=Mus musculus GN=Psmc6 PE=1 SV=1

 Score =  499 bits (1284), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 238/286 (83%), Positives = 259/286 (90%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct: 102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct: 162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct: 222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct: 282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y 
Sbjct: 342 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYK 387

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Mus musculus (taxid: 10090)

>sp|P62333|PRS10_HUMAN 26S protease regulatory subunit 10B OS=Homo sapiens GN=PSMC6 PE=1 SV=1

 Score =  499 bits (1284), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 238/286 (83%), Positives = 259/286 (90%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct: 102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct: 162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct: 222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct: 282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y 
Sbjct: 342 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYK 387

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Homo sapiens (taxid: 9606)

>sp|Q2KIW6|PRS10_BOVIN 26S protease regulatory subunit 10B OS=Bos taurus GN=PSMC6 PE=2 SV=1

 Score =  495 bits (1274), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 237/286 (82%), Positives = 258/286 (90%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct: 102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct: 162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct: 222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct: 282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           DL NVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y 
Sbjct: 342 DLGNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDYK 387

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Bos taurus (taxid: 9913)

>sp|Q54PJ1|PRS10_DICDI 26S protease regulatory subunit 10B OS=Dictyostelium discoideum GN=psmC6 PE=1 SV=1

 Score =  484 bits (1247), Expect = e-136,   Method: Compositional matrix adjust.
 Identities = 229/279 (82%), Positives = 253/279 (90%)

Query: 8   RALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPK 67
           + LPREVDP+++NM  E PG+VSY  +GGLS+QIRELRE +ELPLM PELF+RVGIK PK
Sbjct: 113 KILPREVDPIIFNMTAESPGSVSYGEIGGLSNQIRELREVVELPLMIPELFIRVGIKAPK 172

Query: 68  GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPC 127
           GVLLYGPPGTGKTLLARAIASN++ANFLKVVSSAI+DKYIGESAR+IREMFGYARDHQPC
Sbjct: 173 GVLLYGPPGTGKTLLARAIASNLEANFLKVVSSAIVDKYIGESARVIREMFGYARDHQPC 232

Query: 128 IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPA 187
           +IFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L KVK+IMATNRPDVLDPA
Sbjct: 233 VIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLSKVKIIMATNRPDVLDPA 292

Query: 188 LLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCT 247
           LLRPGRLDRKIEIPLPNE  R+++LKIHAA I KHG++DYEA+ KLA+GFN ADLRNVCT
Sbjct: 293 LLRPGRLDRKIEIPLPNEAGRVDVLKIHAANITKHGDVDYEAIAKLADGFNAADLRNVCT 352

Query: 248 EAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           EAGM AIRAERDYV+ EDFMKAVRK  EAKKLE    Y 
Sbjct: 353 EAGMFAIRAERDYVMEEDFMKAVRKCQEAKKLEGKLDYQ 391

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Dictyostelium discoideum (taxid: 44689)

>sp|O74445|PRS10_SCHPO Probable 26S protease subunit rpt4 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpt4 PE=3 SV=2

 Score =  469 bits (1208), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 223/286 (77%), Positives = 252/286 (88%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMR LPREVDP+VYNM  EDPG++S++ VGGL++QIRELRE IELPL NPELFLR
Sbjct: 101 MTTLTIMRILPREVDPLVYNMSIEDPGDISFAGVGGLNEQIRELREVIELPLKNPELFLR 160

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARA+A+++  NFLKVVSSAI+DKYIGESAR+IREMFGY
Sbjct: 161 VGIKPPKGVLLYGPPGTGKTLLARAVAASLGVNFLKVVSSAIVDKYIGESARIIREMFGY 220

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           A++H+PC+IFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD LG+ K+IMATNR
Sbjct: 221 AKEHEPCVIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDYLGQTKIIMATNR 280

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRKIEIPLPNE  RMEILKIH   ++K GEIDYEA+VKL +G NGA
Sbjct: 281 PDTLDPALLRPGRLDRKIEIPLPNEVGRMEILKIHLEKVSKQGEIDYEALVKLTDGTNGA 340

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           DLRNV TEAG  AI+ +RDYVI  D M A RK+ + KKLE +  Y 
Sbjct: 341 DLRNVVTEAGFIAIKEDRDYVIQSDLMSAARKVADLKKLEGTIDYQ 386

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P53549|PRS10_YEAST 26S protease subunit RPT4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPT4 PE=1 SV=4

 Score =  435 bits (1118), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 202/286 (70%), Positives = 240/286 (83%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           +TTLTIMR LPRE DP+VYNM   + G +++  +GGL++QIRELRE IELPL NPE+F R
Sbjct: 150 ITTLTIMRILPRETDPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQR 209

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLA+A+A+ I ANF+   +S I+DKYIGESAR+IREMF Y
Sbjct: 210 VGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREMFAY 269

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           A++H+PCIIFMDE+DAIGGRRFSEGTSADREIQRTLMELL Q+DGFD LG+ K+IMATNR
Sbjct: 270 AKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNR 329

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRK+EIPLPNE  R+EI KIH A + K GE D+EA VK+++GFNGA
Sbjct: 330 PDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGA 389

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           D+RN  TEAG  AIR +RD++  +D MKAVRK+ E KKLE +  Y 
Sbjct: 390 DIRNCATEAGFFAIRDDRDHINPDDLMKAVRKVAEVKKLEGTIEYQ 435

The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	292
255538750	399	26S protease regulatory subunit S10b, pu	1.0	0.731	1.0	1e-169
118486132	399	unknown [Populus trichocarpa]	1.0	0.731	0.993	1e-168
225458173	398	PREDICTED: 26S protease regulatory subun	1.0	0.733	0.996	1e-168
225428386	399	PREDICTED: 26S protease regulatory subun	1.0	0.731	0.989	1e-168
224105337	392	predicted protein [Populus trichocarpa]	1.0	0.744	0.993	1e-168
255538752	399	26S protease regulatory subunit S10b, pu	1.0	0.731	0.993	1e-168
224080385	399	predicted protein [Populus trichocarpa]	1.0	0.731	0.993	1e-168
224085722	402	predicted protein [Populus trichocarpa]	1.0	0.726	0.993	1e-168
356564312	833	PREDICTED: proteasome-activating nucleot	1.0	0.350	0.979	1e-168
449469943	398	PREDICTED: 26S protease regulatory subun	1.0	0.733	0.993	1e-168

>gi|255538750|ref|XP_002510440.1| 26S protease regulatory subunit S10b, putative [Ricinus communis] gi|223551141|gb|EEF52627.1| 26S protease regulatory subunit S10b, putative [Ricinus communis]

 Score =  600 bits (1547), Expect = e-169,   Method: Compositional matrix adjust.
 Identities = 292/292 (100%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 108 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 167

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 227

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 228 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 287

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA
Sbjct: 288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 347

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE
Sbjct: 348 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 399

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118486132|gb|ABK94909.1| unknown [Populus trichocarpa]

 Score =  597 bits (1540), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 290/292 (99%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 108 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 167

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 227

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 228 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 287

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG+IDYEAVVKLAEGFNGA
Sbjct: 288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGDIDYEAVVKLAEGFNGA 347

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 348 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 399

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458173|ref|XP_002281107.1| PREDICTED: 26S protease regulatory subunit S10B homolog B [Vitis vinifera] gi|147800891|emb|CAN75568.1| hypothetical protein VITISV_010255 [Vitis vinifera] gi|302142551|emb|CBI19754.3| unnamed protein product [Vitis vinifera]

 Score =  597 bits (1539), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 291/292 (99%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 107 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 166

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 167 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 226

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 227 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 286

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA
Sbjct: 287 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 346

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 347 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 398

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225428386|ref|XP_002283544.1| PREDICTED: 26S protease regulatory subunit S10B homolog B isoform 1 [Vitis vinifera] gi|297744432|emb|CBI37694.3| unnamed protein product [Vitis vinifera]

 Score =  597 bits (1538), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 289/292 (98%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSY+AVGGLSDQIRELRESIELPLMNPELF+R
Sbjct: 108 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYAAVGGLSDQIRELRESIELPLMNPELFIR 167

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 227

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 228 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 287

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA
Sbjct: 288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 347

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 348 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 399

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224105337|ref|XP_002313775.1| predicted protein [Populus trichocarpa] gi|222850183|gb|EEE87730.1| predicted protein [Populus trichocarpa]

 Score =  597 bits (1538), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 290/292 (99%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 101 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 160

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 161 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 220

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 221 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 280

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG+IDYEAVVKLAEGFNGA
Sbjct: 281 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGDIDYEAVVKLAEGFNGA 340

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 341 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 392

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255538752|ref|XP_002510441.1| 26S protease regulatory subunit S10b, putative [Ricinus communis] gi|223551142|gb|EEF52628.1| 26S protease regulatory subunit S10b, putative [Ricinus communis]

 Score =  597 bits (1538), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 290/292 (99%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 108 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 167

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 227

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 228 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 287

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG+IDYEAVVKLAEGFNGA
Sbjct: 288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGDIDYEAVVKLAEGFNGA 347

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 348 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 399

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224080385|ref|XP_002306121.1| predicted protein [Populus trichocarpa] gi|222849085|gb|EEE86632.1| predicted protein [Populus trichocarpa]

 Score =  596 bits (1537), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 290/292 (99%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 108 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 167

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 227

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 228 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 287

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG+IDYEAVVKLAEGFNGA
Sbjct: 288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGDIDYEAVVKLAEGFNGA 347

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 348 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 399

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224085722|ref|XP_002307679.1| predicted protein [Populus trichocarpa] gi|222857128|gb|EEE94675.1| predicted protein [Populus trichocarpa]

 Score =  596 bits (1536), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 290/292 (99%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 111 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 170

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 171 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 230

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 231 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 290

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG+IDYEAVVKLAEGFNGA
Sbjct: 291 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGDIDYEAVVKLAEGFNGA 350

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 351 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 402

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356564312|ref|XP_003550399.1| PREDICTED: proteasome-activating nucleotidase-like [Glycine max]

 Score =  595 bits (1535), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 286/292 (97%), Positives = 292/292 (100%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGN+SYSAVGGLSDQIRELRESIELPLMNPELF+R
Sbjct: 542 MTTLTIMRALPREVDPVVYNMLHEDPGNISYSAVGGLSDQIRELRESIELPLMNPELFIR 601

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 602 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 661

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 662 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 721

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA
Sbjct: 722 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 781

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGM+AIRAERDYVIHEDFMKAVRKLN+AKKLESSAHY+ADFGK+
Sbjct: 782 DLRNVCTEAGMAAIRAERDYVIHEDFMKAVRKLNDAKKLESSAHYSADFGKD 833

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449469943|ref|XP_004152678.1| PREDICTED: 26S protease regulatory subunit S10B homolog B-like [Cucumis sativus] gi|449515750|ref|XP_004164911.1| PREDICTED: 26S protease regulatory subunit S10B homolog B-like [Cucumis sativus]

 Score =  595 bits (1533), Expect = e-168,   Method: Compositional matrix adjust.
 Identities = 290/292 (99%), Positives = 291/292 (99%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct: 107 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 166

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY
Sbjct: 167 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 226

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct: 227 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 286

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PDVLDPALLRPGRLDRKIEIPLPNEQSR EILKIHAAGIAKHGEIDYEAVVKLAEGFNGA
Sbjct: 287 PDVLDPALLRPGRLDRKIEIPLPNEQSRTEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 346

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
           DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK+
Sbjct: 347 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKD 398

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	292
UNIPROTKB|Q9FXT8	400	OsRPT4 "Os02g0199900 protein"	1.0	0.73	0.969	1.4e-149
TAIR|locus:2028200	399	AT1G45000 [Arabidopsis thalian	1.0	0.731	0.962	4.3e-148
TAIR|locus:2159996	399	RPT4A "regulatory particle tri	1.0	0.731	0.962	5.5e-148
FB|FBgn0028685	397	Rpt4 "Regulatory particle trip	0.976	0.717	0.859	1.5e-129
UNIPROTKB|F1MLV1	389	PSMC6 "26S protease regulatory	0.976	0.732	0.835	6.1e-126
UNIPROTKB|J9P1N0	395	PSMC6 "Uncharacterized protein	0.976	0.721	0.835	6.1e-126
UNIPROTKB|P62333	389	PSMC6 "26S protease regulatory	0.976	0.732	0.835	6.1e-126
UNIPROTKB|F1SFE6	403	PSMC6 "Uncharacterized protein	0.976	0.707	0.835	6.1e-126
UNIPROTKB|P62335	389	PSMC6 "26S protease regulatory	0.976	0.732	0.835	6.1e-126
MGI|MGI:1914339	389	Psmc6 "proteasome (prosome, ma	0.976	0.732	0.835	6.1e-126

UNIPROTKB|Q9FXT8 OsRPT4 "Os02g0199900 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 1460 (519.0 bits), Expect = 1.4e-149, P = 1.4e-149
 Identities = 283/292 (96%), Positives = 291/292 (99%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR
Sbjct:   109 MTTLTIMRTLPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 168

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK+VSSAIIDKYIGESARLIREMFGY
Sbjct:   169 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKIVSSAIIDKYIGESARLIREMFGY 228

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD+LGKVKMIMATNR
Sbjct:   229 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDELGKVKMIMATNR 288

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PDVLDPALLRPGRLDRKIEIPLPNEQ+RME+LKIHAAGIAKHGEIDYEAVVKLAEGFNGA
Sbjct:   289 PDVLDPALLRPGRLDRKIEIPLPNEQARMEVLKIHAAGIAKHGEIDYEAVVKLAEGFNGA 348

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
             DLRNVCTEAGM+AIRAERDYV+HEDFMKAVRKLN+AKKLESSAHY+ADFGKE
Sbjct:   349 DLRNVCTEAGMAAIRAERDYVVHEDFMKAVRKLNDAKKLESSAHYSADFGKE 400

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2028200 AT1G45000 [Arabidopsis thaliana (taxid:3702)]

 Score = 1446 (514.1 bits), Expect = 4.3e-148, P = 4.3e-148
 Identities = 281/292 (96%), Positives = 288/292 (98%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMRALPREVDPVVYNMLHEDPGN+SYSAVGGL DQIRELRESIELPLMNPELFLR
Sbjct:   108 MTTLTIMRALPREVDPVVYNMLHEDPGNISYSAVGGLGDQIRELRESIELPLMNPELFLR 167

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMF Y
Sbjct:   168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFNY 227

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             AR+HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR
Sbjct:   228 AREHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 287

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHA+GIAKHGEIDYEA+VKL EGFNGA
Sbjct:   288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHASGIAKHGEIDYEAIVKLGEGFNGA 347

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
             DLRN+CTEAGM AIRAERDYVIHEDFMKAVRKL+EAKKLESS+HYNADFGKE
Sbjct:   348 DLRNICTEAGMFAIRAERDYVIHEDFMKAVRKLSEAKKLESSSHYNADFGKE 399

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

GO:0030244 "cellulose biosynthetic process" evidence=RCA

GO:0048193 "Golgi vesicle transport" evidence=RCA

TAIR|locus:2159996 RPT4A "regulatory particle triple-A ATPase 4A" [Arabidopsis thaliana (taxid:3702)]

 Score = 1445 (513.7 bits), Expect = 5.5e-148, P = 5.5e-148
 Identities = 281/292 (96%), Positives = 288/292 (98%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMRALPREVDPVVYNMLHEDPGN+SYSAVGGL DQIRELRESIELPLMNPELFLR
Sbjct:   108 MTTLTIMRALPREVDPVVYNMLHEDPGNISYSAVGGLGDQIRELRESIELPLMNPELFLR 167

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMF Y
Sbjct:   168 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFNY 227

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             AR+HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD LGKVKMIMATNR
Sbjct:   228 AREHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDNLGKVKMIMATNR 287

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PDVLDPALLRPGRLDRKIEIPLPNEQSRM+ILKIHAAGIAKHGEIDYEA+VKLAEGFNGA
Sbjct:   288 PDVLDPALLRPGRLDRKIEIPLPNEQSRMDILKIHAAGIAKHGEIDYEAIVKLAEGFNGA 347

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGKE 292
             DLRN+CTEAGM AIRAERDYVIHEDFMKAVRKL+EAKKLESS+HYNADFGKE
Sbjct:   348 DLRNICTEAGMFAIRAERDYVIHEDFMKAVRKLSEAKKLESSSHYNADFGKE 399

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;TAS

GO:0005737 "cytoplasm" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=IGI;ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0005618 "cell wall" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=RCA

GO:0043248 "proteasome assembly" evidence=RCA

GO:0051788 "response to misfolded protein" evidence=RCA

GO:0008540 "proteasome regulatory particle, base subcomplex" evidence=IDA

FB|FBgn0028685 Rpt4 "Regulatory particle triple-A ATPase 4" [Drosophila melanogaster (taxid:7227)]

 Score = 1271 (452.5 bits), Expect = 1.5e-129, P = 1.5e-129
 Identities = 245/285 (85%), Positives = 266/285 (93%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDP+VYNM HEDPG+V+YSA+GGL+DQIRELRE IELPL+NPELFLR
Sbjct:   110 MTTLTIMRYLPREVDPLVYNMSHEDPGDVTYSAIGGLTDQIRELREVIELPLLNPELFLR 169

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGI PPKG LLYGPPGTGKTLLARA+AS +DANFLKVVSSAI+DKYIGESARLIREMF Y
Sbjct:   170 VGITPPKGCLLYGPPGTGKTLLARAVASQLDANFLKVVSSAIVDKYIGESARLIREMFNY 229

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD LG+VKMIMATNR
Sbjct:   230 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDSLGQVKMIMATNR 289

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PD LDPALLRPGRLDRKIEIPLPNEQ+R+EILKIHA  IAKHGEIDYEA+VKL++ FNGA
Sbjct:   290 PDSLDPALLRPGRLDRKIEIPLPNEQARLEILKIHALKIAKHGEIDYEAIVKLSDNFNGA 349

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             DLRNVCTEAG+ AIRAER+YVI  DFMKAVRK+++ KKLES   Y
Sbjct:   350 DLRNVCTEAGLFAIRAEREYVIQGDFMKAVRKVSDNKKLESKLDY 394

GO:0008540 "proteasome regulatory particle, base subcomplex" evidence=ISS;NAS

GO:0006508 "proteolysis" evidence=ISS;IDA

GO:0004175 "endopeptidase activity" evidence=IDA

GO:0005838 "proteasome regulatory particle" evidence=ISS;IDA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0022008 "neurogenesis" evidence=IMP

GO:1901838 "positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0001163 "RNA polymerase I regulatory region sequence-specific DNA binding" evidence=IDA

UNIPROTKB|F1MLV1 PSMC6 "26S protease regulatory subunit 10B" [Bos taurus (taxid:9913)]

 Score = 1237 (440.5 bits), Expect = 6.1e-126, P = 6.1e-126
 Identities = 238/285 (83%), Positives = 259/285 (90%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct:   102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct:   162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct:   222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct:   282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y
Sbjct:   342 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDY 386

GO:0022624 "proteasome accessory complex" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

UNIPROTKB|J9P1N0 PSMC6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 1237 (440.5 bits), Expect = 6.1e-126, P = 6.1e-126
 Identities = 238/285 (83%), Positives = 259/285 (90%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct:   108 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 167

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct:   168 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 227

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct:   228 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 287

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct:   288 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 347

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y
Sbjct:   348 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDY 392

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|P62333 PSMC6 "26S protease regulatory subunit 10B" [Homo sapiens (taxid:9606)]

 Score = 1237 (440.5 bits), Expect = 6.1e-126, P = 6.1e-126
 Identities = 238/285 (83%), Positives = 259/285 (90%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct:   102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct:   162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct:   222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct:   282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y
Sbjct:   342 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDY 386

GO:0005524 "ATP binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=IDA

GO:0016887 "ATPase activity" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

GO:0030674 "protein binding, bridging" evidence=NAS

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IC

GO:0022624 "proteasome accessory complex" evidence=ISS

GO:0000075 "cell cycle checkpoint" evidence=TAS

GO:0000082 "G1/S transition of mitotic cell cycle" evidence=TAS

GO:0000084 "S phase of mitotic cell cycle" evidence=TAS

GO:0000209 "protein polyubiquitination" evidence=TAS

GO:0000216 "M/G1 transition of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0002474 "antigen processing and presentation of peptide antigen via MHC class I" evidence=TAS

GO:0002479 "antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006521 "regulation of cellular amino acid metabolic process" evidence=TAS

GO:0006915 "apoptotic process" evidence=TAS

GO:0006977 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0031145 "anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0034641 "cellular nitrogen compound metabolic process" evidence=TAS

GO:0042590 "antigen processing and presentation of exogenous peptide antigen via MHC class I" evidence=TAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0044281 "small molecule metabolic process" evidence=TAS

GO:0051436 "negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051437 "positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0051439 "regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0006200 "ATP catabolic process" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

UNIPROTKB|F1SFE6 PSMC6 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 1237 (440.5 bits), Expect = 6.1e-126, P = 6.1e-126
 Identities = 238/285 (83%), Positives = 259/285 (90%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct:   116 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 175

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct:   176 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 235

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct:   236 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 295

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct:   296 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 355

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y
Sbjct:   356 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDY 400

GO:0022624 "proteasome accessory complex" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

UNIPROTKB|P62335 PSMC6 "26S protease regulatory subunit 10B" [Spermophilus tridecemlineatus (taxid:43179)]

 Score = 1237 (440.5 bits), Expect = 6.1e-126, P = 6.1e-126
 Identities = 238/285 (83%), Positives = 259/285 (90%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct:   102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct:   162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct:   222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct:   282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y
Sbjct:   342 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDY 386

GO:0022624 "proteasome accessory complex" evidence=ISS

MGI|MGI:1914339 Psmc6 "proteasome (prosome, macropain) 26S subunit, ATPase, 6" [Mus musculus (taxid:10090)]

 Score = 1237 (440.5 bits), Expect = 6.1e-126, P = 6.1e-126
 Identities = 238/285 (83%), Positives = 259/285 (90%)

Query:     1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             MTTLTIMR LPREVDP+VYNM HEDPGNVSYS +GGLS+QIRELRE IELPL NPELF R
Sbjct:   102 MTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQIRELREVIELPLTNPELFQR 161

Query:    61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
             VGI PPKG LLYGPPGTGKTLLARA+AS +D NFLKVVSS+I+DKYIGESARLIREMF Y
Sbjct:   162 VGIIPPKGCLLYGPPGTGKTLLARAVASQLDCNFLKVVSSSIVDKYIGESARLIREMFNY 221

Query:   121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
             ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ+DGFD L +VKMIMATNR
Sbjct:   222 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVKMIMATNR 281

Query:   181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
             PD LDPALLRPGRLDRKI I LPNEQ+R++ILKIHA  I KHGEIDYEA+VKL++GFNGA
Sbjct:   282 PDTLDPALLRPGRLDRKIHIDLPNEQARLDILKIHAGPITKHGEIDYEAIVKLSDGFNGA 341

Query:   241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             DLRNVCTEAGM AIRA+ D+V+ EDFMKAVRK+ ++KKLES   Y
Sbjct:   342 DLRNVCTEAGMFAIRADHDFVVQEDFMKAVRKVADSKKLESKLDY 386

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=ISO

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0022624 "proteasome accessory complex" evidence=IDA

GO:0030163 "protein catabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
A4G0S4	PAN_METM5	No assigned EC number	0.5398	0.9417	0.6756	yes	no
A3CV35	PAN_METMJ	No assigned EC number	0.5620	0.9760	0.6917	yes	no
Q9MAK9	PS10B_ARATH	No assigned EC number	0.9623	1.0	0.7318	yes	no
O28303	PAN_ARCFU	No assigned EC number	0.5535	0.9280	0.6809	yes	no
P53549	PRS10_YEAST	No assigned EC number	0.7062	0.9794	0.6544	yes	no
Q2KIW6	PRS10_BOVIN	No assigned EC number	0.8286	0.9794	0.7352	yes	no
O57940	PAN_PYRHO	No assigned EC number	0.5344	0.9828	0.7192	yes	no
Q9V287	PAN_PYRAB	No assigned EC number	0.5344	0.9828	0.7247	yes	no
Q58576	PAN_METJA	No assigned EC number	0.5387	0.9280	0.6302	yes	no
Q6LWR0	PAN_METMP	No assigned EC number	0.5434	0.9417	0.6756	yes	no
O74445	PRS10_SCHPO	No assigned EC number	0.7797	0.9794	0.7371	yes	no
Q54PJ1	PRS10_DICDI	No assigned EC number	0.8207	0.9554	0.7099	yes	no
Q9SEI3	PS10A_ARATH	No assigned EC number	0.9623	1.0	0.7318	yes	no
O26824	PAN_METTH	No assigned EC number	0.5590	0.9760	0.6951	yes	no
A7I8B8	PAN_METB6	No assigned EC number	0.5461	0.9280	0.6215	yes	no
C5A6P8	PAN_THEGJ	No assigned EC number	0.5398	0.9417	0.6926	yes	no
O17071	PRS10_CAEEL	No assigned EC number	0.8280	0.9760	0.7019	yes	no
Q8U4H3	PAN_PYRFU	No assigned EC number	0.5344	0.9828	0.7247	yes	no
A6UQT3	PAN_METVS	No assigned EC number	0.5137	0.9828	0.7051	yes	no
Q5JHS5	PAN_PYRKO	No assigned EC number	0.5241	0.9828	0.7229	yes	no
C3NFW6	PAN_SULIN	No assigned EC number	0.5370	0.9246	0.6870	yes	no
C3N7K8	PAN_SULIY	No assigned EC number	0.5370	0.9246	0.6870	yes	no
Q980M1	PAN_SULSO	No assigned EC number	0.5431	0.9486	0.7048	yes	no
Q8TX03	PAN_METKA	No assigned EC number	0.5316	0.9691	0.6490	yes	no
C3MY47	PAN_SULIM	No assigned EC number	0.5370	0.9246	0.6870	yes	no
B6YXR2	PAN_THEON	No assigned EC number	0.5571	0.9246	0.6783	yes	no
P62333	PRS10_HUMAN	No assigned EC number	0.8321	0.9794	0.7352	yes	no
P62334	PRS10_MOUSE	No assigned EC number	0.8321	0.9794	0.7352	yes	no
P62335	PRS10_SPETR	No assigned EC number	0.8321	0.9794	0.7352	N/A	no
A6VHR1	PAN_METM7	No assigned EC number	0.5434	0.9417	0.6756	yes	no
A9A916	PAN_METM6	No assigned EC number	0.5434	0.9417	0.6756	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00014552001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotgun sequence); (398 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00014791001	SubName- Full=Putative uncharacterized protein (Chromosome chr18 scaffold_1, whole genome shotg [...] (309 aa)				•	•	•	•		0.843
	GSVIVG00010470001	SubName- Full=Chromosome chr17 scaffold_263, whole genome shotgun sequence; (386 aa)				•	•	•	•		0.811
	GSVIVG00036762001	SubName- Full=Chromosome chr4 scaffold_83, whole genome shotgun sequence; (440 aa)				•	•	•	•		0.787
	GSVIVG00024499001	RecName- Full=Proteasome subunit beta type; EC=3.4.25.1;; The proteasome is a multicatalytic pr [...] (245 aa)				•	•	•	•		0.649
	GSVIVG00034204001	RecName- Full=Ubiquitin carboxyl-terminal hydrolase; EC=3.1.2.15; (479 aa)				•	•		•		0.648
	GSVIVG00018640001	SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (629 aa)				•	•	•	•		0.625
	GSVIVG00019352001	SubName- Full=Chromosome chr7 scaffold_20, whole genome shotgun sequence; (320 aa)				•	•	•	•		0.622
	GSVIVG00006696001	SubName- Full=Chromosome chr2 scaffold_176, whole genome shotgun sequence; (267 aa)				•	•	•	•		0.615
	GSVIVG00023752001	SubName- Full=Putative uncharacterized protein (Chromosome chr7 scaffold_31, whole genome shotg [...] (205 aa)				•	•	•	•		0.613
	GSVIVG00015634001	SubName- Full=Chromosome chr2 scaffold_11, whole genome shotgun sequence; (365 aa)				•	•	•	•		0.607

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	292
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	1e-168
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	1e-146
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	1e-126
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	1e-106
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-102
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-82
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-72
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	2e-72
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	6e-67
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	9e-64
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	2e-59
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	8e-58
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	2e-53
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	1e-52
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	5e-47
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	8e-43
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	5e-26
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	3e-21
smart00382	148	smart00382, AAA, ATPases associated with a variety	1e-18
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-10
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	9e-10
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	4e-07
COG0714	329	COG0714, COG0714, MoxR-like ATPases [General funct	1e-06
TIGR00382	413	TIGR00382, clpX, endopeptidase Clp ATP-binding reg	2e-06
TIGR03922	557	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPas	7e-06
PRK13341	725	PRK13341, PRK13341, recombination factor protein R	1e-05
COG0593	408	COG0593, DnaA, ATPase involved in DNA replication	1e-05
pfam00910	105	pfam00910, RNA_helicase, RNA helicase	1e-05
TIGR00763	775	TIGR00763, lon, ATP-dependent protease La	2e-05
COG2255	332	COG2255, RuvB, Holliday junction resolvasome, heli	3e-05
CHL00206	2281	CHL00206, ycf2, Ycf2; Provisional	3e-05
COG1219	408	COG1219, ClpX, ATP-dependent protease Clp, ATPase	4e-05
pfam07726	131	pfam07726, AAA_3, ATPase family associated with va	6e-05
PRK00080	328	PRK00080, ruvB, Holliday junction DNA helicase Ruv	9e-05
PRK05342	412	PRK05342, clpX, ATP-dependent protease ATP-binding	9e-05
pfam07728	135	pfam07728, AAA_5, AAA domain (dynein-related subfa	9e-05
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	9e-05
pfam05496	231	pfam05496, RuvB_N, Holliday junction DNA helicase	1e-04
TIGR00635	305	TIGR00635, ruvB, Holliday junction DNA helicase, R	1e-04
cd03223	166	cd03223, ABCD_peroxisomal_ALDP, ATP-binding casset	3e-04
COG1474	366	COG1474, CDC6, Cdc6-related protein, AAA superfami	4e-04
pfam07724	168	pfam07724, AAA_2, AAA domain (Cdc48 subfamily)	4e-04
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	6e-04
pfam00158	168	pfam00158, Sigma54_activat, Sigma-54 interaction d	6e-04
pfam01057	271	pfam01057, Parvo_NS1, Parvovirus non-structural pr	9e-04
cd01120	165	cd01120, RecA-like_NTPases, RecA-like NTPases	0.001
PRK08116	268	PRK08116, PRK08116, hypothetical protein; Validate	0.002
pfam13401	124	pfam13401, AAA_22, AAA domain	0.002
pfam01078	207	pfam01078, Mg_chelatase, Magnesium chelatase, subu	0.002
PRK06835	329	PRK06835, PRK06835, DNA replication protein DnaC;	0.003
COG1484	254	COG1484, DnaC, DNA replication protein [DNA replic	0.003

>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

 Score =  472 bits (1216), Expect = e-168
 Identities = 176/287 (61%), Positives = 219/287 (76%), Gaps = 1/287 (0%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
             + +I+R LP EVDP V  M  E+  +V+Y  +GGL +QI+E+RE +ELPL NPELF  
Sbjct: 120 RDSYSIVRVLPPEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEE 179

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           +GI PPKGVLLYGPPGTGKTLLA+A+A+  DA F++VV S ++ KYIGE ARL+RE+F  
Sbjct: 180 LGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFEL 239

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           AR+  P IIF+DEIDAIG +RF  GTS DRE+QRT++ELLNQLDGFD  G VK+IMATNR
Sbjct: 240 AREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMATNR 299

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD+LDPALLRPGR DRKIE PLP+E+ R EILKIH   +    ++D E + +L EGF+GA
Sbjct: 300 PDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGA 359

Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK-LNEAKKLESSAHYN 286
           DL+ +CTEAGM AIR  RD V  EDF+KAV K + + KKL S+A Y 
Sbjct: 360 DLKAICTEAGMFAIRERRDEVTMEDFLKAVEKVVKKKKKLSSTARYL 406

Length = 406

>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score =  415 bits (1070), Expect = e-146
 Identities = 159/288 (55%), Positives = 208/288 (72%)

Query: 3   TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG 62
           +L I+  LP E DP V  M   +  NV+Y  +GGL +QIRE+RE++ELPL  PELF  VG
Sbjct: 102 SLAIVEVLPSEKDPRVQAMEVIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVG 161

Query: 63  IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR 122
           I+PPKGVLLYGPPGTGKTLLA+A+A   +A F++VV S ++ K+IGE ARL+RE+F  AR
Sbjct: 162 IEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAR 221

Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD 182
           +  P IIF+DEIDAI  +R   GTS DRE+QRTLM+LL ++DGFD  G VK+I ATNR D
Sbjct: 222 EKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRID 281

Query: 183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL 242
           +LDPA+LRPGR DR IE+PLP+E+ R+EILKIH   +    ++D E + +L EG +GADL
Sbjct: 282 ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADL 341

Query: 243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFG 290
           + +CTEAGM AIR +R  V  EDF+KA+ K+   ++ +S       F 
Sbjct: 342 KAICTEAGMFAIRDDRTEVTMEDFLKAIEKVMGKEEKDSMEEPGVMFA 389

Length = 389

>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family

 Score =  364 bits (937), Expect = e-126
 Identities = 166/271 (61%), Positives = 209/271 (77%)

Query: 3   TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG 62
           TLTI+  LP   DP+V  M  E+  NVSY  +GGL +QIRE+RE++ELPL +PELF  VG
Sbjct: 93  TLTIVDVLPTSKDPLVKGMEVEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVG 152

Query: 63  IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR 122
           I+PPKGVLLYGPPGTGKTLLA+A+A   +A F++VV S ++ KYIGE ARL+RE+F  A+
Sbjct: 153 IEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVREIFELAK 212

Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD 182
           +  P IIF+DEIDAI  +R   GTS DRE+QRTLM+LL +LDGFD  G VK+I ATNRPD
Sbjct: 213 EKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPD 272

Query: 183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL 242
           +LDPALLRPGR DR IE+PLP+ + R+EILKIH   +    ++D EA+ K+ EG +GADL
Sbjct: 273 ILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADL 332

Query: 243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKL 273
           + +CTEAGM AIR ERDYV  +DF+KAV K+
Sbjct: 333 KAICTEAGMFAIREERDYVTMDDFIKAVEKV 363

Many proteins may score above the trusted cutoff because an internal. Length = 364

>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional

 Score =  314 bits (807), Expect = e-106
 Identities = 138/276 (50%), Positives = 197/276 (71%)

Query: 3   TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG 62
           T +++  L  EVDP+V  M  +     SY+ +GGL  QI+E++E++ELPL +PEL+  +G
Sbjct: 154 THSVVGILLDEVDPLVSVMKVDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIG 213

Query: 63  IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR 122
           IKPPKGV+LYGPPGTGKTLLA+A+A+   A FL+VV S +I KY+G+  +L+RE+F  A 
Sbjct: 214 IKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAE 273

Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD 182
           ++ P I+F+DEIDAIG +R+   +  ++EIQRT++ELLNQLDGFD  G VK+IMATNR +
Sbjct: 274 ENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSRGDVKVIMATNRIE 333

Query: 183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL 242
            LDPAL+RPGR+DRKIE P P+E+++  I +IH + +    ++D E  +   +  +GAD+
Sbjct: 334 SLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADI 393

Query: 243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK 278
           + +CTEAG+ A+R  R  V   DF KA  K+   KK
Sbjct: 394 KAICTEAGLLALRERRMKVTQADFRKAKEKVLYRKK 429

Length = 438

>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional

 Score =  304 bits (780), Expect = e-102
 Identities = 131/263 (49%), Positives = 182/263 (69%)

Query: 10  LPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGV 69
           LP E D  +  +   +  +V+YS +GGL  Q +E+RE++ELPL  PEL+ ++GI PP+GV
Sbjct: 123 LPPEADSSIQLLQMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGV 182

Query: 70  LLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCII 129
           LLYGPPGTGKT+LA+A+A +  A F++VV S  + KY+GE  R++R++F  AR++ P II
Sbjct: 183 LLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSII 242

Query: 130 FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALL 189
           F+DE+D+I  +RF   T ADRE+QR L+ELLNQ+DGFDQ   VK+IMATNR D LDPALL
Sbjct: 243 FIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALL 302

Query: 190 RPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEA 249
           RPGRLDRKIE PLP+ + +  I +   + +    E+D E  V   E  + AD+  +C EA
Sbjct: 303 RPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEA 362

Query: 250 GMSAIRAERDYVIHEDFMKAVRK 272
           GM A+R  R  ++ +DF K  + 
Sbjct: 363 GMQAVRKNRYVILPKDFEKGYKT 385

Length = 398

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score =  257 bits (657), Expect = 1e-82
 Identities = 118/252 (46%), Positives = 167/252 (66%), Gaps = 7/252 (2%)

Query: 24  EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA 83
           ED  +V+   +GGL +   EL+E+IE PL  PELF ++G++PPKGVLLYGPPGTGKTLLA
Sbjct: 235 EDE-DVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLA 293

Query: 84  RAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFS 143
           +A+A    + F+ V  S ++ K++GES + IRE+F  AR   P IIF+DEID++   R  
Sbjct: 294 KAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGR-- 351

Query: 144 EGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLP 203
            G S D   +R + +LL +LDG ++   V +I ATNRPD LDPALLRPGR DR I +PLP
Sbjct: 352 -GPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFDRLIYVPLP 410

Query: 204 NEQSRMEILKIHAAGIAKH--GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR-AERDY 260
           + + R+EI KIH          ++D E + ++ EG++GAD+  +  EA + A+R A R  
Sbjct: 411 DLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREARRRE 470

Query: 261 VIHEDFMKAVRK 272
           V  +DF+ A++K
Sbjct: 471 VTLDDFLDALKK 482

Length = 494

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score =  236 bits (603), Expect = 2e-72
 Identities = 120/267 (44%), Positives = 168/267 (62%), Gaps = 26/267 (9%)

Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
           NV +S +GGL +  +ELRE++E PL +PE+F ++GI+PPKGVLL+GPPGTGKTLLA+A+A
Sbjct: 449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVA 508

Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIG---GRRFSE 144
           +   ANF+ V    I+ K++GES + IRE+F  AR   P IIF DEIDAI    G RF  
Sbjct: 509 TESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDT 568

Query: 145 GTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPN 204
             +      R + +LL ++DG  +L  V +I ATNRPD+LDPALLRPGR DR I +P P+
Sbjct: 569 SVT-----DRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPD 623

Query: 205 EQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE 264
           E++R EI KIH   +    ++D E + ++ EG+ GAD+  VC EA M+A+R        E
Sbjct: 624 EEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKE 683

Query: 265 ------------------DFMKAVRKL 273
                              F++A++K+
Sbjct: 684 KLEVGEEEFLKDLKVEMRHFLEALKKV 710

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733

>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH

 Score =  230 bits (589), Expect = 2e-72
 Identities = 106/252 (42%), Positives = 158/252 (62%), Gaps = 1/252 (0%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           +L+E+   V++  V G+ +   EL E ++  L NP  F ++G K PKGVLL GPPGTGKT
Sbjct: 44  LLNEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKT 102

Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
           LLA+A+A      F  +  S  ++ ++G  A  +R++F  A+ + PCIIF+DEIDA+G +
Sbjct: 103 LLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQ 162

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R +     + E ++TL +LL ++DGF     V +I ATNRPDVLDPALLRPGR DR++ +
Sbjct: 163 RGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVV 222

Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
            LP+ + R EILK+HA       ++D +AV +   GF+GADL N+  EA + A R  +  
Sbjct: 223 DLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTE 282

Query: 261 VIHEDFMKAVRK 272
           +   D  +A+ +
Sbjct: 283 ITMNDIEEAIDR 294

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 495

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score =  221 bits (564), Expect = 6e-67
 Identities = 108/228 (47%), Positives = 155/228 (67%), Gaps = 3/228 (1%)

Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
            V+Y  +GGL +   ++RE +ELP+ +PELF  +GI+PPKGVLLYGPPGTGKTLLA+A+A
Sbjct: 174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVA 233

Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
           +   A F+ +    I+ KY GES   +RE+F  A ++ P IIF+DEIDAI  +R  E  +
Sbjct: 234 NEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKR--EEVT 291

Query: 148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS 207
            + E +R + +LL  +DG    G+V +I ATNRPD LDPAL RPGR DR+I I +P++++
Sbjct: 292 GEVE-KRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRA 350

Query: 208 RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           R EILK+H   +    ++D + + ++  GF GADL  +  EA M+A+R
Sbjct: 351 RKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALR 398

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733

>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

 Score =  210 bits (536), Expect = 9e-64
 Identities = 105/254 (41%), Positives = 157/254 (61%), Gaps = 3/254 (1%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           +  ED   V+++ V G+ +   EL E ++  L NP+ +  +G K PKGVLL GPPGTGKT
Sbjct: 139 LYLEDQVKVTFADVAGVDEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGPPGTGKT 197

Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
           LLA+A+A      F  +  S  ++ ++G  A  +R++F  A+ + PCIIF+DEIDA+G +
Sbjct: 198 LLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQ 257

Query: 141 R-FSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
           R    G   D E ++TL +LL ++DGF     V +I ATNRPDVLDPALLRPGR DR+I 
Sbjct: 258 RGAGLGGGND-EREQTLNQLLVEMDGFGGNEGVIVIAATNRPDVLDPALLRPGRFDRQIL 316

Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
           + LP+ + R +ILK+HA       ++D + + +   GF+GADL N+  EA + A R  + 
Sbjct: 317 VELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARRNKK 376

Query: 260 YVIHEDFMKAVRKL 273
            +   D  +A+ ++
Sbjct: 377 EITMRDIEEAIDRV 390

Length = 596

>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated

 Score =  199 bits (508), Expect = 2e-59
 Identities = 95/245 (38%), Positives = 150/245 (61%), Gaps = 1/245 (0%)

Query: 29  VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIAS 88
           +++  + G+ +   E  E +   L  PE F  VG K PKGVLL GPPGTGKTLLA+AIA 
Sbjct: 180 ITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAG 238

Query: 89  NIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSA 148
             +  F  +  S  ++ ++G  A  +R++F  A+++ PCI+F+DEIDA+G +R +     
Sbjct: 239 EAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGG 298

Query: 149 DREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSR 208
           + E ++TL +LL ++DGF     V +I ATNR D+LD ALLRPGR DR+I + LP+ + R
Sbjct: 299 NDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGR 358

Query: 209 MEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMK 268
           ++ILK+HA       ++  E + +   GF+GADL N+  EA +   R ++  +  ++   
Sbjct: 359 LDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATITMKEIDT 418

Query: 269 AVRKL 273
           A+ ++
Sbjct: 419 AIDRV 423

Length = 638

>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed

 Score =  195 bits (497), Expect = 8e-58
 Identities = 112/278 (40%), Positives = 164/278 (58%), Gaps = 13/278 (4%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           ML ED    +++ V G  +   E+ E +E  L  P  F ++G K PKGVL+ GPPGTGKT
Sbjct: 141 MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT 199

Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
           LLA+AIA      F  +  S  ++ ++G  A  +R+MF  A+   PCIIF+DEIDA+G +
Sbjct: 200 LLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQ 259

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R +       E ++TL ++L ++DGF+    + +I ATNRPDVLDPALLRPGR DR++ +
Sbjct: 260 RGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVV 319

Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
            LP+ + R +ILK+H   +    +ID   + +   GF+GADL N+  EA + A R  +  
Sbjct: 320 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRV 379

Query: 261 VIHEDFMKAVRK-----------LNEAKKLESSAHYNA 287
           V   +F KA  K           + EA+K ES+A++ A
Sbjct: 380 VSMVEFEKAKDKIMMGAERRSMVMTEAQK-ESTAYHEA 416

Length = 644

>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular activities (AAA)

 Score =  170 bits (432), Expect = 2e-53
 Identities = 74/135 (54%), Positives = 96/135 (71%), Gaps = 5/135 (3%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCI 128
           +LLYGPPGTGKT LA+A+A  + A F+++  S ++ KY+GES + +RE+F  A+   PC+
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60

Query: 129 IFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ-LGKVKMIMATNRPDVLDPA 187
           IF+DEIDA+ G R S G   D E +R + +LL +LDGF   L KV +I ATNRPD LDPA
Sbjct: 61  IFIDEIDALAGSRGSGG---DSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDKLDPA 117

Query: 188 LLRPGRLDRKIEIPL 202
           LLR GR DR IE PL
Sbjct: 118 LLR-GRFDRIIEFPL 131

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131

>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase

 Score =  179 bits (456), Expect = 1e-52
 Identities = 95/223 (42%), Positives = 146/223 (65%), Gaps = 21/223 (9%)

Query: 8   RALPR-EVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPP 66
            A+PR EV+ +V   L E P +V+Y+ +GGL  QI ++R+++ELP ++PEL+   G+KPP
Sbjct: 161 EAIPRTEVEDLV---LEEVP-DVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPP 216

Query: 67  KGVLLYGPPGTGKTLLARAIASNIDAN----------FLKVVSSAIIDKYIGESARLIRE 116
           KGVLLYGPPG GKTL+A+A+A+++ A           FL +    +++KY+GE+ R IR 
Sbjct: 217 KGVLLYGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRL 276

Query: 117 MFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKV 172
           +F  AR    + +P I+F DE+D++   R S G S+D E    + +LL ++DG + L  V
Sbjct: 277 IFQRAREKASEGRPVIVFFDEMDSLFRTRGS-GVSSDVETT-VVPQLLAEIDGVESLDNV 334

Query: 173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIH 215
            +I A+NR D++DPA+LRPGRLD KI I  P+ ++  +I   +
Sbjct: 335 IVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFAKY 377

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 512

>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General function prediction only]

 Score =  161 bits (408), Expect = 5e-47
 Identities = 94/253 (37%), Positives = 140/253 (55%), Gaps = 11/253 (4%)

Query: 22  LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL 81
             E   +++   V G  +  R+ R  I   L NPE F   G   PK VL YGPPGTGKT+
Sbjct: 111 DREIISDITLDDVIGQEEAKRKCR-LIMEYLENPERF---GDWAPKNVLFYGPPGTGKTM 166

Query: 82  LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIG-GR 140
           +A+A+A+      L V ++ +I +++G+ AR I E++  AR   PCI+F+DE+DAI   R
Sbjct: 167 MAKALANEAKVPLLLVKATELIGEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDR 226

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R+ E      EI   +  LL +LDG  +   V  I ATNRP++LDPA+    R + +IE 
Sbjct: 227 RYQELRGDVSEI---VNALLTELDGIKENEGVVTIAATNRPELLDPAI--RSRFEEEIEF 281

Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRN-VCTEAGMSAIRAERD 259
            LPN++ R+EIL+ +A       + D   +    +G +G D++  V   A   AI  +R+
Sbjct: 282 KLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLKTALHRAIAEDRE 341

Query: 260 YVIHEDFMKAVRK 272
            V  ED  KA++K
Sbjct: 342 KVEREDIEKALKK 354

Length = 368

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score =  152 bits (386), Expect = 8e-43
 Identities = 104/231 (45%), Positives = 142/231 (61%), Gaps = 11/231 (4%)

Query: 49  ELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIG 108
           ELPL  PELF ++GI+PPKGVLL+GPPGTGKTLLARA+A+   A FL +    I+ KY+G
Sbjct: 1   ELPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVG 59

Query: 109 ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ 168
           ES   +RE+F  A    P IIF+DEIDA+  +R S+    +R +   L   L  +DG  +
Sbjct: 60  ESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQGEVERRVVAQL---LALMDGLKR 116

Query: 169 LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYE 228
            G+V +I ATNRPD LDPA  RPGR DR+IE+ LP+E  R+EIL+IH   +        +
Sbjct: 117 -GQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTRLMFLGPPGTGK 175

Query: 229 AVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIH------EDFMKAVRKL 273
            +     G +GADL  +  EA +  +R   D V        +DF +A++K+
Sbjct: 176 TLAARTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKV 226

Length = 494

>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

 Score =   99 bits (249), Expect = 5e-26
 Identities = 63/175 (36%), Positives = 87/175 (49%), Gaps = 31/175 (17%)

Query: 35  GGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA---SNID 91
            G  + I  LRE++ELP             PPK +LLYGPPGTGKT LARAIA       
Sbjct: 1   VGQEEAIEALREALELP-------------PPKNLLLYGPPGTGKTTLARAIANELFRPG 47

Query: 92  ANFLKVVSSAIIDKYIGESAR---LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSA 148
           A FL + +S +++  +        L+R +F  A   +P ++F+DEID++           
Sbjct: 48  APFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLS---------- 97

Query: 149 DREIQRTLMELLNQL-DGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPL 202
            R  Q  L+ +L  L D       V++I ATNRP + D       RLD +I IPL
Sbjct: 98  -RGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases. Length = 151

>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional

 Score = 92.8 bits (231), Expect = 3e-21
 Identities = 63/217 (29%), Positives = 106/217 (48%), Gaps = 13/217 (5%)

Query: 62  GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYA 121
           G+  P+G+LL G  GTGK+L A+AIA++     L++    +    +GES   +R+M   A
Sbjct: 255 GLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIA 314

Query: 122 RDHQPCIIFMDEID-AIGGRRFS--EGTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT 178
               PCI+++DEID A          GT+      R L   +  L   ++   V ++   
Sbjct: 315 EALSPCILWIDEIDKAFSNSESKGDSGTTN-----RVLATFITWLS--EKKSPVFVVATA 367

Query: 179 NRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG--EIDYEAVVKLAEG 236
           N  D+L   +LR GR D    + LP+ + R +I KIH          + D + + KL+  
Sbjct: 368 NNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNK 427

Query: 237 FNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKL 273
           F+GA++     EA   A   +R++   +D + A+++ 
Sbjct: 428 FSGAEIEQSIIEAMYIAFYEKREFTT-DDILLALKQF 463

Length = 489

>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular activities

 Score = 80.1 bits (197), Expect = 1e-18
 Identities = 44/157 (28%), Positives = 66/157 (42%), Gaps = 26/157 (16%)

Query: 65  PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS-----------------SAIIDKYI 107
           P + +L+ GPPG+GKT LARA+A  +      V+                       K  
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 108 GESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD 167
           G     +R     AR  +P ++ +DEI ++          A++E    L+E L  L    
Sbjct: 61  GSGELRLRLALALARKLKPDVLILDEITSL--------LDAEQEALLLLLEELRLLLLLK 112

Query: 168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPN 204
               + +I+ TN    L PALLR  R DR+I + L  
Sbjct: 113 SEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 59.9 bits (146), Expect = 4e-10
 Identities = 64/193 (33%), Positives = 94/193 (48%), Gaps = 45/193 (23%)

Query: 64  KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV--------SSAIIDKYIGESARLIR 115
           KP K +LLYGPPG GKT LA A+A++      +V+        ++ +I++  GE+A    
Sbjct: 37  KPKKALLLYGPPGVGKTSLAHALANDYG---WEVIELNASDQRTADVIERVAGEAATS-G 92

Query: 116 EMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMI 175
            +FG  R     +I +DE+D I G         DR   R ++EL+ +        K  +I
Sbjct: 93  SLFGARRK----LILLDEVDGIHGN-------EDRGGARAILELIKK-------AKQPII 134

Query: 176 MATNRPDVLDPAL--LRPGRLDRKIEI-PLPNEQSRMEILK-IHAA-GIAKHGEIDYEAV 230
           +  N  D  DP+L  LR       IE   L   +S + +LK I    GI    E D EA+
Sbjct: 135 LTAN--DPYDPSLRELRN--ACLMIEFKRLS-TRSIVPVLKRICRKEGI----ECDDEAL 185

Query: 231 VKLAEGFNGADLR 243
            ++AE  +G DLR
Sbjct: 186 KEIAER-SGGDLR 197

Length = 482

>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed

 Score = 58.6 bits (143), Expect = 9e-10
 Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 11/70 (15%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDH---- 124
           ++L+GPPGTGKT LAR IA   DA F  +  SA+    + +    +RE+   AR      
Sbjct: 39  MILWGPPGTGKTTLARIIAGATDAPFEAL--SAVTSG-VKD----LREVIEEARQRRSAG 91

Query: 125 QPCIIFMDEI 134
           +  I+F+DEI
Sbjct: 92  RRTILFIDEI 101

Length = 413

>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

 Score = 50.3 bits (121), Expect = 4e-07
 Identities = 64/214 (29%), Positives = 99/214 (46%), Gaps = 42/214 (19%)

Query: 71  LYGPPGTGKTLLARAIASNIDANFLKV--VSSAIID-KYIGESARLIREMFGYARDHQPC 127
           L+GPPGTGKT LAR IA   +A F  +  V+S + D + I E A   R+     R  +  
Sbjct: 53  LWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGVKDLREIIEEA---RKNRLLGR--RT- 106

Query: 128 IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT--NRPDVLD 185
           I+F+DEI      RF      ++  Q  L+  +         G + +I AT  N    L+
Sbjct: 107 ILFLDEI-----HRF------NKAQQDALLPHVEN-------GTIILIGATTENPSFELN 148

Query: 186 PALLRPGRLDRKIEI-PLPNEQSRMEILKIHAAGIAKHG------EIDYEAVVKLAEGFN 238
           PALL   R+    E+ PL + +   ++LK  A    + G       +D EA+  L    N
Sbjct: 149 PALLSRARV---FELKPL-SSEDIKKLLK-RALLDEERGLGGQIIVLDEEALDYLVRLSN 203

Query: 239 GADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK 272
           G D R       ++A+ AE D V+  + ++ + +
Sbjct: 204 G-DARRALNLLELAALSAEPDEVLILELLEEILQ 236

Length = 436

>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction only]

 Score = 48.6 bits (116), Expect = 1e-06
 Identities = 52/244 (21%), Positives = 91/244 (37%), Gaps = 42/244 (17%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKV------VSSAIIDKYIGESARLIREMF---- 118
           VLL GPPG GKTLLARA+A  +   F+++      + S ++  Y   +  L    F    
Sbjct: 46  VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105

Query: 119 GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN----QLDGFDQLGKVK- 173
           G        I+ +DEI+            A  E+Q  L+E L      + G   +     
Sbjct: 106 GPLFAAVRVILLLDEINR-----------APPEVQNALLEALEERQVTVPGLTTIRLPPP 154

Query: 174 -MIMATNRP------DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE-- 224
            +++AT  P        L  ALL   R   +I +  P+ +    I+     G+ +     
Sbjct: 155 FIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEERIILARVGGVDELDLES 212

Query: 225 -----IDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKL 279
                +  E +++L +      + +   +  ++ + A R+             L     L
Sbjct: 213 LVKPVLSDEELLRLQKEVKKVPVSDEVIDYIVTLVAALREAPDVALGASPRASLALLAAL 272

Query: 280 ESSA 283
            + A
Sbjct: 273 RALA 276

Length = 329

>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit (clpX)

 Score = 48.2 bits (115), Expect = 2e-06
 Identities = 35/109 (32%), Positives = 54/109 (49%), Gaps = 25/109 (22%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-------YIGESA-----RLIRE 116
           +LL GP G+GKTLLA+ +A  ++  F      AI D        Y+GE       +L++ 
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPF------AIADATTLTEAGYVGEDVENILLKLLQA 172

Query: 117 MFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADRE-----IQRTLMELL 160
                   Q  II++DEID I   R SE  S  R+     +Q+ L++++
Sbjct: 173 ADYDVEKAQKGIIYIDEIDKIS--RKSENPSITRDVSGEGVQQALLKII 219

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 413

>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA

 Score = 46.8 bits (111), Expect = 7e-06
 Identities = 35/126 (27%), Positives = 53/126 (42%), Gaps = 13/126 (10%)

Query: 40  QIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA------- 92
           Q+  L+ S  + L   E  L V       +L  GPPGTGKT +AR +A  I         
Sbjct: 287 QVAALKSSTAMALARAERGLPVAQTS-NHMLFAGPPGTGKTTIARVVA-KIYCGLGVLRK 344

Query: 93  -NFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADRE 151
               +V  + +I +YIGES     E+   A      ++F+DE   +    + +      E
Sbjct: 345 PLVREVSRADLIGQYIGESEAKTNEIIDSALGG---VLFLDEAYTLVETGYGQKDPFGLE 401

Query: 152 IQRTLM 157
              TL+
Sbjct: 402 AIDTLL 407

This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc [Protein fate, Protein and peptide secretion and trafficking]. Length = 557

>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed

 Score = 46.2 bits (110), Expect = 1e-05
 Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 8/68 (11%)

Query: 70  LLYGPPGTGKTLLARAIASNIDANF--LKVVSSAIID-KYIGESARLIREMFGYARDHQP 126
           +LYGPPG GKT LAR IA++  A+F  L  V + + D +   + A+   E  G     + 
Sbjct: 56  ILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAGVKDLRAEVDRAKERLERHG-----KR 110

Query: 127 CIIFMDEI 134
            I+F+DE+
Sbjct: 111 TILFIDEV 118

Length = 725

>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 45/194 (23%), Positives = 82/194 (42%), Gaps = 34/194 (17%)

Query: 69  VLLYGPPGTGKTLLARAI-----ASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARD 123
           + +YG  G GKT L +AI     A+  +A  + + S    + ++   A    EM  +   
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFV--KALRDNEMEKFKEK 173

Query: 124 HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD- 182
           +   ++ +D+I  + G             Q       N L    + GK ++++ ++RP  
Sbjct: 174 YSLDLLLIDDIQFLAG---------KERTQEEFFHTFNAL---LENGK-QIVLTSDRPPK 220

Query: 183 ---VLDPALLRPGRLDR--KIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGF 237
               L+  L    RL+    +EI  P++++R+ IL+  A    +  EI  E +  LA+  
Sbjct: 221 ELNGLEDRLRS--RLEWGLVVEIEPPDDETRLAILRKKAE--DRGIEIPDEVLEFLAKRL 276

Query: 238 NGADLRNVCTEAGM 251
           +    RNV    G 
Sbjct: 277 D----RNVRELEGA 286

Length = 408

>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase

 Score = 42.6 bits (101), Expect = 1e-05
 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 18/74 (24%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII-----DKYIGESARLIREMFGYARD 123
           + LYGPPG GK+ LA+ +A  +  +       ++      D +            GY   
Sbjct: 1   IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSRNPDDDF----------WDGY--T 48

Query: 124 HQPCIIFMDEIDAI 137
            QP +I +D+    
Sbjct: 49  GQPVVI-IDDFGQN 61

This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses. Length = 105

>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La

 Score = 45.7 bits (109), Expect = 2e-05
 Identities = 58/211 (27%), Positives = 89/211 (42%), Gaps = 54/211 (25%)

Query: 71  LYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK---------YIGE-SARLIREMFGY 120
           L GPPG GKT L ++IA  ++  F++     + D+         Y+G    R+I+ +   
Sbjct: 352 LVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGL-KK 410

Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELL----------NQLD-GFDQL 169
           A+   P +  +DEID IG     +  SA       L+E+L          + LD  FD L
Sbjct: 411 AKTKNP-LFLLDEIDKIGSSFRGDPASA-------LLEVLDPEQNNAFSDHYLDVPFD-L 461

Query: 170 GKVKMIMATNRPDVLDPALLRPGRLDRK--IEIPLPNEQSRMEILKIH-------AAGIA 220
            KV  I   N  D +   L     LDR   IE+    E+ ++EI K +         G+ 
Sbjct: 462 SKVIFIATANSIDTIPRPL-----LDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLK 516

Query: 221 K-HGEIDYEAVVKLAEGFNGADLRNVCTEAG 250
               +I  EA++ L + +          EAG
Sbjct: 517 PDELKITDEALLLLIKYY--------TREAG 539

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 775

>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

 Score = 44.5 bits (106), Expect = 3e-05
 Identities = 19/37 (51%), Positives = 25/37 (67%), Gaps = 1/37 (2%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK 105
           VLL+GPPG GKT LA  IA+ +  N LK+ S   ++K
Sbjct: 55  VLLFGPPGLGKTTLAHIIANELGVN-LKITSGPALEK 90

Length = 332

>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional

 Score = 44.9 bits (106), Expect = 3e-05
 Identities = 28/129 (21%), Positives = 53/129 (41%), Gaps = 19/129 (14%)

Query: 37   LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK 96
               Q      S   P       LR+ + P +G+L+ G  GTG++ L + +A+N    F+ 
Sbjct: 1601 TYSQTSCGANSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFIT 1660

Query: 97   VVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL 156
            V     ++K++               D++P    +D+ID        +    DR++   L
Sbjct: 1661 V----FLNKFL---------------DNKPKGFLIDDIDIDDSDDIDDSDDIDRDLDTEL 1701

Query: 157  MELLNQLDG 165
            + ++N L  
Sbjct: 1702 LTMMNALTM 1710

Length = 2281

>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

 Score = 44.5 bits (106), Expect = 4e-05
 Identities = 34/96 (35%), Positives = 47/96 (48%), Gaps = 20/96 (20%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-------YIGESARLIREMFGYA 121
           +LL GP G+GKTLLA+ +A  ++  F      AI D        Y+GE    I      A
Sbjct: 100 ILLIGPTGSGKTLLAQTLAKILNVPF------AIADATTLTEAGYVGEDVENILLKLLQA 153

Query: 122 RDH-----QPCIIFMDEIDAIGGRRFSEGTSADREI 152
            D+     +  II++DEID I   R SE  S  R++
Sbjct: 154 ADYDVERAERGIIYIDEIDKIA--RKSENPSITRDV 187

Length = 408

>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular activities (AAA)

 Score = 41.8 bits (99), Expect = 6e-05
 Identities = 14/26 (53%), Positives = 18/26 (69%)

Query: 69 VLLYGPPGTGKTLLARAIASNIDANF 94
          VLL G PG  KTLLAR +A ++  +F
Sbjct: 2  VLLEGVPGLAKTLLARTLARSLGLDF 27

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 131

>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed

 Score = 43.2 bits (103), Expect = 9e-05
 Identities = 18/37 (48%), Positives = 25/37 (67%), Gaps = 1/37 (2%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK 105
           VLLYGPPG GKT LA  IA+ +  N +++ S   ++K
Sbjct: 54  VLLYGPPGLGKTTLANIIANEMGVN-IRITSGPALEK 89

Length = 328

>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional

 Score = 43.2 bits (103), Expect = 9e-05
 Identities = 35/101 (34%), Positives = 50/101 (49%), Gaps = 30/101 (29%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-------KYIGES-----ARLIRE 116
           +LL GP G+GKTLLA+ +A  +D  F      AI D        Y+GE       +L++ 
Sbjct: 111 ILLIGPTGSGKTLLAQTLARILDVPF------AIADATTLTEAGYVGEDVENILLKLLQ- 163

Query: 117 MFGYARDH-----QPCIIFMDEIDAIGGRRFSEGTSADREI 152
               A D+     Q  I+++DEID I   R SE  S  R++
Sbjct: 164 ----AADYDVEKAQRGIVYIDEIDKIA--RKSENPSITRDV 198

Length = 412

>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily)

 Score = 41.1 bits (97), Expect = 9e-05
 Identities = 35/148 (23%), Positives = 55/148 (37%), Gaps = 40/148 (27%)

Query: 68  GVLLYGPPGTGKTLLARAIASNID-ANFLKVVSSAIIDKYIGES----ARLIREMFGYAR 122
           GVLL GPPGTGK+ LA  +A+ +       V     + +   E      R I        
Sbjct: 1   GVLLVGPPGTGKSELAERLAAALSNRPVFYVQ----LTRDTTEEDLKGRRNIDPGGASWV 56

Query: 123 D-------HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN-----QLDGFDQLG 170
           D        +  I  +DEI+            A+ ++  +L+ LL+       +G + + 
Sbjct: 57  DGPLVRAAREGEIAVLDEIN-----------RANPDVLNSLLSLLDERRLLLPEGGELVK 105

Query: 171 K----VKMIMATNRPD----VLDPALLR 190
                 ++I   N  D     L PAL  
Sbjct: 106 AAPDGFRLIATMNPLDRGLNELSPALRS 133

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 135

>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 41.4 bits (97), Expect = 9e-05
 Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 10/63 (15%)

Query: 36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL 95
          G  +++  L +++           R     P  VLL GP GTGKT L R +   +     
Sbjct: 4  GREEELERLLDALR----------RARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAG 53

Query: 96 KVV 98
          K  
Sbjct: 54 KCD 56

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 154

>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus

 Score = 42.0 bits (100), Expect = 1e-04
 Identities = 18/37 (48%), Positives = 24/37 (64%), Gaps = 1/37 (2%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK 105
           VLLYGPPG GKT LA  IA+ +  N  ++ S   ++K
Sbjct: 53  VLLYGPPGLGKTTLANIIANEMGVNI-RITSGPALEK 88

The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. Length = 231

>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit

 Score = 42.3 bits (100), Expect = 1e-04
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 8/54 (14%)

Query: 59  LRVGIKPPKG-------VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK 105
           L++ I+  K        +LLYGPPG GKT LA  IA+ +  N LK+ S   ++K
Sbjct: 16  LQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVN-LKITSGPALEK 68

All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions [DNA metabolism, DNA replication, recombination, and repair]. Length = 305

>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of peroxisomal transporter, subfamily D

 Score = 40.2 bits (95), Expect = 3e-04
 Identities = 39/141 (27%), Positives = 52/141 (36%), Gaps = 59/141 (41%)

Query: 59  LRVGIKPPKGVLLYGPPGTGKTLLARAIA-------SNI----DANFL------------ 95
           L   IKP   +L+ GP GTGK+ L RA+A         I      + L            
Sbjct: 20  LSFEIKPGDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFLPQRPYLPLGT 79

Query: 96  ----------KVVSSAIIDKYIGESARLIREMFGYARD--HQPCIIFMDEIDAIGGRRFS 143
                      V+S        GE  RL      +AR   H+P  +F+D           
Sbjct: 80  LREQLIYPWDDVLSG-------GEQQRL-----AFARLLLHKPKFVFLD----------- 116

Query: 144 EGTSA-DREIQRTLMELLNQL 163
           E TSA D E +  L +LL +L
Sbjct: 117 EATSALDEESEDRLYQLLKEL 137

Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic). Length = 166

>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

 Score = 41.2 bits (97), Expect = 4e-04
 Identities = 53/251 (21%), Positives = 86/251 (34%), Gaps = 53/251 (21%)

Query: 66  PKGVLLYGPPGTGKTLLARAIASNIDANFLKV---------------VSSAIIDKYIGES 110
           P  +++YGP GTGKT   + +   ++ +   V               V S I++K     
Sbjct: 42  PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVP 101

Query: 111 ARLIREMFGYAR--DHQPC-----IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQL 163
                 +    R  D+        I+ +DE+DA+  +               L  LL   
Sbjct: 102 LTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKD-----------GEVLYSLLRAP 150

Query: 164 DGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKI---EIPLPNEQSRMEILKIHAAGIA 220
                  KVK+ +     D      L P R+   +   EI  P   +  E+  I      
Sbjct: 151 G----ENKVKVSIIAVSNDDKFLDYLDP-RVKSSLGPSEIVFP-PYTAEELYDILRER-V 203

Query: 221 KHGEIDY---EAVVKLAEGFNGA---DLR---NVCTEAGMSAIRAERDYVIHEDFMKAVR 271
           + G       + V+KL      A   D R   ++   AG  A R E    + ED ++  +
Sbjct: 204 EEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAER-EGSRKVSEDHVREAQ 262

Query: 272 KLNEAKKLESS 282
           +  E   LE  
Sbjct: 263 EEIERDVLEEV 273

Length = 366

>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily)

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 30/112 (26%), Positives = 44/112 (39%), Gaps = 31/112 (27%)

Query: 66  PKGV-LLYGPPGTGKTLLARAIAS--NIDANFLKVV--SSAIIDKYIGESARLIREMFGY 120
           P G  L  GP G GKT LA+A+A     D   L  +  S  + +  +   +RLI    GY
Sbjct: 2   PIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSV---SRLIGAPPGY 58

Query: 121 A------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELL 160
                        R     I+ +DEI+            A   +Q  L+++L
Sbjct: 59  VGYEEGGQLTEAVRRKPYSIVLIDEIE-----------KAHPGVQNDLLQIL 99

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168

>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional

 Score = 40.4 bits (95), Expect = 6e-04
 Identities = 42/178 (23%), Positives = 72/178 (40%), Gaps = 41/178 (23%)

Query: 70  LLYGP-PGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARL--IR-EMFGYA---- 121
           LL+ P PGTGKT +A+A+ + + A  L V          G   R+  +R  +  +A    
Sbjct: 46  LLHSPSPGTGKTTVAKALCNEVGAEVLFV---------NGSDCRIDFVRNRLTRFASTVS 96

Query: 122 RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGK-VKMIMATNR 180
                 +I +DE D         G +  +   R+ ME            K    I+  N 
Sbjct: 97  LTGGGKVIIIDEFD-------RLGLADAQRHLRSFME---------AYSKNCSFIITANN 140

Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILK--IH-AAGIAKHGEIDYEAVVKLAE 235
            + +   L    R  R I+  +P ++ ++E++K  I    GI +   ++ +  V LA 
Sbjct: 141 KNGIIEPLR--SRC-RVIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKV-LAA 194

Length = 316

>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain

 Score = 39.3 bits (93), Expect = 6e-04
 Identities = 28/84 (33%), Positives = 40/84 (47%), Gaps = 24/84 (28%)

Query: 69  VLLYGPPGTGKTLLARAI--ASN-IDANFLKVVSSAIIDKYIGESARLIREMFGYAR--- 122
           VL+ G  GTGK L ARAI   S   D  F+ V  +AI ++ + ES     E+FG+ +   
Sbjct: 25  VLITGESGTGKELFARAIHQLSPRADGPFVAVNCAAIPEELL-ES-----ELFGHEKGAF 78

Query: 123 -----DHQPCI-------IFMDEI 134
                D +          +F+DEI
Sbjct: 79  TGAVSDRKGLFELADGGTLFLDEI 102

Length = 168

>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1

 Score = 39.6 bits (93), Expect = 9e-04
 Identities = 13/23 (56%), Positives = 15/23 (65%)

Query: 69  VLLYGPPGTGKTLLARAIASNID 91
           V  YGP  TGKT LA+AIA  + 
Sbjct: 116 VWFYGPASTGKTNLAQAIAHAVP 138

This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA. NS1, is the major non-structural protein. It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein. It has DNA helicase and ATPase activity. Length = 271

>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases

 Score = 38.2 bits (89), Expect = 0.001
 Identities = 28/120 (23%), Positives = 41/120 (34%), Gaps = 27/120 (22%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII-------------------DKYI-- 107
           +L++GP G+GKT LA  +A NI     KVV   I                    D  I  
Sbjct: 2   ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61

Query: 108 -----GESARLIREMFGYARDHQPC-IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN 161
                  +A  +       R+     +I +DE+  +             E+   L ELL 
Sbjct: 62  FATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLE 121

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. Length = 165

>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 13/20 (65%), Positives = 15/20 (75%)

Query: 68  GVLLYGPPGTGKTLLARAIA 87
           G+LL+G  GTGKT LA  IA
Sbjct: 116 GLLLWGSVGTGKTYLAACIA 135

Length = 268

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 37.3 bits (87), Expect = 0.002
 Identities = 18/92 (19%), Positives = 35/92 (38%), Gaps = 16/92 (17%)

Query: 69  VLLYGPPGTGKTLLARAIASN--------IDAN-------FLKVVSSAI-IDKYIGESAR 112
            +L G  G+GKT L R +A          ++A         L+ +  A+ +    G +A 
Sbjct: 7   GVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTAE 66

Query: 113 LIREMFGYARDHQPCIIFMDEIDAIGGRRFSE 144
           L+  +    +     ++ +DE   +      E
Sbjct: 67  LLEAILDALKRRGRPLLIIDEAQHLSLEALEE 98

Length = 124

>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 10/20 (50%), Positives = 16/20 (80%)

Query: 69 VLLYGPPGTGKTLLARAIAS 88
          +L+ GPPG+GKT+LA+ +  
Sbjct: 25 LLMIGPPGSGKTMLAKRLPG 44

Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. Length = 207

>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated

 Score = 38.3 bits (90), Expect = 0.003
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 38  SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASN-IDANFL 95
            D+    R+++E  L   + F+    K  + +L YG  GTGKT L+  IA   +D    
Sbjct: 155 DDEPLSPRKNMEKILEKCKNFIENFDKNNENLLFYGNTGTGKTFLSNCIAKELLDRGKS 213

Length = 329

>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication, recombination, and repair]

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 12/25 (48%), Positives = 17/25 (68%)

Query: 66  PKGVLLYGPPGTGKTLLARAIASNI 90
            + ++L GPPG GKT LA AI + +
Sbjct: 105 GENLVLLGPPGVGKTHLAIAIGNEL 129

Length = 254

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	292
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
PRK03992	389	proteasome-activating nucleotidase; Provisional	100.0
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	100.0
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	100.0
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	100.0
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	100.0
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	100.0
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	100.0
CHL00176	638	ftsH cell division protein; Validated	100.0
CHL00195	489	ycf46 Ycf46; Provisional	100.0
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	100.0
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	100.0
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	100.0
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	100.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	100.0
CHL00206	2281	ycf2 Ycf2; Provisional	99.97
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.97
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.97
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.95
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.95
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.94
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.91
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.91
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.9
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.9
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.89
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.89
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.89
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.88
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.88
CHL00181	287	cbbX CbbX; Provisional	99.88
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.88
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.88
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.88
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.87
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.87
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.86
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.86
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.86
PF00004	132	AAA: ATPase family associated with various cellula	99.86
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.86
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.85
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.85
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.85
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.84
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK13342	413	recombination factor protein RarA; Reviewed	99.84
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.84
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.84
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.83
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.83
PRK04195	482	replication factor C large subunit; Provisional	99.83
PLN03025	319	replication factor C subunit; Provisional	99.83
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.83
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.82
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.82
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.82
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.81
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.81
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.81
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.81
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.81
PRK12402	337	replication factor C small subunit 2; Reviewed	99.81
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.81
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.8
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.8
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.8
PRK13341	725	recombination factor protein RarA/unknown domain f	99.8
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.8
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.8
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.8
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.8
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.8
PHA02544	316	44 clamp loader, small subunit; Provisional	99.79
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.79
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.79
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.79
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.79
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.79
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.79
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.78
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.78
PRK06893	229	DNA replication initiation factor; Validated	99.77
KOG2028	554	consensus ATPase related to the helicase subunit o	99.77
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.77
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.77
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.77
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.77
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.77
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.77
PRK08084	235	DNA replication initiation factor; Provisional	99.77
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.77
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.76
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.76
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.75
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.75
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.75
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.75
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.75
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.74
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.73
PRK08727	233	hypothetical protein; Validated	99.73
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.73
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.73
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.72
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.71
CHL00095	821	clpC Clp protease ATP binding subunit	99.71
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.71
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.71
PRK05642	234	DNA replication initiation factor; Validated	99.7
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.7
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.69
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.69
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.68
PRK10865	857	protein disaggregation chaperone; Provisional	99.68
PRK12422	445	chromosomal replication initiation protein; Provis	99.67
PRK06620	214	hypothetical protein; Validated	99.67
PRK09087	226	hypothetical protein; Validated	99.66
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.66
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.66
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.65
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.64
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.63
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.62
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.62
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.6
PRK13531	498	regulatory ATPase RavA; Provisional	99.58
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.58
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.58
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.58
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.58
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.57
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.56
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.56
COG0714	329	MoxR-like ATPases [General function prediction onl	99.56
smart00350	509	MCM minichromosome maintenance proteins.	99.55
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.55
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	99.55
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	99.54
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.54
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.54
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.54
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.52
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	99.51
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.51
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.5
COG2204	464	AtoC Response regulator containing CheY-like recei	99.5
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	99.49
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.49
PRK04132	846	replication factor C small subunit; Provisional	99.49
PHA02244	383	ATPase-like protein	99.48
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.48
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.47
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.47
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.47
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	99.46
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.46
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.46
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.46
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	99.45
KOG1514	767	consensus Origin recognition complex, subunit 1, a	99.45
PRK10865	857	protein disaggregation chaperone; Provisional	99.44
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.44
PRK09862	506	putative ATP-dependent protease; Provisional	99.44
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	99.43
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.43
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.43
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.42
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.42
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.42
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.4
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.4
CHL00095	821	clpC Clp protease ATP binding subunit	99.4
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.39
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	99.39
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.38
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.37
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.36
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.35
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.35
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.34
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.34
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.34
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.34
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.33
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.33
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	99.31
PRK13765	637	ATP-dependent protease Lon; Provisional	99.3
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	99.3
smart00382	148	AAA ATPases associated with a variety of cellular	99.26
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	99.26
PF07726	131	AAA_3: ATPase family associated with various cellu	99.26
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.25
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	99.25
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.24
PRK12377	248	putative replication protein; Provisional	99.22
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	99.21
COG0606	490	Predicted ATPase with chaperone activity [Posttran	99.2
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.19
PRK08116	268	hypothetical protein; Validated	99.19
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.19
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.18
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	99.18
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.18
PRK08699	325	DNA polymerase III subunit delta'; Validated	99.18
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	99.16
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.15
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	99.15
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.13
PRK15115	444	response regulator GlrR; Provisional	99.11
COG1241	682	MCM2 Predicted ATPase involved in replication cont	99.11
PRK07952	244	DNA replication protein DnaC; Validated	99.1
PRK08181	269	transposase; Validated	99.09
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	99.09
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.08
PF13173	128	AAA_14: AAA domain	99.07
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	99.07
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	99.06
PRK05917	290	DNA polymerase III subunit delta'; Validated	99.0
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.99
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	98.99
PRK06526	254	transposase; Provisional	98.99
PRK06835	329	DNA replication protein DnaC; Validated	98.98
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	98.97
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.93
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.93
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.93
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.92
PRK08939	306	primosomal protein DnaI; Reviewed	98.91
PRK06921	266	hypothetical protein; Provisional	98.91
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.9
PRK09183	259	transposase/IS protein; Provisional	98.9
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.9
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.88
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.87
PF14516	331	AAA_35: AAA-like domain	98.86
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.85
PF05729	166	NACHT: NACHT domain	98.84
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.81
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.8
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	98.79
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	98.75
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.74
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.74
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.73
KOG0481	729	consensus DNA replication licensing factor, MCM5 c	98.69
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	98.66
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.65
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.63
COG1485	367	Predicted ATPase [General function prediction only	98.62
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	98.6
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	98.59
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	98.57
TIGR02237	209	recomb_radB DNA repair and recombination protein R	98.5
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	98.43
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.42
PRK06581	263	DNA polymerase III subunit delta'; Validated	98.42
cd03216	163	ABC_Carb_Monos_I This family represents the domain	98.41
PRK11823	446	DNA repair protein RadA; Provisional	98.41
COG4178	604	ABC-type uncharacterized transport system, permeas	98.4
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	98.4
KOG2383	467	consensus Predicted ATPase [General function predi	98.39
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	98.38
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	98.38
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	98.37
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	98.37
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	98.35
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.34
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	98.34
cd00983	325	recA RecA is a bacterial enzyme which has roles in	98.33
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.32
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.31
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	98.31
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.3
PRK08533	230	flagellar accessory protein FlaH; Reviewed	98.3
COG4650	531	RtcR Sigma54-dependent transcription regulator con	98.3
PRK04841	903	transcriptional regulator MalT; Provisional	98.29
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	98.28
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	98.28
COG2884	223	FtsE Predicted ATPase involved in cell division [C	98.27
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	98.26
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	98.26
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	98.26
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	98.25
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	98.25
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	98.24
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	98.24
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	98.23
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.22
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	98.22
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	98.21
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	98.21
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	98.21
PRK06067	234	flagellar accessory protein FlaH; Validated	98.21
PRK10536	262	hypothetical protein; Provisional	98.2
PHA00729	226	NTP-binding motif containing protein	98.2
COG4619	223	ABC-type uncharacterized transport system, ATPase	98.2
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	98.19
PRK04296	190	thymidine kinase; Provisional	98.17
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	98.17
KOG0479	818	consensus DNA replication licensing factor, MCM3 c	98.17
PHA02624	647	large T antigen; Provisional	98.16
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	98.16
cd03246	173	ABCC_Protease_Secretion This family represents the	98.15
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	98.15
cd01394	218	radB RadB. The archaeal protein radB shares simila	98.15
PRK08118	167	topology modulation protein; Reviewed	98.14
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	98.14
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	98.13
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	98.13
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	98.13
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	98.13
PRK07261	171	topology modulation protein; Provisional	98.12
COG3899	849	Predicted ATPase [General function prediction only	98.11
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	98.11
PRK09354	349	recA recombinase A; Provisional	98.11
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	98.1
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	98.09
PRK15455	644	PrkA family serine protein kinase; Provisional	98.09
PRK05973	237	replicative DNA helicase; Provisional	98.09
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	98.07
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	98.07
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	98.07
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	98.07
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	98.06
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	98.06
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	98.06
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	98.06
PHA02774	613	E1; Provisional	98.05
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	98.05
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	98.05
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	98.05
COG1118	345	CysA ABC-type sulfate/molybdate transport systems,	98.04
cd01128	249	rho_factor Transcription termination factor rho is	98.04
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	98.04
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	98.03
TIGR02533	486	type_II_gspE general secretory pathway protein E.	98.03
cd03215	182	ABC_Carb_Monos_II This family represents domain II	98.03
PRK09376	416	rho transcription termination factor Rho; Provisio	98.02
PRK00771	437	signal recognition particle protein Srp54; Provisi	98.02
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	98.02
PRK00131	175	aroK shikimate kinase; Reviewed	98.02
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	98.02
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.01
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	98.01
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	98.0
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	97.99
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	97.99
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	97.99
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	97.98
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	97.98
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	97.98
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.97
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	97.97
PRK04328	249	hypothetical protein; Provisional	97.97
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	97.97
COG1127	263	Ttg2A ABC-type transport system involved in resist	97.96
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	97.95
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	97.94
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	97.94
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	97.94
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.93
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	97.93
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.93
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	97.93
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	97.92
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	97.92
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	97.91
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	97.91
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.91
TIGR01188	302	drrA daunorubicin resistance ABC transporter ATP-b	97.91
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	97.91
PRK10436	462	hypothetical protein; Provisional	97.9
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	97.9
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	97.9
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	97.9
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	97.9
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	97.9
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	97.89
PRK06762	166	hypothetical protein; Provisional	97.89
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.89
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	97.88
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	97.88
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	97.87
cd03269	210	ABC_putative_ATPase This subfamily is involved in	97.87
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.87
PRK13537	306	nodulation ABC transporter NodI; Provisional	97.87
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	97.87
PRK11650	356	ugpC glycerol-3-phosphate transporter ATP-binding	97.86
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	97.86
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	97.85
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	97.85
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	97.85
KOG0056	790	consensus Heavy metal exporter HMT1, ABC superfami	97.84
COG4555	245	NatA ABC-type Na+ transport system, ATPase compone	97.84
TIGR02314	343	ABC_MetN D-methionine ABC transporter, ATP-binding	97.84
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	97.84
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	97.84
PTZ00202	550	tuzin; Provisional	97.84
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	97.83
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	97.83
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	97.83
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.83
PRK03839	180	putative kinase; Provisional	97.83
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	97.82
PRK04301	317	radA DNA repair and recombination protein RadA; Va	97.82
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	97.82
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	97.81
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.81
PRK00625	173	shikimate kinase; Provisional	97.81
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	97.81
PRK13947	171	shikimate kinase; Provisional	97.81
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	97.8
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	97.8
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	97.8
TIGR02236	310	recomb_radA DNA repair and recombination protein R	97.8
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	97.8
PRK09452	375	potA putrescine/spermidine ABC transporter ATPase	97.8
PRK09536	402	btuD corrinoid ABC transporter ATPase; Reviewed	97.8
PRK13833	323	conjugal transfer protein TrbB; Provisional	97.8
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	97.8
PRK11607	377	potG putrescine transporter ATP-binding subunit; P	97.79
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	97.79
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	97.79
TIGR00767	415	rho transcription termination factor Rho. Members	97.79
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	97.79
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	97.79
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	97.78
PRK13695	174	putative NTPase; Provisional	97.78
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	97.78
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	97.77
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	97.77
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	97.76
PRK13536	340	nodulation factor exporter subunit NodI; Provision	97.76
PRK11432	351	fbpC ferric transporter ATP-binding subunit; Provi	97.76
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	97.76
PRK13949	169	shikimate kinase; Provisional	97.76
PRK06217	183	hypothetical protein; Validated	97.76
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	97.75
PTZ00035	337	Rad51 protein; Provisional	97.75
PRK14530	215	adenylate kinase; Provisional	97.75
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.75
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.75
COG4133	209	CcmA ABC-type transport system involved in cytochr	97.75
PRK13546	264	teichoic acids export protein ATP-binding subunit;	97.74
TIGR03265	353	PhnT2 putative 2-aminoethylphosphonate ABC transpo	97.74
PRK14532	188	adenylate kinase; Provisional	97.74
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.74
TIGR01288	303	nodI ATP-binding ABC transporter family nodulation	97.74
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.74
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.74
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	97.74
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	97.73
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	97.73
PRK12339	197	2-phosphoglycerate kinase; Provisional	97.72
PRK11153	343	metN DL-methionine transporter ATP-binding subunit	97.72
PRK09519	790	recA DNA recombination protein RecA; Reviewed	97.72
PRK11000	369	maltose/maltodextrin transporter ATP-binding prote	97.72
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	97.71
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	97.71
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	97.71
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	97.7
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.7
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	97.7
PRK06547	172	hypothetical protein; Provisional	97.7
PRK13948	182	shikimate kinase; Provisional	97.7
TIGR03258	362	PhnT 2-aminoethylphosphonate ABC transport system,	97.7
COG4181	228	Predicted ABC-type transport system involved in ly	97.7
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	97.69
COG3840	231	ThiQ ABC-type thiamine transport system, ATPase co	97.69
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	97.69
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	97.69
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	97.69
COG4586	325	ABC-type uncharacterized transport system, ATPase	97.69
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	97.68
PRK14531	183	adenylate kinase; Provisional	97.68
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	97.68
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	97.68
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.68
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	97.67
PF05872	502	DUF853: Bacterial protein of unknown function (DUF	97.67
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.67
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	97.67

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-54  Score=364.47  Aligned_cols=277  Identities=62%  Similarity=1.035  Sum_probs=270.6

Q ss_pred             chhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHH
Q 022768            2 TTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL   81 (292)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~   81 (292)
                      .++++..-+|.+.+|.+..|--++.|.++++++.|+++++++|.+.+..|+.+.+.|.++|+.|+.+||+|||||||||.
T Consensus       121 ~s~~Iv~vLp~~~Dp~V~~M~v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTL  200 (406)
T COG1222         121 DSYSIVRVLPPEVDPRVSVMEVEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTL  200 (406)
T ss_pred             CcceeeeeCCCccCchhheeeeccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHH
Confidence            46788889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHH
Q 022768           82 LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN  161 (292)
Q Consensus        82 l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~  161 (292)
                      +||++|+..+..|+++..+++..+|.|+..+.++++|..++...|+||||||+|.++.++.+.+++.+.+.|++++++|+
T Consensus       201 LAkAVA~~T~AtFIrvvgSElVqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~  280 (406)
T COG1222         201 LAKAVANQTDATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLN  280 (406)
T ss_pred             HHHHHHhccCceEEEeccHHHHHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHH
Q 022768          162 QLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGAD  241 (292)
Q Consensus       162 ~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~d  241 (292)
                      +++++.+.+++-||++||.++.++|++++++||+..|+||.|+.+.|.+|++-+.+......++|++.|+..++|+|++|
T Consensus       281 qlDGFD~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAd  360 (406)
T COG1222         281 QLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGAD  360 (406)
T ss_pred             hccCCCCCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          242 LRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       242 i~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      +..+|.+|.+.|++..+..||++||.+|++.+.....
T Consensus       361 lkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV~~~~~  397 (406)
T COG1222         361 LKAICTEAGMFAIRERRDEVTMEDFLKAVEKVVKKKK  397 (406)
T ss_pred             HHHHHHHHhHHHHHhccCeecHHHHHHHHHHHHhccc
Confidence            9999999999999999999999999999999987543

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.6e-45  Score=328.45  Aligned_cols=273  Identities=44%  Similarity=0.753  Sum_probs=254.4

Q ss_pred             CChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           14 VDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      ..|+...-+--+.|+++|+++.|+++.|++|++.+.+|++..+.|.++|+.++++||+|||||+|||++||++|++.+.+
T Consensus       416 i~psa~Re~~ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~n  495 (693)
T KOG0730|consen  416 IRPSALREILVEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMN  495 (693)
T ss_pred             CCchhhhheeccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCC
Confidence            44555555667889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           94 FLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      |+.+.+.++.++++|+.++.++.+|+.++...|+|+||||+|.+...++++.+   .-..+.|..+|++++++....+++
T Consensus       496 FlsvkgpEL~sk~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~---~v~~RVlsqLLtEmDG~e~~k~V~  572 (693)
T KOG0730|consen  496 FLSVKGPELFSKYVGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSS---GVTDRVLSQLLTEMDGLEALKNVL  572 (693)
T ss_pred             eeeccCHHHHHHhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCcc---chHHHHHHHHHHHcccccccCcEE
Confidence            99999999999999999999999999999999999999999999988875444   455678889999999998888999


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      ||++||+|+.+++++.+++||+..+++++||.+.|.+|++.++++.+...++|++.|+..|+|||++||..+|++|...|
T Consensus       573 ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq~A~~~a  652 (693)
T KOG0730|consen  573 VIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQEAALLA  652 (693)
T ss_pred             EEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhcC--CcccHHHHHHHHHHHhhhhhhchhhhhhhhc
Q 022768          254 IRAER--DYVIHEDFMKAVRKLNEAKKLESSAHYNADF  289 (292)
Q Consensus       254 ~~~~~--~~i~~~~~~~a~~~~~~~~~~~~~~~~~~~~  289 (292)
                      +++.-  ..|+.+++.+|++.+.+.-.......|+++.
T Consensus       653 ~~e~i~a~~i~~~hf~~al~~~r~s~~~~~~~~Ye~fa  690 (693)
T KOG0730|consen  653 LRESIEATEITWQHFEEALKAVRPSLTSELLEKYEDFA  690 (693)
T ss_pred             HHHhcccccccHHHHHHHHHhhcccCCHHHHHHHHHHh
Confidence            99854  4799999999999999988888888887763

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.6e-42  Score=279.08  Aligned_cols=269  Identities=49%  Similarity=0.864  Sum_probs=258.8

Q ss_pred             hCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHH
Q 022768            9 ALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      -+|-+.+++++.+-....|.+++.++.|++-+++++.+.+..|+.+.+++.+.|+.|++++|++||||+|||.+++++|+
T Consensus       132 vlppeadssi~ml~~~ekpdvsy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~  211 (408)
T KOG0727|consen  132 VLPPEADSSISMLGPDEKPDVSYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAN  211 (408)
T ss_pred             ccCCcccccccccCCCCCCCccccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhh
Confidence            36888999999887888899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           89 NIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        89 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                      .....|++++.+++..++.|+..+.++.+|+.++.+.|+|+||||+|.++.++.+.+++.+.+.++.|.+++++++++..
T Consensus       212 ~t~a~firvvgsefvqkylgegprmvrdvfrlakenapsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq  291 (408)
T KOG0727|consen  212 HTTAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQ  291 (408)
T ss_pred             ccchheeeeccHHHHHHHhccCcHHHHHHHHHHhccCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHH
Q 022768          169 LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       169 ~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      .-++-+|.+||..+.++|++++++|.+..|.||.|+..+++-++....+....+.++|++.+..+.+..|+.||..+|++
T Consensus       292 ~~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicqe  371 (408)
T KOG0727|consen  292 TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQE  371 (408)
T ss_pred             ccceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHHH
Confidence            88999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCcccHHHHHHHHHHHhhhh
Q 022768          249 AGMSAIRAERDYVIHEDFMKAVRKLNEAK  277 (292)
Q Consensus       249 a~~~a~~~~~~~i~~~~~~~a~~~~~~~~  277 (292)
                      |.+.|.+.++-.|...|+.++++......
T Consensus       372 agm~avr~nryvvl~kd~e~ay~~~vk~~  400 (408)
T KOG0727|consen  372 AGMLAVRENRYVVLQKDFEKAYKTVVKKD  400 (408)
T ss_pred             HhHHHHHhcceeeeHHHHHHHHHhhcCCc
Confidence            99999999999999999999998876543

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=100.00  E-value=1.3e-41  Score=302.34  Aligned_cols=274  Identities=48%  Similarity=0.845  Sum_probs=253.9

Q ss_pred             hhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768            3 TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      +..+...+|.+.++.+..+.-...|.++|++|.|++.++++|.+.+..|+...+.|.++|+.++.++||+||||||||++
T Consensus       116 ~~~~~~~l~~~~~~~~~~~~~~~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~L  195 (398)
T PTZ00454        116 SHAVVDILPPEADSSIQLLQMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTML  195 (398)
T ss_pred             chhHHHhccccccchhhhhcccCCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHH
Confidence            44566778988999888777788999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           83 ARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        83 ~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      ++++|+.++.+++.+....+...+.+.....++.+|..+....|+||||||+|.++.++.+..++.+...+..+.+++..
T Consensus       196 AkalA~~l~~~fi~i~~s~l~~k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~  275 (398)
T PTZ00454        196 AKAVAHHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQ  275 (398)
T ss_pred             HHHHHHhcCCCEEEEehHHHHHHhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHH
Confidence            99999999999999999988888899999999999999999999999999999998877666556667788899999999


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di  242 (292)
                      +++.....++.+|++||.++.+++++++++||+..|+++.|+.++|..||+.++.......++++..++..+.||+++||
T Consensus       276 ld~~~~~~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI  355 (398)
T PTZ00454        276 MDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADI  355 (398)
T ss_pred             hhccCCCCCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHH
Confidence            98877777899999999999999999999999999999999999999999999988888888999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      ..+|++|...|.++++..|+.+|+.+|++.+...
T Consensus       356 ~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v~~~  389 (398)
T PTZ00454        356 AAICQEAGMQAVRKNRYVILPKDFEKGYKTVVRK  389 (398)
T ss_pred             HHHHHHHHHHHHHcCCCccCHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999998764

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.1e-42  Score=279.62  Aligned_cols=275  Identities=49%  Similarity=0.855  Sum_probs=264.4

Q ss_pred             hhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHH
Q 022768            6 IMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARA   85 (292)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~   85 (292)
                      +.-++|.+-++.+-.|.-...|+-.++++.|++.++++|.+.+..|+..++.|..+|+.++.++|+|||||+|||.++++
T Consensus       145 iletLP~eyDsrVkaMevDekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARA  224 (424)
T KOG0652|consen  145 ILETLPSEYDSRVKAMEVDEKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARA  224 (424)
T ss_pred             ehhcCChhhhhhcceeeeccCCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHH
Confidence            56678999899888888889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768           86 IASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus        86 la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      .|...+..|+.+....+...+.|+..+.++..|..++...|+|+||||+|.++.++.++-..++++.++.++++++++++
T Consensus       225 cAaqT~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDG  304 (424)
T KOG0652|consen  225 CAAQTNATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDG  304 (424)
T ss_pred             HHHhccchHHHhcchHHHhhhhcchHHHHHHHHHHhhccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcC
Confidence            99999999999999999999999999999999999999999999999999999999998888999999999999999999


Q ss_pred             CCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHH
Q 022768          166 FDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNV  245 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l  245 (292)
                      +.+..++-||++||+.+-++|++++++|.+..|.||.|+.+.|..|++-+........+++++.|++-+++|++.++..+
T Consensus       305 Fss~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTddFNGAQcKAV  384 (424)
T KOG0652|consen  305 FSSDDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTDDFNGAQCKAV  384 (424)
T ss_pred             CCCccceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhcccccCchhheee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhhc
Q 022768          246 CTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLE  280 (292)
Q Consensus       246 ~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~~  280 (292)
                      |-+|.+.|++++...|+.+|+.+.+.+++..++.+
T Consensus       385 cVEAGMiALRr~atev~heDfmegI~eVqakKka~  419 (424)
T KOG0652|consen  385 CVEAGMIALRRGATEVTHEDFMEGILEVQAKKKAS  419 (424)
T ss_pred             ehhhhHHHHhcccccccHHHHHHHHHHHHHhhhhc
Confidence            99999999999999999999999999999876643

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=7.3e-42  Score=303.72  Aligned_cols=260  Identities=39%  Similarity=0.692  Sum_probs=238.6

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      -.|.++|+++.++++++.+|+.++.+|++..+.|..+|+..+.+||++||||+|||.+||++|++.+.+|+.+...++.+
T Consensus       504 tVPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPELlN  583 (802)
T KOG0733|consen  504 TVPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPELLN  583 (802)
T ss_pred             ecCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHHHHH
Confidence            45889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      +|+|+.++.++.+|.+++.+.|||||+||+|.|.+.++...+   ....+.+.++|.++++.....++.||++||+|+.+
T Consensus       584 kYVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~s---~~s~RvvNqLLtElDGl~~R~gV~viaATNRPDiI  660 (802)
T KOG0733|consen  584 KYVGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEGS---SVSSRVVNQLLTELDGLEERRGVYVIAATNRPDII  660 (802)
T ss_pred             HHhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCCc---hhHHHHHHHHHHHhcccccccceEEEeecCCCccc
Confidence            999999999999999999999999999999999999877654   34456777888899999888999999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc--CccCCCCCCHHHHHHHcC--CCCHHHHHHHHHHHHHHHHHhcC--
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA--GIAKHGEIDYEAVVKLAE--GFNGADLRNVCTEAGMSAIRAER--  258 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~--~~~~~~~~~~~~l~~~~~--g~~~~di~~l~~~a~~~a~~~~~--  258 (292)
                      ++++++++||+..++++.|+.++|.+|++....  ......+++++.++..+.  ||++.|+..+|++|...|+++..  
T Consensus       661 DpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvreAsi~AL~~~~~~  740 (802)
T KOG0733|consen  661 DPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVREASILALRESLFE  740 (802)
T ss_pred             chhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999999999999999998  667779999999999877  99999999999999999988621  


Q ss_pred             --------------CcccHHHHHHHHHHHhhhhhhchhhhhhh
Q 022768          259 --------------DYVIHEDFMKAVRKLNEAKKLESSAHYNA  287 (292)
Q Consensus       259 --------------~~i~~~~~~~a~~~~~~~~~~~~~~~~~~  287 (292)
                                    -.++..+|++|++.+.+.-.+.....|+.
T Consensus       741 ~~~~~~~~~~~~~~~~~t~~hF~eA~~~i~pSv~~~dr~~Yd~  783 (802)
T KOG0733|consen  741 IDSSEDDVTVRSSTIIVTYKHFEEAFQRIRPSVSERDRKKYDR  783 (802)
T ss_pred             ccccCcccceeeeeeeecHHHHHHHHHhcCCCccHHHHHHHHH
Confidence                          14778899999999999777666555553

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=5.4e-42  Score=278.05  Aligned_cols=276  Identities=54%  Similarity=0.941  Sum_probs=264.4

Q ss_pred             chhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHH
Q 022768            2 TTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL   81 (292)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~   81 (292)
                      .+..|+-.+|.-.+|++..|.-+..|.++++++.|+.++++.|.+.+..|+.+.+.|..+|+.|+.++|+|||||+|||.
T Consensus       147 nkyqi~lplppkidpsvtmm~veekpdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl  226 (435)
T KOG0729|consen  147 NKYQIQLPLPPKIDPSVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTL  226 (435)
T ss_pred             cceeEeccCCCCCCCceeEEEeecCCCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhH
Confidence            45566777888899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHH
Q 022768           82 LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN  161 (292)
Q Consensus        82 l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~  161 (292)
                      .++++|++.+..|+++-.+++..+++|+..+.++++|..++..+.|++|+||+|.+++.+.+...+++++.|+.++++++
T Consensus       227 ~aravanrtdacfirvigselvqkyvgegarmvrelf~martkkaciiffdeidaiggarfddg~ggdnevqrtmleli~  306 (435)
T KOG0729|consen  227 CARAVANRTDACFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELIN  306 (435)
T ss_pred             HHHHHhcccCceEEeehhHHHHHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHH
Q 022768          162 QLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGAD  241 (292)
Q Consensus       162 ~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~d  241 (292)
                      +++++.+.+++-|+.+||.|+.+++++.+++|.+..++|..|+.+.|.+|++-+........++-++.++++..+.++.+
T Consensus       307 qldgfdprgnikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcpnstgae  386 (435)
T KOG0729|consen  307 QLDGFDPRGNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPNSTGAE  386 (435)
T ss_pred             hccCCCCCCCeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCCCCcchH
Confidence            99999999999999999999999999999999999999999999999999999999889999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhh
Q 022768          242 LRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAK  277 (292)
Q Consensus       242 i~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~  277 (292)
                      |+++|.+|.+.|++.-+...|..|+.+|+..+..-+
T Consensus       387 irsvcteagmfairarrk~atekdfl~av~kvvkgy  422 (435)
T KOG0729|consen  387 IRSVCTEAGMFAIRARRKVATEKDFLDAVNKVVKGY  422 (435)
T ss_pred             HHHHHHHhhHHHHHHHhhhhhHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999998877533

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.8e-41  Score=270.86  Aligned_cols=274  Identities=53%  Similarity=0.902  Sum_probs=263.3

Q ss_pred             hhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHH
Q 022768            5 TIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLAR   84 (292)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~   84 (292)
                      .+-+-+|.-++|.++-|.-+..|..+++-+.|++.+++++++.+..|...+++|..+|+..+.++|++||||+|||.+++
T Consensus       120 ~lhkiLpnKvDpLVsLMmVeKvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlar  199 (404)
T KOG0728|consen  120 TLHKILPNKVDPLVSLMMVEKVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLAR  199 (404)
T ss_pred             HHHHhcccccchhhHHHhhhhCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHH
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh
Q 022768           85 AIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD  164 (292)
Q Consensus        85 ~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~  164 (292)
                      ++|+...+.|++++.+++..++.|+..+.++++|-.++...|+|+|+||+|.++..+.+++++++.+.++.+++++++++
T Consensus       200 aVahht~c~firvsgselvqk~igegsrmvrelfvmarehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqld  279 (404)
T KOG0728|consen  200 AVAHHTDCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLD  279 (404)
T ss_pred             HHHhhcceEEEEechHHHHHHHhhhhHHHHHHHHHHHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhcc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHH
Q 022768          165 GFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRN  244 (292)
Q Consensus       165 ~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~  244 (292)
                      ++....++-+|.+||.-+-+++++++++|++..|.||+|+.+.|.+|++-+.........+++..++....|.|+.++..
T Consensus       280 gfeatknikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~  359 (404)
T KOG0728|consen  280 GFEATKNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKG  359 (404)
T ss_pred             ccccccceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhh
Confidence            99999999999999999999999999999999999999999999999999999888899999999999999999999999


Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          245 VCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       245 l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      +|.+|.++|++.-+-+||.+|+.-|...+....+
T Consensus       360 vcteagm~alrerrvhvtqedfemav~kvm~k~~  393 (404)
T KOG0728|consen  360 VCTEAGMYALRERRVHVTQEDFEMAVAKVMQKDS  393 (404)
T ss_pred             hhhhhhHHHHHHhhccccHHHHHHHHHHHHhccc
Confidence            9999999999999999999999999988876544

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=100.00  E-value=2.5e-40  Score=295.55  Aligned_cols=276  Identities=57%  Similarity=0.955  Sum_probs=252.2

Q ss_pred             hhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHH
Q 022768            5 TIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLAR   84 (292)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~   84 (292)
                      .+..-+|...++.+..+.-...|.++|++|.|++++++++.+++..++.....|..+|+.++.++||+||||||||++|+
T Consensus       104 ~~~~~l~~~~~~~~~~~~~~~~p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAk  183 (389)
T PRK03992        104 AIVEVLPSEKDPRVQAMEVIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAK  183 (389)
T ss_pred             hhhhcccccccchhheeeecCCCCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHH
Confidence            44556777777776666667788999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh
Q 022768           85 AIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD  164 (292)
Q Consensus        85 ~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~  164 (292)
                      ++|++++.+++.+++..+...+.+.....++.+|..+....|+||||||+|.++..+.+.....+.+.+..+..++..++
T Consensus       184 aia~~~~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld  263 (389)
T PRK03992        184 AVAHETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMD  263 (389)
T ss_pred             HHHHHhCCCEEEeehHHHhHhhccchHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhcc
Confidence            99999999999999999998888998999999999999999999999999999988776666566778888889998888


Q ss_pred             CCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHH
Q 022768          165 GFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRN  244 (292)
Q Consensus       165 ~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~  244 (292)
                      +....+++.||+|||.++.+++++++++||+..+.+++|+.++|.+||+.++.......++++..++..+.||+++|+..
T Consensus       264 ~~~~~~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~  343 (389)
T PRK03992        264 GFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKA  343 (389)
T ss_pred             ccCCCCCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHH
Confidence            77777789999999999999999999999999999999999999999999998887777899999999999999999999


Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhhc
Q 022768          245 VCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLE  280 (292)
Q Consensus       245 l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~~  280 (292)
                      +|++|...|.+++...|+.+|+.+|+..+......+
T Consensus       344 l~~eA~~~a~~~~~~~i~~~d~~~A~~~~~~~~~~~  379 (389)
T PRK03992        344 ICTEAGMFAIRDDRTEVTMEDFLKAIEKVMGKEEKD  379 (389)
T ss_pred             HHHHHHHHHHHcCCCCcCHHHHHHHHHHHhcccccc
Confidence            999999999999999999999999999998866654

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.3e-40  Score=282.20  Aligned_cols=269  Identities=37%  Similarity=0.620  Sum_probs=234.6

Q ss_pred             hhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           18 VYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        18 ~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ....+-+..|.+.|++|.|++++++-|++.+..|+.-++.|.... .|.+++|++||||||||.|||++|.+++..|+.|
T Consensus       198 lerdIl~~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~Gir-rPWkgvLm~GPPGTGKTlLAKAvATEc~tTFFNV  276 (491)
T KOG0738|consen  198 LERDILQRNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATECGTTFFNV  276 (491)
T ss_pred             HHHHHhccCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcc-cccceeeeeCCCCCcHHHHHHHHHHhhcCeEEEe
Confidence            345566778899999999999999999999999999999988755 6789999999999999999999999999999999


Q ss_pred             eccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC----CCeE
Q 022768           98 VSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL----GKVK  173 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~----~~~~  173 (292)
                      +.+.+.+++.|+.++.++.+|..++.+.|++|||||||.|+..++..+  ......+.=.++|-++++....    .-|+
T Consensus       277 SsstltSKwRGeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s~--EHEaSRRvKsELLvQmDG~~~t~e~~k~Vm  354 (491)
T KOG0738|consen  277 SSSTLTSKWRGESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGSS--EHEASRRVKSELLVQMDGVQGTLENSKVVM  354 (491)
T ss_pred             chhhhhhhhccchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCcc--chhHHHHHHHHHHHHhhccccccccceeEE
Confidence            999999999999999999999999999999999999999998885543  2333333334556565544222    2388


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      |+++||.|++++.++++  ||...|++|.|+.+.|..+++..+.......+++++.++..++|||+.||..+|++|.+.+
T Consensus       355 VLAATN~PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvCreAsm~~  432 (491)
T KOG0738|consen  355 VLAATNFPWDIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVCREASMMA  432 (491)
T ss_pred             EEeccCCCcchHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHHHHHHHHH
Confidence            88999999999999999  9999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhc-----------------CCcccHHHHHHHHHHHhhhhh---hchhhhhhhhcCC
Q 022768          254 IRAE-----------------RDYVIHEDFMKAVRKLNEAKK---LESSAHYNADFGK  291 (292)
Q Consensus       254 ~~~~-----------------~~~i~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~  291 (292)
                      .++.                 ...|+.+||.+|++.+++.-+   ....+.|.+.||+
T Consensus       433 mRR~i~g~~~~ei~~lakE~~~~pv~~~Dfe~Al~~v~pSvs~~d~~k~ekW~~efGS  490 (491)
T KOG0738|consen  433 MRRKIAGLTPREIRQLAKEEPKMPVTNEDFEEALRKVRPSVSAADLEKYEKWMDEFGS  490 (491)
T ss_pred             HHHHHhcCCcHHhhhhhhhccccccchhhHHHHHHHcCcCCCHHHHHHHHHHHHHhcC
Confidence            8852                 125899999999999998655   4457788899986

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.3e-41  Score=280.75  Aligned_cols=285  Identities=79%  Similarity=1.200  Sum_probs=272.4

Q ss_pred             CchhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHH
Q 022768            1 MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT   80 (292)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT   80 (292)
                      +++++|++-+|++++ .++++.++.+..++|+++.|...+..++.+.+..|+.+..++.++|+.++.+++||||||+|||
T Consensus       102 ittltIm~~lprevd-~vy~m~~e~~~~~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKT  180 (388)
T KOG0651|consen  102 ITTLTIMRGLPREVD-LVYNMSHEDPRNISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKT  180 (388)
T ss_pred             eeeeehhcccchHHH-HHHHhhhcCccccCHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchh
Confidence            367899999999999 9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHH
Q 022768           81 LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELL  160 (292)
Q Consensus        81 ~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l  160 (292)
                      .+|++++..+++.++.+..+.+.+.+.|+..+.+++.|+.++...||++|+||+|.+++.+..+.+..+++++.+|++++
T Consensus       181 lla~~Vaa~mg~nfl~v~ss~lv~kyiGEsaRlIRemf~yA~~~~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLl  260 (388)
T KOG0651|consen  181 LLARAVAATMGVNFLKVVSSALVDKYIGESARLIRDMFRYAREVIPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELL  260 (388)
T ss_pred             HHHHHHHHhcCCceEEeeHhhhhhhhcccHHHHHHHHHHHHhhhCceEEeehhhhhhccEEeccccchhHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999998888889999999999999


Q ss_pred             HHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHH
Q 022768          161 NQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA  240 (292)
Q Consensus       161 ~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~  240 (292)
                      +++++.....++-+|.|+|+++.++++|.+++|++..+..|.|+...|..|++-..........++.+.+..+++|+++.
T Consensus       261 nqmdgfd~l~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~f~ga  340 (388)
T KOG0651|consen  261 NQMDGFDTLHRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDGFNGA  340 (388)
T ss_pred             HhhccchhcccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhccChH
Confidence            99999999999999999999999999999999999999999999999999999888877777889999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhhchhhhhh
Q 022768          241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN  286 (292)
Q Consensus       241 di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~~~~~~~~  286 (292)
                      |++..|.+|-..|....+..+..+++..++..+...+..+...+|.
T Consensus       341 d~rn~~tEag~Fa~~~~~~~vl~Ed~~k~vrk~~~~kkle~~~~Y~  386 (388)
T KOG0651|consen  341 DLRNVCTEAGMFAIPEERDEVLHEDFMKLVRKQADAKKLELSLDYK  386 (388)
T ss_pred             HHhhhcccccccccchhhHHHhHHHHHHHHHHHHHHHHhhhhhhhc
Confidence            9999999999999999999999999999999998877766666664

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=100.00  E-value=4.7e-40  Score=294.07  Aligned_cols=276  Identities=50%  Similarity=0.872  Sum_probs=254.5

Q ss_pred             hhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768            3 TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      +..+...+|.++++.+..+.-...|+.+|++|.|++++++++.+++..++.....+..+|+.++.+++|+||||||||++
T Consensus       154 ~~~~~~~~~~~~d~~~~~~~~~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~L  233 (438)
T PTZ00361        154 THSVVGILLDEVDPLVSVMKVDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLL  233 (438)
T ss_pred             CCceEecCccccchhhhhcccccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHH
Confidence            34566678888999998887788899999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           83 ARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        83 ~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      ++++|++++.+++.+....+...+.+.....++.+|..+....|+||||||+|.++.++.+..++...+.+..+.+++..
T Consensus       234 AraIA~el~~~fi~V~~seL~~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~  313 (438)
T PTZ00361        234 AKAVANETSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQ  313 (438)
T ss_pred             HHHHHHhhCCCEEEEecchhhhhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHH
Confidence            99999999999999999999888889999999999999999999999999999999887766666777888889999999


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di  242 (292)
                      ++++....++.||++||.++.+++++.+++||+..|.|+.|+.++|.+||+.++.......+++++.++..+.|++++||
T Consensus       314 Ldg~~~~~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI  393 (438)
T PTZ00361        314 LDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADI  393 (438)
T ss_pred             HhhhcccCCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHH
Confidence            88776667899999999999999999998999999999999999999999999988877788999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      ..+|.+|...|.++++..|+.+||.+|+..+...+.
T Consensus       394 ~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v~~~~~  429 (438)
T PTZ00361        394 KAICTEAGLLALRERRMKVTQADFRKAKEKVLYRKK  429 (438)
T ss_pred             HHHHHHHHHHHHHhcCCccCHHHHHHHHHHHHhhcc
Confidence            999999999999999999999999999999866443

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.8e-40  Score=290.83  Aligned_cols=244  Identities=41%  Similarity=0.678  Sum_probs=230.7

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      -+++|+++.|+++++++|++.+.. ++++..|.++|-.-+.+|||.||||||||.||+++|.+.+.||++...+++-..+
T Consensus       299 ~nv~F~dVkG~DEAK~ELeEiVef-LkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdEm~  377 (752)
T KOG0734|consen  299 KNVTFEDVKGVDEAKQELEEIVEF-LKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMF  377 (752)
T ss_pred             cccccccccChHHHHHHHHHHHHH-hcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhhhh
Confidence            467899999999999999999987 8999999999999999999999999999999999999999999999999999999


Q ss_pred             cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCCh
Q 022768          107 IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDP  186 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~  186 (292)
                      +|...+.++.+|+.++.+.||||||||+|.+++++...   ........+.+++-+++++..+.+++||++||.|+.+++
T Consensus       378 VGvGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~---~~~y~kqTlNQLLvEmDGF~qNeGiIvigATNfpe~LD~  454 (752)
T KOG0734|consen  378 VGVGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPS---DQHYAKQTLNQLLVEMDGFKQNEGIIVIGATNFPEALDK  454 (752)
T ss_pred             hcccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCcc---HHHHHHHHHHHHHHHhcCcCcCCceEEEeccCChhhhhH
Confidence            99999999999999999999999999999998777332   122677889999999999999999999999999999999


Q ss_pred             hhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHH
Q 022768          187 ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDF  266 (292)
Q Consensus       187 ~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~  266 (292)
                      ++.+++||+.+|.+|.||..-|.+|++.|+.......++|+..+++-+.||++.|+.++++.|..+|...+...|++.++
T Consensus       455 AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlVNqAAlkAa~dga~~VtM~~L  534 (752)
T KOG0734|consen  455 ALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLVNQAALKAAVDGAEMVTMKHL  534 (752)
T ss_pred             HhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHHHHHHHHHHhcCcccccHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHh
Q 022768          267 MKAVRKLN  274 (292)
Q Consensus       267 ~~a~~~~~  274 (292)
                      +-|..++.
T Consensus       535 E~akDrIl  542 (752)
T KOG0734|consen  535 EFAKDRIL  542 (752)
T ss_pred             hhhhhhee
Confidence            99988765

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1e-40  Score=273.40  Aligned_cols=269  Identities=51%  Similarity=0.901  Sum_probs=258.3

Q ss_pred             CCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           10 LPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +-.+++|-++-|.-+..|.-++.++.|++.++++|++.+..|+.+++.|...|+.++.+|++||+||||||.||+++|+.
T Consensus       163 L~d~~dpmv~vmK~eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANq  242 (440)
T KOG0726|consen  163 LQDDTDPMVSVMKVEKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQ  242 (440)
T ss_pred             eccCCCccceeeecccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcc
Confidence            44668888888888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC
Q 022768           90 IDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL  169 (292)
Q Consensus        90 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~  169 (292)
                      ....|+++..++++.++.|+..+.++++|+.+..+.|+|+||||+|.++.++.+..++..+++|+.+++++++++++...
T Consensus       243 TSATFlRvvGseLiQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFdsr  322 (440)
T KOG0726|consen  243 TSATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSR  322 (440)
T ss_pred             cchhhhhhhhHHHHHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHH
Q 022768          170 GKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEA  249 (292)
Q Consensus       170 ~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a  249 (292)
                      +.+-||.+||.-+.++|++.+++|++..|.|+.||...+..|+.-+.+......+++++.+...-+.+|+.||..+|.+|
T Consensus       323 gDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAictEa  402 (440)
T KOG0726|consen  323 GDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAICTEA  402 (440)
T ss_pred             CCeEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHHHHH
Confidence            99999999999999999999999999999999999999999999998888888999999999998999999999999999


Q ss_pred             HHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          250 GMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       250 ~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      ..+|++..+-.|+++||..|.+.+--.+.
T Consensus       403 GllAlRerRm~vt~~DF~ka~e~V~~~K~  431 (440)
T KOG0726|consen  403 GLLALRERRMKVTMEDFKKAKEKVLYKKK  431 (440)
T ss_pred             hHHHHHHHHhhccHHHHHHHHHHHHHhcc
Confidence            99999999999999999999998876553

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.4e-39  Score=286.81  Aligned_cols=268  Identities=41%  Similarity=0.660  Sum_probs=234.6

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      +..++++++|.++.|++....+|.+.+.. +..++.|..+|+.|++++|||||||+|||.+|+++|++++.|++.++..+
T Consensus       180 ~~~~~snv~f~diGG~d~~~~el~~li~~-i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApe  258 (802)
T KOG0733|consen  180 LEFPESNVSFSDIGGLDKTLAELCELIIH-IKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPE  258 (802)
T ss_pred             cCCCCCCcchhhccChHHHHHHHHHHHHH-hcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchh
Confidence            44566789999999999999999999988 89999999999999999999999999999999999999999999999999


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-CCCCCeEEEEEeCC
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-DQLGKVKMIMATNR  180 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~vi~t~~~  180 (292)
                      +.+...|+.++.++++|+.++...|||+||||+|.+.+++...+-+..+.+...|...++.+... .....++||++||+
T Consensus       259 ivSGvSGESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnR  338 (802)
T KOG0733|consen  259 IVSGVSGESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNR  338 (802)
T ss_pred             hhcccCcccHHHHHHHHHHHhccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCC
Confidence            99999999999999999999999999999999999988885544444444444444444444321 22357999999999


Q ss_pred             CCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC--
Q 022768          181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER--  258 (292)
Q Consensus       181 ~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~--  258 (292)
                      |+.++++|++.+||+.+|-+..|+..+|.+|++..+.+..+..++++..|+..+.||.+.|+..+|.+|...|++|..  
T Consensus       339 PDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~~Aa~vAikR~ld~  418 (802)
T KOG0733|consen  339 PDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALCREAAFVAIKRILDQ  418 (802)
T ss_pred             CcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999988621  


Q ss_pred             ------------------------------------------------------------CcccHHHHHHHHHHHhhhhh
Q 022768          259 ------------------------------------------------------------DYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       259 ------------------------------------------------------------~~i~~~~~~~a~~~~~~~~~  278 (292)
                                                                                  -.|+.+||.+|+..+++...
T Consensus       419 ~~~p~~~~~~~ed~~~~~~~~d~S~i~~~~~~~~~~~ld~v~~~~i~~~~d~~S~E~~~~L~i~~eDF~~Al~~iQPSak  498 (802)
T KOG0733|consen  419 SSSPLTKVPISEDSSNKDAEEDQSSIKITSNAERPLELDRVVQDAILNNPDPLSKELLEGLSIKFEDFEEALSKIQPSAK  498 (802)
T ss_pred             ccCccccCCccccccCCCccchhhhhhcCCcccccccHHHHHHHHHHhCCCCcChHHhccceecHHHHHHHHHhcCcchh
Confidence                                                                        03567888888888888877


Q ss_pred             hch-----hhhhhhhcC
Q 022768          279 LES-----SAHYNADFG  290 (292)
Q Consensus       279 ~~~-----~~~~~~~~~  290 (292)
                      ++.     .+.|+++++
T Consensus       499 REGF~tVPdVtW~dIGa  515 (802)
T KOG0733|consen  499 REGFATVPDVTWDDIGA  515 (802)
T ss_pred             cccceecCCCChhhccc
Confidence            776     567888765

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-38  Score=289.18  Aligned_cols=263  Identities=38%  Similarity=0.667  Sum_probs=233.3

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      .-++..|.++|+|+.|++++|.+|++.++.|+..+++|.. |+.+..+||+|||||||||.+||++|.++...|+.+...
T Consensus       661 iGAPKIPnV~WdDVGGLeevK~eIldTIqlPL~hpeLfss-glrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGP  739 (953)
T KOG0736|consen  661 IGAPKIPNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGP  739 (953)
T ss_pred             cCCCCCCccchhcccCHHHHHHHHHHHhcCcccChhhhhc-cccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCH
Confidence            3457899999999999999999999999999999998864 666677899999999999999999999999999999999


Q ss_pred             chhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCc--chHHHHHHHHHHHHHhhCCC--CCCCeEEEE
Q 022768          101 AIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS--ADREIQRTLMELLNQLDGFD--QLGKVKMIM  176 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~--~~~~~~~~l~~~l~~~~~~~--~~~~~~vi~  176 (292)
                      ++.++|+|+.+.+++++|.+++...|||||+||+|.++++++.++++  ...   +...+++.+++++.  ....++||+
T Consensus       740 ELLNMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~sGDSGGVMD---RVVSQLLAELDgls~~~s~~VFViG  816 (953)
T KOG0736|consen  740 ELLNMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGRSGDSGGVMD---RVVSQLLAELDGLSDSSSQDVFVIG  816 (953)
T ss_pred             HHHHHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCCCCCccccHH---HHHHHHHHHhhcccCCCCCceEEEe
Confidence            99999999999999999999999999999999999999998776543  344   44455666666665  556899999


Q ss_pred             EeCCCCCCChhhcCCCCcceEEEccCC-CHHHHHHHHHHHHcCccCCCCCCHHHHHHHc-CCCCHHHHHHHHHHHHHHHH
Q 022768          177 ATNRPDVLDPALLRPGRLDRKIEIPLP-NEQSRMEILKIHAAGIAKHGEIDYEAVVKLA-EGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       177 t~~~~~~l~~~l~~~~r~~~~i~l~~p-~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~-~g~~~~di~~l~~~a~~~a~  254 (292)
                      +||+|+.+++++++++||+.-+++.++ |.+.+..+++...+.+..+.++++..++... ..|+++|+..+|..|+..|.
T Consensus       817 ATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TGADlYsLCSdA~l~Ai  896 (953)
T KOG0736|consen  817 ATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTGADLYSLCSDAMLAAI  896 (953)
T ss_pred             cCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCchhHHHHHHHHHHHHHH
Confidence            999999999999999999999999887 5567788999999999999999999999876 57999999999999999999


Q ss_pred             HhcC-----------------CcccHHHHHHHHHHHhhhhhhchhhhhhh
Q 022768          255 RAER-----------------DYVIHEDFMKAVRKLNEAKKLESSAHYNA  287 (292)
Q Consensus       255 ~~~~-----------------~~i~~~~~~~a~~~~~~~~~~~~~~~~~~  287 (292)
                      +|.-                 -.|+++|+.++.+++++..+......||.
T Consensus       897 kR~i~~ie~g~~~~~e~~~~~v~V~~eDflks~~~l~PSvS~~EL~~ye~  946 (953)
T KOG0736|consen  897 KRTIHDIESGTISEEEQESSSVRVTMEDFLKSAKRLQPSVSEQELLRYEM  946 (953)
T ss_pred             HHHHHHhhhccccccccCCceEEEEHHHHHHHHHhcCCcccHHHHHHHHH
Confidence            8721                 16899999999999999988888877764

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=100.00  E-value=8.7e-38  Score=278.15  Aligned_cols=268  Identities=61%  Similarity=1.020  Sum_probs=242.6

Q ss_pred             hhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHH
Q 022768            6 IMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARA   85 (292)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~   85 (292)
                      +..-+|...++.+..+--...|.++|+++.|+++++++|.+++..++.+...+..+|+.++.+++|+||||||||+++++
T Consensus        96 ~~~~l~~~~~~~~~~~~~~~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~laka  175 (364)
T TIGR01242        96 IVDVLPTSKDPLVKGMEVEERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKA  175 (364)
T ss_pred             EEeecccccccccccceeccCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHH
Confidence            34446766777666666678899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768           86 IASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus        86 la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      +++.++.+++.+....+...+.+.....++.+|..+....|++|+|||+|.++.++.+...+.+.+.+..+..++..+++
T Consensus       176 ia~~l~~~~~~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~  255 (364)
T TIGR01242       176 VAHETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDG  255 (364)
T ss_pred             HHHhCCCCEEecchHHHHHHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhC
Confidence            99999999999998888888888888889999999988899999999999998777666666677788889999988887


Q ss_pred             CCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHH
Q 022768          166 FDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNV  245 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l  245 (292)
                      ....+++.+|+|||.++.+++++++++||+..+.++.|+.++|.+|++.+........++++..++..+.||+++|+..+
T Consensus       256 ~~~~~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l  335 (364)
T TIGR01242       256 FDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAI  335 (364)
T ss_pred             CCCCCCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHH
Confidence            66667899999999999999999998999999999999999999999999887777777899999999999999999999


Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 022768          246 CTEAGMSAIRAERDYVIHEDFMKAVRKL  273 (292)
Q Consensus       246 ~~~a~~~a~~~~~~~i~~~~~~~a~~~~  273 (292)
                      +.+|...|..+++..|+.+|+.+|+..+
T Consensus       336 ~~~A~~~a~~~~~~~i~~~d~~~a~~~~  363 (364)
T TIGR01242       336 CTEAGMFAIREERDYVTMDDFIKAVEKV  363 (364)
T ss_pred             HHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence            9999999999999999999999999875

Many proteins may score above the trusted cutoff because an internal

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=100.00  E-value=8.3e-39  Score=258.33  Aligned_cols=243  Identities=37%  Similarity=0.581  Sum_probs=216.9

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      ...+.++|++++|++++++...-.+.. +.+++.|..|.   +++|||+||||||||++|+++|++.+.|++.+....++
T Consensus       113 e~~~~it~ddViGqEeAK~kcrli~~y-LenPe~Fg~WA---PknVLFyGppGTGKTm~Akalane~kvp~l~vkat~li  188 (368)
T COG1223         113 EIISDITLDDVIGQEEAKRKCRLIMEY-LENPERFGDWA---PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELI  188 (368)
T ss_pred             hhhccccHhhhhchHHHHHHHHHHHHH-hhChHHhcccC---cceeEEECCCCccHHHHHHHHhcccCCceEEechHHHH
Confidence            456889999999999999887655554 77778887765   77999999999999999999999999999999999999


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      +.++|+..+.+.+++..+....|||+||||+|.++-.+.-+.-  -.+..+....++..++++..+.+++.|++||+++.
T Consensus       189 GehVGdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQel--RGDVsEiVNALLTelDgi~eneGVvtIaaTN~p~~  266 (368)
T COG1223         189 GEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQEL--RGDVSEIVNALLTELDGIKENEGVVTIAATNRPEL  266 (368)
T ss_pred             HHHhhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHh--cccHHHHHHHHHHhccCcccCCceEEEeecCChhh
Confidence            9999999999999999999999999999999999643322111  12344666788888888888899999999999999


Q ss_pred             CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHH-HHHHHHHHHHHHhcCCccc
Q 022768          184 LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLR-NVCTEAGMSAIRAERDYVI  262 (292)
Q Consensus       184 l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~-~l~~~a~~~a~~~~~~~i~  262 (292)
                      +++++++  ||...|.|..|+.++|.+|++.++...+..-+.++..++..+.|+|++||. .++..|...|+..++..|+
T Consensus       267 LD~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikekvlK~aLh~Ai~ed~e~v~  344 (368)
T COG1223         267 LDPAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLKTALHRAIAEDREKVE  344 (368)
T ss_pred             cCHHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHHHHHHHHHHHHHhchhhhh
Confidence            9999999  999999999999999999999999999888888999999999999999998 8999999999999999999


Q ss_pred             HHHHHHHHHHHh
Q 022768          263 HEDFMKAVRKLN  274 (292)
Q Consensus       263 ~~~~~~a~~~~~  274 (292)
                      .+|+..|+..-.
T Consensus       345 ~edie~al~k~r  356 (368)
T COG1223         345 REDIEKALKKER  356 (368)
T ss_pred             HHHHHHHHHhhc
Confidence            999999998743

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3.1e-37  Score=284.98  Aligned_cols=248  Identities=42%  Similarity=0.707  Sum_probs=233.3

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      ..++|.|+.|+++++++|++++.. +++++.|.++|+..++++||+||||||||.|||++|.+.+.||+.++.+++...+
T Consensus       306 t~V~FkDVAG~deAK~El~E~V~f-LKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE~~  384 (774)
T KOG0731|consen  306 TGVKFKDVAGVDEAKEELMEFVKF-LKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEMF  384 (774)
T ss_pred             CCCccccccCcHHHHHHHHHHHHH-hcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHHHHh
Confidence            349999999999999999999987 9999999999999999999999999999999999999999999999999999999


Q ss_pred             cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCC-CCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          107 IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFS-EGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~-~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      .+.....++.+|..++...|+|++|||+|.++..+++ .....+.+....|.+++-++++......++++++||.++.++
T Consensus       385 ~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~a~tnr~d~ld  464 (774)
T KOG0731|consen  385 VGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVLAATNRPDILD  464 (774)
T ss_pred             cccchHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEEeccCCccccC
Confidence            9999999999999999999999999999999988853 344667888899999999999998888899999999999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHH
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE  264 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~  264 (292)
                      +++++++||+..++++.|+...|.+|++.+++..... .+.++..++.++.||++.||.++|++|...|.++....|+..
T Consensus       465 ~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r~~~~~i~~~  544 (774)
T KOG0731|consen  465 PALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCNEAALLAARKGLREIGTK  544 (774)
T ss_pred             HHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHHhccCccchh
Confidence            9999999999999999999999999999999987764 778899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhh
Q 022768          265 DFMKAVRKLNE  275 (292)
Q Consensus       265 ~~~~a~~~~~~  275 (292)
                      ++.+|++++..
T Consensus       545 ~~~~a~~Rvi~  555 (774)
T KOG0731|consen  545 DLEYAIERVIA  555 (774)
T ss_pred             hHHHHHHHHhc
Confidence            99999996654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=100.00  E-value=3.4e-36  Score=289.39  Aligned_cols=264  Identities=45%  Similarity=0.783  Sum_probs=235.2

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      ..|.++|+++.|++++++.|.+.+.+++.....+..+|+.++.++||+||||||||++++++|++++.+++.+.+.++.+
T Consensus       446 ~~~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~  525 (733)
T TIGR01243       446 EVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILS  525 (733)
T ss_pred             cccccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhh
Confidence            45788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      .+.|+.+..++.+|..++...|+||||||+|.+++.++....  .......+.+++..+++.....+++||+|||.++.+
T Consensus       526 ~~vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~--~~~~~~~~~~lL~~ldg~~~~~~v~vI~aTn~~~~l  603 (733)
T TIGR01243       526 KWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFD--TSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDIL  603 (733)
T ss_pred             cccCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCC--ccHHHHHHHHHHHHhhcccCCCCEEEEEeCCChhhC
Confidence            999999999999999999999999999999999887643322  223455666788888877777899999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhc-------
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAE-------  257 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~-------  257 (292)
                      ++++++++||+..+++++|+.++|.+||+.+..+.....+++++.++..+.||+++||..+|++|...|+.+.       
T Consensus       604 d~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~~~A~~~a~~~~~~~~~~~  683 (733)
T TIGR01243       604 DPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKE  683 (733)
T ss_pred             CHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhccch
Confidence            9999999999999999999999999999999988888888999999999999999999999999999988742       


Q ss_pred             -----------CCcccHHHHHHHHHHHhhhhhhch---hhhhhhhcC
Q 022768          258 -----------RDYVIHEDFMKAVRKLNEAKKLES---SAHYNADFG  290 (292)
Q Consensus       258 -----------~~~i~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~  290 (292)
                                 ...|+.+|+.+|++.+.+..+.+.   ...|.+.|+
T Consensus       684 ~~~~~~~~~~~~~~i~~~~f~~al~~~~ps~~~~~~~~~~~~~~~~~  730 (733)
T TIGR01243       684 KLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYERLAKELK  730 (733)
T ss_pred             hhhcccccccccCcccHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhc
Confidence                       126999999999999998766654   445555554

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=100.00  E-value=5e-36  Score=276.57  Aligned_cols=251  Identities=42%  Similarity=0.715  Sum_probs=227.7

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      ...|.++|++++|++++++++.+.+.. +.....+.++|...++++||+||||||||++++++|++++.+++.+++..+.
T Consensus        47 ~~~~~~~~~di~g~~~~k~~l~~~~~~-l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~  125 (495)
T TIGR01241        47 EEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFV  125 (495)
T ss_pred             CCCCCCCHHHhCCHHHHHHHHHHHHHH-HHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHH
Confidence            456889999999999999999998876 7888889999999999999999999999999999999999999999999988


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      ..+.+.....++.+|..++...|+||||||+|.++.++..............+..++..++++....+++||+|||.++.
T Consensus       126 ~~~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~~~~  205 (495)
T TIGR01241       126 EMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDV  205 (495)
T ss_pred             HHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCChhh
Confidence            88888888899999999999999999999999998777655444455666778888888888777788999999999999


Q ss_pred             CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccH
Q 022768          184 LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIH  263 (292)
Q Consensus       184 l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~  263 (292)
                      +++++++++||+..+.++.|+.++|.+|++.++.......+.++..++..+.||+++||..++++|...|.+++...|+.
T Consensus       206 ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~~~~~~i~~  285 (495)
T TIGR01241       206 LDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITM  285 (495)
T ss_pred             cCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCCCCH
Confidence            99999999999999999999999999999999987766677889999999999999999999999999998888889999


Q ss_pred             HHHHHHHHHHhh
Q 022768          264 EDFMKAVRKLNE  275 (292)
Q Consensus       264 ~~~~~a~~~~~~  275 (292)
                      +|+.+|+..+..
T Consensus       286 ~~l~~a~~~~~~  297 (495)
T TIGR01241       286 NDIEEAIDRVIA  297 (495)
T ss_pred             HHHHHHHHHHhc
Confidence            999999998864

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.2e-37  Score=254.52  Aligned_cols=263  Identities=37%  Similarity=0.672  Sum_probs=225.4

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      ...|++.|+++.|++.+++.|++.+..|+.-+.+|..-. .|.+++||+||||||||+||+++|.+.+..|+.++.+++.
T Consensus       125 ~EKPNVkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR-~PwrgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLv  203 (439)
T KOG0739|consen  125 REKPNVKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKR-KPWRGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV  203 (439)
T ss_pred             ccCCCCchhhhccchhHHHHHHhheeecccchhhhcCCC-CcceeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHHH
Confidence            356899999999999999999999999988777775422 5688999999999999999999999999999999999999


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-CCCCCeEEEEEeCCCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-DQLGKVKMIMATNRPD  182 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~vi~t~~~~~  182 (292)
                      +++.|+.++.++.+|..++.++|+||||||+|.+++.++++-+...+.+.   .+++-++++. ....++.|+++||.|+
T Consensus       204 SKWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enEseasRRIK---TEfLVQMqGVG~d~~gvLVLgATNiPw  280 (439)
T KOG0739|consen  204 SKWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENESEASRRIK---TEFLVQMQGVGNDNDGVLVLGATNIPW  280 (439)
T ss_pred             HHHhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCchHHHHHHH---HHHHHhhhccccCCCceEEEecCCCch
Confidence            99999999999999999999999999999999999887665554444333   3555556544 4445899999999999


Q ss_pred             CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC---
Q 022768          183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER---  258 (292)
Q Consensus       183 ~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~---  258 (292)
                      .++.++++  ||...|++|.|+...|..+++.++...... .+.|+..|+..++|||+.||.-+++.|.+...++..   
T Consensus       281 ~LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivVrDalmePvRkvqsAt  358 (439)
T KOG0739|consen  281 VLDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVVRDALMEPVRKVQSAT  358 (439)
T ss_pred             hHHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEehhhhhhhHHHhhhhh
Confidence            99999999  999999999999999999999998876544 778999999999999999999999988887765411   


Q ss_pred             -------------------------------------------CcccHHHHHHHHHHHhhhhh---hchhhhhhhhcCCC
Q 022768          259 -------------------------------------------DYVIHEDFMKAVRKLNEAKK---LESSAHYNADFGKE  292 (292)
Q Consensus       259 -------------------------------------------~~i~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~  292 (292)
                                                                 +.||+.|+..+++...+.-.   ...+..|...||.|
T Consensus       359 hFk~v~~~s~~~~~~~lltpcspgd~ga~em~w~dv~~dkl~eP~vt~~D~~k~l~~tkPTvn~~Dl~k~~~Ft~dFGqE  438 (439)
T KOG0739|consen  359 HFKKVSGPSNPSEVDDLLTPCSPGDPGAIEMSWMDVPADKLLEPPVTMRDFLKSLSRTKPTVNEDDLLKHEKFTEDFGQE  438 (439)
T ss_pred             hhhccCCCCChhhhccccCCCCCCCcchhhhhhccCCHhhccCCCccHHHHHHHHhhcCCCCCHHHHHHHHHHHHhhccC
Confidence                                                       36899999999999988543   44467888888876

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.4e-35  Score=268.07  Aligned_cols=256  Identities=40%  Similarity=0.689  Sum_probs=243.6

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .+...+....++|.++.|.+++++++.+.++. +++...|..+|..-+.+++++||||||||.+||++|.+.+.|++.++
T Consensus       137 ak~~~~~~~~v~F~DVAG~dEakeel~EiVdf-Lk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iS  215 (596)
T COG0465         137 AKLYLEDQVKVTFADVAGVDEAKEELSELVDF-LKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSIS  215 (596)
T ss_pred             HHHhcccccCcChhhhcCcHHHHHHHHHHHHH-HhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCceecc
Confidence            34444557789999999999999999999987 89999999999999999999999999999999999999999999999


Q ss_pred             ccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEe
Q 022768           99 SSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT  178 (292)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~  178 (292)
                      .+++...++|.....++.+|..++.+.|||+||||+|.++..++.+..+...+....+.+++.+++++..+..++++++|
T Consensus       216 GS~FVemfVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~~gviviaaT  295 (596)
T COG0465         216 GSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVIVIAAT  295 (596)
T ss_pred             chhhhhhhcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCCCceEEEecC
Confidence            99999999999999999999999999999999999999999998887888899999999999999999888899999999


Q ss_pred             CCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC
Q 022768          179 NRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER  258 (292)
Q Consensus       179 ~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~  258 (292)
                      |.++.+++++++++||+..+.++.||...|.+|++.++.......++++..+++.+.|+++.|+.+++++|...|.+++.
T Consensus       296 NRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~NEAal~aar~n~  375 (596)
T COG0465         296 NRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAALLAARRNK  375 (596)
T ss_pred             CCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccchHhhhHHHHHHHHHHhcC
Confidence            99999999999999999999999999999999999999988888999999999999999999999999999999999999


Q ss_pred             CcccHHHHHHHHHHHhh
Q 022768          259 DYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       259 ~~i~~~~~~~a~~~~~~  275 (292)
                      ..|++.++.+|..++..
T Consensus       376 ~~i~~~~i~ea~drv~~  392 (596)
T COG0465         376 KEITMRDIEEAIDRVIA  392 (596)
T ss_pred             eeEeccchHHHHHHHhc
Confidence            99999999999999874

>CHL00176 ftsH cell division protein; Validated

Probab=100.00  E-value=5.4e-35  Score=272.97  Aligned_cols=249  Identities=38%  Similarity=0.693  Sum_probs=225.7

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      ..+.++|++++|++++++++.+.+.. +.....+..+|...+.++||+||||||||++++++|.+.+.+++.+++..+..
T Consensus       176 ~~~~~~f~dv~G~~~~k~~l~eiv~~-lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~~  254 (638)
T CHL00176        176 ADTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVE  254 (638)
T ss_pred             cCCCCCHHhccChHHHHHHHHHHHHH-HhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHHH
Confidence            34568999999999999999998876 77788899999999999999999999999999999999999999999998887


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      .+.+.....++.+|..+....|+||||||+|.++..++........+.+..+..++..+++.....++++|++||.++.+
T Consensus       255 ~~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaaTN~~~~L  334 (638)
T CHL00176        255 MFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDIL  334 (638)
T ss_pred             HhhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEecCchHhh
Confidence            77777778889999999999999999999999987776555555667778888999888887777789999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHH
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE  264 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~  264 (292)
                      ++++++++||+..+.++.|+.++|.+|++.++.......+.++..++..+.||+++||..++++|...|.+++...|+.+
T Consensus       335 D~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~~~~~It~~  414 (638)
T CHL00176        335 DAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATITMK  414 (638)
T ss_pred             hhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCcCHH
Confidence            99999999999999999999999999999999876666778899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHh
Q 022768          265 DFMKAVRKLN  274 (292)
Q Consensus       265 ~~~~a~~~~~  274 (292)
                      |+.+|+.++.
T Consensus       415 dl~~Ai~rv~  424 (638)
T CHL00176        415 EIDTAIDRVI  424 (638)
T ss_pred             HHHHHHHHHH
Confidence            9999999874

>CHL00195 ycf46 Ycf46; Provisional

Probab=100.00  E-value=2.1e-34  Score=261.40  Aligned_cols=248  Identities=28%  Similarity=0.412  Sum_probs=210.5

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      +...+++.+|++|.|++..++.+.+....+   .....++|+.+++++||+||||||||++|+++|++++.+++.+++..
T Consensus       218 le~~~~~~~~~dvgGl~~lK~~l~~~~~~~---~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~  294 (489)
T CHL00195        218 LEFYSVNEKISDIGGLDNLKDWLKKRSTSF---SKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGK  294 (489)
T ss_pred             ccccCCCCCHHHhcCHHHHHHHHHHHHHHh---hHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHH
Confidence            344567889999999999999988765432   12345678889999999999999999999999999999999999999


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      +.+.+.|+.+..++.+|..+....||||+|||+|.++.+.....  ........+..++..+..  ...+++||+|||.+
T Consensus       295 l~~~~vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~--d~~~~~rvl~~lL~~l~~--~~~~V~vIaTTN~~  370 (489)
T CHL00195        295 LFGGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKG--DSGTTNRVLATFITWLSE--KKSPVFVVATANNI  370 (489)
T ss_pred             hcccccChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCC--CchHHHHHHHHHHHHHhc--CCCceEEEEecCCh
Confidence            99999999999999999999999999999999999986543222  223344555566665552  34579999999999


Q ss_pred             CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC--CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCC
Q 022768          182 DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH--GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD  259 (292)
Q Consensus       182 ~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~--~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~  259 (292)
                      +.+++++++++||+..++++.|+.++|.+||+.++......  .+.+++.++..+.|||++||.++|.+|...|..+++ 
T Consensus       371 ~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~~~A~~~~~-  449 (489)
T CHL00195        371 DLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYEKR-  449 (489)
T ss_pred             hhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHHHHHHHcCC-
Confidence            99999999999999999999999999999999999865432  468899999999999999999999999999987765 


Q ss_pred             cccHHHHHHHHHHHhhhh
Q 022768          260 YVIHEDFMKAVRKLNEAK  277 (292)
Q Consensus       260 ~i~~~~~~~a~~~~~~~~  277 (292)
                      .++.+|+.+|++.+.+.+
T Consensus       450 ~lt~~dl~~a~~~~~Pls  467 (489)
T CHL00195        450 EFTTDDILLALKQFIPLA  467 (489)
T ss_pred             CcCHHHHHHHHHhcCCCc
Confidence            589999999999999853

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=4.7e-34  Score=264.17  Aligned_cols=251  Identities=45%  Similarity=0.787  Sum_probs=229.7

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      ...+.++|.++.|++++++.+.+.+..++...+.+...++.++.++||+||||||||++++++|++++.+++.+...++.
T Consensus       234 ~~~~~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~  313 (494)
T COG0464         234 FEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELL  313 (494)
T ss_pred             cCCCCcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHHHh
Confidence            35688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      +++.|++++.++.+|..++...|+||||||+|.++..++....+..   .+.+.+++..+++.....+++||++||.++.
T Consensus       314 sk~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~~~~---~r~~~~lL~~~d~~e~~~~v~vi~aTN~p~~  390 (494)
T COG0464         314 SKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSG---RRVVGQLLTELDGIEKAEGVLVIAATNRPDD  390 (494)
T ss_pred             ccccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCCCchHH---HHHHHHHHHHhcCCCccCceEEEecCCCccc
Confidence            9999999999999999999999999999999999887754333222   5677788888888888889999999999999


Q ss_pred             CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccC--CCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhc-CCc
Q 022768          184 LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAK--HGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAE-RDY  260 (292)
Q Consensus       184 l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~--~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~-~~~  260 (292)
                      +++++++++||+..+++++|+.++|.++++.++.....  ..++++..++..+.||++.||..+|++|...+..+. ...
T Consensus       391 ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~~~~~~~~  470 (494)
T COG0464         391 LDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREARRRE  470 (494)
T ss_pred             cCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhccCC
Confidence            99999999999999999999999999999999985443  467899999999999999999999999999999998 678


Q ss_pred             ccHHHHHHHHHHHhhhh
Q 022768          261 VIHEDFMKAVRKLNEAK  277 (292)
Q Consensus       261 i~~~~~~~a~~~~~~~~  277 (292)
                      |+.+|+.+|++.+.+..
T Consensus       471 ~~~~~~~~a~~~~~p~~  487 (494)
T COG0464         471 VTLDDFLDALKKIKPSV  487 (494)
T ss_pred             ccHHHHHHHHHhcCCCC
Confidence            99999999999976653

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-33  Score=238.98  Aligned_cols=261  Identities=38%  Similarity=0.682  Sum_probs=222.2

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcC-CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG-IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~-~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      .--.++|+++.|++++++.+++.+..|++.++.|..-+ ..+..+||++||||+|||.+|+++|++.+..++.+..+.+.
T Consensus        85 ~~I~v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt  164 (386)
T KOG0737|consen   85 SEIGVSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLT  164 (386)
T ss_pred             hhceeehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccc
Confidence            33458999999999999999999999999999996433 47788999999999999999999999999999999999999


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHH-HHHHHHhhCCCCCC--CeEEEEEeCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL-MELLNQLDGFDQLG--KVKMIMATNR  180 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l-~~~l~~~~~~~~~~--~~~vi~t~~~  180 (292)
                      +++.|+.++.++.+|..+..-.|+|+||||+|.+.+.++    ..+.+....+ .+++...+++....  +++|+++||+
T Consensus       165 ~KWfgE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R~----s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgATNR  240 (386)
T KOG0737|consen  165 SKWFGEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRR----STDHEATAMMKNEFMALWDGLSSKDSERVLVLGATNR  240 (386)
T ss_pred             hhhHHHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhcc----cchHHHHHHHHHHHHHHhccccCCCCceEEEEeCCCC
Confidence            999999999999999999999999999999999987772    2233444333 36666666665555  4999999999


Q ss_pred             CCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh----
Q 022768          181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRA----  256 (292)
Q Consensus       181 ~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~----  256 (292)
                      |.+++.++.+  |+...++++.|+..+|.+|++.++.......++|+..++..++|||+.||..+|..|.....+.    
T Consensus       241 P~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSDLkelC~~Aa~~~ire~~~~  318 (386)
T KOG0737|consen  241 PFDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSDLKELCRLAALRPIRELLVS  318 (386)
T ss_pred             CccHHHHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHHHHHHHHHHhHhHHHHHHHh
Confidence            9999999999  9999999999999999999999999999999999999999999999999999999998877653    


Q ss_pred             c------------------------CCcccHHHHHHHHHHHhhhhh-----hchhhhhhhhcCC
Q 022768          257 E------------------------RDYVIHEDFMKAVRKLNEAKK-----LESSAHYNADFGK  291 (292)
Q Consensus       257 ~------------------------~~~i~~~~~~~a~~~~~~~~~-----~~~~~~~~~~~~~  291 (292)
                      +                        ...+.++|+..+...+.....     -.....|++.+|+
T Consensus       319 ~~~~~d~d~~~~d~~~~~~~~~~~~~r~l~~eDf~~a~~~v~~~~~~~~t~~~a~~~~~~~~~e  382 (386)
T KOG0737|consen  319 ETGLLDLDKAIADLKPTQAAASSCLLRPLEQEDFPKAINRVSASVAMDATRMNALKQWNELYGE  382 (386)
T ss_pred             cccchhhhhhhhhccCCcccccccccCcccHHHHHHHHHhhhhHHHHhhhhhHHHHHHHhhhcc
Confidence            1                        246789999999996655311     1225567776665

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=4.3e-33  Score=251.61  Aligned_cols=225  Identities=41%  Similarity=0.761  Sum_probs=212.5

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccC
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIG  108 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~  108 (292)
                      +.|.++.|+.++++.|++.+.+|-+-...|.+.+++-..++|+|||||+|||.+|.+++...+..++.+...++.+++.|
T Consensus       664 i~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fisvKGPElL~KyIG  743 (952)
T KOG0735|consen  664 IRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFISVKGPELLSKYIG  743 (952)
T ss_pred             CCceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEEecCHHHHHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhh
Q 022768          109 ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPAL  188 (292)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l  188 (292)
                      ..++.++.+|.++..++|||||+||+|.++++++-..++...   +...+++.++++...-.++.++++|.+|+.+++++
T Consensus       744 aSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDsTGVTD---RVVNQlLTelDG~Egl~GV~i~aaTsRpdliDpAL  820 (952)
T KOG0735|consen  744 ASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHDSTGVTD---RVVNQLLTELDGAEGLDGVYILAATSRPDLIDPAL  820 (952)
T ss_pred             ccHHHHHHHHHHhhccCCeEEEeccccccCcccCCCCCCchH---HHHHHHHHhhccccccceEEEEEecCCccccCHhh
Confidence            999999999999999999999999999999999777777655   45566777888777778999999999999999999


Q ss_pred             cCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh
Q 022768          189 LRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       189 ~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~  256 (292)
                      ++++|++..++-+.|+..+|.+|++..........++|++.++..++||+++|+..++..|...|..+
T Consensus       821 LRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll~~A~l~avh~  888 (952)
T KOG0735|consen  821 LRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLLYNAQLAAVHE  888 (952)
T ss_pred             cCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999998888889999999999999999999999999999988765

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=100.00  E-value=4.6e-32  Score=255.88  Aligned_cols=250  Identities=41%  Similarity=0.677  Sum_probs=224.9

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      ......|+++.|.+.+++++.+.+.. +.....+..++...+.+++|+||||+|||+++++++++++.+++.+++..+..
T Consensus       145 ~~~~~~~~di~g~~~~~~~l~~i~~~-~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~  223 (644)
T PRK10733        145 DQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVE  223 (644)
T ss_pred             hhhhCcHHHHcCHHHHHHHHHHHHHH-hhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHH
Confidence            34567899999999999999998876 55666777777777888999999999999999999999999999999998888


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      .+.+.....++.+|..+....|+||||||+|.++..+.........+....+..++..++++....++++|++||.++.+
T Consensus       224 ~~~g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN~p~~l  303 (644)
T PRK10733        224 MFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVL  303 (644)
T ss_pred             hhhcccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecCChhhc
Confidence            88888888899999999999999999999999988776655555566677888888888888778899999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHH
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE  264 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~  264 (292)
                      ++++++++||+..+.++.|+.++|.+||+.++.......++++..++..+.||+++|+..+|++|...|.+++...|+.+
T Consensus       304 D~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~eAa~~a~r~~~~~i~~~  383 (644)
T PRK10733        304 DPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVSMV  383 (644)
T ss_pred             CHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHHcCCCcccHH
Confidence            99999999999999999999999999999999988777889999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhh
Q 022768          265 DFMKAVRKLNE  275 (292)
Q Consensus       265 ~~~~a~~~~~~  275 (292)
                      |+.+|...+..
T Consensus       384 d~~~a~~~v~~  394 (644)
T PRK10733        384 EFEKAKDKIMM  394 (644)
T ss_pred             HHHHHHHHHhc
Confidence            99999987754

>TIGR03689 pup_AAA proteasome ATPase

Probab=100.00  E-value=9.8e-32  Score=243.67  Aligned_cols=256  Identities=38%  Similarity=0.639  Sum_probs=206.2

Q ss_pred             hhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc----
Q 022768           18 VYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN----   93 (292)
Q Consensus        18 ~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~----   93 (292)
                      ...+.-...|+++|++|.|++++++++.+.+..++..+..|..+|+.+++++||+||||||||++++++|+.++.+    
T Consensus       168 ~~~l~~~~~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~  247 (512)
T TIGR03689       168 VEDLVLEEVPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAE  247 (512)
T ss_pred             HhcceeecCCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccc
Confidence            3445557889999999999999999999999999999999999999999999999999999999999999998654    


Q ss_pred             ------EEEEeccchhccccChHHHHHHHHHHHhhhC----CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHh
Q 022768           94 ------FLKVVSSAIIDKYIGESARLIREMFGYARDH----QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQL  163 (292)
Q Consensus        94 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~  163 (292)
                            ++.+...++...+.++++..++.+|..++..    .|+||||||+|.++.+++.+.+.  ......+..++..+
T Consensus       248 ~~~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~--d~e~~il~~LL~~L  325 (512)
T TIGR03689       248 TGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSS--DVETTVVPQLLSEL  325 (512)
T ss_pred             cCCceeEEeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccc--hHHHHHHHHHHHHh
Confidence                  4456666777888899999999999888753    68999999999998776443222  12234556778888


Q ss_pred             hCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc-cCC---------CCCCHHHHHHH
Q 022768          164 DGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI-AKH---------GEIDYEAVVKL  233 (292)
Q Consensus       164 ~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~-~~~---------~~~~~~~l~~~  233 (292)
                      ++....+++++|+|||.++.+++++++++||+..|+|++|+.++|.+||+.++... ...         ...+...+...
T Consensus       326 Dgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~~l~l~~~l~~~~g~~~a~~~al~~~  405 (512)
T TIGR03689       326 DGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTDSLPLDADLAEFDGDREATAAALIQR  405 (512)
T ss_pred             cccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhccCCchHHHHHhcCCCHHHHHHHHHH
Confidence            87777778999999999999999999999999999999999999999999988642 210         01112222211


Q ss_pred             -----------------------------cCCCCHHHHHHHHHHHHHHHHHhc----CCcccHHHHHHHHHHHhh
Q 022768          234 -----------------------------AEGFNGADLRNVCTEAGMSAIRAE----RDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       234 -----------------------------~~g~~~~di~~l~~~a~~~a~~~~----~~~i~~~~~~~a~~~~~~  275 (292)
                                                   ++.+|++.|..++.+|...|+++.    ...++.+|+..|+.+--.
T Consensus       406 av~~~~a~~~~~~~l~~~~~~g~~~~l~~~d~~sGa~i~~iv~~a~~~ai~~~~~~~~~~~~~~~l~~a~~~e~~  480 (512)
T TIGR03689       406 AVDHLYATSEENRYVEVTYANGSTEVLYFKDFVSGAMIANIVDRAKKRAIKDHITGGQVGLRIEHLLAAVLDEFR  480 (512)
T ss_pred             HHHHHhhhhcccceeEEEecCCceeeEeecccccHHHHHHHHHHHHHHHHHHHHhcCCcCcCHHHHHHHHHHhhc
Confidence                                         235689999999999999998773    347899999998876543

In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=100.00  E-value=7.3e-31  Score=252.57  Aligned_cols=263  Identities=43%  Similarity=0.730  Sum_probs=226.1

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      ..+.++|++|.|++++++.+.+++..++..+..+..+|+.++.+++|+||||||||++++++|++++.+++.+++..+..
T Consensus       171 ~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~~  250 (733)
T TIGR01243       171 KVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMS  250 (733)
T ss_pred             CCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHhc
Confidence            35779999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      .+.+.....++.+|..+....|++|+|||+|.++.++..............   ++..++.......+++|+++|.++.+
T Consensus       251 ~~~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~---Ll~~ld~l~~~~~vivI~atn~~~~l  327 (733)
T TIGR01243       251 KYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQ---LLTLMDGLKGRGRVIVIGATNRPDAL  327 (733)
T ss_pred             ccccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHH---HHHHhhccccCCCEEEEeecCChhhc
Confidence            888899999999999999999999999999999877644433333444444   44444444555689999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC------
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER------  258 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~------  258 (292)
                      ++++++++||...+.++.|+.++|.+|++.+........+.+++.++..+.||++.|+..+++.|...+..+..      
T Consensus       328 d~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~~~a~~~al~r~~~~~~~~  407 (733)
T TIGR01243       328 DPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRRFIREGKIN  407 (733)
T ss_pred             CHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHhhccccc
Confidence            99999989999999999999999999999988877777788899999999999999999999999998876521      


Q ss_pred             -------------CcccHHHHHHHHHHHhhhhhhch-----hhhhhhhcC
Q 022768          259 -------------DYVIHEDFMKAVRKLNEAKKLES-----SAHYNADFG  290 (292)
Q Consensus       259 -------------~~i~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~  290 (292)
                                   ..++.+|+.+|+..+.+....+.     ...|+++.|
T Consensus       408 ~~~~~i~~~~~~~~~v~~~df~~Al~~v~ps~~~~~~~~~~~~~~~di~g  457 (733)
T TIGR01243       408 FEAEEIPAEVLKELKVTMKDFMEALKMVEPSAIREVLVEVPNVRWSDIGG  457 (733)
T ss_pred             cccccccchhcccccccHHHHHHHHhhccccccchhhccccccchhhccc
Confidence                         25788999999999887654333     457777766

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.97  E-value=3.1e-30  Score=254.26  Aligned_cols=216  Identities=22%  Similarity=0.310  Sum_probs=178.9

Q ss_pred             cCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc-------------------------
Q 022768           52 LMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY-------------------------  106 (292)
Q Consensus        52 ~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~-------------------------  106 (292)
                      .++++...++|+.++++||++||||||||.+||++|.+.+.|++.+++.++...+                         
T Consensus      1616 s~~kP~slrLGl~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~ 1695 (2281)
T CHL00206       1616 SHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDR 1695 (2281)
T ss_pred             ccCcCHHHHcCCCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhccccccccccccccccccccccccccc
Confidence            3567788999999999999999999999999999999999999999998887532                         


Q ss_pred             ----------------cChH--HHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC--
Q 022768          107 ----------------IGES--ARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF--  166 (292)
Q Consensus       107 ----------------~~~~--~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~--  166 (292)
                                      .+..  ...++.+|..|+...||||+|||+|.++.+.       ...  ..+..++..+++.  
T Consensus      1696 ~~~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~~d-------s~~--ltL~qLLneLDg~~~ 1766 (2281)
T CHL00206       1696 DLDTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVNE-------SNY--LSLGLLVNSLSRDCE 1766 (2281)
T ss_pred             ccchhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCCCc-------cce--ehHHHHHHHhccccc
Confidence                            0111  1237889999999999999999999996541       111  1244555566543  


Q ss_pred             -CCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHH--cCccCCC-CCCHHHHHHHcCCCCHHHH
Q 022768          167 -DQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHA--AGIAKHG-EIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       167 -~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~--~~~~~~~-~~~~~~l~~~~~g~~~~di  242 (292)
                       ....+++||||||.|+.+|+++++++||+..|.++.|+..+|.+++....  .+..... .++++.++..+.||+++|+
T Consensus      1767 ~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADL 1846 (2281)
T CHL00206       1767 RCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDL 1846 (2281)
T ss_pred             cCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHH
Confidence             34568999999999999999999999999999999999999998877543  3333332 3689999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      ..+|++|...|..+++..|+.+++..|+.++...
T Consensus      1847 anLvNEAaliAirq~ks~Id~~~I~~Al~Rq~~g 1880 (2281)
T CHL00206       1847 VALTNEALSISITQKKSIIDTNTIRSALHRQTWD 1880 (2281)
T ss_pred             HHHHHHHHHHHHHcCCCccCHHHHHHHHHHHHhh
Confidence            9999999999999999999999999999998764

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=3e-30  Score=232.50  Aligned_cols=255  Identities=39%  Similarity=0.669  Sum_probs=228.4

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      +++. .++.|.......+...+..++.....+...|+.+++++|+|||||+|||.+++++|++.+..++.+++.++...+
T Consensus       180 ~~~~-~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~peli~k~  258 (693)
T KOG0730|consen  180 PEVG-DDIGGLKRQLSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGPELISKF  258 (693)
T ss_pred             cccc-cccchhHHHHHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHhCceeEecccHHHHHhc
Confidence            5666 789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cChHHHHHHHHHHHhhhCC-CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          107 IGESARLIREMFGYARDHQ-PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~-~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      .|+++..++..|..+.... |++++|||+|.+++++..... ........++.   .+++..+.+++++|+++|++..++
T Consensus       259 ~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~~-~e~Rv~sqllt---L~dg~~~~~~vivl~atnrp~sld  334 (693)
T KOG0730|consen  259 PGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREGADD-VESRVVSQLLT---LLDGLKPDAKVIVLAATNRPDSLD  334 (693)
T ss_pred             ccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccccch-HHHHHHHHHHH---HHhhCcCcCcEEEEEecCCccccC
Confidence            9999999999999999988 999999999999987644322 33444444444   444445667999999999999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHH
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHED  265 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~  265 (292)
                      +++++ +||+..+.+..|+..+|.+|++.+........+.++..++..+.||.++|+..+|.+|...+.++     +.++
T Consensus       335 ~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~~ea~~~~~r~-----~~~~  408 (693)
T KOG0730|consen  335 PALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALCREASLQATRR-----TLEI  408 (693)
T ss_pred             hhhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHHHHHHHHHhhh-----hHHH
Confidence            99998 89999999999999999999999999887777789999999999999999999999999999888     8899


Q ss_pred             HHHHHHHHhhhhhhch-----hhhhhhhcCCC
Q 022768          266 FMKAVRKLNEAKKLES-----SAHYNADFGKE  292 (292)
Q Consensus       266 ~~~a~~~~~~~~~~~~-----~~~~~~~~~~~  292 (292)
                      +..|...+++...++.     ++.|++++|-|
T Consensus       409 ~~~A~~~i~psa~Re~~ve~p~v~W~dIGGlE  440 (693)
T KOG0730|consen  409 FQEALMGIRPSALREILVEMPNVSWDDIGGLE  440 (693)
T ss_pred             HHHHHhcCCchhhhheeccCCCCChhhccCHH
Confidence            9999999999877655     78999999854

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=2.4e-30  Score=226.76  Aligned_cols=269  Identities=35%  Similarity=0.621  Sum_probs=224.3

Q ss_pred             hhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           17 VVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        17 ~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .+.+-+-..-+++.|+++.|++.+++.+.+++.+|......|..+. .+.+++|+.||||+|||.+++++|.+.+..++.
T Consensus       138 ~i~~EI~~~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr-~p~rglLLfGPpgtGKtmL~~aiAsE~~atff~  216 (428)
T KOG0740|consen  138 GIRNEIGDTLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLR-EPVRGLLLFGPPGTGKTMLAKAIATESGATFFN  216 (428)
T ss_pred             HHHHHHhccCCcccccCCcchhhHHHHhhhhhhhcccchHhhhccc-cccchhheecCCCCchHHHHHHHHhhhcceEee
Confidence            3344455667889999999999999999999999999888888766 457789999999999999999999999999999


Q ss_pred             EeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh--CCCCCCCeEE
Q 022768           97 VVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD--GFDQLGKVKM  174 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~--~~~~~~~~~v  174 (292)
                      +....+.++++|+.+..++.+|..++...|+|+||||+|.++.++.++....+..   ...+++-+..  ...+.+++++
T Consensus       217 iSassLtsK~~Ge~eK~vralf~vAr~~qPsvifidEidslls~Rs~~e~e~srr---~ktefLiq~~~~~s~~~drvlv  293 (428)
T KOG0740|consen  217 ISASSLTSKYVGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKRSDNEHESSRR---LKTEFLLQFDGKNSAPDDRVLV  293 (428)
T ss_pred             ccHHHhhhhccChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhcCCcccccchh---hhhHHHhhhccccCCCCCeEEE
Confidence            9999999999999999999999999999999999999999998885544433332   2233333322  1244458999


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc-CCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA-KHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~-~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      |+|||.|+.++.++++  ||...+++|.|+.+.|..+|+..+.... ...+.+++.++..++||+++||.++|.+|.+--
T Consensus       294 igaTN~P~e~Dea~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~kea~~~p  371 (428)
T KOG0740|consen  294 IGATNRPWELDEAARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCKEAAMGP  371 (428)
T ss_pred             EecCCCchHHHHHHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHHHhhcCc
Confidence            9999999999999998  9999999999999999999999998663 335578999999999999999999999998755


Q ss_pred             HHhc-------------CCcccHHHHHHHHHHHhhhhhhch---hhhhhhhcCC
Q 022768          254 IRAE-------------RDYVIHEDFMKAVRKLNEAKKLES---SAHYNADFGK  291 (292)
Q Consensus       254 ~~~~-------------~~~i~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~~  291 (292)
                      ++..             ...++..|+..+...+.+.-+.+.   ...|++.||.
T Consensus       372 ~r~~~~~~~~~~~~~~~~r~i~~~df~~a~~~i~~~~s~~~l~~~~~~~~~fg~  425 (428)
T KOG0740|consen  372 LRELGGTTDLEFIDADKIRPITYPDFKNAFKNIKPSVSLEGLEKYEKWDKEFGS  425 (428)
T ss_pred             hhhcccchhhhhcchhccCCCCcchHHHHHHhhccccCccccchhHHHhhhhcc
Confidence            4432             236788899999999998665554   5677787774

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=99.95  E-value=9.5e-28  Score=227.80  Aligned_cols=256  Identities=39%  Similarity=0.658  Sum_probs=214.0

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cEEE
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NFLK   96 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~~~   96 (292)
                      +-.....+.|+++.|++.++..|++.+..|+...+.|..+++.+++++|++||||||||..++++|..+..     .++-
T Consensus       255 p~~~~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffm  334 (1080)
T KOG0732|consen  255 PLSVDSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFM  334 (1080)
T ss_pred             chhhhcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhh
Confidence            33445678999999999999999999999999999999999999999999999999999999999998833     3344


Q ss_pred             EeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768           97 VVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      -...+..++++|+.++.++.+|..++.+.|+|+|+||+|-+++.+++.+......+...|+   ..++++...+.++||+
T Consensus       335 rkgaD~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSskqEqih~SIvSTLL---aLmdGldsRgqVvvig  411 (1080)
T KOG0732|consen  335 RKGADCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLL---ALMDGLDSRGQVVVIG  411 (1080)
T ss_pred             hcCchhhccccCcHHHHHHHHHHHHhccCceEEeccccccccccccchHHHhhhhHHHHHH---HhccCCCCCCceEEEc
Confidence            4456677889999999999999999999999999999999988876655544444444444   4555667778999999


Q ss_pred             EeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Q 022768          177 ATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       177 t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      +||++..+++++++++||+.+++|+.|+.+.|.+|+..+...+... ..--...++..+.||.++||+.+|.+|...+.+
T Consensus       412 ATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLCTeAal~~~~  491 (1080)
T KOG0732|consen  412 ATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALCTEAALIALR  491 (1080)
T ss_pred             ccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHHHHHhhhhhc
Confidence            9999999999999999999999999999999999999887765422 112357789999999999999999999999988


Q ss_pred             hcCC----------------cccHHHHHHHHHHHhhhhhhc
Q 022768          256 AERD----------------YVIHEDFMKAVRKLNEAKKLE  280 (292)
Q Consensus       256 ~~~~----------------~i~~~~~~~a~~~~~~~~~~~  280 (292)
                      +..+                .|...|+..|+..+.+...++
T Consensus       492 r~~Pq~y~s~~kl~~d~~~ikV~~~~f~~A~~~i~ps~~R~  532 (1080)
T KOG0732|consen  492 RSFPQIYSSSDKLLIDVALIKVEVRDFVEAMSRITPSSRRS  532 (1080)
T ss_pred             cccCeeecccccccccchhhhhhhHhhhhhhhccCCCCCcc
Confidence            7432                467777888877777655443

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=99.95  E-value=1.4e-26  Score=198.54  Aligned_cols=205  Identities=19%  Similarity=0.278  Sum_probs=151.0

Q ss_pred             CCCccccccc-cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc
Q 022768           27 GNVSYSAVGG-LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK  105 (292)
Q Consensus        27 ~~~~~~~l~g-~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~  105 (292)
                      ...+|+++.| +.-...-+.+.+..  ..+.....+|+.++..++|+||||+|||.+|+++|++++.+++.++..++.+.
T Consensus       110 ~~~~f~~~~g~~~~~p~f~dk~~~h--i~kn~l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk  187 (413)
T PLN00020        110 RTRSFDNLVGGYYIAPAFMDKVAVH--IAKNFLALPNIKVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESE  187 (413)
T ss_pred             hhcchhhhcCccccCHHHHHHHHHH--HHhhhhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcC
Confidence            4567777733 33222222222211  12223334678899999999999999999999999999999999999999999


Q ss_pred             ccChHHHHHHHHHHHhhh-----CCCEEEEEcccccccCCcCCCCCcchHHH-HHHHHHHHHHh-----hC----CCCCC
Q 022768          106 YIGESARLIREMFGYARD-----HQPCIIFMDEIDAIGGRRFSEGTSADREI-QRTLMELLNQL-----DG----FDQLG  170 (292)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~-----~~~~il~lDe~d~l~~~~~~~~~~~~~~~-~~~l~~~l~~~-----~~----~~~~~  170 (292)
                      +.|+.++.++.+|..+..     ..||||||||+|.+++++...+....... ...|+.+++..     .+    .....
T Consensus       188 ~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~  267 (413)
T PLN00020        188 NAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIP  267 (413)
T ss_pred             cCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCC
Confidence            999999999999999875     36999999999999988753322222211 23444443321     11    13456


Q ss_pred             CeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCC
Q 022768          171 KVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEG  236 (292)
Q Consensus       171 ~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g  236 (292)
                      +++||+|||+++.|++++++++||+..+  ..|+.++|.+|++.++.....+ ..++..|+..+.|
T Consensus       268 ~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~-~~dv~~Lv~~f~g  330 (413)
T PLN00020        268 RVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVS-REDVVKLVDTFPG  330 (413)
T ss_pred             CceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCC-HHHHHHHHHcCCC
Confidence            8999999999999999999999998864  6899999999999999875443 3555666666655

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.94  E-value=1.1e-26  Score=204.43  Aligned_cols=249  Identities=37%  Similarity=0.614  Sum_probs=203.4

Q ss_pred             CCCcccc--ccccHHHHHHHH-HHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-cEEEEeccch
Q 022768           27 GNVSYSA--VGGLSDQIRELR-ESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-NFLKVVSSAI  102 (292)
Q Consensus        27 ~~~~~~~--l~g~~~~~~~l~-~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-~~~~~~~~~~  102 (292)
                      |.-.|.+  +.|++.....+. ++...-.--+....++|+..-.++|||||||||||.+||.+.+.++. +=-.+|..++
T Consensus       214 Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPeI  293 (744)
T KOG0741|consen  214 PDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPEI  293 (744)
T ss_pred             CCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHHH
Confidence            5566666  678877765543 33333345578899999999999999999999999999999998854 3455788899


Q ss_pred             hccccChHHHHHHHHHHHhhh--------CCCEEEEEcccccccCCcCCCC--CcchHHHHHHHHHHHHHhhCCCCCCCe
Q 022768          103 IDKYIGESARLIREMFGYARD--------HQPCIIFMDEIDAIGGRRFSEG--TSADREIQRTLMELLNQLDGFDQLGKV  172 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~--------~~~~il~lDe~d~l~~~~~~~~--~~~~~~~~~~l~~~l~~~~~~~~~~~~  172 (292)
                      .++|+|+++..++.+|..+..        ..-.|+++||+|.++..+++..  ++....   ...+++..+++.....++
T Consensus       294 L~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~---VVNQLLsKmDGVeqLNNI  370 (744)
T KOG0741|consen  294 LNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDT---VVNQLLSKMDGVEQLNNI  370 (744)
T ss_pred             HHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCCCCCccHH---HHHHHHHhcccHHhhhcE
Confidence            999999999999999998854        2235999999999998886643  334443   344555666666666799


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcC----ccCCCCCCHHHHHHHcCCCCHHHHHHHHHH
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAG----IAKHGEIDYEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~----~~~~~~~~~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      .||+.||+.+.++++|++++|+...++++.||...|.+|++-+...    -....++|++.|+.++.+||++++..+++.
T Consensus       371 LVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVks  450 (744)
T KOG0741|consen  371 LVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGAELEGLVKS  450 (744)
T ss_pred             EEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHHH
Confidence            9999999999999999999999999999999999999998855542    245688999999999999999999999999


Q ss_pred             HHHHHHHhcC---------------CcccHHHHHHHHHHHhhhhh
Q 022768          249 AGMSAIRAER---------------DYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       249 a~~~a~~~~~---------------~~i~~~~~~~a~~~~~~~~~  278 (292)
                      |...|..+.-               -.|+++|+..|+.++.+.+-
T Consensus       451 A~S~A~nR~vk~~~~~~~~~~~~e~lkV~r~DFl~aL~dVkPAFG  495 (744)
T KOG0741|consen  451 AQSFAMNRHVKAGGKVEVDPVAIENLKVTRGDFLNALEDVKPAFG  495 (744)
T ss_pred             HHHHHHHhhhccCcceecCchhhhheeecHHHHHHHHHhcCcccC
Confidence            9999988732               27899999999999998654

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=99.91  E-value=7.9e-24  Score=170.65  Aligned_cols=204  Identities=24%  Similarity=0.294  Sum_probs=138.4

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      ..++...+|.+|++++|+++.+..+.-++......        ..+-.+++||||||+||||+|+.+|++++.++...+.
T Consensus        12 ~~l~~~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r--------~~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg   83 (233)
T PF05496_consen   12 APLAERLRPKSLDEFIGQEHLKGNLKILIRAAKKR--------GEALDHMLFYGPPGLGKTTLARIIANELGVNFKITSG   83 (233)
T ss_dssp             S-HHHHTS-SSCCCS-S-HHHHHHHHHHHHHHHCT--------TS---EEEEESSTTSSHHHHHHHHHHHCT--EEEEEC
T ss_pred             hhhHHhcCCCCHHHccCcHHHHhhhHHHHHHHHhc--------CCCcceEEEECCCccchhHHHHHHHhccCCCeEeccc
Confidence            45566788999999999999999988777643211        1334689999999999999999999999999988776


Q ss_pred             cchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-----CCC-------
Q 022768          100 SAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-----GFD-------  167 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-----~~~-------  167 (292)
                      ..+..  .++    +..++...  ....||||||+|++           +...++.|+..++...     +..       
T Consensus        84 ~~i~k--~~d----l~~il~~l--~~~~ILFIDEIHRl-----------nk~~qe~LlpamEd~~idiiiG~g~~ar~~~  144 (233)
T PF05496_consen   84 PAIEK--AGD----LAAILTNL--KEGDILFIDEIHRL-----------NKAQQEILLPAMEDGKIDIIIGKGPNARSIR  144 (233)
T ss_dssp             CC--S--CHH----HHHHHHT----TT-EEEECTCCC-------------HHHHHHHHHHHHCSEEEEEBSSSSS-BEEE
T ss_pred             hhhhh--HHH----HHHHHHhc--CCCcEEEEechhhc-----------cHHHHHHHHHHhccCeEEEEeccccccceee
Confidence            44321  112    22222222  23479999999999           8899999999888532     111       


Q ss_pred             -CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHH
Q 022768          168 -QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNV  245 (292)
Q Consensus       168 -~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l  245 (292)
                       +.+++.+|++|+....+++++++  ||+...++..++.++..+|++.......+. .+.....++.++.| +|+-...+
T Consensus       145 ~~l~~FTligATTr~g~ls~pLrd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrG-tPRiAnrl  221 (233)
T PF05496_consen  145 INLPPFTLIGATTRAGLLSSPLRD--RFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRG-TPRIANRL  221 (233)
T ss_dssp             EE----EEEEEESSGCCTSHCCCT--TSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTT-SHHHHHHH
T ss_pred             ccCCCceEeeeeccccccchhHHh--hcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCC-ChHHHHHH
Confidence             11368999999999999999999  999999999999999999999777654443 22345778888998 99998888


Q ss_pred             HHHHHHHH
Q 022768          246 CTEAGMSA  253 (292)
Q Consensus       246 ~~~a~~~a  253 (292)
                      ++++..+|
T Consensus       222 l~rvrD~a  229 (233)
T PF05496_consen  222 LRRVRDFA  229 (233)
T ss_dssp             HHHHCCCC
T ss_pred             HHHHHHHH
Confidence            88765443

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.91  E-value=6e-23  Score=186.32  Aligned_cols=247  Identities=21%  Similarity=0.246  Sum_probs=191.8

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEeccchhcccc
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSSAIIDKYI  107 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~~~~~~~~  107 (292)
                      .+++-...++++..+....|           +...++++|.||+|+|||.|++++++++.    +++..++|..+.....
T Consensus       408 ~d~i~~~s~kke~~n~~~sp-----------v~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~  476 (952)
T KOG0735|consen  408 HDFIQVPSYKKENANQELSP-----------VFRHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSL  476 (952)
T ss_pred             Cceeecchhhhhhhhhhccc-----------ccccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchhH
Confidence            56666777777776665555           45578899999999999999999999884    4677788988887777


Q ss_pred             ChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-CC-CCCCCeEEEEEeCCCCCCC
Q 022768          108 GESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-GF-DQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~-~~~~~~~vi~t~~~~~~l~  185 (292)
                      ...++.+..+|..+.++.|+|++||++|.+++....+.+ .+......+..+++++. .+ ..+..+.+|+|.+..+.++
T Consensus       477 e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~s~~e~~-q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~  555 (952)
T KOG0735|consen  477 EKIQKFLNNVFSEALWYAPSIIVLDDLDCLASASSNENG-QDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLN  555 (952)
T ss_pred             HHHHHHHHHHHHHHHhhCCcEEEEcchhhhhccCcccCC-cchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcC
Confidence            788999999999999999999999999999983332222 22223333333332221 11 3334578999999999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh----cCCc
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRA----ERDY  260 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~----~~~~  260 (292)
                      +.+.++.+|+.++.++.|+..+|.+|++..++..... ..-|++.++..++||...|+..++++|...|+..    ..+.
T Consensus       556 ~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifVeRai~~a~leris~~~kl  635 (952)
T KOG0735|consen  556 PLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFVERAIHEAFLERISNGPKL  635 (952)
T ss_pred             hhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHHHHHHHHHHHHHhccCccc
Confidence            9999999999999999999999999999998865422 2234566999999999999999999999999842    2237


Q ss_pred             ccHHHHHHHHHHHhhhhhhch------hhhhhhhcC
Q 022768          261 VIHEDFMKAVRKLNEAKKLES------SAHYNADFG  290 (292)
Q Consensus       261 i~~~~~~~a~~~~~~~~~~~~------~~~~~~~~~  290 (292)
                      +|.+++.++++.+.+...++.      ...|+++.|
T Consensus       636 ltke~f~ksL~~F~P~aLR~ik~~k~tgi~w~digg  671 (952)
T KOG0735|consen  636 LTKELFEKSLKDFVPLALRGIKLVKSTGIRWEDIGG  671 (952)
T ss_pred             chHHHHHHHHHhcChHHhhhccccccCCCCceeccc
Confidence            899999999999998655433      456777776

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=99.90  E-value=3.2e-22  Score=164.54  Aligned_cols=226  Identities=19%  Similarity=0.200  Sum_probs=180.5

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      ......+|..|++.+|++++++.|.-++......        -..-.|+||+||||.||||+|..+|++++..+...+..
T Consensus        15 ~~e~~lRP~~l~efiGQ~~vk~~L~ifI~AAk~r--------~e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp   86 (332)
T COG2255          15 KIERSLRPKTLDEFIGQEKVKEQLQIFIKAAKKR--------GEALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGP   86 (332)
T ss_pred             hhhcccCcccHHHhcChHHHHHHHHHHHHHHHhc--------CCCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccc
Confidence            4566778999999999999999999998765332        24466899999999999999999999999888766655


Q ss_pred             chhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-------CC------C
Q 022768          101 AIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-------GF------D  167 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-------~~------~  167 (292)
                      .+-.      ...+-.++...  ...+||||||+|++           .....+.|...++...       +.      -
T Consensus        87 ~leK------~gDlaaiLt~L--e~~DVLFIDEIHrl-----------~~~vEE~LYpaMEDf~lDI~IG~gp~Arsv~l  147 (332)
T COG2255          87 ALEK------PGDLAAILTNL--EEGDVLFIDEIHRL-----------SPAVEEVLYPAMEDFRLDIIIGKGPAARSIRL  147 (332)
T ss_pred             cccC------hhhHHHHHhcC--CcCCeEEEehhhhc-----------ChhHHHHhhhhhhheeEEEEEccCCccceEec
Confidence            4422      11222333332  23479999999999           7777788877776431       11      1


Q ss_pred             CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      +.+++.+|++|.....+...+++  ||+...++..++.++..+|+.+........ .+-....++.++.| +|+-...++
T Consensus       148 dLppFTLIGATTr~G~lt~PLrd--RFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRG-TPRIAnRLL  224 (332)
T COG2255         148 DLPPFTLIGATTRAGMLTNPLRD--RFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRG-TPRIANRLL  224 (332)
T ss_pred             cCCCeeEeeeccccccccchhHH--hcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccC-CcHHHHHHH
Confidence            22378999999999999999999  999999999999999999999888655444 33346778999998 999999999


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          247 TEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       247 ~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      ++....|.-++...|+.+...+|+..+...
T Consensus       225 rRVRDfa~V~~~~~I~~~ia~~aL~~L~Vd  254 (332)
T COG2255         225 RRVRDFAQVKGDGDIDRDIADKALKMLDVD  254 (332)
T ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHhCcc
Confidence            999999999999999999999999998864

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.90  E-value=1.8e-22  Score=184.75  Aligned_cols=223  Identities=22%  Similarity=0.354  Sum_probs=186.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFS  143 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~  143 (292)
                      .-...+|++|+||+|||++++++|.+++.++++++|.++.......++..+..+|..++.+.|+||||-++|.+..... 
T Consensus       429 ~~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~d-  507 (953)
T KOG0736|consen  429 TLNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQD-  507 (953)
T ss_pred             ccceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCC-
Confidence            3455799999999999999999999999999999999999999889999999999999999999999999999963221 


Q ss_pred             CCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCC
Q 022768          144 EGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG  223 (292)
Q Consensus       144 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~  223 (292)
                        .+.+......+..++..-....+..++++|++++..+.+++.+++  .|-.++.++.|+.++|.+++++++.....+.
T Consensus       508 --gged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y~~~~~~n~  583 (953)
T KOG0736|consen  508 --GGEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWYLNHLPLNQ  583 (953)
T ss_pred             --CchhHHHHHHHHHHHhcccccCCCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHhccccch
Confidence              134445555555555422233566789999999999999999998  7878999999999999999999999888888


Q ss_pred             CCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh---cC-----------------CcccHHHHHHHHHHHhhhhhhch--
Q 022768          224 EIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRA---ER-----------------DYVIHEDFMKAVRKLNEAKKLES--  281 (292)
Q Consensus       224 ~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~---~~-----------------~~i~~~~~~~a~~~~~~~~~~~~--  281 (292)
                      ++....++..+.||+.+++.+++..+-..+..+   ..                 ..++.+|+.+|+.+++..++...  
T Consensus       584 ~v~~k~~a~~t~gfs~~~L~~l~~~~s~~~~~~i~~~~l~g~~~~~~~~~~~~~~~~l~~edf~kals~~~~~fs~aiGA  663 (953)
T KOG0736|consen  584 DVNLKQLARKTSGFSFGDLEALVAHSSLAAKTRIKNKGLAGGLQEEDEGELCAAGFLLTEEDFDKALSRLQKEFSDAIGA  663 (953)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHhcCchHHHHHHHHhhcccccchhccccccccccceecHHHHHHHHHHHHHhhhhhcCC
Confidence            899999999999999999999988773333222   11                 47899999999999998766443  


Q ss_pred             ----hhhhhhhcCC
Q 022768          282 ----SAHYNADFGK  291 (292)
Q Consensus       282 ----~~~~~~~~~~  291 (292)
                          ++.|+|++|-
T Consensus       664 PKIPnV~WdDVGGL  677 (953)
T KOG0736|consen  664 PKIPNVSWDDVGGL  677 (953)
T ss_pred             CCCCccchhcccCH
Confidence                7799999984

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=99.89  E-value=7.2e-22  Score=169.79  Aligned_cols=221  Identities=29%  Similarity=0.416  Sum_probs=163.0

Q ss_pred             hcccCCCCCccccccccHHHH---HHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           21 MLHEDPGNVSYSAVGGLSDQI---RELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~---~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +++...+|.++++++|+++-.   .-|.+.+..             ..-.+++||||||+||||+++.++...+..|..+
T Consensus        13 PLA~rmRP~~lde~vGQ~HLlg~~~~lrr~v~~-------------~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~   79 (436)
T COG2256          13 PLAERLRPKSLDEVVGQEHLLGEGKPLRRAVEA-------------GHLHSMILWGPPGTGKTTLARLIAGTTNAAFEAL   79 (436)
T ss_pred             ChHHHhCCCCHHHhcChHhhhCCCchHHHHHhc-------------CCCceeEEECCCCCCHHHHHHHHHHhhCCceEEe
Confidence            666778899999999999865   445555443             3455799999999999999999999999999999


Q ss_pred             eccchhccccChHHHHHHHHHHHhhhC----CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           98 VSSAIIDKYIGESARLIREMFGYARDH----QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      +...       ...+.++.++..++..    ..-||||||+|++           +...|..|+-.++.       +.++
T Consensus        80 sAv~-------~gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRf-----------nK~QQD~lLp~vE~-------G~ii  134 (436)
T COG2256          80 SAVT-------SGVKDLREIIEEARKNRLLGRRTILFLDEIHRF-----------NKAQQDALLPHVEN-------GTII  134 (436)
T ss_pred             cccc-------ccHHHHHHHHHHHHHHHhcCCceEEEEehhhhc-----------ChhhhhhhhhhhcC-------CeEE
Confidence            8765       3455667777777432    2469999999999           78888888887764       5678


Q ss_pred             EEEEe--CCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc--CC---CCCCH---HHHHHHcCCCCHHHHH
Q 022768          174 MIMAT--NRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA--KH---GEIDY---EAVVKLAEGFNGADLR  243 (292)
Q Consensus       174 vi~t~--~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~--~~---~~~~~---~~l~~~~~g~~~~di~  243 (292)
                      +|++|  |+.-.++++++|  |+ .++.|.+.+.++..+++++.+....  ..   ..++-   +.++..++|    |.+
T Consensus       135 lIGATTENPsF~ln~ALlS--R~-~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~G----D~R  207 (436)
T COG2256         135 LIGATTENPSFELNPALLS--RA-RVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNG----DAR  207 (436)
T ss_pred             EEeccCCCCCeeecHHHhh--hh-heeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCc----hHH
Confidence            88865  555689999999  66 6789999999999999988443221  11   11333   334444444    888


Q ss_pred             HHHHHHHHHHHHhcCC-cccHHHHHHHHHHHhhhhhhchhhhhh
Q 022768          244 NVCTEAGMSAIRAERD-YVIHEDFMKAVRKLNEAKKLESSAHYN  286 (292)
Q Consensus       244 ~l~~~a~~~a~~~~~~-~i~~~~~~~a~~~~~~~~~~~~~~~~~  286 (292)
                      .+++..-..+...... .++.+++.+.+++-....+++...+|+
T Consensus       208 ~aLN~LE~~~~~~~~~~~~~~~~l~~~l~~~~~~~Dk~gD~hYd  251 (436)
T COG2256         208 RALNLLELAALSAEPDEVLILELLEEILQRRSARFDKDGDAHYD  251 (436)
T ss_pred             HHHHHHHHHHHhcCCCcccCHHHHHHHHhhhhhccCCCcchHHH
Confidence            7777766666554332 345899999999888877777666665

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.89  E-value=2.7e-21  Score=170.09  Aligned_cols=224  Identities=20%  Similarity=0.188  Sum_probs=165.8

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ...++|.+|++++|+++.++.+..++......        -.+..+++|+||||+|||++++.+|++++..+...+....
T Consensus        16 ~~~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~--------~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~   87 (328)
T PRK00080         16 ERSLRPKSLDEFIGQEKVKENLKIFIEAAKKR--------GEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL   87 (328)
T ss_pred             hhhcCcCCHHHhcCcHHHHHHHHHHHHHHHhc--------CCCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccc
Confidence            56778889999999999999999887642111        2345689999999999999999999999988776654432


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC-------C------CCC
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG-------F------DQL  169 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~-------~------~~~  169 (292)
                      ..      ...+..++...  ..+++|+|||+|.+           ....++.+...++....       .      ...
T Consensus        88 ~~------~~~l~~~l~~l--~~~~vl~IDEi~~l-----------~~~~~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l  148 (328)
T PRK00080         88 EK------PGDLAAILTNL--EEGDVLFIDEIHRL-----------SPVVEEILYPAMEDFRLDIMIGKGPAARSIRLDL  148 (328)
T ss_pred             cC------hHHHHHHHHhc--ccCCEEEEecHhhc-----------chHHHHHHHHHHHhcceeeeeccCccccceeecC
Confidence            11      11222333322  34579999999998           44445555555543210       0      012


Q ss_pred             CCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHH
Q 022768          170 GKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       170 ~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      +++.+|++++....+++++++  ||+..+.|++|+.+++.++++......... .+-....++..+.| +++.+..+++.
T Consensus       149 ~~~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G-~pR~a~~~l~~  225 (328)
T PRK00080        149 PPFTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRG-TPRIANRLLRR  225 (328)
T ss_pred             CCceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCC-CchHHHHHHHH
Confidence            357889999999999999988  998899999999999999999887754433 22235677778887 77899999999


Q ss_pred             HHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          249 AGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       249 a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      +..+|.......|+.+++.+++..+...
T Consensus       226 ~~~~a~~~~~~~I~~~~v~~~l~~~~~~  253 (328)
T PRK00080        226 VRDFAQVKGDGVITKEIADKALDMLGVD  253 (328)
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence            9988887766789999999999876543

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.89  E-value=2.1e-21  Score=180.52  Aligned_cols=196  Identities=16%  Similarity=0.234  Sum_probs=146.0

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |..+..+++|.+|++|+|++++++.|.+++..-            ...+.+||+||+|+||||+++.+++.+++.     
T Consensus         3 Y~vLarKYRPqtFdEVIGQe~Vv~~L~~aL~~g------------RL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~   70 (830)
T PRK07003          3 YQVLARKWRPKDFASLVGQEHVVRALTHALDGG------------RLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTS   70 (830)
T ss_pred             cHhHHHHhCCCcHHHHcCcHHHHHHHHHHHhcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCC
Confidence            567788999999999999999999999998652            335568999999999999999999998753     


Q ss_pred             -------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchH
Q 022768           94 -------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        94 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                         +++++...      ....+.++.++..+..    ....|+||||+|.|           +.
T Consensus        71 ~PCG~C~sCr~I~~G~h~DviEIDAas------~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~L-----------T~  133 (830)
T PRK07003         71 QPCGVCRACREIDEGRFVDYVEMDAAS------NRGVDEMAALLERAVYAPVDARFKVYMIDEVHML-----------TN  133 (830)
T ss_pred             CCCcccHHHHHHhcCCCceEEEecccc------cccHHHHHHHHHHHHhccccCCceEEEEeChhhC-----------CH
Confidence                               12222111      1122334444444332    34579999999999           66


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      .....|+..|++     ...++.+|++||.++.+.+.+++  || ..+.|+.++.++..+.++..+....+. .+..+..
T Consensus       134 ~A~NALLKtLEE-----PP~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~l  205 (830)
T PRK07003        134 HAFNAMLKTLEE-----PPPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAGHIVSHLERILGEERIAFEPQALRL  205 (830)
T ss_pred             HHHHHHHHHHHh-----cCCCeEEEEEECChhhccchhhh--he-EEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            566666666554     33588899999999999999999  88 889999999999999999887644332 2233566


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMS  252 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~  252 (292)
                      +++.++| +.++..+++..+..+
T Consensus       206 IA~~A~G-smRdALsLLdQAia~  227 (830)
T PRK07003        206 LARAAQG-SMRDALSLTDQAIAY  227 (830)
T ss_pred             HHHHcCC-CHHHHHHHHHHHHHh
Confidence            7778887 788888888877744

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.88  E-value=3.7e-22  Score=166.57  Aligned_cols=242  Identities=24%  Similarity=0.331  Sum_probs=181.6

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcC-CCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEecc
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVG-IKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSS  100 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~-~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~  100 (292)
                      |+.|+=-...|+++..|+...+.-.+...+-. +..++-+|++||||||||+|||++|+.+         ....+++++.
T Consensus       141 WEsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinsh  220 (423)
T KOG0744|consen  141 WESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSH  220 (423)
T ss_pred             HHHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehh
Confidence            55566667789999998765432211111111 2346679999999999999999999988         3457999999


Q ss_pred             chhccccChHHHHHHHHHHHhhhC-----CCEEEEEcccccccCCcCC-CCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768          101 AIIDKYIGESARLIREMFGYARDH-----QPCIIFMDEIDAIGGRRFS-EGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~-----~~~il~lDe~d~l~~~~~~-~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      .+.+++.++..+.+..+|+.+..-     .--.++|||++.++..+.+ .+.....+..+....++.+++.+...+++.+
T Consensus       221 sLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~Nvli  300 (423)
T KOG0744|consen  221 SLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLI  300 (423)
T ss_pred             HHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEE
Confidence            999999999999999999887541     1246689999999877744 4445677888899999999998888899999


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc-----CCCC-------------CCHHHHHHH-cC
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA-----KHGE-------------IDYEAVVKL-AE  235 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~-----~~~~-------------~~~~~l~~~-~~  235 (292)
                      ++|+|..+.++.++.+  |-+.+.++.+|+...+.+|++.+.....     ....             .....+... +.
T Consensus       301 L~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~IlkscieEL~~~gIi~~~~~s~~~~~~i~~~~~~~~~~~~~~~~  378 (423)
T KOG0744|consen  301 LATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCIEELISSGIILFHQRSTGVKEFIKYQKALRNILIELSTV  378 (423)
T ss_pred             EeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHHHHHHhcCeeeeeccchhhhHHhHhhHhHHHHHHHHhhc
Confidence            9999999999999999  9999999999999999999997775321     1100             112233333 47


Q ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          236 GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       236 g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      |.|+|-++++=--|.  |..-...+|+.+++..|+.....+
T Consensus       379 gLSGRtlrkLP~Lah--a~y~~~~~v~~~~fl~al~ea~~k  417 (423)
T KOG0744|consen  379 GLSGRTLRKLPLLAH--AEYFRTFTVDLSNFLLALLEAAKK  417 (423)
T ss_pred             CCccchHhhhhHHHH--HhccCCCccChHHHHHHHHHHHHH
Confidence            999999998766554  333334579999998888776554

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.88  E-value=1.4e-21  Score=170.70  Aligned_cols=209  Identities=22%  Similarity=0.324  Sum_probs=164.2

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      .|.+|+.|+=..+.+++|.+-++.+..++.-|.+.|....++.|||||||||||+++.++|+.++..++.+...+.... 
T Consensus       196 HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n-  274 (457)
T KOG0743|consen  196 HPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLD-  274 (457)
T ss_pred             CCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCc-
Confidence            3489999999999999999999999999999999999999999999999999999999999999999999888776432 


Q ss_pred             cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCC---cch-HHHHHHHHHHHHHhhCCCCCC--CeEEEEEeCC
Q 022768          107 IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGT---SAD-REIQRTLMELLNQLDGFDQLG--KVKMIMATNR  180 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~---~~~-~~~~~~l~~~l~~~~~~~~~~--~~~vi~t~~~  180 (292)
                          .. ++.++......  +||+|+|||+-+.-+.....   ... ....-+|.-+|+.+++++...  .-++|+|||.
T Consensus       275 ----~d-Lr~LL~~t~~k--SIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh  347 (457)
T KOG0743|consen  275 ----SD-LRHLLLATPNK--SILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNH  347 (457)
T ss_pred             ----HH-HHHHHHhCCCC--cEEEEeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCC
Confidence                22 55655544443  79999999998643322211   111 123345667888888777666  6789999999


Q ss_pred             CCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCC--CCHHHHHHH
Q 022768          181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEG--FNGADLRNV  245 (292)
Q Consensus       181 ~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g--~~~~di~~l  245 (292)
                      .+.++|+|.+++|++..|++++-+......++..|+..-.  ...-++.+.....+  .||+++...
T Consensus       348 ~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~--~h~L~~eie~l~~~~~~tPA~V~e~  412 (457)
T KOG0743|consen  348 KEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEE--DHRLFDEIERLIEETEVTPAQVAEE  412 (457)
T ss_pred             hhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCC--CcchhHHHHHHhhcCccCHHHHHHH
Confidence            9999999999999999999999999999999999996432  12234445544443  488877643

>CHL00181 cbbX CbbX; Provisional

Probab=99.88  E-value=8.3e-21  Score=162.88  Aligned_cols=212  Identities=22%  Similarity=0.312  Sum_probs=147.8

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCC---CCceEEEEcCCCChHHHHHHHHHHhc-------CCcEEEEeccc
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIK---PPKGVLLYGPPGTGKTLLARAIASNI-------DANFLKVVSSA  101 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~---~~~~vll~G~~G~GKT~l~~~la~~l-------~~~~~~~~~~~  101 (292)
                      .+++|++++|+++.+.+... .-.....+.|+.   ++.+++|+||||||||++|+++++.+       ..+++.++...
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~~-~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~  101 (287)
T CHL00181         23 EELVGLAPVKTRIREIAALL-LIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDD  101 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHHH-HHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHH
Confidence            37999999999999987663 233455556653   35569999999999999999999875       23588888888


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      +.+.+.|.+......++..+   .++||||||+|.+....+  ..+...+.+..|..+++.     ...+++||++++..
T Consensus       102 l~~~~~g~~~~~~~~~l~~a---~ggVLfIDE~~~l~~~~~--~~~~~~e~~~~L~~~me~-----~~~~~~vI~ag~~~  171 (287)
T CHL00181        102 LVGQYIGHTAPKTKEVLKKA---MGGVLFIDEAYYLYKPDN--ERDYGSEAIEILLQVMEN-----QRDDLVVIFAGYKD  171 (287)
T ss_pred             HHHHHhccchHHHHHHHHHc---cCCEEEEEccchhccCCC--ccchHHHHHHHHHHHHhc-----CCCCEEEEEeCCcH
Confidence            88777777766666666654   347999999999864321  122234555555555542     22467777776532


Q ss_pred             C-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHH----c--CCC-CHHHHHHHHHH
Q 022768          182 D-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKL----A--EGF-NGADLRNVCTE  248 (292)
Q Consensus       182 ~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~----~--~g~-~~~di~~l~~~  248 (292)
                      .     ..++.+++  ||...+.|++|+.+++.+|+..++...... .+-....+...    .  ..+ +.++++.+++.
T Consensus       172 ~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~ve~  249 (287)
T CHL00181        172 RMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQPLFANARSVRNALDR  249 (287)
T ss_pred             HHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHHHH
Confidence            1     34688998  999999999999999999999998754322 11122222322    1  223 58999999998


Q ss_pred             HHHHHHHh
Q 022768          249 AGMSAIRA  256 (292)
Q Consensus       249 a~~~a~~~  256 (292)
                      |......+
T Consensus       250 ~~~~~~~r  257 (287)
T CHL00181        250 ARMRQANR  257 (287)
T ss_pred             HHHHHHHH
Confidence            88766555

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.88  E-value=5.9e-21  Score=162.59  Aligned_cols=213  Identities=22%  Similarity=0.257  Sum_probs=146.3

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCC---CCceEEEEcCCCChHHHHHHHHHHhc-------CCcEEEEec
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIK---PPKGVLLYGPPGTGKTLLARAIASNI-------DANFLKVVS   99 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~---~~~~vll~G~~G~GKT~l~~~la~~l-------~~~~~~~~~   99 (292)
                      .+++++|++++|++|.+++.++... ......|..   ...+++|+||||||||++|+.+++.+       ..+++.+++
T Consensus         4 ~l~~~~Gl~~vk~~i~~~~~~~~~~-~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~   82 (261)
T TIGR02881         4 ELSRMVGLDEVKALIKEIYAWIQIN-EKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVER   82 (261)
T ss_pred             HHHHhcChHHHHHHHHHHHHHHHHH-HHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecH
Confidence            4678999999999999998775333 222334443   34579999999999999999999865       236788888


Q ss_pred             cchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          100 SAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      ..+.+.+.++....+..+|..+.   ++||||||+|.+....      ........+..++..++..  ...+++|+++.
T Consensus        83 ~~l~~~~~g~~~~~~~~~~~~a~---~~VL~IDE~~~L~~~~------~~~~~~~~i~~Ll~~~e~~--~~~~~vila~~  151 (261)
T TIGR02881        83 ADLVGEYIGHTAQKTREVIKKAL---GGVLFIDEAYSLARGG------EKDFGKEAIDTLVKGMEDN--RNEFVLILAGY  151 (261)
T ss_pred             HHhhhhhccchHHHHHHHHHhcc---CCEEEEechhhhccCC------ccchHHHHHHHHHHHHhcc--CCCEEEEecCC
Confidence            88888888888888888887654   4799999999985211      0111223344455554432  24566666654


Q ss_pred             CCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHH-------c--CCCCHHHHHH
Q 022768          180 RPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKL-------A--EGFNGADLRN  244 (292)
Q Consensus       180 ~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~-------~--~g~~~~di~~  244 (292)
                      ..+     .+++++++  ||...+.|+.++.+++.+|++.++...... .+.....+...       .  ...+.+.+++
T Consensus       152 ~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n  229 (261)
T TIGR02881       152 SDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRN  229 (261)
T ss_pred             cchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHH
Confidence            322     36788988  998899999999999999999988754322 11112233221       1  1237788888


Q ss_pred             HHHHHHHHHHHh
Q 022768          245 VCTEAGMSAIRA  256 (292)
Q Consensus       245 l~~~a~~~a~~~  256 (292)
                      +++.|......+
T Consensus       230 ~~e~a~~~~~~r  241 (261)
T TIGR02881       230 IIEKAIRRQAVR  241 (261)
T ss_pred             HHHHHHHHHHHH
Confidence            888888766555

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.88  E-value=5.3e-21  Score=171.63  Aligned_cols=210  Identities=15%  Similarity=0.190  Sum_probs=151.6

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      +..+...++|.+|++++|++++++.|...+...            ..++.+||+||+|+||||+|+.+|+.+++.     
T Consensus         5 ~~~L~~KyRP~~f~dvVGQe~iv~~L~~~i~~~------------ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~   72 (484)
T PRK14956          5 HEVLSRKYRPQFFRDVIHQDLAIGALQNALKSG------------KIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGN   72 (484)
T ss_pred             cchhHHHhCCCCHHHHhChHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCc
Confidence            355677899999999999999999999988652            335568999999999999999999998763     


Q ss_pred             -------------------EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchH
Q 022768           94 -------------------FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        94 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                         +++++...      ......++.+...+.    .....|+||||+|.+           ..
T Consensus        73 ~pCg~C~sC~~i~~g~~~dviEIdaas------~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~L-----------s~  135 (484)
T PRK14956         73 EPCNECTSCLEITKGISSDVLEIDAAS------NRGIENIRELRDNVKFAPMGGKYKVYIIDEVHML-----------TD  135 (484)
T ss_pred             cccCCCcHHHHHHccCCccceeechhh------cccHHHHHHHHHHHHhhhhcCCCEEEEEechhhc-----------CH
Confidence                               12222111      011233444443332    234579999999999           66


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      ..+..|+..++     .+..++++|++|+.++.+.+.+++  || ..+.|.+++.++..+.++..+....+. .+..+..
T Consensus       136 ~A~NALLKtLE-----EPp~~viFILaTte~~kI~~TI~S--RC-q~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~  207 (484)
T PRK14956        136 QSFNALLKTLE-----EPPAHIVFILATTEFHKIPETILS--RC-QDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFW  207 (484)
T ss_pred             HHHHHHHHHhh-----cCCCceEEEeecCChhhccHHHHh--hh-heeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            66666665554     344688899999999999999999  88 778999999998888888887644332 2334567


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      ++..++| +.|+...+++.+...+    ...|+.+++.+.+
T Consensus       208 Ia~~S~G-d~RdAL~lLeq~i~~~----~~~it~~~V~~~l  243 (484)
T PRK14956        208 IAKKGDG-SVRDMLSFMEQAIVFT----DSKLTGVKIRKMI  243 (484)
T ss_pred             HHHHcCC-hHHHHHHHHHHHHHhC----CCCcCHHHHHHHh
Confidence            7788887 7888888887766432    2347777776544

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.88  E-value=6.1e-21  Score=163.84  Aligned_cols=211  Identities=22%  Similarity=0.308  Sum_probs=149.8

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCC---CCceEEEEcCCCChHHHHHHHHHHhcC-------CcEEEEeccch
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIK---PPKGVLLYGPPGTGKTLLARAIASNID-------ANFLKVVSSAI  102 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~---~~~~vll~G~~G~GKT~l~~~la~~l~-------~~~~~~~~~~~  102 (292)
                      +++|++++|+++.+.+.. ......+.+.|+.   ++.+++|+||||||||++|+++++.+.       .+++.+++.++
T Consensus        23 ~l~Gl~~vk~~i~e~~~~-~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~~~l  101 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAAL-LLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDL  101 (284)
T ss_pred             hccCHHHHHHHHHHHHHH-HHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecHHHH
Confidence            699999999999998877 4455566677765   355899999999999999999988762       36888888888


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC-
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP-  181 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~-  181 (292)
                      ...+.|.+...+..++..+   .+++|||||++.+.....  ......+.+..|..+++.     ...++++|++++.. 
T Consensus       102 ~~~~~g~~~~~~~~~~~~a---~~gvL~iDEi~~L~~~~~--~~~~~~~~~~~Ll~~le~-----~~~~~~vI~a~~~~~  171 (284)
T TIGR02880       102 VGQYIGHTAPKTKEILKRA---MGGVLFIDEAYYLYRPDN--ERDYGQEAIEILLQVMEN-----QRDDLVVILAGYKDR  171 (284)
T ss_pred             hHhhcccchHHHHHHHHHc---cCcEEEEechhhhccCCC--ccchHHHHHHHHHHHHhc-----CCCCEEEEEeCCcHH
Confidence            7777777766666666654   348999999998853321  112234455555555542     22567777776542 


Q ss_pred             -C---CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHc------C-CCCHHHHHHHHHHH
Q 022768          182 -D---VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLA------E-GFNGADLRNVCTEA  249 (292)
Q Consensus       182 -~---~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~------~-g~~~~di~~l~~~a  249 (292)
                       +   .+++.+++  ||...++|++++.+++..|++.++...... .+.....+....      . --|.+.++++++.+
T Consensus       172 ~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve~~  249 (284)
T TIGR02880       172 MDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALRRTQPHFANARSIRNAIDRA  249 (284)
T ss_pred             HHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHH
Confidence             2   35789998  999999999999999999999998864322 111123333321      1 12789999999998


Q ss_pred             HHHHHHh
Q 022768          250 GMSAIRA  256 (292)
Q Consensus       250 ~~~a~~~  256 (292)
                      ......+
T Consensus       250 ~~~~~~r  256 (284)
T TIGR02880       250 RLRQANR  256 (284)
T ss_pred             HHHHHHH
Confidence            8776655

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.87  E-value=1e-20  Score=165.12  Aligned_cols=215  Identities=20%  Similarity=0.233  Sum_probs=155.2

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccCh
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGE  109 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~  109 (292)
                      +|++++|+++.++.|..++......        .....+++|+||||+|||++++.+|++++.++..........  .+.
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~--------~~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~--~~~   71 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMR--------QEALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEK--PGD   71 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhc--------CCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcC--chh
Confidence            6899999999999999988642111        133567999999999999999999999988776555332211  111


Q ss_pred             HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-------------CCCCCeEEEE
Q 022768          110 SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-------------DQLGKVKMIM  176 (292)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-------------~~~~~~~vi~  176 (292)
                          +...+...  ..+.+|+|||+|.+           ....++.+..+++.....             ...+.+.+|+
T Consensus        72 ----l~~~l~~~--~~~~vl~iDEi~~l-----------~~~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~  134 (305)
T TIGR00635        72 ----LAAILTNL--EEGDVLFIDEIHRL-----------SPAVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVG  134 (305)
T ss_pred             ----HHHHHHhc--ccCCEEEEehHhhh-----------CHHHHHHhhHHHhhhheeeeeccCccccceeecCCCeEEEE
Confidence                21222222  24579999999998           455556666665432200             1223578899


Q ss_pred             EeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Q 022768          177 ATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       177 t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      +++.+..+++++++  ||...+.+.+|+.++..++++..+...... .+...+.++..+.| .++.+..++..+...|..
T Consensus       135 ~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G-~pR~~~~ll~~~~~~a~~  211 (305)
T TIGR00635       135 ATTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRG-TPRIANRLLRRVRDFAQV  211 (305)
T ss_pred             ecCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCC-CcchHHHHHHHHHHHHHH
Confidence            99998899999998  998889999999999999999887643332 12234567777777 667888889888877766


Q ss_pred             hcCCcccHHHHHHHHHHHh
Q 022768          256 AERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       256 ~~~~~i~~~~~~~a~~~~~  274 (292)
                      .....|+.+++.+++..+.
T Consensus       212 ~~~~~it~~~v~~~l~~l~  230 (305)
T TIGR00635       212 RGQKIINRDIALKALEMLM  230 (305)
T ss_pred             cCCCCcCHHHHHHHHHHhC
Confidence            6667799999999998853

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=2.8e-21  Score=177.55  Aligned_cols=201  Identities=17%  Similarity=0.236  Sum_probs=144.2

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |+.+..+++|.+|++|+|++++++.|.+.+..-            ...+.+||+||+|+||||+++.+++.+++.     
T Consensus         3 y~vLarKYRPqtFddVIGQe~vv~~L~~al~~g------------RLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~   70 (700)
T PRK12323          3 YQVLARKWRPRDFTTLVGQEHVVRALTHALEQQ------------RLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGE   70 (700)
T ss_pred             chhHHHHhCCCcHHHHcCcHHHHHHHHHHHHhC------------CCceEEEEECCCCCCHHHHHHHHHHHhcCCCcccc
Confidence            567788999999999999999999999998752            335668999999999999999999999762     


Q ss_pred             -------EEEEeccch------hccc-----cChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHH
Q 022768           94 -------FLKVVSSAI------IDKY-----IGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADRE  151 (292)
Q Consensus        94 -------~~~~~~~~~------~~~~-----~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~  151 (292)
                             +..+..+..      .+.+     .....+.++++.....    .....|+||||+|.|           +..
T Consensus        71 ~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~L-----------s~~  139 (700)
T PRK12323         71 GGITAQPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHML-----------TNH  139 (700)
T ss_pred             ccCCCCCCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhc-----------CHH
Confidence                   111111100      0000     0112333444444433    234579999999999           555


Q ss_pred             HHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC-CCHHHH
Q 022768          152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE-IDYEAV  230 (292)
Q Consensus       152 ~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~-~~~~~l  230 (292)
                      ....|+..|+     .+..++.+|++|+.++.+.+.++|  || ..+.|+.++.++..+.++..+....+..+ ..+..+
T Consensus       140 AaNALLKTLE-----EPP~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~I  211 (700)
T PRK12323        140 AFNAMLKTLE-----EPPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLL  211 (700)
T ss_pred             HHHHHHHhhc-----cCCCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            5555555544     244678899999999999999999  87 88899999999999988887764333321 224667


Q ss_pred             HHHcCCCCHHHHHHHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEAGM  251 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a~~  251 (292)
                      +..++| ++++..++++.+..
T Consensus       212 A~~A~G-s~RdALsLLdQaia  231 (700)
T PRK12323        212 AQAAQG-SMRDALSLTDQAIA  231 (700)
T ss_pred             HHHcCC-CHHHHHHHHHHHHH
Confidence            778887 88899999887664

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.87  E-value=1.7e-20  Score=172.87  Aligned_cols=211  Identities=17%  Similarity=0.227  Sum_probs=153.2

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |..+...++|.+|++++|++.+++.|...+..-            ..++.+||+||+|+|||++|+.+|+.+++.     
T Consensus         2 Y~~LarKyRPktFddVIGQe~vv~~L~~aI~~g------------rl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~   69 (702)
T PRK14960          2 YQVLARKYRPRNFNELVGQNHVSRALSSALERG------------RLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTS   69 (702)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCC
Confidence            456778899999999999999999999998752            445678999999999999999999998762     


Q ss_pred             -------------------EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchH
Q 022768           94 -------------------FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        94 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                         ++.++....      .....++.+...+.    ..+..|++|||+|.|           +.
T Consensus        70 ~pCg~C~sC~~I~~g~hpDviEIDAAs~------~~VddIReli~~~~y~P~~gk~KV~IIDEVh~L-----------S~  132 (702)
T PRK14960         70 TPCEVCATCKAVNEGRFIDLIEIDAASR------TKVEDTRELLDNVPYAPTQGRFKVYLIDEVHML-----------ST  132 (702)
T ss_pred             CCCccCHHHHHHhcCCCCceEEeccccc------CCHHHHHHHHHHHhhhhhcCCcEEEEEechHhc-----------CH
Confidence                               222222211      12333444444432    234579999999999           66


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      .....|...++.     +.+.+.+|++|+.+..+...+++  || ..+.|.+++.++..+.++..+....+. .+..+..
T Consensus       133 ~A~NALLKtLEE-----PP~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~  204 (702)
T PRK14960        133 HSFNALLKTLEE-----PPEHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQ  204 (702)
T ss_pred             HHHHHHHHHHhc-----CCCCcEEEEEECChHhhhHHHHH--hh-heeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            666666666553     33567788888888888888887  77 789999999999999998888654433 2233566


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ++..+.| +.|++..++..+..+    +...|+.+++.+.+.
T Consensus       205 IA~~S~G-dLRdALnLLDQaIay----g~g~IT~edV~~lLG  241 (702)
T PRK14960        205 IAESAQG-SLRDALSLTDQAIAY----GQGAVHHQDVKEMLG  241 (702)
T ss_pred             HHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHhc
Confidence            7777776 888888888776643    345677777766544

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=2.4e-20  Score=165.82  Aligned_cols=211  Identities=17%  Similarity=0.253  Sum_probs=150.1

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----   94 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----   94 (292)
                      +..+...++|.+|++++|+++.++.+...+...            ..++.++|+||+|+||||+|+.+++.+.+..    
T Consensus         3 ~~~l~~kyrP~~~~~iiGq~~~~~~l~~~~~~~------------~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~   70 (363)
T PRK14961          3 YQILARKWRPQYFRDIIGQKHIVTAISNGLSLG------------RIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITS   70 (363)
T ss_pred             cHHHHHHhCCCchhhccChHHHHHHHHHHHHcC------------CCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            567788999999999999999999999988652            3356689999999999999999999986421    


Q ss_pred             --------------------EEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchH
Q 022768           95 --------------------LKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        95 --------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                          +.++...      ......++.+...+..    ....|++|||+|.+           ..
T Consensus        71 ~pc~~c~~c~~~~~~~~~d~~~~~~~~------~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l-----------~~  133 (363)
T PRK14961         71 NPCRKCIICKEIEKGLCLDLIEIDAAS------RTKVEEMREILDNIYYSPSKSRFKVYLIDEVHML-----------SR  133 (363)
T ss_pred             CCCCCCHHHHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhcCcccCCceEEEEEChhhc-----------CH
Confidence                                1111110      0122334444444322    23469999999998           55


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      ..+..+...++.     +.+.+.+|++++.++.+.+.+++  |+ ..+.|++++.++..++++..+...... .+..+..
T Consensus       134 ~a~naLLk~lEe-----~~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~  205 (363)
T PRK14961        134 HSFNALLKTLEE-----PPQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKL  205 (363)
T ss_pred             HHHHHHHHHHhc-----CCCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            555555555443     33567778888888889999998  77 788999999999999998877654322 2223455


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ++..+.| +++++..+++.+..+    +...|+.+++.+++.
T Consensus       206 ia~~s~G-~~R~al~~l~~~~~~----~~~~It~~~v~~~l~  242 (363)
T PRK14961        206 IAYHAHG-SMRDALNLLEHAINL----GKGNINIKNVTDMLG  242 (363)
T ss_pred             HHHHcCC-CHHHHHHHHHHHHHh----cCCCCCHHHHHHHHC
Confidence            6777776 777888888776543    355788888887665

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.86  E-value=2.6e-20  Score=173.57  Aligned_cols=211  Identities=18%  Similarity=0.269  Sum_probs=152.7

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----   94 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----   94 (292)
                      |..++..++|.+|++++|++.+++.|.+.+..-            .-++.+||+||+|+||||+++.+|+.+++..    
T Consensus         3 y~~La~KyRP~~f~divGQe~vv~~L~~~l~~~------------rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~   70 (647)
T PRK07994          3 YQVLARKWRPQTFAEVVGQEHVLTALANALDLG------------RLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITA   70 (647)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCC
Confidence            567788999999999999999999999988652            3345589999999999999999999987631    


Q ss_pred             --------------------EEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchH
Q 022768           95 --------------------LKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        95 --------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                          ++++...      ......++.+...+.    .....|++|||+|.|           ..
T Consensus        71 ~pCg~C~~C~~i~~g~~~D~ieidaas------~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~L-----------s~  133 (647)
T PRK07994         71 TPCGECDNCREIEQGRFVDLIEIDAAS------RTKVEDTRELLDNVQYAPARGRFKVYLIDEVHML-----------SR  133 (647)
T ss_pred             CCCCCCHHHHHHHcCCCCCceeecccc------cCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhC-----------CH
Confidence                                2222111      011233444443332    234579999999999           66


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      ..+..|+..+++     +.+.+.+|++|+.++.+.+.+++  || ..+.|++++.++....++..+....+. .+..+..
T Consensus       134 ~a~NALLKtLEE-----Pp~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~  205 (647)
T PRK07994        134 HSFNALLKTLEE-----PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQL  205 (647)
T ss_pred             HHHHHHHHHHHc-----CCCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            667777776663     44678888888899999999999  87 889999999999999998877543332 2233556


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ++..+.| +.|++..+++.+...    +...|+.+++.+.+.
T Consensus       206 Ia~~s~G-s~R~Al~lldqaia~----~~~~it~~~v~~~lg  242 (647)
T PRK07994        206 LARAADG-SMRDALSLTDQAIAS----GNGQVTTDDVSAMLG  242 (647)
T ss_pred             HHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHHc
Confidence            7778887 888999988776533    223466666655543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=1.4e-20  Score=172.85  Aligned_cols=214  Identities=15%  Similarity=0.191  Sum_probs=153.9

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |..+...++|.+|++++|++++++.|...+..-            ..++.+||+||+|+|||++|+.+|+.+++.     
T Consensus         3 y~~l~~kyRP~~f~divGq~~v~~~L~~~~~~~------------~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~   70 (509)
T PRK14958          3 HQVLARKWRPRCFQEVIGQAPVVRALSNALDQQ------------YLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSA   70 (509)
T ss_pred             chhHHHHHCCCCHHHhcCCHHHHHHHHHHHHhC------------CCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCc
Confidence            556778999999999999999999999998652            345668999999999999999999998653     


Q ss_pred             -------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchH
Q 022768           94 -------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        94 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                         +++++...      ......++.+...+..    ....|++|||+|.+           ..
T Consensus        71 ~pCg~C~~C~~i~~g~~~d~~eidaas------~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~l-----------s~  133 (509)
T PRK14958         71 NPCNDCENCREIDEGRFPDLFEVDAAS------RTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHML-----------SG  133 (509)
T ss_pred             ccCCCCHHHHHHhcCCCceEEEEcccc------cCCHHHHHHHHHHHhhccccCCcEEEEEEChHhc-----------CH
Confidence                               23333221      1122334444444332    34579999999999           55


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      .....|+..++.     +.+.+.+|++|++++.+.+.+++  |+ ..+.|++++.++....++..+....+. .+..+..
T Consensus       134 ~a~naLLk~LEe-----pp~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~  205 (509)
T PRK14958        134 HSFNALLKTLEE-----PPSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDL  205 (509)
T ss_pred             HHHHHHHHHHhc-----cCCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            556666665553     34578888888888899888998  77 778899999998888888777654433 2233566


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ++..+.| +.+++.++++.+..+    +...|+.+++.+.+....
T Consensus       206 ia~~s~G-slR~al~lLdq~ia~----~~~~It~~~V~~~lg~~~  245 (509)
T PRK14958        206 LARAANG-SVRDALSLLDQSIAY----GNGKVLIADVKTMLGTIE  245 (509)
T ss_pred             HHHHcCC-cHHHHHHHHHHHHhc----CCCCcCHHHHHHHHCCCC
Confidence            7777776 888888888877543    244677777776654433

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=99.86  E-value=8.9e-21  Score=144.74  Aligned_cols=131  Identities=42%  Similarity=0.753  Sum_probs=107.3

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCC-CEEEEEcccccccCCcCCCCCc
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQ-PCIIFMDEIDAIGGRRFSEGTS  147 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~il~lDe~d~l~~~~~~~~~~  147 (292)
                      +||+||||+|||++++.+|+.++.+++.+++..+.+.+.+.....+..++..+.... |+||+|||+|.+..+.......
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~~~~~~~   80 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKSQPSSSS   80 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHCSTSSSH
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccccccccc
Confidence            689999999999999999999999999999999998888899999999999998887 9999999999998776333333


Q ss_pred             chHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccC
Q 022768          148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPL  202 (292)
Q Consensus       148 ~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~  202 (292)
                      ........+...++...  ....++++|+|+|.++.+++.+.+ +||...+.++.
T Consensus        81 ~~~~~~~~L~~~l~~~~--~~~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   81 FEQRLLNQLLSLLDNPS--SKNSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             HHHHHHHHHHHHHHTTT--TTSSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             ccccccceeeecccccc--cccccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence            44444555555554433  223579999999999999999996 69999998863

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.86  E-value=4.1e-20  Score=174.97  Aligned_cols=200  Identities=19%  Similarity=0.221  Sum_probs=143.8

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----   94 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----   94 (292)
                      |..+...++|.+|++++|++++++.|.+++..-            .-++.+||+||+|+|||++++.+|+.+++..    
T Consensus         3 Y~~LaeKyRP~tFddIIGQe~Iv~~LknaI~~~------------rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~   70 (944)
T PRK14949          3 YQVLARKWRPATFEQMVGQSHVLHALTNALTQQ------------RLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTA   70 (944)
T ss_pred             chhHHHHhCCCCHHHhcCcHHHHHHHHHHHHhC------------CCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCC
Confidence            567788999999999999999999999987652            3355679999999999999999999997641    


Q ss_pred             ---EEEecc-chhcc-------cc---ChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHH
Q 022768           95 ---LKVVSS-AIIDK-------YI---GESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL  156 (292)
Q Consensus        95 ---~~~~~~-~~~~~-------~~---~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l  156 (292)
                         ..++.+ .+...       ..   ......++.+...+.    .....|+||||+|.|           ....+..|
T Consensus        71 ~pCg~C~sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~L-----------T~eAqNAL  139 (944)
T PRK14949         71 TPCGVCSSCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHML-----------SRSSFNAL  139 (944)
T ss_pred             CCCCCchHHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhc-----------CHHHHHHH
Confidence               111100 00000       00   011223444443332    234579999999999           77777777


Q ss_pred             HHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcC
Q 022768          157 MELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAE  235 (292)
Q Consensus       157 ~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~  235 (292)
                      +..++.     +...+.+|++|+.+..+.+.+++  || ..+.|++++.++....++..+....+. .+-.+..++..+.
T Consensus       140 LKtLEE-----PP~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~  211 (944)
T PRK14949        140 LKTLEE-----PPEHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAAN  211 (944)
T ss_pred             HHHHhc-----cCCCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            766653     44577888888889999999999  77 889999999999999998887643322 2223566777888


Q ss_pred             CCCHHHHHHHHHHHH
Q 022768          236 GFNGADLRNVCTEAG  250 (292)
Q Consensus       236 g~~~~di~~l~~~a~  250 (292)
                      | ++|++..++..+.
T Consensus       212 G-d~R~ALnLLdQal  225 (944)
T PRK14949        212 G-SMRDALSLTDQAI  225 (944)
T ss_pred             C-CHHHHHHHHHHHH
Confidence            7 8889998888766

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.85  E-value=5e-20  Score=167.65  Aligned_cols=211  Identities=18%  Similarity=0.236  Sum_probs=144.8

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC--------
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA--------   92 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~--------   92 (292)
                      .+...++|.+|++++|++++++.|...+...            ..++.+||+||||+||||+|+.+|+.+++        
T Consensus         3 ~l~~kyRP~~~~divGq~~i~~~L~~~i~~~------------~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~p   70 (472)
T PRK14962          3 ALYRKYRPKTFSEVVGQDHVKKLIINALKKN------------SISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEP   70 (472)
T ss_pred             hhHHHHCCCCHHHccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCC
Confidence            4567889999999999999999999887653            34566899999999999999999999865        


Q ss_pred             ----------------cEEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHH
Q 022768           93 ----------------NFLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREI  152 (292)
Q Consensus        93 ----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~  152 (292)
                                      .++.++...      ......++.+...+..    ....+|+|||+|.+           ....
T Consensus        71 c~~c~~c~~i~~g~~~dv~el~aa~------~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~L-----------t~~a  133 (472)
T PRK14962         71 CNECRACRSIDEGTFMDVIELDAAS------NRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHML-----------TKEA  133 (472)
T ss_pred             CcccHHHHHHhcCCCCccEEEeCcc------cCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHh-----------HHHH
Confidence                            233333221      1112233444433332    34579999999998           5555


Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHH
Q 022768          153 QRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVV  231 (292)
Q Consensus       153 ~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~  231 (292)
                      +..|...+..     +.+.+++|++++.+..+++++++  |+ ..+.|.+++.++...+++..+...... .+..++.++
T Consensus       134 ~~~LLk~LE~-----p~~~vv~Ilattn~~kl~~~L~S--R~-~vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia  205 (472)
T PRK14962        134 FNALLKTLEE-----PPSHVVFVLATTNLEKVPPTIIS--RC-QVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIA  205 (472)
T ss_pred             HHHHHHHHHh-----CCCcEEEEEEeCChHhhhHHHhc--Cc-EEEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            5555555542     33567788888888889999998  77 689999999999999988877643322 222345566


Q ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 022768          232 KLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKL  273 (292)
Q Consensus       232 ~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~  273 (292)
                      ..+.| ..+++.+.++.+..+   .+ ..|+.+++.+++...
T Consensus       206 ~~s~G-dlR~aln~Le~l~~~---~~-~~It~e~V~~~l~~~  242 (472)
T PRK14962        206 KRASG-GLRDALTMLEQVWKF---SE-GKITLETVHEALGLI  242 (472)
T ss_pred             HHhCC-CHHHHHHHHHHHHHh---cC-CCCCHHHHHHHHcCC
Confidence            66665 555555555544332   22 348888888877544

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.85  E-value=9.4e-20  Score=166.49  Aligned_cols=223  Identities=16%  Similarity=0.206  Sum_probs=156.1

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE---
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL---   95 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~---   95 (292)
                      |.++...++|.+|++++|+++.++.|...+..-            ..++++||+||+|+||||+|+.+|+.+++...   
T Consensus         8 y~~la~kyRP~~f~dliGq~~vv~~L~~ai~~~------------ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~   75 (507)
T PRK06645          8 YIPFARKYRPSNFAELQGQEVLVKVLSYTILND------------RLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITE   75 (507)
T ss_pred             ccchhhhhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHHhcCcccccc
Confidence            677888999999999999999999998877542            44678999999999999999999999865321   


Q ss_pred             -----EEecc----chhc----------cccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHH
Q 022768           96 -----KVVSS----AIID----------KYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREI  152 (292)
Q Consensus        96 -----~~~~~----~~~~----------~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~  152 (292)
                           .+..+    .+..          .........++.++..+..    ....|++|||+|.+           ....
T Consensus        76 ~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~L-----------s~~a  144 (507)
T PRK06645         76 NTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHML-----------SKGA  144 (507)
T ss_pred             CcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhc-----------CHHH
Confidence                 00000    0000          0001123445555555532    34579999999998           5555


Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHH
Q 022768          153 QRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVV  231 (292)
Q Consensus       153 ~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~  231 (292)
                      ...|...++     .+.+.+.+|++++..+.+.+.+++  |+ ..+.|.+++.++...+++..+...... .+..+..++
T Consensus       145 ~naLLk~LE-----epp~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia  216 (507)
T PRK06645        145 FNALLKTLE-----EPPPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIA  216 (507)
T ss_pred             HHHHHHHHh-----hcCCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            555555544     244577888888888889999998  77 778999999999999999888754433 222356677


Q ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          232 KLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       232 ~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ..+.| +.+++.++++.+..++... ...||.+++.+.+....
T Consensus       217 ~~s~G-slR~al~~Ldkai~~~~~~-~~~It~~~V~~llg~~~  257 (507)
T PRK06645        217 YKSEG-SARDAVSILDQAASMSAKS-DNIISPQVINQMLGLVD  257 (507)
T ss_pred             HHcCC-CHHHHHHHHHHHHHhhccC-CCCcCHHHHHHHHCCCC
Confidence            77877 8888888888887654321 23577777766654433

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.85  E-value=1.5e-19  Score=155.40  Aligned_cols=238  Identities=24%  Similarity=0.386  Sum_probs=172.7

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      +.-.|++++-...-..+|......- .+.+..    -.+=++++||||||||||.+++.+|...|..+-.+...++--. 
T Consensus       350 gk~pl~~ViL~psLe~Rie~lA~aT-aNTK~h----~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPl-  423 (630)
T KOG0742|consen  350 GKDPLEGVILHPSLEKRIEDLAIAT-ANTKKH----QAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPL-  423 (630)
T ss_pred             CCCCcCCeecCHHHHHHHHHHHHHh-cccccc----cchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCcccc-
Confidence            3445788888888888887765542 221111    2345689999999999999999999999998877776665321 


Q ss_pred             cChHHHHHHHHHHHhhhCC-CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          107 IGESARLIREMFGYARDHQ-PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~-~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      -.+....+..+|+-++... .-+|||||+|.++-.++..  -.+.....+|..+|-...  .....++++.++|.|..++
T Consensus       424 G~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnkt--ymSEaqRsaLNAlLfRTG--dqSrdivLvlAtNrpgdlD  499 (630)
T KOG0742|consen  424 GAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKT--YMSEAQRSALNALLFRTG--DQSRDIVLVLATNRPGDLD  499 (630)
T ss_pred             chHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchh--hhcHHHHHHHHHHHHHhc--ccccceEEEeccCCccchh
Confidence            1234566788998887754 4577999999998665332  122333344545443322  2335799999999999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC----C-------------------CCC----HHHHHHHcCCCC
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH----G-------------------EID----YEAVVKLAEGFN  238 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~----~-------------------~~~----~~~l~~~~~g~~  238 (292)
                      .++-+  |++..++|+.|..++|..++..|+..+...    .                   ..+    ....+..++|||
T Consensus       500 sAV~D--Ride~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfS  577 (630)
T KOG0742|consen  500 SAVND--RIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFS  577 (630)
T ss_pred             HHHHh--hhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCc
Confidence            99998  999999999999999999999888643211    0                   011    355677899999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          239 GADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      +++|.+++..-...++.+....++...+++.+......
T Consensus       578 GREiakLva~vQAavYgsedcvLd~~lf~e~v~ykv~e  615 (630)
T KOG0742|consen  578 GREIAKLVASVQAAVYGSEDCVLDEALFDERVDYKVQE  615 (630)
T ss_pred             HHHHHHHHHHHHHHHhcccchhhHHHHHHHHHHHHHHH
Confidence            99999999999998988888877777777776665543

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.84  E-value=1.3e-19  Score=168.38  Aligned_cols=220  Identities=18%  Similarity=0.226  Sum_probs=154.9

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----   94 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----   94 (292)
                      |+.+..+++|.+|++|+|++++++.|...+...            ..++.+||+||+|+|||++++.+++.+++.-    
T Consensus         3 y~vLarKYRP~tFddIIGQe~vv~~L~~ai~~~------------rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~   70 (709)
T PRK08691          3 YQVLARKWRPKTFADLVGQEHVVKALQNALDEG------------RLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHG   70 (709)
T ss_pred             chhHHHHhCCCCHHHHcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCC
Confidence            566778999999999999999999999998752            4456799999999999999999999886531    


Q ss_pred             ---EEEec------cchhc-----cccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHH
Q 022768           95 ---LKVVS------SAIID-----KYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL  156 (292)
Q Consensus        95 ---~~~~~------~~~~~-----~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l  156 (292)
                         ..+..      ..+.+     .........++.++..+.    .....|+||||+|.+           +......|
T Consensus        71 ~pCg~C~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~L-----------s~~A~NAL  139 (709)
T PRK08691         71 EPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHML-----------SKSAFNAM  139 (709)
T ss_pred             CCCcccHHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECcccc-----------CHHHHHHH
Confidence               11100      00000     000112334555554432    234579999999988           55555555


Q ss_pred             HHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcC
Q 022768          157 MELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAE  235 (292)
Q Consensus       157 ~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~  235 (292)
                      +..++.     +.+.+.+|++++.+..+...+++  || ..+.|+.++.++....++..+....+. .+..+..|+..+.
T Consensus       140 LKtLEE-----Pp~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~  211 (709)
T PRK08691        140 LKTLEE-----PPEHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAA  211 (709)
T ss_pred             HHHHHh-----CCCCcEEEEEeCCccccchHHHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhC
Confidence            555553     33577888888999999999988  77 778899999999999999888754433 2223567777777


Q ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          236 GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       236 g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      | +.+++..+++.+..+    +...|+.+++.+.+....
T Consensus       212 G-slRdAlnLLDqaia~----g~g~It~e~V~~lLG~~d  245 (709)
T PRK08691        212 G-SMRDALSLLDQAIAL----GSGKVAENDVRQMIGAVD  245 (709)
T ss_pred             C-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHHcccC
Confidence            6 888998888887754    234577777776655443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=1.4e-19  Score=164.12  Aligned_cols=209  Identities=18%  Similarity=0.236  Sum_probs=152.0

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC--------
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA--------   92 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~--------   92 (292)
                      .++..++|.+|++++|++..++.|...+..-            ..++++||+||+|+||||+|+.+|+.+++        
T Consensus         2 ~la~KyRP~~f~dliGQe~vv~~L~~a~~~~------------ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~p   69 (491)
T PRK14964          2 NLALKYRPSSFKDLVGQDVLVRILRNAFTLN------------KIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDP   69 (491)
T ss_pred             ChhHHhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCC
Confidence            4567899999999999999999999887652            44678999999999999999999997743        


Q ss_pred             ----------------cEEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHH
Q 022768           93 ----------------NFLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREI  152 (292)
Q Consensus        93 ----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~  152 (292)
                                      .+++++....      ...+.++.+...+..    ....|++|||+|.+           ....
T Consensus        70 Cg~C~~C~~i~~~~~~Dv~eidaas~------~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~L-----------s~~A  132 (491)
T PRK14964         70 CGTCHNCISIKNSNHPDVIEIDAASN------TSVDDIKVILENSCYLPISSKFKVYIIDEVHML-----------SNSA  132 (491)
T ss_pred             ccccHHHHHHhccCCCCEEEEecccC------CCHHHHHHHHHHHHhccccCCceEEEEeChHhC-----------CHHH
Confidence                            2344433221      123345555554432    34579999999998           5555


Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHH
Q 022768          153 QRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVV  231 (292)
Q Consensus       153 ~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~  231 (292)
                      ...|...++     .+.+.+.+|++++....+.+.+++  |+ ..+.|.+++.++....++..+...... .+..+..++
T Consensus       133 ~NaLLK~LE-----ePp~~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa  204 (491)
T PRK14964        133 FNALLKTLE-----EPAPHVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIA  204 (491)
T ss_pred             HHHHHHHHh-----CCCCCeEEEEEeCChHHHHHHHHH--hh-eeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            555555554     344578888888888889999998  77 778999999999999988887654433 223356677


Q ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          232 KLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       232 ~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ..++| +.+++.++++.+..++    ...||.+++.+.+.
T Consensus       205 ~~s~G-slR~alslLdqli~y~----~~~It~e~V~~llg  239 (491)
T PRK14964        205 ENSSG-SMRNALFLLEQAAIYS----NNKISEKSVRDLLG  239 (491)
T ss_pred             HHcCC-CHHHHHHHHHHHHHhc----CCCCCHHHHHHHHc
Confidence            77776 8888888888876543    23688888777643

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.84  E-value=2.3e-19  Score=162.38  Aligned_cols=207  Identities=30%  Similarity=0.400  Sum_probs=146.1

Q ss_pred             cccCCCCCccccccccHHHHHH---HHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRE---LRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~---l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +.+.++|.+|++++|+++.+..   |.+.+..             ....+++|+||||+||||+++.+++.++.+++.++
T Consensus         2 la~~~RP~~l~d~vGq~~~v~~~~~L~~~i~~-------------~~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~   68 (413)
T PRK13342          2 LAERMRPKTLDEVVGQEHLLGPGKPLRRMIEA-------------GRLSSMILWGPPGTGKTTLARIIAGATDAPFEALS   68 (413)
T ss_pred             hhhhhCCCCHHHhcCcHHHhCcchHHHHHHHc-------------CCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEe
Confidence            4567889999999999999766   7777654             23457999999999999999999999999999888


Q ss_pred             ccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           99 SSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      .....       ...++.++..+.    .....+|+|||+|.+           ....+..|...++.       +.+++
T Consensus        69 a~~~~-------~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l-----------~~~~q~~LL~~le~-------~~iil  123 (413)
T PRK13342         69 AVTSG-------VKDLREVIEEARQRRSAGRRTILFIDEIHRF-----------NKAQQDALLPHVED-------GTITL  123 (413)
T ss_pred             ccccc-------HHHHHHHHHHHHHhhhcCCceEEEEechhhh-----------CHHHHHHHHHHhhc-------CcEEE
Confidence            65421       222333333332    235689999999998           56666666665542       45666


Q ss_pred             EEEe--CCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCC-CCC---HHHHHHHcCCCCHHHHHHHHHH
Q 022768          175 IMAT--NRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG-EID---YEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       175 i~t~--~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~-~~~---~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      |+++  |....+++++++  || ..+.|++++.++...+++..+....... .++   ++.++..+.| .++.+.++++.
T Consensus       124 I~att~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~G-d~R~aln~Le~  199 (413)
T PRK13342        124 IGATTENPSFEVNPALLS--RA-QVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANG-DARRALNLLEL  199 (413)
T ss_pred             EEeCCCChhhhccHHHhc--cc-eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCC-CHHHHHHHHHH
Confidence            6654  334578899998  77 7789999999999999988765321111 233   3455666654 55666666665


Q ss_pred             HHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          249 AGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       249 a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      +...     ...|+.+++.+++.....
T Consensus       200 ~~~~-----~~~It~~~v~~~~~~~~~  221 (413)
T PRK13342        200 AALG-----VDSITLELLEEALQKRAA  221 (413)
T ss_pred             HHHc-----cCCCCHHHHHHHHhhhhh
Confidence            5433     456999999999887543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=2e-19  Score=167.36  Aligned_cols=211  Identities=15%  Similarity=0.223  Sum_probs=150.2

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |..+..+++|.+|++++|++++++.|.+.+..-            .-++.+||+||+|+||||+++.+|+.+++.     
T Consensus         3 y~vla~KyRP~~f~dviGQe~vv~~L~~~l~~~------------rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~   70 (618)
T PRK14951          3 YLVLARKYRPRSFSEMVGQEHVVQALTNALTQQ------------RLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQ   70 (618)
T ss_pred             hHHHHHHHCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccc
Confidence            556778999999999999999999999998752            335668999999999999999999998752     


Q ss_pred             ------------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCC
Q 022768           94 ------------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEG  145 (292)
Q Consensus        94 ------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~  145 (292)
                                              ++.++...      ....+.++.+...+..    ....|++|||+|.|        
T Consensus        71 ~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas------~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~L--------  136 (618)
T PRK14951         71 GGITATPCGVCQACRDIDSGRFVDYTELDAAS------NRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHML--------  136 (618)
T ss_pred             cCCCCCCCCccHHHHHHHcCCCCceeecCccc------ccCHHHHHHHHHHHHhCcccCCceEEEEEChhhC--------
Confidence                                    11111111      1122344555544332    23579999999999        


Q ss_pred             CcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CC
Q 022768          146 TSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GE  224 (292)
Q Consensus       146 ~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~  224 (292)
                         +......|+..++     .+.+.+.+|++|++++.+...+++  |+ ..+.|+.++.++..+.++..+....+. .+
T Consensus       137 ---s~~a~NaLLKtLE-----EPP~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~egi~ie~  205 (618)
T PRK14951        137 ---TNTAFNAMLKTLE-----EPPEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAENVPAEP  205 (618)
T ss_pred             ---CHHHHHHHHHhcc-----cCCCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHcCCCCCH
Confidence               5555555554444     244577788888888888888998  77 889999999999999988887654443 22


Q ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          225 IDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       225 ~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ..+..|+..+.| +.+++.++++.+..+    +...|+.+++.+.+.
T Consensus       206 ~AL~~La~~s~G-slR~al~lLdq~ia~----~~~~It~~~V~~~Lg  247 (618)
T PRK14951        206 QALRLLARAARG-SMRDALSLTDQAIAF----GSGQLQEAAVRQMLG  247 (618)
T ss_pred             HHHHHHHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHHc
Confidence            235667777777 888888888766644    234577777666553

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.84  E-value=2.9e-19  Score=164.20  Aligned_cols=212  Identities=18%  Similarity=0.248  Sum_probs=148.7

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |..+...++|.+|++++|++.+++.|...+..-            ..++.+||+||+|+|||++|+.+|+.+.+.     
T Consensus         3 y~~La~KyRP~~f~diiGq~~~v~~L~~~i~~~------------rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~   70 (546)
T PRK14957          3 YQALARKYRPQSFAEVAGQQHALNSLVHALETQ------------KVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTA   70 (546)
T ss_pred             chhHHHHHCcCcHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC
Confidence            556778899999999999999999999988652            334568999999999999999999988651     


Q ss_pred             -------------------EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchH
Q 022768           94 -------------------FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        94 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                         ++.++....      .....++.+...+.    .....|++|||+|.+           +.
T Consensus        71 ~pCg~C~sC~~i~~~~~~dlieidaas~------~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~l-----------s~  133 (546)
T PRK14957         71 EPCNKCENCVAINNNSFIDLIEIDAASR------TGVEETKEILDNIQYMPSQGRYKVYLIDEVHML-----------SK  133 (546)
T ss_pred             CCCcccHHHHHHhcCCCCceEEeecccc------cCHHHHHHHHHHHHhhhhcCCcEEEEEechhhc-----------cH
Confidence                               222221110      11122333333322    234579999999999           66


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      ..+..|+..++.     +.+.+.+|++|+++..+.+.+++  |+ ..++|.+++.++....++..+....+. .+..+..
T Consensus       134 ~a~naLLK~LEe-----pp~~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~  205 (546)
T PRK14957        134 QSFNALLKTLEE-----PPEYVKFILATTDYHKIPVTILS--RC-IQLHLKHISQADIKDQLKIILAKENINSDEQSLEY  205 (546)
T ss_pred             HHHHHHHHHHhc-----CCCCceEEEEECChhhhhhhHHH--he-eeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            666666666653     33567778778888888888988  77 889999999999888888777644332 2233456


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      ++..+.| +.+++..+++.+..+.   + ..|+.+++.+++..
T Consensus       206 Ia~~s~G-dlR~alnlLek~i~~~---~-~~It~~~V~~~l~~  243 (546)
T PRK14957        206 IAYHAKG-SLRDALSLLDQAISFC---G-GELKQAQIKQMLGI  243 (546)
T ss_pred             HHHHcCC-CHHHHHHHHHHHHHhc---c-CCCCHHHHHHHHcc
Confidence            6677776 7778888887766442   1 45777777765443

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.83  E-value=1.3e-19  Score=167.90  Aligned_cols=226  Identities=25%  Similarity=0.350  Sum_probs=159.0

Q ss_pred             hhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc------
Q 022768           17 VVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI------   90 (292)
Q Consensus        17 ~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l------   90 (292)
                      ....++.+.++|.+|++++|+++.++.+...+..             ..+.+++|+||||||||++|+++.+..      
T Consensus        50 ~~~~~~~~~~rp~~f~~iiGqs~~i~~l~~al~~-------------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s  116 (531)
T TIGR02902        50 RLTEPLSEKTRPKSFDEIIGQEEGIKALKAALCG-------------PNPQHVIIYGPPGVGKTAAARLVLEEAKKNPAS  116 (531)
T ss_pred             hhcchHHHhhCcCCHHHeeCcHHHHHHHHHHHhC-------------CCCceEEEECCCCCCHHHHHHHHHHHhhhccCC
Confidence            3455777888999999999999999999876432             335689999999999999999998642      


Q ss_pred             ----CCcEEEEeccchh--c-----cccChHHHHH---HHHH----------HHhhhCCCEEEEEcccccccCCcCCCCC
Q 022768           91 ----DANFLKVVSSAII--D-----KYIGESARLI---REMF----------GYARDHQPCIIFMDEIDAIGGRRFSEGT  146 (292)
Q Consensus        91 ----~~~~~~~~~~~~~--~-----~~~~~~~~~~---~~~~----------~~~~~~~~~il~lDe~d~l~~~~~~~~~  146 (292)
                          +.+++.+++....  .     ...+.....+   ...+          ........++|||||++.+         
T Consensus       117 ~~~~~~~fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L---------  187 (531)
T TIGR02902       117 PFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGEL---------  187 (531)
T ss_pred             CcCCCCCEEEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhC---------
Confidence                3578888876421  1     0011000000   0000          0112234589999999999         


Q ss_pred             cchHHHHHHHHHHHHHhhCC-----------------------CCCCCeEEE-EEeCCCCCCChhhcCCCCcceEEEccC
Q 022768          147 SADREIQRTLMELLNQLDGF-----------------------DQLGKVKMI-MATNRPDVLDPALLRPGRLDRKIEIPL  202 (292)
Q Consensus       147 ~~~~~~~~~l~~~l~~~~~~-----------------------~~~~~~~vi-~t~~~~~~l~~~l~~~~r~~~~i~l~~  202 (292)
                        +...+..|..+++.....                       .-...+.+| +|++.++.+++++++  || ..+.|++
T Consensus       188 --~~~~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrs--R~-~~I~f~p  262 (531)
T TIGR02902       188 --HPVQMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRS--RC-VEIFFRP  262 (531)
T ss_pred             --CHHHHHHHHHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhh--hh-heeeCCC
Confidence              888888888887652100                       001134444 556778999999998  77 6789999


Q ss_pred             CCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          203 PNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       203 p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ++.+++..+++..+...... .+..++.+...+  ++.+++.++++.|...|..+++..|+.+|+..++.
T Consensus       263 L~~eei~~Il~~~a~k~~i~is~~al~~I~~y~--~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~  330 (531)
T TIGR02902       263 LLDEEIKEIAKNAAEKIGINLEKHALELIVKYA--SNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE  330 (531)
T ss_pred             CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhh--hhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence            99999999999988754432 111234444443  37899999999999999888888999999999986

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.83  E-value=2e-19  Score=166.32  Aligned_cols=211  Identities=18%  Similarity=0.252  Sum_probs=151.3

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----   94 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----   94 (292)
                      |..+...++|.+|++++|++++++.|...+...            ..++.+||+||+|+|||++|+.+++.+.+..    
T Consensus         3 ~~~l~~k~rP~~f~divGq~~v~~~L~~~i~~~------------~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~   70 (527)
T PRK14969          3 YQVLARKWRPKSFSELVGQEHVVRALTNALEQQ------------RLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTA   70 (527)
T ss_pred             cHHHHHHhCCCcHHHhcCcHHHHHHHHHHHHcC------------CCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            566788899999999999999999999988752            3456689999999999999999999986521    


Q ss_pred             --------------------EEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchH
Q 022768           95 --------------------LKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        95 --------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                          +.++...      ......++.+...+..    ....|++|||+|.+           ..
T Consensus        71 ~pcg~C~~C~~i~~~~~~d~~ei~~~~------~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~l-----------s~  133 (527)
T PRK14969         71 TPCGVCSACLEIDSGRFVDLIEVDAAS------NTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHML-----------SK  133 (527)
T ss_pred             CCCCCCHHHHHHhcCCCCceeEeeccc------cCCHHHHHHHHHHHhhCcccCCceEEEEcCcccC-----------CH
Confidence                                1111110      1123345555554432    34579999999998           55


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      .....|+..++.     +.+.+.+|++|++++.+...+++  |+ ..+.|+.++.++....+...+....+. .+..+..
T Consensus       134 ~a~naLLK~LEe-----pp~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~  205 (527)
T PRK14969        134 SAFNAMLKTLEE-----PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQL  205 (527)
T ss_pred             HHHHHHHHHHhC-----CCCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            555555555543     34577888888888888888888  77 788999999999998888777543333 2223456


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ++..+.| +.+++.++++.+..+    +...|+.+++.+.+.
T Consensus       206 la~~s~G-slr~al~lldqai~~----~~~~I~~~~v~~~~~  242 (527)
T PRK14969        206 LARAAAG-SMRDALSLLDQAIAY----GGGTVNESEVRAMLG  242 (527)
T ss_pred             HHHHcCC-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHHC
Confidence            6777776 888888888887654    345678877776654

>PRK04195 replication factor C large subunit; Provisional

Probab=99.83  E-value=5.1e-19  Score=163.03  Aligned_cols=211  Identities=31%  Similarity=0.366  Sum_probs=147.6

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      -+.++|.++++++|++++++.|..++.....+         .+..++||+||||+|||++++++|++++.+++.++..+.
T Consensus         5 ~eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~g---------~~~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~   75 (482)
T PRK04195          5 VEKYRPKTLSDVVGNEKAKEQLREWIESWLKG---------KPKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQ   75 (482)
T ss_pred             hhhcCCCCHHHhcCCHHHHHHHHHHHHHHhcC---------CCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEccccc
Confidence            35789999999999999999999998764211         336789999999999999999999999999999988764


Q ss_pred             hccccChHHHHHHHHHHHhhh------CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768          103 IDKYIGESARLIREMFGYARD------HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~------~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      ..      ...+..+...+..      ..+.+|+|||+|.+..+       .+......+..++..       .+..+|+
T Consensus        76 r~------~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~-------~d~~~~~aL~~~l~~-------~~~~iIl  135 (482)
T PRK04195         76 RT------ADVIERVAGEAATSGSLFGARRKLILLDEVDGIHGN-------EDRGGARAILELIKK-------AKQPIIL  135 (482)
T ss_pred             cc------HHHHHHHHHHhhccCcccCCCCeEEEEecCcccccc-------cchhHHHHHHHHHHc-------CCCCEEE
Confidence            32      1222222222211      24689999999998431       133444555555542       2345777


Q ss_pred             EeCCCCCCCh-hhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Q 022768          177 ATNRPDVLDP-ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       177 t~~~~~~l~~-~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      ++|.+..+.. .+++  ++ ..+.|++|+..+...+++..+......  ++.+.+..+... +++|++.+++....++  
T Consensus       136 i~n~~~~~~~k~Lrs--r~-~~I~f~~~~~~~i~~~L~~i~~~egi~--i~~eaL~~Ia~~-s~GDlR~ain~Lq~~a--  207 (482)
T PRK04195        136 TANDPYDPSLRELRN--AC-LMIEFKRLSTRSIVPVLKRICRKEGIE--CDDEALKEIAER-SGGDLRSAINDLQAIA--  207 (482)
T ss_pred             eccCccccchhhHhc--cc-eEEEecCCCHHHHHHHHHHHHHHcCCC--CCHHHHHHHHHH-cCCCHHHHHHHHHHHh--
Confidence            8888887776 6765  55 789999999999999999888644332  344444444332 3448888888777643  


Q ss_pred             hcCCcccHHHHHHHH
Q 022768          256 AERDYVIHEDFMKAV  270 (292)
Q Consensus       256 ~~~~~i~~~~~~~a~  270 (292)
                      .+...++.+++....
T Consensus       208 ~~~~~it~~~v~~~~  222 (482)
T PRK04195        208 EGYGKLTLEDVKTLG  222 (482)
T ss_pred             cCCCCCcHHHHHHhh
Confidence            344567777776554

>PLN03025 replication factor C subunit; Provisional

Probab=99.83  E-value=4.5e-19  Score=155.35  Aligned_cols=206  Identities=19%  Similarity=0.212  Sum_probs=138.2

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cEEE
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NFLK   96 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~~~   96 (292)
                      ..++++|.+|++++|++++++.|..++..             ....+++|+||||+||||+++++|+++..     .++.
T Consensus         3 w~~kyrP~~l~~~~g~~~~~~~L~~~~~~-------------~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~e   69 (319)
T PLN03025          3 WVEKYRPTKLDDIVGNEDAVSRLQVIARD-------------GNMPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLE   69 (319)
T ss_pred             hhhhcCCCCHHHhcCcHHHHHHHHHHHhc-------------CCCceEEEECCCCCCHHHHHHHHHHHHhcccCccceee
Confidence            34688999999999999999999887654             22347999999999999999999998732     3555


Q ss_pred             EeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCe
Q 022768           97 VVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKV  172 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  172 (292)
                      ++.++..+.  ......++. +....    ...+.+++|||+|.+           ....+..|...++..     ...+
T Consensus        70 ln~sd~~~~--~~vr~~i~~-~~~~~~~~~~~~~kviiiDE~d~l-----------t~~aq~aL~~~lE~~-----~~~t  130 (319)
T PLN03025         70 LNASDDRGI--DVVRNKIKM-FAQKKVTLPPGRHKIVILDEADSM-----------TSGAQQALRRTMEIY-----SNTT  130 (319)
T ss_pred             ecccccccH--HHHHHHHHH-HHhccccCCCCCeEEEEEechhhc-----------CHHHHHHHHHHHhcc-----cCCc
Confidence            555432211  111111211 11111    123579999999999           666777777766532     2345


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHH
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGM  251 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~  251 (292)
                      .+|+++|..+.+.+++++  |+ ..+.|++|+.++....++..+...... .+..++.+...+.|    |++.++.....
T Consensus       131 ~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~g----DlR~aln~Lq~  203 (319)
T PLN03025        131 RFALACNTSSKIIEPIQS--RC-AIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADG----DMRQALNNLQA  203 (319)
T ss_pred             eEEEEeCCccccchhHHH--hh-hcccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC----CHHHHHHHHHH
Confidence            678889988899999998  76 678999999999999988887644332 22234555555554    66666555543


Q ss_pred             HHHHhcCCcccHHHHHH
Q 022768          252 SAIRAERDYVIHEDFMK  268 (292)
Q Consensus       252 ~a~~~~~~~i~~~~~~~  268 (292)
                      .+.  +...|+.+++.+
T Consensus       204 ~~~--~~~~i~~~~v~~  218 (319)
T PLN03025        204 THS--GFGFVNQENVFK  218 (319)
T ss_pred             HHh--cCCCCCHHHHHH
Confidence            222  234566666654

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.83  E-value=2.8e-19  Score=148.74  Aligned_cols=203  Identities=20%  Similarity=0.255  Sum_probs=141.6

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------E
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------F   94 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------~   94 (292)
                      .+-+.+.|-+|++++|++++++.|.+.+..             .-..++|||||||||||+.++++|+++.++      +
T Consensus        25 swteKYrPkt~de~~gQe~vV~~L~~a~~~-------------~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rv   91 (346)
T KOG0989|consen   25 SWTEKYRPKTFDELAGQEHVVQVLKNALLR-------------RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRV   91 (346)
T ss_pred             chHHHhCCCcHHhhcchHHHHHHHHHHHhh-------------cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccch
Confidence            345789999999999999999999999865             235689999999999999999999999662      2


Q ss_pred             EEEeccchhccccChHHHHHHHHHHHhh---------hCCC-EEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGYAR---------DHQP-CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD  164 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~-~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~  164 (292)
                      ...+.++..+..+..   .-..-|....         .+.| .|++|||.|.|           ..+.+.+|...++.  
T Consensus        92 l~lnaSderGisvvr---~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsm-----------tsdaq~aLrr~mE~--  155 (346)
T KOG0989|consen   92 LELNASDERGISVVR---EKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSM-----------TSDAQAALRRTMED--  155 (346)
T ss_pred             hhhcccccccccchh---hhhcCHHHHhhccccccCCCCCcceEEEEechhhh-----------hHHHHHHHHHHHhc--
Confidence            333444433332111   1111222221         1333 79999999999           88888888888764  


Q ss_pred             CCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCC-CCCHHHHHHHcCCCCHHHHH
Q 022768          165 GFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG-EIDYEAVVKLAEGFNGADLR  243 (292)
Q Consensus       165 ~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~-~~~~~~l~~~~~g~~~~di~  243 (292)
                         ....+.+|..||..+.+...+.+  |+ ..+.|+....+...+-++.++....+.- +-.++.++..++|    |++
T Consensus       156 ---~s~~trFiLIcnylsrii~pi~S--RC-~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~G----dLR  225 (346)
T KOG0989|consen  156 ---FSRTTRFILICNYLSRIIRPLVS--RC-QKFRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISDG----DLR  225 (346)
T ss_pred             ---cccceEEEEEcCChhhCChHHHh--hH-HHhcCCCcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC----cHH
Confidence               23578899999999999999999  87 6678888888888888888877554442 2234555666665    666


Q ss_pred             HHHHHHHHHHHHhcCCcccHH
Q 022768          244 NVCTEAGMSAIRAERDYVIHE  264 (292)
Q Consensus       244 ~l~~~a~~~a~~~~~~~i~~~  264 (292)
                      .++......+.  ....|+..
T Consensus       226 ~Ait~Lqsls~--~gk~It~~  244 (346)
T KOG0989|consen  226 RAITTLQSLSL--LGKRITTS  244 (346)
T ss_pred             HHHHHHHHhhc--cCcccchH
Confidence            55555544443  33344433

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.82  E-value=1.1e-18  Score=160.20  Aligned_cols=206  Identities=18%  Similarity=0.255  Sum_probs=143.0

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---------
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---------   93 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---------   93 (292)
                      ...++|.+|++++|++++++.|..++...            ..++.+||+||||+||||+++++++.+.+.         
T Consensus         5 ~~KyRP~~~~dvvGq~~v~~~L~~~i~~~------------~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~   72 (504)
T PRK14963          5 YQRARPITFDEVVGQEHVKEVLLAALRQG------------RLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGE   72 (504)
T ss_pred             HHhhCCCCHHHhcChHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCc
Confidence            46789999999999999999999998752            335567999999999999999999988541         


Q ss_pred             --------------EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHH
Q 022768           94 --------------FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRT  155 (292)
Q Consensus        94 --------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~  155 (292)
                                    ++.++...      ......++.+...+.    ...+.+++|||+|.+           ....+..
T Consensus        73 C~sc~~i~~~~h~dv~el~~~~------~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~l-----------s~~a~na  135 (504)
T PRK14963         73 CESCLAVRRGAHPDVLEIDAAS------NNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMM-----------SKSAFNA  135 (504)
T ss_pred             ChhhHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhhccccCCCeEEEEECcccc-----------CHHHHHH
Confidence                          23333221      111233334333322    235679999999987           4444445


Q ss_pred             HHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHc
Q 022768          156 LMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLA  234 (292)
Q Consensus       156 l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~  234 (292)
                      |...++.     +...+++|++++.+..+.+.+++  |+ ..+.|++++.++....++..+...... .+..+..++..+
T Consensus       136 LLk~LEe-----p~~~t~~Il~t~~~~kl~~~I~S--Rc-~~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s  207 (504)
T PRK14963        136 LLKTLEE-----PPEHVIFILATTEPEKMPPTILS--RT-QHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLA  207 (504)
T ss_pred             HHHHHHh-----CCCCEEEEEEcCChhhCChHHhc--ce-EEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            5444432     33467788888888899999998  77 678999999999999999887654433 222356677777


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          235 EGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       235 ~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      .| ..+++.++++.+...     ...||.+++.+.+.
T Consensus       208 ~G-dlR~aln~Lekl~~~-----~~~It~~~V~~~l~  238 (504)
T PRK14963        208 DG-AMRDAESLLERLLAL-----GTPVTRKQVEEALG  238 (504)
T ss_pred             CC-CHHHHHHHHHHHHhc-----CCCCCHHHHHHHHC
Confidence            76 666666666665432     33688777766643

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.82  E-value=8.1e-19  Score=168.98  Aligned_cols=230  Identities=25%  Similarity=0.333  Sum_probs=168.7

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------   90 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------   90 (292)
                      ++.....+-++++++|+++.++++...+..             ....+++|+||||+|||++++.+|..+          
T Consensus       171 ~l~~~~r~~~l~~~igr~~ei~~~~~~L~~-------------~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~  237 (731)
T TIGR02639       171 DLTEKAKNGKIDPLIGREDELERTIQVLCR-------------RKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLK  237 (731)
T ss_pred             hHHHHHhcCCCCcccCcHHHHHHHHHHHhc-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhc
Confidence            333455677889999999999998887754             235579999999999999999999987          


Q ss_pred             CCcEEEEeccchh--ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           91 DANFLKVVSSAII--DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        91 ~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                      +..++.+++..+.  ..+.|+.+..++.+++.+....+.||||||+|.+.+....  .+........|...+.       
T Consensus       238 ~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~--~~~~~~~~~~L~~~l~-------  308 (731)
T TIGR02639       238 NAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGAT--SGGSMDASNLLKPALS-------  308 (731)
T ss_pred             CCeEEEecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCC--CCccHHHHHHHHHHHh-------
Confidence            6678888877776  4677889999999999988777899999999999754321  1122233444444332       


Q ss_pred             CCCeEEEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-----CCCCHHHHHHHcCCC-
Q 022768          169 LGKVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-----GEIDYEAVVKLAEGF-  237 (292)
Q Consensus       169 ~~~~~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-----~~~~~~~l~~~~~g~-  237 (292)
                      .+.+.+|++|+..+     ..++++.+  ||. .+.++.|+.+++.+|++.....+...     .+-.+..++..+..| 
T Consensus       309 ~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi  385 (731)
T TIGR02639       309 SGKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYI  385 (731)
T ss_pred             CCCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhccc
Confidence            25788999998632     46889998  994 79999999999999999766532211     122344555556554 


Q ss_pred             ----CHHHHHHHHHHHHHHHHHhc----CCcccHHHHHHHHHHHhh
Q 022768          238 ----NGADLRNVCTEAGMSAIRAE----RDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       238 ----~~~di~~l~~~a~~~a~~~~----~~~i~~~~~~~a~~~~~~  275 (292)
                          -|.-...++++|......+.    ...|+.+|+.+++..+..
T Consensus       386 ~~r~~P~kai~lld~a~a~~~~~~~~~~~~~v~~~~i~~~i~~~tg  431 (731)
T TIGR02639       386 NDRFLPDKAIDVIDEAGASFRLRPKAKKKANVSVKDIENVVAKMAH  431 (731)
T ss_pred             ccccCCHHHHHHHHHhhhhhhcCcccccccccCHHHHHHHHHHHhC
Confidence                35566788888876554332    346999999999998863

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=99.82  E-value=8.8e-20  Score=166.81  Aligned_cols=168  Identities=27%  Similarity=0.401  Sum_probs=130.2

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-------
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-------  104 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-------  104 (292)
                      .+.+|++++++++.+|+.-....       +...+..++|+||||+|||++++++|+.++..|+++..+.+.+       
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~-------~~~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGH  395 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLT-------KKLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGH  395 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHh-------ccCCCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhccc
Confidence            35689999999999998653111       2234677899999999999999999999999999999887664       


Q ss_pred             --cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH----------hhCCCCCCCe
Q 022768          105 --KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ----------LDGFDQLGKV  172 (292)
Q Consensus       105 --~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~----------~~~~~~~~~~  172 (292)
                        .|+|.....+-+....+....| +++|||+|.+...-       ..+...+|++.|+-          ++.-...+.+
T Consensus       396 RRTYIGamPGrIiQ~mkka~~~NP-v~LLDEIDKm~ss~-------rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~V  467 (782)
T COG0466         396 RRTYIGAMPGKIIQGMKKAGVKNP-VFLLDEIDKMGSSF-------RGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKV  467 (782)
T ss_pred             cccccccCChHHHHHHHHhCCcCC-eEEeechhhccCCC-------CCChHHHHHhhcCHhhcCchhhccccCccchhhe
Confidence              3666666666677777777665 99999999995322       22223444444432          2233455689


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      ++|+|+|..+.++.+|++  || .+|.++.++.++..+|.+.++-
T Consensus       468 mFiaTANsl~tIP~PLlD--RM-EiI~lsgYt~~EKl~IAk~~Li  509 (782)
T COG0466         468 MFIATANSLDTIPAPLLD--RM-EVIRLSGYTEDEKLEIAKRHLI  509 (782)
T ss_pred             EEEeecCccccCChHHhc--ce-eeeeecCCChHHHHHHHHHhcc
Confidence            999999999999999999  88 8999999999999999998874

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.81  E-value=1.7e-18  Score=160.17  Aligned_cols=212  Identities=17%  Similarity=0.230  Sum_probs=144.6

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------   93 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------   93 (292)
                      ..+...++|.+|++|+|++.+++.|.+++..-            .-.+.+||+||+|+|||++|+.+|+.+.+.      
T Consensus         4 ~~la~KyRP~sf~dIiGQe~v~~~L~~ai~~~------------ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~   71 (624)
T PRK14959          4 ASLTARYRPQTFAEVAGQETVKAILSRAAQEN------------RVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGE   71 (624)
T ss_pred             chHHHHhCCCCHHHhcCCHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCC
Confidence            35567899999999999999999999998652            235689999999999999999999999753      


Q ss_pred             ------------------EEEEeccchhccccChHHHHHHHHHHHh-hhCCCEEEEEcccccccCCcCCCCCcchHHHHH
Q 022768           94 ------------------FLKVVSSAIIDKYIGESARLIREMFGYA-RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQR  154 (292)
Q Consensus        94 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~  154 (292)
                                        +++++....  ..+. ..+.+...+... ......|++|||+|.|           ....+.
T Consensus        72 pCg~C~sC~~i~~g~hpDv~eId~a~~--~~Id-~iR~L~~~~~~~p~~g~~kVIIIDEad~L-----------t~~a~n  137 (624)
T PRK14959         72 PCNTCEQCRKVTQGMHVDVVEIDGASN--RGID-DAKRLKEAIGYAPMEGRYKVFIIDEAHML-----------TREAFN  137 (624)
T ss_pred             CCcccHHHHHHhcCCCCceEEEecccc--cCHH-HHHHHHHHHHhhhhcCCceEEEEEChHhC-----------CHHHHH
Confidence                              222322110  0111 112222222222 2234579999999999           566666


Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHH
Q 022768          155 TLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKL  233 (292)
Q Consensus       155 ~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~  233 (292)
                      .|...++.     +.+.+++|++|+.++.+...+++  |+ ..+.|++++.++...+++..+...... ....++.++..
T Consensus       138 aLLk~LEE-----P~~~~ifILaTt~~~kll~TI~S--Rc-q~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~~  209 (624)
T PRK14959        138 ALLKTLEE-----PPARVTFVLATTEPHKFPVTIVS--RC-QHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARR  209 (624)
T ss_pred             HHHHHhhc-----cCCCEEEEEecCChhhhhHHHHh--hh-hccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            66555543     33578888889888888888988  77 678999999999999888877643322 22235566667


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          234 AEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       234 ~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      +.| +.+++.++++.+.    ..+...|+.+++.+++
T Consensus       210 s~G-dlR~Al~lLeqll----~~g~~~It~d~V~~~l  241 (624)
T PRK14959        210 AAG-SVRDSMSLLGQVL----ALGESRLTIDGARGVL  241 (624)
T ss_pred             cCC-CHHHHHHHHHHHH----HhcCCCcCHHHHHHHh
Confidence            776 6666666666542    2233467777766554

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.81  E-value=6.2e-18  Score=151.20  Aligned_cols=226  Identities=23%  Similarity=0.303  Sum_probs=151.3

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC---------CcEEEEe
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID---------ANFLKVV   98 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~---------~~~~~~~   98 (292)
                      .+-.++++|++++++.|..++...+.+         ..+.+++|+||||+|||++++.+++.+.         ..+++++
T Consensus        11 ~~~p~~l~gRe~e~~~l~~~l~~~~~~---------~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in   81 (365)
T TIGR02928        11 DYVPDRIVHRDEQIEELAKALRPILRG---------SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVN   81 (365)
T ss_pred             CCCCCCCCCcHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEE
Confidence            333457899999999999998753221         3356799999999999999999998763         4677788


Q ss_pred             ccchhccc--c----------C--------hHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHH
Q 022768           99 SSAIIDKY--I----------G--------ESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLM  157 (292)
Q Consensus        99 ~~~~~~~~--~----------~--------~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~  157 (292)
                      +....+..  .          +        ........++..... ..+.+|+|||+|.+...           .+..+.
T Consensus        82 ~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~-----------~~~~L~  150 (365)
T TIGR02928        82 CQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGD-----------DDDLLY  150 (365)
T ss_pred             CCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccC-----------CcHHHH
Confidence            76543210  0          0        112223344444332 34678999999999521           112344


Q ss_pred             HHHHHhh-CCCCCCCeEEEEEeCCCC---CCChhhcCCCCcc-eEEEccCCCHHHHHHHHHHHHcCccCCCCCCH---HH
Q 022768          158 ELLNQLD-GFDQLGKVKMIMATNRPD---VLDPALLRPGRLD-RKIEIPLPNEQSRMEILKIHAAGIAKHGEIDY---EA  229 (292)
Q Consensus       158 ~~l~~~~-~~~~~~~~~vi~t~~~~~---~l~~~l~~~~r~~-~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~---~~  229 (292)
                      .+++... ...+..++.+|+++|.+.   .+++.+.+  ||. ..+.|++++.++..++++.++........++.   +.
T Consensus       151 ~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~~  228 (365)
T TIGR02928       151 QLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKS--SLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIPL  228 (365)
T ss_pred             hHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHHH
Confidence            4443311 112335788899998875   47777777  664 57899999999999999988752111111222   22


Q ss_pred             H---HHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          230 V---VKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       230 l---~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      +   +..+.| ..+.+..++..|...|..++...|+.+++.+|+..+...
T Consensus       229 i~~~~~~~~G-d~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~  277 (365)
T TIGR02928       229 CAALAAQEHG-DARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKD  277 (365)
T ss_pred             HHHHHHHhcC-CHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence            2   333445 677778899999999988888899999999999888543

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.81  E-value=3.7e-19  Score=160.93  Aligned_cols=216  Identities=21%  Similarity=0.281  Sum_probs=158.8

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----   94 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----   94 (292)
                      |+.+...++|..|++++|++.++..|...+..-            .-.+.++|.||.|+||||++|.+|+.++|.-    
T Consensus         3 yq~L~rKyRP~~F~evvGQe~v~~~L~nal~~~------------ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~   70 (515)
T COG2812           3 YQVLARKYRPKTFDDVVGQEHVVKTLSNALENG------------RIAHAYLFSGPRGVGKTTIARILAKALNCENGPTA   70 (515)
T ss_pred             hHHHHHHhCcccHHHhcccHHHHHHHHHHHHhC------------cchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCC
Confidence            455677899999999999999999999998763            4567899999999999999999999997642    


Q ss_pred             ---EEEecc-ch-----hc-----cccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHH
Q 022768           95 ---LKVVSS-AI-----ID-----KYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL  156 (292)
Q Consensus        95 ---~~~~~~-~~-----~~-----~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l  156 (292)
                         ..+..+ .+     .+     .......+.++.+.+.+..    .+..|.+|||+|.|           ...   ++
T Consensus        71 ePC~~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHML-----------S~~---af  136 (515)
T COG2812          71 EPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHML-----------SKQ---AF  136 (515)
T ss_pred             CcchhhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhh-----------hHH---HH
Confidence               111110 01     00     0001133445666665543    45689999999999           444   44


Q ss_pred             HHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC-CCHHHHHHHcC
Q 022768          157 MELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE-IDYEAVVKLAE  235 (292)
Q Consensus       157 ~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~-~~~~~l~~~~~  235 (292)
                      ..+|+.++  .++.++.+|++|..+++++..++|  || ..+.|+..+.++....+...+.+..+..+ -.+..+++.++
T Consensus       137 NALLKTLE--EPP~hV~FIlATTe~~Kip~TIlS--Rc-q~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~  211 (515)
T COG2812         137 NALLKTLE--EPPSHVKFILATTEPQKIPNTILS--RC-QRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAE  211 (515)
T ss_pred             HHHhcccc--cCccCeEEEEecCCcCcCchhhhh--cc-ccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcC
Confidence            45555555  566799999999999999999999  77 77899999999999999999887666533 34567778888


Q ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          236 GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       236 g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      | +.||...+++.+....-    ..|+.+.+.+.+
T Consensus       212 G-s~RDalslLDq~i~~~~----~~It~~~v~~~l  241 (515)
T COG2812         212 G-SLRDALSLLDQAIAFGE----GEITLESVRDML  241 (515)
T ss_pred             C-ChhhHHHHHHHHHHccC----CcccHHHHHHHh
Confidence            8 89999999999886642    334444444333

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.81  E-value=2.9e-18  Score=156.96  Aligned_cols=207  Identities=18%  Similarity=0.220  Sum_probs=147.6

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------   93 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------   93 (292)
                      .+...++|.+|++++|++++++.|...+..-            .-++.+||+||+|+|||++++.+++.+.+.       
T Consensus         3 ~l~~KyRP~~fdeiiGqe~v~~~L~~~I~~g------------rl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~p   70 (535)
T PRK08451          3 ALALKYRPKHFDELIGQESVSKTLSLALDNN------------RLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTP   70 (535)
T ss_pred             cHHHHHCCCCHHHccCcHHHHHHHHHHHHcC------------CCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCC
Confidence            4567899999999999999999999998652            345667999999999999999999988431       


Q ss_pred             -----------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHH
Q 022768           94 -----------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREI  152 (292)
Q Consensus        94 -----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~  152 (292)
                                       ++.++...      ....+.++.+......    ....|++|||+|.+           ....
T Consensus        71 C~~C~~C~~~~~~~h~dv~eldaas------~~gId~IRelie~~~~~P~~~~~KVvIIDEad~L-----------t~~A  133 (535)
T PRK08451         71 CDTCIQCQSALENRHIDIIEMDAAS------NRGIDDIRELIEQTKYKPSMARFKIFIIDEVHML-----------TKEA  133 (535)
T ss_pred             CcccHHHHHHhhcCCCeEEEecccc------ccCHHHHHHHHHHHhhCcccCCeEEEEEECcccC-----------CHHH
Confidence                             22222111      0112344444433221    23479999999999           6667


Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHH
Q 022768          153 QRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVV  231 (292)
Q Consensus       153 ~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~  231 (292)
                      +..|+..++.     +.+.+.+|++++.+..+.+.+++  |+ ..++|.+++.++....++..+...... .+..+..++
T Consensus       134 ~NALLK~LEE-----pp~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia  205 (535)
T PRK08451        134 FNALLKTLEE-----PPSYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILA  205 (535)
T ss_pred             HHHHHHHHhh-----cCCceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            7777666654     33567788888888999999999  76 788999999999988888777654333 223456677


Q ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          232 KLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       232 ~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      ..+.| +.+++..+++.+..++    ...||.+++.+.
T Consensus       206 ~~s~G-dlR~alnlLdqai~~~----~~~It~~~V~~~  238 (535)
T PRK08451        206 RSGNG-SLRDTLTLLDQAIIYC----KNAITESKVADM  238 (535)
T ss_pred             HHcCC-cHHHHHHHHHHHHHhc----CCCCCHHHHHHH
Confidence            77776 8888888888777654    234666655544

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.81  E-value=4.2e-18  Score=157.96  Aligned_cols=212  Identities=17%  Similarity=0.201  Sum_probs=143.6

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------EE
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------FL   95 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------~~   95 (292)
                      ...++|.+|++++|++++++.|..++..-            ..++.+||+||+|+|||++++.+|+.+.+.       +-
T Consensus         4 ~~kyRP~~f~eivGq~~i~~~L~~~i~~~------------r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg   71 (584)
T PRK14952          4 YRKYRPATFAEVVGQEHVTEPLSSALDAG------------RINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCG   71 (584)
T ss_pred             HHHhCCCcHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCccc
Confidence            35789999999999999999999998752            345568999999999999999999988652       11


Q ss_pred             EEecc-c----------hh--ccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHH
Q 022768           96 KVVSS-A----------II--DKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLME  158 (292)
Q Consensus        96 ~~~~~-~----------~~--~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~  158 (292)
                      .+..+ .          +.  +.......+.++.+...+.    .....|++|||+|.+           ....+..|+.
T Consensus        72 ~C~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~L-----------t~~A~NALLK  140 (584)
T PRK14952         72 VCESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMV-----------TTAGFNALLK  140 (584)
T ss_pred             ccHHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcC-----------CHHHHHHHHH
Confidence            11000 0          00  0000011233333333332    234579999999999           6666666665


Q ss_pred             HHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCC
Q 022768          159 LLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGF  237 (292)
Q Consensus       159 ~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~  237 (292)
                      .++.     +...+++|++|+.++.+.+.+++  |+ ..+.|..++.++..+.+..++...... .+..+..++..+.| 
T Consensus       141 ~LEE-----pp~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~~s~G-  211 (584)
T PRK14952        141 IVEE-----PPEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIRAGGG-  211 (584)
T ss_pred             HHhc-----CCCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-
Confidence            5553     44578888888888999999999  76 789999999999988888877654432 12223445566665 


Q ss_pred             CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          238 NGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       238 ~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      +.+++.++++.+..++   +...|+.+++.+.
T Consensus       212 dlR~aln~Ldql~~~~---~~~~It~~~v~~l  240 (584)
T PRK14952        212 SPRDTLSVLDQLLAGA---ADTHVTYQRALGL  240 (584)
T ss_pred             CHHHHHHHHHHHHhcc---CCCCcCHHHHHHH
Confidence            7888888888765432   2345666665544

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.81  E-value=5.6e-18  Score=149.84  Aligned_cols=212  Identities=20%  Similarity=0.310  Sum_probs=141.7

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC-----CcEEEE
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID-----ANFLKV   97 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~-----~~~~~~   97 (292)
                      .+.+.|.+|++++|++++++.|..++...             ...+++|+||||+|||++++++++++.     .+++.+
T Consensus         6 ~~ky~P~~~~~~~g~~~~~~~L~~~~~~~-------------~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i   72 (337)
T PRK12402          6 TEKYRPALLEDILGQDEVVERLSRAVDSP-------------NLPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEF   72 (337)
T ss_pred             HHhhCCCcHHHhcCCHHHHHHHHHHHhCC-------------CCceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEe
Confidence            45788999999999999999999987642             223799999999999999999999884     345677


Q ss_pred             eccchhcccc-------------Ch-------HHHHHHHHHHHhhh-----CCCEEEEEcccccccCCcCCCCCcchHHH
Q 022768           98 VSSAIIDKYI-------------GE-------SARLIREMFGYARD-----HQPCIIFMDEIDAIGGRRFSEGTSADREI  152 (292)
Q Consensus        98 ~~~~~~~~~~-------------~~-------~~~~~~~~~~~~~~-----~~~~il~lDe~d~l~~~~~~~~~~~~~~~  152 (292)
                      ++.++.....             +.       ....++.+......     ..+.+|+|||+|.+           ....
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l-----------~~~~  141 (337)
T PRK12402         73 NVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEAL-----------REDA  141 (337)
T ss_pred             chhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccC-----------CHHH
Confidence            7665432110             00       11222222222211     23469999999988           5555


Q ss_pred             HHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHH
Q 022768          153 QRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVV  231 (292)
Q Consensus       153 ~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~  231 (292)
                      +..|..+++...     ..+.+|++++.+..+.+.+++  |+ ..+.+.+|+.++...+++..+...... .+..+..++
T Consensus       142 ~~~L~~~le~~~-----~~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~  213 (337)
T PRK12402        142 QQALRRIMEQYS-----RTCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIA  213 (337)
T ss_pred             HHHHHHHHHhcc-----CCCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence            666666665422     345567777777777788887  66 678999999999999999887654433 222344555


Q ss_pred             HHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          232 KLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       232 ~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      ..+.    ++++.++..+..++.  ....||.+++.+++..
T Consensus       214 ~~~~----gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~  248 (337)
T PRK12402        214 YYAG----GDLRKAILTLQTAAL--AAGEITMEAAYEALGD  248 (337)
T ss_pred             HHcC----CCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCC
Confidence            5554    366666666555442  2236888988887664

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.81  E-value=2.9e-18  Score=159.69  Aligned_cols=209  Identities=19%  Similarity=0.261  Sum_probs=148.3

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------   93 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------   93 (292)
                      ..+...++|.+|++++|+++.++.|...+...            ..++.+||+||+|+|||++++.+++.+.+.      
T Consensus         4 ~al~~k~rP~~f~~viGq~~v~~~L~~~i~~~------------~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~   71 (559)
T PRK05563          4 QALYRKWRPQTFEDVVGQEHITKTLKNAIKQG------------KISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGE   71 (559)
T ss_pred             HHHHHHhCCCcHHhccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC
Confidence            34556789999999999999999999998752            446679999999999999999999988642      


Q ss_pred             ------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHH
Q 022768           94 ------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADRE  151 (292)
Q Consensus        94 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~  151 (292)
                                        ++.++...      ......++.+...+..    ....|++|||+|.|           ...
T Consensus        72 pC~~C~~C~~i~~g~~~dv~eidaas------~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~L-----------t~~  134 (559)
T PRK05563         72 PCNECEICKAITNGSLMDVIEIDAAS------NNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHML-----------STG  134 (559)
T ss_pred             CCCccHHHHHHhcCCCCCeEEeeccc------cCCHHHHHHHHHHHhhCcccCCeEEEEEECcccC-----------CHH
Confidence                              12222111      1223445555555442    34579999999998           454


Q ss_pred             HHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHH
Q 022768          152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAV  230 (292)
Q Consensus       152 ~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l  230 (292)
                      ....|...+   +  .+...+++|++|+.++.+.+.+++  |+ ..+.|++|+.++....++..+...... .+..+..+
T Consensus       135 a~naLLKtL---E--epp~~~ifIlatt~~~ki~~tI~S--Rc-~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~i  206 (559)
T PRK05563        135 AFNALLKTL---E--EPPAHVIFILATTEPHKIPATILS--RC-QRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLI  206 (559)
T ss_pred             HHHHHHHHh---c--CCCCCeEEEEEeCChhhCcHHHHh--Hh-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            444454444   4  334577788888888999999998  77 678999999999999988887654433 22235566


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      +..+.| +.+++..+++.+..++    ...|+.+++.+++
T Consensus       207 a~~s~G-~~R~al~~Ldq~~~~~----~~~It~~~V~~vl  241 (559)
T PRK05563        207 ARAAEG-GMRDALSILDQAISFG----DGKVTYEDALEVT  241 (559)
T ss_pred             HHHcCC-CHHHHHHHHHHHHHhc----cCCCCHHHHHHHh
Confidence            777776 8888888888776542    3457777665543

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.80  E-value=4.8e-18  Score=163.17  Aligned_cols=212  Identities=19%  Similarity=0.172  Sum_probs=144.1

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------E
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------F   94 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------~   94 (292)
                      +..+++|.+|++|+|++++++.|..++..-            ..++.+||+||+|+|||++++.|++.+.|.       +
T Consensus         5 l~~KyRP~~f~eiiGqe~v~~~L~~~i~~~------------ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pC   72 (824)
T PRK07764          5 LYRRYRPATFAEVIGQEHVTEPLSTALDSG------------RINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPC   72 (824)
T ss_pred             HHHHhCCCCHHHhcCcHHHHHHHHHHHHhC------------CCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCC
Confidence            557899999999999999999999998652            334568999999999999999999999752       1


Q ss_pred             EEEeccc-----------hh--ccccChHHHHHHHHHHHh----hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHH
Q 022768           95 LKVVSSA-----------II--DKYIGESARLIREMFGYA----RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLM  157 (292)
Q Consensus        95 ~~~~~~~-----------~~--~~~~~~~~~~~~~~~~~~----~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~  157 (292)
                      -.|..+.           +.  +.......+.++.+...+    ......|+||||+|.|           ....+..|+
T Consensus        73 g~C~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~l-----------t~~a~NaLL  141 (824)
T PRK07764         73 GECDSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMV-----------TPQGFNALL  141 (824)
T ss_pred             cccHHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhc-----------CHHHHHHHH
Confidence            1111000           00  000001123333333322    2245679999999999           676777777


Q ss_pred             HHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCC
Q 022768          158 ELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEG  236 (292)
Q Consensus       158 ~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g  236 (292)
                      .+|+.     ....+++|++|+..+.|.+.|++  |+ ..+.|..++.++..++++..+....+. ....+..++..+.|
T Consensus       142 K~LEE-----pP~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgG  213 (824)
T PRK07764        142 KIVEE-----PPEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGG  213 (824)
T ss_pred             HHHhC-----CCCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            76664     33578888888888889999998  77 788999999999998888877644433 11224456667776


Q ss_pred             CCHHHHHHHHHHHHHHHHHhcCCcccHHHHHH
Q 022768          237 FNGADLRNVCTEAGMSAIRAERDYVIHEDFMK  268 (292)
Q Consensus       237 ~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~  268 (292)
                       +.+++..+++.+...+   +...|+.+++.+
T Consensus       214 -dlR~Al~eLEKLia~~---~~~~IT~e~V~a  241 (824)
T PRK07764        214 -SVRDSLSVLDQLLAGA---GPEGVTYERAVA  241 (824)
T ss_pred             -CHHHHHHHHHHHHhhc---CCCCCCHHHHHH
Confidence             7778888777765332   233466555443

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.80  E-value=5.5e-18  Score=157.97  Aligned_cols=222  Identities=19%  Similarity=0.194  Sum_probs=156.4

Q ss_pred             ChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           15 DPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      ....|..++..++|.+|++|+|++..++.|...+..-            ..++.+||+||+|+|||++++.+|+.+.+..
T Consensus         7 ~~~~y~~la~KyRP~~f~dliGq~~~v~~L~~~~~~g------------ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~   74 (598)
T PRK09111          7 AATPYRVLARKYRPQTFDDLIGQEAMVRTLTNAFETG------------RIAQAFMLTGVRGVGKTTTARILARALNYEG   74 (598)
T ss_pred             CCccchhHHhhhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHhhCcCC
Confidence            3445888999999999999999999999999988652            4466899999999999999999999986542


Q ss_pred             EEEe------ccc-------hh-----cc--c---cChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCc
Q 022768           95 LKVV------SSA-------II-----DK--Y---IGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTS  147 (292)
Q Consensus        95 ~~~~------~~~-------~~-----~~--~---~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~  147 (292)
                      ...+      .+.       +.     +-  .   .......++.++..+..    ....|++|||+|.+          
T Consensus        75 ~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~L----------  144 (598)
T PRK09111         75 PDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHML----------  144 (598)
T ss_pred             ccccCCCccccCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhC----------
Confidence            2111      000       00     00  0   00123345555555432    34579999999999          


Q ss_pred             chHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCC
Q 022768          148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEID  226 (292)
Q Consensus       148 ~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~  226 (292)
                       .......|+..++.     +.+.+.+|++++..+.+.+.+++  |+ ..+.|..++.++....++..+...... ....
T Consensus       145 -s~~a~naLLKtLEe-----Pp~~~~fIl~tte~~kll~tI~S--Rc-q~~~f~~l~~~el~~~L~~i~~kegi~i~~eA  215 (598)
T PRK09111        145 -STAAFNALLKTLEE-----PPPHVKFIFATTEIRKVPVTVLS--RC-QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEA  215 (598)
T ss_pred             -CHHHHHHHHHHHHh-----CCCCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence             55555666655553     33567788888888888888988  77 689999999999999888887644332 1223


Q ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          227 YEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       227 ~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      +..++..+.| +.+++.++++.+..+    +...|+.+++.+.+..
T Consensus       216 l~lIa~~a~G-dlr~al~~Ldkli~~----g~g~It~e~V~~llg~  256 (598)
T PRK09111        216 LALIARAAEG-SVRDGLSLLDQAIAH----GAGEVTAEAVRDMLGL  256 (598)
T ss_pred             HHHHHHHcCC-CHHHHHHHHHHHHhh----cCCCcCHHHHHHHhCC
Confidence            4556777776 788888888776543    2346888888877653

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.80  E-value=3.1e-18  Score=160.14  Aligned_cols=209  Identities=20%  Similarity=0.261  Sum_probs=149.4

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |..+...++|.+|++|+|++++++.|...+..-            ..++.+||+||+|+|||++++.+++.+.+.     
T Consensus         3 y~~l~~k~RP~~f~~iiGq~~v~~~L~~~i~~~------------~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~   70 (576)
T PRK14965          3 YLVLARKYRPQTFSDLTGQEHVSRTLQNAIDTG------------RVAHAFLFTGARGVGKTSTARILAKALNCEQGLTA   70 (576)
T ss_pred             cHHHHHHhCCCCHHHccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC
Confidence            455678899999999999999999999998652            345678999999999999999999998653     


Q ss_pred             -------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchH
Q 022768           94 -------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        94 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                         +++++...      ....+.++.+...+..    ....|++|||+|.|           ..
T Consensus        71 ~~c~~c~~c~~i~~g~~~d~~eid~~s------~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~L-----------t~  133 (576)
T PRK14965         71 EPCNVCPPCVEITEGRSVDVFEIDGAS------NTGVDDIRELRENVKYLPSRSRYKIFIIDEVHML-----------ST  133 (576)
T ss_pred             CCCCccHHHHHHhcCCCCCeeeeeccC------ccCHHHHHHHHHHHHhccccCCceEEEEEChhhC-----------CH
Confidence                               12222111      1122334454444432    34579999999999           66


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      .....|...++.     +.+.+.+|++|+.++.+.+.+++  |+ ..+.|..++.++....+...+....+. ....+..
T Consensus       134 ~a~naLLk~LEe-----pp~~~~fIl~t~~~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~  205 (576)
T PRK14965        134 NAFNALLKTLEE-----PPPHVKFIFATTEPHKVPITILS--RC-QRFDFRRIPLQKIVDRLRYIADQEGISISDAALAL  205 (576)
T ss_pred             HHHHHHHHHHHc-----CCCCeEEEEEeCChhhhhHHHHH--hh-hhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            666666666653     44578888888889999999998  77 678999999998888888777654433 2234566


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      ++..+.| +.+++..+++.+..+.-    ..|+.+++.+.
T Consensus       206 la~~a~G-~lr~al~~Ldqliay~g----~~It~edV~~l  240 (576)
T PRK14965        206 VARKGDG-SMRDSLSTLDQVLAFCG----DAVGDDDVAEL  240 (576)
T ss_pred             HHHHcCC-CHHHHHHHHHHHHHhcc----CCCCHHHHHHH
Confidence            6777776 77788888776664432    24777776554

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.80  E-value=2.9e-18  Score=162.90  Aligned_cols=228  Identities=21%  Similarity=0.273  Sum_probs=145.0

Q ss_pred             hcccCCCCCccccccccHHHHH---HHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIR---ELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~---~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ++...++|.+|++++|+++.+.   .|.+.+..             ....+++|+||||+||||+++.+++.++.+++.+
T Consensus        17 PLaek~RP~tldd~vGQe~ii~~~~~L~~~i~~-------------~~~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~l   83 (725)
T PRK13341         17 PLADRLRPRTLEEFVGQDHILGEGRLLRRAIKA-------------DRVGSLILYGPPGVGKTTLARIIANHTRAHFSSL   83 (725)
T ss_pred             ChHHhcCCCcHHHhcCcHHHhhhhHHHHHHHhc-------------CCCceEEEECCCCCCHHHHHHHHHHHhcCcceee
Confidence            4566788999999999999885   45555543             2345799999999999999999999999888887


Q ss_pred             eccchhccccChHHHHHHHHHHHhh-hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768           98 VSSAIIDKYIGESARLIREMFGYAR-DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      ++....   .......+........ .....+|||||+|.+           +...+..|...+..       +.+++|+
T Consensus        84 na~~~~---i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~L-----------n~~qQdaLL~~lE~-------g~IiLI~  142 (725)
T PRK13341         84 NAVLAG---VKDLRAEVDRAKERLERHGKRTILFIDEVHRF-----------NKAQQDALLPWVEN-------GTITLIG  142 (725)
T ss_pred             hhhhhh---hHHHHHHHHHHHHHhhhcCCceEEEEeChhhC-----------CHHHHHHHHHHhcC-------ceEEEEE
Confidence            764311   1111111222111111 124579999999998           56666666655432       3566666


Q ss_pred             EeC--CCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc-----CCCCCC---HHHHHHHcCCCCHHHHHHHH
Q 022768          177 ATN--RPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA-----KHGEID---YEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       177 t~~--~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~-----~~~~~~---~~~l~~~~~g~~~~di~~l~  246 (292)
                      +++  ....+++++++  |+ ..+.|++++.++...+++..+....     ..-.++   ++.|+..+.| +.+.+..++
T Consensus       143 aTTenp~~~l~~aL~S--R~-~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~G-D~R~lln~L  218 (725)
T PRK13341        143 ATTENPYFEVNKALVS--RS-RLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANG-DARSLLNAL  218 (725)
T ss_pred             ecCCChHhhhhhHhhc--cc-cceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCC-CHHHHHHHH
Confidence            553  23468889998  65 5689999999999999998876210     111233   3445555544 555555555


Q ss_pred             HHHHHHHHHhcC--CcccHHHHHHHHHHHhhhhhhchhhhhh
Q 022768          247 TEAGMSAIRAER--DYVIHEDFMKAVRKLNEAKKLESSAHYN  286 (292)
Q Consensus       247 ~~a~~~a~~~~~--~~i~~~~~~~a~~~~~~~~~~~~~~~~~  286 (292)
                      +.+...+.....  ..|+.+++.+++.......+.....+|+
T Consensus       219 e~a~~~~~~~~~~~i~It~~~~~e~l~~~~~~ydk~gd~hyd  260 (725)
T PRK13341        219 ELAVESTPPDEDGLIDITLAIAEESIQQRAVLYDKEGDAHFD  260 (725)
T ss_pred             HHHHHhcccCCCCceeccHHHHHHHHHHhhhhcccCCCCCHH
Confidence            555432221222  2388888999888765544443334443

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=99.80  E-value=5.9e-19  Score=160.82  Aligned_cols=168  Identities=27%  Similarity=0.424  Sum_probs=131.6

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-------
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-------  104 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-------  104 (292)
                      ++.+|++++++++.+++.--       .-.|-..+..++|+||||+|||++++++|+.++..|++++.+.+.+       
T Consensus       411 eDHYgm~dVKeRILEfiAV~-------kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGH  483 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVG-------KLRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGH  483 (906)
T ss_pred             ccccchHHHHHHHHHHHHHH-------hhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhccc
Confidence            46799999999999998642       1223455778999999999999999999999999999998776543       


Q ss_pred             --cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH----------hhCCCCCCCe
Q 022768          105 --KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ----------LDGFDQLGKV  172 (292)
Q Consensus       105 --~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~----------~~~~~~~~~~  172 (292)
                        .|+|.....+.+.+..+..+.| +++|||+|.++..-       ......+|+++++-          ++.....+++
T Consensus       484 RRTYVGAMPGkiIq~LK~v~t~NP-liLiDEvDKlG~g~-------qGDPasALLElLDPEQNanFlDHYLdVp~DLSkV  555 (906)
T KOG2004|consen  484 RRTYVGAMPGKIIQCLKKVKTENP-LILIDEVDKLGSGH-------QGDPASALLELLDPEQNANFLDHYLDVPVDLSKV  555 (906)
T ss_pred             ceeeeccCChHHHHHHHhhCCCCc-eEEeehhhhhCCCC-------CCChHHHHHHhcChhhccchhhhccccccchhhe
Confidence              4667777777777778887776 89999999996322       11223344444432          2333444589


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      .+|+|+|..+.++++|++  |+ ..|.++.+..++..+|.+.|+-
T Consensus       556 LFicTAN~idtIP~pLlD--RM-EvIelsGYv~eEKv~IA~~yLi  597 (906)
T KOG2004|consen  556 LFICTANVIDTIPPPLLD--RM-EVIELSGYVAEEKVKIAERYLI  597 (906)
T ss_pred             EEEEeccccccCChhhhh--hh-heeeccCccHHHHHHHHHHhhh
Confidence            999999999999999999  88 8899999999999999998875

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.80  E-value=3.5e-18  Score=157.40  Aligned_cols=208  Identities=17%  Similarity=0.196  Sum_probs=145.1

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------   93 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------   93 (292)
                      ..+...++|.+|++++|++.+++.|...+..-            ..++.+||+||+|+|||++|+.+|+.+.+.      
T Consensus         4 ~~~~~KyRP~~F~dIIGQe~iv~~L~~aI~~~------------rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~   71 (605)
T PRK05896          4 ITFYRKYRPHNFKQIIGQELIKKILVNAILNN------------KLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGD   71 (605)
T ss_pred             hhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC
Confidence            45677899999999999999999999987542            335679999999999999999999988542      


Q ss_pred             ------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHH
Q 022768           94 ------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADRE  151 (292)
Q Consensus        94 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~  151 (292)
                                        ++.++...      ......++.+...+..    ....|++|||+|.+           ...
T Consensus        72 ~Cg~C~sCr~i~~~~h~DiieIdaas------~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~L-----------t~~  134 (605)
T PRK05896         72 CCNSCSVCESINTNQSVDIVELDAAS------NNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHML-----------STS  134 (605)
T ss_pred             CCcccHHHHHHHcCCCCceEEecccc------ccCHHHHHHHHHHHHhchhhCCcEEEEEechHhC-----------CHH
Confidence                              11121111      0112234444433322    34579999999998           555


Q ss_pred             HHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHH
Q 022768          152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAV  230 (292)
Q Consensus       152 ~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l  230 (292)
                      .+..|...++.     +.+.+++|++|+.++.+.+.+++  |+ ..+.|++++.++....++..+...... .+..+..+
T Consensus       135 A~NaLLKtLEE-----Pp~~tvfIL~Tt~~~KLl~TI~S--Rc-q~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~L  206 (605)
T PRK05896        135 AWNALLKTLEE-----PPKHVVFIFATTEFQKIPLTIIS--RC-QRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKI  206 (605)
T ss_pred             HHHHHHHHHHh-----CCCcEEEEEECCChHhhhHHHHh--hh-hhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            55666666653     34578888888888999999998  77 678999999999998888877643322 22235566


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      +..+.| +.+++..+++.+..+.   + ..|+.+++.+.
T Consensus       207 a~lS~G-dlR~AlnlLekL~~y~---~-~~It~e~V~el  240 (605)
T PRK05896        207 ADLADG-SLRDGLSILDQLSTFK---N-SEIDIEDINKT  240 (605)
T ss_pred             HHHcCC-cHHHHHHHHHHHHhhc---C-CCCCHHHHHHH
Confidence            677776 7777777777754332   2 23777766664

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.80  E-value=4e-18  Score=151.84  Aligned_cols=211  Identities=19%  Similarity=0.292  Sum_probs=145.4

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      ++++.+.++|.+|++++|++++++.|.+.+...            ..++.+||+||+|+|||++++.+++.+.+.     
T Consensus         1 ~~~~~~~~rp~~~~~iig~~~~~~~l~~~~~~~------------~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~   68 (355)
T TIGR02397         1 YQVLARKYRPQTFEDVIGQEHIVQTLKNAIKNG------------RIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDG   68 (355)
T ss_pred             CccHHHHhCCCcHhhccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            356678899999999999999999999988642            345679999999999999999999987543     


Q ss_pred             -------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchH
Q 022768           94 -------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        94 -------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                                         ++.++...      ......++.++..+..    ....+++|||+|.+           ..
T Consensus        69 ~~c~~c~~c~~~~~~~~~~~~~~~~~~------~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l-----------~~  131 (355)
T TIGR02397        69 EPCNECESCKEINSGSSLDVIEIDAAS------NNGVDDIREILDNVKYAPSSGKYKVYIIDEVHML-----------SK  131 (355)
T ss_pred             CCCCCCHHHHHHhcCCCCCEEEeeccc------cCCHHHHHHHHHHHhcCcccCCceEEEEeChhhc-----------CH
Confidence                               22222211      1122234455544432    34579999999988           44


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEA  229 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~  229 (292)
                      .....+...+   +  .+...+.+|++++.+..+.+.+++  |+ ..+.+++|+.++..+++..++...... .+..+..
T Consensus       132 ~~~~~Ll~~l---e--~~~~~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~  203 (355)
T TIGR02397       132 SAFNALLKTL---E--EPPEHVVFILATTEPHKIPATILS--RC-QRFDFKRIPLEDIVERLKKILDKEGIKIEDEALEL  203 (355)
T ss_pred             HHHHHHHHHH---h--CCccceeEEEEeCCHHHHHHHHHh--he-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            4444444444   3  233567788888888888888988  77 678999999999999999887654432 1223445


Q ss_pred             HHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       230 l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ++..+.| +++.+.+.++.+..++    ...|+.+++.+++.
T Consensus       204 l~~~~~g-~~~~a~~~lekl~~~~----~~~it~~~v~~~~~  240 (355)
T TIGR02397       204 IARAADG-SLRDALSLLDQLISFG----NGNITYEDVNELLG  240 (355)
T ss_pred             HHHHcCC-ChHHHHHHHHHHHhhc----CCCCCHHHHHHHhC
Confidence            5666665 6777777776666543    23488888776653

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.80  E-value=8.8e-18  Score=157.64  Aligned_cols=216  Identities=17%  Similarity=0.260  Sum_probs=148.4

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE-
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV-   97 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~-   97 (292)
                      +..+...++|.+|++++|++.+++.|...+..-            ..++.+||+||+|+|||++|+.+|+.+.+..... 
T Consensus         5 y~~l~~KyRP~~f~dIiGQe~~v~~L~~aI~~~------------rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~   72 (725)
T PRK07133          5 YKALYRKYRPKTFDDIVGQDHIVQTLKNIIKSN------------KISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDL   72 (725)
T ss_pred             hhhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCC
Confidence            445667899999999999999999999998652            3456789999999999999999999986632100 


Q ss_pred             --eccc-------hhccc--cC---hHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHH
Q 022768           98 --VSSA-------IIDKY--IG---ESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMEL  159 (292)
Q Consensus        98 --~~~~-------~~~~~--~~---~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~  159 (292)
                        .|..       ..+..  .+   .....++.+...+..    ....|++|||+|.+           .......|+..
T Consensus        73 ~~pC~~C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~L-----------T~~A~NALLKt  141 (725)
T PRK07133         73 LEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHML-----------SKSAFNALLKT  141 (725)
T ss_pred             CCchhHHHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhC-----------CHHHHHHHHHH
Confidence              0000       00000  00   113334555444432    45579999999998           55555555555


Q ss_pred             HHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCC
Q 022768          160 LNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFN  238 (292)
Q Consensus       160 l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~  238 (292)
                      ++.     +++.+++|++|+.++.+.+.+++  || ..+.|.+++.++....++..+....+. ....+..++..+.| +
T Consensus       142 LEE-----PP~~tifILaTte~~KLl~TI~S--Rc-q~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~G-s  212 (725)
T PRK07133        142 LEE-----PPKHVIFILATTEVHKIPLTILS--RV-QRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSG-S  212 (725)
T ss_pred             hhc-----CCCceEEEEEcCChhhhhHHHHh--hc-eeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-C
Confidence            543     44578888888888999999998  77 689999999999998888876644332 12235667777877 7


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          239 GADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      .+++..+++.+..+.    ...|+.+++.+++
T Consensus       213 lR~AlslLekl~~y~----~~~It~e~V~ell  240 (725)
T PRK07133        213 LRDALSIAEQVSIFG----NNKITLKNVEELF  240 (725)
T ss_pred             HHHHHHHHHHHHHhc----cCCCCHHHHHHHH
Confidence            778888887765432    2337777766543

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.80  E-value=6.5e-18  Score=154.55  Aligned_cols=217  Identities=19%  Similarity=0.220  Sum_probs=147.1

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      +.++...++|.+|++++|++.+++.|...+..-            ..++.+||+||+|+|||++++.+|+.+++.     
T Consensus         3 y~~~~~kyRP~~f~diiGq~~i~~~L~~~i~~~------------~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~   70 (486)
T PRK14953          3 YIPFARKYRPKFFKEVIGQEIVVRILKNAVKLQ------------RVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEG   70 (486)
T ss_pred             chHHHHhhCCCcHHHccChHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCC
Confidence            456778899999999999999999999998652            345668899999999999999999988641     


Q ss_pred             --EEEE-eccchhc----------cccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHH
Q 022768           94 --FLKV-VSSAIID----------KYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL  156 (292)
Q Consensus        94 --~~~~-~~~~~~~----------~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l  156 (292)
                        +-.+ +|..+..          .........++.+...+..    ..+.|++|||+|.+           .......|
T Consensus        71 ~pc~~c~nc~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~L-----------t~~a~naL  139 (486)
T PRK14953         71 EPCGKCENCVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHML-----------TKEAFNAL  139 (486)
T ss_pred             CCCCccHHHHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhc-----------CHHHHHHH
Confidence              1111 0000000          0000112233344333322    34579999999988           45455555


Q ss_pred             HHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcC
Q 022768          157 MELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAE  235 (292)
Q Consensus       157 ~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~  235 (292)
                      ...+.     .+++.+++|++++.++.+.+.+++  |+ ..+.|++++.++....+..++...... .+..+..++..+.
T Consensus       140 Lk~LE-----epp~~~v~Il~tt~~~kl~~tI~S--Rc-~~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~  211 (486)
T PRK14953        140 LKTLE-----EPPPRTIFILCTTEYDKIPPTILS--RC-QRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASE  211 (486)
T ss_pred             HHHHh-----cCCCCeEEEEEECCHHHHHHHHHH--hc-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            55544     234567777777778888888888  77 578999999999999999887754433 2223456677777


Q ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          236 GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       236 g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      | +.+++.++++.+..+    +...+|.+++.+++.
T Consensus       212 G-~lr~al~~Ldkl~~~----~~~~It~~~V~~~lg  242 (486)
T PRK14953        212 G-GMRDAASLLDQASTY----GEGKVTIKVVEEFLG  242 (486)
T ss_pred             C-CHHHHHHHHHHHHHh----cCCCcCHHHHHHHhC
Confidence            6 777888888777643    234588887777553

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.79  E-value=7.9e-18  Score=147.60  Aligned_cols=211  Identities=20%  Similarity=0.243  Sum_probs=138.5

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      +..+.++|.+|++++|++++++.+..++...            ..+..++++||+|+|||++++++++.++.+++.+++.
T Consensus        10 ~w~~kyrP~~~~~~~~~~~~~~~l~~~~~~~------------~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~~~   77 (316)
T PHA02544         10 MWEQKYRPSTIDECILPAADKETFKSIVKKG------------RIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGS   77 (316)
T ss_pred             cceeccCCCcHHHhcCcHHHHHHHHHHHhcC------------CCCeEEEeeCcCCCCHHHHHHHHHHHhCccceEeccC
Confidence            3446899999999999999999999988641            2345566799999999999999999999889888877


Q ss_pred             chhccccChHHHHHHHHHHHhh-hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          101 AIIDKYIGESARLIREMFGYAR-DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      .  .. .......+........ ...+.+|+|||+|.+.          ....+..+..+++..     ..++.+|+++|
T Consensus        78 ~--~~-~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~----------~~~~~~~L~~~le~~-----~~~~~~Ilt~n  139 (316)
T PHA02544         78 D--CR-IDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLG----------LADAQRHLRSFMEAY-----SKNCSFIITAN  139 (316)
T ss_pred             c--cc-HHHHHHHHHHHHHhhcccCCCeEEEEECccccc----------CHHHHHHHHHHHHhc-----CCCceEEEEcC
Confidence            6  21 2122222222222111 1346899999999872          233455666655542     24677889999


Q ss_pred             CCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc-----cCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Q 022768          180 RPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI-----AKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       180 ~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~-----~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~  254 (292)
                      .+..+.+.+++  || ..+.++.|+.+++.++++.+....     .....++.+.+...... +.++++.++.....++.
T Consensus       140 ~~~~l~~~l~s--R~-~~i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~~-~~~d~r~~l~~l~~~~~  215 (316)
T PHA02544        140 NKNGIIEPLRS--RC-RVIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKK-NFPDFRRTINELQRYAS  215 (316)
T ss_pred             ChhhchHHHHh--hc-eEEEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHh-cCCCHHHHHHHHHHHHc
Confidence            99999999998  88 578999999999987766543321     11122343344444332 22366666655554442


Q ss_pred             HhcCCcccHHHHHH
Q 022768          255 RAERDYVIHEDFMK  268 (292)
Q Consensus       255 ~~~~~~i~~~~~~~  268 (292)
                         ...++.+++..
T Consensus       216 ---~~~i~~~~l~~  226 (316)
T PHA02544        216 ---TGKIDAGILSE  226 (316)
T ss_pred             ---cCCCCHHHHHH
Confidence               23455544433

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.79  E-value=9.8e-18  Score=157.27  Aligned_cols=222  Identities=16%  Similarity=0.226  Sum_probs=148.1

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEEeccc
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVSSA  101 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~~~~~  101 (292)
                      +.|.|+++.+++|..++...+.+        -.++..++|+|+||||||++++.+++++          ...+++++|..
T Consensus       755 D~LPhREeEIeeLasfL~paIkg--------sgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~  826 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQ--------SGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMN  826 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhc--------CCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCc
Confidence            67999999999999998765332        2334456799999999999999998876          24578888854


Q ss_pred             hhccc--------------c--C-hHHHHHHHHHHHhhh--CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768          102 IIDKY--------------I--G-ESARLIREMFGYARD--HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus       102 ~~~~~--------------~--~-~~~~~~~~~~~~~~~--~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      +....              .  + .....+..+|.....  ....||+|||+|.|..           ..+..|..+++.
T Consensus       827 Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~k-----------K~QDVLYnLFR~  895 (1164)
T PTZ00112        827 VVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLIT-----------KTQKVLFTLFDW  895 (1164)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCc-----------cHHHHHHHHHHH
Confidence            33211              0  0 122344455554422  2346999999999942           235667777765


Q ss_pred             hhCCCCCCCeEEEEEeCC---CCCCChhhcCCCCcce-EEEccCCCHHHHHHHHHHHHcCcc-CCCCCCHHHHHHHcCCC
Q 022768          163 LDGFDQLGKVKMIMATNR---PDVLDPALLRPGRLDR-KIEIPLPNEQSRMEILKIHAAGIA-KHGEIDYEAVVKLAEGF  237 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~---~~~l~~~l~~~~r~~~-~i~l~~p~~~~r~~i~~~~~~~~~-~~~~~~~~~l~~~~~g~  237 (292)
                      ..  ....++.||+++|.   ++.+.+++++  |+.. .+.|++++.+++.+|++.++.... .-.+..++.++..... 
T Consensus       896 ~~--~s~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIArkVAq-  970 (1164)
T PTZ00112        896 PT--KINSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCARKVAN-  970 (1164)
T ss_pred             hh--ccCCeEEEEEecCchhcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHHHhhhh-
Confidence            43  23357889999986   4456788888  5543 578999999999999999987531 1111223444443333 


Q ss_pred             CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhh
Q 022768          238 NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAK  277 (292)
Q Consensus       238 ~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~  277 (292)
                      ..||+|.++.-+...+..+....|+.+++.+|...+....
T Consensus       971 ~SGDARKALDILRrAgEikegskVT~eHVrkAleeiE~sr 1010 (1164)
T PTZ00112        971 VSGDIRKALQICRKAFENKRGQKIVPRDITEATNQLFDSP 1010 (1164)
T ss_pred             cCCHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHHHhhh
Confidence            2347776665555444444556899999999998775543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.79  E-value=3.2e-18  Score=153.96  Aligned_cols=220  Identities=12%  Similarity=0.180  Sum_probs=146.9

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE--
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK--   96 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~--   96 (292)
                      ++.+...++|.+|++++|++.+++.|...+..-            ..++.+||+||+|+|||++|+.+|+.+.+.-..  
T Consensus         3 ~~~l~~k~RP~~~~eiiGq~~~~~~L~~~~~~~------------~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~   70 (397)
T PRK14955          3 YQVIARKYRPKKFADITAQEHITRTIQNSLRMG------------RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDD   70 (397)
T ss_pred             cHHHHHhcCCCcHhhccChHHHHHHHHHHHHhC------------CcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCc
Confidence            456778999999999999999999999988652            345669999999999999999999999663100  


Q ss_pred             --------Eeccc-----------hhc--cccC---hHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcc
Q 022768           97 --------VVSSA-----------IID--KYIG---ESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSA  148 (292)
Q Consensus        97 --------~~~~~-----------~~~--~~~~---~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~  148 (292)
                              -.|..           ..+  .+.+   ...+.++.+...+.    .....+++|||+|.+           
T Consensus        71 ~~~~~~~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l-----------  139 (397)
T PRK14955         71 ADYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHML-----------  139 (397)
T ss_pred             ccccccCCCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhC-----------
Confidence                    00000           000  0001   11233444433332    234479999999998           


Q ss_pred             hHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCH
Q 022768          149 DREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDY  227 (292)
Q Consensus       149 ~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~  227 (292)
                      ....+..+...++     .+.+.+++|++++....+.+.+++  |+ ..+.|++++.++....+...+...... .+...
T Consensus       140 ~~~~~~~LLk~LE-----ep~~~t~~Il~t~~~~kl~~tl~s--R~-~~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al  211 (397)
T PRK14955        140 SIAAFNAFLKTLE-----EPPPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPLEEIQQQLQGICEAEGISVDADAL  211 (397)
T ss_pred             CHHHHHHHHHHHh-----cCCCCeEEEEEeCChHHhHHHHHH--HH-HHhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            5545555555544     333566777777777888888887  66 578999999999888888877643322 22234


Q ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHHH-hcCCcccHHHHHHHH
Q 022768          228 EAVVKLAEGFNGADLRNVCTEAGMSAIR-AERDYVIHEDFMKAV  270 (292)
Q Consensus       228 ~~l~~~~~g~~~~di~~l~~~a~~~a~~-~~~~~i~~~~~~~a~  270 (292)
                      +.++..+.| +.+.+...++.+..++.. .....|+.+++.+.+
T Consensus       212 ~~l~~~s~g-~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v  254 (397)
T PRK14955        212 QLIGRKAQG-SMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL  254 (397)
T ss_pred             HHHHHHcCC-CHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence            566667776 777777777776665532 224468887776654

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.79  E-value=2.9e-17  Score=148.40  Aligned_cols=236  Identities=20%  Similarity=0.258  Sum_probs=156.5

Q ss_pred             hhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CC
Q 022768           18 VYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DA   92 (292)
Q Consensus        18 ~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~   92 (292)
                      +.+.+..-.|....+.++|+++..++|...+...+.+         ..+.+++|+||||+|||++++.+++.+     +.
T Consensus        16 ~~~~~~~l~~~~~P~~l~~Re~e~~~l~~~l~~~~~~---------~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~   86 (394)
T PRK00411         16 IFKDEEVLEPDYVPENLPHREEQIEELAFALRPALRG---------SRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKV   86 (394)
T ss_pred             eeCChhhCCCCCcCCCCCCHHHHHHHHHHHHHHHhCC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCc
Confidence            4444444445556678999999999999998653221         335679999999999999999999877     46


Q ss_pred             cEEEEeccchhcc----------cc-------C-hHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHH
Q 022768           93 NFLKVVSSAIIDK----------YI-------G-ESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQ  153 (292)
Q Consensus        93 ~~~~~~~~~~~~~----------~~-------~-~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~  153 (292)
                      .++++++....+.          ..       + .....+..+...... ..+.||+|||+|.+...          ...
T Consensus        87 ~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~----------~~~  156 (394)
T PRK00411         87 VYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEK----------EGN  156 (394)
T ss_pred             EEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhcc----------CCc
Confidence            6888887643221          00       0 112223333333332 34579999999998511          112


Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEEeCCCC---CCChhhcCCCCc-ceEEEccCCCHHHHHHHHHHHHcCccCC---CCCC
Q 022768          154 RTLMELLNQLDGFDQLGKVKMIMATNRPD---VLDPALLRPGRL-DRKIEIPLPNEQSRMEILKIHAAGIAKH---GEID  226 (292)
Q Consensus       154 ~~l~~~l~~~~~~~~~~~~~vi~t~~~~~---~l~~~l~~~~r~-~~~i~l~~p~~~~r~~i~~~~~~~~~~~---~~~~  226 (292)
                      ..+..+++...... ..++.+|+++|...   .+++.+.+  |+ ...+.|++++.++..++++.++......   .+..
T Consensus       157 ~~l~~l~~~~~~~~-~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~  233 (394)
T PRK00411        157 DVLYSLLRAHEEYP-GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEV  233 (394)
T ss_pred             hHHHHHHHhhhccC-CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhH
Confidence            34455554433222 23788899888753   46677776  44 3578999999999999999887532111   1222


Q ss_pred             HHHHHHHcCC--CCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          227 YEAVVKLAEG--FNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       227 ~~~l~~~~~g--~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      ++.++..+.+  ...+.+.+++..|...|..++...|+.+++.+|+..+..
T Consensus       234 l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~  284 (394)
T PRK00411        234 LDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEI  284 (394)
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHH
Confidence            4555555532  145666688888888898888889999999999998854

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.79  E-value=6e-18  Score=161.43  Aligned_cols=223  Identities=24%  Similarity=0.350  Sum_probs=157.9

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEE
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKV   97 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~   97 (292)
                      .=.++.++|.++.++++.+.+..             ....+++|+||||+|||++++.++...          ++.++.+
T Consensus       182 ~g~~~~liGR~~ei~~~i~iL~r-------------~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l  248 (758)
T PRK11034        182 VGGIDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL  248 (758)
T ss_pred             cCCCCcCcCCCHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEec
Confidence            34567789999988888887655             235678999999999999999999865          3445555


Q ss_pred             eccchh--ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEE
Q 022768           98 VSSAII--DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMI  175 (292)
Q Consensus        98 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi  175 (292)
                      +...+.  ..+.|+.+..++.++..+....++||||||+|.+++....  +....+....|..++.       .+.+.+|
T Consensus       249 ~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~--~~g~~d~~nlLkp~L~-------~g~i~vI  319 (758)
T PRK11034        249 DIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAA--SGGQVDAANLIKPLLS-------SGKIRVI  319 (758)
T ss_pred             cHHHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCC--CCcHHHHHHHHHHHHh-------CCCeEEE
Confidence            544444  3456778888889998888778899999999999765422  1122233333444433       2678899


Q ss_pred             EEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCH--HHH---HHHc-----CCCCHH
Q 022768          176 MATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDY--EAV---VKLA-----EGFNGA  240 (292)
Q Consensus       176 ~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~--~~l---~~~~-----~g~~~~  240 (292)
                      ++|+..+     ..++++.+  || ..|.++.|+.+++..|++.+...+.....+.+  +.+   ...+     ..+-|.
T Consensus       320 gATt~~E~~~~~~~D~AL~r--RF-q~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~lPd  396 (758)
T PRK11034        320 GSTTYQEFSNIFEKDRALAR--RF-QKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPD  396 (758)
T ss_pred             ecCChHHHHHHhhccHHHHh--hC-cEEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhccccCccChH
Confidence            9998754     46899998  99 58999999999999999987665444433333  222   2223     334677


Q ss_pred             HHHHHHHHHHHHHHH----hcCCcccHHHHHHHHHHHhh
Q 022768          241 DLRNVCTEAGMSAIR----AERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       241 di~~l~~~a~~~a~~----~~~~~i~~~~~~~a~~~~~~  275 (292)
                      ....++++|......    .....|+.+|+.+.+.....
T Consensus       397 Kaidlldea~a~~~~~~~~~~~~~v~~~~i~~v~~~~tg  435 (758)
T PRK11034        397 KAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIAR  435 (758)
T ss_pred             HHHHHHHHHHHhhccCcccccccccChhhHHHHHHHHhC
Confidence            899999999875532    22346888999998877664

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.79  E-value=2.3e-17  Score=150.02  Aligned_cols=210  Identities=19%  Similarity=0.255  Sum_probs=143.0

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      ++.+++.++|.+|++++|++.+++.|...+..-            ..++.+||+||+|+|||++|+.+|+.+.+.     
T Consensus         4 ~~~~~~kyRP~~~~diiGq~~~v~~L~~~i~~~------------~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~   71 (451)
T PRK06305          4 YQVSSRKYRPQTFSEILGQDAVVAVLKNALRFN------------RAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTED   71 (451)
T ss_pred             hHHHHHHhCCCCHHHhcCcHHHHHHHHHHHHcC------------CCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccC
Confidence            677888999999999999999999999988652            345679999999999999999999988542     


Q ss_pred             --------------------EEEEeccchhccccChHHHHHHHHHHHh----hhCCCEEEEEcccccccCCcCCCCCcch
Q 022768           94 --------------------FLKVVSSAIIDKYIGESARLIREMFGYA----RDHQPCIIFMDEIDAIGGRRFSEGTSAD  149 (292)
Q Consensus        94 --------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~il~lDe~d~l~~~~~~~~~~~~  149 (292)
                                          ++.++....      .....++.+....    ......|++|||+|.+           .
T Consensus        72 ~~~c~~c~~C~~i~~~~~~d~~~i~g~~~------~gid~ir~i~~~l~~~~~~~~~kvvIIdead~l-----------t  134 (451)
T PRK06305         72 QEPCNQCASCKEISSGTSLDVLEIDGASH------RGIEDIRQINETVLFTPSKSRYKIYIIDEVHML-----------T  134 (451)
T ss_pred             CCCCcccHHHHHHhcCCCCceEEeecccc------CCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhh-----------C
Confidence                                112211110      0112232222222    2245689999999998           5


Q ss_pred             HHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHH
Q 022768          150 REIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYE  228 (292)
Q Consensus       150 ~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~  228 (292)
                      ...+..|...++.     +.+.+.+|++++.+..+.+.+++  |+ ..+.|++++.++....+...+...... ....+.
T Consensus       135 ~~~~n~LLk~lEe-----p~~~~~~Il~t~~~~kl~~tI~s--Rc-~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~  206 (451)
T PRK06305        135 KEAFNSLLKTLEE-----PPQHVKFFLATTEIHKIPGTILS--RC-QKMHLKRIPEETIIDKLALIAKQEGIETSREALL  206 (451)
T ss_pred             HHHHHHHHHHhhc-----CCCCceEEEEeCChHhcchHHHH--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            5555555555443     33577788888888889999998  77 678999999999998888877643322 222355


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          229 AVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       229 ~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      .++..+.| +.+++...++.+..+   .+ ..|+.+++.+++
T Consensus       207 ~L~~~s~g-dlr~a~~~Lekl~~~---~~-~~It~~~V~~l~  243 (451)
T PRK06305        207 PIARAAQG-SLRDAESLYDYVVGL---FP-KSLDPDSVAKAL  243 (451)
T ss_pred             HHHHHcCC-CHHHHHHHHHHHHHh---cc-CCcCHHHHHHHH
Confidence            66677766 566666666554432   22 347777665544

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.79  E-value=1.1e-17  Score=149.68  Aligned_cols=216  Identities=17%  Similarity=0.191  Sum_probs=142.6

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE-
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV-   97 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~-   97 (292)
                      +...++.++|.+|++++|++.+++.+...+...            ..+++++|+||+|+|||++++.+++.+.++.... 
T Consensus         4 ~~~~~~k~rP~~~~~iig~~~~~~~l~~~i~~~------------~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~   71 (367)
T PRK14970          4 FVVSARKYRPQTFDDVVGQSHITNTLLNAIENN------------HLAQALLFCGPRGVGKTTCARILARKINQPGYDDP   71 (367)
T ss_pred             hHHHHHHHCCCcHHhcCCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            455678899999999999999999999998652            3456899999999999999999999886521110 


Q ss_pred             ------eccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC
Q 022768           98 ------VSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD  167 (292)
Q Consensus        98 ------~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  167 (292)
                            +..++. .........++.++..+.    ...+.+++|||+|.+           .......+...+   +.  
T Consensus        72 ~~~~~~~~~~l~-~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l-----------~~~~~~~ll~~l---e~--  134 (367)
T PRK14970         72 NEDFSFNIFELD-AASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHML-----------SSAAFNAFLKTL---EE--  134 (367)
T ss_pred             CCCCCcceEEec-cccCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhc-----------CHHHHHHHHHHH---hC--
Confidence                  000000 001111234445444432    234579999999988           343444444433   32  


Q ss_pred             CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      +...+.+|++++.+..+.+.+++  |+ ..+.+++|+.++...++...+...... .+..++.++..+.| +.+.+...+
T Consensus       135 ~~~~~~~Il~~~~~~kl~~~l~s--r~-~~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~g-dlr~~~~~l  210 (367)
T PRK14970        135 PPAHAIFILATTEKHKIIPTILS--RC-QIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADG-ALRDALSIF  210 (367)
T ss_pred             CCCceEEEEEeCCcccCCHHHHh--cc-eeEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCC-CHHHHHHHH
Confidence            33456777778888888899988  66 568999999999998888877654432 22334556666665 666666666


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          247 TEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       247 ~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      +....++   +.. |+.+++.+.+.
T Consensus       211 ekl~~y~---~~~-it~~~v~~~~~  231 (367)
T PRK14970        211 DRVVTFC---GKN-ITRQAVTENLN  231 (367)
T ss_pred             HHHHHhc---CCC-CCHHHHHHHhC
Confidence            6555443   222 77777776654

>TIGR00763 lon ATP-dependent protease La

Probab=99.78  E-value=1.1e-17  Score=161.92  Aligned_cols=166  Identities=28%  Similarity=0.411  Sum_probs=120.2

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc--------
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID--------  104 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~--------  104 (292)
                      +++|++++++++.+++......       +...+.+++|+||||+|||++++++|+.++.+++.+++....+        
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~-------~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~  393 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLR-------GKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHR  393 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhh-------cCCCCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCC
Confidence            4889999999999987653211       1233557999999999999999999999999999998654321        


Q ss_pred             -cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHh----------hCCCCCCCeE
Q 022768          105 -KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQL----------DGFDQLGKVK  173 (292)
Q Consensus       105 -~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~----------~~~~~~~~~~  173 (292)
                       .+.+.....+...+..+....| |++|||+|.+....       ......+|.++++..          ......++++
T Consensus       394 ~~~~g~~~g~i~~~l~~~~~~~~-villDEidk~~~~~-------~~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~  465 (775)
T TIGR00763       394 RTYVGAMPGRIIQGLKKAKTKNP-LFLLDEIDKIGSSF-------RGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVI  465 (775)
T ss_pred             CceeCCCCchHHHHHHHhCcCCC-EEEEechhhcCCcc-------CCCHHHHHHHhcCHHhcCccccccCCceeccCCEE
Confidence             2344444445556666655554 89999999996422       111234555555421          0011224789


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHA  216 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~  216 (292)
                      +|+|+|..+.+++++++  || ..+.|+.|+.+++.+|++.++
T Consensus       466 ~I~TtN~~~~i~~~L~~--R~-~vi~~~~~~~~e~~~I~~~~l  505 (775)
T TIGR00763       466 FIATANSIDTIPRPLLD--RM-EVIELSGYTEEEKLEIAKKYL  505 (775)
T ss_pred             EEEecCCchhCCHHHhC--Ce-eEEecCCCCHHHHHHHHHHHH
Confidence            99999999999999999  88 578999999999999998776

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.78  E-value=1.8e-17  Score=153.87  Aligned_cols=216  Identities=17%  Similarity=0.194  Sum_probs=147.1

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----   93 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----   93 (292)
                      |..+...++|.+|++++|++++++.|+..+..-            ..++.+||+||+|+|||++++.+|+.+.+.     
T Consensus         3 y~~l~~kyRP~~f~diiGqe~iv~~L~~~i~~~------------~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~   70 (563)
T PRK06647          3 YRGTATKRRPRDFNSLEGQDFVVETLKHSIESN------------KIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP   70 (563)
T ss_pred             cHHHHHHhCCCCHHHccCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCC
Confidence            445677899999999999999999999998652            345679999999999999999999998652     


Q ss_pred             --EEEEecc-c-----hhc--cccC---hHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHH
Q 022768           94 --FLKVVSS-A-----IID--KYIG---ESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL  156 (292)
Q Consensus        94 --~~~~~~~-~-----~~~--~~~~---~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l  156 (292)
                        +-.+..+ .     ..+  ...+   .....++.+...+.    .....+++|||+|.+           ....+..|
T Consensus        71 ~pC~~C~~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~L-----------s~~a~naL  139 (563)
T PRK06647         71 MPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHML-----------SNSAFNAL  139 (563)
T ss_pred             CCCccchHHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhc-----------CHHHHHHH
Confidence              1111000 0     000  0001   11233444433322    245679999999998           55555555


Q ss_pred             HHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcC
Q 022768          157 MELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAE  235 (292)
Q Consensus       157 ~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~  235 (292)
                      +..++     .+.+.+++|++++.+..+.+.+++  |+ ..+.|.+++.++..+.++..+...... .+..+..++..+.
T Consensus       140 LK~LE-----epp~~~vfI~~tte~~kL~~tI~S--Rc-~~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~  211 (563)
T PRK06647        140 LKTIE-----EPPPYIVFIFATTEVHKLPATIKS--RC-QHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKST  211 (563)
T ss_pred             HHhhc-----cCCCCEEEEEecCChHHhHHHHHH--hc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            44443     344678888888888889999998  77 578999999999998888877543332 2233455666777


Q ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          236 GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       236 g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      | +.+++..+++.+..++    ...++.+++.+++
T Consensus       212 G-dlR~alslLdklis~~----~~~It~e~V~~ll  241 (563)
T PRK06647        212 G-SVRDAYTLFDQVVSFS----DSDITLEQIRSKM  241 (563)
T ss_pred             C-CHHHHHHHHHHHHhhc----CCCCCHHHHHHHh
Confidence            6 7888888887765432    2457777766654

>PRK06893 DNA replication initiation factor; Validated

Probab=99.77  E-value=4.3e-17  Score=136.03  Aligned_cols=212  Identities=13%  Similarity=0.165  Sum_probs=132.9

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      .+++.+|++.++.+... .+......       .   .....+.++|+||||+||||+++++|+++   +..+.++....
T Consensus         9 ~~~~~~fd~f~~~~~~~-~~~~~~~~-------~---~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~   77 (229)
T PRK06893          9 QIDDETLDNFYADNNLL-LLDSLRKN-------F---IDLQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSK   77 (229)
T ss_pred             CCCcccccccccCChHH-HHHHHHHH-------h---hccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHH
Confidence            45678999998765432 11111111       1   11223468999999999999999999886   34455555432


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC-C
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN-R  180 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~-~  180 (292)
                      ...        .....+...  ....+|+|||++.+.+         +...+..+..+++....   .++.++|.|++ .
T Consensus        78 ~~~--------~~~~~~~~~--~~~dlLilDDi~~~~~---------~~~~~~~l~~l~n~~~~---~~~~illits~~~  135 (229)
T PRK06893         78 SQY--------FSPAVLENL--EQQDLVCLDDLQAVIG---------NEEWELAIFDLFNRIKE---QGKTLLLISADCS  135 (229)
T ss_pred             hhh--------hhHHHHhhc--ccCCEEEEeChhhhcC---------ChHHHHHHHHHHHHHHH---cCCcEEEEeCCCC
Confidence            110        111222222  2347999999998743         33445567777776542   23344455554 4


Q ss_pred             CCCCC---hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh
Q 022768          181 PDVLD---PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       181 ~~~l~---~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~  256 (292)
                      |..++   ++++++.+++..+.+++|+.+++.++++..+...... .+...+.|+....| +.+.+..+++.....+...
T Consensus       136 p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~-d~r~l~~~l~~l~~~~~~~  214 (229)
T PRK06893        136 PHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDR-DMHTLFDALDLLDKASLQA  214 (229)
T ss_pred             hHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccC-CHHHHHHHHHHHHHHHHhc
Confidence            55443   7888855567789999999999999999887644332 22224455666665 7778888888775545433


Q ss_pred             cCCcccHHHHHHHHH
Q 022768          257 ERDYVIHEDFMKAVR  271 (292)
Q Consensus       257 ~~~~i~~~~~~~a~~  271 (292)
                      ++ .||.+.+++++.
T Consensus       215 ~~-~it~~~v~~~L~  228 (229)
T PRK06893        215 QR-KLTIPFVKEILG  228 (229)
T ss_pred             CC-CCCHHHHHHHhc
Confidence            44 699999988763

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=99.77  E-value=7.7e-18  Score=143.12  Aligned_cols=223  Identities=26%  Similarity=0.358  Sum_probs=149.9

Q ss_pred             hcccCCCCCccccccccHHHHHH---HHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---E
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRE---LRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---F   94 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~---l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---~   94 (292)
                      ++++..+|-++++.+|+++.+.+   |..++..             ..-..++||||||+|||++|+.++.....+   +
T Consensus       127 PLaermRPktL~dyvGQ~hlv~q~gllrs~ieq-------------~~ipSmIlWGppG~GKTtlArlia~tsk~~Syrf  193 (554)
T KOG2028|consen  127 PLAERMRPKTLDDYVGQSHLVGQDGLLRSLIEQ-------------NRIPSMILWGPPGTGKTTLARLIASTSKKHSYRF  193 (554)
T ss_pred             ChhhhcCcchHHHhcchhhhcCcchHHHHHHHc-------------CCCCceEEecCCCCchHHHHHHHHhhcCCCceEE
Confidence            66778899999999999987643   3333322             234469999999999999999999988776   4


Q ss_pred             EEEeccchhccccChHHHHHHHHHHHhhh-----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGYARD-----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL  169 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~  169 (292)
                      ++++...       .....++.+|..++.     ...-||||||+|++           +...|..++-.++.       
T Consensus       194 velSAt~-------a~t~dvR~ife~aq~~~~l~krkTilFiDEiHRF-----------NksQQD~fLP~VE~-------  248 (554)
T KOG2028|consen  194 VELSATN-------AKTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRF-----------NKSQQDTFLPHVEN-------  248 (554)
T ss_pred             EEEeccc-------cchHHHHHHHHHHHHHHhhhcceeEEEeHHhhhh-----------hhhhhhcccceecc-------
Confidence            4444333       233445566666543     23469999999998           56566666554432       


Q ss_pred             CCeEEEEEe--CCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc---C-----ccCCC---CCC---HHHHHHH
Q 022768          170 GKVKMIMAT--NRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA---G-----IAKHG---EID---YEAVVKL  233 (292)
Q Consensus       170 ~~~~vi~t~--~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~---~-----~~~~~---~~~---~~~l~~~  233 (292)
                      +.+.+|++|  |+.-.++.++.+  || .++.+...+.+....|+.+...   +     .....   .++   ++.++..
T Consensus       249 G~I~lIGATTENPSFqln~aLlS--RC-~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~l  325 (554)
T KOG2028|consen  249 GDITLIGATTENPSFQLNAALLS--RC-RVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYL  325 (554)
T ss_pred             CceEEEecccCCCccchhHHHHh--cc-ceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHh
Confidence            578888876  445578999999  66 5677888888888888776432   1     11111   122   3445556


Q ss_pred             cCCCCHHHHHHHHHHHHH---HHHHhc----CCcccHHHHHHHHHHHhhhhhhchhhhhhhh
Q 022768          234 AEGFNGADLRNVCTEAGM---SAIRAE----RDYVIHEDFMKAVRKLNEAKKLESSAHYNAD  288 (292)
Q Consensus       234 ~~g~~~~di~~l~~~a~~---~a~~~~----~~~i~~~~~~~a~~~~~~~~~~~~~~~~~~~  288 (292)
                      +.|    |.+..++...+   .+..+.    +..++.+|+.++++.-...+++...++|+-+
T Consensus       326 sdG----DaR~aLN~Lems~~m~~tr~g~~~~~~lSidDvke~lq~s~~~YDr~Ge~HYntI  383 (554)
T KOG2028|consen  326 SDG----DARAALNALEMSLSMFCTRSGQSSRVLLSIDDVKEGLQRSHILYDRAGEEHYNTI  383 (554)
T ss_pred             cCc----hHHHHHHHHHHHHHHHHhhcCCcccceecHHHHHHHHhhccceecccchhHHHHH
Confidence            665    55544443333   233332    3479999999999998888888777777643

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.77  E-value=2.6e-17  Score=148.89  Aligned_cols=221  Identities=21%  Similarity=0.263  Sum_probs=143.2

Q ss_pred             CCCcccc-ccccHH--HHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEEEEe
Q 022768           27 GNVSYSA-VGGLSD--QIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFLKVV   98 (292)
Q Consensus        27 ~~~~~~~-l~g~~~--~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~~~   98 (292)
                      +..+|++ ++|...  +...+..+...+          + .....++|+||+|+|||+|++++++++     +..+++++
T Consensus       105 ~~~tfd~fi~g~~n~~a~~~~~~~~~~~----------~-~~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       105 PKYTFDNFVVGKSNRLAHAAALAVAENP----------G-KAYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CCCcccccccCCcHHHHHHHHHHHHhCc----------C-ccCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE
Confidence            5688888 556544  334444443322          1 224568999999999999999999987     56788888


Q ss_pred             ccchhccccChHHH-HHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEE
Q 022768           99 SSAIIDKYIGESAR-LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMA  177 (292)
Q Consensus        99 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t  177 (292)
                      +..+...+...... .+........  ...+|+|||+|.+.+         ....+..+..+++.+..   .+..++|++
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~dlLiiDDi~~l~~---------~~~~~~~l~~~~n~~~~---~~~~iiits  239 (405)
T TIGR00362       174 SEKFTNDFVNALRNNKMEEFKEKYR--SVDLLLIDDIQFLAG---------KERTQEEFFHTFNALHE---NGKQIVLTS  239 (405)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHH--hCCEEEEehhhhhcC---------CHHHHHHHHHHHHHHHH---CCCCEEEec
Confidence            77665433221111 1111112222  247999999998843         22345566666665532   123334444


Q ss_pred             eCCCCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          178 TNRPDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       178 ~~~~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      ...+..   +++.++++...+..+.+++|+.++|..|++..+...... .+-.++.++....+ +.+++..++.....+|
T Consensus       240 ~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~-~~r~l~~~l~~l~~~a  318 (405)
T TIGR00362       240 DRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRS-NVRELEGALNRLLAYA  318 (405)
T ss_pred             CCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHHHH
Confidence            334443   567888833334689999999999999999998754333 22234556666665 8889999999998888


Q ss_pred             HHhcCCcccHHHHHHHHHHHh
Q 022768          254 IRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ...+ ..||.+.+.+++....
T Consensus       319 ~~~~-~~it~~~~~~~L~~~~  338 (405)
T TIGR00362       319 SLTG-KPITLELAKEALKDLL  338 (405)
T ss_pred             HHhC-CCCCHHHHHHHHHHhc
Confidence            6655 4599999999998763

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.77  E-value=1.9e-17  Score=151.61  Aligned_cols=221  Identities=22%  Similarity=0.276  Sum_probs=144.3

Q ss_pred             CCCCcccccc-ccHH--HHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEEEE
Q 022768           26 PGNVSYSAVG-GLSD--QIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFLKV   97 (292)
Q Consensus        26 ~~~~~~~~l~-g~~~--~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~~   97 (292)
                      .+..+|++.+ |...  +...+..+...+          + ....+++|+||+|+|||||++++++++     +..++++
T Consensus       116 ~~~~tfd~fv~g~~n~~a~~~~~~~~~~~----------~-~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi  184 (450)
T PRK00149        116 NPKYTFDNFVVGKSNRLAHAAALAVAENP----------G-KAYNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYV  184 (450)
T ss_pred             CCCCcccccccCCCcHHHHHHHHHHHhCc----------C-ccCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEE
Confidence            3667888854 4333  455555554432          1 223569999999999999999999987     4567888


Q ss_pred             eccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEE
Q 022768           98 VSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMA  177 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t  177 (292)
                      ++..+...+...........|.... ..+.+|+|||+|.+.+         ....+..+..+++.+...   +..++|++
T Consensus       185 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~dlLiiDDi~~l~~---------~~~~~~~l~~~~n~l~~~---~~~iiits  251 (450)
T PRK00149        185 TSEKFTNDFVNALRNNTMEEFKEKY-RSVDVLLIDDIQFLAG---------KERTQEEFFHTFNALHEA---GKQIVLTS  251 (450)
T ss_pred             EHHHHHHHHHHHHHcCcHHHHHHHH-hcCCEEEEehhhhhcC---------CHHHHHHHHHHHHHHHHC---CCcEEEEC
Confidence            8877654433222111111222211 2457999999999843         223456666666655421   23344444


Q ss_pred             eCCCCC---CChhhcCCCCc--ceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHH
Q 022768          178 TNRPDV---LDPALLRPGRL--DRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGM  251 (292)
Q Consensus       178 ~~~~~~---l~~~l~~~~r~--~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~  251 (292)
                      ...|..   +++++++  ||  +..+.+.+|+.++|.+|++..+...... .+..++.++....| +.+.+..++.....
T Consensus       252 ~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~-~~R~l~~~l~~l~~  328 (450)
T PRK00149        252 DRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITS-NVRELEGALNRLIA  328 (450)
T ss_pred             CCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCC-CHHHHHHHHHHHHH
Confidence            444444   6688888  66  4689999999999999999988753322 11224445555554 78888889998888


Q ss_pred             HHHHhcCCcccHHHHHHHHHHHh
Q 022768          252 SAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       252 ~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ++...++ .||.+.+.+++..+.
T Consensus       329 ~~~~~~~-~it~~~~~~~l~~~~  350 (450)
T PRK00149        329 YASLTGK-PITLELAKEALKDLL  350 (450)
T ss_pred             HHHhhCC-CCCHHHHHHHHHHhh
Confidence            8766654 599999999999873

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.77  E-value=3.1e-17  Score=153.24  Aligned_cols=220  Identities=11%  Similarity=0.201  Sum_probs=146.8

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE---
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL---   95 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~---   95 (292)
                      +..++..++|.+|++++|++.+++.|.+.+..-            .-++.+||+||+|+||||+|+.+|+.+.+...   
T Consensus         3 ~~~l~~kyRP~~f~eivGQe~i~~~L~~~i~~~------------ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~   70 (620)
T PRK14954          3 YQVIARKYRPSKFADITAQEHITHTIQNSLRMD------------RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDD   70 (620)
T ss_pred             cHHHHHHHCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCc
Confidence            456778899999999999999999999987642            34567999999999999999999999976321   


Q ss_pred             --------E-Eecc---------chhc--cccC---hHHHHHHHHHHHh----hhCCCEEEEEcccccccCCcCCCCCcc
Q 022768           96 --------K-VVSS---------AIID--KYIG---ESARLIREMFGYA----RDHQPCIIFMDEIDAIGGRRFSEGTSA  148 (292)
Q Consensus        96 --------~-~~~~---------~~~~--~~~~---~~~~~~~~~~~~~----~~~~~~il~lDe~d~l~~~~~~~~~~~  148 (292)
                              . +..+         ...+  .+.+   ...+.++.+....    ......|++|||+|.+           
T Consensus        71 ~~~~~~~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~L-----------  139 (620)
T PRK14954         71 PVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHML-----------  139 (620)
T ss_pred             cccccccCCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhc-----------
Confidence                    0 0000         0000  0011   1123444444333    2234579999999998           


Q ss_pred             hHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCH
Q 022768          149 DREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDY  227 (292)
Q Consensus       149 ~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~  227 (292)
                      ....+..|+..++.     +.+.+++|++++....+.+.+++  |+ ..+.|.+++.++....+...+...... .+...
T Consensus       140 t~~a~naLLK~LEe-----Pp~~tv~IL~t~~~~kLl~TI~S--Rc-~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal  211 (620)
T PRK14954        140 STAAFNAFLKTLEE-----PPPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPLDEIQSQLQMICRAEGIQIDADAL  211 (620)
T ss_pred             CHHHHHHHHHHHhC-----CCCCeEEEEEeCChhhhhHHHHh--hc-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            55555555555543     33467777777778888889988  66 789999999999888888776543322 22335


Q ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHHH-hcCCcccHHHHHHHH
Q 022768          228 EAVVKLAEGFNGADLRNVCTEAGMSAIR-AERDYVIHEDFMKAV  270 (292)
Q Consensus       228 ~~l~~~~~g~~~~di~~l~~~a~~~a~~-~~~~~i~~~~~~~a~  270 (292)
                      +.++..+.| +.+++...++....++.. .....|+.+++.+.+
T Consensus       212 ~~La~~s~G-dlr~al~eLeKL~~y~~~~~~~~~It~~~V~~lv  254 (620)
T PRK14954        212 QLIARKAQG-SMRDAQSILDQVIAFSVGSEAEKVIAYQGVAELL  254 (620)
T ss_pred             HHHHHHhCC-CHHHHHHHHHHHHHhccccccCCccCHHHHHHHH
Confidence            666677776 666777777666554421 124467777776654

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.77  E-value=5.8e-17  Score=152.11  Aligned_cols=199  Identities=19%  Similarity=0.241  Sum_probs=138.7

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE---
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL---   95 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~---   95 (292)
                      +.++...++|.+|++++|++++++.|..++..-            .-.+++||+||+|+|||++|+.+|+.+.+...   
T Consensus         3 ~~pl~~kyRP~~f~~liGq~~i~~~L~~~l~~~------------rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~   70 (620)
T PRK14948          3 YEPLHHKYRPQRFDELVGQEAIATTLKNALISN------------RIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKP   70 (620)
T ss_pred             cchHHHHhCCCcHhhccChHHHHHHHHHHHHcC------------CCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCC
Confidence            567788999999999999999999999988752            23567999999999999999999999876311   


Q ss_pred             ------EEecc---------ch--hccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHH
Q 022768           96 ------KVVSS---------AI--IDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQR  154 (292)
Q Consensus        96 ------~~~~~---------~~--~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~  154 (292)
                            .+..+         ++  .........+.+++++..+..    ....|++|||+|.|           ......
T Consensus        71 ~~~~Cg~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~L-----------t~~a~n  139 (620)
T PRK14948         71 TPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHML-----------STAAFN  139 (620)
T ss_pred             CCCCCcccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECcccc-----------CHHHHH
Confidence                  11000         00  000111234455666655543    34579999999999           555556


Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHH
Q 022768          155 TLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKL  233 (292)
Q Consensus       155 ~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~  233 (292)
                      .|+..++     .+...+++|+++++++.+.+.+++  |+ ..+.|+.++.++....+.+.+...... ....+..++..
T Consensus       140 aLLK~LE-----ePp~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~  211 (620)
T PRK14948        140 ALLKTLE-----EPPPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQR  211 (620)
T ss_pred             HHHHHHh-----cCCcCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            6655554     344577888888888888899998  77 778999999888888777776543222 12235666777


Q ss_pred             cCCCCHHHHHHHHHHH
Q 022768          234 AEGFNGADLRNVCTEA  249 (292)
Q Consensus       234 ~~g~~~~di~~l~~~a  249 (292)
                      +.| +.+++..+++..
T Consensus       212 s~G-~lr~A~~lLekl  226 (620)
T PRK14948        212 SQG-GLRDAESLLDQL  226 (620)
T ss_pred             cCC-CHHHHHHHHHHH
Confidence            776 566777666654

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.77  E-value=1.4e-17  Score=133.49  Aligned_cols=191  Identities=19%  Similarity=0.241  Sum_probs=139.1

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-C----CcEEEEe
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-D----ANFLKVV   98 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-~----~~~~~~~   98 (292)
                      +.|+|+.+++++|+++.+++|.-....             ..-.+++|.||||+||||-+.++|+++ |    ..++++|
T Consensus        19 eKYrP~~l~dIVGNe~tv~rl~via~~-------------gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELN   85 (333)
T KOG0991|consen   19 EKYRPSVLQDIVGNEDTVERLSVIAKE-------------GNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELN   85 (333)
T ss_pred             HhhCchHHHHhhCCHHHHHHHHHHHHc-------------CCCCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhcc
Confidence            478999999999999999999887654             234579999999999999999999987 3    2456777


Q ss_pred             ccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           99 SSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      .++-.+-   +..+.....|..-+.    ....|++|||+|.+           ....|.++...++...     ....+
T Consensus        86 ASdeRGI---DvVRn~IK~FAQ~kv~lp~grhKIiILDEADSM-----------T~gAQQAlRRtMEiyS-----~ttRF  146 (333)
T KOG0991|consen   86 ASDERGI---DVVRNKIKMFAQKKVTLPPGRHKIIILDEADSM-----------TAGAQQALRRTMEIYS-----NTTRF  146 (333)
T ss_pred             Ccccccc---HHHHHHHHHHHHhhccCCCCceeEEEeeccchh-----------hhHHHHHHHHHHHHHc-----ccchh
Confidence            6664432   223333344554443    33479999999999           7778888888777654     35568


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      ..+||..+++-+++.+  || ..+++...+..+...-+........+. .+..++.+...++|    |+++.++......
T Consensus       147 alaCN~s~KIiEPIQS--RC-AiLRysklsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiifta~G----DMRQalNnLQst~  219 (333)
T KOG0991|consen  147 ALACNQSEKIIEPIQS--RC-AILRYSKLSDQQILKRLLEVAKAEKVNYTDDGLEAIIFTAQG----DMRQALNNLQSTV  219 (333)
T ss_pred             hhhhcchhhhhhhHHh--hh-HhhhhcccCHHHHHHHHHHHHHHhCCCCCcchHHHhhhhccc----hHHHHHHHHHHHh
Confidence            8899999999999999  77 556777777776655444444433333 34456777777777    9999998876544

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.77  E-value=7.3e-17  Score=134.80  Aligned_cols=202  Identities=16%  Similarity=0.191  Sum_probs=137.2

Q ss_pred             CCCCcccccc--ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           26 PGNVSYSAVG--GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        26 ~~~~~~~~l~--g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      .++.+|++++  +.+.+...+..+...            .....+++|+||+|+|||++++++++..   +.+++++++.
T Consensus        12 ~~~~~~d~f~~~~~~~~~~~l~~~~~~------------~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~   79 (227)
T PRK08903         12 PPPPTFDNFVAGENAELVARLRELAAG------------PVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAA   79 (227)
T ss_pred             CChhhhcccccCCcHHHHHHHHHHHhc------------cCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehH
Confidence            3557899977  345566666665432            2446789999999999999999999876   5577777765


Q ss_pred             chhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          101 AIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      .....            +.  ......+|+|||+|.+           +...+..+..+++....   .+..++|++++.
T Consensus        80 ~~~~~------------~~--~~~~~~~liiDdi~~l-----------~~~~~~~L~~~~~~~~~---~~~~~vl~~~~~  131 (227)
T PRK08903         80 SPLLA------------FD--FDPEAELYAVDDVERL-----------DDAQQIALFNLFNRVRA---HGQGALLVAGPA  131 (227)
T ss_pred             HhHHH------------Hh--hcccCCEEEEeChhhc-----------CchHHHHHHHHHHHHHH---cCCcEEEEeCCC
Confidence            54211            11  1223479999999988           44556677777766542   234345555543


Q ss_pred             CC---CCChhhcCCCCc--ceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Q 022768          181 PD---VLDPALLRPGRL--DRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       181 ~~---~l~~~l~~~~r~--~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~  254 (292)
                      +.   .+.+.+.+  |+  ...+.+++|+.+++..+++......... .+..+..|+....| +.+++..+++....+|.
T Consensus       132 ~~~~~~l~~~L~s--r~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~~g-n~~~l~~~l~~l~~~~~  208 (227)
T PRK08903        132 APLALPLREDLRT--RLGWGLVYELKPLSDADKIAALKAAAAERGLQLADEVPDYLLTHFRR-DMPSLMALLDALDRYSL  208 (227)
T ss_pred             CHHhCCCCHHHHH--HHhcCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccC-CHHHHHHHHHHHHHHHH
Confidence            22   24567776  55  5789999999998888888776543332 22234556665555 88888889998777665


Q ss_pred             HhcCCcccHHHHHHHHH
Q 022768          255 RAERDYVIHEDFMKAVR  271 (292)
Q Consensus       255 ~~~~~~i~~~~~~~a~~  271 (292)
                      ..+ ..||...+.+++.
T Consensus       209 ~~~-~~i~~~~~~~~l~  224 (227)
T PRK08903        209 EQK-RPVTLPLLREMLA  224 (227)
T ss_pred             HhC-CCCCHHHHHHHHh
Confidence            555 5799999999875

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.77  E-value=1e-16  Score=134.23  Aligned_cols=210  Identities=13%  Similarity=0.175  Sum_probs=136.7

Q ss_pred             CCCCCcccccc--ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEec
Q 022768           25 DPGNVSYSAVG--GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID---ANFLKVVS   99 (292)
Q Consensus        25 ~~~~~~~~~l~--g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~   99 (292)
                      .++..+|++.+  ++..++..+..+...             ....+++|+||+|+||||+++++++.+.   ..+.++..
T Consensus        15 ~~~~~~fd~f~~~~n~~a~~~l~~~~~~-------------~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~   81 (235)
T PRK08084         15 LPDDETFASFYPGDNDSLLAALQNALRQ-------------EHSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPL   81 (235)
T ss_pred             CCCcCCccccccCccHHHHHHHHHHHhC-------------CCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEH
Confidence            44556788876  456667777666533             2345799999999999999999998763   34555554


Q ss_pred             cchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          100 SAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      ......        ..........  ..+|+|||++.+.+         +...+..+..+++...+   .+++.+|+|++
T Consensus        82 ~~~~~~--------~~~~~~~~~~--~dlliiDdi~~~~~---------~~~~~~~lf~l~n~~~e---~g~~~li~ts~  139 (235)
T PRK08084         82 DKRAWF--------VPEVLEGMEQ--LSLVCIDNIECIAG---------DELWEMAIFDLYNRILE---SGRTRLLITGD  139 (235)
T ss_pred             HHHhhh--------hHHHHHHhhh--CCEEEEeChhhhcC---------CHHHHHHHHHHHHHHHH---cCCCeEEEeCC
Confidence            332111        1122222222  25899999998832         34566777777776542   23444666665


Q ss_pred             C-CCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Q 022768          180 R-PDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       180 ~-~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~  254 (292)
                      . +..   +.++++++...+.++.+.+|+.+++.++++..+...... .+-..+.|+....| +.+.+..+++.....+.
T Consensus       140 ~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~-d~r~l~~~l~~l~~~~l  218 (235)
T PRK08084        140 RPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDR-EMRTLFMTLDQLDRASI  218 (235)
T ss_pred             CChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcC-CHHHHHHHHHHHHHHHH
Confidence            4 443   578999944445899999999999999998866543322 22224556666665 78888888888654444


Q ss_pred             HhcCCcccHHHHHHHHH
Q 022768          255 RAERDYVIHEDFMKAVR  271 (292)
Q Consensus       255 ~~~~~~i~~~~~~~a~~  271 (292)
                      ..+ ..||.+.+++++.
T Consensus       219 ~~~-~~it~~~~k~~l~  234 (235)
T PRK08084        219 TAQ-RKLTIPFVKEILK  234 (235)
T ss_pred             hcC-CCCCHHHHHHHHc
Confidence            444 4599999988764

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.77  E-value=5.7e-17  Score=142.33  Aligned_cols=212  Identities=22%  Similarity=0.239  Sum_probs=138.8

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cEEE
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NFLK   96 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~~~   96 (292)
                      ..+.+.|.+|++++|.+++++.+..++...             ...+++|+||+|+|||++++.+++.+..     .++.
T Consensus         7 w~~kyrP~~~~~~~g~~~~~~~l~~~i~~~-------------~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~   73 (319)
T PRK00440          7 WVEKYRPRTLDEIVGQEEIVERLKSYVKEK-------------NMPHLLFAGPPGTGKTTAALALARELYGEDWRENFLE   73 (319)
T ss_pred             cchhhCCCcHHHhcCcHHHHHHHHHHHhCC-------------CCCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEE
Confidence            457889999999999999999999987642             2336899999999999999999998733     3444


Q ss_pred             EeccchhccccChHHHHHHHHHHHh-hh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           97 VVSSAIIDKYIGESARLIREMFGYA-RD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      ++......  .......+....... .. ..+.+|+|||+|.+           ....+..|..+++..     ...+.+
T Consensus        74 ~~~~~~~~--~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l-----------~~~~~~~L~~~le~~-----~~~~~l  135 (319)
T PRK00440         74 LNASDERG--IDVIRNKIKEFARTAPVGGAPFKIIFLDEADNL-----------TSDAQQALRRTMEMY-----SQNTRF  135 (319)
T ss_pred             eccccccc--hHHHHHHHHHHHhcCCCCCCCceEEEEeCcccC-----------CHHHHHHHHHHHhcC-----CCCCeE
Confidence            43322111  001111222221111 11 23579999999998           455555666655432     234667


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      |++++.+..+.+.+++  |+ ..+.|++++.++...+++.++...... .+..+..++..+.| +.+.+...++.+.   
T Consensus       136 Il~~~~~~~l~~~l~s--r~-~~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~g-d~r~~~~~l~~~~---  208 (319)
T PRK00440        136 ILSCNYSSKIIDPIQS--RC-AVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEG-DMRKAINALQAAA---  208 (319)
T ss_pred             EEEeCCccccchhHHH--Hh-heeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH---
Confidence            7788888888888887  76 468999999999999999888754432 22235556666655 4444444444333   


Q ss_pred             HHhcCCcccHHHHHHHHHHH
Q 022768          254 IRAERDYVIHEDFMKAVRKL  273 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a~~~~  273 (292)
                      ..  ...||.+++.+++...
T Consensus       209 ~~--~~~it~~~v~~~~~~~  226 (319)
T PRK00440        209 AT--GKEVTEEAVYKITGTA  226 (319)
T ss_pred             Hc--CCCCCHHHHHHHhCCC
Confidence            22  3568888888776543

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.76  E-value=5.8e-17  Score=152.31  Aligned_cols=215  Identities=18%  Similarity=0.216  Sum_probs=143.2

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE----
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL----   95 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~----   95 (292)
                      +.+.+.++|.+|++|+|++++++.|..++..-            ..++.+||+||+|+|||++++.+++.+.+...    
T Consensus         4 ~~l~~kyRP~~~~eiiGq~~~~~~L~~~i~~~------------~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~   71 (585)
T PRK14950          4 QVLYRKWRSQTFAELVGQEHVVQTLRNAIAEG------------RVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKG   71 (585)
T ss_pred             HHHHHHhCCCCHHHhcCCHHHHHHHHHHHHhC------------CCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC
Confidence            44567899999999999999999999988652            33566899999999999999999998864221    


Q ss_pred             -EEeccc------------hh--ccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHH
Q 022768           96 -KVVSSA------------II--DKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL  156 (292)
Q Consensus        96 -~~~~~~------------~~--~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l  156 (292)
                       .++.+.            +.  +.......+.++.+...+..    ....|++|||+|.|           .......|
T Consensus        72 ~~c~~c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L-----------~~~a~naL  140 (585)
T PRK14950         72 RPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHML-----------STAAFNAL  140 (585)
T ss_pred             CCCccCHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhC-----------CHHHHHHH
Confidence             000000            00  00001122334444433322    34579999999998           55555555


Q ss_pred             HHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcC
Q 022768          157 MELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAE  235 (292)
Q Consensus       157 ~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~  235 (292)
                      +..++.     +...+++|++++..+.+.+.+++  |+ ..+.|..++..+....+...+...... ....+..++..+.
T Consensus       141 Lk~LEe-----pp~~tv~Il~t~~~~kll~tI~S--R~-~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~  212 (585)
T PRK14950        141 LKTLEE-----PPPHAIFILATTEVHKVPATILS--RC-QRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAAT  212 (585)
T ss_pred             HHHHhc-----CCCCeEEEEEeCChhhhhHHHHh--cc-ceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            554443     33567777788878888888888  66 678999999999998888877654332 1223456667777


Q ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          236 GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       236 g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      | +.+++.+.++....+    ....|+.+++.+.+
T Consensus       213 G-dlr~al~~LekL~~y----~~~~It~e~V~~ll  242 (585)
T PRK14950        213 G-SMRDAENLLQQLATT----YGGEISLSQVQSLL  242 (585)
T ss_pred             C-CHHHHHHHHHHHHHh----cCCCCCHHHHHHHh
Confidence            6 777777777765432    23458887776543

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.76  E-value=9.3e-17  Score=155.97  Aligned_cols=224  Identities=22%  Similarity=0.310  Sum_probs=156.9

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC----------
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID----------   91 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~----------   91 (292)
                      +.....+-+++.++|+++.++++...+..             ....+++|+||||+|||++++.+|+.+.          
T Consensus       177 L~~~~r~~~ld~~iGr~~ei~~~i~~l~r-------------~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~  243 (852)
T TIGR03345       177 LTAQAREGKIDPVLGRDDEIRQMIDILLR-------------RRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRN  243 (852)
T ss_pred             HHHHhcCCCCCcccCCHHHHHHHHHHHhc-------------CCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccC
Confidence            33455778899999999998888887654             2345799999999999999999999862          


Q ss_pred             CcEEEEeccchh--ccccChHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           92 ANFLKVVSSAII--DKYIGESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        92 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                      ..++.++...+.  ..+.|+.+..++.++..+.. ..+.||||||+|.+.+..+...   .......|...+       .
T Consensus       244 ~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~---~~d~~n~Lkp~l-------~  313 (852)
T TIGR03345       244 VRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAG---QGDAANLLKPAL-------A  313 (852)
T ss_pred             CeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccc---cccHHHHhhHHh-------h
Confidence            346666666654  35678888999999998865 3578999999999976442211   111122233333       2


Q ss_pred             CCCeEEEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-----CCCCHHHHHHHcCCC-
Q 022768          169 LGKVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-----GEIDYEAVVKLAEGF-  237 (292)
Q Consensus       169 ~~~~~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-----~~~~~~~l~~~~~g~-  237 (292)
                      .+.+.+|++|+..+     .+++++.+  || ..|.++.|+.+++..|++.....+...     .+..+..++..+.+| 
T Consensus       314 ~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf-~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi  390 (852)
T TIGR03345       314 RGELRTIAATTWAEYKKYFEKDPALTR--RF-QVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYI  390 (852)
T ss_pred             CCCeEEEEecCHHHHhhhhhccHHHHH--hC-eEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHccccc
Confidence            36788999998642     47899999  99 689999999999999987665543221     223355666777766 


Q ss_pred             ----CHHHHHHHHHHHHHHHHHh-cCCcccHHHHHHHHH
Q 022768          238 ----NGADLRNVCTEAGMSAIRA-ERDYVIHEDFMKAVR  271 (292)
Q Consensus       238 ----~~~di~~l~~~a~~~a~~~-~~~~i~~~~~~~a~~  271 (292)
                          -|.....++++|+...... ....+..+++.+.+.
T Consensus       391 ~~r~LPDKAIdlldea~a~~~~~~~~~p~~~~~~~~~~~  429 (852)
T TIGR03345       391 PGRQLPDKAVSLLDTACARVALSQNATPAALEDLRRRIA  429 (852)
T ss_pred             ccccCccHHHHHHHHHHHHHHHhccCCchhHHHHHHHHH
Confidence                4677788899887766543 333444455554443

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=99.75  E-value=9e-17  Score=131.62  Aligned_cols=196  Identities=20%  Similarity=0.292  Sum_probs=135.4

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      ..+.++.+++|+|++.+++.|.+....++.+         .+..++||+|++|||||+++|++..+.   |..++++...
T Consensus        19 ~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G---------~pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~   89 (249)
T PF05673_consen   19 KHPDPIRLDDLIGIERQKEALIENTEQFLQG---------LPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKE   89 (249)
T ss_pred             CCCCCCCHHHhcCHHHHHHHHHHHHHHHHcC---------CCCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHH
Confidence            3567899999999999999999999887655         568899999999999999999999987   4456666554


Q ss_pred             chhccccChHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          101 AIIDKYIGESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      .+..         +..+++..+. ..+=|||+||+.          .+........|..+|+-.-+ ..+.++++.+|+|
T Consensus        90 ~L~~---------l~~l~~~l~~~~~kFIlf~DDLs----------Fe~~d~~yk~LKs~LeGgle-~~P~NvliyATSN  149 (249)
T PF05673_consen   90 DLGD---------LPELLDLLRDRPYKFILFCDDLS----------FEEGDTEYKALKSVLEGGLE-ARPDNVLIYATSN  149 (249)
T ss_pred             Hhcc---------HHHHHHHHhcCCCCEEEEecCCC----------CCCCcHHHHHHHHHhcCccc-cCCCcEEEEEecc
Confidence            4422         2344444432 234699999863          12233444666666654322 4456899999999


Q ss_pred             CCCCCChhhcC---------------------CCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCC---CHHH--HHHH
Q 022768          180 RPDVLDPALLR---------------------PGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI---DYEA--VVKL  233 (292)
Q Consensus       180 ~~~~l~~~l~~---------------------~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~---~~~~--l~~~  233 (292)
                      ..+.++.....                     ..||+..+.|.+|+.++..+|++.++....+.-+.   ..+.  .+..
T Consensus       150 RRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~  229 (249)
T PF05673_consen  150 RRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELRQEALQWALR  229 (249)
T ss_pred             hhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence            76543332111                     13999999999999999999999999755443221   1111  2233


Q ss_pred             cCCCCHHHHHHHHHH
Q 022768          234 AEGFNGADLRNVCTE  248 (292)
Q Consensus       234 ~~g~~~~di~~l~~~  248 (292)
                      -.|.|++-..+.+..
T Consensus       230 rg~RSGRtA~QF~~~  244 (249)
T PF05673_consen  230 RGGRSGRTARQFIDD  244 (249)
T ss_pred             cCCCCHHHHHHHHHH
Confidence            456788877777764

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.75  E-value=6.4e-17  Score=146.94  Aligned_cols=223  Identities=16%  Similarity=0.204  Sum_probs=142.0

Q ss_pred             CCCCcccccc-ccHH--HHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEEEE
Q 022768           26 PGNVSYSAVG-GLSD--QIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFLKV   97 (292)
Q Consensus        26 ~~~~~~~~l~-g~~~--~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~~   97 (292)
                      .|..+|++.+ |...  +...+..+...+            ....+++|+||+|+|||||++++++++     +..++++
T Consensus        99 ~~~~tFdnFv~g~~n~~a~~~~~~~~~~~------------~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi  166 (440)
T PRK14088         99 NPDYTFENFVVGPGNSFAYHAALEVAKNP------------GRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYI  166 (440)
T ss_pred             CCCCcccccccCCchHHHHHHHHHHHhCc------------CCCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEE
Confidence            3668899876 5433  233444433221            123469999999999999999999986     3467888


Q ss_pred             eccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEE
Q 022768           98 VSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMA  177 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t  177 (292)
                      ++..+...........-..-|.......+.+|+|||++.+.+         ....+..+..+++.+..   .+..+++++
T Consensus       167 ~~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~---------~~~~q~elf~~~n~l~~---~~k~iIits  234 (440)
T PRK14088        167 TSEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIG---------KTGVQTELFHTFNELHD---SGKQIVICS  234 (440)
T ss_pred             EHHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcC---------cHHHHHHHHHHHHHHHH---cCCeEEEEC
Confidence            876655433221111001122222223468999999998743         22344556666665542   123444444


Q ss_pred             eCCCCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          178 TNRPDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       178 ~~~~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      .+.|..   +.+++.++...+..+.+.+|+.+.|..|++..+...... .+..++.++....| +.+++..++.....++
T Consensus       235 d~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~-~~R~L~g~l~~l~~~~  313 (440)
T PRK14088        235 DREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDD-NLRRLRGAIIKLLVYK  313 (440)
T ss_pred             CCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhcccc-CHHHHHHHHHHHHHHH
Confidence            455554   456788833345688999999999999999888643322 11224455555555 7889999999888877


Q ss_pred             HHhcCCcccHHHHHHHHHHHh
Q 022768          254 IRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ...++ .+|.+.+.++++.+.
T Consensus       314 ~~~~~-~it~~~a~~~L~~~~  333 (440)
T PRK14088        314 ETTGE-EVDLKEAILLLKDFI  333 (440)
T ss_pred             HHhCC-CCCHHHHHHHHHHHh
Confidence            66665 599999999998874

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.75  E-value=1.3e-16  Score=133.15  Aligned_cols=205  Identities=19%  Similarity=0.297  Sum_probs=137.9

Q ss_pred             CCCCcccccc--ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           26 PGNVSYSAVG--GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        26 ~~~~~~~~l~--g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      +.+.+|++.+  +....++.+.+++..             ..+.+++|+||+|||||++++++++.+   +.+++++++.
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~l~~~~~~-------------~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~   75 (226)
T TIGR03420         9 PDDPTFDNFYAGGNAELLAALRQLAAG-------------KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLA   75 (226)
T ss_pred             CCchhhcCcCcCCcHHHHHHHHHHHhc-------------CCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHH
Confidence            3446778876  356677888777532             346789999999999999999999876   4577888877


Q ss_pred             chhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          101 AIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      .+....        ...+...  ..+.+|+|||+|.+..         ....+..+..+++.....   +. .+|+|++.
T Consensus        76 ~~~~~~--------~~~~~~~--~~~~lLvIDdi~~l~~---------~~~~~~~L~~~l~~~~~~---~~-~iIits~~  132 (226)
T TIGR03420        76 ELAQAD--------PEVLEGL--EQADLVCLDDVEAIAG---------QPEWQEALFHLYNRVREA---GG-RLLIAGRA  132 (226)
T ss_pred             HHHHhH--------HHHHhhc--ccCCEEEEeChhhhcC---------ChHHHHHHHHHHHHHHHc---CC-eEEEECCC
Confidence            764321        1222222  2236999999998821         123356677777654321   22 45566654


Q ss_pred             -CCCCC---hhhcCCCCc--ceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          181 -PDVLD---PALLRPGRL--DRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       181 -~~~l~---~~l~~~~r~--~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                       +..+.   +.+.+  |+  ...+.+++|+.+++..+++.+....... .+..+..|+....| ++++++.+++.+...+
T Consensus       133 ~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~~~g-n~r~L~~~l~~~~~~~  209 (226)
T TIGR03420       133 APAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSR-DMGSLMALLDALDRAS  209 (226)
T ss_pred             ChHHCCcccHHHHH--HHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccC-CHHHHHHHHHHHHHHH
Confidence             33322   56666  54  4789999999999999998876543322 22234556665554 8999999999998877


Q ss_pred             HHhcCCcccHHHHHHHH
Q 022768          254 IRAERDYVIHEDFMKAV  270 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a~  270 (292)
                      ...+. .|+.+.+.+.+
T Consensus       210 ~~~~~-~i~~~~~~~~~  225 (226)
T TIGR03420       210 LAAKR-KITIPFVKEVL  225 (226)
T ss_pred             HHhCC-CCCHHHHHHHh
Confidence            66554 69999888765

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.75  E-value=1.2e-16  Score=139.05  Aligned_cols=225  Identities=18%  Similarity=0.248  Sum_probs=144.8

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-------cE--EEE
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-------NF--LKV   97 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-------~~--~~~   97 (292)
                      .+++|++++|++++++.+.-++..+             ...++||.|+||+|||++++++++.++.       ++  ..+
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~~~-------------~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~   69 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAIDP-------------GIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARP   69 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHhcc-------------CCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcc
Confidence            5788999999999999988765322             1368999999999999999999999842       11  100


Q ss_pred             ecc---------chhc---------------cccChH--HHHHH-H--HHH--HhhhCCCEEEEEcccccccCCcCCCCC
Q 022768           98 VSS---------AIID---------------KYIGES--ARLIR-E--MFG--YARDHQPCIIFMDEIDAIGGRRFSEGT  146 (292)
Q Consensus        98 ~~~---------~~~~---------------~~~~~~--~~~~~-~--~~~--~~~~~~~~il~lDe~d~l~~~~~~~~~  146 (292)
                      ...         .+..               ...|..  ...+. .  .+.  .......++|++||++.+         
T Consensus        70 ~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl---------  140 (334)
T PRK13407         70 EDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLL---------  140 (334)
T ss_pred             cCCcccccccCCcccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhC---------
Confidence            000         0000               011110  00000 0  010  001133479999999999         


Q ss_pred             cchHHHHHHHHHHHHHhh------C--CCCCCCeEEEEEeCCCC-CCChhhcCCCCcceEEEccCCCH-HHHHHHHHHHH
Q 022768          147 SADREIQRTLMELLNQLD------G--FDQLGKVKMIMATNRPD-VLDPALLRPGRLDRKIEIPLPNE-QSRMEILKIHA  216 (292)
Q Consensus       147 ~~~~~~~~~l~~~l~~~~------~--~~~~~~~~vi~t~~~~~-~l~~~l~~~~r~~~~i~l~~p~~-~~r~~i~~~~~  216 (292)
                        +...+..|.+.+....      +  .....++++++|.|..+ .+++.+.+  ||...+.+++|.. +++.++++...
T Consensus       141 --~~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~~~e~~~il~~~~  216 (334)
T PRK13407        141 --EDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRDVETRVEVIRRRD  216 (334)
T ss_pred             --CHHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHhh
Confidence              8889999998887532      0  11234788888888644 58889998  9999999988866 88899988754


Q ss_pred             cCcc----C------CCCCCHHH-----------------------HHHHcC-CCCHHHHHHHHHHHHHHHHHhcCCccc
Q 022768          217 AGIA----K------HGEIDYEA-----------------------VVKLAE-GFNGADLRNVCTEAGMSAIRAERDYVI  262 (292)
Q Consensus       217 ~~~~----~------~~~~~~~~-----------------------l~~~~~-g~~~~di~~l~~~a~~~a~~~~~~~i~  262 (292)
                      ....    .      ......+.                       ++..+. ....+++. +++.|..+|..+++..|+
T Consensus       217 ~~~~~~~~~~~~~~~~~~~~~~~i~~a~~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~-l~~aA~a~A~l~Gr~~V~  295 (334)
T PRK13407        217 AYDADHDAFMAKWGAEDMQLRGRILGARARLPQLKTPNTVLHDCAALCIALGSDGLRGELT-LLRAARALAAFEGAEAVG  295 (334)
T ss_pred             cccccchhhhccccccccCCHHHHHHHHHhcCCcccCHHHHHHHHHHHHHHCCCCchHHHH-HHHHHHHHHHHcCCCeeC
Confidence            2110    0      00111111                       112222 12445555 999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhh
Q 022768          263 HEDFMKAVRKLNEAKK  278 (292)
Q Consensus       263 ~~~~~~a~~~~~~~~~  278 (292)
                      .+|+.++..-+-.+..
T Consensus       296 ~~Di~~~~~~vl~hR~  311 (334)
T PRK13407        296 RSHLRSVATMALSHRL  311 (334)
T ss_pred             HHHHHHHHHHhhhhhc
Confidence            9999988876665443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.75  E-value=2.4e-16  Score=145.46  Aligned_cols=193  Identities=19%  Similarity=0.214  Sum_probs=133.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc-----CCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI-----DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR  141 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~  141 (292)
                      ..++|+|++|+|||||++++++++     +..++++.+.++...+...........|... .....+|+|||++.+..  
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~-y~~~DLLlIDDIq~l~g--  391 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRR-YREMDILLVDDIQFLED--  391 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHH-hhcCCEEEEehhccccC--
Confidence            359999999999999999999976     4577888887766544332222111223222 23458999999998853  


Q ss_pred             CCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC-C---CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          142 FSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP-D---VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       142 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~-~---~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                             ....+..++++++.+...   ++ .+|+|++.+ .   .+.+.|+++..++.++.+..|+.+.|..|++..+.
T Consensus       392 -------ke~tqeeLF~l~N~l~e~---gk-~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka~  460 (617)
T PRK14086        392 -------KESTQEEFFHTFNTLHNA---NK-QIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKAV  460 (617)
T ss_pred             -------CHHHHHHHHHHHHHHHhc---CC-CEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHHH
Confidence                   344567777888776532   22 355566653 3   46788999544577889999999999999999887


Q ss_pred             CccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          218 GIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       218 ~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      ...+. .+--++.|+....+ +.+.+..++.....++...++ .|+.+.+.++++.+..
T Consensus       461 ~r~l~l~~eVi~yLa~r~~r-nvR~LegaL~rL~a~a~~~~~-~itl~la~~vL~~~~~  517 (617)
T PRK14086        461 QEQLNAPPEVLEFIASRISR-NIRELEGALIRVTAFASLNRQ-PVDLGLTEIVLRDLIP  517 (617)
T ss_pred             hcCCCCCHHHHHHHHHhccC-CHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHHhhc
Confidence            65433 11123445555543 788999999988887766654 5999999999987754

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.74  E-value=1.5e-16  Score=141.84  Aligned_cols=184  Identities=17%  Similarity=0.276  Sum_probs=123.4

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE---------------
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF---------------   94 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~---------------   94 (292)
                      .|++|+|++++++.|.+.+.....   .+..++...++.+||+||+|+|||++|+.+|+.+.+..               
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~---~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~   79 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARA---DVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTV   79 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccc---cccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHH
Confidence            589999999999999999976421   11122233567899999999999999999999875531               


Q ss_pred             --------EEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           95 --------LKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        95 --------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                              ..+....   .  ......++.++..+..    ....|++|||+|.+           +...+..|+..+++
T Consensus        80 ~~~~hpD~~~i~~~~---~--~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m-----------~~~aanaLLk~LEe  143 (394)
T PRK07940         80 LAGTHPDVRVVAPEG---L--SIGVDEVRELVTIAARRPSTGRWRIVVIEDADRL-----------TERAANALLKAVEE  143 (394)
T ss_pred             hcCCCCCEEEecccc---c--cCCHHHHHHHHHHHHhCcccCCcEEEEEechhhc-----------CHHHHHHHHHHhhc
Confidence                    1111100   0  1123335566555543    34579999999999           66666666666643


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di  242 (292)
                           +.+++++|.+|++++.+.+.++|  |+ ..+.|++|+.++..+.+....   ... ......++..+.|. ++..
T Consensus       144 -----p~~~~~fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~~~i~~~L~~~~---~~~-~~~a~~la~~s~G~-~~~A  210 (394)
T PRK07940        144 -----PPPRTVWLLCAPSPEDVLPTIRS--RC-RHVALRTPSVEAVAEVLVRRD---GVD-PETARRAARASQGH-IGRA  210 (394)
T ss_pred             -----CCCCCeEEEEECChHHChHHHHh--hC-eEEECCCCCHHHHHHHHHHhc---CCC-HHHHHHHHHHcCCC-HHHH
Confidence                 33456677777778999999999  77 789999999998887776322   121 12245677788874 4444


Q ss_pred             HHH
Q 022768          243 RNV  245 (292)
Q Consensus       243 ~~l  245 (292)
                      ..+
T Consensus       211 ~~l  213 (394)
T PRK07940        211 RRL  213 (394)
T ss_pred             HHH
Confidence            333

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.73  E-value=5.6e-16  Score=131.48  Aligned_cols=145  Identities=24%  Similarity=0.250  Sum_probs=111.2

Q ss_pred             CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC------------CCCCChhhcCCC
Q 022768          125 QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR------------PDVLDPALLRPG  192 (292)
Q Consensus       125 ~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~------------~~~l~~~l~~~~  192 (292)
                      -|+||||||+|.|           +-++-..|...+..     . -..++|.++|.            |+.++.++++  
T Consensus       291 VpGVLFIDEvHmL-----------DIE~FsFlnrAlEs-----e-~aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLD--  351 (450)
T COG1224         291 VPGVLFIDEVHML-----------DIECFSFLNRALES-----E-LAPIIILATNRGMTKIRGTDIESPHGIPLDLLD--  351 (450)
T ss_pred             ecceEEEechhhh-----------hHHHHHHHHHHhhc-----c-cCcEEEEEcCCceeeecccCCcCCCCCCHhhhh--
Confidence            4789999999999           66666666666543     1 23456666653            5678889998  


Q ss_pred             CcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       193 r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      |+ ..|...+++.++.+.|++.++....+. .+-.++.|+.+...-|.+...+|+..|...|.+++...|..+|+.+|..
T Consensus       352 Rl-lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~  430 (450)
T COG1224         352 RL-LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE  430 (450)
T ss_pred             he-eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence            77 778889999999999999988765444 3344677777777778999999999999999999999999999999999


Q ss_pred             HHhh-hhhhchhhhhhhhc
Q 022768          272 KLNE-AKKLESSAHYNADF  289 (292)
Q Consensus       272 ~~~~-~~~~~~~~~~~~~~  289 (292)
                      -+.. +.+-+....|+++|
T Consensus       431 lF~D~krSv~~v~~~~~~~  449 (450)
T COG1224         431 LFLDVKRSVEYVEKYEGLL  449 (450)
T ss_pred             HHhhHHHHHHHHHHHHhhc
Confidence            8876 34444455666544

>PRK08727 hypothetical protein; Validated

Probab=99.73  E-value=1e-15  Score=128.11  Aligned_cols=207  Identities=20%  Similarity=0.289  Sum_probs=129.4

Q ss_pred             CCCCccccccccHH-HHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           26 PGNVSYSAVGGLSD-QIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        26 ~~~~~~~~l~g~~~-~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      ++..+|++.++-.. ....+......             .....++|+||+|+||||++.++++.+   +..+.++...+
T Consensus        13 ~~~~~f~~f~~~~~n~~~~~~~~~~~-------------~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~   79 (233)
T PRK08727         13 PSDQRFDSYIAAPDGLLAQLQALAAG-------------QSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQA   79 (233)
T ss_pred             CCcCChhhccCCcHHHHHHHHHHHhc-------------cCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHH
Confidence            34568888665443 33333322211             123469999999999999999998765   44555665433


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC-
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR-  180 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~-  180 (292)
                      ..        ..+...+....  ...+|+|||++.+..         ....+..+.++++....    .+..+|+|++. 
T Consensus        80 ~~--------~~~~~~~~~l~--~~dlLiIDDi~~l~~---------~~~~~~~lf~l~n~~~~----~~~~vI~ts~~~  136 (233)
T PRK08727         80 AA--------GRLRDALEALE--GRSLVALDGLESIAG---------QREDEVALFDFHNRARA----AGITLLYTARQM  136 (233)
T ss_pred             hh--------hhHHHHHHHHh--cCCEEEEeCcccccC---------ChHHHHHHHHHHHHHHH----cCCeEEEECCCC
Confidence            22        12223333333  336999999998843         23345667777776542    23446666664 


Q ss_pred             CCC---CChhhcCCCCc--ceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Q 022768          181 PDV---LDPALLRPGRL--DRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       181 ~~~---l~~~l~~~~r~--~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~  254 (292)
                      +..   +.+++++  |+  ...+.+++|+.+++.++++.++...... .+..++.|+..+.| ..+.+..+++.....+.
T Consensus       137 p~~l~~~~~dL~S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~r-d~r~~l~~L~~l~~~~~  213 (233)
T PRK08727        137 PDGLALVLPDLRS--RLAQCIRIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTHGER-ELAGLVALLDRLDRESL  213 (233)
T ss_pred             hhhhhhhhHHHHH--HHhcCceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCC-CHHHHHHHHHHHHHHHH
Confidence            444   4688988  64  5788999999999999999876543322 11223445555554 45555555777766565


Q ss_pred             HhcCCcccHHHHHHHHHH
Q 022768          255 RAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       255 ~~~~~~i~~~~~~~a~~~  272 (292)
                      ..++ .||.+.+.+.+..
T Consensus       214 ~~~~-~it~~~~~~~l~~  230 (233)
T PRK08727        214 AAKR-RVTVPFLRRVLEE  230 (233)
T ss_pred             HhCC-CCCHHHHHHHHhh
Confidence            5544 6999999888754

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=99.73  E-value=1.1e-15  Score=134.89  Aligned_cols=227  Identities=20%  Similarity=0.299  Sum_probs=161.6

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----EEEEeccchh
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----FLKVVSSAII  103 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----~~~~~~~~~~  103 (292)
                      .--+.+.++++.++++..++...+.+         ..+.+++++|+||||||.+++.+++++...     ++++||....
T Consensus        14 ~iP~~l~~Re~ei~~l~~~l~~~~~~---------~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~   84 (366)
T COG1474          14 YIPEELPHREEEINQLASFLAPALRG---------ERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELR   84 (366)
T ss_pred             CCcccccccHHHHHHHHHHHHHHhcC---------CCCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCC
Confidence            33344999999999999998776544         445669999999999999999999988444     8999988765


Q ss_pred             cccc---------------C-hHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC
Q 022768          104 DKYI---------------G-ESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF  166 (292)
Q Consensus       104 ~~~~---------------~-~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~  166 (292)
                      +.+.               | ........++..... ...-||+|||+|.|..+.           ...|..++......
T Consensus        85 t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~-----------~~~LY~L~r~~~~~  153 (366)
T COG1474          85 TPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKD-----------GEVLYSLLRAPGEN  153 (366)
T ss_pred             CHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhcccc-----------chHHHHHHhhcccc
Confidence            4321               0 011222233333322 345799999999996432           16777777765543


Q ss_pred             CCCCCeEEEEEeCCCC---CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCH---HHH---HHHcCCC
Q 022768          167 DQLGKVKMIMATNRPD---VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDY---EAV---VKLAEGF  237 (292)
Q Consensus       167 ~~~~~~~vi~t~~~~~---~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~---~~l---~~~~~g~  237 (292)
                        ..++.+|+.+|...   .+++.+.++... ..|.|++++.+|..+|+..+.........++-   ...   +....| 
T Consensus       154 --~~~v~vi~i~n~~~~~~~ld~rv~s~l~~-~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~G-  229 (366)
T COG1474         154 --KVKVSIIAVSNDDKFLDYLDPRVKSSLGP-SEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESG-  229 (366)
T ss_pred             --ceeEEEEEEeccHHHHHHhhhhhhhccCc-ceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCc-
Confidence              45788999998863   578888884333 46899999999999999988875433333322   222   233334 


Q ss_pred             CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhh
Q 022768          238 NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKL  279 (292)
Q Consensus       238 ~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~  279 (292)
                      ..+-...+++.|...|.+++...++.+++.+|...+......
T Consensus       230 DAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~~~~~~  271 (366)
T COG1474         230 DARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIERDVLE  271 (366)
T ss_pred             cHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhhHHHHH
Confidence            566666999999999999999999999999997776655443

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.73  E-value=4e-16  Score=136.13  Aligned_cols=230  Identities=17%  Similarity=0.186  Sum_probs=155.4

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-------cE
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-------NF   94 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-------~~   94 (292)
                      .....+.++|++++|+++.+..|...+..|             ...+++|.|++|||||++++.+++.+..       +|
T Consensus         7 ~~~~~~~~pf~~ivGq~~~k~al~~~~~~p-------------~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf   73 (350)
T CHL00081          7 KKKERPVFPFTAIVGQEEMKLALILNVIDP-------------KIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPF   73 (350)
T ss_pred             hhccCCCCCHHHHhChHHHHHHHHHhccCC-------------CCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCC
Confidence            334566789999999999999999998775             2347999999999999999999877632       22


Q ss_pred             EEEecc-------chhcc-------------------ccChHHHH------HHHHHHHh---------hhCCCEEEEEcc
Q 022768           95 LKVVSS-------AIIDK-------------------YIGESARL------IREMFGYA---------RDHQPCIIFMDE  133 (292)
Q Consensus        95 ~~~~~~-------~~~~~-------------------~~~~~~~~------~~~~~~~~---------~~~~~~il~lDe  133 (292)
                      . ....       .....                   ..+.+...      +...+...         .....++|++||
T Consensus        74 ~-~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDE  152 (350)
T CHL00081         74 N-SHPSDPELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDE  152 (350)
T ss_pred             C-CCCCChhhhchhhhhhhcccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecC
Confidence            1 0000       00000                   00111111      11111111         123457999999


Q ss_pred             cccccCCcCCCCCcchHHHHHHHHHHHHHhh------C--CCCCCCeEEEEEeCCCC-CCChhhcCCCCcceEEEccCCC
Q 022768          134 IDAIGGRRFSEGTSADREIQRTLMELLNQLD------G--FDQLGKVKMIMATNRPD-VLDPALLRPGRLDRKIEIPLPN  204 (292)
Q Consensus       134 ~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~------~--~~~~~~~~vi~t~~~~~-~l~~~l~~~~r~~~~i~l~~p~  204 (292)
                      ++.+           +...+..|.+.+....      +  .....++++|+|.|..+ .+++.+.+  ||...+.+.+|+
T Consensus       153 InrL-----------~~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--Rf~l~i~l~~~~  219 (350)
T CHL00081        153 VNLL-----------DDHLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGMHAEIRTVK  219 (350)
T ss_pred             hHhC-----------CHHHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--HhCceeecCCCC
Confidence            9999           8888999988886521      1  11234677888777654 58899998  999999999997


Q ss_pred             -HHHHHHHHHHHHcCc--cC--------CCCCCH-----------------------HHHHHHcCCCCHHHHHHHHHHHH
Q 022768          205 -EQSRMEILKIHAAGI--AK--------HGEIDY-----------------------EAVVKLAEGFNGADLRNVCTEAG  250 (292)
Q Consensus       205 -~~~r~~i~~~~~~~~--~~--------~~~~~~-----------------------~~l~~~~~g~~~~di~~l~~~a~  250 (292)
                       .+.+.+|++......  ..        ......                       ..++..+..-++|--..+++.|.
T Consensus       220 ~~~~e~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~ar~~~~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raAr  299 (350)
T CHL00081        220 DPELRVKIVEQRTSFDKNPQEFREKYEESQEELRSKIVAAQNLLPKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAK  299 (350)
T ss_pred             ChHHHHHHHHhhhccccChhhhhhhhccccccCHHHHHHHHHhcCCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHH
Confidence             589999988753210  00        000111                       11222333346788889999999


Q ss_pred             HHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          251 MSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       251 ~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      .+|..+++..|+.+|+..+...+-.+..
T Consensus       300 A~Aal~GR~~V~pdDv~~~a~~vL~HR~  327 (350)
T CHL00081        300 ALAAFEGRTEVTPKDIFKVITLCLRHRL  327 (350)
T ss_pred             HHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence            9999999999999999999998887665

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.72  E-value=6.3e-16  Score=145.19  Aligned_cols=207  Identities=17%  Similarity=0.235  Sum_probs=142.6

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------   93 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------   93 (292)
                      ..+..++|.+|++++|++++++.|...+..-            ..++.+||+||+|+|||++++.+++.+.+.       
T Consensus         6 ~~~~kyRP~~f~~viGq~~~~~~L~~~i~~~------------~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~   73 (614)
T PRK14971          6 VSARKYRPSTFESVVGQEALTTTLKNAIATN------------KLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGE   73 (614)
T ss_pred             HHHHHHCCCCHHHhcCcHHHHHHHHHHHHcC------------CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCC
Confidence            4467889999999999999999999998652            345669999999999999999999988642       


Q ss_pred             ------------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHH
Q 022768           94 ------------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADRE  151 (292)
Q Consensus        94 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~  151 (292)
                                        ++.++...      ......++.+...+..    ....|++|||+|.+           ...
T Consensus        74 ~Cg~C~sC~~~~~~~~~n~~~ld~~~------~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~L-----------s~~  136 (614)
T PRK14971         74 ACNECESCVAFNEQRSYNIHELDAAS------NNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHML-----------SQA  136 (614)
T ss_pred             CCCcchHHHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhhCcccCCcEEEEEECcccC-----------CHH
Confidence                              11111110      0113344455444332    34579999999999           555


Q ss_pred             HHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC-CCHHHH
Q 022768          152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE-IDYEAV  230 (292)
Q Consensus       152 ~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~-~~~~~l  230 (292)
                      .+..|...++.     +...+++|++++....+.+.+++  |+ ..+.|.+++.++....++..+....+.-+ ..+..+
T Consensus       137 a~naLLK~LEe-----pp~~tifIL~tt~~~kIl~tI~S--Rc-~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~L  208 (614)
T PRK14971        137 AFNAFLKTLEE-----PPSYAIFILATTEKHKILPTILS--RC-QIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVI  208 (614)
T ss_pred             HHHHHHHHHhC-----CCCCeEEEEEeCCchhchHHHHh--hh-heeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            66666666553     33567788888888899999998  77 67999999999999888887765544322 235667


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      +..+.| +.+++...++.+..++   +.. |+.+++.+.
T Consensus       209 a~~s~g-dlr~al~~Lekl~~y~---~~~-It~~~V~~~  242 (614)
T PRK14971        209 AQKADG-GMRDALSIFDQVVSFT---GGN-ITYKSVIEN  242 (614)
T ss_pred             HHHcCC-CHHHHHHHHHHHHHhc---cCC-ccHHHHHHH
Confidence            777766 6666666666654433   211 555554443

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=99.71  E-value=2.8e-16  Score=129.97  Aligned_cols=200  Identities=21%  Similarity=0.283  Sum_probs=124.8

Q ss_pred             CCCcccccc-c--cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEEEEe
Q 022768           27 GNVSYSAVG-G--LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFLKVV   98 (292)
Q Consensus        27 ~~~~~~~l~-g--~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~~~   98 (292)
                      |..+|++.+ |  ++.+...++.....+           -.....++|+||+|+|||||++++++++     +..+++++
T Consensus         3 ~~~tFdnfv~g~~N~~a~~~~~~ia~~~-----------~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~   71 (219)
T PF00308_consen    3 PKYTFDNFVVGESNELAYAAAKAIAENP-----------GERYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLS   71 (219)
T ss_dssp             TT-SCCCS--TTTTHHHHHHHHHHHHST-----------TTSSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEE
T ss_pred             CCCccccCCcCCcHHHHHHHHHHHHhcC-----------CCCCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeec
Confidence            567899975 5  344555555554442           1123468999999999999999999875     55688888


Q ss_pred             ccchhccccChHHH-HHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEE
Q 022768           99 SSAIIDKYIGESAR-LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMA  177 (292)
Q Consensus        99 ~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t  177 (292)
                      ..++...+...... .+........  ...+|+|||+|.+.+         ....+..+..+++....   .++.+|+.+
T Consensus        72 ~~~f~~~~~~~~~~~~~~~~~~~~~--~~DlL~iDDi~~l~~---------~~~~q~~lf~l~n~~~~---~~k~li~ts  137 (219)
T PF00308_consen   72 AEEFIREFADALRDGEIEEFKDRLR--SADLLIIDDIQFLAG---------KQRTQEELFHLFNRLIE---SGKQLILTS  137 (219)
T ss_dssp             HHHHHHHHHHHHHTTSHHHHHHHHC--TSSEEEEETGGGGTT---------HHHHHHHHHHHHHHHHH---TTSEEEEEE
T ss_pred             HHHHHHHHHHHHHcccchhhhhhhh--cCCEEEEecchhhcC---------chHHHHHHHHHHHHHHh---hCCeEEEEe
Confidence            87776543322211 1122222222  347999999999843         45678888888887653   134444444


Q ss_pred             eCCCCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCH---HHHHHHcCCCCHHHHHHHHHHHHH
Q 022768          178 TNRPDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDY---EAVVKLAEGFNGADLRNVCTEAGM  251 (292)
Q Consensus       178 ~~~~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~---~~l~~~~~g~~~~di~~l~~~a~~  251 (292)
                      ...|..   +.+.+.++...+..+.+.+|+.+.|..+++.++......  ++.   +-|+....+ +.+++..+++....
T Consensus       138 ~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~--l~~~v~~~l~~~~~~-~~r~L~~~l~~l~~  214 (219)
T PF00308_consen  138 DRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKAKERGIE--LPEEVIEYLARRFRR-DVRELEGALNRLDA  214 (219)
T ss_dssp             SS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHHHHHTT----S-HHHHHHHHHHTTS-SHHHHHHHHHHHHH
T ss_pred             CCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHHHhCCC--CcHHHHHHHHHhhcC-CHHHHHHHHHHHHH
Confidence            444544   567888843456689999999999999999988765444  333   344455443 88889888888776


Q ss_pred             HHH
Q 022768          252 SAI  254 (292)
Q Consensus       252 ~a~  254 (292)
                      ++.
T Consensus       215 ~~~  217 (219)
T PF00308_consen  215 YAQ  217 (219)
T ss_dssp             HHH
T ss_pred             Hhh
Confidence            653

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.71  E-value=9.2e-16  Score=149.55  Aligned_cols=205  Identities=23%  Similarity=0.331  Sum_probs=149.7

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEE
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFL   95 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~   95 (292)
                      ...-.++.++|+++.++++.+.+..             ....+++|+||||+|||++++.+|..+          +.+++
T Consensus       173 a~~~~~~~~igr~~ei~~~~~~L~r-------------~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~  239 (821)
T CHL00095        173 AIDGNLDPVIGREKEIERVIQILGR-------------RTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVI  239 (821)
T ss_pred             HHcCCCCCCCCcHHHHHHHHHHHcc-------------cccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEE
Confidence            3445678999999999999998765             345689999999999999999999876          36788


Q ss_pred             EEeccchh--ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           96 KVVSSAII--DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        96 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      .++...+.  ..+.|+.+..++.++..+....+.||||||+|.+.+..+...   .......|...+.       .+.+.
T Consensus       240 ~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g---~~~~a~lLkp~l~-------rg~l~  309 (821)
T CHL00095        240 TLDIGLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEG---AIDAANILKPALA-------RGELQ  309 (821)
T ss_pred             EeeHHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCC---cccHHHHhHHHHh-------CCCcE
Confidence            88887765  456788899999999998887889999999999976543211   1223333443333       25788


Q ss_pred             EEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc----cCC-CCCCHHHHHHHcCCC-----C
Q 022768          174 MIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI----AKH-GEIDYEAVVKLAEGF-----N  238 (292)
Q Consensus       174 vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~----~~~-~~~~~~~l~~~~~g~-----~  238 (292)
                      +|++|+..+     ..++.+.+  || ..+.++.|+.++...|++.....+    ... .+-.+..+...+.+|     -
T Consensus       310 ~IgaTt~~ey~~~ie~D~aL~r--Rf-~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi~~r~l  386 (821)
T CHL00095        310 CIGATTLDEYRKHIEKDPALER--RF-QPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIADRFL  386 (821)
T ss_pred             EEEeCCHHHHHHHHhcCHHHHh--cc-eEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCccccC
Confidence            999988653     46788888  88 568999999999988887554321    111 122245556666665     4


Q ss_pred             HHHHHHHHHHHHHHHHHh
Q 022768          239 GADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~~  256 (292)
                      |.....++++|.......
T Consensus       387 Pdkaidlld~a~a~~~~~  404 (821)
T CHL00095        387 PDKAIDLLDEAGSRVRLI  404 (821)
T ss_pred             chHHHHHHHHHHHHHHhh
Confidence            667788889888766554

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.71  E-value=7.7e-16  Score=148.13  Aligned_cols=220  Identities=19%  Similarity=0.259  Sum_probs=142.1

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc--------
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID--------  104 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~--------  104 (292)
                      +++|++++|+++.+++.....       .+...+..++|+||||+|||++++.+|+.++.+++.++.....+        
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~-------~~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~  395 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSR-------VNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHR  395 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHh-------cccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccch
Confidence            389999999999998874311       11234667999999999999999999999999999988766432        


Q ss_pred             -cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHh----------hCCCCCCCeE
Q 022768          105 -KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQL----------DGFDQLGKVK  173 (292)
Q Consensus       105 -~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~----------~~~~~~~~~~  173 (292)
                       .+.|.....+...+..+.... .|++|||+|.+....       ......+|+++++.-          ......++++
T Consensus       396 ~~~~g~~~G~~~~~l~~~~~~~-~villDEidk~~~~~-------~g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~  467 (784)
T PRK10787        396 RTYIGSMPGKLIQKMAKVGVKN-PLFLLDEIDKMSSDM-------RGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVM  467 (784)
T ss_pred             hccCCCCCcHHHHHHHhcCCCC-CEEEEEChhhccccc-------CCCHHHHHHHHhccccEEEEecccccccccCCceE
Confidence             122332223333333333333 489999999984321       112346677766531          1112346899


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc-----c---CCCCCCHHHHHHHcCCCC----HHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI-----A---KHGEIDYEAVVKLAEGFN----GAD  241 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~-----~---~~~~~~~~~l~~~~~g~~----~~d  241 (292)
                      +|+|+|.. .+++++++  || ..+.+..++.++..+|++.++...     .   ..-.++-+.+..+..+|+    .|.
T Consensus       468 ~i~TaN~~-~i~~aLl~--R~-~ii~~~~~t~eek~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~~ii~~yt~e~GaR~  543 (784)
T PRK10787        468 FVATSNSM-NIPAPLLD--RM-EVIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRS  543 (784)
T ss_pred             EEEcCCCC-CCCHHHhc--ce-eeeecCCCCHHHHHHHHHHhhhHHHHHHhCCCCCeEEECHHHHHHHHHhCCcccCCcH
Confidence            99999887 59999999  99 678999999999999999887411     0   111233344444434443    355


Q ss_pred             HHHHHHHHHHHHHHh----cC---CcccHHHHHHHHH
Q 022768          242 LRNVCTEAGMSAIRA----ER---DYVIHEDFMKAVR  271 (292)
Q Consensus       242 i~~l~~~a~~~a~~~----~~---~~i~~~~~~~a~~  271 (292)
                      +...++.....+..+    +.   -.|+.+++.+.+.
T Consensus       544 LeR~I~~i~r~~l~~~~~~~~~~~v~v~~~~~~~~lg  580 (784)
T PRK10787        544 LEREISKLCRKAVKQLLLDKSLKHIEINGDNLHDYLG  580 (784)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCceeeecHHHHHHHhC
Confidence            554444444433332    21   2577777776665

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.71  E-value=8.9e-16  Score=139.64  Aligned_cols=192  Identities=14%  Similarity=0.221  Sum_probs=133.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc-----CCcEEEEeccchhccccChHHH---HHHHHHHHhhhCCCEEEEEccccccc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI-----DANFLKVVSSAIIDKYIGESAR---LIREMFGYARDHQPCIIFMDEIDAIG  138 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~il~lDe~d~l~  138 (292)
                      .+++|+|++|+|||||++++++.+     +..++++++.++...+......   .+......  .....+|+|||++.+.
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~--~~~~dvLiIDDiq~l~  219 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNE--ICQNDVLIIDDVQFLS  219 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHH--hccCCEEEEecccccc
Confidence            469999999999999999999965     4567888877766544333221   11111111  2345799999999883


Q ss_pred             CCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC-CC---CCChhhcCCCCcceEEEccCCCHHHHHHHHHH
Q 022768          139 GRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR-PD---VLDPALLRPGRLDRKIEIPLPNEQSRMEILKI  214 (292)
Q Consensus       139 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~-~~---~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~  214 (292)
                      +         ....++.+..+++.....   ++ .+|+|++. |.   .+.+++.++...+.++.+.+|+.++|.++++.
T Consensus       220 ~---------k~~~~e~lf~l~N~~~~~---~k-~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~  286 (450)
T PRK14087        220 Y---------KEKTNEIFFTIFNNFIEN---DK-QLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKK  286 (450)
T ss_pred             C---------CHHHHHHHHHHHHHHHHc---CC-cEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHH
Confidence            2         345677788888776532   22 36666654 33   35688888444467889999999999999999


Q ss_pred             HHcCccCCCCCC---HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhc-CCcccHHHHHHHHHHHh
Q 022768          215 HAAGIAKHGEID---YEAVVKLAEGFNGADLRNVCTEAGMSAIRAE-RDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       215 ~~~~~~~~~~~~---~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~-~~~i~~~~~~~a~~~~~  274 (292)
                      .+........++   ++.++..+.| ++|.+..++..+...+.... ...|+.+.+.++++++.
T Consensus       287 ~~~~~gl~~~l~~evl~~Ia~~~~g-d~R~L~gaL~~l~~~a~~~~~~~~it~~~v~~~l~~~~  349 (450)
T PRK14087        287 EIKNQNIKQEVTEEAINFISNYYSD-DVRKIKGSVSRLNFWSQQNPEEKIITIEIVSDLFRDIP  349 (450)
T ss_pred             HHHhcCCCCCCCHHHHHHHHHccCC-CHHHHHHHHHHHHHHHhcccCCCCCCHHHHHHHHhhcc
Confidence            887543211233   3445556665 88899999999887776653 25799999999998864

>PRK05642 DNA replication initiation factor; Validated

Probab=99.70  E-value=3.4e-15  Score=124.96  Aligned_cols=182  Identities=15%  Similarity=0.242  Sum_probs=119.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRF  142 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~  142 (292)
                      ...++|+||+|+|||||++++++++   +..+++++..++...        ...+.......  .+|+|||++.+.+   
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~~~--------~~~~~~~~~~~--d~LiiDDi~~~~~---  111 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDR--------GPELLDNLEQY--ELVCLDDLDVIAG---  111 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHHhh--------hHHHHHhhhhC--CEEEEechhhhcC---
Confidence            3679999999999999999999765   567777777665432        11222233333  5899999998733   


Q ss_pred             CCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc
Q 022768          143 SEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI  219 (292)
Q Consensus       143 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~  219 (292)
                            ....+..+.++++....   .++.++++++..+..   ..++++++...+..+.+.+|+.+++..+++.++...
T Consensus       112 ------~~~~~~~Lf~l~n~~~~---~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~~~  182 (234)
T PRK05642        112 ------KADWEEALFHLFNRLRD---SGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRASRR  182 (234)
T ss_pred             ------ChHHHHHHHHHHHHHHh---cCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHc
Confidence                  23456678888876532   234444444444433   368888833336788999999999999999665543


Q ss_pred             cCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          220 AKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       220 ~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      ... .+-..+-++....+ +.+.+..+++.....+...+ ..||..-+++++.
T Consensus       183 ~~~l~~ev~~~L~~~~~~-d~r~l~~~l~~l~~~~l~~~-~~it~~~~~~~L~  233 (234)
T PRK05642        183 GLHLTDEVGHFILTRGTR-SMSALFDLLERLDQASLQAQ-RKLTIPFLKETLG  233 (234)
T ss_pred             CCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHHHHHHcC-CcCCHHHHHHHhc
Confidence            222 12223445555554 77888888888876554444 4599998888764

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.70  E-value=1.7e-15  Score=148.04  Aligned_cols=209  Identities=22%  Similarity=0.312  Sum_probs=150.4

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------C
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------D   91 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~   91 (292)
                      +.....+-.++.++|+++.++++...+..             ....+++|+||||+|||++++.++..+          +
T Consensus       163 l~~~~~~~~~~~~igr~~ei~~~~~~l~r-------------~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~  229 (852)
T TIGR03346       163 LTERAREGKLDPVIGRDEEIRRTIQVLSR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKN  229 (852)
T ss_pred             HHHHhhCCCCCcCCCcHHHHHHHHHHHhc-------------CCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcC
Confidence            44455677889999999999999888755             335678999999999999999999886          5


Q ss_pred             CcEEEEeccchh--ccccChHHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           92 ANFLKVVSSAII--DKYIGESARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        92 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                      .+++.++...+.  ..+.++.+..++.++..+... .+.||||||+|.+.+.....   ........|...+       .
T Consensus       230 ~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~---~~~d~~~~Lk~~l-------~  299 (852)
T TIGR03346       230 KRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAE---GAMDAGNMLKPAL-------A  299 (852)
T ss_pred             CeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCc---chhHHHHHhchhh-------h
Confidence            567777766654  356677888888999887653 57899999999997532111   1122223332222       3


Q ss_pred             CCCeEEEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCC-----CHHHHHHHcCCC-
Q 022768          169 LGKVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI-----DYEAVVKLAEGF-  237 (292)
Q Consensus       169 ~~~~~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~-----~~~~l~~~~~g~-  237 (292)
                      .+.+.+|++|+..+     ..++++.+  || ..+.++.|+.+++..|++.....+.....+     .+...+.++.+| 
T Consensus       300 ~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf-~~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~~yi  376 (852)
T TIGR03346       300 RGELHCIGATTLDEYRKYIEKDAALER--RF-QPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYI  376 (852)
T ss_pred             cCceEEEEeCcHHHHHHHhhcCHHHHh--cC-CEEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhccccc
Confidence            36788999988753     47899998  99 568999999999999999776654333222     234445556555 


Q ss_pred             ----CHHHHHHHHHHHHHHHHHh
Q 022768          238 ----NGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       238 ----~~~di~~l~~~a~~~a~~~  256 (292)
                          -|.-...++++|...+...
T Consensus       377 ~~r~lPdkAidlld~a~a~~~~~  399 (852)
T TIGR03346       377 TDRFLPDKAIDLIDEAAARIRME  399 (852)
T ss_pred             cccCCchHHHHHHHHHHHHHHhh
Confidence                4677888999988766543

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.69  E-value=1.1e-15  Score=130.03  Aligned_cols=192  Identities=21%  Similarity=0.294  Sum_probs=127.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc--cccCh----HHH-HHHH-------------------HH
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID--KYIGE----SAR-LIRE-------------------MF  118 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~--~~~~~----~~~-~~~~-------------------~~  118 (292)
                      .+.+++|+||||||||++|+++++.++.+++.+++..-..  ...|.    ... ....                   .+
T Consensus        20 ~g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l   99 (262)
T TIGR02640        20 SGYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRL   99 (262)
T ss_pred             cCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCchH
Confidence            3678999999999999999999999999999998764221  11111    000 0000                   01


Q ss_pred             HHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh----C-------CCCCCCeEEEEEeCCCC-----
Q 022768          119 GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD----G-------FDQLGKVKMIMATNRPD-----  182 (292)
Q Consensus       119 ~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~----~-------~~~~~~~~vi~t~~~~~-----  182 (292)
                      ..+. ..+.+|+|||++.+           +.+.+..|..+++...    +       +..++.+.+|+|+|...     
T Consensus       100 ~~A~-~~g~~lllDEi~r~-----------~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~  167 (262)
T TIGR02640       100 TLAV-REGFTLVYDEFTRS-----------KPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVH  167 (262)
T ss_pred             HHHH-HcCCEEEEcchhhC-----------CHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCcccccee
Confidence            1111 23469999999998           7888888888886421    0       01234678999999752     


Q ss_pred             CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHH---HH----cCCCCHHHHHHHHHHHHHHHHH
Q 022768          183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVV---KL----AEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       183 ~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~---~~----~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      .+++++.+  || ..+.+++|+.++..+|++.+.. .  ... ..+.+.   ..    .....++ ++.++.-+...+..
T Consensus       168 ~l~~aL~~--R~-~~i~i~~P~~~~e~~Il~~~~~-~--~~~-~~~~iv~~~~~~R~~~~~~~~~-~r~~i~~~~~~~~~  239 (262)
T TIGR02640       168 ETQDALLD--RL-ITIFMDYPDIDTETAILRAKTD-V--AED-SAATIVRLVREFRASGDEITSG-LRASLMIAEVATQQ  239 (262)
T ss_pred             cccHHHHh--hc-EEEECCCCCHHHHHHHHHHhhC-C--CHH-HHHHHHHHHHHHHhhCCccCCc-HHHHHHHHHHHHHc
Confidence            46788888  88 7889999999999999998753 1  111 111111   11    1112332 66666666666666


Q ss_pred             hcCCcccHHHHHHHHHHHhhh
Q 022768          256 AERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       256 ~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      ..+..++.+|+.+.+..+-.+
T Consensus       240 ~~~~~~~~~~~~~~~~~~~~~  260 (262)
T TIGR02640       240 DIPVDVDDEDFVDLCIDILAS  260 (262)
T ss_pred             CCCCCCCcHHHHHHHHHHhcc
Confidence            667899999999998887653

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.69  E-value=2e-15  Score=131.75  Aligned_cols=221  Identities=19%  Similarity=0.216  Sum_probs=146.9

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC-------CcEE-------
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID-------ANFL-------   95 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~-------~~~~-------   95 (292)
                      +|..++|+++.+..|.-.+..+             ...+++|.|++|+||||++++++..+.       +++-       
T Consensus         2 pf~~ivgq~~~~~al~~~~~~~-------------~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~   68 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVIDP-------------KIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPE   68 (337)
T ss_pred             CccccccHHHHHHHHHHHhcCC-------------CCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCcc
Confidence            6899999999999998877653             245799999999999999999998772       2111       


Q ss_pred             -EE-eccc----------------hhc--------cccChHHHHHHHHHH---------HhhhCCCEEEEEcccccccCC
Q 022768           96 -KV-VSSA----------------IID--------KYIGESARLIREMFG---------YARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        96 -~~-~~~~----------------~~~--------~~~~~~~~~~~~~~~---------~~~~~~~~il~lDe~d~l~~~  140 (292)
                       .+ +|..                +.+        ...|..  .+...+.         .......++|||||++.+   
T Consensus        69 ~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~l~G~~--d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L---  143 (337)
T TIGR02030        69 MMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDRVCGTL--DIERALTEGVKAFEPGLLARANRGILYIDEVNLL---  143 (337)
T ss_pred             ccChHHhhhhhcccccccccCCCCcCCCCCCCcccceecch--hHhhHhhcCCEEeecCcceeccCCEEEecChHhC---
Confidence             00 0000                000        111110  0111100         011134579999999999   


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHhh------C--CCCCCCeEEEEEeCCCC-CCChhhcCCCCcceEEEccCCCH-HHHHH
Q 022768          141 RFSEGTSADREIQRTLMELLNQLD------G--FDQLGKVKMIMATNRPD-VLDPALLRPGRLDRKIEIPLPNE-QSRME  210 (292)
Q Consensus       141 ~~~~~~~~~~~~~~~l~~~l~~~~------~--~~~~~~~~vi~t~~~~~-~l~~~l~~~~r~~~~i~l~~p~~-~~r~~  210 (292)
                              +...+..|.+.+....      +  .....++++|+|.|..+ .+++.+.+  ||...+.+++|+. +++.+
T Consensus       144 --------~~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p~~~eer~e  213 (337)
T TIGR02030       144 --------EDHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTVRDVELRVE  213 (337)
T ss_pred             --------CHHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--hcceEEECCCCCCHHHHHH
Confidence                    8888898988886531      0  01223677888877654 68899998  9999999999876 88888


Q ss_pred             HHHHHHcCc----c----CC-----------------CC--CC------HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhc
Q 022768          211 ILKIHAAGI----A----KH-----------------GE--ID------YEAVVKLAEGFNGADLRNVCTEAGMSAIRAE  257 (292)
Q Consensus       211 i~~~~~~~~----~----~~-----------------~~--~~------~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~  257 (292)
                      |++......    .    ..                 ..  ++      +..++..+..-++|-...+++.|...|..++
T Consensus       214 IL~~~~~~~~~~~~~~~~~~~e~~~~~~~I~~a~~~~~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~G  293 (337)
T TIGR02030       214 IVERRTEYDADPHAFCEKWQTEQEALQAKIVNAQNLLPQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEG  293 (337)
T ss_pred             HHHhhhhcccCchhhhhhhhhhhhcCHHHHHHHHHHhccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcC
Confidence            888743210    0    00                 00  11      1122233333367788899999999999999


Q ss_pred             CCcccHHHHHHHHHHHhhhhh
Q 022768          258 RDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       258 ~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      +..|+.+|+..+..-+-.+..
T Consensus       294 R~~V~~dDv~~~a~~vL~HR~  314 (337)
T TIGR02030       294 RTEVTVDDIRRVAVLALRHRL  314 (337)
T ss_pred             CCCCCHHHHHHHHHHHHHHhC
Confidence            999999999999988877654

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.68  E-value=2.2e-15  Score=142.02  Aligned_cols=225  Identities=21%  Similarity=0.297  Sum_probs=147.1

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc--------
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI--------   90 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l--------   90 (292)
                      .+.+....+|.+|++++|++..++.+...+..             ..+.+++|+||+||||||+++.+++..        
T Consensus       141 ~~~~~~~~rp~~~~~iiGqs~~~~~l~~~ia~-------------~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~  207 (615)
T TIGR02903       141 HKSAQSLLRPRAFSEIVGQERAIKALLAKVAS-------------PFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPF  207 (615)
T ss_pred             hhHHhhhcCcCcHHhceeCcHHHHHHHHHHhc-------------CCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcc
Confidence            34555677899999999999999988776643             235579999999999999999998755        


Q ss_pred             --CCcEEEEeccchhcc-------ccChHHH----HHHHHHHH----------hhhCCCEEEEEcccccccCCcCCCCCc
Q 022768           91 --DANFLKVVSSAIIDK-------YIGESAR----LIREMFGY----------ARDHQPCIIFMDEIDAIGGRRFSEGTS  147 (292)
Q Consensus        91 --~~~~~~~~~~~~~~~-------~~~~~~~----~~~~~~~~----------~~~~~~~il~lDe~d~l~~~~~~~~~~  147 (292)
                        +.+++.+++..+...       ..+....    .....+..          ......++|||||++.|          
T Consensus       208 ~~~~~fv~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~L----------  277 (615)
T TIGR02903       208 AEDAPFVEVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGEL----------  277 (615)
T ss_pred             cCCCCeEEEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccC----------
Confidence              346788887654210       0111000    00000110          11234579999999999          


Q ss_pred             chHHHHHHHHHHHHHhhC-----------------------CCCCCCeEEEEE-eCCCCCCChhhcCCCCcceEEEccCC
Q 022768          148 ADREIQRTLMELLNQLDG-----------------------FDQLGKVKMIMA-TNRPDVLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       148 ~~~~~~~~l~~~l~~~~~-----------------------~~~~~~~~vi~t-~~~~~~l~~~l~~~~r~~~~i~l~~p  203 (292)
                       +...+..|..+++....                       .....++++|++ ++.++.+++++++  || ..+.++++
T Consensus       278 -d~~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrS--R~-~~i~~~pl  353 (615)
T TIGR02903       278 -DPLLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRS--RC-AEVFFEPL  353 (615)
T ss_pred             -CHHHHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHh--ce-eEEEeCCC
Confidence             88888888888865320                       001123555554 4567789999998  88 46789999


Q ss_pred             CHHHHHHHHHHHHcCccCCCCCCH---HHHHHHcCCCCHHHHHHHHHHHHHHHHHhc--------CCcccHHHHHHHHHH
Q 022768          204 NEQSRMEILKIHAAGIAKHGEIDY---EAVVKLAEGFNGADLRNVCTEAGMSAIRAE--------RDYVIHEDFMKAVRK  272 (292)
Q Consensus       204 ~~~~r~~i~~~~~~~~~~~~~~~~---~~l~~~~~g~~~~di~~l~~~a~~~a~~~~--------~~~i~~~~~~~a~~~  272 (292)
                      +.++...|++..+......  ++.   +.+...+  +.++.....+..+..++..+.        ...|+.+|+.++++.
T Consensus       354 s~edi~~Il~~~a~~~~v~--ls~eal~~L~~ys--~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~  429 (615)
T TIGR02903       354 TPEDIALIVLNAAEKINVH--LAAGVEELIARYT--IEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQI  429 (615)
T ss_pred             CHHHHHHHHHHHHHHcCCC--CCHHHHHHHHHCC--CcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCC
Confidence            9999999999988754322  222   3333332  245666666666665543221        236899999999876


Q ss_pred             Hh
Q 022768          273 LN  274 (292)
Q Consensus       273 ~~  274 (292)
                      -.
T Consensus       430 ~r  431 (615)
T TIGR02903       430 SR  431 (615)
T ss_pred             Cc
Confidence            43

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.68  E-value=8.9e-16  Score=149.59  Aligned_cols=172  Identities=23%  Similarity=0.353  Sum_probs=130.7

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------C
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------D   91 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~   91 (292)
                      +.....+-.++.++|+++.++++.+.+.+             ....+++|+||||+|||++++.++..+          +
T Consensus       168 l~~~~r~~~l~~vigr~~ei~~~i~iL~r-------------~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~  234 (857)
T PRK10865        168 LTERAEQGKLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKG  234 (857)
T ss_pred             HHHHHhcCCCCcCCCCHHHHHHHHHHHhc-------------CCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCC
Confidence            33455667889999999999999888765             335579999999999999999999987          5


Q ss_pred             CcEEEEeccchh--ccccChHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           92 ANFLKVVSSAII--DKYIGESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        92 ~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                      .+++.++...+.  ..+.|+.+..++.++..... ..+.||||||+|.+.+...+.   ........|...+       .
T Consensus       235 ~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~---~~~d~~~~lkp~l-------~  304 (857)
T PRK10865        235 RRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKAD---GAMDAGNMLKPAL-------A  304 (857)
T ss_pred             CEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCc---cchhHHHHhcchh-------h
Confidence            677888777765  34667888889999987654 467899999999997543221   1222333443333       3


Q ss_pred             CCCeEEEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc
Q 022768          169 LGKVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI  219 (292)
Q Consensus       169 ~~~~~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~  219 (292)
                      .+.+.+|++|+..+     +.++++.+  ||. .|.++.|+.+++..+++.....+
T Consensus       305 ~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~~iL~~l~~~~  357 (857)
T PRK10865        305 RGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAILRGLKERY  357 (857)
T ss_pred             cCCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHHHHHHHHhhhh
Confidence            36889999998765     47899998  995 68899999999999998776544

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.67  E-value=6.2e-15  Score=133.74  Aligned_cols=223  Identities=17%  Similarity=0.240  Sum_probs=136.8

Q ss_pred             CCCCcccccc-ccHHH--HHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           26 PGNVSYSAVG-GLSDQ--IRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        26 ~~~~~~~~l~-g~~~~--~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      -|..+|++.+ |....  ...+..+...+-.      . +-....+++|+||+|+|||||++++++++   +..++++..
T Consensus       105 ~~~~tFdnFv~g~~N~~a~~~a~~~a~~~~~------~-~~~~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~  177 (445)
T PRK12422        105 DPLMTFANFLVTPENDLPHRILQEFTKVSEQ------G-KGFPFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRS  177 (445)
T ss_pred             CccccccceeeCCcHHHHHHHHHHHHhcccc------c-cCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeH
Confidence            3567888866 54333  3444444332100      0 00123569999999999999999999876   577888887


Q ss_pred             cchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          100 SAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      ..+...............|.... ....+|+|||++.+.+         ....++.+..+++.+..   .+. .+|+|++
T Consensus       178 ~~f~~~~~~~l~~~~~~~f~~~~-~~~dvLiIDDiq~l~~---------k~~~qeelf~l~N~l~~---~~k-~IIlts~  243 (445)
T PRK12422        178 ELFTEHLVSAIRSGEMQRFRQFY-RNVDALFIEDIEVFSG---------KGATQEEFFHTFNSLHT---EGK-LIVISST  243 (445)
T ss_pred             HHHHHHHHHHHhcchHHHHHHHc-ccCCEEEEcchhhhcC---------ChhhHHHHHHHHHHHHH---CCC-cEEEecC
Confidence            66543322111111111232222 3457999999998843         23455666677665432   123 3555555


Q ss_pred             C-CC---CCChhhcCCCCc--ceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHH---HHcCCCCHHHHHHHHHHHH
Q 022768          180 R-PD---VLDPALLRPGRL--DRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVV---KLAEGFNGADLRNVCTEAG  250 (292)
Q Consensus       180 ~-~~---~l~~~l~~~~r~--~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~---~~~~g~~~~di~~l~~~a~  250 (292)
                      . |.   .+.+++++  ||  +..+.+.+|+.+++..+++..+.....  .++.+.+.   ....+ +.+.+..++....
T Consensus       244 ~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~--~l~~evl~~la~~~~~-dir~L~g~l~~l~  318 (445)
T PRK12422        244 CAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLRSFLERKAEALSI--RIEETALDFLIEALSS-NVKSLLHALTLLA  318 (445)
T ss_pred             CCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHHHHHHHHHHHcCC--CCCHHHHHHHHHhcCC-CHHHHHHHHHHHH
Confidence            4 43   46688888  66  588999999999999999998876443  24444444   44443 5666666666664


Q ss_pred             HH-HHHh-cCCcccHHHHHHHHHHHh
Q 022768          251 MS-AIRA-ERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       251 ~~-a~~~-~~~~i~~~~~~~a~~~~~  274 (292)
                      .. |+.. ....++.+++.++++++.
T Consensus       319 ~~~a~~~~~~~~i~~~~~~~~l~~~~  344 (445)
T PRK12422        319 KRVAYKKLSHQLLYVDDIKALLHDVL  344 (445)
T ss_pred             HHHHHHHhhCCCCCHHHHHHHHHHhh
Confidence            21 3332 224699999999998763

>PRK06620 hypothetical protein; Validated

Probab=99.67  E-value=5.9e-15  Score=121.54  Aligned_cols=196  Identities=12%  Similarity=0.127  Sum_probs=123.7

Q ss_pred             CCCccccccc-c--HHHHHHHHHHhhcccCChHHHHhcCCCC-CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           27 GNVSYSAVGG-L--SDQIRELRESIELPLMNPELFLRVGIKP-PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        27 ~~~~~~~l~g-~--~~~~~~l~~~l~~~~~~~~~~~~~~~~~-~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      +..+|++++- .  ..+...+..+...+          +..+ ...++|+||+|+||||+++++++..+..++.  ....
T Consensus        11 ~~~tfd~Fvvg~~N~~a~~~~~~~~~~~----------~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~--~~~~   78 (214)
T PRK06620         11 SKYHPDEFIVSSSNDQAYNIIKNWQCGF----------GVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYIIK--DIFF   78 (214)
T ss_pred             CCCCchhhEecccHHHHHHHHHHHHHcc----------ccCCCcceEEEECCCCCCHHHHHHHHHhccCCEEcc--hhhh
Confidence            4567787543 3  34556665554321          1222 3679999999999999999999987643221  1000


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                                 ....+     ....+|+|||+|.+           ..   ..+..+++.+.+   .++.++++++..|.
T Consensus        79 -----------~~~~~-----~~~d~lliDdi~~~-----------~~---~~lf~l~N~~~e---~g~~ilits~~~p~  125 (214)
T PRK06620         79 -----------NEEIL-----EKYNAFIIEDIENW-----------QE---PALLHIFNIINE---KQKYLLLTSSDKSR  125 (214)
T ss_pred             -----------chhHH-----hcCCEEEEeccccc-----------hH---HHHHHHHHHHHh---cCCEEEEEcCCCcc
Confidence                       00111     12268999999865           21   356666666543   24555555554444


Q ss_pred             C--CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCC
Q 022768          183 V--LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD  259 (292)
Q Consensus       183 ~--l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~  259 (292)
                      .  + ++++++...+.++.+.+|+.+.+..+++..+...... .+-..+.|+....+ +.+.+..+++.....+...+ .
T Consensus       126 ~l~l-~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev~~~L~~~~~~-d~r~l~~~l~~l~~~~~~~~-~  202 (214)
T PRK06620        126 NFTL-PDLSSRIKSVLSILLNSPDDELIKILIFKHFSISSVTISRQIIDFLLVNLPR-EYSKIIEILENINYFALISK-R  202 (214)
T ss_pred             ccch-HHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccC-CHHHHHHHHHHHHHHHHHcC-C
Confidence            3  5 7888843345588999999999999998887644332 22234556666665 77888888888665555544 4


Q ss_pred             cccHHHHHHHH
Q 022768          260 YVIHEDFMKAV  270 (292)
Q Consensus       260 ~i~~~~~~~a~  270 (292)
                      .||.+.+++++
T Consensus       203 ~it~~~~~~~l  213 (214)
T PRK06620        203 KITISLVKEVL  213 (214)
T ss_pred             CCCHHHHHHHh
Confidence            69999888875

>PRK09087 hypothetical protein; Validated

Probab=99.66  E-value=4.7e-15  Score=123.14  Aligned_cols=201  Identities=17%  Similarity=0.143  Sum_probs=127.3

Q ss_pred             CCCCCccccccc---cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           25 DPGNVSYSAVGG---LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        25 ~~~~~~~~~l~g---~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      ..+..+|++.+.   +..+...+.+...              ..++.++|+||+|+|||||++++++..+..++  +...
T Consensus        14 ~~~~~~~~~Fi~~~~N~~a~~~l~~~~~--------------~~~~~l~l~G~~GsGKThLl~~~~~~~~~~~i--~~~~   77 (226)
T PRK09087         14 HDPAYGRDDLLVTESNRAAVSLVDHWPN--------------WPSPVVVLAGPVGSGKTHLASIWREKSDALLI--HPNE   77 (226)
T ss_pred             CCCCCChhceeecCchHHHHHHHHhccc--------------CCCCeEEEECCCCCCHHHHHHHHHHhcCCEEe--cHHH
Confidence            345568999874   3334453333211              12445999999999999999999988654433  3222


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC-C
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN-R  180 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~-~  180 (292)
                      +..           ..+.....   .+|+|||++.+.            ..+..+.++++.....   ++. +|+|++ .
T Consensus        78 ~~~-----------~~~~~~~~---~~l~iDDi~~~~------------~~~~~lf~l~n~~~~~---g~~-ilits~~~  127 (226)
T PRK09087         78 IGS-----------DAANAAAE---GPVLIEDIDAGG------------FDETGLFHLINSVRQA---GTS-LLMTSRLW  127 (226)
T ss_pred             cch-----------HHHHhhhc---CeEEEECCCCCC------------CCHHHHHHHHHHHHhC---CCe-EEEECCCC
Confidence            211           11111111   489999999761            1134577777665431   233 455444 3


Q ss_pred             CCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh
Q 022768          181 PDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       181 ~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~  256 (292)
                      +..   ..++++++...+.++.+.+|+.+++.++++.++...... .+..++.|+....+ +.+.+..++......+...
T Consensus       128 p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~~~~r-~~~~l~~~l~~L~~~~~~~  206 (226)
T PRK09087        128 PSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVSRMER-SLFAAQTIVDRLDRLALER  206 (226)
T ss_pred             hHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHHh
Confidence            432   357888844456889999999999999999998764332 22224555555554 6666777777777667665


Q ss_pred             cCCcccHHHHHHHHHHH
Q 022768          257 ERDYVIHEDFMKAVRKL  273 (292)
Q Consensus       257 ~~~~i~~~~~~~a~~~~  273 (292)
                      ++ .+|...++++++.+
T Consensus       207 ~~-~it~~~~~~~l~~~  222 (226)
T PRK09087        207 KS-RITRALAAEVLNEM  222 (226)
T ss_pred             CC-CCCHHHHHHHHHhh
Confidence            54 59999999999875

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.66  E-value=4.5e-15  Score=130.65  Aligned_cols=195  Identities=17%  Similarity=0.193  Sum_probs=130.5

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------E
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------F   94 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------~   94 (292)
                      ....+.|..+++|+|++++++.|...+..-            .-++.+||+||+|+|||++++.+++.+.+.       .
T Consensus        13 ~~~~~~P~~~~~l~Gh~~a~~~L~~a~~~g------------rl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~   80 (351)
T PRK09112         13 LDGVPSPSENTRLFGHEEAEAFLAQAYREG------------KLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPE   80 (351)
T ss_pred             ccCCCCCCchhhccCcHHHHHHHHHHHHcC------------CCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCcc
Confidence            344578899999999999999999998752            335569999999999999999999988551       1


Q ss_pred             EEE-ec--c---ch-----------hcc---c------cChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCC
Q 022768           95 LKV-VS--S---AI-----------IDK---Y------IGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSE  144 (292)
Q Consensus        95 ~~~-~~--~---~~-----------~~~---~------~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~  144 (292)
                      ... .+  +   ..           ...   .      ..-..+.++.+.....    .....|++|||+|.+       
T Consensus        81 ~~~~~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l-------  153 (351)
T PRK09112         81 TLADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDM-------  153 (351)
T ss_pred             ccCCCCCCCHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhc-------
Confidence            000 00  0   00           000   0      0001233333333322    234579999999999       


Q ss_pred             CCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC
Q 022768          145 GTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE  224 (292)
Q Consensus       145 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~  224 (292)
                          +......|+..+++     +..++.+|..++.++.+.+.+++  |+ ..+.|++|+.++..++++......... +
T Consensus       154 ----~~~aanaLLk~LEE-----pp~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~~~~~L~~~~~~~~~~-~  220 (351)
T PRK09112        154 ----NRNAANAILKTLEE-----PPARALFILISHSSGRLLPTIRS--RC-QPISLKPLDDDELKKALSHLGSSQGSD-G  220 (351)
T ss_pred             ----CHHHHHHHHHHHhc-----CCCCceEEEEECChhhccHHHHh--hc-cEEEecCCCHHHHHHHHHHhhcccCCC-H
Confidence                77777777776654     33466667777888888899998  77 689999999999999988743221111 1


Q ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHH
Q 022768          225 IDYEAVVKLAEGFNGADLRNVCTEA  249 (292)
Q Consensus       225 ~~~~~l~~~~~g~~~~di~~l~~~a  249 (292)
                      .....+...+.| +++....++...
T Consensus       221 ~~~~~i~~~s~G-~pr~Al~ll~~~  244 (351)
T PRK09112        221 EITEALLQRSKG-SVRKALLLLNYG  244 (351)
T ss_pred             HHHHHHHHHcCC-CHHHHHHHHhcC
Confidence            124556677776 777777666443

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=99.66  E-value=9.2e-15  Score=129.00  Aligned_cols=225  Identities=19%  Similarity=0.240  Sum_probs=153.2

Q ss_pred             cCCCCCccccccc-cH--HHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEE
Q 022768           24 EDPGNVSYSAVGG-LS--DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFL   95 (292)
Q Consensus        24 ~~~~~~~~~~l~g-~~--~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~   95 (292)
                      ...|.++|++++. ..  -+......+-..+          | .+...++|+||.|+|||||++++++..     +..++
T Consensus        79 ~l~~~ytFdnFv~g~~N~~A~aa~~~va~~~----------g-~~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~  147 (408)
T COG0593          79 GLNPKYTFDNFVVGPSNRLAYAAAKAVAENP----------G-GAYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVV  147 (408)
T ss_pred             cCCCCCchhheeeCCchHHHHHHHHHHHhcc----------C-CcCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEE
Confidence            3456788888543 32  2333333333322          1 235679999999999999999999977     23577


Q ss_pred             EEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEE
Q 022768           96 KVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMI  175 (292)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi  175 (292)
                      ++....+...++......-..-|..-+  .-.+|+|||++.+.+         ....++.+..+++.+...   ++ .+|
T Consensus       148 y~~se~f~~~~v~a~~~~~~~~Fk~~y--~~dlllIDDiq~l~g---------k~~~qeefFh~FN~l~~~---~k-qIv  212 (408)
T COG0593         148 YLTSEDFTNDFVKALRDNEMEKFKEKY--SLDLLLIDDIQFLAG---------KERTQEEFFHTFNALLEN---GK-QIV  212 (408)
T ss_pred             eccHHHHHHHHHHHHHhhhHHHHHHhh--ccCeeeechHhHhcC---------ChhHHHHHHHHHHHHHhc---CC-EEE
Confidence            777776655544443333334454444  336999999999854         345578888888876532   34 455


Q ss_pred             EEe-CCCCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC-CCHHHHHHHcCCCCHHHHHHHHHHHH
Q 022768          176 MAT-NRPDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE-IDYEAVVKLAEGFNGADLRNVCTEAG  250 (292)
Q Consensus       176 ~t~-~~~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~-~~~~~l~~~~~g~~~~di~~l~~~a~  250 (292)
                      .|+ ..|..   +.++++++.-++..+.+.+|+.+.|..+++..+......-+ --..-++..... +.+++..++....
T Consensus       213 ltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~~~-nvReLegaL~~l~  291 (408)
T COG0593         213 LTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRLDR-NVRELEGALNRLD  291 (408)
T ss_pred             EEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhc-cHHHHHHHHHHHH
Confidence            555 44554   44889994445678899999999999999997765544422 223445555543 7889999999999


Q ss_pred             HHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          251 MSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       251 ~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      .+|...++ .||.+.+.++++.+...
T Consensus       292 ~~a~~~~~-~iTi~~v~e~L~~~~~~  316 (408)
T COG0593         292 AFALFTKR-AITIDLVKEILKDLLRA  316 (408)
T ss_pred             HHHHhcCc-cCcHHHHHHHHHHhhcc
Confidence            88877777 69999999999988765

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.65  E-value=1.4e-15  Score=130.68  Aligned_cols=139  Identities=16%  Similarity=0.237  Sum_probs=103.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc--ccChHHHHH----------HHHHHHhhhCCCEEEEEc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK--YIGESARLI----------REMFGYARDHQPCIIFMD  132 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~--~~~~~~~~~----------~~~~~~~~~~~~~il~lD  132 (292)
                      .+++++|.|+||+|||++++.+|+.++.+++.+++......  ..|.....+          ...+..+. ..+.+|++|
T Consensus        63 ~~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~-~~g~illlD  141 (327)
T TIGR01650        63 YDRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWAL-QHNVALCFD  141 (327)
T ss_pred             cCCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHH-hCCeEEEec
Confidence            36789999999999999999999999999999998776544  333321111          01112222 245789999


Q ss_pred             ccccccCCcCCCCCcchHHHHHHHHHHHHH---------hhCCCCCCCeEEEEEeCCCC------------CCChhhcCC
Q 022768          133 EIDAIGGRRFSEGTSADREIQRTLMELLNQ---------LDGFDQLGKVKMIMATNRPD------------VLDPALLRP  191 (292)
Q Consensus       133 e~d~l~~~~~~~~~~~~~~~~~~l~~~l~~---------~~~~~~~~~~~vi~t~~~~~------------~l~~~l~~~  191 (292)
                      |+|..           ..+.+..|..+++.         ...+.+.+.+.+|+|+|...            .++.++++ 
T Consensus       142 Ein~a-----------~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lD-  209 (327)
T TIGR01650       142 EYDAG-----------RPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMD-  209 (327)
T ss_pred             hhhcc-----------CHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHh-
Confidence            99988           77788888888763         12234556799999999743            36889998 


Q ss_pred             CCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          192 GRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       192 ~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                       ||..++.+.+|+.++..+|+.....
T Consensus       210 -RF~i~~~~~Yp~~e~E~~Il~~~~~  234 (327)
T TIGR01650       210 -RWSIVTTLNYLEHDNEAAIVLAKAK  234 (327)
T ss_pred             -heeeEeeCCCCCHHHHHHHHHhhcc
Confidence             9988889999999999999887654

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.64  E-value=2e-14  Score=127.25  Aligned_cols=190  Identities=18%  Similarity=0.230  Sum_probs=129.7

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE--------
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF--------   94 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~--------   94 (292)
                      ...+.|.++++|+|++++++.|.+.+..-            .-++.+||+||+|+||++++..+|+.+-+.-        
T Consensus        10 ~~~~~P~~~~~iiGq~~~~~~L~~~~~~~------------rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~   77 (365)
T PRK07471         10 EGAPHPRETTALFGHAAAEAALLDAYRSG------------RLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAV   77 (365)
T ss_pred             cCCCCCCchhhccChHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccc
Confidence            33478889999999999999999998762            4466799999999999999999999873311        


Q ss_pred             --------------------------EEEecc--chhccc-cChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCc
Q 022768           95 --------------------------LKVVSS--AIIDKY-IGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRR  141 (292)
Q Consensus        95 --------------------------~~~~~~--~~~~~~-~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~  141 (292)
                                                +.+...  +-.+.. ..-..+.++.+.....    ...+.|++|||+|.+    
T Consensus        78 ~~~~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m----  153 (365)
T PRK07471         78 PPPTSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEM----  153 (365)
T ss_pred             cccccccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhc----
Confidence                                      001000  000000 0011233444444332    245789999999999    


Q ss_pred             CCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccC
Q 022768          142 FSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAK  221 (292)
Q Consensus       142 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~  221 (292)
                             +......|+..+++     +.+++++|.+|+.++.+.+.+++  |+ ..+.|++|+.++..+++......   
T Consensus       154 -------~~~aanaLLK~LEe-----pp~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~i~~~L~~~~~~---  215 (365)
T PRK07471        154 -------NANAANALLKVLEE-----PPARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPEDVIDALAAAGPD---  215 (365)
T ss_pred             -------CHHHHHHHHHHHhc-----CCCCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHHHHHHHHHhccc---
Confidence                   77777777776663     33567788889888888889988  77 78999999999999888875421   


Q ss_pred             CCCCCHHHHHHHcCCCCHHHHHHHHH
Q 022768          222 HGEIDYEAVVKLAEGFNGADLRNVCT  247 (292)
Q Consensus       222 ~~~~~~~~l~~~~~g~~~~di~~l~~  247 (292)
                      ..+.....+...+.| +++....++.
T Consensus       216 ~~~~~~~~l~~~s~G-sp~~Al~ll~  240 (365)
T PRK07471        216 LPDDPRAALAALAEG-SVGRALRLAG  240 (365)
T ss_pred             CCHHHHHHHHHHcCC-CHHHHHHHhc
Confidence            111112456677776 7766666654

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.63  E-value=4e-14  Score=131.44  Aligned_cols=234  Identities=42%  Similarity=0.642  Sum_probs=192.1

Q ss_pred             cCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEE
Q 022768           52 LMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFM  131 (292)
Q Consensus        52 ~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~l  131 (292)
                      +.....+..++..++.+++++||+|+|||.+++.++.. +.....++.......+.+.....+...+..+....|+++++
T Consensus         4 ~~~~~~~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~   82 (494)
T COG0464           4 LKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFI   82 (494)
T ss_pred             ccCHHHHHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEee
Confidence            44566788888999999999999999999999999999 65557777888888889999999999999999999999999


Q ss_pred             cccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHH
Q 022768          132 DEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEI  211 (292)
Q Consensus       132 De~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i  211 (292)
                      ||+|.+.+.+..............+...+..+.   ... +.+++.++.+..+++.++.+++|...+.+..|+...+.++
T Consensus        83 d~~~~~~~~~~~~~~~~~~~v~~~l~~~~d~~~---~~~-v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ei  158 (494)
T COG0464          83 DEIDALAPKRSSDQGEVERRVVAQLLALMDGLK---RGQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEI  158 (494)
T ss_pred             chhhhcccCccccccchhhHHHHHHHHhccccc---CCc-eEEEeecCCccccChhHhCccccceeeecCCCCHHHHHHH
Confidence            999999888766333344444555555555444   333 7788888999999999999999999999999999999999


Q ss_pred             HHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhc------CCcccHHHHHHHHHHHhhh---hhhchh
Q 022768          212 LKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAE------RDYVIHEDFMKAVRKLNEA---KKLESS  282 (292)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~------~~~i~~~~~~~a~~~~~~~---~~~~~~  282 (292)
                      +...........+.+.+.++..+.|+.+.++..++..+...+..+.      ...++.+++.++++.+.+.   ......
T Consensus       159 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  238 (494)
T COG0464         159 LQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGEYIGVTEDDFEEALKKVLPSRGVLFEDED  238 (494)
T ss_pred             HHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHHHHHHHHHHHhhhccCcccccccHHHHHHHHHhcCcccccccCCCC
Confidence            9988877766667889999999999999999999999998888885      3368999999999999774   112235


Q ss_pred             hhhhhhcC
Q 022768          283 AHYNADFG  290 (292)
Q Consensus       283 ~~~~~~~~  290 (292)
                      ..|+++.|
T Consensus       239 v~~~digg  246 (494)
T COG0464         239 VTLDDIGG  246 (494)
T ss_pred             cceehhhc
Confidence            56666654

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.62  E-value=5.3e-14  Score=113.62  Aligned_cols=198  Identities=18%  Similarity=0.243  Sum_probs=139.7

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      -+.++++.+.+|+|.+.+++.|.+....+..+         .+..+||++|..|||||+++|++.+++   +..+++++-
T Consensus        51 v~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G---------~pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLVEV~k  121 (287)
T COG2607          51 VPDPDPIDLADLVGVDRQKEALVRNTEQFAEG---------LPANNVLLWGARGTGKSSLVKALLNEYADEGLRLVEVDK  121 (287)
T ss_pred             CCCCCCcCHHHHhCchHHHHHHHHHHHHHHcC---------CcccceEEecCCCCChHHHHHHHHHHHHhcCCeEEEEcH
Confidence            35677899999999999999999998887554         567889999999999999999999988   445666665


Q ss_pred             cchhccccChHHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEe
Q 022768          100 SAIIDKYIGESARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT  178 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~  178 (292)
                      .++..         +..++...+.. ..-|||.||+-          .+......+.|...++---+ ..+.+|++.+|+
T Consensus       122 ~dl~~---------Lp~l~~~Lr~~~~kFIlFcDDLS----------Fe~gd~~yK~LKs~LeG~ve-~rP~NVl~YATS  181 (287)
T COG2607         122 EDLAT---------LPDLVELLRARPEKFILFCDDLS----------FEEGDDAYKALKSALEGGVE-GRPANVLFYATS  181 (287)
T ss_pred             HHHhh---------HHHHHHHHhcCCceEEEEecCCC----------CCCCchHHHHHHHHhcCCcc-cCCCeEEEEEec
Confidence            55432         33555555543 24688999972          22344556667676654322 233489999999


Q ss_pred             CCCCCCChh--------------------hcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC---CCHHHHHHH--
Q 022768          179 NRPDVLDPA--------------------LLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE---IDYEAVVKL--  233 (292)
Q Consensus       179 ~~~~~l~~~--------------------l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~---~~~~~l~~~--  233 (292)
                      |..+.++..                    +.-+.||+..+.|.+++.++...++..++....++-.   ++.+.+...  
T Consensus       182 NRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e~l~~eAl~WAt~  261 (287)
T COG2607         182 NRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDEELHAEALQWATT  261 (287)
T ss_pred             CCcccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHh
Confidence            987654421                    1223499999999999999999999999986655532   223333332  


Q ss_pred             cCCCCHHHHHHHHHHH
Q 022768          234 AEGFNGADLRNVCTEA  249 (292)
Q Consensus       234 ~~g~~~~di~~l~~~a  249 (292)
                      -.|.|++-..|.++..
T Consensus       262 rg~RSGR~A~QF~~~~  277 (287)
T COG2607         262 RGGRSGRVAWQFIRDL  277 (287)
T ss_pred             cCCCccHhHHHHHHHH
Confidence            3466777777777653

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=99.62  E-value=8.4e-14  Score=119.29  Aligned_cols=193  Identities=17%  Similarity=0.260  Sum_probs=120.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCC-cEEEEe--ccch-----h----cc----ccCh-HHHHHHHHH----HHhhhC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDA-NFLKVV--SSAI-----I----DK----YIGE-SARLIREMF----GYARDH  124 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~-~~~~~~--~~~~-----~----~~----~~~~-~~~~~~~~~----~~~~~~  124 (292)
                      +..++|+||+|+||||+++.+++.+.. .+..+.  ....     .    ..    ..+. ....+..+.    ......
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~  122 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAG  122 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCC
Confidence            346889999999999999999998763 222111  0000     0    00    0001 111111111    222345


Q ss_pred             CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC--CCC----ChhhcCCCCcceEE
Q 022768          125 QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP--DVL----DPALLRPGRLDRKI  198 (292)
Q Consensus       125 ~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~--~~l----~~~l~~~~r~~~~i  198 (292)
                      .+.+|+|||+|.+           .......+..+.+...  .....+.++++....  +.+    ...+.+  |+...+
T Consensus       123 ~~~vliiDe~~~l-----------~~~~~~~l~~l~~~~~--~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~--r~~~~~  187 (269)
T TIGR03015       123 KRALLVVDEAQNL-----------TPELLEELRMLSNFQT--DNAKLLQIFLVGQPEFRETLQSPQLQQLRQ--RIIASC  187 (269)
T ss_pred             CCeEEEEECcccC-----------CHHHHHHHHHHhCccc--CCCCeEEEEEcCCHHHHHHHcCchhHHHHh--heeeee
Confidence            5689999999988           4444444443332211  111233444544321  111    123444  677788


Q ss_pred             EccCCCHHHHHHHHHHHHcCccCC-----CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 022768          199 EIPLPNEQSRMEILKIHAAGIAKH-----GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKL  273 (292)
Q Consensus       199 ~l~~p~~~~r~~i~~~~~~~~~~~-----~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~  273 (292)
                      .+++++.++..+++...+......     .+..++.+...+.| .++.+..++..+...|..++...|+.+++.+++..+
T Consensus       188 ~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G-~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~  266 (269)
T TIGR03015       188 HLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRG-IPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEI  266 (269)
T ss_pred             eCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCC-cccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            999999999999999887643211     22345667888888 567899999999999999999999999999999987


Q ss_pred             h
Q 022768          274 N  274 (292)
Q Consensus       274 ~  274 (292)
                      +
T Consensus       267 ~  267 (269)
T TIGR03015       267 D  267 (269)
T ss_pred             h
Confidence            6

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.60  E-value=7.9e-14  Score=121.98  Aligned_cols=175  Identities=14%  Similarity=0.226  Sum_probs=118.9

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--------EEEEeccc
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--------FLKVVSSA  101 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--------~~~~~~~~  101 (292)
                      +|++++|++.+++.+...+..-            .-++.+||+||+|+|||++++.+++.+-+.        +..+... 
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~~------------~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~-   68 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIKN------------RFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPI-   68 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHcC------------CCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccc-
Confidence            5899999999999999988652            345678999999999999999999987432        2222211 


Q ss_pred             hhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEE
Q 022768          102 IIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMA  177 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t  177 (292)
                       .+..  .....++.+...+.    .....|++||++|.+           +......|...++.     +++++.+|.+
T Consensus        69 -~~~~--i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m-----------~~~a~naLLK~LEe-----pp~~t~~il~  129 (313)
T PRK05564         69 -NKKS--IGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKM-----------TEQAQNAFLKTIEE-----PPKGVFIILL  129 (313)
T ss_pred             -cCCC--CCHHHHHHHHHHHhcCcccCCceEEEEechhhc-----------CHHHHHHHHHHhcC-----CCCCeEEEEE
Confidence             1111  12233444444332    234579999999998           66666666666653     4467777778


Q ss_pred             eCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHH
Q 022768          178 TNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLR  243 (292)
Q Consensus       178 ~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~  243 (292)
                      |+.++.+.+.+++  |+ ..+.|++|+.++....+.....+.   .......++..+.| +++.+.
T Consensus       130 ~~~~~~ll~TI~S--Rc-~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~~~l~~~~~g-~~~~a~  188 (313)
T PRK05564        130 CENLEQILDTIKS--RC-QIYKLNRLSKEEIEKFISYKYNDI---KEEEKKSAIAFSDG-IPGKVE  188 (313)
T ss_pred             eCChHhCcHHHHh--hc-eeeeCCCcCHHHHHHHHHHHhcCC---CHHHHHHHHHHcCC-CHHHHH
Confidence            8888999999999  77 689999999998887776654321   11223455666665 444443

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.58  E-value=1.5e-13  Score=123.62  Aligned_cols=218  Identities=17%  Similarity=0.157  Sum_probs=135.5

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEeccc-hhccccC
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSSA-IIDKYIG  108 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~~-~~~~~~~  108 (292)
                      ..++|.+++++.+..++.               .+.++||.||||+|||++|++++...+.  ++....+.. ......|
T Consensus        20 ~~i~gre~vI~lll~aal---------------ag~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG   84 (498)
T PRK13531         20 KGLYERSHAIRLCLLAAL---------------SGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFG   84 (498)
T ss_pred             hhccCcHHHHHHHHHHHc---------------cCCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcC
Confidence            347888888888877763               3778999999999999999999997753  333333221 1111222


Q ss_pred             hH-HHHH--HHHHHHhh-h--CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-----CCCCCeEEEEE
Q 022768          109 ES-ARLI--REMFGYAR-D--HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-----DQLGKVKMIMA  177 (292)
Q Consensus       109 ~~-~~~~--~~~~~~~~-~--~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-----~~~~~~~vi~t  177 (292)
                      .. ....  ...|.... .  ....+||+||++.+           +...+..|+..+++-...     .+.+..+++++
T Consensus        85 ~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~ra-----------sp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~A  153 (498)
T PRK13531         85 PLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWKA-----------GPAILNTLLTAINERRFRNGAHEEKIPMRLLVTA  153 (498)
T ss_pred             cHHHhhhhhcCchhhhcCCccccccEEeecccccC-----------CHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEE
Confidence            11 0000  01111111 1  02248999999988           888999999988654311     11122344555


Q ss_pred             eCCCCC---CChhhcCCCCcceEEEccCCC-HHHHHHHHHHHHc--CccC--CCCCCHHH--------------------
Q 022768          178 TNRPDV---LDPALLRPGRLDRKIEIPLPN-EQSRMEILKIHAA--GIAK--HGEIDYEA--------------------  229 (292)
Q Consensus       178 ~~~~~~---l~~~l~~~~r~~~~i~l~~p~-~~~r~~i~~~~~~--~~~~--~~~~~~~~--------------------  229 (292)
                      +|...+   ..+++.+  ||...+.+++|+ .++..+++.....  ....  ...++.+.                    
T Consensus       154 TN~LPE~g~~leAL~D--RFliri~vp~l~~~~~e~~lL~~~~~~~~~~~~~~~vis~eel~~lq~~v~~V~v~d~v~ey  231 (498)
T PRK13531        154 SNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPASLQITDEEYQQWQKEIGKITLPDHVFEL  231 (498)
T ss_pred             CCCCcccCCchHHhHh--hEEEEEECCCCCchHHHHHHHHcccccccCCCcccCCCCHHHHHHHHHHhcceeCCHHHHHH
Confidence            564322   2247777  898889999997 4565777765322  1111  11122111                    


Q ss_pred             ---HHHH---cC---CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          230 ---VVKL---AE---GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       230 ---l~~~---~~---g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                         |...   +.   ..|+|...++++.|.+.|+..++..|+.+|+. .+..+-+++.
T Consensus       232 I~~L~~~lr~~r~~~~~SpR~~~~l~~~akA~A~l~GR~~V~p~Dv~-ll~~vL~HRl  288 (498)
T PRK13531        232 IFQLRQQLDALPNAPYVSDRRWKKAIRLLQASAFFSGRDAIAPIDLI-LLKDCLWHDA  288 (498)
T ss_pred             HHHHHHHHhcCCCCCCcCcHHHHHHHHHHHHHHHHCCCCCCCHHHHH-HhHHHhccCH
Confidence               2221   11   26899999999999999999999999999999 7777666544

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.58  E-value=1e-13  Score=122.22  Aligned_cols=244  Identities=22%  Similarity=0.310  Sum_probs=154.9

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcC-CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-cccC-h
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVG-IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIG-E  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~-~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~~-~  109 (292)
                      .++|++++++.+...+...+........+. -.++.+++|+||||+|||++++++++.++.+++.++...+.. .+.| .
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~~~e~g~vG~d   92 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRD   92 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeEEEeecceeecCCcccCC
Confidence            489999999999888765433221111111 123578999999999999999999999999999999776542 3333 2


Q ss_pred             HHHHHHHHHHHh--------------------------------------------------------------------
Q 022768          110 SARLIREMFGYA--------------------------------------------------------------------  121 (292)
Q Consensus       110 ~~~~~~~~~~~~--------------------------------------------------------------------  121 (292)
                      .+..++.++..+                                                                    
T Consensus        93 vE~i~r~l~e~A~~~i~~d~i~~~r~~a~~~ae~riv~~Ll~~~~~~~~~~~~~~~~~~~r~~~~~~l~~g~ldd~~iei  172 (441)
T TIGR00390        93 VESMVRDLTDAAVKLVKEEAIEKVRDRAEELAEERIVDVLLPPAKNQWGQTEQQQEPESAREAFRKKLREGELDDKEIEI  172 (441)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCccccccccccccchHHHHHHHHHHHhcCCccCcEEEE
Confidence            222222221111                                                                    


Q ss_pred             -----------------------------------------------------------------------hhCCCEEEE
Q 022768          122 -----------------------------------------------------------------------RDHQPCIIF  130 (292)
Q Consensus       122 -----------------------------------------------------------------------~~~~~~il~  130 (292)
                                                                                             .....+|||
T Consensus       173 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ea~~~l~~~e~~~lid~~~v~~~a~~~~e~~GIVf  252 (441)
T TIGR00390       173 DVSAKMPSGIEIMAPPGMEEMTMQLQSLFQNLGGQKKKKRKLKIKDAKKALIAEEAAKLVDPEEIKQEAIDAVEQSGIIF  252 (441)
T ss_pred             eecCCCCCccccCCCcchhHHHhhHHHHHHhhcCCCCceEEeEHHHHHHHHHHHHHHhccChHHHHHHHHHHHHcCCEEE
Confidence                                                                                   012457999


Q ss_pred             EcccccccCCcCCCCC-cchHHHHHHHHHHHHHhh-----CCCCCCCeEEEEEe----CCCCCCChhhcCCCCcceEEEc
Q 022768          131 MDEIDAIGGRRFSEGT-SADREIQRTLMELLNQLD-----GFDQLGKVKMIMAT----NRPDVLDPALLRPGRLDRKIEI  200 (292)
Q Consensus       131 lDe~d~l~~~~~~~~~-~~~~~~~~~l~~~l~~~~-----~~~~~~~~~vi~t~----~~~~~l~~~l~~~~r~~~~i~l  200 (292)
                      |||+|.++.+..+.+. -+....|..|+.+++.-.     ..-...++.+|++.    ..|+.+-|.+..  ||...+.+
T Consensus       253 iDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~G--R~Pi~v~L  330 (441)
T TIGR00390       253 IDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQG--RFPIRVEL  330 (441)
T ss_pred             EEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhC--ccceEEEC
Confidence            9999999976533332 344567888877776421     11233467777765    236667788887  99999999


Q ss_pred             cCCCHHHHHHHHH----HHHcCc-------cCC---CCCCHHHHHHHc-------CCCCHHHHHHHHHHHHHHHHHhcC-
Q 022768          201 PLPNEQSRMEILK----IHAAGI-------AKH---GEIDYEAVVKLA-------EGFNGADLRNVCTEAGMSAIRAER-  258 (292)
Q Consensus       201 ~~p~~~~r~~i~~----~~~~~~-------~~~---~~~~~~~l~~~~-------~g~~~~di~~l~~~a~~~a~~~~~-  258 (292)
                      .+++.++...|+.    ....++       .+.   .+-.+..++...       .+.-.|-++.++.....-+..... 
T Consensus       331 ~~L~~edL~rILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtilE~~l~d~~fe~p~  410 (441)
T TIGR00390       331 QALTTDDFERILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLLEDISFEAPD  410 (441)
T ss_pred             CCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEeHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHhcCCC
Confidence            9999999988773    111111       111   122244444443       355567788777777765544422 


Q ss_pred             -----CcccHHHHHHHHHHHhhhhh
Q 022768          259 -----DYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       259 -----~~i~~~~~~~a~~~~~~~~~  278 (292)
                           -.|+.+.+.+.+..+....+
T Consensus       411 ~~~~~v~I~~~~V~~~l~~~~~~~D  435 (441)
T TIGR00390       411 LSGQNITIDADYVSKKLGALVADED  435 (441)
T ss_pred             CCCCEEEECHHHHHhHHHHHHhcCC
Confidence                 26788888888877765443

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.58  E-value=9e-14  Score=131.89  Aligned_cols=221  Identities=21%  Similarity=0.269  Sum_probs=146.6

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC------------------
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID------------------   91 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~------------------   91 (292)
                      .|.+|+|+++++..|.-....+             ...++||.|++|+|||++++++++.+.                  
T Consensus         2 pf~~ivGq~~~~~al~~~av~~-------------~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~   68 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAVDP-------------RIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPE   68 (633)
T ss_pred             CcchhcChHHHHHHHHHHhhCC-------------CCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCcc
Confidence            6889999999999988777653             224699999999999999999999882                  


Q ss_pred             -----------------CcEEEEeccchhccccChHHHHHHHHHH---------HhhhCCCEEEEEcccccccCCcCCCC
Q 022768           92 -----------------ANFLKVVSSAIIDKYIGESARLIREMFG---------YARDHQPCIIFMDEIDAIGGRRFSEG  145 (292)
Q Consensus        92 -----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~il~lDe~d~l~~~~~~~~  145 (292)
                                       .+++.+.+........|...  +...+.         .......++|||||++.+        
T Consensus        69 ~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d--~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l--------  138 (633)
T TIGR02442        69 EWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLD--IERALREGEKAFQPGLLAEAHRGILYIDEVNLL--------  138 (633)
T ss_pred             ccChhhhhcccccccCCCCeeeCCCCCcHHHcCCccc--HHHHhhcCCeeecCcceeecCCCeEEeChhhhC--------
Confidence                             23444333222122222210  011110         011224479999999999        


Q ss_pred             CcchHHHHHHHHHHHHHhh--------CCCCCCCeEEEEEeCCC-CCCChhhcCCCCcceEEEccCCC-HHHHHHHHHHH
Q 022768          146 TSADREIQRTLMELLNQLD--------GFDQLGKVKMIMATNRP-DVLDPALLRPGRLDRKIEIPLPN-EQSRMEILKIH  215 (292)
Q Consensus       146 ~~~~~~~~~~l~~~l~~~~--------~~~~~~~~~vi~t~~~~-~~l~~~l~~~~r~~~~i~l~~p~-~~~r~~i~~~~  215 (292)
                         +...+..|...++...        ......++.+|+|+|.. ..+++.+.+  ||...+.++.+. .+++.++++..
T Consensus       139 ---~~~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~~l~i~v~~~~~~~~~~~il~~~  213 (633)
T TIGR02442       139 ---DDHLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RFGLCVDVAAPRDPEERVEIIRRR  213 (633)
T ss_pred             ---CHHHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--hcceEEEccCCCchHHHHHHHHHH
Confidence               8888999998887531        01112368899988864 357888998  999889887764 56777777643


Q ss_pred             HcCc-------------------------cCCC--CCC---HHHHHHHc--CCC-CHHHHHHHHHHHHHHHHHhcCCccc
Q 022768          216 AAGI-------------------------AKHG--EID---YEAVVKLA--EGF-NGADLRNVCTEAGMSAIRAERDYVI  262 (292)
Q Consensus       216 ~~~~-------------------------~~~~--~~~---~~~l~~~~--~g~-~~~di~~l~~~a~~~a~~~~~~~i~  262 (292)
                      ....                         ....  .++   .+.+....  .|. +.+-...+++.|...|..+++..|+
T Consensus       214 ~~~~~~~~~~~~~~~~~~~~l~~~i~~ar~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~  293 (633)
T TIGR02442       214 LAFDADPEAFAARWAAEQEELRNRIARARSLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVT  293 (633)
T ss_pred             HhhccCcHHHHHHhhhhHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCC
Confidence            2200                         0000  111   12222222  233 4667778999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhh
Q 022768          263 HEDFMKAVRKLNEAKK  278 (292)
Q Consensus       263 ~~~~~~a~~~~~~~~~  278 (292)
                      .+|+.+|+..+-.+..
T Consensus       294 ~~Dv~~A~~lvL~hR~  309 (633)
T TIGR02442       294 AEDVREAAELVLPHRR  309 (633)
T ss_pred             HHHHHHHHHHHhhhhc
Confidence            9999999999886544

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.58  E-value=2.2e-13  Score=118.42  Aligned_cols=185  Identities=17%  Similarity=0.233  Sum_probs=127.6

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE---------------
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF---------------   94 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~---------------   94 (292)
                      .|++|+|++++++.|.+.+..-            .-++.+||+||+|+||+++|.++++.+-+.-               
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~~------------rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~h   69 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQN------------RIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNH   69 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHhC------------CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCC
Confidence            5899999999999999998762            4467899999999999999999999873321               


Q ss_pred             ---EEEeccchh-ccc--------c-------C-hHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchH
Q 022768           95 ---LKVVSSAII-DKY--------I-------G-ESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADR  150 (292)
Q Consensus        95 ---~~~~~~~~~-~~~--------~-------~-~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~  150 (292)
                         ..+...... +..        .       + -..+.++.+...+.    .....|++||++|.+           +.
T Consensus        70 PDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m-----------~~  138 (314)
T PRK07399         70 PDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETM-----------NE  138 (314)
T ss_pred             CCEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhc-----------CH
Confidence               111111000 000        0       0 01123344433332    245689999999999           67


Q ss_pred             HHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHH
Q 022768          151 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAV  230 (292)
Q Consensus       151 ~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l  230 (292)
                      .....|+..+++     ++ +..+|.+++.++.+.+.++|  |+ ..+.|++++.++..++++......  ..+.+...+
T Consensus       139 ~aaNaLLK~LEE-----Pp-~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~~~~~~~L~~~~~~~--~~~~~~~~l  207 (314)
T PRK07399        139 AAANALLKTLEE-----PG-NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLSDEQLEQVLKRLGDEE--ILNINFPEL  207 (314)
T ss_pred             HHHHHHHHHHhC-----CC-CCeEEEEECChHhCcHHHHh--hc-eEEecCCCCHHHHHHHHHHhhccc--cchhHHHHH
Confidence            677777776654     22 45677788889999999999  77 889999999999998888764311  111224677


Q ss_pred             HHHcCCCCHHHHHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEA  249 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a  249 (292)
                      ...+.| +++.+.++++..
T Consensus       208 ~~~a~G-s~~~al~~l~~~  225 (314)
T PRK07399        208 LALAQG-SPGAAIANIEQL  225 (314)
T ss_pred             HHHcCC-CHHHHHHHHHHH
Confidence            888887 887887777543

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.58  E-value=1.9e-13  Score=122.60  Aligned_cols=221  Identities=21%  Similarity=0.234  Sum_probs=132.5

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHh---cCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-cccCh
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLR---VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGE  109 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~---~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~~~  109 (292)
                      ++|++++++.+...+...+........   -...+..++||+||||+|||++|+++++.++.+++.+++..+.. .+.|.
T Consensus        73 ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~gyvG~  152 (412)
T PRK05342         73 VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGE  152 (412)
T ss_pred             eeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcccc
Confidence            899999999997776443222111000   00123578999999999999999999999999999999887643 34444


Q ss_pred             H-HHHHHHHHHH----hhhCCCEEEEEcccccccCCcCCC---CCcchHHHHHHHHHHHHHhh--------CCCCCCCeE
Q 022768          110 S-ARLIREMFGY----ARDHQPCIIFMDEIDAIGGRRFSE---GTSADREIQRTLMELLNQLD--------GFDQLGKVK  173 (292)
Q Consensus       110 ~-~~~~~~~~~~----~~~~~~~il~lDe~d~l~~~~~~~---~~~~~~~~~~~l~~~l~~~~--------~~~~~~~~~  173 (292)
                      . ...+..++..    .....++||||||+|.+..+....   .+......|..|+.+++...        ...+...++
T Consensus       153 d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v~~~gg~~~~~~~~~  232 (412)
T PRK05342        153 DVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFI  232 (412)
T ss_pred             hHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHhcCeEEeCCCCCcCcCCCCeE
Confidence            2 2333333332    123467899999999997652111   11123467888888886321        011222345


Q ss_pred             EEEEeCCCC----------------------------------------------------CCChhhcCCCCcceEEEcc
Q 022768          174 MIMATNRPD----------------------------------------------------VLDPALLRPGRLDRKIEIP  201 (292)
Q Consensus       174 vi~t~~~~~----------------------------------------------------~l~~~l~~~~r~~~~i~l~  201 (292)
                      +|.|+|...                                                    .+.|.+..  |++.++.|.
T Consensus       233 ~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEflg--Rld~iv~f~  310 (412)
T PRK05342        233 QVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFIG--RLPVVATLE  310 (412)
T ss_pred             EeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHhC--CCCeeeecC
Confidence            555554400                                                    02334444  888899999


Q ss_pred             CCCHHHHHHHHHH----HHc-------CccCCCCCC---HHHHHHH--cCCCCHHHHHHHHHHHHHHHHHh
Q 022768          202 LPNEQSRMEILKI----HAA-------GIAKHGEID---YEAVVKL--AEGFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       202 ~p~~~~r~~i~~~----~~~-------~~~~~~~~~---~~~l~~~--~~g~~~~di~~l~~~a~~~a~~~  256 (292)
                      +++.++..+|+..    ...       ...+.-.++   .+.++..  ..++-.|.++.+++....-...+
T Consensus       311 ~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~~~~~~GAR~Lrriie~~l~~~~~~  381 (412)
T PRK05342        311 ELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMFE  381 (412)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhCCCCCCCCchHHHHHHHHhHHHHHh
Confidence            9999999988872    222       111221222   2334443  23445677777777666655543

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=99.57  E-value=1.1e-13  Score=106.79  Aligned_cols=140  Identities=44%  Similarity=0.708  Sum_probs=94.1

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChHHH
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGESAR  112 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~~~  112 (292)
                      |.+...+.+..++..             ..+.+++|+||+|+|||++++.+++.+   +.+++.+++.............
T Consensus         2 ~~~~~~~~i~~~~~~-------------~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~   68 (151)
T cd00009           2 GQEEAIEALREALEL-------------PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELF   68 (151)
T ss_pred             chHHHHHHHHHHHhC-------------CCCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHh
Confidence            566777777777644             246689999999999999999999998   7888888877655432211111


Q ss_pred             H---HHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-CCCCCeEEEEEeCCCC--CCCh
Q 022768          113 L---IREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-DQLGKVKMIMATNRPD--VLDP  186 (292)
Q Consensus       113 ~---~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-~~~~~~~vi~t~~~~~--~l~~  186 (292)
                      .   ............+.+|+|||++.+           .......+...+...... ....++.+|++++...  .+++
T Consensus        69 ~~~~~~~~~~~~~~~~~~~lilDe~~~~-----------~~~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~  137 (151)
T cd00009          69 GHFLVRLLFELAEKAKPGVLFIDEIDSL-----------SRGAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDR  137 (151)
T ss_pred             hhhhHhHHHHhhccCCCeEEEEeChhhh-----------hHHHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcCh
Confidence            1   112223334456789999999887           444555566655554321 0135788899988776  6777


Q ss_pred             hhcCCCCcceEEEcc
Q 022768          187 ALLRPGRLDRKIEIP  201 (292)
Q Consensus       187 ~l~~~~r~~~~i~l~  201 (292)
                      .+.+  ||...+.++
T Consensus       138 ~~~~--r~~~~i~~~  150 (151)
T cd00009         138 ALYD--RLDIRIVIP  150 (151)
T ss_pred             hHHh--hhccEeecC
Confidence            7777  887666665

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.56  E-value=1.4e-13  Score=121.47  Aligned_cols=244  Identities=23%  Similarity=0.320  Sum_probs=154.8

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCC-CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-cccC-h
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGI-KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIG-E  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~-~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~~-~  109 (292)
                      .++|++++++.+..++...++.......... ..+.+++|+||||+|||++++.+++.++.+++.+++..+.. .+.| +
T Consensus        16 ~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~f~e~GyvG~d   95 (443)
T PRK05201         16 YIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRD   95 (443)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchhhccCCcccCC
Confidence            3899999999999888543222111101110 12578999999999999999999999999999999876653 3444 1


Q ss_pred             HHHHHHHHHHHh--------------------------------------------------------------------
Q 022768          110 SARLIREMFGYA--------------------------------------------------------------------  121 (292)
Q Consensus       110 ~~~~~~~~~~~~--------------------------------------------------------------------  121 (292)
                      .+..++.++..+                                                                    
T Consensus        96 ~e~~ir~L~~~A~~~~~~~~~~~~~~~a~~~~e~ri~~~l~~~~~~~~~~~~~~~~~~~~r~~~~~~l~~g~ldd~~iei  175 (443)
T PRK05201         96 VESIIRDLVEIAVKMVREEKREKVREKAEEAAEERILDALLPPAKNNWGEEEEKEEISATRQKFRKKLREGELDDKEIEI  175 (443)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCccCCccccccchhhhHHHHHHHHHHHcCCcCCcEEEE
Confidence            122222221111                                                                    


Q ss_pred             ----------------------------------------------------------------------hhCCCEEEEE
Q 022768          122 ----------------------------------------------------------------------RDHQPCIIFM  131 (292)
Q Consensus       122 ----------------------------------------------------------------------~~~~~~il~l  131 (292)
                                                                                            .....+||||
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~eA~~~l~~~e~~~lid~~~v~~~ai~~ae~~GIVfi  255 (443)
T PRK05201        176 EVAEAAPMMEIMGPPGMEEMTIQLQDMFGNLGPKKKKKRKLKVKEARKILIEEEAAKLIDMEEIKQEAIERVEQNGIVFI  255 (443)
T ss_pred             EecCCCCcccCCCCcchhHHHHHHHHHHHhhCCCCCceEEeEHHHHHHHHHHHHHHhccChHHHHHHHHHHHHcCCEEEE
Confidence                                                                                  0124579999


Q ss_pred             cccccccCCcCCCC-CcchHHHHHHHHHHHHHhh-----CCCCCCCeEEEEEe----CCCCCCChhhcCCCCcceEEEcc
Q 022768          132 DEIDAIGGRRFSEG-TSADREIQRTLMELLNQLD-----GFDQLGKVKMIMAT----NRPDVLDPALLRPGRLDRKIEIP  201 (292)
Q Consensus       132 De~d~l~~~~~~~~-~~~~~~~~~~l~~~l~~~~-----~~~~~~~~~vi~t~----~~~~~l~~~l~~~~r~~~~i~l~  201 (292)
                      ||+|.++.+....+ +-+....|..|+.+++.-.     ..-...++.+|++.    ..|+.+-|.|..  ||...+.+.
T Consensus       256 DEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~G--R~Pi~v~L~  333 (443)
T PRK05201        256 DEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQG--RFPIRVELD  333 (443)
T ss_pred             EcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhC--ccceEEECC
Confidence            99999997653322 2334567888877776421     11233467777765    335667788887  999999999


Q ss_pred             CCCHHHHHHHHHH----HHcCc-------cCC---CCCCHHHHHHHc-------CCCCHHHHHHHHHHHHHHHHHhcC--
Q 022768          202 LPNEQSRMEILKI----HAAGI-------AKH---GEIDYEAVVKLA-------EGFNGADLRNVCTEAGMSAIRAER--  258 (292)
Q Consensus       202 ~p~~~~r~~i~~~----~~~~~-------~~~---~~~~~~~l~~~~-------~g~~~~di~~l~~~a~~~a~~~~~--  258 (292)
                      +++.++...|+..    ...++       .+.   .+..+..++..+       .+.-.|-++.+++....-+.....  
T Consensus       334 ~L~~~dL~~ILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtI~E~~L~d~~Fe~p~~  413 (443)
T PRK05201        334 ALTEEDFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLEDISFEAPDM  413 (443)
T ss_pred             CCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHHHHhccCCCC
Confidence            9999999887741    22211       111   122344455443       344567788888777766543322  


Q ss_pred             ----CcccHHHHHHHHHHHhhhhh
Q 022768          259 ----DYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       259 ----~~i~~~~~~~a~~~~~~~~~  278 (292)
                          -.|+.+.+.+.+..+....+
T Consensus       414 ~~~~v~I~~~~V~~~l~~l~~~~D  437 (443)
T PRK05201        414 SGETVTIDAAYVDEKLGDLVKDED  437 (443)
T ss_pred             CCCEEEECHHHHHHHHHHHHhcCC
Confidence                26788888888877765444

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.56  E-value=2.1e-13  Score=130.58  Aligned_cols=168  Identities=20%  Similarity=0.293  Sum_probs=117.4

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc-----cc
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-----YI  107 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~-----~~  107 (292)
                      .++|++++++.|...+.....+.   .. .-.|..++||+||||+|||.+|+.+|+.++.+++.+++.++...     +.
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl---~~-~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~Li  534 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGL---GH-EHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLI  534 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccc---cC-CCCCcceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHc
Confidence            47999999999999987532110   00 01234569999999999999999999999999999998876431     11


Q ss_pred             Ch----HHH-HHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCCeEEEE
Q 022768          108 GE----SAR-LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLGKVKMIM  176 (292)
Q Consensus       108 ~~----~~~-~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~~~vi~  176 (292)
                      |.    ... .-..+....+....+||+|||+|.+           ..+.+..|+++++...-.      ....++++|+
T Consensus       535 G~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka-----------~~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~  603 (758)
T PRK11034        535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKA-----------HPDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVM  603 (758)
T ss_pred             CCCCCcccccccchHHHHHHhCCCcEEEeccHhhh-----------hHHHHHHHHHHHhcCeeecCCCceecCCCcEEEE
Confidence            11    000 0112223334455689999999999           788888888888753211      1123678999


Q ss_pred             EeCCC-------------------------CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          177 ATNRP-------------------------DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       177 t~~~~-------------------------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      |+|..                         ..+.|.+..  |++.++.|++++.++..+|+...+.
T Consensus       604 TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~~~~l~~I~~~~l~  667 (758)
T PRK11034        604 TTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_pred             eCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCCHHHHHHHHHHHHH
Confidence            99832                         114466666  8999999999999999998886654

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.56  E-value=2.8e-13  Score=119.25  Aligned_cols=215  Identities=25%  Similarity=0.256  Sum_probs=138.8

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc--cChHH
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY--IGESA  111 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~--~~~~~  111 (292)
                      ++|.++++..+...+..               +.+++|.||||+|||++++.+|..++.+++++.+.......  .|...
T Consensus        26 ~~g~~~~~~~~l~a~~~---------------~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~   90 (329)
T COG0714          26 VVGDEEVIELALLALLA---------------GGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYA   90 (329)
T ss_pred             eeccHHHHHHHHHHHHc---------------CCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchh
Confidence            77888888777776543               67899999999999999999999999999999988654321  12111


Q ss_pred             HHHH----HHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh------C-CCCCCCeEEEE
Q 022768          112 RLIR----EMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD------G-FDQLGKVKMIM  176 (292)
Q Consensus       112 ~~~~----~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~------~-~~~~~~~~vi~  176 (292)
                      ....    ..+.....    ...+++++|||+..           ....+..|+..++...      . ..-...+++++
T Consensus        91 ~~~~~~~~~~~~~~~gpl~~~~~~ill~DEInra-----------~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~via  159 (329)
T COG0714          91 YAALLLEPGEFRFVPGPLFAAVRVILLLDEINRA-----------PPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIA  159 (329)
T ss_pred             HhhhhccCCeEEEecCCcccccceEEEEeccccC-----------CHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEE
Confidence            1110    00000000    00139999999988           8889999999998731      2 33445788888


Q ss_pred             EeC-----CCCCCChhhcCCCCcceEEEccCC-CHHHHHHHHHHHHcCc------cCCCCCCHHH---------------
Q 022768          177 ATN-----RPDVLDPALLRPGRLDRKIEIPLP-NEQSRMEILKIHAAGI------AKHGEIDYEA---------------  229 (292)
Q Consensus       177 t~~-----~~~~l~~~l~~~~r~~~~i~l~~p-~~~~r~~i~~~~~~~~------~~~~~~~~~~---------------  229 (292)
                      |.|     ....+++++++  ||...+.+++| +.++...+........      .....+....               
T Consensus       160 T~Np~e~~g~~~l~eA~ld--Rf~~~~~v~yp~~~~e~~~i~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~  237 (329)
T COG0714         160 TQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEERIILARVGGVDELDLESLVKPVLSDEELLRLQKEVKKVPVSD  237 (329)
T ss_pred             ccCccccCCCcCCCHHHHh--hEEEEEecCCCCchHHHHHHHHhCccccccccchhhhhhhCHHHHHHHHhhhccCCchH
Confidence            888     34568999999  99889999999 4444444444333201      1111111111               


Q ss_pred             --------HHHH-------cCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          230 --------VVKL-------AEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       230 --------l~~~-------~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                              +...       ..|.+++....++..+...|...++..+..+++.........+
T Consensus       238 ~~~~~~~~l~~~~~~~~~~~~~~s~r~~~~~~~~~~~~a~~~~~~~~~~~dv~~~~~~~~~~  299 (329)
T COG0714         238 EVIDYIVTLVAALREAPDVALGASPRASLALLAALRALALLDGRDAVIPDDVKALAEPALAH  299 (329)
T ss_pred             HHHHHHHHHHHhhccccchhccCCchhHHHHHHHHHhhhhhcCccccCHHHHHHHhhhhhhh
Confidence                    1111       1133566667777777777777777788888877766665543

>smart00350 MCM minichromosome maintenance proteins

Probab=99.55  E-value=1.5e-13  Score=127.31  Aligned_cols=226  Identities=18%  Similarity=0.157  Sum_probs=140.4

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE----eccchhccccCh
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV----VSSAIIDKYIGE  109 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~----~~~~~~~~~~~~  109 (292)
                      +.|.+.++..+.-.+..-.. +.......+....++||+|+||+|||++++++++......+..    ++..+.......
T Consensus       205 i~G~~~~k~~l~l~l~gg~~-~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~~l~~~~~~~  283 (509)
T smart00350      205 IYGHEDIKKAILLLLFGGVH-KNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTAAVTRD  283 (509)
T ss_pred             ccCcHHHHHHHHHHHhCCCc-cccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcCCccccceEc
Confidence            67777777776666543110 0000001123345899999999999999999999876543222    111111100000


Q ss_pred             ---HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh------C--CCCCCCeEEEEEe
Q 022768          110 ---SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD------G--FDQLGKVKMIMAT  178 (292)
Q Consensus       110 ---~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~------~--~~~~~~~~vi~t~  178 (292)
                         ....++  -+.......++++|||++.+           ....+..|.+.++.-.      +  ..-+.++.+|+|+
T Consensus       284 ~~~g~~~~~--~G~l~~A~~Gil~iDEi~~l-----------~~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~  350 (509)
T smart00350      284 PETREFTLE--GGALVLADNGVCCIDEFDKM-----------DDSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAA  350 (509)
T ss_pred             cCcceEEec--CccEEecCCCEEEEechhhC-----------CHHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEe
Confidence               000000  00111234579999999999           7888888888886422      0  0112478899999


Q ss_pred             CCCC-------------CCChhhcCCCCcceEE-EccCCCHHHHHHHHHHHHcCcc------------------------
Q 022768          179 NRPD-------------VLDPALLRPGRLDRKI-EIPLPNEQSRMEILKIHAAGIA------------------------  220 (292)
Q Consensus       179 ~~~~-------------~l~~~l~~~~r~~~~i-~l~~p~~~~r~~i~~~~~~~~~------------------------  220 (292)
                      |+.+             .+++.+++  ||+..+ ....|+.+...+|.++.+....                        
T Consensus       351 NP~~g~y~~~~~~~~n~~l~~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~~~~~~~~~~~~~~~~~~~~~~~l~~yi~  428 (509)
T smart00350      351 NPIGGRYDPKLTPEENIDLPAPILS--RFDLLFVVLDEVDEERDRELAKHVVDLHRYSHPEPDEADEVPISQEFLRKYIA  428 (509)
T ss_pred             CCCCcccCCCcChhhccCCChHHhC--ceeeEEEecCCCChHHHHHHHHHHHHhhcccCccccccccccCCHHHHHHHHH
Confidence            9753             48899999  997755 5588999988888877542110                        


Q ss_pred             -----CCCCCCHHH---HH-----HH----------cCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          221 -----KHGEIDYEA---VV-----KL----------AEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       221 -----~~~~~~~~~---l~-----~~----------~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                           ....+.-+.   +.     .+          ..+.++|.+..+++-|.+.|..+.+..|+.+|+.+|++-+..
T Consensus       429 ~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~Dv~~ai~l~~~  506 (509)
T smart00350      429 YAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEADVEEAIRLLRE  506 (509)
T ss_pred             HHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHHH
Confidence                 000111111   10     01          113488999999999999999999999999999999988764

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.55  E-value=5.6e-13  Score=122.58  Aligned_cols=214  Identities=21%  Similarity=0.254  Sum_probs=141.6

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHH----hc-------------------CCCCCceEEEEcCCCChHH
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFL----RV-------------------GIKPPKGVLLYGPPGTGKT   80 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~----~~-------------------~~~~~~~vll~G~~G~GKT   80 (292)
                      +.+.|..|.+|.|.+.+-+.++.++..-  +.+.|.    ++                   +-++.+.+||+||||.|||
T Consensus       263 dky~Pk~FtdLLsDe~tNR~~L~WLK~W--D~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGKT  340 (877)
T KOG1969|consen  263 DKYRPKKFTDLLSDEKTNRRMLGWLKQW--DPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGKT  340 (877)
T ss_pred             cccChhHHHHHhcchhHHHHHHHHHHhh--cHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCChh
Confidence            4789999999999999999999887531  112222    11                   2234556889999999999


Q ss_pred             HHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHH
Q 022768           81 LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTL  156 (292)
Q Consensus        81 ~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l  156 (292)
                      |||+.+|+..|..++++|.++-.+  .......+..+.....    ...|..|+|||||--           ......++
T Consensus       341 TLAHViAkqaGYsVvEINASDeRt--~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa-----------~~~~Vdvi  407 (877)
T KOG1969|consen  341 TLAHVIAKQAGYSVVEINASDERT--APMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGA-----------PRAAVDVI  407 (877)
T ss_pred             HHHHHHHHhcCceEEEeccccccc--HHHHHHHHHHHHhhccccccCCCcceEEEecccCC-----------cHHHHHHH
Confidence            999999999999999999887543  2223333333332222    156899999999754           56667777


Q ss_pred             HHHHHHh--h--CCCC------------CCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc
Q 022768          157 MELLNQL--D--GFDQ------------LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA  220 (292)
Q Consensus       157 ~~~l~~~--~--~~~~------------~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~  220 (292)
                      ..++..-  .  +...            .-.-.||+.||+..  .|+|+.-..|..++.|.+|......+=++..+....
T Consensus       408 lslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdLY--aPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~  485 (877)
T KOG1969|consen  408 LSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDLY--APALRPLRPFAEIIAFVPPSQSRLVERLNEICHREN  485 (877)
T ss_pred             HHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCcc--chhhhhcccceEEEEecCCChhHHHHHHHHHHhhhc
Confidence            7777621  1  1100            01234888999765  455554336889999999988766655555554333


Q ss_pred             CC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC
Q 022768          221 KH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER  258 (292)
Q Consensus       221 ~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~  258 (292)
                      .. ..-.+..|+.++++    ||+..++.....+....+
T Consensus       486 mr~d~~aL~~L~el~~~----DIRsCINtLQfLa~~~~r  520 (877)
T KOG1969|consen  486 MRADSKALNALCELTQN----DIRSCINTLQFLASNVDR  520 (877)
T ss_pred             CCCCHHHHHHHHHHhcc----hHHHHHHHHHHHHHhccc
Confidence            22 11234455555555    999999999988866433

>TIGR00368 Mg chelatase-related protein

Probab=99.55  E-value=2.9e-13  Score=124.16  Aligned_cols=216  Identities=19%  Similarity=0.319  Sum_probs=135.4

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC----cEEEEeccc-h
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA----NFLKVVSSA-I  102 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~----~~~~~~~~~-~  102 (292)
                      ...|+++.|++.+++.+.-.+               ..+.+++|.||||+|||++++.++..+..    ..+...... .
T Consensus       188 ~~d~~dv~Gq~~~~~al~~aa---------------~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~le~~~i~s~  252 (499)
T TIGR00368       188 DLDLKDIKGQQHAKRALEIAA---------------AGGHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSL  252 (499)
T ss_pred             CCCHHHhcCcHHHHhhhhhhc---------------cCCCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEEeccccccc
Confidence            458999999999988776654               34678999999999999999999975522    111111100 0


Q ss_pred             hcc-----------cc----ChHH-HHHHH----HHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768          103 IDK-----------YI----GESA-RLIRE----MFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus       103 ~~~-----------~~----~~~~-~~~~~----~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      ...           +.    ..+. ..+..    --........++|||||++.+           +...+..|.+.++.
T Consensus       253 ~g~~~~~~~~~~~Pf~~p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~-----------~~~~~~~L~~~LE~  321 (499)
T TIGR00368       253 VGKLIDRKQIKQRPFRSPHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEF-----------KRSVLDALREPIED  321 (499)
T ss_pred             hhhhccccccccCCccccccccchhhhhCCccccchhhhhccCCCeEecCChhhC-----------CHHHHHHHHHHHHc
Confidence            000           00    0000 00000    001122334589999999998           78888888888864


Q ss_pred             hh--------CCCCCCCeEEEEEeCCC------C-----------------CCChhhcCCCCcceEEEccCCCHHHH---
Q 022768          163 LD--------GFDQLGKVKMIMATNRP------D-----------------VLDPALLRPGRLDRKIEIPLPNEQSR---  208 (292)
Q Consensus       163 ~~--------~~~~~~~~~vi~t~~~~------~-----------------~l~~~l~~~~r~~~~i~l~~p~~~~r---  208 (292)
                      -.        ......++.+|+++|.-      .                 .++..+++  ||+..+.++.++..+.   
T Consensus       322 ~~v~i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllD--R~dl~~~~~~~~~~~l~~~  399 (499)
T TIGR00368       322 GSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLD--RIDLSVEVPLLPPEKLLST  399 (499)
T ss_pred             CcEEEEecCcceeccCCeEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHh--hCCEEEEEcCCCHHHHhcc
Confidence            32        11112478899999862      1                 47778888  9999999987654321   


Q ss_pred             ----------HHHHHH------HHcCc---cCCCCCCHHHHHH----------------HcCCCCHHHHHHHHHHHHHHH
Q 022768          209 ----------MEILKI------HAAGI---AKHGEIDYEAVVK----------------LAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       209 ----------~~i~~~------~~~~~---~~~~~~~~~~l~~----------------~~~g~~~~di~~l~~~a~~~a  253 (292)
                                ..+.+.      ++.+.   ..+..+....+.+                ...++|.|-...+++-|...|
T Consensus       400 ~~~e~s~~ir~rV~~Ar~~q~~R~~~~~~~~~N~~l~~~~l~~~~~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiA  479 (499)
T TIGR00368       400 GSGESSAEVKQRVIKAREIQNIRYEKFANINKNADLNSDEIEQFCKLSAIDANDLEGALNKLGLSSRATHRILKVARTIA  479 (499)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHhcCCCCCcccccCCHHHHHhhcCCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHH
Confidence                      222221      11111   1122222222211                122578999999999999999


Q ss_pred             HHhcCCcccHHHHHHHHH
Q 022768          254 IRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a~~  271 (292)
                      ..++...|+.+|+.+|+.
T Consensus       480 dL~g~~~i~~~hv~eA~~  497 (499)
T TIGR00368       480 DLKEEKNISREHLAEAIE  497 (499)
T ss_pred             hhcCCCCCCHHHHHHHHh
Confidence            999999999999999985

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=99.54  E-value=2.9e-13  Score=127.28  Aligned_cols=137  Identities=19%  Similarity=0.270  Sum_probs=92.2

Q ss_pred             CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh----CC------------CCCCCeEEEEEeCCC--CCCChh
Q 022768          126 PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD----GF------------DQLGKVKMIMATNRP--DVLDPA  187 (292)
Q Consensus       126 ~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~----~~------------~~~~~~~vi~t~~~~--~~l~~~  187 (292)
                      .++|+|||++.|           ....+..|.+.++.-.    +.            .-.-++.+|+++|..  ..+++.
T Consensus       218 gGtL~Ldei~~L-----------~~~~q~~Ll~~L~~~~i~~~g~~e~~~~~~~~~~~ip~dvrvIa~~~~~~l~~l~~~  286 (608)
T TIGR00764       218 KGVLYIDEIKTM-----------PLEVQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLDDLEGMHPA  286 (608)
T ss_pred             CCEEEEEChHhC-----------CHHHHHHHHHHHHhCcEEecCccccccccccCCCCCccceEEEEECCHHHHhhcCHH
Confidence            368899999888           6778888888886532    00            011267788888864  578999


Q ss_pred             hcCCCCcc---eEEEccC---CCHHHHHHHHHHHHcC---ccCCCCCCHHHHHHHcC------------CCCHHHHHHHH
Q 022768          188 LLRPGRLD---RKIEIPL---PNEQSRMEILKIHAAG---IAKHGEIDYEAVVKLAE------------GFNGADLRNVC  246 (292)
Q Consensus       188 l~~~~r~~---~~i~l~~---p~~~~r~~i~~~~~~~---~~~~~~~~~~~l~~~~~------------g~~~~di~~l~  246 (292)
                      +++  ||.   ..+.++.   .+.+.+.++++.....   ......++.+.+..+..            ..+.+++..++
T Consensus       287 l~~--rf~~y~v~v~~~~~~~~~~e~~~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~ll  364 (608)
T TIGR00764       287 LRS--RIRGYGYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLV  364 (608)
T ss_pred             HHH--HhcCCeEEEEeeccCCCCHHHHHHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHH
Confidence            998  887   5565533   3456666555543332   11122444444433321            12579999999


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          247 TEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       247 ~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      +.|...|..++...|+.+|+.+|++....
T Consensus       365 R~A~~iA~~~~~~~I~~ehV~~Ai~~~~~  393 (608)
T TIGR00764       365 RAAGDIAKSSGKVYVTAEHVLKAKKLAKT  393 (608)
T ss_pred             HHHHHHHHhcCCceecHHHHHHHHHHHHH
Confidence            99988888888889999999999887764

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.54  E-value=3.8e-13  Score=125.91  Aligned_cols=227  Identities=15%  Similarity=0.188  Sum_probs=133.7

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE-Eec
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK-VVS   99 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~-~~~   99 (292)
                      +..+.+.|.++++|+|.++.++.+..++....        ++..+++.++|+||+|+||||+++.+++.++..+.+ .+.
T Consensus        73 pW~eKyrP~~ldel~~~~~ki~~l~~~l~~~~--------~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~np  144 (637)
T TIGR00602        73 PWVEKYKPETQHELAVHKKKIEEVETWLKAQV--------LENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWSNP  144 (637)
T ss_pred             chHHHhCCCCHHHhcCcHHHHHHHHHHHHhcc--------cccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHhhh
Confidence            45568999999999999999999998876531        123455669999999999999999999998765433 111


Q ss_pred             c---chhcc------------ccChHHHHHHHHHHHhh----------hCCCEEEEEcccccccCCcCCCCCcchHHHHH
Q 022768          100 S---AIIDK------------YIGESARLIREMFGYAR----------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQR  154 (292)
Q Consensus       100 ~---~~~~~------------~~~~~~~~~~~~~~~~~----------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~  154 (292)
                      .   ...+.            ........+..++..+.          .....||+|||++.++..           ...
T Consensus       145 v~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r-----------~~~  213 (637)
T TIGR00602       145 TLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYR-----------DTR  213 (637)
T ss_pred             hhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchh-----------hHH
Confidence            1   00000            00112223333333332          124579999999887421           222


Q ss_pred             HHHHHHH-HhhCCCCCCCeEEEEEeCC-CC--------------CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcC
Q 022768          155 TLMELLN-QLDGFDQLGKVKMIMATNR-PD--------------VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAG  218 (292)
Q Consensus       155 ~l~~~l~-~~~~~~~~~~~~vi~t~~~-~~--------------~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~  218 (292)
                      .+..++. ...   ..+.+.+|++++. +.              .+.+.+++..|+ .+|.|.+.+.....+.++..+..
T Consensus       214 ~lq~lLr~~~~---e~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv-~~I~FnPia~t~l~K~L~rIl~~  289 (637)
T TIGR00602       214 ALHEILRWKYV---SIGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRV-SNISFNPIAPTIMKKFLNRIVTI  289 (637)
T ss_pred             HHHHHHHHHhh---cCCCceEEEEecCCccccccccccccchhcccCHhHhcccce-eEEEeCCCCHHHHHHHHHHHHHh
Confidence            3334443 111   1234445554442 21              133667754455 57899999999988888777764


Q ss_pred             ccCC--CC--C-CHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh-------cCCcccHHHHHHHHH
Q 022768          219 IAKH--GE--I-DYEAVVKLAEGFNGADLRNVCTEAGMSAIRA-------ERDYVIHEDFMKAVR  271 (292)
Q Consensus       219 ~~~~--~~--~-~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~-------~~~~i~~~~~~~a~~  271 (292)
                      ....  .+  + +.+.+..+... +.||+|.++.....++...       ....++..++..+..
T Consensus       290 E~~~~~~~~~~p~~~~l~~I~~~-s~GDiRsAIn~LQf~~~~~g~~a~~~~~~~vs~~hv~~a~~  353 (637)
T TIGR00602       290 EAKKNGEKIKVPKKTSVELLCQG-CSGDIRSAINSLQFSSSKSGSLPIKKRMSTKSDAHASKSKI  353 (637)
T ss_pred             hhhccccccccCCHHHHHHHHHh-CCChHHHHHHHHHHHHhcCCccccccccccccHHHhhhccc
Confidence            2111  11  1 22334333332 4459999999888876542       122455555555543

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.54  E-value=5.8e-13  Score=128.64  Aligned_cols=165  Identities=25%  Similarity=0.405  Sum_probs=117.9

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCC----CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc-
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGI----KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY-  106 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~----~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~-  106 (292)
                      ..++|++++++.+.+.+...        +.|+    .+..+++|+||+|+|||++|+++|+.++.+++.+++.++.... 
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~--------~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~  525 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRS--------RAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHT  525 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHH--------hcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhccc
Confidence            35889999999998887653        1122    2334589999999999999999999999999999987764321 


Q ss_pred             ----cChH-----HHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCC
Q 022768          107 ----IGES-----ARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLGK  171 (292)
Q Consensus       107 ----~~~~-----~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~  171 (292)
                          .|..     ......+...++....+||+|||+|.+           ....+..|+++++...-.      ....+
T Consensus       526 ~~~lig~~~gyvg~~~~~~l~~~~~~~p~~VvllDEieka-----------~~~~~~~Ll~~ld~g~~~d~~g~~vd~~~  594 (731)
T TIGR02639       526 VSRLIGAPPGYVGFEQGGLLTEAVRKHPHCVLLLDEIEKA-----------HPDIYNILLQVMDYATLTDNNGRKADFRN  594 (731)
T ss_pred             HHHHhcCCCCCcccchhhHHHHHHHhCCCeEEEEechhhc-----------CHHHHHHHHHhhccCeeecCCCcccCCCC
Confidence                1110     001122333444566789999999998           788888888888753211      11236


Q ss_pred             eEEEEEeCCCC-------------------------CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          172 VKMIMATNRPD-------------------------VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       172 ~~vi~t~~~~~-------------------------~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      +++|+|+|...                         .+.|.+..  |++.++.|.+++.++..+|++..+.
T Consensus       595 ~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs~e~l~~Iv~~~L~  663 (731)
T TIGR02639       595 VILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLSEEVLEKIVQKFVD  663 (731)
T ss_pred             CEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCCHHHHHHHHHHHHH
Confidence            77899887632                         13456665  8999999999999999999997775

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.54  E-value=5.7e-13  Score=125.54  Aligned_cols=222  Identities=23%  Similarity=0.315  Sum_probs=155.2

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcE
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANF   94 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~   94 (292)
                      ....-.++.++|+++.++++.+.+.+.             ..++-+++|+||+|||.++..+|.+.          +..+
T Consensus       163 ~Ar~gklDPvIGRd~EI~r~iqIL~RR-------------~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i  229 (786)
T COG0542         163 LAREGKLDPVIGRDEEIRRTIQILSRR-------------TKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRI  229 (786)
T ss_pred             HHhcCCCCCCcChHHHHHHHHHHHhcc-------------CCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEE
Confidence            345567788999999999999998763             34567888999999999999999876          4456


Q ss_pred             EEEeccchh--ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCe
Q 022768           95 LKVVSSAII--DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKV  172 (292)
Q Consensus        95 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  172 (292)
                      +.++...+.  .++.|+.+..++.+...+....+.||||||+|.+.+.-+...+  .-+....|.-.+..       +.+
T Consensus       230 ~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~--a~DAaNiLKPaLAR-------GeL  300 (786)
T COG0542         230 YSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGG--AMDAANLLKPALAR-------GEL  300 (786)
T ss_pred             EEecHHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCccccc--ccchhhhhHHHHhc-------CCe
Confidence            777777665  4688999999999999999888899999999999764432221  22333344443332       567


Q ss_pred             EEEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCC-----CHHHHHHHc-----CCC
Q 022768          173 KMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI-----DYEAVVKLA-----EGF  237 (292)
Q Consensus       173 ~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~-----~~~~l~~~~-----~g~  237 (292)
                      .+|++|...+     +-+++|.+  || ..|.+..|+.++...|++..-..+.....+     .+...+.++     +.+
T Consensus       301 ~~IGATT~~EYRk~iEKD~AL~R--RF-Q~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~D~Al~aAv~LS~RYI~dR~  377 (786)
T COG0542         301 RCIGATTLDEYRKYIEKDAALER--RF-QKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPDRF  377 (786)
T ss_pred             EEEEeccHHHHHHHhhhchHHHh--cC-ceeeCCCCCHHHHHHHHHHHHHHHHHccCceecHHHHHHHHHHHHhhcccCC
Confidence            7888886533     35788888  99 888999999999999999766544333222     223333333     334


Q ss_pred             CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          238 NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       238 ~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      -|.-...++++|..............+.+.+-+.
T Consensus       378 LPDKAIDLiDeA~a~~~l~~~~p~~l~~~~~~~~  411 (786)
T COG0542         378 LPDKAIDLLDEAGARVRLEIDKPEELDELERELA  411 (786)
T ss_pred             CCchHHHHHHHHHHHHHhcccCCcchhHHHHHHH
Confidence            5556678888888766554333333333333333

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.52  E-value=8e-13  Score=118.01  Aligned_cols=221  Identities=20%  Similarity=0.289  Sum_probs=133.6

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHh----cCC-CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-ccc
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLR----VGI-KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYI  107 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~----~~~-~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~  107 (292)
                      ++|++++++.+...+...+........    .++ ....++||+||||+|||++|+++|+.++.++..+++..+.. .+.
T Consensus        79 ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L~~~gyv  158 (413)
T TIGR00382        79 VIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYV  158 (413)
T ss_pred             ecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhccccccc
Confidence            799999999998877432222110000    001 12468999999999999999999999999999888776542 344


Q ss_pred             ChH-HHHHHHHHHHh----hhCCCEEEEEcccccccCCcCCCC---CcchHHHHHHHHHHHHHhh--------CCCCCCC
Q 022768          108 GES-ARLIREMFGYA----RDHQPCIIFMDEIDAIGGRRFSEG---TSADREIQRTLMELLNQLD--------GFDQLGK  171 (292)
Q Consensus       108 ~~~-~~~~~~~~~~~----~~~~~~il~lDe~d~l~~~~~~~~---~~~~~~~~~~l~~~l~~~~--------~~~~~~~  171 (292)
                      |.. ...+...+...    ....+++|+|||+|.+..+....+   +......+..|+++++...        ...+...
T Consensus       159 G~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~~~~v~~~~gr~~~~~~  238 (413)
T TIGR00382       159 GEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQE  238 (413)
T ss_pred             cccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccccccccchhHHHHHHHHhhccceecccCCCccccCCC
Confidence            542 33333433322    234568999999999975432211   1122367777888774211        0112235


Q ss_pred             eEEEEEeCCC---------------------------C-----------------------CCChhhcCCCCcceEEEcc
Q 022768          172 VKMIMATNRP---------------------------D-----------------------VLDPALLRPGRLDRKIEIP  201 (292)
Q Consensus       172 ~~vi~t~~~~---------------------------~-----------------------~l~~~l~~~~r~~~~i~l~  201 (292)
                      +++|.|+|..                           .                       .+.|.+..  |++.++.|.
T Consensus       239 ~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEflg--Rld~Iv~f~  316 (413)
T TIGR00382       239 FIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIG--RLPVIATLE  316 (413)
T ss_pred             eEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHhC--CCCeEeecC
Confidence            6777777651                           0                       02234444  888889999


Q ss_pred             CCCHHHHHHHHHHH----HcCc-------cCCCCCC---HHHHHHH--cCCCCHHHHHHHHHHHHHHHHHh
Q 022768          202 LPNEQSRMEILKIH----AAGI-------AKHGEID---YEAVVKL--AEGFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       202 ~p~~~~r~~i~~~~----~~~~-------~~~~~~~---~~~l~~~--~~g~~~~di~~l~~~a~~~a~~~  256 (292)
                      +++.++..+|+...    ..++       .+.-.++   .+.++..  ...+-.|.++.+++....-+...
T Consensus       317 pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~Lr~iie~~l~~~m~e  387 (413)
T TIGR00382       317 KLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVMFD  387 (413)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchHHHHHHHHhhHHHHhh
Confidence            99999999887642    2211       1111122   3334443  23455788888888777766554

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=99.51  E-value=1.6e-12  Score=108.09  Aligned_cols=132  Identities=24%  Similarity=0.261  Sum_probs=99.3

Q ss_pred             CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC-------------CCCCChhhcCC
Q 022768          125 QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR-------------PDVLDPALLRP  191 (292)
Q Consensus       125 ~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~-------------~~~l~~~l~~~  191 (292)
                      -|++|||||+|.|           +-++-..|...+..     + -..++|+++|.             |+.+++.+++ 
T Consensus       296 vPGVLFIDEVhML-----------DiEcFTyL~kalES-----~-iaPivifAsNrG~~~irGt~d~~sPhGip~dllD-  357 (456)
T KOG1942|consen  296 VPGVLFIDEVHML-----------DIECFTYLHKALES-----P-IAPIVIFASNRGMCTIRGTEDILSPHGIPPDLLD-  357 (456)
T ss_pred             cCcceEeeehhhh-----------hhHHHHHHHHHhcC-----C-CCceEEEecCCcceeecCCcCCCCCCCCCHHHhh-
Confidence            5899999999998           66666666665542     1 23445665553             4568888988 


Q ss_pred             CCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          192 GRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       192 ~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                       |. ..|...+++.++.++|++.+....... .+-.+..|+.+....+.+...+++..|...|...++..|..+|+.+..
T Consensus       358 -Rl-~Iirt~~y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~  435 (456)
T KOG1942|consen  358 -RL-LIIRTLPYDEEEIRQIIKIRAQVEGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVT  435 (456)
T ss_pred             -he-eEEeeccCCHHHHHHHHHHHHhhhcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHH
Confidence             77 667777788889999999888754443 333466677776667888999999999999999999999999999988


Q ss_pred             HHHhhh
Q 022768          271 RKLNEA  276 (292)
Q Consensus       271 ~~~~~~  276 (292)
                      .-+...
T Consensus       436 ~Lf~Da  441 (456)
T KOG1942|consen  436 ELFLDA  441 (456)
T ss_pred             HHHHhc
Confidence            877654

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.51  E-value=7e-13  Score=116.62  Aligned_cols=147  Identities=21%  Similarity=0.360  Sum_probs=104.6

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCc-eEEEEcCCCChHHHHHHHHHHhcC-------------------
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPK-GVLLYGPPGTGKTLLARAIASNID-------------------   91 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~-~vll~G~~G~GKT~l~~~la~~l~-------------------   91 (292)
                      ++++|.+++..++..+....            .... .+||+||||+|||++|.++|+.+.                   
T Consensus         1 ~~~~~~~~~~~~l~~~~~~~------------~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~   68 (325)
T COG0470           1 DELVPWQEAVKRLLVQALES------------GRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLI   68 (325)
T ss_pred             CCcccchhHHHHHHHHHHhc------------CCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHH
Confidence            35788888888888887642            2233 499999999999999999999886                   


Q ss_pred             -----CcEEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           92 -----ANFLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        92 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                           ..+++++..+.....  .....++.+......    ....|++|||+|.+           ....+.++...+.+
T Consensus        69 ~~~~~~d~lel~~s~~~~~~--i~~~~vr~~~~~~~~~~~~~~~kviiidead~m-----------t~~A~nallk~lEe  135 (325)
T COG0470          69 PAGNHPDFLELNPSDLRKID--IIVEQVRELAEFLSESPLEGGYKVVIIDEADKL-----------TEDAANALLKTLEE  135 (325)
T ss_pred             hhcCCCceEEecccccCCCc--chHHHHHHHHHHhccCCCCCCceEEEeCcHHHH-----------hHHHHHHHHHHhcc
Confidence                 456667666654321  123334444433322    34579999999999           66666666666653


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEI  211 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i  211 (292)
                           +..+..+|.+||.++.+-+.+++  |+ ..+.|++|+.......
T Consensus       136 -----p~~~~~~il~~n~~~~il~tI~S--Rc-~~i~f~~~~~~~~i~~  176 (325)
T COG0470         136 -----PPKNTRFILITNDPSKILPTIRS--RC-QRIRFKPPSRLEAIAW  176 (325)
T ss_pred             -----CCCCeEEEEEcCChhhccchhhh--cc-eeeecCCchHHHHHHH
Confidence                 44678899999999999999999  77 7788888654444333

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=99.50  E-value=4e-13  Score=115.89  Aligned_cols=106  Identities=27%  Similarity=0.276  Sum_probs=69.7

Q ss_pred             CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC------------CCCCChhhcCCC
Q 022768          125 QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR------------PDVLDPALLRPG  192 (292)
Q Consensus       125 ~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~------------~~~l~~~l~~~~  192 (292)
                      -|+||||||+|.|           +-++-..|...++.     . -..++|.+||+            |+.+|.++++  
T Consensus       278 vpGVLFIDEvHmL-----------DiEcFsfLnralEs-----~-~sPiiIlATNRg~~~irGt~~~sphGiP~DlLD--  338 (398)
T PF06068_consen  278 VPGVLFIDEVHML-----------DIECFSFLNRALES-----E-LSPIIILATNRGITKIRGTDIISPHGIPLDLLD--  338 (398)
T ss_dssp             EE-EEEEESGGGS-----------BHHHHHHHHHHHTS-----T-T--EEEEEES-SEEE-BTTS-EEETT--HHHHT--
T ss_pred             ecceEEecchhhc-----------cHHHHHHHHHHhcC-----C-CCcEEEEecCceeeeccCccCcCCCCCCcchHh--
Confidence            3789999999999           88777777777653     1 24556666663            4578889998  


Q ss_pred             CcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHH
Q 022768          193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAG  250 (292)
Q Consensus       193 r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~  250 (292)
                      |+ ..|...+++.++..+|++.++....+. .+-.++.|.......+.+...+++..|.
T Consensus       339 Rl-lII~t~py~~~ei~~Il~iR~~~E~v~i~~~al~~L~~ig~~~SLRYAiqLi~~a~  396 (398)
T PF06068_consen  339 RL-LIIRTKPYSEEEIKQILKIRAKEEDVEISEDALDLLTKIGVETSLRYAIQLITPAS  396 (398)
T ss_dssp             TE-EEEEE----HHHHHHHHHHHHHHCT--B-HHHHHHHHHHHHHS-HHHHHHCHHHHH
T ss_pred             hc-EEEECCCCCHHHHHHHHHhhhhhhcCcCCHHHHHHHHHHhhhccHHHHHHhhhhhh
Confidence            88 888999999999999999888754333 2234566667766678888888887664

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=99.50  E-value=5.2e-13  Score=119.67  Aligned_cols=208  Identities=25%  Similarity=0.305  Sum_probs=144.8

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK  105 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~  105 (292)
                      ..+..++|...+.+++.+.+...           .....+|||+|++||||..+|+++.+..   +.||+.+||..+...
T Consensus       138 ~~~~~liG~S~am~~l~~~i~kv-----------A~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~  206 (464)
T COG2204         138 SLGGELVGESPAMQQLRRLIAKV-----------APSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPEN  206 (464)
T ss_pred             cccCCceecCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHH
Confidence            46788999999999999998775           4557789999999999999999999877   459999999987544


Q ss_pred             ccChHHHHHHHHHHHhh---------------hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC--
Q 022768          106 YIGESARLIREMFGYAR---------------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ--  168 (292)
Q Consensus       106 ~~~~~~~~~~~~~~~~~---------------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~--  168 (292)
                      ...+      ++|...+               ....+.||||||..+           .-..|..|+.+++.-.-.+-  
T Consensus       207 l~ES------ELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~m-----------pl~~Q~kLLRvLqe~~~~rvG~  269 (464)
T COG2204         207 LLES------ELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEM-----------PLELQVKLLRVLQEREFERVGG  269 (464)
T ss_pred             HHHH------HhhcccccCcCCcccccCcceeEcCCceEEeeccccC-----------CHHHHHHHHHHHHcCeeEecCC
Confidence            3222      4555433               245689999999998           88999999999986431111  


Q ss_pred             ----CCCeEEEEEeCCC-------CCCChhhcCCCCcceEEEccCCCHHHHHH----HHHHHHc----Cc-cCCCCCCHH
Q 022768          169 ----LGKVKMIMATNRP-------DVLDPALLRPGRLDRKIEIPLPNEQSRME----ILKIHAA----GI-AKHGEIDYE  228 (292)
Q Consensus       169 ----~~~~~vi~t~~~~-------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~~~~~~----~~-~~~~~~~~~  228 (292)
                          .-++.||++||..       ...-++|..  |+ .++.+..|...+|.+    ++.+++.    .. .....++.+
T Consensus       270 ~~~i~vdvRiIaaT~~dL~~~v~~G~FReDLyy--RL-nV~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~~~~~s~~  346 (464)
T COG2204         270 NKPIKVDVRIIAATNRDLEEEVAAGRFREDLYY--RL-NVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPE  346 (464)
T ss_pred             CcccceeeEEEeecCcCHHHHHHcCCcHHHHHh--hh-ccceecCCcccccchhHHHHHHHHHHHHHHHcCCCCCCCCHH
Confidence                1157899998853       123333433  44 456777777777764    4444444    22 223567778


Q ss_pred             HHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Q 022768          229 AVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFM  267 (292)
Q Consensus       229 ~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~  267 (292)
                      .+..+...-.||.+++|-+.+...++......|+.+++.
T Consensus       347 a~~~L~~y~WPGNVREL~N~ver~~il~~~~~i~~~~l~  385 (464)
T COG2204         347 ALAALLAYDWPGNVRELENVVERAVILSEGPEIEVEDLP  385 (464)
T ss_pred             HHHHHHhCCCChHHHHHHHHHHHHHhcCCccccchhhcc
Confidence            888887755666777666666666666666566665543

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.49  E-value=2.9e-12  Score=105.71  Aligned_cols=181  Identities=15%  Similarity=0.210  Sum_probs=126.9

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-cE--EE----
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-NF--LK----   96 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-~~--~~----   96 (292)
                      +.+.|-+++.+.+.++....++.+...             ..-.|+++|||+|+||-|.+.++.+++.. .+  +.    
T Consensus         5 dkyrpksl~~l~~~~e~~~~Lksl~~~-------------~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~   71 (351)
T KOG2035|consen    5 DKYRPKSLDELIYHEELANLLKSLSST-------------GDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETR   71 (351)
T ss_pred             hhcCcchhhhcccHHHHHHHHHHhccc-------------CCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeE
Confidence            467888999999999999999888652             12358999999999999999999988822 11  11    


Q ss_pred             --------------Eeccchhcc---ccCh-HHHHHHHHHHHhhh---------CCCEEEEEcccccccCCcCCCCCcch
Q 022768           97 --------------VVSSAIIDK---YIGE-SARLIREMFGYARD---------HQPCIIFMDEIDAIGGRRFSEGTSAD  149 (292)
Q Consensus        97 --------------~~~~~~~~~---~~~~-~~~~~~~~~~~~~~---------~~~~il~lDe~d~l~~~~~~~~~~~~  149 (292)
                                    +....+..-   ..|. ....+++++....+         ..-.+++|.|+|.|           .
T Consensus        72 t~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~L-----------T  140 (351)
T KOG2035|consen   72 TFTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADEL-----------T  140 (351)
T ss_pred             EEecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhh-----------h
Confidence                          111111100   1111 12223444443332         22369999999999           8


Q ss_pred             HHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCC-CHH
Q 022768          150 REIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI-DYE  228 (292)
Q Consensus       150 ~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~-~~~  228 (292)
                      .+.|.+|...++...     +.+.+|..+|..+.+-+++++  |+ ..+.++.|+.++...++...+......-+. -..
T Consensus       141 ~dAQ~aLRRTMEkYs-----~~~RlIl~cns~SriIepIrS--RC-l~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~  212 (351)
T KOG2035|consen  141 RDAQHALRRTMEKYS-----SNCRLILVCNSTSRIIEPIRS--RC-LFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLK  212 (351)
T ss_pred             HHHHHHHHHHHHHHh-----cCceEEEEecCcccchhHHhh--he-eEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHH
Confidence            899999998887654     478899999999999999999  76 778999999999999999888755444222 234


Q ss_pred             HHHHHcCC
Q 022768          229 AVVKLAEG  236 (292)
Q Consensus       229 ~l~~~~~g  236 (292)
                      .++..++|
T Consensus       213 rIa~kS~~  220 (351)
T KOG2035|consen  213 RIAEKSNR  220 (351)
T ss_pred             HHHHHhcc
Confidence            45555554

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.49  E-value=1.7e-12  Score=121.95  Aligned_cols=200  Identities=21%  Similarity=0.236  Sum_probs=134.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEeccchhccccChHH--HHHHH-HHH----HhhhCCCEEEEEccccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSSAIIDKYIGESA--RLIRE-MFG----YARDHQPCIIFMDEIDA  136 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~~~~~~~~~~~~--~~~~~-~~~----~~~~~~~~il~lDe~d~  136 (292)
                      -.+|||.|++|+|||++++++++.++.  +|+.+......+...|...  ..+.. .+.    .......++|||||++.
T Consensus        16 ~g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~lDEi~r   95 (589)
T TIGR02031        16 LGGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYVDMANL   95 (589)
T ss_pred             cceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcEeccchhh
Confidence            357999999999999999999998764  5777765333333333321  00100 000    01113447999999999


Q ss_pred             ccCCcCCCCCcchHHHHHHHHHHHHHhh------C--CCCCCCeEEEEEeCCCC---CCChhhcCCCCcceEEEccC-CC
Q 022768          137 IGGRRFSEGTSADREIQRTLMELLNQLD------G--FDQLGKVKMIMATNRPD---VLDPALLRPGRLDRKIEIPL-PN  204 (292)
Q Consensus       137 l~~~~~~~~~~~~~~~~~~l~~~l~~~~------~--~~~~~~~~vi~t~~~~~---~l~~~l~~~~r~~~~i~l~~-p~  204 (292)
                      +           +...+..|.+.++...      +  .....++.+|+|+|..+   .+++.+.+  ||...+.+.. |+
T Consensus        96 l-----------~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld--Rf~l~v~~~~~~~  162 (589)
T TIGR02031        96 L-----------DDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD--RLALHVSLEDVAS  162 (589)
T ss_pred             C-----------CHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH--hccCeeecCCCCC
Confidence            9           8889999999887532      1  11123688899888765   68889998  9988887754 57


Q ss_pred             HHHHHHHHHHHHcCcc-------------------CCC--CCC---HHHHHHH--cCCC-CHHHHHHHHHHHHHHHHHhc
Q 022768          205 EQSRMEILKIHAAGIA-------------------KHG--EID---YEAVVKL--AEGF-NGADLRNVCTEAGMSAIRAE  257 (292)
Q Consensus       205 ~~~r~~i~~~~~~~~~-------------------~~~--~~~---~~~l~~~--~~g~-~~~di~~l~~~a~~~a~~~~  257 (292)
                      .++|.+|++.......                   ...  .+.   +..+...  ..|. +.+--..+++.|...|..++
T Consensus       163 ~~er~eil~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~g  242 (589)
T TIGR02031       163 QDLRVEIVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHG  242 (589)
T ss_pred             HHHHHHHHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhC
Confidence            7788888877542110                   000  011   1112221  1233 36777789999999999999


Q ss_pred             CCcccHHHHHHHHHHHhhhhh
Q 022768          258 RDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       258 ~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      +.+|+.+|+..|..-+-.+..
T Consensus       243 r~~V~~~Dv~~a~~lvl~hR~  263 (589)
T TIGR02031       243 RTEVTEEDLKLAVELVLLPRA  263 (589)
T ss_pred             CCCCCHHHHHHHHHHHhhhhc
Confidence            999999999999999887654

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>PRK04132 replication factor C small subunit; Provisional

Probab=99.49  E-value=1.2e-12  Score=125.69  Aligned_cols=173  Identities=21%  Similarity=0.229  Sum_probs=120.8

Q ss_pred             CceEEEEc--CCCChHHHHHHHHHHhc-----CCcEEEEeccchhccccChHHHHHHHHHHHhhh------CCCEEEEEc
Q 022768           66 PKGVLLYG--PPGTGKTLLARAIASNI-----DANFLKVVSSAIIDKYIGESARLIREMFGYARD------HQPCIIFMD  132 (292)
Q Consensus        66 ~~~vll~G--~~G~GKT~l~~~la~~l-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~il~lD  132 (292)
                      +-+-++.|  |++.||||+|+++|+++     +.+++++|+++..+      ...++.+......      .+..|++||
T Consensus       564 ~~~~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rg------id~IR~iIk~~a~~~~~~~~~~KVvIID  637 (846)
T PRK04132        564 GYHNFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERG------INVIREKVKEFARTKPIGGASFKIIFLD  637 (846)
T ss_pred             chhhhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCccc------HHHHHHHHHHHHhcCCcCCCCCEEEEEE
Confidence            44567779  99999999999999998     45789999887532      1233333322211      123799999


Q ss_pred             ccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHH
Q 022768          133 EIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEIL  212 (292)
Q Consensus       133 e~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~  212 (292)
                      |+|.|           +...+.+|..+++.     +...+.+|++||+++.+.+++++  || ..+.|++|+.++....+
T Consensus       638 EaD~L-----------t~~AQnALLk~lEe-----p~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~~i~~~L  698 (846)
T PRK04132        638 EADAL-----------TQDAQQALRRTMEM-----FSSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRL  698 (846)
T ss_pred             CcccC-----------CHHHHHHHHHHhhC-----CCCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHHHHHHHH
Confidence            99999           77788888887764     33578899999999999999999  77 88999999999999888


Q ss_pred             HHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          213 KIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       213 ~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      ++.+...... .+..+..++..++| +.+.+.++++.+.   ...  ..|+.+++...
T Consensus       699 ~~I~~~Egi~i~~e~L~~Ia~~s~G-DlR~AIn~Lq~~~---~~~--~~It~~~V~~~  750 (846)
T PRK04132        699 RYIAENEGLELTEEGLQAILYIAEG-DMRRAINILQAAA---ALD--DKITDENVFLV  750 (846)
T ss_pred             HHHHHhcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH---Hhc--CCCCHHHHHHH
Confidence            8877643322 23345667777777 4445555554433   221  24555554443

>PHA02244 ATPase-like protein

Probab=99.48  E-value=2.2e-12  Score=112.29  Aligned_cols=127  Identities=24%  Similarity=0.275  Sum_probs=85.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccC---hHHHHHHHHHHHhhhCCCEEEEEcccccccCC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIG---ESARLIREMFGYARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~  140 (292)
                      ..+.+++|+||+|||||++|+++|..++.+++.++...-.....+   ........-+-.+. ..+++|+|||++.+   
T Consensus       117 ~~~~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~-~~GgvLiLDEId~a---  192 (383)
T PHA02244        117 NANIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAF-KKGGLFFIDEIDAS---  192 (383)
T ss_pred             hcCCCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHh-hcCCEEEEeCcCcC---
Confidence            346689999999999999999999999999999884311000111   00000001111122 34579999999988   


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHh-----h-CCCCCCCeEEEEEeCCC-----------CCCChhhcCCCCcceEEEccCC
Q 022768          141 RFSEGTSADREIQRTLMELLNQL-----D-GFDQLGKVKMIMATNRP-----------DVLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       141 ~~~~~~~~~~~~~~~l~~~l~~~-----~-~~~~~~~~~vi~t~~~~-----------~~l~~~l~~~~r~~~~i~l~~p  203 (292)
                              ....+..|..++...     . .....+++.+|+|+|..           ..+++++++  || ..+.+.+|
T Consensus       193 --------~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllD--RF-v~I~~dyp  261 (383)
T PHA02244        193 --------IPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLD--RF-APIEFDYD  261 (383)
T ss_pred             --------CHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHh--hc-EEeeCCCC
Confidence                    677777777777521     1 11234688999999973           457889998  99 67899999


Q ss_pred             CH
Q 022768          204 NE  205 (292)
Q Consensus       204 ~~  205 (292)
                      +.
T Consensus       262 ~~  263 (383)
T PHA02244        262 EK  263 (383)
T ss_pred             cH
Confidence            84

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.48  E-value=1.3e-12  Score=114.66  Aligned_cols=191  Identities=21%  Similarity=0.240  Sum_probs=120.9

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcccc
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYI  107 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~  107 (292)
                      +++++|.....+++.+.+...           ...+.+|+|+|++||||+++|+++....   +.+++.++|..+.....
T Consensus         5 ~~~liG~S~~~~~~~~~i~~~-----------a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~~~~   73 (326)
T PRK11608          5 KDNLLGEANSFLEVLEQVSRL-----------APLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNENLL   73 (326)
T ss_pred             cCccEECCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCHHHH
Confidence            567999999999999988775           3456789999999999999999998765   46899999987632110


Q ss_pred             ChHHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-----
Q 022768          108 GESARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-----  167 (292)
Q Consensus       108 ~~~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-----  167 (292)
                            -..+|+.               ......+.|||||++.+           ....+..|..+++......     
T Consensus        74 ------~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L-----------~~~~Q~~L~~~l~~~~~~~~g~~~  136 (326)
T PRK11608         74 ------DSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATA-----------PMLVQEKLLRVIEYGELERVGGSQ  136 (326)
T ss_pred             ------HHHHccccccccCCcccccCCchhccCCCeEEeCChhhC-----------CHHHHHHHHHHHhcCcEEeCCCCc
Confidence                  1112211               12234589999999999           8888999988886532111     


Q ss_pred             -CCCCeEEEEEeCCC-------CCCChhhcCCCCc-ceEEEccCCCH--HHHHHHHHHHHcCc----cCC--CCCCHHHH
Q 022768          168 -QLGKVKMIMATNRP-------DVLDPALLRPGRL-DRKIEIPLPNE--QSRMEILKIHAAGI----AKH--GEIDYEAV  230 (292)
Q Consensus       168 -~~~~~~vi~t~~~~-------~~l~~~l~~~~r~-~~~i~l~~p~~--~~r~~i~~~~~~~~----~~~--~~~~~~~l  230 (292)
                       ...++.+|++++..       ..+.+.+..  |+ ...|.+|+...  ++...++.+++...    ...  ..++.+.+
T Consensus       137 ~~~~~~RiI~~s~~~l~~l~~~g~f~~dL~~--~l~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al  214 (326)
T PRK11608        137 PLQVNVRLVCATNADLPAMVAEGKFRADLLD--RLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERAR  214 (326)
T ss_pred             eeeccEEEEEeCchhHHHHHHcCCchHHHHH--hcCCCEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHH
Confidence             01257888887653       234556655  56 23445554432  23334555554322    111  24566666


Q ss_pred             HHHcCCC---CHHHHHHHHHHHHH
Q 022768          231 VKLAEGF---NGADLRNVCTEAGM  251 (292)
Q Consensus       231 ~~~~~g~---~~~di~~l~~~a~~  251 (292)
                      ..+...-   |.+++.++++.+..
T Consensus       215 ~~L~~y~WPGNvrEL~~vl~~a~~  238 (326)
T PRK11608        215 ETLLNYRWPGNIRELKNVVERSVY  238 (326)
T ss_pred             HHHHhCCCCcHHHHHHHHHHHHHH
Confidence            6665433   44555566666554

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.47  E-value=2.3e-12  Score=112.61  Aligned_cols=156  Identities=20%  Similarity=0.355  Sum_probs=105.4

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCc------------------------EEEEeccchhccccChHHHHHHHHHHH
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDAN------------------------FLKVVSSAIIDKYIGESARLIREMFGY  120 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (292)
                      -++.+||+||+|+||+++|+.+|+.+.+.                        ++.+....- +  ..-..+.++.+...
T Consensus        21 ~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~-~--~~i~id~iR~l~~~   97 (328)
T PRK05707         21 HPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEA-D--KTIKVDQVRELVSF   97 (328)
T ss_pred             cceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCC-C--CCCCHHHHHHHHHH
Confidence            36679999999999999999999988542                        111211100 0  01123444454444


Q ss_pred             hh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcce
Q 022768          121 AR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDR  196 (292)
Q Consensus       121 ~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~  196 (292)
                      +.    .....|++||++|.+           +......|+..+++     +.+++.+|.+|+.++.+.+.++|  |+ .
T Consensus        98 ~~~~~~~~~~kv~iI~~a~~m-----------~~~aaNaLLK~LEE-----Pp~~~~fiL~t~~~~~ll~TI~S--Rc-~  158 (328)
T PRK05707         98 VVQTAQLGGRKVVLIEPAEAM-----------NRNAANALLKSLEE-----PSGDTVLLLISHQPSRLLPTIKS--RC-Q  158 (328)
T ss_pred             HhhccccCCCeEEEECChhhC-----------CHHHHHHHHHHHhC-----CCCCeEEEEEECChhhCcHHHHh--hc-e
Confidence            43    244679999999999           77777777777664     44688899999999999999999  88 6


Q ss_pred             EEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          197 KIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       197 ~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      .+.|++|+.++..+.+......   ..+.+...+...+.| +++....+.
T Consensus       159 ~~~~~~~~~~~~~~~L~~~~~~---~~~~~~~~~l~la~G-sp~~A~~l~  204 (328)
T PRK05707        159 QQACPLPSNEESLQWLQQALPE---SDERERIELLTLAGG-SPLRALQLH  204 (328)
T ss_pred             eeeCCCcCHHHHHHHHHHhccc---CChHHHHHHHHHcCC-CHHHHHHHH
Confidence            6999999999888777754321   112223455667776 555554443

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.47  E-value=7.3e-13  Score=124.03  Aligned_cols=209  Identities=23%  Similarity=0.271  Sum_probs=132.9

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccch
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAI  102 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~  102 (292)
                      .+..+++.++|.....+++.+.+...           .....+|+|+|++||||+++|+++....   +.+++.++|..+
T Consensus       190 ~~~~~~~~liG~s~~~~~~~~~~~~~-----------a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~  258 (534)
T TIGR01817       190 RRSGKEDGIIGKSPAMRQVVDQARVV-----------ARSNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAAL  258 (534)
T ss_pred             cccCccCceEECCHHHHHHHHHHHHH-----------hCcCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCC
Confidence            34578999999999999999988765           3456789999999999999999999875   569999999876


Q ss_pred             hccccChHHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC
Q 022768          103 IDKYIGESARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD  167 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  167 (292)
                      ....      .-..+|+.               ......++|||||++.+           +...|..|..+++......
T Consensus       259 ~~~~------~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L-----------~~~~Q~~Ll~~l~~~~~~~  321 (534)
T TIGR01817       259 SETL------LESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEI-----------SPAFQAKLLRVLQEGEFER  321 (534)
T ss_pred             CHHH------HHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhC-----------CHHHHHHHHHHHhcCcEEE
Confidence            3311      11122221               11234579999999999           8888999988887532100


Q ss_pred             ------CCCCeEEEEEeCCC-------CCCChhhcCCCCcc-eEEEccCCC--HHHHHHHHHHHHcCc----cCCCCCCH
Q 022768          168 ------QLGKVKMIMATNRP-------DVLDPALLRPGRLD-RKIEIPLPN--EQSRMEILKIHAAGI----AKHGEIDY  227 (292)
Q Consensus       168 ------~~~~~~vi~t~~~~-------~~l~~~l~~~~r~~-~~i~l~~p~--~~~r~~i~~~~~~~~----~~~~~~~~  227 (292)
                            ...++.+|++++..       ..+.+.+..  |+. ..|.+|+..  .++...++..++...    .....++.
T Consensus       322 ~~~~~~~~~~~riI~~s~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~s~  399 (534)
T TIGR01817       322 VGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYY--RINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITP  399 (534)
T ss_pred             CCCCceEeecEEEEEeCCCCHHHHHHcCCCCHHHHH--HhcCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCCCH
Confidence                  01147788887653       123334443  442 345555554  234445666665432    12234566


Q ss_pred             HHHHHHcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Q 022768          228 EAVVKLAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDFM  267 (292)
Q Consensus       228 ~~l~~~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~~  267 (292)
                      +.+..+...-   |.++++++++.|.   .......|+.+++.
T Consensus       400 ~a~~~L~~~~WPGNvrEL~~v~~~a~---~~~~~~~I~~~~l~  439 (534)
T TIGR01817       400 SAIRVLMSCKWPGNVRELENCLERTA---TLSRSGTITRSDFS  439 (534)
T ss_pred             HHHHHHHhCCCCChHHHHHHHHHHHH---HhCCCCcccHHHCc
Confidence            6666655533   4445555555554   44445678888875

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.47  E-value=2.6e-12  Score=122.81  Aligned_cols=209  Identities=22%  Similarity=0.276  Sum_probs=131.9

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhc
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIID  104 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~  104 (292)
                      ..+|++++|.....+++.+.+...           .....+|+|+|++||||+++|+++.+..   +.+++.++|..+..
T Consensus       321 ~~~~~~l~g~s~~~~~~~~~~~~~-----------a~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~  389 (638)
T PRK11388        321 SHTFDHMPQDSPQMRRLIHFGRQA-----------AKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPD  389 (638)
T ss_pred             cccccceEECCHHHHHHHHHHHHH-----------hCcCCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCCh
Confidence            457999999999999888887764           3446679999999999999999999876   46999999987642


Q ss_pred             cccChHHHHHHHHHHHh------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC---
Q 022768          105 KYIGESARLIREMFGYA------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL---  169 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~---  169 (292)
                      .      .....+|...            .....++|||||++.+           +...|..|..+++.....+..   
T Consensus       390 ~------~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l-----------~~~~Q~~Ll~~l~~~~~~~~~~~~  452 (638)
T PRK11388        390 E------ALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYL-----------SPELQSALLQVLKTGVITRLDSRR  452 (638)
T ss_pred             H------HHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhC-----------CHHHHHHHHHHHhcCcEEeCCCCc
Confidence            1      1112333321            1234589999999999           888999999888653211111   


Q ss_pred             ---CCeEEEEEeCCCC-------CCChhhcCCCCcceEEEccCCCHHHHH----HHHHHHHcCc----cCCCCCCHHHHH
Q 022768          170 ---GKVKMIMATNRPD-------VLDPALLRPGRLDRKIEIPLPNEQSRM----EILKIHAAGI----AKHGEIDYEAVV  231 (292)
Q Consensus       170 ---~~~~vi~t~~~~~-------~l~~~l~~~~r~~~~i~l~~p~~~~r~----~i~~~~~~~~----~~~~~~~~~~l~  231 (292)
                         -++.+|+|++..-       .+.+.+..  |+ ..+.+..|...+|.    .++..++...    .....++.+.+.
T Consensus       453 ~~~~~~riI~~t~~~l~~~~~~~~f~~dL~~--~l-~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~  529 (638)
T PRK11388        453 LIPVDVRVIATTTADLAMLVEQNRFSRQLYY--AL-HAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALA  529 (638)
T ss_pred             eEEeeEEEEEeccCCHHHHHhcCCChHHHhh--hh-ceeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHHH
Confidence               1567888887531       22233332  33 24455666666664    3455554432    112235666666


Q ss_pred             HHcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          232 KLAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       232 ~~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      .+...-   |.++++++++.+..   ......|+.+++...+
T Consensus       530 ~L~~y~WPGNvreL~~~l~~~~~---~~~~~~i~~~~lp~~~  568 (638)
T PRK11388        530 RLVSYRWPGNDFELRSVIENLAL---SSDNGRIRLSDLPEHL  568 (638)
T ss_pred             HHHcCCCCChHHHHHHHHHHHHH---hCCCCeecHHHCchhh
Confidence            665432   44555555555443   3344567777776655

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=99.46  E-value=2.7e-12  Score=112.20  Aligned_cols=224  Identities=20%  Similarity=0.227  Sum_probs=145.3

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc------c
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS------A  101 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~------~  101 (292)
                      .+.|..++|++..+..|......|             .-.++||.|+.|+||||++++++..+..--+...|.      +
T Consensus        13 ~~pf~aivGqd~lk~aL~l~av~P-------------~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~   79 (423)
T COG1239          13 NLPFTAIVGQDPLKLALGLNAVDP-------------QIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDD   79 (423)
T ss_pred             ccchhhhcCchHHHHHHhhhhccc-------------ccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCC
Confidence            478889999999999888776554             344799999999999999999999884322111110      0


Q ss_pred             --------------------------hhccccChHHHHH------HHHHHH---------hhhCCCEEEEEcccccccCC
Q 022768          102 --------------------------IIDKYIGESARLI------REMFGY---------ARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus       102 --------------------------~~~~~~~~~~~~~------~~~~~~---------~~~~~~~il~lDe~d~l~~~  140 (292)
                                                +...-.+.+++.+      ......         ....+.+||++||++.|   
T Consensus        80 P~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL---  156 (423)
T COG1239          80 PEEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLL---  156 (423)
T ss_pred             hhhhhHHHHhhccccccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEeccccc---
Confidence                                      0111112233311      111110         11234579999999999   


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHh--------hCCCCCCCeEEEEEeCCCC-CCChhhcCCCCcceEEEccCC-CHHHHHH
Q 022768          141 RFSEGTSADREIQRTLMELLNQL--------DGFDQLGKVKMIMATNRPD-VLDPALLRPGRLDRKIEIPLP-NEQSRME  210 (292)
Q Consensus       141 ~~~~~~~~~~~~~~~l~~~l~~~--------~~~~~~~~~~vi~t~~~~~-~l~~~l~~~~r~~~~i~l~~p-~~~~r~~  210 (292)
                              +...+..|++.+...        -.+....++++|+|+|+.+ +|-+.|++  ||+..+.+.+| +.++|.+
T Consensus       157 --------~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqLlD--Rfg~~v~~~~~~~~~~rv~  226 (423)
T COG1239         157 --------DDHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQLLD--RFGLEVDTHYPLDLEERVE  226 (423)
T ss_pred             --------cHHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhhHh--hhcceeeccCCCCHHHHHH
Confidence                    889999999888773        1223444899999999864 68899999  99999988665 7789998


Q ss_pred             HHHHHHcCccCCCC----------------------------CCHH------HHHHHcCCCCHHHHHHHHHHHHHHHHHh
Q 022768          211 ILKIHAAGIAKHGE----------------------------IDYE------AVVKLAEGFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       211 i~~~~~~~~~~~~~----------------------------~~~~------~l~~~~~g~~~~di~~l~~~a~~~a~~~  256 (292)
                      |+++.+.- ....+                            ++..      .+.....-...+-..-+++.+...|...
T Consensus       227 Ii~r~~~f-~~~Pe~f~~~~~~~~~~lR~~ii~ar~~l~~V~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~  305 (423)
T COG1239         227 IIRRRLAF-EAVPEAFLEKYADAQRALRARIIAARSLLSEVELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALR  305 (423)
T ss_pred             HHHHHHHh-hcCcHHHHHHHHHHHHHHHHHHHHHHhccccccCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhc
Confidence            88866541 11000                            0000      0111111111233345667777788888


Q ss_pred             cCCcccHHHHHHHHHHHhhhhh
Q 022768          257 ERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       257 ~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      ++..++.+|+++|..-.-....
T Consensus       306 Gr~~v~~~Di~~a~~l~l~hR~  327 (423)
T COG1239         306 GRTEVEEEDIREAAELALLHRR  327 (423)
T ss_pred             CceeeehhhHHHHHhhhhhhhh
Confidence            9999999999999887766543

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.46  E-value=1.5e-12  Score=114.33  Aligned_cols=149  Identities=17%  Similarity=0.227  Sum_probs=106.2

Q ss_pred             ccccccc-cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---------------
Q 022768           30 SYSAVGG-LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---------------   93 (292)
Q Consensus        30 ~~~~l~g-~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---------------   93 (292)
                      .|+.|+| ++.+++.|...+..-            .-++.+||+||+|+||+++++.+++.+-+.               
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~~~------------~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~   70 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIAKN------------RLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCK   70 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHHcC------------CCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHH
Confidence            4788899 888999999887642            446678999999999999999999987432               


Q ss_pred             ---------EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHH
Q 022768           94 ---------FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELL  160 (292)
Q Consensus        94 ---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l  160 (292)
                               +..+...   +..  ...+.++.+.....    .....|++|||+|.+           +...+..|+..+
T Consensus        71 ~~~~~~hpD~~~i~~~---~~~--i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~-----------~~~a~NaLLK~L  134 (329)
T PRK08058         71 RIDSGNHPDVHLVAPD---GQS--IKKDQIRYLKEEFSKSGVESNKKVYIIEHADKM-----------TASAANSLLKFL  134 (329)
T ss_pred             HHhcCCCCCEEEeccc---ccc--CCHHHHHHHHHHHhhCCcccCceEEEeehHhhh-----------CHHHHHHHHHHh
Confidence                     1111110   000  11233444443332    234579999999999           666666666666


Q ss_pred             HHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHH
Q 022768          161 NQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKI  214 (292)
Q Consensus       161 ~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~  214 (292)
                      ++     +++.+.+|.+++.++.+.+.+++  |+ ..+.|++|+.++..+.++.
T Consensus       135 EE-----Pp~~~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        135 EE-----PSGGTTAILLTENKHQILPTILS--RC-QVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             cC-----CCCCceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCHHHHHHHHHH
Confidence            53     44678888888889999999999  77 7899999999888777654

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.46  E-value=2.8e-12  Score=112.51  Aligned_cols=188  Identities=23%  Similarity=0.255  Sum_probs=116.2

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChH
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGES  110 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~  110 (292)
                      |+|.....+++.+.+...           .....+|+|+|++||||+++|+++....   +.|++.++|..+.....   
T Consensus         1 liG~S~~m~~~~~~~~~~-----------a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~~~l---   66 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRL-----------APLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLL---   66 (329)
T ss_pred             CCcCCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCChHHH---
Confidence            467778888887777664           3446789999999999999999998755   46999999987542211   


Q ss_pred             HHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCC
Q 022768          111 ARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQL  169 (292)
Q Consensus       111 ~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~  169 (292)
                         -..+|..               ......++|||||++.|           +...|..|..+++.....      ...
T Consensus        67 ---~~~lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L-----------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~  132 (329)
T TIGR02974        67 ---DSELFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATA-----------SLLVQEKLLRVIEYGEFERVGGSQTLQ  132 (329)
T ss_pred             ---HHHHhccccccccCcccccCCchhhCCCCEEEeCChHhC-----------CHHHHHHHHHHHHcCcEEecCCCceec
Confidence               1122221               11234589999999999           888999999888753210      112


Q ss_pred             CCeEEEEEeCCC-------CCCChhhcCCCCcceEEEccCCCHHHHH----HHHHHHHcCc----cCC--CCCCHHHHHH
Q 022768          170 GKVKMIMATNRP-------DVLDPALLRPGRLDRKIEIPLPNEQSRM----EILKIHAAGI----AKH--GEIDYEAVVK  232 (292)
Q Consensus       170 ~~~~vi~t~~~~-------~~l~~~l~~~~r~~~~i~l~~p~~~~r~----~i~~~~~~~~----~~~--~~~~~~~l~~  232 (292)
                      .++.+|++++..       ..+.+.+..  |+. .+.+..|...+|.    .++..++...    ...  ..++.+.+..
T Consensus       133 ~~~RiI~at~~~l~~~~~~g~fr~dL~~--rl~-~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~  209 (329)
T TIGR02974       133 VDVRLVCATNADLPALAAEGRFRADLLD--RLA-FDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQ  209 (329)
T ss_pred             cceEEEEechhhHHHHhhcCchHHHHHH--Hhc-chhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHH
Confidence            357888888653       123455554  552 3345555555554    4555554422    212  2456666666


Q ss_pred             HcCCC---CHHHHHHHHHHHHHH
Q 022768          233 LAEGF---NGADLRNVCTEAGMS  252 (292)
Q Consensus       233 ~~~g~---~~~di~~l~~~a~~~  252 (292)
                      +...-   |.++++++++.+...
T Consensus       210 L~~y~WPGNvrEL~n~i~~~~~~  232 (329)
T TIGR02974       210 LLEYHWPGNVRELKNVVERSVYR  232 (329)
T ss_pred             HHhCCCCchHHHHHHHHHHHHHh
Confidence            65533   444555555555443

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.46  E-value=3.1e-12  Score=103.70  Aligned_cols=143  Identities=21%  Similarity=0.358  Sum_probs=95.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCc------------------------EEEEeccchhccccChHHHHHHHHHHH
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDAN------------------------FLKVVSSAIIDKYIGESARLIREMFGY  120 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (292)
                      .++.+||+||+|+|||++++.+++.+.+.                        +..+....   ..  .....++.+...
T Consensus        13 ~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~---~~--~~~~~i~~i~~~   87 (188)
T TIGR00678        13 LAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEG---QS--IKVDQVRELVEF   87 (188)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEecccc---Cc--CCHHHHHHHHHH
Confidence            45679999999999999999999987542                        11111110   00  122344444444


Q ss_pred             hhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcce
Q 022768          121 ARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDR  196 (292)
Q Consensus       121 ~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~  196 (292)
                      +..    ....+++|||+|.+           ....+..|...++.     +.+...+|++++.+..+.+.+++  |+ .
T Consensus        88 ~~~~~~~~~~kviiide~~~l-----------~~~~~~~Ll~~le~-----~~~~~~~il~~~~~~~l~~~i~s--r~-~  148 (188)
T TIGR00678        88 LSRTPQESGRRVVIIEDAERM-----------NEAAANALLKTLEE-----PPPNTLFILITPSPEKLLPTIRS--RC-Q  148 (188)
T ss_pred             HccCcccCCeEEEEEechhhh-----------CHHHHHHHHHHhcC-----CCCCeEEEEEECChHhChHHHHh--hc-E
Confidence            432    34579999999999           55555555555542     33467777778888889999998  77 6


Q ss_pred             EEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCC
Q 022768          197 KIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEG  236 (292)
Q Consensus       197 ~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g  236 (292)
                      .+.|.+|+.++..+++...  +  +. +.....++..+.|
T Consensus       149 ~~~~~~~~~~~~~~~l~~~--g--i~-~~~~~~i~~~~~g  183 (188)
T TIGR00678       149 VLPFPPLSEEALLQWLIRQ--G--IS-EEAAELLLALAGG  183 (188)
T ss_pred             EeeCCCCCHHHHHHHHHHc--C--CC-HHHHHHHHHHcCC
Confidence            8999999999998888776  2  22 2234555555555

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.45  E-value=9.7e-12  Score=103.74  Aligned_cols=144  Identities=22%  Similarity=0.257  Sum_probs=105.8

Q ss_pred             CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC------------CCCCCChhhcCCC
Q 022768          125 QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN------------RPDVLDPALLRPG  192 (292)
Q Consensus       125 ~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~------------~~~~l~~~l~~~~  192 (292)
                      .|+||||||+|.|           +-++-..|...+..-      -..++|.++|            .|+.++-.+++  
T Consensus       288 vpGVLFIDEvHML-----------DIEcFsFlNrAlE~d------~~PiiimaTNrgit~iRGTn~~SphGiP~D~lD--  348 (454)
T KOG2680|consen  288 VPGVLFIDEVHML-----------DIECFSFLNRALEND------MAPIIIMATNRGITRIRGTNYRSPHGIPIDLLD--  348 (454)
T ss_pred             ccceEEEeeehhh-----------hhHHHHHHHHHhhhc------cCcEEEEEcCCceEEeecCCCCCCCCCcHHHhh--
Confidence            4789999999999           777777776666531      1233444444            25678888888  


Q ss_pred             CcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       193 r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      |+ ..|...+++.++..+|++.++....+. .+..++.|......-+.+...+++..|...|.++....+..+|+.++++
T Consensus       349 R~-lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~  427 (454)
T KOG2680|consen  349 RM-LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR  427 (454)
T ss_pred             hh-heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence            77 678888899999999999888754433 2333556666666678899999999999999999999999999999999


Q ss_pred             HHhhhh-hhchhhhhhhh
Q 022768          272 KLNEAK-KLESSAHYNAD  288 (292)
Q Consensus       272 ~~~~~~-~~~~~~~~~~~  288 (292)
                      -+-..+ +.+-..+|.+-
T Consensus       428 LFlD~~Rs~~yl~E~~~~  445 (454)
T KOG2680|consen  428 LFLDEKRSMKYLTEYQSG  445 (454)
T ss_pred             HHhhhhhhhHHHHHhhhc
Confidence            887643 32333444443

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=99.45  E-value=8.5e-12  Score=114.61  Aligned_cols=221  Identities=16%  Similarity=0.227  Sum_probs=147.9

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEEeccch
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVSSAI  102 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~~~~~~  102 (292)
                      .|.+++...+.|..++..++..        -..+.+++|.|-||||||.+++.+.+.+          ...++++|...+
T Consensus       397 sLpcRe~E~~~I~~f~~~~i~~--------~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l  468 (767)
T KOG1514|consen  397 SLPCRENEFSEIEDFLRSFISD--------QGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRL  468 (767)
T ss_pred             cccchhHHHHHHHHHHHhhcCC--------CCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceee
Confidence            3677788888888888775322        0224579999999999999999999866          356788887665


Q ss_pred             hccc----------cCh------HHHHHHHHHHHh-hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          103 IDKY----------IGE------SARLIREMFGYA-RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       103 ~~~~----------~~~------~~~~~~~~~~~~-~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      .+..          .+.      .-..+..-|... ....+.||+|||+|.|           -...|..|..+++... 
T Consensus       469 ~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~L-----------vtr~QdVlYn~fdWpt-  536 (767)
T KOG1514|consen  469 ASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDIL-----------VTRSQDVLYNIFDWPT-  536 (767)
T ss_pred             cCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHH-----------hcccHHHHHHHhcCCc-
Confidence            4310          000      000111111100 1135689999999999           4455788889888755 


Q ss_pred             CCCCCCeEEEEEeCCCCC----CChhhcCCCCcc-eEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCC--C
Q 022768          166 FDQLGKVKMIMATNRPDV----LDPALLRPGRLD-RKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGF--N  238 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~~----l~~~l~~~~r~~-~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~--~  238 (292)
                       .++.+.+||+.+|..+.    +...+-+  |++ ..+.|.+++.++..+|+..++.+...-.....+.+++...-.  .
T Consensus       537 -~~~sKLvvi~IaNTmdlPEr~l~nrvsS--Rlg~tRi~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSGD  613 (767)
T KOG1514|consen  537 -LKNSKLVVIAIANTMDLPERLLMNRVSS--RLGLTRICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSGD  613 (767)
T ss_pred             -CCCCceEEEEecccccCHHHHhccchhh--hccceeeecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhcccc
Confidence             55568889998887543    2333444  443 578999999999999999999876222222223333322222  4


Q ss_pred             HHHHHHHHHHHHHHHHHhcC-------CcccHHHHHHHHHHHhhh
Q 022768          239 GADLRNVCTEAGMSAIRAER-------DYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~~~~-------~~i~~~~~~~a~~~~~~~  276 (292)
                      .+....+|++|...|-.+..       ..|+..++.+|+..|-..
T Consensus       614 aRraldic~RA~Eia~~~~~~~k~~~~q~v~~~~v~~Ai~em~~~  658 (767)
T KOG1514|consen  614 ARRALDICRRAAEIAEERNVKGKLAVSQLVGILHVMEAINEMLAS  658 (767)
T ss_pred             HHHHHHHHHHHHHHhhhhcccccccccceeehHHHHHHHHHHhhh
Confidence            45666889999998888765       578999999999988754

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.44  E-value=9.2e-12  Score=121.74  Aligned_cols=206  Identities=20%  Similarity=0.300  Sum_probs=130.0

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc-
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY-  106 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~-  106 (292)
                      ...++|++++++.+.+.+.....+   ... .-.|...++|+||+|+|||++|++++..+   +.+++.+++.++.... 
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~g---l~~-~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~  642 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAG---LSD-PNRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHS  642 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhc---ccC-CCCCCceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhh
Confidence            346899999999999988653110   000 01122468999999999999999999987   4578888887764321 


Q ss_pred             ----cChH----H-HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCC
Q 022768          107 ----IGES----A-RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLGK  171 (292)
Q Consensus       107 ----~~~~----~-~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~  171 (292)
                          .|..    . ..-..+....+....++|+|||++.+           ....+..|..+++...-.      ....+
T Consensus       643 ~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka-----------~~~v~~~Ll~ile~g~l~d~~gr~vd~rn  711 (857)
T PRK10865        643 VSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKA-----------HPDVFNILLQVLDDGRLTDGQGRTVDFRN  711 (857)
T ss_pred             HHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhC-----------CHHHHHHHHHHHhhCceecCCceEEeecc
Confidence                1000    0 00011222233344589999999988           788888888888653211      11235


Q ss_pred             eEEEEEeCCCC-------------------------CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc-------
Q 022768          172 VKMIMATNRPD-------------------------VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI-------  219 (292)
Q Consensus       172 ~~vi~t~~~~~-------------------------~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~-------  219 (292)
                      +++|+|+|...                         .+.+.+..  |++..+.|.+++.+....|++.++...       
T Consensus       712 ~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELln--Rld~iivF~PL~~edl~~Iv~~~L~~l~~rl~~~  789 (857)
T PRK10865        712 TVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEER  789 (857)
T ss_pred             cEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHH--hCCeeEecCCCCHHHHHHHHHHHHHHHHHHHHhC
Confidence            67888988631                         13456666  888899999999999998888776532       


Q ss_pred             cCCCCCCHHHHHHHcC-CCC----HHHHHHHHHHHHHHH
Q 022768          220 AKHGEIDYEAVVKLAE-GFN----GADLRNVCTEAGMSA  253 (292)
Q Consensus       220 ~~~~~~~~~~l~~~~~-g~~----~~di~~l~~~a~~~a  253 (292)
                      ...-.++.+.+..+.. ||+    .+.++.+++.-....
T Consensus       790 gi~l~is~~al~~L~~~gy~~~~GARpL~r~I~~~i~~~  828 (857)
T PRK10865        790 GYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQIENP  828 (857)
T ss_pred             CCcCcCCHHHHHHHHHcCCCccCChHHHHHHHHHHHHHH
Confidence            2222345555554432 443    466666666554433

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=99.44  E-value=7.7e-14  Score=112.15  Aligned_cols=124  Identities=26%  Similarity=0.354  Sum_probs=72.5

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----EEEeccc----
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----LKVVSSA----  101 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----~~~~~~~----  101 (292)
                      .|++|+|++.+|+.|+-+...               ++++|++||||+|||++|+.+...+..--    +++....    
T Consensus         1 Df~dI~GQe~aKrAL~iAAaG---------------~h~lLl~GppGtGKTmlA~~l~~lLP~l~~~e~le~~~i~s~~~   65 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAAG---------------GHHLLLIGPPGTGKTMLARRLPSLLPPLTEEEALEVSKIYSVAG   65 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHHC---------------C--EEEES-CCCTHHHHHHHHHHCS--CCEECCESS--S-TT--
T ss_pred             ChhhhcCcHHHHHHHHHHHcC---------------CCCeEEECCCCCCHHHHHHHHHHhCCCCchHHHhhhcccccccc
Confidence            478999999999999988764               57899999999999999999998763211    0000000    


Q ss_pred             ------hhc----cccChHHHHHHHHHHH--------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHh
Q 022768          102 ------IID----KYIGESARLIREMFGY--------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQL  163 (292)
Q Consensus       102 ------~~~----~~~~~~~~~~~~~~~~--------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~  163 (292)
                            +..    .....+ .....++.-        +.....+||||||+..+           +....+.|.+.++..
T Consensus        66 ~~~~~~~~~~~Pfr~phhs-~s~~~liGgg~~~~PGeislAh~GVLflDE~~ef-----------~~~vld~Lr~ple~g  133 (206)
T PF01078_consen   66 LGPDEGLIRQRPFRAPHHS-ASEAALIGGGRPPRPGEISLAHRGVLFLDELNEF-----------DRSVLDALRQPLEDG  133 (206)
T ss_dssp             -S---EEEE---EEEE-TT---HHHHHEEGGGEEE-CGGGGTTSEEEECETTTS------------HHHHHHHHHHHHHS
T ss_pred             CCCCCceecCCCcccCCCC-cCHHHHhCCCcCCCcCHHHHhcCCEEEechhhhc-----------CHHHHHHHHHHHHCC
Confidence                  000    000000 001111211        12245589999999888           888888888888764


Q ss_pred             hC--------CCCCCCeEEEEEeCC
Q 022768          164 DG--------FDQLGKVKMIMATNR  180 (292)
Q Consensus       164 ~~--------~~~~~~~~vi~t~~~  180 (292)
                      ..        ..-..++.+|+|+|.
T Consensus       134 ~v~i~R~~~~~~~Pa~f~lv~a~NP  158 (206)
T PF01078_consen  134 EVTISRAGGSVTYPARFLLVAAMNP  158 (206)
T ss_dssp             BEEEEETTEEEEEB--EEEEEEE-S
T ss_pred             eEEEEECCceEEEecccEEEEEecc
Confidence            21        112227889999884

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>PRK09862 putative ATP-dependent protease; Provisional

Probab=99.44  E-value=4.2e-12  Score=116.13  Aligned_cols=217  Identities=21%  Similarity=0.234  Sum_probs=135.3

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc----EEEEecc----
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN----FLKVVSS----  100 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~----~~~~~~~----  100 (292)
                      .+|.+++|...+++.+.-.               ...+.+++|+||+|+|||++++.++..+...    .+++..-    
T Consensus       188 ~d~~~v~Gq~~~~~al~la---------------a~~G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~  252 (506)
T PRK09862        188 HDLSDVIGQEQGKRGLEIT---------------AAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLV  252 (506)
T ss_pred             cCeEEEECcHHHHhhhhee---------------ccCCcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhh
Confidence            4788999998877765433               2457889999999999999999999866321    1111110    


Q ss_pred             -------chhcc-c--cC--hHHH-HHH----HHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHh
Q 022768          101 -------AIIDK-Y--IG--ESAR-LIR----EMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQL  163 (292)
Q Consensus       101 -------~~~~~-~--~~--~~~~-~~~----~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~  163 (292)
                             .+... +  ..  .+.. .+.    .--........++|||||++.+           +...+..|.+.++.-
T Consensus       253 g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG~l~~A~gGvLfLDEi~e~-----------~~~~~~~L~~~LE~g  321 (506)
T PRK09862        253 NAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEF-----------ERRTLDALREPIESG  321 (506)
T ss_pred             ccccccCCcCCCCccCCCccchHHHHhCCCceehhhHhhhccCCEEecCCchhC-----------CHHHHHHHHHHHHcC
Confidence                   00000 0  00  0011 110    0001222344589999999988           788888888887553


Q ss_pred             hC--------CCCCCCeEEEEEeCCCC---------------------CCChhhcCCCCcceEEEccCCCHHH-------
Q 022768          164 DG--------FDQLGKVKMIMATNRPD---------------------VLDPALLRPGRLDRKIEIPLPNEQS-------  207 (292)
Q Consensus       164 ~~--------~~~~~~~~vi~t~~~~~---------------------~l~~~l~~~~r~~~~i~l~~p~~~~-------  207 (292)
                      ..        .....++.+|+|+|...                     .++..+++  ||+..+.+++++.++       
T Consensus       322 ~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~~l~~~~~~  399 (506)
T PRK09862        322 QIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPGILSKTVVP  399 (506)
T ss_pred             cEEEecCCcceeccCCEEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHh--hccEEEEeCCCCHHHHhcccCC
Confidence            21        11234789999998742                     36678888  999999998875321       


Q ss_pred             ---HHHHHHHHH----cC----ccCCCCCCHHHHH----------------HHcCCCCHHHHHHHHHHHHHHHHHhcCCc
Q 022768          208 ---RMEILKIHA----AG----IAKHGEIDYEAVV----------------KLAEGFNGADLRNVCTEAGMSAIRAERDY  260 (292)
Q Consensus       208 ---r~~i~~~~~----~~----~~~~~~~~~~~l~----------------~~~~g~~~~di~~l~~~a~~~a~~~~~~~  260 (292)
                         ...+-+...    .+    ...+..+....+.                ....|+|.|....+++-|...|..+++..
T Consensus       400 ~ess~~i~~rV~~ar~~q~~r~~~~n~~l~~~~l~~~~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~  479 (506)
T PRK09862        400 GESSATVKQRVMAARERQFKRQNKLNAWLDSPEIRQFCKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDI  479 (506)
T ss_pred             CCChHHHHHHHhhHHHHHHHHHHHHhcccCHHHHHHHhCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCC
Confidence               111111100    00    0111222111111                12236799999999999999999999999


Q ss_pred             ccHHHHHHHHHHH
Q 022768          261 VIHEDFMKAVRKL  273 (292)
Q Consensus       261 i~~~~~~~a~~~~  273 (292)
                      |+.+|+.+|+..-
T Consensus       480 V~~~hv~eAl~yR  492 (506)
T PRK09862        480 ITRQHLQEAVSYR  492 (506)
T ss_pred             CCHHHHHHHHHhh
Confidence            9999999999864

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=99.43  E-value=1.1e-11  Score=105.05  Aligned_cols=211  Identities=18%  Similarity=0.215  Sum_probs=130.0

Q ss_pred             cccccHHHH---HHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC---------CcEEEEecc
Q 022768           33 AVGGLSDQI---RELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID---------ANFLKVVSS  100 (292)
Q Consensus        33 ~l~g~~~~~---~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~---------~~~~~~~~~  100 (292)
                      .-+|+..+.   ++|.+.+..|          ......+++|+|++|.|||++++.+++...         .|++.+...
T Consensus        35 rWIgY~~A~~~L~~L~~Ll~~P----------~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P  104 (302)
T PF05621_consen   35 RWIGYPRAKEALDRLEELLEYP----------KRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMP  104 (302)
T ss_pred             CeecCHHHHHHHHHHHHHHhCC----------cccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecC
Confidence            345665554   4455555444          123356799999999999999999997662         356666543


Q ss_pred             chhcc----------------ccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh
Q 022768          101 AIIDK----------------YIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD  164 (292)
Q Consensus       101 ~~~~~----------------~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~  164 (292)
                      .-.+.                ...........+....+..+..+|+|||+|.++.+        ....+..++++++.+.
T Consensus       105 ~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaG--------s~~~qr~~Ln~LK~L~  176 (302)
T PF05621_consen  105 PEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAG--------SYRKQREFLNALKFLG  176 (302)
T ss_pred             CCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcc--------cHHHHHHHHHHHHHHh
Confidence            22210                01112333344556667778899999999997532        3445666777776663


Q ss_pred             CCCCCCCeEEEEEeC--CCC--CCChhhcCCCCcceEEEccCCC-HHHHHHHHHHHHcCccCC--CCCC----HHHHHHH
Q 022768          165 GFDQLGKVKMIMATN--RPD--VLDPALLRPGRLDRKIEIPLPN-EQSRMEILKIHAAGIAKH--GEID----YEAVVKL  233 (292)
Q Consensus       165 ~~~~~~~~~vi~t~~--~~~--~l~~~l~~~~r~~~~i~l~~p~-~~~r~~i~~~~~~~~~~~--~~~~----~~~l~~~  233 (292)
                      .   .-++.+|+...  -..  .-++.+.+  || ..+.++.-. .++...++..+....+..  ..+.    ...+..+
T Consensus       177 N---eL~ipiV~vGt~~A~~al~~D~QLa~--RF-~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~  250 (302)
T PF05621_consen  177 N---ELQIPIVGVGTREAYRALRTDPQLAS--RF-EPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHER  250 (302)
T ss_pred             h---ccCCCeEEeccHHHHHHhccCHHHHh--cc-CCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Confidence            2   12334444332  112  23456666  88 445554432 245555666555433322  2222    2456677


Q ss_pred             cCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHH
Q 022768          234 AEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMK  268 (292)
Q Consensus       234 ~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~  268 (292)
                      ++| +.|++..++..|...|+..+...||.+.+..
T Consensus       251 s~G-~iG~l~~ll~~aA~~AI~sG~E~It~~~l~~  284 (302)
T PF05621_consen  251 SEG-LIGELSRLLNAAAIAAIRSGEERITREILDK  284 (302)
T ss_pred             cCC-chHHHHHHHHHHHHHHHhcCCceecHHHHhh
Confidence            888 5559999999999999999999999988876

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.43  E-value=4.5e-12  Score=117.88  Aligned_cols=210  Identities=21%  Similarity=0.243  Sum_probs=129.1

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccch
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAI  102 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~  102 (292)
                      ....+|++++|.....+++.+.+...           .....+|+|+|++||||+++|+++....   ..+++.++|..+
T Consensus       198 ~~~~~f~~~ig~s~~~~~~~~~~~~~-----------A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~  266 (520)
T PRK10820        198 NDDSAFSQIVAVSPKMRQVVEQARKL-----------AMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASI  266 (520)
T ss_pred             cccccccceeECCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccC
Confidence            35679999999999888888777653           2346679999999999999999987654   468999999886


Q ss_pred             hccccChHHHHHHHHHHHh---------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC
Q 022768          103 IDKYIGESARLIREMFGYA---------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD  167 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~---------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  167 (292)
                      ....      .-..+|...               .....+.|||||++.+           +...|..|..+++.....+
T Consensus       267 ~~~~------~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L-----------~~~~Q~~Ll~~l~~~~~~~  329 (520)
T PRK10820        267 PDDV------VESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEM-----------SPRMQAKLLRFLNDGTFRR  329 (520)
T ss_pred             CHHH------HHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEEeChhhC-----------CHHHHHHHHHHHhcCCccc
Confidence            4311      111223211               1234579999999999           8888999988887532101


Q ss_pred             ------CCCCeEEEEEeCCC-------CCCChhhcCCCCcceEEEccCCCHHHHH----HHHHHHHcC----ccC-CCCC
Q 022768          168 ------QLGKVKMIMATNRP-------DVLDPALLRPGRLDRKIEIPLPNEQSRM----EILKIHAAG----IAK-HGEI  225 (292)
Q Consensus       168 ------~~~~~~vi~t~~~~-------~~l~~~l~~~~r~~~~i~l~~p~~~~r~----~i~~~~~~~----~~~-~~~~  225 (292)
                            ...++.+|++++..       ....+.+..  |+. .+.+..|+..+|.    .++..++..    ... ...+
T Consensus       330 ~g~~~~~~~~vRiI~st~~~l~~l~~~g~f~~dL~~--rL~-~~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~l  406 (520)
T PRK10820        330 VGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYY--RLN-VLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKL  406 (520)
T ss_pred             CCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHh--hcC-eeEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCc
Confidence                  11256788887653       123444554  542 2455555555554    344444432    222 1246


Q ss_pred             CHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHH
Q 022768          226 DYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDF  266 (292)
Q Consensus       226 ~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~  266 (292)
                      +.+.+..+...-.|++++++-+.....+.......|+.+++
T Consensus       407 s~~a~~~L~~y~WPGNvreL~nvl~~a~~~~~~~~i~~~~~  447 (520)
T PRK10820        407 AADLNTVLTRYGWPGNVRQLKNAIYRALTQLEGYELRPQDI  447 (520)
T ss_pred             CHHHHHHHhcCCCCCHHHHHHHHHHHHHHhCCCCcccHHHc
Confidence            67777776654344455554444443333334445666664

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.43  E-value=1.8e-11  Score=106.32  Aligned_cols=168  Identities=13%  Similarity=0.209  Sum_probs=110.1

Q ss_pred             HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------------------------
Q 022768           38 SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------------------------   93 (292)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------------------------   93 (292)
                      ....+.|.+.+..-            .-++.+||+||+|+||+++|+.+|+.+-+.                        
T Consensus         8 ~~~~~~l~~~~~~~------------rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD   75 (325)
T PRK06871          8 QPTYQQITQAFQQG------------LGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPD   75 (325)
T ss_pred             HHHHHHHHHHHHcC------------CcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCC
Confidence            34566666665441            346789999999999999999999988442                        


Q ss_pred             EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC
Q 022768           94 FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL  169 (292)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~  169 (292)
                      +..+...+  +..  -..+.++.+...+.    .....|++||++|.|           .......|+..++     .++
T Consensus        76 ~~~i~p~~--~~~--I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m-----------~~~AaNaLLKtLE-----EPp  135 (325)
T PRK06871         76 FHILEPID--NKD--IGVDQVREINEKVSQHAQQGGNKVVYIQGAERL-----------TEAAANALLKTLE-----EPR  135 (325)
T ss_pred             EEEEcccc--CCC--CCHHHHHHHHHHHhhccccCCceEEEEechhhh-----------CHHHHHHHHHHhc-----CCC
Confidence            11111100  010  12334444444332    234579999999999           7777777777666     456


Q ss_pred             CCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHH
Q 022768          170 GKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNV  245 (292)
Q Consensus       170 ~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l  245 (292)
                      +++.+|.+|+.++.+.+.++|  |+ ..+.|++|+.++..+.+......    .......+...+.| +++...++
T Consensus       136 ~~~~fiL~t~~~~~llpTI~S--RC-~~~~~~~~~~~~~~~~L~~~~~~----~~~~~~~~~~l~~g-~p~~A~~~  203 (325)
T PRK06871        136 PNTYFLLQADLSAALLPTIYS--RC-QTWLIHPPEEQQALDWLQAQSSA----EISEILTALRINYG-RPLLALTF  203 (325)
T ss_pred             CCeEEEEEECChHhCchHHHh--hc-eEEeCCCCCHHHHHHHHHHHhcc----ChHHHHHHHHHcCC-CHHHHHHH
Confidence            788999999999999999999  88 77899999998888777654321    11123344555665 44444433

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=99.42  E-value=5.3e-12  Score=99.56  Aligned_cols=134  Identities=25%  Similarity=0.379  Sum_probs=90.8

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc----------------------
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN----------------------   93 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~----------------------   93 (292)
                      |++++++.|.+.+..-            .-++.+||+||+|+||+++|..+++.+-+.                      
T Consensus         1 gq~~~~~~L~~~~~~~------------~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~   68 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSG------------RLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHP   68 (162)
T ss_dssp             S-HHHHHHHHHHHHCT------------C--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CT
T ss_pred             CcHHHHHHHHHHHHcC------------CcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCc
Confidence            7888999999888652            446779999999999999999999877321                      


Q ss_pred             -EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           94 -FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        94 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                       ++.+.......   .-..+.++.+......    ....|++|||+|.+           ..+.+.+|+..+++     +
T Consensus        69 d~~~~~~~~~~~---~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l-----------~~~a~NaLLK~LEe-----p  129 (162)
T PF13177_consen   69 DFIIIKPDKKKK---SIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKL-----------TEEAQNALLKTLEE-----P  129 (162)
T ss_dssp             TEEEEETTTSSS---SBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS------------HHHHHHHHHHHHS-----T
T ss_pred             ceEEEecccccc---hhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhh-----------hHHHHHHHHHHhcC-----C
Confidence             22232221100   0123444454444432    35689999999999           88888888888874     4


Q ss_pred             CCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCC
Q 022768          169 LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       169 ~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p  203 (292)
                      ..++.+|.+|+.++.+.+.++|  |+ ..+.|++.
T Consensus       130 p~~~~fiL~t~~~~~il~TI~S--Rc-~~i~~~~l  161 (162)
T PF13177_consen  130 PENTYFILITNNPSKILPTIRS--RC-QVIRFRPL  161 (162)
T ss_dssp             TTTEEEEEEES-GGGS-HHHHT--TS-EEEEE---
T ss_pred             CCCEEEEEEECChHHChHHHHh--hc-eEEecCCC
Confidence            5689999999999999999999  77 66777654

...

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.42  E-value=1.5e-11  Score=120.64  Aligned_cols=207  Identities=19%  Similarity=0.298  Sum_probs=133.4

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc--
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY--  106 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~--  106 (292)
                      ..++|++++++.+.+.+.....+   .. ..-.|...++|.||+|+|||++|++++..+   +.+++.++++.+....  
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~g---l~-~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~  640 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAG---LS-DPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSV  640 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhcc---CC-CCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchH
Confidence            46899999999999998763111   00 001234568999999999999999999987   4578888887654321  


Q ss_pred             ---cChH----H-HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------CCCCe
Q 022768          107 ---IGES----A-RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------QLGKV  172 (292)
Q Consensus       107 ---~~~~----~-~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~~~~~  172 (292)
                         .|..    . ..-..+....+....+||+|||++.+           ....+..|+++++...-..      ...++
T Consensus       641 ~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka-----------~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~  709 (852)
T TIGR03346       641 ARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKA-----------HPDVFNVLLQVLDDGRLTDGQGRTVDFRNT  709 (852)
T ss_pred             HHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccC-----------CHHHHHHHHHHHhcCceecCCCeEEecCCc
Confidence               1100    0 00112333334455679999999998           8888999999887542111      12367


Q ss_pred             EEEEEeCCCCC-------------------------CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc-------c
Q 022768          173 KMIMATNRPDV-------------------------LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI-------A  220 (292)
Q Consensus       173 ~vi~t~~~~~~-------------------------l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~-------~  220 (292)
                      +||+|+|....                         ..+.+..  |++.++.|.+++.+...+|+...+...       .
T Consensus       710 iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL~~e~l~~I~~l~L~~l~~~l~~~~  787 (852)
T TIGR03346       710 VIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERK  787 (852)
T ss_pred             EEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCcCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            79999987321                         2344554  888899999999999999888665421       1


Q ss_pred             CCCCCCHHHHHHHcC-----CCCHHHHHHHHHHHHHHHHH
Q 022768          221 KHGEIDYEAVVKLAE-----GFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       221 ~~~~~~~~~l~~~~~-----g~~~~di~~l~~~a~~~a~~  255 (292)
                      +.-.++.+.+..+..     .+..+.++.+++......+.
T Consensus       788 ~~l~i~~~a~~~L~~~~~~~~~gaR~L~~~i~~~i~~~l~  827 (852)
T TIGR03346       788 ITLELSDAALDFLAEAGYDPVYGARPLKRAIQREIENPLA  827 (852)
T ss_pred             CeecCCHHHHHHHHHhCCCCCCCchhHHHHHHHHHHHHHH
Confidence            122334443333322     34567888777776655544

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.42  E-value=1.7e-12  Score=114.35  Aligned_cols=201  Identities=25%  Similarity=0.286  Sum_probs=130.7

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEec
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVS   99 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~   99 (292)
                      .......+++|+|.....+++.+.+...           .+.+.+|||+|++|+||+.+|+.+....    ..|++.+||
T Consensus        70 ~~~~~~~~~~LIG~~~~~~~~~eqik~~-----------ap~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NC  138 (403)
T COG1221          70 PYLKSEALDDLIGESPSLQELREQIKAY-----------APSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNC  138 (403)
T ss_pred             hhccchhhhhhhccCHHHHHHHHHHHhh-----------CCCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEH
Confidence            3456678899999999999988888764           4668889999999999999999888533    569999999


Q ss_pred             cchhccccChHHHHHHHHHHHhhh---------------CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh
Q 022768          100 SAIIDKYIGESARLIREMFGYARD---------------HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD  164 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~  164 (292)
                      ..+.......      .+|+..+.               ...++|||||++.+           ....|..|+.+++...
T Consensus       139 a~~~en~~~~------eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~L-----------P~~~Q~kLl~~le~g~  201 (403)
T COG1221         139 AAYSENLQEA------ELFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRL-----------PPEGQEKLLRVLEEGE  201 (403)
T ss_pred             HHhCcCHHHH------HHhccccceeecccCCcCchheecCCCEEehhhhhhC-----------CHhHHHHHHHHHHcCc
Confidence            9886654322      24443321               34579999999999           8899999999998742


Q ss_pred             CC------CCCCCeEEEEEeCCC--CCCCh--hhcCCCCcceEEEccCCCH--HHHHHHHHHHHc----CccCCCCCCH-
Q 022768          165 GF------DQLGKVKMIMATNRP--DVLDP--ALLRPGRLDRKIEIPLPNE--QSRMEILKIHAA----GIAKHGEIDY-  227 (292)
Q Consensus       165 ~~------~~~~~~~vi~t~~~~--~~l~~--~l~~~~r~~~~i~l~~p~~--~~r~~i~~~~~~----~~~~~~~~~~-  227 (292)
                      -.      .....+.+|++|+..  +.+-.  .+.++ ++...|++|+...  +++..++++++.    ........+. 
T Consensus       202 ~~rvG~~~~~~~dVRli~AT~~~l~~~~~~g~dl~~r-l~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~~~  280 (403)
T COG1221         202 YRRVGGSQPRPVDVRLICATTEDLEEAVLAGADLTRR-LNILTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVDSP  280 (403)
T ss_pred             eEecCCCCCcCCCceeeeccccCHHHHHHhhcchhhh-hcCceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCCCH
Confidence            11      122367788877542  22333  34331 3334555555432  233344555544    3333322222 


Q ss_pred             HHHHHHc----CCCCHHHHHHHHHHHHHHHH
Q 022768          228 EAVVKLA----EGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       228 ~~l~~~~----~g~~~~di~~l~~~a~~~a~  254 (292)
                      +.+....    .| |.+++.++++.++..+.
T Consensus       281 ~a~~~L~~y~~pG-NirELkN~Ve~~~~~~~  310 (403)
T COG1221         281 EALRALLAYDWPG-NIRELKNLVERAVAQAS  310 (403)
T ss_pred             HHHHHHHhCCCCC-cHHHHHHHHHHHHHHhc
Confidence            3333322    33 77888888888887774

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=99.40  E-value=4.5e-12  Score=113.91  Aligned_cols=210  Identities=25%  Similarity=0.330  Sum_probs=138.1

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      ....++|++|+|...+..++.+.+...           .....+|||.|.+||||..+|+++-+..   +.||+.+||..
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~-----------A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaA  306 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRI-----------AKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAA  306 (560)
T ss_pred             cccccchhhhccCCHHHHHHHHHHHhh-----------cCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEeccc
Confidence            445689999999999999998888765           4567789999999999999999999876   56999999998


Q ss_pred             hhccccChHHHHHHHHHHHhhh----------------CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          102 IIDKYIGESARLIREMFGYARD----------------HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~----------------~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      +......+      ++|+....                ...+.|||||+..|           +-..|..|+..+++.+-
T Consensus       307 iPe~LlES------ELFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgem-----------pl~LQaKLLRVLQEkei  369 (560)
T COG3829         307 IPETLLES------ELFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEM-----------PLPLQAKLLRVLQEKEI  369 (560)
T ss_pred             CCHHHHHH------HHhCcCCccccccccCCCCcceeeccCCeEEehhhccC-----------CHHHHHHHHHHHhhceE
Confidence            76543322      44444321                34579999999988           88899999999987531


Q ss_pred             C------CCCCCeEEEEEeCCC-C------CCChhhcCCCCcceEEEccCCCHHHHHH----HHHHHHc----CccCC-C
Q 022768          166 F------DQLGKVKMIMATNRP-D------VLDPALLRPGRLDRKIEIPLPNEQSRME----ILKIHAA----GIAKH-G  223 (292)
Q Consensus       166 ~------~~~~~~~vi~t~~~~-~------~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~~~~~~----~~~~~-~  223 (292)
                      .      .-.-++.+|++||.. .      ..-.+|--  |. -++.+..|...+|.+    +..+++.    .+... .
T Consensus       370 ~rvG~t~~~~vDVRIIAATN~nL~~~i~~G~FReDLYY--RL-NV~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~  446 (560)
T COG3829         370 ERVGGTKPIPVDVRIIAATNRNLEKMIAEGTFREDLYY--RL-NVIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVK  446 (560)
T ss_pred             EecCCCCceeeEEEEEeccCcCHHHHHhcCcchhhhee--ee-ceeeecCCCcccCcchHHHHHHHHHHHHHHHcCCCcc
Confidence            1      111168899999863 1      12222222  33 345666666666653    3333333    23222 3


Q ss_pred             CCCHHHHHHHcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Q 022768          224 EIDYEAVVKLAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDFM  267 (292)
Q Consensus       224 ~~~~~~l~~~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~~  267 (292)
                      .+..+.+......-   |.|++.+++.++...+  .....|+.+|+.
T Consensus       447 ~ls~~a~~~L~~y~WPGNVRELeNviER~v~~~--~~~~~I~~~~lp  491 (560)
T COG3829         447 GLSPDALALLLRYDWPGNVRELENVIERAVNLV--ESDGLIDADDLP  491 (560)
T ss_pred             cCCHHHHHHHHhCCCCchHHHHHHHHHHHHhcc--CCcceeehhhcc
Confidence            35556666554422   6677778888887632  222235555544

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.40  E-value=1.2e-11  Score=120.60  Aligned_cols=167  Identities=20%  Similarity=0.315  Sum_probs=113.1

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc---
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK---  105 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~---  105 (292)
                      ..++|++++++.+.+.+.....+   ... .-.|-..++|+||+|+|||.+|+++|..+   ...++.+++.++...   
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~g---l~~-~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~  641 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAG---LED-PRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTV  641 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcC---CCC-CCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhh
Confidence            46899999999999988653111   000 01222358999999999999999999988   457788887765322   


Q ss_pred             ---------ccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------CCC
Q 022768          106 ---------YIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------QLG  170 (292)
Q Consensus       106 ---------~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~~~  170 (292)
                               +.|..+.  ..+....+.+.++||+|||++..           ++.....|+++++...-..      ...
T Consensus       642 ~~l~g~~~gyvg~~~~--g~L~~~v~~~p~svvllDEieka-----------~~~v~~~Llq~ld~g~l~d~~Gr~vd~~  708 (852)
T TIGR03345       642 SRLKGSPPGYVGYGEG--GVLTEAVRRKPYSVVLLDEVEKA-----------HPDVLELFYQVFDKGVMEDGEGREIDFK  708 (852)
T ss_pred             ccccCCCCCccccccc--chHHHHHHhCCCcEEEEechhhc-----------CHHHHHHHHHHhhcceeecCCCcEEecc
Confidence                     1111110  12233445567799999999987           7788888888887542111      113


Q ss_pred             CeEEEEEeCCCC-----------------------------CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcC
Q 022768          171 KVKMIMATNRPD-----------------------------VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAG  218 (292)
Q Consensus       171 ~~~vi~t~~~~~-----------------------------~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~  218 (292)
                      ++++|+|+|...                             .+.+.+++  |+. .+.|.+++.++..+|+...+..
T Consensus       709 n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv~~~L~~  782 (852)
T TIGR03345       709 NTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIPYLPLDDDVLAAIVRLKLDR  782 (852)
T ss_pred             ccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEEeCCCCHHHHHHHHHHHHHH
Confidence            688999988521                             13445565  775 7899999999999998876653

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.40  E-value=2.6e-11  Score=118.63  Aligned_cols=169  Identities=22%  Similarity=0.319  Sum_probs=114.6

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc--
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY--  106 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~--  106 (292)
                      ..++|++++++.+...+.....+   ... .-.|-..++|+||+|+|||++|+.+|+.+   +.++++++++++....  
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~g---l~~-~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVG---LKN-PNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTV  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhc---ccC-CCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccH
Confidence            55899999999999888653111   000 01223458999999999999999999987   3578888877654321  


Q ss_pred             ---cChH-----HHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCCe
Q 022768          107 ---IGES-----ARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLGKV  172 (292)
Q Consensus       107 ---~~~~-----~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~~  172 (292)
                         .|..     ......+....+....+||+|||+|.+           .......|+++++...-.      -...++
T Consensus       585 ~~l~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDeieka-----------~~~v~~~Llq~le~g~~~d~~g~~v~~~~~  653 (821)
T CHL00095        585 SKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKA-----------HPDIFNLLLQILDDGRLTDSKGRTIDFKNT  653 (821)
T ss_pred             HHhcCCCCcccCcCccchHHHHHHhCCCeEEEECChhhC-----------CHHHHHHHHHHhccCceecCCCcEEecCce
Confidence               1110     000113344445555689999999998           788888888888753210      112478


Q ss_pred             EEEEEeCCCCC-------------------------------------CChhhcCCCCcceEEEccCCCHHHHHHHHHHH
Q 022768          173 KMIMATNRPDV-------------------------------------LDPALLRPGRLDRKIEIPLPNEQSRMEILKIH  215 (292)
Q Consensus       173 ~vi~t~~~~~~-------------------------------------l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~  215 (292)
                      ++|+|+|....                                     ..|.+..  |++.++.|.+++.++..+|+...
T Consensus       654 i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln--Rid~ii~F~pL~~~~l~~Iv~~~  731 (821)
T CHL00095        654 LIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN--RLDEIIVFRQLTKNDVWEIAEIM  731 (821)
T ss_pred             EEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhc--cCCeEEEeCCCCHHHHHHHHHHH
Confidence            89999875321                                     1234555  88889999999999999998876


Q ss_pred             Hc
Q 022768          216 AA  217 (292)
Q Consensus       216 ~~  217 (292)
                      +.
T Consensus       732 l~  733 (821)
T CHL00095        732 LK  733 (821)
T ss_pred             HH
Confidence            65

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.39  E-value=1.6e-11  Score=107.57  Aligned_cols=169  Identities=15%  Similarity=0.197  Sum_probs=109.8

Q ss_pred             HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------------------------
Q 022768           38 SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------------------------   93 (292)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------------------------   93 (292)
                      ....+++.+.+..-            .-++.+||+||+|+||+++|.++|+.+-+.                        
T Consensus         8 ~~~~~~l~~~~~~~------------rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD   75 (334)
T PRK07993          8 RPDYEQLVGSYQAG------------RGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPD   75 (334)
T ss_pred             hHHHHHHHHHHHcC------------CcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCC
Confidence            34556666665431            446789999999999999999999988431                        


Q ss_pred             EEEEeccchhccccChHHHHHHHHHHHh----hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC
Q 022768           94 FLKVVSSAIIDKYIGESARLIREMFGYA----RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL  169 (292)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~  169 (292)
                      +..+....- +.  .-..+.++.+...+    ......|++||++|.|           .......|+..++     .+.
T Consensus        76 ~~~i~p~~~-~~--~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m-----------~~~AaNaLLKtLE-----EPp  136 (334)
T PRK07993         76 YYTLTPEKG-KS--SLGVDAVREVTEKLYEHARLGGAKVVWLPDAALL-----------TDAAANALLKTLE-----EPP  136 (334)
T ss_pred             EEEEecccc-cc--cCCHHHHHHHHHHHhhccccCCceEEEEcchHhh-----------CHHHHHHHHHHhc-----CCC
Confidence            111111100 00  01233344444333    2345679999999999           7777777777666     456


Q ss_pred             CCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHH
Q 022768          170 GKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNV  245 (292)
Q Consensus       170 ~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l  245 (292)
                      +++++|.+|+.++.+.+.++|  |+ ..+.|++|+.++..+.+....   ..+ ......++..+.| +++....+
T Consensus       137 ~~t~fiL~t~~~~~lLpTIrS--RC-q~~~~~~~~~~~~~~~L~~~~---~~~-~~~a~~~~~la~G-~~~~Al~l  204 (334)
T PRK07993        137 ENTWFFLACREPARLLATLRS--RC-RLHYLAPPPEQYALTWLSREV---TMS-QDALLAALRLSAG-APGAALAL  204 (334)
T ss_pred             CCeEEEEEECChhhChHHHHh--cc-ccccCCCCCHHHHHHHHHHcc---CCC-HHHHHHHHHHcCC-CHHHHHHH
Confidence            789999999999999999999  88 568999999888777665422   111 1123345666666 55544444

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=99.39  E-value=3.1e-12  Score=107.54  Aligned_cols=203  Identities=19%  Similarity=0.189  Sum_probs=137.6

Q ss_pred             CChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           14 VDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      ..+.-..+..+.++|..++++++.++.+..+.++...             ..-.+.|+|||||+|||+...+.|+.+..+
T Consensus        23 ~~~~~~~pwvekyrP~~l~dv~~~~ei~st~~~~~~~-------------~~lPh~L~YgPPGtGktsti~a~a~~ly~~   89 (360)
T KOG0990|consen   23 QSPQYPQPWVEKYRPPFLGIVIKQEPIWSTENRYSGM-------------PGLPHLLFYGPPGTGKTSTILANARDFYSP   89 (360)
T ss_pred             CCcccCCCCccCCCCchhhhHhcCCchhhHHHHhccC-------------CCCCcccccCCCCCCCCCchhhhhhhhcCC
Confidence            3444444555789999999999999999999998543             233389999999999999999999998764


Q ss_pred             E------EEEeccchhccccChHHHHHHHHHHHhhh-------CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHH
Q 022768           94 F------LKVVSSAIIDKYIGESARLIREMFGYARD-------HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELL  160 (292)
Q Consensus        94 ~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l  160 (292)
                      .      ..++.++-.+.   ...+.-...|...+.       ..+..++|||+|.+           ....|.+|...+
T Consensus        90 ~~~~~m~lelnaSd~rgi---d~vr~qi~~fast~~~~~fst~~~fKlvILDEADaM-----------T~~AQnALRRvi  155 (360)
T KOG0990|consen   90 HPTTSMLLELNASDDRGI---DPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAM-----------TRDAQNALRRVI  155 (360)
T ss_pred             CCchhHHHHhhccCccCC---cchHHHHHHHHhhccceeccccCceeEEEecchhHh-----------hHHHHHHHHHHH
Confidence            2      12222222211   122333344555442       25679999999999           888888888766


Q ss_pred             HHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCH
Q 022768          161 NQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNG  239 (292)
Q Consensus       161 ~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~  239 (292)
                      ....     .++.++..+|.+..+.+++++  || ..+.|.+.+.......+.+....-... .......+...    +.
T Consensus       156 ek~t-----~n~rF~ii~n~~~ki~pa~qs--Rc-trfrf~pl~~~~~~~r~shi~e~e~~~~~~~~~~a~~r~----s~  223 (360)
T KOG0990|consen  156 EKYT-----ANTRFATISNPPQKIHPAQQS--RC-TRFRFAPLTMAQQTERQSHIRESEQKETNPEGYSALGRL----SV  223 (360)
T ss_pred             HHhc-----cceEEEEeccChhhcCchhhc--cc-ccCCCCCCChhhhhhHHHHHHhcchhhcCHHHHHHHHHH----hH
Confidence            5543     466677889999999999999  77 667788888777777777666532222 11122333333    34


Q ss_pred             HHHHHHHHHHHHHHHH
Q 022768          240 ADLRNVCTEAGMSAIR  255 (292)
Q Consensus       240 ~di~~l~~~a~~~a~~  255 (292)
                      +|++.+++-....+..
T Consensus       224 gDmr~a~n~Lqs~~~~  239 (360)
T KOG0990|consen  224 GDMRVALNYLQSILKK  239 (360)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4888777665555444

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.38  E-value=5.1e-12  Score=116.80  Aligned_cols=207  Identities=23%  Similarity=0.290  Sum_probs=126.7

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHh-----------cCCcEEEE
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASN-----------IDANFLKV   97 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~-----------l~~~~~~~   97 (292)
                      .+|++++|.....+++.+.+...           .....+|||+|++||||+++|+++.+.           .+.||+.+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~-----------A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~i  284 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLY-----------ARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAV  284 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEe
Confidence            57899999999999999888764           345678999999999999999999887           35699999


Q ss_pred             eccchhccccChHHHHHHHHHHH----------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHH
Q 022768           98 VSSAIIDKYIGESARLIREMFGY----------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN  161 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~  161 (292)
                      +|..+.....      -..+|..                ......+.|||||++.|           +...|..|..+++
T Consensus       285 nCaal~e~ll------eseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~L-----------p~~~Q~kLl~~L~  347 (538)
T PRK15424        285 NCGAIAESLL------EAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEM-----------PLPLQTRLLRVLE  347 (538)
T ss_pred             ecccCChhhH------HHHhcCCccccccCccccccCCchhccCCCEEEEcChHhC-----------CHHHHHHHHhhhh
Confidence            9988643211      1122221                11234579999999999           8889999999887


Q ss_pred             HhhCCC------CCCCeEEEEEeCCCC-C------CChhhcCCCCcceEEEccCCCHHHHH----HHHHHHHcCc--cCC
Q 022768          162 QLDGFD------QLGKVKMIMATNRPD-V------LDPALLRPGRLDRKIEIPLPNEQSRM----EILKIHAAGI--AKH  222 (292)
Q Consensus       162 ~~~~~~------~~~~~~vi~t~~~~~-~------l~~~l~~~~r~~~~i~l~~p~~~~r~----~i~~~~~~~~--~~~  222 (292)
                      .....+      -.-++.+|++++..- .      +.+.+..  |+ ..+.+..|...+|.    .++.+++...  ...
T Consensus       348 e~~~~r~G~~~~~~~dvRiIaat~~~L~~~v~~g~Fr~dL~y--rL-~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~  424 (538)
T PRK15424        348 EKEVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFY--RL-SILRLQLPPLRERVADILPLAESFLKQSLAALS  424 (538)
T ss_pred             cCeEEecCCCceeccceEEEEecCCCHHHHHhcccchHHHHH--Hh-cCCeecCCChhhchhHHHHHHHHHHHHHHHHcC
Confidence            642111      112467888886531 1      2222322  33 23455556555554    4555665432  111


Q ss_pred             CCCCHHHH-------HHHcC-CC--CHHHHHHHHHHHHHHHHHhcCCcccHHHH
Q 022768          223 GEIDYEAV-------VKLAE-GF--NGADLRNVCTEAGMSAIRAERDYVIHEDF  266 (292)
Q Consensus       223 ~~~~~~~l-------~~~~~-g~--~~~di~~l~~~a~~~a~~~~~~~i~~~~~  266 (292)
                      ..+..+.+       ..+.. .|  |.++++++++++..++.......++.+++
T Consensus       425 ~~~~~~a~~~~~~a~~~L~~y~WPGNvREL~nvier~~i~~~~~~~~~i~~~~l  478 (538)
T PRK15424        425 APFSAALRQGLQQCETLLLHYDWPGNVRELRNLMERLALFLSVEPTPDLTPQFL  478 (538)
T ss_pred             CCCCHHHHHhhHHHHHHHHhCCCCchHHHHHHHHHHHHHhcCCCCcCccCHHHh
Confidence            12333222       12221 12  66777777777776542222234555554

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.37  E-value=1.8e-11  Score=113.84  Aligned_cols=194  Identities=24%  Similarity=0.277  Sum_probs=126.2

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY  106 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~  106 (292)
                      ++.+++|....++++.+.+...           ...+.+|+|+|++||||+++|+++....   +.+++.++|..+....
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~-----------a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~~~  253 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVV-----------AASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESL  253 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCChHH
Confidence            5788999999999999988774           3457789999999999999999999875   4699999998874321


Q ss_pred             cChHHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC----
Q 022768          107 IGESARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD----  167 (292)
Q Consensus       107 ~~~~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~----  167 (292)
                      .      -..+|..               ......+.|||||++.|           ....+..|..+++.....+    
T Consensus       254 ~------e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L-----------~~~~Q~~Ll~~l~~~~~~~~g~~  316 (509)
T PRK05022        254 A------ESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGEL-----------PLALQAKLLRVLQYGEIQRVGSD  316 (509)
T ss_pred             H------HHHhcCccccccCCCcccCCcchhhcCCCEEEecChhhC-----------CHHHHHHHHHHHhcCCEeeCCCC
Confidence            1      1122221               11234579999999999           8888888988886532100    


Q ss_pred             --CCCCeEEEEEeCCC-------CCCChhhcCCCCcceEEEccCCCHHHHH----HHHHHHHcCcc-----CCCCCCHHH
Q 022768          168 --QLGKVKMIMATNRP-------DVLDPALLRPGRLDRKIEIPLPNEQSRM----EILKIHAAGIA-----KHGEIDYEA  229 (292)
Q Consensus       168 --~~~~~~vi~t~~~~-------~~l~~~l~~~~r~~~~i~l~~p~~~~r~----~i~~~~~~~~~-----~~~~~~~~~  229 (292)
                        ...++.+|++++..       ..+...+..  |+. .+.+..|+..+|.    .++.+++....     ....++.+.
T Consensus       317 ~~~~~~~RiI~~t~~~l~~~~~~~~f~~dL~~--rl~-~~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a  393 (509)
T PRK05022        317 RSLRVDVRVIAATNRDLREEVRAGRFRADLYH--RLS-VFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAA  393 (509)
T ss_pred             cceecceEEEEecCCCHHHHHHcCCccHHHHh--ccc-ccEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHH
Confidence              11257888888753       124444443  442 3344555555554    34455544321     123456666


Q ss_pred             HHHHcCCC---CHHHHHHHHHHHHHHHH
Q 022768          230 VVKLAEGF---NGADLRNVCTEAGMSAI  254 (292)
Q Consensus       230 l~~~~~g~---~~~di~~l~~~a~~~a~  254 (292)
                      +..+...-   |.++++++++.|...+.
T Consensus       394 ~~~L~~y~WPGNvrEL~~~i~ra~~~~~  421 (509)
T PRK05022        394 QAALLAYDWPGNVRELEHVISRAALLAR  421 (509)
T ss_pred             HHHHHhCCCCCcHHHHHHHHHHHHHhcC
Confidence            66554421   66777788888776654

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.36  E-value=1.7e-11  Score=113.42  Aligned_cols=211  Identities=23%  Similarity=0.291  Sum_probs=128.6

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhc
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIID  104 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~  104 (292)
                      ..+|++++|.....+++.+.+...           .....+|+|+|++||||+++|+++.+..   +.|++.++|..+..
T Consensus       208 ~~~f~~iiG~S~~m~~~~~~i~~~-----------A~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~e  276 (526)
T TIGR02329       208 RYRLDDLLGASAPMEQVRALVRLY-----------ARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAE  276 (526)
T ss_pred             ccchhheeeCCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCCh
Confidence            477899999999999999888764           3456789999999999999999998764   56999999987643


Q ss_pred             cccChHHHHHHHHHHH----------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-
Q 022768          105 KYIGESARLIREMFGY----------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-  167 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~----------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-  167 (292)
                      ..      .-..+|..                ......+.|||||++.|           +...|..|..+++.....+ 
T Consensus       277 ~l------leseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~L-----------p~~~Q~~Ll~~L~~~~~~r~  339 (526)
T TIGR02329       277 SL------LEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEM-----------PLPLQTRLLRVLEEREVVRV  339 (526)
T ss_pred             hH------HHHHhcCCcccccccccccccccchhhcCCceEEecChHhC-----------CHHHHHHHHHHHhcCcEEec
Confidence            21      11123321                11134579999999999           8889999999887543111 


Q ss_pred             -----CCCCeEEEEEeCCCC-------CCChhhcCCCCcceEEEccCCCHHHHH----HHHHHHHcCccC--CCCCCHHH
Q 022768          168 -----QLGKVKMIMATNRPD-------VLDPALLRPGRLDRKIEIPLPNEQSRM----EILKIHAAGIAK--HGEIDYEA  229 (292)
Q Consensus       168 -----~~~~~~vi~t~~~~~-------~l~~~l~~~~r~~~~i~l~~p~~~~r~----~i~~~~~~~~~~--~~~~~~~~  229 (292)
                           ..-++.+|++++..-       .+.+.+..  |+. .+.+..|+..+|.    .++..++.....  ...++.+.
T Consensus       340 g~~~~~~~dvRiIaat~~~l~~~v~~g~fr~dL~~--rL~-~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a  416 (526)
T TIGR02329       340 GGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFY--RLS-ILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAA  416 (526)
T ss_pred             CCCceeeecceEEeccCCCHHHHhhhcchhHHHHH--hcC-CcEEeCCCchhchhHHHHHHHHHHHHHHHHcCCCCCHHH
Confidence                 111457888876531       12223332  331 2344455545544    455555543311  11244444


Q ss_pred             HHH-------HcC-CC--CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          230 VVK-------LAE-GF--NGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       230 l~~-------~~~-g~--~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      +..       +.. .|  |.+++.++++++...+.......|+.+++...
T Consensus       417 ~~~~~~~~~~L~~y~WPGNvrEL~nvier~~i~~~~~~~~~I~~~~l~~~  466 (526)
T TIGR02329       417 AQVLAGVADPLQRYPWPGNVRELRNLVERLALELSAMPAGALTPDVLRAL  466 (526)
T ss_pred             HHHhHHHHHHHHhCCCCchHHHHHHHHHHHHHhcccCCCCccCHHHhhhh
Confidence            332       322 12  55666666666654432222346777776543

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.35  E-value=9.4e-11  Score=101.64  Aligned_cols=167  Identities=16%  Similarity=0.208  Sum_probs=109.7

Q ss_pred             HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----------------------E
Q 022768           38 SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----------------------F   94 (292)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----------------------~   94 (292)
                      .+..+++...+..-            .-++.+||+||.|+||+++|+.+|+.+-+.                       +
T Consensus         9 ~~~~~~l~~~~~~~------------rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~   76 (319)
T PRK06090          9 VPVWQNWKAGLDAG------------RIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDL   76 (319)
T ss_pred             HHHHHHHHHHHHcC------------CcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCE
Confidence            45666777666542            446789999999999999999999877332                       2


Q ss_pred             EEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCC
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG  170 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~  170 (292)
                      ..+....- +..  -..+.++.+...+.    .....|++||++|.+           .......|+..++     .+.+
T Consensus        77 ~~i~p~~~-~~~--I~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m-----------~~~AaNaLLKtLE-----EPp~  137 (319)
T PRK06090         77 HVIKPEKE-GKS--ITVEQIRQCNRLAQESSQLNGYRLFVIEPADAM-----------NESASNALLKTLE-----EPAP  137 (319)
T ss_pred             EEEecCcC-CCc--CCHHHHHHHHHHHhhCcccCCceEEEecchhhh-----------CHHHHHHHHHHhc-----CCCC
Confidence            22221100 000  12233444433332    234579999999999           6767777777666     3556


Q ss_pred             CeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          171 KVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       171 ~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      ++.+|.+|+.++.+.+.++|  |+ ..+.|++|+.++..+.+...  +  ..   ....+...+.| ++.....+.
T Consensus       138 ~t~fiL~t~~~~~lLpTI~S--RC-q~~~~~~~~~~~~~~~L~~~--~--~~---~~~~~l~l~~G-~p~~A~~~~  202 (319)
T PRK06090        138 NCLFLLVTHNQKRLLPTIVS--RC-QQWVVTPPSTAQAMQWLKGQ--G--IT---VPAYALKLNMG-SPLKTLAMM  202 (319)
T ss_pred             CeEEEEEECChhhChHHHHh--cc-eeEeCCCCCHHHHHHHHHHc--C--Cc---hHHHHHHHcCC-CHHHHHHHh
Confidence            89999999999999999999  88 78899999998887776542  1  11   12344555665 554444443

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.35  E-value=7.9e-11  Score=102.21  Aligned_cols=172  Identities=19%  Similarity=0.239  Sum_probs=110.1

Q ss_pred             HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE----EEEeccchh------cc--
Q 022768           38 SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF----LKVVSSAII------DK--  105 (292)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~----~~~~~~~~~------~~--  105 (292)
                      ..+++.+...+..-            .-++.+||+||+|+||+++|..+|+.+-+.-    -.+.++...      +.  
T Consensus        10 ~~~~~~l~~~~~~~------------rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~   77 (319)
T PRK08769         10 QRAYDQTVAALDAG------------RLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQL   77 (319)
T ss_pred             HHHHHHHHHHHHcC------------CcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEE
Confidence            45566676665541            3456799999999999999999998774321    001110000      00  


Q ss_pred             ---c---------cChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC
Q 022768          106 ---Y---------IGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL  169 (292)
Q Consensus       106 ---~---------~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~  169 (292)
                         .         ..-..+.++.+...+..    ....|++||++|.|           +......|+..+++     +.
T Consensus        78 i~~~p~~~~~k~~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m-----------~~~AaNaLLKtLEE-----Pp  141 (319)
T PRK08769         78 VSFIPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAI-----------NRAACNALLKTLEE-----PS  141 (319)
T ss_pred             EecCCCcccccccccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhh-----------CHHHHHHHHHHhhC-----CC
Confidence               0         00123344555444432    23479999999999           77777777777664     45


Q ss_pred             CCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          170 GKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       170 ~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      +++.+|.+++.++.+.+.++|  |+ ..+.|++|+.++..+.+...    ... ..+...+...+.| +++....++
T Consensus       142 ~~~~fiL~~~~~~~lLpTIrS--RC-q~i~~~~~~~~~~~~~L~~~----~~~-~~~a~~~~~l~~G-~p~~A~~~~  209 (319)
T PRK08769        142 PGRYLWLISAQPARLPATIRS--RC-QRLEFKLPPAHEALAWLLAQ----GVS-ERAAQEALDAARG-HPGLAAQWL  209 (319)
T ss_pred             CCCeEEEEECChhhCchHHHh--hh-eEeeCCCcCHHHHHHHHHHc----CCC-hHHHHHHHHHcCC-CHHHHHHHh
Confidence            688888899999999999999  88 77899999998777766542    111 1123355666776 554444443

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.34  E-value=4.1e-11  Score=115.46  Aligned_cols=200  Identities=25%  Similarity=0.327  Sum_probs=124.2

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhc
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIID  104 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~  104 (292)
                      ...|++++|....++.+.+.+...           .....+|+|+|++|||||++|+++....   +.+++.++|..+..
T Consensus       372 n~~~~~liG~S~~~~~~~~~~~~~-----------a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~  440 (686)
T PRK15429        372 DSEFGEIIGRSEAMYSVLKQVEMV-----------AQSDSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPA  440 (686)
T ss_pred             cccccceeecCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCCh
Confidence            357889999999999998888764           2446689999999999999999998865   56999999987642


Q ss_pred             cc-----cChHH----HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCC
Q 022768          105 KY-----IGESA----RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQL  169 (292)
Q Consensus       105 ~~-----~~~~~----~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~  169 (292)
                      ..     .|...    ...............++|||||++.+           +...+..|..+++.....      ...
T Consensus       441 ~~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L-----------~~~~Q~~L~~~l~~~~~~~~g~~~~~~  509 (686)
T PRK15429        441 GLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDM-----------PLELQPKLLRVLQEQEFERLGSNKIIQ  509 (686)
T ss_pred             hHhhhhhcCcccccccccccchhhHHHhcCCCeEEEechhhC-----------CHHHHHHHHHHHHhCCEEeCCCCCccc
Confidence            21     11000    00001111122334589999999999           888999999988753210      111


Q ss_pred             CCeEEEEEeCCCC-------CCChhhcCCCCcceEEEccCCCHHHHHH----HHHHHHcCc----cCC-CCCCHHHHHHH
Q 022768          170 GKVKMIMATNRPD-------VLDPALLRPGRLDRKIEIPLPNEQSRME----ILKIHAAGI----AKH-GEIDYEAVVKL  233 (292)
Q Consensus       170 ~~~~vi~t~~~~~-------~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~~~~~~~~----~~~-~~~~~~~l~~~  233 (292)
                      .++.+|++++..-       .+...+..  |+ ..+.+..|+..+|.+    +++.++...    ... ..+..+.+..+
T Consensus       510 ~~~RiI~~t~~~l~~~~~~~~f~~~L~~--~l-~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~~al~~L  586 (686)
T PRK15429        510 TDVRLIAATNRDLKKMVADREFRSDLYY--RL-NVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTL  586 (686)
T ss_pred             ceEEEEEeCCCCHHHHHHcCcccHHHHh--cc-CeeEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHH
Confidence            3578888886531       12233332  33 234556666666643    555554432    111 23555666655


Q ss_pred             cCCC---CHHHHHHHHHHHHHH
Q 022768          234 AEGF---NGADLRNVCTEAGMS  252 (292)
Q Consensus       234 ~~g~---~~~di~~l~~~a~~~  252 (292)
                      ...-   |.+++.++++.|...
T Consensus       587 ~~y~WPGNvrEL~~~i~~a~~~  608 (686)
T PRK15429        587 SNMEWPGNVRELENVIERAVLL  608 (686)
T ss_pred             HhCCCCCcHHHHHHHHHHHHHh
Confidence            4422   566677777776653

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=99.34  E-value=2.2e-11  Score=108.19  Aligned_cols=195  Identities=28%  Similarity=0.389  Sum_probs=132.5

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhc
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIID  104 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~  104 (292)
                      ...+.++||...+...+.+.+...           .....+|||.|.+||||..+|+++-...   ..|++.+||..+..
T Consensus       219 ~~~~~~iIG~S~am~~ll~~i~~V-----------A~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPe  287 (550)
T COG3604         219 VLEVGGIIGRSPAMRQLLKEIEVV-----------AKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPE  287 (550)
T ss_pred             hcccccceecCHHHHHHHHHHHHH-----------hcCCCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccch
Confidence            567889999999999999998765           4567789999999999999999999876   56999999998865


Q ss_pred             cccChHHHHHHHHHHHhhh---------------CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh--CCC
Q 022768          105 KYIGESARLIREMFGYARD---------------HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD--GFD  167 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~---------------~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~--~~~  167 (292)
                      ....+      ++|+..+.               ...+.||||||..|           .-..|..|+..++..+  -..
T Consensus       288 sLlES------ELFGHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGel-----------PL~lQaKLLRvLQegEieRvG  350 (550)
T COG3604         288 SLLES------ELFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGEL-----------PLALQAKLLRVLQEGEIERVG  350 (550)
T ss_pred             HHHHH------HHhcccccccccchhccCcceeecCCCeEechhhccC-----------CHHHHHHHHHHHhhcceeecC
Confidence            43322      44444332               34579999999888           7889999999988643  111


Q ss_pred             CCC----CeEEEEEeCCC-C------CCChhhcCCCCcceEEEccCCCHHHHHH----HHHHHHc----CccC-CCCCCH
Q 022768          168 QLG----KVKMIMATNRP-D------VLDPALLRPGRLDRKIEIPLPNEQSRME----ILKIHAA----GIAK-HGEIDY  227 (292)
Q Consensus       168 ~~~----~~~vi~t~~~~-~------~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~~~~~~----~~~~-~~~~~~  227 (292)
                      ...    .+.||++||.- +      +.-.++.-  |. -++-+..|...+|..    +.++++.    .... .-.++.
T Consensus       351 ~~r~ikVDVRiIAATNRDL~~~V~~G~FRaDLYy--RL-sV~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~  427 (550)
T COG3604         351 GDRTIKVDVRVIAATNRDLEEMVRDGEFRADLYY--RL-SVFPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSA  427 (550)
T ss_pred             CCceeEEEEEEEeccchhHHHHHHcCcchhhhhh--cc-cccccCCCCcccCCccHHHHHHHHHHHHHHhcCCcccccCH
Confidence            111    58899999862 1      12222222  33 244455566666542    3334433    2222 233455


Q ss_pred             HHHHHHcCC-C--CHHHHHHHHHHHHHHH
Q 022768          228 EAVVKLAEG-F--NGADLRNVCTEAGMSA  253 (292)
Q Consensus       228 ~~l~~~~~g-~--~~~di~~l~~~a~~~a  253 (292)
                      +.+...++- |  |.+++.+++++|...|
T Consensus       428 ~Al~~L~~y~wPGNVRELen~veRavlla  456 (550)
T COG3604         428 EALELLSSYEWPGNVRELENVVERAVLLA  456 (550)
T ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHHHHHh
Confidence            666665541 1  7789999999999877

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.34  E-value=1.2e-12  Score=100.86  Aligned_cols=113  Identities=32%  Similarity=0.433  Sum_probs=72.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc--ccChHHHH-H-----HHHHHHhhhCCCEEEEEcccccccC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK--YIGESARL-I-----REMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~--~~~~~~~~-~-----~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      +|+|+||||+|||++++.+|+.++.+++.+.+....+.  ..+..... -     ...+..+. ..+.+++|||++..  
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~-~~~~il~lDEin~a--   77 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAM-RKGGILVLDEINRA--   77 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTH-HEEEEEEESSCGG---
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeecccccccccccccccc-cceeEEEECCcccC--
Confidence            58999999999999999999999999988887654321  00000000 0     00000000 14689999999988  


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCC--------CCCC------CeEEEEEeCCCC----CCChhhcCCCCc
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGF--------DQLG------KVKMIMATNRPD----VLDPALLRPGRL  194 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~--------~~~~------~~~vi~t~~~~~----~l~~~l~~~~r~  194 (292)
                               .......|..+++.....        ....      ++.+|+|+|+..    .+++++++  ||
T Consensus        78 ---------~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~--Rf  139 (139)
T PF07728_consen   78 ---------PPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLD--RF  139 (139)
T ss_dssp             ----------HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHT--T-
T ss_pred             ---------CHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHh--hC
Confidence                     777888888887643211        0011      389999999987    78999998  76

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.34  E-value=1.1e-10  Score=102.10  Aligned_cols=133  Identities=19%  Similarity=0.311  Sum_probs=93.0

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcE-------------------------EEEeccchh---------------
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANF-------------------------LKVVSSAII---------------  103 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~-------------------------~~~~~~~~~---------------  103 (292)
                      .-++.+||+||+|+||+++|+.+|+.+.+.-                         ..+......               
T Consensus        19 rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~~~   98 (342)
T PRK06964         19 RLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEADA   98 (342)
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccchh
Confidence            4467899999999999999999999885421                         111110000               


Q ss_pred             ---cc----c-cChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCC
Q 022768          104 ---DK----Y-IGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGK  171 (292)
Q Consensus       104 ---~~----~-~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~  171 (292)
                         +.    . ..-..+.++.+...+.    .....|++||++|.+           .......|+..++     .+.++
T Consensus        99 ~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m-----------~~~AaNaLLKtLE-----EPp~~  162 (342)
T PRK06964         99 DEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEAL-----------NVAAANALLKTLE-----EPPPG  162 (342)
T ss_pred             hcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhc-----------CHHHHHHHHHHhc-----CCCcC
Confidence               00    0 0012233444444332    234579999999999           7777777777666     46678


Q ss_pred             eEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHH
Q 022768          172 VKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIH  215 (292)
Q Consensus       172 ~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~  215 (292)
                      +++|.+|+.++.+.+.++|  |+ ..+.|++|+.++..+.+...
T Consensus       163 t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        163 TVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             cEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            9999999999999999999  88 78999999998888877653

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.33  E-value=1.9e-11  Score=115.37  Aligned_cols=167  Identities=22%  Similarity=0.340  Sum_probs=119.1

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEeccchhccc--
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID---ANFLKVVSSAIIDKY--  106 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~~~~~~~~--  106 (292)
                      ..++|+++++..+-+.+...-.+   +.. .-.|...+||.||+|+|||-+|+++|..+.   ..+++++++++..+.  
T Consensus       491 ~rViGQd~AV~avs~aIrraRaG---L~d-p~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsV  566 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAG---LGD-PNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSV  566 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcC---CCC-CCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHH
Confidence            45899999999999998764111   111 113445689999999999999999999995   789999999886431  


Q ss_pred             ----------cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCC------
Q 022768          107 ----------IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG------  170 (292)
Q Consensus       107 ----------~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~------  170 (292)
                                +|..+  =..+-..++....+||+|||++.-           .+.+...|+++++...-....+      
T Consensus       567 SrLIGaPPGYVGyee--GG~LTEaVRr~PySViLlDEIEKA-----------HpdV~nilLQVlDdGrLTD~~Gr~VdFr  633 (786)
T COG0542         567 SRLIGAPPGYVGYEE--GGQLTEAVRRKPYSVILLDEIEKA-----------HPDVFNLLLQVLDDGRLTDGQGRTVDFR  633 (786)
T ss_pred             HHHhCCCCCCceecc--ccchhHhhhcCCCeEEEechhhhc-----------CHHHHHHHHHHhcCCeeecCCCCEEecc
Confidence                      11111  123334445566799999999987           8888889998887643222222      


Q ss_pred             CeEEEEEeCCCCC----------------------------CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          171 KVKMIMATNRPDV----------------------------LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       171 ~~~vi~t~~~~~~----------------------------l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      ++++|+|+|.-..                            ..|.++.  |++.+|.|.+.+.+...+|+...+.
T Consensus       634 NtiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~L~  706 (786)
T COG0542         634 NTIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQLN  706 (786)
T ss_pred             eeEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHHHH
Confidence            6888999874211                            2334444  8888999999999999998886665

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=99.33  E-value=4.3e-11  Score=94.74  Aligned_cols=119  Identities=31%  Similarity=0.443  Sum_probs=82.6

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChH
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGES  110 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~  110 (292)
                      |+|.....+++.+.+...           ...+.+|+|+|++||||+.+|+++.+..   +.|++.++|..+...     
T Consensus         1 liG~s~~m~~~~~~~~~~-----------a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~~-----   64 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRA-----------ASSDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPEE-----   64 (168)
T ss_dssp             SS--SHHHHHHHHHHHHH-----------TTSTS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-HH-----
T ss_pred             CEeCCHHHHHHHHHHHHH-----------hCCCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhcc-----
Confidence            578888888888887765           3446789999999999999999999876   468999999886432     


Q ss_pred             HHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------CC
Q 022768          111 ARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------QL  169 (292)
Q Consensus       111 ~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~~  169 (292)
                       ..-..+|..               ......++|||||++.|           +...|..|..+++...-.+      ..
T Consensus        65 -~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L-----------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~  132 (168)
T PF00158_consen   65 -LLESELFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDL-----------PPELQAKLLRVLEEGKFTRLGSDKPVP  132 (168)
T ss_dssp             -HHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS------------HHHHHHHHHHHHHSEEECCTSSSEEE
T ss_pred             -hhhhhhhccccccccccccccCCceeeccceEEeecchhhh-----------HHHHHHHHHHHHhhchhcccccccccc
Confidence             112234432               22345589999999999           8999999999998643111      11


Q ss_pred             CCeEEEEEeCC
Q 022768          170 GKVKMIMATNR  180 (292)
Q Consensus       170 ~~~~vi~t~~~  180 (292)
                      .++.+|++|+.
T Consensus       133 ~~~RiI~st~~  143 (168)
T PF00158_consen  133 VDVRIIASTSK  143 (168)
T ss_dssp             --EEEEEEESS
T ss_pred             ccceEEeecCc
Confidence            27889999885

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=99.31  E-value=1.7e-10  Score=101.80  Aligned_cols=223  Identities=20%  Similarity=0.207  Sum_probs=143.6

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cEEEEeccchhc
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NFLKVVSSAIID  104 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~~~~~~~~~~~  104 (292)
                      .-+.+.|.+...+.+.+++...+..         ..+..+++.|.||+|||..+.-+...+..     ..++++|..+..
T Consensus       148 ~p~~l~gRe~e~~~v~~F~~~hle~---------~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~  218 (529)
T KOG2227|consen  148 PPGTLKGRELEMDIVREFFSLHLEL---------NTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTE  218 (529)
T ss_pred             CCCCccchHHHHHHHHHHHHhhhhc---------ccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccc
Confidence            4467899999999999998876433         56778999999999999999877766632     347777775432


Q ss_pred             cc---------------cChHHHHHHHHHHH-hhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC
Q 022768          105 KY---------------IGESARLIREMFGY-ARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD  167 (292)
Q Consensus       105 ~~---------------~~~~~~~~~~~~~~-~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  167 (292)
                      ..               .+.+.......|.. .... .+-++++||+|.|+           ...+..|..++..-.  .
T Consensus       219 ~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~-----------tr~~~vLy~lFewp~--l  285 (529)
T KOG2227|consen  219 ASAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLI-----------TRSQTVLYTLFEWPK--L  285 (529)
T ss_pred             hHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHh-----------hcccceeeeehhccc--C
Confidence            10               00011111222222 2222 36789999999994           333445555554322  4


Q ss_pred             CCCCeEEEEEeCCCCCCC---hhhcC-CCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC--CCHHHHHHHcCCCCHHH
Q 022768          168 QLGKVKMIMATNRPDVLD---PALLR-PGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE--IDYEAVVKLAEGFNGAD  241 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~---~~l~~-~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~--~~~~~l~~~~~g~~~~d  241 (292)
                      ++.++++|+.+|..+.-+   +.+.. ...-...+.|++++.++..+|+...+........  ..++..++...+.|| |
T Consensus       286 p~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SG-D  364 (529)
T KOG2227|consen  286 PNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSG-D  364 (529)
T ss_pred             CcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCch-h
Confidence            556899999999765322   22222 1223467899999999999999999986654433  345667777777555 8


Q ss_pred             HH---HHHHHHHHHHHHhcCC----------------cccHHHHHHHHHHHhh
Q 022768          242 LR---NVCTEAGMSAIRAERD----------------YVIHEDFMKAVRKLNE  275 (292)
Q Consensus       242 i~---~l~~~a~~~a~~~~~~----------------~i~~~~~~~a~~~~~~  275 (292)
                      ++   .+|+.|...+....+.                .|-.+++..++..+..
T Consensus       365 lRkaLdv~R~aiEI~E~e~r~~~~~~l~~~~~p~~~~~v~~~~va~viSk~~~  417 (529)
T KOG2227|consen  365 LRKALDVCRRAIEIAEIEKRKILDDPLSPGTSPEKKKKVGVEHVAAVISKVDG  417 (529)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhccccCCCCCCCcccccccchHHHHHHhhhhcc
Confidence            87   4566666666554332                3446667666666654

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=99.30  E-value=1.9e-10  Score=108.28  Aligned_cols=134  Identities=21%  Similarity=0.291  Sum_probs=89.1

Q ss_pred             CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-------------C---CCCeEEEEEeCCC--CCCChh
Q 022768          126 PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-------------Q---LGKVKMIMATNRP--DVLDPA  187 (292)
Q Consensus       126 ~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-------------~---~~~~~vi~t~~~~--~~l~~~  187 (292)
                      .++|+|||++.|           +...+..|.++++...-..             +   .-++.+|++++..  +.++++
T Consensus       227 GGtL~LDei~~L-----------~~~~q~~Llr~L~~~~i~i~g~~e~~~~~~~~~~~ip~dvrvI~a~~~~ll~~~dpd  295 (637)
T PRK13765        227 KGVLFIDEINTL-----------DLESQQSLLTAMQEKKFPITGQSERSSGAMVRTEPVPCDFIMVAAGNLDALENMHPA  295 (637)
T ss_pred             CcEEEEeChHhC-----------CHHHHHHHHHHHHhCCEEecccccccccccCCCcceeeeeEEEEecCcCHHHhhhHH
Confidence            368899999888           6778888888876432100             1   1156788888764  467888


Q ss_pred             hcCCCCcc---eEEEccC---CCHHHHHHHHHHHHcCccC---CCCCCHHHHHHHcC------C------CCHHHHHHHH
Q 022768          188 LLRPGRLD---RKIEIPL---PNEQSRMEILKIHAAGIAK---HGEIDYEAVVKLAE------G------FNGADLRNVC  246 (292)
Q Consensus       188 l~~~~r~~---~~i~l~~---p~~~~r~~i~~~~~~~~~~---~~~~~~~~l~~~~~------g------~~~~di~~l~  246 (292)
                      +..  ||.   ..+.|..   -+.+.+..+++...+....   ...++.+.+..+..      |      ...+++..++
T Consensus       296 L~~--rfk~~~v~v~f~~~~~d~~e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~  373 (637)
T PRK13765        296 LRS--RIKGYGYEVYMRDTMEDTPENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLV  373 (637)
T ss_pred             HHH--HhccCeEEEEcccccCCCHHHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHH
Confidence            887  664   5566643   2356666666644433211   23455444443222      1      2478999999


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          247 TEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       247 ~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      +.|..+|...+...++.+++.+|...
T Consensus       374 r~a~~~a~~~~~~~i~~~~v~~a~~~  399 (637)
T PRK13765        374 RVAGDIARSEGAELTTAEHVLEAKKI  399 (637)
T ss_pred             HHHHHHHHhhccceecHHHHHHHHHh
Confidence            99999999999999999999988754

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=99.30  E-value=1.2e-10  Score=111.61  Aligned_cols=229  Identities=16%  Similarity=0.100  Sum_probs=138.0

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHH--------HhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------EEEE
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELF--------LRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------FLKV   97 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~--------~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------~~~~   97 (292)
                      .|.|.+++|+.|.-.+..-.......        ..-.++...+|||+|+||+|||++++++++.....       +..+
T Consensus       451 ~I~G~e~vK~ailL~L~gG~~k~~~~~~~~dg~~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~v  530 (915)
T PTZ00111        451 SIKARNNVKIGLLCQLFSGNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSV  530 (915)
T ss_pred             eEECCHHHHHHHHHHHhcCCccccccccccccccccccccCCceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccc
Confidence            47899999988876664321110000        00123445689999999999999999999865432       2222


Q ss_pred             eccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh------CC--CCC
Q 022768           98 VSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD------GF--DQL  169 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~------~~--~~~  169 (292)
                      .+..........+.. ...--+.......++++|||++.+           ....+..|.+++++-.      +.  .-+
T Consensus       531 gLTa~~~~~d~~tG~-~~le~GaLvlAdgGtL~IDEidkm-----------s~~~Q~aLlEaMEqqtIsI~KaGi~~tL~  598 (915)
T PTZ00111        531 GLTASIKFNESDNGR-AMIQPGAVVLANGGVCCIDELDKC-----------HNESRLSLYEVMEQQTVTIAKAGIVATLK  598 (915)
T ss_pred             cccchhhhcccccCc-ccccCCcEEEcCCCeEEecchhhC-----------CHHHHHHHHHHHhCCEEEEecCCcceecC
Confidence            222211100000000 000000011234579999999999           7888888888886532      10  122


Q ss_pred             CCeEEEEEeCCCC-------------CCChhhcCCCCcceEE-EccCCCHHHHHHHHHHHHcCc----------------
Q 022768          170 GKVKMIMATNRPD-------------VLDPALLRPGRLDRKI-EIPLPNEQSRMEILKIHAAGI----------------  219 (292)
Q Consensus       170 ~~~~vi~t~~~~~-------------~l~~~l~~~~r~~~~i-~l~~p~~~~r~~i~~~~~~~~----------------  219 (292)
                      .++.||+++|+..             .+++.+++  ||+..+ .++.|+.+.-..|..+.+...                
T Consensus       599 ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLS--RFDLIf~l~D~~d~~~D~~lA~hI~~~~~~~h~~~~~~~~~~~~  676 (915)
T PTZ00111        599 AETAILASCNPINSRYNKNKAVIENINISPSLFT--RFDLIYLVLDHIDQDTDQLISLSIAKDFLLPHMTGSGNDEDTYD  676 (915)
T ss_pred             CCeEEEEEcCCcccccCcccCcccccCCChHHhh--hhcEEEEecCCCChHHHHHHHHHHHHhhcccccccccccccchh
Confidence            4789999999742             37789999  997665 557787765555544332100                


Q ss_pred             -----------------------------------cCCCCCCH---HHH-------HHH---------------------
Q 022768          220 -----------------------------------AKHGEIDY---EAV-------VKL---------------------  233 (292)
Q Consensus       220 -----------------------------------~~~~~~~~---~~l-------~~~---------------------  233 (292)
                                                         .+.+.+.-   +.|       -..                     
T Consensus       677 ~~~~~~~~~~~~~~~~~~~~i~~~lLrkYI~YAR~~~~P~Ls~eA~~~i~~~Yv~mR~~~~~~~~~~~~~~~~~~~~~~~  756 (915)
T PTZ00111        677 RSNTMHVEDESLRSEKDYNKNDLDMLRMYIKFSKLHCFPKLSDEAKKVITREYVKMRQGNFQTSNLDELEHAQEDDDDDL  756 (915)
T ss_pred             ccccccccccccccccccCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHhhhhcccccccccccccccccccc
Confidence                                               00011110   111       110                     


Q ss_pred             ---cC-----CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          234 ---AE-----GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       234 ---~~-----g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                         ..     -.++|.+..+++-|.+.|..+.+..|+.+|+.+|++-+..
T Consensus       757 ~~~~~~~~~i~iT~RqLEsLIRLsEA~AK~rLs~~Vt~~Dv~~Ai~L~~~  806 (915)
T PTZ00111        757 YYQSSGTRMIYVSSRMISSIIRISVSLARMRLSTVVTPADALQAVQIVKS  806 (915)
T ss_pred             ccccccCCcccccHHHHHHHHHHHHHHhhhcCcCcccHHHHHHHHHHHHH
Confidence               01     1478999999999999999999999999999999998864

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.26  E-value=1.3e-10  Score=88.76  Aligned_cols=125  Identities=30%  Similarity=0.460  Sum_probs=76.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCc---EEEEeccchhccc--------------cChHHHHHHHHHHHhhhCCCEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDAN---FLKVVSSAIIDKY--------------IGESARLIREMFGYARDHQPCI  128 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~---~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~~~~~i  128 (292)
                      +.+++|+||||+|||++++.++..+...   ++.+++.......              ...........+..+....+.+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            4679999999999999999999999775   7777766543221              1223445567777777766799


Q ss_pred             EEEcccccccCCcCCCCCcchHHHHHHHHHH---HHHhhCCCCCCCeEEEEEeCC-CCCCChhhcCCCCcceEEEccCC
Q 022768          129 IFMDEIDAIGGRRFSEGTSADREIQRTLMEL---LNQLDGFDQLGKVKMIMATNR-PDVLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       129 l~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~---l~~~~~~~~~~~~~vi~t~~~-~~~l~~~l~~~~r~~~~i~l~~p  203 (292)
                      |++||++.+..           .........   ..............+|+++|. ....+..+..  ++...+.+..+
T Consensus        82 iiiDei~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~--~~~~~~~~~~~  147 (148)
T smart00382       82 LILDEITSLLD-----------AEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR--RFDRRIVLLLI  147 (148)
T ss_pred             EEEECCcccCC-----------HHHHHHHHhhhhhHHHHHHHhcCCCEEEEEeCCCccCchhhhhh--ccceEEEecCC
Confidence            99999998842           111111111   000000022246778888886 2333444444  66666655443

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=99.26  E-value=3.8e-11  Score=106.51  Aligned_cols=229  Identities=17%  Similarity=0.146  Sum_probs=144.1

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHH
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESAR  112 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~  112 (292)
                      +|+|.+++|+.|.-.+..-..+ .....+.++-.-+|++.|.||+.||.|++++.+.....++...-+.   .-+|-+..
T Consensus       343 EIyGheDVKKaLLLlLVGgvd~-~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlapRgvYTTGrGS---SGVGLTAA  418 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLVGGVDK-SPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAPRGVYTTGRGS---SGVGLTAA  418 (721)
T ss_pred             hhccchHHHHHHHHHhhCCCCC-CCCCCceeecceeEEecCCCchhHHHHHHHHHhcCcccceecCCCC---Cccccchh
Confidence            5799999999999988764322 1111222344567999999999999999999998766665543222   11222222


Q ss_pred             HHHHHHHH-h-------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-CC-------CCCCCeEEEE
Q 022768          113 LIREMFGY-A-------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-GF-------DQLGKVKMIM  176 (292)
Q Consensus       113 ~~~~~~~~-~-------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~-------~~~~~~~vi~  176 (292)
                      .++.-... .       -....+|-+|||||.+           +.....++.+.+++-. ++       .-+.++.+++
T Consensus       419 VmkDpvTgEM~LEGGALVLAD~GICCIDEfDKM-----------~e~DRtAIHEVMEQQTISIaKAGI~TtLNAR~sILa  487 (721)
T KOG0482|consen  419 VMKDPVTGEMVLEGGALVLADGGICCIDEFDKM-----------DESDRTAIHEVMEQQTISIAKAGINTTLNARTSILA  487 (721)
T ss_pred             hhcCCCCCeeEeccceEEEccCceEeehhhhhh-----------hhhhhHHHHHHHHhhhhhhhhhccccchhhhHHhhh
Confidence            22211110 0       0134578999999999           3333334444444321 11       2223678899


Q ss_pred             EeCCCC-------------CCChhhcCCCCcceEEEc-cCCCHHHHHHHHHHHHcC--ccCCC-----CCCHHHHHHHc-
Q 022768          177 ATNRPD-------------VLDPALLRPGRLDRKIEI-PLPNEQSRMEILKIHAAG--IAKHG-----EIDYEAVVKLA-  234 (292)
Q Consensus       177 t~~~~~-------------~l~~~l~~~~r~~~~i~l-~~p~~~~r~~i~~~~~~~--~~~~~-----~~~~~~l~~~~-  234 (292)
                      ++|+..             .++.+|++  ||+..+.+ ..|+.+.-..+.++...-  ....+     .++++.+-... 
T Consensus       488 AANPayGRYnprrs~e~NI~LPaALLS--RFDll~Li~D~pdrd~D~~LA~HiTyVH~H~~qp~~~fepl~~~~mR~yI~  565 (721)
T KOG0482|consen  488 AANPAYGRYNPRRSPEQNINLPAALLS--RFDLLWLIQDRPDRDNDLRLAQHITYVHQHEEQPPLDFEPLDPNLMRRYIS  565 (721)
T ss_pred             hcCccccccCcccChhHhcCCcHHHHH--hhhhhhhhccCCcccchHHHHHHhHhhhccCCCCCccCCCCCHHHHHHHHH
Confidence            988642             47889999  99876644 778877666666654431  11111     12322211110 


Q ss_pred             ------------------------------C----CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          235 ------------------------------E----GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       235 ------------------------------~----g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                                                    .    -.+++.+..+++-+.+.|..+....|..+|+.+|++-|...++
T Consensus       566 ~ak~~~P~vp~~l~dyi~~AYv~~Rrea~~~~~~t~ttpRtLL~IlRls~AlarLRls~~V~~~DV~EALRLme~sK~  643 (721)
T KOG0482|consen  566 LAKRKNPVVPEALADYITGAYVELRREARSSKDFTYTTPRTLLGILRLSTALARLRLSDSVEEDDVNEALRLMEMSKD  643 (721)
T ss_pred             HHhhcCCCCCHHHHHHHHHHHHHHHHHhhccCCCcccCHHHHHHHHHHHHHHHHhhhccccchhhHHHHHHHHHhhhc
Confidence                                          0    2378999999999999999999999999999999999987544

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=99.26  E-value=3.8e-11  Score=88.90  Aligned_cols=111  Identities=26%  Similarity=0.369  Sum_probs=62.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh--ccccCh----HHHHHHHHHHHhhh-CCCEEEEEcccccccCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII--DKYIGE----SARLIREMFGYARD-HQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~--~~~~~~----~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~  140 (292)
                      |+||.|+||+|||++++++|+.++..+.++.+..-.  +...|.    ...   ..|...+. --..|+++||+++.   
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~---~~f~~~~GPif~~ill~DEiNra---   74 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQET---GEFEFRPGPIFTNILLADEINRA---   74 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTT---TEEEEEE-TT-SSEEEEETGGGS---
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCC---CeeEeecChhhhceeeecccccC---
Confidence            689999999999999999999999999888764211  000000    000   00000000 00159999999998   


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHhhC------CCCCCCeEEEEEeCCCC-----CCChhhcCCCCc
Q 022768          141 RFSEGTSADREIQRTLMELLNQLDG------FDQLGKVKMIMATNRPD-----VLDPALLRPGRL  194 (292)
Q Consensus       141 ~~~~~~~~~~~~~~~l~~~l~~~~~------~~~~~~~~vi~t~~~~~-----~l~~~l~~~~r~  194 (292)
                              ....|.++++.+.+...      ..-...++||+|.|+.+     .++.++++  ||
T Consensus        75 --------ppktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~D--RF  129 (131)
T PF07726_consen   75 --------PPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLD--RF  129 (131)
T ss_dssp             ---------HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHT--TS
T ss_pred             --------CHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhc--cc
Confidence                    88899999999987531      22233588888888755     57888888  77

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.25  E-value=1.5e-10  Score=106.42  Aligned_cols=203  Identities=26%  Similarity=0.339  Sum_probs=123.4

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY  106 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~  106 (292)
                      .+..++|.....+.+...+...           .....+++|+|++|+||+++|+.+....   +.+++.++|..+....
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~-----------a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~~~  205 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKI-----------APSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPENL  205 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCChHH
Confidence            4556888888877777766542           2345679999999999999999998765   4589999998763221


Q ss_pred             cChHHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC----
Q 022768          107 IGESARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD----  167 (292)
Q Consensus       107 ~~~~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~----  167 (292)
                            .-..+|+.               .....+++|||||++.|           +...+..|..+++.....+    
T Consensus       206 ------~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l-----------~~~~q~~l~~~l~~~~~~~~~~~  268 (445)
T TIGR02915       206 ------LESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDL-----------PLNLQAKLLRFLQERVIERLGGR  268 (445)
T ss_pred             ------HHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhC-----------CHHHHHHHHHHHhhCeEEeCCCC
Confidence                  11122221               11244689999999999           8889999998887532100    


Q ss_pred             --CCCCeEEEEEeCCC-------CCCChhhcCCCCcceEEEccCCCHHHHHH----HHHHHHcCc----cCC-CCCCHHH
Q 022768          168 --QLGKVKMIMATNRP-------DVLDPALLRPGRLDRKIEIPLPNEQSRME----ILKIHAAGI----AKH-GEIDYEA  229 (292)
Q Consensus       168 --~~~~~~vi~t~~~~-------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~~~~~~~~----~~~-~~~~~~~  229 (292)
                        ...++.+|++++..       ..+.+.+..  |+ ..+.+..|...+|.+    ++..++...    ... ..++.+.
T Consensus       269 ~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~--~l-~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a  345 (445)
T TIGR02915       269 EEIPVDVRIVCATNQDLKRMIAEGTFREDLFY--RI-AEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDA  345 (445)
T ss_pred             ceeeeceEEEEecCCCHHHHHHcCCccHHHHH--Hh-ccceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHHH
Confidence              01257788888754       234444443  44 234455555555543    444444432    111 2355566


Q ss_pred             HHHHcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHH
Q 022768          230 VVKLAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDF  266 (292)
Q Consensus       230 l~~~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~  266 (292)
                      +..+...-   |.++++++++.|...   .....|+.+++
T Consensus       346 ~~~L~~~~wpgNvreL~~~i~~a~~~---~~~~~i~~~~l  382 (445)
T TIGR02915       346 LRALEAHAWPGNVRELENKVKRAVIM---AEGNQITAEDL  382 (445)
T ss_pred             HHHHHhCCCCChHHHHHHHHHHHHHh---CCCCcccHHHc
Confidence            66554422   556666666666543   33335555554

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=99.25  E-value=4e-10  Score=103.88  Aligned_cols=211  Identities=15%  Similarity=0.225  Sum_probs=123.6

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe-ccc
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV-SSA  101 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~-~~~  101 (292)
                      -+.+.|.+.++|.-....++++..++.....        +..+.+.++|+||+|+||||+++.+|++++..+.+-. ...
T Consensus        10 ~~ky~P~~~~eLavhkkKv~eV~~wl~~~~~--------~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~Ew~np~~   81 (519)
T PF03215_consen   10 VEKYAPKTLDELAVHKKKVEEVRSWLEEMFS--------GSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQEWINPVS   81 (519)
T ss_pred             chhcCCCCHHHhhccHHHHHHHHHHHHHHhc--------cCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEEecCCCC
Confidence            3578899999999999999999999875321        1233556888999999999999999999988776632 222


Q ss_pred             hh------ccccCh---HH------HHHHHH-HHHhh-----------hCCCEEEEEcccccccCCcCCCCCcchHHHHH
Q 022768          102 II------DKYIGE---SA------RLIREM-FGYAR-----------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQR  154 (292)
Q Consensus       102 ~~------~~~~~~---~~------~~~~~~-~~~~~-----------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~  154 (292)
                      ..      ..+.+.   ..      ...... +...+           ...+.||+|||+=.++...       ......
T Consensus        82 ~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~~-------~~~f~~  154 (519)
T PF03215_consen   82 FRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHRD-------TSRFRE  154 (519)
T ss_pred             ccccccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccchh-------HHHHHH
Confidence            10      001000   00      001111 11111           1246799999996653211       233444


Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEEe-CC------C--------CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc
Q 022768          155 TLMELLNQLDGFDQLGKVKMIMAT-NR------P--------DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI  219 (292)
Q Consensus       155 ~l~~~l~~~~~~~~~~~~~vi~t~-~~------~--------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~  219 (292)
                      .|..++..    .....+++|+|- +.      .        ..+++.++...++ ..|.|.+-...-.++.+...+...
T Consensus       155 ~L~~~l~~----~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i-~~I~FNpIa~T~mkKaL~rI~~~E  229 (519)
T PF03215_consen  155 ALRQYLRS----SRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGI-TRIKFNPIAPTFMKKALKRILKKE  229 (519)
T ss_pred             HHHHHHHc----CCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCc-eEEEecCCCHHHHHHHHHHHHHHH
Confidence            44444432    111155666661 11      1        1345666654344 788999988877777777665532


Q ss_pred             -----cCCCCCC-HHHHHHHcCCCCHHHHHHHHHHHHHHHH
Q 022768          220 -----AKHGEID-YEAVVKLAEGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       220 -----~~~~~~~-~~~l~~~~~g~~~~di~~l~~~a~~~a~  254 (292)
                           ......+ .+.+..+..+ +.||||.++.....++.
T Consensus       230 ~~~~~~~~~~p~~~~~l~~I~~~-s~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  230 ARSSSGKNKVPDKQSVLDSIAES-SNGDIRSAINNLQFWCL  269 (519)
T ss_pred             hhhhcCCccCCChHHHHHHHHHh-cCchHHHHHHHHHHHhc
Confidence                 1111112 1223333332 33499999999999997

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.24  E-value=2.3e-11  Score=96.54  Aligned_cols=117  Identities=23%  Similarity=0.311  Sum_probs=72.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCC----cEEEEeccchhccc--cChHHHHHHHHHHHhhhCCCEEEEEcccccccC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDA----NFLKVVSSAIIDKY--IGESARLIREMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~----~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      -.+++|.||+|+|||.++++++..+..    +++.+++..+....  .......+...-........+||+|||+|....
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~~   82 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAHP   82 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCSH
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhHHHhhccc
Confidence            457999999999999999999999995    99999999887610  001111111111111122224999999999943


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCCeEEEEEeCCCC
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGF------DQLGKVKMIMATNRPD  182 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~~~vi~t~~~~~  182 (292)
                      ..+...+-.....+..|+.+++...-.      -...++++|+|+|-..
T Consensus        83 ~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~  131 (171)
T PF07724_consen   83 SNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGA  131 (171)
T ss_dssp             TTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSST
T ss_pred             cccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccccc
Confidence            311111112237788888888764211      1223788999998643

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK12377 putative replication protein; Provisional

Probab=99.22  E-value=9.2e-11  Score=98.36  Aligned_cols=155  Identities=15%  Similarity=0.199  Sum_probs=90.3

Q ss_pred             cCCCCCcccccc----ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEE
Q 022768           24 EDPGNVSYSAVG----GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLK   96 (292)
Q Consensus        24 ~~~~~~~~~~l~----g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~   96 (292)
                      +.....+|++..    |...++.....++..+       .    ....+++|+||||+|||||+.++++.+   +..++.
T Consensus        66 ~~~~~~tFdnf~~~~~~~~~a~~~a~~~a~~~-------~----~~~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~  134 (248)
T PRK12377         66 PLHRKCSFANYQVQNDGQRYALSQAKSIADEL-------M----TGCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIV  134 (248)
T ss_pred             cccccCCcCCcccCChhHHHHHHHHHHHHHHH-------H----hcCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEE
Confidence            344556788775    3333455555555442       1    124579999999999999999999987   566777


Q ss_pred             EeccchhccccChHHH--HHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           97 VVSSAIIDKYIGESAR--LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      +...++..........  .....+...  ....+|+|||+....         .....+..+..+++.-..    ....+
T Consensus       135 i~~~~l~~~l~~~~~~~~~~~~~l~~l--~~~dLLiIDDlg~~~---------~s~~~~~~l~~ii~~R~~----~~~pt  199 (248)
T PRK12377        135 VTVPDVMSRLHESYDNGQSGEKFLQEL--CKVDLLVLDEIGIQR---------ETKNEQVVLNQIIDRRTA----SMRSV  199 (248)
T ss_pred             EEHHHHHHHHHHHHhccchHHHHHHHh--cCCCEEEEcCCCCCC---------CCHHHHHHHHHHHHHHHh----cCCCE
Confidence            7766655432111000  111222222  345799999996542         144567788888876432    23447


Q ss_pred             EEEeCCCC-----CCChhhcCCCCc--ceEEEccCCC
Q 022768          175 IMATNRPD-----VLDPALLRPGRL--DRKIEIPLPN  204 (292)
Q Consensus       175 i~t~~~~~-----~l~~~l~~~~r~--~~~i~l~~p~  204 (292)
                      |+|+|...     .+..++.++.+.  ...+.+...+
T Consensus       200 iitSNl~~~~l~~~~~~ri~dRl~~~~~~~v~~~g~s  236 (248)
T PRK12377        200 GMLTNLNHEAMSTLLGERVMDRMTMNGGRWVNFNWES  236 (248)
T ss_pred             EEEcCCCHHHHHHHhhHHHHHHHhhCCCeEEEeCCcC
Confidence            88888642     244455552221  2345555544

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.21  E-value=1.6e-10  Score=97.97  Aligned_cols=86  Identities=28%  Similarity=0.398  Sum_probs=64.1

Q ss_pred             CEEEEEcccccccCCcCCCC-CcchHHHHHHHHHHHHHhh-----CCCCCCCeEEEEEe----CCCCCCChhhcCCCCcc
Q 022768          126 PCIIFMDEIDAIGGRRFSEG-TSADREIQRTLMELLNQLD-----GFDQLGKVKMIMAT----NRPDVLDPALLRPGRLD  195 (292)
Q Consensus       126 ~~il~lDe~d~l~~~~~~~~-~~~~~~~~~~l~~~l~~~~-----~~~~~~~~~vi~t~----~~~~~l~~~l~~~~r~~  195 (292)
                      .+|+||||+|.++.+...+. +-+-...|+.|+-++.--.     +.-..+++.+|++.    ..|+++-|.|+.  ||.
T Consensus       251 ~GIvFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQG--RfP  328 (444)
T COG1220         251 NGIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQG--RFP  328 (444)
T ss_pred             cCeEEEehhhHHHhcCCCCCCCcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcC--CCc
Confidence            47999999999987765443 3344567777777765432     33444578888875    457888899988  999


Q ss_pred             eEEEccCCCHHHHHHHHH
Q 022768          196 RKIEIPLPNEQSRMEILK  213 (292)
Q Consensus       196 ~~i~l~~p~~~~r~~i~~  213 (292)
                      ..+.+...+.+....|+.
T Consensus       329 IRVEL~~Lt~~Df~rILt  346 (444)
T COG1220         329 IRVELDALTKEDFERILT  346 (444)
T ss_pred             eEEEcccCCHHHHHHHHc
Confidence            999999999988887665

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=99.20  E-value=6.5e-11  Score=105.14  Aligned_cols=216  Identities=22%  Similarity=0.277  Sum_probs=122.8

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc----EEEEe-----
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN----FLKVV-----   98 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~----~~~~~-----   98 (292)
                      ...|.|++|++.+++.+.-....               ++++|++||||||||++++-+...+..-    .+++.     
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAAAG---------------gHnLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s~I~s~  239 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAAAG---------------GHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHSL  239 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHHhc---------------CCcEEEecCCCCchHHhhhhhcccCCCCChHHHHHHHHHhhh
Confidence            45899999999999999888654               7899999999999999999988766321    11111     


Q ss_pred             ccchhc----------cccChHHHHHHHHHHH--------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHH
Q 022768           99 SSAIID----------KYIGESARLIREMFGY--------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELL  160 (292)
Q Consensus        99 ~~~~~~----------~~~~~~~~~~~~~~~~--------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l  160 (292)
                      ...+..          ...+.+. ....+...        +...+.+||||||+-.+           ...+.+.|.+-|
T Consensus       240 ~g~~~~~~~~~~~rPFr~PHHsa-S~~aLvGGG~~p~PGeIsLAH~GVLFLDElpef-----------~~~iLe~LR~PL  307 (490)
T COG0606         240 AGDLHEGCPLKIHRPFRAPHHSA-SLAALVGGGGVPRPGEISLAHNGVLFLDELPEF-----------KRSILEALREPL  307 (490)
T ss_pred             cccccccCccceeCCccCCCccc-hHHHHhCCCCCCCCCceeeecCCEEEeeccchh-----------hHHHHHHHhCcc
Confidence            000000          0000100 01111111        11134589999998555           443333333333


Q ss_pred             HHhhC--------CCCCCCeEEEEEeCCC-----------------------CCCChhhcCCCCcceEEEccCCCHHHHH
Q 022768          161 NQLDG--------FDQLGKVKMIMATNRP-----------------------DVLDPALLRPGRLDRKIEIPLPNEQSRM  209 (292)
Q Consensus       161 ~~~~~--------~~~~~~~~vi~t~~~~-----------------------~~l~~~l~~~~r~~~~i~l~~p~~~~r~  209 (292)
                      +...-        ..-.-++.+|+++|..                       .+++..+++  |++..+.++.++..++.
T Consensus       308 E~g~i~IsRa~~~v~ypa~Fqlv~AmNpcpcG~~~~~~~~C~c~~~~~~~Y~~klSgp~lD--RiDl~vev~~~~~~e~~  385 (490)
T COG0606         308 ENGKIIISRAGSKVTYPARFQLVAAMNPCPCGNLGAPLRRCPCSPRQIKRYLNKLSGPFLD--RIDLMVEVPRLSAGELI  385 (490)
T ss_pred             ccCcEEEEEcCCeeEEeeeeEEhhhcCCCCccCCCCCCCCcCCCHHHHHHHHHHhhHHHHh--hhhheecccCCCHHHhh
Confidence            22110        0111156777887742                       135556777  88888888776533221


Q ss_pred             --------------HHHHHHHc----Ccc--CCCCCCHHHHHH----------------HcCCCCHHHHHHHHHHHHHHH
Q 022768          210 --------------EILKIHAA----GIA--KHGEIDYEAVVK----------------LAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       210 --------------~i~~~~~~----~~~--~~~~~~~~~l~~----------------~~~g~~~~di~~l~~~a~~~a  253 (292)
                                    .+++.+..    ...  .+..++-..|.+                ..-++|.+....+++-|..+|
T Consensus       386 ~~~~~~ess~~v~~rVa~AR~~Q~~R~~~~~~Na~l~~~~l~k~~~L~~~~~~~L~~al~~~~lS~R~~~rILKvarTiA  465 (490)
T COG0606         386 RQVPTGESSAGVRERVAKAREAQIARAGRIGINAELSEEALRKFCALQREDADLLKAALERLGLSARAYHRILKVARTIA  465 (490)
T ss_pred             cCCCCCCCcHHHHHHHHHHHHHHHHHhhccCcchhcCHHHHHHhcccCHhHHHHHHHHHHhcchhHHHHHHHHHHHhhhh
Confidence                          12221111    111  122222222222                122567788888888888888


Q ss_pred             HHhcCCcccHHHHHHHHHH
Q 022768          254 IRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a~~~  272 (292)
                      -..+...|...++.+|++.
T Consensus       466 DL~g~~~i~~~hl~eAi~y  484 (490)
T COG0606         466 DLEGSEQIERSHLAEAISY  484 (490)
T ss_pred             cccCcchhhHHHHHHHHhh
Confidence            8888888999999988864

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.19  E-value=7e-10  Score=96.78  Aligned_cols=166  Identities=16%  Similarity=0.192  Sum_probs=106.4

Q ss_pred             cc-cccccHHHHHHHHHHhhcccCChHHHHhcCC-CCCceEEEEcCCCChHHHHHHHHHHhcCC-------cEEEEec--
Q 022768           31 YS-AVGGLSDQIRELRESIELPLMNPELFLRVGI-KPPKGVLLYGPPGTGKTLLARAIASNIDA-------NFLKVVS--   99 (292)
Q Consensus        31 ~~-~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~-~~~~~vll~G~~G~GKT~l~~~la~~l~~-------~~~~~~~--   99 (292)
                      |+ +++|+++++.++.+++.....        |. .....++|+||||+||||+++++++.++.       +++.+..  
T Consensus        49 F~~~~~G~~~~i~~lv~~l~~~a~--------g~~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~~~  120 (361)
T smart00763       49 FDHDFFGMEEAIERFVNYFKSAAQ--------GLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKWNG  120 (361)
T ss_pred             cchhccCcHHHHHHHHHHHHHHHh--------cCCCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEecC
Confidence            45 799999999999998876421        12 23466899999999999999999999865       6666654  


Q ss_pred             --cchhccccChHHHH----------------------------------------------------------------
Q 022768          100 --SAIIDKYIGESARL----------------------------------------------------------------  113 (292)
Q Consensus       100 --~~~~~~~~~~~~~~----------------------------------------------------------------  113 (292)
                        +.+.....+-....                                                                
T Consensus       121 ~~sp~~e~Pl~l~p~~~r~~~~~~~~~~~~~~~~~l~p~c~~~l~~e~~gd~~~~~V~~~~~s~~~~~gi~~~~P~D~~~  200 (361)
T smart00763      121 EESPMHEDPLHLFPDELREDLEDEYGIPRRRLEGDLSPWCRKRLDEEYGGDIEKFEVVRVNFSELRRIGIGKFEPKDENN  200 (361)
T ss_pred             CCCCCccCCcccCCHHHHHHHHHHhCCChhhcCCCCCHHHHHHHHHHhCCCcceEEEEEecCCeecceEEEEECCCCCCc
Confidence              22211100000000                                                                


Q ss_pred             --HHHHHHHh----------------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC--
Q 022768          114 --IREMFGYA----------------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD--  167 (292)
Q Consensus       114 --~~~~~~~~----------------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~--  167 (292)
                        +..+.+.+                      .....+++-|+|+...           +.+.+..|+..+++..-.-  
T Consensus       201 qdi~~L~G~vd~~k~~~~~~~dp~a~~~~G~l~~aNrGi~~f~Ei~K~-----------~~~~l~~LL~~~qE~~v~~~~  269 (361)
T smart00763      201 QDISELTGKVDIRKLEIYSESDPRAFSYDGALNRANRGILEFVEMFKA-----------DIKFLHPLLTATQEGNIKGTG  269 (361)
T ss_pred             ccHHHHhcccCHHHhcccCCCCCeEEeccCccccccCceEEEeehhcC-----------CHHHHHHHhhhhhcceEecCC
Confidence              00000000                      0023478888888777           7778888888877643211  


Q ss_pred             ----CCCCeEEEEEeCCCC-------CCChhhcCCCCcceEEEccCC-CHHHHHHHHHHHHcC
Q 022768          168 ----QLGKVKMIMATNRPD-------VLDPALLRPGRLDRKIEIPLP-NEQSRMEILKIHAAG  218 (292)
Q Consensus       168 ----~~~~~~vi~t~~~~~-------~l~~~l~~~~r~~~~i~l~~p-~~~~r~~i~~~~~~~  218 (292)
                          -.-..++|+++|..+       +..+++++  || ..++++++ +.++-.+|.+..+..
T Consensus       270 ~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~d--R~-~~i~vpY~l~~~~E~~Iy~k~~~~  329 (361)
T smart00763      270 GFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLD--RI-IKVKVPYCLRVSEEAQIYEKLLRN  329 (361)
T ss_pred             cccccccceEEEEeCCHHHHhhhhccccchhhhh--ce-EEEeCCCcCCHHHHHHHHHHHhcc
Confidence                111467888888762       56788988  88 47888887 557777888877753

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK08116 hypothetical protein; Validated

Probab=99.19  E-value=1.8e-10  Score=98.25  Aligned_cols=123  Identities=18%  Similarity=0.245  Sum_probs=76.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChH----HHHHHHHHHHhhhCCCEEEEEccccccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGES----ARLIREMFGYARDHQPCIIFMDEIDAIG  138 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~il~lDe~d~l~  138 (292)
                      +.+++|+|++|+|||+|+.++++.+   +.+++.++..++........    ......++....  ...+|+|||+... 
T Consensus       114 ~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~--~~dlLviDDlg~e-  190 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLV--NADLLILDDLGAE-  190 (268)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhc--CCCEEEEecccCC-
Confidence            4579999999999999999999986   67788888766554321110    011112232222  3369999999542 


Q ss_pred             CCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC-CC----CChhhcCCCCc---ceEEEccCCCH
Q 022768          139 GRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP-DV----LDPALLRPGRL---DRKIEIPLPNE  205 (292)
Q Consensus       139 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~-~~----l~~~l~~~~r~---~~~i~l~~p~~  205 (292)
                              ......+..+..+++....    .+..+|+|+|.+ ..    ++.++.+  |+   ...+.+..++.
T Consensus       191 --------~~t~~~~~~l~~iin~r~~----~~~~~IiTsN~~~~eL~~~~~~ri~s--Rl~e~~~~v~~~g~d~  251 (268)
T PRK08116        191 --------RDTEWAREKVYNIIDSRYR----KGLPTIVTTNLSLEELKNQYGKRIYD--RILEMCTPVENEGKSY  251 (268)
T ss_pred             --------CCCHHHHHHHHHHHHHHHH----CCCCEEEECCCCHHHHHHHHhHHHHH--HHHHcCEEEEeeCcCh
Confidence                    1145566777777776421    233478888764 22    3456666  52   35667777764

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=99.19  E-value=3.6e-10  Score=104.53  Aligned_cols=208  Identities=21%  Similarity=0.285  Sum_probs=127.9

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY  106 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~  106 (292)
                      ++.+++|.....+++.+.+...           ......++|.|++||||+++|+++....   +.+++.++|..+....
T Consensus       136 ~~~~lig~s~~~~~l~~~~~~~-----------~~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~~~  204 (469)
T PRK10923        136 PTTDIIGEAPAMQDVFRIIGRL-----------SRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDL  204 (469)
T ss_pred             ccccceecCHHHHHHHHHHHHH-----------hccCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCHHH
Confidence            4567889888888877776543           2446779999999999999999999876   4689999998763211


Q ss_pred             cChHHHHHHHHHHHh---------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC----
Q 022768          107 IGESARLIREMFGYA---------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD----  167 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~---------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~----  167 (292)
                            .-..+|+..               ....++.|||||++.+           +...+..|..+++......    
T Consensus       205 ------~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l-----------~~~~q~~L~~~l~~~~~~~~~~~  267 (469)
T PRK10923        205 ------IESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDM-----------PLDVQTRLLRVLADGQFYRVGGY  267 (469)
T ss_pred             ------HHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccC-----------CHHHHHHHHHHHhcCcEEeCCCC
Confidence                  111233211               1234579999999999           8888888888887532110    


Q ss_pred             --CCCCeEEEEEeCCC-------CCCChhhcCCCCc-ceEEEccCCCH--HHHHHHHHHHHcCc----cCC-CCCCHHHH
Q 022768          168 --QLGKVKMIMATNRP-------DVLDPALLRPGRL-DRKIEIPLPNE--QSRMEILKIHAAGI----AKH-GEIDYEAV  230 (292)
Q Consensus       168 --~~~~~~vi~t~~~~-------~~l~~~l~~~~r~-~~~i~l~~p~~--~~r~~i~~~~~~~~----~~~-~~~~~~~l  230 (292)
                        ...++.+|+|++..       ..+.+.+..  |+ ...|.+|+...  ++...++.+++...    ... ..++.+.+
T Consensus       268 ~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~--~l~~~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~  345 (469)
T PRK10923        268 APVKVDVRIIAATHQNLEQRVQEGKFREDLFH--RLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETE  345 (469)
T ss_pred             CeEEeeEEEEEeCCCCHHHHHHcCCchHHHHH--HhcceeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHH
Confidence              01246788888653       134455554  55 23444444422  23334555555432    111 23555666


Q ss_pred             HHHcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          231 VKLAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       231 ~~~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      ..+...-   |.++++++++.+.   .......|+.+++...+
T Consensus       346 ~~L~~~~wpgNv~eL~~~i~~~~---~~~~~~~i~~~~l~~~~  385 (469)
T PRK10923        346 AALTRLAWPGNVRQLENTCRWLT---VMAAGQEVLIQDLPGEL  385 (469)
T ss_pred             HHHHhCCCCChHHHHHHHHHHHH---HhCCCCcccHHHCcHhh
Confidence            6655533   4455555555554   44445578888876544

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.18  E-value=4.5e-10  Score=100.53  Aligned_cols=144  Identities=24%  Similarity=0.354  Sum_probs=86.0

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------EEEEecc---
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------FLKVVSS---  100 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------~~~~~~~---  100 (292)
                      ++++.+.++..+.+...+.               .+.+++|+||||||||++|+.+|..+...       .+.++..   
T Consensus       174 l~d~~i~e~~le~l~~~L~---------------~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySY  238 (459)
T PRK11331        174 LNDLFIPETTIETILKRLT---------------IKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSY  238 (459)
T ss_pred             hhcccCCHHHHHHHHHHHh---------------cCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccH
Confidence            5667777777777766654               25689999999999999999999987431       1222211   


Q ss_pred             -chhccccCh-H-----HHHHHHHHHHhhh--CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH---------
Q 022768          101 -AIIDKYIGE-S-----ARLIREMFGYARD--HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ---------  162 (292)
Q Consensus       101 -~~~~~~~~~-~-----~~~~~~~~~~~~~--~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~---------  162 (292)
                       ++...+... .     ......+...+..  ..|.+|+|||+++--.          ......+..+++.         
T Consensus       239 eDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani----------~kiFGel~~lLE~~~rg~~~~v  308 (459)
T PRK11331        239 EDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANL----------SKVFGEVMMLMEHDKRGENWSV  308 (459)
T ss_pred             HHHhcccCCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCH----------HHhhhhhhhhccccccccccce
Confidence             111111000 0     0112233334443  3578999999987621          1122222333321         


Q ss_pred             --------hhCCCCCCCeEEEEEeCCCC----CCChhhcCCCCcceEEEccC
Q 022768          163 --------LDGFDQLGKVKMIMATNRPD----VLDPALLRPGRLDRKIEIPL  202 (292)
Q Consensus       163 --------~~~~~~~~~~~vi~t~~~~~----~l~~~l~~~~r~~~~i~l~~  202 (292)
                              .+.+..+.++.+|+|+|..+    .++.++++  || ..+.+.+
T Consensus       309 ~l~y~e~d~e~f~iP~Nl~IIgTMNt~Drs~~~lD~AlrR--RF-~fi~i~p  357 (459)
T PRK11331        309 PLTYSENDEERFYVPENVYIIGLMNTADRSLAVVDYALRR--RF-SFIDIEP  357 (459)
T ss_pred             eeeccccccccccCCCCeEEEEecCccccchhhccHHHHh--hh-heEEecC
Confidence                    01234456899999999876    68999999  88 4456654

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=99.18  E-value=9.2e-10  Score=100.28  Aligned_cols=231  Identities=17%  Similarity=0.143  Sum_probs=145.8

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc----
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY----  106 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~----  106 (292)
                      |..+.|.+.+|.-|.-.+-.-...... ....++..-+|+|.|.||+|||.+++++++-++..++...-..-...+    
T Consensus       344 ~PsIyGhe~VK~GilL~LfGGv~K~a~-eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsPR~vYtsGkaSSaAGLTaaV  422 (764)
T KOG0480|consen  344 FPSIYGHELVKAGILLSLFGGVHKSAG-EGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSPRSVYTSGKASSAAGLTAAV  422 (764)
T ss_pred             CccccchHHHHhhHHHHHhCCccccCC-CCccccCCceEEEeCCCCccHHHHHHHHhccCCcceEecCcccccccceEEE
Confidence            456789999998887665432221111 233345567899999999999999999999887776654322211100    


Q ss_pred             c--ChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-CCCCC-------CCeEEEE
Q 022768          107 I--GESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-GFDQL-------GKVKMIM  176 (292)
Q Consensus       107 ~--~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~~~~-------~~~~vi~  176 (292)
                      +  +.+.+..-+ .+.......+|-+|||||.+           +...+.++.+.+++-. ++.+.       .+..|||
T Consensus       423 vkD~esgdf~iE-AGALmLADnGICCIDEFDKM-----------d~~dqvAihEAMEQQtISIaKAGv~aTLnARtSIlA  490 (764)
T KOG0480|consen  423 VKDEESGDFTIE-AGALMLADNGICCIDEFDKM-----------DVKDQVAIHEAMEQQTISIAKAGVVATLNARTSILA  490 (764)
T ss_pred             EecCCCCceeee-cCcEEEccCceEEechhccc-----------ChHhHHHHHHHHHhheehheecceEEeecchhhhhh
Confidence            0  000000000 00112234589999999999           6767778888777632 22211       2566788


Q ss_pred             EeCCCC-------------CCChhhcCCCCcceEE-EccCCCHHHHHHHHHHHHcCc-cC--------------------
Q 022768          177 ATNRPD-------------VLDPALLRPGRLDRKI-EIPLPNEQSRMEILKIHAAGI-AK--------------------  221 (292)
Q Consensus       177 t~~~~~-------------~l~~~l~~~~r~~~~i-~l~~p~~~~r~~i~~~~~~~~-~~--------------------  221 (292)
                      ++|+..             .+++++.+  ||+..+ .+..|++..-..|-++.+... .+                    
T Consensus       491 AANPv~GhYdR~ktl~eNi~msApimS--RFDL~FiLlD~~nE~~D~~ia~hIld~h~~i~~~~~~~~~~~~e~vrkYi~  568 (764)
T KOG0480|consen  491 AANPVGGHYDRKKTLRENINMSAPIMS--RFDLFFILLDDCNEVVDYAIARHILDLHRGIDDATERVCVYTLEQVRKYIR  568 (764)
T ss_pred             hcCCcCCccccccchhhhcCCCchhhh--hhcEEEEEecCCchHHHHHHHHHHHHHhccccccccccccccHHHHHHHHH
Confidence            888642             37789999  998755 668888877666666554310 00                    


Q ss_pred             -----CCCCCH----------HHHHHHc--------CCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          222 -----HGEIDY----------EAVVKLA--------EGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       222 -----~~~~~~----------~~l~~~~--------~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                           .+.+..          ..|-...        -..+.+++..+++-+.+.|...-...+|.+++.+|.+-++..
T Consensus       569 yAR~~~P~ls~ea~~~lve~Y~~lR~~~~~~~~~~s~~ITvRqLESlIRLsEA~Ar~~~~devt~~~v~ea~eLlk~S  646 (764)
T KOG0480|consen  569 YARNFKPKLSKEASEMLVEKYKGLRQRDAQGNNRSSYRITVRQLESLIRLSEARARVECRDEVTKEDVEEAVELLKKS  646 (764)
T ss_pred             HHHhcCccccHHHHHHHHHHHHHHHHhhccccCcccccccHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHHHHHHhh
Confidence                 000110          0011111        134789999999999999999999999999999999998865

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=99.18  E-value=2e-10  Score=95.82  Aligned_cols=186  Identities=22%  Similarity=0.365  Sum_probs=100.2

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---EEEEeccchhc-----c
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---FLKVVSSAIID-----K  105 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---~~~~~~~~~~~-----~  105 (292)
                      .+|++...+.|.+++..             .+...++|+||+|+|||++++.+...+...   .+++.......     .
T Consensus         1 F~gR~~el~~l~~~l~~-------------~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~   67 (234)
T PF01637_consen    1 FFGREKELEKLKELLES-------------GPSQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRS   67 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH---------------SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHh-------------hcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHH
Confidence            36889999999887754             346789999999999999999999988332   11111100000     0


Q ss_pred             c------------------------------cChHHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHHHHH
Q 022768          106 Y------------------------------IGESARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQR  154 (292)
Q Consensus       106 ~------------------------------~~~~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~  154 (292)
                      .                              .......+..++...... ...+|+|||++.+..     ..........
T Consensus        68 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~-----~~~~~~~~~~  142 (234)
T PF01637_consen   68 FIEETSLADELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAI-----ASEEDKDFLK  142 (234)
T ss_dssp             HHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGB-----CTTTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhh-----cccchHHHHH
Confidence            0                              001122334444444333 238999999999950     0112345555


Q ss_pred             HHHHHHHHhhCCCCCCCeEEEEEeCCCCC------CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccC--CCCCC
Q 022768          155 TLMELLNQLDGFDQLGKVKMIMATNRPDV------LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAK--HGEID  226 (292)
Q Consensus       155 ~l~~~l~~~~~~~~~~~~~vi~t~~~~~~------l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~--~~~~~  226 (292)
                      .+..+++..   ....++.+|+++.....      -...+..  |+.. +.+++.+.++..+++...+.....  ..+.+
T Consensus       143 ~l~~~~~~~---~~~~~~~~v~~~S~~~~~~~~~~~~~~~~~--~~~~-~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~  216 (234)
T PF01637_consen  143 SLRSLLDSL---LSQQNVSIVITGSSDSLMEEFLDDKSPLFG--RFSH-IELKPLSKEEAREFLKELFKELIKLPFSDED  216 (234)
T ss_dssp             HHHHHHHH-------TTEEEEEEESSHHHHHHTT-TTSTTTT-----E-EEE----HHHHHHHHHHHHHCC------HHH
T ss_pred             HHHHHHhhc---cccCCceEEEECCchHHHHHhhcccCcccc--ccce-EEEeeCCHHHHHHHHHHHHHHhhcccCCHHH
Confidence            566655542   23346666666554211      1122333  6645 999999999999999987765411  13445


Q ss_pred             HHHHHHHcCCCCHHHHHH
Q 022768          227 YEAVVKLAEGFNGADLRN  244 (292)
Q Consensus       227 ~~~l~~~~~g~~~~di~~  244 (292)
                      ++.+...+.| .|+.|..
T Consensus       217 ~~~i~~~~gG-~P~~l~~  233 (234)
T PF01637_consen  217 IEEIYSLTGG-NPRYLQE  233 (234)
T ss_dssp             HHHHHHHHTT--HHHHHH
T ss_pred             HHHHHHHhCC-CHHHHhc
Confidence            6777788888 6666654

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=99.18  E-value=5.2e-10  Score=97.76  Aligned_cols=132  Identities=19%  Similarity=0.346  Sum_probs=92.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCc-------------------------EEEEeccch---hccc-cChHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDAN-------------------------FLKVVSSAI---IDKY-IGESARLI  114 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------------------------~~~~~~~~~---~~~~-~~~~~~~~  114 (292)
                      .-++.+||+||+|+|||++++.+|+.+.+.                         ++.+....-   .++. ..-..+.+
T Consensus        19 r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~i   98 (325)
T PRK08699         19 RRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDAV   98 (325)
T ss_pred             CcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHHH
Confidence            346679999999999999999999987431                         222322110   0000 00123445


Q ss_pred             HHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcC
Q 022768          115 REMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLR  190 (292)
Q Consensus       115 ~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~  190 (292)
                      +.+...+..    ....|++||+++.+           +...+..+...+++..     .++.+|.+++.++.+.+.+++
T Consensus        99 R~l~~~~~~~p~~~~~kV~iiEp~~~L-----------d~~a~naLLk~LEep~-----~~~~~Ilvth~~~~ll~ti~S  162 (325)
T PRK08699         99 REIIDNVYLTSVRGGLRVILIHPAESM-----------NLQAANSLLKVLEEPP-----PQVVFLLVSHAADKVLPTIKS  162 (325)
T ss_pred             HHHHHHHhhCcccCCceEEEEechhhC-----------CHHHHHHHHHHHHhCc-----CCCEEEEEeCChHhChHHHHH
Confidence            555555443    34579999999999           8888888888887632     356788899999999999998


Q ss_pred             CCCcceEEEccCCCHHHHHHHHHH
Q 022768          191 PGRLDRKIEIPLPNEQSRMEILKI  214 (292)
Q Consensus       191 ~~r~~~~i~l~~p~~~~r~~i~~~  214 (292)
                        |+ ..+.|++|+.++..+.+..
T Consensus       163 --Rc-~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        163 --RC-RKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             --Hh-hhhcCCCCCHHHHHHHHHh
Confidence              77 7789999998887776654

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=99.16  E-value=1.7e-09  Score=101.21  Aligned_cols=198  Identities=15%  Similarity=0.147  Sum_probs=132.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEeccchhccccChH--HHHHHHH---H--HHhhhCCCEEEEEcccccc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSSAIIDKYIGES--ARLIREM---F--GYARDHQPCIIFMDEIDAI  137 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~~~~~~~~~~~--~~~~~~~---~--~~~~~~~~~il~lDe~d~l  137 (292)
                      .+|+|.|++|+|||++++.++..+..  ||..+....-....+|..  +..+..-   +  ......+.+||||||++.+
T Consensus        26 gGv~i~g~~G~~ks~~~r~l~~llp~~~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~~pGlla~Ah~GvL~lDe~n~~  105 (584)
T PRK13406         26 GGVVLRARAGPVRDRWLAALRALLPAGTPLRRLPPGIADDRLLGGLDLAATLRAGRPVAQRGLLAEADGGVLVLAMAERL  105 (584)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhcCCCCCcccCCCCCcHHHccCCchHHhHhhcCCcCCCCCceeeccCCEEEecCcccC
Confidence            57999999999999999999999865  776665544444444432  1111110   0  0111234589999999998


Q ss_pred             cCCcCCCCCcchHHHHHHHHHHHHHhh--------CCCCCCCeEEEEEeCCC---CCCChhhcCCCCcceEEEccCCCHH
Q 022768          138 GGRRFSEGTSADREIQRTLMELLNQLD--------GFDQLGKVKMIMATNRP---DVLDPALLRPGRLDRKIEIPLPNEQ  206 (292)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~l~~~l~~~~--------~~~~~~~~~vi~t~~~~---~~l~~~l~~~~r~~~~i~l~~p~~~  206 (292)
                                 +...+..|.+.+....        ...-..++++|++.|..   ..+++.+++  ||...+.+.+++..
T Consensus       106 -----------~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLD--Rf~l~v~v~~~~~~  172 (584)
T PRK13406        106 -----------EPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALAD--RLAFHLDLDGLALR  172 (584)
T ss_pred             -----------CHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHh--heEEEEEcCCCChH
Confidence                       8888999988887531        11222368888874332   348889999  99999999988754


Q ss_pred             HHH-------HHHH--HHHcCccCCCCCCHHHHHHH--cCCC-CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          207 SRM-------EILK--IHAAGIAKHGEIDYEAVVKL--AEGF-NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       207 ~r~-------~i~~--~~~~~~~~~~~~~~~~l~~~--~~g~-~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      +..       .|..  ..+.+..++ +..+..++..  .-|. +.+--..+++.|...|..+++..|+.+||.+|+..+-
T Consensus       173 ~~~~~~~~~~~I~~AR~rl~~v~v~-~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~lvL  251 (584)
T PRK13406        173 DAREIPIDADDIAAARARLPAVGPP-PEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAARLVL  251 (584)
T ss_pred             HhcccCCCHHHHHHHHHHHccCCCC-HHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence            322       2322  222221111 1112222221  2354 7788889999999999999999999999999999988


Q ss_pred             hhhh
Q 022768          275 EAKK  278 (292)
Q Consensus       275 ~~~~  278 (292)
                      .+..
T Consensus       252 ~hR~  255 (584)
T PRK13406        252 APRA  255 (584)
T ss_pred             Hhhc
Confidence            7655

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.15  E-value=1e-09  Score=101.21  Aligned_cols=206  Identities=25%  Similarity=0.306  Sum_probs=122.4

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcccc
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYI  107 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~  107 (292)
                      +..++|.......+.+.+...           ......++++|++|+||+++++++....   +.+++.++|..+.... 
T Consensus       142 ~~~ii~~S~~~~~~~~~~~~~-----------a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~~~-  209 (457)
T PRK11361        142 WGHILTNSPAMMDICKDTAKI-----------ALSQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESL-  209 (457)
T ss_pred             ccceecccHHHhHHHHHHHHH-----------cCCCcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCHHH-
Confidence            445677766666665555443           2345679999999999999999998764   4689999998763211 


Q ss_pred             ChHHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC--C---
Q 022768          108 GESARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF--D---  167 (292)
Q Consensus       108 ~~~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~--~---  167 (292)
                           .-..+|..               ......++|||||++.+           +...+..|..++......  .   
T Consensus       210 -----~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l-----------~~~~q~~L~~~l~~~~~~~~~~~~  273 (457)
T PRK11361        210 -----LESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEM-----------PLVLQAKLLRILQEREFERIGGHQ  273 (457)
T ss_pred             -----HHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhC-----------CHHHHHHHHHHHhcCcEEeCCCCc
Confidence                 11122221               11234579999999999           788888888888653210  0   


Q ss_pred             -CCCCeEEEEEeCCCC-------CCChhhcCCCCcceEEEccCCCHHHHHH----HHHHHHcCcc----CC-CCCCHHHH
Q 022768          168 -QLGKVKMIMATNRPD-------VLDPALLRPGRLDRKIEIPLPNEQSRME----ILKIHAAGIA----KH-GEIDYEAV  230 (292)
Q Consensus       168 -~~~~~~vi~t~~~~~-------~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~~~~~~~~~----~~-~~~~~~~l  230 (292)
                       ...++.+|++++..-       .+.+.+..  |+ ..+.+..|+..+|.+    ++..++....    .. ..++.+.+
T Consensus       274 ~~~~~~rii~~t~~~l~~~~~~g~~~~~l~~--~l-~~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~  350 (457)
T PRK11361        274 TIKVDIRIIAATNRDLQAMVKEGTFREDLFY--RL-NVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAM  350 (457)
T ss_pred             eeeeceEEEEeCCCCHHHHHHcCCchHHHHH--Hh-ccceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHH
Confidence             012478888887531       23333333  33 235566666665543    4444444321    11 23556666


Q ss_pred             HHHcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          231 VKLAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       231 ~~~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      ..+...-   +.+++.++++.|..   ......|+.+++...+
T Consensus       351 ~~L~~~~wpgNv~eL~~~~~~~~~---~~~~~~i~~~~l~~~~  390 (457)
T PRK11361        351 SLLTAWSWPGNIRELSNVIERAVV---MNSGPIIFSEDLPPQI  390 (457)
T ss_pred             HHHHcCCCCCcHHHHHHHHHHHHH---hCCCCcccHHHChHhh
Confidence            5555422   45566666666553   3344567777776443

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=99.15  E-value=9.4e-10  Score=100.95  Aligned_cols=227  Identities=21%  Similarity=0.190  Sum_probs=136.4

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcC-CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh-cc-----c
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVG-IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII-DK-----Y  106 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~-~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~-~~-----~  106 (292)
                      |+|.+++|+-|.-.+-.  ...+.+..-| ....-+||++|.||+|||.+++++.+.+....+.-.-..-. +.     .
T Consensus       431 Iye~edvKkglLLqLfG--Gt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVtr  508 (804)
T KOG0478|consen  431 IYELEDVKKGLLLQLFG--GTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVTK  508 (804)
T ss_pred             hhcccchhhhHHHHHhc--CCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEEe
Confidence            68888888887766532  1112222221 33456899999999999999999999886655442211100 00     0


Q ss_pred             cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC-C-------CCCCCeEEEEEe
Q 022768          107 IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG-F-------DQLGKVKMIMAT  178 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~-~-------~~~~~~~vi~t~  178 (292)
                      .+++.+.+-+ -...-....++-+|||||.|           .......|.+.+++-+. +       .-+.++.|||++
T Consensus       509 d~dtkqlVLe-sGALVLSD~GiCCIDEFDKM-----------~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaA  576 (804)
T KOG0478|consen  509 DPDTRQLVLE-SGALVLSDNGICCIDEFDKM-----------SDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAA  576 (804)
T ss_pred             cCccceeeee-cCcEEEcCCceEEchhhhhh-----------hHHHHHHHHHHHHHhhhhHhhcceeeeccccceeeeee
Confidence            0011111100 00111244579999999999           66777788888776321 1       122367899999


Q ss_pred             CCCC-------------CCChhhcCCCCcceEE-EccCCCHHHHHHHHH----HHHcCcc--------------------
Q 022768          179 NRPD-------------VLDPALLRPGRLDRKI-EIPLPNEQSRMEILK----IHAAGIA--------------------  220 (292)
Q Consensus       179 ~~~~-------------~l~~~l~~~~r~~~~i-~l~~p~~~~r~~i~~----~~~~~~~--------------------  220 (292)
                      |+..             .+++.|++  ||+.++ -+..||...-+.|..    .|+....                    
T Consensus       577 NP~~skynp~k~i~eNI~LpptLLS--RFDLIylllD~~DE~~Dr~La~HivsLy~e~~~~~~~~~~d~~~lr~yi~yAr  654 (804)
T KOG0478|consen  577 NPIRSKYNPNKSIIENINLPPTLLS--RFDLIFLLLDKPDERSDRRLADHIVALYPETGEKQGSEAIDMNLLRDYIRYAR  654 (804)
T ss_pred             ccccccCCCCCchhhccCCChhhhh--hhcEEEEEecCcchhHHHHHHHHHHHhcccccccchhHHHhHHHHHHHHHHHh
Confidence            9532             37789999  998766 558887763333333    2222110                    


Q ss_pred             --CCCCCCHHHHH----------HHc--CC---CCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          221 --KHGEIDYEAVV----------KLA--EG---FNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       221 --~~~~~~~~~l~----------~~~--~g---~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                        +...+..+..-          ...  .|   .+++.+..+++.+.+.|..+....+...|+++|..-....
T Consensus       655 k~i~p~l~~ea~~~l~~ayvd~rk~~~~~~~itat~rQlesLiRlsEahak~r~s~~ve~~dV~eA~~l~R~a  727 (804)
T KOG0478|consen  655 KNIHPALSPEASQALIQAYVDMRKIGEGAGQITATPRQLESLIRLSEAHAKMRLSNRVEEIDVEEAVRLLREA  727 (804)
T ss_pred             ccCCccccHHHHHHHHHHhhhhhhhcccccccchhHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHH
Confidence              11111111100          000  12   2678999999999999999999999999999999877754

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.13  E-value=7.6e-10  Score=98.99  Aligned_cols=143  Identities=29%  Similarity=0.364  Sum_probs=96.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh-ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII-DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSE  144 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~  144 (292)
                      -..+|+.||||+|||+||..+|...+.||+.+-..+-. +......-..++.+|..++...-++|++|+++.|..-.   
T Consensus       538 lvSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD~v---  614 (744)
T KOG0741|consen  538 LVSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYV---  614 (744)
T ss_pred             ceEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhccc---
Confidence            44599999999999999999999999999987655443 33333344568899999999888999999999986322   


Q ss_pred             CCcchHHHHHHHHHHHHHhhCCCCCC-CeEEEEEeCCCCCCCh-hhcCCCCcceEEEccCCCH-HHHHHHHHH
Q 022768          145 GTSADREIQRTLMELLNQLDGFDQLG-KVKMIMATNRPDVLDP-ALLRPGRLDRKIEIPLPNE-QSRMEILKI  214 (292)
Q Consensus       145 ~~~~~~~~~~~l~~~l~~~~~~~~~~-~~~vi~t~~~~~~l~~-~l~~~~r~~~~i~l~~p~~-~~r~~i~~~  214 (292)
                       .-+.+..+..+..++-.+....+.+ +.+|++||+..+-+.. .+..  .|+.++.+|..+. ++...+++.
T Consensus       615 -pIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~--~F~~~i~Vpnl~~~~~~~~vl~~  684 (744)
T KOG0741|consen  615 -PIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILD--CFSSTIHVPNLTTGEQLLEVLEE  684 (744)
T ss_pred             -ccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHH--hhhheeecCccCchHHHHHHHHH
Confidence             1122333344444444444434444 4556666665443322 3444  7888888888765 666666654

>PRK15115 response regulator GlrR; Provisional

Probab=99.11  E-value=1.7e-09  Score=99.37  Aligned_cols=204  Identities=23%  Similarity=0.276  Sum_probs=119.3

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccCh
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGE  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~  109 (292)
                      .++|.....+++.+.+...           ......++|+|++|+||+++|+.+.+..   +.+++.++|..+....   
T Consensus       135 ~lig~s~~~~~~~~~~~~~-----------a~~~~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~~~---  200 (444)
T PRK15115        135 AIVTRSPLMLRLLEQARMV-----------AQSDVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQL---  200 (444)
T ss_pred             cccccCHHHHHHHHHHHhh-----------ccCCCeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCHHH---
Confidence            4566665555555444332           2335679999999999999999998875   4689999998763221   


Q ss_pred             HHHHHHHHHHHh---------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------C
Q 022768          110 SARLIREMFGYA---------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------Q  168 (292)
Q Consensus       110 ~~~~~~~~~~~~---------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~  168 (292)
                         .-..+|...               .....++|||||+|.|           +...+..|..+++......      .
T Consensus       201 ---~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l-----------~~~~q~~L~~~l~~~~~~~~g~~~~~  266 (444)
T PRK15115        201 ---LESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDM-----------PAPLQVKLLRVLQERKVRPLGSNRDI  266 (444)
T ss_pred             ---HHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEccccC-----------CHHHHHHHHHHHhhCCEEeCCCCcee
Confidence               111223211               1234579999999999           8888899988887532100      0


Q ss_pred             CCCeEEEEEeCCCC-------CCChhhcCCCCcceEEEccCCCHHHHHH----HHHHHHcCc----cCC-CCCCHHHHHH
Q 022768          169 LGKVKMIMATNRPD-------VLDPALLRPGRLDRKIEIPLPNEQSRME----ILKIHAAGI----AKH-GEIDYEAVVK  232 (292)
Q Consensus       169 ~~~~~vi~t~~~~~-------~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~~~~~~~~----~~~-~~~~~~~l~~  232 (292)
                      ..++.+|+|++..-       .+.+.+..  |+ ..+.+..|...+|.+    ++..++...    ... ..++.+.+..
T Consensus       267 ~~~~rii~~~~~~l~~~~~~~~f~~~l~~--~l-~~~~i~lPpLr~R~eDi~~l~~~~l~~~~~~~~~~~~~~~~~a~~~  343 (444)
T PRK15115        267 DIDVRIISATHRDLPKAMARGEFREDLYY--RL-NVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKR  343 (444)
T ss_pred             eeeEEEEEeCCCCHHHHHHcCCccHHHHH--hh-ceeeecCCChHhccccHHHHHHHHHHHHHHHhCCCCCCcCHHHHHH
Confidence            11577888887430       12222222  23 245666676777653    445554432    111 2355666665


Q ss_pred             HcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          233 LAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       233 ~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      +...-   |.++++++++.|.   .......|+.+++...+
T Consensus       344 L~~~~WpgNvreL~~~i~~~~---~~~~~~~i~~~~l~~~~  381 (444)
T PRK15115        344 LMTASWPGNVRQLVNVIEQCV---ALTSSPVISDALVEQAL  381 (444)
T ss_pred             HHhCCCCChHHHHHHHHHHHH---HhCCCCccChhhhhhhh
Confidence            55422   4455555555554   33444567777775444

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=99.11  E-value=6e-10  Score=104.42  Aligned_cols=227  Identities=19%  Similarity=0.172  Sum_probs=138.6

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHh-cCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChH
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLR-VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGES  110 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~-~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~  110 (292)
                      ..+.|.+++++.|.-.+-.-...  ...+ -.++..-|+||.|.||+|||.+++.+++.+...++...-+.-.   .|-+
T Consensus       286 PsIyG~e~VKkAilLqLfgGv~k--~~~~g~~iRGDInILLvGDPgtaKSqlLk~v~~~aPr~vytsgkgss~---~GLT  360 (682)
T COG1241         286 PSIYGHEDVKKAILLQLFGGVKK--NLPDGTRIRGDIHILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSSA---AGLT  360 (682)
T ss_pred             ccccCcHHHHHHHHHHhcCCCcc--cCCCCcccccceeEEEcCCCchhHHHHHHHHHhhCCceEEEccccccc---cCce
Confidence            34789999988887766432111  0000 0122245799999999999999999999887665543211110   1111


Q ss_pred             HHHHH-----HHHHHh---hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-CCCC-------CCCeEE
Q 022768          111 ARLIR-----EMFGYA---RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-GFDQ-------LGKVKM  174 (292)
Q Consensus       111 ~~~~~-----~~~~~~---~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~~~-------~~~~~v  174 (292)
                      ....+     ++.-.+   -...++|.+|||+|.+           +.....++.+.+.+-. .+.+       +.++.+
T Consensus       361 Aav~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm-----------~~~dr~aihEaMEQQtIsIaKAGI~atLnARcsv  429 (682)
T COG1241         361 AAVVRDKVTGEWVLEAGALVLADGGVCCIDEFDKM-----------NEEDRVAIHEAMEQQTISIAKAGITATLNARCSV  429 (682)
T ss_pred             eEEEEccCCCeEEEeCCEEEEecCCEEEEEeccCC-----------ChHHHHHHHHHHHhcEeeecccceeeecchhhhh
Confidence            11111     110011   1245689999999998           7777788888887642 2222       226778


Q ss_pred             EEEeCCCC-------------CCChhhcCCCCcceEEEc-cCCCHHHHHHHHHHHHcCc---------------------
Q 022768          175 IMATNRPD-------------VLDPALLRPGRLDRKIEI-PLPNEQSRMEILKIHAAGI---------------------  219 (292)
Q Consensus       175 i~t~~~~~-------------~l~~~l~~~~r~~~~i~l-~~p~~~~r~~i~~~~~~~~---------------------  219 (292)
                      +|++|+..             .+++.+++  ||+..+-+ ..|+.+.-..+..+.+...                     
T Consensus       430 LAAaNP~~Gryd~~~~~~enI~l~~~lLS--RFDLifvl~D~~d~~~D~~ia~hil~~h~~~~~~~~~~~~~~~~~~~~~  507 (682)
T COG1241         430 LAAANPKFGRYDPKKTVAENINLPAPLLS--RFDLIFVLKDDPDEEKDEEIAEHILDKHRGEEPEETISLDGVDEVEERD  507 (682)
T ss_pred             hhhhCCCCCcCCCCCCHHHhcCCChhHHh--hCCeeEEecCCCCccchHHHHHHHHHHHhccccccccccccccccccCc
Confidence            88998754             37788999  99886644 5566543333322222110                     


Q ss_pred             -------------cCCCCCC---HHHHHH-----Hc----------CCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHH
Q 022768          220 -------------AKHGEID---YEAVVK-----LA----------EGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMK  268 (292)
Q Consensus       220 -------------~~~~~~~---~~~l~~-----~~----------~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~  268 (292)
                                   ...+.+.   .+.|..     +.          -..+.+++..+++-|.+.|..+.+..|+.+|+.+
T Consensus       508 ~~~lrkYI~YAR~~v~P~lt~ea~e~l~~~Yv~~Rk~~~~~~~~~~~piT~RqLEsiiRLaeA~Ak~rLS~~V~~eD~~e  587 (682)
T COG1241         508 FELLRKYISYARKNVTPVLTEEAREELEDYYVEMRKKSALVEEKRTIPITARQLESIIRLAEAHAKMRLSDVVEEEDVDE  587 (682)
T ss_pred             HHHHHHHHHHHhccCCcccCHHHHHHHHHHHHHhhhccccccccCcccccHHHHHHHHHHHHHHHhhhccCCCCHHHHHH
Confidence                         0101111   111111     11          1146899999999999999999999999999999


Q ss_pred             HHHHHhhh
Q 022768          269 AVRKLNEA  276 (292)
Q Consensus       269 a~~~~~~~  276 (292)
                      |++-+...
T Consensus       588 Ai~lv~~~  595 (682)
T COG1241         588 AIRLVDFS  595 (682)
T ss_pred             HHHHHHHH
Confidence            99998853

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.10  E-value=8.5e-10  Score=92.33  Aligned_cols=132  Identities=18%  Similarity=0.198  Sum_probs=80.2

Q ss_pred             cCCCCCcccccccc----HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEE
Q 022768           24 EDPGNVSYSAVGGL----SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLK   96 (292)
Q Consensus        24 ~~~~~~~~~~l~g~----~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~   96 (292)
                      +.....+|++..-.    ..++..+..++..+           .....+++|+|++|+|||+++.++++.+   +..++.
T Consensus        64 ~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~-----------~~~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~  132 (244)
T PRK07952         64 PLHQNCSFENYRVECEGQMNALSKARQYVEEF-----------DGNIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLI  132 (244)
T ss_pred             ccccCCccccccCCCchHHHHHHHHHHHHHhh-----------ccCCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEE
Confidence            34456788887532    23444444444332           0113479999999999999999999988   667888


Q ss_pred             EeccchhccccChH---HHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           97 VVSSAIIDKYIGES---ARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        97 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      +...++........   ......++....  ...+|+|||++...         ........+..+++.-..    ....
T Consensus       133 it~~~l~~~l~~~~~~~~~~~~~~l~~l~--~~dlLvIDDig~~~---------~s~~~~~~l~~Ii~~Ry~----~~~~  197 (244)
T PRK07952        133 ITVADIMSAMKDTFSNSETSEEQLLNDLS--NVDLLVIDEIGVQT---------ESRYEKVIINQIVDRRSS----SKRP  197 (244)
T ss_pred             EEHHHHHHHHHHHHhhccccHHHHHHHhc--cCCEEEEeCCCCCC---------CCHHHHHHHHHHHHHHHh----CCCC
Confidence            87766654322111   011122333322  45799999997752         134445667777775321    2345


Q ss_pred             EEEEeCCC
Q 022768          174 MIMATNRP  181 (292)
Q Consensus       174 vi~t~~~~  181 (292)
                      +|+|+|..
T Consensus       198 tiitSNl~  205 (244)
T PRK07952        198 TGMLTNSN  205 (244)
T ss_pred             EEEeCCCC
Confidence            78888864

>PRK08181 transposase; Validated

Probab=99.09  E-value=7.7e-10  Score=93.93  Aligned_cols=128  Identities=20%  Similarity=0.330  Sum_probs=79.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChH-HHHHHHHHHHhhhCCCEEEEEcccccccCC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGES-ARLIREMFGYARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~il~lDe~d~l~~~  140 (292)
                      .+.+++|+||+|+|||+++.++++++   +..++++...++........ .......+...  ..+.+|+|||++.... 
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l--~~~dLLIIDDlg~~~~-  181 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKL--DKFDLLILDDLAYVTK-  181 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHH--hcCCEEEEeccccccC-
Confidence            46789999999999999999999755   66788887776655432110 01112223322  2447999999987632 


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC-C---------CChhhcCCCCc---ceEEEccCCCHHH
Q 022768          141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD-V---------LDPALLRPGRL---DRKIEIPLPNEQS  207 (292)
Q Consensus       141 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~-~---------l~~~l~~~~r~---~~~i~l~~p~~~~  207 (292)
                              +...+..+.++++....     +..+|+|+|.+. .         +..++.+  |+   ...+.+...+...
T Consensus       182 --------~~~~~~~Lf~lin~R~~-----~~s~IiTSN~~~~~w~~~~~D~~~a~aild--RL~h~~~~i~~~g~s~R~  246 (269)
T PRK08181        182 --------DQAETSVLFELISARYE-----RRSILITANQPFGEWNRVFPDPAMTLAAVD--RLVHHATIFEMNVESYRR  246 (269)
T ss_pred             --------CHHHHHHHHHHHHHHHh-----CCCEEEEcCCCHHHHHHhcCCccchhhHHH--hhhcCceEEecCCccchh
Confidence                    45566788888876542     124788888652 1         2233344  33   3456666666554


Q ss_pred             HHH
Q 022768          208 RME  210 (292)
Q Consensus       208 r~~  210 (292)
                      +..
T Consensus       247 ~~~  249 (269)
T PRK08181        247 RTA  249 (269)
T ss_pred             HHH
Confidence            443

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.09  E-value=4.4e-09  Score=94.61  Aligned_cols=213  Identities=14%  Similarity=0.160  Sum_probs=119.9

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc---
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS---  100 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~---  100 (292)
                      +++.|.+.++|.=....+.+++.++.....    + . ....++.+||+||+|+||||+++.+++++|..+.+-...   
T Consensus        74 eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~----~-~-~~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew~Npi~~  147 (634)
T KOG1970|consen   74 EKYKPRTLEELAVHKKKISEVKQWLKQVAE----F-T-PKLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIEWSNPINL  147 (634)
T ss_pred             HhcCcccHHHHhhhHHhHHHHHHHHHHHHH----h-c-cCCCceEEEEeCCCCCCchhHHHHHHHhhCceeeeecCCccc
Confidence            366777888888888888888888772100    0 0 122356788999999999999999999999887664411   


Q ss_pred             ----chhccccChH---HHHH---HHHHHHh------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHH
Q 022768          101 ----AIIDKYIGES---ARLI---REMFGYA------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLME  158 (292)
Q Consensus       101 ----~~~~~~~~~~---~~~~---~~~~~~~------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~  158 (292)
                          .+-+...+..   ...+   ......+            ....+.+|++||+=..+..          ...+.+.+
T Consensus       148 ~~~~~~h~~t~~~~~~~~s~L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~----------d~~~~f~e  217 (634)
T KOG1970|consen  148 KEPENLHNETSFLMFPYQSQLAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYR----------DDSETFRE  217 (634)
T ss_pred             cccccccccchhcccchhhHHHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhh----------hhHHHHHH
Confidence                1111000000   1111   1111111            1134569999998655321          12233333


Q ss_pred             HHHHhhCCCCCCCeEEEEEeC-CCCCCCh------hhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCC----CCCH
Q 022768          159 LLNQLDGFDQLGKVKMIMATN-RPDVLDP------ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG----EIDY  227 (292)
Q Consensus       159 ~l~~~~~~~~~~~~~vi~t~~-~~~~l~~------~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~----~~~~  227 (292)
                      .|..+...... .+++|+|-. .....++      .+.-..|. ..|.|.+-...-.++.++.++.......    ..+.
T Consensus       218 vL~~y~s~g~~-PlIf~iTd~~~~g~nnq~rlf~~d~q~~~ri-~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k~~~~  295 (634)
T KOG1970|consen  218 VLRLYVSIGRC-PLIFIITDSLSNGNNNQDRLFPKDIQEEPRI-SNISFNPIAPTIMKKFLKRICRIEANKKSGIKVPDT  295 (634)
T ss_pred             HHHHHHhcCCC-cEEEEEeccccCCCcchhhhchhhhhhccCc-ceEeecCCcHHHHHHHHHHHHHHhcccccCCcCchh
Confidence            33333222222 345555532 2222222      22222244 6789988888888888887776432221    1234


Q ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHHHHH
Q 022768          228 EAVVKLAEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       228 ~~l~~~~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      ..+..+..+ ++||||.++......+.+
T Consensus       296 ~~v~~i~~~-s~GDIRsAInsLQlsssk  322 (634)
T KOG1970|consen  296 AEVELICQG-SGGDIRSAINSLQLSSSK  322 (634)
T ss_pred             HHHHHHHHh-cCccHHHHHhHhhhhccc
Confidence            445555555 555999999999988733

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.08  E-value=2.4e-09  Score=98.91  Aligned_cols=207  Identities=24%  Similarity=0.310  Sum_probs=126.3

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcccc
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYI  107 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~  107 (292)
                      ...++|.....+++.+.+...           ......+++.|.+||||+++++++....   +.+++.++|..+.....
T Consensus       133 ~~~lig~s~~~~~v~~~i~~~-----------a~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~~~~  201 (463)
T TIGR01818       133 SAELIGEAPAMQEVFRAIGRL-----------SRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLI  201 (463)
T ss_pred             ccceeecCHHHHHHHHHHHHH-----------hCcCCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCHHHH
Confidence            345788877777777666542           2345679999999999999999998765   46899999887632211


Q ss_pred             ChHHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-----
Q 022768          108 GESARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-----  167 (292)
Q Consensus       108 ~~~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-----  167 (292)
                            -..+|+.               .....++.|||||++.+           +...+..|..++.......     
T Consensus       202 ------~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l-----------~~~~q~~ll~~l~~~~~~~~~~~~  264 (463)
T TIGR01818       202 ------ESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDM-----------PLDAQTRLLRVLADGEFYRVGGRT  264 (463)
T ss_pred             ------HHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhC-----------CHHHHHHHHHHHhcCcEEECCCCc
Confidence                  1122221               11234689999999999           7888888888886532100     


Q ss_pred             -CCCCeEEEEEeCCCC-------CCChhhcCCCCcc-eEEEccCCC--HHHHHHHHHHHHcCcc----CC-CCCCHHHHH
Q 022768          168 -QLGKVKMIMATNRPD-------VLDPALLRPGRLD-RKIEIPLPN--EQSRMEILKIHAAGIA----KH-GEIDYEAVV  231 (292)
Q Consensus       168 -~~~~~~vi~t~~~~~-------~l~~~l~~~~r~~-~~i~l~~p~--~~~r~~i~~~~~~~~~----~~-~~~~~~~l~  231 (292)
                       ...++.+|++++..-       ...+.+..  |+. ..|.+|+..  .++...++..++....    .. ..++.+.+.
T Consensus       265 ~~~~~~rii~~~~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~  342 (463)
T TIGR01818       265 PIKVDVRIVAATHQNLEALVRQGKFREDLFH--RLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALE  342 (463)
T ss_pred             eeeeeeEEEEeCCCCHHHHHHcCCcHHHHHH--HhCcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHH
Confidence             112567888876531       23344444  442 355666654  3455556665554321    11 235566666


Q ss_pred             HHcCCC---CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          232 KLAEGF---NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       232 ~~~~g~---~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      .+...-   |.++++++++.+..   ......|+.+++...+
T Consensus       343 ~L~~~~wpgNvreL~~~~~~~~~---~~~~~~i~~~~l~~~~  381 (463)
T TIGR01818       343 RLKQLRWPGNVRQLENLCRWLTV---MASGDEVLVSDLPAEL  381 (463)
T ss_pred             HHHhCCCCChHHHHHHHHHHHHH---hCCCCcccHHhchHHH
Confidence            655432   44566666666554   3344568888876555

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PF13173 AAA_14: AAA domain

Probab=99.07  E-value=1.2e-09  Score=82.86  Aligned_cols=119  Identities=24%  Similarity=0.324  Sum_probs=75.2

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcC--CcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNID--ANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSE  144 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~  144 (292)
                      ..++|.||+|+||||+++.+++.+.  ..++++++.+..........  +...+.......+.+|+|||++.+       
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~i~iDEiq~~-------   73 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLADPD--LLEYFLELIKPGKKYIFIDEIQYL-------   73 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHhhhh--hHHHHHHhhccCCcEEEEehhhhh-------
Confidence            4689999999999999999999876  77888887765432111111  222222222225679999999987       


Q ss_pred             CCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC----ChhhcCCCCcceEEEccCCCHHHH
Q 022768          145 GTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL----DPALLRPGRLDRKIEIPLPNEQSR  208 (292)
Q Consensus       145 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l----~~~l~~~~r~~~~i~l~~p~~~~r  208 (292)
                           +.+...+..+.+..      .++.+|+|++....+    ...+..  |+ ..+++.+++..|.
T Consensus        74 -----~~~~~~lk~l~d~~------~~~~ii~tgS~~~~l~~~~~~~l~g--r~-~~~~l~Plsf~E~  127 (128)
T PF13173_consen   74 -----PDWEDALKFLVDNG------PNIKIILTGSSSSLLSKDIAESLAG--RV-IEIELYPLSFREF  127 (128)
T ss_pred             -----ccHHHHHHHHHHhc------cCceEEEEccchHHHhhcccccCCC--eE-EEEEECCCCHHHh
Confidence                 23455555555431      355677777654433    333443  55 5778888887663

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=99.07  E-value=5.4e-10  Score=85.88  Aligned_cols=106  Identities=31%  Similarity=0.522  Sum_probs=74.3

Q ss_pred             cccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC---cEEEEeccchhccccChHH
Q 022768           35 GGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA---NFLKVVSSAIIDKYIGESA  111 (292)
Q Consensus        35 ~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~---~~~~~~~~~~~~~~~~~~~  111 (292)
                      +|.....+++.+.+...           .....+|+|+|++||||+++|+++......   +++.+++....        
T Consensus         1 vG~S~~~~~l~~~l~~~-----------a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~--------   61 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERL-----------AKSSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP--------   61 (138)
T ss_dssp             --SCHHHHHHHHHHHHH-----------HCSSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC--------
T ss_pred             CCCCHHHHHHHHHHHHH-----------hCCCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc--------
Confidence            46677777887777764           245678999999999999999999987754   44444444422        


Q ss_pred             HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          112 RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       112 ~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                         ..++..+   .++.|+|+|+|.+           +...+..|..++....    ..++.+|++++.
T Consensus        62 ---~~~l~~a---~~gtL~l~~i~~L-----------~~~~Q~~L~~~l~~~~----~~~~RlI~ss~~  109 (138)
T PF14532_consen   62 ---AELLEQA---KGGTLYLKNIDRL-----------SPEAQRRLLDLLKRQE----RSNVRLIASSSQ  109 (138)
T ss_dssp             ---HHHHHHC---TTSEEEEECGCCS------------HHHHHHHHHHHHHCT----TTTSEEEEEECC
T ss_pred             ---HHHHHHc---CCCEEEECChHHC-----------CHHHHHHHHHHHHhcC----CCCeEEEEEeCC
Confidence               2333333   5589999999999           8899999999888732    346678887764

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=99.06  E-value=2.6e-11  Score=106.52  Aligned_cols=227  Identities=19%  Similarity=0.194  Sum_probs=124.4

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc----hhccccC
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA----IIDKYIG  108 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~----~~~~~~~  108 (292)
                      .|.|.+.+|..+.-.+......... ..-..+..-++||+|.||+|||.+++.+++.....++......    +......
T Consensus        25 ~i~g~~~iK~aill~L~~~~~~~~~-~~~~~r~~ihiLlvGdpg~gKS~ll~~~~~~~pr~v~~~g~~~s~~gLta~~~~  103 (331)
T PF00493_consen   25 SIYGHEDIKKAILLQLFGGVEKNDP-DGTRIRGNIHILLVGDPGTGKSQLLKYVAKLAPRSVYTSGKGSSAAGLTASVSR  103 (331)
T ss_dssp             TTTT-HHHHHHHCCCCTT--SCCCC-T-TEE--S--EEEECSCHHCHHHHHHCCCCT-SSEEEEECCGSTCCCCCEEECC
T ss_pred             cCcCcHHHHHHHHHHHHhccccccc-cccccccccceeeccchhhhHHHHHHHHHhhCCceEEECCCCcccCCccceecc
Confidence            3689998888886665442211000 0001234568999999999999999998876655443322111    1000000


Q ss_pred             ---hHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-CCCC-------CCCeEEEEE
Q 022768          109 ---ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-GFDQ-------LGKVKMIMA  177 (292)
Q Consensus       109 ---~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~~~-------~~~~~vi~t  177 (292)
                         ..+..+.  .+..-....+|++|||+|.+           .......|.+.+++-. .+..       +.++.|+++
T Consensus       104 d~~~~~~~le--aGalvlad~GiccIDe~dk~-----------~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa  170 (331)
T PF00493_consen  104 DPVTGEWVLE--AGALVLADGGICCIDEFDKM-----------KEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAA  170 (331)
T ss_dssp             CGGTSSECEE--E-HHHHCTTSEEEECTTTT-------------CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEE
T ss_pred             ccccceeEEe--CCchhcccCceeeecccccc-----------cchHHHHHHHHHHcCeeccchhhhcccccchhhhHHH
Confidence               0000000  00111234589999999999           6667788888887632 1111       226889999


Q ss_pred             eCCCC-------------CCChhhcCCCCcceEEEc-cCCCHHHHHHHHHHHHcCccCCC------------CCCH----
Q 022768          178 TNRPD-------------VLDPALLRPGRLDRKIEI-PLPNEQSRMEILKIHAAGIAKHG------------EIDY----  227 (292)
Q Consensus       178 ~~~~~-------------~l~~~l~~~~r~~~~i~l-~~p~~~~r~~i~~~~~~~~~~~~------------~~~~----  227 (292)
                      +|+..             .+++.+.+  ||+..+.+ ..++.+.-..+.++.+.......            .++.    
T Consensus       171 ~NP~~g~~~~~~~~~~ni~l~~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~~~~~~~~~~~~~~~~~~~~~~~~lr  248 (331)
T PF00493_consen  171 ANPKFGRYDPNKSLSENINLPPPLLS--RFDLIFLLRDKPDEEEDERLAEHILDSHRNGKKSKEKKIKKNDKPISEDLLR  248 (331)
T ss_dssp             E--TT--S-TTS-CGCCT-S-CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTTT---S--------SSS-TT-HCCCH
T ss_pred             HhhhhhhcchhhhhHHhcccchhhHh--hcCEEEEeccccccccccccceEEEeccccccccccccccccCCccCHHHHH
Confidence            98754             36678888  99988765 66776666666665554221110            1111    


Q ss_pred             -------------------HHHHHHc-------------CCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          228 -------------------EAVVKLA-------------EGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       228 -------------------~~l~~~~-------------~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                                         +.+....             ...+++.+..+++-|.+.|..+.+..|+.+|+..|+.-+..
T Consensus       249 ~yI~yar~~~~P~ls~ea~~~I~~~Yv~lR~~~~~~~~~~~iT~R~LeSLIRLseA~AKl~lr~~V~~~Dv~~Ai~L~~~  328 (331)
T PF00493_consen  249 KYIAYARQNIHPVLSEEAKELIINYYVELRKESKSNNKSIPITIRQLESLIRLSEAHAKLRLRDEVTEEDVEEAIRLFEE  328 (331)
T ss_dssp             HHHHHHHHHC--EE-HHCHHHHHHHHCCCCHCHHCHSS-B-SSCCCCCHHHHHHHHHHHCTTSSECSHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhcccccCHHHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHHHHHhccCceeHHHHHHHHHHHHh
Confidence                               1111111             02356788899999999999999999999999999987764

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=99.00  E-value=1.1e-08  Score=87.13  Aligned_cols=131  Identities=18%  Similarity=0.227  Sum_probs=88.9

Q ss_pred             HHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc----------------EEEEeccch
Q 022768           39 DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN----------------FLKVVSSAI  102 (292)
Q Consensus        39 ~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~----------------~~~~~~~~~  102 (292)
                      ...+.|...+..-            .-++.+||+||.|+||+++|..+|+.+-+.                +..+....-
T Consensus         4 ~~~~~L~~~i~~~------------rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~   71 (290)
T PRK05917          4 AAWEALIQRVRDQ------------KVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGK   71 (290)
T ss_pred             HHHHHHHHHHHcC------------CcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCC
Confidence            3456666666542            446789999999999999999999987542                111111100


Q ss_pred             hccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEe
Q 022768          103 IDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT  178 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~  178 (292)
                       +..  -..+.++.+.....    .....|++||++|.+           ..+.+..|+.++++     +++++++|..|
T Consensus        72 -~~~--I~idqiR~l~~~~~~~p~e~~~kv~ii~~ad~m-----------t~~AaNaLLK~LEE-----Pp~~~~fiL~~  132 (290)
T PRK05917         72 -GRL--HSIETPRAIKKQIWIHPYESPYKIYIIHEADRM-----------TLDAISAFLKVLED-----PPQHGVIILTS  132 (290)
T ss_pred             -CCc--CcHHHHHHHHHHHhhCccCCCceEEEEechhhc-----------CHHHHHHHHHHhhc-----CCCCeEEEEEe
Confidence             000  12233344433332    234579999999999           77777777777764     55688899999


Q ss_pred             CCCCCCChhhcCCCCcceEEEccCC
Q 022768          179 NRPDVLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       179 ~~~~~l~~~l~~~~r~~~~i~l~~p  203 (292)
                      +.++.+.+.++|  |+ ..+.|+++
T Consensus       133 ~~~~~ll~TI~S--Rc-q~~~~~~~  154 (290)
T PRK05917        133 AKPQRLPPTIRS--RS-LSIHIPME  154 (290)
T ss_pred             CChhhCcHHHHh--cc-eEEEccch
Confidence            999999999999  77 66777765

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=98.99  E-value=1.9e-09  Score=92.04  Aligned_cols=143  Identities=20%  Similarity=0.380  Sum_probs=80.7

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhh-----------hCCCEEEEEcc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR-----------DHQPCIIFMDE  133 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~il~lDe  133 (292)
                      .++++||+||+|+|||.+++.+...+...-+.+....+..   ..+...++.......           ..+..|+||||
T Consensus        32 ~~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~---~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDD  108 (272)
T PF12775_consen   32 NGRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSA---QTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDD  108 (272)
T ss_dssp             CTEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-T---THHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEET
T ss_pred             cCCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccC---CCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecc
Confidence            4789999999999999999998887754332221111111   122333333222111           13446999999


Q ss_pred             cccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-------CCCCeEEEEEeCCCC---CCChhhcCCCCcceEEEccCC
Q 022768          134 IDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-------QLGKVKMIMATNRPD---VLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       134 ~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-------~~~~~~vi~t~~~~~---~l~~~l~~~~r~~~~i~l~~p  203 (292)
                      ++.-...+.     +.....+.|.++++....+.       .-.++.+|+++++..   .+++++.+  .| ..+.++.|
T Consensus       109 lN~p~~d~y-----gtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r--~f-~i~~~~~p  180 (272)
T PF12775_consen  109 LNMPQPDKY-----GTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR--HF-NILNIPYP  180 (272)
T ss_dssp             TT-S---TT-----S--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT--TE-EEEE----
T ss_pred             cCCCCCCCC-----CCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh--he-EEEEecCC
Confidence            987532211     12234455556665432111       112688889888643   36778887  66 67899999


Q ss_pred             CHHHHHHHHHHHHcC
Q 022768          204 NEQSRMEILKIHAAG  218 (292)
Q Consensus       204 ~~~~r~~i~~~~~~~  218 (292)
                      +.+....|+..++..
T Consensus       181 ~~~sl~~If~~il~~  195 (272)
T PF12775_consen  181 SDESLNTIFSSILQS  195 (272)
T ss_dssp             TCCHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHhh
Confidence            999888888776653

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=98.99  E-value=9.9e-09  Score=88.00  Aligned_cols=194  Identities=20%  Similarity=0.282  Sum_probs=122.3

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchh
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAII  103 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~  103 (292)
                      +...|+.+++.....+.+.+.....           ..-...+||.|..||||-.+|++.-...   ..||+.+||..+.
T Consensus       199 ~~~~F~~~v~~S~~mk~~v~qA~k~-----------AmlDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFlalNCA~lP  267 (511)
T COG3283         199 DVSGFEQIVAVSPKMKHVVEQAQKL-----------AMLDAPLLITGETGTGKDLLAKACHLASPRHSKPFLALNCASLP  267 (511)
T ss_pred             cccchHHHhhccHHHHHHHHHHHHh-----------hccCCCeEEecCCCchHHHHHHHHhhcCcccCCCeeEeecCCCc
Confidence            5567888888888777776655442           1224469999999999999999877655   5689999999886


Q ss_pred             ccccChHHHHHHHHHHHhh----------hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCC---
Q 022768          104 DKYIGESARLIREMFGYAR----------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG---  170 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~----------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~---  170 (292)
                      .....      .++|..+.          ....+.+++||+..+           +...|..|+.+++.... +..+   
T Consensus       268 e~~aE------sElFG~apg~~gk~GffE~AngGTVlLDeIgEm-----------Sp~lQaKLLRFL~DGtF-RRVGee~  329 (511)
T COG3283         268 EDAAE------SELFGHAPGDEGKKGFFEQANGGTVLLDEIGEM-----------SPRLQAKLLRFLNDGTF-RRVGEDH  329 (511)
T ss_pred             hhHhH------HHHhcCCCCCCCccchhhhccCCeEEeehhhhc-----------CHHHHHHHHHHhcCCce-eecCCcc
Confidence            54322      24454443          133479999999888           88899999999986432 1111   


Q ss_pred             ----CeEEEEEeCCC-------CCCChhhcCCCCcceEEEccCCCHHHHHH----HH----HHHHcCccCC-CCCCHHHH
Q 022768          171 ----KVKMIMATNRP-------DVLDPALLRPGRLDRKIEIPLPNEQSRME----IL----KIHAAGIAKH-GEIDYEAV  230 (292)
Q Consensus       171 ----~~~vi~t~~~~-------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~----i~----~~~~~~~~~~-~~~~~~~l  230 (292)
                          ++.||++|+.+       .+.-.++..  |. -++++..|...+|.+    +.    ..+..+.... ...+.+.+
T Consensus       330 Ev~vdVRVIcatq~nL~~lv~~g~fReDLfy--RL-NVLtl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~  406 (511)
T COG3283         330 EVHVDVRVICATQVNLVELVQKGKFREDLFY--RL-NVLTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLL  406 (511)
T ss_pred             eEEEEEEEEecccccHHHHHhcCchHHHHHH--Hh-heeeecCCccccCcccchHHHHHHHHHHHHHhCCCCCccCHHHH
Confidence                58888888643       122333333  44 356666676666543    23    3333333333 44566666


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEAGMS  252 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a~~~  252 (292)
                      ...+..-.++.++++-+.....
T Consensus       407 ~~L~~y~WpGNVRqL~N~iyRA  428 (511)
T COG3283         407 TVLTRYAWPGNVRQLKNAIYRA  428 (511)
T ss_pred             HHHHHcCCCccHHHHHHHHHHH
Confidence            6666543444555554444333

>PRK06526 transposase; Provisional

Probab=98.99  E-value=1.6e-09  Score=91.52  Aligned_cols=101  Identities=21%  Similarity=0.328  Sum_probs=62.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChH-HHHHHHHHHHhhhCCCEEEEEcccccccCC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGES-ARLIREMFGYARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~il~lDe~d~l~~~  140 (292)
                      .+.+++|+||||+|||+++.+++.++   |..+.......+........ ...+...+..  ...+.+|+|||++.+.. 
T Consensus        97 ~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~--l~~~dlLIIDD~g~~~~-  173 (254)
T PRK06526         97 GKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVK--LGRYPLLIVDEVGYIPF-  173 (254)
T ss_pred             cCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHH--hccCCEEEEcccccCCC-
Confidence            46789999999999999999998875   55555555544433221100 0011111111  23457999999987621 


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       141 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                              +......+..+++....     +..+|+|+|.+
T Consensus       174 --------~~~~~~~L~~li~~r~~-----~~s~IitSn~~  201 (254)
T PRK06526        174 --------EPEAANLFFQLVSSRYE-----RASLIVTSNKP  201 (254)
T ss_pred             --------CHHHHHHHHHHHHHHHh-----cCCEEEEcCCC
Confidence                    35556677787765432     12378888865

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.98  E-value=3.5e-09  Score=92.55  Aligned_cols=123  Identities=20%  Similarity=0.291  Sum_probs=75.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChH---HHHHHHHHHHhhhCCCEEEEEcccccccC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGES---ARLIREMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      ..+++|+|++|+|||||+.++|+++   +..++++....+........   .......+.....  ..+|+|||+.... 
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~--~DLLIIDDlG~e~-  259 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLIN--CDLLIIDDLGTEK-  259 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhcc--CCEEEEeccCCCC-
Confidence            4789999999999999999999987   66788888777654331110   0011111333333  3699999996542 


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC-CC----CChhhcCCCCcc---eEEEccCCCH
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP-DV----LDPALLRPGRLD---RKIEIPLPNE  205 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~-~~----l~~~l~~~~r~~---~~i~l~~p~~  205 (292)
                              ........+..+++....    .+..+|+|||.+ ..    +++++.+  |+.   ..+.|...|.
T Consensus       260 --------~t~~~~~~Lf~iin~R~~----~~k~tIiTSNl~~~el~~~~~eri~S--RL~~~~~~i~~~G~d~  319 (329)
T PRK06835        260 --------ITEFSKSELFNLINKRLL----RQKKMIISTNLSLEELLKTYSERISS--RLLGNFTLLKFYGEDI  319 (329)
T ss_pred             --------CCHHHHHHHHHHHHHHHH----CCCCEEEECCCCHHHHHHHHhHHHHH--HHHcCCEEEEecCcCh
Confidence                    245666778888876432    123477788763 22    3455555  431   3455554443

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=98.97  E-value=1.2e-07  Score=78.13  Aligned_cols=186  Identities=20%  Similarity=0.240  Sum_probs=116.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcE---EEEeccchhcc-----cc----C--------hHHHHHHHHHHHhhh-CCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANF---LKVVSSAIIDK-----YI----G--------ESARLIREMFGYARD-HQP  126 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~---~~~~~~~~~~~-----~~----~--------~~~~~~~~~~~~~~~-~~~  126 (292)
                      .+.++|+.|+|||+++|++...++..-   +.++...+...     .+    .        .....-..+....+. ..|
T Consensus        53 ~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~  132 (269)
T COG3267          53 ILAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRP  132 (269)
T ss_pred             eEEEEecCCCchhHHHHHHHHhcCCCceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCC
Confidence            577899999999999997777664322   22222211110     00    0        011111222222222 446


Q ss_pred             EEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC-C---hhhcCCCCcceEEEccC
Q 022768          127 CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL-D---PALLRPGRLDRKIEIPL  202 (292)
Q Consensus       127 ~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l-~---~~l~~~~r~~~~i~l~~  202 (292)
                      .++++||++.+           .....+.+.-+.+.-......-++++++-......+ -   ..+..  |+...+.+++
T Consensus       133 v~l~vdEah~L-----------~~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~--R~~ir~~l~P  199 (269)
T COG3267         133 VVLMVDEAHDL-----------NDSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQ--RIDIRIELPP  199 (269)
T ss_pred             eEEeehhHhhh-----------ChhHHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhh--eEEEEEecCC
Confidence            89999999998           555666666666655544433344444432211111 0   12222  7777789999


Q ss_pred             CCHHHHHHHHHHHHcCccCCC----CCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Q 022768          203 PNEQSRMEILKIHAAGIAKHG----EIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFM  267 (292)
Q Consensus       203 p~~~~r~~i~~~~~~~~~~~~----~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~  267 (292)
                      .+.++...++++++.+.....    +-....+...+.| .|+-+.+++..|...|+..+...|+...+.
T Consensus       200 ~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg-~P~lin~~~~~Al~~a~~a~~~~v~~a~~~  267 (269)
T COG3267         200 LTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQG-IPRLINNLATLALDAAYSAGEDGVSEAEIK  267 (269)
T ss_pred             cChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhcc-chHHHHHHHHHHHHHHHHcCCCccchhhcc
Confidence            999999999999988654332    2345667778888 788999999999999999999988876654

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.93  E-value=1e-07  Score=79.71  Aligned_cols=156  Identities=14%  Similarity=0.128  Sum_probs=95.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCc-----EEEEecc------chhccc---c---ChHHHHHHHHHHHh---h-
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDAN-----FLKVVSS------AIIDKY---I---GESARLIREMFGYA---R-  122 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----~~~~~~~------~~~~~~---~---~~~~~~~~~~~~~~---~-  122 (292)
                      .+++.+||+|+.|+||..+|..+|+.+-+.     +-.+..+      .+.+..   .   .-..+.++.+....   . 
T Consensus         5 ~~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s~   84 (261)
T PRK05818          5 NKTHPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPSV   84 (261)
T ss_pred             CCCcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCch
Confidence            457789999999999999999999877332     1110000      000000   0   01122233333322   1 


Q ss_pred             h-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEcc
Q 022768          123 D-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIP  201 (292)
Q Consensus       123 ~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~  201 (292)
                      . ....|++|+++|.+           .......|+.+++     .+++++.+|.+|+.++.+.+.++|  |+ ..+.++
T Consensus        85 e~~~~KV~II~~ae~m-----------~~~AaNaLLK~LE-----EPp~~t~fiLit~~~~~lLpTI~S--RC-q~~~~~  145 (261)
T PRK05818         85 ESNGKKIYIIYGIEKL-----------NKQSANSLLKLIE-----EPPKNTYGIFTTRNENNILNTILS--RC-VQYVVL  145 (261)
T ss_pred             hcCCCEEEEeccHhhh-----------CHHHHHHHHHhhc-----CCCCCeEEEEEECChHhCchHhhh--he-eeeecC
Confidence            1 23589999999999           6666666666665     466789999999999999999999  77 556676


Q ss_pred             CC----------CHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHH
Q 022768          202 LP----------NEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCT  247 (292)
Q Consensus       202 ~p----------~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~  247 (292)
                      .+          +..+..+.+....   .    ++. .++...+| +..++.+++.
T Consensus       146 ~~~~~~~~~~~~~~~~i~~~L~~~~---~----~d~-~i~~~a~g-~~~~a~~l~~  192 (261)
T PRK05818        146 SKEKKVPFKVESNDRYFQYILLSFY---S----VDE-QLQAYNNG-SFSKLKNIIE  192 (261)
T ss_pred             ChhhhcccccccChHHHHHHHHHcc---C----ccH-HHHHHcCC-CHHHHHHHHH
Confidence            66          2222222222221   1    111 56666776 6667777766

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=98.93  E-value=2.6e-08  Score=82.76  Aligned_cols=127  Identities=18%  Similarity=0.259  Sum_probs=80.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG  145 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~  145 (292)
                      ..+-.+.||+|||||.++|.+|+.+|.+++.++|.+..+      ...+..++.-+... .+.+++||++++        
T Consensus        32 ~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~------~~~l~ril~G~~~~-GaW~cfdefnrl--------   96 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMD------YQSLSRILKGLAQS-GAWLCFDEFNRL--------   96 (231)
T ss_dssp             TTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-------HHHHHHHHHHHHHH-T-EEEEETCCCS--------
T ss_pred             CCCCCCcCCCCCCchhHHHHHHHHhCCeEEEeccccccc------HHHHHHHHHHHhhc-Cchhhhhhhhhh--------
Confidence            456778999999999999999999999999999988543      33444555444443 379999999999        


Q ss_pred             CcchHHHHHHHHHHHHHhh----C-----------CCCCCCeEEEEEeCC----CCCCChhhcCCCCcceEEEccCCCHH
Q 022768          146 TSADREIQRTLMELLNQLD----G-----------FDQLGKVKMIMATNR----PDVLDPALLRPGRLDRKIEIPLPNEQ  206 (292)
Q Consensus       146 ~~~~~~~~~~l~~~l~~~~----~-----------~~~~~~~~vi~t~~~----~~~l~~~l~~~~r~~~~i~l~~p~~~  206 (292)
                         +.+....+.+.+..+.    .           +.-++.+.+.+|.|.    ..++|+.++.  -| +.+.+..||.+
T Consensus        97 ---~~~vLS~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~--lF-Rpvam~~PD~~  170 (231)
T PF12774_consen   97 ---SEEVLSVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKA--LF-RPVAMMVPDLS  170 (231)
T ss_dssp             ---SHHHHHHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCT--TE-EEEE--S--HH
T ss_pred             ---hHHHHHHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHH--Hh-heeEEeCCCHH
Confidence               6666666655554431    1           011124556777774    3578899987  56 77899999988


Q ss_pred             HHHHHHH
Q 022768          207 SRMEILK  213 (292)
Q Consensus       207 ~r~~i~~  213 (292)
                      ...+++-
T Consensus       171 ~I~ei~L  177 (231)
T PF12774_consen  171 LIAEILL  177 (231)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7776644

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.93  E-value=1.2e-07  Score=81.20  Aligned_cols=170  Identities=12%  Similarity=0.191  Sum_probs=102.7

Q ss_pred             cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------EEEEec------cchh
Q 022768           37 LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------FLKVVS------SAII  103 (292)
Q Consensus        37 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------~~~~~~------~~~~  103 (292)
                      +..+++.+...+..-            .-++.+||+||  .||+++|+.+|+.+-+.       +-.+..      ..+.
T Consensus         7 q~~~~~~L~~~~~~~------------rl~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HP   72 (290)
T PRK07276          7 QPKVFQRFQTILEQD------------RLNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFS   72 (290)
T ss_pred             HHHHHHHHHHHHHcC------------CcceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCC
Confidence            455667777766542            45678999996  68999999999877332       111110      0111


Q ss_pred             cc----ccC--hHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768          104 DK----YIG--ESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus       104 ~~----~~~--~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      +-    ..+  -..+.++.+.....    .....|++||++|.+           .......|+..++     .+.++++
T Consensus        73 D~~~i~p~~~~I~idqIR~l~~~~~~~p~~~~~kV~II~~ad~m-----------~~~AaNaLLKtLE-----EPp~~t~  136 (290)
T PRK07276         73 DVTVIEPQGQVIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKM-----------HVNAANSLLKVIE-----EPQSEIY  136 (290)
T ss_pred             CeeeecCCCCcCCHHHHHHHHHHHhhCcccCCcEEEEeehhhhc-----------CHHHHHHHHHHhc-----CCCCCeE
Confidence            10    001  12233444443332    234579999999999           6666666666665     3556788


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCT  247 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~  247 (292)
                      +|.+|+.++.+.+.++|  |+ ..+.|+. +.+...+++...    ...  .+...+.....| +++.+..+..
T Consensus       137 ~iL~t~~~~~lLpTI~S--Rc-q~i~f~~-~~~~~~~~L~~~----g~~--~~~a~~la~~~~-s~~~A~~l~~  199 (290)
T PRK07276        137 IFLLTNDENKVLPTIKS--RT-QIFHFPK-NEAYLIQLLEQK----GLL--KTQAELLAKLAQ-STSEAEKLAQ  199 (290)
T ss_pred             EEEEECChhhCchHHHH--cc-eeeeCCC-cHHHHHHHHHHc----CCC--hHHHHHHHHHCC-CHHHHHHHhC
Confidence            99999999999999999  77 7788866 555544554421    111  111233334445 6777776663

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.92  E-value=5.2e-09  Score=91.65  Aligned_cols=96  Identities=33%  Similarity=0.575  Sum_probs=72.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-cccCh-HHHHHHHHHHHhh----hCCCEEEEEcccccccCC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGE-SARLIREMFGYAR----DHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~  140 (292)
                      .+||+.||+|+|||.+++.+|+.++.|+.-++|..+.. .|+|+ .+..+..++..+.    .+..+|+||||+|.+..+
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~~  306 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITKK  306 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhccc
Confidence            46999999999999999999999999999999998864 35555 3445556655543    245589999999999744


Q ss_pred             cCC-CCC--cchHHHHHHHHHHHHH
Q 022768          141 RFS-EGT--SADREIQRTLMELLNQ  162 (292)
Q Consensus       141 ~~~-~~~--~~~~~~~~~l~~~l~~  162 (292)
                      ..+ ++.  -.....|..|+.+++-
T Consensus       307 ~~~i~~~RDVsGEGVQQaLLKllEG  331 (564)
T KOG0745|consen  307 AESIHTSRDVSGEGVQQALLKLLEG  331 (564)
T ss_pred             CccccccccccchhHHHHHHHHhcc
Confidence            333 222  2456788888888864

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.91  E-value=9.1e-09  Score=89.25  Aligned_cols=102  Identities=20%  Similarity=0.276  Sum_probs=63.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChHH-HHHHHHHHHhhhCCCEEEEEcccccccCC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGESA-RLIREMFGYARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~il~lDe~d~l~~~  140 (292)
                      .+.+++|+|++|+|||+|+.++|+++   +..+..+....+......... ......+....  ...+|+|||+..-.  
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l~--~~dlLiIDDiG~e~--  230 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIRELKNSISDGSVKEKIDAVK--EAPVLMLDDIGAEQ--  230 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHhc--CCCEEEEecCCCcc--
Confidence            35789999999999999999999988   677777777666543321111 11223333333  34699999996431  


Q ss_pred             cCCCCCcchHHHH-HHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          141 RFSEGTSADREIQ-RTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       141 ~~~~~~~~~~~~~-~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                             .+.... ..+..+++.-    ...+..+|+|+|.+
T Consensus       231 -------~s~~~~~~ll~~Il~~R----~~~~~~ti~TSNl~  261 (306)
T PRK08939        231 -------MSSWVRDEVLGVILQYR----MQEELPTFFTSNFD  261 (306)
T ss_pred             -------ccHHHHHHHHHHHHHHH----HHCCCeEEEECCCC
Confidence                   133333 3344455432    11345688898864

>PRK06921 hypothetical protein; Provisional

Probab=98.91  E-value=9.6e-09  Score=87.47  Aligned_cols=105  Identities=17%  Similarity=0.257  Sum_probs=61.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEccccc-ccC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDA-IGG  139 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~-l~~  139 (292)
                      ...+++|+|++|+|||+|+.++++++    +..++++...++........ ......+...  ....+|+|||++. +.+
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~~~-~~~~~~~~~~--~~~dlLiIDDl~~~~~g  192 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGDLKDDF-DLLEAKLNRM--KKVEVLFIDDLFKPVNG  192 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHHHH-HHHHHHHHHh--cCCCEEEEeccccccCC
Confidence            35789999999999999999999976    45667776655443221111 1111222222  2347999999954 111


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      .     ..........+..+++....    .+..+|+|+|.+
T Consensus       193 ~-----e~~t~~~~~~lf~iin~R~~----~~k~tIitsn~~  225 (266)
T PRK06921        193 K-----PRATEWQIEQMYSVLNYRYL----NHKPILISSELT  225 (266)
T ss_pred             C-----ccCCHHHHHHHHHHHHHHHH----CCCCEEEECCCC
Confidence            1     11134445667777776432    122367787753

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.90  E-value=3.3e-08  Score=90.77  Aligned_cols=207  Identities=22%  Similarity=0.280  Sum_probs=115.7

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccCh
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGE  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~  109 (292)
                      .++|.....+.+...+...           ......++++|.+|+||+++++++....   +.+++.++|.......   
T Consensus       140 ~lig~s~~~~~~~~~i~~~-----------~~~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~~~---  205 (441)
T PRK10365        140 GMVGKSPAMQHLLSEIALV-----------APSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNESL---  205 (441)
T ss_pred             ceEecCHHHHHHHHHHhhc-----------cCCCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCHHH---
Confidence            3555555555554444332           2346679999999999999999998655   4689999998753211   


Q ss_pred             HHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------C
Q 022768          110 SARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------Q  168 (292)
Q Consensus       110 ~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~  168 (292)
                         .-..+|+.               .....+++|||||++.|           +...+..|..++.......      .
T Consensus       206 ---~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l-----------~~~~q~~l~~~l~~~~~~~~~~~~~~  271 (441)
T PRK10365        206 ---LESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDI-----------SPMMQVRLLRAIQEREVQRVGSNQTI  271 (441)
T ss_pred             ---HHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccC-----------CHHHHHHHHHHHccCcEEeCCCCcee
Confidence               11122221               12234689999999999           7788888888776532110      0


Q ss_pred             CCCeEEEEEeCCCC-------CCChhhcCCCCcceEEEccCCCHHHHH----HHHHHHHcCc----cCC-CCCCHHHHHH
Q 022768          169 LGKVKMIMATNRPD-------VLDPALLRPGRLDRKIEIPLPNEQSRM----EILKIHAAGI----AKH-GEIDYEAVVK  232 (292)
Q Consensus       169 ~~~~~vi~t~~~~~-------~l~~~l~~~~r~~~~i~l~~p~~~~r~----~i~~~~~~~~----~~~-~~~~~~~l~~  232 (292)
                      ..++.+|++++..-       .+.+.+..  ++ ..+.+..|+..+|.    .++..++...    ... ..++.+.+..
T Consensus       272 ~~~~rii~~t~~~~~~~~~~~~~~~~l~~--~l-~~~~i~~ppLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~  348 (441)
T PRK10365        272 SVDVRLIAATHRDLAAEVNAGRFRQDLYY--RL-NVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDL  348 (441)
T ss_pred             eeceEEEEeCCCCHHHHHHcCCchHHHHH--Hh-ccceecCCChhhcchhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHH
Confidence            11466787775531       12222222  22 23455556555554    3555555432    111 2355666665


Q ss_pred             HcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          233 LAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       233 ~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      +...-.|++++++.+.....+.......|+.+++...+
T Consensus       349 L~~~~wpgN~reL~~~~~~~~~~~~~~~i~~~~l~~~~  386 (441)
T PRK10365        349 LIHYDWPGNIRELENAVERAVVLLTGEYISERELPLAI  386 (441)
T ss_pred             HHhCCCCCHHHHHHHHHHHHHHhCCCCccchHhCchhh
Confidence            55422244555444444333344444567777765443

>PRK09183 transposase/IS protein; Provisional

Probab=98.90  E-value=1.1e-08  Score=86.88  Aligned_cols=103  Identities=18%  Similarity=0.284  Sum_probs=64.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccCh-HHHHHHHHHHHhhhCCCEEEEEcccccccC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGE-SARLIREMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      ..+.+++|+||+|+||||++.+++...   |..+.+++..++....... ....+...+... ...+.+++|||++....
T Consensus       100 ~~~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~-~~~~dlLiiDdlg~~~~  178 (259)
T PRK09183        100 ERNENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRG-VMAPRLLIIDEIGYLPF  178 (259)
T ss_pred             hcCCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHH-hcCCCEEEEcccccCCC
Confidence            457789999999999999999998764   6667777766554322111 011122333322 23557999999976521


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                               +......+..+++....    .+ .+|+|+|.+
T Consensus       179 ---------~~~~~~~lf~li~~r~~----~~-s~iiTsn~~  206 (259)
T PRK09183        179 ---------SQEEANLFFQVIAKRYE----KG-SMILTSNLP  206 (259)
T ss_pred             ---------ChHHHHHHHHHHHHHHh----cC-cEEEecCCC
Confidence                     34455667777766432    12 367788764

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.90  E-value=6.9e-09  Score=87.64  Aligned_cols=97  Identities=27%  Similarity=0.514  Sum_probs=70.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-cccChHHHH-HHHHHHHhh----hCCCEEEEEcccccccC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGESARL-IREMFGYAR----DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~----~~~~~il~lDe~d~l~~  139 (292)
                      ..++|+.||.|+|||.||+.+|+.++.||--.++..+.. .|+|+...+ +..+++.+-    ....+|++|||+|.+..
T Consensus        97 KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIar  176 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIAR  176 (408)
T ss_pred             eccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhc
Confidence            346999999999999999999999999999988888763 356654333 334443332    23448999999999976


Q ss_pred             CcCCC---CCcchHHHHHHHHHHHHH
Q 022768          140 RRFSE---GTSADREIQRTLMELLNQ  162 (292)
Q Consensus       140 ~~~~~---~~~~~~~~~~~l~~~l~~  162 (292)
                      +....   .+-+....|.+|+.++.-
T Consensus       177 kSeN~SITRDVSGEGVQQALLKiiEG  202 (408)
T COG1219         177 KSENPSITRDVSGEGVQQALLKIIEG  202 (408)
T ss_pred             cCCCCCcccccCchHHHHHHHHHHcC
Confidence            55332   122456788888888864

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.88  E-value=3.6e-09  Score=84.71  Aligned_cols=102  Identities=25%  Similarity=0.379  Sum_probs=62.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChH-HHHHHHHHHHhhhCCCEEEEEcccccccC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGES-ARLIREMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      ..+.+++|+|++|+|||++|.++++++   +.++.+++..++........ .......+.....  ..+|+|||+...  
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~--~dlLilDDlG~~--  120 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKR--VDLLILDDLGYE--  120 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHT--SSCEEEETCTSS--
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCcccc--ccEeccccccee--
Confidence            446789999999999999999999866   77888888887765432211 0111233333333  369999998543  


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                             ..+......+.++++.-..    .+ ..|+|+|..
T Consensus       121 -------~~~~~~~~~l~~ii~~R~~----~~-~tIiTSN~~  150 (178)
T PF01695_consen  121 -------PLSEWEAELLFEIIDERYE----RK-PTIITSNLS  150 (178)
T ss_dssp             ----------HHHHHCTHHHHHHHHH----T--EEEEEESS-
T ss_pred             -------eecccccccchhhhhHhhc----cc-CeEeeCCCc
Confidence                   1244556677777776542    12 467788864

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.87  E-value=1.2e-08  Score=86.24  Aligned_cols=101  Identities=21%  Similarity=0.329  Sum_probs=64.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChHHH-H-HHHHHHHhhhCCCEEEEEcccccccC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGESAR-L-IREMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      .+.+++|+||||+|||+|+-++++++   |..++.+...++.......... . -..+....  ....+|+|||+-..- 
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~~Lk~~~~~~~~~~~l~~~l--~~~dlLIiDDlG~~~-  180 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEGRLEEKLLREL--KKVDLLIIDDIGYEP-  180 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhcCchHHHHHHHh--hcCCEEEEecccCcc-
Confidence            57789999999999999999999987   6788888888876654322221 1 11122212  234699999996641 


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                              .+......+.+++...-.    .+-. ++|+|.+
T Consensus       181 --------~~~~~~~~~~q~I~~r~~----~~~~-~~tsN~~  209 (254)
T COG1484         181 --------FSQEEADLLFQLISRRYE----SRSL-IITSNLS  209 (254)
T ss_pred             --------CCHHHHHHHHHHHHHHHh----hccc-eeecCCC
Confidence                    133344555555544321    1222 8888865

>PF14516 AAA_35: AAA-like domain

Probab=98.86  E-value=1.4e-06  Score=76.84  Aligned_cols=186  Identities=17%  Similarity=0.212  Sum_probs=106.9

Q ss_pred             cccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChHH
Q 022768           35 GGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGESA  111 (292)
Q Consensus        35 ~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~~  111 (292)
                      +.+..+.+++.+.+..              ++..+.|.||..+|||+++..+.+.+   +..++.+++..+.........
T Consensus        14 i~R~~~e~~~~~~i~~--------------~G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~~~~~~~~~   79 (331)
T PF14516_consen   14 IERPPAEQECYQEIVQ--------------PGSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLGSAIFSDLE   79 (331)
T ss_pred             cCchHHHHHHHHHHhc--------------CCCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCCCcccCCHH
Confidence            4555566777666643              47889999999999999998888766   566777776654332111111


Q ss_pred             HHH-------------------------------HHHHHHh---hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHH
Q 022768          112 RLI-------------------------------REMFGYA---RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLM  157 (292)
Q Consensus       112 ~~~-------------------------------~~~~~~~---~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~  157 (292)
                      ..+                               ...+...   ....|-||+|||+|.++..         ......+.
T Consensus        80 ~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~---------~~~~~dF~  150 (331)
T PF14516_consen   80 QFLRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEY---------PQIADDFF  150 (331)
T ss_pred             HHHHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccC---------cchHHHHH
Confidence            100                               1111111   1146789999999999632         12223334


Q ss_pred             HHHHHhhCCCC----CCCeEEEEEeCCCCCCChhh-cCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHH
Q 022768          158 ELLNQLDGFDQ----LGKVKMIMATNRPDVLDPAL-LRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVK  232 (292)
Q Consensus       158 ~~l~~~~~~~~----~~~~~vi~t~~~~~~l~~~l-~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~  232 (292)
                      .+++.....+.    ..++.+|++......+.... .++..++..+.++..+.++...+++.+-...  .. ..++.+..
T Consensus       151 ~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~--~~-~~~~~l~~  227 (331)
T PF14516_consen  151 GLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLEF--SQ-EQLEQLMD  227 (331)
T ss_pred             HHHHHHHHhcccCcccceEEEEEecCcccccccCCCCCCcccccceeCCCCCHHHHHHHHHhhhccC--CH-HHHHHHHH
Confidence            44443322121    12344555443322222222 3433455688999999999999988775432  21 22788888


Q ss_pred             HcCCCCHHHHHHHHH
Q 022768          233 LAEGFNGADLRNVCT  247 (292)
Q Consensus       233 ~~~g~~~~di~~l~~  247 (292)
                      .+.|. |.=++.+|.
T Consensus       228 ~tgGh-P~Lv~~~~~  241 (331)
T PF14516_consen  228 WTGGH-PYLVQKACY  241 (331)
T ss_pred             HHCCC-HHHHHHHHH
Confidence            88884 334444443

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.85  E-value=2.8e-08  Score=75.32  Aligned_cols=72  Identities=21%  Similarity=0.368  Sum_probs=46.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc--------CCcEEEEeccchhcc--------------cc--ChHHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI--------DANFLKVVSSAIIDK--------------YI--GESARLIREMFGYA  121 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l--------~~~~~~~~~~~~~~~--------------~~--~~~~~~~~~~~~~~  121 (292)
                      +..++|+|++|+|||++++.+++.+        ..+++.+++....+.              ..  .........+.+..
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l   83 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDAL   83 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHH
Confidence            5679999999999999999999987        667777776544310              00  11233334444444


Q ss_pred             hhCCCEEEEEcccccc
Q 022768          122 RDHQPCIIFMDEIDAI  137 (292)
Q Consensus       122 ~~~~~~il~lDe~d~l  137 (292)
                      ......+|+|||+|.+
T Consensus        84 ~~~~~~~lviDe~~~l   99 (131)
T PF13401_consen   84 DRRRVVLLVIDEADHL   99 (131)
T ss_dssp             HHCTEEEEEEETTHHH
T ss_pred             HhcCCeEEEEeChHhc
Confidence            4455469999999997

>PF05729 NACHT: NACHT domain

Probab=98.84  E-value=4.2e-08  Score=77.33  Aligned_cols=140  Identities=20%  Similarity=0.287  Sum_probs=77.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCC--------cE-EEEeccchhcccc-ChHHHHH-----------HH-HHHHhhhCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDA--------NF-LKVVSSAIIDKYI-GESARLI-----------RE-MFGYARDHQ  125 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~--------~~-~~~~~~~~~~~~~-~~~~~~~-----------~~-~~~~~~~~~  125 (292)
                      .++|+|++|+|||++++.++..+..        ++ +............ ......+           .. .........
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~   81 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKNK   81 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcCC
Confidence            5889999999999999999987611        12 2222222221110 0111111           11 111223345


Q ss_pred             CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC--CChhhcCCCCcceEEEccCC
Q 022768          126 PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV--LDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       126 ~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~--l~~~l~~~~r~~~~i~l~~p  203 (292)
                      ..+++||.+|.+......   .........+..++..    ...+++.++.|++....  +...+..    ...+.+.+.
T Consensus        82 ~~llilDglDE~~~~~~~---~~~~~~~~~l~~l~~~----~~~~~~~liit~r~~~~~~~~~~~~~----~~~~~l~~~  150 (166)
T PF05729_consen   82 RVLLILDGLDELEEQDQS---QERQRLLDLLSQLLPQ----ALPPGVKLIITSRPRAFPDLRRRLKQ----AQILELEPF  150 (166)
T ss_pred             ceEEEEechHhcccchhh---hHHHHHHHHHHHHhhh----ccCCCCeEEEEEcCChHHHHHHhcCC----CcEEEECCC
Confidence            679999999998432100   0011222333344433    22346677777764332  2222222    156899999


Q ss_pred             CHHHHHHHHHHHHcC
Q 022768          204 NEQSRMEILKIHAAG  218 (292)
Q Consensus       204 ~~~~r~~i~~~~~~~  218 (292)
                      +.++..++++.++++
T Consensus       151 ~~~~~~~~~~~~f~~  165 (166)
T PF05729_consen  151 SEEDIKQYLRKYFSN  165 (166)
T ss_pred             CHHHHHHHHHHHhhc
Confidence            999999999988763

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.81  E-value=4.8e-07  Score=78.11  Aligned_cols=126  Identities=12%  Similarity=0.117  Sum_probs=86.4

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCc-------------EEEEeccchhccccChHHHHHHHHHHHhhh-----CCC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDAN-------------FLKVVSSAIIDKYIGESARLIREMFGYARD-----HQP  126 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~-------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~  126 (292)
                      -++.+||+|+.|.||+++++.+++.+-|.             +..++.   .+..  ...+.++.+......     ...
T Consensus        17 l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~---~g~~--i~vd~Ir~l~~~~~~~~~~~~~~   91 (299)
T PRK07132         17 ISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDI---FDKD--LSKSEFLSAINKLYFSSFVQSQK   91 (299)
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEecc---CCCc--CCHHHHHHHHHHhccCCcccCCc
Confidence            35678899999999999999999987331             111210   0111  112334444433321     256


Q ss_pred             EEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHH
Q 022768          127 CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQ  206 (292)
Q Consensus       127 ~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~  206 (292)
                      .|++||++|.+           .......|+..++.     +++.+.+|.+++.++.+-+.+++  |+ ..+.|.+++.+
T Consensus        92 KvvII~~~e~m-----------~~~a~NaLLK~LEE-----Pp~~t~~il~~~~~~kll~TI~S--Rc-~~~~f~~l~~~  152 (299)
T PRK07132         92 KILIIKNIEKT-----------SNSLLNALLKTIEE-----PPKDTYFLLTTKNINKVLPTIVS--RC-QVFNVKEPDQQ  152 (299)
T ss_pred             eEEEEeccccc-----------CHHHHHHHHHHhhC-----CCCCeEEEEEeCChHhChHHHHh--Ce-EEEECCCCCHH
Confidence            89999999988           66566666666653     45678888888888889999998  77 77999999988


Q ss_pred             HHHHHHHH
Q 022768          207 SRMEILKI  214 (292)
Q Consensus       207 ~r~~i~~~  214 (292)
                      +..+.+..
T Consensus       153 ~l~~~l~~  160 (299)
T PRK07132        153 KILAKLLS  160 (299)
T ss_pred             HHHHHHHH
Confidence            88766654

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=98.80  E-value=2.2e-08  Score=88.66  Aligned_cols=103  Identities=22%  Similarity=0.323  Sum_probs=64.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCC-cEEEEeccchhccccChH------HHHHHHHHHHhhhCCCEEEEEcccc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDA-NFLKVVSSAIIDKYIGES------ARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~-~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      ..++++++|+|+.|+|||+|+..+...+.. .-.+++..++....-...      ...+..+.+... ....+|+|||++
T Consensus        59 ~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~-~~~~lLcfDEF~  137 (362)
T PF03969_consen   59 PPPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELA-KESRLLCFDEFQ  137 (362)
T ss_pred             CCCCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHH-hcCCEEEEeeee
Confidence            456899999999999999999999998865 333344333332110010      111222222222 222599999998


Q ss_pred             cccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          136 AIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       136 ~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      .-           +......|..++..+-.    .++++|+|+|.+
T Consensus       138 V~-----------DiaDAmil~rLf~~l~~----~gvvlVaTSN~~  168 (362)
T PF03969_consen  138 VT-----------DIADAMILKRLFEALFK----RGVVLVATSNRP  168 (362)
T ss_pred             cc-----------chhHHHHHHHHHHHHHH----CCCEEEecCCCC
Confidence            75           44444555566665532    488999999974

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=98.79  E-value=3.6e-08  Score=89.90  Aligned_cols=227  Identities=19%  Similarity=0.213  Sum_probs=123.3

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHH
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARL  113 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~  113 (292)
                      ++|.+++|..+--.+-.-... .....-.++---++||+|.||||||.++|++++.....++....+.-.   +|-+...
T Consensus       451 IyGh~~VK~AvAlaLfGGv~k-n~~~khkvRGDinvLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGASa---vGLTa~v  526 (854)
T KOG0477|consen  451 IYGHEDVKRAVALALFGGVPK-NPGGKHKVRGDINVLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGASA---VGLTAYV  526 (854)
T ss_pred             hhchHHHHHHHHHHHhcCCcc-CCCCCceeccceeEEEecCCCccHHHHHHHHHhcCcceeEeccCCccc---cceeEEE
Confidence            689999988887766432111 000000122244699999999999999999999887666553322111   1111000


Q ss_pred             -----HHHHHHHhh---hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-CC-------CCCCCeEEEEE
Q 022768          114 -----IREMFGYAR---DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-GF-------DQLGKVKMIMA  177 (292)
Q Consensus       114 -----~~~~~~~~~---~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~~-------~~~~~~~vi~t  177 (292)
                           .++|.-.+-   ....+|-+|||||.+-..           ....+.+.+.+-. ++       .-+.++.+|++
T Consensus       527 ~KdPvtrEWTLEaGALVLADkGvClIDEFDKMndq-----------DRtSIHEAMEQQSISISKAGIVtsLqArctvIAA  595 (854)
T KOG0477|consen  527 RKDPVTREWTLEAGALVLADKGVCLIDEFDKMNDQ-----------DRTSIHEAMEQQSISISKAGIVTSLQARCTVIAA  595 (854)
T ss_pred             eeCCccceeeeccCeEEEccCceEEeehhhhhccc-----------ccchHHHHHHhcchhhhhhhHHHHHHhhhhhhee
Confidence                 011111111   133479999999998311           1111112221100 00       11147889999


Q ss_pred             eCCC---C----------CCChhhcCCCCcceEEEc---cCCCHHHHHH--HHHHHHcC---------------------
Q 022768          178 TNRP---D----------VLDPALLRPGRLDRKIEI---PLPNEQSRME--ILKIHAAG---------------------  218 (292)
Q Consensus       178 ~~~~---~----------~l~~~l~~~~r~~~~i~l---~~p~~~~r~~--i~~~~~~~---------------------  218 (292)
                      +|+.   .          ++...+++  ||+..--+   -.|-.+++..  ++..+...                     
T Consensus       596 anPigGRY~~s~tFaqNV~ltePIlS--RFDiLcVvkD~vd~~~De~lA~fVV~Sh~r~hp~~~~~~~~~e~~~~~~v~~  673 (854)
T KOG0477|consen  596 ANPIGGRYNPSLTFAQNVDLTEPILS--RFDILCVVKDTVDPVQDEKLAKFVVGSHVRHHPSNKEEDGLEEPQMPARVEP  673 (854)
T ss_pred             cCCCCCccCCccchhhccccccchhh--hcceeeeeecccCchhHHHHHHHHHHhHhhcCCcccccCccccccccccccc
Confidence            9872   1          35567777  77542111   1122222221  12222210                     


Q ss_pred             -----------------ccCCCCCCHHHHHHHcC---------C---CCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          219 -----------------IAKHGEIDYEAVVKLAE---------G---FNGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       219 -----------------~~~~~~~~~~~l~~~~~---------g---~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                                       .+.....|.+.++....         |   .+.+.|..+++.+.+.|..+.+..|+.+|+..|
T Consensus       674 ipq~lLrkyI~yar~~v~PkL~q~d~~K~s~vya~lRkES~~tGs~piTvRHieS~ir~seAhArm~Lr~~V~~~d~~~A  753 (854)
T KOG0477|consen  674 IPQELLRKYIIYAREKVRPKLNQMDMDKISSVYADLRKESMATGSLPITVRHIESMIRMSEAHARMHLREYVTEEDVDMA  753 (854)
T ss_pred             ChHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHhhccccCCchhhHHHHHHHHHHHHHHHHHHHHhhccHhHHHHH
Confidence                             01112233333333221         2   156889999999999999999999999999999


Q ss_pred             HHHHhhhh
Q 022768          270 VRKLNEAK  277 (292)
Q Consensus       270 ~~~~~~~~  277 (292)
                      ++.+....
T Consensus       754 I~v~ldSf  761 (854)
T KOG0477|consen  754 IRVMLDSF  761 (854)
T ss_pred             HHHHHHHH
Confidence            99887653

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=98.75  E-value=3.7e-07  Score=77.93  Aligned_cols=164  Identities=20%  Similarity=0.305  Sum_probs=102.7

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHH---hcCCcEEEEeccchhcc--
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIAS---NIDANFLKVVSSAIIDK--  105 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~---~l~~~~~~~~~~~~~~~--  105 (292)
                      ...+.|..+..+.+-+.+.+-..         ...+..+++.||.|+|||++......   +.+..++.+........  
T Consensus        23 ~~~l~g~~~~~~~l~~~lkqt~~---------~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk   93 (408)
T KOG2228|consen   23 HINLFGVQDEQKHLSELLKQTIL---------HGESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDK   93 (408)
T ss_pred             CcceeehHHHHHHHHHHHHHHHH---------hcCCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhH
Confidence            35678888888888777765321         25577899999999999998766554   45777777766554432  


Q ss_pred             -------------------ccChHHHHHHHHHHHhhh-----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHH
Q 022768          106 -------------------YIGESARLIREMFGYARD-----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN  161 (292)
Q Consensus       106 -------------------~~~~~~~~~~~~~~~~~~-----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~  161 (292)
                                         ..|.....+..+....+.     ..+.|.++||+|.+++          ..-|..+.++++
T Consensus        94 ~al~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~----------h~rQtllYnlfD  163 (408)
T KOG2228|consen   94 IALKGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAP----------HSRQTLLYNLFD  163 (408)
T ss_pred             HHHHHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhcccc----------chhhHHHHHHHH
Confidence                               001111111111111111     2235667889998863          345566677777


Q ss_pred             HhhCCCCCCCeEEEEEeCCC---CCCChhhcCCCCcceE-EEc-cCCCHHHHHHHHHHHHc
Q 022768          162 QLDGFDQLGKVKMIMATNRP---DVLDPALLRPGRLDRK-IEI-PLPNEQSRMEILKIHAA  217 (292)
Q Consensus       162 ~~~~~~~~~~~~vi~t~~~~---~~l~~~l~~~~r~~~~-i~l-~~p~~~~r~~i~~~~~~  217 (292)
                      ....  ..-.+.+|+.|...   +.+.+++++  ||... |.+ +.....+..++++..+.
T Consensus       164 isqs--~r~Piciig~Ttrld~lE~LEKRVKS--RFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  164 ISQS--ARAPICIIGVTTRLDILELLEKRVKS--RFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             HHhh--cCCCeEEEEeeccccHHHHHHHHHHh--hcccceeeccCCCChHHHHHHHHHHhc
Confidence            6552  23466777766543   456788888  99775 555 44567888899888774

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.74  E-value=1.1e-07  Score=91.46  Aligned_cols=130  Identities=23%  Similarity=0.397  Sum_probs=93.2

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchh------
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAII------  103 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~------  103 (292)
                      .++|+++++..+-+.+...-.+   ..+.  .+...++|.||.|+|||-+|+++|..+   ...++.+++.++.      
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~g---l~~~--~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskli  637 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAG---LKDP--NPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKLI  637 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhcc---cCCC--CCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhcc
Confidence            4889999999998888654211   1111  356679999999999999999999988   4467888888532      


Q ss_pred             cc---ccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCC------CeEE
Q 022768          104 DK---YIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG------KVKM  174 (292)
Q Consensus       104 ~~---~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~------~~~v  174 (292)
                      +.   |.|..+  ...+....+....+||+|||+|.-           +...+..|.++++...-....+      +++|
T Consensus       638 gsp~gyvG~e~--gg~LteavrrrP~sVVLfdeIEkA-----------h~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~  704 (898)
T KOG1051|consen  638 GSPPGYVGKEE--GGQLTEAVKRRPYSVVLFEEIEKA-----------HPDVLNILLQLLDRGRLTDSHGREVDFKNAIF  704 (898)
T ss_pred             CCCcccccchh--HHHHHHHHhcCCceEEEEechhhc-----------CHHHHHHHHHHHhcCccccCCCcEeeccceEE
Confidence            21   333322  235666667777899999999987           7888888888888654333223      6889


Q ss_pred             EEEeCC
Q 022768          175 IMATNR  180 (292)
Q Consensus       175 i~t~~~  180 (292)
                      |+|+|.
T Consensus       705 IMTsn~  710 (898)
T KOG1051|consen  705 IMTSNV  710 (898)
T ss_pred             EEeccc
Confidence            999875

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=98.74  E-value=1.3e-06  Score=75.42  Aligned_cols=174  Identities=21%  Similarity=0.245  Sum_probs=93.8

Q ss_pred             HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHh--cCCcE---EEEeccchhcc-------
Q 022768           38 SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASN--IDANF---LKVVSSAIIDK-------  105 (292)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~--l~~~~---~~~~~~~~~~~-------  105 (292)
                      +..+++|.+.+...           -.....+.|+|++|+|||++|..+++.  ....+   +.++.......       
T Consensus         2 e~~~~~l~~~L~~~-----------~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i   70 (287)
T PF00931_consen    2 EKEIEKLKDWLLDN-----------SNEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQI   70 (287)
T ss_dssp             HHHHHHHHHHHHTT-----------TTSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHH
T ss_pred             HHHHHHHHHHhhCC-----------CCCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccc
Confidence            55677777776552           134667889999999999999999987  43322   22332221110       


Q ss_pred             ------c------cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768          106 ------Y------IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus       106 ------~------~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                            .      ...... ....+.......+.+|+||+++..           .     .+..+...+.  ....+..
T Consensus        71 ~~~l~~~~~~~~~~~~~~~-~~~~l~~~L~~~~~LlVlDdv~~~-----------~-----~~~~l~~~~~--~~~~~~k  131 (287)
T PF00931_consen   71 LRQLGEPDSSISDPKDIEE-LQDQLRELLKDKRCLLVLDDVWDE-----------E-----DLEELREPLP--SFSSGSK  131 (287)
T ss_dssp             HHHHTCC-STSSCCSSHHH-HHHHHHHHHCCTSEEEEEEEE-SH-----------H-----HH-------H--CHHSS-E
T ss_pred             ccccccccccccccccccc-ccccchhhhccccceeeeeeeccc-----------c-----cccccccccc--ccccccc
Confidence                  0      011222 223333333455899999998754           1     2212221111  1113567


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc---CC-CCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA---KH-GEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~---~~-~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      +|+||+.... ......  . ...+.++..+.++-.++++.......   .. .......+...+.| .|--|..+.
T Consensus       132 ilvTTR~~~v-~~~~~~--~-~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~g-lPLal~~~a  203 (287)
T PF00931_consen  132 ILVTTRDRSV-AGSLGG--T-DKVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGG-LPLALKLIA  203 (287)
T ss_dssp             EEEEESCGGG-GTTHHS--C-EEEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT--HHHHHHHH
T ss_pred             cccccccccc-cccccc--c-cccccccccccccccccccccccccccccccccccccccccccccc-ccccccccc
Confidence            8888875432 111111  1 36789999999999999998876443   11 12224678888887 554555443

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PLN03210 Resistant to P

Probab=98.73  E-value=1.4e-06  Score=88.98  Aligned_cols=178  Identities=21%  Similarity=0.306  Sum_probs=101.3

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE---EEEeccch
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF---LKVVSSAI  102 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~---~~~~~~~~  102 (292)
                      .++..+++++|.++..++|...+...           ....+.+.|+|++|+||||+|+++++.+...+   +.++...+
T Consensus       178 ~~~~~~~~~vG~~~~l~~l~~lL~l~-----------~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~g~vfv~~~~v  246 (1153)
T PLN03210        178 TPSNDFEDFVGIEDHIAKMSSLLHLE-----------SEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAFI  246 (1153)
T ss_pred             ccCcccccccchHHHHHHHHHHHccc-----------cCceEEEEEEcCCCCchHHHHHHHHHHHhhcCCeEEEeecccc
Confidence            35567899999999999998887532           34467789999999999999999998774432   11211000


Q ss_pred             hc---ccc-------C----hHHHHHHH-------------HHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHH
Q 022768          103 ID---KYI-------G----ESARLIRE-------------MFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRT  155 (292)
Q Consensus       103 ~~---~~~-------~----~~~~~~~~-------------~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~  155 (292)
                      ..   .+.       .    .....+..             ........++.+|+|||++..             .....
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~-------------~~l~~  313 (1153)
T PLN03210        247 SKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQ-------------DVLDA  313 (1153)
T ss_pred             ccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCH-------------HHHHH
Confidence            00   000       0    00001111             111122345678999998643             12222


Q ss_pred             HHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCH----HHHH
Q 022768          156 LMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDY----EAVV  231 (292)
Q Consensus       156 l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~----~~l~  231 (292)
                      +.   ....  ....+..||+||++.+     +.........+.++.|+.++-.++++.++...... ..++    ..++
T Consensus       314 L~---~~~~--~~~~GsrIIiTTrd~~-----vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~~~-~~~~~~l~~~iv  382 (1153)
T PLN03210        314 LA---GQTQ--WFGSGSRIIVITKDKH-----FLRAHGIDHIYEVCLPSNELALEMFCRSAFKKNSP-PDGFMELASEVA  382 (1153)
T ss_pred             HH---hhCc--cCCCCcEEEEEeCcHH-----HHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCCCC-cHHHHHHHHHHH
Confidence            22   1111  1123556788888543     22212345678899999999999999887643221 1222    2345


Q ss_pred             HHcCCCC
Q 022768          232 KLAEGFN  238 (292)
Q Consensus       232 ~~~~g~~  238 (292)
                      ....|.+
T Consensus       383 ~~c~GLP  389 (1153)
T PLN03210        383 LRAGNLP  389 (1153)
T ss_pred             HHhCCCc
Confidence            5666644

syringae 6; Provisional

>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]

Probab=98.69  E-value=1.5e-07  Score=84.24  Aligned_cols=241  Identities=17%  Similarity=0.182  Sum_probs=137.1

Q ss_pred             ChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           15 DPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      .|.+|..++.+..|.    +.|.++.++.+--.+-.- ..+.+-..+-..-.-+||+-|.||+.||.++|.+-+-....+
T Consensus       318 ~~d~Ye~is~sIAPS----IfG~~DiKkAiaClLFgG-srK~LpDg~~lRGDINVLLLGDPgtAKSQlLKFvEkvsPIaV  392 (729)
T KOG0481|consen  318 SPDVYERISKSIAPS----IFGHEDIKKAIACLLFGG-SRKRLPDGVTLRGDINVLLLGDPGTAKSQLLKFVEKVSPIAV  392 (729)
T ss_pred             CccHHHHHhhccCch----hcCchhHHHHHHHHhhcC-ccccCCCcceeccceeEEEecCCchhHHHHHHHHHhcCceEE
Confidence            344455555554443    789999999887765321 111111111123345699999999999999999888766555


Q ss_pred             EEEeccchhccccChHHHHHHHHHHH--------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-C
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGY--------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-G  165 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~  165 (292)
                      +...-+.-   ..|-+...++.-..+        .-....+|++|||||.+           ..+...++.+.+++-. +
T Consensus       393 YTSGKGSS---AAGLTASV~RD~~tReFylEGGAMVLADgGVvCIDEFDKM-----------re~DRVAIHEAMEQQTIS  458 (729)
T KOG0481|consen  393 YTSGKGSS---AAGLTASVIRDPSTREFYLEGGAMVLADGGVVCIDEFDKM-----------REDDRVAIHEAMEQQTIS  458 (729)
T ss_pred             EecCCCcc---cccceeeEEecCCcceEEEecceEEEecCCEEEeehhhcc-----------CchhhhHHHHHHHhhhHH
Confidence            54332111   111111111110000        01134589999999999           3333444444444321 1


Q ss_pred             C-------CCCCCeEEEEEeCCCC-----------C--CChhhcCCCCcceEEEccCCCHHHH-HHHHHHHHc----Cc-
Q 022768          166 F-------DQLGKVKMIMATNRPD-----------V--LDPALLRPGRLDRKIEIPLPNEQSR-MEILKIHAA----GI-  219 (292)
Q Consensus       166 ~-------~~~~~~~vi~t~~~~~-----------~--l~~~l~~~~r~~~~i~l~~p~~~~r-~~i~~~~~~----~~-  219 (292)
                      +       .-+.++.|++++|...           .  .-+.+++  ||+..+-++.-..+++ ..|.++...    .. 
T Consensus       459 IAKAGITT~LNSRtSVLAAANpvfGRyDd~Kt~~dNIDf~~TILS--RFDmIFIVKD~h~~~~D~~lAkHVI~vH~~~~n  536 (729)
T KOG0481|consen  459 IAKAGITTTLNSRTSVLAAANPVFGRYDDTKTGEDNIDFMPTILS--RFDMIFIVKDEHDEERDITLAKHVINVHVSKAN  536 (729)
T ss_pred             HhhhcceeeecchhhhhhhcCCccccccccCCcccccchhhhHhh--hccEEEEEeccCcchhhhHHHHHhhhhhccccc
Confidence            1       2234778899998642           1  3367788  9988877765443333 333333322    00 


Q ss_pred             -c------CCCCCCHHHHHHHc--------------------C----------------------CCCHHHHHHHHHHHH
Q 022768          220 -A------KHGEIDYEAVVKLA--------------------E----------------------GFNGADLRNVCTEAG  250 (292)
Q Consensus       220 -~------~~~~~~~~~l~~~~--------------------~----------------------g~~~~di~~l~~~a~  250 (292)
                       .      ....+.++.+.+..                    .                      -.+.+++..+++-+.
T Consensus       537 ~~~~~~~~~~~ei~~~~~KryI~YcR~kc~PrLs~~AaekL~~~yV~~R~~~~q~e~~s~~rssIPITVRQLEAIiRI~E  616 (729)
T KOG0481|consen  537 AQTDSQEENEGEIPIEKLKRYIQYCRLKCGPRLSAEAAEKLSSRYVTMRKGVRQHEQDSDKRSSIPITVRQLEAIIRIAE  616 (729)
T ss_pred             cccCccccCCCcccHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHhHHHHHHHHhhhcccccCCCceeHHHHHHHHHHHH
Confidence             0      01112222222111                    0                      126789999999999


Q ss_pred             HHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          251 MSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       251 ~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      .+|..+..+..|.+++.+|++-++..
T Consensus       617 SLAKm~Ls~~ate~hV~EA~RLF~vS  642 (729)
T KOG0481|consen  617 SLAKMELSPFATEAHVEEALRLFQVS  642 (729)
T ss_pred             HHHhhcCCccccHHHHHHHHHHHhHh
Confidence            99999999999999999999988864

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=98.66  E-value=1.1e-06  Score=73.99  Aligned_cols=220  Identities=16%  Similarity=0.167  Sum_probs=118.6

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE-------eccchhcc
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV-------VSSAIIDK  105 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~-------~~~~~~~~  105 (292)
                      .|.|+.-+++.+...+...+.+..      -..+-.+=++|++||||+++++.+|+.+...-...       ...++...
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~~------p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~  156 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANPN------PRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHA  156 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCCC------CCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCCh
Confidence            478998888888888877654411      12233455889999999999999998773221111       11111111


Q ss_pred             -ccCh-HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC--CCCCCeEEEEEeCCC
Q 022768          106 -YIGE-SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF--DQLGKVKMIMATNRP  181 (292)
Q Consensus       106 -~~~~-~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~--~~~~~~~vi~t~~~~  181 (292)
                       .+.. ..+....+.+.+..|..++.++||+|.|           .+...+.+.-+++.....  ....+.++|+-+|..
T Consensus       157 ~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKm-----------p~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~g  225 (344)
T KOG2170|consen  157 SKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKL-----------PPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAG  225 (344)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCceEEechhhhc-----------CHhHHHHHhhhhccccccccccccceEEEEEcCCc
Confidence             1111 1223344555566788899999999999           788888888888753222  223356677777664


Q ss_pred             C-CCCh---hhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCC---HHHHHHHHHHHHHHHH
Q 022768          182 D-VLDP---ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFN---GADLRNVCTEAGMSAI  254 (292)
Q Consensus       182 ~-~l~~---~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~---~~di~~l~~~a~~~a~  254 (292)
                      . .+..   ...++++-...+.+....+.-..........+...+..++-..+..... |-   .+++++.++...   .
T Consensus       226 g~eI~~~aL~~~~~g~~re~~~l~~~E~~L~~~~~n~~~~Gl~~S~li~~~lid~fIP-FLPLek~hV~~C~r~el---~  301 (344)
T KOG2170|consen  226 GSEIARIALENARNGKPREQLRLKSFEPALMQSAFNEKAGGLVHSRLISNNLIDHFIP-FLPLEKRHVRSCIRAEL---R  301 (344)
T ss_pred             chHHHHHHHHHHHcCCCcccchhhhhhHHHHHhhhccccccccccccchhhHHhhccC-cCcccHHHHHHHHHHHH---H
Confidence            4 3332   1222233334445554444433333333333334444343333333222 33   355555555332   2


Q ss_pred             HhcCCcccHHHHHHHHHHHh
Q 022768          255 RAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       255 ~~~~~~i~~~~~~~a~~~~~  274 (292)
                      +++ .....+-+.+.+..+.
T Consensus       302 ~rg-~~~d~~~~erva~~l~  320 (344)
T KOG2170|consen  302 KRG-LAPDQDFVERVANSLS  320 (344)
T ss_pred             hcc-cccchHHHHHHHHhhc
Confidence            333 3344555555555544

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.65  E-value=2.7e-07  Score=72.37  Aligned_cols=110  Identities=26%  Similarity=0.353  Sum_probs=62.4

Q ss_pred             EEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc------------------------cChHHHHHHHHHHHh
Q 022768           69 VLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY------------------------IGESARLIREMFGYA  121 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~------------------------~~~~~~~~~~~~~~~  121 (292)
                      ++|+|+||+|||+++..++...   +.+++.++........                        ..............+
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATADDPAAARLLSKAERLR   81 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcchHHHHHHHhhhhhccccccEEEEEcCCCCCcHHHHHHHHHHHH
Confidence            7899999999999999999877   4556665544322100                        001111122334445


Q ss_pred             hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          122 RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       122 ~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      ....+.+++|||+..+..................+..++.....    .++.+|++++...
T Consensus        82 ~~~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~----~~~~vv~~~~~~~  138 (165)
T cd01120          82 ERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARK----GGVTVIFTLQVPS  138 (165)
T ss_pred             hCCCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhc----CCceEEEEEecCC
Confidence            55778999999999875322100001122334455555544432    3666777776553

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.63  E-value=1.3e-07  Score=75.99  Aligned_cols=59  Identities=25%  Similarity=0.455  Sum_probs=38.1

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---EEEEeccch
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---FLKVVSSAI  102 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---~~~~~~~~~  102 (292)
                      ++|++++.++|..++.. ..         -..++.++|+|++|+|||++++.+...+...   ++.+.+...
T Consensus         2 fvgR~~e~~~l~~~l~~-~~---------~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    2 FVGREEEIERLRDLLDA-AQ---------SGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             -TT-HHHHHHHHHTTGG-TS---------S-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHHH-HH---------cCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            68999999999999852 11         1446789999999999999999988777433   555554444

>COG1485 Predicted ATPase [General function prediction only]

Probab=98.62  E-value=1.9e-07  Score=80.36  Aligned_cols=101  Identities=21%  Similarity=0.293  Sum_probs=62.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcE-EEEeccchhcc-------ccChHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANF-LKVVSSAIIDK-------YIGESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~-~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      .++++++++|+-|.|||+|+..+...+..+- .++....+...       ..|+..-.-....+.+...  .+|+|||++
T Consensus        63 ~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~FM~~vH~~l~~l~g~~dpl~~iA~~~~~~~--~vLCfDEF~  140 (367)
T COG1485          63 GPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQGQTDPLPPIADELAAET--RVLCFDEFE  140 (367)
T ss_pred             CCCceEEEECCCCccHHHHHHHHHhhCCccccccccHHHHHHHHHHHHHHHcCCCCccHHHHHHHHhcC--CEEEeeeee
Confidence            4678999999999999999999999886543 33333332211       1122211111111222223  599999997


Q ss_pred             cccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          136 AIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       136 ~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      .-           +-...-.|..+++.+-.    .+|++++|+|.+
T Consensus       141 Vt-----------DI~DAMiL~rL~~~Lf~----~GV~lvaTSN~~  171 (367)
T COG1485         141 VT-----------DIADAMILGRLLEALFA----RGVVLVATSNTA  171 (367)
T ss_pred             ec-----------ChHHHHHHHHHHHHHHH----CCcEEEEeCCCC
Confidence            65           44444555566666543    489999999974

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=98.60  E-value=2.3e-07  Score=89.92  Aligned_cols=211  Identities=18%  Similarity=0.209  Sum_probs=131.1

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCC-hHHHHhcCCCCCc--eEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMN-PELFLRVGIKPPK--GVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~~--~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      ...+.+.+..++.|.......+.+.+...... +..|...+.....  .++++||||+|||+.+..+|..++..+++.|.
T Consensus       311 ~~k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g~~v~E~Na  390 (871)
T KOG1968|consen  311 TEKYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELGFKVVEKNA  390 (871)
T ss_pred             ccccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhcccceeecCc
Confidence            35667777788888888888888877653111 1112221111111  36899999999999999999999999999998


Q ss_pred             cchhccccCh-------HHHHHHHHH-----HHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC
Q 022768          100 SAIIDKYIGE-------SARLIREMF-----GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD  167 (292)
Q Consensus       100 ~~~~~~~~~~-------~~~~~~~~~-----~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  167 (292)
                      ....+.....       ....+...+     .........+|++||+|.++.        .++.....+..+...     
T Consensus       391 s~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~--------~dRg~v~~l~~l~~k-----  457 (871)
T KOG1968|consen  391 SDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG--------EDRGGVSKLSSLCKK-----  457 (871)
T ss_pred             cccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc--------hhhhhHHHHHHHHHh-----
Confidence            8776543211       001111111     000112234999999999853        245555555555552     


Q ss_pred             CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHH
Q 022768          168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCT  247 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~  247 (292)
                        ...-+|.+||+.......-..  +.+..++|+.|+...+..-+..++......  ++-..+..++.. +++||++.+.
T Consensus       458 --s~~Piv~~cndr~~p~sr~~~--~~~~~l~f~kP~~~~i~~ri~si~~se~~k--i~~~~l~~~s~~-~~~DiR~~i~  530 (871)
T KOG1968|consen  458 --SSRPLVCTCNDRNLPKSRALS--RACSDLRFSKPSSELIRSRIMSICKSEGIK--ISDDVLEEISKL-SGGDIRQIIM  530 (871)
T ss_pred             --ccCCeEEEecCCCCccccchh--hhcceeeecCCcHHHHHhhhhhhhccccee--cCcHHHHHHHHh-cccCHHHHHH
Confidence              234588899887665543333  445778999999988877666555432222  333444444442 4559999888


Q ss_pred             HHHHHH
Q 022768          248 EAGMSA  253 (292)
Q Consensus       248 ~a~~~a  253 (292)
                      ....+.
T Consensus       531 ~lq~~~  536 (871)
T KOG1968|consen  531 QLQFWS  536 (871)
T ss_pred             HHhhhh
Confidence            887774

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=98.59  E-value=3e-07  Score=84.57  Aligned_cols=187  Identities=28%  Similarity=0.319  Sum_probs=109.8

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc--CCcEEEEeccchhccccChHHHH
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI--DANFLKVVSSAIIDKYIGESARL  113 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l--~~~~~~~~~~~~~~~~~~~~~~~  113 (292)
                      +.....+.+.+.+...           ....-++++.|.+|+||-.+++++-...  ..|++.+||..+.....++    
T Consensus       317 ~~d~s~a~l~rk~~rv-----------~~~~~pvll~GEtGtGKe~laraiH~~s~~~gpfvAvNCaAip~~lies----  381 (606)
T COG3284         317 LLDPSRATLLRKAERV-----------AATDLPVLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPEALIES----  381 (606)
T ss_pred             ccCHHHHHHHHHHHHH-----------hhcCCCeEecCCcchhHHHHHHHHHhcccccCCeEEEEeccchHHhhhH----
Confidence            4555555555544432           2335679999999999999999999766  4589999998876543332    


Q ss_pred             HHHHHHHhh----------------hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-----CCCCCe
Q 022768          114 IREMFGYAR----------------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-----DQLGKV  172 (292)
Q Consensus       114 ~~~~~~~~~----------------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-----~~~~~~  172 (292)
                        ++|.+..                ....+.||+||+..|           .-..|..|+..+.+....     ...=.+
T Consensus       382 --ELFGy~~GafTga~~kG~~g~~~~A~gGtlFldeIgd~-----------p~~~Qs~LLrVl~e~~v~p~g~~~~~vdi  448 (606)
T COG3284         382 --ELFGYVAGAFTGARRKGYKGKLEQADGGTLFLDEIGDM-----------PLALQSRLLRVLQEGVVTPLGGTRIKVDI  448 (606)
T ss_pred             --HHhccCccccccchhccccccceecCCCccHHHHhhhc-----------hHHHHHHHHHHHhhCceeccCCcceeEEE
Confidence              3443321                234479999999988           888999999999875321     111157


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcce-------EEEccCCCHHHHH---HHHHHHHcCc-cCCCCCCHHHHHHHcCCC---C
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDR-------KIEIPLPNEQSRM---EILKIHAAGI-AKHGEIDYEAVVKLAEGF---N  238 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~-------~i~l~~p~~~~r~---~i~~~~~~~~-~~~~~~~~~~l~~~~~g~---~  238 (292)
                      .||++|+..-   ..+...++|..       ...+..|...+|.   .++.+++... ...-.++-+.+..+..--   |
T Consensus       449 rvi~ath~dl---~~lv~~g~fredLyyrL~~~~i~lP~lr~R~d~~~~l~~~~~~~~~~~~~l~~~~~~~l~~~~WPGN  525 (606)
T COG3284         449 RVIAATHRDL---AQLVEQGRFREDLYYRLNAFVITLPPLRERSDRIPLLDRILKRENDWRLQLDDDALARLLAYRWPGN  525 (606)
T ss_pred             EEEeccCcCH---HHHHHcCCchHHHHHHhcCeeeccCchhcccccHHHHHHHHHHccCCCccCCHHHHHHHHhCCCCCc
Confidence            7888887531   11222223321       2334445555554   3444444322 222345555555554433   4


Q ss_pred             HHHHHHHHHHHHHHH
Q 022768          239 GADLRNVCTEAGMSA  253 (292)
Q Consensus       239 ~~di~~l~~~a~~~a  253 (292)
                      .++++++++.+...+
T Consensus       526 irel~~v~~~~~~l~  540 (606)
T COG3284         526 IRELDNVIERLAALS  540 (606)
T ss_pred             HHHHHHHHHHHHHcC
Confidence            555555555555433

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=98.57  E-value=1.9e-07  Score=77.82  Aligned_cols=58  Identities=22%  Similarity=0.322  Sum_probs=43.4

Q ss_pred             HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCCh
Q 022768          115 REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDP  186 (292)
Q Consensus       115 ~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~  186 (292)
                      +.+++++....|.+++|||-          ..+.+...+..+.+++..+..    .++.|+..+++...+..
T Consensus       147 RV~lARAL~~~p~lllLDEP----------~~gvD~~~~~~i~~lL~~l~~----eg~tIl~vtHDL~~v~~  204 (254)
T COG1121         147 RVLLARALAQNPDLLLLDEP----------FTGVDVAGQKEIYDLLKELRQ----EGKTVLMVTHDLGLVMA  204 (254)
T ss_pred             HHHHHHHhccCCCEEEecCC----------cccCCHHHHHHHHHHHHHHHH----CCCEEEEEeCCcHHhHh
Confidence            44556666788999999994          345588889999999988753    26778888888765544

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=98.50  E-value=5.3e-07  Score=74.25  Aligned_cols=78  Identities=19%  Similarity=0.399  Sum_probs=51.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchh-ccccC----------------------hHHHHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAII-DKYIG----------------------ESARLIR  115 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~-~~~~~----------------------~~~~~~~  115 (292)
                      |++.+..++|+||||+|||+++..++...   +..+++++...+. .....                      +....+.
T Consensus         8 Gi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~~~~~rl~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~   87 (209)
T TIGR02237         8 GVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIAEDRPERALSNFIVFEVFDFDEQGVAIQ   87 (209)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCCHHHHHHHHHhChHHHhcCEEEEECCCHHHHHHHHH
Confidence            67888899999999999999999988644   5677888776411 10000                      0111133


Q ss_pred             HHHHHhhhCCCEEEEEcccccccC
Q 022768          116 EMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       116 ~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      .+...+....+++|+||-+..++.
T Consensus        88 ~l~~~~~~~~~~lvVIDSis~l~~  111 (209)
T TIGR02237        88 KTSKFIDRDSASLVVVDSFTALYR  111 (209)
T ss_pred             HHHHHHhhcCccEEEEeCcHHHhH
Confidence            333334444688999999998753

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=98.43  E-value=2.7e-06  Score=75.85  Aligned_cols=78  Identities=21%  Similarity=0.411  Sum_probs=52.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcccc------Ch--------HHHHHHHHHHHhhhC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYI------GE--------SARLIREMFGYARDH  124 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~------~~--------~~~~~~~~~~~~~~~  124 (292)
                      |+.++..++|.|+||+|||+++..++..+   +.++++++..+......      +.        ....+..+...+...
T Consensus        78 Gi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EEs~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~  157 (372)
T cd01121          78 GLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEESPEQIKLRADRLGISTENLYLLAETNLEDILASIEEL  157 (372)
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCcCHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHHhc
Confidence            57888889999999999999999998765   34677776543221100      00        011234455555566


Q ss_pred             CCEEEEEcccccccC
Q 022768          125 QPCIIFMDEIDAIGG  139 (292)
Q Consensus       125 ~~~il~lDe~d~l~~  139 (292)
                      .|.+|+||+++.+..
T Consensus       158 ~~~lVVIDSIq~l~~  172 (372)
T cd01121         158 KPDLVIIDSIQTVYS  172 (372)
T ss_pred             CCcEEEEcchHHhhc
Confidence            889999999998854

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.42  E-value=4.6e-07  Score=66.30  Aligned_cols=23  Identities=43%  Similarity=0.959  Sum_probs=20.8

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcC
Q 022768           69 VLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      |+|+|+||+|||++++.+++.+.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHH
Confidence            57999999999999999998774

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=98.42  E-value=1e-05  Score=66.70  Aligned_cols=139  Identities=12%  Similarity=0.076  Sum_probs=95.0

Q ss_pred             CCceEEEEcCCC-ChHHHHHHHHHHhcCC---------cEEEEeccchhcc-ccChHHHHHHHHHHHhh----hCCCEEE
Q 022768           65 PPKGVLLYGPPG-TGKTLLARAIASNIDA---------NFLKVVSSAIIDK-YIGESARLIREMFGYAR----DHQPCII  129 (292)
Q Consensus        65 ~~~~vll~G~~G-~GKT~l~~~la~~l~~---------~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~----~~~~~il  129 (292)
                      -.+.+||.|..+ +||..++..++..+-+         .+..+........ ...-..+.++++.....    .....|+
T Consensus        14 LshAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~~~p~~g~~KVi   93 (263)
T PRK06581         14 LYNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLSKTSAISGYKVA   93 (263)
T ss_pred             chheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHhhCcccCCcEEE
Confidence            356799999998 9999998888877633         2333322110000 00012333444444332    3456899


Q ss_pred             EEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHH
Q 022768          130 FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRM  209 (292)
Q Consensus       130 ~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~  209 (292)
                      +|+++|.+           ......+|+..++     .+++++.+|.+|+.++.+.+.++|  || ..+.++.|+.....
T Consensus        94 II~~ae~m-----------t~~AANALLKtLE-----EPP~~t~fILit~~~~~LLpTIrS--RC-q~i~~~~p~~~~~~  154 (263)
T PRK06581         94 IIYSAELM-----------NLNAANSCLKILE-----DAPKNSYIFLITSRAASIISTIRS--RC-FKINVRSSILHAYN  154 (263)
T ss_pred             EEechHHh-----------CHHHHHHHHHhhc-----CCCCCeEEEEEeCChhhCchhHhh--ce-EEEeCCCCCHHHHH
Confidence            99999999           6666677766665     355678888888889999999999  87 78899999998888


Q ss_pred             HHHHHHHcCccCC
Q 022768          210 EILKIHAAGIAKH  222 (292)
Q Consensus       210 ~i~~~~~~~~~~~  222 (292)
                      +.+...+......
T Consensus       155 e~~~~~~~p~~~~  167 (263)
T PRK06581        155 ELYSQFIQPIADN  167 (263)
T ss_pred             HHHHHhccccccc
Confidence            8888777654433

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=98.41  E-value=3.7e-06  Score=66.42  Aligned_cols=107  Identities=17%  Similarity=0.188  Sum_probs=68.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchhc--------ccc-----ChHHHHHHHHHHHhhhCCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAIID--------KYI-----GESARLIREMFGYARDHQP  126 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~~--------~~~-----~~~~~~~~~~~~~~~~~~~  126 (292)
                      .+.++..+.|.||+|+||||+++.++......  -+.++...+..        ...     =......+..+..+....|
T Consensus        22 ~i~~Ge~~~l~G~nGsGKSTLl~~i~G~~~~~~G~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~~qrl~laral~~~p  101 (163)
T cd03216          22 SVRRGEVHALLGENGAGKSTLMKILSGLYKPDSGEILVDGKEVSFASPRDARRAGIAMVYQLSVGERQMVEIARALARNA  101 (163)
T ss_pred             EEeCCCEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECCEECCcCCHHHHHhcCeEEEEecCHHHHHHHHHHHHHhcCC
Confidence            36778899999999999999999999876321  12222211110        000     0112233455666677889


Q ss_pred             EEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          127 CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       127 ~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      .++++||...          ..+......+.+++..+..    .+..+|.++++.+
T Consensus       102 ~illlDEP~~----------~LD~~~~~~l~~~l~~~~~----~~~tiii~sh~~~  143 (163)
T cd03216         102 RLLILDEPTA----------ALTPAEVERLFKVIRRLRA----QGVAVIFISHRLD  143 (163)
T ss_pred             CEEEEECCCc----------CCCHHHHHHHHHHHHHHHH----CCCEEEEEeCCHH
Confidence            9999999643          3377777788888876531    2456777777654

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK11823 DNA repair protein RadA; Provisional

Probab=98.41  E-value=3.2e-06  Score=77.37  Aligned_cols=79  Identities=20%  Similarity=0.360  Sum_probs=54.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccCh--------------HHHHHHHHHHHhhhC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGE--------------SARLIREMFGYARDH  124 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~  124 (292)
                      |+.++..++|+|+||+|||+++..++...   +.++++++..+........              ....+..++..+...
T Consensus        76 Gi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~  155 (446)
T PRK11823         76 GLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEE  155 (446)
T ss_pred             CccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccccHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHHhh
Confidence            57888889999999999999999998765   5677777755432211000              001133444555556


Q ss_pred             CCEEEEEcccccccCC
Q 022768          125 QPCIIFMDEIDAIGGR  140 (292)
Q Consensus       125 ~~~il~lDe~d~l~~~  140 (292)
                      .|.+|+||.+..+...
T Consensus       156 ~~~lVVIDSIq~l~~~  171 (446)
T PRK11823        156 KPDLVVIDSIQTMYSP  171 (446)
T ss_pred             CCCEEEEechhhhccc
Confidence            7899999999988643

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=98.40  E-value=6.4e-07  Score=83.10  Aligned_cols=107  Identities=27%  Similarity=0.423  Sum_probs=68.3

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-------c----EEEEe------ccchhc--cc------cCh------
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-------N----FLKVV------SSAIID--KY------IGE------  109 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-------~----~~~~~------~~~~~~--~~------~~~------  109 (292)
                      +.++++..++|.|++|+|||++.|++|..-..       |    .+.+.      ...+..  .+      .++      
T Consensus       414 ~~v~~G~~llI~G~SG~GKTsLlRaiaGLWP~g~G~I~~P~~~~~lflpQ~PY~p~GtLre~l~YP~~~~~~~d~~l~~v  493 (604)
T COG4178         414 FEVRPGERLLITGESGAGKTSLLRALAGLWPWGSGRISMPADSALLFLPQRPYLPQGTLREALCYPNAAPDFSDAELVAV  493 (604)
T ss_pred             eeeCCCCEEEEECCCCCCHHHHHHHHhccCccCCCceecCCCCceEEecCCCCCCCccHHHHHhCCCCCCCCChHHHHHH
Confidence            34788999999999999999999999965411       1    11111      000000  00      000      


Q ss_pred             ------------------------HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          110 ------------------------SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       110 ------------------------~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                                              ....-+..|.++...+|.++||||+-          +.-+.+.+..++++++.-  
T Consensus       494 L~~vgL~~L~~rl~~~~~W~~vLS~GEqQRlafARilL~kP~~v~LDEAT----------sALDe~~e~~l~q~l~~~--  561 (604)
T COG4178         494 LHKVGLGDLAERLDEEDRWDRVLSGGEQQRLAFARLLLHKPKWVFLDEAT----------SALDEETEDRLYQLLKEE--  561 (604)
T ss_pred             HHHcCcHHHHHHHhccCcHhhhcChhHHHHHHHHHHHHcCCCEEEEecch----------hccChHHHHHHHHHHHhh--
Confidence                                    01112445666677899999999973          334777888888888752  


Q ss_pred             CCCCCCeEEEEEeCCCC
Q 022768          166 FDQLGKVKMIMATNRPD  182 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~  182 (292)
                         -+++.+|..++.+.
T Consensus       562 ---lp~~tvISV~Hr~t  575 (604)
T COG4178         562 ---LPDATVISVGHRPT  575 (604)
T ss_pred             ---CCCCEEEEeccchh
Confidence               25778888888654

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=98.40  E-value=3.4e-06  Score=68.05  Aligned_cols=52  Identities=21%  Similarity=0.394  Sum_probs=35.3

Q ss_pred             HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          115 REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       115 ~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      +-.+.++....|.++++||.-          +.-+++.....+..+..+..    .+..+|+.|+.
T Consensus       144 RVAIARALaM~P~vmLFDEPT----------SALDPElv~EVL~vm~~LA~----eGmTMivVTHE  195 (240)
T COG1126         144 RVAIARALAMDPKVMLFDEPT----------SALDPELVGEVLDVMKDLAE----EGMTMIIVTHE  195 (240)
T ss_pred             HHHHHHHHcCCCCEEeecCCc----------ccCCHHHHHHHHHHHHHHHH----cCCeEEEEech
Confidence            344555666889999999963          44477777777777766542    35667777764

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=98.39  E-value=4.8e-06  Score=72.82  Aligned_cols=161  Identities=22%  Similarity=0.289  Sum_probs=88.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcE--EEEeccchhccc---------------cC----hHHHHHHHHHHHhh
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANF--LKVVSSAIIDKY---------------IG----ESARLIREMFGYAR  122 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~--~~~~~~~~~~~~---------------~~----~~~~~~~~~~~~~~  122 (292)
                      .++++++|||.-|+|||+|+..+...+....  -+++...+....               .+    ..-+-+.-+.+.+.
T Consensus       112 ~~PkGlYlYG~VGcGKTmLMDlFy~~~~~i~rkqRvHFh~fM~~VH~r~H~~k~~~~~~~~~~a~~~~~Dpl~~vA~eIa  191 (467)
T KOG2383|consen  112 GPPKGLYLYGSVGCGKTMLMDLFYDALPPIWRKQRVHFHGFMLSVHKRMHELKQEQGAEKPGYAKSWEIDPLPVVADEIA  191 (467)
T ss_pred             CCCceEEEecccCcchhHHHHHHhhcCCchhhhhhhhHHHHHHHHHHHHHHHHHhccccCccccccccCCccHHHHHHHh
Confidence            3478999999999999999999997664311  111111111100               00    00011111111111


Q ss_pred             hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC-CCCCChhhcCCCCcceEEEcc
Q 022768          123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR-PDVLDPALLRPGRLDRKIEIP  201 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~-~~~l~~~l~~~~r~~~~i~l~  201 (292)
                       ..-.+|++||+..-           +-...-+|..++..+-.    .++++++|+|+ |+++...-..+.-|       
T Consensus       192 -~ea~lLCFDEfQVT-----------DVADAmiL~rLf~~Lf~----~GvVlvATSNR~P~dLYknGlQR~~F-------  248 (467)
T KOG2383|consen  192 -EEAILLCFDEFQVT-----------DVADAMILKRLFEHLFK----NGVVLVATSNRAPEDLYKNGLQRENF-------  248 (467)
T ss_pred             -hhceeeeechhhhh-----------hHHHHHHHHHHHHHHHh----CCeEEEEeCCCChHHHhhcchhhhhh-------
Confidence             22369999999765           44444455566655432    48999999987 45555433331123       


Q ss_pred             CCCHHHHHHHHHHHHcCccCCCCCCHHHHHH-HcCCC---CHHHHHHHHHHHHH
Q 022768          202 LPNEQSRMEILKIHAAGIAKHGEIDYEAVVK-LAEGF---NGADLRNVCTEAGM  251 (292)
Q Consensus       202 ~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~-~~~g~---~~~di~~l~~~a~~  251 (292)
                          ---..+++.++.-..+...+|+...+. ...+|   +..|...++++-..
T Consensus       249 ----~PfI~~L~~rc~vi~ldS~vDYR~~~~~~~~~~yf~~~~d~~~~l~~~fk  298 (467)
T KOG2383|consen  249 ----IPFIALLEERCKVIQLDSGVDYRRKAKSAGENYYFISETDVETVLKEWFK  298 (467)
T ss_pred             ----hhHHHHHHHhheEEecCCccchhhccCCCCceeEecChhhHHHHHHHHHH
Confidence                123467777787777777777762221 11222   23367777766654

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.38  E-value=7.7e-07  Score=73.38  Aligned_cols=29  Identities=34%  Similarity=0.479  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+||||||+++.+|.-.
T Consensus        25 ~v~~GEfvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          25 SVEKGEFVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778889999999999999999999655

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=98.38  E-value=3.4e-06  Score=69.28  Aligned_cols=62  Identities=18%  Similarity=0.328  Sum_probs=41.6

Q ss_pred             HHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhc
Q 022768          116 EMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALL  189 (292)
Q Consensus       116 ~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~  189 (292)
                      .++.++.-..|.+|+|||--          .+.+....+.+.+.+..+-.  ..+...+|..|+..+++++.+-
T Consensus       180 vLiaRALv~~P~LLiLDEP~----------~GLDl~~re~ll~~l~~~~~--~~~~~~ll~VtHh~eEi~~~~t  241 (257)
T COG1119         180 VLIARALVKDPELLILDEPA----------QGLDLIAREQLLNRLEELAA--SPGAPALLFVTHHAEEIPPCFT  241 (257)
T ss_pred             HHHHHHHhcCCCEEEecCcc----------ccCChHHHHHHHHHHHHHhc--CCCCceEEEEEcchhhcccccc
Confidence            34555556789999999952          22355555667777766652  3345668888999988888554

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=98.37  E-value=4.4e-06  Score=66.71  Aligned_cols=107  Identities=20%  Similarity=0.149  Sum_probs=65.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccch---hccccChHHHHHHHHHHHhhhCCCEEEEEcccccc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAI---IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAI  137 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l  137 (292)
                      +.++..+.|.||+|+|||||++.++......  -+.++...+   .....=......+..+..+....|.++++||--. 
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~~~p~lllLDEPts-  100 (177)
T cd03222          22 VKEGEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSA-  100 (177)
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHhcCCCEEEEECCcc-
Confidence            5678889999999999999999999876322  122221111   0100001222334455566667889999999643 


Q ss_pred             cCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          138 GGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                               ..+......+.+++.....   ..+..+|.++++.+
T Consensus       101 ---------~LD~~~~~~l~~~l~~~~~---~~~~tiiivsH~~~  133 (177)
T cd03222         101 ---------YLDIEQRLNAARAIRRLSE---EGKKTALVVEHDLA  133 (177)
T ss_pred             ---------cCCHHHHHHHHHHHHHHHH---cCCCEEEEEECCHH
Confidence                     3366777777777766531   12245777777654

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=98.37  E-value=2.8e-05  Score=70.19  Aligned_cols=121  Identities=17%  Similarity=0.250  Sum_probs=74.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS  147 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~  147 (292)
                      .++|.||.++||||+++.+.+......++++..+....... ..+.+ ..+..........++|||++.+          
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~~~-l~d~~-~~~~~~~~~~~~yifLDEIq~v----------  106 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIE-LLDLL-RAYIELKEREKSYIFLDEIQNV----------  106 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcchhh-HHHHH-HHHHHhhccCCceEEEecccCc----------
Confidence            78999999999999999999888666777776665443211 11112 2222222224479999999986          


Q ss_pred             chHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC--CCCCChhhcCCCCcceEEEccCCCHHHHHH
Q 022768          148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNR--PDVLDPALLRPGRLDRKIEIPLPNEQSRME  210 (292)
Q Consensus       148 ~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~--~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~  210 (292)
                        ..+...+..+.+...     .++++.+++..  ...+...+..  |. ..+.+.|.+..+...
T Consensus       107 --~~W~~~lk~l~d~~~-----~~v~itgsss~ll~~~~~~~L~G--R~-~~~~l~PlSF~Efl~  161 (398)
T COG1373         107 --PDWERALKYLYDRGN-----LDVLITGSSSSLLSKEISESLAG--RG-KDLELYPLSFREFLK  161 (398)
T ss_pred             --hhHHHHHHHHHcccc-----ceEEEECCchhhhccchhhhcCC--Cc-eeEEECCCCHHHHHh
Confidence              445566666655421     13333332221  1234445544  63 778899999999865

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=98.35  E-value=5.7e-06  Score=66.66  Aligned_cols=102  Identities=21%  Similarity=0.214  Sum_probs=58.1

Q ss_pred             EEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc-------------------------------cChHH---
Q 022768           69 VLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY-------------------------------IGESA---  111 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~-------------------------------~~~~~---  111 (292)
                      ++|.||||+|||+++..++...   +.+++++...+.....                               .+...   
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~e~~~~~~~~~~~~~g~~~~~l~~~g~l~~~d~~~~~~s~~~~~~~~   81 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEGLLAIVDADPDEIGPAESSLRL   81 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEECCCCHHHHHHHHHHcCCChHHHHhcCCeEEEecCccccchhhhhhhH
Confidence            7899999999999998887644   5666666543221100                               00000   


Q ss_pred             HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          112 RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       112 ~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      ..+..+...+....|.+++||++..+...       ........+..++..+..    .++.+|++++..
T Consensus        82 ~~~~~i~~~~~~~~~~~lviD~~~~~~~~-------~~~~~~~~i~~l~~~l~~----~g~tvi~v~~~~  140 (187)
T cd01124          82 ELIQRLKDAIEEFKAKRVVIDSVSGLLLM-------EQSTARLEIRRLLFALKR----FGVTTLLTSEQS  140 (187)
T ss_pred             HHHHHHHHHHHHhCCCEEEEeCcHHHhhc-------ChHHHHHHHHHHHHHHHH----CCCEEEEEeccc
Confidence            11233444445567899999999876421       113333444555555432    245566666544

A related protein is found in archaea.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.34  E-value=1.2e-05  Score=61.84  Aligned_cols=25  Identities=36%  Similarity=0.619  Sum_probs=22.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...++++|+||+||||++.-++..+
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHH
Confidence            4569999999999999999999877

>TIGR02012 tigrfam_recA protein RecA

Probab=98.34  E-value=6.3e-06  Score=71.68  Aligned_cols=78  Identities=19%  Similarity=0.231  Sum_probs=51.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |++++..++|+||||+|||+|+-.++...   +.++++++..+....                .....+..+..+...++
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~  130 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVR  130 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhh
Confidence            47888899999999999999988877654   566777665432210                11112233333333344


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+.+|+||-+..+.+
T Consensus       131 ~~~~~lIVIDSv~al~~  147 (321)
T TIGR02012       131 SGAVDIIVVDSVAALVP  147 (321)
T ss_pred             ccCCcEEEEcchhhhcc
Confidence            45678999999998864

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=98.33  E-value=7e-06  Score=71.42  Aligned_cols=78  Identities=18%  Similarity=0.227  Sum_probs=51.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |++.++.+.|+||||+|||++|-.++...   +..+++++..+....                .+...+..+..+-..+.
T Consensus        51 Glp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~  130 (325)
T cd00983          51 GYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSLVR  130 (325)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHHHh
Confidence            47788889999999999999999888544   667777765432110                11112223333333334


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+++|+||-+..+.+
T Consensus       131 s~~~~lIVIDSvaal~~  147 (325)
T cd00983         131 SGAVDLIVVDSVAALVP  147 (325)
T ss_pred             ccCCCEEEEcchHhhcc
Confidence            45678999999998875

RecA couples ATP hydrolysis to DNA strand exchange.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.32  E-value=1e-05  Score=81.66  Aligned_cols=139  Identities=20%  Similarity=0.260  Sum_probs=97.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc--ccCh----HHH---HHHHHHHHhhhCCCEEEEEccc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK--YIGE----SAR---LIREMFGYARDHQPCIIFMDEI  134 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~--~~~~----~~~---~~~~~~~~~~~~~~~il~lDe~  134 (292)
                      .....+||.||.-+|||++..++|+..|..+++++..++.+.  +.|.    ...   .-..++-.+.... -.++|||+
T Consensus       886 ~~~fP~LiQGpTSSGKTSMI~yla~~tghkfVRINNHEHTdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~G-yWIVLDEL  964 (4600)
T COG5271         886 LSNFPLLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEGVLVEALRRG-YWIVLDEL  964 (4600)
T ss_pred             hcCCcEEEecCCCCCcchHHHHHHHHhCccEEEecCcccchHHHHhhceeecCCCceeeehhHHHHHHhcC-cEEEeecc
Confidence            346679999999999999999999999999999997766431  1111    000   0011222222222 58999999


Q ss_pred             ccccCCcCCCCCcchHHHHHHHHHHHHHhh---------CCCCCCCeEEEEEeCCCC------CCChhhcCCCCcceEEE
Q 022768          135 DAIGGRRFSEGTSADREIQRTLMELLNQLD---------GFDQLGKVKMIMATNRPD------VLDPALLRPGRLDRKIE  199 (292)
Q Consensus       135 d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~---------~~~~~~~~~vi~t~~~~~------~l~~~l~~~~r~~~~i~  199 (292)
                      +.-           .....++|..+++.-.         ...+++.+.+.+|-|+|.      .++.+++.  || ..++
T Consensus       965 NLA-----------pTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRN--RF-lE~h 1030 (4600)
T COG5271         965 NLA-----------PTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRN--RF-LEMH 1030 (4600)
T ss_pred             ccC-----------cHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHh--hh-Hhhh
Confidence            765           6778888888887532         225666788888888764      36778887  88 7788


Q ss_pred             ccCCCHHHHHHHHHHHHc
Q 022768          200 IPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       200 l~~p~~~~r~~i~~~~~~  217 (292)
                      |..-..++...|+...+.
T Consensus      1031 FddipedEle~ILh~rc~ 1048 (4600)
T COG5271        1031 FDDIPEDELEEILHGRCE 1048 (4600)
T ss_pred             cccCcHHHHHHHHhccCc
Confidence            888788888888776553

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.31  E-value=1e-05  Score=78.28  Aligned_cols=199  Identities=22%  Similarity=0.262  Sum_probs=124.1

Q ss_pred             ccccccc-HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEEec
Q 022768           31 YSAVGGL-SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVS   99 (292)
Q Consensus        31 ~~~l~g~-~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~~~   99 (292)
                      ++.++|. ++.++++.+.+.+             ...++-+|+|.||+|||.++.-++...          +..++.++.
T Consensus       185 ldPvigr~deeirRvi~iL~R-------------rtk~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~  251 (898)
T KOG1051|consen  185 LDPVIGRHDEEIRRVIEILSR-------------KTKNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDF  251 (898)
T ss_pred             CCCccCCchHHHHHHHHHHhc-------------cCCCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEh
Confidence            5778888 8888888888765             233678999999999999999999876          234555555


Q ss_pred             cchh--ccccChHHHHHHHHHHHhh-hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768          100 SAII--DKYIGESARLIREMFGYAR-DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus       100 ~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      ..+.  ..+.++.+..++.+...+. .....||+|||+|.+.+....       ..   .....+.+......+.+++|+
T Consensus       252 g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg~g~~-------~~---~~d~~nlLkp~L~rg~l~~IG  321 (898)
T KOG1051|consen  252 GSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGELHWLVGSGSN-------YG---AIDAANLLKPLLARGGLWCIG  321 (898)
T ss_pred             hhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecceeeeecCCCc-------ch---HHHHHHhhHHHHhcCCeEEEe
Confidence            5433  3456778888888888877 445678899999999654322       11   222222222112234599999


Q ss_pred             EeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC--------CCCCHHHHH--HHcCCCCHHH
Q 022768          177 ATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH--------GEIDYEAVV--KLAEGFNGAD  241 (292)
Q Consensus       177 t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~--------~~~~~~~l~--~~~~g~~~~d  241 (292)
                      ||...+     .-+|++.+  || ..+.++.|+.+....++......+..+        .......+.  ..+..+-+.-
T Consensus       322 atT~e~Y~k~iekdPalEr--rw-~l~~v~~pS~~~~~~iL~~l~~~~e~~hg~~~s~~a~~~a~~~s~~~~t~r~lpd~  398 (898)
T KOG1051|consen  322 ATTLETYRKCIEKDPALER--RW-QLVLVPIPSVENLSLILPGLSERYEVHHGVRISDESLFSAAQLSARYITLSFLPDC  398 (898)
T ss_pred             cccHHHHHHHHhhCcchhh--Cc-ceeEeccCcccchhhhhhhhhhhhccccCCcccccccccccchhhhhcccCcCchh
Confidence            886422     35788887  88 556788888766555655444331111        001111122  2233445556


Q ss_pred             HHHHHHHHHHHHHH
Q 022768          242 LRNVCTEAGMSAIR  255 (292)
Q Consensus       242 i~~l~~~a~~~a~~  255 (292)
                      ...++++|......
T Consensus       399 aidl~dEa~a~~~~  412 (898)
T KOG1051|consen  399 AIDLEDEAAALVKS  412 (898)
T ss_pred             cccHHHHHHHHHhh
Confidence            66777777765533

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=98.31  E-value=8.8e-06  Score=62.86  Aligned_cols=104  Identities=21%  Similarity=0.264  Sum_probs=64.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE--EEEeccchhcccc-ChHHHHHHHHHHHhhhCCCEEEEEccccccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANF--LKVVSSAIIDKYI-GESARLIREMFGYARDHQPCIIFMDEIDAIG  138 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~--~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~  138 (292)
                      .+.++..+.|.|++|+||||+++.++......-  +.++......... =......+..+..+....|.++++||...  
T Consensus        22 ~~~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~~i~~~~~lS~G~~~rv~laral~~~p~illlDEP~~--   99 (144)
T cd03221          22 TINPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQLSGGEKMRLALAKLLLENPNLLLLDEPTN--   99 (144)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCeEEEEEEccCCHHHHHHHHHHHHHhcCCCEEEEeCCcc--
Confidence            357788999999999999999999998764321  1111110000000 01222333445666667889999999643  


Q ss_pred             CCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          139 GRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       139 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                              ..+......+.+++..+       +..++.++++.+
T Consensus       100 --------~LD~~~~~~l~~~l~~~-------~~til~~th~~~  128 (144)
T cd03221         100 --------HLDLESIEALEEALKEY-------PGTVILVSHDRY  128 (144)
T ss_pred             --------CCCHHHHHHHHHHHHHc-------CCEEEEEECCHH
Confidence                    23666677777777654       135777777654

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=98.30  E-value=1.9e-05  Score=68.71  Aligned_cols=163  Identities=18%  Similarity=0.187  Sum_probs=93.3

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc------
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK------  105 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~------  105 (292)
                      ..+.+.+.+++.+...+-.- .         -.-+.+++|+|.+|||||.+++.+.+.++.+.+.+++.+....      
T Consensus         6 ~~v~~Re~qi~~L~~Llg~~-~---------~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~   75 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGNN-S---------CTIPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEK   75 (438)
T ss_pred             cCccchHHHHHHHHHHhCCC-C---------cccceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHH
Confidence            45678888888888876331 0         0234567999999999999999999999888877776544321      


Q ss_pred             ---------ccChH----HHHHHHH---HHH---hhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          106 ---------YIGES----ARLIREM---FGY---ARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       106 ---------~~~~~----~~~~~~~---~~~---~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                               ..|..    ...+...   +..   +... ..-.|++|.+|.+-        +.+......+..+...   
T Consensus        76 IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lr--------D~~a~ll~~l~~L~el---  144 (438)
T KOG2543|consen   76 ILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALR--------DMDAILLQCLFRLYEL---  144 (438)
T ss_pred             HHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhh--------ccchHHHHHHHHHHHH---
Confidence                     01110    1111111   111   1111 23578999999982        2223333333333333   


Q ss_pred             CCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          166 FDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                       .+.+.+.++.+....+..-..=.+ ...-.+++||.|+.++...|+.+--.
T Consensus       145 -~~~~~i~iils~~~~e~~y~~n~g-~~~i~~l~fP~Ys~~e~~~Il~~~~p  194 (438)
T KOG2543|consen  145 -LNEPTIVIILSAPSCEKQYLINTG-TLEIVVLHFPQYSVEETQVILSRDNP  194 (438)
T ss_pred             -hCCCceEEEEeccccHHHhhcccC-CCCceEEecCCCCHHHHHHHHhcCCc
Confidence             223455555555443321110001 12236789999999999998875443

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=98.30  E-value=1.2e-05  Score=67.11  Aligned_cols=110  Identities=18%  Similarity=0.335  Sum_probs=61.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc-----------------------------c--
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY-----------------------------I--  107 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~-----------------------------~--  107 (292)
                      |++++..+++.|++|+|||+++..++...   +..++++...+.....                             .  
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~   99 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGN   99 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccCh
Confidence            46778899999999999999976555433   4555555533211100                             0  


Q ss_pred             ChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          108 GESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      ......+..+........|.+++||++-.+...      ..+......+.+++..+..   . +..+++|++..
T Consensus       100 ~~~~~~l~~il~~~~~~~~~~lVIDe~t~~l~~------~~d~~~~~~l~~~l~~l~~---~-g~tvi~t~~~~  163 (230)
T PRK08533        100 SEKRKFLKKLMNTRRFYEKDVIIIDSLSSLISN------DASEVAVNDLMAFFKRISS---L-NKVIILTANPK  163 (230)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEECccHHhcC------CcchHHHHHHHHHHHHHHh---C-CCEEEEEeccc
Confidence            001223333444444456889999999765311      1122333455566555432   1 33566666543

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.30  E-value=2.6e-06  Score=71.65  Aligned_cols=85  Identities=27%  Similarity=0.548  Sum_probs=60.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHH------hcCCcEEEEeccchhccccChHHHHHHHHHHHhh-------------
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIAS------NIDANFLKVVSSAIIDKYIGESARLIREMFGYAR-------------  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~------~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------  122 (292)
                      .+.+...+|+.||.|.|||.+++.+..      .+..+++++||..+.+...      +..+|..++             
T Consensus       204 a~rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~a------msalfghvkgaftga~~~r~gl  277 (531)
T COG4650         204 AIRSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTA------MSALFGHVKGAFTGARESREGL  277 (531)
T ss_pred             HhhccCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchH------HHHHHhhhccccccchhhhhhh
Confidence            445566799999999999999998873      4577899999999876432      223333332             


Q ss_pred             --hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHh
Q 022768          123 --DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQL  163 (292)
Q Consensus       123 --~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~  163 (292)
                        ....++||+||+..++           ...+..|+..+++.
T Consensus       278 lrsadggmlfldeigelg-----------adeqamllkaieek  309 (531)
T COG4650         278 LRSADGGMLFLDEIGELG-----------ADEQAMLLKAIEEK  309 (531)
T ss_pred             hccCCCceEehHhhhhcC-----------ccHHHHHHHHHHhh
Confidence              2456899999998883           34455666666654

>PRK04841 transcriptional regulator MalT; Provisional

Probab=98.29  E-value=6e-05  Score=75.48  Aligned_cols=183  Identities=18%  Similarity=0.217  Sum_probs=100.1

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc-
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-  105 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~-  105 (292)
                      ||..-..++-.+.-.+.|...                ...+.++|+||+|.||||++..++...+ ++.-+......+. 
T Consensus         9 ~p~~~~~~~~R~rl~~~l~~~----------------~~~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l~~~d~~~   71 (903)
T PRK04841          9 RPVRLHNTVVRERLLAKLSGA----------------NNYRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSLDESDNQP   71 (903)
T ss_pred             CCCCccccCcchHHHHHHhcc----------------cCCCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEecCcccCCH
Confidence            333345666666555555332                2345799999999999999999998766 5444333211100 


Q ss_pred             --c----c--------C---------------hHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHH
Q 022768          106 --Y----I--------G---------------ESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRT  155 (292)
Q Consensus       106 --~----~--------~---------------~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~  155 (292)
                        +    .        +               .....+..++..... ..|.+|+|||+|.+-          +......
T Consensus        72 ~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~----------~~~~~~~  141 (903)
T PRK04841         72 ERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLIT----------NPEIHEA  141 (903)
T ss_pred             HHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCC----------ChHHHHH
Confidence              0    0        0               001112222222222 568899999999871          2334445


Q ss_pred             HHHHHHHhhCCCCCCCeEEEEEeCCCCCCC-hhhcCCCCcceEEEcc--CCCHHHHHHHHHHHHcCccCCCCCCHHHHHH
Q 022768          156 LMELLNQLDGFDQLGKVKMIMATNRPDVLD-PALLRPGRLDRKIEIP--LPNEQSRMEILKIHAAGIAKHGEIDYEAVVK  232 (292)
Q Consensus       156 l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~-~~l~~~~r~~~~i~l~--~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~  232 (292)
                      +..++...     .+++.+|++++....++ ..++..+.+ ..+...  +.+.++..+++.......  ........+..
T Consensus       142 l~~l~~~~-----~~~~~lv~~sR~~~~~~~~~l~~~~~~-~~l~~~~l~f~~~e~~~ll~~~~~~~--~~~~~~~~l~~  213 (903)
T PRK04841        142 MRFFLRHQ-----PENLTLVVLSRNLPPLGIANLRVRDQL-LEIGSQQLAFDHQEAQQFFDQRLSSP--IEAAESSRLCD  213 (903)
T ss_pred             HHHHHHhC-----CCCeEEEEEeCCCCCCchHhHHhcCcc-eecCHHhCCCCHHHHHHHHHhccCCC--CCHHHHHHHHH
Confidence            55666542     24566666665532232 122211122 233333  779999999988765421  12334577888


Q ss_pred             HcCCCCHHHHHHH
Q 022768          233 LAEGFNGADLRNV  245 (292)
Q Consensus       233 ~~~g~~~~di~~l  245 (292)
                      .+.|+ |.-++.+
T Consensus       214 ~t~Gw-p~~l~l~  225 (903)
T PRK04841        214 DVEGW-ATALQLI  225 (903)
T ss_pred             HhCCh-HHHHHHH
Confidence            88884 4344433

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=98.28  E-value=8.1e-06  Score=66.62  Aligned_cols=31  Identities=26%  Similarity=0.553  Sum_probs=25.0

Q ss_pred             hcCCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           60 RVGIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        60 ~~~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.+..+..++|.||+|+||||+++.++...
T Consensus        19 ~i~l~~g~~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          19 DIDMEKKNGILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             eEEEcCCcEEEEECCCCCChHHHHHHHHHHH
Confidence            3445556789999999999999999998533

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=98.28  E-value=1.1e-05  Score=63.27  Aligned_cols=107  Identities=27%  Similarity=0.394  Sum_probs=65.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcE--EEEeccchhc-------c---cc--ChHHHHHHHHHHHhhhCCCEE
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANF--LKVVSSAIID-------K---YI--GESARLIREMFGYARDHQPCI  128 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~--~~~~~~~~~~-------~---~~--~~~~~~~~~~~~~~~~~~~~i  128 (292)
                      +.++..+.|.|++|+||||+++.++..+...-  +.++......       .   +.  =......+..+..+....|.+
T Consensus        22 i~~g~~~~i~G~nGsGKStll~~l~g~~~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~r~~l~~~l~~~~~i  101 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARALLLNPDL  101 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCCCCccEEEECCEEcccCCHHHHHhceEEEeeCCHHHHHHHHHHHHHhcCCCE
Confidence            56788899999999999999999998774322  2333221110       0   00  011222334455556667899


Q ss_pred             EEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          129 IFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       129 l~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      +++||...=          .+......+.+++.....    .+..++.+++..+.
T Consensus       102 ~ilDEp~~~----------lD~~~~~~l~~~l~~~~~----~~~tii~~sh~~~~  142 (157)
T cd00267         102 LLLDEPTSG----------LDPASRERLLELLRELAE----EGRTVIIVTHDPEL  142 (157)
T ss_pred             EEEeCCCcC----------CCHHHHHHHHHHHHHHHH----CCCEEEEEeCCHHH
Confidence            999997532          256666777777766532    13457777776543

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=98.27  E-value=1.5e-05  Score=62.99  Aligned_cols=54  Identities=20%  Similarity=0.386  Sum_probs=37.7

Q ss_pred             HHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          118 FGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       118 ~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      ++.+....|.+|+=||-          +...++.....++.++.+++.    .+..|+.+|++.+.++
T Consensus       148 IARAiV~~P~vLlADEP----------TGNLDp~~s~~im~lfeeinr----~GtTVl~ATHd~~lv~  201 (223)
T COG2884         148 IARAIVNQPAVLLADEP----------TGNLDPDLSWEIMRLFEEINR----LGTTVLMATHDLELVN  201 (223)
T ss_pred             HHHHHccCCCeEeecCC----------CCCCChHHHHHHHHHHHHHhh----cCcEEEEEeccHHHHH
Confidence            33444478899999984          444578888888888888753    3667888888654433

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=98.26  E-value=1.2e-05  Score=68.57  Aligned_cols=101  Identities=20%  Similarity=0.281  Sum_probs=62.9

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC---cEEEE
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA---NFLKV   97 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~---~~~~~   97 (292)
                      .+....+..+++++.-.++..+.|++.+..              +...++|.|++|+||||+++++...+..   .++.+
T Consensus        49 ~~~~~~~~~~l~~lg~~~~~~~~l~~~~~~--------------~~GlilisG~tGSGKTT~l~all~~i~~~~~~iiti  114 (264)
T cd01129          49 ILDKKNQILDLEKLGLKPENLEIFRKLLEK--------------PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITV  114 (264)
T ss_pred             EeCCccCCCCHHHcCCCHHHHHHHHHHHhc--------------CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEE
Confidence            333444456778876556666777666543              2456899999999999999999877743   23333


Q ss_pred             ecc-ch-----hccc-cChHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768           98 VSS-AI-----IDKY-IGESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        98 ~~~-~~-----~~~~-~~~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      ... ++     .... ...........+..+....|.+++++|+-
T Consensus       115 Edp~E~~~~~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR  159 (264)
T cd01129         115 EDPVEYQIPGINQVQVNEKAGLTFARGLRAILRQDPDIIMVGEIR  159 (264)
T ss_pred             CCCceecCCCceEEEeCCcCCcCHHHHHHHHhccCCCEEEeccCC
Confidence            211 11     1000 11112234566667777899999999994

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=98.26  E-value=6.4e-06  Score=67.69  Aligned_cols=30  Identities=27%  Similarity=0.405  Sum_probs=25.4

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.+.++..+.|.||+|||||||+..++.-.
T Consensus        26 l~i~~Ge~vaI~GpSGSGKSTLLniig~ld   55 (226)
T COG1136          26 LEIEAGEFVAIVGPSGSGKSTLLNLLGGLD   55 (226)
T ss_pred             EEEcCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            346778889999999999999999998533

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=98.26  E-value=9.9e-06  Score=64.64  Aligned_cols=107  Identities=15%  Similarity=0.163  Sum_probs=62.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-------------EEEEe---------ccch-hccccCh--HHHHHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-------------FLKVV---------SSAI-IDKYIGE--SARLIRE  116 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-------------~~~~~---------~~~~-~~~~~~~--~~~~~~~  116 (292)
                      .+.++..+.|.||+|+|||||++.++...|..             +..+.         .... .......  .....+.
T Consensus        17 ~i~~G~~~~l~G~nG~GKSTLl~~il~~~G~v~~~~~~~~~~~~~~~~~~q~~~l~~~~L~~~~~~~~~~~LSgGq~qrl   96 (176)
T cd03238          17 SIPLNVLVVVTGVSGSGKSTLVNEGLYASGKARLISFLPKFSRNKLIFIDQLQFLIDVGLGYLTLGQKLSTLSGGELQRV   96 (176)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhhcCCcEEECCcccccccccEEEEhHHHHHHHcCCCccccCCCcCcCCHHHHHHH
Confidence            35778889999999999999999996422211             11110         0000 0000000  1122334


Q ss_pred             HHHHhhhCC--CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          117 MFGYARDHQ--PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       117 ~~~~~~~~~--~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      .+..+....  |.++++||.-.          ..+......+.+.+..+..    .+..+|.++++.+
T Consensus        97 ~laral~~~~~p~llLlDEPt~----------~LD~~~~~~l~~~l~~~~~----~g~tvIivSH~~~  150 (176)
T cd03238          97 KLASELFSEPPGTLFILDEPST----------GLHQQDINQLLEVIKGLID----LGNTVILIEHNLD  150 (176)
T ss_pred             HHHHHHhhCCCCCEEEEeCCcc----------cCCHHHHHHHHHHHHHHHh----CCCEEEEEeCCHH
Confidence            455555667  89999999643          2366777777777766531    2455777777654

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=98.25  E-value=6.3e-06  Score=68.65  Aligned_cols=39  Identities=26%  Similarity=0.501  Sum_probs=32.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |+..+..++|+|+||+|||+++..++...   +..+++++..
T Consensus        19 Gi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         19 GFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            57778889999999999999999999744   6677777765

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=98.25  E-value=8.9e-06  Score=68.21  Aligned_cols=86  Identities=21%  Similarity=0.212  Sum_probs=50.3

Q ss_pred             HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCc
Q 022768          115 REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRL  194 (292)
Q Consensus       115 ~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~  194 (292)
                      +.+++.+....|.+|++||--..          -+-..|-.+++++..+..   ..+..+|++.++.   +-+.+-+.++
T Consensus       146 rv~iArALaQ~~~iLLLDEPTs~----------LDi~~Q~evl~ll~~l~~---~~~~tvv~vlHDl---N~A~ryad~~  209 (258)
T COG1120         146 RVLIARALAQETPILLLDEPTSH----------LDIAHQIEVLELLRDLNR---EKGLTVVMVLHDL---NLAARYADHL  209 (258)
T ss_pred             HHHHHHHHhcCCCEEEeCCCccc----------cCHHHHHHHHHHHHHHHH---hcCCEEEEEecCH---HHHHHhCCEE
Confidence            34455566688899999996433          366677777777777652   2356788888754   3333322221


Q ss_pred             -----ceEEEccCCCHHHHHHHHHHHH
Q 022768          195 -----DRKIEIPLPNEQSRMEILKIHA  216 (292)
Q Consensus       195 -----~~~i~l~~p~~~~r~~i~~~~~  216 (292)
                           +..+....|..--..+.++..+
T Consensus       210 i~lk~G~i~a~G~p~evlT~e~l~~Vy  236 (258)
T COG1120         210 ILLKDGKIVAQGTPEEVLTEENLREVY  236 (258)
T ss_pred             EEEECCeEEeecCcchhcCHHHHHHHh
Confidence                 2334455565444445555544

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=98.24  E-value=1e-06  Score=65.80  Aligned_cols=31  Identities=29%  Similarity=0.682  Sum_probs=27.5

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      |+|.|+||+||||+++.++..++.+++.++.
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEecc
Confidence            7899999999999999999999888776554

...

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=98.24  E-value=2.3e-05  Score=65.22  Aligned_cols=134  Identities=16%  Similarity=0.309  Sum_probs=76.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcE--EEEeccchhccc---c-----------ChHHHHH-------HHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANF--LKVVSSAIIDKY---I-----------GESARLI-------REMFGY  120 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~--~~~~~~~~~~~~---~-----------~~~~~~~-------~~~~~~  120 (292)
                      ..+..+++.|++|||||++++.+...+...+  +.+........+   .           ...+..+       ......
T Consensus        11 ~~~fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~~k   90 (241)
T PF04665_consen   11 KDPFRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYIKK   90 (241)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHhhh
Confidence            3355799999999999999999998774422  222211111110   0           0001111       111111


Q ss_pred             hhh---CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceE
Q 022768          121 ARD---HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRK  197 (292)
Q Consensus       121 ~~~---~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~  197 (292)
                      ...   ..+.+|++||+-.            .......+..++..    ...-++.+|..++....+++.++.  -....
T Consensus        91 ~~~~k~~~~~LiIlDD~~~------------~~~k~~~l~~~~~~----gRH~~is~i~l~Q~~~~lp~~iR~--n~~y~  152 (241)
T PF04665_consen   91 SPQKKNNPRFLIILDDLGD------------KKLKSKILRQFFNN----GRHYNISIIFLSQSYFHLPPNIRS--NIDYF  152 (241)
T ss_pred             hcccCCCCCeEEEEeCCCC------------chhhhHHHHHHHhc----ccccceEEEEEeeecccCCHHHhh--cceEE
Confidence            111   2367999999732            11123345555543    223468899999999999999987  55555


Q ss_pred             EEccCCCHHHHHHHHHHHH
Q 022768          198 IEIPLPNEQSRMEILKIHA  216 (292)
Q Consensus       198 i~l~~p~~~~r~~i~~~~~  216 (292)
                      +-+. .+......+++.+.
T Consensus       153 i~~~-~s~~dl~~i~~~~~  170 (241)
T PF04665_consen  153 IIFN-NSKRDLENIYRNMN  170 (241)
T ss_pred             EEec-CcHHHHHHHHHhcc
Confidence            5565 46666666666544

This is thought to be an ATPase involved in viral DNA packaging [].

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=98.23  E-value=9.1e-06  Score=64.69  Aligned_cols=108  Identities=24%  Similarity=0.366  Sum_probs=66.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchhc------------------cccCh-------HHHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAIID------------------KYIGE-------SARLI  114 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~~------------------~~~~~-------~~~~~  114 (292)
                      .+.++..+.|.||+|+||||+++.++......  -+.++...+..                  .+...       .....
T Consensus        24 ~i~~G~~~~l~G~nGsGKstLl~~i~G~~~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~~~~~~~~~t~~e~lLS~G~~~  103 (171)
T cd03228          24 TIKPGEKVAIVGPSGSGKSTLLKLLLRLYDPTSGEILIDGVDLRDLDLESLRKNIAYVPQDPFLFSGTIRENILSGGQRQ  103 (171)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHHcCCCCCCCEEEECCEEhhhcCHHHHHhhEEEEcCCchhccchHHHHhhCHHHHH
Confidence            36778899999999999999999999876321  11122111100                  00000       01112


Q ss_pred             HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          115 REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       115 ~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      +..+..+....|.++++||--.          +.+......+.+++..+..     +..+|+++++.+.+
T Consensus       104 rl~la~al~~~p~llllDEP~~----------gLD~~~~~~l~~~l~~~~~-----~~tii~~sh~~~~~  158 (171)
T cd03228         104 RIAIARALLRDPPILILDEATS----------ALDPETEALILEALRALAK-----GKTVIVIAHRLSTI  158 (171)
T ss_pred             HHHHHHHHhcCCCEEEEECCCc----------CCCHHHHHHHHHHHHHhcC-----CCEEEEEecCHHHH
Confidence            2334555567889999999643          3366777778887776531     35677888876544

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.22  E-value=1.3e-05  Score=80.94  Aligned_cols=138  Identities=22%  Similarity=0.244  Sum_probs=93.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc------cc-cCh--HHHHH-HHHHHHhhhCCCEEEEEcccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID------KY-IGE--SARLI-REMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~------~~-~~~--~~~~~-~~~~~~~~~~~~~il~lDe~d  135 (292)
                      ++++++-|.||+|||++..++|+..|..+++++.++-.+      .. +++  .+-.. ..-|-.+.. ....++|||++
T Consensus      1543 ~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr-~G~WVlLDEiN 1621 (4600)
T COG5271        1543 GKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMR-DGGWVLLDEIN 1621 (4600)
T ss_pred             CCceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhh-cCCEEEeehhh
Confidence            567999999999999999999999999999999765322      11 111  00000 111212222 23689999997


Q ss_pred             cccCCcCCCCCcchHHHHHHHHHHHHHhh---------CCCCCCCeEEEEEeCCCC------CCChhhcCCCCcceEEEc
Q 022768          136 AIGGRRFSEGTSADREIQRTLMELLNQLD---------GFDQLGKVKMIMATNRPD------VLDPALLRPGRLDRKIEI  200 (292)
Q Consensus       136 ~l~~~~~~~~~~~~~~~~~~l~~~l~~~~---------~~~~~~~~~vi~t~~~~~------~l~~~l~~~~r~~~~i~l  200 (292)
                      .-           .+...+.|...++.-.         .+..++++.|.++-|+.+      .++..+..  || .++.+
T Consensus      1622 La-----------SQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qggGRKgLPkSF~n--RF-svV~~ 1687 (4600)
T COG5271        1622 LA-----------SQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGGGRKGLPKSFLN--RF-SVVKM 1687 (4600)
T ss_pred             hh-----------HHHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCCCcccCCHHHhh--hh-heEEe
Confidence            65           5666666666665422         223345676777766533      48888887  89 77888


Q ss_pred             cCCCHHHHHHHHHHHHcC
Q 022768          201 PLPNEQSRMEILKIHAAG  218 (292)
Q Consensus       201 ~~p~~~~r~~i~~~~~~~  218 (292)
                      ..++.+....|......+
T Consensus      1688 d~lt~dDi~~Ia~~~yp~ 1705 (4600)
T COG5271        1688 DGLTTDDITHIANKMYPQ 1705 (4600)
T ss_pred             cccccchHHHHHHhhCCc
Confidence            999888888888777663

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=98.22  E-value=1.2e-05  Score=64.58  Aligned_cols=109  Identities=22%  Similarity=0.308  Sum_probs=65.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchhcc-------ccC----------------------hH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAIIDK-------YIG----------------------ES  110 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~~~-------~~~----------------------~~  110 (292)
                      .+.++..+.|.||+|+||||+++.++......  -+.++.......       ..+                      ..
T Consensus        21 ~i~~G~~~~l~G~nGsGKStLl~~i~G~~~~~~G~v~~~g~~~~~~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~  100 (180)
T cd03214          21 SIEAGEIVGILGPNGAGKSTLLKTLAGLLKPSSGEILLDGKDLASLSPKELARKIAYVPQALELLGLAHLADRPFNELSG  100 (180)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEECCEECCcCCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCH
Confidence            35778899999999999999999999876321  222322211100       000                      00


Q ss_pred             HHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          111 ARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       111 ~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      ....+..+..+....|.++++||.-.          ..+......+.+++..+..   ..+..+|+++++.+.
T Consensus       101 G~~qrl~laral~~~p~llllDEP~~----------~LD~~~~~~~~~~l~~~~~---~~~~tiii~sh~~~~  160 (180)
T cd03214         101 GERQRVLLARALAQEPPILLLDEPTS----------HLDIAHQIELLELLRRLAR---ERGKTVVMVLHDLNL  160 (180)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeCCcc----------CCCHHHHHHHHHHHHHHHH---hcCCEEEEEeCCHHH
Confidence            11122334444557889999999643          2366677777777776532   113467777776553

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>TIGR00416 sms DNA repair protein RadA

Probab=98.21  E-value=1.9e-05  Score=72.33  Aligned_cols=78  Identities=23%  Similarity=0.364  Sum_probs=52.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcccc------Ch--------HHHHHHHHHHHhhhC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYI------GE--------SARLIREMFGYARDH  124 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~------~~--------~~~~~~~~~~~~~~~  124 (292)
                      |+.++..++|.|+||+||||++..++...   +.++++++..+......      +.        ....+..+...+...
T Consensus        90 Gi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EEs~~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i~~~  169 (454)
T TIGR00416        90 GIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICANIEEE  169 (454)
T ss_pred             CccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcCCHHHHHHHHHHcCCChHHeEEcCCCCHHHHHHHHHhc
Confidence            67888899999999999999999998755   34677777543322110      00        001123444455556


Q ss_pred             CCEEEEEcccccccC
Q 022768          125 QPCIIFMDEIDAIGG  139 (292)
Q Consensus       125 ~~~il~lDe~d~l~~  139 (292)
                      +|.+++||.+..+..
T Consensus       170 ~~~~vVIDSIq~l~~  184 (454)
T TIGR00416       170 NPQACVIDSIQTLYS  184 (454)
T ss_pred             CCcEEEEecchhhcc
Confidence            789999999998754

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=98.21  E-value=1.8e-05  Score=63.40  Aligned_cols=108  Identities=17%  Similarity=0.241  Sum_probs=66.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchhc-----------------cccC----------hHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAIID-----------------KYIG----------ESAR  112 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~~-----------------~~~~----------~~~~  112 (292)
                      .+.++..+.|.||+|+||||+++.++......  -+.++...+..                 .+..          ....
T Consensus        24 ~i~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~~~LS~G~  103 (178)
T cd03247          24 ELKQGEKIALLGRSGSGKSTLLQLLTGDLKPQQGEITLDGVPVSDLEKALSSLISVLNQRPYLFDTTLRNNLGRRFSGGE  103 (178)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhccCCCCCCEEEECCEEHHHHHHHHHhhEEEEccCCeeecccHHHhhcccCCHHH
Confidence            36778899999999999999999999875321  12222111100                 0000          0112


Q ss_pred             HHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          113 LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       113 ~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      ..+..+..+....|.++++||.-.          ..+......+.+++..+.    . +..+|+++++.+.+
T Consensus       104 ~qrv~laral~~~p~~lllDEP~~----------~LD~~~~~~l~~~l~~~~----~-~~tii~~sh~~~~~  160 (178)
T cd03247         104 RQRLALARILLQDAPIVLLDEPTV----------GLDPITERQLLSLIFEVL----K-DKTLIWITHHLTGI  160 (178)
T ss_pred             HHHHHHHHHHhcCCCEEEEECCcc----------cCCHHHHHHHHHHHHHHc----C-CCEEEEEecCHHHH
Confidence            223445556667899999999643          236777777888777653    1 34677777766543

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=98.21  E-value=1.1e-05  Score=59.75  Aligned_cols=53  Identities=26%  Similarity=0.355  Sum_probs=41.2

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..|.|++-+++.+.+.+...+.+.      .-..+..+-|+|++|||||.+++.+|+.+
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~------~p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANP------NPRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCC------CCCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            458999999999999988765431      12223445589999999999999999986

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=98.21  E-value=8.6e-06  Score=68.27  Aligned_cols=39  Identities=26%  Similarity=0.451  Sum_probs=31.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |++.+..++++|+||+|||+++.+++...   +.+++++...
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~e   62 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE   62 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEcC
Confidence            57888999999999999999999997543   5566665543

>PRK10536 hypothetical protein; Provisional

Probab=98.20  E-value=2.7e-05  Score=65.18  Aligned_cols=46  Identities=22%  Similarity=0.245  Sum_probs=35.4

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+..+.+.......+...+..               ...+++.||+|||||+++.+++..
T Consensus        52 ~~~~~i~p~n~~Q~~~l~al~~---------------~~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         52 RDTSPILARNEAQAHYLKAIES---------------KQLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             cCCccccCCCHHHHHHHHHHhc---------------CCeEEEECCCCCCHHHHHHHHHHH
Confidence            4556677777777777666532               347899999999999999999884

>PHA00729 NTP-binding motif containing protein

Probab=98.20  E-value=4.2e-06  Score=68.81  Aligned_cols=25  Identities=28%  Similarity=0.525  Sum_probs=23.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+++|+|+||+||||+|.+++..++
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4799999999999999999999875

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=98.20  E-value=1.4e-05  Score=62.05  Aligned_cols=29  Identities=31%  Similarity=0.550  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..++|+||+|+|||++.|.+|...
T Consensus        25 ~v~~Ge~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          25 SVRAGEFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             eecCCceEEEeCCCCccHHHHHHHHHhcc
Confidence            45778889999999999999999999755

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=98.19  E-value=0.00033  Score=61.59  Aligned_cols=78  Identities=17%  Similarity=0.228  Sum_probs=50.3

Q ss_pred             CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC---------------CCChh-
Q 022768          124 HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD---------------VLDPA-  187 (292)
Q Consensus       124 ~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~---------------~l~~~-  187 (292)
                      ..+-|++|||+|++           ..+....+++.++.+-.   .+++++|.+.+...               ..... 
T Consensus       171 ~~~iViiIDdLDR~-----------~~~~i~~~l~~ik~~~~---~~~i~~Il~~D~~~l~~ai~~~~~~~~~~~~~~~y  236 (325)
T PF07693_consen  171 KKRIVIIIDDLDRC-----------SPEEIVELLEAIKLLLD---FPNIIFILAFDPEILEKAIEKNYGEGFDEIDGREY  236 (325)
T ss_pred             CceEEEEEcchhcC-----------CcHHHHHHHHHHHHhcC---CCCeEEEEEecHHHHHHHHHhhcCcccccccHHHH
Confidence            34679999999999           55555555555555433   36788888775321               01111 


Q ss_pred             hcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          188 LLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       188 l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      +..  .++..+.+|.|+..+...++...+.
T Consensus       237 LeK--iiq~~~~lP~~~~~~~~~~~~~~~~  264 (325)
T PF07693_consen  237 LEK--IIQVPFSLPPPSPSDLERYLNELLE  264 (325)
T ss_pred             HHh--hcCeEEEeCCCCHHHHHHHHHHHHH
Confidence            222  5677889999998888877776644

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>PRK04296 thymidine kinase; Provisional

Probab=98.17  E-value=3.5e-05  Score=62.43  Aligned_cols=31  Identities=26%  Similarity=0.253  Sum_probs=24.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc---CCcEEEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI---DANFLKV   97 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~   97 (292)
                      ...+++||+|+||||++..++.++   +..++.+
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            457899999999999998888765   4455544

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=98.17  E-value=2.5e-05  Score=61.85  Aligned_cols=104  Identities=29%  Similarity=0.428  Sum_probs=63.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEe--------ccc--hhc-----c----ccC--hHHHHHHHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVV--------SSA--IID-----K----YIG--ESARLIREMF  118 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~--------~~~--~~~-----~----~~~--~~~~~~~~~~  118 (292)
                      .+.++..+.|.||+|+||||+++.++......  -+.++        ..+  +..     .    ...  ......+..+
T Consensus        23 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~~~~~LS~G~~~rv~l  102 (166)
T cd03223          23 EIKPGDRLLITGPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYPWDDVLSGGEQQRLAF  102 (166)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEECCCCccccccHHHHhhccCCCCCCHHHHHHHHH
Confidence            35778899999999999999999999876321  01111        000  000     0    000  0112223445


Q ss_pred             HHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          119 GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       119 ~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      ..+....|.++++||-..          ..+......+.+++...       ...+|.++++.+
T Consensus       103 aral~~~p~~lllDEPt~----------~LD~~~~~~l~~~l~~~-------~~tiiivsh~~~  149 (166)
T cd03223         103 ARLLLHKPKFVFLDEATS----------ALDEESEDRLYQLLKEL-------GITVISVGHRPS  149 (166)
T ss_pred             HHHHHcCCCEEEEECCcc----------ccCHHHHHHHHHHHHHh-------CCEEEEEeCChh
Confidence            555667889999999643          23666777777777653       245777777653

The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt

>KOG0479 consensus DNA replication licensing factor, MCM3 component [Replication, recombination and repair]

Probab=98.17  E-value=4.5e-05  Score=69.73  Aligned_cols=155  Identities=17%  Similarity=0.182  Sum_probs=87.6

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcC--CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc-------chh
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVG--IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS-------AII  103 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~--~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~-------~~~  103 (292)
                      .|.|.+.+|+.|.-.+-.   +.+....-|  ++-.-++|++|.|-+.||.|++++.+......-...-+       .-.
T Consensus       302 SI~GH~~vKkAillLLlG---GvEk~L~NGshlRGDINiLlvGDPSvAKSQLLRyVLntAplAI~TTGRGSSGVGLTAAV  378 (818)
T KOG0479|consen  302 SIYGHDYVKKAILLLLLG---GVEKNLENGSHLRGDINILLVGDPSVAKSQLLRYVLNTAPLAIATTGRGSSGVGLTAAV  378 (818)
T ss_pred             ccccHHHHHHHHHHHHhc---cceeccCCCceeccceeEEEecCchHHHHHHHHHHHhcccccccccCCCCCCccceeEE
Confidence            378999999999887643   222221111  33355699999999999999999998763322111000       000


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh------CC--CCCCCeEEE
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD------GF--DQLGKVKMI  175 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~------~~--~~~~~~~vi  175 (292)
                      .......++.+..  +..-....+|++|||||.+           +.....++.+.+++-.      ++  .-+.+|.|+
T Consensus       379 TtD~eTGERRLEA--GAMVLADRGVVCIDEFDKM-----------sDiDRvAIHEVMEQqtVTIaKAGIHasLNARCSVl  445 (818)
T KOG0479|consen  379 TTDQETGERRLEA--GAMVLADRGVVCIDEFDKM-----------SDIDRVAIHEVMEQQTVTIAKAGIHASLNARCSVL  445 (818)
T ss_pred             eeccccchhhhhc--CceEEccCceEEehhcccc-----------cchhHHHHHHHHhcceEEeEeccchhhhccceeee
Confidence            0001111222210  1111134589999999998           3333345556665532      11  223489999


Q ss_pred             EEeCCCC-------------CCChhhcCCCCcceEE-EccCCCH
Q 022768          176 MATNRPD-------------VLDPALLRPGRLDRKI-EIPLPNE  205 (292)
Q Consensus       176 ~t~~~~~-------------~l~~~l~~~~r~~~~i-~l~~p~~  205 (292)
                      +++|+..             .++..+++  ||+..+ .+...+.
T Consensus       446 AAANPvyG~Yd~~k~P~eNIgLpDSLLS--RFDLlFv~lD~~d~  487 (818)
T KOG0479|consen  446 AAANPVYGQYDQSKTPMENIGLPDSLLS--RFDLLFVVLDDIDA  487 (818)
T ss_pred             eecCccccccCCCCChhhccCCcHHHHh--hhcEEEEEeccccc
Confidence            9998642             26677888  887644 3344433

>PHA02624 large T antigen; Provisional

Probab=98.16  E-value=1.3e-05  Score=74.37  Aligned_cols=40  Identities=28%  Similarity=0.321  Sum_probs=33.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      |++..+.++|+||+|||||+++.++++.++..++.+++..
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt  466 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP  466 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCc
Confidence            4566778999999999999999999999977777777443

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=98.16  E-value=1.5e-05  Score=66.84  Aligned_cols=40  Identities=23%  Similarity=0.406  Sum_probs=31.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~  101 (292)
                      |++.+..+.|+|+||+|||+++..++...         +..+++++..+
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            57788889999999999999999998543         25667776544

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=98.15  E-value=3.1e-05  Score=61.74  Aligned_cols=106  Identities=25%  Similarity=0.406  Sum_probs=65.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchh---------------c---cccC-------hHHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAII---------------D---KYIG-------ESARLIR  115 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~---------------~---~~~~-------~~~~~~~  115 (292)
                      +.++..+.|.||+|+|||||++.++......  -+.++...+.               .   .+..       ......+
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~lLS~G~~qr  104 (173)
T cd03246          25 IEPGESLAIIGPSGSGKSTLARLILGLLRPTSGRVRLDGADISQWDPNELGDHVGYLPQDDELFSGSIAENILSGGQRQR  104 (173)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHhccCCCCCeEEECCEEcccCCHHHHHhheEEECCCCccccCcHHHHCcCHHHHHH
Confidence            5678889999999999999999999865321  1112111110               0   0000       1122234


Q ss_pred             HHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          116 EMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       116 ~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      ..+..+....|.++++||.-.          ..+......+.+++..+..    .+..+|+++++.+
T Consensus       105 v~la~al~~~p~~lllDEPt~----------~LD~~~~~~l~~~l~~~~~----~~~tii~~sh~~~  157 (173)
T cd03246         105 LGLARALYGNPRILVLDEPNS----------HLDVEGERALNQAIAALKA----AGATRIVIAHRPE  157 (173)
T ss_pred             HHHHHHHhcCCCEEEEECCcc----------ccCHHHHHHHHHHHHHHHh----CCCEEEEEeCCHH
Confidence            455666668899999999643          3377777777777776532    2456777777654

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=98.15  E-value=2.6e-05  Score=62.18  Aligned_cols=106  Identities=25%  Similarity=0.346  Sum_probs=65.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchh-----------------ccccC-h--------HHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAII-----------------DKYIG-E--------SARLI  114 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~-----------------~~~~~-~--------~~~~~  114 (292)
                      +.++..+.|.||+|+||||+++.++......  -+.++.....                 ..+.+ .        .....
T Consensus        23 i~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~~tv~~~~~LS~G~~q  102 (173)
T cd03230          23 VEKGEIYGLLGPNGAGKTTLIKIILGLLKPDSGEIKVLGKDIKKEPEEVKRRIGYLPEEPSLYENLTVRENLKLSGGMKQ  102 (173)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECCEEcccchHhhhccEEEEecCCccccCCcHHHHhhcCHHHHH
Confidence            5678889999999999999999999865221  1111110000                 00111 1        11122


Q ss_pred             HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          115 REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       115 ~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      +..+..+....|.++++||...          ..+......+.+++..+..    .+..+|+++++.+
T Consensus       103 rv~laral~~~p~illlDEPt~----------~LD~~~~~~l~~~l~~~~~----~g~tiii~th~~~  156 (173)
T cd03230         103 RLALAQALLHDPELLILDEPTS----------GLDPESRREFWELLRELKK----EGKTILLSSHILE  156 (173)
T ss_pred             HHHHHHHHHcCCCEEEEeCCcc----------CCCHHHHHHHHHHHHHHHH----CCCEEEEECCCHH
Confidence            3455566668899999999643          3367777788888776542    1345777777654

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd01394 radB RadB

Probab=98.15  E-value=1.5e-05  Score=66.09  Aligned_cols=39  Identities=31%  Similarity=0.511  Sum_probs=31.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |+..+..++|+|+||+|||+++..+|...   +.++++++..
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~e   56 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTE   56 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            57788889999999999999999999765   4566666543

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK08118 topology modulation protein; Reviewed

Probab=98.14  E-value=7.1e-06  Score=65.03  Aligned_cols=33  Identities=24%  Similarity=0.474  Sum_probs=30.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      .|+|+|+||+||||+++.+++.++.+++.++..
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l   35 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDAL   35 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchh
Confidence            589999999999999999999999998887743

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=98.14  E-value=2.7e-05  Score=68.59  Aligned_cols=100  Identities=20%  Similarity=0.370  Sum_probs=67.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC--CcEEEEeccchhccccC--------------hHHHHHHHHHHHhhhCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID--ANFLKVVSSAIIDKYIG--------------ESARLIREMFGYARDHQ  125 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~--~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~~~~~  125 (292)
                      |+-++..+||-|.||.|||||+-.++..+.  .+++++...+-.+....              -.+..+..+.+.+...+
T Consensus        89 G~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~~~vLYVsGEES~~QiklRA~RL~~~~~~l~l~aEt~~e~I~~~l~~~~  168 (456)
T COG1066          89 GLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGKVLYVSGEESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAELEQEK  168 (456)
T ss_pred             CcccccEEEEccCCCCCHHHHHHHHHHHHHhcCcEEEEeCCcCHHHHHHHHHHhCCCccceEEehhcCHHHHHHHHHhcC
Confidence            456778899999999999999988887762  37888886654332111              12344567777777889


Q ss_pred             CEEEEEcccccccCCcCCCCCcch---HHHHHHHHHHHH
Q 022768          126 PCIIFMDEIDAIGGRRFSEGTSAD---REIQRTLMELLN  161 (292)
Q Consensus       126 ~~il~lDe~d~l~~~~~~~~~~~~---~~~~~~l~~~l~  161 (292)
                      |.+++||-++.++...-++..+.-   +++...|.++-+
T Consensus       169 p~lvVIDSIQT~~s~~~~SapGsVsQVRe~t~~L~~~AK  207 (456)
T COG1066         169 PDLVVIDSIQTLYSEEITSAPGSVSQVREVAAELMRLAK  207 (456)
T ss_pred             CCEEEEeccceeecccccCCCCcHHHHHHHHHHHHHHHH
Confidence            999999999999765544333333   334444444443

>cd01131 PilT Pilus retraction ATPase PilT

Probab=98.13  E-value=1.8e-05  Score=64.50  Aligned_cols=67  Identities=24%  Similarity=0.419  Sum_probs=41.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCc----EEEEecc-chhc---------cccChHHHHHHHHHHHhhhCCCEEEEEcc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDAN----FLKVVSS-AIID---------KYIGESARLIREMFGYARDHQPCIIFMDE  133 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~----~~~~~~~-~~~~---------~~~~~~~~~~~~~~~~~~~~~~~il~lDe  133 (292)
                      .++|.||+|+||||++++++..+..+    ++.+... ++..         ...+.........+..+....|.++++||
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~~~~~~~i~t~e~~~E~~~~~~~~~i~q~~vg~~~~~~~~~i~~aLr~~pd~ii~gE   82 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEFVHESKRSLINQREVGLDTLSFENALKAALRQDPDVILVGE   82 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhhcCCcEEEEEcCCccccccCccceeeecccCCCccCHHHHHHHHhcCCcCEEEEcC
Confidence            48899999999999999999877422    2222111 1100         00111122344555666667899999999


Q ss_pred             c
Q 022768          134 I  134 (292)
Q Consensus       134 ~  134 (292)
                      +
T Consensus        83 i   83 (198)
T cd01131          83 M   83 (198)
T ss_pred             C
Confidence            8

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=98.13  E-value=5.4e-05  Score=63.60  Aligned_cols=39  Identities=33%  Similarity=0.410  Sum_probs=30.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |++++..++|.|+||+|||+++..++...   +.+++++...
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~e   58 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALE   58 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEee
Confidence            57889999999999999999998776532   5566665533

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=98.13  E-value=1.5e-05  Score=76.49  Aligned_cols=29  Identities=28%  Similarity=0.454  Sum_probs=26.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++++..+.|.|++|+||||++|.+.+..
T Consensus       495 ~I~~Ge~vaIvG~SGsGKSTL~KLL~gly  523 (709)
T COG2274         495 EIPPGEKVAIVGRSGSGKSTLLKLLLGLY  523 (709)
T ss_pred             EeCCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            46778889999999999999999999766

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.13  E-value=4.1e-05  Score=61.79  Aligned_cols=28  Identities=36%  Similarity=0.476  Sum_probs=23.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..+...-|+||+|+||||+++.+-+..
T Consensus        30 i~~~~VTAlIGPSGcGKST~LR~lNRmn   57 (253)
T COG1117          30 IPKNKVTALIGPSGCGKSTLLRCLNRMN   57 (253)
T ss_pred             ccCCceEEEECCCCcCHHHHHHHHHhhc
Confidence            5667778999999999999999998643

>PRK07261 topology modulation protein; Provisional

Probab=98.12  E-value=8.4e-06  Score=64.88  Aligned_cols=34  Identities=24%  Similarity=0.434  Sum_probs=29.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      .++|+|+||+||||+++.+++.++.+++..+...
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~   35 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLH   35 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEE
Confidence            4899999999999999999999998887766443

>COG3899 Predicted ATPase [General function prediction only]

Probab=98.11  E-value=0.00014  Score=71.65  Aligned_cols=192  Identities=11%  Similarity=0.164  Sum_probs=116.6

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe---ccchhcc-ccCh
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV---SSAIIDK-YIGE  109 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~---~~~~~~~-~~~~  109 (292)
                      ++|++.....|..+....          ....+..+++.|.+|+|||.+++.+.+.......++-   +..+... ....
T Consensus         2 l~GRe~ev~~Ll~~f~~v----------~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~~~~~i~~~f~q~~~~ipl~~   71 (849)
T COG3899           2 LYGRETELAQLLAAFDRV----------SKGRGEVVLVAGESGIGKSALVNEVHKPITQQRGYFIKGKFDQFERNIPLSP   71 (849)
T ss_pred             CCchHhHHHHHHHHHHHH----------hCCCeEEEEEeecCCCcHHHHHHHHHHHHhccceeeeHhhcccccCCCchHH
Confidence            689999999998887764          1234557889999999999999999987744311111   1101000 0000


Q ss_pred             HHHHHHHHH-------------------------------------------------------------------HHhh
Q 022768          110 SARLIREMF-------------------------------------------------------------------GYAR  122 (292)
Q Consensus       110 ~~~~~~~~~-------------------------------------------------------------------~~~~  122 (292)
                      ..+.++.++                                                                   ..+.
T Consensus        72 lvq~~r~l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~  151 (849)
T COG3899          72 LVQAFRDLMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTA  151 (849)
T ss_pred             HHHHHHHHHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHh
Confidence            000000000                                                                   0111


Q ss_pred             hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh--CCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEc
Q 022768          123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD--GFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI  200 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~--~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l  200 (292)
                      ..+|-|+|+||+|-.           +......+..++....  .++.   .-+..+.+....+....++...+ ..|.+
T Consensus       152 ~~~plVi~leDlhWa-----------D~~SL~lL~~lm~~~~~~~~~~---n~v~~~h~~~~~~~~~~~~~~~i-~~I~L  216 (849)
T COG3899         152 EEHPLVIVLEDLHWA-----------DSASLKLLQLLMDRIAIGAYRD---NEVLLLHPLRPTLGEILKSATNI-TTITL  216 (849)
T ss_pred             ccCCeEEEEeccccc-----------ChhHHHHHHHHHHhcchhhhhc---cccccCCCccchhhHHhhcCCce-eEEec
Confidence            245889999999876           6666666666666543  1111   11222222223334444443233 68899


Q ss_pred             cCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHH
Q 022768          201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGM  251 (292)
Q Consensus       201 ~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~  251 (292)
                      .+.+..+-..++...++..........+.+.+.+.| +|-=+.++++....
T Consensus       217 ~PL~~~d~~~lV~~~l~~~~~~~~p~~~~i~~kt~G-nPfFi~e~lk~l~~  266 (849)
T COG3899         217 APLSRADTNQLVAATLGCTKLLPAPLLELIFEKTKG-NPFFIEEFLKALYE  266 (849)
T ss_pred             CcCchhhHHHHHHHHhCCcccccchHHHHHHHHhcC-CCccHHHHHHHHHh
Confidence            999999999999998876444444557788889999 88778777776665

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=98.11  E-value=3.2e-05  Score=62.99  Aligned_cols=94  Identities=26%  Similarity=0.285  Sum_probs=55.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc--------CCcEEEEeccch-hccccCh--HH-----------HHHHHHHHHhhh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI--------DANFLKVVSSAI-IDKYIGE--SA-----------RLIREMFGYARD  123 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l--------~~~~~~~~~~~~-~~~~~~~--~~-----------~~~~~~~~~~~~  123 (292)
                      ..+.|+.||||+||||+++-+|+-+        +..+..++...- .....+.  ..           -.-..+...++.
T Consensus       137 ~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cpk~~gmmmaIrs  216 (308)
T COG3854         137 WLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCPKAEGMMMAIRS  216 (308)
T ss_pred             ceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccchHHHHHHHHHHh
Confidence            4568999999999999999999866        222333332211 1111111  00           011234444566


Q ss_pred             CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          124 HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       124 ~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      ..|.|+++||+...             +...++...++        .++.+|.|++-
T Consensus       217 m~PEViIvDEIGt~-------------~d~~A~~ta~~--------~GVkli~TaHG  252 (308)
T COG3854         217 MSPEVIIVDEIGTE-------------EDALAILTALH--------AGVKLITTAHG  252 (308)
T ss_pred             cCCcEEEEeccccH-------------HHHHHHHHHHh--------cCcEEEEeecc
Confidence            88999999999543             22233334433        47889998863

>PRK09354 recA recombinase A; Provisional

Probab=98.11  E-value=3.2e-05  Score=67.86  Aligned_cols=78  Identities=19%  Similarity=0.225  Sum_probs=51.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |++.++.+.|+||+|+|||+++-.++...   +..+++++..+-...                .....+..+..+-..++
T Consensus        56 Gip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~  135 (349)
T PRK09354         56 GLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVR  135 (349)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhh
Confidence            47788889999999999999998887543   666777665542211                01112222323333334


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+.+|+||-+-.+.+
T Consensus       136 s~~~~lIVIDSvaaL~~  152 (349)
T PRK09354        136 SGAVDLIVVDSVAALVP  152 (349)
T ss_pred             cCCCCEEEEeChhhhcc
Confidence            45678999999988864

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=98.10  E-value=1.2e-05  Score=66.23  Aligned_cols=23  Identities=43%  Similarity=0.771  Sum_probs=20.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +..+||||+||+||||+|+.++.
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcCC
Confidence            45699999999999999999863

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=98.09  E-value=2.4e-05  Score=70.53  Aligned_cols=28  Identities=29%  Similarity=0.542  Sum_probs=25.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+-|+||+|+||||++|.+....
T Consensus       359 l~~G~~lgIIGPSgSGKSTLaR~lvG~w  386 (580)
T COG4618         359 LQAGEALGIIGPSGSGKSTLARLLVGIW  386 (580)
T ss_pred             ecCCceEEEECCCCccHHHHHHHHHccc
Confidence            5778899999999999999999999654

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=98.09  E-value=4.4e-06  Score=77.07  Aligned_cols=62  Identities=18%  Similarity=0.318  Sum_probs=46.5

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC-CcEEEE
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID-ANFLKV   97 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~-~~~~~~   97 (292)
                      .-|++++|++++++++.+++.....      .++ .....++|.||||+|||++++.+++.+. .+++.+
T Consensus        73 ~fF~d~yGlee~ieriv~~l~~Aa~------gl~-~~~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~  135 (644)
T PRK15455         73 PAFEEFYGMEEAIEQIVSYFRHAAQ------GLE-EKKQILYLLGPVGGGKSSLAERLKSLMERVPIYVL  135 (644)
T ss_pred             cchhcccCcHHHHHHHHHHHHHHHH------hcC-CCCceEEEecCCCCCchHHHHHHHHHHHhCcceee
Confidence            3578999999999999999854321      112 3456788999999999999999999773 244443

>PRK05973 replicative DNA helicase; Provisional

Probab=98.09  E-value=7.9e-05  Score=62.13  Aligned_cols=39  Identities=33%  Similarity=0.364  Sum_probs=31.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |+.++..++|.|+||+|||+++-.++...   |.++++++..
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSlE  101 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLE  101 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEEe
Confidence            67888899999999999999998887644   6666666544

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=98.07  E-value=6.8e-06  Score=70.43  Aligned_cols=100  Identities=19%  Similarity=0.323  Sum_probs=61.9

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---EEEEecc-
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---FLKVVSS-  100 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---~~~~~~~-  100 (292)
                      ...+.+++++.-.....+.+.+++...           +....+++|.|++|+||||++++++..+...   ++.+... 
T Consensus        97 ~~~~~sle~l~~~~~~~~~~~~~l~~~-----------v~~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~  165 (270)
T PF00437_consen   97 SSKPFSLEDLGESGSIPEEIAEFLRSA-----------VRGRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPP  165 (270)
T ss_dssp             TSS--CHCCCCHTHHCHHHHHHHHHHC-----------HHTTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS
T ss_pred             ccccccHhhccCchhhHHHHHHHHhhc-----------cccceEEEEECCCccccchHHHHHhhhccccccceEEecccc
Confidence            445668888877666666666666543           2346789999999999999999999988544   2222211 


Q ss_pred             chh--c----cccC-hHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768          101 AII--D----KYIG-ESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus       101 ~~~--~----~~~~-~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      ++.  +    .... ........++..+....|.++++.|+-
T Consensus       166 E~~l~~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR  207 (270)
T PF00437_consen  166 ELRLPGPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIGEIR  207 (270)
T ss_dssp             -S--SCSSEEEEEEETTTBSHHHHHHHHTTS--SEEEESCE-
T ss_pred             ceeecccceEEEEeecCcccHHHHHHHHhcCCCCcccccccC
Confidence            110  0    0000 122334566777788899999999995

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=98.07  E-value=3.2e-05  Score=70.10  Aligned_cols=101  Identities=20%  Similarity=0.260  Sum_probs=65.8

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      .+....-..+++++.......+.+.+.+..|              ..-+|++||.|+||||++.++...++.+...+...
T Consensus       227 il~~~~~~l~l~~Lg~~~~~~~~~~~~~~~p--------------~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~Ti  292 (500)
T COG2804         227 ILDKDQVILDLEKLGMSPFQLARLLRLLNRP--------------QGLILVTGPTGSGKTTTLYAALSELNTPERNIITI  292 (500)
T ss_pred             EeccccccCCHHHhCCCHHHHHHHHHHHhCC--------------CeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEe
Confidence            3344445677888877777788888887653              45688999999999999999999886544322211


Q ss_pred             ---------chhccccCh-HHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768          101 ---------AIIDKYIGE-SARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus       101 ---------~~~~~~~~~-~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                               .+....+.. ..-.....++....+.|+||++.|+-
T Consensus       293 EDPVE~~~~gI~Q~qVN~k~gltfa~~LRa~LRqDPDvImVGEIR  337 (500)
T COG2804         293 EDPVEYQLPGINQVQVNPKIGLTFARALRAILRQDPDVIMVGEIR  337 (500)
T ss_pred             eCCeeeecCCcceeecccccCCCHHHHHHHHhccCCCeEEEeccC
Confidence                     111110000 11112345556667899999999994

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=98.07  E-value=5.7e-05  Score=64.26  Aligned_cols=39  Identities=26%  Similarity=0.296  Sum_probs=30.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |++++..++|+|+||+|||+++-.++...   +.+++++...
T Consensus        32 Gip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~E   73 (259)
T TIGR03878        32 GIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVE   73 (259)
T ss_pred             CeECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec
Confidence            56778889999999999999999887643   5566666643

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=98.07  E-value=1.3e-05  Score=68.39  Aligned_cols=26  Identities=35%  Similarity=0.549  Sum_probs=23.6

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+++|.||+|+||||+++.++..+..
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~~  137 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILST  137 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccCC
Confidence            68999999999999999999998743

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=98.06  E-value=2.7e-05  Score=64.45  Aligned_cols=30  Identities=33%  Similarity=0.504  Sum_probs=25.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+..+.-+.|.||+||||||++|.+-+...
T Consensus        23 ~I~~gef~vliGpSGsGKTTtLkMINrLie   52 (309)
T COG1125          23 TIEEGEFLVLIGPSGSGKTTTLKMINRLIE   52 (309)
T ss_pred             EecCCeEEEEECCCCCcHHHHHHHHhcccC
Confidence            356677789999999999999999997663

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=98.06  E-value=7.7e-05  Score=66.68  Aligned_cols=82  Identities=15%  Similarity=0.275  Sum_probs=47.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc--CCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI--DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR  141 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~  141 (292)
                      ..+.++++.||+||||||++.+++...  ... ..+....+....    .   .....  ......+|+|||+..+.-  
T Consensus       207 e~~~Nli~lGp~GTGKThla~~l~~~~a~~sG-~f~T~a~Lf~~L----~---~~~lg--~v~~~DlLI~DEvgylp~--  274 (449)
T TIGR02688       207 EPNYNLIELGPKGTGKSYIYNNLSPYVILISG-GTITVAKLFYNI----S---TRQIG--LVGRWDVVAFDEVATLKF--  274 (449)
T ss_pred             hcCCcEEEECCCCCCHHHHHHHHhHHHHHHcC-CcCcHHHHHHHH----H---HHHHh--hhccCCEEEEEcCCCCcC--
Confidence            557899999999999999999988762  100 111111211110    0   11111  123457999999988632  


Q ss_pred             CCCCCcchHHHHHHHHHHHHH
Q 022768          142 FSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus       142 ~~~~~~~~~~~~~~l~~~l~~  162 (292)
                           ....+....+...+..
T Consensus       275 -----~~~~~~v~imK~yMes  290 (449)
T TIGR02688       275 -----AKPKELIGILKNYMES  290 (449)
T ss_pred             -----CchHHHHHHHHHHHHh
Confidence                 1244455666665554

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=98.06  E-value=5.6e-05  Score=61.46  Aligned_cols=106  Identities=21%  Similarity=0.260  Sum_probs=63.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc--CCcE--EEEeccch---------------hccccC-hHH-----------
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI--DANF--LKVVSSAI---------------IDKYIG-ESA-----------  111 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l--~~~~--~~~~~~~~---------------~~~~~~-~~~-----------  111 (292)
                      +.++..+.|.||+|+|||||++.++...  ...-  +.++...+               ...+.. ...           
T Consensus        32 i~~Ge~~~l~G~nGsGKStLl~~i~Gl~~~~~~~G~i~~~g~~~~~~~~~~~i~~~~q~~~~~~~~t~~~~i~~~~~~~~  111 (194)
T cd03213          32 AKPGELTAIMGPSGAGKSTLLNALAGRRTGLGVSGEVLINGRPLDKRSFRKIIGYVPQDDILHPTLTVRETLMFAAKLRG  111 (194)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCCCCCCCceEEEECCEeCchHhhhheEEEccCcccCCCCCcHHHHHHHHHHhcc
Confidence            5778899999999999999999999876  3211  11111000               000000 111           


Q ss_pred             ----HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          112 ----RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       112 ----~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                          ...+..+..+....|.++++||...          ..+......+.+++..+..    .+..+|.++++.+
T Consensus       112 LS~G~~qrv~laral~~~p~illlDEP~~----------~LD~~~~~~l~~~l~~~~~----~~~tiii~sh~~~  172 (194)
T cd03213         112 LSGGERKRVSIALELVSNPSLLFLDEPTS----------GLDSSSALQVMSLLRRLAD----TGRTIICSIHQPS  172 (194)
T ss_pred             CCHHHHHHHHHHHHHHcCCCEEEEeCCCc----------CCCHHHHHHHHHHHHHHHh----CCCEEEEEecCch
Confidence                1112334444557889999999643          3367777778787776532    1445777777653

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=98.06  E-value=8.7e-06  Score=66.16  Aligned_cols=123  Identities=16%  Similarity=0.177  Sum_probs=56.1

Q ss_pred             EEEEcCCCChHHHHHHHH-HH-hc--CCcEEEEeccchhcc-ccChHHHHH----------------HHHHHHhhhCCCE
Q 022768           69 VLLYGPPGTGKTLLARAI-AS-NI--DANFLKVVSSAIIDK-YIGESARLI----------------REMFGYARDHQPC  127 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~l-a~-~l--~~~~~~~~~~~~~~~-~~~~~~~~~----------------~~~~~~~~~~~~~  127 (292)
                      .+++|.||+|||..|-.. .. .+  |.+++. |...+.-. ........+                .....-......+
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t-ni~gL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT-NIPGLNIEKIQPVLGYDIPTRLIDLSDPDFEEDWDDPDDWRKLPKGS   81 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE---TTB-S--EEEE--TTT-S-----S--SSSEEGGGHHHHTTSGTT-
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE-ccCCcchhhhhhhccccccccccccccccchhhhhhhhhhcccCCCc
Confidence            688999999999977444 32 22  555554 43322110 000000000                0011111111468


Q ss_pred             EEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCC
Q 022768          128 IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       128 il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p  203 (292)
                      +++|||++.+++.+.....    .....+ +.+..    ....+.-++.+|..+..+++.++.  .....+.+..+
T Consensus        82 liviDEa~~~~~~r~~~~~----~~~~~~-~~l~~----hRh~g~diiliTQ~~~~id~~ir~--lve~~~~~~k~  146 (193)
T PF05707_consen   82 LIVIDEAQNFFPSRSWKGK----KVPEII-EFLAQ----HRHYGWDIILITQSPSQIDKFIRD--LVEYHYHCRKL  146 (193)
T ss_dssp             EEEETTGGGTSB---T-T--------HHH-HGGGG----CCCTT-EEEEEES-GGGB-HHHHC--CEEEEEEEEE-
T ss_pred             EEEEECChhhcCCCccccc----cchHHH-HHHHH----hCcCCcEEEEEeCCHHHHhHHHHH--HHheEEEEEee
Confidence            9999999999876533111    111222 33333    333477899999999999999986  66666655433

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>PHA02774 E1; Provisional

Probab=98.05  E-value=3.2e-05  Score=71.50  Aligned_cols=57  Identities=23%  Similarity=0.399  Sum_probs=39.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcE-EEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEccc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANF-LKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEI  134 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~  134 (292)
                      .+..++++|+||||||||+++.++++.++..+ ..+|.....             .++.+..+  .+++|||+
T Consensus       431 ~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s~F-------------wLqpl~d~--ki~vlDD~  488 (613)
T PHA02774        431 IPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKSHF-------------WLQPLADA--KIALLDDA  488 (613)
T ss_pred             CCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECcccc-------------ccchhccC--CEEEEecC
Confidence            44456899999999999999999999986554 335542211             02222222  59999998

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=98.05  E-value=5.1e-05  Score=62.10  Aligned_cols=26  Identities=27%  Similarity=0.401  Sum_probs=22.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +..+..++|+||+|+||||+++.++.
T Consensus        26 l~~~~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          26 LGSGRLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             EcCCeEEEEECCCCCccHHHHHHHHH
Confidence            34556799999999999999999993

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=98.05  E-value=3.1e-05  Score=64.44  Aligned_cols=40  Identities=23%  Similarity=0.359  Sum_probs=31.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---C------CcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---D------ANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~------~~~~~~~~~~  101 (292)
                      |+..+..+.|+|+||+|||+++..++...   +      ..+++++...
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            57788889999999999999999998653   2      4566666543

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=98.05  E-value=8e-05  Score=61.45  Aligned_cols=22  Identities=23%  Similarity=0.499  Sum_probs=20.2

Q ss_pred             ceEEEEcCCCChHHHHHHHHHH
Q 022768           67 KGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +.++|+||+|+||||+++.++.
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            6799999999999999999983

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>COG1118 CysA ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=98.04  E-value=8.2e-06  Score=69.15  Aligned_cols=29  Identities=45%  Similarity=0.560  Sum_probs=25.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+..+..+-+.||+|+||||+++.+|...
T Consensus        24 ~i~~Ge~vaLlGpSGaGKsTlLRiIAGLe   52 (345)
T COG1118          24 DIKSGELVALLGPSGAGKSTLLRIIAGLE   52 (345)
T ss_pred             eecCCcEEEEECCCCCcHHHHHHHHhCcC
Confidence            35678889999999999999999999654

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.04  E-value=0.00011  Score=61.84  Aligned_cols=30  Identities=37%  Similarity=0.510  Sum_probs=26.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      +..+..++|.||+|+||||+++.+++.+..
T Consensus        13 i~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          13 IGKGQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            456788999999999999999999998754

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=98.04  E-value=7.4e-05  Score=59.86  Aligned_cols=108  Identities=22%  Similarity=0.327  Sum_probs=65.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchh--------------------ccccC-----------h
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAII--------------------DKYIG-----------E  109 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~--------------------~~~~~-----------~  109 (292)
                      +.++..+.|.||+|+||||+++.++......  -+.++...+.                    ..+.+           .
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~g~~~~~~~~~~~~~~~~i~~~~q~~~~~~~~t~~~~l~~~lS  102 (178)
T cd03229          23 IEAGEIVALLGPSGSGKSTLLRCIAGLEEPDSGSILIDGEDLTDLEDELPPLRRRIGMVFQDFALFPHLTVLENIALGLS  102 (178)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCCCCceEEEECCEEccccchhHHHHhhcEEEEecCCccCCCCCHHHheeecCC
Confidence            5678889999999999999999999765321  1111111000                    00000           0


Q ss_pred             HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          110 SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      .....+..+..+....|.++++||-.          .+.+......+.+++..+..   ..+..+|.++++.+.
T Consensus       103 ~G~~qr~~la~al~~~p~llilDEP~----------~~LD~~~~~~l~~~l~~~~~---~~~~tiii~sH~~~~  163 (178)
T cd03229         103 GGQQQRVALARALAMDPDVLLLDEPT----------SALDPITRREVRALLKSLQA---QLGITVVLVTHDLDE  163 (178)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEeCCc----------ccCCHHHHHHHHHHHHHHHH---hcCCEEEEEeCCHHH
Confidence            11223344556666788999999963          33377777788887776542   113457777776543

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=98.03  E-value=6.7e-06  Score=72.04  Aligned_cols=29  Identities=48%  Similarity=0.538  Sum_probs=24.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++.-+-|-||+||||||+++.+|.--
T Consensus        27 ~i~~Gef~~lLGPSGcGKTTlLR~IAGfe   55 (352)
T COG3842          27 DIKKGEFVTLLGPSGCGKTTLLRMIAGFE   55 (352)
T ss_pred             eecCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            35667778899999999999999999543

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=98.03  E-value=6.2e-05  Score=69.62  Aligned_cols=98  Identities=21%  Similarity=0.277  Sum_probs=61.7

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC---cEEEEec-
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA---NFLKVVS-   99 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~---~~~~~~~-   99 (292)
                      ......+++++.-.++..+.+.+.+..              +...++++||+|+||||+++++.+.+..   .++.+.. 
T Consensus       214 ~~~~~~~l~~Lg~~~~~~~~l~~~~~~--------------~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDp  279 (486)
T TIGR02533       214 KTAVRLDLETLGMSPELLSRFERLIRR--------------PHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDP  279 (486)
T ss_pred             CccCCCCHHHcCCCHHHHHHHHHHHhc--------------CCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCC
Confidence            334456788876566667777776643              2445889999999999999988887743   2333321 


Q ss_pred             -----cchhcccc-ChHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768          100 -----SAIIDKYI-GESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus       100 -----~~~~~~~~-~~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                           .......+ .............+....|.++++.|+-
T Consensus       280 vE~~~~~~~q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEiR  321 (486)
T TIGR02533       280 VEYQIEGIGQIQVNPKIGLTFAAGLRAILRQDPDIIMVGEIR  321 (486)
T ss_pred             eeeecCCCceEEEccccCccHHHHHHHHHhcCCCEEEEeCCC
Confidence                 11111111 1111233455666677899999999984

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=98.03  E-value=2.8e-05  Score=62.49  Aligned_cols=106  Identities=16%  Similarity=0.215  Sum_probs=63.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccch----------------hc------ccc-ChHHHHH---
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAI----------------ID------KYI-GESARLI---  114 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~----------------~~------~~~-~~~~~~~---  114 (292)
                      +.++..+.|.|++|+||||+++.++......  -+.++...+                ..      .+. ....+.+   
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G~~~~~~G~i~~~g~~~~~~~~~~~~~~~i~~~~q~~~~~~~~~~~t~~e~l~~~  102 (182)
T cd03215          23 VRAGEIVGIAGLVGNGQTELAEALFGLRPPASGEITLDGKPVTRRSPRDAIRAGIAYVPEDRKREGLVLDLSVAENIALS  102 (182)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCCCCCCceEEECCEECCccCHHHHHhCCeEEecCCcccCcccCCCcHHHHHHHH
Confidence            5778889999999999999999999865321  111111000                00      000 0111111   


Q ss_pred             ---------HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          115 ---------REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       115 ---------~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                               +..+..+....|.++++||--.          ..+......+.+++..+..    .+..+|.++++.+
T Consensus       103 ~~LS~G~~qrl~la~al~~~p~llllDEP~~----------~LD~~~~~~l~~~l~~~~~----~~~tiii~sh~~~  165 (182)
T cd03215         103 SLLSGGNQQKVVLARWLARDPRVLILDEPTR----------GVDVGAKAEIYRLIRELAD----AGKAVLLISSELD  165 (182)
T ss_pred             hhcCHHHHHHHHHHHHHccCCCEEEECCCCc----------CCCHHHHHHHHHHHHHHHH----CCCEEEEEeCCHH
Confidence                     2234444557889999999633          3367777777777776532    2456777777653

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.02  E-value=7.5e-05  Score=66.20  Aligned_cols=116  Identities=16%  Similarity=0.287  Sum_probs=62.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cEEEEeccch----------------hccccChHHHHH---HHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NFLKVVSSAI----------------IDKYIGESARLI---REMF  118 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~~~~~~~~~----------------~~~~~~~~~~~~---~~~~  118 (292)
                      +..+...+|.||+|+||||+++.+++....     .++.+...+.                .+.+.......+   ..++
T Consensus       166 IGkGQR~lIvgppGvGKTTLaK~Ian~I~~nhFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~i  245 (416)
T PRK09376        166 IGKGQRGLIVAPPKAGKTVLLQNIANSITTNHPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVI  245 (416)
T ss_pred             cccCceEEEeCCCCCChhHHHHHHHHHHHhhcCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHH
Confidence            344677999999999999999999987633     2222222221                011111111111   1222


Q ss_pred             HHhh----hCCCEEEEEcccccccCCcCC-------C-CCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEe
Q 022768          119 GYAR----DHQPCIIFMDEIDAIGGRRFS-------E-GTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT  178 (292)
Q Consensus       119 ~~~~----~~~~~il~lDe~d~l~~~~~~-------~-~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~  178 (292)
                      ..+.    .....+|++||++++...-..       . +.+.+......+..++..-......+.+.+|+|+
T Consensus       246 e~Ae~~~e~G~dVlL~iDsItR~arAqrev~~~sG~~~sgG~~~~~~~~~~r~f~~Arn~e~~GSlT~i~T~  317 (416)
T PRK09376        246 EKAKRLVEHGKDVVILLDSITRLARAYNTVVPSSGKVLSGGVDANALHRPKRFFGAARNIEEGGSLTIIATA  317 (416)
T ss_pred             HHHHHHHHcCCCEEEEEEChHHHHHHHHhhhhccCCCCCCCCChhHhhhhHHHHHhhcCCCCCcceEEEEEE
Confidence            2222    234579999999998532211       1 1223444444455555544333345678888875

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=98.02  E-value=0.00035  Score=63.59  Aligned_cols=193  Identities=15%  Similarity=0.173  Sum_probs=95.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc---------------c-----ChHHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY---------------I-----GESARLIREMFGYA  121 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~---------------~-----~~~~~~~~~~~~~~  121 (292)
                      ++..++++|++|+||||++..+|..+   +..+..+.+..+....               .     ......+...+..+
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~R~aa~eQL~~la~~~gvp~~~~~~~~d~~~i~~~al~~~  173 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYRPAAYDQLKQLAEKIGVPFYGDPDNKDAVEIAKEGLEKF  173 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCCCHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHHh
Confidence            46779999999999999999999876   4455555544332100               0     01112223333333


Q ss_pred             hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC-CCh--hhcCCCCcceEE
Q 022768          122 RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV-LDP--ALLRPGRLDRKI  198 (292)
Q Consensus       122 ~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~-l~~--~l~~~~r~~~~i  198 (292)
                      ...  .+|+||..-.+.         .+......+..+...    .....+++++.+..... ++.  .+.....+ .-+
T Consensus       174 ~~~--DvVIIDTAGr~~---------~d~~lm~El~~l~~~----~~pdevlLVvda~~gq~av~~a~~F~~~l~i-~gv  237 (437)
T PRK00771        174 KKA--DVIIVDTAGRHA---------LEEDLIEEMKEIKEA----VKPDEVLLVIDATIGQQAKNQAKAFHEAVGI-GGI  237 (437)
T ss_pred             hcC--CEEEEECCCccc---------chHHHHHHHHHHHHH----hcccceeEEEeccccHHHHHHHHHHHhcCCC-CEE
Confidence            333  689999885441         122223333333222    22235555555443322 111  11110011 122


Q ss_pred             EccCCCHHHHHH-HHHHHHc----------CccC--CCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHH---------Hh
Q 022768          199 EIPLPNEQSRME-ILKIHAA----------GIAK--HGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAI---------RA  256 (292)
Q Consensus       199 ~l~~p~~~~r~~-i~~~~~~----------~~~~--~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~---------~~  256 (292)
                      -+.-.|...+.. ++.....          +..+  -...+.+.++.+.-|  -+|+..+++.|...-.         +-
T Consensus       238 IlTKlD~~a~~G~~ls~~~~~~~Pi~fig~Ge~v~Dle~f~~~~~~~~ilg--mgd~~~l~e~~~~~~~~~~~~~~~~~~  315 (437)
T PRK00771        238 IITKLDGTAKGGGALSAVAETGAPIKFIGTGEKIDDLERFDPDRFISRLLG--MGDLESLLEKVEEALDEEEEEKDVEKM  315 (437)
T ss_pred             EEecccCCCcccHHHHHHHHHCcCEEEEecCCCcccCCcCCHHHHHHHHhC--CCChHHHHHHHHHhhhHHHHHHHHHHH
Confidence            334444444432 2221111          1111  133466777776654  3488888876655311         11


Q ss_pred             cCCcccHHHHHHHHHHHhh
Q 022768          257 ERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       257 ~~~~i~~~~~~~a~~~~~~  275 (292)
                      .....+.+|+.+-++.+..
T Consensus       316 ~~~~f~l~d~~~q~~~~~k  334 (437)
T PRK00771        316 MKGKFTLKDMYKQLEAMNK  334 (437)
T ss_pred             HcCCcCHHHHHHHHHHHHh
Confidence            2346788888887777764

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=98.02  E-value=0.0012  Score=59.19  Aligned_cols=53  Identities=23%  Similarity=0.439  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHH-HHHHHhcCCcEEEEeccchhc
Q 022768           38 SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA-RAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~-~~la~~l~~~~~~~~~~~~~~  104 (292)
                      .+..+.|+.++..             .+..-|+++||.|+||+.++ ..+.+. ...++.++|..+..
T Consensus         2 ~e~~~~L~~wL~e-------------~~~TFIvV~GPrGSGK~elV~d~~L~~-r~~vL~IDC~~i~~   55 (431)
T PF10443_consen    2 KEAIEQLKSWLNE-------------NPNTFIVVQGPRGSGKRELVMDHVLKD-RKNVLVIDCDQIVK   55 (431)
T ss_pred             chHHHHHHHHHhc-------------CCCeEEEEECCCCCCccHHHHHHHHhC-CCCEEEEEChHhhh
Confidence            3566778888765             34556888899999999999 444443 33488888876654

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PRK00131 aroK shikimate kinase; Reviewed

Probab=98.02  E-value=6.6e-06  Score=65.43  Aligned_cols=35  Identities=23%  Similarity=0.420  Sum_probs=30.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .++..++|+|+||+||||+++.++..++.+++..+
T Consensus         2 ~~~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d   36 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD   36 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            35678999999999999999999999998887544

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=98.02  E-value=5e-05  Score=63.25  Aligned_cols=108  Identities=24%  Similarity=0.337  Sum_probs=63.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEeccchhcc--------------------------c-----
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVSSAIIDK--------------------------Y-----  106 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~~~~~~~--------------------------~-----  106 (292)
                      |++.+..+++.|+||+|||+++..++...    +.+++++...+....                          .     
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee~~~~l~~~~~s~g~d~~~~~~~g~l~~~d~~~~~~~   94 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEEPPEELIENMKSFGWDLEEYEDSGKLKIIDAFPERIG   94 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS-HHHHHHHHHTTTS-HHHHHHTTSEEEEESSGGGST
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecCCHHHHHHHHHHcCCcHHHHhhcCCEEEEeccccccc
Confidence            57888999999999999999998877433    677777664322210                          0     


Q ss_pred             --cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          107 --IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       107 --~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                        .......+..+...+...++.+++||-+..+..      ..........+..+...+..    .++.++++.+
T Consensus        95 ~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls~l~~------~~~~~~~r~~l~~l~~~l~~----~~~t~llt~~  159 (226)
T PF06745_consen   95 WSPNDLEELLSKIREAIEELKPDRVVIDSLSALLL------YDDPEELRRFLRALIKFLKS----RGVTTLLTSE  159 (226)
T ss_dssp             -TSCCHHHHHHHHHHHHHHHTSSEEEEETHHHHTT------SSSGGGHHHHHHHHHHHHHH----TTEEEEEEEE
T ss_pred             ccccCHHHHHHHHHHHHHhcCCCEEEEECHHHHhh------cCCHHHHHHHHHHHHHHHHH----CCCEEEEEEc
Confidence              012233344444555555668999999988821      11123333444445544432    3555666655

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.01  E-value=2.4e-05  Score=63.71  Aligned_cols=35  Identities=31%  Similarity=0.551  Sum_probs=25.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      .+.++|.|++|||||++++.+...+   +..++.+...
T Consensus        18 ~~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT   55 (196)
T PF13604_consen   18 DRVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPT   55 (196)
T ss_dssp             CSEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESS
T ss_pred             CeEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCc
Confidence            4568889999999999999988665   4455544433

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=98.01  E-value=4.2e-05  Score=67.83  Aligned_cols=71  Identities=18%  Similarity=0.386  Sum_probs=45.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCC----cEEEEecc-chh---------ccccChHHHHHHHHHHHhhhCCCEEEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDA----NFLKVVSS-AII---------DKYIGESARLIREMFGYARDHQPCIIF  130 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~----~~~~~~~~-~~~---------~~~~~~~~~~~~~~~~~~~~~~~~il~  130 (292)
                      +...++|.||+|+||||+++++++.+..    .++.+... ++.         ....+.........+..+....|.+|+
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~~~~~~~i~q~evg~~~~~~~~~l~~~lr~~pd~i~  200 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVHRNKRSLINQREVGLDTLSFANALRAALREDPDVIL  200 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhccCccceEEccccCCCCcCHHHHHHHhhccCCCEEE
Confidence            3567999999999999999999987642    22222111 110         001121122345556667778999999


Q ss_pred             Ecccc
Q 022768          131 MDEID  135 (292)
Q Consensus       131 lDe~d  135 (292)
                      +||+-
T Consensus       201 vgEir  205 (343)
T TIGR01420       201 IGEMR  205 (343)
T ss_pred             EeCCC
Confidence            99983

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=98.00  E-value=2.2e-05  Score=64.58  Aligned_cols=28  Identities=32%  Similarity=0.433  Sum_probs=25.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+-|.|++|+||||+++.++.-.
T Consensus        30 i~~Ge~lgivGeSGsGKSTL~r~l~Gl~   57 (252)
T COG1124          30 IERGETLGIVGESGSGKSTLARLLAGLE   57 (252)
T ss_pred             ecCCCEEEEEcCCCCCHHHHHHHHhccc
Confidence            6778999999999999999999999644

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.99  E-value=7.8e-05  Score=61.25  Aligned_cols=29  Identities=38%  Similarity=0.606  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.|++|+||||+++.++...
T Consensus        24 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   52 (207)
T PRK13539         24 TLAAGEALVLTGPNGSGKTTLLRLIAGLL   52 (207)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            35778899999999999999999999865

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=97.99  E-value=0.00011  Score=60.13  Aligned_cols=107  Identities=23%  Similarity=0.288  Sum_probs=63.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc--CC--cEEEEeccchhc-------------------cccCh---------
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI--DA--NFLKVVSSAIID-------------------KYIGE---------  109 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l--~~--~~~~~~~~~~~~-------------------~~~~~---------  109 (292)
                      .+.++..+.|.|++|+||||+++.++...  ..  --+.++...+..                   .+.+.         
T Consensus        22 ~i~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~p~~G~i~~~g~~~~~~~~~~~~~~~i~~v~q~~~~~~~~~~~~~l~~~  101 (200)
T cd03217          22 TIKKGEVHALMGPNGSGKSTLAKTIMGHPKYEVTEGEILFKGEDITDLPPEERARLGIFLAFQYPPEIPGVKNADFLRYV  101 (200)
T ss_pred             EECCCcEEEEECCCCCCHHHHHHHHhCCCcCCCCccEEEECCEECCcCCHHHHhhCcEEEeecChhhccCccHHHHHhhc
Confidence            35778899999999999999999999873  11  112222111100                   00000         


Q ss_pred             -----HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          110 -----SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       110 -----~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                           .....+..+..+....|.++++||--          ...+......+.+++..+..    .+..+|.+++..+
T Consensus       102 ~~~LS~G~~qrv~laral~~~p~illlDEPt----------~~LD~~~~~~l~~~L~~~~~----~~~tiii~sh~~~  165 (200)
T cd03217         102 NEGFSGGEKKRNEILQLLLLEPDLAILDEPD----------SGLDIDALRLVAEVINKLRE----EGKSVLIITHYQR  165 (200)
T ss_pred             cccCCHHHHHHHHHHHHHhcCCCEEEEeCCC----------ccCCHHHHHHHHHHHHHHHH----CCCEEEEEecCHH
Confidence                 01112233444555788999999963          23366677777777776532    1345777777654

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.99  E-value=9.1e-05  Score=60.62  Aligned_cols=29  Identities=38%  Similarity=0.701  Sum_probs=26.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++....
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          30 VKPGEMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHhcccCC
Confidence            57788999999999999999999998754

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=97.98  E-value=5.3e-05  Score=66.18  Aligned_cols=74  Identities=18%  Similarity=0.396  Sum_probs=47.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEecc-chh----c---cc-----cChHHHHHHHHHHHhhhCCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSS-AII----D---KY-----IGESARLIREMFGYARDHQP  126 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~-~~~----~---~~-----~~~~~~~~~~~~~~~~~~~~  126 (292)
                      -+..+.+++|.||+|+||||++++++..+...  .+.+... ++.    .   ..     .+........++..+....|
T Consensus       140 ~v~~~~~ili~G~tGsGKTTll~al~~~~~~~~~iv~ied~~El~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~Lr~~p  219 (308)
T TIGR02788       140 AIASRKNIIISGGTGSGKTTFLKSLVDEIPKDERIITIEDTREIFLPHPNYVHLFYSKGGQGLAKVTPKDLLQSCLRMRP  219 (308)
T ss_pred             HhhCCCEEEEECCCCCCHHHHHHHHHccCCccccEEEEcCccccCCCCCCEEEEEecCCCCCcCccCHHHHHHHHhcCCC
Confidence            35668899999999999999999999877432  2222110 100    0   00     01112234566777777889


Q ss_pred             EEEEEcccc
Q 022768          127 CIIFMDEID  135 (292)
Q Consensus       127 ~il~lDe~d  135 (292)
                      .++++||+-
T Consensus       220 d~ii~gE~r  228 (308)
T TIGR02788       220 DRIILGELR  228 (308)
T ss_pred             CeEEEeccC
Confidence            999999983

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=97.98  E-value=4.3e-05  Score=64.30  Aligned_cols=38  Identities=32%  Similarity=0.444  Sum_probs=31.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~   99 (292)
                      |+.++..++|.|+||+|||+++..++...    +.++++++.
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~   50 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSL   50 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeC
Confidence            67888899999999999999988877644    667776663

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=97.98  E-value=5.6e-05  Score=71.13  Aligned_cols=29  Identities=31%  Similarity=0.625  Sum_probs=26.3

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ++++..+.|.||+|+||||+++.+++...
T Consensus       358 i~~G~~vaIvG~SGsGKSTLl~lL~g~~~  386 (529)
T TIGR02868       358 LPPGERVAILGPSGSGKSTLLMLLTGLLD  386 (529)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            67899999999999999999999997663

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.97  E-value=5.9e-05  Score=61.30  Aligned_cols=111  Identities=22%  Similarity=0.293  Sum_probs=62.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR  141 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~  141 (292)
                      |......++|.|+-|+|||++++.|+...     ..+.  .....   ..+....    +..+  -++.|||++.+    
T Consensus        48 g~k~d~~lvl~G~QG~GKStf~~~L~~~~-----~~d~--~~~~~---~kd~~~~----l~~~--~iveldEl~~~----  107 (198)
T PF05272_consen   48 GCKNDTVLVLVGKQGIGKSTFFRKLGPEY-----FSDS--INDFD---DKDFLEQ----LQGK--WIVELDELDGL----  107 (198)
T ss_pred             CCcCceeeeEecCCcccHHHHHHHHhHHh-----ccCc--cccCC---CcHHHHH----HHHh--HheeHHHHhhc----
Confidence            44555668899999999999999996551     1111  11110   0111111    1111  38999999887    


Q ss_pred             CCCCCcchHHHHHHHHHHHHHhhCC----------CCCCCeEEEEEeCCCCCCCh-hhcCCCCcceEEEccC
Q 022768          142 FSEGTSADREIQRTLMELLNQLDGF----------DQLGKVKMIMATNRPDVLDP-ALLRPGRLDRKIEIPL  202 (292)
Q Consensus       142 ~~~~~~~~~~~~~~l~~~l~~~~~~----------~~~~~~~vi~t~~~~~~l~~-~l~~~~r~~~~i~l~~  202 (292)
                             .......+..++..-...          .-....++|+|+|..+-+.. .--+  || ..+.+..
T Consensus       108 -------~k~~~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnR--Rf-~~v~v~~  169 (198)
T PF05272_consen  108 -------SKKDVEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNR--RF-WPVEVSK  169 (198)
T ss_pred             -------chhhHHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCe--EE-EEEEEcC
Confidence                   344445666666543211          11125778999998764432 2333  66 5555544

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.97  E-value=0.00013  Score=59.24  Aligned_cols=29  Identities=31%  Similarity=0.417  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.|++|+|||||++.++...
T Consensus        22 ~i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   50 (195)
T PRK13541         22 TFLPSAITYIKGANGCGKSSLLRMIAGIM   50 (195)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            36778899999999999999999999865

>PRK04328 hypothetical protein; Provisional

Probab=97.97  E-value=0.00018  Score=60.87  Aligned_cols=38  Identities=34%  Similarity=0.411  Sum_probs=29.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      |++++..++|.|+||+|||+++..++...   +.++++++.
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~   59 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVAL   59 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEe
Confidence            57788999999999999999998776532   445555543

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=97.97  E-value=4.1e-05  Score=66.33  Aligned_cols=49  Identities=29%  Similarity=0.449  Sum_probs=35.4

Q ss_pred             hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      ...|.+++|||-          +++-+......+.+++..+..   .++..|+.+++.++++
T Consensus       152 ~~~P~lliLDEP----------t~GLDp~~~~~~~~~l~~l~~---~g~~tvlissH~l~e~  200 (293)
T COG1131         152 LHDPELLILDEP----------TSGLDPESRREIWELLRELAK---EGGVTILLSTHILEEA  200 (293)
T ss_pred             hcCCCEEEECCC----------CcCCCHHHHHHHHHHHHHHHh---CCCcEEEEeCCcHHHH
Confidence            467899999995          345577777888888777642   1337789999877654

>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=97.96  E-value=0.00011  Score=60.38  Aligned_cols=29  Identities=24%  Similarity=0.381  Sum_probs=25.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+-|.||+|+|||+++|.+...+
T Consensus        30 ~V~~Gei~~iiGgSGsGKStlLr~I~Gll   58 (263)
T COG1127          30 DVPRGEILAILGGSGSGKSTLLRLILGLL   58 (263)
T ss_pred             eecCCcEEEEECCCCcCHHHHHHHHhccC
Confidence            35678889999999999999999999766

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.95  E-value=6.1e-05  Score=63.13  Aligned_cols=108  Identities=22%  Similarity=0.225  Sum_probs=68.3

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE--EEEeccchhcc-------------------------ccCh--HH
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF--LKVVSSAIIDK-------------------------YIGE--SA  111 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~--~~~~~~~~~~~-------------------------~~~~--~~  111 (292)
                      +.+..+..+-|.|++|+||||+++.+.+.....-  +.+...++...                         +..+  ..
T Consensus        34 f~i~~ge~~glVGESG~GKSTlgr~i~~L~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGG  113 (268)
T COG4608          34 FSIKEGETLGLVGESGCGKSTLGRLILGLEEPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGG  113 (268)
T ss_pred             EEEcCCCEEEEEecCCCCHHHHHHHHHcCcCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCch
Confidence            3467789999999999999999999998775332  22222211110                         0000  11


Q ss_pred             HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          112 RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       112 ~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      +.-+-.++++..-.|.+++.||.-..+          +...+..+.+++..+...   -++..++.+++.
T Consensus       114 QrQRi~IARALal~P~liV~DEpvSaL----------DvSiqaqIlnLL~dlq~~---~~lt~lFIsHDL  170 (268)
T COG4608         114 QRQRIGIARALALNPKLIVADEPVSAL----------DVSVQAQILNLLKDLQEE---LGLTYLFISHDL  170 (268)
T ss_pred             hhhhHHHHHHHhhCCcEEEecCchhhc----------chhHHHHHHHHHHHHHHH---hCCeEEEEEEEH
Confidence            222344555666789999999986553          566777777777766522   255677777654

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.94  E-value=0.00011  Score=59.55  Aligned_cols=106  Identities=20%  Similarity=0.315  Sum_probs=62.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEeccch-----------h---ccccC-hHHHH----------
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSSAI-----------I---DKYIG-ESARL----------  113 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~~~-----------~---~~~~~-~~~~~----------  113 (292)
                      +.++..+.|.||+|+||||+++.++....    .--+.++...+           .   ..+.. .....          
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~~~~~~~G~i~~~g~~~~~~~~~~i~~~~q~~~~~~~~tv~~~l~~~~~~~~L  109 (192)
T cd03232          30 VKPGTLTALMGESGAGKTTLLDVLAGRKTAGVITGEILINGRPLDKNFQRSTGYVEQQDVHSPNLTVREALRFSALLRGL  109 (192)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhCCCcCCCcceEEEECCEehHHHhhhceEEecccCccccCCcHHHHHHHHHHHhcC
Confidence            56788899999999999999999997421    11111111110           0   00010 11111          


Q ss_pred             -----HHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          114 -----IREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       114 -----~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                           .+..+..+....|.++++||...          ..+......+.+++..+..    .+..+|.++++.+
T Consensus       110 SgGe~qrv~la~al~~~p~vlllDEP~~----------~LD~~~~~~l~~~l~~~~~----~~~tiiivtH~~~  169 (192)
T cd03232         110 SVEQRKRLTIGVELAAKPSILFLDEPTS----------GLDSQAAYNIVRFLKKLAD----SGQAILCTIHQPS  169 (192)
T ss_pred             CHHHhHHHHHHHHHhcCCcEEEEeCCCc----------CCCHHHHHHHHHHHHHHHH----cCCEEEEEEcCCh
Confidence                 12223444457889999999643          3367777777777776542    2455777777654

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=97.94  E-value=1.1e-05  Score=65.05  Aligned_cols=72  Identities=21%  Similarity=0.338  Sum_probs=45.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEecc-chh-------cc------ccChHHHHHHHHHHHhhhCCCE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSS-AII-------DK------YIGESARLIREMFGYARDHQPC  127 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~-~~~-------~~------~~~~~~~~~~~~~~~~~~~~~~  127 (292)
                      ..+..++|.||+|+||||++++++..+..  ..+.+... ++.       ..      ..+.........+..+....|.
T Consensus        23 ~~g~~i~I~G~tGSGKTTll~aL~~~i~~~~~~i~ied~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~lR~~pd  102 (186)
T cd01130          23 EARKNILISGGTGSGKTTLLNALLAFIPPDERIITIEDTAELQLPHPNWVRLVTRPGNVEGSGEVTMADLLRSALRMRPD  102 (186)
T ss_pred             hCCCEEEEECCCCCCHHHHHHHHHhhcCCCCCEEEECCccccCCCCCCEEEEEEecCCCCCCCccCHHHHHHHHhccCCC
Confidence            45788999999999999999999987742  12222111 000       00      0001122345666667778899


Q ss_pred             EEEEcccc
Q 022768          128 IIFMDEID  135 (292)
Q Consensus       128 il~lDe~d  135 (292)
                      ++++.|+-
T Consensus       103 ~i~igEir  110 (186)
T cd01130         103 RIIVGEVR  110 (186)
T ss_pred             EEEEEccC
Confidence            99999983

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=97.94  E-value=0.00016  Score=58.56  Aligned_cols=29  Identities=21%  Similarity=0.307  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        14 ~i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   42 (190)
T TIGR01166        14 AAERGEVLALLGANGAGKSTLLLHLNGLL   42 (190)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778899999999999999999999755

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=97.93  E-value=3.5e-05  Score=59.14  Aligned_cols=32  Identities=34%  Similarity=0.739  Sum_probs=25.8

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ++++|+||+||||+++.+++.++  ...++...+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~--~~~i~~D~~   33 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLG--AVVISQDEI   33 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHST--EEEEEHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHCC--CEEEeHHHH
Confidence            78999999999999999999988  444444443

...

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=97.93  E-value=0.00015  Score=59.18  Aligned_cols=25  Identities=20%  Similarity=0.469  Sum_probs=21.5

Q ss_pred             CCCC-ceEEEEcCCCChHHHHHHHHH
Q 022768           63 IKPP-KGVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        63 ~~~~-~~vll~G~~G~GKT~l~~~la   87 (292)
                      +.++ +.++|+||+|+||||+++.++
T Consensus        24 i~~~~~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          24 LGENKRVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             ECCCceEEEEECCCCCChHHHHHHHH
Confidence            4455 469999999999999999998

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.93  E-value=3.4e-05  Score=66.97  Aligned_cols=70  Identities=21%  Similarity=0.334  Sum_probs=44.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC-----CcEEEEecc-chh-------ccccChHHHHHHHHHHHhhhCCCEEEEEc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID-----ANFLKVVSS-AII-------DKYIGESARLIREMFGYARDHQPCIIFMD  132 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~-----~~~~~~~~~-~~~-------~~~~~~~~~~~~~~~~~~~~~~~~il~lD  132 (292)
                      ..+++|.|++|+||||+++++++.+.     ..++.+... ++.       ..........+..++..+....|..+++.
T Consensus       132 ~~~ilI~G~tGSGKTTll~al~~~i~~~~~~~ri~tiEd~~El~~~~~~~v~~~~~~~~~~~~~~l~~aLR~~pD~iivG  211 (299)
T TIGR02782       132 RKNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQLRTSDDAISMTRLLKATLRLRPDRIIVG  211 (299)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhccCCCceEEEECCchhhcCCCCCEEEEEecCCCCCHHHHHHHHhcCCCCEEEEe
Confidence            56899999999999999999998863     222222211 000       00001111145567777778889999999


Q ss_pred             ccc
Q 022768          133 EID  135 (292)
Q Consensus       133 e~d  135 (292)
                      |+-
T Consensus       212 EiR  214 (299)
T TIGR02782       212 EVR  214 (299)
T ss_pred             ccC
Confidence            983

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.93  E-value=7.3e-05  Score=62.38  Aligned_cols=30  Identities=33%  Similarity=0.578  Sum_probs=26.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..++|.|++|+||||+++.++.-+.
T Consensus        26 ~i~~Ge~~~i~G~nGsGKSTL~~~l~GLl~   55 (235)
T COG1122          26 EIEKGERVLLIGPNGSGKSTLLKLLNGLLK   55 (235)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHcCcCc
Confidence            367788899999999999999999998763

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=97.92  E-value=3.7e-05  Score=63.59  Aligned_cols=29  Identities=28%  Similarity=0.342  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        25 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   53 (216)
T TIGR00960        25 HITKGEMVFLVGHSGAGKSTFLKLILGIE   53 (216)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            35778899999999999999999999865

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=97.92  E-value=8.6e-05  Score=63.62  Aligned_cols=38  Identities=21%  Similarity=0.332  Sum_probs=30.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~   99 (292)
                      |+.++..++|.|+||+|||+++..++..+    +.++++++.
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~~g~~vl~iS~   67 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISL   67 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHhcCceEEEEEc
Confidence            46778889999999999999999887654    556666554

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=97.91  E-value=0.00012  Score=60.02  Aligned_cols=28  Identities=36%  Similarity=0.457  Sum_probs=25.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+|||||++.++...
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   50 (205)
T cd03226          23 LYAGEIIALTGKNGAGKTTLAKILAGLI   50 (205)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            5678889999999999999999999865

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=97.91  E-value=0.00024  Score=57.28  Aligned_cols=19  Identities=32%  Similarity=0.574  Sum_probs=18.1

Q ss_pred             EEEEcCCCChHHHHHHHHH
Q 022768           69 VLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la   87 (292)
                      ++|+||.|+|||++++.++
T Consensus         2 ~~ltG~N~~GKst~l~~i~   20 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVG   20 (185)
T ss_pred             EEEECCCCCcHHHHHHHHH
Confidence            6899999999999999999

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.91  E-value=8.4e-05  Score=58.99  Aligned_cols=34  Identities=21%  Similarity=0.336  Sum_probs=29.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      .++|.|+||+|||++|..++..++.+++++....
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~~   36 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATAQ   36 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCCC
Confidence            5899999999999999999999887777766544

>TIGR01188 drrA daunorubicin resistance ABC transporter ATP-binding subunit

Probab=97.91  E-value=2.6e-05  Score=67.98  Aligned_cols=29  Identities=24%  Similarity=0.418  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++..+
T Consensus        15 ~i~~Ge~~~l~G~NGaGKSTLl~~l~Gl~   43 (302)
T TIGR01188        15 KVREGEVFGFLGPNGAGKTTTIRMLTTLL   43 (302)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778889999999999999999999865

This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc.

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.91  E-value=5.4e-05  Score=61.84  Aligned_cols=28  Identities=32%  Similarity=0.387  Sum_probs=25.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~i~G~~   51 (200)
T PRK13540         24 LPAGGLLHLKGSNGAGKTTLLKLIAGLL   51 (200)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            5678899999999999999999999765

>PRK10436 hypothetical protein; Provisional

Probab=97.90  E-value=8.8e-05  Score=67.97  Aligned_cols=103  Identities=18%  Similarity=0.348  Sum_probs=64.2

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---EE
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---FL   95 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---~~   95 (292)
                      ...+.......+++++.-.+...+.+++.+..              +...++++||.|+||||++.++...++.+   ++
T Consensus       185 lRll~~~~~~~~L~~LG~~~~~~~~l~~~~~~--------------~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~  250 (462)
T PRK10436        185 LRLLQQVQQALDLETLGMTPAQLAQFRQALQQ--------------PQGLILVTGPTGSGKTVTLYSALQTLNTAQINIC  250 (462)
T ss_pred             EEEeccccCCCCHHHcCcCHHHHHHHHHHHHh--------------cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEE
Confidence            33333444456788876556667777777654              35669999999999999998888777433   22


Q ss_pred             EEec------cchhccccC-hHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768           96 KVVS------SAIIDKYIG-ESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        96 ~~~~------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      .+-.      .......++ .........+..+....|.+|++.|+-
T Consensus       251 TiEDPvE~~l~gi~Q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEIR  297 (462)
T PRK10436        251 SVEDPVEIPLAGINQTQIHPKAGLTFQRVLRALLRQDPDVIMVGEIR  297 (462)
T ss_pred             EecCCccccCCCcceEeeCCccCcCHHHHHHHHhcCCCCEEEECCCC
Confidence            2221      111110111 112234566667777899999999984

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=97.90  E-value=8.9e-05  Score=70.03  Aligned_cols=103  Identities=20%  Similarity=0.258  Sum_probs=65.2

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---EE
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---FL   95 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---~~   95 (292)
                      ...+....+..+++++.-.++..+.+.+++..+              ...++++||+|+||||++.++.+.++.+   ++
T Consensus       283 lRll~~~~~~~~l~~lg~~~~~~~~l~~~~~~~--------------~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~  348 (564)
T TIGR02538       283 LRILDSSAAQLDIDKLGFEPDQKALFLEAIHKP--------------QGMVLVTGPTGSGKTVSLYTALNILNTEEVNIS  348 (564)
T ss_pred             EEeecCccccCCHHHcCCCHHHHHHHHHHHHhc--------------CCeEEEECCCCCCHHHHHHHHHHhhCCCCceEE
Confidence            334444445567888766666777777776542              5568999999999999999888877432   22


Q ss_pred             EEe------ccchhccccC-hHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768           96 KVV------SSAIIDKYIG-ESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        96 ~~~------~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      .+-      .......... .........+..+....|.+|++.|+-
T Consensus       349 tiEdpvE~~~~~~~q~~v~~~~g~~~~~~l~~~LR~dPDvI~vGEiR  395 (564)
T TIGR02538       349 TAEDPVEINLPGINQVNVNPKIGLTFAAALRSFLRQDPDIIMVGEIR  395 (564)
T ss_pred             EecCCceecCCCceEEEeccccCCCHHHHHHHHhccCCCEEEeCCCC
Confidence            211      1111111111 111234566667778899999999994

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=97.90  E-value=0.00021  Score=59.21  Aligned_cols=25  Identities=24%  Similarity=0.283  Sum_probs=22.3

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ..+..++|.||+|+|||++++.++.
T Consensus        29 ~~g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          29 EGGYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4567789999999999999999987

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.90  E-value=0.00013  Score=59.88  Aligned_cols=29  Identities=34%  Similarity=0.450  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.|++|+|||||++.++...
T Consensus        23 ~i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   51 (204)
T PRK13538         23 TLNAGELVQIEGPNGAGKTSLLRILAGLA   51 (204)
T ss_pred             EECCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778899999999999999999999865

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=97.90  E-value=0.00011  Score=64.67  Aligned_cols=116  Identities=16%  Similarity=0.197  Sum_probs=62.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccchhc--c-------c---------------cC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSAIID--K-------Y---------------IG  108 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~~~~--~-------~---------------~~  108 (292)
                      |+..+..+.|+|+||+|||++|..+|-..         +..+++++...-..  +       +               ..
T Consensus       122 Gi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~~g~d~~~~l~~I~~~~~~  201 (344)
T PLN03187        122 GIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAERFGMDADAVLDNIIYARAY  201 (344)
T ss_pred             CCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHHcCCChhhhcCeEEEecCC
Confidence            57778889999999999999999987422         24567776544110  0       0               00


Q ss_pred             hHH---HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEe
Q 022768          109 ESA---RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT  178 (292)
Q Consensus       109 ~~~---~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~  178 (292)
                      ...   ..+..+........+.+|+||-+-.++.....+... ..+.+..+..++..+..+....++.+|+|.
T Consensus       202 ~~e~~~~~l~~l~~~i~~~~~~LvVIDSital~r~~~~~rg~-l~~rq~~L~~~~~~L~~lA~~~~vavvvTN  273 (344)
T PLN03187        202 TYEHQYNLLLGLAAKMAEEPFRLLIVDSVIALFRVDFTGRGE-LAERQQKLAQMLSRLTKIAEEFNVAVYMTN  273 (344)
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHhhhccccCccc-hHHHHHHHHHHHHHHHHHHHHcCCEEEEEe
Confidence            011   112222222333457899999998876543222111 122233344444433322222366677664

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=97.90  E-value=0.00021  Score=58.44  Aligned_cols=25  Identities=24%  Similarity=0.345  Sum_probs=21.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ..+..++|.||+|+|||++++.++.
T Consensus        27 ~~~~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          27 GSSRFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4457799999999999999999873

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=97.89  E-value=8.4e-05  Score=64.83  Aligned_cols=40  Identities=18%  Similarity=0.268  Sum_probs=31.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~  101 (292)
                      |+..+..+.|+|+||+|||+++..+|-..         +..+++++..+
T Consensus        92 Gi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~  140 (313)
T TIGR02238        92 GIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEG  140 (313)
T ss_pred             CCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCC
Confidence            57788889999999999999999887422         34677777554

This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.

>PRK06762 hypothetical protein; Provisional

Probab=97.89  E-value=4.1e-05  Score=60.54  Aligned_cols=37  Identities=22%  Similarity=0.406  Sum_probs=30.2

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      ..++|+|+||+||||+++.+++.++..+..++...+.
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~~D~~r   39 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQERLGRGTLLVSQDVVR   39 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCeEEecHHHHH
Confidence            4688999999999999999999997666666655444

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.89  E-value=1.1e-05  Score=61.02  Aligned_cols=33  Identities=30%  Similarity=0.628  Sum_probs=29.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      ..++|++|.||+||||++..+|..++.+++.+.
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~~i~is   39 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLEYIEIS   39 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCceEehh
Confidence            457999999999999999999999998888765

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=97.88  E-value=9.5e-05  Score=65.05  Aligned_cols=72  Identities=21%  Similarity=0.313  Sum_probs=46.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEecc-chh-----------cc--ccChHHHHHHHHHHHhhhCCCE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSS-AII-----------DK--YIGESARLIREMFGYARDHQPC  127 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~-~~~-----------~~--~~~~~~~~~~~~~~~~~~~~~~  127 (292)
                      ....+++|.|++|+||||++++++.....  .++.+... ++.           ..  ..+........++..+....|.
T Consensus       158 ~~~~nili~G~tgSGKTTll~aL~~~ip~~~ri~tiEd~~El~l~~~~n~~~~~~~~~~~~~~~~~~~~ll~~~LR~~PD  237 (332)
T PRK13900        158 ISKKNIIISGGTSTGKTTFTNAALREIPAIERLITVEDAREIVLSNHPNRVHLLASKGGQGRAKVTTQDLIEACLRLRPD  237 (332)
T ss_pred             HcCCcEEEECCCCCCHHHHHHHHHhhCCCCCeEEEecCCCccccccCCCEEEEEecCCCCCcCcCcHHHHHHHHhccCCC
Confidence            34678999999999999999999988753  22222100 000           00  0111122355677777888899


Q ss_pred             EEEEcccc
Q 022768          128 IIFMDEID  135 (292)
Q Consensus       128 il~lDe~d  135 (292)
                      .+++.|+-
T Consensus       238 ~IivGEiR  245 (332)
T PRK13900        238 RIIVGELR  245 (332)
T ss_pred             eEEEEecC
Confidence            99999984

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=97.88  E-value=0.00017  Score=59.46  Aligned_cols=31  Identities=29%  Similarity=0.342  Sum_probs=27.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      +..+..+-|.|++|+|||||++.++......
T Consensus        50 i~~Ge~vGiiG~NGaGKSTLlkliaGi~~Pt   80 (249)
T COG1134          50 IYKGERVGIIGHNGAGKSTLLKLIAGIYKPT   80 (249)
T ss_pred             EeCCCEEEEECCCCCcHHHHHHHHhCccCCC
Confidence            5668889999999999999999999877543

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=97.87  E-value=6.3e-05  Score=62.89  Aligned_cols=29  Identities=34%  Similarity=0.399  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        22 ~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   50 (232)
T cd03218          22 SVKQGEIVGLLGPNGAGKTTTFYMIVGLV   50 (232)
T ss_pred             EecCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            35678889999999999999999999765

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=97.87  E-value=0.0002  Score=58.91  Aligned_cols=29  Identities=34%  Similarity=0.423  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        22 ~i~~G~~~~i~G~nGsGKSTLl~~l~G~~   50 (210)
T cd03269          22 SVEKGEIFGLLGPNGAGKTTTIRMILGII   50 (210)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            35778889999999999999999999765

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.87  E-value=0.00018  Score=57.03  Aligned_cols=106  Identities=14%  Similarity=0.211  Sum_probs=58.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcccc-----------------ChHHHHHHHHHHHhhhCCCEEEEE
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYI-----------------GESARLIREMFGYARDHQPCIIFM  131 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~il~l  131 (292)
                      ++|.|++|+|||++|..++...+.+++++......+...                 .+....+...+....  .+.+++|
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~~~~d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~--~~~~VLI   79 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATAEAFDDEMAERIARHRKRRPAHWRTIETPRDLVSALKELD--PGDVVLI   79 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEccCcCCHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcC--CCCEEEE
Confidence            689999999999999999988777787776554332110                 011122233322211  4569999


Q ss_pred             cccccccCCcCCCCCcc-hHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          132 DEIDAIGGRRFSEGTSA-DREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       132 De~d~l~~~~~~~~~~~-~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      |-+..+..+-....... .......+..++..+..    ....+|+++|.
T Consensus        80 Dclt~~~~n~l~~~~~~~~~~~~~~i~~l~~~l~~----~~~~~viVsnE  125 (169)
T cd00544          80 DCLTLWVTNLLFADLEEWEAAIADEIDALLAAVRN----KPGTLILVSNE  125 (169)
T ss_pred             EcHhHHHHHhCCCccccchhHHHHHHHHHHHHHHc----CCCcEEEEECC
Confidence            99888754332211000 12233444555555542    23345555653

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=97.87  E-value=9.7e-05  Score=64.49  Aligned_cols=29  Identities=28%  Similarity=0.358  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++..+
T Consensus        29 ~i~~Gei~gllGpNGaGKSTLl~~l~Gl~   57 (306)
T PRK13537         29 HVQRGECFGLLGPNGAGKTTTLRMLLGLT   57 (306)
T ss_pred             EEeCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            35678889999999999999999999866

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=97.87  E-value=0.00016  Score=59.62  Aligned_cols=28  Identities=43%  Similarity=0.487  Sum_probs=25.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+|||||++.++..+
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~   50 (213)
T cd03301          23 IADGEFVVLLGPSGCGKTTTLRMIAGLE   50 (213)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            5778899999999999999999999865

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>PRK11650 ugpC glycerol-3-phosphate transporter ATP-binding subunit; Provisional

Probab=97.86  E-value=4.4e-05  Score=67.98  Aligned_cols=29  Identities=31%  Similarity=0.484  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        26 ~i~~Ge~~~llG~sGsGKSTLLr~iaGl~   54 (356)
T PRK11650         26 DVADGEFIVLVGPSGCGKSTLLRMVAGLE   54 (356)
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            35678889999999999999999999765

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=97.86  E-value=0.00026  Score=58.92  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=31.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |++++..++|.|+||+|||+++..++...   +.++++++..
T Consensus        12 Gi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~g~~~~y~s~e   53 (224)
T TIGR03880        12 GFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLE   53 (224)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECC
Confidence            57788899999999999999998887543   6666666654

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=97.85  E-value=0.00013  Score=65.03  Aligned_cols=70  Identities=24%  Similarity=0.281  Sum_probs=44.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC-----CcEEEEecc-chh-----------ccccChHHHHHHHHHHHhhhCCCEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID-----ANFLKVVSS-AII-----------DKYIGESARLIREMFGYARDHQPCI  128 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~-----~~~~~~~~~-~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~i  128 (292)
                      ...++++||+|+||||+++++++.+.     ..++.+... ++.           ....+.........+..+....|.+
T Consensus       149 ~GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~~~~~~~~~~~q~evg~~~~~~~~~l~~aLR~~PD~  228 (372)
T TIGR02525       149 AGLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYILGSPDDLLPPAQSQIGRDVDSFANGIRLALRRAPKI  228 (372)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhccCCCceeecccccccCCCccCHHHHHHHhhccCCCE
Confidence            44689999999999999999988762     234433211 110           0111111123445666777789999


Q ss_pred             EEEcccc
Q 022768          129 IFMDEID  135 (292)
Q Consensus       129 l~lDe~d  135 (292)
                      +++.|+-
T Consensus       229 I~vGEiR  235 (372)
T TIGR02525       229 IGVGEIR  235 (372)
T ss_pred             EeeCCCC
Confidence            9999984

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=97.85  E-value=0.00022  Score=58.80  Aligned_cols=29  Identities=34%  Similarity=0.503  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++..+
T Consensus        23 ~i~~G~~~~i~G~nGsGKSTLl~~l~G~~   51 (214)
T cd03292          23 SISAGEFVFLVGPSGAGKSTLLKLIYKEE   51 (214)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            35778889999999999999999999865

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=97.85  E-value=0.00021  Score=58.73  Aligned_cols=28  Identities=32%  Similarity=0.393  Sum_probs=25.3

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+|||||++.++...
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~Gl~   50 (208)
T cd03268          23 VKKGEIYGFLGPNGAGKTTTMKIILGLI   50 (208)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCc
Confidence            5678899999999999999999999764

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>KOG0056 consensus Heavy metal exporter HMT1, ABC superfamily [Inorganic ion transport and metabolism]

Probab=97.84  E-value=4.6e-05  Score=68.57  Aligned_cols=28  Identities=36%  Similarity=0.636  Sum_probs=25.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+-+.||+|.||||+++.+.+-.
T Consensus       561 v~pGktvAlVG~SGaGKSTimRlLfRff  588 (790)
T KOG0056|consen  561 VQPGKTVALVGPSGAGKSTIMRLLFRFF  588 (790)
T ss_pred             ecCCcEEEEECCCCCchhHHHHHHHHHh
Confidence            5778999999999999999999999866

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]

Probab=97.84  E-value=0.00017  Score=57.81  Aligned_cols=28  Identities=36%  Similarity=0.388  Sum_probs=25.3

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..+..+-+-||+|+||||+++.+|.-+
T Consensus        25 ae~Gei~GlLG~NGAGKTT~LRmiatlL   52 (245)
T COG4555          25 AEEGEITGLLGENGAGKTTLLRMIATLL   52 (245)
T ss_pred             eccceEEEEEcCCCCCchhHHHHHHHhc
Confidence            4668889999999999999999999877

>TIGR02314 ABC_MetN D-methionine ABC transporter, ATP-binding protein

Probab=97.84  E-value=4.1e-05  Score=67.74  Aligned_cols=29  Identities=21%  Similarity=0.235  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        27 ~i~~Gei~gIiG~sGaGKSTLlr~I~gl~   55 (343)
T TIGR02314        27 HVPAGQIYGVIGASGAGKSTLIRCVNLLE   55 (343)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            35778889999999999999999999765

Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=97.84  E-value=0.0002  Score=59.55  Aligned_cols=29  Identities=28%  Similarity=0.409  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++..+
T Consensus        22 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (223)
T TIGR03740        22 TVPKNSVYGLLGPNGAGKSTLLKMITGIL   50 (223)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            35678899999999999999999999865

Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=97.84  E-value=0.00017  Score=59.08  Aligned_cols=28  Identities=29%  Similarity=0.312  Sum_probs=25.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++..+
T Consensus        21 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   48 (206)
T TIGR03608        21 IEKGKMYAIIGESGSGKSTLLNIIGLLE   48 (206)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            5678889999999999999999999865

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>PTZ00202 tuzin; Provisional

Probab=97.84  E-value=0.0013  Score=59.32  Aligned_cols=61  Identities=16%  Similarity=0.117  Sum_probs=48.7

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      ...+.+|.+.....|...+...          ....+..+.|.|++|+|||++++.+...++.+.+.++..
T Consensus       260 ~~~~FVGReaEla~Lr~VL~~~----------d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNpr  320 (550)
T PTZ00202        260 VIRQFVSREAEESWVRQVLRRL----------DTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVR  320 (550)
T ss_pred             CccCCCCcHHHHHHHHHHHhcc----------CCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCC
Confidence            3467899999999999887642          123345788999999999999999999998777776655

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=97.83  E-value=0.00016  Score=59.96  Aligned_cols=28  Identities=21%  Similarity=0.299  Sum_probs=25.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+|||||++.++...
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (220)
T cd03263          25 VYKGEIFGLLGHNGAGKTTTLKMLTGEL   52 (220)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            5778889999999999999999999765

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=97.83  E-value=0.00018  Score=60.38  Aligned_cols=29  Identities=31%  Similarity=0.497  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        23 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   51 (236)
T TIGR03864        23 TVRPGEFVALLGPNGAGKSTLFSLLTRLY   51 (236)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            36778899999999999999999999765

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=97.83  E-value=4.8e-05  Score=66.38  Aligned_cols=29  Identities=41%  Similarity=0.539  Sum_probs=25.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+..+..+.|.||+||||||+++.+|.-.
T Consensus        25 ~i~~Gef~vllGPSGcGKSTlLr~IAGLe   53 (338)
T COG3839          25 DIEDGEFVVLLGPSGCGKSTLLRMIAGLE   53 (338)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            35667889999999999999999999644

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.83  E-value=0.00031  Score=62.94  Aligned_cols=25  Identities=32%  Similarity=0.484  Sum_probs=22.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..++++||+|+||||++..+|..+
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~  198 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIY  198 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5678999999999999999998765

>PRK03839 putative kinase; Provisional

Probab=97.83  E-value=1.7e-05  Score=63.63  Aligned_cols=31  Identities=23%  Similarity=0.555  Sum_probs=27.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .++|.|+||+||||+++.+|+.++.+++.++
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            4889999999999999999999998886654

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=97.82  E-value=7.2e-05  Score=61.14  Aligned_cols=28  Identities=32%  Similarity=0.510  Sum_probs=25.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.|++|+||||+++.++...
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (201)
T cd03231          23 LAAGEALQVTGPNGSGKTTLLRILAGLS   50 (201)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            5778899999999999999999999765

The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=97.82  E-value=0.00014  Score=63.93  Aligned_cols=40  Identities=25%  Similarity=0.451  Sum_probs=31.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~  101 (292)
                      |++.+..+.|+|+||+|||+++-.++...         +..+++++..+
T Consensus        98 Gi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~  146 (317)
T PRK04301         98 GIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEG  146 (317)
T ss_pred             CccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCC
Confidence            57778889999999999999999998653         33677777654

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.82  E-value=6.7e-05  Score=61.99  Aligned_cols=29  Identities=31%  Similarity=0.515  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.|++|+||||+++.++...
T Consensus        33 ~i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   61 (214)
T PRK13543         33 HVDAGEALLVQGDNGAGKTTLLRVLAGLL   61 (214)
T ss_pred             EECCCCEEEEEcCCCCCHHHHHHHHhCCC
Confidence            36778899999999999999999999765

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.81  E-value=5.2e-05  Score=71.24  Aligned_cols=29  Identities=34%  Similarity=0.560  Sum_probs=26.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++|+..+-+.||+|+||||++..+-+-.
T Consensus       490 ti~pGe~vALVGPSGsGKSTiasLL~rfY  518 (716)
T KOG0058|consen  490 TIRPGEVVALVGPSGSGKSTIASLLLRFY  518 (716)
T ss_pred             eeCCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            37889999999999999999999998755

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.81  E-value=1.9e-05  Score=63.10  Aligned_cols=36  Identities=25%  Similarity=0.398  Sum_probs=29.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      ++.+++.|+||+||||+++.+++.++.+++.++...
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~~~~~~~~~~D~   37 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVLAEPWLHFGVDS   37 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhhCCCccccCccH
Confidence            457899999999999999999999887776554433

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK00625 shikimate kinase; Provisional

Probab=97.81  E-value=2.2e-05  Score=62.52  Aligned_cols=31  Identities=29%  Similarity=0.498  Sum_probs=28.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +|+|+|.||+||||+++.+++.++.+++.++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhh
Confidence            5899999999999999999999999988776

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=97.81  E-value=4.5e-05  Score=66.44  Aligned_cols=29  Identities=24%  Similarity=0.389  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        24 ~i~~Gei~~l~G~NGaGKTTLl~~l~Gl~   52 (301)
T TIGR03522        24 EAQKGRIVGFLGPNGAGKSTTMKIITGYL   52 (301)
T ss_pred             EEeCCeEEEEECCCCCCHHHHHHHHhCCC
Confidence            35778899999999999999999999765

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK13947 shikimate kinase; Provisional

Probab=97.81  E-value=2.2e-05  Score=62.36  Aligned_cols=31  Identities=29%  Similarity=0.536  Sum_probs=28.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +|+|.|+||+||||+++.+|+.++.+++..+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d   33 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTD   33 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            5899999999999999999999999987655

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=97.80  E-value=0.00014  Score=69.33  Aligned_cols=29  Identities=31%  Similarity=0.510  Sum_probs=26.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++++..+.|.|++|+||||+++.+++..
T Consensus       372 ~i~~G~~vaIvG~SGsGKSTL~~lL~g~~  400 (588)
T PRK11174        372 TLPAGQRIALVGPSGAGKTSLLNALLGFL  400 (588)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            36789999999999999999999999876

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=97.80  E-value=0.001  Score=63.88  Aligned_cols=179  Identities=17%  Similarity=0.186  Sum_probs=100.1

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc--CCcEEEEeccchhc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI--DANFLKVVSSAIID  104 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l--~~~~~~~~~~~~~~  104 (292)
                      ||....+.+-.......|.+.                ...+-++|.-|.|.||||++-.++...  +..+.-+++.+-.+
T Consensus        14 ~P~~~~~~v~R~rL~~~L~~~----------------~~~RL~li~APAGfGKttl~aq~~~~~~~~~~v~Wlslde~dn   77 (894)
T COG2909          14 RPVRPDNYVVRPRLLDRLRRA----------------NDYRLILISAPAGFGKTTLLAQWRELAADGAAVAWLSLDESDN   77 (894)
T ss_pred             CCCCcccccccHHHHHHHhcC----------------CCceEEEEeCCCCCcHHHHHHHHHHhcCcccceeEeecCCccC
Confidence            444455555555555544332                335679999999999999999998633  23332223222111


Q ss_pred             c-------cc----------C-------------hHHHHHHHHHHHhh-hCCCEEEEEcccccccCCcCCCCCcchHHHH
Q 022768          105 K-------YI----------G-------------ESARLIREMFGYAR-DHQPCIIFMDEIDAIGGRRFSEGTSADREIQ  153 (292)
Q Consensus       105 ~-------~~----------~-------------~~~~~~~~~~~~~~-~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~  153 (292)
                      .       ..          +             .....+..++.... ..+|..|||||.|.+-          +....
T Consensus        78 dp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~----------~~~l~  147 (894)
T COG2909          78 DPARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLIS----------DPALH  147 (894)
T ss_pred             CHHHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccC----------cccHH
Confidence            0       00          0             01122334444333 3568899999999983          45566


Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC-hhhcCCCCcceEE--EccCCCHHHHHHHHHHHHcCccCCCCCCHHHH
Q 022768          154 RTLMELLNQLDGFDQLGKVKMIMATNRPDVLD-PALLRPGRLDRKI--EIPLPNEQSRMEILKIHAAGIAKHGEIDYEAV  230 (292)
Q Consensus       154 ~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~-~~l~~~~r~~~~i--~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l  230 (292)
                      ..+..+++.     .++++.+|+++.....+. ..++-++-. .+|  .-=..+.+|-.+++....+- . -...+.+.|
T Consensus       148 ~~l~fLl~~-----~P~~l~lvv~SR~rP~l~la~lRlr~~l-lEi~~~~Lrf~~eE~~~fl~~~~~l-~-Ld~~~~~~L  219 (894)
T COG2909         148 EALRFLLKH-----APENLTLVVTSRSRPQLGLARLRLRDEL-LEIGSEELRFDTEEAAAFLNDRGSL-P-LDAADLKAL  219 (894)
T ss_pred             HHHHHHHHh-----CCCCeEEEEEeccCCCCcccceeehhhH-HhcChHhhcCChHHHHHHHHHcCCC-C-CChHHHHHH
Confidence            666666664     446888888886644332 222211111 122  11235677888887766531 1 234567778


Q ss_pred             HHHcCCCCH
Q 022768          231 VKLAEGFNG  239 (292)
Q Consensus       231 ~~~~~g~~~  239 (292)
                      ...++|+..
T Consensus       220 ~~~teGW~~  228 (894)
T COG2909         220 YDRTEGWAA  228 (894)
T ss_pred             HhhcccHHH
Confidence            888888643

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=97.80  E-value=0.00024  Score=58.92  Aligned_cols=29  Identities=24%  Similarity=0.401  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++..+
T Consensus        22 ~i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   50 (220)
T cd03265          22 RVRRGEIFGLLGPNGAGKTTTIKMLTTLL   50 (220)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            35678889999999999999999999765

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=97.80  E-value=0.00017  Score=63.15  Aligned_cols=40  Identities=23%  Similarity=0.395  Sum_probs=32.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~  101 (292)
                      |+..+..+.|+|+||+|||+++-.+|...         +..+++++..+
T Consensus        91 Gi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~  139 (310)
T TIGR02236        91 GIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTEN  139 (310)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCC
Confidence            57778888999999999999999998663         23677777655

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=97.80  E-value=9.7e-05  Score=60.81  Aligned_cols=28  Identities=39%  Similarity=0.602  Sum_probs=25.3

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+|||||++.++...
T Consensus        24 i~~G~~~~l~G~nGsGKSTLl~~l~G~~   51 (211)
T cd03225          24 IKKGEFVLIVGPNGSGKSTLLRLLNGLL   51 (211)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhcCC
Confidence            5678889999999999999999999765

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>PRK09452 potA putrescine/spermidine ABC transporter ATPase protein; Reviewed

Probab=97.80  E-value=8.2e-05  Score=66.64  Aligned_cols=29  Identities=38%  Similarity=0.444  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        36 ~i~~Ge~~~LlGpsGsGKSTLLr~IaGl~   64 (375)
T PRK09452         36 TINNGEFLTLLGPSGCGKTTVLRLIAGFE   64 (375)
T ss_pred             EEeCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35678889999999999999999999755

>PRK09536 btuD corrinoid ABC transporter ATPase; Reviewed

Probab=97.80  E-value=9.5e-05  Score=66.75  Aligned_cols=29  Identities=41%  Similarity=0.581  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||++|.++..+
T Consensus        25 ~i~~Geiv~liGpNGaGKSTLLk~LaGll   53 (402)
T PRK09536         25 SVREGSLVGLVGPNGAGKTTLLRAINGTL   53 (402)
T ss_pred             EECCCCEEEEECCCCchHHHHHHHHhcCC
Confidence            35778889999999999999999999765

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=97.80  E-value=7.6e-05  Score=65.13  Aligned_cols=69  Identities=19%  Similarity=0.287  Sum_probs=43.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC-----CcEEEEecc-chh----c--cccChHHHHHHHHHHHhhhCCCEEEEEcc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID-----ANFLKVVSS-AII----D--KYIGESARLIREMFGYARDHQPCIIFMDE  133 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~-----~~~~~~~~~-~~~----~--~~~~~~~~~~~~~~~~~~~~~~~il~lDe  133 (292)
                      ..+++|.|++|+||||++++++....     ..++.+... ++.    .  ............++..+....|..+++-|
T Consensus       144 ~~nilI~G~tGSGKTTll~aL~~~i~~~~~~~rivtiEd~~El~~~~~n~v~l~~~~~~~~~~lv~~aLR~~PD~IivGE  223 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTAEIQCAAENAVALHTSDTVDMARLLKSTMRLRPDRIIVGE  223 (323)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHhcCCCCceEEEecCCcccccCCCCEEEeccCCCcCHHHHHHHHhCCCCCEEEEee
Confidence            56799999999999999999998762     122222211 110    0  00011122345666777778899999999


Q ss_pred             c
Q 022768          134 I  134 (292)
Q Consensus       134 ~  134 (292)
                      +
T Consensus       224 i  224 (323)
T PRK13833        224 V  224 (323)
T ss_pred             c
Confidence            8

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=97.80  E-value=6.7e-05  Score=61.78  Aligned_cols=27  Identities=41%  Similarity=0.550  Sum_probs=23.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++ .+.|.||+|+||||+++.++..+
T Consensus        23 i~~g-~~~i~G~nGsGKSTLl~~l~Gl~   49 (211)
T cd03264          23 LGPG-MYGLLGPNGAGKTTLMRILATLT   49 (211)
T ss_pred             EcCC-cEEEECCCCCCHHHHHHHHhCCC
Confidence            5567 88999999999999999999755

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional

Probab=97.79  E-value=5.2e-05  Score=67.96  Aligned_cols=29  Identities=31%  Similarity=0.326  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        41 ~i~~Ge~~~llGpsGsGKSTLLr~IaGl~   69 (377)
T PRK11607         41 TIYKGEIFALLGASGCGKSTLLRMLAGFE   69 (377)
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35678889999999999999999999755

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=97.79  E-value=7.4e-05  Score=61.84  Aligned_cols=29  Identities=38%  Similarity=0.542  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.|++|+|||||++.++...
T Consensus        27 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (218)
T cd03266          27 TVKPGEVTGLLGPNGAGKTTTLRMLAGLL   55 (218)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCc
Confidence            35678889999999999999999999765

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=97.79  E-value=0.00041  Score=54.63  Aligned_cols=24  Identities=29%  Similarity=0.484  Sum_probs=20.6

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHH
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      .+...+|+||.|+|||+++++++-
T Consensus        20 ~~~~~~i~G~NgsGKS~~l~~i~~   43 (162)
T cd03227          20 EGSLTIITGPNGSGKSTILDAIGL   43 (162)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            345789999999999999999864

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>TIGR00767 rho transcription termination factor Rho

Probab=97.79  E-value=0.00018  Score=64.05  Aligned_cols=29  Identities=38%  Similarity=0.542  Sum_probs=25.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +..+..++|.||+|+|||++++.+++...
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHHHHHHHhhc
Confidence            56688899999999999999999999763

Members of this family differ in the specificity of RNA binding.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=97.79  E-value=0.00025  Score=67.63  Aligned_cols=28  Identities=32%  Similarity=0.444  Sum_probs=26.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ++++..+.|.|++|+||||+++.++...
T Consensus       366 i~~G~~~aIvG~sGsGKSTLl~ll~gl~  393 (582)
T PRK11176        366 IPAGKTVALVGRSGSGKSTIANLLTRFY  393 (582)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            6788999999999999999999999876

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=97.79  E-value=0.00038  Score=58.07  Aligned_cols=37  Identities=32%  Similarity=0.356  Sum_probs=28.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      |+.++..++|.|+||+|||+++..++...   +.++++++
T Consensus        16 Gi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is   55 (229)
T TIGR03881        16 GIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVT   55 (229)
T ss_pred             CCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEE
Confidence            57889999999999999999998876432   44555554

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=97.78  E-value=0.00029  Score=58.43  Aligned_cols=29  Identities=38%  Similarity=0.486  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        26 ~i~~G~~~~i~G~nGsGKSTLl~~l~Gl~   54 (220)
T cd03293          26 SVEEGEFVALVGPSGCGKSTLLRIIAGLE   54 (220)
T ss_pred             EEeCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            35678889999999999999999999865

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13695 putative NTPase; Provisional

Probab=97.78  E-value=0.00063  Score=54.20  Aligned_cols=23  Identities=43%  Similarity=0.664  Sum_probs=20.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++|.|++|+||||+++.++..+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999987765

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=97.78  E-value=6.4e-05  Score=60.75  Aligned_cols=139  Identities=19%  Similarity=0.215  Sum_probs=63.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS  147 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~  147 (292)
                      .++|+||+|||||.++-.+|+.++.|++..+...........+.+..   -..... - .=++|||-..-         +
T Consensus         3 v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Driq~y~~l~v~Sgrp~---~~el~~-~-~RiyL~~r~l~---------~   68 (233)
T PF01745_consen    3 VYLIVGPTGTGKTALAIALAQKTGAPVISLDRIQCYPELSVGSGRPT---PSELKG-T-RRIYLDDRPLS---------D   68 (233)
T ss_dssp             EEEEE-STTSSHHHHHHHHHHHH--EEEEE-SGGG-GGGTTTTT------SGGGTT---EEEES----GG---------G
T ss_pred             EEEEECCCCCChhHHHHHHHHHhCCCEEEecceecccccccccCCCC---HHHHcc-c-ceeeecccccc---------C
Confidence            47899999999999999999999999999886554433221111111   001111 1 23788875332         1


Q ss_pred             chHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCC---CCcc-eEEEccCCCHHHHHHHHHHHHcCccCC
Q 022768          148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRP---GRLD-RKIEIPLPNEQSRMEILKIHAAGIAKH  222 (292)
Q Consensus       148 ~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~---~r~~-~~i~l~~p~~~~r~~i~~~~~~~~~~~  222 (292)
                      +.-...+....++..+...... + .+|.-...-+.++.-..+.   ..|. .+..++.|+.+....-.+.+..+....
T Consensus        69 G~i~a~ea~~~Li~~v~~~~~~-~-~~IlEGGSISLl~~m~~~~~w~~~f~w~i~rl~l~d~~~f~~ra~~Rv~~ML~p  145 (233)
T PF01745_consen   69 GIINAEEAHERLISEVNSYSAH-G-GLILEGGSISLLNCMAQDPYWSLDFRWHIRRLRLPDEEVFMARAKRRVRQMLRP  145 (233)
T ss_dssp             -S--HHHHHHHHHHHHHTTTTS-S-EEEEEE--HHHHHHHHH-TTTSSSSEEEEEE-----HHHHHHHHHHHHHHHHS-
T ss_pred             CCcCHHHHHHHHHHHHHhcccc-C-ceEEeCchHHHHHHHHhcccccCCCeEEEEEEECCChHHHHHHHHHHHHHhcCC
Confidence            1223334445555555554442 3 3555544433333322221   1233 344778899887776666555544333

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=97.77  E-value=0.00031  Score=58.46  Aligned_cols=29  Identities=28%  Similarity=0.367  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        44 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   72 (224)
T cd03220          44 EVPRGERIGLIGRNGAGKSTLLRLLAGIY   72 (224)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778899999999999999999999865

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=97.77  E-value=0.00011  Score=60.66  Aligned_cols=29  Identities=41%  Similarity=0.563  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        22 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (213)
T cd03259          22 TVEPGEFLALLGPSGCGKTTLLRLIAGLE   50 (213)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            35778889999999999999999999765

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=97.76  E-value=0.0002  Score=60.89  Aligned_cols=29  Identities=31%  Similarity=0.510  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        23 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   51 (255)
T PRK11248         23 TLESGELLVVLGPSGCGKTTLLNLIAGFV   51 (255)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778899999999999999999999765

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=97.76  E-value=0.00018  Score=63.70  Aligned_cols=29  Identities=31%  Similarity=0.454  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++..+
T Consensus        63 ~i~~Gei~gLlGpNGaGKSTLl~~L~Gl~   91 (340)
T PRK13536         63 TVASGECFGLLGPNGAGKSTIARMILGMT   91 (340)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            36778889999999999999999999865

>PRK11432 fbpC ferric transporter ATP-binding subunit; Provisional

Probab=97.76  E-value=9.5e-05  Score=65.70  Aligned_cols=29  Identities=41%  Similarity=0.495  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        28 ~i~~Ge~~~llGpsGsGKSTLLr~IaGl~   56 (351)
T PRK11432         28 TIKQGTMVTLLGPSGCGKTTVLRLVAGLE   56 (351)
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            35678889999999999999999999765

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=97.76  E-value=0.00013  Score=59.43  Aligned_cols=29  Identities=31%  Similarity=0.523  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        22 ~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~   50 (198)
T TIGR01189        22 TLNAGEALQVTGPNGIGKTTLLRILAGLL   50 (198)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778899999999999999999999865

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>PRK13949 shikimate kinase; Provisional

Probab=97.76  E-value=2.8e-05  Score=61.77  Aligned_cols=31  Identities=32%  Similarity=0.577  Sum_probs=28.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .++|+|+||+||||+++.+|+.++.+++..+
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~~id~D   33 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLSFIDLD   33 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCeeccc
Confidence            5899999999999999999999998887765

>PRK06217 hypothetical protein; Validated

Probab=97.76  E-value=2.9e-05  Score=62.56  Aligned_cols=31  Identities=29%  Similarity=0.471  Sum_probs=28.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .|+|.|++|+||||+++.+++.++.+++..+
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcC
Confidence            4899999999999999999999998876655

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=97.75  E-value=0.00012  Score=64.10  Aligned_cols=71  Identities=21%  Similarity=0.349  Sum_probs=44.9

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---C--CcEEEEecc-chh------ccccChHHHHHHHHHHHhhhCCCEEEEEc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---D--ANFLKVVSS-AII------DKYIGESARLIREMFGYARDHQPCIIFMD  132 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~--~~~~~~~~~-~~~------~~~~~~~~~~~~~~~~~~~~~~~~il~lD  132 (292)
                      ...+++|.|++|+||||++++++...   .  ..++.+... ++.      ..+.......+..++..+....|..|++.
T Consensus       147 ~~~~ilI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El~~~~~~~v~~~~~~~~~~~~ll~~aLR~~PD~IivG  226 (319)
T PRK13894        147 AHRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYVQYHTSIDVNMTALLKTTLRMRPDRILVG  226 (319)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCccccCCCCEEEEecCCCCCHHHHHHHHhcCCCCEEEEe
Confidence            36789999999999999999999864   1  122221111 110      00000112235567777788899999999


Q ss_pred             ccc
Q 022768          133 EID  135 (292)
Q Consensus       133 e~d  135 (292)
                      |+-
T Consensus       227 EiR  229 (319)
T PRK13894        227 EVR  229 (319)
T ss_pred             ccC
Confidence            983

>PTZ00035 Rad51 protein; Provisional

Probab=97.75  E-value=0.00025  Score=62.61  Aligned_cols=28  Identities=32%  Similarity=0.420  Sum_probs=24.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      |+..+..+.|+|++|+|||+++..++..
T Consensus       114 Gi~~G~iteI~G~~GsGKT~l~~~l~~~  141 (337)
T PTZ00035        114 GIETGSITELFGEFRTGKTQLCHTLCVT  141 (337)
T ss_pred             CCCCCeEEEEECCCCCchhHHHHHHHHH
Confidence            6777888999999999999999998853

>PRK14530 adenylate kinase; Provisional

Probab=97.75  E-value=3.1e-05  Score=64.00  Aligned_cols=31  Identities=26%  Similarity=0.515  Sum_probs=27.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ..++|.|+||+||||+++.+++.++.+++..
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            4699999999999999999999998777644

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.75  E-value=2.8e-05  Score=62.50  Aligned_cols=29  Identities=31%  Similarity=0.515  Sum_probs=25.3

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ++|.|+||+||||+++.++..++..++.+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is~   30 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLSA   30 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            78999999999999999999998655544

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=97.75  E-value=0.00068  Score=55.12  Aligned_cols=102  Identities=22%  Similarity=0.358  Sum_probs=53.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcccc--------------------ChHHHHHHHHHHHhh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYI--------------------GESARLIREMFGYAR  122 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~  122 (292)
                      ++.++|.||+|+||||.+--+|..+   +..+--+....+.....                    ......+...+....
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~D~~R~ga~eQL~~~a~~l~vp~~~~~~~~~~~~~~~~~l~~~~   80 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLKGKKVALISADTYRIGAVEQLKTYAEILGVPFYVARTESDPAEIAREALEKFR   80 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEESTSSTHHHHHHHHHHHHHTEEEEESSTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhccccceeecCCCCCccHHHHHHHHHHHhccccchhhcchhhHHHHHHHHHHHh
Confidence            3568999999999999887777655   44444444333221000                    011222333344443


Q ss_pred             hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      ...-.+++||=.-+.         ..+......+..++....    ...+.++..++.
T Consensus        81 ~~~~D~vlIDT~Gr~---------~~d~~~~~el~~~~~~~~----~~~~~LVlsa~~  125 (196)
T PF00448_consen   81 KKGYDLVLIDTAGRS---------PRDEELLEELKKLLEALN----PDEVHLVLSATM  125 (196)
T ss_dssp             HTTSSEEEEEE-SSS---------STHHHHHHHHHHHHHHHS----SSEEEEEEEGGG
T ss_pred             hcCCCEEEEecCCcc---------hhhHHHHHHHHHHhhhcC----CccceEEEeccc
Confidence            333468888876332         224455556666665542    235566666544

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=97.75  E-value=0.00046  Score=54.68  Aligned_cols=29  Identities=31%  Similarity=0.557  Sum_probs=25.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||.|+||||++|.+|.-+.
T Consensus        25 l~~Ge~~~i~G~NG~GKTtLLRilaGLl~   53 (209)
T COG4133          25 LNAGEALQITGPNGAGKTTLLRILAGLLR   53 (209)
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHHcccC
Confidence            46788899999999999999999998763

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=97.74  E-value=0.00031  Score=59.93  Aligned_cols=29  Identities=24%  Similarity=0.313  Sum_probs=26.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++..+
T Consensus        46 ~i~~Ge~~~liG~NGsGKSTLlk~L~Gl~   74 (264)
T PRK13546         46 KAYEGDVIGLVGINGSGKSTLSNIIGGSL   74 (264)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            46778889999999999999999999875

>TIGR03265 PhnT2 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein

Probab=97.74  E-value=0.00011  Score=65.43  Aligned_cols=28  Identities=46%  Similarity=0.542  Sum_probs=25.3

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        27 i~~Ge~~~l~GpsGsGKSTLLr~iaGl~   54 (353)
T TIGR03265        27 VKKGEFVCLLGPSGCGKTTLLRIIAGLE   54 (353)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHCCC
Confidence            5678889999999999999999999765

This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.

>PRK14532 adenylate kinase; Provisional

Probab=97.74  E-value=3e-05  Score=62.64  Aligned_cols=30  Identities=27%  Similarity=0.530  Sum_probs=26.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +++|.|+||+||||+++.+|+.++.+++.+
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            489999999999999999999998766544

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=97.74  E-value=3.2e-05  Score=60.18  Aligned_cols=31  Identities=29%  Similarity=0.521  Sum_probs=27.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +++|+|+||+||||+++.++..++.+++..+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d   31 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD   31 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            4889999999999999999999998887655

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>TIGR01288 nodI ATP-binding ABC transporter family nodulation protein NodI

Probab=97.74  E-value=0.00027  Score=61.63  Aligned_cols=28  Identities=36%  Similarity=0.519  Sum_probs=25.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        27 i~~Ge~~~l~G~NGaGKSTLl~~l~Gl~   54 (303)
T TIGR01288        27 IARGECFGLLGPNGAGKSTIARMLLGMI   54 (303)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            6778899999999999999999999765

This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.74  E-value=0.00023  Score=63.63  Aligned_cols=102  Identities=22%  Similarity=0.405  Sum_probs=59.3

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC---cEEEEeccchhcccc--ChHHHHHHHHHH-------------------
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA---NFLKVVSSAIIDKYI--GESARLIREMFG-------------------  119 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~---~~~~~~~~~~~~~~~--~~~~~~~~~~~~-------------------  119 (292)
                      ..+..++|.|+.|||||++.+++...+..   .++.+..........  |.+.   ...|.                   
T Consensus        20 ~~~~~~fv~G~~GtGKs~l~~~i~~~~~~~~~~~~~~a~tg~AA~~i~~G~T~---hs~f~i~~~~~~~~~~~~~~~~~~   96 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSFLIKAIIDYLRSRGKKVLVTAPTGIAAFNIPGGRTI---HSFFGIPINNNEKSQCKISKNSRL   96 (364)
T ss_pred             cCCcEEEEEcCCCCChhHHHHHHHHHhccccceEEEecchHHHHHhccCCcch---HHhcCccccccccccccccccchh
Confidence            45678999999999999999999987743   344333332222111  1110   01110                   


Q ss_pred             HhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC----CCCCCCeEEEEEeC
Q 022768          120 YARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG----FDQLGKVKMIMATN  179 (292)
Q Consensus       120 ~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~----~~~~~~~~vi~t~~  179 (292)
                      ......-.+|+|||+-.+           .......+...++.+..    ..+.+++.+|+...
T Consensus        97 ~~~l~~~~~lIiDEism~-----------~~~~l~~i~~~lr~i~~~~~~~~pFGG~~vil~GD  149 (364)
T PF05970_consen   97 RERLRKADVLIIDEISMV-----------SADMLDAIDRRLRDIRKSKDSDKPFGGKQVILFGD  149 (364)
T ss_pred             hhhhhhheeeecccccch-----------hHHHHHHHHHhhhhhhcccchhhhcCcceEEeehh
Confidence            001122369999999776           66666666666665543    23455676666553

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.74  E-value=0.00047  Score=64.08  Aligned_cols=39  Identities=31%  Similarity=0.387  Sum_probs=31.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh----cCCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN----IDANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~----l~~~~~~~~~~  100 (292)
                      |++++..++|.|+||+|||+++..++..    .+.+++++...
T Consensus        17 Glp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e   59 (484)
T TIGR02655        17 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE   59 (484)
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe
Confidence            5788999999999999999999988543    25677666644

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=97.74  E-value=0.00031  Score=59.50  Aligned_cols=29  Identities=38%  Similarity=0.646  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++..+
T Consensus        26 ~i~~Ge~~~I~G~NGsGKSTLl~~i~Gl~   54 (251)
T PRK09544         26 ELKPGKILTLLGPNGAGKSTLVRVVLGLV   54 (251)
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhCCC
Confidence            36778899999999999999999999765

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=97.73  E-value=0.00032  Score=66.93  Aligned_cols=28  Identities=32%  Similarity=0.568  Sum_probs=25.8

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.|++|+||||+++.+++..
T Consensus       358 i~~G~~v~IvG~sGsGKSTLl~lL~gl~  385 (588)
T PRK13657        358 AKPGQTVAIVGPTGAGKSTLINLLQRVF  385 (588)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            6789999999999999999999999766

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=97.73  E-value=0.00033  Score=58.74  Aligned_cols=29  Identities=28%  Similarity=0.391  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.|++|+|||||++.++...
T Consensus        43 ~i~~Ge~~~i~G~NGsGKSTLl~~i~Gl~   71 (236)
T cd03267          43 TIEKGEIVGFIGPNGAGKTTTLKILSGLL   71 (236)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            35678889999999999999999999765

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=97.72  E-value=0.00037  Score=56.64  Aligned_cols=37  Identities=11%  Similarity=0.063  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          239 GADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      ...|+.+-+-....|...+-+.|...++.++...+..
T Consensus       157 ~~~ir~i~~~l~~~a~~~~i~~i~~~~~~~~~~~~~~  193 (197)
T PRK12339        157 LPEYRTIMDYSIADARGYNIKVIDTDNYREARNPLLD  193 (197)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCeecCccHHHHHHHHHH
Confidence            3467777777777788888899999999999887654

>PRK11153 metN DL-methionine transporter ATP-binding subunit; Provisional

Probab=97.72  E-value=0.00011  Score=65.29  Aligned_cols=29  Identities=28%  Similarity=0.266  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        27 ~i~~Gei~~iiG~nGsGKSTLlk~L~Gl~   55 (343)
T PRK11153         27 HIPAGEIFGVIGASGAGKSTLIRCINLLE   55 (343)
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35778889999999999999999999765

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=97.72  E-value=0.00039  Score=67.19  Aligned_cols=78  Identities=18%  Similarity=0.213  Sum_probs=50.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh---cCCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN---IDANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~---l~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |+..+..++|+||+|+|||+++..++..   .+..+++++..+-...                .....+..+..+-..+.
T Consensus        56 Gip~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t~~~~~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~  135 (790)
T PRK09519         56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (790)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchhHHHHHHcCCChhHeEEecCCCHHHHHHHHHHHhh
Confidence            5778889999999999999999776653   3556666664442220                01112222323333334


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+.+|+||-+..++.
T Consensus       136 ~~~~~LVVIDSI~aL~~  152 (790)
T PRK09519        136 SGALDIVVIDSVAALVP  152 (790)
T ss_pred             cCCCeEEEEcchhhhcc
Confidence            45689999999998874

>PRK11000 maltose/maltodextrin transporter ATP-binding protein; Provisional

Probab=97.72  E-value=0.00012  Score=65.55  Aligned_cols=29  Identities=38%  Similarity=0.499  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        25 ~i~~Ge~~~l~G~nGsGKSTLL~~iaGl~   53 (369)
T PRK11000         25 DIHEGEFVVFVGPSGCGKSTLLRMIAGLE   53 (369)
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35678889999999999999999999765

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=97.71  E-value=0.00027  Score=67.50  Aligned_cols=30  Identities=27%  Similarity=0.330  Sum_probs=26.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .++++..+.|.|++|+||||+++.+++...
T Consensus       363 ~i~~Ge~iaIvG~SGsGKSTLl~lL~gl~~  392 (592)
T PRK10790        363 SVPSRGFVALVGHTGSGKSTLASLLMGYYP  392 (592)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcccC
Confidence            367899999999999999999999998763

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=97.71  E-value=0.00023  Score=69.23  Aligned_cols=28  Identities=29%  Similarity=0.488  Sum_probs=25.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ++++..+.|.|++|+||||+++.+++..
T Consensus       488 i~~G~~iaIvG~sGsGKSTLlklL~gl~  515 (694)
T TIGR03375       488 IRPGEKVAIIGRIGSGKSTLLKLLLGLY  515 (694)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            6789999999999999999999999766

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=97.71  E-value=0.00033  Score=56.55  Aligned_cols=126  Identities=22%  Similarity=0.361  Sum_probs=71.7

Q ss_pred             cCChHHHHhcC--CCCCceEEEEcCCCChHHHHHHHHHHhc---CCcE--------------------------------
Q 022768           52 LMNPELFLRVG--IKPPKGVLLYGPPGTGKTLLARAIASNI---DANF--------------------------------   94 (292)
Q Consensus        52 ~~~~~~~~~~~--~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~--------------------------------   94 (292)
                      ..+.++-.++|  ++-+.-++|-|+.|+|||.++..++--+   +..+                                
T Consensus        12 ~gndelDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l   91 (235)
T COG2874          12 SGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRL   91 (235)
T ss_pred             CCcHHHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHHHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhccee
Confidence            44555666664  5666668888999999999999998432   1111                                


Q ss_pred             --EEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCe
Q 022768           95 --LKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKV  172 (292)
Q Consensus        95 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  172 (292)
                        +.++...+. .........+..+....+.+...+++||-+..+...          .......+++..+..+...++ 
T Consensus        92 ~~~~~~~~~~~-~~~~~~~~~L~~l~~~~k~~~~dViIIDSls~~~~~----------~~~~~vl~fm~~~r~l~d~gK-  159 (235)
T COG2874          92 LFFPVNLEPVN-WGRRSARKLLDLLLEFIKRWEKDVIIIDSLSAFATY----------DSEDAVLNFMTFLRKLSDLGK-  159 (235)
T ss_pred             EEEEecccccc-cChHHHHHHHHHHHhhHHhhcCCEEEEecccHHhhc----------ccHHHHHHHHHHHHHHHhCCC-
Confidence              222211111 112234455666666667777789999999877421          112234444444433333444 


Q ss_pred             EEEEEeCCCCCCChhhcC
Q 022768          173 KMIMATNRPDVLDPALLR  190 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~  190 (292)
                      ++|.|.| |+.++++...
T Consensus       160 vIilTvh-p~~l~e~~~~  176 (235)
T COG2874         160 VIILTVH-PSALDEDVLT  176 (235)
T ss_pred             EEEEEeC-hhhcCHHHHH
Confidence            3555555 5556665444

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=97.70  E-value=0.00071  Score=57.13  Aligned_cols=28  Identities=29%  Similarity=0.514  Sum_probs=24.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        22 i~~Ge~~~i~G~NGsGKSTLlk~L~G~~   49 (246)
T cd03237          22 ISESEVIGILGPNGIGKTTFIKMLAGVL   49 (246)
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4567889999999999999999999875

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.70  E-value=0.0001  Score=55.76  Aligned_cols=31  Identities=29%  Similarity=0.398  Sum_probs=27.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      +.++..++|.|+.|+||||+++.+++.++..
T Consensus        19 l~~~~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        19 LDFGTVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CCCCCEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            3557789999999999999999999999754

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=97.70  E-value=0.00033  Score=59.68  Aligned_cols=91  Identities=15%  Similarity=0.188  Sum_probs=58.0

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHH
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESAR  112 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~  112 (292)
                      +|+-.+++++.+.+...-.           ..++.+.|+.|.+|+||+++++..|...+..++.+....-.  ...+...
T Consensus         9 ~lVlf~~ai~hi~ri~RvL-----------~~~~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~y--~~~~f~~   75 (268)
T PF12780_consen    9 NLVLFDEAIEHIARISRVL-----------SQPRGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITKGY--SIKDFKE   75 (268)
T ss_dssp             -----HHHHHHHHHHHHHH-----------CSTTEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTSTTT--HHHHHHH
T ss_pred             ceeeHHHHHHHHHHHHHHH-----------cCCCCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeCCc--CHHHHHH
Confidence            4566777777776665442           24567899999999999999999999888888877654321  2234455


Q ss_pred             HHHHHHHHhhh-CCCEEEEEccccc
Q 022768          113 LIREMFGYARD-HQPCIIFMDEIDA  136 (292)
Q Consensus       113 ~~~~~~~~~~~-~~~~il~lDe~d~  136 (292)
                      .++.++..+.. ..+.+++++|-+.
T Consensus        76 dLk~~~~~ag~~~~~~vfll~d~qi  100 (268)
T PF12780_consen   76 DLKKALQKAGIKGKPTVFLLTDSQI  100 (268)
T ss_dssp             HHHHHHHHHHCS-S-EEEEEECCCS
T ss_pred             HHHHHHHHHhccCCCeEEEecCccc
Confidence            66666655543 4578888887543

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>PRK06547 hypothetical protein; Provisional

Probab=97.70  E-value=5.7e-05  Score=60.05  Aligned_cols=35  Identities=31%  Similarity=0.381  Sum_probs=29.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .....|+|.|++|+||||+++.+++.++.+++..+
T Consensus        13 ~~~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         13 GGMITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            44567888899999999999999999887776554

>PRK13948 shikimate kinase; Provisional

Probab=97.70  E-value=5.4e-05  Score=60.72  Aligned_cols=35  Identities=26%  Similarity=0.377  Sum_probs=31.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .++.+++|+|.+|+||||+++.+++.++.+++..+
T Consensus         8 ~~~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D   42 (182)
T PRK13948          8 RPVTWVALAGFMGTGKSRIGWELSRALMLHFIDTD   42 (182)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEECC
Confidence            45688999999999999999999999999998655

>TIGR03258 PhnT 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT

Probab=97.70  E-value=0.00047  Score=61.56  Aligned_cols=28  Identities=43%  Similarity=0.534  Sum_probs=25.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        28 i~~Ge~~~llGpsGsGKSTLLr~iaGl~   55 (362)
T TIGR03258        28 IEAGELLALIGKSGCGKTTLLRAIAGFV   55 (362)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            5678889999999999999999999754

This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.

>COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=97.70  E-value=0.00042  Score=54.14  Aligned_cols=26  Identities=35%  Similarity=0.621  Sum_probs=23.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +.++..+-|+||+|+||||++..+|.
T Consensus        33 v~~Ge~vaiVG~SGSGKSTLl~vlAG   58 (228)
T COG4181          33 VKRGETVAIVGPSGSGKSTLLAVLAG   58 (228)
T ss_pred             ecCCceEEEEcCCCCcHHhHHHHHhc
Confidence            57788999999999999999999983

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=97.69  E-value=4.4e-05  Score=60.98  Aligned_cols=29  Identities=38%  Similarity=0.780  Sum_probs=25.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .++|.||||+||||+|+.+++.++.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~hls   30 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLPHLD   30 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEc
Confidence            48999999999999999999997665544

>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]

Probab=97.69  E-value=8.3e-05  Score=58.54  Aligned_cols=31  Identities=29%  Similarity=0.410  Sum_probs=26.6

Q ss_pred             hcCCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           60 RVGIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        60 ~~~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ++.+..+..+-|.||+|+||||+...+|.-.
T Consensus        19 dl~v~~ge~vAi~GpSGaGKSTLLnLIAGF~   49 (231)
T COG3840          19 DLTVPAGEIVAILGPSGAGKSTLLNLIAGFE   49 (231)
T ss_pred             EEeecCCcEEEEECCCCccHHHHHHHHHhcc
Confidence            4456778889999999999999999999644

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=97.69  E-value=0.00026  Score=69.04  Aligned_cols=29  Identities=31%  Similarity=0.543  Sum_probs=26.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++++..+.|.|++|+||||+++.++...
T Consensus       501 ~i~~Ge~vaIvG~sGsGKSTLlklL~gl~  529 (710)
T TIGR03796       501 TLQPGQRVALVGGSGSGKSTIAKLVAGLY  529 (710)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            36789999999999999999999999766

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=97.69  E-value=0.0002  Score=62.71  Aligned_cols=40  Identities=25%  Similarity=0.320  Sum_probs=30.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc------C---CcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI------D---ANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l------~---~~~~~~~~~~  101 (292)
                      |+.++..+.++|+||+|||+++..++...      +   ..+++++..+
T Consensus        92 Gi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~  140 (316)
T TIGR02239        92 GIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEG  140 (316)
T ss_pred             CCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCC
Confidence            57778889999999999999999988532      1   2556666554

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=97.69  E-value=0.00046  Score=65.59  Aligned_cols=28  Identities=36%  Similarity=0.526  Sum_probs=25.8

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.|++|+||||+++.+++..
T Consensus       355 i~~G~~v~IvG~sGsGKSTLl~lL~gl~  382 (571)
T TIGR02203       355 IEPGETVALVGRSGSGKSTLVNLIPRFY  382 (571)
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            5778999999999999999999999766

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.69  E-value=0.00028  Score=59.09  Aligned_cols=30  Identities=20%  Similarity=0.228  Sum_probs=26.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .++++..+.+.|+.|+||||++|.+...+-
T Consensus        46 ~IP~G~ivgflGaNGAGKSTtLKmLTGll~   75 (325)
T COG4586          46 EIPKGEIVGFLGANGAGKSTTLKMLTGLLL   75 (325)
T ss_pred             ecCCCcEEEEEcCCCCcchhhHHHHhCccc
Confidence            468888899999999999999999997663

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=97.68  E-value=0.00018  Score=68.35  Aligned_cols=28  Identities=32%  Similarity=0.457  Sum_probs=25.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ++++..+.|.||+|+||||+++.+++..
T Consensus       363 i~~G~~~aivG~sGsGKSTL~~ll~g~~  390 (574)
T PRK11160        363 IKAGEKVALLGRTGCGKSTLLQLLTRAW  390 (574)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            6789999999999999999999999766

>PRK14531 adenylate kinase; Provisional

Probab=97.68  E-value=4.9e-05  Score=61.19  Aligned_cols=30  Identities=30%  Similarity=0.533  Sum_probs=27.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .+++.||||+||||+++.++..++.+++.+
T Consensus         4 ~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          4 RLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            589999999999999999999998877654

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=97.68  E-value=0.00041  Score=58.08  Aligned_cols=29  Identities=34%  Similarity=0.502  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        24 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (234)
T cd03251          24 DIPAGETVALVGPSGSGKSTLVNLIPRFY   52 (234)
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            35778889999999999999999999765

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=97.68  E-value=0.00035  Score=66.50  Aligned_cols=29  Identities=31%  Similarity=0.544  Sum_probs=26.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.|++|+||||+++.++..+
T Consensus       362 ~i~~Ge~i~IvG~sGsGKSTLlklL~gl~  390 (576)
T TIGR02204       362 TVRPGETVALVGPSGAGKSTLFQLLLRFY  390 (576)
T ss_pred             EecCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            36789999999999999999999999876

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.68  E-value=0.00017  Score=64.24  Aligned_cols=23  Identities=43%  Similarity=0.668  Sum_probs=21.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++|.|.||||||.++-.++..+
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh
Confidence            57899999999999999999988

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=97.67  E-value=0.00032  Score=65.22  Aligned_cols=77  Identities=22%  Similarity=0.294  Sum_probs=53.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcccc------C----------------------hH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYI------G----------------------ES  110 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~------~----------------------~~  110 (292)
                      |+.++..++|.||||+|||+++-.++...   +.+++++...+-.....      |                      ..
T Consensus       259 G~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~ge~~~y~s~eEs~~~i~~~~~~lg~~~~~~~~~g~l~~~~~~p~~~~~  338 (484)
T TIGR02655       259 GFFKDSIILATGATGTGKTLLVSKFLENACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGL  338 (484)
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCHHHHHHHHHHcCCChHHHhhCCcEEEEEcccccCCh
Confidence            57888999999999999999998888755   55666666443322110      0                      11


Q ss_pred             HHHHHHHHHHhhhCCCEEEEEccccccc
Q 022768          111 ARLIREMFGYARDHQPCIIFMDEIDAIG  138 (292)
Q Consensus       111 ~~~~~~~~~~~~~~~~~il~lDe~d~l~  138 (292)
                      ...+..+...+....|.+|+||-+..+.
T Consensus       339 ~~~~~~i~~~i~~~~~~~vvIDsi~~~~  366 (484)
T TIGR02655       339 EDHLQIIKSEIADFKPARIAIDSLSALA  366 (484)
T ss_pred             HHHHHHHHHHHHHcCCCEEEEcCHHHHH
Confidence            3445556666666788999999998763

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PF05872 DUF853: Bacterial protein of unknown function (DUF853); InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold

Probab=97.67  E-value=0.00047  Score=61.81  Aligned_cols=89  Identities=15%  Similarity=0.268  Sum_probs=59.4

Q ss_pred             CCE-EEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEE--Ecc
Q 022768          125 QPC-IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKI--EIP  201 (292)
Q Consensus       125 ~~~-il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i--~l~  201 (292)
                      +|. |+||||+|.++...       .....+.+.++.+.+.+    .++-|++.|..|.+++..+++  .++..|  -+.
T Consensus       254 kPklVfFfDEAHLLF~da-------~kall~~ieqvvrLIRS----KGVGv~fvTQ~P~DiP~~VL~--QLGnrIQHaLR  320 (502)
T PF05872_consen  254 KPKLVFFFDEAHLLFNDA-------PKALLDKIEQVVRLIRS----KGVGVYFVTQNPTDIPDDVLG--QLGNRIQHALR  320 (502)
T ss_pred             CceEEEEEechhhhhcCC-------CHHHHHHHHHHHHHhhc----cCceEEEEeCCCCCCCHHHHH--hhhhHHHHHHh
Confidence            454 56799999997433       55555555566655543    478899999999999999987  555555  566


Q ss_pred             CCCHHHHHHHHHHHHcCccCCCCCCH
Q 022768          202 LPNEQSRMEILKIHAAGIAKHGEIDY  227 (292)
Q Consensus       202 ~p~~~~r~~i~~~~~~~~~~~~~~~~  227 (292)
                      .+++.+++.+ +.....+..+...|.
T Consensus       321 AfTP~DqKav-k~aa~tfr~np~~d~  345 (502)
T PF05872_consen  321 AFTPKDQKAV-KAAAETFRPNPAFDT  345 (502)
T ss_pred             cCCHhHHHHH-HHHHHhCCCCccccH
Confidence            6777777665 334444444444443

This family is restricted to bacterial proteins, none of which have currently been characterised.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.67  E-value=4.3e-05  Score=59.28  Aligned_cols=28  Identities=29%  Similarity=0.686  Sum_probs=24.7

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ++|+|+||+||||+++.+++.++..++.
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~   29 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFID   29 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEe
Confidence            6899999999999999999998776553

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=97.67  E-value=0.0069  Score=52.92  Aligned_cols=47  Identities=19%  Similarity=0.171  Sum_probs=31.4

Q ss_pred             EEEccCCCHHHHHHHHHHHHcCccCCC-CC---CHHHHHHHcCCCCHHHHHH
Q 022768          197 KIEIPLPNEQSRMEILKIHAAGIAKHG-EI---DYEAVVKLAEGFNGADLRN  244 (292)
Q Consensus       197 ~i~l~~p~~~~r~~i~~~~~~~~~~~~-~~---~~~~l~~~~~g~~~~di~~  244 (292)
                      .+.++.++.+|-..+++.+........ ..   ..+.+...+.| +++++..
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~~~~~~~~~e~~~~~s~G-Np~el~k  308 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRSRVDEELVLEKLFLSSNG-NPRELEK  308 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCccccCCCCHHHHHHHHHhcCC-CHHHhcc
Confidence            789999999999999998876543332 11   22334444454 8888754

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	292
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-122
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		4e-86
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		7e-82
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		2e-78
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		2e-76
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-74
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		3e-65
2ce7_A	476	Edta Treated Length = 476		4e-53
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		1e-52
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-52
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		2e-52
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		2e-52
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		1e-51
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		2e-51
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		2e-51
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		2e-51
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		1e-49
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		9e-47
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		1e-44
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		4e-44
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		7e-44
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		8e-44
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		9e-44
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		1e-43
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		2e-38
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		2e-38
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		2e-38
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		3e-38
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		4e-38
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		7e-36
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		1e-35
3b9p_A	297	Spastin Length = 297		2e-35
3vfd_A	389	Human Spastin Aaa Domain Length = 389		4e-35
4a3v_B	95	Yeast Regulatory Particle Proteasome Assembly Chape		8e-12
2krk_A	86	Solution Nmr Structure Of 26s Protease Regulatory S		2e-10
3kw6_A	78	Crystal Structure Of A Domain Of 26s Proteasome Reg		3e-10
3vlf_B	88	Crystal Structure Of Yeast Proteasome Interacting P		1e-09
1ofh_A	310	Asymmetric Complex Between Hslv And I-domain Delete		2e-08
3t15_A	293	Structure Of Green-Type Rubisco Activase From Tobac		3e-06
1um8_A	376	Crystal Structure Of Helicobacter Pylori Clpx Lengt		5e-06
3hte_A	363	Crystal Structure Of Nucleotide-Free Hexameric Clpx		1e-04
3hws_A	363	Crystal Structure Of Nucleotide-Bound Hexameric Clp		1e-04
1g4a_E	443	Crystal Structures Of The Hslvu Peptidase-Atpase Co		7e-04
1do2_A	442	Trigonal Crystal Form Of Heat Shock Locus U (Hslu)		7e-04
1e94_E	449	Hslv-Hslu From E.Coli Length = 449		7e-04
2dvw_B	83	Structure Of The Oncoprotein Gankyrin In Complex Wi		8e-04

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  435 bits (1118), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 202/286 (70%), Positives = 240/286 (83%)
Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
           +TTLTIMR LPRE DP+VYNM   + G +++  +GGL++QIRELRE IELPL NPE+F R
Sbjct: 150 ITTLTIMRILPRETDPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQR 209
Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGY 120
           VGIKPPKGVLLYGPPGTGKTLLA+A+A+ I ANF+   +S I+DKYIGESAR+IREMF Y
Sbjct: 210 VGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDKYIGESARIIREMFAY 269
Query: 121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR 180
           A++H+PCIIFMDE+DAIGGRRFSEGTSADREIQRTLMELL Q+DGFD LG+ K+IMATNR
Sbjct: 270 AKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIMATNR 329
Query: 181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGA 240
           PD LDPALLRPGRLDRK+EIPLPNE  R+EI KIH A + K GE D+EA VK+++GFNGA
Sbjct: 330 PDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGA 389
Query: 241 DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYN 286
           D+RN  TEAG  AIR +RD++  +D MKAVRK+ E KKLE +  Y 
Sbjct: 390 DIRNCATEAGFFAIRDDRDHINPDDLMKAVRKVAEVKKLEGTIEYQ 435

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score =  314 bits (804), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 147/277 (53%), Positives = 198/277 (71%), Gaps = 1/277 (0%)
Query: 10  LPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGV 69
           LP  +DP V  M  E+  +V+YS VGG  DQI +LRE +ELPL++PE F  +GI PPKG+
Sbjct: 187 LPPRIDPSVTMMTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGI 246
Query: 70  LLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCII 129
           LLYGPPGTGKTL ARA+A+  DA F++V+ S ++ KY+GE AR++RE+F  AR  + CII
Sbjct: 247 LLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACII 306
Query: 130 FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALL 189
           F DEIDA+GG RF +G   D E+QRT++EL+ QLDGFD  G +K++ ATNRP+ LDPALL
Sbjct: 307 FFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALL 366
Query: 190 RPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEA 249
           RPGR+DRK+E  LP+ + R  I +IH+  ++    I +E + +L     GA+LR+VCTEA
Sbjct: 367 RPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEA 426
Query: 250 GMSAIRAERDYVIHEDFMKAVRK-LNEAKKLESSAHY 285
           GM AIRA R     +DF+KAV K ++  KK  S++ Y
Sbjct: 427 GMFAIRARRKVATEKDFLKAVDKVISGYKKFSSTSRY 463

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score =  300 bits (768), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 147/267 (55%), Positives = 196/267 (73%), Gaps = 9/267 (3%)
Query: 7   MRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPP 66
           MRA   EVD        E P NV Y  +GGL  Q++E+RE +ELPL +PELF +VGI+PP
Sbjct: 1   MRAKAMEVD--------ERP-NVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPP 51
Query: 67  KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQP 126
           KG+LLYGPPGTGKTLLA+A+A+  +A F++VV S ++ K+IGE A L++++F  A++  P
Sbjct: 52  KGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAP 111
Query: 127 CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDP 186
            IIF+DEIDAI  +R    T  DRE+QRTLM+LL ++DGFD  G VK+I ATNRPD+LDP
Sbjct: 112 SIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDP 171
Query: 187 ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVC 246
           A+LRPGR DR IE+P P+E+ R+EILKIH   +    +++ E + K+ EG  GA+L+ +C
Sbjct: 172 AILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAIC 231
Query: 247 TEAGMSAIRAERDYVIHEDFMKAVRKL 273
           TEAGM+AIR  RDYV  +DF KAV K+
Sbjct: 232 TEAGMNAIRELRDYVTMDDFRKAVEKI 258

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score =  288 bits (737), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 140/266 (52%), Positives = 188/266 (70%)
Query: 8   RALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPK 67
           + L  + DP+V  M+ E   + +Y  VGGL+ QI+E++E IELP+ +PELF  +GI  PK
Sbjct: 124 KVLENKADPLVSLMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPK 183
Query: 68  GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPC 127
           GV+LYGPPGTGKTLLARA+A + D  F++V  + ++ KYIGE +R++RE+F  AR+H P 
Sbjct: 184 GVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPS 243
Query: 128 IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPA 187
           IIFMDEID+IG  R       D E+QRT++ELLNQLDGF+    +K+IMATNR D+LDPA
Sbjct: 244 IIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMATNRLDILDPA 303
Query: 188 LLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCT 247
           LLRPGR+DRKIE P P+  +R EIL+IH+  +     I+   V +   G +GAD++ VCT
Sbjct: 304 LLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCT 363
Query: 248 EAGMSAIRAERDYVIHEDFMKAVRKL 273
           EAGM A+R  R +V  EDF  AV K+
Sbjct: 364 EAGMYALRERRIHVTQEDFELAVGKV 389

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score =  282 bits (721), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 139/280 (49%), Positives = 193/280 (68%), Gaps = 1/280 (0%)
Query: 6   IMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKP 65
           I+  LP E D  V  M  ++    +YS VGGL  QI EL E+I LP+   + F  +GI+ 
Sbjct: 155 ILDTLPSEFDSRVKAMEVDEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRA 214
Query: 66  PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQ 125
           PKG L+YGPPGTGKTLLARA A+  +A FLK+ +  ++  YIGE A+L+R+ F  A++  
Sbjct: 215 PKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQMYIGEGAKLVRDAFALAKEKA 274
Query: 126 PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD 185
           P IIF+DE+DAIG +RF    S DRE+QRT++ELLNQLDGF    +VK++ ATNR DVLD
Sbjct: 275 PTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSSDDRVKVLAATNRVDVLD 334
Query: 186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNV 245
           PALLR GRLDRKIE PLP+E SR +IL+IH+  +    +I+++ + +  + FNGA L+ V
Sbjct: 335 PALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAV 394
Query: 246 CTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
             EAGM A+R  +  V HEDF++ + ++ +A+K +S + Y
Sbjct: 395 TVEAGMIALRNGQSSVKHEDFVEGISEV-QARKSKSVSFY 433

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  276 bits (705), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 133/275 (48%), Positives = 194/275 (70%)
Query: 3   TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG 62
           T++I+  L  + DP+V  M  +     SYS +GGL  QI+E++ES+ELPL +PEL+  +G
Sbjct: 153 TMSIVGVLQDDADPMVSVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMG 212
Query: 63  IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR 122
           IKPPKGV+LYG PGTGKTLLA+A+A+   A FL++V S +I KY+G+  RL R++F  A 
Sbjct: 213 IKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELIQKYLGDGPRLCRQIFKVAG 272
Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD 182
           ++ P I+F+DEIDAIG +R+   +  +REIQRT++ELLNQLDGFD  G VK+IMATN+ +
Sbjct: 273 ENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIE 332
Query: 183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL 242
            LDPAL+RPGR+DRKI    P+  ++ +IL IH + +    +++ E +V   +  +GAD+
Sbjct: 333 TLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADI 392
Query: 243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAK 277
           + +CTEAG+ A+R  R  V  EDF +A  ++ + K
Sbjct: 393 QAMCTEAGLLALRERRMQVTAEDFKQAKERVMKNK 427

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score =  244 bits (624), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 120/261 (45%), Positives = 178/261 (68%), Gaps = 1/261 (0%)
Query: 10  LPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGV 69
           LP + D  +  M   +  +V+Y+ VGGL  Q +E+RE++ELPL+  +L+ ++GI PP+GV
Sbjct: 150 LPPDSDSSISVMGENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGV 209
Query: 70  LLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCII 129
           LLYGPPGTGKT+L +A+A++  A F++V  S  + KY+GE  R++R++F  AR++ P II
Sbjct: 210 LLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSII 269
Query: 130 FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALL 189
           F+DE+D+I  +RF   T +DRE+QR L+ELL Q+DGFDQ   VK+IMATNR D LDPALL
Sbjct: 270 FIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALL 329
Query: 190 RPGRLDRKIEIP-LPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTE 248
           RPGRLDRKIE P L + + R  I    A+ ++   E D ++++   +  +GA +  +  E
Sbjct: 330 RPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQE 389
Query: 249 AGMSAIRAERDYVIHEDFMKA 269
           AG+ A+R  R  ++  D  +A
Sbjct: 390 AGLRAVRKNRYVILQSDLEEA 410

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score =  204 bits (520), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 106/254 (41%), Positives = 159/254 (62%), Gaps = 3/254 (1%)
Query: 22  LHEDPGN--VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGK 79
           +++  GN  V++  VGG  + I EL+E +E  L +P  F R+G + PKG+LL GPPGTGK
Sbjct: 4   MYKPSGNKRVTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGK 62
Query: 80  TLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGG 139
           TLLARA+A   +  F  +  S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G 
Sbjct: 63  TLLARAVAGEANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGR 122
Query: 140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
            R +       E ++TL +LL ++DGFD    + ++ ATNRPD+LDPALLRPGR D+KI 
Sbjct: 123 HRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIV 182
Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
           +  P+   R +IL+IH        +++ E + K   GF GADL N+  EA + A R  RD
Sbjct: 183 VDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAREGRD 242
Query: 260 YVIHEDFMKAVRKL 273
            +  +DF +A+ ++
Sbjct: 243 KITMKDFEEAIDRV 256

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score =  202 bits (515), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 96/222 (43%), Positives = 140/222 (63%)
Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
            V++  +GGL D  REL+E ++ P+ +P+ FL+ G+ P KGVL YGPPG GKTLLA+AIA
Sbjct: 11  QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIA 70
Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
           +   ANF+ +    ++  + GES   +RE+F  AR   PC++F DE+D+I   R      
Sbjct: 71  NECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD 130
Query: 148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS 207
                 R + ++L ++DG      V +I ATNRPD++DPA+LRPGRLD+ I IPLP+E+S
Sbjct: 131 GGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKS 190
Query: 208 RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEA 249
           R+ ILK +        ++D E + K+  GF+GADL  +C  A
Sbjct: 191 RVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRA 232

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score =  202 bits (514), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 105/254 (41%), Positives = 158/254 (62%), Gaps = 3/254 (1%)
Query: 22  LHEDPGN--VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGK 79
           +++  GN  V++  VGG  + I EL+E +E  L +P  F R+G + PKG+LL GPPGTG 
Sbjct: 4   MYKPSGNKRVTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGA 62
Query: 80  TLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGG 139
           TLLARA+A   +  F  +  S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G 
Sbjct: 63  TLLARAVAGEANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGR 122
Query: 140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
            R +       E ++TL +LL ++DGFD    + ++ ATNRPD+LDPALLRPGR D+KI 
Sbjct: 123 HRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKKIV 182
Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
           +  P+   R +IL+IH        +++ E + K   GF GADL N+  EA + A R  RD
Sbjct: 183 VDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAREGRD 242
Query: 260 YVIHEDFMKAVRKL 273
            +  +DF +A+ ++
Sbjct: 243 KITMKDFEEAIDRV 256

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score =  199 bits (507), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 107/253 (42%), Positives = 154/253 (60%), Gaps = 3/253 (1%)
Query: 13  EVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLY 72
           E +P+      E    V Y  VGG   Q+ +++E +ELPL +P LF  +G+KPP+G+LLY
Sbjct: 185 EGEPIKREDEEESLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLY 244
Query: 73  GPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMD 132
           GPPGTGKTL+ARA+A+   A F  +    I+ K  GES   +R+ F  A  + P IIF+D
Sbjct: 245 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFID 304
Query: 133 EIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPG 192
           E+DAI  +R  E T  + E +R + +LL  +DG  Q   V ++ ATNRP+ +DPAL R G
Sbjct: 305 ELDAIAPKR--EKTHGEVE-RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG 361
Query: 193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMS 252
           R DR+++I +P+   R+EIL+IH   +    ++D E V     G  GADL  +C+EA + 
Sbjct: 362 RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQ 421
Query: 253 AIRAERDYVIHED 265
           AIR + D +  ED
Sbjct: 422 AIRKKMDLIDLED 434

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score =  199 bits (505), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/253 (41%), Positives = 154/253 (60%), Gaps = 3/253 (1%)
Query: 13  EVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLY 72
           E +P+      E    V Y  +GG   Q+ +++E +ELPL +P LF  +G+KPP+G+LLY
Sbjct: 185 EGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLY 244
Query: 73  GPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMD 132
           GPPGTGKTL+ARA+A+   A F  +    I+ K  GES   +R+ F  A  + P IIF+D
Sbjct: 245 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFID 304
Query: 133 EIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPG 192
           E+DAI  +R  E T  + E +R + +LL  +DG  Q   V ++ ATNRP+ +DPAL R G
Sbjct: 305 ELDAIAPKR--EKTHGEVE-RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG 361
Query: 193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMS 252
           R DR+++I +P+   R+EIL+IH   +    ++D E V     G  GADL  +C+EA + 
Sbjct: 362 RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQ 421
Query: 253 AIRAERDYVIHED 265
           AIR + D +  ED
Sbjct: 422 AIRKKMDLIDLED 434

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score =  199 bits (506), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 107/253 (42%), Positives = 154/253 (60%), Gaps = 3/253 (1%)
Query: 13  EVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLY 72
           E +P+      E    V Y  VGG   Q+ +++E +ELPL +P LF  +G+KPP+G+LLY
Sbjct: 185 EGEPIKREDEEESLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLY 244
Query: 73  GPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMD 132
           GPPGTGKTL+ARA+A+   A F  +    I+ K  GES   +R+ F  A  + P IIF+D
Sbjct: 245 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFID 304
Query: 133 EIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPG 192
           E+DAI  +R  E T  + E +R + +LL  +DG  Q   V ++ ATNRP+ +DPAL R G
Sbjct: 305 ELDAIAPKR--EKTHGEVE-RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG 361
Query: 193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMS 252
           R DR+++I +P+   R+EIL+IH   +    ++D E V     G  GADL  +C+EA + 
Sbjct: 362 RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQ 421
Query: 253 AIRAERDYVIHED 265
           AIR + D +  ED
Sbjct: 422 AIRKKMDLIDLED 434

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  199 bits (505), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/253 (41%), Positives = 154/253 (60%), Gaps = 3/253 (1%)
Query: 13  EVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLY 72
           E +P+      E    V Y  +GG   Q+ +++E +ELPL +P LF  +G+KPP+G+LLY
Sbjct: 185 EGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLY 244
Query: 73  GPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMD 132
           GPPGTGKTL+ARA+A+   A F  +    I+ K  GES   +R+ F  A  + P IIF+D
Sbjct: 245 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFID 304
Query: 133 EIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPG 192
           E+DAI  +R  E T  + E +R + +LL  +DG  Q   V ++ ATNRP+ +DPAL R G
Sbjct: 305 ELDAIAPKR--EKTHGEVE-RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG 361
Query: 193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMS 252
           R DR+++I +P+   R+EIL+IH   +    ++D E V     G  GADL  +C+EA + 
Sbjct: 362 RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQ 421
Query: 253 AIRAERDYVIHED 265
           AIR + D +  ED
Sbjct: 422 AIRKKMDLIDLED 434

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  199 bits (505), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/253 (41%), Positives = 154/253 (60%), Gaps = 3/253 (1%)
Query: 13  EVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLY 72
           E +P+      E    V Y  +GG   Q+ +++E +ELPL +P LF  +G+KPP+G+LLY
Sbjct: 185 EGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLY 244
Query: 73  GPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMD 132
           GPPGTGKTL+ARA+A+   A F  +    I+ K  GES   +R+ F  A  + P IIF+D
Sbjct: 245 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFID 304
Query: 133 EIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPG 192
           E+DAI  +R  E T  + E +R + +LL  +DG  Q   V ++ ATNRP+ +DPAL R G
Sbjct: 305 ELDAIAPKR--EKTHGEVE-RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG 361
Query: 193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMS 252
           R DR+++I +P+   R+EIL+IH   +    ++D E V     G  GADL  +C+EA + 
Sbjct: 362 RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQ 421
Query: 253 AIRAERDYVIHED 265
           AIR + D +  ED
Sbjct: 422 AIRKKMDLIDLED 434

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  199 bits (505), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/253 (41%), Positives = 154/253 (60%), Gaps = 3/253 (1%)
Query: 13  EVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLY 72
           E +P+      E    V Y  +GG   Q+ +++E +ELPL +P LF  +G+KPP+G+LLY
Sbjct: 185 EGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLY 244
Query: 73  GPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMD 132
           GPPGTGKTL+ARA+A+   A F  +    I+ K  GES   +R+ F  A  + P IIF+D
Sbjct: 245 GPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFID 304
Query: 133 EIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPG 192
           E+DAI  +R  E T  + E +R + +LL  +DG  Q   V ++ ATNRP+ +DPAL R G
Sbjct: 305 ELDAIAPKR--EKTHGEVE-RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG 361
Query: 193 RLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMS 252
           R DR+++I +P+   R+EIL+IH   +    ++D E V     G  GADL  +C+EA + 
Sbjct: 362 RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQ 421
Query: 253 AIRAERDYVIHED 265
           AIR + D +  ED
Sbjct: 422 AIRKKMDLIDLED 434

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score =  193 bits (490), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 105/253 (41%), Positives = 153/253 (60%), Gaps = 1/253 (0%)
Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           ML ED    +++ V G  +   E+ E +E  L  P  F ++G K PKGVL+ GPPGTGKT
Sbjct: 1   MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT 59
Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
           LLA+AIA      F  +  S  ++ ++G  A  +R+MF  A+   PCIIF+DEIDA+G +
Sbjct: 60  LLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQ 119
Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R +       E ++TL ++L ++DGF+    + +I ATNRPDVLDPALLRPGR DR++ +
Sbjct: 120 RGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVV 179
Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
            LP+ + R +ILK+H   +    +ID   + +   GF+GADL N+  EA + A R  +  
Sbjct: 180 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRV 239
Query: 261 VIHEDFMKAVRKL 273
           V   +F KA  K+
Sbjct: 240 VSMVEFEKAKDKI 252

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score =  183 bits (465), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 100/247 (40%), Positives = 150/247 (60%), Gaps = 3/247 (1%)
Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
           NV +  + G  +   E+ E ++  L  PE +  +G K PKGVLL GPPGTGKTLLA+A+A
Sbjct: 7   NVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVA 65
Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG-T 146
                 F  +  S+ I+ ++G  A  +R++F  A+   P IIF+DEIDAIG  R + G  
Sbjct: 66  GEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVV 125
Query: 147 SADREIQRTLMELLNQLDGF-DQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNE 205
           S + E ++TL +LL ++DGF  +   V ++ ATNRP++LDPAL+RPGR DR++ +  P+ 
Sbjct: 126 SGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDF 185
Query: 206 QSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHED 265
             R+EILK+H  G+    +++ + V KL  G  GADL N+  EA + A R  +  V  + 
Sbjct: 186 NGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKEVRQQH 245
Query: 266 FMKAVRK 272
             +AV +
Sbjct: 246 LKEAVER 252

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score =  176 bits (446), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 157/274 (57%), Gaps = 26/274 (9%)
Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
           NV+++ +G L D   EL  +I  P+ NP+ F  +G+  P GVLL GPPG GKTLLA+A+A
Sbjct: 6   NVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVA 65
Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
           +    NF+ V    +++ Y+GES R +R++F  A++  PC+IF DE+DA+  RR    T 
Sbjct: 66  NESGLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETG 125
Query: 148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS 207
           A     R + +LL ++DG +   +V ++ ATNRPD++DPA+LRPGRLD+ + + LP    
Sbjct: 126 AS---VRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPAD 182
Query: 208 RMEILKIHAAGIAKHG-------EIDYEAVVK--LAEGFNGADLRNVCTEAGMSAIRAER 258
           R+ ILK     I K+G       +++ EA+      + + GADL  +  EA + A+R E 
Sbjct: 183 RLAILKT----ITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASICALRQE- 237
Query: 259 DYVIHEDFMKAVRKLNEAKKLE-SSAHYNADFGK 291
                   M   +  NE  +L+ S  H+   F K
Sbjct: 238 --------MARQKSGNEKGELKVSHKHFEEAFKK 263

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score =  174 bits (442), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 96/249 (38%), Positives = 148/249 (59%), Gaps = 4/249 (1%)
Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
            VS+  V G+ +   E+RE ++  L +PE FL++G K PKG LL GPPG GKTLLA+A+A
Sbjct: 2   GVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVA 60
Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
           +     FL +  +  ++   G  A  +R +F  AR   PCI+++DEIDA+G +R +  + 
Sbjct: 61  TEAQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSG 120
Query: 148 -ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQ 206
            ++ E ++TL +LL ++DG      V ++ +TNR D+LD AL+RPGRLDR + I LP  Q
Sbjct: 121 FSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQ 180
Query: 207 SRMEILKIH--AAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE 264
            R EI + H  +  + +      + + +L  GF+GAD+ N+C EA + A R     V   
Sbjct: 181 ERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAAREGHTSVHTL 240
Query: 265 DFMKAVRKL 273
           +F  AV ++
Sbjct: 241 NFEYAVERV 249

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score =  174 bits (440), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 105/254 (41%), Positives = 154/254 (60%), Gaps = 2/254 (0%)
Query: 20  NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGK 79
            +L E P  V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GK
Sbjct: 20  RVLTEAP-KVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGK 77
Query: 80  TLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGG 139
           T LARA+A      F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G 
Sbjct: 78  THLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGR 137
Query: 140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
           +R S     + E ++TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I 
Sbjct: 138 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 197
Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
           I  P+ + R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R 
Sbjct: 198 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRR 257
Query: 260 YVIHEDFMKAVRKL 273
            +  +D  +A  ++
Sbjct: 258 KITMKDLEEAADRV 271

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score =  173 bits (439), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 105/254 (41%), Positives = 154/254 (60%), Gaps = 2/254 (0%)
Query: 20  NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGK 79
            +L E P  V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GK
Sbjct: 29  RVLTEAP-KVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGK 86
Query: 80  TLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGG 139
           T LARA+A      F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G 
Sbjct: 87  THLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGR 146
Query: 140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
           +R S     + E ++TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I 
Sbjct: 147 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 206
Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
           I  P+ + R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R 
Sbjct: 207 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRR 266
Query: 260 YVIHEDFMKAVRKL 273
            +  +D  +A  ++
Sbjct: 267 KITMKDLEEAADRV 280

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score =  173 bits (439), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 105/250 (42%), Positives = 153/250 (61%), Gaps = 2/250 (0%)
Query: 20  NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGK 79
           ++L E P  V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GK
Sbjct: 5   SVLTEAP-KVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGK 62
Query: 80  TLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGG 139
           T LARA+A      F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G 
Sbjct: 63  THLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGR 122
Query: 140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
           +R S     + E ++TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I 
Sbjct: 123 KRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 182
Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
           I  P+ + R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R 
Sbjct: 183 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRR 242
Query: 260 YVIHEDFMKA 269
            +  +D  +A
Sbjct: 243 KITMKDLEEA 252

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score =  173 bits (439), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 105/249 (42%), Positives = 152/249 (61%), Gaps = 2/249 (0%)
Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           +L E P  V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GKT
Sbjct: 30  VLTEAP-KVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKT 87
Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
            LARA+A      F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G +
Sbjct: 88  HLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRK 147
Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R S     + E ++TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I I
Sbjct: 148 RGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAI 207
Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
             P+ + R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R  
Sbjct: 208 DAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRK 267
Query: 261 VIHEDFMKA 269
           +  +D  +A
Sbjct: 268 ITMKDLEEA 276

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score =  156 bits (394), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 92/243 (37%), Positives = 146/243 (60%), Gaps = 8/243 (3%)
Query: 14  VDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYG 73
           +DP    +L E P NV +  V GL      L+E++ LP+  P LF +   KP  G+LLYG
Sbjct: 2   IDPFTA-ILSEKP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-KGNRKPTSGILLYG 58
Query: 74  PPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDE 133
           PPGTGK+ LA+A+A+  ++ F  V SS ++ K++GES +L++++F  AR+++P IIF+D+
Sbjct: 59  PPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQ 118
Query: 134 IDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGR 193
           +DA+ G R    + A R I+  L+  +N + G D  G V ++ ATN P  LD A+ R  R
Sbjct: 119 VDALTGTRGEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLGATNIPWQLDSAIRR--R 174
Query: 194 LDRKIEIPLPNEQSRMEILKIHAAGI-AKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMS 252
            +R+I IPLP+  +R  + +I+         + DY  +  + EG++G+D+  V  +A M 
Sbjct: 175 FERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQ 234
Query: 253 AIR 255
            IR
Sbjct: 235 PIR 237

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score =  155 bits (393), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 90/236 (38%), Positives = 144/236 (61%), Gaps = 7/236 (2%)
Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           +L E P NV +  V GL      L+E++ LP+  P LF +   KP  G+LLYGPPGTGK+
Sbjct: 41  ILSEKP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-KGNRKPTSGILLYGPPGTGKS 98
Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
            LA+A+A+  ++ F  V SS ++ K++GES +L++++F  AR+++P IIF+D++DA+ G 
Sbjct: 99  YLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGT 158
Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R    + A R I+  L+  +N + G D  G V ++ ATN P  LD A+ R  R +R+I I
Sbjct: 159 RGEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLGATNIPWQLDSAIRR--RFERRIYI 214
Query: 201 PLPNEQSRMEILKIHAAGI-AKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           PLP+  +R  + +I+     +   + DY  +  + EG++G+D+  V  +A M  IR
Sbjct: 215 PLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIR 270

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score =  155 bits (393), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 91/235 (38%), Positives = 142/235 (60%), Gaps = 7/235 (2%)
Query: 22  LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL 81
           L E P NV +  V GL      L+E++ LP+  P LF +   KP  G+LLYGPPGTGK+ 
Sbjct: 18  LSEKP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-KGNRKPTSGILLYGPPGTGKSY 75
Query: 82  LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR 141
           LA+A+A+  ++ F  V SS ++ K++GES +L++++F  AR+++P IIF+DE+DA+ G R
Sbjct: 76  LAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDEVDALTGTR 135
Query: 142 FSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIP 201
               + A R I+  L+  +N + G D  G V ++ ATN P  LD A+ R  R +R+I IP
Sbjct: 136 GEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLGATNIPWQLDSAIRR--RFERRIYIP 191
Query: 202 LPNEQSRMEILKIHAAGI-AKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           LP+  +R  + +I+         + DY  +  + EG++G+D+  V  +A M  IR
Sbjct: 192 LPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIR 246

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score =  155 bits (391), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 90/236 (38%), Positives = 143/236 (60%), Gaps = 7/236 (2%)
Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           +L E P NV +  V GL      L+E++ LP+  P LF +   KP  G+LLYGPPGTGK+
Sbjct: 26  ILSEKP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-KGNRKPTSGILLYGPPGTGKS 83
Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
            LA+A+A+  ++ F  V SS ++ K++GES +L++++F  AR+++P IIF+D++DA+ G 
Sbjct: 84  YLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGT 143
Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R    + A R I+  L+  +N + G D  G V ++ ATN P  LD A+ R  R +R+I I
Sbjct: 144 RGEGESEASRRIKTELLVQMNGV-GNDSQG-VLVLGATNIPWQLDSAIRR--RFERRIYI 199
Query: 201 PLPNEQSRMEILKIHAAGI-AKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           PLP+  +R  + +I+         + DY  +  + EG++G+D+  V  +A M  IR
Sbjct: 200 PLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIR 255

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score =  155 bits (391), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 92/299 (30%), Positives = 161/299 (53%), Gaps = 27/299 (9%)
Query: 11  PREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIK-PPKGV 69
           P+ ++ ++  ++   P  V++  + G+      ++E +  P++ P++F   G++ PPKG+
Sbjct: 64  PKMIELIMNEIMDHGP-PVNWEDIAGVEFAKATIKEIVVWPMLRPDIF--TGLRGPPKGI 120
Query: 70  LLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCII 129
           LL+GPPGTGKTL+ + IAS   A F  + +S++  K++GE  +++R +F  AR  QP +I
Sbjct: 121 LLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVI 180
Query: 130 FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG--KVKMIMATNRPDVLDPA 187
           F+DEID++  +R   G       +R   E L QLDG       ++ ++ ATNRP  +D A
Sbjct: 181 FIDEIDSLLSQR---GDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEA 237
Query: 188 LLRPGRLDRKIEIPLPNEQSRMEI-LKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVC 246
             R  RL +++ IPLP   +R +I + + +       E + E +V+ ++ F+GAD+  +C
Sbjct: 238 ARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLC 295
Query: 247 TEAGMSAIRAERD---------------YVIHEDFMKAVRKLNEAKKLESSAHYNADFG 290
            EA +  IR+ +                Y+  E+  + VR     K LE   ++N  FG
Sbjct: 296 REASLGPIRSLQTADIATITPDQVRPIAYIDFENAFRTVRPSVSPKDLELYENWNKTFG 354

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score =  147 bits (371), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 85/233 (36%), Positives = 140/233 (60%), Gaps = 13/233 (5%)
Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPP-KGVLLYGPPGTGKTLLARAI 86
           NV +S V GL      L+E++ LP+  P LF   G + P +G+LL+GPPGTGK+ LA+A+
Sbjct: 130 NVKWSDVAGLEGAKEALKEAVILPIKFPHLF--TGKRTPWRGILLFGPPGTGKSYLAKAV 187
Query: 87  ASNID-ANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG 145
           A+  + + F  + SS ++ K++GES +L++ +F  AR+++P IIF+DEID++ G R    
Sbjct: 188 ATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENE 247
Query: 146 TSADREIQRTLMELLNQLD--GFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLP 203
           + A R I+    E L Q+   G D  G + ++ ATN P VLD A+ R  R +++I IPLP
Sbjct: 248 SEAARRIK---TEFLVQMQGVGVDNDG-ILVLGATNIPWVLDSAIRR--RFEKRIYIPLP 301
Query: 204 NEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
              +R  + ++H         E D++ + +  +G++GAD+  +  +A M  +R
Sbjct: 302 EAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVR 354

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score =  146 bits (369), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 86/233 (36%), Positives = 139/233 (59%), Gaps = 13/233 (5%)
Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPP-KGVLLYGPPGTGKTLLARAI 86
           NV +S V GL      L+E++ LP+  P LF   G + P +G+LL+GPPGTGK+ LA+A+
Sbjct: 8   NVKWSDVAGLEGAKEALKEAVILPIKFPHLF--TGKRTPWRGILLFGPPGTGKSYLAKAV 65
Query: 87  ASNID-ANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG 145
           A+  + + F  + SS ++ K++GES +L++ +F  AR+++P IIF+DEID++ G R    
Sbjct: 66  ATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENE 125
Query: 146 TSADREIQRTLMELLNQLD--GFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLP 203
           + A R I+    E L Q+   G D  G + ++ ATN P VLD A+ R  R +++I IPLP
Sbjct: 126 SEAARRIK---TEFLVQMQGVGVDNDG-ILVLGATNIPWVLDSAIRR--RFEKRIYIPLP 179
Query: 204 NEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
              +R  + K+H         E D+  + +  +G++GAD+  +  +A M  +R
Sbjct: 180 EPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVR 232

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score =  145 bits (366), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 94/294 (31%), Positives = 161/294 (54%), Gaps = 27/294 (9%)
Query: 17  VVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPP-KGVLLYGPP 75
           ++ + + E    V ++ + G     + L+E + LP + PELF   G++ P KG+LL+GPP
Sbjct: 6   LILDEIVEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELF--TGLRAPAKGLLLFGPP 63
Query: 76  GTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEID 135
           G GKTLLARA+A+   A FL + ++++  KY+G+  +L+R +F  AR  QP IIF+DE+D
Sbjct: 64  GNGKTLLARAVATECSATFLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVD 123
Query: 136 AIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLD 195
           ++   R S    A R ++   +   + L G     ++ ++ ATNRP  LD A LR  R  
Sbjct: 124 SLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFT 181
Query: 196 RKIEIPLPNEQSRMEILKIHAAGIAKHGE-IDYEAVVKLA---EGFNGADLRNVCTEAGM 251
           +++ + LP+EQ+R  +L      + K G  +D EA+ +LA   +G++G+DL  +  +A +
Sbjct: 182 KRVYVSLPDEQTRELLLN---RLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAAL 238
Query: 252 SAIR------------AERDYVIHEDF---MKAVRKLNEAKKLESSAHYNADFG 290
             IR            +    +  +DF   +K +R+    + L S   ++ D+G
Sbjct: 239 EPIRELNVEQVKCLDISAMRAITEQDFHSSLKRIRRSVAPQSLNSYEKWSQDYG 292

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score =  144 bits (364), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 96/305 (31%), Positives = 168/305 (55%), Gaps = 36/305 (11%)
Query: 12  REVDPVVYNMLHE---DPGN-VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPP- 66
           R VD  + N++     D G  V +  + G     + L+E + LP + PELF   G++ P 
Sbjct: 91  RNVDSNLANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELF--TGLRAPA 148
Query: 67  KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQP 126
           +G+LL+GPPG GKT+LA+A+A+  +A F  + ++++  KY+GE  +L+R +F  AR+ QP
Sbjct: 149 RGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQP 208
Query: 127 CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG--KVKMIMATNRPDVL 184
            IIF+D++D++   R      A R ++    E L + DG    G  +V ++ ATNRP  L
Sbjct: 209 SIIFIDQVDSLLCERREGEHDASRRLK---TEFLIEFDGVQSAGDDRVLVMGATNRPQEL 265
Query: 185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG----EIDYEAVVKLAEGFNGA 240
           D A+LR  R  +++ + LPNE++R+ +LK       K G    + +   + ++ +G++G+
Sbjct: 266 DEAVLR--RFIKRVYVSLPNEETRLLLLKNLL---CKQGSPLTQKELAQLARMTDGYSGS 320
Query: 241 DLRNVCTEAGMSAIR------------AERDYVIHEDFMKAVRKLNEA---KKLESSAHY 285
           DL  +  +A +  IR            +E   +   DF ++++K+  +   + LE+   +
Sbjct: 321 DLTALAKDAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRW 380
Query: 286 NADFG 290
           N DFG
Sbjct: 381 NKDFG 385

>pdb|4A3V|B Chain B, Yeast Regulatory Particle Proteasome Assembly Chaperone Hsm3 In Complex With Rpt1 C-Terminal Fragment Length = 95

Iteration: 1
 Score = 67.4 bits (163), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 35/85 (41%), Positives = 52/85 (61%), Gaps = 1/85 (1%)
Query: 202 LPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYV 261
           LP+ + R  I +IH+  ++    I +E + +L     GA+LR+VCTEAGM AIRA R   
Sbjct: 7   LPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVA 66
Query: 262 IHEDFMKAVRK-LNEAKKLESSAHY 285
             +DF+KAV K ++  KK  S++ Y
Sbjct: 67  TEKDFLKAVDKVISGYKKFSSTSRY 91

>pdb|2KRK|A Chain A, Solution Nmr Structure Of 26s Protease Regulatory Subunit 8 From H.Sapiens, Northeast Structural Genomics Consortium Target Target Hr3102a Length = 86

Iteration: 1
 Score = 62.8 bits (151), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/71 (43%), Positives = 47/71 (66%)
Query: 203 PNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVI 262
           PNE++R++ILKIH+  +     I+   + +L  G +GA+++ VCTEAGM A+R  R +V 
Sbjct: 11  PNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVT 70
Query: 263 HEDFMKAVRKL 273
            EDF  AV K+
Sbjct: 71  QEDFEMAVAKV 81

>pdb|3KW6|A Chain A, Crystal Structure Of A Domain Of 26s Proteasome Regulatory Subunit 8 From Homo Sapiens. Northeast Structural Genomics Consortium Target Id Hr3102a Length = 78

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 47/75 (62%)
Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
           P PNE++R++ILKIH+        I+   + +L  G +GA+++ VCTEAG  A+R  R +
Sbjct: 1   PPPNEEARLDILKIHSRKXNLTRGINLRKIAELXPGASGAEVKGVCTEAGXYALRERRVH 60
Query: 261 VIHEDFMKAVRKLNE 275
           V  EDF  AV K+ +
Sbjct: 61  VTQEDFEXAVAKVXQ 75

>pdb|3VLF|B Chain B, Crystal Structure Of Yeast Proteasome Interacting Protein Length = 88

Iteration: 1
 Score = 60.5 bits (145), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 1/81 (1%)
Query: 206 QSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHED 265
           + R  I +IH+   +    I +E + +L     GA+LR+VCTEAG  AIRA R     +D
Sbjct: 4   EGRANIFRIHSKSXSVERGIRWELISRLCPNSTGAELRSVCTEAGXFAIRARRKVATEKD 63
Query: 266 FMKAVRK-LNEAKKLESSAHY 285
           F+KAV K ++  KK  S++ Y
Sbjct: 64  FLKAVDKVISGYKKFSSTSRY 84

>pdb|1OFH|A Chain A, Asymmetric Complex Between Hslv And I-domain Deleted Hslu (h. Influenzae) Length = 310

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/150 (34%), Positives = 78/150 (52%), Gaps = 15/150 (10%)
Query: 66  PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIG-ESARLIREMF---GY 120
           PK +L+ GP G GKT +AR +A   +A F+KV ++   +  Y+G E   +IR++    G 
Sbjct: 50  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGG 109
Query: 121 ARD--HQPCIIFMDEIDAIGGRRFSEGTSADRE-IQRTLMELLNQLDGFDQLGKVK---- 173
           A D   Q  I+F+DEID I  +    G    RE +QR L+ L+       + G VK    
Sbjct: 110 AIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHI 169
Query: 174 MIMATNRPDVLDPALLRP---GRLDRKIEI 200
           + +A+    V  P+ L P   GRL  ++E+
Sbjct: 170 LFIASGAFQVARPSDLIPELQGRLPIRVEL 199

>pdb|3T15|A Chain A, Structure Of Green-Type Rubisco Activase From Tobacco Length = 293

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 49/200 (24%), Positives = 92/200 (46%), Gaps = 21/200 (10%)
Query: 58  FLRV-GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIRE 116
           FL++  IK P  + ++G  G GK+     +   +  N + + +  +     GE A+LIR+
Sbjct: 27  FLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQ 86
Query: 117 MFGYA----RDHQPCIIFMDEIDAIGGRR--FSEGTSADREIQRTLMELLN-----QLDG 165
            +  A    R    C +F++++DA  GR    ++ T  ++ +  TLM + +     QL G
Sbjct: 87  RYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPG 146
Query: 166 F---DQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH 222
                +  +V +I+  N    L   L+R GR+++      P  + R+ +      GI + 
Sbjct: 147 MYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTREDRIGV----CTGIFRT 200
Query: 223 GEIDYEAVVKLAEGFNGADL 242
             +  E VVK+ + F G  +
Sbjct: 201 DNVPAEDVVKIVDNFPGQSI 220

>pdb|1UM8|A Chain A, Crystal Structure Of Helicobacter Pylori Clpx Length = 376

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 50/90 (55%), Gaps = 8/90 (8%)
Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-YIGES-----ARLIREMFGYAR 122
           +LL GP G+GKTL+A+ +A ++D       ++++ +  Y+GE       RL++      +
Sbjct: 75  ILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQ 134
Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADREI 152
             Q  I+F+DEID I   R SE  S  R++
Sbjct: 135 KAQKGIVFIDEIDKIS--RLSENRSITRDV 162

>pdb|3HTE|A Chain A, Crystal Structure Of Nucleotide-Free Hexameric Clpx Length = 363

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 56/103 (54%), Gaps = 13/103 (12%)
Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-YIGESA-----RLIREMFGYAR 122
           +LL GP G+GKTLLA  +A  +D  F    ++ + +  Y+GE       +L+++     +
Sbjct: 54  ILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQ 113
Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADRE-----IQRTLMELL 160
             Q  I+++D+ID I   R S+  S  R+     +Q+ L++L+
Sbjct: 114 KAQRGIVYIDQIDKIS--RKSDNPSITRDVSGEGVQQALLKLI 154

>pdb|3HWS|A Chain A, Crystal Structure Of Nucleotide-Bound Hexameric Clpx Length = 363

Iteration: 1
 Score = 43.9 bits (102), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 56/103 (54%), Gaps = 13/103 (12%)
Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-YIGESA-----RLIREMFGYAR 122
           +LL GP G+GKTLLA  +A  +D  F    ++ + +  Y+GE       +L+++     +
Sbjct: 54  ILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQ 113
Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADRE-----IQRTLMELL 160
             Q  I+++D+ID I   R S+  S  R+     +Q+ L++L+
Sbjct: 114 KAQRGIVYIDQIDKI--SRKSDNPSITRDVSGEGVQQALLKLI 154

>pdb|1G4A|E Chain E, Crystal Structures Of The Hslvu Peptidase-Atpase Complex Reveal An Atp-Dependent Proteolysis Mechanism Length = 443

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 66  PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGESARLIREMFGYARDH 124
           PK +L+ GP G GKT +AR +A   +A F+KV ++   +  Y+G      +E+    RD 
Sbjct: 50  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVG------KEVDSIIRDL 103
Query: 125 QPCIIFMDEIDAIGGRRF 142
               + M  + AI   R+
Sbjct: 104 TDAAVKMVRVQAIEKNRY 121

>pdb|1DO2|A Chain A, Trigonal Crystal Form Of Heat Shock Locus U (Hslu) From Escherichia Coli Length = 442

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 66  PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGESARLIREMFGYARDH 124
           PK +L+ GP G GKT +AR +A   +A F+KV ++   +  Y+G      +E+    RD 
Sbjct: 49  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVG------KEVDSIIRDL 102
Query: 125 QPCIIFMDEIDAIGGRRF 142
               + M  + AI   R+
Sbjct: 103 TDAAVKMVRVQAIEKNRY 120

>pdb|1E94|E Chain E, Hslv-Hslu From E.Coli Length = 449

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 40/78 (51%), Gaps = 7/78 (8%)
Query: 66  PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGESARLIREMFGYARDH 124
           PK +L+ GP G GKT +AR +A   +A F+KV ++   +  Y+G      +E+    RD 
Sbjct: 56  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVG------KEVDSIIRDL 109
Query: 125 QPCIIFMDEIDAIGGRRF 142
               + M  + AI   R+
Sbjct: 110 TDAAVKMVRVQAIEKNRY 127

>pdb|2DVW|B Chain B, Structure Of The Oncoprotein Gankyrin In Complex With S6 Atpase Of The 26s Proteasome Length = 83

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 30/48 (62%)
Query: 224 EIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR 271
           E+D E  V   +  +GAD+ ++C E+GM A+R  R  V+ +DF KA +
Sbjct: 22  EVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYK 69

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	292
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	1e-172
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	1e-106
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-102
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	1e-101
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	8e-96
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	4e-84
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	1e-95
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	1e-86
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	4e-86
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	2e-85
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	8e-85
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	2e-84
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	2e-80
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	3e-78
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	9e-76
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	1e-75
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	1e-75
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	7e-75
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	2e-74
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	4e-68
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	9e-68
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	8e-61
2krk_A	86	26S protease regulatory subunit 8; structural geno	3e-39
3kw6_A	78	26S protease regulatory subunit 8; structural geno	1e-36
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	5e-28
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	6e-28
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	5e-21
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	5e-17
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	3e-14
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-12
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	2e-10
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	2e-10
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	2e-10
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	6e-10
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	9e-10
3pvs_A	447	Replication-associated recombination protein A; ma	1e-09
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	6e-08
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	9e-08
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	4e-07
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	4e-05
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	5e-05
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	6e-05
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	1e-04
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	1e-04
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	1e-04
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	2e-04
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	2e-04
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	3e-04
2wg5_A	109	General control protein GCN4, proteasome-activatin	5e-04
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	5e-04
2qgz_A	308	Helicase loader, putative primosome component; str	5e-04
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	7e-04
2r44_A	331	Uncharacterized protein; putative ATPase, structur	8e-04

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score =  477 bits (1230), Expect = e-172
 Identities = 143/265 (53%), Positives = 196/265 (73%)

Query: 18  VYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGT 77
              M  ++  NV Y  +GGL  Q++E+RE +ELPL +PELF +VGI+PPKG+LLYGPPGT
Sbjct: 3   AKAMEVDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGT 62

Query: 78  GKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAI 137
           GKTLLA+A+A+  +A F++VV S ++ K+IGE A L++++F  A++  P IIF+DEIDAI
Sbjct: 63  GKTLLAKAVATETNATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAI 122

Query: 138 GGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRK 197
             +R    T  DRE+QRTLM+LL ++DGFD  G VK+I ATNRPD+LDPA+LRPGR DR 
Sbjct: 123 AAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAILRPGRFDRI 182

Query: 198 IEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAE 257
           IE+P P+E+ R+EILKIH   +    +++ E + K+ EG  GA+L+ +CTEAGM+AIR  
Sbjct: 183 IEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIREL 242

Query: 258 RDYVIHEDFMKAVRKLNEAKKLESS 282
           RDYV  +DF KAV K+ E KK++  
Sbjct: 243 RDYVTMDDFRKAVEKIMEKKKVKVK 267

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score =  317 bits (813), Expect = e-106
 Identities = 109/289 (37%), Positives = 161/289 (55%), Gaps = 20/289 (6%)

Query: 3   TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG 62
            +     +  E +P+      E    V Y  +GG   Q+ +++E +ELPL +P LF  +G
Sbjct: 175 IVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG 234

Query: 63  IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR 122
           +KPP+G+LLYGPPGTGKTL+ARA+A+   A F  +    I+ K  GES   +R+ F  A 
Sbjct: 235 VKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAE 294

Query: 123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD 182
            + P IIF+DE+DAI  +R  E T  + E +R + +LL  +DG  Q   V ++ ATNRP+
Sbjct: 295 KNAPAIIFIDELDAIAPKR--EKTHGEVE-RRIVSQLLTLMDGLKQRAHVIVMAATNRPN 351

Query: 183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL 242
            +DPAL R GR DR+++I +P+   R+EIL+IH   +    ++D E V     G  GADL
Sbjct: 352 SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADL 411

Query: 243 RNVCTEAGMSAIRAERDY-----------------VIHEDFMKAVRKLN 274
             +C+EA + AIR + D                  V  +DF  A+ + N
Sbjct: 412 AALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSN 460

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus} Length = 301

 Score =  299 bits (769), Expect = e-102
 Identities = 99/228 (43%), Positives = 143/228 (62%)

Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
            V++  +GGL D  REL+E ++ P+ +P+ FL+ G+ P KGVL YGPPG GKTLLA+AIA
Sbjct: 11  QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIA 70

Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
           +   ANF+ +    ++  + GES   +RE+F  AR   PC++F DE+D+I   R      
Sbjct: 71  NECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD 130

Query: 148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS 207
                 R + ++L ++DG      V +I ATNRPD++DPA+LRPGRLD+ I IPLP+E+S
Sbjct: 131 GGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKS 190

Query: 208 RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           R+ ILK +        ++D E + K+  GF+GADL  +C  A   AIR
Sbjct: 191 RVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIR 238

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score =  295 bits (758), Expect = e-101
 Identities = 97/262 (37%), Positives = 150/262 (57%), Gaps = 19/262 (7%)

Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
           NV+++ +G L D   EL  +I  P+ NP+ F  +G+  P GVLL GPPG GKTLLA+A+A
Sbjct: 6   NVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVA 65

Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
           +    NF+ V    +++ Y+GES R +R++F  A++  PC+IF DE+DA+  RR    T 
Sbjct: 66  NESGLNFISVKGPELLNMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETG 125

Query: 148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS 207
           A     R + +LL ++DG +   +V ++ ATNRPD++DPA+LRPGRLD+ + + LP    
Sbjct: 126 A---SVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPAD 182

Query: 208 RMEILKIHAAGIAK---HGEIDYEAVVKLA--EGFNGADLRNVCTEAGMSAIR------- 255
           R+ ILK       K     +++ EA+      + + GADL  +  EA + A+R       
Sbjct: 183 RLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASICALRQEMARQK 242

Query: 256 ----AERDYVIHEDFMKAVRKL 273
                    V H+ F +A +K+
Sbjct: 243 SGNEKGELKVSHKHFEEAFKKV 264

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score =  282 bits (724), Expect = 1e-95
 Identities = 58/272 (21%), Positives = 107/272 (39%), Gaps = 28/272 (10%)

Query: 34  VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN 93
           + G       + + +     N        IK P  + ++G  G GK+     +   +  N
Sbjct: 6   LDGFYIAPAFMDKLVVHITKN--FLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKMGIN 63

Query: 94  FLKVVSSAIIDKYIGESARLIREMFGYA----RDHQPCIIFMDEIDAIGGRR--FSEGTS 147
            + + +  +     GE A+LIR+ +  A    R    C +F++++DA  GR    ++ T 
Sbjct: 64  PIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAGRMGGTTQYTV 123

Query: 148 ADREIQRTLMELLN-----QLDGFD---QLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
            ++ +  TLM + +     QL G     +  +V +I+  N    L   L+R GR+++   
Sbjct: 124 NNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW 183

Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
            P   +  R+ +      GI +   +  E VVK+ + F G  +       G    R   D
Sbjct: 184 APTRED--RIGVCT----GIFRTDNVPAEDVVKIVDNFPGQSIDFF----GALRARVYDD 233

Query: 260 YVIHEDFMKAVRKLNEAKKLESSAHYNADFGK 291
            V        + K+    KL +S      F +
Sbjct: 234 EVRKWVSGTGIEKIG--DKLLNSFDGPPTFEQ 263

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score =  260 bits (666), Expect = 1e-86
 Identities = 89/298 (29%), Positives = 152/298 (51%), Gaps = 25/298 (8%)

Query: 12  REVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLL 71
           +++  ++ + + E    V ++ + G     + L+E + LP + PELF  +   P KG+LL
Sbjct: 1   QKLVQLILDEIVEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLL 59

Query: 72  YGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFM 131
           +GPPG GKTLLARA+A+   A FL + ++++  KY+G+  +L+R +F  AR  QP IIF+
Sbjct: 60  FGPPGNGKTLLARAVATECSATFLNISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFI 119

Query: 132 DEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM---ATNRPDVLDPAL 188
           DE+D++   R S    A R   R   E L + DG         I+   ATNRP  LD A 
Sbjct: 120 DEVDSLLSERSSSEHEASR---RLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAA 176

Query: 189 LRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCT 247
           LR  R  +++ + LP+EQ+R  +L                  + K+ +G++G+DL  +  
Sbjct: 177 LR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAK 234

Query: 248 EAGMSAIR------------AERDYVIHEDFMKAVRKLN---EAKKLESSAHYNADFG 290
           +A +  IR            +    +  +DF  +++++      + L S   ++ D+G
Sbjct: 235 DAALEPIRELNVEQVKCLDISAMRAITEQDFHSSLKRIRRSVAPQSLNSYEKWSQDYG 292

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Length = 322

 Score =  259 bits (664), Expect = 4e-86
 Identities = 90/237 (37%), Positives = 141/237 (59%), Gaps = 11/237 (4%)

Query: 22  LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL 81
           L E P NV +  V GL      L+E++ LP+  P LF +   KP  G+LLYGPPGTGK+ 
Sbjct: 9   LSEKP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-KGNRKPTSGILLYGPPGTGKSY 66

Query: 82  LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR 141
           LA+A+A+  ++ F  V SS ++ K++GES +L++++F  AR+++P IIF+D++DA+ G R
Sbjct: 67  LAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTR 126

Query: 142 FSEGTSADREIQRTLMELLNQLDGF-DQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
               + A R   R   ELL Q++G  +    V ++ ATN P  LD A+ R  R +R+I I
Sbjct: 127 GEGESEASR---RIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIYI 181

Query: 201 PLPNEQSRMEILKIHAAGIAKH--GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           PLP+  +R  + +I+          + DY  +  + EG++G+D+  V  +A M  IR
Sbjct: 182 PLPDLAARTTMFEINVGDT-PCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIR 237

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Length = 357

 Score =  259 bits (663), Expect = 2e-85
 Identities = 93/301 (30%), Positives = 159/301 (52%), Gaps = 31/301 (10%)

Query: 11  PREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVL 70
           P+ ++ ++  ++   P  V++  + G+      ++E +  P++ P++F  +   PPKG+L
Sbjct: 64  PKMIELIMNEIMDHGP-PVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGIL 121

Query: 71  LYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIF 130
           L+GPPGTGKTL+ + IAS   A F  + +S++  K++GE  +++R +F  AR  QP +IF
Sbjct: 122 LFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIF 181

Query: 131 MDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF--DQLGKVKMIMATNRPDVLDPAL 188
           +DEID++  +R      + R   R   E L QLDG       ++ ++ ATNRP  +D A 
Sbjct: 182 IDEIDSLLSQRGDGEHESSR---RIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAA 238

Query: 189 LRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG----EIDYEAVVKLAEGFNGADLRN 244
            R  RL +++ IPLP   +R +I+      ++K      E + E +V+ ++ F+GAD+  
Sbjct: 239 RR--RLVKRLYIPLPEASARKQIVINL---MSKEQCCLSEEEIEQIVQQSDAFSGADMTQ 293

Query: 245 VCTEAGMSAIRAERDYVIH------------EDFMKAVRKLN---EAKKLESSAHYNADF 289
           +C EA +  IR+ +   I              DF  A R +      K LE   ++N  F
Sbjct: 294 LCREASLGPIRSLQTADIATITPDQVRPIAYIDFENAFRTVRPSVSPKDLELYENWNKTF 353

Query: 290 G 290
           G
Sbjct: 354 G 354

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score =  256 bits (656), Expect = 8e-85
 Identities = 85/238 (35%), Positives = 139/238 (58%), Gaps = 12/238 (5%)

Query: 22  LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL 81
           + E P NV +S V GL      L+E++ LP+  P LF      P +G+LL+GPPGTGK+ 
Sbjct: 3   VIERP-NVKWSDVAGLEGAKEALKEAVILPIKFPHLF-TGKRTPWRGILLFGPPGTGKSY 60

Query: 82  LARAIASNID-ANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
           LA+A+A+  + + F  + SS ++ K++GES +L++ +F  AR+++P IIF+DEID++ G 
Sbjct: 61  LAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGS 120

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGK-VKMIMATNRPDVLDPALLRPGRLDRKIE 199
           R    + A R   R   E L Q+ G       + ++ ATN P VLD A+ R  R +++I 
Sbjct: 121 RSENESEAAR---RIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRIY 175

Query: 200 IPLPNEQSRMEILKIHAAGIAKHG--EIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           IPLP   +R  + K+H     ++   E D+  + +  +G++GAD+  +  +A M  +R
Sbjct: 176 IPLPEPHARAAMFKLHLGTT-QNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVR 232

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score =  257 bits (658), Expect = 2e-84
 Identities = 88/300 (29%), Positives = 157/300 (52%), Gaps = 25/300 (8%)

Query: 11  PREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVL 70
               + ++  ++      V +  + G     + L+E + LP + PELF  +   P +G+L
Sbjct: 95  SNLANLIMNEIVDNGT-AVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLR-APARGLL 152

Query: 71  LYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIF 130
           L+GPPG GKT+LA+A+A+  +A F  + ++++  KY+GE  +L+R +F  AR+ QP IIF
Sbjct: 153 LFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIF 212

Query: 131 MDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGK--VKMIMATNRPDVLDPAL 188
           +D++D++   R      A R   R   E L + DG    G   V ++ ATNRP  LD A+
Sbjct: 213 IDQVDSLLCERREGEHDASR---RLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAV 269

Query: 189 LRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA-KHGEIDYEAVVKLAEGFNGADLRNVCT 247
           LR  R  +++ + LPNE++R+ +LK           + +   + ++ +G++G+DL  +  
Sbjct: 270 LR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAK 327

Query: 248 EAGMSAIR------------AERDYVIHEDFMKAVRKLN---EAKKLESSAHYNADFGKE 292
           +A +  IR            +E   +   DF ++++K+      + LE+   +N DFG  
Sbjct: 328 DAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKDFGDT 387

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A* Length = 355

 Score =  246 bits (629), Expect = 2e-80
 Identities = 90/237 (37%), Positives = 142/237 (59%), Gaps = 9/237 (3%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           +L E P NV +  V GL      L+E++ LP+  P LF +   KP  G+LLYGPPGTGK+
Sbjct: 41  ILSEKP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLF-KGNRKPTSGILLYGPPGTGKS 98

Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
            LA+A+A+  ++ F  V SS ++ K++GES +L++++F  AR+++P IIF+D++DA+ G 
Sbjct: 99  YLAKAVATEANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGT 158

Query: 141 RFSEGTSADREIQRTLMELLNQLDGF-DQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
           R    + A R   R   ELL Q++G  +    V ++ ATN P  LD A+ R  R +R+I 
Sbjct: 159 RGEGESEASR---RIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIRR--RFERRIY 213

Query: 200 IPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
           IPLP+  +R  + +I+         + DY  +  + EG++G+D+  V  +A M  IR
Sbjct: 214 IPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIR 270

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A Length = 444

 Score =  243 bits (621), Expect = 3e-78
 Identities = 84/239 (35%), Positives = 141/239 (58%), Gaps = 12/239 (5%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           ++ E P NV +S V GL      L+E++ LP+  P LF      P +G+LL+GPPGTGK+
Sbjct: 124 IVIERP-NVKWSDVAGLEGAKEALKEAVILPIKFPHLF-TGKRTPWRGILLFGPPGTGKS 181

Query: 81  LLARAIASNID-ANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGG 139
            LA+A+A+  + + F  + SS ++ K++GES +L++ +F  AR+++P IIF+DEID++ G
Sbjct: 182 YLAKAVATEANNSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCG 241

Query: 140 RRFSEGTSADREIQRTLMELLNQLDGF-DQLGKVKMIMATNRPDVLDPALLRPGRLDRKI 198
            R    + A R   R   E L Q+ G       + ++ ATN P VLD A+ R  R +++I
Sbjct: 242 SRSENESEAAR---RIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRR--RFEKRI 296

Query: 199 EIPLPNEQSRMEILKIHAAGIAKHG--EIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
            IPLP   +R  + ++H     ++   E D++ + +  +G++GAD+  +  +A M  +R
Sbjct: 297 YIPLPEAHARAAMFRLHLGST-QNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVR 354

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score =  231 bits (590), Expect = 9e-76
 Identities = 105/253 (41%), Positives = 153/253 (60%), Gaps = 1/253 (0%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           ML ED    +++ V G  +   E+ E +E  L  P  F ++G K PKGVL+ GPPGTGKT
Sbjct: 1   MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT 59

Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
           LLA+AIA      F  +  S  ++ ++G  A  +R+MF  A+   PCIIF+DEIDA+G +
Sbjct: 60  LLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQ 119

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R +       E ++TL ++L ++DGF+    + +I ATNRPDVLDPALLRPGR DR++ +
Sbjct: 120 RGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVV 179

Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
            LP+ + R +ILK+H   +    +ID   + +   GF+GADL N+  EA + A R  +  
Sbjct: 180 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRV 239

Query: 261 VIHEDFMKAVRKL 273
           V   +F KA  K+
Sbjct: 240 VSMVEFEKAKDKI 252

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Length = 254

 Score =  230 bits (588), Expect = 1e-75
 Identities = 102/250 (40%), Positives = 150/250 (60%), Gaps = 1/250 (0%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
            +  +   V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GKT
Sbjct: 5   SVLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKT 63

Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
            LARA+A      F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G +
Sbjct: 64  HLARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRK 123

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R S     + E ++TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I I
Sbjct: 124 RGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAI 183

Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
             P+ + R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R  
Sbjct: 184 DAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRK 243

Query: 261 VIHEDFMKAV 270
           +  +D  +A 
Sbjct: 244 ITMKDLEEAA 253

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A* Length = 268

 Score =  230 bits (590), Expect = 1e-75
 Identities = 100/256 (39%), Positives = 152/256 (59%), Gaps = 7/256 (2%)

Query: 22  LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL 81
           ++ +  NV +  + G  +   E+ E ++  L  PE +  +G K PKGVLL GPPGTGKTL
Sbjct: 1   INAEKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTL 59

Query: 82  LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR 141
           LA+A+A      F  +  S+ I+ ++G  A  +R++F  A+   P IIF+DEIDAIG  R
Sbjct: 60  LAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSR 119

Query: 142 FSEGTSA---DREIQRTLMELLNQLDGFDQLGK-VKMIMATNRPDVLDPALLRPGRLDRK 197
            + G  +   +RE  +TL +LL ++DGF      V ++ ATNRP++LDPAL+RPGR DR+
Sbjct: 120 AAGGVVSGNDERE--QTLNQLLAEMDGFGSENAPVIVLAATNRPEILDPALMRPGRFDRQ 177

Query: 198 IEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAE 257
           + +  P+   R+EILK+H  G+    +++ + V KL  G  GADL N+  EA + A R  
Sbjct: 178 VLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNN 237

Query: 258 RDYVIHEDFMKAVRKL 273
           +  V  +   +AV + 
Sbjct: 238 QKEVRQQHLKEAVERG 253

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Length = 262

 Score =  229 bits (585), Expect = 7e-75
 Identities = 96/248 (38%), Positives = 144/248 (58%), Gaps = 4/248 (1%)

Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
            VS+  V G+ +   E+RE ++  L +PE FL++G K PKG LL GPPG GKTLLA+A+A
Sbjct: 2   GVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVA 60

Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR-FSEGT 146
           +     FL +  +  ++   G  A  +R +F  AR   PCI+++DEIDA+G +R  +   
Sbjct: 61  TEAQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSG 120

Query: 147 SADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQ 206
            ++ E ++TL +LL ++DG      V ++ +TNR D+LD AL+RPGRLDR + I LP  Q
Sbjct: 121 FSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQ 180

Query: 207 SRMEILKIHAAGIAKHGEIDYEAVV--KLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE 264
            R EI + H   +       + +    +L  GF+GAD+ N+C EA + A R     V   
Sbjct: 181 ERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAAREGHTSVHTL 240

Query: 265 DFMKAVRK 272
           +F  AV +
Sbjct: 241 NFEYAVER 248

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score =  228 bits (583), Expect = 2e-74
 Identities = 102/249 (40%), Positives = 150/249 (60%), Gaps = 1/249 (0%)

Query: 22  LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL 81
           +  +   V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GKT 
Sbjct: 30  VLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTH 88

Query: 82  LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR 141
           LARA+A      F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G +R
Sbjct: 89  LARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 148

Query: 142 FSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIP 201
            S     + E ++TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I I 
Sbjct: 149 GSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAID 208

Query: 202 LPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYV 261
            P+ + R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R  +
Sbjct: 209 APDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKI 268

Query: 262 IHEDFMKAV 270
             +D  +A 
Sbjct: 269 TMKDLEEAA 277

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score =  218 bits (558), Expect = 4e-68
 Identities = 104/253 (41%), Positives = 153/253 (60%), Gaps = 5/253 (1%)

Query: 22  LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL 81
           +  +   V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GKT 
Sbjct: 21  VLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTH 79

Query: 82  LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR 141
           LARA+A      F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G +R
Sbjct: 80  LARAVAGEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKR 139

Query: 142 FS--EGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE 199
            S   G + +RE  +TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I 
Sbjct: 140 GSGVGGGNDERE--QTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIA 197

Query: 200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD 259
           I  P+ + R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R 
Sbjct: 198 IDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRR 257

Query: 260 YVIHEDFMKAVRK 272
            +  +D  +A  +
Sbjct: 258 KITMKDLEEAADR 270

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E* Length = 476

 Score =  217 bits (555), Expect = 9e-68
 Identities = 107/255 (41%), Positives = 156/255 (61%), Gaps = 6/255 (2%)

Query: 21  MLHEDPGN-VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGK 79
           M        V++  VGG  + I EL+E +E  L +P  F R+G + PKG+LL GPPGTGK
Sbjct: 4   MYKPSGNKRVTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGK 62

Query: 80  TLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGG 139
           TLLARA+A   +  F  +  S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G 
Sbjct: 63  TLLARAVAGEANVPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGR 122

Query: 140 RRFS--EGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRK 197
            R +   G   +RE  +TL +LL ++DGFD    + ++ ATNRPD+LDPALLRPGR D+K
Sbjct: 123 HRGAGLGGGHDERE--QTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPGRFDKK 180

Query: 198 IEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAE 257
           I +  P+   R +IL+IH        +++ E + K   GF GADL N+  EA + A R  
Sbjct: 181 IVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAREG 240

Query: 258 RDYVIHEDFMKAVRK 272
           RD +  +DF +A+ +
Sbjct: 241 RDKITMKDFEEAIDR 255

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A* Length = 272

 Score =  193 bits (492), Expect = 8e-61
 Identities = 52/270 (19%), Positives = 99/270 (36%), Gaps = 21/270 (7%)

Query: 7   MRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPP 66
                 ++ P  +    ED  +   + +    D +  + +  EL +   +   R    P 
Sbjct: 9   HHGSTMDIKPA-FGTNQEDYASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDR---TPL 64

Query: 67  KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGES-ARLIREMFGYARDHQ 125
             VLL GPP +GKT LA  IA   +  F+K+ S   +  +   +  + ++++F  A   Q
Sbjct: 65  VSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQ 124

Query: 126 PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG-KVKMIMATNRPDVL 184
              + +D+I+ +            R     L  LL  L      G K+ +I  T+R DVL
Sbjct: 125 LSCVVVDDIERLLDYV----PIGPRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKDVL 180

Query: 185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEG---FNGAD 241
              +         I +  PN  +  ++L+          + +   + +  +G   + G  
Sbjct: 181 Q-EMEMLNAFSTTIHV--PNIATGEQLLEALELL-GNFKDKERTTIAQQVKGKKVWIGIK 236

Query: 242 LRNVCTEAGMSAIRAERDYVIHEDFMKAVR 271
              +  E  +      R       F+  +R
Sbjct: 237 KLLMLIEMSLQMDPEYR----VRKFLALLR 262

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Length = 86

 Score =  131 bits (332), Expect = 3e-39
 Identities = 31/80 (38%), Positives = 48/80 (60%)

Query: 198 IEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAE 257
                PNE++R++ILKIH+  +     I+   + +L  G +GA+++ VCTEAGM A+R  
Sbjct: 6   HHHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRER 65

Query: 258 RDYVIHEDFMKAVRKLNEAK 277
           R +V  EDF  AV K+ +  
Sbjct: 66  RVHVTQEDFEMAVAKVMQKD 85

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens} Length = 78

 Score =  124 bits (314), Expect = 1e-36
 Identities = 32/77 (41%), Positives = 49/77 (63%)

Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
           P PNE++R++ILKIH+  +     I+   + +L  G +GA+++ VCTEAGM A+R  R +
Sbjct: 1   PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVH 60

Query: 261 VIHEDFMKAVRKLNEAK 277
           V  EDF  AV K+ +  
Sbjct: 61  VTQEDFEMAVAKVMQKD 77

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B* Length = 83

 Score =  102 bits (256), Expect = 5e-28
 Identities = 23/82 (28%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 204 NEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIH 263
           + + +  I     + +    E+D E  V   +  +GAD+ ++C E+GM A+R  R  V+ 
Sbjct: 2   DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLA 61

Query: 264 EDFMKAVRKLNEAKKLESSAHY 285
           +DF KA + +   KK E    +
Sbjct: 62  KDFEKAYKTV--IKKDEQEHEF 81

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B* Length = 88

 Score =  102 bits (256), Expect = 6e-28
 Identities = 33/83 (39%), Positives = 50/83 (60%), Gaps = 1/83 (1%)

Query: 204 NEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIH 263
           + + R  I +IH+  ++    I +E + +L     GA+LR+VCTEAGM AIRA R     
Sbjct: 2   DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATE 61

Query: 264 EDFMKAVRK-LNEAKKLESSAHY 285
           +DF+KAV K ++  KK  S++ Y
Sbjct: 62  KDFLKAVDKVISGYKKFSSTSRY 84

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B Length = 82

 Score = 83.9 bits (208), Expect = 5e-21
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 208 RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFM 267
           R  I    A+ ++   E D ++++   +  +GA +  +  EAG+ A+R  R  ++  D  
Sbjct: 3   RRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLE 62

Query: 268 KAVRKLNEAKKLESSAHY 285
           +A                
Sbjct: 63  EAYAT-QVKTDNTVDKFD 79

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A* Length = 309

 Score = 78.6 bits (193), Expect = 5e-17
 Identities = 47/237 (19%), Positives = 87/237 (36%), Gaps = 36/237 (15%)

Query: 36  GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVL---LYGPPGTGKTLLARAIASNI-- 90
           GL      +RE+  L L+      ++G+      L     G PGTGKT +A  +A  +  
Sbjct: 35  GLKPVKDRIRETAAL-LLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHR 93

Query: 91  -----DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG 145
                  + + V    ++ +YIG +A   +E+   A      ++F+DE   +   R    
Sbjct: 94  LGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRAM---GGVLFIDEAYYLY--RPDNE 148

Query: 146 TSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPG---RLDRKIEIPL 202
               +E    L++++           + +I+A     + +     PG   R+   IE P 
Sbjct: 149 RDYGQEAIEILLQVMEN-----NRDDLVVILAGYADRMENFFQSNPGFRSRIAHHIEFPD 203

Query: 203 PNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGF----------NGADLRNVCTEA 249
            +++   EI         ++ ++  EA   L              N   +RN    A
Sbjct: 204 YSDEELFEIAGHMLDD--QNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDRA 258

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20 Length = 516

 Score = 71.5 bits (175), Expect = 3e-14
 Identities = 35/196 (17%), Positives = 68/196 (34%), Gaps = 42/196 (21%)

Query: 67  KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS-----AIIDKYIGESAR---LIREMF 118
           +  +LYGPPG GKT  A  +A  +  + L+  +S      +++  +  +     ++    
Sbjct: 78  RAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFK 137

Query: 119 GYARDHQPC----IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM 174
                        +I MDE+D +        +  DR     L +   +           +
Sbjct: 138 HNEEAQNLNGKHFVIIMDEVDGM--------SGGDRGGVGQLAQFCRKT-------STPL 182

Query: 175 IMATNRPDVLDPALLRPGRLDRKIEI----PLPNEQSRMEILKI-HAAGIAKHGEIDYEA 229
           I+  N  +   P  +RP   DR               +  ++ I          ++D   
Sbjct: 183 ILICN--ERNLPK-MRP--FDRVCLDIQFRRPDANSIKSRLMTIAIREKF----KLDPNV 233

Query: 230 VVKLAEGFNGADLRNV 245
           + +L +   G D+R V
Sbjct: 234 IDRLIQTTRG-DIRQV 248

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 66.8 bits (162), Expect = 2e-12
 Identities = 55/374 (14%), Positives = 103/374 (27%), Gaps = 143/374 (38%)

Query: 20  NMLHED-----PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGP 74
           + L+ D       NVS            +LR++    L+         ++P K VL+ G 
Sbjct: 117 DRLYNDNQVFAKYNVSRL------QPYLKLRQA----LLE--------LRPAKNVLIDGV 158

Query: 75  PGTGKTLLARAIASN-----------------------------------IDANFLKVVS 99
            G+GKT +A  +  +                                   ID N+     
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSD 218

Query: 100 SAIIDKYIGESARLIREMFGYARDHQPCIIFMDE------IDAIGGRRFSEG-----TSA 148
            +   K    S +        ++ ++ C++ +         +A     F+       T+ 
Sbjct: 219 HSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNA-----FNLSCKILLTTR 273

Query: 149 DREI-------QRTLMELLNQLDGFDQ------LGK-VKMIMATNRPDVLD--P------ 186
            +++         T + L +             L K +         +VL   P      
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSII 333

Query: 187 -ALLRPG-------------RLDRKIEIPL----PNEQSRM----EIL----KIHAAGIA 220
              +R G             +L   IE  L    P E  +M     +      I    ++
Sbjct: 334 AESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLS 393

Query: 221 KH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD-----YVIHEDFMKAVRKLN 274
               ++    V+ +    +   L              E+        I   +++   KL 
Sbjct: 394 LIWFDVIKSDVMVVVNKLHKYSL-------------VEKQPKESTISIPSIYLELKVKLE 440

Query: 275 EAKKLESS--AHYN 286
               L  S   HYN
Sbjct: 441 NEYALHRSIVDHYN 454

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 386

 Score = 60.1 bits (145), Expect = 2e-10
 Identities = 51/275 (18%), Positives = 90/275 (32%), Gaps = 53/275 (19%)

Query: 39  DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV 98
           DQIR++   +       +         P  + +YG  GTGKT + + + S +   FL   
Sbjct: 27  DQIRKIASILAPLYREEK---------PNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKF 77

Query: 99  SSAII-------------------DKYIGESARLIREMFGYARDH-----QPCIIFMDEI 134
               I                   D  +  +   I E++              +I +DEI
Sbjct: 78  KHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEI 137

Query: 135 DAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV---LDPALLRP 191
           DA   +        + +I   L  + ++++      K+  I  TN       LDP +   
Sbjct: 138 DAFVKKY-------NDDILYKLSRINSEVNK----SKISFIGITNDVKFVDLLDPRVKSS 186

Query: 192 GRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAE--GFNGADLR---NVC 246
              +  I  P   E+   +IL   A    K G +    +   A        D R   ++ 
Sbjct: 187 LSEEEIIFPPYNAEEL-EDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLL 245

Query: 247 TEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLES 281
             +G  A R +   V  E    A  ++   +  + 
Sbjct: 246 RVSGEIAERMKDTKVKEEYVYMAKEEIERDRVRDI 280

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A* Length = 456

 Score = 59.6 bits (144), Expect = 2e-10
 Identities = 48/248 (19%), Positives = 81/248 (32%), Gaps = 34/248 (13%)

Query: 58  FLRVGIKPPKGVLLYGPPGTGKTLLARAIAS--NIDANFLKVVSSAIIDKYIGESARLIR 115
            ++      + VLL GPPGTGKT LA AIA        F  +V S +    I ++  L  
Sbjct: 55  LIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYSTEIKKTEVL-M 113

Query: 116 EMFGYA---RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG------- 165
           E F  A   R  +   ++  E+  +             +    ++  L    G       
Sbjct: 114 ENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLD 173

Query: 166 ---FDQLGK--------VKMIMATNRPDVLDPALLRPGRLDRKIE--IPLPNEQSRMEIL 212
              F+ L K        + +   +                D + E  +PLP      +  
Sbjct: 174 PSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKE 233

Query: 213 KIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK 272
            I    +    ++D    V  A    G D+ ++  +  M   + E    +  +  K V K
Sbjct: 234 IIQDVTL---HDLD----VANARPQGGQDILSMMGQL-MKPKKTEITDKLRGEINKVVNK 285

Query: 273 LNEAKKLE 280
             +    E
Sbjct: 286 YIDQGIAE 293

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus} Length = 384

 Score = 59.4 bits (143), Expect = 2e-10
 Identities = 48/287 (16%), Positives = 88/287 (30%), Gaps = 60/287 (20%)

Query: 39  DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-------- 90
           D +R+   +I   + N               L  G  GTGKT +++ I + I        
Sbjct: 27  DILRDAAIAIRYFVKNEV---------KFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDE 77

Query: 91  ---DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQ------------------PCII 129
              D     V    +        + L  ++ G++                        II
Sbjct: 78  EYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAII 137

Query: 130 FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV---LDP 186
           ++DE+D +  R         R     L +L            + +IM +N  +V   ++P
Sbjct: 138 YLDEVDTLVKR---------RGGDIVLYQL------LRSDANISVIMISNDINVRDYMEP 182

Query: 187 ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAE--GFNGADLRN 244
            +L    L   +     + +    IL  +A      G  D E +  +A        D R 
Sbjct: 183 RVL--SSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARK 240

Query: 245 VCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK 291
                  +A  A    +I ++ +       E ++L  +        K
Sbjct: 241 AVNLLFRAAQLASGGGIIRKEHVDKAIVDYEQERLIEAVKALPFHYK 287

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A* Length = 412

 Score = 58.4 bits (140), Expect = 6e-10
 Identities = 36/295 (12%), Positives = 80/295 (27%), Gaps = 54/295 (18%)

Query: 39  DQIRELRESIELPLMNPELFLRVGIKPPKGVLLY---GPPGTGKTLLARAI-------AS 88
            +   L       L++       G       ++Y   G  G GKT LA+         A+
Sbjct: 29  GEAEALARIYLNRLLS-------GAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAA 81

Query: 89  NIDANFLKV------------VSSAIIDKYIGE--------SARLIREMFGYARDHQPCI 128
                  +             + S I+ +               L   +     ++   +
Sbjct: 82  KEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLL 141

Query: 129 IFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPAL 188
           + +DE                 E   TL+ +  ++   D + ++  ++  +    L    
Sbjct: 142 VILDEFQ-----SMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMR 196

Query: 189 LRPGR----LDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLA-----EGFNG 239
            +  +    +  K+ +P    +    IL+  A    +    +   +  ++     +    
Sbjct: 197 EKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGD 256

Query: 240 ADLR---NVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADFGK 291
              R        A   A    RD +  +   KAV +   A          +    
Sbjct: 257 GSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELEALSIHEL 311

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20 Length = 389

 Score = 57.9 bits (139), Expect = 9e-10
 Identities = 43/282 (15%), Positives = 85/282 (30%), Gaps = 54/282 (19%)

Query: 39  DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF-LKV 97
            Q+++L   +   L NP               L G PGTGKT+  R +          + 
Sbjct: 24  QQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARF 76

Query: 98  V---------SSAIIDKYI----------GESARLIREMF--GYARDHQPCIIFMDEIDA 136
           V          +AII +            G S      +             + +D+   
Sbjct: 77  VYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFN 136

Query: 137 IGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDR 196
           +             +I  T + L  + D      ++ +++  +   VL+        +  
Sbjct: 137 LA-----------PDILSTFIRLGQEADKLGA-FRIALVIVGHNDAVLNNLDPSTRGIMG 184

Query: 197 KIEIPLP--NEQSRMEILKIHAAGIAKHGEIDYEAVVKLAE--------GFNGADLR--- 243
           K  I      +    +IL   A      G    + +  +A+          N  D R   
Sbjct: 185 KYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAI 244

Query: 244 NVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHY 285
           ++   +  +A +  R ++  ED  K+ +++      E     
Sbjct: 245 DILYRSAYAAQQNGRKHIAPEDVRKSSKEVLFGISEEVLIGL 286

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 57.9 bits (141), Expect = 1e-09
 Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 15/72 (20%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKV--VSSAIIDKYIGESARLIREMFGYARDH-- 124
           ++L+GPPGTGKT LA  IA   +A+  ++  V+S + +         IRE    AR +  
Sbjct: 53  MILWGPPGTGKTTLAEVIARYANADVERISAVTSGVKE---------IREAIERARQNRN 103

Query: 125 --QPCIIFMDEI 134
             +  I+F+DE+
Sbjct: 104 AGRRTILFVDEV 115

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A* Length = 310

 Score = 51.9 bits (125), Expect = 6e-08
 Identities = 36/104 (34%), Positives = 55/104 (52%), Gaps = 8/104 (7%)

Query: 65  PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIG--ESARLIR--EMFG 119
            PK +L+ GP G GKT +AR +A   +A F+KV ++   +  Y+G    + +    +  G
Sbjct: 49  TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAG 108

Query: 120 YARDH--QPCIIFMDEIDAIGGRRFSEGTSADRE-IQRTLMELL 160
            A D   Q  I+F+DEID I  +    G    RE +QR L+ L+
Sbjct: 109 GAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLV 152

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Length = 387

 Score = 51.7 bits (123), Expect = 9e-08
 Identities = 51/277 (18%), Positives = 86/277 (31%), Gaps = 52/277 (18%)

Query: 39  DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA------ 92
            ++R L E +   L           + P   LLYG  GTGKT +AR +   ++A      
Sbjct: 26  AELRRLAEVLAPALRG---------EKPSNALLYGLTGTGKTAVARLVLRRLEARASSLG 76

Query: 93  --------NFLKVVSSAIIDKYIGESARLIREMFGYARDH-------------QPCIIFM 131
                   N     +   +   I E+  +     G +                   II +
Sbjct: 77  VLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVL 136

Query: 132 DEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPAL--L 189
           DEID +  R            Q  L  +            V ++  TN    ++     +
Sbjct: 137 DEIDFLPKR---------PGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRV 187

Query: 190 RPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAE--GFNGADLR---N 244
           +    + ++  P        +IL+  A      G +D + V   A        D R   +
Sbjct: 188 KSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALD 247

Query: 245 VCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLES 281
           +   AG  A R   + V  E    A  ++   +  E 
Sbjct: 248 LLRVAGEIAERRREERVRREHVYSARAEIERDRVSEV 284

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli} Length = 500

 Score = 50.1 bits (120), Expect = 4e-07
 Identities = 34/190 (17%), Positives = 66/190 (34%), Gaps = 43/190 (22%)

Query: 69  VLLYGPPGTGKTLLARAIASNI-DANFLKV----------VSSAIIDKYIGESARLIREM 117
           V L GPPG  K+L+AR +     +A   +           V   +  + + +  R  R  
Sbjct: 44  VFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYERLT 103

Query: 118 FGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ----LDGFD-QLGKV 172
            GY  + +  I+F+DEI     +           I  TL+  +N+          ++   
Sbjct: 104 SGYLPEAE--IVFLDEIW----K-----AGP--AILNTLLTAINERQFRNGAHVEKIPMR 150

Query: 173 KMIMATNRP----DVLDPALLRPGRLDR---KIEIPLPNEQSRMEILKIHAAGIAKHGEI 225
            ++ A+N        L+ AL      DR   ++ +    +++    +         +  +
Sbjct: 151 LLVAASNELPEADSSLE-AL-----YDRMLIRLWLDKVQDKANFRSMLTSQQDENDN-PV 203

Query: 226 DYEAVVKLAE 235
                V   E
Sbjct: 204 PDALQVTDEE 213

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20 Length = 376

 Score = 43.8 bits (104), Expect = 4e-05
 Identities = 33/94 (35%), Positives = 46/94 (48%), Gaps = 20/94 (21%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-------YIGES-----ARLIRE 116
           +LL GP G+GKTL+A+ +A ++D         AI D        Y+GE       RL++ 
Sbjct: 75  ILLIGPTGSGKTLMAQTLAKHLDIPI------AISDATSLTEAGYVGEDVENILTRLLQA 128

Query: 117 MFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADR 150
                +  Q  I+F+DEID I   R SE  S  R
Sbjct: 129 SDWNVQKAQKGIVFIDEIDKIS--RLSENRSITR 160

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A* 3vkh_C* Length = 3245

 Score = 43.7 bits (103), Expect = 5e-05
 Identities = 20/112 (17%), Positives = 41/112 (36%), Gaps = 13/112 (11%)

Query: 58   FLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA------NFLKVVSSAIIDKYI---- 107
             L   +   + ++L GPPG+GKT+   +             NF    +  ++ K      
Sbjct: 1296 VLHAWLSEHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHC 1355

Query: 108  -GESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLME 158
              +       +    +  +  ++F DEI+     ++  GT       R ++E
Sbjct: 1356 EYKRTPSGETVLRPTQLGKWLVVFCDEINLPSTDKY--GTQRVITFIRQMVE 1405

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A Length = 363

 Score = 43.0 bits (102), Expect = 6e-05
 Identities = 30/99 (30%), Positives = 45/99 (45%), Gaps = 30/99 (30%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-------YIGES-----ARLIRE 116
           +LL GP G+GKTLLA  +A  +D  F       + D        Y+GE       +L++ 
Sbjct: 54  ILLIGPTGSGKTLLAETLARLLDVPF------TMADATTLTEAGYVGEDVENIIQKLLQ- 106

Query: 117 MFGYARDH-----QPCIIFMDEIDAIGGRRFSEGTSADR 150
                 D+     Q  I+++D+ID I   R S+  S  R
Sbjct: 107 ----KCDYDVQKAQRGIVYIDQIDKIS--RKSDNPSITR 139

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp} Length = 338

 Score = 42.2 bits (100), Expect = 1e-04
 Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCI 128
           +L  GP G GKT LA  I+  + AN  K  ++ +I+K  G+ A ++  +     D    I
Sbjct: 58  ILFSGPAGLGKTTLANIISYEMSANI-KTTAAPMIEK-SGDLAAILTNL--SEGD----I 109

Query: 129 IFMDEI 134
           +F+DEI
Sbjct: 110 LFIDEI 115

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A* Length = 180

 Score = 40.8 bits (96), Expect = 1e-04
 Identities = 11/24 (45%), Positives = 13/24 (54%)

Query: 64 KPPKGVLLYGPPGTGKTLLARAIA 87
          +  KG+   G PG GKT LA A  
Sbjct: 36 EEGKGLTFVGSPGVGKTHLAVATL 59

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A* Length = 334

 Score = 41.8 bits (99), Expect = 1e-04
 Identities = 26/66 (39%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCI 128
           VLL GPPG GKT LA  IAS +  N   V S  ++ K  G+ A ++  +     D    +
Sbjct: 54  VLLAGPPGLGKTTLAHIIASELQTNI-HVTSGPVLVK-QGDMAAILTSL--ERGD----V 105

Query: 129 IFMDEI 134
           +F+DEI
Sbjct: 106 LFIDEI 111

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 63 IKPPKGVLLYGPPGTGKTLLARAIA 87
           K  KG+ L+G  G GKT L  AIA
Sbjct: 51 GKKMKGLYLHGSFGVGKTYLLAAIA 75

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C* Length = 324

 Score = 41.4 bits (98), Expect = 2e-04
 Identities = 26/66 (39%), Positives = 36/66 (54%), Gaps = 7/66 (10%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCI 128
           +LL+GPPG GKT LA  IA  +  N  +V S   I+K  G+ A ++        D    I
Sbjct: 41  LLLFGPPGLGKTTLAHVIAHELGVNL-RVTSGPAIEK-PGDLAAILANSLE-EGD----I 93

Query: 129 IFMDEI 134
           +F+DEI
Sbjct: 94  LFIDEI 99

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus} Length = 193

 Score = 39.9 bits (93), Expect = 3e-04
 Identities = 12/34 (35%), Positives = 22/34 (64%)

Query: 62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL 95
          G++ P  +++ G P TGKT L++A+A+ +    L
Sbjct: 1  GMQTPALIIVTGHPATGKTTLSQALATGLRLPLL 34

>2wg5_A General control protein GCN4, proteasome-activating nucleotidase; transcription hydrolase complex, nucleotide-binding; 2.10A {Saccharomyces cerevisiae} PDB: 2wg6_A Length = 109

 Score = 37.9 bits (88), Expect = 5e-04
 Identities = 10/25 (40%), Positives = 13/25 (52%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHED 25
             TL I+  LP   DP+VY    E+
Sbjct: 85  QQTLAIVNVLPTSKDPMVYGFEVEE 109

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A Length = 2695

 Score = 40.6 bits (95), Expect = 5e-04
 Identities = 32/198 (16%), Positives = 68/198 (34%), Gaps = 26/198 (13%)

Query: 58   FLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS-SA---------IIDKYI 107
                 +   +G++L GPPG+GKT++      N     +  ++ S           + ++ 
Sbjct: 1259 IFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHT 1318

Query: 108  GESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMEL-----LNQ 162
                           D +  ++F DEI+     ++  G+       R LME        +
Sbjct: 1319 NYVTTSKGLTLLPKSDIKNLVLFCDEINLPKLDKY--GSQNVVLFLRQLMEKQGFWKTPE 1376

Query: 163  LDGFDQLGKVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA 217
               +  + ++ ++ A N P       +     R   +   + +  P+ +S  +I +I+  
Sbjct: 1377 NK-WVTIERIHIVGACNPPTDPGRIPMSERFTRHAAI---LYLGYPSGKSLSQIYEIYYK 1432

Query: 218  GIAKHGEIDYEAVVKLAE 235
             I K            A 
Sbjct: 1433 AIFKLVPEFRSYTEPFAR 1450

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 11/24 (45%), Positives = 14/24 (58%)

Query: 64  KPPKGVLLYGPPGTGKTLLARAIA 87
              KG+ LYG  G GK+ L  A+A
Sbjct: 150 AEQKGLYLYGDMGIGKSYLLAAMA 173

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G Length = 350

 Score = 39.8 bits (93), Expect = 7e-04
 Identities = 11/21 (52%), Positives = 16/21 (76%)

Query: 68 GVLLYGPPGTGKTLLARAIAS 88
          GVL++G  GTGK+   RA+A+
Sbjct: 47 GVLVFGDRGTGKSTAVRALAA 67

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406} Length = 331

 Score = 39.4 bits (93), Expect = 8e-04
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 69 VLLYGPPGTGKTLLARAIASNIDANF 94
          +LL G PG  KTL    +A  +D +F
Sbjct: 49 ILLEGVPGLAKTLSVNTLAKTMDLDF 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	292
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	100.0
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	100.0
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	100.0
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	100.0
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	100.0
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	100.0
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	100.0
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	100.0
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	100.0
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	100.0
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	100.0
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	100.0
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	100.0
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	100.0
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	100.0
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	100.0
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	100.0
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	100.0
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.97
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.96
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.92
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.91
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.91
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.9
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.89
3pvs_A	447	Replication-associated recombination protein A; ma	99.88
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.88
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.88
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.88
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.85
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.85
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.84
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.83
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.83
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.83
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.83
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.83
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.83
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.82
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.82
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.82
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.82
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.82
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.82
3bos_A	242	Putative DNA replication factor; P-loop containing	99.81
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.81
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.81
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.81
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.81
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.8
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.79
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.78
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.78
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.77
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.77
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.76
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.76
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.75
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.74
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.73
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.73
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.72
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.72
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.72
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.72
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.7
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.68
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.67
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.66
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.64
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.62
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.61
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.59
3co5_A	143	Putative two-component system transcriptional RES	99.59
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.58
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.42
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.37
3f8t_A	506	Predicted ATPase involved in replication control,	99.35
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.35
2fna_A	357	Conserved hypothetical protein; structural genomic	99.33
3kw6_A	78	26S protease regulatory subunit 8; structural geno	99.31
2krk_A	86	26S protease regulatory subunit 8; structural geno	99.28
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	99.22
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.2
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.2
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	99.15
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	99.12
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	99.11
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.08
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.06
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.95
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.94
2qgz_A	308	Helicase loader, putative primosome component; str	98.9
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.89
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.89
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	98.85
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.73
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.69
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.68
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.68
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.62
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	98.52
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.5
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	98.41
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	98.36
2cvh_A	220	DNA repair and recombination protein RADB; filamen	98.35
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	98.35
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	98.35
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	98.29
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.28
1xp8_A	366	RECA protein, recombinase A; recombination, radior	98.28
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	98.25
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	98.23
4a74_A	231	DNA repair and recombination protein RADA; hydrola	98.22
2z43_A	324	DNA repair and recombination protein RADA; archaea	98.19
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	98.18
1u94_A	356	RECA protein, recombinase A; homologous recombinat	98.18
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	98.15
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	98.14
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	98.11
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.1
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	98.1
2eyu_A	261	Twitching motility protein PILT; pilus retraction	98.1
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	98.09
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	98.04
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	98.04
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.04
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	98.03
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	98.0
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	98.0
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.99
3io5_A	333	Recombination and repair protein; storage dimer, i	97.98
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.98
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	97.97
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	97.97
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	97.97
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	97.96
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.95
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	97.95
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	97.94
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.92
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	97.92
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	97.9
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	97.9
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	97.89
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.88
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	97.88
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.88
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.86
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.85
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	97.85
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	97.84
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	97.83
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	97.83
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.81
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	97.81
2ewv_A	372	Twitching motility protein PILT; pilus retraction	97.81
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.8
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.79
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.79
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	97.78
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	97.78
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	97.78
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.78
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	97.77
2r6a_A	454	DNAB helicase, replicative helicase; replication,	97.77
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	97.77
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	97.76
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	97.76
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.75
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	97.75
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.74
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	97.74
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.74
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	97.73
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.73
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	97.72
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.7
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	97.69
1via_A	175	Shikimate kinase; structural genomics, transferase	97.68
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	97.68
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	97.68
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.65
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.65
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	97.65
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	97.64
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.64
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	97.64
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.64
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	97.63
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.61
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.61
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.61
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	97.61
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.6
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.6
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	97.6
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.6
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.59
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	97.59
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.58
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.57
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.57
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.57
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	97.56
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.56
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.56
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.55
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.55
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.54
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	97.54
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	97.54
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	97.54
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.54
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.53
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	97.53
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.53
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	97.52
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	97.52
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	97.51
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.51
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	97.51
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	97.49
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	97.48
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	97.47
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.47
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	97.47
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.47
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	97.47
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	97.47
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	97.46
1p9r_A	418	General secretion pathway protein E; bacterial typ	97.46
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.46
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	97.45
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	97.44
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	97.43
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	97.42
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	97.42
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	97.41
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	97.41
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	97.41
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.41
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	97.38
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	97.36
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	97.36
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	97.35
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	97.34
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	97.34
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	97.33
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	97.33
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	97.33
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	97.33
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	97.33
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	97.33
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	97.31
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	97.31
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	97.31
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	97.31
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.31
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	97.3
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	97.3
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	97.28
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	97.28
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	97.28
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	97.27
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	97.26
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	97.25
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	97.25
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	97.25
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	97.24
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	97.24
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	97.24
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	97.23
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.23
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	97.22
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	97.22
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	97.22
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	97.21
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	97.21
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	97.2
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	97.18
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	97.17
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	97.17
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	97.17
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	97.16
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	97.16
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	97.16
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.16
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	97.16
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	97.16
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	97.14
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	97.14
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	97.14
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	97.14
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	97.12
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	97.12
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	97.11
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	97.11
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	97.06
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	97.05
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	97.04
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	97.04
2og2_A	359	Putative signal recognition particle receptor; nuc	97.03
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	97.02
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.02
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.01
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	97.01
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	97.01
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	97.01
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	96.98
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.97
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	96.97
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	96.96
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	96.96
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	96.96
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	96.93
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	96.92
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	96.92
1b0u_A	262	Histidine permease; ABC transporter, transport pro	96.89
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	96.88
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	96.88
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	96.87
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.86
1g6h_A	257	High-affinity branched-chain amino acid transport	96.84
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	96.83
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	96.83
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.83
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	96.83
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	96.83
2ghi_A	260	Transport protein; multidrug resistance protein, M	96.82
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.82
1ji0_A	240	ABC transporter; ATP binding protein, structural g	96.82
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	96.81
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	96.8
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	96.79
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	96.78
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	96.76
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	96.76
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.75
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	96.75
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	96.73
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	96.73
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	96.71
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	96.71
3b6e_A	216	Interferon-induced helicase C domain-containing P;	96.7
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	96.7
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	96.69
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	96.66
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.65
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	96.62
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	96.6
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	96.6
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	96.6
3bor_A	237	Human initiation factor 4A-II; translation initiat	96.58
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	96.58
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.56
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	96.56
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	96.54
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	96.54
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	96.53
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	96.53
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	96.52
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	96.52
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	96.5
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	96.48
3kta_A	182	Chromosome segregation protein SMC; structural mai	96.48
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	96.48
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	96.47
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	96.47
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	96.46
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	96.42
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	96.41
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	96.41
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	96.4
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	96.37
2xxa_A	433	Signal recognition particle protein; protein trans	96.37
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	96.37
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	96.31
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	96.3
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	96.29
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	96.26
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	96.26
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	96.26
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	96.23
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	96.23
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	96.23
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	96.22
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	96.19
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	96.19
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	96.19
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	96.18
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	96.17
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	96.14
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	96.14
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	96.14
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	96.11
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	96.1
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.09
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	96.09
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	96.09
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	96.08
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	96.06
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	96.06
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	96.04
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	96.03
2ged_A	193	SR-beta, signal recognition particle receptor beta	96.03
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	96.01
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	95.99
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	95.99
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	95.96
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	95.96
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.93
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	95.91
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	95.9
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	95.88
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	95.87
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	95.84
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	95.84
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.83
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	95.81
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	95.78
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	95.76
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	95.76
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	95.75
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	95.74
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	95.74
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	95.73
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	95.71
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	95.69
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	95.69
2hf9_A	226	Probable hydrogenase nickel incorporation protein	95.68
1nrj_B	218	SR-beta, signal recognition particle receptor beta	95.65
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	95.65
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	95.64
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	95.62
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	95.61
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	95.61
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	95.6
2wji_A	165	Ferrous iron transport protein B homolog; membrane	95.6
3pih_A	916	Uvrabc system protein A; hydrolase, ABC ATPase, DN	95.59
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	95.59
3i8s_A	274	Ferrous iron transport protein B; GTPase, GPCR, ir	95.57
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	95.55
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	95.54
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	95.54
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	95.52
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	95.52
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	95.51
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	95.49
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	95.48
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	95.47
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	95.47
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	95.44
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	95.43
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	95.43
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	95.41
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	95.41
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	95.4
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	95.4
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	95.38
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	95.38
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	95.38
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	95.37
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	95.36
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	95.33
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	95.33
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	95.33
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	95.31
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	95.29
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	95.28
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	95.28
3ice_A	422	Transcription termination factor RHO; transcriptio	95.26
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	95.24
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	95.24
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	95.23
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	95.2
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	95.2
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	95.18
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	95.18
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	95.17
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	95.16
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	95.14
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	95.14
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	95.13
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	95.12
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	95.1
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	95.1
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	95.09
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	95.09
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	95.08
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	95.08
3a1s_A	258	Iron(II) transport protein B; FEOB, iron transport	95.07

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.2e-51  Score=358.25  Aligned_cols=286  Identities=50%  Similarity=0.836  Sum_probs=264.2

Q ss_pred             hhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768            3 TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      .+.++.-+|.+++|.+..+.-.+.|+++|++|.|+++++++|++.+..|+..++.|.++|+.+++++||+||||||||++
T Consensus       119 ~~~~~~~l~~~~~~~~~~~~~~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTll  198 (405)
T 4b4t_J          119 SYMLHKVLENKADPLVSLMMVEKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLL  198 (405)
T ss_dssp             TCSCCEECCCCCSCCTTSCEEECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHH
T ss_pred             cceeeeecCcccCchhhhccccCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHH
Confidence            45667789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           83 ARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        83 ~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      |+++|++++.+++.+++.++.+.+.|+++..++.+|..++...||||||||+|.+++++.+..++.+......+..++..
T Consensus       199 AkAiA~e~~~~f~~v~~s~l~sk~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~  278 (405)
T 4b4t_J          199 ARAVAHHTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQ  278 (405)
T ss_dssp             HHHHHHHHTCEEEEEEGGGGSCSSTTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHH
T ss_pred             HHHHHHhhCCCceEEEhHHhhccccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999988777777778888999999999


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di  242 (292)
                      ++++....+++||+|||.++.+++++++++||+..|+++.|+.++|.+||+.++.......+++++.++..+.|||++||
T Consensus       279 lDg~~~~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi  358 (405)
T 4b4t_J          279 LDGFETSKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADV  358 (405)
T ss_dssp             HHTTTCCCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHH
T ss_pred             hhccCCCCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHH
Confidence            99988888999999999999999999999999999999999999999999999998888888999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhhchhhhhhhhc
Q 022768          243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNADF  289 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~~~~~~~~~~~  289 (292)
                      ..+|++|...|.++++..|+.+||.+|+..+..... +....+.+.|
T Consensus       359 ~~l~~eA~~~Air~~~~~vt~~Df~~Al~~v~~~~~-~~~~s~~k~~  404 (405)
T 4b4t_J          359 KGVCTEAGMYALRERRIHVTQEDFELAVGKVMNKNQ-ETAISVAKLF  404 (405)
T ss_dssp             HHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHHHHHT-CC--------
T ss_pred             HHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhCccc-cccchhHhhh
Confidence            999999999999999999999999999999987544 3344444443

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.7e-50  Score=357.07  Aligned_cols=285  Identities=71%  Similarity=1.155  Sum_probs=263.2

Q ss_pred             hhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768            3 TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      .+.+...+|++++|.+.++.-...|.++|++|.|+++++++|.+.+..|+..+..|.++|+.+++++|||||||||||++
T Consensus       152 ~~~~~~~l~~~~d~~~~~~~~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTll  231 (437)
T 4b4t_L          152 TLTIMRILPRETDPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLL  231 (437)
T ss_dssp             SCSEEEECCCCSCCCCSSCEEEESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHH
T ss_pred             chhHHHhcCcccCchhheeeeccCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHH
Confidence            45567789999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           83 ARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        83 ~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      |+++|++++.+++.+++.++.+.+.|.+...++.+|..++...||||||||+|.++.++.+.....+......+..+|..
T Consensus       232 AkAiA~e~~~~~~~v~~s~l~sk~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~  311 (437)
T 4b4t_L          232 AKAVAATIGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQ  311 (437)
T ss_dssp             HHHHHHHHTCEEEEEEGGGTCCSSSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCEEEEehhhhccccchHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999988777766777888899999999


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di  242 (292)
                      +++.....+++||+|||.++.+++++++++||+..|+|+.|+.++|.+||+.++.......++|++.++..+.|||++||
T Consensus       312 lDg~~~~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi  391 (437)
T 4b4t_L          312 MDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADI  391 (437)
T ss_dssp             HHSSSCTTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHH
T ss_pred             hhcccCCCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHH
Confidence            99988888999999999999999999999999999999999999999999999998888888999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhhchhhhhhh
Q 022768          243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLESSAHYNA  287 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~~~~~~~~~  287 (292)
                      ..+|++|...|.++++..|+.+||.+|++.+.+....+...+|++
T Consensus       392 ~~l~~eA~~~air~~~~~i~~~d~~~Al~~v~~~~k~e~~~e~~K  436 (437)
T 4b4t_L          392 RNCATEAGFFAIRDDRDHINPDDLMKAVRKVAEVKKLEGTIEYQK  436 (437)
T ss_dssp             HHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHHHTCC---------
T ss_pred             HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHhccCcccchhhhc
Confidence            999999999999999999999999999999998777777777765

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.5e-49  Score=348.95  Aligned_cols=279  Identities=48%  Similarity=0.839  Sum_probs=262.8

Q ss_pred             hhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768            3 TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      .+.+..-+|.+.+|.+..+.-...|+++|++|.|+++++++|.+.+..|+..++.|.++|+.+++++|||||||||||++
T Consensus       153 ~~~~~~~l~~~~d~~~~~~~~~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlL  232 (437)
T 4b4t_I          153 TMSIVGVLQDDADPMVSVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLL  232 (437)
T ss_dssp             TCCEEEEECCCSSCCCCCCEEESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHH
T ss_pred             CccceeecCCccCCcceeeeeccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHH
Confidence            34556678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           83 ARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        83 ~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      |+++|++++.+++.++..++.+.+.|+++..++.+|..++...|+||||||+|.++.++.......+......+..+|+.
T Consensus       233 AkAiA~e~~~~fi~v~~s~l~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~  312 (437)
T 4b4t_I          233 AKAVANQTSATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQ  312 (437)
T ss_dssp             HHHHHHHHTCEEEEEESGGGCCSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCEEEEEHHHhhhccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999988777776677788889999999


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di  242 (292)
                      +++.....+++||+|||.++.+++++++++||+..|+|+.|+.++|.+||+.++.......+++++.|+..+.|||++||
T Consensus       313 lDg~~~~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI  392 (437)
T 4b4t_I          313 LDGFDDRGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADI  392 (437)
T ss_dssp             HHHCCCSSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHH
T ss_pred             hhCcCCCCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHH
Confidence            98888888999999999999999999999999999999999999999999999998888888999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhhch
Q 022768          243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLES  281 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~~~  281 (292)
                      ..+|++|...|+++++..|+.+||.+|++.+.....++.
T Consensus       393 ~~l~~eA~~~Air~~~~~It~eDf~~Al~rv~~~~~~e~  431 (437)
T 4b4t_I          393 QAMCTEAGLLALRERRMQVTAEDFKQAKERVMKNKVEEN  431 (437)
T ss_dssp             HHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHHHHHCCCS
T ss_pred             HHHHHHHHHHHHHcCCCccCHHHHHHHHHHHhCCCChhh
Confidence            999999999999999999999999999999987665544

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.4e-48  Score=348.24  Aligned_cols=275  Identities=52%  Similarity=0.931  Sum_probs=263.0

Q ss_pred             chhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHH
Q 022768            2 TTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTL   81 (292)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~   81 (292)
                      +++.+..-+|.+++|.+..|.-+..|.++|++|.|+++++++|.+.+..|+..++.|.++|+.+++++||+||||||||+
T Consensus       179 ~~~~i~~~lp~~~d~~v~~m~v~e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTl  258 (467)
T 4b4t_H          179 SKYNIELPLPPRIDPSVTMMTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTL  258 (467)
T ss_dssp             TSCCCCCSSCSSSCCCCCCCEEESSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHH
T ss_pred             CcceeeecCCCccCCccceeeecCCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHH
Confidence            46788899999999999999889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHH
Q 022768           82 LARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN  161 (292)
Q Consensus        82 l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~  161 (292)
                      +|+++|++++.+++.+++..+.+.+.|.++..++.+|..++...|+||||||+|.++.++.+...+........+..+|.
T Consensus       259 LAkAiA~e~~~~fi~vs~s~L~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~  338 (467)
T 4b4t_H          259 CARAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELIT  338 (467)
T ss_dssp             HHHHHHHHHTCEEEEEEGGGGCCCSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCeEEEEhHHhhcccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998887777777888889999999


Q ss_pred             HhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHH
Q 022768          162 QLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGAD  241 (292)
Q Consensus       162 ~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~d  241 (292)
                      .+++.....+++||+|||.++.+++++++++||+..|+|+.|+.++|.+||+.++.......+++++.|+..+.|||++|
T Consensus       339 ~lDg~~~~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGAD  418 (467)
T 4b4t_H          339 QLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAE  418 (467)
T ss_dssp             HHHSSCCTTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHH
T ss_pred             HhhccCCCCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHH
Confidence            99988888899999999999999999999999999999999999999999999999888888899999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          242 LRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       242 i~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      |..+|++|...|.++++..|+.+||.+|+..+...
T Consensus       419 I~~l~~eAa~~Air~~~~~it~~Df~~Al~kV~~g  453 (467)
T 4b4t_H          419 LRSVCTEAGMFAIRARRKVATEKDFLKAVDKVISG  453 (467)
T ss_dssp             HHHHHHHHHHHHHHHTCSSBCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHhcC
Confidence            99999999999999999999999999999998764

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=7.9e-49  Score=350.91  Aligned_cols=277  Identities=49%  Similarity=0.837  Sum_probs=261.6

Q ss_pred             hhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768            3 TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      .+.+...+|.+.+|.+..+.-...|+++|++|.|+++++++|.+.+..|+..++.|.++|+.+++++|||||||||||++
T Consensus       152 ~~~~~~~l~~~~d~~~~~~~~~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTll  231 (434)
T 4b4t_M          152 SYLILDTLPSEFDSRVKAMEVDEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLL  231 (434)
T ss_dssp             SCSEEEEEEESSSCSCSCCEEESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHH
T ss_pred             chhhheecCcccCchhhhcccCCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHH
Confidence            34556678899999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           83 ARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        83 ~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      |+++|++++.+++.+++..+.+.+.|.++..++.+|..++...||||||||+|.++.++.+...+........+..+++.
T Consensus       232 AkAiA~e~~~~f~~v~~s~l~~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~  311 (434)
T 4b4t_M          232 ARACAAQTNATFLKLAAPQLVQMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQ  311 (434)
T ss_dssp             HHHHHHHHTCEEEEEEGGGGCSSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCEEEEehhhhhhcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999988777666777888899999999


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADL  242 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di  242 (292)
                      ++++....+++||+|||.++.+++++++++||+..|+++.|+.++|.+||+.++.......+++++.|+..+.|||++||
T Consensus       312 ldg~~~~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi  391 (434)
T 4b4t_M          312 LDGFSSDDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQL  391 (434)
T ss_dssp             HTTSCSSCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHH
T ss_pred             hhccCCCCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHH
Confidence            99988888999999999999999999999999999999999999999999999998888888999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhhh
Q 022768          243 RNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKL  279 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~~  279 (292)
                      ..+|++|...|.+++...|+.+||.+|+..+.+..++
T Consensus       392 ~~l~~eA~~~a~r~~~~~i~~~Df~~Al~~v~~~~~~  428 (434)
T 4b4t_M          392 KAVTVEAGMIALRNGQSSVKHEDFVEGISEVQARKSK  428 (434)
T ss_dssp             HHHHHHHHHHHHHHTCSSBCHHHHHHHHHSCSSSCCC
T ss_pred             HHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhCCCCc
Confidence            9999999999999999999999999999998876553

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.6e-47  Score=339.96  Aligned_cols=273  Identities=44%  Similarity=0.781  Sum_probs=257.1

Q ss_pred             hhhhhhhCCCCCChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768            3 TLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      .+.+...+|.+.++.+..+.-...|.++|+++.|+++++++|.+.+..|+..++.|.++|+.+++++||+||||||||++
T Consensus       143 ~~~~~~~l~~~~d~~v~~~~~~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~l  222 (428)
T 4b4t_K          143 SNALVDILPPDSDSSISVMGENEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTML  222 (428)
T ss_dssp             SCCEEEEECSCCCCSSCCCEEESSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHH
T ss_pred             hhhHHhhcCcccCcchhhccCCCCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHH
Confidence            45566778999999999888899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           83 ARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        83 ~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      |+++|++++.+++.+++.++.+.+.|.+...++.+|..++...|+|+||||+|.++.++.......+......+..++..
T Consensus       223 akAiA~~~~~~~~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~  302 (428)
T 4b4t_K          223 VKAVANSTKAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQ  302 (428)
T ss_dssp             HHHHHHHHTCEEEEEEGGGTCCSSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCeEEEecchhhccccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999988777777777788889999999


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEcc-CCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIP-LPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGAD  241 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~-~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~d  241 (292)
                      ++++....+++||+|||.++.+++++++++||+..|+|| +|+.++|..||+.++.......+++++.++..+.|||++|
T Consensus       303 ldg~~~~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgad  382 (428)
T 4b4t_K          303 MDGFDQSTNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAV  382 (428)
T ss_dssp             HHHSCSSCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHH
T ss_pred             hhCCCCCCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHH
Confidence            998888889999999999999999999999999999996 8999999999999999888888899999999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          242 LRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       242 i~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      |..+|++|...|.++++..|+.+|+.+|+.....
T Consensus       383 i~~l~~eA~~~a~r~~~~~i~~~d~~~A~~~~~~  416 (428)
T 4b4t_K          383 IAAIMQEAGLRAVRKNRYVILQSDLEEAYATQVK  416 (428)
T ss_dssp             HHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHhhC
Confidence            9999999999999999999999999999987543

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=1.5e-41  Score=323.63  Aligned_cols=267  Identities=38%  Similarity=0.680  Sum_probs=195.3

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ....|+++|+++.|++++++.|++.+.+|+.....|.++|..+++++||+||||||||++|+++|++++.+++.++..++
T Consensus       468 ~~~~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~l  547 (806)
T 3cf2_A          468 VVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPEL  547 (806)
T ss_dssp             CCBCCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHHH
T ss_pred             cccCCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccchh
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      .+.+.|++++.++.+|..++...||||||||+|.++++++....+........+.++|.+++++....+++||+|||.++
T Consensus       548 ~s~~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~aTN~p~  627 (806)
T 3cf2_A          548 LTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPD  627 (806)
T ss_dssp             HTTTCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC-CCSS
T ss_pred             hccccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEeCCCch
Confidence            99999999999999999999999999999999999988765544444555677888899999888888999999999999


Q ss_pred             CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC----
Q 022768          183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER----  258 (292)
Q Consensus       183 ~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~----  258 (292)
                      .+++++++++||+..++++.|+.++|.+||+.++.......+++++.|+..+.|||++||..+|++|...|+++..    
T Consensus       628 ~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~~A~~~a~r~~~~~~~  707 (806)
T 3cf2_A          628 IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEI  707 (806)
T ss_dssp             SSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHHHHHHHHHHHHHC---
T ss_pred             hCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            9999999999999999999999999999999999888888889999999999999999999999999999987631    


Q ss_pred             ---------------------CcccHHHHHHHHHHHhhhhhhchhh---hhhhhc
Q 022768          259 ---------------------DYVIHEDFMKAVRKLNEAKKLESSA---HYNADF  289 (292)
Q Consensus       259 ---------------------~~i~~~~~~~a~~~~~~~~~~~~~~---~~~~~~  289 (292)
                                           ..|+.+||.+|++.+.+.-+.+...   .|.+.|
T Consensus       708 ~~~~~~~~~~~~~~~~~~~~~~~i~~~df~~al~~~~pSvs~~~l~~y~~~~~~f  762 (806)
T 3cf2_A          708 RRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL  762 (806)
T ss_dssp             --------------------CCC----CCTTTC---------------CCCC---
T ss_pred             hhhhhhccCccccccccccccCccCHHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence                                 2589999999999999875555544   444444

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=4.2e-39  Score=306.81  Aligned_cols=265  Identities=40%  Similarity=0.688  Sum_probs=235.1

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ....|.++|++|.|+++++++|++.+..|+..++.|..+|+.+++++||+||||||||++|+++|++++.+++.+++.++
T Consensus       195 ~~~~~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l  274 (806)
T 3cf2_A          195 EESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEI  274 (806)
T ss_dssp             SCCSSSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHH
T ss_pred             cccCCCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHh
Confidence            34568899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      .+.+.+..+..++.+|..++...|+||||||+|.+++++.+.........   +.+++..++++....+++||++||.++
T Consensus       275 ~sk~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~ri---v~~LL~~mdg~~~~~~V~VIaaTN~~d  351 (806)
T 3cf2_A          275 MSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRI---VSQLLTLMDGLKQRAHVIVMAATNRPN  351 (806)
T ss_dssp             HSSCTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHH---HHHHHTHHHHCCGGGCEEEEEECSSTT
T ss_pred             hcccchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHH---HHHHHHHHhcccccCCEEEEEecCChh
Confidence            99999999999999999999999999999999999988766555444444   444455555555567899999999999


Q ss_pred             CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC----
Q 022768          183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER----  258 (292)
Q Consensus       183 ~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~----  258 (292)
                      .+++++++++||+..|+++.|+.++|.+||+.++.......++++..++..+.||+++||..+|++|...|..+..    
T Consensus       352 ~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~eA~~~A~~r~~~~i~  431 (806)
T 3cf2_A          352 SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLID  431 (806)
T ss_dssp             TSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             hcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcccccc
Confidence            9999999999999999999999999999999999988888899999999999999999999999999999987632    


Q ss_pred             -------------CcccHHHHHHHHHHHhhhhhhch-----hhhhhhhcC
Q 022768          259 -------------DYVIHEDFMKAVRKLNEAKKLES-----SAHYNADFG  290 (292)
Q Consensus       259 -------------~~i~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~  290 (292)
                                   ..|+.+|+..|+..+.+...++.     ...|+++.|
T Consensus       432 ~~~~~~~~e~~~~~~v~~~Df~~Al~~~~ps~~r~~~~~~p~v~w~digg  481 (806)
T 3cf2_A          432 LEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGG  481 (806)
T ss_dssp             GTCCCCSHHHHHHCEECTTHHHHHHSSSSCCCCCCCCCBCCCCCSTTCCS
T ss_pred             ccccccchhhhccceeeHHHHHHHHHhCCCcccccccccCCCCCHHHhCC
Confidence                         25788999999999988655433     456777766

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=100.00  E-value=2.6e-37  Score=265.82  Aligned_cols=255  Identities=56%  Similarity=0.978  Sum_probs=237.3

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      ...|+++|++++|++++++.|.+++..++.....+.++|+.++.+++|+||||||||++++++++.++.+++.+++..+.
T Consensus         9 ~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~   88 (285)
T 3h4m_A            9 DERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELV   88 (285)
T ss_dssp             ESSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGGC
T ss_pred             cCCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHHH
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      ..+.+.....+..+|..+....|++|+|||+|.+..++.+.....+...+..+..+++.++......++++|+|+|.++.
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~  168 (285)
T 3h4m_A           89 KKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDI  168 (285)
T ss_dssp             CCSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSSSSEEEEEECSCGGG
T ss_pred             HhccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCchh
Confidence            99999999999999999999999999999999999887777666778888999999998887777778999999999999


Q ss_pred             CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccH
Q 022768          184 LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIH  263 (292)
Q Consensus       184 l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~  263 (292)
                      +++.+++++||...+.++.|+.++|.+|++.++.......+.++..++..+.|++++++..+++.|...|..++...|+.
T Consensus       169 l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~~a~~~a~~~~~~~I~~  248 (285)
T 3h4m_A          169 LDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGMNAIRELRDYVTM  248 (285)
T ss_dssp             BCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHHHHHHTTCSSBCH
T ss_pred             cCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCcCCH
Confidence            99999998899999999999999999999999988777778899999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhh
Q 022768          264 EDFMKAVRKLNEAKK  278 (292)
Q Consensus       264 ~~~~~a~~~~~~~~~  278 (292)
                      +|+.+|+..+.....
T Consensus       249 ~d~~~al~~~~~~~~  263 (285)
T 3h4m_A          249 DDFRKAVEKIMEKKK  263 (285)
T ss_dssp             HHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhccc
Confidence            999999999987544

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=100.00  E-value=2.1e-37  Score=268.42  Aligned_cols=266  Identities=38%  Similarity=0.686  Sum_probs=223.4

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII  103 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~  103 (292)
                      ...|+++|++++|++++++.|.+.+..++.....+..+++.++.+++|+||||||||++|+++++.++.+++.+++..+.
T Consensus         7 ~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~   86 (301)
T 3cf0_A            7 VEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELL   86 (301)
T ss_dssp             EECCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHH
T ss_pred             ccCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHH
Confidence            35688999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      ..+.+.....+..+|..+....|++|||||+|.+...++.............+..++..+++.....+++||++||.++.
T Consensus        87 ~~~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~atn~~~~  166 (301)
T 3cf0_A           87 TMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDI  166 (301)
T ss_dssp             HHHHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEESCGGG
T ss_pred             hhhcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEecCCccc
Confidence            87778877888899999998899999999999997654332211111112233445555555555668999999999999


Q ss_pred             CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC-----
Q 022768          184 LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER-----  258 (292)
Q Consensus       184 l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~-----  258 (292)
                      +++++++++||...++++.|+.++|.+|++.++.......+++++.++..+.||+++||..+|++|...|..+..     
T Consensus       167 ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~~~a~~~a~~~~~~~~~~  246 (301)
T 3cf0_A          167 IDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIR  246 (301)
T ss_dssp             SCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHHHHHHC-
T ss_pred             cChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            999999989999999999999999999999999877766788999999999999999999999999998876521     


Q ss_pred             --------------------CcccHHHHHHHHHHHhhhhhhch---hhhhhhhc
Q 022768          259 --------------------DYVIHEDFMKAVRKLNEAKKLES---SAHYNADF  289 (292)
Q Consensus       259 --------------------~~i~~~~~~~a~~~~~~~~~~~~---~~~~~~~~  289 (292)
                                          ..|+.+||.+|++.+.+..+...   ...|.+.|
T Consensus       247 ~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~al~~~~~s~~~~~~~~~~~~~~~~  300 (301)
T 3cf0_A          247 RERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTL  300 (301)
T ss_dssp             -------------------CCCBCHHHHHHHHTTCCCSSCHHHHHHHHHHHHHH
T ss_pred             hhhhcccccccccccccccCCccCHHHHHHHHHHcCCCCCHHHHHHHHHHHHHh
Confidence                                36899999999999987655544   34455544

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=100.00  E-value=3.3e-37  Score=269.62  Aligned_cols=267  Identities=34%  Similarity=0.626  Sum_probs=220.6

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      ..-...|+++|++++|++++++.|.+.+..++.....+.. +..++.++||+||||||||++|+++|++++.+++.+++.
T Consensus         7 ~~~~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~   85 (322)
T 3eie_A            7 AILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSS   85 (322)
T ss_dssp             CSEEECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCT-TCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHH
T ss_pred             ceeecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhc-CCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchH
Confidence            3445788999999999999999999999888777666655 446678999999999999999999999999999999999


Q ss_pred             chhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          101 AIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      .+...+.+.....++.+|..+....|+||||||+|.+..++...........+..++..+....  ....+++||++||.
T Consensus        86 ~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~--~~~~~v~vi~atn~  163 (322)
T 3eie_A           86 DLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVG--NDSQGVLVLGATNI  163 (322)
T ss_dssp             HHHTTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGG--TSCCCEEEEEEESC
T ss_pred             HHhhcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhcccc--ccCCceEEEEecCC
Confidence            9999999999999999999999999999999999999877655444444555555555544432  24457999999999


Q ss_pred             CCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC-
Q 022768          181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER-  258 (292)
Q Consensus       181 ~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~-  258 (292)
                      ++.+++++++  ||...++++.|+.++|.+|++.++...... .+.+++.++..+.||+++||..+|+.|...|+++.. 
T Consensus       164 ~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~a~~~a~r~~~~  241 (322)
T 3eie_A          164 PWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQS  241 (322)
T ss_dssp             GGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHHHTTHHHHHHHH
T ss_pred             hhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999  999999999999999999999998865433 455788999999999999999999999999988631 


Q ss_pred             ------------------------------------------CcccHHHHHHHHHHHhhhhhhch---hhhhhhhcCCC
Q 022768          259 ------------------------------------------DYVIHEDFMKAVRKLNEAKKLES---SAHYNADFGKE  292 (292)
Q Consensus       259 ------------------------------------------~~i~~~~~~~a~~~~~~~~~~~~---~~~~~~~~~~~  292 (292)
                                                                ..|+.+|+.+|++.+.+..+.+.   ...|.+.||++
T Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~it~~df~~al~~~~ps~~~~~~~~~~~~~~~~~~~  320 (322)
T 3eie_A          242 ATHFKDVSTEDDETRKLTPCSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQE  320 (322)
T ss_dssp             CEEEEECC----CCCCEEECCSSCTTEEEEEGGGSCSSCBCCCCCCHHHHHHHHHHSCCSSCTTHHHHHHHHHHHHC--
T ss_pred             hhhhhhhccccccccccccccccccccccccccccccccccCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhcCC
Confidence                                                      34999999999999998655444   56788889875

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=100.00  E-value=2.4e-36  Score=263.86  Aligned_cols=262  Identities=33%  Similarity=0.622  Sum_probs=222.2

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-CCcEEEEeccchh
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-DANFLKVVSSAII  103 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-~~~~~~~~~~~~~  103 (292)
                      ..|+++|++|+|++++++.|.+.+..|+.....+.. +..+++++||+||||||||++|+++|+++ +.+++.+++.++.
T Consensus         5 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~   83 (322)
T 1xwi_A            5 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLV   83 (322)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCT-TCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSC
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhC-CCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHH
Confidence            568899999999999999999999988877777653 24567899999999999999999999999 8899999999999


Q ss_pred             ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-CCCCeEEEEEeCCCC
Q 022768          104 DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-QLGKVKMIMATNRPD  182 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-~~~~~~vi~t~~~~~  182 (292)
                      ..+.+.....++.+|..+....|+||||||+|.+.+++......   .....+..++..+++.. ...+++||++||.++
T Consensus        84 ~~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~---~~~~~~~~ll~~ld~~~~~~~~v~vI~atn~~~  160 (322)
T 1xwi_A           84 SKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESE---AARRIKTEFLVQMQGVGVDNDGILVLGATNIPW  160 (322)
T ss_dssp             CSSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTT---HHHHHHHHHHHHHHCSSSCCTTEEEEEEESCTT
T ss_pred             hhhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccch---HHHHHHHHHHHHHhcccccCCCEEEEEecCCcc
Confidence            88889999999999999999999999999999998776554332   23344556666666543 356899999999999


Q ss_pred             CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC---
Q 022768          183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER---  258 (292)
Q Consensus       183 ~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~---  258 (292)
                      .+++++++  ||...+.++.|+.++|.+|++.++...... .+.+++.++..+.||+++||..+|++|...|.++..   
T Consensus       161 ~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~A~~~a~r~~~~~~  238 (322)
T 1xwi_A          161 VLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVRKVQSAT  238 (322)
T ss_dssp             TSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHHHHTHHHHHHHHCS
T ss_pred             cCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence            99999999  999999999999999999999998765443 456788999999999999999999999999887521   


Q ss_pred             ----------------------------------------------CcccHHHHHHHHHHHhhhhhh---chhhhhhhhc
Q 022768          259 ----------------------------------------------DYVIHEDFMKAVRKLNEAKKL---ESSAHYNADF  289 (292)
Q Consensus       259 ----------------------------------------------~~i~~~~~~~a~~~~~~~~~~---~~~~~~~~~~  289 (292)
                                                                    ..|+.+|+.+|++.+.+.-+.   +....|.+.|
T Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~al~~~~ps~~~~~~~~~~~~~~~~  318 (322)
T 1xwi_A          239 HFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMSDMLRSLSNTKPTVNEHDLLKLKKFTEDF  318 (322)
T ss_dssp             EEEEEEEECSSCTTSEEEEEEEECCSSSTTEEECCGGGSCGGGBCCCCBCHHHHHHHHHTCCCSCCHHHHHHHHHHHHTT
T ss_pred             hhhhhccccccccccccccccccccccccchhhccccccccccccCCCcCHHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence                                                          259999999999999986554   3467888888


Q ss_pred             CCC
Q 022768          290 GKE  292 (292)
Q Consensus       290 ~~~  292 (292)
                      |.+
T Consensus       319 ~~~  321 (322)
T 1xwi_A          319 GQE  321 (322)
T ss_dssp             CSC
T ss_pred             ccC
Confidence            875

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=100.00  E-value=2.8e-36  Score=266.83  Aligned_cols=273  Identities=34%  Similarity=0.613  Sum_probs=210.4

Q ss_pred             ChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           15 DPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      ...+...+....|+++|++|+|++++++.|.+.+..++.....+.. +..++.++||+||||||||++|+++|+.++.++
T Consensus        34 ~~~~~~~~~~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~  112 (355)
T 2qp9_X           34 RGALSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTF  112 (355)
T ss_dssp             -------------CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCS-SCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEE
T ss_pred             HHHHhhhhcccCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhc-CCCCCceEEEECCCCCcHHHHHHHHHHHhCCCE
Confidence            3344445556788999999999999999999999888777777665 456678899999999999999999999999999


Q ss_pred             EEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      +.+++..+...+.+.....++.+|..+....|+||||||+|.+...+..............++..++.+.  ....+++|
T Consensus       113 ~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~--~~~~~v~v  190 (355)
T 2qp9_X          113 FSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVG--NDSQGVLV  190 (355)
T ss_dssp             EEEEHHHHHSCC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC-----CCEEE
T ss_pred             EEeeHHHHhhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhccc--ccCCCeEE
Confidence            9999999988888888999999999999889999999999999776544333333444444444444322  23457999


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      |++||.++.+++++++  ||...+.++.|+.++|.+|++.++...... .+.+++.|+..+.||+++||..+|++|...|
T Consensus       191 I~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~~A~~~a  268 (355)
T 2qp9_X          191 LGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQP  268 (355)
T ss_dssp             EEEESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHH
T ss_pred             EeecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999998  999999999999999999999998765432 4567889999999999999999999999999


Q ss_pred             HHhc-------------------------------------------CCcccHHHHHHHHHHHhhhhhhc---hhhhhhh
Q 022768          254 IRAE-------------------------------------------RDYVIHEDFMKAVRKLNEAKKLE---SSAHYNA  287 (292)
Q Consensus       254 ~~~~-------------------------------------------~~~i~~~~~~~a~~~~~~~~~~~---~~~~~~~  287 (292)
                      +.+.                                           ...|+.+||.+|++.+.+..+.+   ....|.+
T Consensus       269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~Al~~~~ps~~~~~~~~~~~~~~  348 (355)
T 2qp9_X          269 IRKIQSATHFKDVSTEDDETRKLTPSSPGDDGAIEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTR  348 (355)
T ss_dssp             HHHHHHCSEEEECCC-----CCEEEECTTSSSEEECCGGGSCGGGBCCCCBCHHHHHHHHHHSCCSSCHHHHHHHHHHHH
T ss_pred             HHHHHHhhhhhhhccccccccccCcCCccccchhhcccccccccccccCCccHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            8762                                           12499999999999999875554   3678888


Q ss_pred             hcCCC
Q 022768          288 DFGKE  292 (292)
Q Consensus       288 ~~~~~  292 (292)
                      .||.+
T Consensus       349 ~~~~~  353 (355)
T 2qp9_X          349 DFGQE  353 (355)
T ss_dssp             HTC--
T ss_pred             HhccC
Confidence            88864

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=100.00  E-value=3.9e-35  Score=248.56  Aligned_cols=251  Identities=41%  Similarity=0.681  Sum_probs=216.4

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      .+..++.+|++++|++++++.+.+.+.. +.....+..++...+.+++|+||||||||++++++++.++.+++.+++..+
T Consensus         3 ~~~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~   81 (257)
T 1lv7_A            3 TEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDF   81 (257)
T ss_dssp             EECSSCCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSS
T ss_pred             CccCCCCCHHHhcCcHHHHHHHHHHHHH-HhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHH
Confidence            4567889999999999999999988765 555666777777788899999999999999999999999999999999998


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      ...+.+.....+..+|..+....|++++|||+|.+...+..............+..++..++......++++|+++|.++
T Consensus        82 ~~~~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~vI~~tn~~~  161 (257)
T 1lv7_A           82 VEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPD  161 (257)
T ss_dssp             TTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCTT
T ss_pred             HHHhhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCEEEEEeeCCch
Confidence            88888888888899999998888999999999999876655444344445566677777777766667899999999999


Q ss_pred             CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCccc
Q 022768          183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVI  262 (292)
Q Consensus       183 ~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~  262 (292)
                      .+++++.+++||...+.++.|+.++|.+|++.++.......+.+...++..+.||+++|+..+++.|...|..++...|+
T Consensus       162 ~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~~a~~~a~~~~~~~i~  241 (257)
T 1lv7_A          162 VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVS  241 (257)
T ss_dssp             TSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBC
T ss_pred             hCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccc
Confidence            99999999889999999999999999999999998777777888999999999999999999999999999999888999


Q ss_pred             HHHHHHHHHHHh
Q 022768          263 HEDFMKAVRKLN  274 (292)
Q Consensus       263 ~~~~~~a~~~~~  274 (292)
                      .+|+.+|+..+.
T Consensus       242 ~~~~~~a~~~~~  253 (257)
T 1lv7_A          242 MVEFEKAKDKIM  253 (257)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            999999999875

>2ce7_A Cell division protein FTSH; metalloprotease; HET: ADP; 2.44A {Thermotoga maritima} SCOP: a.269.1.1 c.37.1.20 PDB: 2cea_A* 3kds_E*

Probab=100.00  E-value=4.5e-35  Score=265.95  Aligned_cols=252  Identities=41%  Similarity=0.730  Sum_probs=219.1

Q ss_pred             ccC-CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           23 HED-PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        23 ~~~-~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      .+. .+.++|++++|++++++++.+.+.. +.....+.++|...+.+++|+||||||||+++++++++++.+++.+++.+
T Consensus         6 ~~~~~~~~~f~di~G~~~~~~~l~e~v~~-l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~   84 (476)
T 2ce7_A            6 KPSGNKRVTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSD   84 (476)
T ss_dssp             CCCCSCCCCGGGCCSCHHHHHHHHHHHHH-HHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGG
T ss_pred             ccCCCCCCCHHHhCCcHHHHHHHHHHHHH-hhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHH
Confidence            344 6788999999999999999999876 67778889999988999999999999999999999999999999999999


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      +...+.+.....++.+|..+....|+||||||+|.+..+++....+.+......+..++..++++....+++||++||.+
T Consensus        85 ~~~~~~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn~~  164 (476)
T 2ce7_A           85 FVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRP  164 (476)
T ss_dssp             TTTCCTTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEESCG
T ss_pred             HHHHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecCCh
Confidence            99888888888899999999999999999999999987765544444555566677777777655555689999999999


Q ss_pred             CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcc
Q 022768          182 DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYV  261 (292)
Q Consensus       182 ~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i  261 (292)
                      +.+++++++++||+..+.++.|+.++|.+|++.++.......++++..++..+.|++++||.++|++|...|..++...|
T Consensus       165 ~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~~Aal~A~~~~~~~I  244 (476)
T 2ce7_A          165 DILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAALLAAREGRDKI  244 (476)
T ss_dssp             GGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSB
T ss_pred             hhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHHHHHHHHHHcCCCee
Confidence            99999999989999999999999999999999999887777788899999999999999999999999999998888899


Q ss_pred             cHHHHHHHHHHHhh
Q 022768          262 IHEDFMKAVRKLNE  275 (292)
Q Consensus       262 ~~~~~~~a~~~~~~  275 (292)
                      +.+|+.+|+..+..
T Consensus       245 ~~~dl~~al~~v~~  258 (476)
T 2ce7_A          245 TMKDFEEAIDRVIA  258 (476)
T ss_dssp             CHHHHHHHHHHHC-
T ss_pred             cHHHHHHHHHHHhc
Confidence            99999999998864

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=100.00  E-value=3.8e-35  Score=268.43  Aligned_cols=264  Identities=39%  Similarity=0.688  Sum_probs=226.2

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      ..++.+|++++|+++++++|.+.+..++.....+..+|..++.++||+||||||||++|++++++++.+++.+++..+..
T Consensus       197 ~~~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~~  276 (489)
T 3hu3_A          197 SLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMS  276 (489)
T ss_dssp             HHTCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHHT
T ss_pred             ccCCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhhh
Confidence            34667999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      .+.+.....++.+|..+....|++|||||+|.+..++...........+..|+.+++.   .....+++||+|||.++.+
T Consensus       277 ~~~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~---~~~~~~v~vIaaTn~~~~L  353 (489)
T 3hu3_A          277 KLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDG---LKQRAHVIVMAATNRPNSI  353 (489)
T ss_dssp             SCTTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHH---SCTTSCEEEEEEESCGGGB
T ss_pred             hhcchhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhc---cccCCceEEEEecCCcccc
Confidence            9999999999999999999999999999999998776554444445555556655554   3445689999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCC-----
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERD-----  259 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~-----  259 (292)
                      ++++++++||...+.++.|+.++|.+|++.++.......+.++..++..+.||+++|+..++++|...|..+...     
T Consensus       354 d~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~~~A~~~a~r~~~~~i~~~  433 (489)
T 3hu3_A          354 DPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLE  433 (489)
T ss_dssp             CGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTTTTCCTT
T ss_pred             CHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHHHHHHHHHHHhcccccccc
Confidence            999999899999999999999999999999998887778889999999999999999999999999999887532     


Q ss_pred             ------------cccHHHHHHHHHHHhhhhhhch-----hhhhhhhcCC
Q 022768          260 ------------YVIHEDFMKAVRKLNEAKKLES-----SAHYNADFGK  291 (292)
Q Consensus       260 ------------~i~~~~~~~a~~~~~~~~~~~~-----~~~~~~~~~~  291 (292)
                                  .|+.+|+.+|++.+.+...++.     ...|+|++|-
T Consensus       434 ~~~~~~~~~~~~~vt~edf~~Al~~~~ps~~re~~~e~p~v~W~dig~~  482 (489)
T 3hu3_A          434 DETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGR  482 (489)
T ss_dssp             CSSCCHHHHHHCCBCHHHHHHHHTSHHHHHHHGGGC-------------
T ss_pred             ccccchhhcccCcCCHHHHHHHHHhCCchhhhcccccCCCCCHHHcCCC
Confidence                        5899999999999998776554     6789999984

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=100.00  E-value=2.2e-35  Score=251.89  Aligned_cols=253  Identities=38%  Similarity=0.665  Sum_probs=205.1

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      ..|+++|+++.|++++++.|.+.+..++.....+..+++..+.+++|+||||+|||++++++|..++.+++.++..++..
T Consensus         3 ~~~~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~~   82 (274)
T 2x8a_A            3 TVPNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLN   82 (274)
T ss_dssp             ---------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTCS
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHHh
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999988887


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      .+.+.....+..+|..+....|+++++||+|.++..+.....   ......+..++..+++......+++++++|.++.+
T Consensus        83 ~~~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~~---~~~~~~~~~~l~~Lsgg~~~~~~i~ia~tn~p~~L  159 (274)
T 2x8a_A           83 MYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRET---GASVRVVNQLLTEMDGLEARQQVFIMAATNRPDII  159 (274)
T ss_dssp             STTHHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC------------CTTHHHHHHHHHHTCCSTTCEEEEEEESCGGGS
T ss_pred             hhhhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCcc---hHHHHHHHHHHHhhhcccccCCEEEEeecCChhhC
Confidence            777788888999999988888999999999998754422111   11223455677777766666788999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcC---ccCCCCCCHHHHHHHc--CCCCHHHHHHHHHHHHHHHHHhc--
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAG---IAKHGEIDYEAVVKLA--EGFNGADLRNVCTEAGMSAIRAE--  257 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~---~~~~~~~~~~~l~~~~--~g~~~~di~~l~~~a~~~a~~~~--  257 (292)
                      ++++++++||+..++++.|+.++|.+||+.++..   .....+++++.++..+  .||+++||..+|++|...|.++.  
T Consensus       160 D~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~~a~~~a~~~~~~  239 (274)
T 2x8a_A          160 DPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASICALRQEMA  239 (274)
T ss_dssp             CHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHHHHHHHHHHHHC-
T ss_pred             CHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999998854   2345678999999864  59999999999999999998752  


Q ss_pred             ---------CCcccHHHHHHHHHHHhhhhhhc
Q 022768          258 ---------RDYVIHEDFMKAVRKLNEAKKLE  280 (292)
Q Consensus       258 ---------~~~i~~~~~~~a~~~~~~~~~~~  280 (292)
                               ...|+.+|+.+|++.+.+..+.+
T Consensus       240 ~~~~~~~~~~~~i~~~df~~al~~~~ps~~~~  271 (274)
T 2x8a_A          240 RQKSGNEKGELKVSHKHFEEAFKKVRSSISKK  271 (274)
T ss_dssp             ----------CCBCHHHHHHHHTTCCCCC---
T ss_pred             hccccccccCCeecHHHHHHHHHHhcCCCChh
Confidence                     23699999999999998865543

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=100.00  E-value=2.3e-34  Score=244.28  Aligned_cols=251  Identities=38%  Similarity=0.647  Sum_probs=193.5

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      |+++|++++|++++++.|.+.+.. +.....+..+|...+.+++|+||||||||+++++++++++.+++.+++..+...+
T Consensus         1 ~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~   79 (262)
T 2qz4_A            1 MGVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVI   79 (262)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHH-HHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSS
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHH-HHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhc
Confidence            568999999999999999998876 5666777788888899999999999999999999999999999999999998888


Q ss_pred             cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCc-chHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          107 IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS-ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~-~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      .+.....+..+|..+....|++|+|||+|.+..++...... .....+..+..++..++......++++|+|+|.++.++
T Consensus        80 ~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~tn~~~~ld  159 (262)
T 2qz4_A           80 GGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILD  159 (262)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCCEEEEEEESCGGGGG
T ss_pred             cChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEecCCChhhcC
Confidence            88888888999999988889999999999997655332211 13344566777777777666667899999999999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCC--HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccH
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEID--YEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIH  263 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~--~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~  263 (292)
                      +.+++++||...++++.|+.++|.++++.++.........+  ...++..+.|++++++..+++.|...|..++...|+.
T Consensus       160 ~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~~a~~~a~~~~~~~i~~  239 (262)
T 2qz4_A          160 GALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHAAREGHTSVHT  239 (262)
T ss_dssp             SGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHHHHHTC--------CCB
T ss_pred             HHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCCCCCCH
Confidence            99998889999999999999999999999987654443322  3678889999999999999999999999888889999


Q ss_pred             HHHHHHHHHHhhhhh
Q 022768          264 EDFMKAVRKLNEAKK  278 (292)
Q Consensus       264 ~~~~~a~~~~~~~~~  278 (292)
                      +|+.+|++.+.....
T Consensus       240 ~d~~~a~~~~~~~~~  254 (262)
T 2qz4_A          240 LNFEYAVERVLAGTA  254 (262)
T ss_dssp             CCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhccChh
Confidence            999999999887544

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A

Probab=100.00  E-value=1.4e-34  Score=262.88  Aligned_cols=268  Identities=33%  Similarity=0.606  Sum_probs=212.5

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-CCcEEEE
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-DANFLKV   97 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-~~~~~~~   97 (292)
                      ...+....|+++|++|+|++++++.|.+.+..++.....+.. +..+++++||+||||||||++|+++|+.+ +.+++.+
T Consensus       121 ~~~i~~~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v  199 (444)
T 2zan_A          121 QGAIVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSI  199 (444)
T ss_dssp             ---CBCCCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSG-GGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEE
T ss_pred             hcceeccCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhc-cCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEE
Confidence            444556789999999999999999999999877666555543 23567899999999999999999999999 8899999


Q ss_pred             eccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-CCCCeEEEE
Q 022768           98 VSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-QLGKVKMIM  176 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-~~~~~~vi~  176 (292)
                      ++.++...+.+.....++.+|..+....|+||||||+|.+.+.+.........   ..+..++..+++.. ...+++||+
T Consensus       200 ~~~~l~~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~---~~~~~lL~~l~~~~~~~~~v~vI~  276 (444)
T 2zan_A          200 SSSDLVSKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAAR---RIKTEFLVQMQGVGVDNDGILVLG  276 (444)
T ss_dssp             CCC---------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGH---HHHHHHHTTTTCSSCCCSSCEEEE
T ss_pred             eHHHHHhhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHH---HHHHHHHHHHhCcccCCCCEEEEe
Confidence            99998888888777788899999998899999999999998766554333333   34455566665543 356899999


Q ss_pred             EeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Q 022768          177 ATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       177 t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      |||.++.+++++++  ||...+.++.|+.++|..|++.++...... .+.+++.|+..+.||+++||..+|++|...|++
T Consensus       277 atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~a~~~a~r  354 (444)
T 2zan_A          277 ATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVR  354 (444)
T ss_dssp             EESCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHH
T ss_pred             cCCCccccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999999  999999999999999999999998765432 456789999999999999999999999998887


Q ss_pred             hc-------------------------------------------------CCcccHHHHHHHHHHHhhhhhh---chhh
Q 022768          256 AE-------------------------------------------------RDYVIHEDFMKAVRKLNEAKKL---ESSA  283 (292)
Q Consensus       256 ~~-------------------------------------------------~~~i~~~~~~~a~~~~~~~~~~---~~~~  283 (292)
                      +.                                                 ...|+.+||.+|++.+.+.-+.   ....
T Consensus       355 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~a~~~~~ps~~~~~~~~~~  434 (444)
T 2zan_A          355 KVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLK  434 (444)
T ss_dssp             HHHHCSEEEEECCBCSSCTTSBCSCEEEEECTTSTTEEECCTTTSCTTCBCCCCEEHHHHHHHHHTCCCSCCHHHHHHHH
T ss_pred             HHHhhhhhhhhccccccccccccccccccCCCCcccchhcccccCchhhccCCccCHHHHHHHHHhCCCCCCHHHHHHHH
Confidence            52                                                 0258999999999999986544   3467


Q ss_pred             hhhhhcCCC
Q 022768          284 HYNADFGKE  292 (292)
Q Consensus       284 ~~~~~~~~~  292 (292)
                      .|.+.||.|
T Consensus       435 ~~~~~~~~~  443 (444)
T 2zan_A          435 KFTEDFGQE  443 (444)
T ss_dssp             HHTSSCTTT
T ss_pred             HHHHHHcCC
Confidence            888889875

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=100.00  E-value=1.1e-33  Score=250.45  Aligned_cols=268  Identities=33%  Similarity=0.581  Sum_probs=215.8

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .+.+....++.+|++++|++++++.|.+.+..++.....+...+ .++.++||+||||||||++|+++++.++.+++.++
T Consensus        71 ~~~i~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~  149 (357)
T 3d8b_A           71 MNEIMDHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQSGATFFSIS  149 (357)
T ss_dssp             HHHTBCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-SCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEE
T ss_pred             HhhcccCCCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhcc-CCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEe
Confidence            34455677899999999999999999999988766655554443 55788999999999999999999999999999999


Q ss_pred             ccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC--CCCCeEEEE
Q 022768           99 SSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD--QLGKVKMIM  176 (292)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~--~~~~~~vi~  176 (292)
                      +..+...+.+.....++.+|..+....|++|||||+|.+...+.........   ..+..++..+.+..  ...+++||+
T Consensus       150 ~~~l~~~~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~---~~~~~lL~~l~~~~~~~~~~v~vI~  226 (357)
T 3d8b_A          150 ASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSR---RIKTEFLVQLDGATTSSEDRILVVG  226 (357)
T ss_dssp             GGGGCCSSTTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHH---HHHHHHHHHHHC----CCCCEEEEE
T ss_pred             hHHhhccccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHH---HHHHHHHHHHhcccccCCCCEEEEE
Confidence            9999988888888999999999998889999999999997655332222222   33344444444332  345799999


Q ss_pred             EeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Q 022768          177 ATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       177 t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      +||.++.+++++++  ||...+.++.|+.++|.++++.++...... .+.++..++..+.||+++++..+|+.|...+++
T Consensus       227 atn~~~~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~a~~~~ir  304 (357)
T 3d8b_A          227 ATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLGPIR  304 (357)
T ss_dssp             EESCGGGBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHH
T ss_pred             ecCChhhCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999999  998899999999999999999988654332 334578899999999999999999999998887


Q ss_pred             hc------------CCcccHHHHHHHHHHHhhhhhh---chhhhhhhhcCCC
Q 022768          256 AE------------RDYVIHEDFMKAVRKLNEAKKL---ESSAHYNADFGKE  292 (292)
Q Consensus       256 ~~------------~~~i~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~~~  292 (292)
                      +.            ...|+.+|+.+|+..+.+....   +..+.|++.||.+
T Consensus       305 ~l~~~~~~~~~~~~~~~i~~~d~~~al~~~~ps~~~~~~~~~~~~~~~~g~~  356 (357)
T 3d8b_A          305 SLQTADIATITPDQVRPIAYIDFENAFRTVRPSVSPKDLELYENWNKTFGCG  356 (357)
T ss_dssp             HCCC----------CCCBCHHHHHHHHHHHGGGCCCCCHHHHHHHHHHHSCC
T ss_pred             HhhhhhhccccccccCCcCHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhCCC
Confidence            43            2479999999999999985443   4467999999974

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A*

Probab=100.00  E-value=1.1e-32  Score=233.08  Aligned_cols=247  Identities=41%  Similarity=0.709  Sum_probs=209.3

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ....|+++|++++|++++++++.+.... +.....+...++..+.+++|+||||+||||+++++++.++.+++.++...+
T Consensus         7 ~~~~~~~~~~~i~g~~~~~~~l~~l~~~-~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~   85 (254)
T 1ixz_A            7 LTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF   85 (254)
T ss_dssp             -CCCCSCCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             ccCCCCCCHHHhCCcHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHH
Confidence            4567889999999999999999988766 566778888888888889999999999999999999999999999998887


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      .....+.....+..+|+.+....|+++++||+|.+...+..............+..++..+++......+++++++|.++
T Consensus        86 ~~~~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~t~~p~  165 (254)
T 1ixz_A           86 VEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPD  165 (254)
T ss_dssp             HHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGG
T ss_pred             HHHHhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEccCCch
Confidence            77777777777888998887777899999999998765533222233455566777777777666666788999999999


Q ss_pred             CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCccc
Q 022768          183 VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVI  262 (292)
Q Consensus       183 ~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~  262 (292)
                      .+++++++++||+..+.++.|+.++|.+|++.+........+.++..++..+.|++++|+..++++|...|..++...|+
T Consensus       166 ~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~~a~~~a~~~~~~~I~  245 (254)
T 1ixz_A          166 ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKIT  245 (254)
T ss_dssp             GSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBC
T ss_pred             hCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCCcC
Confidence            99999999999999999999999999999999988777777888999999999999999999999999999888888899


Q ss_pred             HHHHHHHH
Q 022768          263 HEDFMKAV  270 (292)
Q Consensus       263 ~~~~~~a~  270 (292)
                      .+|+.+|+
T Consensus       246 ~~dl~~a~  253 (254)
T 1ixz_A          246 MKDLEEAA  253 (254)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHh
Confidence            99999885

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=100.00  E-value=2.2e-33  Score=242.67  Aligned_cols=272  Identities=31%  Similarity=0.592  Sum_probs=212.1

Q ss_pred             hhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           17 VVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        17 ~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .+....-...|+.+|++++|++++++.|.+.+..+......+..++ .++.+++|+||||||||++++++++.++.+++.
T Consensus         6 ~~~~~~~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~   84 (297)
T 3b9p_A            6 LILDEIVEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLARAVATECSATFLN   84 (297)
T ss_dssp             HHHTTTBCCSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGG-CCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEE
T ss_pred             HHHHHhccCCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCC-CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEE
Confidence            4445556678899999999999999999999988766666555544 457899999999999999999999999999999


Q ss_pred             EeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768           97 VVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      +++..+...+.+.....++.+|..+....|++|+|||+|.+...+..............+...++.........++++|+
T Consensus        85 i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~  164 (297)
T 3b9p_A           85 ISAASLTSKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLA  164 (297)
T ss_dssp             EESTTTSSSSCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CEEEEE
T ss_pred             eeHHHHhhcccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEe
Confidence            99999988888888888999999999889999999999999876654433334444445555555433222235799999


Q ss_pred             EeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Q 022768          177 ATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR  255 (292)
Q Consensus       177 t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~  255 (292)
                      +||.++.+++.+++  ||...+.++.|+.++|..+++.++...... .+.++..++..+.|++++++..+++.|...|.+
T Consensus       165 ~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~~a~~~a~r  242 (297)
T 3b9p_A          165 ATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAALEPIR  242 (297)
T ss_dssp             EESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHH
T ss_pred             ecCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999998  999999999999999999999988754332 234567888999999999999999999999887


Q ss_pred             hc------------CCcccHHHHHHHHHHHhhhhhh---chhhhhhhhcCC
Q 022768          256 AE------------RDYVIHEDFMKAVRKLNEAKKL---ESSAHYNADFGK  291 (292)
Q Consensus       256 ~~------------~~~i~~~~~~~a~~~~~~~~~~---~~~~~~~~~~~~  291 (292)
                      +.            ...|+.+|+.+|+..+.+....   ...+.|++.||+
T Consensus       243 ~~~~~~~~~~~~~~~~~i~~~d~~~a~~~~~~s~~~~~~~~~~~~~~~~~~  293 (297)
T 3b9p_A          243 ELNVEQVKCLDISAMRAITEQDFHSSLKRIRRSVAPQSLNSYEKWSQDYGD  293 (297)
T ss_dssp             TCC--------CCCCCCCCHHHHHHHTTSCCCSSCHHHHHHHHHHC-----
T ss_pred             HHhhhhcccccccccCCcCHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCC
Confidence            64            2479999999999998874333   346678888875

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=100.00  E-value=4.9e-33  Score=253.96  Aligned_cols=249  Identities=41%  Similarity=0.700  Sum_probs=220.0

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      ++++|++++|++++++++.+.+.. +.....+.+++...+.+++|+||||||||+++++++..++.+++.+++..+...+
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~~-l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~  104 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF  104 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHH-HHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSC
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHHH-hhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhh
Confidence            789999999999999999998876 6667778888888888999999999999999999999999999999999988888


Q ss_pred             cChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCCh
Q 022768          107 IGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDP  186 (292)
Q Consensus       107 ~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~  186 (292)
                      .+.....+..+|..+....|+++||||+|.+...+.........+....+..++..+++......+++++++|.++.+++
T Consensus       105 ~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviAatn~p~~LD~  184 (499)
T 2dhr_A          105 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDP  184 (499)
T ss_dssp             TTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEECCSCGGGSCT
T ss_pred             hhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEEecCChhhcCc
Confidence            88888888888988877778999999999997665443333355666778888888887666667899999999999999


Q ss_pred             hhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHH
Q 022768          187 ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDF  266 (292)
Q Consensus       187 ~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~  266 (292)
                      ++++++||+..+.++.|+.++|.+|++.++.......++++..++..+.|++++|+.+++++|...|..++...|+.+|+
T Consensus       185 aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~Aa~~A~~~~~~~It~~dl  264 (499)
T 2dhr_A          185 ALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMKDL  264 (499)
T ss_dssp             TTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHHHHHHTTTCCSSCCSHHH
T ss_pred             ccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHH
Confidence            99999999999999999999999999999887777778889999999999999999999999999998888788999999


Q ss_pred             HHHHHHHhhh
Q 022768          267 MKAVRKLNEA  276 (292)
Q Consensus       267 ~~a~~~~~~~  276 (292)
                      .+|+..+...
T Consensus       265 ~~al~~v~~~  274 (499)
T 2dhr_A          265 EEAADRVMML  274 (499)
T ss_dssp             HHHHHHHTTC
T ss_pred             HHHHHHHhcc
Confidence            9999998753

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=100.00  E-value=7.9e-33  Score=247.92  Aligned_cols=275  Identities=30%  Similarity=0.597  Sum_probs=210.6

Q ss_pred             CChhhhhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           14 VDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        14 ~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      ....+.+..-..+++.+|++++|++++++.|.+++..+......+...+ .++.++||+||||||||++|+++|++++.+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~vLL~GppGtGKT~la~aia~~~~~~  175 (389)
T 3vfd_A           97 LANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLR-APARGLLLFGPPGNGKTMLAKAVAAESNAT  175 (389)
T ss_dssp             CCTTGGGTTBCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-CCCSEEEEESSTTSCHHHHHHHHHHHTTCE
T ss_pred             HHHHHHhhhhccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccC-CCCceEEEECCCCCCHHHHHHHHHHhhcCc
Confidence            3344455556678999999999999999999999988766666665555 457899999999999999999999999999


Q ss_pred             EEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           94 FLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      ++.+++..+...+.+.....+..+|..+....|+||||||+|.++..+...........+..+...+..... ....+++
T Consensus       176 ~~~v~~~~l~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~~~v~  254 (389)
T 3vfd_A          176 FFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQS-AGDDRVL  254 (389)
T ss_dssp             EEEECSCCC-------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC------CEE
T ss_pred             EEEeeHHHhhccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccc-cCCCCEE
Confidence            999999999988888888889999999999999999999999998766544444445555555555544332 2235799


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMS  252 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~  252 (292)
                      ||+++|.++.+++.+++  ||...+.++.|+.++|.++|+.++...... .+.++..++..+.|++++++..+++.|...
T Consensus       255 vI~atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~~a~~~  332 (389)
T 3vfd_A          255 VMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALG  332 (389)
T ss_dssp             EEEEESCGGGCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTH
T ss_pred             EEEecCCchhcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            99999999999999999  998899999999999999999988754322 233567889999999999999999999999


Q ss_pred             HHHh------------cCCcccHHHHHHHHHHHhhhhh---hchhhhhhhhcCCC
Q 022768          253 AIRA------------ERDYVIHEDFMKAVRKLNEAKK---LESSAHYNADFGKE  292 (292)
Q Consensus       253 a~~~------------~~~~i~~~~~~~a~~~~~~~~~---~~~~~~~~~~~~~~  292 (292)
                      +..+            ....|+.+|+.+++..+.+...   .+....|++.||+.
T Consensus       333 ~~rel~~~~~~~~~~~~~~~i~~~d~~~al~~~~~s~~~~~l~~~~~~~~~~g~~  387 (389)
T 3vfd_A          333 PIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKDFGDT  387 (389)
T ss_dssp             HHHTSCCC---CCSSSCCCCCCHHHHHHHHHHCCCSSCHHHHHHHHHHHHHCC--
T ss_pred             HHHhhhhhhhhccchhhcCCcCHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhCCc
Confidence            9876            2347999999999998876543   34467888899863

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=100.00  E-value=2.1e-31  Score=228.22  Aligned_cols=244  Identities=42%  Similarity=0.717  Sum_probs=207.7

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK  105 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~  105 (292)
                      .|+++|++++|.+++++++.+.... +.....+..+++..+.+++|+||||+||||++++++..++.+++.+++..+...
T Consensus        34 ~~~~~~~~i~g~~~~~~~l~~l~~~-~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~~~~  112 (278)
T 1iy2_A           34 APKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM  112 (278)
T ss_dssp             CCCCCGGGSSSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHS
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHHHHH
Confidence            3789999999999999999988776 566778888888888889999999999999999999999999999998887776


Q ss_pred             ccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          106 YIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      ..+.....+..+|..+....|+++++||+|.+.............+....+..++..+++......+++++++|.++.++
T Consensus       113 ~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a~t~~p~~ld  192 (278)
T 1iy2_A          113 FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILD  192 (278)
T ss_dssp             TTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEEEESCTTSSC
T ss_pred             HhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEEecCCchhCC
Confidence            66777777888898888778899999999998655432222223455667778888887666556788999999999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHH
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHED  265 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~  265 (292)
                      +++++++||...+.++.|+.++|.+|++.++.......+.++..++..+.|++++||..+++.|...|..++...|+.+|
T Consensus       193 ~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~~~a~~~a~~~~~~~I~~~d  272 (278)
T 1iy2_A          193 PALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMKD  272 (278)
T ss_dssp             HHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCCSBCHHH
T ss_pred             HhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCcCHHH
Confidence            99999899999999999999999999999988777777888999999999999999999999999999888888899999


Q ss_pred             HHHHH
Q 022768          266 FMKAV  270 (292)
Q Consensus       266 ~~~a~  270 (292)
                      +.+|+
T Consensus       273 l~~a~  277 (278)
T 1iy2_A          273 LEEAA  277 (278)
T ss_dssp             HHHHT
T ss_pred             HHHHh
Confidence            99885

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A*

Probab=100.00  E-value=3.5e-35  Score=250.32  Aligned_cols=261  Identities=39%  Similarity=0.661  Sum_probs=207.3

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      .+..|+.+|++++|++++++.+.+.+.. +.....+..++...+.+++|+||||||||++|+++++.++.+++.+++..+
T Consensus         2 ~~~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~   80 (268)
T 2r62_A            2 NAEKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSF   80 (268)
T ss_dssp             CCCCCCCCSTTSSSCTTTHHHHHHHHHH-HHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTT
T ss_pred             CccCCCCCHHHhCCcHHHHHHHHHHHHH-HHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHH
Confidence            4567889999999999999999998876 677788888888888999999999999999999999999999999998888


Q ss_pred             hccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCC-cchHHHHHHHHHHHHHhhCCCC-CCCeEEEEEeCC
Q 022768          103 IDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGT-SADREIQRTLMELLNQLDGFDQ-LGKVKMIMATNR  180 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~-~~~~~~~~~l~~~l~~~~~~~~-~~~~~vi~t~~~  180 (292)
                      ...+.+.....+..+|..+....|++|+|||+|.+...+..+.. ..+......+..++..+++... ..++++|+|+|.
T Consensus        81 ~~~~~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~vi~ttn~  160 (268)
T 2r62_A           81 IEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNR  160 (268)
T ss_dssp             TTSCSSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEEEECBSC
T ss_pred             HHhhcchHHHHHHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEEEEecCC
Confidence            77666665555667788888788899999999999765422110 0111111233445555544332 335899999999


Q ss_pred             CCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCc
Q 022768          181 PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY  260 (292)
Q Consensus       181 ~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~  260 (292)
                      ++.+++.+.+++||...+.++.|+.++|.++|+.++.......+.+++.++..+.|++++++..+++.|...|..++...
T Consensus       161 ~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~~a~~~a~~~~~~~  240 (268)
T 2r62_A          161 PEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEAALLAGRNNQKE  240 (268)
T ss_dssp             CTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHHHHHHTTSSSCCCS
T ss_pred             chhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCC
Confidence            99999999998899999999999999999999999987766677788889999999999999999999999998777788


Q ss_pred             ccHHHHHHHHHHHhhhhhhchhhh
Q 022768          261 VIHEDFMKAVRKLNEAKKLESSAH  284 (292)
Q Consensus       261 i~~~~~~~a~~~~~~~~~~~~~~~  284 (292)
                      |+.+++.+|+..+.+....+...+
T Consensus       241 i~~~~~~~a~~~~~~~~~~~~~~~  264 (268)
T 2r62_A          241 VRQQHLKEAVERGIAGLEKKLEHH  264 (268)
T ss_dssp             CCHHHHHTSCTTCCCCCC------
T ss_pred             cCHHHHHHHHHHHhhcchhhhhhc
Confidence            999999999999888766655443

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.92  E-value=6.4e-25  Score=189.08  Aligned_cols=176  Identities=24%  Similarity=0.392  Sum_probs=131.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHh----hhCCCEEEEEcccccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYA----RDHQPCIIFMDEIDAI  137 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~il~lDe~d~l  137 (292)
                      +..++.++||+||||||||++|+++|+.++.+++.+++..+.+.+.|.....+...|..+    +...|+||+|||+|.+
T Consensus        32 ~~~~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~  111 (293)
T 3t15_A           32 NIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDAG  111 (293)
T ss_dssp             TCCCCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC--
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechhhh
Confidence            456778999999999999999999999999999999999999999999999999999888    4667899999999999


Q ss_pred             cCCcCCCC--CcchHHHHHHHHHHHHHhh--------CCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHH
Q 022768          138 GGRRFSEG--TSADREIQRTLMELLNQLD--------GFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS  207 (292)
Q Consensus       138 ~~~~~~~~--~~~~~~~~~~l~~~l~~~~--------~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~  207 (292)
                      +++..+..  .......+..|+++++...        ......++++|+|||.++.+++++++++||...+.  .|+.++
T Consensus       112 ~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~--~P~~~~  189 (293)
T 3t15_A          112 AGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--APTRED  189 (293)
T ss_dssp             ------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE--CCCHHH
T ss_pred             cCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe--CcCHHH
Confidence            77443211  1133455667777765221        12244579999999999999999998778987776  479999


Q ss_pred             HHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHH
Q 022768          208 RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLR  243 (292)
Q Consensus       208 r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~  243 (292)
                      |.+|++.++..    ..++.+.++..+.+|++.++.
T Consensus       190 r~~Il~~~~~~----~~~~~~~l~~~~~~~~~~~l~  221 (293)
T 3t15_A          190 RIGVCTGIFRT----DNVPAEDVVKIVDNFPGQSID  221 (293)
T ss_dssp             HHHHHHHHHGG----GCCCHHHHHHHHHHSCSCCHH
T ss_pred             HHHHHHHhccC----CCCCHHHHHHHhCCCCcccHH
Confidence            99999988763    356788999999999887765

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.91  E-value=2.4e-23  Score=184.92  Aligned_cols=236  Identities=20%  Similarity=0.260  Sum_probs=160.1

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEeccchhc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSSAIID  104 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~~~~~  104 (292)
                      |..+|++++|++++++.+........        .+..+++++||+||||+|||++|+++++.++.  +++.+++..+..
T Consensus        39 p~~~~~~ivG~~~~~~~l~~l~~~~~--------~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~  110 (368)
T 3uk6_A           39 PRQASQGMVGQLAARRAAGVVLEMIR--------EGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFS  110 (368)
T ss_dssp             BCSEETTEESCHHHHHHHHHHHHHHH--------TTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGGGSC
T ss_pred             cCcchhhccChHHHHHHHHHHHHHHH--------cCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchhhhh
Confidence            44559999999999988766654321        12345679999999999999999999999975  777777655332


Q ss_pred             cccCh-------------------------------------------------HHHHHHHHHHHhhh---------CCC
Q 022768          105 KYIGE-------------------------------------------------SARLIREMFGYARD---------HQP  126 (292)
Q Consensus       105 ~~~~~-------------------------------------------------~~~~~~~~~~~~~~---------~~~  126 (292)
                      ...+.                                                 ....++..+..+..         ..|
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~  190 (368)
T 3uk6_A          111 LEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIP  190 (368)
T ss_dssp             SSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CB
T ss_pred             cccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccC
Confidence            22111                                                 11222233322221         125


Q ss_pred             EEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEe-----------CCCCCCChhhcCCCCcc
Q 022768          127 CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMAT-----------NRPDVLDPALLRPGRLD  195 (292)
Q Consensus       127 ~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~-----------~~~~~l~~~l~~~~r~~  195 (292)
                      +||||||+|.+           ....+..|..+++.     ....++++++.           |.+..+++.+++  ||.
T Consensus       191 ~vl~IDEi~~l-----------~~~~~~~L~~~le~-----~~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~~  252 (368)
T 3uk6_A          191 GVLFIDEVHML-----------DIESFSFLNRALES-----DMAPVLIMATNRGITRIRGTSYQSPHGIPIDLLD--RLL  252 (368)
T ss_dssp             CEEEEESGGGS-----------BHHHHHHHHHHTTC-----TTCCEEEEEESCSEEECBTSSCEEETTCCHHHHT--TEE
T ss_pred             ceEEEhhcccc-----------ChHHHHHHHHHhhC-----cCCCeeeeecccceeeeeccCCCCcccCCHHHHh--hcc
Confidence            79999999999           56566655555432     22345444443           236678999999  885


Q ss_pred             eEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH-
Q 022768          196 RKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKL-  273 (292)
Q Consensus       196 ~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~-  273 (292)
                      . +.|++|+.+++.++++.++...... .+..++.++..+.+.+++++.++++.|...|..++...|+.+++.+++..+ 
T Consensus       253 ~-i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~~~~~~~It~~~v~~a~~~~~  331 (368)
T 3uk6_A          253 I-VSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCRKRKGTEVQVDDIKRVYSLFL  331 (368)
T ss_dssp             E-EEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHSB
T ss_pred             E-EEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHhc
Confidence            4 8999999999999999887643322 222356677777734999999999999999999999999999999999884 


Q ss_pred             hhhhhhchhhhhhhhc
Q 022768          274 NEAKKLESSAHYNADF  289 (292)
Q Consensus       274 ~~~~~~~~~~~~~~~~  289 (292)
                      ....+.+....+++.|
T Consensus       332 ~~~~~~~~~~~~~~~~  347 (368)
T 3uk6_A          332 DESRSTQYMKEYQDAF  347 (368)
T ss_dssp             CHHHHHHHHC------
T ss_pred             CHHHHHHHHHHhhhhh
Confidence            3334444455555543

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.91  E-value=1.6e-22  Score=177.63  Aligned_cols=225  Identities=18%  Similarity=0.176  Sum_probs=169.2

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      .+...+.|.+|++++|.++.++.+..++.....        ...+..+++|+||||||||++|+++++.++.+++.+++.
T Consensus        18 ~~~~~~~p~~~~~iiG~~~~~~~l~~~l~~~~~--------~~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~~~   89 (338)
T 3pfi_A           18 TYETSLRPSNFDGYIGQESIKKNLNVFIAAAKK--------RNECLDHILFSGPAGLGKTTLANIISYEMSANIKTTAAP   89 (338)
T ss_dssp             -----CCCCSGGGCCSCHHHHHHHHHHHHHHHH--------TTSCCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             hhhhccCCCCHHHhCChHHHHHHHHHHHHHHHh--------cCCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEecch
Confidence            455678888999999999999999998875311        113456799999999999999999999999999999987


Q ss_pred             chhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-------------C
Q 022768          101 AIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-------------D  167 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-------------~  167 (292)
                      .+..      ...+...+..  ...+++|||||+|.+           ....+..|...++.....             .
T Consensus        90 ~~~~------~~~~~~~~~~--~~~~~vl~lDEi~~l-----------~~~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~  150 (338)
T 3pfi_A           90 MIEK------SGDLAAILTN--LSEGDILFIDEIHRL-----------SPAIEEVLYPAMEDYRLDIIIGSGPAAQTIKI  150 (338)
T ss_dssp             GCCS------HHHHHHHHHT--CCTTCEEEEETGGGC-----------CHHHHHHHHHHHHTSCC---------CCCCCC
T ss_pred             hccc------hhHHHHHHHh--ccCCCEEEEechhhc-----------CHHHHHHHHHHHHhccchhhcccCccccceec
Confidence            6521      1122222222  345689999999999           667777777777653210             1


Q ss_pred             CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      ..+++.+|+++|....+++++++  ||+..+.+++|+.+++..+++.++...... .+.....++..+.| +++.+..++
T Consensus       151 ~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G-~~r~l~~~l  227 (338)
T 3pfi_A          151 DLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRS-TPRIALRLL  227 (338)
T ss_dssp             CCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTT-CHHHHHHHH
T ss_pred             CCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCc-CHHHHHHHH
Confidence            11258899999998889999998  898999999999999999999888654322 22234556665555 888999999


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          247 TEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       247 ~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      +.+..++.......|+.+++..++.....
T Consensus       228 ~~~~~~a~~~~~~~i~~~~~~~~~~~~~~  256 (338)
T 3pfi_A          228 KRVRDFADVNDEEIITEKRANEALNSLGV  256 (338)
T ss_dssp             HHHHHHHHHTTCSEECHHHHHHHHHHHTC
T ss_pred             HHHHHHHHhhcCCccCHHHHHHHHHHhCC
Confidence            99998888888888999999999877543

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=99.90  E-value=1.3e-22  Score=185.03  Aligned_cols=249  Identities=20%  Similarity=0.206  Sum_probs=178.3

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC--CcEEEEeccchh
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID--ANFLKVVSSAII  103 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~--~~~~~~~~~~~~  103 (292)
                      .|...|++++|++++++.+..++...        ..+..+++++||+||||||||++|+++|+.++  .+++.+++..+.
T Consensus        31 ~~~~~~~~iiG~~~~~~~l~~~~~~~--------~~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~  102 (456)
T 2c9o_A           31 LAKQAASGLVGQENAREACGVIVELI--------KSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVY  102 (456)
T ss_dssp             CBCSEETTEESCHHHHHHHHHHHHHH--------HTTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGC
T ss_pred             ChhhchhhccCHHHHHHHHHHHHHHH--------HhCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHH
Confidence            45678999999999999998887643        22456678999999999999999999999998  899999999999


Q ss_pred             ccccChHHHHHHHHHHHh---hhCCCEEEEEcccccccCCcCCCCCcc--------------------------------
Q 022768          104 DKYIGESARLIREMFGYA---RDHQPCIIFMDEIDAIGGRRFSEGTSA--------------------------------  148 (292)
Q Consensus       104 ~~~~~~~~~~~~~~~~~~---~~~~~~il~lDe~d~l~~~~~~~~~~~--------------------------------  148 (292)
                      ..+.+.... +...|..+   +...|++|||||+|.+++++.....+.                                
T Consensus       103 ~~~~~~~~~-~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~  181 (456)
T 2c9o_A          103 STEIKKTEV-LMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQ  181 (456)
T ss_dssp             CSSSCHHHH-HHHHHHHTEEEEEEEEEEEEEEEEEEEEEC--------------CEEEEEEETTEEEEEEECHHHHHHHH
T ss_pred             HHhhhhhHH-HHHHHHHHHhhhhcCCcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccchhHhhhHHHHHHHh
Confidence            999998887 88999988   667889999999999885543321000                                


Q ss_pred             ------------------------------------------h------------------------------------H
Q 022768          149 ------------------------------------------D------------------------------------R  150 (292)
Q Consensus       149 ------------------------------------------~------------------------------------~  150 (292)
                                                                .                                    .
T Consensus       182 ~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~~~dl~~~a~~t~ggadl~~l~~  261 (456)
T 2c9o_A          182 KERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPQGGQDILSMMG  261 (456)
T ss_dssp             HTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEEHHHHHHTC--------------
T ss_pred             hccCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHHHHHHHHHHHhCCChhHHHHHHh
Confidence                                                      0                                    0


Q ss_pred             H---------------------------------------------HHHHHHHHHHHhhCCCCCCCeEEEEE--------
Q 022768          151 E---------------------------------------------IQRTLMELLNQLDGFDQLGKVKMIMA--------  177 (292)
Q Consensus       151 ~---------------------------------------------~~~~l~~~l~~~~~~~~~~~~~vi~t--------  177 (292)
                      .                                             .......+++.++.  +...+++++|        
T Consensus       262 ~i~~p~~~~I~~~lr~~I~~~l~~~~~~g~~~v~~~VliIDEa~~l~~~a~~aLlk~lEe--~~~~~~il~tn~~~~~i~  339 (456)
T 2c9o_A          262 QLMKPKKTEITDKLRGEINKVVNKYIDQGIAELVPGVLFVDEVHMLDIECFTYLHRALES--SIAPIVIFASNRGNCVIR  339 (456)
T ss_dssp             ---------------CHHHHHHHHHHHTTSEEEEECEEEEESGGGCBHHHHHHHHHHTTS--TTCCEEEEEECCSEEECB
T ss_pred             hhcccchhhHHHHHHHHHHHHHHHHHHhccccccceEEEEechhhcCHHHHHHHHHHhhc--cCCCEEEEecCCcccccc
Confidence            0                                             00122233333332  2234444444        


Q ss_pred             -eC---CCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHc-CCCCHHHHHHHHHHHHH
Q 022768          178 -TN---RPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLA-EGFNGADLRNVCTEAGM  251 (292)
Q Consensus       178 -~~---~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~-~g~~~~di~~l~~~a~~  251 (292)
                       ++   .+..+++.+++  ||.. +.|++|+.++..++++..+...... .+.....++..+ .| +++....+++.|..
T Consensus       340 ~~~~~~~~~~l~~~i~s--R~~~-~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g-~~r~a~~ll~~a~~  415 (456)
T 2c9o_A          340 GTEDITSPHGIPLDLLD--RVMI-IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKT-TLRYSVQLLTPANL  415 (456)
T ss_dssp             TTSSCEEETTCCHHHHT--TEEE-EECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHS-CHHHHHHTHHHHHH
T ss_pred             ccccccccccCChhHHh--hcce-eeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCC-CHHHHHHHHHHHHH
Confidence             22   16678899999  8855 6999999999999999877532221 122345566776 65 89999999999999


Q ss_pred             HHHHhcCCcccHHHHHHHHHHHh-hhhhhchhhhhhhhc
Q 022768          252 SAIRAERDYVIHEDFMKAVRKLN-EAKKLESSAHYNADF  289 (292)
Q Consensus       252 ~a~~~~~~~i~~~~~~~a~~~~~-~~~~~~~~~~~~~~~  289 (292)
                      .|..++...|+.+++.+++..+. ...+.+....|+..|
T Consensus       416 ~A~~~~~~~v~~~~v~~~~~~~~d~~~~~~~~~~~~~~~  454 (456)
T 2c9o_A          416 LAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKY  454 (456)
T ss_dssp             HHHHTTCSSBCHHHHHHHHHHSCCHHHHHHHHHC-----
T ss_pred             HHhhcCCCccCHHHHHHHHHHhcChHHHHHHHHHHHHhc
Confidence            99999999999999999998874 344444555555544

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=99.89  E-value=6.2e-22  Score=172.71  Aligned_cols=221  Identities=20%  Similarity=0.243  Sum_probs=166.6

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ...+.|.+|++++|.++.++.+..++.....       . ...+.+++|+||+|+|||++|+++++.++.+++.+++..+
T Consensus         3 ~~~~~p~~~~~~ig~~~~~~~l~~~l~~~~~-------~-~~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~   74 (324)
T 1hqc_A            3 DLALRPKTLDEYIGQERLKQKLRVYLEAAKA-------R-KEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAI   74 (324)
T ss_dssp             --CCCCCSTTTCCSCHHHHHHHHHHHHHHHH-------H-CSCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTC
T ss_pred             ccccCcccHHHhhCHHHHHHHHHHHHHHHHc-------c-CCCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEecccc
Confidence            4567888999999999999999988765310       0 1245689999999999999999999999999998887665


Q ss_pred             hccccChHHHHHHHHHHHhhh--CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-----C--------
Q 022768          103 IDKYIGESARLIREMFGYARD--HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-----D--------  167 (292)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~--~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-----~--------  167 (292)
                      ..      ..   .++.....  ..+++|||||+|.+           ....+..+..+++.....     .        
T Consensus        75 ~~------~~---~l~~~l~~~~~~~~~l~lDEi~~l-----------~~~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~  134 (324)
T 1hqc_A           75 EK------PG---DLAAILANSLEEGDILFIDEIHRL-----------SRQAEEHLYPAMEDFVMDIVIGQGPAARTIRL  134 (324)
T ss_dssp             CS------HH---HHHHHHTTTCCTTCEEEETTTTSC-----------CHHHHHHHHHHHHHSEEEECCSSSSSCCCEEE
T ss_pred             CC------hH---HHHHHHHHhccCCCEEEEECCccc-----------ccchHHHHHHHHHhhhhHHhcccccccccccc
Confidence            32      11   22222222  45689999999998           666777777777753200     0        


Q ss_pred             CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      ...++.+|+++|.+..+++++.+  ||...+.+++|+.+++..+++.++...... .+.....++..+.| +++.+..++
T Consensus       135 ~~~~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~r~l~~~l  211 (324)
T 1hqc_A          135 ELPRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG-TMRVAKRLF  211 (324)
T ss_dssp             ECCCCEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCS-CHHHHHHHH
T ss_pred             CCCCEEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccC-CHHHHHHHH
Confidence            11357899999999999999988  898899999999999999999888654332 12234566777766 888999999


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          247 TEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       247 ~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      +.+...+.......|+.+++.+++....
T Consensus       212 ~~~~~~a~~~~~~~i~~~~~~~~~~~~~  239 (324)
T 1hqc_A          212 RRVRDFAQVAGEEVITRERALEALAALG  239 (324)
T ss_dssp             HHHTTTSTTTSCSCCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHhc
Confidence            9988777666677899999998887654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.88  E-value=1.7e-22  Score=183.13  Aligned_cols=217  Identities=21%  Similarity=0.255  Sum_probs=154.6

Q ss_pred             hhcccCCCCCccccccccHHHH---HHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQI---RELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~---~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .++...++|.+|++++|+++.+   +.|...+...             ...+++|+||||||||++++.+++.++.+++.
T Consensus        14 ~pla~r~rP~~l~~ivGq~~~~~~~~~L~~~i~~~-------------~~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~   80 (447)
T 3pvs_A           14 QPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAG-------------HLHSMILWGPPGTGKTTLAEVIARYANADVER   80 (447)
T ss_dssp             CCHHHHTCCCSTTTCCSCHHHHSTTSHHHHHHHHT-------------CCCEEEEECSTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             CChHHHhCCCCHHHhCCcHHHHhchHHHHHHHHcC-------------CCcEEEEECCCCCcHHHHHHHHHHHhCCCeEE
Confidence            4666778889999999999999   7777777652             23689999999999999999999999999999


Q ss_pred             EeccchhccccChHHHHHHHHHHHh----hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCe
Q 022768           97 VVSSAIIDKYIGESARLIREMFGYA----RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKV  172 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  172 (292)
                      +++....       ...++.++..+    ....+.+|||||+|.+           ....+..|+..++.       +.+
T Consensus        81 l~a~~~~-------~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l-----------~~~~q~~LL~~le~-------~~v  135 (447)
T 3pvs_A           81 ISAVTSG-------VKEIREAIERARQNRNAGRRTILFVDEVHRF-----------NKSQQDAFLPHIED-------GTI  135 (447)
T ss_dssp             EETTTCC-------HHHHHHHHHHHHHHHHTTCCEEEEEETTTCC-----------------CCHHHHHT-------TSC
T ss_pred             EEeccCC-------HHHHHHHHHHHHHhhhcCCCcEEEEeChhhh-----------CHHHHHHHHHHHhc-------Cce
Confidence            8865421       22233333333    2356799999999998           44455566666653       456


Q ss_pred             EEEEEe--CCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc-----CCCCC---CHHHHHHHcCCCCHHHH
Q 022768          173 KMIMAT--NRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA-----KHGEI---DYEAVVKLAEGFNGADL  242 (292)
Q Consensus       173 ~vi~t~--~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~-----~~~~~---~~~~l~~~~~g~~~~di  242 (292)
                      ++|+++  |....+++++.+  |+ .++.|++|+.+++..+++.++....     ....+   .++.++..+.| +.+.+
T Consensus       136 ~lI~att~n~~~~l~~aL~s--R~-~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~G-d~R~l  211 (447)
T 3pvs_A          136 TFIGATTENPSFELNSALLS--RA-RVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNG-DARRA  211 (447)
T ss_dssp             EEEEEESSCGGGSSCHHHHT--TE-EEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCS-CHHHH
T ss_pred             EEEecCCCCcccccCHHHhC--ce-eEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCC-CHHHH
Confidence            777766  444578999999  77 5788999999999999999886521     11112   34666677766 78888


Q ss_pred             HHHHHHHHHHHHHh--cCCcccHHHHHHHHHHHhhhhh
Q 022768          243 RNVCTEAGMSAIRA--ERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       243 ~~l~~~a~~~a~~~--~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      ..+++.+...+...  +...|+.+++.+++.......+
T Consensus       212 ln~Le~a~~~a~~~~~~~~~It~e~v~~~l~~~~~~~d  249 (447)
T 3pvs_A          212 LNTLEMMADMAEVDDSGKRVLKPELLTEIAGERSARFD  249 (447)
T ss_dssp             HHHHHHHHHHSCBCTTSCEECCHHHHHHHHTCCCCC--
T ss_pred             HHHHHHHHHhcccccCCCCccCHHHHHHHHhhhhhccC
Confidence            88888887766422  3457999999999876644333

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.88  E-value=4.9e-22  Score=172.29  Aligned_cols=224  Identities=19%  Similarity=0.256  Sum_probs=160.8

Q ss_pred             cc-cccccHHHHHHHHHHhhcccCChHHHHhcCC---CCCceEEEEcCCCChHHHHHHHHHHhc-------CCcEEEEec
Q 022768           31 YS-AVGGLSDQIRELRESIELPLMNPELFLRVGI---KPPKGVLLYGPPGTGKTLLARAIASNI-------DANFLKVVS   99 (292)
Q Consensus        31 ~~-~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~---~~~~~vll~G~~G~GKT~l~~~la~~l-------~~~~~~~~~   99 (292)
                      ++ +++|++++++.|.+.+..+.. .....++|+   .++.+++|+||||||||++++++++.+       ..+++.+++
T Consensus        29 l~~~i~G~~~~~~~l~~~~~~~~~-~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~  107 (309)
T 3syl_A           29 LDRELIGLKPVKDRIRETAALLLV-ERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTR  107 (309)
T ss_dssp             HHHHSSSCHHHHHHHHHHHHHHHH-HHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECG
T ss_pred             HHHHccChHHHHHHHHHHHHHHHh-HHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcH
Confidence            44 799999999999999876432 344444444   335579999999999999999999988       338999999


Q ss_pred             cchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          100 SAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      ..+...+.+.....+...|..+   .+++|+|||+|.++....+  .......+..|..+++..     ..++.+|+++|
T Consensus       108 ~~l~~~~~g~~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~~--~~~~~~~~~~Ll~~l~~~-----~~~~~~i~~~~  177 (309)
T 3syl_A          108 DDLVGQYIGHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPDNE--RDYGQEAIEILLQVMENN-----RDDLVVILAGY  177 (309)
T ss_dssp             GGTCCSSTTCHHHHHHHHHHHH---TTSEEEEETGGGSCCCC-----CCTHHHHHHHHHHHHHC-----TTTCEEEEEEC
T ss_pred             HHhhhhcccccHHHHHHHHHhc---CCCEEEEEChhhhccCCCc--ccccHHHHHHHHHHHhcC-----CCCEEEEEeCC
Confidence            9998888888887777777766   3579999999999754422  223456666666666642     25778888887


Q ss_pred             CCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHH-------cCCCCHHHHHHHH
Q 022768          180 RPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKL-------AEGFNGADLRNVC  246 (292)
Q Consensus       180 ~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~-------~~g~~~~di~~l~  246 (292)
                      ...     .+++.+++  ||...+.|++|+.+++..|++.++...... .+.....++..       ....+.+++..++
T Consensus       178 ~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l  255 (309)
T 3syl_A          178 ADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNAL  255 (309)
T ss_dssp             HHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHH
T ss_pred             hHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            643     24688888  999999999999999999999988754322 11123334443       2223689999999


Q ss_pred             HHHHHHHHHh----cCCcccHHHHH
Q 022768          247 TEAGMSAIRA----ERDYVIHEDFM  267 (292)
Q Consensus       247 ~~a~~~a~~~----~~~~i~~~~~~  267 (292)
                      +.|...+..+    ....++.+++.
T Consensus       256 ~~a~~~~~~r~~~~~~~~~~~~~l~  280 (309)
T 3syl_A          256 DRARLRQANRLFTASSGPLDARALS  280 (309)
T ss_dssp             HHHHHHHHHHHHHC---CEEHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCCCHHHHh
Confidence            9998766555    23456666554

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=99.88  E-value=7.3e-21  Score=156.35  Aligned_cols=210  Identities=20%  Similarity=0.209  Sum_probs=151.3

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEEE
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFLK   96 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~   96 (292)
                      ....++|..|++++|.++.++.+..++...             ...+++|+||+|+|||++++.+++.+     ...++.
T Consensus         7 ~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~-------------~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~   73 (226)
T 2chg_A            7 WVEKYRPRTLDEVVGQDEVIQRLKGYVERK-------------NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIE   73 (226)
T ss_dssp             HHHHTSCSSGGGCCSCHHHHHHHHHHHHTT-------------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEE
T ss_pred             HHHhcCCCCHHHHcCcHHHHHHHHHHHhCC-------------CCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEE
Confidence            345678889999999999999999988652             23459999999999999999999876     345777


Q ss_pred             EeccchhccccChHHHHHHHHHHH--hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           97 VVSSAIIDKYIGESARLIREMFGY--ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      +++......  ......+......  .....+.+|+|||+|.+           .......+..+++..     ..++.+
T Consensus        74 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l-----------~~~~~~~l~~~l~~~-----~~~~~~  135 (226)
T 2chg_A           74 MNASDERGI--DVVRHKIKEFARTAPIGGAPFKIIFLDEADAL-----------TADAQAALRRTMEMY-----SKSCRF  135 (226)
T ss_dssp             EETTCTTCH--HHHHHHHHHHHTSCCSTTCSCEEEEEETGGGS-----------CHHHHHHHHHHHHHT-----TTTEEE
T ss_pred             eccccccCh--HHHHHHHHHHhcccCCCccCceEEEEeChhhc-----------CHHHHHHHHHHHHhc-----CCCCeE
Confidence            776543221  0111111111111  01245789999999998           555666777777652     247888


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      |+++|.+..+.+.+.+  |+. .+.+++|+.++..++++.++...... .+.....++..+.| +++.+..+++.+...+
T Consensus       136 i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~l~~~l~~~~~~~  211 (226)
T 2chg_A          136 ILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGG-DFRKAINALQGAAAIG  211 (226)
T ss_dssp             EEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHHHHHHHHHHHHTC
T ss_pred             EEEeCChhhcCHHHHH--hCc-eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHHhcC
Confidence            9999998889999998  785 88999999999999999887643322 12234566677766 7777777777766544


Q ss_pred             HHhcCCcccHHHHHHHHH
Q 022768          254 IRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a~~  271 (292)
                           ..|+.+++.+++.
T Consensus       212 -----~~I~~~~v~~~~~  224 (226)
T 2chg_A          212 -----EVVDADTIYQITA  224 (226)
T ss_dssp             -----SCBCHHHHHHHHH
T ss_pred             -----ceecHHHHHHHhc
Confidence                 5899999999875

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.88  E-value=4.9e-21  Score=170.59  Aligned_cols=225  Identities=21%  Similarity=0.225  Sum_probs=163.0

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEec
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVS   99 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~   99 (292)
                      ...++++|+++.++.+..++...+..         ..+.+++|+||||+|||++++.+++.+         +.+++.+++
T Consensus        16 ~~p~~~~gr~~~~~~l~~~l~~~~~~---------~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~   86 (387)
T 2v1u_A           16 YVPDVLPHREAELRRLAEVLAPALRG---------EKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNA   86 (387)
T ss_dssp             CCCSCCTTCHHHHHHHHHTTGGGTSS---------CCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEET
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEEC
Confidence            34488999999999999988653221         446789999999999999999999988         778888887


Q ss_pred             cchhccc----------------cCh-HHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHH--HHHHHHHH
Q 022768          100 SAIIDKY----------------IGE-SARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADRE--IQRTLMEL  159 (292)
Q Consensus       100 ~~~~~~~----------------~~~-~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~--~~~~l~~~  159 (292)
                      ....+..                .+. ....+..++...... .+.+|+|||+|.+           ...  .+..+..+
T Consensus        87 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l-----------~~~~~~~~~l~~l  155 (387)
T 2v1u_A           87 RHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFL-----------PKRPGGQDLLYRI  155 (387)
T ss_dssp             TTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHH-----------HHSTTHHHHHHHH
T ss_pred             CcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhh-----------cccCCCChHHHhH
Confidence            6532210                011 222334444443333 3679999999998           333  56677777


Q ss_pred             HHHhhCCCCCCCeEEEEEeCCC---CCCChhhcCCCCcce-EEEccCCCHHHHHHHHHHHHcCc---cCCCCCCHHHHHH
Q 022768          160 LNQLDGFDQLGKVKMIMATNRP---DVLDPALLRPGRLDR-KIEIPLPNEQSRMEILKIHAAGI---AKHGEIDYEAVVK  232 (292)
Q Consensus       160 l~~~~~~~~~~~~~vi~t~~~~---~~l~~~l~~~~r~~~-~i~l~~p~~~~r~~i~~~~~~~~---~~~~~~~~~~l~~  232 (292)
                      ++.........++.+|+++|.+   ..+++.+.+  ||.. .+.|++|+.++..++++.++...   ....+...+.++.
T Consensus       156 ~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~  233 (387)
T 2v1u_A          156 TRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAA  233 (387)
T ss_dssp             HHGGGCC-----CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHH
T ss_pred             hhchhhcCCCceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHH
Confidence            7765533214578899999887   678889988  7765 88999999999999999887531   1112334566777


Q ss_pred             HcC---CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          233 LAE---GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       233 ~~~---g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      .+.   | +++.+..+++.|...|...+...|+.+++.+++..+...
T Consensus       234 ~~~~~~G-~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~~~~  279 (387)
T 2v1u_A          234 LAAREHG-DARRALDLLRVAGEIAERRREERVRREHVYSARAEIERD  279 (387)
T ss_dssp             HHHSSSC-CHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHHHH
T ss_pred             HHHHhcc-CHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhhc
Confidence            776   6 888999999999988887788889999999999887543

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=99.85  E-value=1.1e-20  Score=165.00  Aligned_cols=207  Identities=18%  Similarity=0.182  Sum_probs=140.3

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      +..+.++|.+|++++|++++++.+..++...            ..+..++++||||+|||++++++++.++.+++++++.
T Consensus        15 ~~~~k~rP~~~~~ivg~~~~~~~l~~~l~~~------------~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~~~   82 (324)
T 3u61_B           15 ILEQKYRPSTIDECILPAFDKETFKSITSKG------------KIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGS   82 (324)
T ss_dssp             SHHHHSCCCSTTTSCCCHHHHHHHHHHHHTT------------CCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEETT
T ss_pred             hHHHhhCCCCHHHHhCcHHHHHHHHHHHHcC------------CCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEccc
Confidence            3445688899999999999999999998742            3456678889999999999999999999999999976


Q ss_pred             chhccccChHHHHHHHHHHHhhh-----CCCEEEEEcccccccCCcCCCCCcch-HHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768          101 AIIDKYIGESARLIREMFGYARD-----HQPCIIFMDEIDAIGGRRFSEGTSAD-REIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~-----~~~~il~lDe~d~l~~~~~~~~~~~~-~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      ...       ...++..+.....     ..+.+|+|||+|.+           . ...+..|..+++...     .++.+
T Consensus        83 ~~~-------~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l-----------~~~~~~~~L~~~le~~~-----~~~~i  139 (324)
T 3u61_B           83 DCK-------IDFVRGPLTNFASAASFDGRQKVIVIDEFDRS-----------GLAESQRHLRSFMEAYS-----SNCSI  139 (324)
T ss_dssp             TCC-------HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCG-----------GGHHHHHHHHHHHHHHG-----GGCEE
T ss_pred             ccC-------HHHHHHHHHHHHhhcccCCCCeEEEEECCccc-----------CcHHHHHHHHHHHHhCC-----CCcEE
Confidence            532       2223332222221     25689999999999           5 667778888877643     46789


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc-------CccCC-CC-CCHHHHHHHcCCCCHHHHHHH
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA-------GIAKH-GE-IDYEAVVKLAEGFNGADLRNV  245 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~-------~~~~~-~~-~~~~~l~~~~~g~~~~di~~l  245 (292)
                      |+++|.+..+++++++  || ..+.|++|+.+++.++++.+..       ..... .+ ..++.++..+.| +.+++...
T Consensus       140 I~~~n~~~~l~~~l~s--R~-~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~g-d~R~a~~~  215 (324)
T 3u61_B          140 IITANNIDGIIKPLQS--RC-RVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFP-DFRKTIGE  215 (324)
T ss_dssp             EEEESSGGGSCTTHHH--HS-EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCS-CTTHHHHH
T ss_pred             EEEeCCccccCHHHHh--hC-cEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCC-CHHHHHHH
Confidence            9999999999999999  88 5799999999998766554332       11111 12 234556666665 44444444


Q ss_pred             HHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          246 CTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       246 ~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      ++.   .+   ....|+.+++.+++..
T Consensus       216 L~~---~~---~~~~i~~~~v~~~~~~  236 (324)
T 3u61_B          216 LDS---YS---SKGVLDAGILSLVTND  236 (324)
T ss_dssp             HHH---HG---GGTCBCC---------
T ss_pred             HHH---Hh---ccCCCCHHHHHHHhCC
Confidence            444   33   3345777777766544

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.85  E-value=9.6e-20  Score=151.51  Aligned_cols=209  Identities=17%  Similarity=0.244  Sum_probs=150.8

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------   93 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------   93 (292)
                      .+....++|..|++++|.++.++.|...+...            ..+..++|+||+|+|||++++.+++.+...      
T Consensus        11 ~~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~   78 (250)
T 1njg_A           11 QVLARKWRPQTFADVVGQEHVLTALANGLSLG------------RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITAT   78 (250)
T ss_dssp             CCHHHHTCCCSGGGCCSCHHHHHHHHHHHHHT------------CCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSS
T ss_pred             HHHhhccCCccHHHHhCcHHHHHHHHHHHHcC------------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCC
Confidence            34456778889999999999999999988652            334579999999999999999999987542      


Q ss_pred             ------------------EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHH
Q 022768           94 ------------------FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADRE  151 (292)
Q Consensus        94 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~  151 (292)
                                        ++.+....      ......+..++....    ...+.+|+|||+|.+           +..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l-----------~~~  141 (250)
T 1njg_A           79 PCGVCDNCREIEQGRFVDLIEIDAAS------RTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHML-----------SRH  141 (250)
T ss_dssp             CCSCSHHHHHHHTTCCSSEEEEETTC------GGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGS-----------CHH
T ss_pred             CCcccHHHHHHhccCCcceEEecCcc------cccHHHHHHHHHHhhhchhcCCceEEEEECcccc-----------cHH
Confidence                              12222111      112233444444432    234689999999998           555


Q ss_pred             HHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHH
Q 022768          152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAV  230 (292)
Q Consensus       152 ~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l  230 (292)
                      ....+..++..     ...++.+|++++.+..+.+.+.+  |+ ..+.+++++.++..++++.++...... .+.....+
T Consensus       142 ~~~~l~~~l~~-----~~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l  213 (250)
T 1njg_A          142 SFNALLKTLEE-----PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLL  213 (250)
T ss_dssp             HHHHHHHHHHS-----CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHH
T ss_pred             HHHHHHHHHhc-----CCCceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            56666665542     23578899999988888888888  65 789999999999999999887643222 22235677


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      +..+.| +++.+..+++.|...+    ...|+.+++.+++
T Consensus       214 ~~~~~G-~~~~~~~~~~~~~~~~----~~~i~~~~v~~~~  248 (250)
T 1njg_A          214 ARAAEG-SLRDALSLTDQAIASG----DGQVSTQAVSAML  248 (250)
T ss_dssp             HHHHTT-CHHHHHHHHHHHHTTT----TSSBCHHHHHHHS
T ss_pred             HHHcCC-CHHHHHHHHHHHHhcc----CceecHHHHHHHh
Confidence            888877 8999999998875332    3479999998875

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=99.84  E-value=7.4e-20  Score=165.88  Aligned_cols=221  Identities=17%  Similarity=0.230  Sum_probs=152.9

Q ss_pred             CCCCCcccccc-c--cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEEE
Q 022768           25 DPGNVSYSAVG-G--LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFLK   96 (292)
Q Consensus        25 ~~~~~~~~~l~-g--~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~   96 (292)
                      -.|..+|++++ |  ...+...+..+...+            ....+++|+||||+||||+++++++.+     +.++++
T Consensus        98 l~~~~tfd~fv~g~~n~~a~~~~~~~a~~~------------~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~  165 (440)
T 2z4s_A           98 LNPDYTFENFVVGPGNSFAYHAALEVAKHP------------GRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMY  165 (440)
T ss_dssp             CCTTCSGGGCCCCTTTHHHHHHHHHHHHST------------TSSCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEE
T ss_pred             CCCCCChhhcCCCCchHHHHHHHHHHHhCC------------CCCCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEE
Confidence            34557999988 5  344455555554432            115689999999999999999999988     788899


Q ss_pred             EeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768           97 VVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      +++..+...+...........|.......+.+|+|||+|.+..         ....+..+..+++.+..   .+.. +|+
T Consensus       166 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~---------~~~~q~~l~~~l~~l~~---~~~~-iIi  232 (440)
T 2z4s_A          166 ITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIG---------KTGVQTELFHTFNELHD---SGKQ-IVI  232 (440)
T ss_dssp             EEHHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSS---------CHHHHHHHHHHHHHHHT---TTCE-EEE
T ss_pred             eeHHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccC---------ChHHHHHHHHHHHHHHH---CCCe-EEE
Confidence            9887764433222111111122222222678999999999842         22456667777665532   2344 444


Q ss_pred             EeCC-CCC---CChhhcCCCCcc--eEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHH
Q 022768          177 ATNR-PDV---LDPALLRPGRLD--RKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEA  249 (292)
Q Consensus       177 t~~~-~~~---l~~~l~~~~r~~--~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a  249 (292)
                      +++. +..   +++++++  ||.  ..+.+++|+.+++..+++..+...... .+..++.++..+.| +.+++..+++.+
T Consensus       233 tt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~g-n~R~l~~~L~~~  309 (440)
T 2z4s_A          233 CSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDD-NLRRLRGAIIKL  309 (440)
T ss_dssp             EESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCS-CHHHHHHHHHHH
T ss_pred             EECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHH
Confidence            5544 443   7889988  664  788999999999999999887643322 22336778888876 999999999999


Q ss_pred             HHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          250 GMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       250 ~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ...|...+. .|+.+++.++++...
T Consensus       310 ~~~a~~~~~-~It~~~~~~~l~~~~  333 (440)
T 2z4s_A          310 LVYKETTGK-EVDLKEAILLLKDFI  333 (440)
T ss_dssp             HHHHHHSSS-CCCHHHHHHHTSTTT
T ss_pred             HHHHHHhCC-CCCHHHHHHHHHHHh
Confidence            998876654 699999999998765

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=99.83  E-value=2e-19  Score=158.34  Aligned_cols=230  Identities=17%  Similarity=0.172  Sum_probs=148.2

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE----Ee
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK----VV   98 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~----~~   98 (292)
                      ....++.+|++++|.++.++.+......             ....++||+||||||||++|+++++.++.....    ++
T Consensus        15 ~~~~~~~~f~~i~G~~~~~~~l~~~~~~-------------~~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~   81 (350)
T 1g8p_A           15 AKTRPVFPFSAIVGQEDMKLALLLTAVD-------------PGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVS   81 (350)
T ss_dssp             ---CCCCCGGGSCSCHHHHHHHHHHHHC-------------GGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTC
T ss_pred             CCCCCCCCchhccChHHHHHHHHHHhhC-------------CCCceEEEECCCCccHHHHHHHHHHhCcccccccccccc
Confidence            3456788999999999988776554432             123469999999999999999999988631100    11


Q ss_pred             ccchhc---------------------cccChHHH-HH-----HHHHHHh---------hhCCCEEEEEcccccccCCcC
Q 022768           99 SSAIID---------------------KYIGESAR-LI-----REMFGYA---------RDHQPCIIFMDEIDAIGGRRF  142 (292)
Q Consensus        99 ~~~~~~---------------------~~~~~~~~-~~-----~~~~~~~---------~~~~~~il~lDe~d~l~~~~~  142 (292)
                      +.....                     ...+.... ..     ...+...         ....+++|+|||+|.+     
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l-----  156 (350)
T 1g8p_A           82 SPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLL-----  156 (350)
T ss_dssp             CSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGS-----
T ss_pred             ccccccccchhhhhccccccCCCcccccCCCcchhhheeechhhhhhcCCceeecCceeeecCCCEEEEeChhhC-----
Confidence            111000                     00001011 00     1111111         1123689999999999     


Q ss_pred             CCCCcchHHHHHHHHHHHHHhh----CC----CCCCCeEEEEEeCCCC-CCChhhcCCCCcceEEEccCC-CHHHHHHHH
Q 022768          143 SEGTSADREIQRTLMELLNQLD----GF----DQLGKVKMIMATNRPD-VLDPALLRPGRLDRKIEIPLP-NEQSRMEIL  212 (292)
Q Consensus       143 ~~~~~~~~~~~~~l~~~l~~~~----~~----~~~~~~~vi~t~~~~~-~l~~~l~~~~r~~~~i~l~~p-~~~~r~~i~  212 (292)
                            ....+..|..+++...    ..    ....++.+|+|+|..+ .+++++++  ||...+.+++| +.+++.+|+
T Consensus       157 ------~~~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~~~~~~il  228 (350)
T 1g8p_A          157 ------EDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVI  228 (350)
T ss_dssp             ------CHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHH
T ss_pred             ------CHHHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCCcHHHHHHHH
Confidence                  6777788888877521    00    0012688999999744 79999999  99888999998 677777887


Q ss_pred             HHHHc---------------------------CccCCCCCCH---HHHHHHcCC--C-CHHHHHHHHHHHHHHHHHhcCC
Q 022768          213 KIHAA---------------------------GIAKHGEIDY---EAVVKLAEG--F-NGADLRNVCTEAGMSAIRAERD  259 (292)
Q Consensus       213 ~~~~~---------------------------~~~~~~~~~~---~~l~~~~~g--~-~~~di~~l~~~a~~~a~~~~~~  259 (292)
                      +..+.                           .....-.++.   ..+.....+  . +.+.+..+++.|...|..+++.
T Consensus       229 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ls~~~~~~l~~~~~~~~~~~~R~~~~ll~~a~~~A~~~~~~  308 (350)
T 1g8p_A          229 RRRDTYDADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGAT  308 (350)
T ss_dssp             HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHhcccCchhhccccccchHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCC
Confidence            65311                           0000112332   333333322  2 6799999999999999999988


Q ss_pred             cccHHHHHHHHHHHhhhhh
Q 022768          260 YVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       260 ~i~~~~~~~a~~~~~~~~~  278 (292)
                      .|+.+|+.+|+..+..+..
T Consensus       309 ~v~~~~v~~a~~~~l~~r~  327 (350)
T 1g8p_A          309 AVGRDHLKRVATMALSHRL  327 (350)
T ss_dssp             BCCHHHHHHHHHHHHGGGC
T ss_pred             cCCHHHHHHHHHHHHhhcc
Confidence            9999999999998876654

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.83  E-value=1.4e-19  Score=159.41  Aligned_cols=216  Identities=15%  Similarity=0.183  Sum_probs=152.5

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC------Cc
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID------AN   93 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~------~~   93 (292)
                      .+....++|.+|++++|++++++.+...+...             ...+++|+||||+|||++++++++.++      ..
T Consensus        25 ~~~~~k~~p~~~~~i~g~~~~~~~l~~~l~~~-------------~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~   91 (353)
T 1sxj_D           25 QPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSA-------------NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSR   91 (353)
T ss_dssp             -CHHHHTCCSSTTTCCSCCTTHHHHHHHTTCT-------------TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTS
T ss_pred             ccHHHhcCCCCHHHhhCCHHHHHHHHHHHhcC-------------CCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccc
Confidence            35556789999999999999999999987542             224599999999999999999999864      35


Q ss_pred             EEEEeccchhccccChHHHHHHHHHHHh-------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHH
Q 022768           94 FLKVVSSAIIDKYIGESARLIREMFGYA-------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELL  160 (292)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l  160 (292)
                      ++.+++......  +.....+.. +...             ....+.+|+|||+|.+           ....+..+..++
T Consensus        92 ~~~~~~~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l-----------~~~~~~~Ll~~l  157 (353)
T 1sxj_D           92 ILELNASDERGI--SIVREKVKN-FARLTVSKPSKHDLENYPCPPYKIIILDEADSM-----------TADAQSALRRTM  157 (353)
T ss_dssp             EEEECSSSCCCH--HHHTTHHHH-HHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGS-----------CHHHHHHHHHHH
T ss_pred             eEEEccccccch--HHHHHHHHH-HhhhcccccchhhcccCCCCCceEEEEECCCcc-----------CHHHHHHHHHHH
Confidence            777776553210  011111111 1110             1134579999999998           666677777777


Q ss_pred             HHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCH
Q 022768          161 NQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNG  239 (292)
Q Consensus       161 ~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~  239 (292)
                      +...     ....+|+++|.+..+.+.+++  |+ ..+.+++|+.++...+++..+...... .+..++.++..+.| ++
T Consensus       158 e~~~-----~~~~~il~~~~~~~l~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G-~~  228 (353)
T 1sxj_D          158 ETYS-----GVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAG-DL  228 (353)
T ss_dssp             HHTT-----TTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS-CH
T ss_pred             HhcC-----CCceEEEEeCchhhCcchhhc--cC-ceEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CH
Confidence            7532     456778888998889999998  77 488999999999999999887543322 22235667777776 77


Q ss_pred             HHHHHHHHHHHHHHHHhcCC-cccHHHHHHHHH
Q 022768          240 ADLRNVCTEAGMSAIRAERD-YVIHEDFMKAVR  271 (292)
Q Consensus       240 ~di~~l~~~a~~~a~~~~~~-~i~~~~~~~a~~  271 (292)
                      +.+.++++.+...+...+.. .|+.+++.+++.
T Consensus       229 r~~~~~l~~~~~~~~~~~~~~~It~~~v~~~~~  261 (353)
T 1sxj_D          229 RRGITLLQSASKGAQYLGDGKNITSTQVEELAG  261 (353)
T ss_dssp             HHHHHHHHHTHHHHHHHCSCCCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCCCccCccccHHHHHHHhC
Confidence            77777887777665443333 799999887765

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.83  E-value=4.9e-19  Score=154.92  Aligned_cols=220  Identities=20%  Similarity=0.234  Sum_probs=156.7

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch---
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI---  102 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~---  102 (292)
                      ..+..+++++|++++++.+..++..               +.+++|+||||+|||++++++++.++.++..+++...   
T Consensus        21 ~~~~~~~~i~g~~~~~~~l~~~l~~---------------~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~   85 (331)
T 2r44_A           21 VIDEVGKVVVGQKYMINRLLIGICT---------------GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLP   85 (331)
T ss_dssp             HHHHHTTTCCSCHHHHHHHHHHHHH---------------TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCH
T ss_pred             HHHHhccceeCcHHHHHHHHHHHHc---------------CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCCh
Confidence            3444668899999999999887754               4589999999999999999999999999988886421   


Q ss_pred             ---hccccChHHHHHHHHHHHhhhCC---CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC------CCCCC
Q 022768          103 ---IDKYIGESARLIREMFGYARDHQ---PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG------FDQLG  170 (292)
Q Consensus       103 ---~~~~~~~~~~~~~~~~~~~~~~~---~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~------~~~~~  170 (292)
                         .+.......   ...+  .....   .++|+|||+|.+           ....+..|...++....      .....
T Consensus        86 ~~l~g~~~~~~~---~~~~--~~~~g~l~~~vl~iDEi~~~-----------~~~~~~~Ll~~l~~~~~~~~g~~~~~~~  149 (331)
T 2r44_A           86 SDLIGTMIYNQH---KGNF--EVKKGPVFSNFILADEVNRS-----------PAKVQSALLECMQEKQVTIGDTTYPLDN  149 (331)
T ss_dssp             HHHHEEEEEETT---TTEE--EEEECTTCSSEEEEETGGGS-----------CHHHHHHHHHHHHHSEEEETTEEEECCS
T ss_pred             hhcCCceeecCC---CCce--EeccCcccccEEEEEccccC-----------CHHHHHHHHHHHhcCceeeCCEEEECCC
Confidence               111000000   0000  00011   269999999998           67778888888775321      11233


Q ss_pred             CeEEEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccC--------------------CCCC
Q 022768          171 KVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAK--------------------HGEI  225 (292)
Q Consensus       171 ~~~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~--------------------~~~~  225 (292)
                      ++++|+|+|..+     .+++++++  ||...+.+++|+.+++.+|++........                    .-.+
T Consensus       150 ~~~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~v~~  227 (331)
T 2r44_A          150 PFLVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKESELEVMRRVSNMNFNYQVQKIVSKNDVLEIRNEINKVTI  227 (331)
T ss_dssp             SCEEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHHHHHHHHHHHCTTCCCCCCCCSCHHHHHHHHHHHHTCBC
T ss_pred             CEEEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHHHHHHHHhccccCcchhccccCCHHHHHHHHHHhccCCC
Confidence            677888888543     38899999  99888999999999999999988764211                    0111


Q ss_pred             C---HHHHHHHc-------------------CCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          226 D---YEAVVKLA-------------------EGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       226 ~---~~~l~~~~-------------------~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      +   .+.++...                   .|.+++.+..+++.|...|..+++..|+.+|+.+++..+-.+..
T Consensus       228 ~~~~~~~i~~~~~~~r~~~~~~~~~~~~~~~~~~s~R~~~~ll~~a~a~A~l~g~~~v~~~dv~~~~~~vl~~r~  302 (331)
T 2r44_A          228 SESLEKYIIELVFATRFPAEYGLEAEASYILYGASTRAAINLNRVAKAMAFFNNRDYVLPEDIKEVAYDILNHRI  302 (331)
T ss_dssp             CHHHHHHHHHHHHHHHSGGGGTCHHHHHHEEECCCHHHHHHHHHHHHHHHHHTTCSBCCHHHHHHHHHHHHTTTS
T ss_pred             CHHHHHHHHHHHHHHhccccccccccccccccCcChhHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhHhhc
Confidence            2   22222211                   25589999999999999999999999999999999998875443

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=99.83  E-value=2.1e-19  Score=155.44  Aligned_cols=241  Identities=23%  Similarity=0.302  Sum_probs=154.5

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhc-CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-cccCh
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRV-GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGE  109 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~-~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~~~  109 (292)
                      +.++|++++++.+...+..++........+ +...+.+++|+||||||||++++++++.++.+++.+++..+.. .+.+.
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~~~~~~   94 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   94 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGG
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccCCccCc
Confidence            358999999999998886532111000000 0134678999999999999999999999999999999988764 33332


Q ss_pred             -HHHHHHHHHHHh-----hhCCCEEEEEcccccccCCcCCCCCcc-hHHHHHHHHHHHHHhhC-----CCCCCCeEEEEE
Q 022768          110 -SARLIREMFGYA-----RDHQPCIIFMDEIDAIGGRRFSEGTSA-DREIQRTLMELLNQLDG-----FDQLGKVKMIMA  177 (292)
Q Consensus       110 -~~~~~~~~~~~~-----~~~~~~il~lDe~d~l~~~~~~~~~~~-~~~~~~~l~~~l~~~~~-----~~~~~~~~vi~t  177 (292)
                       ....+..++...     ....+++|+|||+|.+........... ....+..|..+++....     .....++++|++
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~  174 (310)
T 1ofh_A           95 EVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIAS  174 (310)
T ss_dssp             STTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEE
T ss_pred             cHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEc
Confidence             223344444422     112357999999999965443221111 11234555555553210     012346788888


Q ss_pred             e----CCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHH-------------cCccCC-CCCCHHHHHHHc-----
Q 022768          178 T----NRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHA-------------AGIAKH-GEIDYEAVVKLA-----  234 (292)
Q Consensus       178 ~----~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~-------------~~~~~~-~~~~~~~l~~~~-----  234 (292)
                      +    +.+..+++++.+  ||...+.|++|+.+++.+|++...             .+.... .+..++.++..+     
T Consensus       175 ~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~  252 (310)
T 1ofh_A          175 GAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNE  252 (310)
T ss_dssp             ECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHHHHHHHHHHHHH
T ss_pred             CCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHHHHHHHhhhhcc
Confidence            5    456678899998  998889999999999999998321             111101 112244555554     


Q ss_pred             --CCCCHHHHHHHHHHHHHHHHHhcCC------cccHHHHHHHHHHHh
Q 022768          235 --EGFNGADLRNVCTEAGMSAIRAERD------YVIHEDFMKAVRKLN  274 (292)
Q Consensus       235 --~g~~~~di~~l~~~a~~~a~~~~~~------~i~~~~~~~a~~~~~  274 (292)
                        .+.+.+.+..+++.+...+......      .|+.+++.+++....
T Consensus       253 ~~~~g~~R~l~~~l~~~~~~~~~~~~~~~~~~~~i~~~~v~~~l~~~~  300 (310)
T 1ofh_A          253 KTENIGARRLHTVMERLMDKISFSASDMNGQTVNIDAAYVADALGEVV  300 (310)
T ss_dssp             HSCCCTTHHHHHHHHHHSHHHHHHGGGCTTCEEEECHHHHHHHTCSSS
T ss_pred             cccccCcHHHHHHHHHHHHhhhcCCccccCCEEEEeeHHHHHHHHhhh
Confidence              1348899999999987665433221      499999999987654

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.83  E-value=1.1e-19  Score=161.88  Aligned_cols=214  Identities=21%  Similarity=0.247  Sum_probs=151.0

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----------CCcEEEEec
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----------DANFLKVVS   99 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----------~~~~~~~~~   99 (292)
                      .++++|+++.++.+...+......         ..+.+++|+||+|+|||++++.+++.+           +.+++.+++
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~---------~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~   89 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKN---------EVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNC   89 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTT---------CCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEEC
Confidence            378999999999999888653221         345689999999999999999999987           888999987


Q ss_pred             cchh-ccc-----------------cCh-HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHH-HHHH
Q 022768          100 SAII-DKY-----------------IGE-SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRT-LMEL  159 (292)
Q Consensus       100 ~~~~-~~~-----------------~~~-~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~-l~~~  159 (292)
                      .... +..                 .+. ....+..++....... .+|+|||+|.+....          .+.. +..+
T Consensus        90 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~vlilDEi~~l~~~~----------~~~~~l~~l  158 (384)
T 2qby_B           90 REVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIR-AIIYLDEVDTLVKRR----------GGDIVLYQL  158 (384)
T ss_dssp             HHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSC-EEEEEETTHHHHHST----------TSHHHHHHH
T ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCC-CEEEEECHHHhccCC----------CCceeHHHH
Confidence            6543 100                 000 1222333333333333 499999999983211          1233 3343


Q ss_pred             HHHhhCCCCCCCeEEEEEeCCC---CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcC-c--cCCCCCCHHHHHHH
Q 022768          160 LNQLDGFDQLGKVKMIMATNRP---DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAG-I--AKHGEIDYEAVVKL  233 (292)
Q Consensus       160 l~~~~~~~~~~~~~vi~t~~~~---~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~-~--~~~~~~~~~~l~~~  233 (292)
                      +...      .++.+|+++|..   ..+++.+.+  ||...+.|++|+.++..++++.++.. .  ....+..++.++..
T Consensus       159 ~~~~------~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~i~~~  230 (384)
T 2qby_B          159 LRSD------ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAI  230 (384)
T ss_dssp             HTSS------SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHHHHHH
T ss_pred             hcCC------cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHHHHHH
Confidence            3321      578899999886   678888888  87779999999999999999988752 1  11122234566666


Q ss_pred             cC---CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          234 AE---GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       234 ~~---g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      +.   | +++.+..+++.|...|.  +...|+.+++.+++..+..
T Consensus       231 ~~~~~G-~~r~a~~~l~~a~~~a~--~~~~i~~~~v~~~~~~~~~  272 (384)
T 2qby_B          231 SAKEHG-DARKAVNLLFRAAQLAS--GGGIIRKEHVDKAIVDYEQ  272 (384)
T ss_dssp             HHTTCC-CHHHHHHHHHHHHHHTT--SSSCCCHHHHHHHHHHHHH
T ss_pred             HHhccC-CHHHHHHHHHHHHHHhc--CCCccCHHHHHHHHHHHhc
Confidence            65   5 67788888888887775  5568999999999988764

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.83  E-value=8.3e-19  Score=156.00  Aligned_cols=226  Identities=24%  Similarity=0.309  Sum_probs=156.0

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc------CCcEEEEecc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI------DANFLKVVSS  100 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l------~~~~~~~~~~  100 (292)
                      +....++++|+++.++.|...+......         ..+..++|+||+|+|||++++.+++.+      +.+++.+++.
T Consensus        15 ~~~~p~~~~gr~~e~~~l~~~l~~~~~~---------~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~   85 (386)
T 2qby_A           15 PDYIPDELPHREDQIRKIASILAPLYRE---------EKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTR   85 (386)
T ss_dssp             SSCCCSCCTTCHHHHHHHHHSSGGGGGT---------CCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHH
T ss_pred             CccCCCCCCChHHHHHHHHHHHHHHHcC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECC
Confidence            3445588999999999999987653221         446789999999999999999999988      7888888865


Q ss_pred             chhcc----------------ccC-hHHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768          101 AIIDK----------------YIG-ESARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus       101 ~~~~~----------------~~~-~~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      .....                ..+ ........++...... .|.+|+|||+|.+....       +   ...+..++..
T Consensus        86 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~-------~---~~~l~~l~~~  155 (386)
T 2qby_A           86 QIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKY-------N---DDILYKLSRI  155 (386)
T ss_dssp             HHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSS-------C---STHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccC-------c---CHHHHHHhhc
Confidence            43210                001 1223334444444433 37899999999984211       1   2234444444


Q ss_pred             hhCCCCCCCeEEEEEeCCC---CCCChhhcCCCCcc-eEEEccCCCHHHHHHHHHHHHcCccCCCCCC---HHHHHHHcC
Q 022768          163 LDGFDQLGKVKMIMATNRP---DVLDPALLRPGRLD-RKIEIPLPNEQSRMEILKIHAAGIAKHGEID---YEAVVKLAE  235 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~---~~l~~~l~~~~r~~-~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~---~~~l~~~~~  235 (292)
                      ++.. ...++.+|++++..   ..+.+.+.+  ||. ..+.+++++.++..++++.++........++   ...++..+.
T Consensus       156 ~~~~-~~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~  232 (386)
T 2qby_A          156 NSEV-NKSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAA  232 (386)
T ss_dssp             HHSC-CC--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHH
T ss_pred             hhhc-CCCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHH
Confidence            4322 33578889999876   456777777  654 4899999999999999998765322112222   344555555


Q ss_pred             ---CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          236 ---GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       236 ---g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                         | +++.+..++..+...|...+...|+.+++.+++..+..
T Consensus       233 ~~~G-~~r~~~~ll~~a~~~a~~~~~~~i~~~~v~~a~~~~~~  274 (386)
T 2qby_A          233 REHG-DARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEIER  274 (386)
T ss_dssp             HTTC-CHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHH
T ss_pred             HhcC-CHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHhh
Confidence               5 78889999999998888777788999999999988764

>1in4_A RUVB, holliday junction DNA helicase RUVB; AAA+-class ATPase, winged-helix domain, ATP hydrolysis, walker A, walker B, sensor 1, sensor 2; HET: ADP; 1.60A {Thermotoga maritima} SCOP: a.4.5.11 c.37.1.20 PDB: 1in5_A* 1in6_A* 1in8_A* 1in7_A* 1j7k_A*

Probab=99.82  E-value=1.7e-18  Score=151.63  Aligned_cols=225  Identities=20%  Similarity=0.225  Sum_probs=159.3

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      ..-....+.+|++++|.+.+++.+...+....       ..+ .+..+++|+||||+||||+++.+++.++.++...+..
T Consensus        14 ~~~~~lr~~~l~~~~g~~~~~~~l~~~i~~~~-------~~~-~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~   85 (334)
T 1in4_A           14 SGVQFLRPKSLDEFIGQENVKKKLSLALEAAK-------MRG-EVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGP   85 (334)
T ss_dssp             ---CTTSCSSGGGCCSCHHHHHHHHHHHHHHH-------HHT-CCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETT
T ss_pred             HHHHHcCCccHHHccCcHHHHHHHHHHHHHHH-------hcC-CCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEech
Confidence            33455677799999999999888887765310       001 2346799999999999999999999999887665543


Q ss_pred             chhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC-------C------C
Q 022768          101 AIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG-------F------D  167 (292)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~-------~------~  167 (292)
                      ....      ...+...+..  ...+.|++|||++.+           ....++.+...+.....       .      .
T Consensus        86 ~~~~------~~~l~~~~~~--~~~~~v~~iDE~~~l-----------~~~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~  146 (334)
T 1in4_A           86 VLVK------QGDMAAILTS--LERGDVLFIDEIHRL-----------NKAVEELLYSAIEDFQIDIMIGKGPSAKSIRI  146 (334)
T ss_dssp             TCCS------HHHHHHHHHH--CCTTCEEEEETGGGC-----------CHHHHHHHHHHHHTSCCCC-------------
T ss_pred             HhcC------HHHHHHHHHH--ccCCCEEEEcchhhc-----------CHHHHHHHHHHHHhcccceeeccCcccccccc
Confidence            3211      1122222222  234579999999998           33445555544432110       0      0


Q ss_pred             CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHH
Q 022768          168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVC  246 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~  246 (292)
                      ....+.++++++.+..+++.+++  ||...+.+++++.++..++++......... .+.....++..+.| +++.+..++
T Consensus       147 ~l~~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G-~~R~a~~ll  223 (334)
T 1in4_A          147 DIQPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIRLT  223 (334)
T ss_dssp             --CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHHHHHHHH
T ss_pred             cCCCeEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCC-ChHHHHHHH
Confidence            11246788888889999999999  998889999999999999999877643322 11224567777777 889999999


Q ss_pred             HHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          247 TEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       247 ~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      +.+...|..++...|+.+++.+++..+..
T Consensus       224 ~~~~~~a~~~~~~~It~~~v~~al~~~~~  252 (334)
T 1in4_A          224 KRVRDMLTVVKADRINTDIVLKTMEVLNI  252 (334)
T ss_dssp             HHHHHHHHHHTCSSBCHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHHHhCC
Confidence            99999998888888999999999998753

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=99.82  E-value=4.4e-19  Score=157.43  Aligned_cols=209  Identities=17%  Similarity=0.238  Sum_probs=148.9

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------   93 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------   93 (292)
                      ..+...+.|.+|++++|+++.++.|...+...            ..++.++|+||+|+|||++++.+++.+++.      
T Consensus         4 ~~l~~k~rp~~~~~~vg~~~~~~~L~~~l~~~------------~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~   71 (373)
T 1jr3_A            4 QVLARKWRPQTFADVVGQEHVLTALANGLSLG------------RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITAT   71 (373)
T ss_dssp             CCHHHHTCCCSTTTSCSCHHHHHHHHHHHHHT------------CCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSS
T ss_pred             HHHHHhhCCCchhhccCcHHHHHHHHHHHHhC------------CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCC
Confidence            34556788889999999999999999988642            334578999999999999999999988642      


Q ss_pred             ------------------EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHH
Q 022768           94 ------------------FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADRE  151 (292)
Q Consensus        94 ------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~  151 (292)
                                        ++.++....  ..    ...++.++..+.    ...+.+|+|||+|.+           +..
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~----~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l-----------~~~  134 (373)
T 1jr3_A           72 PCGVCDNCREIEQGRFVDLIEIDAASR--TK----VEDTRDLLDNVQYAPARGRFKVYLIDEVHML-----------SRH  134 (373)
T ss_dssp             CCSSSHHHHHHHTSCCSSCEEEETTCS--CC----SSCHHHHHHHTTSCCSSSSSEEEEEECGGGS-----------CHH
T ss_pred             CCcccHHHHHHhccCCCceEEeccccc--CC----HHHHHHHHHHHhhccccCCeEEEEEECcchh-----------cHH
Confidence                              222222110  01    112334444443    234689999999998           555


Q ss_pred             HHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHH
Q 022768          152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAV  230 (292)
Q Consensus       152 ~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l  230 (292)
                      ....|...++.     +..++.+|++++.+..+.+.+++  |+ ..+.+++|+.++..++++.++...... .+.....+
T Consensus       135 ~~~~Ll~~le~-----~~~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l  206 (373)
T 1jr3_A          135 SFNALLKTLEE-----PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLL  206 (373)
T ss_dssp             HHHHHHHHHHS-----CCSSEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHH
T ss_pred             HHHHHHHHHhc-----CCCceEEEEEeCChHhCcHHHHh--he-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            66666666543     34578899999888888899988  76 789999999999999999887643322 11224567


Q ss_pred             HHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          231 VKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       231 ~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      +..+.| +++.+.++++.+...+    ...|+.+++.+++
T Consensus       207 ~~~~~G-~~r~~~~~l~~~~~~~----~~~i~~~~v~~~~  241 (373)
T 1jr3_A          207 ARAAEG-SLRDALSLTDQAIASG----DGQVSTQAVSAML  241 (373)
T ss_dssp             HHHSSS-CHHHHHHHHHHHHHHT----TTCBCHHHHHHHT
T ss_pred             HHHCCC-CHHHHHHHHHHHHHhc----CCcccHHHHHHHh
Confidence            777877 8889988888875432    3457877776654

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=99.82  E-value=3.4e-19  Score=155.48  Aligned_cols=219  Identities=15%  Similarity=0.204  Sum_probs=145.6

Q ss_pred             CCCCcccccc-c--cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           26 PGNVSYSAVG-G--LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        26 ~~~~~~~~l~-g--~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      .|..+|++++ |  ...+...+..++..+           ...+.+++|+||||+|||++++++++.+   +.+++++++
T Consensus         5 ~~~~~f~~fv~g~~~~~a~~~~~~~~~~~-----------~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~   73 (324)
T 1l8q_A            5 NPKYTLENFIVGEGNRLAYEVVKEALENL-----------GSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSA   73 (324)
T ss_dssp             CTTCCSSSCCCCTTTHHHHHHHHHHHHTT-----------TTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             CCCCCcccCCCCCcHHHHHHHHHHHHhCc-----------CCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEH
Confidence            4667899987 4  455566666666543           1245789999999999999999999988   889999998


Q ss_pred             cchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          100 SAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      ..+.....+.........|.... ..+++|+|||+|.+..         ....+..+..+++....   .+..+++++++
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~vL~iDEi~~l~~---------~~~~~~~l~~~l~~~~~---~~~~iii~~~~  140 (324)
T 1l8q_A           74 DDFAQAMVEHLKKGTINEFRNMY-KSVDLLLLDDVQFLSG---------KERTQIEFFHIFNTLYL---LEKQIILASDR  140 (324)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHH-HTCSEEEEECGGGGTT---------CHHHHHHHHHHHHHHHH---TTCEEEEEESS
T ss_pred             HHHHHHHHHHHHcCcHHHHHHHh-cCCCEEEEcCcccccC---------ChHHHHHHHHHHHHHHH---CCCeEEEEecC
Confidence            77654433222211112222222 2368999999999832         22456666666665431   13445555555


Q ss_pred             CCC---CCChhhcCCCCcc--eEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHH-
Q 022768          180 RPD---VLDPALLRPGRLD--RKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMS-  252 (292)
Q Consensus       180 ~~~---~l~~~l~~~~r~~--~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~-  252 (292)
                      .+.   .+++++.+  ||.  ..+.+++ +.+++.++++.++...... .+..++.++..+ | +.+++..++..+... 
T Consensus       141 ~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g-~~r~l~~~l~~~~~~~  215 (324)
T 1l8q_A          141 HPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-K-NVREIEGKIKLIKLKG  215 (324)
T ss_dssp             CGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-S-SHHHHHHHHHHHHHHC
T ss_pred             ChHHHHHhhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-C-CHHHHHHHHHHHHHcC
Confidence            544   57889988  764  6789999 9999999999888643322 122256677777 5 788888888887766 


Q ss_pred             --HHH-hcCCcc-cHHHHHHHHHHH
Q 022768          253 --AIR-AERDYV-IHEDFMKAVRKL  273 (292)
Q Consensus       253 --a~~-~~~~~i-~~~~~~~a~~~~  273 (292)
                        ++. .....| +.+++.+++...
T Consensus       216 ~~~l~~~~~~~i~t~~~i~~~~~~~  240 (324)
T 1l8q_A          216 FEGLERKERKERDKLMQIVEFVANY  240 (324)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhccccccCCCCHHHHHHHHHHH
Confidence              111 223457 888888887653

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=99.82  E-value=1.1e-18  Score=152.00  Aligned_cols=196  Identities=21%  Similarity=0.255  Sum_probs=139.3

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cE
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NF   94 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~   94 (292)
                      .+..+.++|.+|++++|++++++.+..++...             ...+++|+||+|+|||++++.+++.+..     .+
T Consensus        13 ~~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~~-------------~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~   79 (327)
T 1iqp_A           13 KPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTG-------------SMPHLLFAGPPGVGKTTAALALARELFGENWRHNF   79 (327)
T ss_dssp             SCHHHHTCCCSTTTCCSCHHHHHHHHHHHHHT-------------CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHE
T ss_pred             CchhhccCCCCHHHhhCCHHHHHHHHHHHHcC-------------CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCce
Confidence            34556789999999999999999999887652             2335999999999999999999998632     36


Q ss_pred             EEEeccchhccccChHHHHHHHHHHHh-h-hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCe
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGYA-R-DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKV  172 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~  172 (292)
                      +.+++....+.  ......+....... . ...+.+|+|||+|.+           ....+..|..+++..     ..++
T Consensus        80 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l-----------~~~~~~~L~~~le~~-----~~~~  141 (327)
T 1iqp_A           80 LELNASDERGI--NVIREKVKEFARTKPIGGASFKIIFLDEADAL-----------TQDAQQALRRTMEMF-----SSNV  141 (327)
T ss_dssp             EEEETTCHHHH--HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGS-----------CHHHHHHHHHHHHHT-----TTTE
T ss_pred             EEeeccccCch--HHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcC-----------CHHHHHHHHHHHHhc-----CCCC
Confidence            67766543211  01111122211111 1 145789999999998           666677777777652     2477


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHH
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAG  250 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~  250 (292)
                      .+|++++.+..+.+.+.+  |+ ..+.+++++.++...+++..+...... .+...+.++..+.| +++.+.++++.+.
T Consensus       142 ~~i~~~~~~~~l~~~l~s--r~-~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~~~~~l~~~~  216 (327)
T 1iqp_A          142 RFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG-DMRRAINILQAAA  216 (327)
T ss_dssp             EEEEEESCGGGSCHHHHH--TE-EEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT-CHHHHHHHHHHHH
T ss_pred             eEEEEeCCccccCHHHHh--hC-cEEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCC-CHHHHHHHHHHHH
Confidence            889999998889999988  77 478999999999999999887644322 22234566777766 7777777776654

>1sxj_A Activator 1 95 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.82  E-value=1.3e-19  Score=167.72  Aligned_cols=227  Identities=19%  Similarity=0.239  Sum_probs=143.2

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCC-hHHHHhcCC---CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMN-PELFLRVGI---KPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~-~~~~~~~~~---~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..+.++|.+|++++|++++++.|.+++...... ...+...|.   .+.++++|+||||+|||++|++++++++.+++.
T Consensus        28 lW~ekyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~~~i~  107 (516)
T 1sxj_A           28 LWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILE  107 (516)
T ss_dssp             CHHHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             CcccccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCCCEEE
Confidence            4445788899999999999999999998652111 111222222   245789999999999999999999999999999


Q ss_pred             EeccchhccccChHHHHH---------HHHHHHh-----hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768           97 VVSSAIIDKYIGESARLI---------REMFGYA-----RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~---------~~~~~~~-----~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      +++.........  ...+         ...|..+     ....+.+|+|||+|.+...        .......+..+++.
T Consensus       108 in~s~~~~~~~~--~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~--------~~~~l~~L~~~l~~  177 (516)
T 1sxj_A          108 QNASDVRSKTLL--NAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGG--------DRGGVGQLAQFCRK  177 (516)
T ss_dssp             ECTTSCCCHHHH--HHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTT--------STTHHHHHHHHHHH
T ss_pred             EeCCCcchHHHH--HHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchh--------hHHHHHHHHHHHHh
Confidence            998775432110  0000         0111111     1245789999999998432        12233455555554


Q ss_pred             hhCCCCCCCeEEEEEeCCC--CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCH
Q 022768          163 LDGFDQLGKVKMIMATNRP--DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNG  239 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~--~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~  239 (292)
                      .       +..+|++++..  ..+ +.++   ++...+.|++|+.+++.+++...+...... .+..+..++..+.|   
T Consensus       178 ~-------~~~iIli~~~~~~~~l-~~l~---~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~G---  243 (516)
T 1sxj_A          178 T-------STPLILICNERNLPKM-RPFD---RVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG---  243 (516)
T ss_dssp             C-------SSCEEEEESCTTSSTT-GGGT---TTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT---
T ss_pred             c-------CCCEEEEEcCCCCccc-hhhH---hceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC---
Confidence            1       22244455443  233 3344   344789999999999999998776533222 22336677777765   


Q ss_pred             HHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          240 ADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       240 ~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                       +++.+++.....+.  ....|+.+++.+++....
T Consensus       244 -diR~~i~~L~~~~~--~~~~It~~~v~~~~~~~~  275 (516)
T 1sxj_A          244 -DIRQVINLLSTIST--TTKTINHENINEISKAWE  275 (516)
T ss_dssp             -CHHHHHHHHTHHHH--HSSCCCTTHHHHHHHHHH
T ss_pred             -cHHHHHHHHHHHHh--cCCCCchHHHHHHHHhhc
Confidence             45555544443333  445688888888877543

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=99.82  E-value=2e-19  Score=156.19  Aligned_cols=211  Identities=21%  Similarity=0.214  Sum_probs=142.2

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEE
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFL   95 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~   95 (292)
                      +....++|.+|++++|++++++.+...+..             ....+++|+||+|+|||++++.+++.+     +.+++
T Consensus         6 ~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~   72 (319)
T 2chq_A            6 IWVEKYRPRTLDEVVGQDEVIQRLKGYVER-------------KNIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFI   72 (319)
T ss_dssp             CTTTTTSCSSGGGSCSCHHHHHHHHTTTTT-------------TCCCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCE
T ss_pred             cHHHhcCCCCHHHHhCCHHHHHHHHHHHhC-------------CCCCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeE
Confidence            455678999999999999999999887754             122359999999999999999999986     33577


Q ss_pred             EEeccchhccccChHHHHHHHHHHHhh--hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           96 KVVSSAIIDKYIGESARLIREMFGYAR--DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      .+++....+.  ......+........  ...+.+++|||+|.+           ....+..|..+++     ....++.
T Consensus        73 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l-----------~~~~~~~L~~~le-----~~~~~~~  134 (319)
T 2chq_A           73 EMNASDERGI--DVVRHKIKEFARTAPIGGAPFKIIFLDEADAL-----------TADAQAALRRTME-----MYSKSCR  134 (319)
T ss_dssp             EEETTSTTCT--TTSSHHHHHHHHSCCSSSCCCEEEEEETGGGS-----------CHHHHHTTGGGTS-----SSSSSEE
T ss_pred             EEeCccccCh--HHHHHHHHHHHhcCCCCCCCceEEEEeCCCcC-----------CHHHHHHHHHHHH-----hcCCCCe
Confidence            7777654321  111222222221111  144789999999998           4444444444432     2335788


Q ss_pred             EEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHH
Q 022768          174 MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMS  252 (292)
Q Consensus       174 vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~  252 (292)
                      +|+++|.+..+.+.+++  |+ ..+.+++|+.++..+++..++...... .+..+..++..+.| +.+.+.++++.+.  
T Consensus       135 ~i~~~~~~~~l~~~l~s--r~-~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G-~~r~~~~~l~~~~--  208 (319)
T 2chq_A          135 FILSCNYVSRIIEPIQS--RC-AVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGG-DFRKAINALQGAA--  208 (319)
T ss_dssp             EEEEESCGGGSCHHHHT--TC-EEEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTT-CHHHHHHHHHHHH--
T ss_pred             EEEEeCChhhcchHHHh--hC-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHHH--
Confidence            99999999899999998  77 489999999999999999887654332 11223445555554 5555555555443  


Q ss_pred             HHHhcCCcccHHHHHHHHH
Q 022768          253 AIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       253 a~~~~~~~i~~~~~~~a~~  271 (292)
                       ..  ...|+.+++.+++.
T Consensus       209 -~~--~~~i~~~~v~~~~~  224 (319)
T 2chq_A          209 -AI--GEVVDADTIYQITA  224 (319)
T ss_dssp             -HS--SSCBCHHHHHHHTT
T ss_pred             -Hc--CCCCCHHHHHHHHC
Confidence             22  34577777765543

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=99.81  E-value=5.3e-19  Score=147.18  Aligned_cols=210  Identities=14%  Similarity=0.162  Sum_probs=144.0

Q ss_pred             ccCCC-CCcccccccc---HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC---CcEE
Q 022768           23 HEDPG-NVSYSAVGGL---SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID---ANFL   95 (292)
Q Consensus        23 ~~~~~-~~~~~~l~g~---~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~---~~~~   95 (292)
                      ....+ +.+|++++|.   ..+++.+..++..             ..+.+++|+||||+|||++++.+++.+.   .+++
T Consensus        18 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~-------------~~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~   84 (242)
T 3bos_A           18 PVHLPDDETFTSYYPAAGNDELIGALKSAASG-------------DGVQAIYLWGPVKSGRTHLIHAACARANELERRSF   84 (242)
T ss_dssp             ECCCCTTCSTTTSCC--CCHHHHHHHHHHHHT-------------CSCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             CCCCCCCCChhhccCCCCCHHHHHHHHHHHhC-------------CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEE
Confidence            33444 4899999972   4666777666543             2467899999999999999999998874   6788


Q ss_pred             EEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEE
Q 022768           96 KVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMI  175 (292)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi  175 (292)
                      .+++..+.......        +.  ....+.+|+|||+|.+..         ....+..+..+++....   ...+.+|
T Consensus        85 ~~~~~~~~~~~~~~--------~~--~~~~~~vliiDe~~~~~~---------~~~~~~~l~~~l~~~~~---~~~~~ii  142 (242)
T 3bos_A           85 YIPLGIHASISTAL--------LE--GLEQFDLICIDDVDAVAG---------HPLWEEAIFDLYNRVAE---QKRGSLI  142 (242)
T ss_dssp             EEEGGGGGGSCGGG--------GT--TGGGSSEEEEETGGGGTT---------CHHHHHHHHHHHHHHHH---HCSCEEE
T ss_pred             EEEHHHHHHHHHHH--------HH--hccCCCEEEEeccccccC---------CHHHHHHHHHHHHHHHH---cCCCeEE
Confidence            88887765443211        11  113457999999999832         22235556666654321   1233355


Q ss_pred             EEeCC-CC---CCChhhcCCCCcc--eEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHH
Q 022768          176 MATNR-PD---VLDPALLRPGRLD--RKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       176 ~t~~~-~~---~l~~~l~~~~r~~--~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      ++++. +.   .+.+.+.+  ||.  ..+.+++|+.+++.+++..++...... .+...+.++..+.| +.+++..+++.
T Consensus       143 ~~~~~~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~l~~~l~~  219 (242)
T 3bos_A          143 VSASASPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMAR-DLRTLFDVLDR  219 (242)
T ss_dssp             EEESSCTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTT-CHHHHHHHHHH
T ss_pred             EEcCCCHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccC-CHHHHHHHHHH
Confidence            55553 33   34577877  664  889999999999999999888643322 12234566677766 89999999999


Q ss_pred             HHHHHHHhcCCcccHHHHHHHHH
Q 022768          249 AGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       249 a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      +..+|...+ ..|+.+++.++++
T Consensus       220 ~~~~a~~~~-~~It~~~v~~~l~  241 (242)
T 3bos_A          220 LDKASMVHQ-RKLTIPFVKEMLR  241 (242)
T ss_dssp             HHHHHHHHT-CCCCHHHHHHHHT
T ss_pred             HHHHHHHhC-CCCcHHHHHHHhh
Confidence            998886555 4699999998874

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.81  E-value=1.7e-18  Score=154.34  Aligned_cols=222  Identities=16%  Similarity=0.184  Sum_probs=155.3

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCc--eEEEEcCCCChHHHHHHHHHHhc----CCcEEEEeccchh
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPK--GVLLYGPPGTGKTLLARAIASNI----DANFLKVVSSAII  103 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~--~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~~~~~  103 (292)
                      .+++++|+++.++.+..++......         ..+.  +++|+||+|+|||++++.+++.+    +..++.+++....
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~---------~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~   85 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRN---------PGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYR   85 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHS---------TTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCC
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcC---------CCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCC
Confidence            3478999999999999988653211         2334  89999999999999999999988    5677888865432


Q ss_pred             cc--c--------------cC-hHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          104 DK--Y--------------IG-ESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       104 ~~--~--------------~~-~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      ..  .              .+ ........+...... ..|.+|+|||+|.+           +......|..++.....
T Consensus        86 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l-----------~~~~~~~L~~~~~~~~~  154 (389)
T 1fnn_A           86 NFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL-----------APDILSTFIRLGQEADK  154 (389)
T ss_dssp             SHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS-----------CHHHHHHHHHHTTCHHH
T ss_pred             CHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc-----------chHHHHHHHHHHHhCCC
Confidence            10  0              01 112222222222222 34789999999988           55555555555533210


Q ss_pred             CCCCCCeEEEEEeCCC---CCCChhhcCCCCcce-EEEccCCCHHHHHHHHHHHHcCccCCCCC---CHHHHHHHc----
Q 022768          166 FDQLGKVKMIMATNRP---DVLDPALLRPGRLDR-KIEIPLPNEQSRMEILKIHAAGIAKHGEI---DYEAVVKLA----  234 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~---~~l~~~l~~~~r~~~-~i~l~~p~~~~r~~i~~~~~~~~~~~~~~---~~~~l~~~~----  234 (292)
                       ....++.+|+++|.+   ..+.+.+.+  ||.. .+.|++++.++..++++..+........+   .+..++..+    
T Consensus       155 -~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~  231 (389)
T 1fnn_A          155 -LGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQT  231 (389)
T ss_dssp             -HSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSS
T ss_pred             -CCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcc
Confidence             001378899999887   567788877  7764 79999999999999999887532111122   345667777    


Q ss_pred             -----CCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          235 -----EGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       235 -----~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                           .| +++.+..+++.|...|..++...|+.+++.+++..+..
T Consensus       232 ~~~~~~G-~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~~~~~~  276 (389)
T 1fnn_A          232 PLDTNRG-DARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVLF  276 (389)
T ss_dssp             TTCTTSC-CHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHSC
T ss_pred             cCCCCCC-cHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHhh
Confidence                 45 78899999999999998888888999999999887653

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.81  E-value=1.4e-18  Score=151.18  Aligned_cols=208  Identities=16%  Similarity=0.156  Sum_probs=148.7

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEE
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFL   95 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~   95 (292)
                      +..+.++|.+|++++|+++.++.|...+...            . ..+++|+||+|+|||++++.+++.+     +.+++
T Consensus        10 ~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~------------~-~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~   76 (323)
T 1sxj_B           10 PWVEKYRPQVLSDIVGNKETIDRLQQIAKDG------------N-MPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVL   76 (323)
T ss_dssp             CHHHHTCCSSGGGCCSCTHHHHHHHHHHHSC------------C-CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEE
T ss_pred             cHHHhcCCCCHHHHHCCHHHHHHHHHHHHcC------------C-CCeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEE
Confidence            3445688889999999999999999987642            2 2349999999999999999999986     33567


Q ss_pred             EEeccchhccccChHHHHHHHHHHHhh-------hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           96 KVVSSAIIDKYIGESARLIREMFGYAR-------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                      .+++....+      ...++..+....       ...+.+|+|||+|.+           ....+..|..+++..     
T Consensus        77 ~~~~~~~~~------~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l-----------~~~~~~~L~~~le~~-----  134 (323)
T 1sxj_B           77 ELNASDDRG------IDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSM-----------TAGAQQALRRTMELY-----  134 (323)
T ss_dssp             EECTTSCCS------HHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGS-----------CHHHHHTTHHHHHHT-----
T ss_pred             EecCccccC------hHHHHHHHHHHHhccccCCCCCceEEEEECcccC-----------CHHHHHHHHHHHhcc-----
Confidence            776554211      223333333322       234789999999998           555666677776652     


Q ss_pred             CCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHH
Q 022768          169 LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCT  247 (292)
Q Consensus       169 ~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~  247 (292)
                      ..++.+|++++.+..+.+.+++  |+ ..+.+++|+.++..++++.++...... .+.....++..+.| +++.+.++++
T Consensus       135 ~~~~~~il~~~~~~~l~~~l~s--r~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~r~a~~~l~  210 (323)
T 1sxj_B          135 SNSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG-DMRQAINNLQ  210 (323)
T ss_dssp             TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHHHHHHHH
T ss_pred             CCCceEEEEeCChhhchhHHHh--hc-eEEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHH
Confidence            2578888899998889999998  77 489999999999999999877543222 12234567777776 7777777776


Q ss_pred             HHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          248 EAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       248 ~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      .+..   ..  ..|+.+++.+++..
T Consensus       211 ~~~~---~~--~~i~~~~v~~~~~~  230 (323)
T 1sxj_B          211 STVA---GH--GLVNADNVFKIVDS  230 (323)
T ss_dssp             HHHH---HH--SSBCHHHHHHHHTS
T ss_pred             HHHh---cC--CCcCHHHHHHHHCC
Confidence            6542   21  45888888777654

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=99.81  E-value=5.1e-19  Score=150.63  Aligned_cols=225  Identities=20%  Similarity=0.223  Sum_probs=141.5

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh-ccccC
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII-DKYIG  108 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~-~~~~~  108 (292)
                      ....++|..+..+.+.......   .......+..++.++||+||||||||++|+++++.++.+++.+++.... +....
T Consensus        31 ~~~~~i~~~~~~~~i~~~~~~l---~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~~~g~~~~  107 (272)
T 1d2n_A           31 IMNGIIKWGDPVTRVLDDGELL---VQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSET  107 (272)
T ss_dssp             CTTCCCCCSHHHHHHHHHHHHH---HHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHH
T ss_pred             HhcCCCCccHHHHHHHHHHHHH---HHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHHhcCCchH
Confidence            3456889888877776642211   1112222345678899999999999999999999999999999876532 11122


Q ss_pred             hHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC-CCCCeEEEEEeCCCCCCCh-
Q 022768          109 ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD-QLGKVKMIMATNRPDVLDP-  186 (292)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~-~~~~~~vi~t~~~~~~l~~-  186 (292)
                      .....+..+|..+....+++|+|||+|.+++..... ..........|..+   +.... ...++++|+|+|.++.+++ 
T Consensus       108 ~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~-~~~~~~~l~~L~~~---~~~~~~~~~~~~ii~ttn~~~~l~~~  183 (272)
T 1d2n_A          108 AKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIG-PRFSNLVLQALLVL---LKKAPPQGRKLLIIGTTSRKDVLQEM  183 (272)
T ss_dssp             HHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTT-TBCCHHHHHHHHHH---TTCCCSTTCEEEEEEEESCHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCC-hhHHHHHHHHHHHH---hcCccCCCCCEEEEEecCChhhcchh
Confidence            233566778887777778999999999997554221 11233334444443   33222 2346778999998877666 


Q ss_pred             hhcCCCCcceEEEccCCCH-HHHHHHHHHHHcCccCCCCCCHHHHHHHcCCC----CHHHHHHHHHHHHHHHHHhcCCcc
Q 022768          187 ALLRPGRLDRKIEIPLPNE-QSRMEILKIHAAGIAKHGEIDYEAVVKLAEGF----NGADLRNVCTEAGMSAIRAERDYV  261 (292)
Q Consensus       187 ~l~~~~r~~~~i~l~~p~~-~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~----~~~di~~l~~~a~~~a~~~~~~~i  261 (292)
                      .+.+  ||...+.+|+++. ++...++....   .. .+.++..++..+.|+    +.+++.++++.|...+     ...
T Consensus       184 ~l~~--rf~~~i~~p~l~~r~~i~~i~~~~~---~~-~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~~-----~~~  252 (272)
T 1d2n_A          184 EMLN--AFSTTIHVPNIATGEQLLEALELLG---NF-KDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMD-----PEY  252 (272)
T ss_dssp             TCTT--TSSEEEECCCEEEHHHHHHHHHHHT---CS-CHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTSC-----GGG
T ss_pred             hhhc--ccceEEcCCCccHHHHHHHHHHhcC---CC-CHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhhc-----hHH
Confidence            5555  8888888877765 44444444321   11 233467788888887    5666666666554322     234


Q ss_pred             cHHHHHHHHHH
Q 022768          262 IHEDFMKAVRK  272 (292)
Q Consensus       262 ~~~~~~~a~~~  272 (292)
                      ..+++.+++..
T Consensus       253 ~~~~~~~~l~~  263 (272)
T 1d2n_A          253 RVRKFLALLRE  263 (272)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            44455554443

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.81  E-value=1.7e-19  Score=155.46  Aligned_cols=160  Identities=8%  Similarity=0.084  Sum_probs=118.5

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEEeccchh
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVSSAII  103 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~~~~~~~  103 (292)
                      |.|++++.+.+..++...+..         ..+.+++|+||||||||++++.+++++          ...+++++|..+.
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~---------~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~   92 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMS---------SQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELA   92 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHT---------TCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC
T ss_pred             cCCHHHHHHHHHHHHHHHhcC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccC
Confidence            889999999999888765332         567889999999999999999999988          3457888876643


Q ss_pred             ccc----------------cChHHHHHHHHHHHh--hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          104 DKY----------------IGESARLIREMFGYA--RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       104 ~~~----------------~~~~~~~~~~~~~~~--~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      +..                .+.....+...|...  ....+.|++|||+|.+.             .+..|..+++... 
T Consensus        93 t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~-------------~q~~L~~l~~~~~-  158 (318)
T 3te6_A           93 GMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL-------------SEKILQYFEKWIS-  158 (318)
T ss_dssp             --HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC-------------CTHHHHHHHHHHH-
T ss_pred             CHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh-------------cchHHHHHHhccc-
Confidence            321                122345566677664  33457899999999993             2356666666433 


Q ss_pred             CCCCCCeEEEEEeCCCCC----CChhhcCCCCcc-eEEEccCCCHHHHHHHHHHHHcCc
Q 022768          166 FDQLGKVKMIMATNRPDV----LDPALLRPGRLD-RKIEIPLPNEQSRMEILKIHAAGI  219 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~~----l~~~l~~~~r~~-~~i~l~~p~~~~r~~i~~~~~~~~  219 (292)
                       ....++.+|+++|..+.    +++++++  ||. ..+.|++++.++..+|++.++...
T Consensus       159 -~~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~~~  214 (318)
T 3te6_A          159 -SKNSKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLKSL  214 (318)
T ss_dssp             -CSSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             -ccCCcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHHhh
Confidence             34468999999998764    3445566  776 578999999999999999888753

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=99.80  E-value=2e-19  Score=166.96  Aligned_cols=225  Identities=22%  Similarity=0.288  Sum_probs=142.2

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc------
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID------  104 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~------  104 (292)
                      ..+++|++++++.+.+++.....      .... ++.+++|+||||+|||+++++++..++.++..+++.....      
T Consensus        80 ~~di~G~~~vk~~i~~~~~l~~~------~~~~-~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~g  152 (543)
T 3m6a_A           80 DEEHHGLEKVKERILEYLAVQKL------TKSL-KGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRG  152 (543)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHHHH------SSSC-CSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC---------
T ss_pred             HHHhccHHHHHHHHHHHHHHHHh------cccC-CCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhhh
Confidence            45699999999999887654210      1112 5778999999999999999999999999999998876543      


Q ss_pred             ---cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh--CC--------CCCCC
Q 022768          105 ---KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD--GF--------DQLGK  171 (292)
Q Consensus       105 ---~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~--~~--------~~~~~  171 (292)
                         .+.+.....+...|..+.... +++||||+|.+....       ....+..|+++++...  .+        ....+
T Consensus       153 ~~~~~ig~~~~~~~~~~~~a~~~~-~vl~lDEid~l~~~~-------~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~  224 (543)
T 3m6a_A          153 HRRTYVGAMPGRIIQGMKKAGKLN-PVFLLDEIDKMSSDF-------RGDPSSAMLEVLDPEQNSSFSDHYIEETFDLSK  224 (543)
T ss_dssp             -----------CHHHHHHTTCSSS-EEEEEEESSSCC----------------CCGGGTCTTTTTBCCCSSSCCCCBCSS
T ss_pred             HHHHHhccCchHHHHHHHHhhccC-CEEEEhhhhhhhhhh-------ccCHHHHHHHHHhhhhcceeecccCCeeecccc
Confidence               233333344445555554444 499999999995332       1113344444443211  00        11146


Q ss_pred             eEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcC-----ccC---CCCCCHHHHHH----HcCCCCH
Q 022768          172 VKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAG-----IAK---HGEIDYEAVVK----LAEGFNG  239 (292)
Q Consensus       172 ~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~-----~~~---~~~~~~~~l~~----~~~g~~~  239 (292)
                      +++|+|+|.++.+++++++  || ..+.++.|+.+++..|++.++..     ...   .-.++.+.+..    .+...+.
T Consensus       225 v~iI~ttN~~~~l~~aL~~--R~-~vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~~~~~~~~v  301 (543)
T 3m6a_A          225 VLFIATANNLATIPGPLRD--RM-EIINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIRYYTREAGV  301 (543)
T ss_dssp             CEEEEECSSTTTSCHHHHH--HE-EEEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHHHHCCCSSS
T ss_pred             eEEEeccCccccCCHHHHh--hc-ceeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHHhCChhhch
Confidence            8999999999999999999  99 57899999999999999987621     111   11223333333    2322356


Q ss_pred             HHHHHHHHHHHHHHHHh------cCCcccHHHHHHHHHHH
Q 022768          240 ADLRNVCTEAGMSAIRA------ERDYVIHEDFMKAVRKL  273 (292)
Q Consensus       240 ~di~~l~~~a~~~a~~~------~~~~i~~~~~~~a~~~~  273 (292)
                      ++++..+..+...+..+      ....|+.+++.+++..-
T Consensus       302 R~L~~~i~~~~~~aa~~~~~~~~~~~~It~~~l~~~Lg~~  341 (543)
T 3m6a_A          302 RSLERQLAAICRKAAKAIVAEERKRITVTEKNLQDFIGKR  341 (543)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCCSCCEECTTTTHHHHCSC
T ss_pred             hHHHHHHHHHHHHHHHHHHhcCCcceecCHHHHHHHhCCc
Confidence            67766666655555443      23368999998887543

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.79  E-value=3.3e-18  Score=150.89  Aligned_cols=196  Identities=16%  Similarity=0.207  Sum_probs=137.3

Q ss_pred             hcccCCCCCccccccccHHHHHHHHHHh-hcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc------
Q 022768           21 MLHEDPGNVSYSAVGGLSDQIRELRESI-ELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN------   93 (292)
Q Consensus        21 ~~~~~~~~~~~~~l~g~~~~~~~l~~~l-~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~------   93 (292)
                      +..+.++|.+|++++|++++++.+...+ ..             ....+++|+||+|+||||+++.+++.+..+      
T Consensus         3 ~w~~kyrP~~~~~~vg~~~~~~~l~~~~~~~-------------~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~   69 (354)
T 1sxj_E            3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQP-------------RDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLK   69 (354)
T ss_dssp             -CTTTTCCCSGGGCCSCHHHHHHHHTTTTCT-------------TCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC--
T ss_pred             cchhccCCCCHHHhcCCHHHHHHHHHHHhhC-------------CCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEE
Confidence            3456789999999999999999998876 32             223349999999999999999999965211      


Q ss_pred             -----------------------EEEEeccchhccccChHHHHHHHHHHHhh--------------hCCCEEEEEccccc
Q 022768           94 -----------------------FLKVVSSAIIDKYIGESARLIREMFGYAR--------------DHQPCIIFMDEIDA  136 (292)
Q Consensus        94 -----------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~il~lDe~d~  136 (292)
                                             ++.++.....   ... ...++..+....              ...|.+++|||++.
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~-~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~  145 (354)
T 1sxj_E           70 IDVRQFVTASNRKLELNVVSSPYHLEITPSDMG---NND-RIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANS  145 (354)
T ss_dssp             ----------------CCEECSSEEEECCC-------CC-HHHHHHHHHHHTTTTC------------CCEEEEEECTTS
T ss_pred             ecceeecccccccceeeeecccceEEecHhhcC---Ccc-hHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccc
Confidence                                   1222211110   000 012233333221              23577999999999


Q ss_pred             ccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHH
Q 022768          137 IGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHA  216 (292)
Q Consensus       137 l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~  216 (292)
                      +           +...+..+...++...     .++.+|++++.++.+.+.+++  |+ ..+.|++|+.++..++++..+
T Consensus       146 L-----------~~~~~~~L~~~le~~~-----~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~~~~~l~~~~  206 (354)
T 1sxj_E          146 L-----------TKDAQAALRRTMEKYS-----KNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVV  206 (354)
T ss_dssp             S-----------CHHHHHHHHHHHHHST-----TTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHH
T ss_pred             c-----------CHHHHHHHHHHHHhhc-----CCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcCHHHHHHHHHHHH
Confidence            7           6777788888777632     468899999999999999998  77 889999999999999999887


Q ss_pred             cCccCC-C-CCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          217 AGIAKH-G-EIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       217 ~~~~~~-~-~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      ...... . +..+..++..+.| +.+++..+++.+...+
T Consensus       207 ~~~~~~~~~~~~l~~i~~~~~G-~~r~a~~~l~~~~~~~  244 (354)
T 1sxj_E          207 TNERIQLETKDILKRIAQASNG-NLRVSLLMLESMALNN  244 (354)
T ss_dssp             HHHTCEECCSHHHHHHHHHHTT-CHHHHHHHHTHHHHTT
T ss_pred             HHcCCCCCcHHHHHHHHHHcCC-CHHHHHHHHHHHHHhC
Confidence            643332 2 3346778888877 7778888887766543

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.78  E-value=5.8e-19  Score=141.59  Aligned_cols=163  Identities=24%  Similarity=0.384  Sum_probs=117.1

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCc
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DAN   93 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~   93 (292)
                      ..+++.+|++++|.++.++++.+.+..             ..+.+++|+||+|+|||++++.+++.+          +.+
T Consensus        14 ~~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~   80 (195)
T 1jbk_A           14 ERAEQGKLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRR   80 (195)
T ss_dssp             HHHHTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCE
T ss_pred             HHHhhccccccccchHHHHHHHHHHhc-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCc
Confidence            345567899999999999999888754             335689999999999999999999986          677


Q ss_pred             EEEEeccchhc--cccChHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCC
Q 022768           94 FLKVVSSAIID--KYIGESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG  170 (292)
Q Consensus        94 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~  170 (292)
                      ++.+++..+..  ...+.....+..++..+.. ..+.+|+|||+|.+.......   ........+..++..       .
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~---~~~~~~~~l~~~~~~-------~  150 (195)
T 1jbk_A           81 VLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKAD---GAMDAGNMLKPALAR-------G  150 (195)
T ss_dssp             EEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT---------CCCCHHHHHHHHHT-------T
T ss_pred             EEEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCccc---chHHHHHHHHHhhcc-------C
Confidence            88888776652  3334455566666665543 457899999999995432111   111223344444432       4


Q ss_pred             CeEEEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHH
Q 022768          171 KVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEIL  212 (292)
Q Consensus       171 ~~~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~  212 (292)
                      ++.+|++++.+.     .+++.+.+  ||. .+.+++|+.+++.+++
T Consensus       151 ~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          151 ELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             SCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             CeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHHh
Confidence            677888888765     68899998  885 6899999999998775

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=99.78  E-value=1e-17  Score=148.36  Aligned_cols=236  Identities=21%  Similarity=0.258  Sum_probs=150.8

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHh-cC-CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc-ccCh
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLR-VG-IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-YIGE  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~-~~-~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~-~~~~  109 (292)
                      .++|++++++.+...+...+........ .+ ..++.+++|+||||||||++|+++|+.++.+++.+++..+... +.|.
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l~~~~~~g~   95 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGE   95 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHTTCHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHhcccccccc
Confidence            3799999999999988533211110000 01 1256789999999999999999999999999999999887643 4444


Q ss_pred             H-HHHHHHHHHHh----hhCCCEEEEEcccccccCCcCCCCCcch---HHHHHHHHHHHHHhh----------------C
Q 022768          110 S-ARLIREMFGYA----RDHQPCIIFMDEIDAIGGRRFSEGTSAD---REIQRTLMELLNQLD----------------G  165 (292)
Q Consensus       110 ~-~~~~~~~~~~~----~~~~~~il~lDe~d~l~~~~~~~~~~~~---~~~~~~l~~~l~~~~----------------~  165 (292)
                      . ...+..++..+    ....+++|||||+|.+...+.......+   ...+..|+.+++...                -
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~  175 (363)
T 3hws_A           96 DVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFL  175 (363)
T ss_dssp             HHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC----------------CC
T ss_pred             cHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccCccccccCCCceE
Confidence            3 44455666554    2334689999999999765443322222   236666777666110                0


Q ss_pred             CCCCCCeEEEEEeCCC----------CC-----------------------------------CChhhcCCCCcceEEEc
Q 022768          166 FDQLGKVKMIMATNRP----------DV-----------------------------------LDPALLRPGRLDRKIEI  200 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~----------~~-----------------------------------l~~~l~~~~r~~~~i~l  200 (292)
                      .-...++.+|++++..          ..                                   +.+.+.+  ||+..+.|
T Consensus       176 ~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~--R~~~~~~~  253 (363)
T 3hws_A          176 QVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG--RLPVVATL  253 (363)
T ss_dssp             CCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT--TCCEEEEC
T ss_pred             EEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc--ccCeeeec
Confidence            1122355566666532          11                                   5777887  99999999


Q ss_pred             cCCCHHHHHHHHHH----HHc-------CccCCCCCC---HHHHHH--HcCCCCHHHHHHHHHHHHHHHHHhcCC-----
Q 022768          201 PLPNEQSRMEILKI----HAA-------GIAKHGEID---YEAVVK--LAEGFNGADLRNVCTEAGMSAIRAERD-----  259 (292)
Q Consensus       201 ~~p~~~~r~~i~~~----~~~-------~~~~~~~~~---~~~l~~--~~~g~~~~di~~l~~~a~~~a~~~~~~-----  259 (292)
                      .+|+.+++.+|+..    +..       .....-.++   .+.|+.  ....++.++++.+++.+...+..+...     
T Consensus       254 ~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie~~~~~~l~~~~~~~~~~  333 (363)
T 3hws_A          254 NELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTMYDLPSMEDVE  333 (363)
T ss_dssp             CCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHHHHHHHHHHSTTTCCCSE
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHHHHHHHHHHhcccccCCc
Confidence            99999999998875    221       111111223   334443  334557789999999999888776422     


Q ss_pred             --cccHHHHHHHH
Q 022768          260 --YVIHEDFMKAV  270 (292)
Q Consensus       260 --~i~~~~~~~a~  270 (292)
                        .|+.+++.+.+
T Consensus       334 ~~~I~~~~v~~~~  346 (363)
T 3hws_A          334 KVVIDESVIDGQS  346 (363)
T ss_dssp             EEECHHHHTTCCS
T ss_pred             eeEEcHHHHhCcC
Confidence              46666665543

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.77  E-value=1.3e-17  Score=161.26  Aligned_cols=224  Identities=22%  Similarity=0.292  Sum_probs=159.8

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEE
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFL   95 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~   95 (292)
                      ..+-+|++++|+++.++++.+.+..             ....+++|+||||+|||++++.++..+          +..++
T Consensus       180 ~~~~~~d~~iGr~~~i~~l~~~l~~-------------~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~  246 (758)
T 1r6b_X          180 ARVGGIDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIY  246 (758)
T ss_dssp             HHTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEE
T ss_pred             HhcCCCCCccCCHHHHHHHHHHHhc-------------cCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEE
Confidence            3456889999999999999888754             346789999999999999999999987          55667


Q ss_pred             EEeccchh--ccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           96 KVVSSAII--DKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        96 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      .++...+.  ..+.+.....++.++..+....+++|||||+|.+.+.....  .......    .++   ...-..+.+.
T Consensus       247 ~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~--~~~~~~~----~~L---~~~l~~~~~~  317 (758)
T 1r6b_X          247 SLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAAS--GGQVDAA----NLI---KPLLSSGKIR  317 (758)
T ss_dssp             ECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSS--SCHHHHH----HHH---SSCSSSCCCE
T ss_pred             EEcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCC--cchHHHH----HHH---HHHHhCCCeE
Confidence            77666655  34667788889999998888778999999999997543221  1122222    222   2223346788


Q ss_pred             EEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccC--CCCCC---HHHHHHHcC-----CCC
Q 022768          174 MIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAK--HGEID---YEAVVKLAE-----GFN  238 (292)
Q Consensus       174 vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~--~~~~~---~~~l~~~~~-----g~~  238 (292)
                      +|++++.++     .+++++.+  ||. .+.++.|+.+++.++++.+...+..  .-.++   +..++..+.     .+.
T Consensus       318 ~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~~~s~~~i~~~~l  394 (758)
T 1r6b_X          318 VIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHL  394 (758)
T ss_dssp             EEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCT
T ss_pred             EEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhcccccC
Confidence            899988642     46788888  895 7999999999999999977653211  11122   333444433     346


Q ss_pred             HHHHHHHHHHHHHHHHH----hcCCcccHHHHHHHHHHHh
Q 022768          239 GADLRNVCTEAGMSAIR----AERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~----~~~~~i~~~~~~~a~~~~~  274 (292)
                      +..+..++++|...+..    .....|+.+++.+++..+.
T Consensus       395 p~~~i~lld~a~~~~~~~~~~~~~~~v~~~di~~~~~~~~  434 (758)
T 1r6b_X          395 PDKAIDVIDEAGARARLMPVSKRKKTVNVADIESVVARIA  434 (758)
T ss_dssp             THHHHHHHHHHHHHHHHSSSCCCCCSCCHHHHHHHHHHHS
T ss_pred             chHHHHHHHHHHHHHhcccccccCCccCHHHHHHHHHHhc
Confidence            77889999998876655    2345799999999998865

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.77  E-value=4.2e-18  Score=149.56  Aligned_cols=213  Identities=19%  Similarity=0.224  Sum_probs=142.6

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cE
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NF   94 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~   94 (292)
                      .+....++|.+|++++|++++++.|...+..-            . ..+++|+||+|+||||+++++++.+..     .+
T Consensus        13 ~~~~~k~rp~~~~~~~g~~~~~~~L~~~i~~g------------~-~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~   79 (340)
T 1sxj_C           13 LPWVEKYRPETLDEVYGQNEVITTVRKFVDEG------------K-LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMV   79 (340)
T ss_dssp             CCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTT------------C-CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHE
T ss_pred             CchHHHhCCCcHHHhcCcHHHHHHHHHHHhcC------------C-CceEEEECCCCCCHHHHHHHHHHHHcCCCccceE
Confidence            34556789999999999999999998887641            1 224999999999999999999998743     25


Q ss_pred             EEEeccchhccccChHHHHHHHHHHHhh------hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGYAR------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                      ..++.....+      ...++..+....      ...+.+++|||+|.+           ....+..|..+++..     
T Consensus        80 ~~~~~~~~~~------~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l-----------~~~~~~~L~~~le~~-----  137 (340)
T 1sxj_C           80 LELNASDDRG------IDVVRNQIKDFASTRQIFSKGFKLIILDEADAM-----------TNAAQNALRRVIERY-----  137 (340)
T ss_dssp             EEECTTSCCS------HHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGS-----------CHHHHHHHHHHHHHT-----
T ss_pred             EEEcCccccc------HHHHHHHHHHHHhhcccCCCCceEEEEeCCCCC-----------CHHHHHHHHHHHhcC-----
Confidence            5555443211      122222222211      123689999999998           566677777777653     


Q ss_pred             CCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHH
Q 022768          169 LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCT  247 (292)
Q Consensus       169 ~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~  247 (292)
                      ...+.+|+++|.+..+.+.+++  |+ ..+.|++++.++..+.+...+...... .+.....++..+.| ..+.+..+++
T Consensus       138 ~~~~~~il~~n~~~~i~~~i~s--R~-~~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G-~~r~~~~~l~  213 (340)
T 1sxj_C          138 TKNTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNG-DMRRVLNVLQ  213 (340)
T ss_dssp             TTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT-CHHHHHHHTT
T ss_pred             CCCeEEEEEecCccccchhHHh--hc-eeEeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHH
Confidence            2467788889999999999999  77 578999999999998888877432221 12234556666766 5555555554


Q ss_pred             HHHHHHHHhcCCcccHHHHHHHHH
Q 022768          248 EAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       248 ~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      .+...+...+...|+.+++.+++.
T Consensus       214 ~~~~~~~~~~~~~it~~~v~~~~~  237 (340)
T 1sxj_C          214 SCKATLDNPDEDEISDDVIYECCG  237 (340)
T ss_dssp             TTTTTTCSSSCCCBCHHHHHHHTT
T ss_pred             HHHHhcCCcccccccHHHHHHHhC
Confidence            443222111122577777765544

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.76  E-value=3.5e-18  Score=156.15  Aligned_cols=210  Identities=24%  Similarity=0.314  Sum_probs=141.2

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCc
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DAN   93 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~   93 (292)
                      ....+.++++++|.++.++++...+..             ....++||+||||+|||++++.+++.+          +.+
T Consensus       172 ~~~r~~~ld~iiGr~~~i~~l~~~l~r-------------~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~  238 (468)
T 3pxg_A          172 AIAKEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKR  238 (468)
T ss_dssp             HHTTSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCC
T ss_pred             HHHhcCCCCCccCcHHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCe
Confidence            356677899999999999999998765             235689999999999999999999997          677


Q ss_pred             EEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeE
Q 022768           94 FLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVK  173 (292)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~  173 (292)
                      ++.+++.   ..+.|.....++.++..+....++|||||    .           ....+..|...+       ..+.+.
T Consensus       239 ~~~l~~~---~~~~g~~e~~~~~~~~~~~~~~~~iLfiD----~-----------~~~a~~~L~~~L-------~~g~v~  293 (468)
T 3pxg_A          239 VMTLDMG---TKYRGEFEDRLKKVMDEIRQAGNIILFID----A-----------AIDASNILKPSL-------ARGELQ  293 (468)
T ss_dssp             EECC-------------CTTHHHHHHHHHTCCCCEEEEC----C-------------------CCCT-------TSSSCE
T ss_pred             EEEeeCC---ccccchHHHHHHHHHHHHHhcCCeEEEEe----C-----------chhHHHHHHHhh-------cCCCEE
Confidence            8888776   44556666677888888888888999999    1           122222222222       235788


Q ss_pred             EEEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC--CCCC---HHHHHHHcCC-----CC
Q 022768          174 MIMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH--GEID---YEAVVKLAEG-----FN  238 (292)
Q Consensus       174 vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~--~~~~---~~~l~~~~~g-----~~  238 (292)
                      +|+++|..+     .+++++++  ||. .+.|+.|+.+++..|++.+...+...  ..++   +..++..+.+     +.
T Consensus       294 vI~at~~~e~~~~~~~~~al~~--Rf~-~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~~l  370 (468)
T 3pxg_A          294 CIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFL  370 (468)
T ss_dssp             EEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCT
T ss_pred             EEecCCHHHHHHHhhcCHHHHH--hCc-cceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccCcC
Confidence            999999876     68899998  995 69999999999999999887653222  2222   3334444433     34


Q ss_pred             HHHHHHHHHHHHHHHHHhcCC-cccHHHHHHHHHHHh
Q 022768          239 GADLRNVCTEAGMSAIRAERD-YVIHEDFMKAVRKLN  274 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~~~~~-~i~~~~~~~a~~~~~  274 (292)
                      +..+..+++.|...+..+... ......+.+.+..+.
T Consensus       371 p~~ai~ll~~a~~~~~~~~~~~p~~i~~l~~~i~~l~  407 (468)
T 3pxg_A          371 PDKAIDLIDEAGSKVRLRSFTTPPNLKELEQKLDEVR  407 (468)
T ss_dssp             THHHHHHHHHHHHHHHHHTTSCCSSTHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHhccCCCchHHHHHHHHHHHHH
Confidence            668889998888766655432 233344444444443

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.76  E-value=1.4e-17  Score=144.20  Aligned_cols=206  Identities=21%  Similarity=0.334  Sum_probs=140.0

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccC
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIG  108 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~  108 (292)
                      .+++|++.+++.+...+......    ......+..+++|+||||||||++|+++++.+   +.+++.+++..+..... 
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~----~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~-   91 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAG----LKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHA-   91 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHT----CSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTH-
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcC----CCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeeccccccccc-
Confidence            45789999999999988653110    00011234579999999999999999999988   45688888876543210 


Q ss_pred             hHHHHH------------HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------CCC
Q 022768          109 ESARLI------------REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------QLG  170 (292)
Q Consensus       109 ~~~~~~------------~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~~~  170 (292)
                       ....+            ..+........+++|+|||+|.+           ....+..|..+++......      ...
T Consensus        92 -~~~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l-----------~~~~~~~Ll~~le~~~~~~~~~~~~~~~  159 (311)
T 4fcw_A           92 -VSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKA-----------HPDVFNILLQMLDDGRLTDSHGRTVDFR  159 (311)
T ss_dssp             -HHHHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGS-----------CHHHHHHHHHHHHHSEEECTTSCEEECT
T ss_pred             -HHHhcCCCCccccccccchHHHHHHhCCCeEEEEeChhhc-----------CHHHHHHHHHHHhcCEEEcCCCCEEECC
Confidence             01100            12223333455689999999999           7788888888887643111      113


Q ss_pred             CeEEEEEeCC--------------------------CCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc----
Q 022768          171 KVKMIMATNR--------------------------PDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA----  220 (292)
Q Consensus       171 ~~~vi~t~~~--------------------------~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~----  220 (292)
                      ++++|+|+|.                          ...+++.+.+  ||+..+.+++|+.+++..|++.++....    
T Consensus       160 ~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~~~  237 (311)
T 4fcw_A          160 NTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQMSYLRARLA  237 (311)
T ss_dssp             TEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHTHHHHHHHH
T ss_pred             CcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            6779999998                          3357778887  9999999999999999999998775421    


Q ss_pred             ---CCCCCC---HHHHHHHcC--CCCHHHHHHHHHHHHHHHHHh
Q 022768          221 ---KHGEID---YEAVVKLAE--GFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       221 ---~~~~~~---~~~l~~~~~--g~~~~di~~l~~~a~~~a~~~  256 (292)
                         ....++   +..|+...-  ..+.++++.+++.+...+..+
T Consensus       238 ~~~~~~~~~~~~~~~l~~~~~~~~gn~R~L~~~i~~~~~~~~~~  281 (311)
T 4fcw_A          238 EKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQ  281 (311)
T ss_dssp             TTTCEEEECHHHHHHHHHHSCBTTTBTTTHHHHHHHHTHHHHHH
T ss_pred             hCCcEEEeCHHHHHHHHHhCCCccCCchhHHHHHHHHHHHHHHH
Confidence               112233   344444433  457888999998887766543

>1um8_A ATP-dependent CLP protease ATP-binding subunit CL; CLPP binding loop, chaperone; HET: ADP; 2.60A {Helicobacter pylori} SCOP: c.37.1.20

Probab=99.75  E-value=2.1e-17  Score=147.09  Aligned_cols=236  Identities=17%  Similarity=0.219  Sum_probs=141.5

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHH-----------------hcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFL-----------------RVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~-----------------~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      .++|++++++.|...+...+.......                 .-...+..+++|+||||||||++|+++++.++.+++
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l~~~~~  101 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIA  101 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEE
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            489999999999988743222211100                 011234678999999999999999999999999999


Q ss_pred             EEeccchhc-cccChH-HHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCc---chHHHHHHHHHHHHHhh-C
Q 022768           96 KVVSSAIID-KYIGES-ARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTS---ADREIQRTLMELLNQLD-G  165 (292)
Q Consensus        96 ~~~~~~~~~-~~~~~~-~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~---~~~~~~~~l~~~l~~~~-~  165 (292)
                      .+++..+.. .+.+.. ...+...+....    ...+++|+|||+|.+...+......   .....+..|+.+++... .
T Consensus       102 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~  181 (376)
T 1um8_A          102 ISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVN  181 (376)
T ss_dssp             EEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHHHHHHHCCEEC
T ss_pred             EecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCceecccchHHHHHHHHHHhhcccee
Confidence            999887642 222322 233444444322    2356899999999996542221111   11236677777776321 0


Q ss_pred             C---------------CCCCCeEEEEEeCC-----------------------------------------CCCCChhhc
Q 022768          166 F---------------DQLGKVKMIMATNR-----------------------------------------PDVLDPALL  189 (292)
Q Consensus       166 ~---------------~~~~~~~vi~t~~~-----------------------------------------~~~l~~~l~  189 (292)
                      +               ....++.+|+++|.                                         ...+.+.+.
T Consensus       182 ~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~~p~l~  261 (376)
T 1um8_A          182 IPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELI  261 (376)
T ss_dssp             ---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHH
T ss_pred             cccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhcCCChHHh
Confidence            0               01135567777762                                         012456777


Q ss_pred             CCCCcceEEEccCCCHHHHHHHHHH----HHc-------CccCCCCCC---HHHHHHHcC--CCCHHHHHHHHHHHHHHH
Q 022768          190 RPGRLDRKIEIPLPNEQSRMEILKI----HAA-------GIAKHGEID---YEAVVKLAE--GFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       190 ~~~r~~~~i~l~~p~~~~r~~i~~~----~~~-------~~~~~~~~~---~~~l~~~~~--g~~~~di~~l~~~a~~~a  253 (292)
                      +  |++..+.|++++.++...++..    +..       .....-.++   +..++....  ..+.+.++.+++.+...+
T Consensus       262 ~--R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le~~~~~~  339 (376)
T 1um8_A          262 G--RLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIEDFCLDI  339 (376)
T ss_dssp             T--TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHHHHHHH
T ss_pred             c--CCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHHHHHHHHHHHHHH
Confidence            7  8888899999999999998862    111       011111123   334444322  247889999999998877


Q ss_pred             HHhcCC------cccHHHHHHHH
Q 022768          254 IRAERD------YVIHEDFMKAV  270 (292)
Q Consensus       254 ~~~~~~------~i~~~~~~~a~  270 (292)
                      +.+...      .|+.+++.++.
T Consensus       340 ~~~~~~~~~~~~~i~~~~v~~~~  362 (376)
T 1um8_A          340 MFDLPKLKGSEVRITKDCVLKQA  362 (376)
T ss_dssp             HHTGGGGTTSEEEECHHHHTTSS
T ss_pred             HhhccCCCCCEEEEeHHHhcCCC
Confidence            765332      58888887644

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=99.74  E-value=3.8e-17  Score=146.52  Aligned_cols=242  Identities=23%  Similarity=0.283  Sum_probs=155.2

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCC-CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc-cccCh
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGI-KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID-KYIGE  109 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~-~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~-~~~~~  109 (292)
                      +.|+|++++++.|..++..++.....+..++. .++.+++|+||||+|||++++++|+.++.+++.+++..+.. .+.|.
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~~~~~g~vG~   94 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   94 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC----CCC
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchhhcccceeec
Confidence            36899999999999998766444333332222 24678999999999999999999999999999999877765 35553


Q ss_pred             -HHHHHHHHHHHh-------------------------------------------------------------------
Q 022768          110 -SARLIREMFGYA-------------------------------------------------------------------  121 (292)
Q Consensus       110 -~~~~~~~~~~~~-------------------------------------------------------------------  121 (292)
                       ....++.+|..+                                                                   
T Consensus        95 d~e~~lr~lf~~a~~~~~~De~d~~~~~~~~~~e~rvl~~LL~~~dg~~~~~~v~a~~TN~~~~ld~aL~rggr~D~~i~  174 (444)
T 1g41_A           95 EVDSIIRDLTDSAMKLVRQQEIAKNRARAEDVAEERILDALLPPAKNQWGEVENHDSHSSTRQAFRKKLREGQLDDKEIE  174 (444)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHSCC------------------------------------------------------
T ss_pred             cHHHHHHHHHHHHHhcchhhhhhhhhccchhhHHHHHHHHHHHHhhccccccccccccccCHHHHHHHHHcCCCcceEEE
Confidence             333333332211                                                                   


Q ss_pred             ------------------------------------------------------------------------hhCCCEEE
Q 022768          122 ------------------------------------------------------------------------RDHQPCII  129 (292)
Q Consensus       122 ------------------------------------------------------------------------~~~~~~il  129 (292)
                                                                                              +....+++
T Consensus       175 i~lP~~~~~~~ei~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~~a~~~l~~~e~~~l~~~~~~~~~ai~~ae~~~il  254 (444)
T 1g41_A          175 IDVSAGVSMGVEIMAPPGMEEMTNQLQSLFQNLGSDKTKKRKMKIKDALKALIDDEAAKLINPEELKQKAIDAVEQNGIV  254 (444)
T ss_dssp             ---------------------------------------------------CCGGGSCSSCCHHHHHHHHHHHHHHHCEE
T ss_pred             EcCCCCccchhhhhcCCChHHHHHHHHHHHHhhcCCCCcceeeeHHHHHHHHHHHHHHHccCHHHHHHHHHHHhccCCee
Confidence                                                                                    00123589


Q ss_pred             EEcccccccCCcCCCCCc-chHHHHHHHHHHHHHhhC-----CCCCCCeEEEEEe----CCCCCCChhhcCCCCcceEEE
Q 022768          130 FMDEIDAIGGRRFSEGTS-ADREIQRTLMELLNQLDG-----FDQLGKVKMIMAT----NRPDVLDPALLRPGRLDRKIE  199 (292)
Q Consensus       130 ~lDe~d~l~~~~~~~~~~-~~~~~~~~l~~~l~~~~~-----~~~~~~~~vi~t~----~~~~~l~~~l~~~~r~~~~i~  199 (292)
                      ++||+|.+..+......+ .....|.+|+.+++.-..     .....++++|+|+    +.+..+.+.+++  ||...+.
T Consensus       255 ~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlipel~~--R~~i~i~  332 (444)
T 1g41_A          255 FIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQG--RLPIRVE  332 (444)
T ss_dssp             EEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCHHHHT--TCCEEEE
T ss_pred             eHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcchHHhc--ccceeee
Confidence            999999997654322222 223467788887763210     0234578889887    234446688998  9999999


Q ss_pred             ccCCCHHHHHHHHH--------HH---HcCccCC---CCCCHHHHHH-------HcCCCCHHHHHHHHHHHHHHHHHhcC
Q 022768          200 IPLPNEQSRMEILK--------IH---AAGIAKH---GEIDYEAVVK-------LAEGFNGADLRNVCTEAGMSAIRAER  258 (292)
Q Consensus       200 l~~p~~~~r~~i~~--------~~---~~~~~~~---~~~~~~~l~~-------~~~g~~~~di~~l~~~a~~~a~~~~~  258 (292)
                      |+.++.++..+|+.        .+   +......   .+-.+..++.       .+.+...|.++.++..+...+..+..
T Consensus       333 l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie~~~~~~~~~~~  412 (444)
T 1g41_A          333 LTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERLMDKISFSAS  412 (444)
T ss_dssp             CCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHHHHHHHHHHHGG
T ss_pred             CCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHHHHHHHHHhhcc
Confidence            99999999999883        11   1111111   1112334443       23556678888777777766554421


Q ss_pred             ------CcccHHHHHHHHHHHhh
Q 022768          259 ------DYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       259 ------~~i~~~~~~~a~~~~~~  275 (292)
                            -.|+.+++.+.+.....
T Consensus       413 ~~~~~~~~i~~~~v~~~l~~~~~  435 (444)
T 1g41_A          413 DMNGQTVNIDAAYVADALGEVVE  435 (444)
T ss_dssp             GCTTCEEEECHHHHHHHHTTTTT
T ss_pred             ccCCCeEEEeHHHHHHhcCcccc
Confidence                  25888888877655443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.73  E-value=1.7e-17  Score=160.21  Aligned_cols=192  Identities=27%  Similarity=0.344  Sum_probs=136.3

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcE
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANF   94 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~   94 (292)
                      ...+-++++++|.++.++++...+..             ....++||+||||||||++|+.+|+.+          +.++
T Consensus       173 ~~~~~~ld~iiG~~~~i~~l~~~l~~-------------~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~  239 (758)
T 3pxi_A          173 IAKEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRV  239 (758)
T ss_dssp             HTTSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCE
T ss_pred             HHhhCCCCCccCchHHHHHHHHHHhC-------------CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeE
Confidence            45667899999999999999998765             345679999999999999999999997          7778


Q ss_pred             EEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           95 LKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      +.+++   ...+.|+.+..++.++..+....++|||||    .           ....+..|...+       ..+.+.+
T Consensus       240 ~~~~~---g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD----~-----------~~~~~~~L~~~l-------~~~~v~~  294 (758)
T 3pxi_A          240 MTLDM---GTKYRGEFEDRLKKVMDEIRQAGNIILFID----A-----------AIDASNILKPSL-------ARGELQC  294 (758)
T ss_dssp             ECC-------------CTTHHHHHHHHHTCCCCEEEEC----C-------------------CCCT-------TSSSCEE
T ss_pred             EEecc---cccccchHHHHHHHHHHHHHhcCCEEEEEc----C-----------chhHHHHHHHHH-------hcCCEEE
Confidence            87776   344566777788889998888888999999    1           112222222222       2357889


Q ss_pred             EEEeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCC--CCC---HHHHHHHc-----CCCCH
Q 022768          175 IMATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG--EID---YEAVVKLA-----EGFNG  239 (292)
Q Consensus       175 i~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~--~~~---~~~l~~~~-----~g~~~  239 (292)
                      |++||..+     .+++++++  || ..+.++.|+.+++.+|++.+...+....  .++   +..++..+     .++.+
T Consensus       295 I~at~~~~~~~~~~~d~al~r--Rf-~~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i~~~~~p  371 (758)
T 3pxi_A          295 IGATTLDEYRKYIEKDAALER--RF-QPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLP  371 (758)
T ss_dssp             EEECCTTTTHHHHTTCSHHHH--SE-EEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTT
T ss_pred             EeCCChHHHHHHhhccHHHHh--hC-cEEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcccccCcCC
Confidence            99999887     68999999  99 6799999999999999998776543222  233   23333332     35677


Q ss_pred             HHHHHHHHHHHHHHHHhc
Q 022768          240 ADLRNVCTEAGMSAIRAE  257 (292)
Q Consensus       240 ~di~~l~~~a~~~a~~~~  257 (292)
                      .....++..|...+..+.
T Consensus       372 ~~ai~ll~~a~~~~~~~~  389 (758)
T 3pxi_A          372 DKAIDLIDEAGSKVRLRS  389 (758)
T ss_dssp             HHHHHHHHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHhhc
Confidence            889999999988776653

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.73  E-value=1.2e-16  Score=154.39  Aligned_cols=203  Identities=19%  Similarity=0.279  Sum_probs=141.0

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccC
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIG  108 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~  108 (292)
                      ..++|++++++.+...+.......    .....+..++||+||||||||++|+++++.+   +.+++.+++..+......
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~----~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~  566 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGL----KDPKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHST  566 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTC----SCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCC
T ss_pred             CcCcChHHHHHHHHHHHHHHHccc----CCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhccccccc
Confidence            468999999999999887642110    0001222369999999999999999999987   678999999998876554


Q ss_pred             hHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCCeEEEEEeCCCC
Q 022768          109 ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLGKVKMIMATNRPD  182 (292)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~~~vi~t~~~~~  182 (292)
                      .    ...+........+++|||||+|.+           ....+..|+.+++.....      ....++++|+|+|.+.
T Consensus       567 ~----~~~l~~~~~~~~~~vl~lDEi~~~-----------~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~  631 (758)
T 3pxi_A          567 S----GGQLTEKVRRKPYSVVLLDAIEKA-----------HPDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGA  631 (758)
T ss_dssp             C-------CHHHHHHCSSSEEEEECGGGS-----------CHHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSST
T ss_pred             c----cchhhHHHHhCCCeEEEEeCcccc-----------CHHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCCh
Confidence            4    112233344456689999999998           788888999988874311      1224678999999754


Q ss_pred             C------------CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc-------cCCCCCCHHHHHHHc-----CCCC
Q 022768          183 V------------LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI-------AKHGEIDYEAVVKLA-----EGFN  238 (292)
Q Consensus       183 ~------------l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~-------~~~~~~~~~~l~~~~-----~g~~  238 (292)
                      .            +.+++.+  ||+..+.|++|+.+++..|++.++...       ...-.++.+.+..+.     ..++
T Consensus       632 ~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~  709 (758)
T 3pxi_A          632 SEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEEGVDLEYG  709 (758)
T ss_dssp             TCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGGGCCTTTT
T ss_pred             hhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHhCCCCCCC
Confidence            4            6788888  998899999999999999998776532       112223444444432     2346


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 022768          239 GADLRNVCTEAGMSAIR  255 (292)
Q Consensus       239 ~~di~~l~~~a~~~a~~  255 (292)
                      .++++.+++.+...+..
T Consensus       710 ~R~L~~~i~~~v~~~l~  726 (758)
T 3pxi_A          710 ARPLRRAIQKHVEDRLS  726 (758)
T ss_dssp             TTTHHHHHHHHTHHHHH
T ss_pred             ChHHHHHHHHHHHHHHH
Confidence            77888888876655443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.72  E-value=6.7e-18  Score=134.82  Aligned_cols=156  Identities=24%  Similarity=0.379  Sum_probs=111.1

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCc
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DAN   93 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~   93 (292)
                      ..+.+.+|++++|.++.++.+.+.+..             ....+++|+||+|+|||++++.+++.+          +.+
T Consensus        14 ~~~~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~   80 (187)
T 2p65_A           14 ALARAGKLDPVIGRDTEIRRAIQILSR-------------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRK   80 (187)
T ss_dssp             HHHHTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCE
T ss_pred             HHHhccccchhhcchHHHHHHHHHHhC-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCe
Confidence            345566899999999999999888754             335689999999999999999999987          677


Q ss_pred             EEEEeccchhc--cccChHHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCC
Q 022768           94 FLKVVSSAIID--KYIGESARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG  170 (292)
Q Consensus        94 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~  170 (292)
                      ++.+++..+..  ...+.....+..++..+... .+.+|+|||+|.+......  ..........+..++..       .
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~--~~~~~~~~~~l~~~~~~-------~  151 (187)
T 2p65_A           81 LVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAV--AEGALDAGNILKPMLAR-------G  151 (187)
T ss_dssp             EEEECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSS--CTTSCCTHHHHHHHHHT-------T
T ss_pred             EEEEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhcccccc--cccchHHHHHHHHHHhc-------C
Confidence            78877766542  23344455566666666554 6789999999999643321  11112233344444432       4


Q ss_pred             CeEEEEEeCCCC-----CCChhhcCCCCcceEEEccCCC
Q 022768          171 KVKMIMATNRPD-----VLDPALLRPGRLDRKIEIPLPN  204 (292)
Q Consensus       171 ~~~vi~t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~  204 (292)
                      ++.+|++++.+.     .+++.+++  ||. .+.++.|+
T Consensus       152 ~~~ii~~~~~~~~~~~~~~~~~l~~--R~~-~i~i~~p~  187 (187)
T 2p65_A          152 ELRCIGATTVSEYRQFIEKDKALER--RFQ-QILVEQPS  187 (187)
T ss_dssp             CSCEEEEECHHHHHHHTTTCHHHHH--HEE-EEECCSCC
T ss_pred             CeeEEEecCHHHHHHHHhccHHHHH--hcC-cccCCCCC
Confidence            677899888764     58899998  896 58888885

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.72  E-value=1.3e-16  Score=155.94  Aligned_cols=206  Identities=22%  Similarity=0.303  Sum_probs=136.5

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcE
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANF   94 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~   94 (292)
                      ...+.+|++++|.++.++++...+..             ....+++|+||||+|||++++.+++.+          +.++
T Consensus       163 ~~r~~~ld~viGr~~~i~~l~~~l~~-------------~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~  229 (854)
T 1qvr_A          163 LAAEGKLDPVIGRDEEIRRVIQILLR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRI  229 (854)
T ss_dssp             HHHTTCSCCCCSCHHHHHHHHHHHHC-------------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEE
T ss_pred             HHhcCCCcccCCcHHHHHHHHHHHhc-------------CCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeE
Confidence            34567899999999999999988754             335679999999999999999999987          7788


Q ss_pred             EEEeccchh--ccccChHHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCC
Q 022768           95 LKVVSSAII--DKYIGESARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGK  171 (292)
Q Consensus        95 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~  171 (292)
                      +.+++..+.  ..+.+.....+..++..+... .+.||||||+|.+.+....   .........+..++..       +.
T Consensus       230 ~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~---~g~~~~~~~L~~~l~~-------~~  299 (854)
T 1qvr_A          230 VSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKA---EGAVDAGNMLKPALAR-------GE  299 (854)
T ss_dssp             EEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC----------------------HHHHHT-------TC
T ss_pred             EEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCc---cchHHHHHHHHHHHhC-------CC
Confidence            999887775  345677788888888888765 6789999999999643321   1112333344444432       46


Q ss_pred             eEEEEEeCCCC----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC--CCCC---HHHHHHHc-----CCC
Q 022768          172 VKMIMATNRPD----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH--GEID---YEAVVKLA-----EGF  237 (292)
Q Consensus       172 ~~vi~t~~~~~----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~--~~~~---~~~l~~~~-----~g~  237 (292)
                      +.+|++++.++    .+++++.+  ||.. +.++.|+.+++.+|++.++......  ..+.   +..++..+     ..+
T Consensus       300 i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~  376 (854)
T 1qvr_A          300 LRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERR  376 (854)
T ss_dssp             CCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSC
T ss_pred             eEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhccccc
Confidence            77888888654    47889998  8964 9999999999999998766533111  1122   23333333     456


Q ss_pred             CHHHHHHHHHHHHHHHHHh
Q 022768          238 NGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       238 ~~~di~~l~~~a~~~a~~~  256 (292)
                      .+..+..++.+|...+..+
T Consensus       377 lp~kai~lldea~a~~~~~  395 (854)
T 1qvr_A          377 LPDKAIDLIDEAAARLRMA  395 (854)
T ss_dssp             THHHHHHHHHHHHHHHHHT
T ss_pred             ChHHHHHHHHHHHHHHHhh
Confidence            7888999999988777655

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=99.72  E-value=6.7e-17  Score=136.94  Aligned_cols=205  Identities=20%  Similarity=0.236  Sum_probs=124.3

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEeccchhcc
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID---ANFLKVVSSAIIDK  105 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~~~~~~~  105 (292)
                      .+|++++|.+..++.+.+.+...           ...+.+++|+||||||||++|+++++.+.   .+++.+++..+...
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~-----------~~~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~~   71 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHL-----------APLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNEN   71 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHH-----------TTSCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCHH
T ss_pred             cccccceeCCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCChh
Confidence            47899999999999988877653           23357899999999999999999999875   68999998876321


Q ss_pred             ccChHHHHHHHHHH---------------HhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC----
Q 022768          106 YIGESARLIREMFG---------------YARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF----  166 (292)
Q Consensus       106 ~~~~~~~~~~~~~~---------------~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~----  166 (292)
                      ..   .   ..+|+               ......+++|+|||+|.+           ....+..|..+++...-.    
T Consensus        72 ~~---~---~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l-----------~~~~q~~Ll~~l~~~~~~~~g~  134 (265)
T 2bjv_A           72 LL---D---SELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATA-----------PMMVQEKLLRVIEYGELERVGG  134 (265)
T ss_dssp             HH---H---HHHHCCC---------CCCCHHHHTTTSEEEEESGGGS-----------CHHHHHHHHHHHHHCEECCCCC
T ss_pred             HH---H---HHhcCCcccccccccccccchhhhcCCcEEEEechHhc-----------CHHHHHHHHHHHHhCCeecCCC
Confidence            10   0   01111               011134579999999999           677788888888753200    


Q ss_pred             --CCCCCeEEEEEeCCC-------CCCChhhcCCCCcc-eEEEccCCCH--HHHHHHHHHHHcC----ccCC--CCCCHH
Q 022768          167 --DQLGKVKMIMATNRP-------DVLDPALLRPGRLD-RKIEIPLPNE--QSRMEILKIHAAG----IAKH--GEIDYE  228 (292)
Q Consensus       167 --~~~~~~~vi~t~~~~-------~~l~~~l~~~~r~~-~~i~l~~p~~--~~r~~i~~~~~~~----~~~~--~~~~~~  228 (292)
                        ....++.+|+|+|..       ..+.+.+.+  ||. ..+.+|+++.  ++...+++.++..    ....  ..++.+
T Consensus       135 ~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~--Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~~  212 (265)
T 2bjv_A          135 SQPLQVNVRLVCATNADLPAMVNEGTFRADLLD--ALAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTER  212 (265)
T ss_dssp             --CEECCCEEEEEESSCHHHHHHHTSSCHHHHH--HHCSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCHH
T ss_pred             cccccCCeEEEEecCcCHHHHHHcCCccHHHHH--hhcCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCHH
Confidence              012357899999874       246778877  774 3556666543  4445555554432    1211  135555


Q ss_pred             HHHHHc-CCC--CHHHHHHHHHHHHHHHHHhcCCcccHHHH
Q 022768          229 AVVKLA-EGF--NGADLRNVCTEAGMSAIRAERDYVIHEDF  266 (292)
Q Consensus       229 ~l~~~~-~g~--~~~di~~l~~~a~~~a~~~~~~~i~~~~~  266 (292)
                      .+..+. ..+  +.+++..+++.+...+   ....|+.+|+
T Consensus       213 a~~~L~~~~~~gn~reL~~~l~~~~~~~---~~~~i~~~~l  250 (265)
T 2bjv_A          213 ARETLLNYRWPGNIRELKNVVERSVYRH---GTSDYPLDDI  250 (265)
T ss_dssp             HHHHHHHSCCTTHHHHHHHHHHHHHHHH---CCSSSCBCCC
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHHhC---CCCcCcHHHc
Confidence            555443 222  5566777777766544   3345555544

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.72  E-value=1.8e-17  Score=151.59  Aligned_cols=210  Identities=17%  Similarity=0.179  Sum_probs=134.9

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEeccc-----hhc
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSSA-----IID  104 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~~-----~~~  104 (292)
                      ..++|.+++++.+..++..               +.++||+||||+|||++|+++++.++.  ++..+.+..     +.+
T Consensus        22 ~~ivGq~~~i~~l~~al~~---------------~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~~t~~dL~G   86 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAALS---------------GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFG   86 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHHH---------------TCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTTCCHHHHHC
T ss_pred             hhhHHHHHHHHHHHHHHhc---------------CCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhcCCHHHhcC
Confidence            3578999999888877644               468999999999999999999998854  444444321     111


Q ss_pred             cccChHHHHHHHHHHHh-hhC--CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC-----CCCCCCeEEEE
Q 022768          105 KYIGESARLIREMFGYA-RDH--QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG-----FDQLGKVKMIM  176 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~-~~~--~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~-----~~~~~~~~vi~  176 (292)
                      ...+..... ...+... ...  .++||||||++.+           ....+..|...++....     ....+..++|+
T Consensus        87 ~~~~~~~~~-~g~~~~~~~g~l~~~~IL~IDEI~r~-----------~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~  154 (500)
T 3nbx_X           87 PLSIQALKD-EGRYERLTSGYLPEAEIVFLDEIWKA-----------GPAILNTLLTAINERQFRNGAHVEKIPMRLLVA  154 (500)
T ss_dssp             CBC-----------CBCCTTSGGGCSEEEEESGGGC-----------CHHHHHHHHHHHHSSEEECSSSEEECCCCEEEE
T ss_pred             cccHHHHhh-chhHHhhhccCCCcceeeeHHhHhhh-----------cHHHHHHHHHHHHHHhccCCCCcCCcchhhhhh
Confidence            111110000 1111111 111  3579999999988           77888888888864320     01112234677


Q ss_pred             EeCCCCC---CChhhcCCCCcceEEEccCCCH-HHHHHHHHHHHcCccC---------------------CCCCC---HH
Q 022768          177 ATNRPDV---LDPALLRPGRLDRKIEIPLPNE-QSRMEILKIHAAGIAK---------------------HGEID---YE  228 (292)
Q Consensus       177 t~~~~~~---l~~~l~~~~r~~~~i~l~~p~~-~~r~~i~~~~~~~~~~---------------------~~~~~---~~  228 (292)
                      +||....   ..+++.+  ||...+.+++|+. +++..|++........                     .-.++   .+
T Consensus       155 ATN~lpe~~~~~~aLld--RF~~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~v~v~d~v~e  232 (500)
T 3nbx_X          155 ASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFE  232 (500)
T ss_dssp             EESSCCCTTCTTHHHHT--TCCEEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHHTTCBCCHHHHH
T ss_pred             ccccCCCccccHHHHHH--HHHHHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcCCcccCchHHHH
Confidence            7775322   3458888  9988999999987 6788888765421100                     00111   12


Q ss_pred             HHHHHc---------CCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHH
Q 022768          229 AVVKLA---------EGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR  271 (292)
Q Consensus       229 ~l~~~~---------~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~  271 (292)
                      .++...         .|.|++.+..+++.|...|..+++..|+.+|+. ++.
T Consensus       233 ~i~~l~~~lr~~r~~~~iS~R~~~~llr~A~A~A~l~gr~~Vt~eDv~-~a~  283 (500)
T 3nbx_X          233 LIFMLRQQLDKLPDAPYVSDRRWKKAIRLLQASAFFSGRSAVAPVDLI-LLK  283 (500)
T ss_dssp             HHHHHHHHHHHCSSSCCCCHHHHHHHHHHHHHHHHHTTCSBCCGGGGG-GGG
T ss_pred             HHHHHHHHhhcCCCCCccchhHHHHHHHHHHHHHhhcCCccccchHHH-HHH
Confidence            233322         477999999999999999999999999999987 443

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.70  E-value=3.5e-16  Score=151.18  Aligned_cols=201  Identities=19%  Similarity=0.304  Sum_probs=138.6

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCC----CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc---
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGI----KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK---  105 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~----~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~---  105 (292)
                      .++|++++++.+...+...        ..|.    .+..++||+||||+|||++|+++++.++.+++.+++.++...   
T Consensus       459 ~v~g~~~~~~~l~~~i~~~--------~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~  530 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMA--------RAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTV  530 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHH--------HTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCC
T ss_pred             hccCHHHHHHHHHHHHHHH--------hcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhH
Confidence            4789999998888877542        1122    234579999999999999999999999999999999887542   


Q ss_pred             --ccC----hHH-HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------CCCCe
Q 022768          106 --YIG----ESA-RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------QLGKV  172 (292)
Q Consensus       106 --~~~----~~~-~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~~~~~  172 (292)
                        ..|    ... ..-..+........++||+|||+|.+           ....+..|..+++......      ...++
T Consensus       531 ~~l~g~~~g~~g~~~~~~l~~~~~~~~~~vl~lDEi~~~-----------~~~~~~~Ll~~le~~~~~~~~g~~~~~~~~  599 (758)
T 1r6b_X          531 SRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKA-----------HPDVFNILLQVMDNGTLTDNNGRKADFRNV  599 (758)
T ss_dssp             SSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGS-----------CHHHHHHHHHHHHHSEEEETTTEEEECTTE
T ss_pred             hhhcCCCCCCcCccccchHHHHHHhCCCcEEEEeCcccc-----------CHHHHHHHHHHhcCcEEEcCCCCEEecCCe
Confidence              111    111 11112334444566799999999998           7788888888887532100      11368


Q ss_pred             EEEEEeCCCC-------------------------CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCc-------c
Q 022768          173 KMIMATNRPD-------------------------VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGI-------A  220 (292)
Q Consensus       173 ~vi~t~~~~~-------------------------~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~-------~  220 (292)
                      ++|+|+|...                         .+.+++++  ||+..+.|++|+.+++..|++.++...       .
T Consensus       600 ~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~  677 (758)
T 1r6b_X          600 VLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIVELQVQLDQKG  677 (758)
T ss_dssp             EEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             EEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCCCHHHHHHHHHHHHHHHHHHHHHCC
Confidence            8999999743                         46778887  998889999999999999999877532       1


Q ss_pred             CCCCCC---HHHHHHHc--CCCCHHHHHHHHHHHHHHHH
Q 022768          221 KHGEID---YEAVVKLA--EGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       221 ~~~~~~---~~~l~~~~--~g~~~~di~~l~~~a~~~a~  254 (292)
                      ..-.++   .+.++...  .++..+++..+++.+...++
T Consensus       678 ~~~~~~~~a~~~l~~~~~~~~~g~R~l~~~i~~~~~~~l  716 (758)
T 1r6b_X          678 VSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPL  716 (758)
T ss_dssp             EEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHHTHHH
T ss_pred             cEEEeCHHHHHHHHHhCCCcCCCchHHHHHHHHHHHHHH
Confidence            111223   33344332  24557788888877766443

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.68  E-value=2.5e-17  Score=154.27  Aligned_cols=226  Identities=18%  Similarity=0.123  Sum_probs=145.6

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe----ccchhcccc
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV----SSAIIDKYI  107 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~----~~~~~~~~~  107 (292)
                      ..++|++++++.+...+..-. .+.. ....+....++||+||||||||++|+++++.++...+...    +..+.....
T Consensus       295 ~~I~G~e~vk~al~~~l~~g~-~~~~-~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~  372 (595)
T 3f9v_A          295 PSIYGHWELKEALALALFGGV-PKVL-EDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVV  372 (595)
T ss_dssp             STTSCCHHHHHHHTTTTTCCC-CEET-TTTEECCSCCEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECS
T ss_pred             chhcChHHHHHHHHHHHhCCC-cccc-cCCCcCCCcceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceee
Confidence            357899998887755443210 0000 0011223348999999999999999999999876654422    111111111


Q ss_pred             ChH-HHH---HHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC--------CCCCCCeEEE
Q 022768          108 GES-ARL---IREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG--------FDQLGKVKMI  175 (292)
Q Consensus       108 ~~~-~~~---~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~--------~~~~~~~~vi  175 (292)
                      ... ...   ....+.   ...+++++|||+|.+           ....+..|.+.++...-        ...+.++.+|
T Consensus       373 ~~~~~g~~~~~~G~l~---~A~~gil~IDEid~l-----------~~~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vI  438 (595)
T 3f9v_A          373 REKGTGEYYLEAGALV---LADGGIAVIDEIDKM-----------RDEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVI  438 (595)
T ss_dssp             SGGGTSSCSEEECHHH---HHSSSEECCTTTTCC-----------CSHHHHHHHHHHHSSSEEEESSSSEEEECCCCEEE
T ss_pred             eccccccccccCCeeE---ecCCCcEEeehhhhC-----------CHhHhhhhHHHHhCCEEEEecCCcEEEecCceEEE
Confidence            000 000   000111   123479999999998           66778888888875321        0112468899


Q ss_pred             EEeCCCC-------------CCChhhcCCCCcce-EEEccCCCHHHHHHHHHHHHcCcc---------------------
Q 022768          176 MATNRPD-------------VLDPALLRPGRLDR-KIEIPLPNEQSRMEILKIHAAGIA---------------------  220 (292)
Q Consensus       176 ~t~~~~~-------------~l~~~l~~~~r~~~-~i~l~~p~~~~r~~i~~~~~~~~~---------------------  220 (292)
                      +|+|...             .+++++++  ||+. .+..+.|+.+ ...|.++.+....                     
T Consensus       439 aatNp~~G~~~~~~~~~~ni~l~~aLl~--RFDl~~~~~~~~~~e-~~~i~~~il~~~~~~~~~~~l~~~~l~~~i~~ar  515 (595)
T 3f9v_A          439 AAGNPKFGRYISERPVSDNINLPPTILS--RFDLIFILKDQPGEQ-DRELANYILDVHSGKSTKNIIDIDTLRKYIAYAR  515 (595)
T ss_dssp             EEECCTTCCSCTTSCSCTTTCSCSSSGG--GCSCCEEECCTTHHH-HHHHHHHHHTTTCCCSSSSTTCCTTTHHHHHHHH
T ss_pred             EEcCCcCCccCcccCchhccCCCHHHHh--hCeEEEEeCCCCCHH-HHHHHHHHHHHhhccccccCCCHHHHHHHHHHHH
Confidence            9999875             78899998  9965 4556777777 7777777665321                     


Q ss_pred             -----CCCCCCHHHHHHH--------------cCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          221 -----KHGEIDYEAVVKL--------------AEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       221 -----~~~~~~~~~l~~~--------------~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                           .-.+...+.+...              ..+.+++.+..+++.|...|..+++..|+.+|+.+|+.-+...
T Consensus       516 ~~~~p~ls~ea~~~l~~~y~~lR~~~~~~~~~~~~~s~R~l~~lirla~a~A~l~~~~~V~~~dv~~Ai~l~~~s  590 (595)
T 3f9v_A          516 KYVTPKITSEAKNLITDFFVEMRKKSSETPDSPILITPRQLEALIRISEAYAKMALKAEVTREDAERAINIMRLF  590 (595)
T ss_dssp             HHHCCCCCCCTHHHHHHHHTTSSCSCCBCSSSCBCSSTTTTTHHHHHHHHHHHTTSSCCSSHHHHHHHHHHHHHH
T ss_pred             HhCCCCCCHHHHHHHHHHHHHHHHhhccCCCccccccHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHHH
Confidence                 1111223444444              2356899999999999999999999999999999999887753

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.67  E-value=6.1e-16  Score=145.59  Aligned_cols=222  Identities=22%  Similarity=0.322  Sum_probs=146.2

Q ss_pred             ccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE---EEEec
Q 022768           23 HEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF---LKVVS   99 (292)
Q Consensus        23 ~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~---~~~~~   99 (292)
                      ...+++..|++++|.+++++.+...+..               +.+++|+||||+||||+++++++.++...   +.+..
T Consensus        32 ~~~~rp~~l~~i~G~~~~l~~l~~~i~~---------------g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~~~~~~~   96 (604)
T 3k1j_A           32 EIEVPEKLIDQVIGQEHAVEVIKTAANQ---------------KRHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFP   96 (604)
T ss_dssp             GSCCCSSHHHHCCSCHHHHHHHHHHHHT---------------TCCEEEECCTTSSHHHHHHHHHHTSCCSSCEEEEEEC
T ss_pred             cccccccccceEECchhhHhhccccccC---------------CCEEEEEeCCCCCHHHHHHHHhccCCcccCCeEEEeC
Confidence            3577899999999999999988887653               56899999999999999999999885432   11111


Q ss_pred             cchhc--c---c--cChHHH-------------------------------------------------HHHHHHHH---
Q 022768          100 SAIID--K---Y--IGESAR-------------------------------------------------LIREMFGY---  120 (292)
Q Consensus       100 ~~~~~--~---~--~~~~~~-------------------------------------------------~~~~~~~~---  120 (292)
                      .....  .   +  .+....                                                 ....+|..   
T Consensus        97 ~~~~~~~p~i~~~p~g~~~~~~e~~~~~~~~~~~~r~~~~~~~~~~~~~nl~v~~~~~~~~~~v~~~~~~~~~L~G~~~~  176 (604)
T 3k1j_A           97 NPEDENMPRIKTVPACQGRRIVEKYREKAKSQESVKSSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRH  176 (604)
T ss_dssp             CTTCTTSCEEEEEETTHHHHHHHHHHHHHHHHTCC-----------CCCEEEECCTTCSSCCEEECTTCCHHHHHCEECC
T ss_pred             CcccccCCcEEEEecchHHHHHHHHHHhhccchhhhhhcccccccccccceeeccccCCCCCEEEcCCCCHHhcCceEEe
Confidence            11000  0   0  000000                                                 01111110   


Q ss_pred             --------------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC--------------
Q 022768          121 --------------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF--------------  166 (292)
Q Consensus       121 --------------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~--------------  166 (292)
                                          .....+++|||||++.+           +...+..|...++...-.              
T Consensus       177 ~~~~~g~~~~g~~~~i~~g~~~~a~~gvL~LDEi~~l-----------~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~  245 (604)
T 3k1j_A          177 DPFQSGGLGTPAHERVEPGMIHRAHKGVLFIDEIATL-----------SLKMQQSLLTAMQEKKFPITGQSEMSSGAMVR  245 (604)
T ss_dssp             CCC----CCCCGGGGEECCHHHHTTTSEEEETTGGGS-----------CHHHHHHHHHHHHHSEECCBCSCTTSGGGGCB
T ss_pred             chhhcCCccccccccccCceeeecCCCEEEEechhhC-----------CHHHHHHHHHHHHcCcEEecccccccccccCC
Confidence                                11234579999999998           778888888888754211              


Q ss_pred             --CCCCCeEEEEEeCCC--CCCChhhcCCCCcc---eEEEccCC---CHHHHHHHHHHHHcCcc---CCCCCCHHH---H
Q 022768          167 --DQLGKVKMIMATNRP--DVLDPALLRPGRLD---RKIEIPLP---NEQSRMEILKIHAAGIA---KHGEIDYEA---V  230 (292)
Q Consensus       167 --~~~~~~~vi~t~~~~--~~l~~~l~~~~r~~---~~i~l~~p---~~~~r~~i~~~~~~~~~---~~~~~~~~~---l  230 (292)
                        ....++.+|+++|..  +.+++++++  ||.   ..+.|+..   +.+....+++.+.....   ....++.+.   +
T Consensus       246 ~~~~p~~~~vI~atn~~~~~~l~~~l~~--R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~L  323 (604)
T 3k1j_A          246 TEPVPCDFVLVAAGNLDTVDKMHPALRS--RIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEI  323 (604)
T ss_dssp             CSCEECCCEEEEEECHHHHHHSCHHHHH--HHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHH
T ss_pred             CCccceeEEEEEecCHHHHhhcCHHHHH--HhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHH
Confidence              111367899999975  578999998  875   45666432   34556666554443221   112333333   3


Q ss_pred             HHHc---CCC------CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          231 VKLA---EGF------NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       231 ~~~~---~g~------~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      ....   .|.      +.+++.++++.|..+|..++...|+.+|+.+|+..
T Consensus       324 i~~~~r~~g~r~~l~~~~R~l~~llr~A~~~A~~~~~~~I~~edv~~A~~~  374 (604)
T 3k1j_A          324 VREAQKRAGRKGHLTLRLRDLGGIVRAAGDIAVKKGKKYVEREDVIEAVKM  374 (604)
T ss_dssp             HHHHHHTTCSTTEEECCHHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHH
T ss_pred             HHHHhhhhccccccccCHHHHHHHHHHHHHHHHhcCcccccHHHHHHHHHh
Confidence            3322   442      69999999999999999999999999999999965

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.66  E-value=2.6e-16  Score=135.83  Aligned_cols=206  Identities=22%  Similarity=0.237  Sum_probs=125.8

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccC
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIG  108 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~  108 (292)
                      ++++|....++++.+.+...           .....+++|+|+||||||++|+++++..   +.+++.++|..+......
T Consensus         2 ~~iig~s~~~~~~~~~~~~~-----------a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~l~~   70 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMV-----------APSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLE   70 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHH-----------CSTTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChHHHH
Confidence            35899999999998888764           2446789999999999999999999965   568999998876431110


Q ss_pred             h---------HH---HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCC
Q 022768          109 E---------SA---RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLG  170 (292)
Q Consensus       109 ~---------~~---~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~  170 (292)
                      .         ..   ......+..   ..+++|||||++.+           ....+..|..+++.....      ....
T Consensus        71 ~~lfg~~~g~~tg~~~~~~g~~~~---a~~g~L~LDEi~~l-----------~~~~q~~Ll~~l~~~~~~~~g~~~~~~~  136 (304)
T 1ojl_A           71 SELFGHEKGAFTGADKRREGRFVE---ADGGTLFLDEIGDI-----------SPLMQVRLLRAIQEREVQRVGSNQTISV  136 (304)
T ss_dssp             HHHTCCCSSCCC---CCCCCHHHH---HTTSEEEEESCTTC-----------CHHHHHHHHHHHHSSBCCBTTBCCCCBC
T ss_pred             HHhcCccccccCchhhhhcCHHHh---cCCCEEEEeccccC-----------CHHHHHHHHHHHhcCEeeecCCcccccC
Confidence            0         00   000111222   23479999999999           667777788777753210      1123


Q ss_pred             CeEEEEEeCCC-------CCCChhhcCCCCcc-eEEEccCCC--HHHHHHHHHHHHcCc----cC-CCCCCHHHHHHHcC
Q 022768          171 KVKMIMATNRP-------DVLDPALLRPGRLD-RKIEIPLPN--EQSRMEILKIHAAGI----AK-HGEIDYEAVVKLAE  235 (292)
Q Consensus       171 ~~~vi~t~~~~-------~~l~~~l~~~~r~~-~~i~l~~p~--~~~r~~i~~~~~~~~----~~-~~~~~~~~l~~~~~  235 (292)
                      ++.+|+++|..       ..+.+++..  |+. ..+.+|++.  .++...++..++...    .. ...++.+.+..+..
T Consensus       137 ~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~  214 (304)
T 1ojl_A          137 DVRLIAATHRDLAEEVSAGRFRQDLYY--RLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIH  214 (304)
T ss_dssp             CCEEEEEESSCHHHHHHHTSSCHHHHH--HHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHH
T ss_pred             CeEEEEecCccHHHHHHhCCcHHHHHh--hcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHc
Confidence            58899999875       235566666  663 345566554  344455666555422    11 12345444444332


Q ss_pred             C---CCHHHHHHHHHHHHHHHHHhcCCcccHHHHH
Q 022768          236 G---FNGADLRNVCTEAGMSAIRAERDYVIHEDFM  267 (292)
Q Consensus       236 g---~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~  267 (292)
                      .   .+.+++.++++.+...+   ....|+.+++.
T Consensus       215 ~~wpGnvReL~~~l~~~~~~~---~~~~i~~~~l~  246 (304)
T 1ojl_A          215 YDWPGNIRELENAIERAVVLL---TGEYISERELP  246 (304)
T ss_dssp             CCCSSHHHHHHHHHHHHHHHC---CSSSBCGGGSC
T ss_pred             CCCCCCHHHHHHHHHHHHHhC---CCCcccHHhhh
Confidence            1   25566667777666543   33456655554

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.64  E-value=1.4e-14  Score=130.08  Aligned_cols=228  Identities=14%  Similarity=0.142  Sum_probs=145.1

Q ss_pred             CccccccccHHHHHHHHHHh-hcccCChHHHHhcCC-CCCceEEE--EcCCCChHHHHHHHHHHhc---------CCcEE
Q 022768           29 VSYSAVGGLSDQIRELRESI-ELPLMNPELFLRVGI-KPPKGVLL--YGPPGTGKTLLARAIASNI---------DANFL   95 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l-~~~~~~~~~~~~~~~-~~~~~vll--~G~~G~GKT~l~~~la~~l---------~~~~~   95 (292)
                      ...+.++|.++..+.|...+ .....        +. ..+..++|  +||+|+|||++++.+++.+         +..++
T Consensus        19 ~~p~~l~gR~~el~~l~~~l~~~~~~--------~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~   90 (412)
T 1w5s_A           19 YIPPELRVRRGEAEALARIYLNRLLS--------GAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQA   90 (412)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHHHHT--------SSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             cCCCCCCChHHHHHHHHHHHhHHHhc--------CCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEE
Confidence            34478999999999999887 54211        00 23567899  9999999999999999876         34567


Q ss_pred             EEeccchhcc--c--------------cCh-HHHHHHHHHHHhh-hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHH
Q 022768           96 KVVSSAIIDK--Y--------------IGE-SARLIREMFGYAR-DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLM  157 (292)
Q Consensus        96 ~~~~~~~~~~--~--------------~~~-~~~~~~~~~~~~~-~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~  157 (292)
                      .+++......  .              .+. .......+..... ...+.+|+|||+|.+....     .........+.
T Consensus        91 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~-----~~~~~~l~~l~  165 (412)
T 1w5s_A           91 YVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSP-----RIAAEDLYTLL  165 (412)
T ss_dssp             EEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCT-----TSCHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhcc-----CcchHHHHHHH
Confidence            7775332110  0              010 1122222222222 2457899999999983210     00223333344


Q ss_pred             HHHHHhhCCCCC--CCeEEEEEeCCCC---CCC---hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCC---C
Q 022768          158 ELLNQLDGFDQL--GKVKMIMATNRPD---VLD---PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI---D  226 (292)
Q Consensus       158 ~~l~~~~~~~~~--~~~~vi~t~~~~~---~l~---~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~---~  226 (292)
                      ..+....  ...  .++.+|++++.++   .+.   +.+.+  ++...+.+++++.++..++++.++.........   .
T Consensus       166 ~~~~~~~--~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~  241 (412)
T 1w5s_A          166 RVHEEIP--SRDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRH  241 (412)
T ss_dssp             THHHHSC--CTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHH
T ss_pred             HHHHhcc--cCCCCceEEEEEEeccccHHHHHhhhcchhhh--hcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHH
Confidence            4443321  112  5788888887554   233   45555  555569999999999999998776422211122   2


Q ss_pred             HHHHHHHcC------CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          227 YEAVVKLAE------GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       227 ~~~l~~~~~------g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ...+...+.      | +++.+..++..+...|..++...++.+++.+++....
T Consensus       242 ~~~i~~~~~~~~~~~G-~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~  294 (412)
T 1w5s_A          242 LELISDVYGEDKGGDG-SARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENE  294 (412)
T ss_dssp             HHHHHHHHCGGGTSCC-CHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHhccCCC-cHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence            456677777      7 8889999999998888877777899999988887653

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=99.62  E-value=6.6e-15  Score=128.84  Aligned_cols=174  Identities=16%  Similarity=0.216  Sum_probs=119.1

Q ss_pred             cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----------------------
Q 022768           37 LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----------------------   93 (292)
Q Consensus        37 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----------------------   93 (292)
                      +++.++.+...+..-            ..++.+||+||+|+|||++++.+++.+.+.                       
T Consensus         7 ~~~~~~~l~~~i~~~------------~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~   74 (334)
T 1a5t_A            7 LRPDFEKLVASYQAG------------RGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHP   74 (334)
T ss_dssp             GHHHHHHHHHHHHTT------------CCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCT
T ss_pred             hHHHHHHHHHHHHcC------------CcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCC
Confidence            466677777776541            345679999999999999999999988543                       


Q ss_pred             -EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC
Q 022768           94 -FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ  168 (292)
Q Consensus        94 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~  168 (292)
                       +..++...- +  .....+.++.++..+..    ..+.|++|||+|.+           ....+..|...+   +  .+
T Consensus        75 d~~~~~~~~~-~--~~~~i~~ir~l~~~~~~~~~~~~~kvviIdead~l-----------~~~a~naLLk~l---E--ep  135 (334)
T 1a5t_A           75 DYYTLAPEKG-K--NTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL-----------TDAAANALLKTL---E--EP  135 (334)
T ss_dssp             TEEEECCCTT-C--SSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGB-----------CHHHHHHHHHHH---T--SC
T ss_pred             CEEEEecccc-C--CCCCHHHHHHHHHHHhhccccCCcEEEEECchhhc-----------CHHHHHHHHHHh---c--CC
Confidence             222222100 0  01123445566555542    34689999999999           555555555554   3  34


Q ss_pred             CCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHH
Q 022768          169 LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       169 ~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      .+++++|++++.++.+.+.+++  |+ ..+.|++|+.++..++++...   .. .+.....++..+.| +++.+..+++.
T Consensus       136 ~~~~~~Il~t~~~~~l~~ti~S--Rc-~~~~~~~~~~~~~~~~L~~~~---~~-~~~~~~~l~~~s~G-~~r~a~~~l~~  207 (334)
T 1a5t_A          136 PAETWFFLATREPERLLATLRS--RC-RLHYLAPPPEQYAVTWLSREV---TM-SQDALLAALRLSAG-SPGAALALFQG  207 (334)
T ss_dssp             CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHC---CC-CHHHHHHHHHHTTT-CHHHHHHTTSS
T ss_pred             CCCeEEEEEeCChHhCcHHHhh--cc-eeeeCCCCCHHHHHHHHHHhc---CC-CHHHHHHHHHHcCC-CHHHHHHHhcc
Confidence            4678899999999999999999  77 679999999999999888765   11 12234556777776 77777666654


Q ss_pred             H
Q 022768          249 A  249 (292)
Q Consensus       249 a  249 (292)
                      +
T Consensus       208 ~  208 (334)
T 1a5t_A          208 D  208 (334)
T ss_dssp             H
T ss_pred             c
Confidence            4

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=99.61  E-value=2.9e-15  Score=146.38  Aligned_cols=209  Identities=20%  Similarity=0.307  Sum_probs=138.9

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc-
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY-  106 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~-  106 (292)
                      +..++|++++++.+...+......   ... .-.+..+++|+||+|||||++|+++++.+   +.+++.+++..+.... 
T Consensus       557 ~~~viG~~~a~~~l~~~i~~~~~g---~~~-~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~  632 (854)
T 1qvr_A          557 HKRVVGQDEAIRAVADAIRRARAG---LKD-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHA  632 (854)
T ss_dssp             HHHSCSCHHHHHHHHHHHHHHGGG---CSC-SSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGG
T ss_pred             hcccCCcHHHHHHHHHHHHHHhcc---cCC-CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhH
Confidence            356899999999998888653110   000 01223579999999999999999999998   7789999988765431 


Q ss_pred             ----cChHH-----HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC------CCCC
Q 022768          107 ----IGESA-----RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD------QLGK  171 (292)
Q Consensus       107 ----~~~~~-----~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~------~~~~  171 (292)
                          .+...     .....+........+++|||||++.+           ....+..|..+++......      ...+
T Consensus       633 ~s~l~g~~~~~~G~~~~g~l~~~~~~~~~~vl~lDEi~~l-----------~~~~~~~Ll~~l~~~~~~~~~g~~vd~~~  701 (854)
T 1qvr_A          633 VSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKA-----------HPDVFNILLQILDDGRLTDSHGRTVDFRN  701 (854)
T ss_dssp             GGGC--------------CHHHHHHHCSSEEEEESSGGGS-----------CHHHHHHHHHHHTTTEECCSSSCCEECTT
T ss_pred             HHHHcCCCCCCcCccccchHHHHHHhCCCeEEEEeccccc-----------CHHHHHHHHHHhccCceECCCCCEeccCC
Confidence                11100     00122333344455689999999998           7778888888877532111      1236


Q ss_pred             eEEEEEeCCC--------------------------CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc-----
Q 022768          172 VKMIMATNRP--------------------------DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA-----  220 (292)
Q Consensus       172 ~~vi~t~~~~--------------------------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~-----  220 (292)
                      +++|+|+|..                          ..+.+.+..  |++..+.+.+|+.++...|+..++....     
T Consensus       702 ~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~pl~~edi~~i~~~~l~~~~~~~~~  779 (854)
T 1qvr_A          702 TVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLSYLRARLAE  779 (854)
T ss_dssp             EEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHHHHHHHHHT
T ss_pred             eEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            7899999962                          235677777  8988888999999999999987775221     


Q ss_pred             --CCCCCC---HHHHHHHcC--CCCHHHHHHHHHHHHHHHHHh
Q 022768          221 --KHGEID---YEAVVKLAE--GFNGADLRNVCTEAGMSAIRA  256 (292)
Q Consensus       221 --~~~~~~---~~~l~~~~~--g~~~~di~~l~~~a~~~a~~~  256 (292)
                        ....++   .+.|+...-  .++.++++.+++.+...+..+
T Consensus       780 ~~~~~~~~~~a~~~L~~~~~~~~gn~R~L~~~i~~~~~~~~~~  822 (854)
T 1qvr_A          780 KRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQ  822 (854)
T ss_dssp             TTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHHHTHHHHHH
T ss_pred             CCceEEECHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHH
Confidence              111233   344444433  457889999988887766544

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=99.59  E-value=7.4e-14  Score=120.29  Aligned_cols=142  Identities=13%  Similarity=0.200  Sum_probs=105.0

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc------CCcEEEEeccchhccccCh
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI------DANFLKVVSSAIIDKYIGE  109 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l------~~~~~~~~~~~~~~~~~~~  109 (292)
                      |++++++.|...+..-            . .+++||+||+|+|||++++.+++.+      ...++.++...-     ..
T Consensus         1 g~~~~~~~L~~~i~~~------------~-~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~-----~~   62 (305)
T 2gno_A            1 GAKDQLETLKRIIEKS------------E-GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE-----NI   62 (305)
T ss_dssp             ---CHHHHHHHHHHTC------------S-SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS-----CB
T ss_pred             ChHHHHHHHHHHHHCC------------C-CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcC-----CC
Confidence            6778888888887652            2 5689999999999999999999864      345666664320     12


Q ss_pred             HHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          110 SARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       110 ~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      ..+.++.++..+..    ....|++|||+|.+           ....+..|...++     .+++.+.+|++|+.++.+.
T Consensus        63 ~id~ir~li~~~~~~p~~~~~kvviIdead~l-----------t~~a~naLLk~LE-----ep~~~t~fIl~t~~~~kl~  126 (305)
T 2gno_A           63 GIDDIRTIKDFLNYSPELYTRKYVIVHDCERM-----------TQQAANAFLKALE-----EPPEYAVIVLNTRRWHYLL  126 (305)
T ss_dssp             CHHHHHHHHHHHTSCCSSSSSEEEEETTGGGB-----------CHHHHHHTHHHHH-----SCCTTEEEEEEESCGGGSC
T ss_pred             CHHHHHHHHHHHhhccccCCceEEEeccHHHh-----------CHHHHHHHHHHHh-----CCCCCeEEEEEECChHhCh
Confidence            23345555555543    23579999999999           6666666666665     3446888888899999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHH
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHA  216 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~  216 (292)
                      +.+++  |   .+.|++|+.++..+.++..+
T Consensus       127 ~tI~S--R---~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          127 PTIKS--R---VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             HHHHT--T---SEEEECCCCHHHHHHHHHHH
T ss_pred             HHHHc--e---eEeCCCCCHHHHHHHHHHHh
Confidence            99999  6   78999999999999888776

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.59  E-value=1.3e-15  Score=116.88  Aligned_cols=132  Identities=18%  Similarity=0.248  Sum_probs=92.3

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHH
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESAR  112 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~  112 (292)
                      +++|.++.++++.+.+...           ...+.+++|+||||||||++|+++++... +++.+++..+....      
T Consensus         5 ~~iG~s~~~~~l~~~~~~~-----------~~~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~~~------   66 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAA-----------AKRTSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLIDM------   66 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHH-----------HTCSSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHHHC------
T ss_pred             CceeCCHHHHHHHHHHHHH-----------hCCCCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCChHh------
Confidence            5789999999999988764           23456799999999999999999999888 88888887764332      


Q ss_pred             HHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC-CCC----Chh
Q 022768          113 LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP-DVL----DPA  187 (292)
Q Consensus       113 ~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~-~~l----~~~  187 (292)
                       ....+..+   .+++|||||+|.+           ....+..+..+++...    ..++.+|+++|.+ ..+    .+.
T Consensus        67 -~~~~~~~a---~~~~l~lDei~~l-----------~~~~q~~Ll~~l~~~~----~~~~~iI~~tn~~~~~~~~~~~~~  127 (143)
T 3co5_A           67 -PMELLQKA---EGGVLYVGDIAQY-----------SRNIQTGITFIIGKAE----RCRVRVIASCSYAAGSDGISCEEK  127 (143)
T ss_dssp             -HHHHHHHT---TTSEEEEEECTTC-----------CHHHHHHHHHHHHHHT----TTTCEEEEEEEECTTTC--CHHHH
T ss_pred             -hhhHHHhC---CCCeEEEeChHHC-----------CHHHHHHHHHHHHhCC----CCCEEEEEecCCCHHHHHhCccHH
Confidence             23344433   3479999999999           6777888888887642    2467788888753 332    233


Q ss_pred             hcCCCCc-ceEEEccCC
Q 022768          188 LLRPGRL-DRKIEIPLP  203 (292)
Q Consensus       188 l~~~~r~-~~~i~l~~p  203 (292)
                      +..  |+ ...+.+|+.
T Consensus       128 L~~--rl~~~~i~lPpL  142 (143)
T 3co5_A          128 LAG--LFSESVVRIPPL  142 (143)
T ss_dssp             HHH--HSSSEEEEECCC
T ss_pred             HHH--HhcCcEEeCCCC
Confidence            443  43 345666653

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.58  E-value=5.2e-15  Score=113.75  Aligned_cols=112  Identities=21%  Similarity=0.289  Sum_probs=82.7

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccCh
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGE  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~  109 (292)
                      +++|....++++.+.+...           ...+.+++|+||||||||++|+++++..   +.+++ +++..+...    
T Consensus         2 ~iiG~s~~~~~~~~~~~~~-----------a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~----   65 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQL-----------SETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNA----   65 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHH-----------TTCCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTS----
T ss_pred             CceeCCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcc----
Confidence            5789999999999888664           2456789999999999999999999987   67888 998876543    


Q ss_pred             HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          110 SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       110 ~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                        ......+..+   .+++|||||+|.+           ....+..|..++..     ...++.+|+++|.+
T Consensus        66 --~~~~~~~~~a---~~g~l~ldei~~l-----------~~~~q~~Ll~~l~~-----~~~~~~~I~~t~~~  116 (145)
T 3n70_A           66 --PQLNDFIALA---QGGTLVLSHPEHL-----------TREQQYHLVQLQSQ-----EHRPFRLIGIGDTS  116 (145)
T ss_dssp             --SCHHHHHHHH---TTSCEEEECGGGS-----------CHHHHHHHHHHHHS-----SSCSSCEEEEESSC
T ss_pred             --hhhhcHHHHc---CCcEEEEcChHHC-----------CHHHHHHHHHHHhh-----cCCCEEEEEECCcC
Confidence              1122333333   3479999999999           67778888777732     22356788888864

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=99.42  E-value=4.4e-13  Score=106.65  Aligned_cols=134  Identities=14%  Similarity=0.084  Sum_probs=82.8

Q ss_pred             cCCCCCccccccc----cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEE
Q 022768           24 EDPGNVSYSAVGG----LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFL   95 (292)
Q Consensus        24 ~~~~~~~~~~l~g----~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~   95 (292)
                      ..+.+.+|+++++    +.++++.+.+++..          +.+..+.+++|+||+|+||||+++++++.+    +..++
T Consensus         2 ~r~~~~~f~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~   71 (180)
T 3ec2_A            2 KRYWNANLDTYHPKNVSQNRALLTIRVFVHN----------FNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGY   71 (180)
T ss_dssp             CSCTTCCSSSCCCCSHHHHHHHHHHHHHHHS----------CCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCC
T ss_pred             chhhhCccccccCCCHHHHHHHHHHHHHHHh----------ccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEE
Confidence            4567788999886    34455555555543          233457889999999999999999999877    55666


Q ss_pred             EEeccchhccccChHHHH-HHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           96 KVVSSAIIDKYIGESARL-IREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        96 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      .++..++........... .......  ...|.+|+|||++...         .+......+..+++....    .+..+
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~llilDE~~~~~---------~~~~~~~~l~~ll~~~~~----~~~~i  136 (180)
T 3ec2_A           72 FFDTKDLIFRLKHLMDEGKDTKFLKT--VLNSPVLVLDDLGSER---------LSDWQRELISYIITYRYN----NLKST  136 (180)
T ss_dssp             EEEHHHHHHHHHHHHHHTCCSHHHHH--HHTCSEEEEETCSSSC---------CCHHHHHHHHHHHHHHHH----TTCEE
T ss_pred             EEEHHHHHHHHHHHhcCchHHHHHHH--hcCCCEEEEeCCCCCc---------CCHHHHHHHHHHHHHHHH----cCCCE
Confidence            666655543221110000 0011111  1256899999997431         155666677777765431    24567


Q ss_pred             EEEeCCCC
Q 022768          175 IMATNRPD  182 (292)
Q Consensus       175 i~t~~~~~  182 (292)
                      |+|+|.+.
T Consensus       137 i~tsn~~~  144 (180)
T 3ec2_A          137 IITTNYSL  144 (180)
T ss_dssp             EEECCCCS
T ss_pred             EEEcCCCh
Confidence            77887653

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.37  E-value=1.2e-10  Score=101.89  Aligned_cols=191  Identities=18%  Similarity=0.175  Sum_probs=115.2

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh---
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII---  103 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~---  103 (292)
                      |+.....++|+++..+.|.+.+..               +..++|+||+|+|||++++.+++..+  ++++++....   
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~---------------~~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~~~~~~~   69 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLEN---------------YPLTLLLGIRRVGKSSLLRAFLNERP--GILIDCRELYAER   69 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHH---------------CSEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHHHHHHTT
T ss_pred             CCCChHhcCChHHHHHHHHHHHhc---------------CCeEEEECCCcCCHHHHHHHHHHHcC--cEEEEeecccccc
Confidence            445567899999999999988753               25799999999999999999999875  6666654321   


Q ss_pred             ---c---------ccc-------------------------ChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCC
Q 022768          104 ---D---------KYI-------------------------GESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGT  146 (292)
Q Consensus       104 ---~---------~~~-------------------------~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~  146 (292)
                         .         ...                         ......+..+...+....|.+|+|||+|.+....    .
T Consensus        70 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~----~  145 (350)
T 2qen_A           70 GHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYG----S  145 (350)
T ss_dssp             TCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBT----T
T ss_pred             cCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccC----c
Confidence               0         000                         0111112222222222237899999999983100    0


Q ss_pred             cchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC---------CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          147 SADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD---------VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       147 ~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~---------~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      .........+..+++..      .++.+|+|++...         .....+..  |+...+.+++++.++..+++...+.
T Consensus       146 ~~~~~~~~~L~~~~~~~------~~~~~il~g~~~~~l~~~l~~~~~~~~l~~--~~~~~i~l~pl~~~e~~~~l~~~~~  217 (350)
T 2qen_A          146 RGGKELLALFAYAYDSL------PNLKIILTGSEVGLLHDFLKITDYESPLYG--RIAGEVLVKPFDKDTSVEFLKRGFR  217 (350)
T ss_dssp             TTTHHHHHHHHHHHHHC------TTEEEEEEESSHHHHHHHHCTTCTTSTTTT--CCCEEEECCCCCHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHHHHHhc------CCeEEEEECCcHHHHHHHHhhcCCCCcccc--CccceeeCCCCCHHHHHHHHHHHHH
Confidence            01223444444444431      3677777765421         11122322  5556899999999999999987765


Q ss_pred             CccCC-CCCCHHHHHHHcCCCCHHHHHHHHH
Q 022768          218 GIAKH-GEIDYEAVVKLAEGFNGADLRNVCT  247 (292)
Q Consensus       218 ~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~  247 (292)
                      ..... .......+...+.| .|.-+..++.
T Consensus       218 ~~~~~~~~~~~~~i~~~tgG-~P~~l~~~~~  247 (350)
T 2qen_A          218 EVNLDVPENEIEEAVELLDG-IPGWLVVFGV  247 (350)
T ss_dssp             TTTCCCCHHHHHHHHHHHTT-CHHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHHHHhCC-CHHHHHHHHH
Confidence            32221 12234566777887 5656666554

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=99.35  E-value=7.3e-11  Score=105.52  Aligned_cols=220  Identities=15%  Similarity=0.055  Sum_probs=131.5

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHH-HHhcCCcEEEEeccc----hhccccC
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAI-ASNIDANFLKVVSSA----IIDKYIG  108 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~l-a~~l~~~~~~~~~~~----~~~~~~~  108 (292)
                      ++|++++++.|.-.+..-...        ....-++||.|+||+ ||++++++ ++.+....+......    +.....+
T Consensus       215 I~G~e~vK~aLll~L~GG~~k--------~rgdihVLL~G~PGt-KS~Lar~i~~~i~pR~~ft~g~~ss~~gLt~s~r~  285 (506)
T 3f8t_A          215 LPGAEEVGKMLALQLFSCVGK--------NSERLHVLLAGYPVV-CSEILHHVLDHLAPRGVYVDLRRTELTDLTAVLKE  285 (506)
T ss_dssp             STTCHHHHHHHHHHHTTCCSS--------GGGCCCEEEESCHHH-HHHHHHHHHHHTCSSEEEEEGGGCCHHHHSEEEEE
T ss_pred             cCCCHHHHHHHHHHHcCCccc--------cCCceeEEEECCCCh-HHHHHHHHHHHhCCCeEEecCCCCCccCceEEEEc
Confidence            788888887777766442100        112238999999999 99999999 776644333211110    1000000


Q ss_pred             hHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh----CCCCCCCeEEEEEeCCCC--
Q 022768          109 ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD----GFDQLGKVKMIMATNRPD--  182 (292)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~----~~~~~~~~~vi~t~~~~~--  182 (292)
                      .+...+  --+.......+++++||++.+           ....+..|.+.+++-.    +..-+.++.||+|+|..+  
T Consensus       286 ~tG~~~--~~G~l~LAdgGvl~lDEIn~~-----------~~~~qsaLlEaMEe~~VtI~G~~lparf~VIAA~NP~~~y  352 (506)
T 3f8t_A          286 DRGWAL--RAGAAVLADGGILAVDHLEGA-----------PEPHRWALMEAMDKGTVTVDGIALNARCAVLAAINPGEQW  352 (506)
T ss_dssp             SSSEEE--EECHHHHTTTSEEEEECCTTC-----------CHHHHHHHHHHHHHSEEEETTEEEECCCEEEEEECCCC--
T ss_pred             CCCccc--CCCeeEEcCCCeeehHhhhhC-----------CHHHHHHHHHHHhCCcEEECCEEcCCCeEEEEEeCccccc
Confidence            000000  000011123479999999998           8889999999988642    111124788999999864  


Q ss_pred             ---------CCChhhcCCCCcceEE-EccCCCHHHHH---------HHHHHH---HcCccCCCCCCH---HHHH------
Q 022768          183 ---------VLDPALLRPGRLDRKI-EIPLPNEQSRM---------EILKIH---AAGIAKHGEIDY---EAVV------  231 (292)
Q Consensus       183 ---------~l~~~l~~~~r~~~~i-~l~~p~~~~r~---------~i~~~~---~~~~~~~~~~~~---~~l~------  231 (292)
                               .+++++++  ||+..+ .+.+|+.+...         +.++.+   .........++-   +.+.      
T Consensus       353 d~~~s~~~~~Lp~alLD--RFDLi~i~~d~pd~e~d~e~~~~~ls~e~L~~yi~~ar~~~~~p~ls~ea~~yI~~~y~~t  430 (506)
T 3f8t_A          353 PSDPPIARIDLDQDFLS--HFDLIAFLGVDPRPGEPEEQDTEVPSYTLLRRYLLYAIREHPAPELTEEARKRLEHWYETR  430 (506)
T ss_dssp             CCSCGGGGCCSCHHHHT--TCSEEEETTC--------------CCHHHHHHHHHHHHHHCSCCEECHHHHHHHHHHHHHH
T ss_pred             CCCCCccccCCChHHhh--heeeEEEecCCCChhHhhcccCCCCCHHHHHHHHHHHHhcCCCceeCHHHHHHHHHHHHHH
Confidence                     68889999  997655 44666543311         122211   110000111111   0111      


Q ss_pred             -H----------HcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhh
Q 022768          232 -K----------LAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAK  277 (292)
Q Consensus       232 -~----------~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~  277 (292)
                       .          ..-|.|++.+..+++.|.+.|..+++..|+.+|+.+|+.-+...-
T Consensus       431 R~~~~~~~~~~~~~~giSpR~leaLiRlA~A~A~L~gR~~V~~eDV~~Ai~L~~~Sl  487 (506)
T 3f8t_A          431 REEVEERLGMGLPTLPVTRRQLESVERLAKAHARMRLSDDVEPEDVDIAAELVDWYL  487 (506)
T ss_dssp             HHHHHHHHHTTCCCCCCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHHHHH
T ss_pred             hcCcccccccccccccccHHHHHHHHHHHHHHHHHcCcCCCCHHHHHHHHHHHHHHH
Confidence             0          234679999999999999999999999999999999999888643

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.35  E-value=1.4e-11  Score=109.66  Aligned_cols=206  Identities=24%  Similarity=0.286  Sum_probs=127.7

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEeccchhcccc
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID---ANFLKVVSSAIIDKYI  107 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~~~~~~~~~  107 (292)
                      +..++|.....+++.+.+...           .....+++|+|++|+||+++++.+....+   .+++.++|..+.... 
T Consensus       136 ~~~~ig~s~~m~~l~~~i~~~-----------a~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~-  203 (387)
T 1ny5_A          136 EEEYVFESPKMKEILEKIKKI-----------SCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDI-  203 (387)
T ss_dssp             CCCCCCCSHHHHHHHHHHHHH-----------TTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHH-
T ss_pred             chhhhhccHHhhHHHHHHHHh-----------cCCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHH-
Confidence            456788888877777776653           24456799999999999999999988764   689999998764321 


Q ss_pred             ChHHHHHHHHHHHh---------------hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------
Q 022768          108 GESARLIREMFGYA---------------RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------  166 (292)
Q Consensus       108 ~~~~~~~~~~~~~~---------------~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------  166 (292)
                           .-..+|+..               .....++|||||++.+           +...+..|..+++...-.      
T Consensus       204 -----~~~elfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l-----------~~~~q~~Ll~~l~~~~~~~~g~~~  267 (387)
T 1ny5_A          204 -----FEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGEL-----------SLEAQAKLLRVIESGKFYRLGGRK  267 (387)
T ss_dssp             -----HHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGC-----------CHHHHHHHHHHHHHSEECCBTCCS
T ss_pred             -----HHHHhcCCCCCCCCCcccccCCceeeCCCcEEEEcChhhC-----------CHHHHHHHHHHHhcCcEEeCCCCc
Confidence                 112333221               1133479999999999           888999999998864211      


Q ss_pred             CCCCCeEEEEEeCCC-------CCCChhhcCCCCc-ceEEEccCCCH--HHHHHHHHHHHcCc----cCC-CCCCHHHHH
Q 022768          167 DQLGKVKMIMATNRP-------DVLDPALLRPGRL-DRKIEIPLPNE--QSRMEILKIHAAGI----AKH-GEIDYEAVV  231 (292)
Q Consensus       167 ~~~~~~~vi~t~~~~-------~~l~~~l~~~~r~-~~~i~l~~p~~--~~r~~i~~~~~~~~----~~~-~~~~~~~l~  231 (292)
                      ....++.+|++||..       ....+.+..  |+ ...+.+|+...  ++...++.+++...    ... ..++.+.+.
T Consensus       268 ~~~~~~rii~at~~~l~~~~~~g~fr~dl~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~  345 (387)
T 1ny5_A          268 EIEVNVRILAATNRNIKELVKEGKFREDLYY--RLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQE  345 (387)
T ss_dssp             BEECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHH
T ss_pred             eeeccEEEEEeCCCCHHHHHHcCCccHHHHH--hhcCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHHH
Confidence            011257799999863       223444443  33 23445554432  34444555554422    211 235556666


Q ss_pred             HHcC-CC--CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHH
Q 022768          232 KLAE-GF--NGADLRNVCTEAGMSAIRAERDYVIHEDFMKA  269 (292)
Q Consensus       232 ~~~~-g~--~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a  269 (292)
                      .+.. .|  |.++++++++.|...+   ....|+.+++...
T Consensus       346 ~l~~~~wpGNvreL~~~i~~~~~~~---~~~~i~~~~l~~~  383 (387)
T 1ny5_A          346 LLLSYPWYGNVRELKNVIERAVLFS---EGKFIDRGELSCL  383 (387)
T ss_dssp             HHHHSCCTTHHHHHHHHHHHHHHHC---CSSEECHHHHHHH
T ss_pred             HHHhCCCCcHHHHHHHHHHHHHHhC---CCCcCcHHHCcHh
Confidence            5543 22  4456666666665443   4557888888654

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.33  E-value=1.6e-10  Score=101.26  Aligned_cols=188  Identities=15%  Similarity=0.160  Sum_probs=116.8

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh---
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII---  103 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~---  103 (292)
                      |+.....++|.++..+.|.+ +..                ..++|+||+|+|||++++.+++..+..++.+++....   
T Consensus         8 ~~~~~~~~~gR~~el~~L~~-l~~----------------~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~   70 (357)
T 2fna_A            8 PKDNRKDFFDREKEIEKLKG-LRA----------------PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERN   70 (357)
T ss_dssp             CCCSGGGSCCCHHHHHHHHH-TCS----------------SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCS
T ss_pred             CCCCHHHhcChHHHHHHHHH-hcC----------------CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchhhcccc
Confidence            44466789999999999988 531                4799999999999999999999987777777765431   


Q ss_pred             --c--cccChH---------------------------------------HHHHHHHHHHhhhC--CCEEEEEccccccc
Q 022768          104 --D--KYIGES---------------------------------------ARLIREMFGYARDH--QPCIIFMDEIDAIG  138 (292)
Q Consensus       104 --~--~~~~~~---------------------------------------~~~~~~~~~~~~~~--~~~il~lDe~d~l~  138 (292)
                        .  ......                                       ...+..++......  .|.+|+|||+|.+.
T Consensus        71 ~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~  150 (357)
T 2fna_A           71 YISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELV  150 (357)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGG
T ss_pred             CCCHHHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhh
Confidence              0  000000                                       01122233333222  37899999999983


Q ss_pred             CCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC---------CChhhcCCCCcceEEEccCCCHHHHH
Q 022768          139 GRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV---------LDPALLRPGRLDRKIEIPLPNEQSRM  209 (292)
Q Consensus       139 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~---------l~~~l~~~~r~~~~i~l~~p~~~~r~  209 (292)
                      ...       .......+..+.+..      .++.+|+|++....         ....+..  |+...+.+++++.++..
T Consensus       151 ~~~-------~~~~~~~l~~~~~~~------~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~--r~~~~i~l~~l~~~e~~  215 (357)
T 2fna_A          151 KLR-------GVNLLPALAYAYDNL------KRIKFIMSGSEMGLLYDYLRVEDPESPLFG--RAFSTVELKPFSREEAI  215 (357)
T ss_dssp             GCT-------TCCCHHHHHHHHHHC------TTEEEEEEESSHHHHHHHTTTTCTTSTTTT--CCCEEEEECCCCHHHHH
T ss_pred             ccC-------chhHHHHHHHHHHcC------CCeEEEEEcCchHHHHHHHhccCCCCcccc--CccceeecCCCCHHHHH
Confidence            210       111223333333321      36777777764321         1112222  55578899999999999


Q ss_pred             HHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHH
Q 022768          210 EILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       210 ~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      +++...+.......+ +...+...+.| +|.-+..++..
T Consensus       216 ~~l~~~~~~~~~~~~-~~~~i~~~t~G-~P~~l~~~~~~  252 (357)
T 2fna_A          216 EFLRRGFQEADIDFK-DYEVVYEKIGG-IPGWLTYFGFI  252 (357)
T ss_dssp             HHHHHHHHHHTCCCC-CHHHHHHHHCS-CHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCC-cHHHHHHHhCC-CHHHHHHHHHH
Confidence            999877643222222 24778888888 66667666554

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=99.31  E-value=1.3e-11  Score=83.99  Aligned_cols=76  Identities=42%  Similarity=0.678  Sum_probs=71.2

Q ss_pred             cCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       201 ~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      |.|+.++|.+||+.++.......+++++.|+..+.|||++||..+|++|...|+.++...|+.+||.+|+..+...
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~d~~~Al~~v~~~   76 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQK   76 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHHC-
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHhc
Confidence            6899999999999999988877889999999999999999999999999999999999999999999999988653

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=99.28  E-value=1.3e-11  Score=85.39  Aligned_cols=77  Identities=40%  Similarity=0.631  Sum_probs=72.4

Q ss_pred             ccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhh
Q 022768          200 IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEA  276 (292)
Q Consensus       200 l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~  276 (292)
                      -.+|+.++|.+||+.++.......+++++.|+..+.|||++||..+|++|...|+++....|+.+||.+|+..+.+.
T Consensus         8 ~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~eAa~~alr~~~~~I~~~df~~Al~~v~p~   84 (86)
T 2krk_A            8 HSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRERRVHVTQEDFEMAVAKVMQK   84 (86)
T ss_dssp             CCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHHCC
T ss_pred             CCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHccC
Confidence            47899999999999999988877889999999999999999999999999999999988999999999999998764

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=99.22  E-value=2.3e-11  Score=93.60  Aligned_cols=100  Identities=18%  Similarity=0.303  Sum_probs=68.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR  141 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~  141 (292)
                      ++..++|+||+|+||||++++++..+   +..+++++..++...               .....+.+|+|||++.+    
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~---------------~~~~~~~lLilDE~~~~----   95 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLT---------------DAAFEAEYLAVDQVEKL----   95 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCC---------------GGGGGCSEEEEESTTCC----
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHH---------------HHHhCCCEEEEeCcccc----
Confidence            46789999999999999999999987   566778877665433               11234689999999886    


Q ss_pred             CCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC-CCCCCC--hhhcCCCCcc
Q 022768          142 FSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN-RPDVLD--PALLRPGRLD  195 (292)
Q Consensus       142 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~-~~~~l~--~~l~~~~r~~  195 (292)
                             ....+..+..+++....   .+..++|+|++ .+..+.  +++.+  |+.
T Consensus        96 -------~~~~~~~l~~li~~~~~---~g~~~iiits~~~p~~l~~~~~L~S--Rl~  140 (149)
T 2kjq_A           96 -------GNEEQALLFSIFNRFRN---SGKGFLLLGSEYTPQQLVIREDLRT--RMA  140 (149)
T ss_dssp             -------CSHHHHHHHHHHHHHHH---HTCCEEEEEESSCTTTSSCCHHHHH--HGG
T ss_pred             -------ChHHHHHHHHHHHHHHH---cCCcEEEEECCCCHHHccccHHHHH--HHh
Confidence                   32236677777766532   12333555666 444332  78887  553

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.20  E-value=4.3e-10  Score=99.36  Aligned_cols=189  Identities=23%  Similarity=0.278  Sum_probs=117.0

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--EEEEeccchhccccCh
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--FLKVVSSAIIDKYIGE  109 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--~~~~~~~~~~~~~~~~  109 (292)
                      ..++|.....+++...+...           ......++++|++|+||+.+++.+....+..  ++.++|..+.....  
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~-----------a~~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~--  195 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKI-----------AKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELA--  195 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHH-----------HTSCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTH--
T ss_pred             ccccccchHHHHHHhhhhhh-----------hccchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHH--
Confidence            46788888887777766543           1335579999999999999999999877543  99999987643321  


Q ss_pred             HHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC------
Q 022768          110 SARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ------  168 (292)
Q Consensus       110 ~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~------  168 (292)
                          -..+|+.               ......++|||||++.+           +...|..|..+++.....+-      
T Consensus       196 ----~~~lfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l-----------~~~~Q~~Ll~~l~~~~~~~~g~~~~~  260 (368)
T 3dzd_A          196 ----ESELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGEL-----------DQRVQAKLLRVLETGSFTRLGGNQKI  260 (368)
T ss_dssp             ----HHHHHEECSCSSSSCCCCEECHHHHTTTSEEEEETGGGS-----------CHHHHHHHHHHHHHSEECCBTCCCBE
T ss_pred             ----HHHhcCccccccCCcccccCChHhhcCCCeEEecChhhC-----------CHHHHHHHHHHHHhCCcccCCCCcce
Confidence                1122221               11234479999999999           88999999999986431111      


Q ss_pred             CCCeEEEEEeCCC-------CCCChhhcCCCCcc-eEEEccCCCH--HHHHHHHHHHHcCc----cCC-CCCCHHHHHHH
Q 022768          169 LGKVKMIMATNRP-------DVLDPALLRPGRLD-RKIEIPLPNE--QSRMEILKIHAAGI----AKH-GEIDYEAVVKL  233 (292)
Q Consensus       169 ~~~~~vi~t~~~~-------~~l~~~l~~~~r~~-~~i~l~~p~~--~~r~~i~~~~~~~~----~~~-~~~~~~~l~~~  233 (292)
                      .-++.+|++||..       ....+.+..  |+. ..+.+|+...  ++...++.+++...    ... ..++.+.+..+
T Consensus       261 ~~~~rii~at~~~l~~~v~~g~fr~dL~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L  338 (368)
T 3dzd_A          261 EVDIRVISATNKNLEEEIKKGNFREDLYY--RLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYL  338 (368)
T ss_dssp             ECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTSEEEECCCGGGSTTHHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHH
T ss_pred             eeeeEEEEecCCCHHHHHHcCCccHHHHH--HhCCeEEeCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHH
Confidence            1156788888853       123334444  442 2456666544  45555666555432    111 34566666666


Q ss_pred             cCCCCHHHHH---HHHHHHH
Q 022768          234 AEGFNGADLR---NVCTEAG  250 (292)
Q Consensus       234 ~~g~~~~di~---~l~~~a~  250 (292)
                      ...-.||+++   ++++.|.
T Consensus       339 ~~~~wpGNvreL~n~i~~~~  358 (368)
T 3dzd_A          339 MKQEWKGNVRELKNLIERAV  358 (368)
T ss_dssp             HTCCCTTHHHHHHHHHHHHH
T ss_pred             HhCCCCcHHHHHHHHHHHHH
Confidence            5532244555   5555544

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.20  E-value=1.1e-10  Score=123.56  Aligned_cols=139  Identities=19%  Similarity=0.311  Sum_probs=93.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc-CCcEEEEeccchhccccChHHHHHHHHHHHhh---------------hCCCEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI-DANFLKVVSSAIIDKYIGESARLIREMFGYAR---------------DHQPCII  129 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~il  129 (292)
                      ++++|++||||||||++|+.++... +..+..+++....+      ...+...+....               ..++.|+
T Consensus      1267 ~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infsa~ts------~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~Vl 1340 (2695)
T 4akg_A         1267 KRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTT------TEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVL 1340 (2695)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECCTTCC------HHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEeecCCC------HHHHHHHHHHHhhhccccCCccccCCCCCceEEE
Confidence            6799999999999999995555544 56667777655432      122223332210               1234799


Q ss_pred             EEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCC-------CCeEEEEEeCCCC-----CCChhhcCCCCcceE
Q 022768          130 FMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQL-------GKVKMIMATNRPD-----VLDPALLRPGRLDRK  197 (292)
Q Consensus       130 ~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~-------~~~~vi~t~~~~~-----~l~~~l~~~~r~~~~  197 (292)
                      ||||+|.....+.     +.+...+.|.++++........       .++.+|+|+|++.     .+++++.+  || ..
T Consensus      1341 FiDEinmp~~d~y-----g~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllR--rf-~v 1412 (2695)
T 4akg_A         1341 FCDEINLPKLDKY-----GSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTR--HA-AI 1412 (2695)
T ss_dssp             EEETTTCSCCCSS-----SCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHT--TE-EE
T ss_pred             Eeccccccccccc-----CchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhh--ee-eE
Confidence            9999987432221     1334556666666532111111       2588999999984     79999998  88 78


Q ss_pred             EEccCCCHHHHHHHHHHHHcC
Q 022768          198 IEIPLPNEQSRMEILKIHAAG  218 (292)
Q Consensus       198 i~l~~p~~~~r~~i~~~~~~~  218 (292)
                      +.++.|+.+++..|+..++..
T Consensus      1413 i~i~~P~~~~l~~I~~~il~~ 1433 (2695)
T 4akg_A         1413 LYLGYPSGKSLSQIYEIYYKA 1433 (2695)
T ss_dssp             EECCCCTTTHHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHH
Confidence            999999999999999987754

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=99.15  E-value=6.4e-11  Score=120.69  Aligned_cols=154  Identities=15%  Similarity=0.173  Sum_probs=100.6

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCC----------hHHHHh---------------c---CCCCCceEEEEcCCCC
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMN----------PELFLR---------------V---GIKPPKGVLLYGPPGT   77 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~----------~~~~~~---------------~---~~~~~~~vll~G~~G~   77 (292)
                      .+.++|+++.|.+++++.+.+.+.+++..          ...+..               +   |++.++.++++|||||
T Consensus      1014 ~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tG~~glD~~lg~GG~p~g~~~l~~G~~g~ 1093 (1706)
T 3cmw_A         1014 ASGSSTGSMSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESS 1093 (1706)
T ss_dssp             ----------CTTHHHHHHHHHHHHHHHHHHCGGGSEEGGGCGGGSCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTS
T ss_pred             cCCceeeecCCccHHHHHHHHHHHHHHhhccCcccchhchhhhhccccccccCchhHHHHhccCCCCCCCEEEEEcCCCC
Confidence            34589999999999999999999887722          122333               1   2456777999999999


Q ss_pred             hHHHHHHHHHHhc---CCcEEEEeccchh------------ccccCh----HHHHHHHHHHHhhhCCCEEEEEccccccc
Q 022768           78 GKTLLARAIASNI---DANFLKVVSSAII------------DKYIGE----SARLIREMFGYARDHQPCIIFMDEIDAIG  138 (292)
Q Consensus        78 GKT~l~~~la~~l---~~~~~~~~~~~~~------------~~~~~~----~~~~~~~~~~~~~~~~~~il~lDe~d~l~  138 (292)
                      |||++|++++.+.   +.+.++++..+..            +.+.++    .++.+..++..++...|+++++|+++.|+
T Consensus      1094 GKT~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~~~~~~i~~d~~~al~ 1173 (1706)
T 3cmw_A         1094 GKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALT 1173 (1706)
T ss_dssp             SHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCC
T ss_pred             ChHHHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHhcCCeEEEeCchHhcC
Confidence            9999999999866   5667777766533            334445    78889999998999999999999999998


Q ss_pred             CCcC---CCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          139 GRRF---SEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       139 ~~~~---~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      +.+.   +.......-..+.+.+++..+.......+++||+|-+
T Consensus      1174 ~~~~~~g~~~~~~~~~~~r~~~q~l~~~~~~~~~~~v~v~~~n~ 1217 (1706)
T 3cmw_A         1174 PKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQ 1217 (1706)
T ss_dssp             CHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHHTTCEEEEEEC
T ss_pred             cccccccccccccccHHHHHHHHHHHHHHhhhccCCeEEEEecc
Confidence            8732   2211112233344666666665444445777775443

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B*

Probab=99.12  E-value=2.9e-10  Score=79.10  Aligned_cols=75  Identities=40%  Similarity=0.636  Sum_probs=68.4

Q ss_pred             CHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          204 NEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       204 ~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      |.++|.+||+.++.+.....+++++.|+..+.||||.||..+|++|...|.++....|+.+||.+|++.+.....
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGADl~~l~~eAa~~a~r~~~~~i~~~df~~Al~~v~~~~~   76 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATEKDFLKAVDKVISGYK   76 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHHHHHHHHHHHHHHHHHSCSSBCHHHHHHHHHHHTC---
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHhcCcc
Confidence            567899999999998888889999999999999999999999999999999999999999999999999987543

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=99.11  E-value=1.5e-10  Score=79.70  Aligned_cols=76  Identities=26%  Similarity=0.459  Sum_probs=68.8

Q ss_pred             CCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhhhhh
Q 022768          203 PNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKK  278 (292)
Q Consensus       203 p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~~~~  278 (292)
                      .+.++|.+||+.++.......+++++.++..+.|||+.||..+|++|...|..+....|+.+|+..|+..+.+..+
T Consensus         1 ~d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~eA~~~a~~~~~~~i~~~df~~Al~~~~ps~~   76 (83)
T 3aji_B            1 MDRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRENRYIVLAKDFEKAYKTVIKKDE   76 (83)
T ss_dssp             CCHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHHHHHGGGTSCCSSBCHHHHHHHHHHHCC---
T ss_pred             CCHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCCcCHHHHHHHHHHHccCch
Confidence            3678999999999998887788999999999999999999999999999999998889999999999999998765

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.08  E-value=1.5e-10  Score=93.58  Aligned_cols=100  Identities=25%  Similarity=0.260  Sum_probs=60.8

Q ss_pred             CCCccccccccHH----HHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           27 GNVSYSAVGGLSD----QIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        27 ~~~~~~~l~g~~~----~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      .+.+|+++++...    +++.+..++.....         ...+.+++|+||+|+|||++++++++.+   +.+++.+++
T Consensus        20 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~   90 (202)
T 2w58_A           20 LRASLSDVDLNDDGRIKAIRFAERFVAEYEP---------GKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYV   90 (202)
T ss_dssp             GCCCTTSSCCSSHHHHHHHHHHHHHHHHCCS---------SCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEH
T ss_pred             HcCCHhhccCCChhHHHHHHHHHHHHHHhhh---------ccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEh
Confidence            4678999887553    34445555443200         0122789999999999999999999987   567777777


Q ss_pred             cchhccccChH-HHHHHHHHHHhhhCCCEEEEEcccccc
Q 022768          100 SAIIDKYIGES-ARLIREMFGYARDHQPCIIFMDEIDAI  137 (292)
Q Consensus       100 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~il~lDe~d~l  137 (292)
                      ..+........ ...+...+.....  +.+|+|||++..
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~lilDei~~~  127 (202)
T 2w58_A           91 PELFRELKHSLQDQTMNEKLDYIKK--VPVLMLDDLGAE  127 (202)
T ss_dssp             HHHHHHHHHC---CCCHHHHHHHHH--SSEEEEEEECCC
T ss_pred             HHHHHHHHHHhccchHHHHHHHhcC--CCEEEEcCCCCC
Confidence            65543221100 0001122222232  359999999765

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=99.06  E-value=8.5e-09  Score=109.53  Aligned_cols=186  Identities=14%  Similarity=0.193  Sum_probs=124.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG  145 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~  145 (292)
                      ..+.++.||+|||||++++.+|+.+|.+++.++|.+..+.      ..+..+|..+.... +++++||++++        
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~------~~lg~~~~g~~~~G-aw~~~DE~nr~--------  709 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDY------QVLSRLLVGITQIG-AWGCFDEFNRL--------  709 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCH------HHHHHHHHHHHHHT-CEEEEETTTSS--------
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCCh------hHhhHHHHHHHhcC-CEeeehhhhhc--------
Confidence            5678999999999999999999999999999999876442      23345555444443 79999999998        


Q ss_pred             CcchHHHHHHHHHHHHHhh---------------CCCCCCCeEEEEEeCC----CCCCChhhcCCCCcceEEEccCCCHH
Q 022768          146 TSADREIQRTLMELLNQLD---------------GFDQLGKVKMIMATNR----PDVLDPALLRPGRLDRKIEIPLPNEQ  206 (292)
Q Consensus       146 ~~~~~~~~~~l~~~l~~~~---------------~~~~~~~~~vi~t~~~----~~~l~~~l~~~~r~~~~i~l~~p~~~  206 (292)
                         ..+....+...+..+.               .+.-++.+.+++|.|+    ..++++.+++  || ..+.+..||.+
T Consensus       710 ---~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~--~F-r~v~m~~Pd~~  783 (2695)
T 4akg_A          710 ---DEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKK--SF-REFSMKSPQSG  783 (2695)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHT--TE-EEEECCCCCHH
T ss_pred             ---ChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHh--he-EEEEeeCCCHH
Confidence               6666666643333210               1123446788999984    4579999998  88 78999999999


Q ss_pred             HHHHHHHHHHcCccCCCCCC------HHHHHHHcC-----CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHhh
Q 022768          207 SRMEILKIHAAGIAKHGEID------YEAVVKLAE-----GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       207 ~r~~i~~~~~~~~~~~~~~~------~~~l~~~~~-----g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~~  275 (292)
                      ...+++-... +........      +..+.....     .+..+.++.++..|...-...   .-....+.+|+.+++.
T Consensus       784 ~i~ei~l~s~-Gf~~a~~la~kiv~~~~l~~e~ls~q~hydfglRalksvL~~ag~lkr~~---~~e~~~l~~al~~~~l  859 (2695)
T 4akg_A          784 TIAEMILQIM-GFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPLISEF---GEGEKTVVESLKRVIL  859 (2695)
T ss_dssp             HHHHHHHHHH-HCSSHHHHHHHHHHHHHHHHHHSCCCTTCCCSHHHHHHHHHHHHHHHHHS---CSSHHHHHHHHHHHTG
T ss_pred             HHHHHHHHhc-CCCchHHHHHHHHHHHHHHHHHhCcCCcccccHHHHHHHHHHHHHhhccC---CcHHHHHHHHHHHhcc
Confidence            8888754322 111111110      011111111     257889999888876554333   2344567788887775


Q ss_pred             h
Q 022768          276 A  276 (292)
Q Consensus       276 ~  276 (292)
                      .
T Consensus       860 p  860 (2695)
T 4akg_A          860 P  860 (2695)
T ss_dssp             G
T ss_pred             c
Confidence            3

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=98.95  E-value=7.9e-09  Score=90.39  Aligned_cols=182  Identities=11%  Similarity=0.020  Sum_probs=112.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcC---C-cEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEccccc-ccC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNID---A-NFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDA-IGG  139 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~---~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~-l~~  139 (292)
                      ..+.++|+||+|.||++.++.+++.+.   . +...+...   +.  .+....+..+..........+++|||+|. +  
T Consensus        17 ~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~---~~--~~~~~l~~~~~~~plf~~~kvvii~~~~~kl--   89 (343)
T 1jr3_D           17 LRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSID---PN--TDWNAIFSLCQAMSLFASRQTLLLLLPENGP--   89 (343)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECC---TT--CCHHHHHHHHHHHHHCCSCEEEEEECCSSCC--
T ss_pred             CCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEec---CC--CCHHHHHHHhcCcCCccCCeEEEEECCCCCC--
Confidence            356899999999999999999988662   1 22222111   11  12233332333333345568999999988 7  


Q ss_pred             CcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC------CCCChhhcCCCCcceEEEccCCCHHHHHHHHH
Q 022768          140 RRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP------DVLDPALLRPGRLDRKIEIPLPNEQSRMEILK  213 (292)
Q Consensus       140 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~  213 (292)
                               ....+..|...++     .+++.+++|++++..      ..+.+.+.+  |+ ..+.+.+++.++....++
T Consensus        90 ---------~~~~~~aLl~~le-----~p~~~~~~il~~~~~~~~~~~~k~~~~i~s--r~-~~~~~~~l~~~~l~~~l~  152 (343)
T 1jr3_D           90 ---------NAAINEQLLTLTG-----LLHDDLLLIVRGNKLSKAQENAAWFTALAN--RS-VQVTCQTPEQAQLPRWVA  152 (343)
T ss_dssp             ---------CTTHHHHHHHHHT-----TCBTTEEEEEEESCCCTTTTTSHHHHHHTT--TC-EEEEECCCCTTHHHHHHH
T ss_pred             ---------ChHHHHHHHHHHh-----cCCCCeEEEEEcCCCChhhHhhHHHHHHHh--Cc-eEEEeeCCCHHHHHHHHH
Confidence                     3444555555554     233566666666543      345667777  66 678999999999988888


Q ss_pred             HHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          214 IHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       214 ~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ..+...... .+.....++..+.| +.+++.+.++....+   .+...||.+++.+.+....
T Consensus       153 ~~~~~~g~~i~~~a~~~l~~~~~g-dl~~~~~elekl~l~---~~~~~It~e~V~~~~~~~~  210 (343)
T 1jr3_D          153 ARAKQLNLELDDAANQVLCYCYEG-NLLALAQALERLSLL---WPDGKLTLPRVEQAVNDAA  210 (343)
T ss_dssp             HHHHHTTCEECHHHHHHHHHSSTT-CHHHHHHHHHHHHHH---CTTCEECHHHHHHHHHHHC
T ss_pred             HHHHHcCCCCCHHHHHHHHHHhch-HHHHHHHHHHHHHHh---cCCCCCCHHHHHHHHhhhh
Confidence            887654332 11223445555555 555555555555433   2345799999888776554

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.94  E-value=1.7e-09  Score=86.50  Aligned_cols=114  Identities=17%  Similarity=0.216  Sum_probs=63.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRF  142 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~  142 (292)
                      ++..++++|+||||||||++|.++++.+...++.+....  ..+          .+...  ....+++|||++.-.    
T Consensus        55 iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~fans~--s~f----------~l~~l--~~~kIiiLDEad~~~----  116 (212)
T 1tue_A           55 TPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNST--SHF----------WLEPL--TDTKVAMLDDATTTC----  116 (212)
T ss_dssp             CTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCSS--SCG----------GGGGG--TTCSSEEEEEECHHH----
T ss_pred             CCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeEEecc--chh----------hhccc--CCCCEEEEECCCchh----
Confidence            455568999999999999999999999865443221100  000          00111  123599999996320    


Q ss_pred             CCCCcchHHHHHHHHHHHHHh----hCCCCC----CCeEEEEEeCCC---CCCChhhcCCCCcceEEEccCC
Q 022768          143 SEGTSADREIQRTLMELLNQL----DGFDQL----GKVKMIMATNRP---DVLDPALLRPGRLDRKIEIPLP  203 (292)
Q Consensus       143 ~~~~~~~~~~~~~l~~~l~~~----~~~~~~----~~~~vi~t~~~~---~~l~~~l~~~~r~~~~i~l~~p  203 (292)
                            -......+..+++.-    +.....    ....+|+|||..   +..-+.+.+  |+ .++.|+.|
T Consensus       117 ------~~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~S--Ri-~~f~F~~~  179 (212)
T 1tue_A          117 ------WTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLES--RI-TVFEFPNA  179 (212)
T ss_dssp             ------HHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHT--SC-EEEECCSC
T ss_pred             ------HHHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhh--hE-EEEEcCCC
Confidence                  122223344444331    111111    135688999873   223356777  77 56666643

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.90  E-value=7.4e-10  Score=95.50  Aligned_cols=98  Identities=17%  Similarity=0.245  Sum_probs=58.4

Q ss_pred             CCccccccccH----HHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEec
Q 022768           28 NVSYSAVGGLS----DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVS   99 (292)
Q Consensus        28 ~~~~~~l~g~~----~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~   99 (292)
                      +.+|+++.+..    .+.+.+..++..+          +...+.+++|+||+|+|||+++.++++.+.    .+++.++.
T Consensus       120 ~~tfd~f~~~~~~~~~~~~~~~~~i~~~----------~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~  189 (308)
T 2qgz_A          120 HIHLSDIDVNNASRMEAFSAILDFVEQY----------PSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHF  189 (308)
T ss_dssp             SCCGGGSCCCSHHHHHHHHHHHHHHHHC----------SCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEH
T ss_pred             hCCHhhCcCCChHHHHHHHHHHHHHHhc----------cccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEH
Confidence            46899988643    2344444555432          111357899999999999999999998664    67777777


Q ss_pred             cchhccccChH-HHHHHHHHHHhhhCCCEEEEEcccccc
Q 022768          100 SAIIDKYIGES-ARLIREMFGYARDHQPCIIFMDEIDAI  137 (292)
Q Consensus       100 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~il~lDe~d~l  137 (292)
                      ..+........ .......+....  ...+|+|||++..
T Consensus       190 ~~l~~~l~~~~~~~~~~~~~~~~~--~~~lLiiDdig~~  226 (308)
T 2qgz_A          190 PSFAIDVKNAISNGSVKEEIDAVK--NVPVLILDDIGAE  226 (308)
T ss_dssp             HHHHHHHHCCCC----CCTTHHHH--TSSEEEEETCCC-
T ss_pred             HHHHHHHHHHhccchHHHHHHHhc--CCCEEEEcCCCCC
Confidence            65543221110 001111122222  2369999999654

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.89  E-value=2.9e-09  Score=85.71  Aligned_cols=126  Identities=19%  Similarity=0.213  Sum_probs=76.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh--------cC-CcEEEEeccchhcccc----------Ch-----HHHHHHHHHHHhh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN--------ID-ANFLKVVSSAIIDKYI----------GE-----SARLIREMFGYAR  122 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~--------l~-~~~~~~~~~~~~~~~~----------~~-----~~~~~~~~~~~~~  122 (292)
                      ..++++|+||+|||++|..++..        .| .+++..+..++.....          ..     ....+..++. ..
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~-~~   84 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIK-KP   84 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTT-SG
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhh-cc
Confidence            36889999999999998776433        24 6666666554432111          00     0111222211 12


Q ss_pred             hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccC
Q 022768          123 DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPL  202 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~  202 (292)
                      ...+++|+|||++.+++.+.+... .    .    .++..+.. ......-+|.+++.+..++..+++  |+...+++..
T Consensus        85 ~~~~~vliIDEAq~l~~~~~~~~e-~----~----rll~~l~~-~r~~~~~iil~tq~~~~l~~~lr~--ri~~~~~l~~  152 (199)
T 2r2a_A           85 ENIGSIVIVDEAQDVWPARSAGSK-I----P----ENVQWLNT-HRHQGIDIFVLTQGPKLLDQNLRT--LVRKHYHIAS  152 (199)
T ss_dssp             GGTTCEEEETTGGGTSBCCCTTCC-C----C----HHHHGGGG-TTTTTCEEEEEESCGGGBCHHHHT--TEEEEEEEEE
T ss_pred             ccCceEEEEEChhhhccCccccch-h----H----HHHHHHHh-cCcCCeEEEEECCCHHHHhHHHHH--HhheEEEEcC
Confidence            234589999999999754422111 1    1    23333322 223456788888889999999998  9988888877


Q ss_pred             CCH
Q 022768          203 PNE  205 (292)
Q Consensus       203 p~~  205 (292)
                      +..
T Consensus       153 ~~~  155 (199)
T 2r2a_A          153 NKM  155 (199)
T ss_dssp             CSS
T ss_pred             ccc
Confidence            543

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=98.89  E-value=1.2e-09  Score=93.55  Aligned_cols=112  Identities=14%  Similarity=0.143  Sum_probs=62.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec--cchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS--SAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~  140 (292)
                      +.++..++|+||||+|||+++.+++...+.++.++..  .+..+.+.......+..+........  +|+||+++.+...
T Consensus       120 i~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~--LLVIDsI~aL~~~  197 (331)
T 2vhj_A          120 RYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHR--VIVIDSLKNVIGA  197 (331)
T ss_dssp             EEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCS--EEEEECCTTTC--
T ss_pred             CCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCC--EEEEecccccccc
Confidence            4567778999999999999999999875545444333  33322222344555555555555544  9999999998543


Q ss_pred             cCCC-C-CcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCC
Q 022768          141 RFSE-G-TSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR  180 (292)
Q Consensus       141 ~~~~-~-~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~  180 (292)
                      ..+. . ..........+..+.....    ..++.+|+++|.
T Consensus       198 ~~~~s~~G~v~~~lrqlL~~L~~~~k----~~gvtVIlttnp  235 (331)
T 2vhj_A          198 AGGNTTSGGISRGAFDLLSDIGAMAA----SRGCVVIASLNP  235 (331)
T ss_dssp             ---------CCHHHHHHHHHHHHHHH----HHTCEEEEECCC
T ss_pred             cccccccchHHHHHHHHHHHHHHHHh----hCCCEEEEEeCC
Confidence            3221 0 0112222333333333222    135667888774

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=98.85  E-value=1e-09  Score=75.21  Aligned_cols=69  Identities=22%  Similarity=0.328  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          206 QSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       206 ~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      ++|.+||+.++.......+++++.++..+.|||+.||..+|++|...|..+....|+.+|+.+|+..+.
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGADi~~l~~eAa~~ai~~~~~~i~~~df~~Al~~v~   69 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRKNRYVILQSDLEEAYATQV   69 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHTTC
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhccCCcCHHHHHHHHHHHH
Confidence            468899999998877777899999999999999999999999999999999989999999999999985

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.73  E-value=8.9e-08  Score=102.61  Aligned_cols=139  Identities=20%  Similarity=0.344  Sum_probs=90.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc-CCcEEEEeccchhccccChHHHHHHHHHHH-h---h------------hCCCE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI-DANFLKVVSSAIIDKYIGESARLIREMFGY-A---R------------DHQPC  127 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~---~------------~~~~~  127 (292)
                      .+.++||+||+|||||.+++.+++.+ +.+++.++++...+      ...+...+.. .   .            ..+..
T Consensus      1303 ~~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tt------a~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~ 1376 (3245)
T 3vkg_A         1303 EHRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATT------PELLLKTFDHHCEYKRTPSGETVLRPTQLGKWL 1376 (3245)
T ss_dssp             TTCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCC------HHHHHHHHHHHEEEEECTTSCEEEEESSTTCEE
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCC------HHHHHHHHhhcceEEeccCCCcccCCCcCCceE
Confidence            36789999999999998887766655 44566666654322      2223233321 0   0            01235


Q ss_pred             EEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC-------CCCeEEEEEeCCCC-----CCChhhcCCCCcc
Q 022768          128 IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ-------LGKVKMIMATNRPD-----VLDPALLRPGRLD  195 (292)
Q Consensus       128 il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~-------~~~~~vi~t~~~~~-----~l~~~l~~~~r~~  195 (292)
                      |+||||++.-...+.     +.+...+.|.++++....+..       ..++.+|+|+|++.     .+++++.+  || 
T Consensus      1377 VlFiDDiNmp~~D~y-----GtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r--~F- 1448 (3245)
T 3vkg_A         1377 VVFCDEINLPSTDKY-----GTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLR--HA- 1448 (3245)
T ss_dssp             EEEETTTTCCCCCTT-----SCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHT--TC-
T ss_pred             EEEecccCCCCcccc-----ccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHh--hc-
Confidence            999999986422111     134466777777765322111       13688999999873     58999998  88 


Q ss_pred             eEEEccCCCHHHHHHHHHHHHc
Q 022768          196 RKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       196 ~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      ..+.++.|+.++...|+..++.
T Consensus      1449 ~vi~i~~ps~esL~~If~til~ 1470 (3245)
T 3vkg_A         1449 PILLVDFPSTSSLTQIYGTFNR 1470 (3245)
T ss_dssp             CEEECCCCCHHHHHHHHHHHHH
T ss_pred             eEEEeCCCCHHHHHHHHHHHHH
Confidence            5689999999999999876654

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.69  E-value=2.4e-06  Score=79.97  Aligned_cols=179  Identities=11%  Similarity=0.092  Sum_probs=100.2

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-------CCcEEEEecc
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-------DANFLKVVSS  100 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-------~~~~~~~~~~  100 (292)
                      |.....++|.+...++|.+.+...           -...+.+.|+|++|+|||++|+.+++..       ...++.++..
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~-----------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~  188 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKL-----------KGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVG  188 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTS-----------TTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEE
T ss_pred             CCCCCeecccHHHHHHHHHHHhcc-----------cCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECC
Confidence            344567999999999999987642           1235678999999999999999997532       2223333322


Q ss_pred             chhcc-----c-----------------cChHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHH
Q 022768          101 AIIDK-----Y-----------------IGESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLM  157 (292)
Q Consensus       101 ~~~~~-----~-----------------~~~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~  157 (292)
                      .....     .                 ..........+...... .++.+|+|||++..                .   
T Consensus       189 ~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~----------------~---  249 (591)
T 1z6t_A          189 KQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS----------------W---  249 (591)
T ss_dssp             SCCHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH----------------H---
T ss_pred             CCchHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH----------------H---
Confidence            21000     0                 00011111112111122 25789999999643                1   


Q ss_pred             HHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEE-ccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCC
Q 022768          158 ELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE-IPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEG  236 (292)
Q Consensus       158 ~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~-l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g  236 (292)
                       .+..+     .++..||+|++....... ...  .. ..+. +.+++.++-.+++.................+...+.|
T Consensus       250 -~l~~l-----~~~~~ilvTsR~~~~~~~-~~~--~~-~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G  319 (591)
T 1z6t_A          250 -VLKAF-----DSQCQILLTTRDKSVTDS-VMG--PK-YVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKG  319 (591)
T ss_dssp             -HHHTT-----CSSCEEEEEESCGGGGTT-CCS--CE-EEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTT
T ss_pred             -HHHHh-----cCCCeEEEECCCcHHHHh-cCC--Cc-eEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCC
Confidence             11211     245678888875432111 111  11 2222 2478999999999988754222223346778888888


Q ss_pred             CCHHHHHHHHH
Q 022768          237 FNGADLRNVCT  247 (292)
Q Consensus       237 ~~~~di~~l~~  247 (292)
                       .|--+..+..
T Consensus       320 -~PLal~~~a~  329 (591)
T 1z6t_A          320 -SPLVVSLIGA  329 (591)
T ss_dssp             -CHHHHHHHHH
T ss_pred             -CcHHHHHHHH
Confidence             5545554433

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=98.68  E-value=1.7e-07  Score=74.04  Aligned_cols=27  Identities=30%  Similarity=0.599  Sum_probs=23.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      .+.|.||+|+||||+++.++..++..+
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~i~~   28 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLGKRA   28 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGGGE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcC
Confidence            478999999999999999999876443

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.68  E-value=1.6e-07  Score=100.62  Aligned_cols=128  Identities=16%  Similarity=0.250  Sum_probs=95.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG  145 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~  145 (292)
                      ..+..+.||+|||||.+++.+|+.+|.+++.++|.+-.+.      ..+..+|..+..+ .+..++|||+++        
T Consensus       604 ~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~------~~~g~i~~G~~~~-GaW~cfDEfNrl--------  668 (3245)
T 3vkg_A          604 RMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDL------QAMSRIFVGLCQC-GAWGCFDEFNRL--------  668 (3245)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCH------HHHHHHHHHHHHH-TCEEEEETTTSS--------
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCH------HHHHHHHhhHhhc-CcEEEehhhhcC--------
Confidence            3456799999999999999999999999999998875432      2344555544444 378999999998        


Q ss_pred             CcchHHHHHHHHHHHHHh----------------hCCCCCCCeEEEEEeCC----CCCCChhhcCCCCcceEEEccCCCH
Q 022768          146 TSADREIQRTLMELLNQL----------------DGFDQLGKVKMIMATNR----PDVLDPALLRPGRLDRKIEIPLPNE  205 (292)
Q Consensus       146 ~~~~~~~~~~l~~~l~~~----------------~~~~~~~~~~vi~t~~~----~~~l~~~l~~~~r~~~~i~l~~p~~  205 (292)
                         +.+....+.+.+..+                ..+.-++.+.+++|.|+    ..++++.++.  +| ..+.+..||.
T Consensus       669 ---~~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~--lF-r~v~m~~Pd~  742 (3245)
T 3vkg_A          669 ---EERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKK--LF-RSMAMIKPDR  742 (3245)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHT--TE-EEEECCSCCH
T ss_pred             ---CHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHh--hc-EEEEEeCCCH
Confidence               666666665544421                11233446889999985    4679999999  88 6799999999


Q ss_pred             HHHHHHHHH
Q 022768          206 QSRMEILKI  214 (292)
Q Consensus       206 ~~r~~i~~~  214 (292)
                      +...+++-.
T Consensus       743 ~~i~ei~L~  751 (3245)
T 3vkg_A          743 EMIAQVMLY  751 (3245)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988888643

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=98.62  E-value=7.6e-08  Score=80.34  Aligned_cols=121  Identities=21%  Similarity=0.275  Sum_probs=70.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSE  144 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~  144 (292)
                      +..+++|+||||||||++++++|+.++. +..++...  ..+          .+..  .....++++||....       
T Consensus       103 ~~n~~~l~GppgtGKt~~a~ala~~~~l-~G~vn~~~--~~f----------~l~~--~~~k~i~l~Ee~~~~-------  160 (267)
T 1u0j_A          103 KRNTIWLFGPATTGKTNIAEAIAHTVPF-YGCVNWTN--ENF----------PFND--CVDKMVIWWEEGKMT-------  160 (267)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHHSSC-EEECCTTC--SSC----------TTGG--GSSCSEEEECSCCEE-------
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHhhhcc-cceeeccc--ccc----------cccc--ccccEEEEeccccch-------
Confidence            3567999999999999999999997643 22222211  000          1111  122357777777554       


Q ss_pred             CCcchHHHHHHHHHHHH----HhhCCC----CCCCeEEEEEeCC-C----------CCCChhhcCCCCcceEEEcc----
Q 022768          145 GTSADREIQRTLMELLN----QLDGFD----QLGKVKMIMATNR-P----------DVLDPALLRPGRLDRKIEIP----  201 (292)
Q Consensus       145 ~~~~~~~~~~~l~~~l~----~~~~~~----~~~~~~vi~t~~~-~----------~~l~~~l~~~~r~~~~i~l~----  201 (292)
                           .+....+..++.    .++...    ...+..+|+|||. .          +...+.|++  |+ ..+.|+    
T Consensus       161 -----~d~~~~lr~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~s--R~-~~f~F~~~~p  232 (267)
T 1u0j_A          161 -----AKVVESAKAILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQD--RM-FKFELTRRLD  232 (267)
T ss_dssp             -----TTTHHHHHHHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHT--TE-EEEECCSCCC
T ss_pred             -----hHHHHHHHHHhCCCcEEEecCcCCcccccCCCEEEEecCCcccccccCccchhhhHHHhh--hE-EEEECCCcCC
Confidence                 122233444443    111111    1135668888886 1          234567888  77 777787    


Q ss_pred             ----CCCHHHHHHHHHHH
Q 022768          202 ----LPNEQSRMEILKIH  215 (292)
Q Consensus       202 ----~p~~~~r~~i~~~~  215 (292)
                          +.+.++-...+++.
T Consensus       233 ~~~~~lt~~~~~~f~~w~  250 (267)
T 1u0j_A          233 HDFGKVTKQEVKDFFRWA  250 (267)
T ss_dssp             TTSCCCCHHHHHHHHHHH
T ss_pred             cccCCCCHHHHHHHHHHH
Confidence                66778888877754

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A*

Probab=98.52  E-value=6e-06  Score=83.55  Aligned_cols=185  Identities=12%  Similarity=0.130  Sum_probs=107.3

Q ss_pred             hhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc-------CC
Q 022768           20 NMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI-------DA   92 (292)
Q Consensus        20 ~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l-------~~   92 (292)
                      ..+.....|.....++|+++.+++|.+.+...           -...+.+.|+|+.|+|||+||+.+++..       ..
T Consensus       112 ~~l~~~~~p~~~~~~vgR~~~~~~l~~~l~~~-----------~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~  180 (1249)
T 3sfz_A          112 TVLCEGGVPQRPVIFVTRKKLVHAIQQKLWKL-----------NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSG  180 (1249)
T ss_dssp             HHHHHTTCCCCCSSCCCCHHHHHHHHHHHHTT-----------TTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTT
T ss_pred             heeccCCCCCCCceeccHHHHHHHHHHHHhhc-----------cCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCC
Confidence            33444445555677999999999999988532           1234568899999999999999988752       22


Q ss_pred             cEEEEeccchhcc---------------------ccChHHHHHHHHHHHhhhC--CCEEEEEcccccccCCcCCCCCcch
Q 022768           93 NFLKVVSSAIIDK---------------------YIGESARLIREMFGYARDH--QPCIIFMDEIDAIGGRRFSEGTSAD  149 (292)
Q Consensus        93 ~~~~~~~~~~~~~---------------------~~~~~~~~~~~~~~~~~~~--~~~il~lDe~d~l~~~~~~~~~~~~  149 (292)
                      .++.++.......                     ........+...+......  ++.+|+||+++..            
T Consensus       181 ~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~------------  248 (1249)
T 3sfz_A          181 GVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP------------  248 (1249)
T ss_dssp             CEEEEECCSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCH------------
T ss_pred             eEEEEEECCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCH------------
Confidence            3334443321100                     0001112222222222222  3689999999643            


Q ss_pred             HHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccC-CCHHHHHHHHHHHHcCccCCCCCCHH
Q 022768          150 REIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPL-PNEQSRMEILKIHAAGIAKHGEIDYE  228 (292)
Q Consensus       150 ~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~-p~~~~r~~i~~~~~~~~~~~~~~~~~  228 (292)
                          ..    +..   +  .++..||+||+.+.......    .....+.++. ++.++-.+++..+.............
T Consensus       249 ----~~----~~~---~--~~~~~ilvTtR~~~~~~~~~----~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~  311 (1249)
T 3sfz_A          249 ----WV----LKA---F--DNQCQILLTTRDKSVTDSVM----GPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAH  311 (1249)
T ss_dssp             ----HH----HTT---T--CSSCEEEEEESSTTTTTTCC----SCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHH
T ss_pred             ----HH----HHh---h--cCCCEEEEEcCCHHHHHhhc----CCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHH
Confidence                11    111   1  24567889988654321111    2234567775 88899999998877533222223356


Q ss_pred             HHHHHcCCCCHHHHHHH
Q 022768          229 AVVKLAEGFNGADLRNV  245 (292)
Q Consensus       229 ~l~~~~~g~~~~di~~l  245 (292)
                      .+.....|. |--|..+
T Consensus       312 ~i~~~~~gl-PLal~~~  327 (1249)
T 3sfz_A          312 SIIKECKGS-PLVVSLI  327 (1249)
T ss_dssp             HHHHHTTTC-HHHHHHH
T ss_pred             HHHHHhCCC-HHHHHHH
Confidence            788888874 4344433

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.50  E-value=3e-07  Score=95.20  Aligned_cols=79  Identities=19%  Similarity=0.262  Sum_probs=58.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |+.++.+++|+||||+|||++|.+++.+.   +..+.+++..+....                .....+..+..+...++
T Consensus      1423 Gi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr 1502 (2050)
T 3cmu_A         1423 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1502 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHHHh
Confidence            37889999999999999999999998765   556777765543211                11123456666677777


Q ss_pred             hCCCEEEEEcccccccCC
Q 022768          123 DHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~  140 (292)
                      ...|++|+||+++.+.+.
T Consensus      1503 ~~~~~lVVIDsi~al~p~ 1520 (2050)
T 3cmu_A         1503 SGAVDVIVVDSVAALTPK 1520 (2050)
T ss_dssp             HTCCSEEEESCGGGCCCH
T ss_pred             cCCCCEEEEcChhHhccc
Confidence            788999999999988653

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=98.41  E-value=2.6e-06  Score=69.62  Aligned_cols=37  Identities=30%  Similarity=0.375  Sum_probs=29.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      |+.++..++|.||+|+||||+++.++...   +..++.++
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            35678889999999999999999999654   44555544

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=98.36  E-value=9.1e-07  Score=72.98  Aligned_cols=78  Identities=15%  Similarity=0.298  Sum_probs=50.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh--c-------CCcEEEEeccchhc---------cc--------------cC-
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN--I-------DANFLKVVSSAIID---------KY--------------IG-  108 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~--l-------~~~~~~~~~~~~~~---------~~--------------~~-  108 (292)
                      |+.++..++|+||+|+||||+++.++..  .       +..+++++......         ..              .. 
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~   99 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAF   99 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHHHHHTTCCHHHHHHTEEEEECC
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHHHHHHHcCCCHHHHhhCeEEEecC
Confidence            3677888999999999999999999984  3       34567766544100         00              00 


Q ss_pred             hHH---HHHHHHHHHhhhCCCEEEEEcccccccC
Q 022768          109 ESA---RLIREMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       109 ~~~---~~~~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      ...   ..+..+...+....|.+|+||++..+..
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~lliiD~~~~~~~  133 (243)
T 1n0w_A          100 NTDHQTQLLYQASAMMVESRYALLIVDSATALYR  133 (243)
T ss_dssp             SHHHHHHHHHHHHHHHHHSCEEEEEEETSSGGGC
T ss_pred             CHHHHHHHHHHHHHHHhcCCceEEEEeCchHHHH
Confidence            011   1122233334456789999999988753

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=98.35  E-value=9.1e-07  Score=71.82  Aligned_cols=40  Identities=28%  Similarity=0.303  Sum_probs=33.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      |+.++..++|.||+|+||||+++.++...+.++++++...
T Consensus        16 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~~   55 (220)
T 2cvh_A           16 GFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEG   55 (220)
T ss_dssp             SBCTTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESSC
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECCC
Confidence            3677888999999999999999999985566777777544

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=98.35  E-value=1.6e-06  Score=75.69  Aligned_cols=78  Identities=17%  Similarity=0.161  Sum_probs=51.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |+.++..++|+||||+||||++..++..+   +..+++++.......                ........+..+.....
T Consensus        57 Gi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~  136 (356)
T 3hr8_A           57 GYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDELVR  136 (356)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHHHhh
Confidence            36778889999999999999999999865   556777775542210                01112222322222333


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+.+++||.+..+.+
T Consensus       137 ~~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          137 SGVVDLIVVDSVAALVP  153 (356)
T ss_dssp             TSCCSEEEEECTTTCCC
T ss_pred             hcCCCeEEehHhhhhcC
Confidence            45678999999988864

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=98.29  E-value=1.1e-06  Score=76.86  Aligned_cols=78  Identities=19%  Similarity=0.214  Sum_probs=50.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc----------------cChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY----------------IGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~  122 (292)
                      |+.++..++|+||||+||||++..++...   +..+++++........                .......+..+...+.
T Consensus        57 Gl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~  136 (349)
T 2zr9_A           57 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVR  136 (349)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            35678889999999999999999998654   5567776654322110                0012222222222333


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...|.+|+||++..+..
T Consensus       137 ~~~~~lIVIDsl~~l~~  153 (349)
T 2zr9_A          137 SGALDIIVIDSVAALVP  153 (349)
T ss_dssp             TTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEcChHhhcc
Confidence            45689999999999863

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=98.28  E-value=1.5e-06  Score=78.93  Aligned_cols=58  Identities=21%  Similarity=0.344  Sum_probs=37.5

Q ss_pred             hhhcccCCCCCcccccc-ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           19 YNMLHEDPGNVSYSAVG-GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~-g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.+..+++.|.+|++|- ++.+++..+...+...              ...++|.|++|||||+++..++..+
T Consensus        11 ~~~~~~~~~p~~~~~Ln~~Q~~av~~~~~~i~~~--------------~~~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           11 SSGLVPRGSHMTFDDLTEGQKNAFNIVMKAIKEK--------------KHHVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             ----------CCSSCCCHHHHHHHHHHHHHHHSS--------------SCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCccccCCCccccCCHHHHHHHHHHHHHHhcC--------------CCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            34556788889999885 5666666666665431              2389999999999999999999877

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=98.28  E-value=3.8e-06  Score=73.80  Aligned_cols=78  Identities=22%  Similarity=0.268  Sum_probs=51.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc----------------cChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY----------------IGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~  122 (292)
                      |+.++..++|+|+||+|||+++..++...   +.++++++........                ....+..+..+.....
T Consensus        70 Gl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~  149 (366)
T 1xp8_A           70 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  149 (366)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHh
Confidence            46778889999999999999999988764   5677777755422110                0112222222222233


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+++|+||.+..+..
T Consensus       150 ~~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          150 SGAIDVVVVDSVAALTP  166 (366)
T ss_dssp             TTCCSEEEEECTTTCCC
T ss_pred             cCCCCEEEEeChHHhcc
Confidence            45678999999999864

>1svm_A Large T antigen; AAA+ fold, viral protein; HET: ATP; 1.94A {Simian virus 40} SCOP: c.37.1.20 PDB: 1svl_A* 1svo_A 1n25_A 2h1l_A

Probab=98.25  E-value=1.1e-06  Score=77.45  Aligned_cols=118  Identities=21%  Similarity=0.263  Sum_probs=66.2

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCC
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~  140 (292)
                      +++.++..++|+||+|+||||+++.++...+..++.+.....      .....    ++  ......++++||++.+..-
T Consensus       164 ~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~~~~~------~~~~~----lg--~~~q~~~~l~dd~~~~~~~  231 (377)
T 1svm_A          164 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLD------RLNFE----LG--VAIDQFLVVFEDVKGTGGE  231 (377)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTT------THHHH----HG--GGTTCSCEEETTCCCSTTT
T ss_pred             cccCCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEeccch------hHHHH----HH--HhcchhHHHHHHHHHHHHH
Confidence            367888899999999999999999999988765544221110      10111    11  1122356799999987531


Q ss_pred             cCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEE
Q 022768          141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIE  199 (292)
Q Consensus       141 ~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~  199 (292)
                      ...... .. ... .+..+.+.+.     +.+.+++++|.++.+ +.+.+++++...+.
T Consensus       232 ~r~l~~-~~-~~~-~~~~l~~~ld-----G~v~v~~~tn~~~~l-~alf~pg~ld~~~~  281 (377)
T 1svm_A          232 SRDLPS-GQ-GIN-NLDNLRDYLD-----GSVKVNLEKKHLNKR-TQIFPPGIVTMNEY  281 (377)
T ss_dssp             TTTCCC-CS-HHH-HHHTTHHHHH-----CSSCEEECCSSSCCE-EECCCCEEEEECSC
T ss_pred             Hhhccc-cC-cch-HHHHHHHHhc-----CCCeEeeccCchhhH-HHhhcCcccChhHH
Confidence            100000 01 110 1122223333     234577788888877 56665555544433

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A*

Probab=98.23  E-value=4.2e-05  Score=71.01  Aligned_cols=169  Identities=13%  Similarity=0.132  Sum_probs=93.5

Q ss_pred             cccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHH----hcCCcE---EEEeccchh----
Q 022768           35 GGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIAS----NIDANF---LKVVSSAII----  103 (292)
Q Consensus        35 ~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~----~l~~~~---~~~~~~~~~----  103 (292)
                      +|+++.+++|.+.+...          +-.....+.|+|+.|+||||+|+.+++    .....|   +.++.....    
T Consensus       131 ~GR~~~~~~l~~~L~~~----------~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~  200 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEM----------CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKST  200 (549)
T ss_dssp             CCCHHHHHHHHHHHHHH----------TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHH
T ss_pred             CCchHHHHHHHHHHhcc----------cCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCH
Confidence            49999999999988542          012346788999999999999999996    333222   222222210    


Q ss_pred             cc--------c--------c----ChHHHHHHHHHHHhhhCC-CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHH
Q 022768          104 DK--------Y--------I----GESARLIREMFGYARDHQ-PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ  162 (292)
Q Consensus       104 ~~--------~--------~----~~~~~~~~~~~~~~~~~~-~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~  162 (292)
                      ..        .        .    ......+...+......+ +.+|+||+++..           ...   .+.   ..
T Consensus       201 ~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~-----------~~~---~~~---~~  263 (549)
T 2a5y_B          201 FDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQE-----------ETI---RWA---QE  263 (549)
T ss_dssp             HHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCH-----------HHH---HHH---HH
T ss_pred             HHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCc-----------hhh---ccc---cc
Confidence            00        0        0    000111222233333343 789999999754           111   111   11


Q ss_pred             hhCCCCCCCeEEEEEeCCCCCCChhhcCCC-CcceEEEccCCCHHHHHHHHHHHHcCccCCCCC--CHHHHHHHcCCCCH
Q 022768          163 LDGFDQLGKVKMIMATNRPDVLDPALLRPG-RLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI--DYEAVVKLAEGFNG  239 (292)
Q Consensus       163 ~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~-r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~--~~~~l~~~~~g~~~  239 (292)
                             .+..||+||+...     +.... .....+.+++++.++-.+++..+..........  ....++....| .|
T Consensus       264 -------~gs~ilvTTR~~~-----v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c~G-lP  330 (549)
T 2a5y_B          264 -------LRLRCLVTTRDVE-----ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSG-NP  330 (549)
T ss_dssp             -------TTCEEEEEESBGG-----GGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTT-CH
T ss_pred             -------CCCEEEEEcCCHH-----HHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHhCC-Ch
Confidence                   3566888887532     22110 122568899999999999999875432110000  13456666776 44


Q ss_pred             HHHH
Q 022768          240 ADLR  243 (292)
Q Consensus       240 ~di~  243 (292)
                      --|.
T Consensus       331 LAl~  334 (549)
T 2a5y_B          331 ATLM  334 (549)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            3443

>4a74_A DNA repair and recombination protein RADA; hydrolase, recombinase; HET: DNA ANP; 1.48A {Pyrococcus furiosus} PDB: 4a6x_A* 4a6p_A* 4a7o_A*

Probab=98.22  E-value=5.2e-06  Score=67.75  Aligned_cols=29  Identities=34%  Similarity=0.515  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      |+.++..+.|.||+|+||||+++.++...
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            46778889999999999999999999844

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=98.19  E-value=2.4e-06  Score=73.99  Aligned_cols=78  Identities=14%  Similarity=0.255  Sum_probs=51.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccchh--c-------cc---------------cC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSAII--D-------KY---------------IG  108 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~~~--~-------~~---------------~~  108 (292)
                      |+.++..++|+|+||+|||+++..++...         +..+++++.....  .       ..               ..
T Consensus       103 Gl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~g~~~~~~~~~l~~~~~~  182 (324)
T 2z43_A          103 GIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDIDNVMNNIYYIRAI  182 (324)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHTTCCHHHHHHTEEEEECC
T ss_pred             CCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHhCCCHHHHhccEEEEeCC
Confidence            56778889999999999999999999865         4567777765421  0       00               00


Q ss_pred             hHH---HHHHHHHHHhhh-CCCEEEEEcccccccC
Q 022768          109 ESA---RLIREMFGYARD-HQPCIIFMDEIDAIGG  139 (292)
Q Consensus       109 ~~~---~~~~~~~~~~~~-~~~~il~lDe~d~l~~  139 (292)
                      ...   ..+..+...... ..+.+|+||.+..+..
T Consensus       183 ~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~  217 (324)
T 2z43_A          183 NTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFR  217 (324)
T ss_dssp             SHHHHHHHHHHHHHHHHHCTTEEEEEETTTTHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhccCCCEEEEeCcHHHhh
Confidence            011   122333344444 6789999999998863

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=98.18  E-value=5.2e-06  Score=72.43  Aligned_cols=78  Identities=15%  Similarity=0.192  Sum_probs=51.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccchhc--c-------c-----------------
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSAIID--K-------Y-----------------  106 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~~~~--~-------~-----------------  106 (292)
                      |+.++..++|+||||+|||+++..++...         +..+++++......  .       .                 
T Consensus       118 Gl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~~g~~~~~~l~~l~~~~~~  197 (343)
T 1v5w_A          118 GIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHDAVLDNVLYARAY  197 (343)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHHTTCCHHHHHHTEEEEECC
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHcCCCHHHHHhceeEeecC
Confidence            57788889999999999999999999862         45677777554211  0       0                 


Q ss_pred             -cChHHHHHHHHHHHhhh--CCCEEEEEcccccccC
Q 022768          107 -IGESARLIREMFGYARD--HQPCIIFMDEIDAIGG  139 (292)
Q Consensus       107 -~~~~~~~~~~~~~~~~~--~~~~il~lDe~d~l~~  139 (292)
                       ..+....+..+...+..  ..+.+|+||.+..+..
T Consensus       198 ~~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~l~~  233 (343)
T 1v5w_A          198 TSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFR  233 (343)
T ss_dssp             STTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGGHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCCCccEEEEechHHHHH
Confidence             00111122223333444  5678999999998863

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=98.18  E-value=3.2e-06  Score=73.98  Aligned_cols=78  Identities=21%  Similarity=0.295  Sum_probs=50.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccc---------------cChHHHHHHHHHH-Hhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKY---------------IGESARLIREMFG-YAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~---------------~~~~~~~~~~~~~-~~~  122 (292)
                      |+.++..++|+|+||+|||++|..++...   +.++++++........               .......+...+. ...
T Consensus        59 Gl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~  138 (356)
T 1u94_A           59 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  138 (356)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHHHHh
Confidence            36778889999999999999999998754   5677777764322110               0011112222222 223


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+.+|+||.+..+..
T Consensus       139 ~~~~~lVVIDsl~~l~~  155 (356)
T 1u94_A          139 SGAVDVIVVDSVAALTP  155 (356)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             ccCCCEEEEcCHHHhcc
Confidence            45678999999998864

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=98.15  E-value=4.8e-06  Score=73.99  Aligned_cols=79  Identities=19%  Similarity=0.281  Sum_probs=49.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccchhcc--------ccC----------------
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSAIIDK--------YIG----------------  108 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~~~~~--------~~~----------------  108 (292)
                      |+.++..+.|+||||+|||||++.++...         +..+++++.......        ..+                
T Consensus       174 GI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~~~a~~~gl~~~~vleni~~~~~~  253 (400)
T 3lda_A          174 GVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLVSIAQRFGLDPDDALNNVAYARAY  253 (400)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHHHHHTTCCHHHHHHTEEEEECC
T ss_pred             CcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHHHHHHHHcCCChHhHhhcEEEeccC
Confidence            67788889999999999999999876432         234666665432110        000                


Q ss_pred             ---hHHHHHHHHHHHhhhCCCEEEEEcccccccCC
Q 022768          109 ---ESARLIREMFGYARDHQPCIIFMDEIDAIGGR  140 (292)
Q Consensus       109 ---~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~  140 (292)
                         .....+..+...+....|.+|+||++..++..
T Consensus       254 ~~~~~~~~l~~~~~~l~~~~~~llVIDs~t~~~~~  288 (400)
T 3lda_A          254 NADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRT  288 (400)
T ss_dssp             SHHHHHHHHHHHHHHHHHSCEEEEEEETGGGGCC-
T ss_pred             ChHHHHHHHHHHHHHHHhcCCceEEecchhhhCch
Confidence               00112222333344467899999999887643

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=98.14  E-value=8.2e-06  Score=71.40  Aligned_cols=98  Identities=19%  Similarity=0.279  Sum_probs=58.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEecc-chh---------ccccChHHHHHHHHHHHhhhCCCEEEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSS-AII---------DKYIGESARLIREMFGYARDHQPCIIF  130 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~-~~~---------~~~~~~~~~~~~~~~~~~~~~~~~il~  130 (292)
                      ++..++|.||+|+||||++++++..+.    ..++.+... ++.         ....+.........+..+....|.+|+
T Consensus       122 ~~g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~~~~~~~~La~aL~~~Pdvil  201 (356)
T 3jvv_A          122 PRGLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIIL  201 (356)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHHHHHHHTTSCCSEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeeeeccccCCHHHHHHHHhhhCcCEEe
Confidence            456799999999999999999998763    233332211 110         001111112234567777788999999


Q ss_pred             EcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          131 MDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       131 lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      +||.-             +.+....+.....        .+..+++|++..+.
T Consensus       202 lDEp~-------------d~e~~~~~~~~~~--------~G~~vl~t~H~~~~  233 (356)
T 3jvv_A          202 VGEMR-------------DLETIRLALTAAE--------TGHLVFGTLHTTSA  233 (356)
T ss_dssp             ESCCC-------------SHHHHHHHHHHHH--------TTCEEEEEESCSSH
T ss_pred             cCCCC-------------CHHHHHHHHHHHh--------cCCEEEEEEccChH
Confidence            99983             2333333333322        14458888887654

>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerizat motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11

Probab=98.11  E-value=5.4e-06  Score=72.48  Aligned_cols=41  Identities=24%  Similarity=0.375  Sum_probs=32.8

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhc---------CCcEEEEeccc
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNI---------DANFLKVVSSA  101 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l---------~~~~~~~~~~~  101 (292)
                      .|+.++..+.|+||+|+||||+++.++...         +..+++++..+
T Consensus       126 ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~  175 (349)
T 1pzn_A          126 GGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN  175 (349)
T ss_dssp             SSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSS
T ss_pred             CCCCCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCC
Confidence            467788889999999999999999999876         23556666543

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=98.10  E-value=1.9e-05  Score=64.30  Aligned_cols=72  Identities=21%  Similarity=0.232  Sum_probs=42.9

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc-------hhccccChH-----HHHHHHHHHHhhh----CC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA-------IIDKYIGES-----ARLIREMFGYARD----HQ  125 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~-------~~~~~~~~~-----~~~~~~~~~~~~~----~~  125 (292)
                      ++..++++|++|+||||++..++..+   +..++.+....       +.+. .+..     ......++..+..    ..
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~sr-lG~~~~~~~~~~~~~i~~~i~~~~~~~~   89 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSR-TGTSLPSVEVESAPEILNYIMSNSFNDE   89 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCC-CCCSSCCEEESSTHHHHHHHHSTTSCTT
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHh-cCCCccccccCCHHHHHHHHHHHhhCCC
Confidence            35668888999999999988888766   45555553221       1111 0100     0011234444433    34


Q ss_pred             CEEEEEcccccc
Q 022768          126 PCIIFMDEIDAI  137 (292)
Q Consensus       126 ~~il~lDe~d~l  137 (292)
                      +.+|+|||++.+
T Consensus        90 ~dvViIDEaQ~l  101 (223)
T 2b8t_A           90 TKVIGIDEVQFF  101 (223)
T ss_dssp             CCEEEECSGGGS
T ss_pred             CCEEEEecCccC
Confidence            789999999877

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=98.10  E-value=1.9e-05  Score=64.99  Aligned_cols=37  Identities=38%  Similarity=0.459  Sum_probs=28.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      |+.++..++|.||||+|||+++..++...   +.++++++
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~   58 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVA   58 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEE
Confidence            46778889999999999999988887543   44555554

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=98.10  E-value=5.6e-06  Score=69.37  Aligned_cols=71  Identities=21%  Similarity=0.432  Sum_probs=44.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC---cEEEEeccch---h--------ccccChHHHHHHHHHHHhhhCCCEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA---NFLKVVSSAI---I--------DKYIGESARLIREMFGYARDHQPCII  129 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~---~~~~~~~~~~---~--------~~~~~~~~~~~~~~~~~~~~~~~~il  129 (292)
                      .++..++|.||+|+||||+++.++..+..   .-+.+....+   .        ....+.....++..+..+....|.+|
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~g~~i~~~~~~~~~~v~q~~~gl~~~~l~~~la~aL~~~p~il  102 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFKHKKSIVNQREVGEDTKSFADALRAALREDPDVI  102 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHHHHHHHHHHCCSEE
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEcCCcceeecCCcceeeeHHHhCCCHHHHHHHHHHHHhhCCCEE
Confidence            56788999999999999999999986632   1222221111   0        00000011123455666666789999


Q ss_pred             EEccc
Q 022768          130 FMDEI  134 (292)
Q Consensus       130 ~lDe~  134 (292)
                      ++||.
T Consensus       103 llDEp  107 (261)
T 2eyu_A          103 FVGEM  107 (261)
T ss_dssp             EESCC
T ss_pred             EeCCC
Confidence            99998

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=98.09  E-value=3.2e-06  Score=71.33  Aligned_cols=29  Identities=24%  Similarity=0.339  Sum_probs=25.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++....
T Consensus        31 i~~Ge~~~iiGpnGsGKSTLl~~l~Gl~~   59 (275)
T 3gfo_A           31 IKRGEVTAILGGNGVGKSTLFQNFNGILK   59 (275)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcCCC
Confidence            56788899999999999999999997663

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=98.04  E-value=7.7e-06  Score=63.92  Aligned_cols=23  Identities=35%  Similarity=0.537  Sum_probs=20.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARA   85 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~   85 (292)
                      +.++..+.|.||+|+||||+++.
T Consensus         6 i~~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            6 IPELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EESSEEEEEECCTTSCHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHH
Confidence            45678899999999999999994

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=98.04  E-value=1.7e-05  Score=66.56  Aligned_cols=28  Identities=32%  Similarity=0.553  Sum_probs=25.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        34 i~~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           34 IASGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             EETTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            5678889999999999999999999765

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.04  E-value=2.1e-06  Score=68.05  Aligned_cols=25  Identities=24%  Similarity=0.174  Sum_probs=20.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..++++||+|+||||++..++..+
T Consensus         3 g~i~vi~G~~gsGKTT~ll~~~~~~   27 (184)
T 2orw_A            3 GKLTVITGPMYSGKTTELLSFVEIY   27 (184)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568899999999999986666543

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=98.03  E-value=4e-06  Score=65.72  Aligned_cols=37  Identities=19%  Similarity=0.365  Sum_probs=31.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      +..++|+|+||+||||+++.+++.++.+++.++...+
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~~D~~   39 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVDSL   39 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCCeEEeccchH
Confidence            3568999999999999999999999988877665443

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=98.00  E-value=7.7e-06  Score=71.52  Aligned_cols=30  Identities=20%  Similarity=0.224  Sum_probs=26.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+|||||++.++....
T Consensus        50 ~i~~Gei~~IiGpnGaGKSTLlr~i~GL~~   79 (366)
T 3tui_C           50 HVPAGQIYGVIGASGAGKSTLIRCVNLLER   79 (366)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEcCCCEEEEEcCCCchHHHHHHHHhcCCC
Confidence            367788899999999999999999997653

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=98.00  E-value=1.1e-05  Score=67.45  Aligned_cols=30  Identities=37%  Similarity=0.434  Sum_probs=26.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+|||||++.++....
T Consensus        37 ~i~~Gei~~l~G~NGsGKSTLlk~l~Gl~~   66 (256)
T 1vpl_A           37 EIEEGEIFGLIGPNGAGKTTTLRIISTLIK   66 (256)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCcEEEEECCCCCCHHHHHHHHhcCCC
Confidence            356788899999999999999999997663

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.99  E-value=3.8e-06  Score=67.30  Aligned_cols=36  Identities=28%  Similarity=0.443  Sum_probs=30.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +.++..++|.|++|+||||+++.+++.++.+++..+
T Consensus        22 ~~~~~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~d   57 (199)
T 3vaa_A           22 SNAMVRIFLTGYMGAGKTTLGKAFARKLNVPFIDLD   57 (199)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             cCCCCEEEEEcCCCCCHHHHHHHHHHHcCCCEEcch
Confidence            456778999999999999999999999988876443

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=97.98  E-value=2.1e-05  Score=67.06  Aligned_cols=77  Identities=19%  Similarity=0.253  Sum_probs=48.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc-----CCcEEEEeccchhcc----------------ccChHHHHHHHHHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI-----DANFLKVVSSAIIDK----------------YIGESARLIREMFGY  120 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l-----~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~  120 (292)
                      |+.++ .++|+||||+|||+++-.++...     +..+++++..+-...                .....+...-.+...
T Consensus        25 Gl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~  103 (333)
T 3io5_A           25 GMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQ  103 (333)
T ss_dssp             CBCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHH
T ss_pred             CCcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHH
Confidence            35666 68999999999999988777654     556777775543210                001122220112222


Q ss_pred             ---hhhCCCEEEEEcccccccC
Q 022768          121 ---ARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       121 ---~~~~~~~il~lDe~d~l~~  139 (292)
                         +....|.+|+||-+..+..
T Consensus       104 l~~i~~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          104 LDAIERGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             HHTCCTTCCEEEEEECSTTCBC
T ss_pred             HHHhhccCceEEEEeccccccc
Confidence               3445789999999999974

>1nlf_A Regulatory protein REPA; replicative DNA helicase structural changes, replication; 1.95A {Escherichia coli} SCOP: c.37.1.11 PDB: 1g8y_A 1olo_A

Probab=97.98  E-value=3.5e-05  Score=65.03  Aligned_cols=29  Identities=31%  Similarity=0.436  Sum_probs=24.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      |+.++..++|+||+|+||||++..++..+
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~~~   54 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAAQI   54 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            35668889999999999999999998644

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=97.97  E-value=0.00014  Score=67.05  Aligned_cols=74  Identities=15%  Similarity=0.325  Sum_probs=53.3

Q ss_pred             EEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC--CCChhhcCCCCcceEEEccCCC
Q 022768          127 CIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD--VLDPALLRPGRLDRKIEIPLPN  204 (292)
Q Consensus       127 ~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~--~l~~~l~~~~r~~~~i~l~~p~  204 (292)
                      -+|+|||++.+....       .......+..+.....    .-++.+|++++.+.  .++..++.  .|...+-|...+
T Consensus       345 ivvVIDE~~~L~~~~-------~~~~~~~L~~Iar~GR----a~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI~lrv~s  411 (574)
T 2iut_A          345 IVVVVDEFADMMMIV-------GKKVEELIARIAQKAR----AAGIHLILATQRPSVDVITGLIKA--NIPTRIAFQVSS  411 (574)
T ss_dssp             EEEEESCCTTHHHHT-------CHHHHHHHHHHHHHCT----TTTEEEEEEESCCCTTTSCHHHHH--TCCEEEEECCSC
T ss_pred             EEEEEeCHHHHhhhh-------hHHHHHHHHHHHHHHh----hCCeEEEEEecCcccccccHHHHh--hhccEEEEEcCC
Confidence            589999999874311       2344455556655532    24899999999887  78888887  788888888888


Q ss_pred             HHHHHHHHH
Q 022768          205 EQSRMEILK  213 (292)
Q Consensus       205 ~~~r~~i~~  213 (292)
                      ..+...++-
T Consensus       412 ~~Dsr~ILd  420 (574)
T 2iut_A          412 KIDSRTILD  420 (574)
T ss_dssp             HHHHHHHHS
T ss_pred             HHHHHHhcC
Confidence            887777763

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=97.97  E-value=3.8e-05  Score=65.66  Aligned_cols=30  Identities=30%  Similarity=0.541  Sum_probs=26.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++..+.
T Consensus        76 ~i~~Ge~vaivG~sGsGKSTLl~ll~gl~~  105 (306)
T 3nh6_A           76 TVMPGQTLALVGPSGAGKSTILRLLFRFYD  105 (306)
T ss_dssp             EECTTCEEEEESSSCHHHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCchHHHHHHHHHcCCC
Confidence            367788999999999999999999997663

>3rlf_A Maltose/maltodextrin import ATP-binding protein M; integral membrane protein, ATPase, ABC transporter, membrane transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia coli} PDB: 1q1e_A 1q12_A* 2awo_A* 3fh6_A 3puv_A* 3puw_A* 3pux_A* 3puy_A* 3puz_A* 3pv0_A* 2awn_A* 2r6g_A* 1q1b_A

Probab=97.97  E-value=7.3e-06  Score=72.10  Aligned_cols=30  Identities=37%  Similarity=0.482  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++....
T Consensus        25 ~i~~Ge~~~llGpsGsGKSTLLr~iaGl~~   54 (381)
T 3rlf_A           25 DIHEGEFVVFVGPSGCGKSTLLRMIAGLET   54 (381)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EECCCCEEEEEcCCCchHHHHHHHHHcCCC
Confidence            356788899999999999999999997663

>3tif_A Uncharacterized ABC transporter ATP-binding prote; nucleotide-binding domain, ABC transporter ATPase; HET: ADP; 1.80A {Methanocaldococcus jannaschii dsm 2661ORGANISM_TAXID} PDB: 1l2t_A* 1f3o_A*

Probab=97.96  E-value=4.6e-05  Score=62.71  Aligned_cols=29  Identities=31%  Similarity=0.426  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        27 ~i~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           27 NIKEGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            35778889999999999999999999765

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=97.95  E-value=1.1e-05  Score=69.66  Aligned_cols=28  Identities=25%  Similarity=0.340  Sum_probs=25.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      |++++..++|+|+||+|||+++..++..
T Consensus        94 Gl~~g~i~~i~G~~gsGKT~la~~la~~  121 (322)
T 2i1q_A           94 GLESQSVTEFAGVFGSGKTQIMHQSCVN  121 (322)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            5677888999999999999999999975

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=97.95  E-value=3.5e-05  Score=62.94  Aligned_cols=29  Identities=24%  Similarity=0.268  Sum_probs=25.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+|||||++.++....
T Consensus        27 i~~Ge~~~iiG~nGsGKSTLl~~l~Gl~~   55 (224)
T 2pcj_A           27 VKKGEFVSIIGASGSGKSTLLYILGLLDA   55 (224)
T ss_dssp             EETTCEEEEEECTTSCHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            56788899999999999999999997663

>3fvq_A Fe(3+) IONS import ATP-binding protein FBPC; nucleotide binding domain, ABC motor domain, ferric iron TRA ATP-binding, cell inner membrane; HET: ATP; 1.90A {Neisseria gonorrhoeae}

Probab=97.94  E-value=9.2e-06  Score=70.92  Aligned_cols=29  Identities=31%  Similarity=0.512  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        26 ~i~~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           26 SLDPGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             EECTTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             EEcCCCEEEEECCCCchHHHHHHHHhcCC
Confidence            35678889999999999999999999765

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=97.92  E-value=9.6e-06  Score=64.30  Aligned_cols=35  Identities=31%  Similarity=0.579  Sum_probs=29.8

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..+..++|.|+||+||||+++.++..++.+++..
T Consensus         2 ~~~~~~I~l~G~~GsGKST~~~~L~~~l~~~~i~~   36 (193)
T 2rhm_A            2 MQTPALIIVTGHPATGKTTLSQALATGLRLPLLSK   36 (193)
T ss_dssp             CSCCEEEEEEESTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEecH
Confidence            44567799999999999999999999998776653

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=97.92  E-value=1.7e-05  Score=69.37  Aligned_cols=29  Identities=34%  Similarity=0.390  Sum_probs=25.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        25 ~i~~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           25 EVKDGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             EEcCCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            35678889999999999999999999765

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=97.90  E-value=1.5e-05  Score=69.54  Aligned_cols=29  Identities=41%  Similarity=0.517  Sum_probs=25.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++....
T Consensus        38 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   66 (355)
T 1z47_A           38 IREGEMVGLLGPSGSGKTTILRLIAGLER   66 (355)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            56688899999999999999999997653

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=97.90  E-value=9e-05  Score=67.66  Aligned_cols=76  Identities=16%  Similarity=0.381  Sum_probs=50.1

Q ss_pred             CCE-EEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC--CCChhhcCCCCcceEEEcc
Q 022768          125 QPC-IIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD--VLDPALLRPGRLDRKIEIP  201 (292)
Q Consensus       125 ~~~-il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~--~l~~~l~~~~r~~~~i~l~  201 (292)
                      .|. +|+|||+..+....       .......+..+.....    .-++.+|++++.+.  .++..++.  .+...+-|.
T Consensus       296 lP~ivlvIDE~~~ll~~~-------~~~~~~~l~~Lar~gR----a~GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lr  362 (512)
T 2ius_A          296 EPYIVVLVDEFADLMMTV-------GKKVEELIARLAQKAR----AAGIHLVLATQRPSVDVITGLIKA--NIPTRIAFT  362 (512)
T ss_dssp             CCEEEEEEETHHHHHHHH-------HHHHHHHHHHHHHHCG----GGTEEEEEEESCCCTTTSCHHHHH--HCCEEEEEC
T ss_pred             CCcEEEEEeCHHHHHhhh-------hHHHHHHHHHHHHHhh----hCCcEEEEEecCCccccccHHHHh--hcCCeEEEE
Confidence            354 88999998774210       1223333333333321    23788889998886  57777877  788888888


Q ss_pred             CCCHHHHHHHHH
Q 022768          202 LPNEQSRMEILK  213 (292)
Q Consensus       202 ~p~~~~r~~i~~  213 (292)
                      ..+..+...++.
T Consensus       363 v~s~~dsr~ilg  374 (512)
T 2ius_A          363 VSSKIDSRTILD  374 (512)
T ss_dssp             CSSHHHHHHHHS
T ss_pred             cCCHHHHHHhcC
Confidence            888888887765

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=97.89  E-value=9.3e-05  Score=62.94  Aligned_cols=38  Identities=16%  Similarity=0.227  Sum_probs=30.1

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEe
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVV   98 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~   98 (292)
                      .++.++..++|.||||+||||+++.++..+    |.+++.++
T Consensus        30 ~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~   71 (296)
T 1cr0_A           30 LGARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAM   71 (296)
T ss_dssp             CSBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEE
T ss_pred             cCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEe
Confidence            356788899999999999999999999765    33555543

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=97.88  E-value=9.5e-06  Score=64.28  Aligned_cols=40  Identities=28%  Similarity=0.306  Sum_probs=32.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      +.++..++|.||+|+||||+++.++...+...+.++...+
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~d~~   45 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDL   45 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTTHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHhccCCCeEEEcccch
Confidence            4667889999999999999999999987767666665443

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=97.88  E-value=7.5e-05  Score=61.93  Aligned_cols=28  Identities=29%  Similarity=0.404  Sum_probs=25.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        32 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           32 IKQGEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            5678889999999999999999999765

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.88  E-value=2.7e-05  Score=80.96  Aligned_cols=78  Identities=19%  Similarity=0.268  Sum_probs=54.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccC----------------hHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIG----------------ESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~  122 (292)
                      +++++.+++++||||+|||+++.+++.+.   |.++.++...+.......                ..+..........+
T Consensus      1077 gi~~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~ 1156 (2050)
T 3cmu_A         1077 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1156 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCcEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHH
Confidence            57889999999999999999999998654   677888887765433220                11122223333344


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...|.+|+||++..+.+
T Consensus      1157 ~~~~dlvVIDsl~~L~~ 1173 (2050)
T 3cmu_A         1157 SGAVDVIVVDSVAALTP 1173 (2050)
T ss_dssp             HTCCSEEEESCGGGCCC
T ss_pred             hCCCCEEEECCcccccc
Confidence            56789999999999854

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.86  E-value=8.9e-06  Score=64.15  Aligned_cols=33  Identities=21%  Similarity=0.236  Sum_probs=28.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +..++|+|++|+||||+++.++..++.+++..+
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~~~~i~~d   37 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTKRILYDSD   37 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            457999999999999999999999998877543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.85  E-value=0.0011  Score=53.69  Aligned_cols=34  Identities=26%  Similarity=0.263  Sum_probs=26.6

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      ..+++.|++|+||||++-.++..+   |..++.++..
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D   43 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVE   43 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeC
Confidence            458899999999999988888765   6666655543

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=97.85  E-value=0.0001  Score=61.28  Aligned_cols=29  Identities=17%  Similarity=0.225  Sum_probs=25.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++....
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           28 LNKGDILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             EETTCEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            56788899999999999999999998763

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=97.84  E-value=5e-05  Score=62.58  Aligned_cols=29  Identities=28%  Similarity=0.355  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        27 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           27 SIPEGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            35778889999999999999999999865

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=97.83  E-value=7e-05  Score=62.98  Aligned_cols=29  Identities=31%  Similarity=0.470  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++..+
T Consensus        41 ~i~~Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           41 TLYPGKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            36778889999999999999999999765

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=97.83  E-value=0.00013  Score=60.99  Aligned_cols=30  Identities=30%  Similarity=0.506  Sum_probs=26.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+|||||++.++....
T Consensus        46 ~i~~Gei~~liG~NGsGKSTLlk~l~Gl~~   75 (263)
T 2olj_A           46 HIREGEVVVVIGPSGSGKSTFLRCLNLLED   75 (263)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEEcCCCCcHHHHHHHHHcCCC
Confidence            357788899999999999999999998663

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.81  E-value=0.00011  Score=61.18  Aligned_cols=39  Identities=28%  Similarity=0.478  Sum_probs=32.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ..+..++|.|+||+||||+++.++..++..++.++...+
T Consensus        30 ~~~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           30 KQPIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             SSCEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            446779999999999999999999999866677776655

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=97.81  E-value=0.00011  Score=58.42  Aligned_cols=24  Identities=42%  Similarity=0.732  Sum_probs=21.6

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.|.||+|+||||+++.++..+
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhhc
Confidence            358899999999999999999876

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=97.81  E-value=2.6e-05  Score=68.75  Aligned_cols=74  Identities=16%  Similarity=0.336  Sum_probs=45.6

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEecc-ch--hc--cccCh-----HHHHHHHHHHHhhhCCC
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSS-AI--ID--KYIGE-----SARLIREMFGYARDHQP  126 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~-~~--~~--~~~~~-----~~~~~~~~~~~~~~~~~  126 (292)
                      +.+.++..++|.||+|+||||+++.++..+.    ..++.+... +.  ..  .++.+     ....+...+..+....|
T Consensus       131 l~~~~g~~i~ivG~~GsGKTTll~~l~~~~~~~~~g~I~~~e~~~e~~~~~~~~~v~Q~~~g~~~~~~~~~l~~~L~~~p  210 (372)
T 2ewv_A          131 LCHRKMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFKHKKSIVNQREVGEDTKSFADALRAALREDP  210 (372)
T ss_dssp             HTTSSSEEEEEECSSSSSHHHHHHHHHHHHHHHSCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCSHHHHHHHTTSCC
T ss_pred             HhhcCCCEEEEECCCCCCHHHHHHHHHhhcCcCCCcEEEEecccHhhhhccCceEEEeeecCCCHHHHHHHHHHHhhhCc
Confidence            3356678899999999999999999998663    223222211 00  00  00000     11123455566666789


Q ss_pred             EEEEEccc
Q 022768          127 CIIFMDEI  134 (292)
Q Consensus       127 ~il~lDe~  134 (292)
                      .+|++||+
T Consensus       211 d~illdE~  218 (372)
T 2ewv_A          211 DVIFVGEM  218 (372)
T ss_dssp             SEEEESCC
T ss_pred             CEEEECCC
Confidence            99999998

>1y63_A LMAJ004144AAA protein; structural genomics, protein structure initiative, PSI, SGPP structural genomics of pathogenic protozoa consortium; HET: ADP; 1.70A {Leishmania major} SCOP: c.37.1.1

Probab=97.80  E-value=1.2e-05  Score=63.51  Aligned_cols=33  Identities=36%  Similarity=0.508  Sum_probs=27.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHh-cCCcEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASN-IDANFLK   96 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~-l~~~~~~   96 (292)
                      ..+..++|+|++|+||||+++.++.. ++.+++.
T Consensus         8 ~~~~~I~l~G~~GsGKSTv~~~La~~l~g~~~id   41 (184)
T 1y63_A            8 PKGINILITGTPGTGKTSMAEMIAAELDGFQHLE   41 (184)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHSTTEEEEE
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhcCCCEEee
Confidence            34667999999999999999999999 6766553

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.79  E-value=1.8e-05  Score=61.57  Aligned_cols=30  Identities=30%  Similarity=0.729  Sum_probs=26.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      +..++|+|++|+||||+++.++..++.+++
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~La~~l~~~~i   33 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFY   33 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCEEE
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCEE
Confidence            356999999999999999999999987554

>3iij_A Coilin-interacting nuclear ATPase protein; alpha and beta proteins (A/B), protein binding, transferase, phosphotransferase; HET: ADP; 1.76A {Homo sapiens} SCOP: c.37.1.1 PDB: 3iik_A 3iil_A* 3iim_A* 1rkb_A

Probab=97.79  E-value=1.5e-05  Score=62.64  Aligned_cols=34  Identities=35%  Similarity=0.592  Sum_probs=28.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ..+..++|+|+||+||||+++.++..++.+++..
T Consensus         9 ~~~~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~   42 (180)
T 3iij_A            9 MLLPNILLTGTPGVGKTTLGKELASKSGLKYINV   42 (180)
T ss_dssp             CCCCCEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             ccCCeEEEEeCCCCCHHHHHHHHHHHhCCeEEEH
Confidence            3456799999999999999999999998766543

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=97.78  E-value=0.00013  Score=60.08  Aligned_cols=38  Identities=32%  Similarity=0.303  Sum_probs=29.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh----cCCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN----IDANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~----l~~~~~~~~~   99 (292)
                      |+.++..++|.|+||+|||++|..+|..    .+.++++++.
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~   67 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTL   67 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeecc
Confidence            4677888999999999999999887643    2566666653

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=97.78  E-value=0.00014  Score=63.89  Aligned_cols=29  Identities=38%  Similarity=0.523  Sum_probs=25.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+|||||++.++....
T Consensus        26 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   54 (372)
T 1g29_1           26 VKDGEFMILLGPSGCGKTTTLRMIAGLEE   54 (372)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EcCCCEEEEECCCCcHHHHHHHHHHcCCC
Confidence            56678899999999999999999997663

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=97.78  E-value=9.2e-05  Score=65.03  Aligned_cols=29  Identities=41%  Similarity=0.480  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        33 ~i~~Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           33 TIKDGEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHHcCC
Confidence            35678889999999999999999999765

>3kb2_A SPBC2 prophage-derived uncharacterized protein YORR; alpha-beta protein., structural genomics, PSI-2, protein structure initiative; HET: G3D; 2.20A {Bacillus subtilis} SCOP: c.37.1.1 PDB: 2axp_A*

Probab=97.78  E-value=1.8e-05  Score=61.43  Aligned_cols=31  Identities=19%  Similarity=0.249  Sum_probs=27.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .++|.|++|+||||+++.+++.++.+++..+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~~~~i~~d   33 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELKYPIIKGS   33 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHCCCEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeeecCc
Confidence            5889999999999999999999998876554

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=97.77  E-value=3.7e-05  Score=67.28  Aligned_cols=30  Identities=37%  Similarity=0.471  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++....
T Consensus        25 ~i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           25 KIKDGEFMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EECCCCEEEEECCCCchHHHHHHHHhcCCC
Confidence            356788899999999999999999997653

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=97.77  E-value=0.00014  Score=65.88  Aligned_cols=38  Identities=26%  Similarity=0.388  Sum_probs=31.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~   99 (292)
                      |+.++..++|.|+||+|||+++..++..+    +.+++.++.
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~  240 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSL  240 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEES
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC
Confidence            68888899999999999999999988754    456776663

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=97.77  E-value=0.00011  Score=60.54  Aligned_cols=28  Identities=29%  Similarity=0.536  Sum_probs=24.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.+ ..+.|.||+|+||||+++.++....
T Consensus        22 i~~-e~~~liG~nGsGKSTLl~~l~Gl~~   49 (240)
T 2onk_A           22 MGR-DYCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             ECS-SEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             ECC-EEEEEECCCCCCHHHHHHHHhCCCC
Confidence            566 7889999999999999999998663

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=97.76  E-value=0.00015  Score=71.24  Aligned_cols=43  Identities=28%  Similarity=0.359  Sum_probs=36.0

Q ss_pred             cccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           35 GGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        35 ~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +|++..+++|.+.+...            ...+.+.|+|+.|+||||+|+.+++.
T Consensus       131 VGRe~eLeeL~elL~~~------------d~~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLEL------------RPAKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHC------------CSSCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHhcc------------CCCeEEEEEcCCCccHHHHHHHHHHh
Confidence            89999999999987642            23467889999999999999999863

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=97.76  E-value=0.00017  Score=62.78  Aligned_cols=30  Identities=30%  Similarity=0.449  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++....
T Consensus        22 ~i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   51 (348)
T 3d31_A           22 KVESGEYFVILGPTGAGKTLFLELIAGFHV   51 (348)
T ss_dssp             EECTTCEEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             EEcCCCEEEEECCCCccHHHHHHHHHcCCC
Confidence            356788899999999999999999997653

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=97.75  E-value=0.00012  Score=58.15  Aligned_cols=103  Identities=15%  Similarity=0.131  Sum_probs=57.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc---------hhcccc-------------C----hHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA---------IIDKYI-------------G----ESARLIRE  116 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~---------~~~~~~-------------~----~~~~~~~~  116 (292)
                      ...+++++++|.||||+|-.++-+.   |..+..+....         +...+.             .    ........
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~  107 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMA  107 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHH
Confidence            3468999999999999998887655   66666653221         122210             0    01222334


Q ss_pred             HHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          117 MFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       117 ~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      .+..++.    ....+|+|||+.....-        .--....+.+++.     ....+.-+|+|+|.+
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~~--------g~l~~~ev~~~l~-----~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVAY--------DYLPLEEVISALN-----ARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHHT--------TSSCHHHHHHHHH-----TSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCccccC--------CCCCHHHHHHHHH-----hCcCCCEEEEECCCC
Confidence            4444433    44689999999653100        0001123444443     233577899999875

>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion, hydrolas binding complex; 2.40A {Helicobacter pylori} SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A

Probab=97.75  E-value=3.2e-05  Score=67.03  Aligned_cols=72  Identities=18%  Similarity=0.222  Sum_probs=46.9

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEeccchhc-----c---ccChHHHHHHHHHHHhhhCCCEEEEEcc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSSAIID-----K---YIGESARLIREMFGYARDHQPCIIFMDE  133 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~~~~~-----~---~~~~~~~~~~~~~~~~~~~~~~il~lDe  133 (292)
                      .++..++|.||+|+||||++++++.....  ..+.++......     .   +........+..+..+....|.+|++||
T Consensus       169 ~~g~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~~~e~~~~~~~~~i~~~~ggg~~~r~~la~aL~~~p~ilildE  248 (330)
T 2pt7_A          169 AIGKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGE  248 (330)
T ss_dssp             HHTCCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEECC
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECCeeccccccchhEEEEEeCCChhHHHHHHHHhhhCCCEEEEcC
Confidence            44778999999999999999999998743  234444321110     0   1100112334556667778899999999


Q ss_pred             cc
Q 022768          134 ID  135 (292)
Q Consensus       134 ~d  135 (292)
                      .-
T Consensus       249 ~~  250 (330)
T 2pt7_A          249 LR  250 (330)
T ss_dssp             CC
T ss_pred             CC
Confidence            73

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.74  E-value=1.7e-05  Score=61.57  Aligned_cols=32  Identities=25%  Similarity=0.404  Sum_probs=28.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      -.+++|.|++|+||||+++.++..++.+++..
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~~lg~~~id~   38 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGLALKLEVLDT   38 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            34799999999999999999999999888754

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=97.74  E-value=0.0001  Score=61.19  Aligned_cols=29  Identities=28%  Similarity=0.450  Sum_probs=25.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+|||||++.++....
T Consensus        23 i~~Ge~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           23 VRAGEILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            56788899999999999999999998764

>2iyv_A Shikimate kinase, SK; transferase, aromatic amino acid biosynthesis, P-loop kinase, metal- binding, shikimate pathway; HET: ADP; 1.35A {Mycobacterium tuberculosis} SCOP: c.37.1.2 PDB: 2iyr_A* 2iyq_A* 2iyt_A 2iyu_A* 2iys_A* 2iyw_A* 2iyx_A* 2iyy_A* 2iyz_A* 2g1k_A* 1l4y_A* 1u8a_A* 1we2_A* 1zyu_A* 2dfn_A* 2dft_A* 2g1j_A 1l4u_A* 3baf_A*

Probab=97.74  E-value=1.6e-05  Score=62.57  Aligned_cols=31  Identities=29%  Similarity=0.572  Sum_probs=27.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .|+|.|+||+||||+++.+++.++.+++..+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg~~~id~D   34 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKALGVGLLDTD   34 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcCCCEEeCc
Confidence            5899999999999999999999998876543

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=97.73  E-value=0.00019  Score=67.23  Aligned_cols=30  Identities=40%  Similarity=0.617  Sum_probs=26.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++....
T Consensus       377 ~i~~G~~~~ivG~sGsGKSTll~~l~g~~~  406 (598)
T 3qf4_B          377 HIKPGQKVALVGPTGSGKTTIVNLLMRFYD  406 (598)
T ss_dssp             ECCTTCEEEEECCTTSSTTHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhcCcC
Confidence            467889999999999999999999997664

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.73  E-value=4.5e-05  Score=64.76  Aligned_cols=39  Identities=33%  Similarity=0.544  Sum_probs=31.2

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ..+..++|.||||+||||+++.++..++..++.++...+
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~D~~   69 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTF   69 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEechHh
Confidence            345678999999999999999999988655666665444

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=97.72  E-value=0.00011  Score=63.11  Aligned_cols=38  Identities=32%  Similarity=0.263  Sum_probs=30.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      |+.++..++|.|+||+|||+++..+|...   +.++++++.
T Consensus        64 Gl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~sl  104 (315)
T 3bh0_A           64 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL  104 (315)
T ss_dssp             SBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEEC
Confidence            68889999999999999999999998654   346666653

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.70  E-value=2.3e-05  Score=61.79  Aligned_cols=31  Identities=32%  Similarity=0.576  Sum_probs=26.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..++|.|++|+||||+++.+++.++.+++.
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l~~~~i~   34 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQELGFKKLS   34 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCeEec
Confidence            4578999999999999999999998866543

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=97.69  E-value=0.00012  Score=61.15  Aligned_cols=38  Identities=24%  Similarity=0.350  Sum_probs=30.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh---cCCcEEEEeccchh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN---IDANFLKVVSSAII  103 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~---l~~~~~~~~~~~~~  103 (292)
                      +..|+|.|+||+||||+++.++..   .+.+++.++...+.
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~D~~~   44 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGSDLIR   44 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECTHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECchHHH
Confidence            457899999999999999999998   67777755554443

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.68  E-value=2.8e-05  Score=60.74  Aligned_cols=29  Identities=41%  Similarity=0.709  Sum_probs=26.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .++|.|+||+||||+++.++..++.+++.
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d   34 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLD   34 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEc
Confidence            58999999999999999999999877654

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=97.68  E-value=0.00063  Score=58.11  Aligned_cols=73  Identities=16%  Similarity=0.226  Sum_probs=45.2

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc--------------------ccChHHHHHHHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK--------------------YIGESARLIREMFGY  120 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~  120 (292)
                      .++..++|.|++|+||||++..+|..+   +..+..+++......                    ..+.........+..
T Consensus       102 ~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~s~~~~~~v~~~al~~  181 (306)
T 1vma_A          102 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTFRAAAIEQLKIWGERVGATVISHSEGADPAAVAFDAVAH  181 (306)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTTCHHHHHHHHHHHHHHTCEEECCSTTCCHHHHHHHHHHH
T ss_pred             CCCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEccccccHHHHHHHHHHHHHcCCcEEecCCccCHHHHHHHHHHH
Confidence            456778999999999999999999866   445554443322110                    001112222234444


Q ss_pred             hhhCCCEEEEEccccc
Q 022768          121 ARDHQPCIIFMDEIDA  136 (292)
Q Consensus       121 ~~~~~~~il~lDe~d~  136 (292)
                      +....+.+++||+.-.
T Consensus       182 a~~~~~dvvIiDtpg~  197 (306)
T 1vma_A          182 ALARNKDVVIIDTAGR  197 (306)
T ss_dssp             HHHTTCSEEEEEECCC
T ss_pred             HHhcCCCEEEEECCCc
Confidence            5556778999998743

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=97.68  E-value=0.00014  Score=63.45  Aligned_cols=29  Identities=34%  Similarity=0.458  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        27 ~i~~Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           27 NIENGERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             EECTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             EECCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35678889999999999999999999765

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.65  E-value=3.9e-05  Score=61.37  Aligned_cols=32  Identities=31%  Similarity=0.620  Sum_probs=26.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      .++..++|.||+|+||||+++.++..+|..++
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~g~~~i   58 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADETGLEFA   58 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHHCCEEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhhCCeEE
Confidence            34678999999999999999999999865443

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=97.65  E-value=4.2e-05  Score=59.66  Aligned_cols=32  Identities=31%  Similarity=0.511  Sum_probs=27.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ++..++|.|++|+||||+++.++..++..++.
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~   38 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQLHAAFLD   38 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHHTCEEEE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhhCcEEEe
Confidence            46679999999999999999999988755543

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=97.65  E-value=0.00019  Score=69.97  Aligned_cols=27  Identities=19%  Similarity=0.320  Sum_probs=23.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      .+..+..++|.||+|+||||+++.++.
T Consensus       669 ~~~~g~i~~ItGPNGaGKSTlLr~i~~  695 (918)
T 3thx_B          669 SEDSERVMIITGPNMGGKSSYIKQVAL  695 (918)
T ss_dssp             CTTSCCEEEEESCCCHHHHHHHHHHHH
T ss_pred             cCCCCeEEEEECCCCCchHHHHHHHHH
Confidence            345677899999999999999999874

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=97.64  E-value=0.00019  Score=64.72  Aligned_cols=38  Identities=24%  Similarity=0.213  Sum_probs=31.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~   99 (292)
                      |+.++..++|.|+||+|||+++..+|...    +.++++++.
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~sl  237 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSL  237 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEES
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            68888889999999999999999888643    456777664

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.64  E-value=2.2e-05  Score=62.35  Aligned_cols=33  Identities=21%  Similarity=0.359  Sum_probs=28.4

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .+..++|.|++|+||||+++.+++.++.+++..
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   40 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   40 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            356799999999999999999999998776544

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=97.64  E-value=0.00027  Score=66.02  Aligned_cols=31  Identities=35%  Similarity=0.530  Sum_probs=26.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+.++..+.|.||+|+||||+++.++.....
T Consensus       365 ~i~~Ge~~~ivG~sGsGKSTll~~l~g~~~~  395 (587)
T 3qf4_A          365 SVKPGSLVAVLGETGSGKSTLMNLIPRLIDP  395 (587)
T ss_dssp             EECTTCEEEEECSSSSSHHHHHHTTTTSSCC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCccC
Confidence            3677889999999999999999999986643

>2cdn_A Adenylate kinase; phosphoryl transfer, associative mechanism, ATP-binding, nucleotide biosynthesis, nucleotide-binding, transferase; HET: ADP; 1.9A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1p4s_A

Probab=97.64  E-value=5.4e-05  Score=60.52  Aligned_cols=34  Identities=32%  Similarity=0.488  Sum_probs=28.9

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ..+..|+|.|+||+||||+++.++..++.+++.+
T Consensus        18 ~~~~~I~l~G~~GsGKST~a~~La~~l~~~~i~~   51 (201)
T 2cdn_A           18 GSHMRVLLLGPPGAGKGTQAVKLAEKLGIPQIST   51 (201)
T ss_dssp             CSCCEEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhCCcEEeh
Confidence            3355689999999999999999999998876654

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=97.63  E-value=0.00013  Score=68.00  Aligned_cols=31  Identities=29%  Similarity=0.368  Sum_probs=26.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+.++..+.|.||+|+||||+++.++.....
T Consensus       363 ~i~~G~~~~ivG~sGsGKSTll~~l~g~~~p  393 (578)
T 4a82_A          363 SIEKGETVAFVGMSGGGKSTLINLIPRFYDV  393 (578)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHTTTTTSSCC
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHhcCCCC
Confidence            3677889999999999999999999987643

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.61  E-value=3.7e-05  Score=64.06  Aligned_cols=32  Identities=31%  Similarity=0.372  Sum_probs=28.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      .++|+||+|+||||+++.+|..++.+++..+.
T Consensus         3 li~I~G~~GSGKSTla~~La~~~~~~~i~~D~   34 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQETGWPVVALDR   34 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCCEEECCS
T ss_pred             EEEEECCCCcCHHHHHHHHHhcCCCeEEeccH
Confidence            47899999999999999999999988877664

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.61  E-value=5.9e-05  Score=70.21  Aligned_cols=33  Identities=30%  Similarity=0.368  Sum_probs=25.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      +..++|.|+||||||+++..++..+   +.+++.+.
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~A  239 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCA  239 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEec
Confidence            4578999999999999999998755   45555443

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.61  E-value=4.6e-05  Score=60.98  Aligned_cols=32  Identities=28%  Similarity=0.531  Sum_probs=27.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..++|.|++|+||||+++.++..++..++..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~   49 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEACGYPFIEG   49 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHHTCCEEEG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCEEEeC
Confidence            45699999999999999999999998776653

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=97.61  E-value=4.9e-05  Score=61.69  Aligned_cols=33  Identities=24%  Similarity=0.472  Sum_probs=28.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      +..++.|+|.||||+||+|.|+.+++.++.+++
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~~~~g~~hI   58 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLVQKFHFNHL   58 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHHHHHCCEEE
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            345667889999999999999999999987655

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=97.60  E-value=6.6e-05  Score=58.80  Aligned_cols=37  Identities=22%  Similarity=0.241  Sum_probs=31.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      ++..+.|.|++|+||||+++.++..+   +.+++.++...
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d~~~   43 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDN   43 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEECChH
Confidence            46778999999999999999999987   88888776443

>1aky_A Adenylate kinase; ATP:AMP phosphotransferase, myokinase, transferase (phosphotransferase); HET: AP5; 1.63A {Saccharomyces cerevisiae} SCOP: c.37.1.1 g.41.2.1 PDB: 2aky_A* 3aky_A* 1dvr_A*

Probab=97.60  E-value=5e-05  Score=61.64  Aligned_cols=32  Identities=31%  Similarity=0.523  Sum_probs=27.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..++|.|+||+||||+++.++..++.+++..
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   35 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERFHAAHLAT   35 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCceEEeh
Confidence            56799999999999999999999998766544

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=97.60  E-value=0.00017  Score=66.58  Aligned_cols=110  Identities=15%  Similarity=0.230  Sum_probs=65.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc--------------------------cc--ChH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK--------------------------YI--GES  110 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~--------------------------~~--~~~  110 (292)
                      ++.++..++|.|++|+||||+++.++...   +.+++++...+....                          ..  -..
T Consensus       277 ~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~~ee~~~~l~~~~~~~g~~~~~~~~~g~~~~~~~~p~~LS~  356 (525)
T 1tf7_A          277 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGL  356 (525)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEESSSCHHHHHHHHHTTSCCHHHHHHTTSEEECCCCGGGSCH
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEEEeCCHHHHHHHHHHcCCCHHHHHhCCCEEEEEeccccCCH
Confidence            46778899999999999999999999755   334555443221100                          00  012


Q ss_pred             HHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          111 ARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       111 ~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      ....+.++..+....|.+|+||=+..+...     . ...+....+..++..+..    .++.+|++++..
T Consensus       357 g~~q~~~~a~~l~~~p~llilDp~~~Ld~~-----~-~~~~~~~~i~~ll~~l~~----~g~tvilvsh~~  417 (525)
T 1tf7_A          357 EDHLQIIKSEINDFKPARIAIDSLSALARG-----V-SNNAFRQFVIGVTGYAKQ----EEITGLFTNTSD  417 (525)
T ss_dssp             HHHHHHHHHHHHTTCCSEEEEECHHHHTSS-----S-CHHHHHHHHHHHHHHHHH----TTCEEEEEEECS
T ss_pred             HHHHHHHHHHHHhhCCCEEEEcChHHHHhh-----C-ChHHHHHHHHHHHHHHHh----CCCEEEEEECcc
Confidence            334455666666788999999965555221     0 112255556666665542    245666666554

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.60  E-value=4.8e-05  Score=60.16  Aligned_cols=31  Identities=29%  Similarity=0.443  Sum_probs=26.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..|+|.|+||+||||+++.++..++.+++.
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~   33 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKYGYTHLS   33 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCeEEe
Confidence            4568999999999999999999999876654

>3tlx_A Adenylate kinase 2; structural genomics, structural genomics consortium, SGC, RO fold, transferase, ATP binding, phosphorylation; HET: ADP ATP AMP; 2.75A {Plasmodium falciparum}

Probab=97.59  E-value=7.2e-05  Score=61.83  Aligned_cols=34  Identities=24%  Similarity=0.361  Sum_probs=29.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .++..|+|.||||+||||+++.++..++.+++.+
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~   60 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLST   60 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            4567799999999999999999999998766654

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=97.59  E-value=0.00096  Score=59.73  Aligned_cols=195  Identities=15%  Similarity=0.140  Sum_probs=99.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhc--------------------cccChHHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIID--------------------KYIGESARLIREMFGYA  121 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~~~  121 (292)
                      ++..+++.|++|+||||++..+|..+   +..+..+.+.....                    .........+...+..+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~R~aa~eqL~~~~~~~gvpv~~~~~~~dp~~i~~~al~~a  178 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGVDYF  178 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCSSTHHHHHHHHHHGGGTCEEECCTTCCCHHHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCcchhHHHHHHHHHHhcCCcEEecCCCCCHHHHHHHHHHHH
Confidence            35678899999999999999998766   55565555433211                    00112333445566666


Q ss_pred             hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC-C--hhhcCCCCcceEE
Q 022768          122 RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL-D--PALLRPGRLDRKI  198 (292)
Q Consensus       122 ~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l-~--~~l~~~~r~~~~i  198 (292)
                      ......+++||..-.+.         .+......+..+.....    ...+++|.-+...+.. +  ..+.....+. -+
T Consensus       179 ~~~~~DvVIIDTaGrl~---------~d~~lm~el~~i~~~~~----pd~vlLVvDA~~gq~a~~~a~~f~~~~~i~-gV  244 (443)
T 3dm5_A          179 KSKGVDIIIVDTAGRHK---------EDKALIEEMKQISNVIH----PHEVILVIDGTIGQQAYNQALAFKEATPIG-SI  244 (443)
T ss_dssp             HHTTCSEEEEECCCCSS---------CCHHHHHHHHHHHHHHC----CSEEEEEEEGGGGGGHHHHHHHHHHSCTTE-EE
T ss_pred             HhCCCCEEEEECCCccc---------chHHHHHHHHHHHHhhc----CceEEEEEeCCCchhHHHHHHHHHhhCCCe-EE
Confidence            66667899999875431         13333333444433322    2345555544332211 0  1222111221 12


Q ss_pred             EccCCCHHHHHHHHHHHH--cCcc---------C--CCCCCHHHHHHHcCCCCHHHHHHHHHHHHH----------HHHH
Q 022768          199 EIPLPNEQSRMEILKIHA--AGIA---------K--HGEIDYEAVVKLAEGFNGADLRNVCTEAGM----------SAIR  255 (292)
Q Consensus       199 ~l~~p~~~~r~~i~~~~~--~~~~---------~--~~~~~~~~l~~~~~g~~~~di~~l~~~a~~----------~a~~  255 (292)
                      -+.-.|...+...+....  .+.+         +  -...+.+.++..--|  .+|+..+++.|..          .+.+
T Consensus       245 IlTKlD~~~~gG~~ls~~~~~g~PI~fig~Ge~vddL~~f~~~~~~~~llg--~gd~~~l~e~~~~~~~~~~~~~~~~~k  322 (443)
T 3dm5_A          245 IVTKLDGSAKGGGALSAVAATGAPIKFIGTGEKIDDIEPFDPPRFVSRLLG--LGDIQGLLEKFKELEKEVEIKEEDIER  322 (443)
T ss_dssp             EEECCSSCSSHHHHHHHHHTTCCCEEEEECSSSTTCEEECCHHHHHHHHTT--TTCHHHHHHHHHHHHTTHHHHHHHHHH
T ss_pred             EEECCCCcccccHHHHHHHHHCCCEEEEEcCCChHHhhhCCHHHHHHHHcC--CCcHHHHHHHHHHhhhhhHHHHHHHHH
Confidence            233333322222111111  1111         1  122456777776654  4488888866533          2222


Q ss_pred             hcCCcccHHHHHHHHHHHhh
Q 022768          256 AERDYVIHEDFMKAVRKLNE  275 (292)
Q Consensus       256 ~~~~~i~~~~~~~a~~~~~~  275 (292)
                      -.....|.+|+.+-++.+..
T Consensus       323 ~~~~~f~l~d~~~q~~~~~k  342 (443)
T 3dm5_A          323 FLRGKFTLKDMYAQLEAMRK  342 (443)
T ss_dssp             HHTTCCCHHHHHHHHHHHHT
T ss_pred             HhhCCcCHHHHHHHHHHHHh
Confidence            23445888888887777653

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.58  E-value=4.3e-05  Score=62.01  Aligned_cols=32  Identities=25%  Similarity=0.436  Sum_probs=28.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..|+|.|+||+||||+++.++..++.+++..
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   36 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKEYGLAHLST   36 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCceEEeh
Confidence            45689999999999999999999998776654

>1e6c_A Shikimate kinase; phosphoryl transfer, ADP, shikimate pathway, P-loop protein, transferase; 1.8A {Erwinia chrysanthemi} SCOP: c.37.1.2 PDB: 1shk_A 2shk_A*

Probab=97.57  E-value=5.1e-05  Score=58.92  Aligned_cols=29  Identities=24%  Similarity=0.533  Sum_probs=26.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .++|.|++|+||||+++.++..++.+++.
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg~~~id   32 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARALGYEFVD   32 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEc
Confidence            58999999999999999999999877654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.57  E-value=3.8e-05  Score=60.24  Aligned_cols=30  Identities=27%  Similarity=0.485  Sum_probs=23.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      +..++|.|++|+||||+++.+++.++.+++
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l~~~~i   34 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERLPGSFV   34 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHSTTCEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhcCCCEE
Confidence            456899999999999999999999998876

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.57  E-value=5.3e-05  Score=61.85  Aligned_cols=33  Identities=21%  Similarity=0.444  Sum_probs=27.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .+..++|.|++|+||||+++.++..++.+++..
T Consensus         6 ~~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   38 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTVSSRITTHFELKHLSS   38 (227)
T ss_dssp             -CCEEEEEECTTSSHHHHHHHHHHHSSSEEEEH
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHHcCCeEEec
Confidence            356799999999999999999999998766543

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=97.56  E-value=0.00025  Score=72.26  Aligned_cols=31  Identities=23%  Similarity=0.381  Sum_probs=27.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .++++..+.|+||+|+||||+++.+.+.+..
T Consensus       440 ~i~~G~~vaivG~sGsGKSTll~ll~~~~~~  470 (1321)
T 4f4c_A          440 RVNAGQTVALVGSSGCGKSTIISLLLRYYDV  470 (1321)
T ss_dssp             EECTTCEEEEEECSSSCHHHHHHHHTTSSCC
T ss_pred             eecCCcEEEEEecCCCcHHHHHHHhcccccc
Confidence            4678899999999999999999999987754

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=97.56  E-value=4.8e-05  Score=60.03  Aligned_cols=26  Identities=31%  Similarity=0.457  Sum_probs=23.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +..++|.|++|+||||+++.++..++
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35689999999999999999999886

>3dl0_A Adenylate kinase; phosphotransferase, zinc coordination, ATP-binding, binding, nucleotide biosynthesis, nucleotide-binding, trans; HET: AP5; 1.58A {Bacillus subtilis} PDB: 1p3j_A* 2ori_A* 2eu8_A* 2oo7_A* 2p3s_A* 2qaj_A* 2osb_A* 3dkv_A* 1zin_A* 1zio_A* 1zip_A* 1s3g_A*

Probab=97.56  E-value=6.3e-05  Score=60.82  Aligned_cols=30  Identities=23%  Similarity=0.430  Sum_probs=26.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .++|.|+||+||||+++.++..++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKYGIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            488999999999999999999998877655

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.55  E-value=3.9e-05  Score=60.99  Aligned_cols=32  Identities=22%  Similarity=0.369  Sum_probs=27.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..|+|.|++|+||||+++.+++.++.+++..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   43 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYGFTHLST   43 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            45799999999999999999999998665543

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=97.55  E-value=5.9e-05  Score=58.44  Aligned_cols=29  Identities=28%  Similarity=0.535  Sum_probs=25.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .++|.|+||+||||+++.+ ..++.+++.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~g~~~i~~   31 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KERGAKVIVM   31 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHTTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCcEEEH
Confidence            5889999999999999999 8888776653

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.54  E-value=4.4e-05  Score=59.60  Aligned_cols=28  Identities=36%  Similarity=0.420  Sum_probs=23.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHH-hcCCcE
Q 022768           67 KGVLLYGPPGTGKTLLARAIAS-NIDANF   94 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~-~l~~~~   94 (292)
                      ..++|.|+||+||||+++.+++ .++..+
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~~~~~~~~   31 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYN   31 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEE
T ss_pred             eEEEEecCCCCCHHHHHHHHHhhcCCcEE
Confidence            4588999999999999999998 454333

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=97.54  E-value=0.0003  Score=62.16  Aligned_cols=29  Identities=34%  Similarity=0.487  Sum_probs=25.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        43 ~i~~Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           43 SISPGQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             EECTTCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            36778889999999999999999999754

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=97.54  E-value=0.00041  Score=67.91  Aligned_cols=25  Identities=20%  Similarity=0.202  Sum_probs=21.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la   87 (292)
                      ...+..++|.||+|+||||+++.++
T Consensus       659 ~~~g~i~~ItGpNGsGKSTlLr~ia  683 (934)
T 3thx_A          659 KDKQMFHIITGPNMGGKSTYIRQTG  683 (934)
T ss_dssp             TTTBCEEEEECCTTSSHHHHHHHHH
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHH
Confidence            3456779999999999999999995

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=97.54  E-value=8e-05  Score=59.53  Aligned_cols=38  Identities=18%  Similarity=0.191  Sum_probs=29.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      .++..+.|.||+|+||||+++.++..+   |...+.++...
T Consensus        23 ~~g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d~d~   63 (200)
T 3uie_A           23 QKGCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILDGDN   63 (200)
T ss_dssp             SCCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEecCch
Confidence            457789999999999999999999988   44434555433

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.54  E-value=6.7e-05  Score=60.62  Aligned_cols=30  Identities=27%  Similarity=0.489  Sum_probs=26.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .|+|.|+||+||||+++.++..++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKYEIPHIST   31 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEeeH
Confidence            478999999999999999999998877654

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.53  E-value=6.1e-05  Score=60.23  Aligned_cols=33  Identities=18%  Similarity=0.297  Sum_probs=27.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +..|+|.|++|+||||+++.+++.++.+++..+
T Consensus        15 ~~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~d   47 (203)
T 1ukz_A           15 VSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG   47 (203)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHSSCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCceEEeHH
Confidence            456889999999999999999999987665543

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=97.53  E-value=0.00028  Score=65.90  Aligned_cols=29  Identities=31%  Similarity=0.407  Sum_probs=26.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus       365 ~i~~G~~~~ivG~sGsGKSTll~~l~g~~  393 (582)
T 3b5x_A          365 SIPQGKTVALVGRSGSGKSTIANLFTRFY  393 (582)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            36778899999999999999999999765

>1qf9_A UMP/CMP kinase, protein (uridylmonophosphate/cytidylmonophosphate kinase); nucleoside monophosphate kinase, NMP kinase; HET: ADP C5P; 1.70A {Dictyostelium discoideum} SCOP: c.37.1.1 PDB: 1uke_A* 2ukd_A* 3ukd_A* 4ukd_A* 5ukd_A*

Probab=97.53  E-value=8.4e-05  Score=58.63  Aligned_cols=32  Identities=28%  Similarity=0.458  Sum_probs=27.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..++|.|++|+||||+++.++..++.+++..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~   37 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEeeH
Confidence            35689999999999999999999998766544

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=97.52  E-value=0.0004  Score=64.82  Aligned_cols=30  Identities=37%  Similarity=0.462  Sum_probs=26.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++....
T Consensus       365 ~i~~G~~~~ivG~sGsGKSTLl~~l~g~~~  394 (582)
T 3b60_A          365 KIPAGKTVALVGRSGSGKSTIASLITRFYD  394 (582)
T ss_dssp             EECTTCEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhhccC
Confidence            367788999999999999999999998663

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=97.52  E-value=0.00027  Score=58.14  Aligned_cols=34  Identities=32%  Similarity=0.368  Sum_probs=28.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      ..++++||+|+|||.++-.++...+.+++.+...
T Consensus       109 ~~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P~  142 (237)
T 2fz4_A          109 KRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPT  142 (237)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHHSCSCEEEEESS
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeCC
Confidence            3599999999999999999988887777666544

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=97.51  E-value=0.00078  Score=60.23  Aligned_cols=197  Identities=13%  Similarity=0.127  Sum_probs=97.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------c----cChHHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------Y----IGESARLIREMFGYA  121 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~----~~~~~~~~~~~~~~~  121 (292)
                      ++..+++.|++|+||||++..+|..+   +..+..+.+......                +    ...........+..+
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D~~r~~a~eqL~~~~~~~gv~~~~~~~~~dp~~i~~~al~~a  175 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIF  175 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEECCSCHHHHHHHHHHHHTTTCCEECCTTCSCHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecCccchhHHHHHHHHHHhcCCceeeccccCCHHHHHHHHHHHH
Confidence            35678899999999999999999766   555555554322110                0    001122233444455


Q ss_pred             hhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC---hhhcCCCCcceEE
Q 022768          122 RDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD---PALLRPGRLDRKI  198 (292)
Q Consensus       122 ~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~---~~l~~~~r~~~~i  198 (292)
                      ....+.+++||....+..       ..+......+..+.....    ...+++|..+...+..-   ..+...... ..+
T Consensus       176 ~~~~~DvvIIDTaGr~~~-------~~d~~lm~el~~i~~~~~----pd~vlLVlDa~~gq~a~~~a~~f~~~~~~-~gV  243 (433)
T 3kl4_A          176 VKNKMDIIIVDTAGRHGY-------GEETKLLEEMKEMYDVLK----PDDVILVIDASIGQKAYDLASRFHQASPI-GSV  243 (433)
T ss_dssp             TTTTCSEEEEEECCCSSS-------CCTTHHHHHHHHHHHHHC----CSEEEEEEEGGGGGGGHHHHHHHHHHCSS-EEE
T ss_pred             HhcCCCEEEEECCCCccc-------cCCHHHHHHHHHHHHhhC----CcceEEEEeCccchHHHHHHHHHhcccCC-cEE
Confidence            545678999998855410       013334444444444432    23555666554332211   112110011 122


Q ss_pred             EccCCCHHHH----HHHHHHHH-c------CccC--CCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh---------
Q 022768          199 EIPLPNEQSR----MEILKIHA-A------GIAK--HGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRA---------  256 (292)
Q Consensus       199 ~l~~p~~~~r----~~i~~~~~-~------~~~~--~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~---------  256 (292)
                      -+.-.|...+    ..+....- .      +...  ....+.+.++..--|  .+|+..+++.+.......         
T Consensus       244 IlTKlD~~a~~G~als~~~~~g~Pi~fig~Ge~v~dL~~f~p~~~~~~llg--~gd~~~l~e~~~~~~~~~~~~~~~~k~  321 (433)
T 3kl4_A          244 IITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILG--MGDIESILEKVKGLEEYDKIQKKMEDV  321 (433)
T ss_dssp             EEECGGGCSCHHHHHHHHHHHTCEEEEEECCSSSSCEEECCHHHHHHHHHC--SSHHHHHHHHHHHC-------------
T ss_pred             EEecccccccchHHHHHHHHHCCCEEEEECCCChHhCccCCHHHHHHHhcC--CchHHHHHHHHHHhhhHHHHHHHHHHH
Confidence            2333332222    22222210 0      1111  123456677765544  248888887776533222         


Q ss_pred             cCC--cccHHHHHHHHHHHhh
Q 022768          257 ERD--YVIHEDFMKAVRKLNE  275 (292)
Q Consensus       257 ~~~--~i~~~~~~~a~~~~~~  275 (292)
                      ...  ..+.+|+.+-++.+..
T Consensus       322 ~~g~~~f~~~d~~~q~~~~~k  342 (433)
T 3kl4_A          322 MEGKGKLTLRDVYAQIIALRK  342 (433)
T ss_dssp             ------CCHHHHHHHHHHHHH
T ss_pred             HcCCCCCCHHHHHHHHHHHHh
Confidence            122  6889999988888774

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.51  E-value=7.8e-05  Score=57.58  Aligned_cols=30  Identities=20%  Similarity=0.390  Sum_probs=26.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .|+|.|++|+||||+++.+++.++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   31 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDV   31 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEEC
Confidence            488999999999999999999999877653

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=97.51  E-value=9.1e-05  Score=59.12  Aligned_cols=34  Identities=18%  Similarity=0.134  Sum_probs=28.6

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc-CCcEEEEe
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI-DANFLKVV   98 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l-~~~~~~~~   98 (292)
                      .+..|+|.|++|+||||+++.+++.+ +.+++.+.
T Consensus         3 ~~~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~   37 (204)
T 2v54_A            3 RGALIVFEGLDKSGKTTQCMNIMESIPANTIKYLN   37 (204)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHTSCGGGEEEEE
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHCCCceEEEe
Confidence            35679999999999999999999998 56666654

>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide monophosphate kinase,, transferase; 1.75A {Escherichia coli} SCOP: c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A* 2fem_A 2feo_A*

Probab=97.49  E-value=8.9e-05  Score=60.29  Aligned_cols=31  Identities=29%  Similarity=0.534  Sum_probs=26.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..+.|.||+|+||||+++.+++.++.+++.
T Consensus         5 ~~~i~i~G~~GsGKSTl~~~L~~~~g~~~~d   35 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCKAMAEALQWHLLD   35 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            3468999999999999999999998866654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=97.48  E-value=7.4e-05  Score=58.72  Aligned_cols=28  Identities=18%  Similarity=0.374  Sum_probs=24.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ..+..+.|.||+|+||||+++.++....
T Consensus         3 ~~g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            3 HMRKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            3467799999999999999999998764

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=97.47  E-value=0.00047  Score=64.45  Aligned_cols=28  Identities=25%  Similarity=0.363  Sum_probs=24.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++..+
T Consensus       100 ~~~Gei~~LvGpNGaGKSTLLkiL~Gll  127 (608)
T 3j16_B          100 PRPGQVLGLVGTNGIGKSTALKILAGKQ  127 (608)
T ss_dssp             CCTTSEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCCEEEEECCCCChHHHHHHHHhcCC
Confidence            3567889999999999999999999765

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.47  E-value=6.3e-05  Score=61.15  Aligned_cols=31  Identities=23%  Similarity=0.441  Sum_probs=26.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..|+|.|++|+||||+++.++..++.+++.
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~   35 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQLAHIS   35 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceec
Confidence            4579999999999999999999999865543

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=97.47  E-value=0.00042  Score=63.93  Aligned_cols=106  Identities=16%  Similarity=0.218  Sum_probs=63.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc----------EEEEeccchhc---------------cc-----------
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN----------FLKVVSSAIID---------------KY-----------  106 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~----------~~~~~~~~~~~---------------~~-----------  106 (292)
                      +.++..+.|.||+|+||||+++.++......          +-.+. .....               ..           
T Consensus       291 i~~Gei~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~~~~i~~~~-q~~~~~~~~tv~~~l~~~~~~~~~~~~~~~~~~  369 (538)
T 3ozx_A          291 AKEGEIIGILGPNGIGKTTFARILVGEITADEGSVTPEKQILSYKP-QRIFPNYDGTVQQYLENASKDALSTSSWFFEEV  369 (538)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSCCSBCCEESSCCCEEEEC-SSCCCCCSSBHHHHHHHHCSSTTCTTSHHHHHT
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEECCeeeEeec-hhcccccCCCHHHHHHHhhhhccchhHHHHHHH
Confidence            4567889999999999999999999865221          11111 00000               00           


Q ss_pred             -------------cCh--HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCC
Q 022768          107 -------------IGE--SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGK  171 (292)
Q Consensus       107 -------------~~~--~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~  171 (292)
                                   +..  ....-+..+..+....|.+|++||-          ++..+......+.+++..+..   ..+
T Consensus       370 l~~~~l~~~~~~~~~~LSGGq~QRv~iAraL~~~p~lLlLDEP----------T~gLD~~~~~~i~~~l~~l~~---~~g  436 (538)
T 3ozx_A          370 TKRLNLHRLLESNVNDLSGGELQKLYIAATLAKEADLYVLDQP----------SSYLDVEERYIVAKAIKRVTR---ERK  436 (538)
T ss_dssp             TTTTTGGGCTTSBGGGCCHHHHHHHHHHHHHHSCCSEEEEEST----------TTTCCHHHHHHHHHHHHHHHH---HTT
T ss_pred             HHHcCCHHHhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEeCC----------ccCCCHHHHHHHHHHHHHHHH---hCC
Confidence                         000  1112244555556688999999995          334477777777777766531   124


Q ss_pred             eEEEEEeCCCC
Q 022768          172 VKMIMATNRPD  182 (292)
Q Consensus       172 ~~vi~t~~~~~  182 (292)
                      ..+|+++++.+
T Consensus       437 ~tvi~vsHdl~  447 (538)
T 3ozx_A          437 AVTFIIDHDLS  447 (538)
T ss_dssp             CEEEEECSCHH
T ss_pred             CEEEEEeCCHH
Confidence            56777777643

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=97.47  E-value=0.0001  Score=60.48  Aligned_cols=32  Identities=34%  Similarity=0.482  Sum_probs=27.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..|+|.|++|+||||+++.++..++.+++..
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   47 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   47 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            45799999999999999999999998766554

>3sr0_A Adenylate kinase; phosphoryl transfer analogue, ALF4, transferase (phosphotran phosphoryl transfer, nucleotide-binding; HET: ADP AMP; 1.56A {Aquifex aeolicus} PDB: 2rh5_A 2rgx_A*

Probab=97.47  E-value=8.7e-05  Score=59.74  Aligned_cols=29  Identities=28%  Similarity=0.494  Sum_probs=25.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .++|.||||+||+|.|+.+++.++.+++.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~g~~~is   30 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEKGFVHIS   30 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            47889999999999999999999877654

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=97.47  E-value=0.00049  Score=63.41  Aligned_cols=113  Identities=20%  Similarity=0.259  Sum_probs=65.3

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHH--HHhc--CCcEEEEeccchhc------cccC------------------------
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAI--ASNI--DANFLKVVSSAIID------KYIG------------------------  108 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~l--a~~l--~~~~~~~~~~~~~~------~~~~------------------------  108 (292)
                      +.++..++|.||+|+|||||++.+  +...  +...++++..+...      ...+                        
T Consensus        36 i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~~~g~i~v~g~~~~~~~~~~~~~~g~~~q~~~~~~~l~~~~~~~~~~~~  115 (525)
T 1tf7_A           36 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQ  115 (525)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEESSSCHHHHHHHHGGGTCCHHHHHHTTSEEEEECCCCSSCC
T ss_pred             CCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEeCCHHHHHHHHHHcCCChHHhhccCcEEEEecCcccchh
Confidence            567889999999999999999994  4333  33445544322100      0000                        


Q ss_pred             ------hHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          109 ------ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       109 ------~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                            .....+...........|.+|+|||+-.+...     ...+......+..++..+..    .++.+|.++++.+
T Consensus       116 ~~l~~~~l~~~~~~~~~~LS~g~~~~lilDe~t~~~~~-----~~lD~~~~~~l~~ll~~l~~----~g~tvl~itH~~~  186 (525)
T 1tf7_A          116 EVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQ-----YDASSVVRRELFRLVARLKQ----IGATTVMTTERIE  186 (525)
T ss_dssp             SCCSSHHHHHHHHHHHHHHHHHTCSEEEEECSTTTSTT-----TCCHHHHHHHHHHHHHHHHH----HTCEEEEEEECSS
T ss_pred             hhhcccCHHHHHHHHHHHHHHcCCCEEEECCHHHHHHh-----cCCHHHHHHHHHHHHHHHHH----CCCEEEEEecCCC
Confidence                  01112223333333456789999998665321     12245566667777766642    2556777777765


Q ss_pred             CC
Q 022768          183 VL  184 (292)
Q Consensus       183 ~l  184 (292)
                      .+
T Consensus       187 ~~  188 (525)
T 1tf7_A          187 EY  188 (525)
T ss_dssp             SS
T ss_pred             Cc
Confidence            54

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=97.46  E-value=5.9e-05  Score=62.63  Aligned_cols=33  Identities=24%  Similarity=0.450  Sum_probs=29.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +..+.|.|++|+||||+++.++..++.+++..+
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~lg~~~~d~d   80 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSLGYTFFDCD   80 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCcEEeCc
Confidence            678999999999999999999999998776543

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=97.46  E-value=0.00022  Score=63.70  Aligned_cols=94  Identities=18%  Similarity=0.271  Sum_probs=52.6

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC---cEEEEecc-ch
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA---NFLKVVSS-AI  102 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~---~~~~~~~~-~~  102 (292)
                      ...+++++.-.......|...+.              .++..++|.||+|+||||++++++..+..   .++..... +.
T Consensus       142 ~~~~l~~Lg~~~~~~~~L~~l~~--------------~~ggii~I~GpnGSGKTTlL~allg~l~~~~g~I~~~ed~ie~  207 (418)
T 1p9r_A          142 TRLDLHSLGMTAHNHDNFRRLIK--------------RPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEF  207 (418)
T ss_dssp             TCCCGGGSCCCHHHHHHHHHHHT--------------SSSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCS
T ss_pred             CCCCHHHcCCCHHHHHHHHHHHH--------------hcCCeEEEECCCCCCHHHHHHHHHhhcCCCCCEEEEecccchh
Confidence            34567776444444444444421              34667899999999999999999998743   23333211 11


Q ss_pred             h-----cc-ccChHHHHHHHHHHHhhhCCCEEEEEccc
Q 022768          103 I-----DK-YIGESARLIREMFGYARDHQPCIIFMDEI  134 (292)
Q Consensus       103 ~-----~~-~~~~~~~~~~~~~~~~~~~~~~il~lDe~  134 (292)
                      .     .. ............+..+....|.++++.|+
T Consensus       208 ~~~~~~q~~v~~~~g~~f~~~lr~~Lrq~pd~i~vgEi  245 (418)
T 1p9r_A          208 DIDGIGQTQVNPRVDMTFARGLRAILRQDPDVVMVGEI  245 (418)
T ss_dssp             CCSSSEEEECBGGGTBCHHHHHHHHGGGCCSEEEESCC
T ss_pred             ccCCcceEEEccccCcCHHHHHHHHhccCCCeEEEcCc
Confidence            0     00 00011112223344445567889988885

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.46  E-value=5e-05  Score=65.90  Aligned_cols=52  Identities=17%  Similarity=0.350  Sum_probs=36.1

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ..+...+.+...+...+..         ....+++|+|++|+||||+++.++..++.+++.
T Consensus         3 ~~~~L~~~il~~l~~~i~~---------g~~~~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A            3 DTHKLADDVLQLLDNRIED---------NYRVCVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             CHHHHHHHHHHHHHHTTTT---------CSCEEEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHhcc---------CCeeEEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            4455566666665443111         223459999999999999999999999877643

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=97.45  E-value=0.00041  Score=64.04  Aligned_cols=28  Identities=32%  Similarity=0.507  Sum_probs=25.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+|||||++.++..+
T Consensus        44 i~~Ge~~~LvG~NGaGKSTLlk~l~Gl~   71 (538)
T 1yqt_A           44 VKEGMVVGIVGPNGTGKSTAVKILAGQL   71 (538)
T ss_dssp             CCTTSEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            5678889999999999999999999755

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=97.44  E-value=0.00049  Score=63.47  Aligned_cols=27  Identities=30%  Similarity=0.395  Sum_probs=23.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++..+.|.||+|+||||+++.++..+
T Consensus        23 ~~Gei~gLiGpNGaGKSTLlkiL~Gl~   49 (538)
T 3ozx_A           23 KNNTILGVLGKNGVGKTTVLKILAGEI   49 (538)
T ss_dssp             CTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            346678899999999999999999755

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=97.43  E-value=0.00011  Score=56.60  Aligned_cols=29  Identities=34%  Similarity=0.424  Sum_probs=26.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||.|+||||+++.++..+
T Consensus        29 ~i~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           29 HTEKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CCSSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            46778889999999999999999999987

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=97.42  E-value=9.6e-05  Score=59.04  Aligned_cols=29  Identities=28%  Similarity=0.524  Sum_probs=24.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++....
T Consensus         4 m~~g~ii~l~Gp~GsGKSTl~~~L~~~~~   32 (205)
T 3tr0_A            4 MNKANLFIISAPSGAGKTSLVRALVKALA   32 (205)
T ss_dssp             -CCCCEEEEECCTTSCHHHHHHHHHHHSS
T ss_pred             CCCCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            45677899999999999999999999864

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=97.42  E-value=0.00041  Score=60.06  Aligned_cols=38  Identities=21%  Similarity=0.218  Sum_probs=30.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      |+.++.-++|.|+||+|||+++..+|...   +.++.+++.
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSl   82 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSL   82 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEES
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeC
Confidence            57888889999999999999999998754   566666553

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=97.41  E-value=0.00013  Score=57.55  Aligned_cols=31  Identities=19%  Similarity=0.132  Sum_probs=27.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      .++|.|++|+||||+++.+++.+   +.+++..+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d   35 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYR   35 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEe
Confidence            47899999999999999999988   88887665

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=97.41  E-value=0.00013  Score=57.62  Aligned_cols=29  Identities=28%  Similarity=0.575  Sum_probs=24.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      +.|+|+||+|+||||+++.+.......+.
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~~~~~   30 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYPDSFG   30 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCCCCeE
Confidence            45999999999999999999988754443

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=97.41  E-value=0.0001  Score=59.13  Aligned_cols=29  Identities=24%  Similarity=0.469  Sum_probs=26.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..++|.||||+||||+++.++..++
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             cccCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            56678899999999999999999999875

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=97.41  E-value=0.00025  Score=72.98  Aligned_cols=121  Identities=17%  Similarity=0.214  Sum_probs=72.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhc----------------cccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIID----------------KYIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~~  122 (292)
                      |.+.++.+.++||+|+||||++-.++.+.   |..+.+++..+-.+                ..+...+..+..+...++
T Consensus      1427 G~prg~~iei~g~~~sGkttl~~~~~a~~~~~g~~~~~i~~e~~~~~~~~~~~Gv~~~~l~~~~p~~~e~~l~~~~~~~~ 1506 (1706)
T 3cmw_A         1427 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1506 (1706)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CCCCCCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEEecCCCCCHHHHHHcCCCHHHeEEeCCCcHHHHHHHHHHHHH
Confidence            45667889999999999999997777533   66666666543222                233345667777777778


Q ss_pred             hCCCEEEEEcccccccCCcCCCCCcc--hHH-HHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          123 DHQPCIIFMDEIDAIGGRRFSEGTSA--DRE-IQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~~~~~~~~~--~~~-~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      ...+++|++|-+..|.++..-.....  .-. ..+.+.+.+..+.+.-...++.+|++....+
T Consensus      1507 s~~~~~vvvDsv~al~~~~e~~~~~~~~~~~~~ar~m~~~lr~l~~~~~~~~~~~i~~~~~~~ 1569 (1706)
T 3cmw_A         1507 SGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQIRM 1569 (1706)
T ss_dssp             HTCCSEEEESCSTTCCCTTTTC-------CCHHHHHHHHHHHHHHHHHHHHTCEEEEEECBC-
T ss_pred             cCCCCEEEEccHHhCCccccccccccccchhHHHHHHHHHHHHHHHHHHhCCcEEEEeecccc
Confidence            88899999999999976542221111  111 1222223333333222224677777765443

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=97.38  E-value=0.00013  Score=58.95  Aligned_cols=30  Identities=23%  Similarity=0.339  Sum_probs=26.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .++|.|+||+||||+++.++..++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~g~~~i~~   31 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            488999999999999999999998777654

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=97.36  E-value=0.00016  Score=60.06  Aligned_cols=31  Identities=29%  Similarity=0.510  Sum_probs=27.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      ++..+.|.||+|+||||+++.+++.++..++
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~Lg~~~~   56 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESLNWRLL   56 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHTTCEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhcCCCcC
Confidence            4567899999999999999999999987654

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=97.36  E-value=0.00011  Score=58.67  Aligned_cols=28  Identities=25%  Similarity=0.360  Sum_probs=24.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++..+
T Consensus         3 i~~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3557789999999999999999999877

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=97.35  E-value=0.001  Score=59.92  Aligned_cols=38  Identities=32%  Similarity=0.263  Sum_probs=31.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      |+.++.-++|.|+||+|||+++-.+|...   +.+++.++.
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSl  233 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSL  233 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEEC
Confidence            68888899999999999999998888654   556766653

>2if2_A Dephospho-COA kinase; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative, northeast structural genomics consortium, NESG; 3.00A {Aquifex aeolicus}

Probab=97.34  E-value=9e-05  Score=59.27  Aligned_cols=30  Identities=27%  Similarity=0.338  Sum_probs=25.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .+.|.|++|+||||+++.++. ++.+++..+
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~i~~d   32 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYVLDAD   32 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEEEEHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEEEEcc
Confidence            588999999999999999999 876665544

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=97.33  E-value=0.00014  Score=57.86  Aligned_cols=28  Identities=18%  Similarity=0.533  Sum_probs=25.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      .++|.|++|+||||+++.+++.++.+++
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~~   29 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEIF   29 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEEE
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcEE
Confidence            4789999999999999999999987654

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=97.33  E-value=0.0019  Score=60.37  Aligned_cols=24  Identities=33%  Similarity=0.570  Sum_probs=21.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.|.||+|+|||||++.++...
T Consensus       379 Eiv~iiG~NGsGKSTLlk~l~Gl~  402 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKLLAGAL  402 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHTSS
T ss_pred             eEEEEECCCCCcHHHHHHHHhcCC
Confidence            558999999999999999999865

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=97.33  E-value=0.00014  Score=62.38  Aligned_cols=33  Identities=36%  Similarity=0.567  Sum_probs=29.3

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      ..++|+||+|+|||++++.+|+.++..++.++.
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds   38 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADALPCELISVDS   38 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHSCEEEEEECT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCcEEeccc
Confidence            468999999999999999999999888777754

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=97.33  E-value=0.00016  Score=59.80  Aligned_cols=30  Identities=33%  Similarity=0.608  Sum_probs=26.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      +..+.|.||+|+||||+++.+++.++....
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg~~~~   56 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFGLQHL   56 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCCCE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEe
Confidence            567999999999999999999998876544

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=97.33  E-value=0.00011  Score=58.69  Aligned_cols=27  Identities=33%  Similarity=0.632  Sum_probs=22.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ++..+.|.||+|+||||+++.++....
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            466799999999999999999998764

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=97.33  E-value=7e-05  Score=60.19  Aligned_cols=29  Identities=17%  Similarity=0.273  Sum_probs=25.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      .+..|+|.|++|+||||+++.+++.++.+
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~~l~~~   37 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVEYLKNN   37 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            45679999999999999999999987544

>3r20_A Cytidylate kinase; structural genomics, seattle structural genomics center for infectious disease, ssgcid, ADP, DCMP, D transferase; 2.00A {Mycobacterium smegmatis} SCOP: c.37.1.0 PDB: 3r8c_A 4die_A*

Probab=97.31  E-value=0.00018  Score=58.91  Aligned_cols=31  Identities=35%  Similarity=0.613  Sum_probs=26.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..+.|.||+|+||||+++.++..++.+++.
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg~~~~d   39 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALGARYLD   39 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            4578899999999999999999999866543

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=97.31  E-value=0.00014  Score=59.13  Aligned_cols=28  Identities=21%  Similarity=0.483  Sum_probs=24.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            5678889999999999999999999977

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=97.31  E-value=0.00016  Score=58.92  Aligned_cols=30  Identities=20%  Similarity=0.527  Sum_probs=25.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .++|.|++|+||||+++.++..++.+++..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~lg~~~i~~   31 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKYSLAHIES   31 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEch
Confidence            478999999999999999999998655443

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=97.31  E-value=0.00015  Score=58.41  Aligned_cols=29  Identities=24%  Similarity=0.410  Sum_probs=25.2

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .++..++|.||+|+||||+++.++..++.
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CCCcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            35677899999999999999999998753

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.31  E-value=0.00068  Score=53.76  Aligned_cols=33  Identities=12%  Similarity=-0.019  Sum_probs=24.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKV   97 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~   97 (292)
                      .+.-.+++||.|+||||.+-.++...   +..++.+
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~   42 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVF   42 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEE
Confidence            35678889999999999888777765   4455444

>2grj_A Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosphocoenzyme kinase, structural genomics, joint center for structural GE JCSG; HET: ADP COD; 2.60A {Thermotoga maritima}

Probab=97.30  E-value=0.00013  Score=58.08  Aligned_cols=31  Identities=23%  Similarity=0.324  Sum_probs=26.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .+.|+|++||||||+++.++..+|.+++..+
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vid~D   44 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVVNVD   44 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEEECc
Confidence            4779999999999999999999887766543

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=97.30  E-value=0.00036  Score=71.20  Aligned_cols=29  Identities=24%  Similarity=0.509  Sum_probs=26.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++++..+-|+|++|+||||+++.+.+-.
T Consensus      1101 ~I~~Ge~vaIVG~SGsGKSTL~~lL~rl~ 1129 (1321)
T 4f4c_A         1101 SVEPGQTLALVGPSGCGKSTVVALLERFY 1129 (1321)
T ss_dssp             EECTTCEEEEECSTTSSTTSHHHHHTTSS
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHhcCc
Confidence            46788999999999999999999999766

>1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1

Probab=97.28  E-value=0.00018  Score=57.67  Aligned_cols=28  Identities=29%  Similarity=0.369  Sum_probs=24.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .+.|.|++|+||||+++.++. +|.+++.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~id   31 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPLVD   31 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcccc
Confidence            578999999999999999988 7777654

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=97.28  E-value=0.0001  Score=58.14  Aligned_cols=24  Identities=25%  Similarity=0.422  Sum_probs=22.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .|+|.|+||+||||+++.+++.++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            588999999999999999999886

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=97.28  E-value=0.00028  Score=56.68  Aligned_cols=28  Identities=32%  Similarity=0.547  Sum_probs=25.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .++..+.|.||+|+||||+++.++..+.
T Consensus        20 ~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           20 PGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            5577889999999999999999999875

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=97.27  E-value=0.00043  Score=63.43  Aligned_cols=39  Identities=10%  Similarity=0.066  Sum_probs=31.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEecc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVSS  100 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~~  100 (292)
                      |+.++..++|.|+||+|||+++..+|...    +.+++.++..
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E  280 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLE  280 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESS
T ss_pred             ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEecc
Confidence            68888899999999999999999988754    4567766643

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=97.26  E-value=0.00019  Score=57.56  Aligned_cols=28  Identities=21%  Similarity=0.229  Sum_probs=24.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      +..|+|.|++|+||||+++.+++.++..
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHhhc
Confidence            4568999999999999999999988763

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=97.25  E-value=0.00014  Score=58.40  Aligned_cols=33  Identities=18%  Similarity=0.271  Sum_probs=26.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc-CCcEE
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI-DANFL   95 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l-~~~~~   95 (292)
                      +.++..+.|.|++|+||||+++.++..+ +..++
T Consensus        18 ~~~~~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i   51 (207)
T 2qt1_A           18 GSKTFIIGISGVTNSGKTTLAKNLQKHLPNCSVI   51 (207)
T ss_dssp             SCCCEEEEEEESTTSSHHHHHHHHHTTSTTEEEE
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHhcCCcEEE
Confidence            4556678899999999999999999987 44443

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=97.25  E-value=0.00018  Score=58.44  Aligned_cols=29  Identities=21%  Similarity=0.337  Sum_probs=25.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+|||||++.++....
T Consensus        13 ~~~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           13 MAQGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            56788899999999999999999999875

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=97.25  E-value=0.0015  Score=63.03  Aligned_cols=26  Identities=23%  Similarity=0.289  Sum_probs=22.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .++..++|.||+|+||||++|.++..
T Consensus       605 ~~g~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          605 PQRRMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             SSSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCChHHHHHHHHHH
Confidence            35677999999999999999999864

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=97.24  E-value=9.9e-05  Score=59.40  Aligned_cols=29  Identities=21%  Similarity=0.276  Sum_probs=24.9

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      ..+..|+|.|++|+||||+++.++..++.
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A            7 RRGALIVLEGVDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             CCCCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            34667999999999999999999998743

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=97.24  E-value=0.00088  Score=62.69  Aligned_cols=28  Identities=36%  Similarity=0.516  Sum_probs=25.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+|||||++.++..+
T Consensus       114 i~~Ge~~~LiG~NGsGKSTLlkiL~Gll  141 (607)
T 3bk7_A          114 VKDGMVVGIVGPNGTGKTTAVKILAGQL  141 (607)
T ss_dssp             CCTTSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            5678889999999999999999999755

>3ake_A Cytidylate kinase; CMP kinase, CMP complex, open conformation, nucleotide metab transferase; HET: C5P; 1.50A {Thermus thermophilus} PDB: 3akc_A* 3akd_A*

Probab=97.23  E-value=0.00026  Score=56.54  Aligned_cols=31  Identities=29%  Similarity=0.485  Sum_probs=27.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .+.|.|++|+||||+++.++..++.+++..+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg~~~~d~d   34 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALGVPYLSSG   34 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCceeccc
Confidence            6889999999999999999999997776544

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.23  E-value=0.0011  Score=52.40  Aligned_cols=35  Identities=20%  Similarity=0.187  Sum_probs=26.1

Q ss_pred             CCceEEEEcCCCChHH-HHHHHHHHhc--CCcEEEEec
Q 022768           65 PPKGVLLYGPPGTGKT-LLARAIASNI--DANFLKVVS   99 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT-~l~~~la~~l--~~~~~~~~~   99 (292)
                      .+.-.+++||.|+||| .|++.+.+..  +..++.+..
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp   56 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKY   56 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEcc
Confidence            3566889999999999 7888877654  556666653

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=97.22  E-value=0.00021  Score=57.41  Aligned_cols=30  Identities=27%  Similarity=0.431  Sum_probs=25.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++..+.
T Consensus        16 ~i~~Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           16 PAAVGRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             ---CCCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            357788899999999999999999999874

>1vht_A Dephospho-COA kinase; structural genomics, transferase; HET: BA3; 1.59A {Escherichia coli} SCOP: c.37.1.1 PDB: 1vhl_A* 1viy_A 1t3h_A 1n3b_A

Probab=97.22  E-value=0.00028  Score=57.01  Aligned_cols=31  Identities=32%  Similarity=0.404  Sum_probs=25.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..+.|.|++|+||||+++.++. ++.+++..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~-lg~~~id~   34 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD-LGINVIDA   34 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH-TTCEEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH-cCCEEEEc
Confidence            45688999999999999999998 77665543

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=97.21  E-value=0.00023  Score=60.76  Aligned_cols=30  Identities=30%  Similarity=0.600  Sum_probs=27.5

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++++..+.|+||+|+|||||++.++..+
T Consensus       121 l~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          121 KGIPKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             HTCTTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEecCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            457889999999999999999999999987

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=97.21  E-value=0.0003  Score=55.94  Aligned_cols=31  Identities=26%  Similarity=0.307  Sum_probs=26.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..|.|.|++|+||||+++.+++. +.+++..
T Consensus         8 ~~~I~i~G~~GsGKST~~~~La~~-g~~~id~   38 (203)
T 1uf9_A            8 PIIIGITGNIGSGKSTVAALLRSW-GYPVLDL   38 (203)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHT-TCCEEEH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHC-CCEEEcc
Confidence            456889999999999999999998 7666543

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=97.20  E-value=0.00031  Score=56.38  Aligned_cols=35  Identities=26%  Similarity=0.316  Sum_probs=27.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .++..+.|.||+|+||||+++.++..++..+..+.
T Consensus         4 ~~~~~i~i~G~~GsGKSTl~~~l~~~~~~~i~~v~   38 (211)
T 3asz_A            4 PKPFVIGIAGGTASGKTTLAQALARTLGERVALLP   38 (211)
T ss_dssp             -CCEEEEEEESTTSSHHHHHHHHHHHHGGGEEEEE
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhCCCeEEEe
Confidence            45667889999999999999999998773333333

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=97.18  E-value=0.00028  Score=56.22  Aligned_cols=29  Identities=24%  Similarity=0.437  Sum_probs=25.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ...+..++|.||+|+||||+++.+++...
T Consensus        16 ~~~g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           16 FQGRKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CCSCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCCCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            34577899999999999999999998865

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=97.17  E-value=0.0011  Score=52.91  Aligned_cols=37  Identities=16%  Similarity=0.124  Sum_probs=28.9

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      ..+..+.|.|++|+||||+++.++..+   +.++...+..
T Consensus        20 ~~~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d   59 (201)
T 1rz3_A           20 AGRLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMD   59 (201)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccC
Confidence            456678899999999999999999876   5555555433

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=97.17  E-value=0.0016  Score=62.72  Aligned_cols=61  Identities=16%  Similarity=0.159  Sum_probs=35.8

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCC--hHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMN--PELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~--~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +..+|.++.-.+...+.+...-..|...  ......  +..+..+++.||+|+|||+++..++..
T Consensus        70 ~~~~f~~~~l~~~~~~~l~~r~~lP~~~q~~~i~~~--l~~~~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A           70 KINPFTGREFTPKYVDILKIRRELPVHAQRDEFLKL--YQNNQIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             SBCTTTCSBCCHHHHHHHHHHTTSGGGGGHHHHHHH--HHHCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCccccCCCHHHHHHHHHhhcCChHHHHHHHHHH--HhCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            3456777755555555555444333211  111111  223567999999999999977777543

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=97.17  E-value=0.0013  Score=61.54  Aligned_cols=27  Identities=26%  Similarity=0.420  Sum_probs=24.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++..+.|.||+|+|||||++.++..+
T Consensus       380 ~~Gei~~i~G~NGsGKSTLlk~l~Gl~  406 (607)
T 3bk7_A          380 RKGEVIGIVGPNGIGKTTFVKMLAGVE  406 (607)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            567889999999999999999999865

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=97.16  E-value=0.0022  Score=59.18  Aligned_cols=27  Identities=30%  Similarity=0.426  Sum_probs=24.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++..+.|.||+|+|||||++.++...
T Consensus       310 ~~Ge~~~i~G~NGsGKSTLlk~l~Gl~  336 (538)
T 1yqt_A          310 KKGEVIGIVGPNGIGKTTFVKMLAGVE  336 (538)
T ss_dssp             ETTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            467889999999999999999999865

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B*

Probab=97.16  E-value=0.0028  Score=62.79  Aligned_cols=22  Identities=36%  Similarity=0.451  Sum_probs=20.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la   87 (292)
                      +..++|+||+|+||||+++.++
T Consensus       789 g~i~~ItGpNgsGKSTlLr~iG  810 (1022)
T 2o8b_B          789 AYCVLVTGPNMGGKSTLMRQAG  810 (1022)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHH
Confidence            5789999999999999999984

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=97.16  E-value=0.00044  Score=57.31  Aligned_cols=39  Identities=15%  Similarity=0.226  Sum_probs=30.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCc--------EEEEeccchhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDAN--------FLKVVSSAIID  104 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~--------~~~~~~~~~~~  104 (292)
                      +..|.|.|++|+||||+++.++..++.+        +..++...+..
T Consensus        22 ~~iI~I~G~~GSGKST~a~~L~~~lg~~~~d~~~~~~~~i~~D~~~~   68 (252)
T 1uj2_A           22 PFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFYR   68 (252)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGGGGBC
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHhhhhcccccCCceEEEecCcccc
Confidence            4568899999999999999999998876        33566655543

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=97.16  E-value=0.00056  Score=64.16  Aligned_cols=25  Identities=28%  Similarity=0.464  Sum_probs=21.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..++++|+|||||||++..+...+
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHH
Confidence            4578999999999999988877654

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=97.16  E-value=0.00031  Score=55.28  Aligned_cols=36  Identities=28%  Similarity=0.309  Sum_probs=28.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEec
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID---ANFLKVVS   99 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~   99 (292)
                      ..+..++|.|++|+||||+++.++..++   .++..++.
T Consensus        11 ~~~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~~   49 (186)
T 2yvu_A           11 EKGIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLDG   49 (186)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEeeH
Confidence            4567799999999999999999998874   34555543

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=97.16  E-value=0.00027  Score=58.38  Aligned_cols=31  Identities=19%  Similarity=0.225  Sum_probs=26.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      +.++..+.|.||+|+||||+++.++..+|..
T Consensus        22 i~~g~iigI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           22 SMRPFLIGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             -CCSEEEEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHhchh
Confidence            4567778899999999999999999987643

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=97.14  E-value=0.00035  Score=59.63  Aligned_cols=28  Identities=25%  Similarity=0.458  Sum_probs=25.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++..+
T Consensus        97 ~~~g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A           97 FRKPAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             SSSCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4567789999999999999999999876

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=97.14  E-value=0.0016  Score=66.33  Aligned_cols=31  Identities=26%  Similarity=0.369  Sum_probs=27.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+.++..+.|.||+|+||||+++.+++....
T Consensus       412 ~i~~G~~~~ivG~sGsGKSTl~~ll~g~~~~  442 (1284)
T 3g5u_A          412 KVKSGQTVALVGNSGCGKSTTVQLMQRLYDP  442 (1284)
T ss_dssp             EECTTCEEEEECCSSSSHHHHHHHTTTSSCC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            3678889999999999999999999987643

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=97.14  E-value=0.00031  Score=55.41  Aligned_cols=32  Identities=25%  Similarity=0.454  Sum_probs=24.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      ..++|.||+|+||||+++.++...+. .+.++.
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~~~~g-~~~i~~   34 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAAQLDN-SAYIEG   34 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSS-EEEEEH
T ss_pred             eEEEEECCCCCcHHHHHHHHhcccCC-eEEEcc
Confidence            45789999999999999999986543 234443

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=97.14  E-value=0.00025  Score=61.17  Aligned_cols=35  Identities=26%  Similarity=0.376  Sum_probs=30.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      +..++|.||+|+|||+++..||+.++..++..+..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~   74 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKM   74 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSS
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHCCCcEEccccc
Confidence            45688999999999999999999998777766654

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=97.12  E-value=0.00042  Score=56.82  Aligned_cols=33  Identities=24%  Similarity=0.476  Sum_probs=28.3

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ..+..+.|.|++|+||||+++.++..++.+++.
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~~lg~~~~d   46 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAKDFGFTYLD   46 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHcCCceec
Confidence            446679999999999999999999999876654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=97.12  E-value=0.0011  Score=62.64  Aligned_cols=48  Identities=23%  Similarity=0.233  Sum_probs=31.8

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      -++.+++.+..++..               ....||+||||||||+++-.+...+   +..++.+.
T Consensus       190 LN~~Q~~AV~~al~~---------------~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a  240 (646)
T 4b3f_X          190 LDTSQKEAVLFALSQ---------------KELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCA  240 (646)
T ss_dssp             CCHHHHHHHHHHHHC---------------SSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCHHHHHHHHHHhcC---------------CCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEc
Confidence            467778888877643               2357999999999998665544333   44444443

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=97.11  E-value=0.0025  Score=61.09  Aligned_cols=24  Identities=33%  Similarity=0.371  Sum_probs=21.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +..++|.||+|+||||+++.++..
T Consensus       576 g~i~~I~GpNGsGKSTlLr~iagl  599 (765)
T 1ewq_A          576 HELVLITGPNMAGKSTFLRQTALI  599 (765)
T ss_dssp             SCEEEEESCSSSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHhh
Confidence            567899999999999999999864

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=97.11  E-value=0.00042  Score=55.78  Aligned_cols=39  Identities=18%  Similarity=0.256  Sum_probs=30.8

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEeccch
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSSAI  102 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~~~  102 (292)
                      ..+..++|.|++|+||||+++.++..++    .+++.++...+
T Consensus        23 ~~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~~d~~   65 (211)
T 1m7g_A           23 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNI   65 (211)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEECChHH
Confidence            4567899999999999999999998774    45666664433

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=97.06  E-value=0.0016  Score=66.26  Aligned_cols=29  Identities=21%  Similarity=0.366  Sum_probs=25.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.+++..
T Consensus      1055 ~i~~Ge~v~ivG~sGsGKSTl~~~l~g~~ 1083 (1284)
T 3g5u_A         1055 EVKKGQTLALVGSSGCGKSTVVQLLERFY 1083 (1284)
T ss_dssp             EECSSSEEEEECSSSTTHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            36778899999999999999999999765

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=97.05  E-value=0.017  Score=46.29  Aligned_cols=59  Identities=15%  Similarity=0.070  Sum_probs=32.5

Q ss_pred             CCccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ..+|+++.-.++..+.|.+.--. +. .+......  +..+..+++.+|+|+|||..+-..+-
T Consensus        13 ~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--~~~~~~~li~~~TGsGKT~~~~~~~~   73 (220)
T 1t6n_A           13 SSGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQ--AILGMDVLCQAKSGMGKTAVFVLATL   73 (220)
T ss_dssp             -CCSTTSCCCHHHHHHHHHTTCCCCCHHHHHHHHH--HHTTCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH--HhCCCCEEEECCCCCchhhhhhHHHH
Confidence            35688875556666666553211 10 01111111  11246799999999999986554443

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=97.04  E-value=0.0043  Score=50.01  Aligned_cols=54  Identities=17%  Similarity=0.046  Sum_probs=31.7

Q ss_pred             CCCccccccccHHHHHHHHHHhhccc--CChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPL--MNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      +..+|+++--.+...+.+...--...  .+......  +..++.+++.+|+|+|||..
T Consensus        12 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--~~~~~~~lv~~pTGsGKT~~   67 (224)
T 1qde_A           12 VVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMP--IIEGHDVLAQAQSGTGKTGT   67 (224)
T ss_dssp             CCCCGGGGTCCHHHHHHHHHHTCCSCCHHHHHHHHH--HHTTCCEEEECCTTSSHHHH
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCcHHHHHHHHH--HhcCCCEEEECCCCCcHHHH
Confidence            44678888655666666665421101  11111111  12356799999999999986

>3foz_A TRNA delta(2)-isopentenylpyrophosphate transferas; nucleoside modification, isopentenyl-tRNA transferase, transferase-RNA complex; 2.50A {Escherichia coli k-12} PDB: 2zxu_A* 2zm5_A

Probab=97.04  E-value=0.0004  Score=59.09  Aligned_cols=34  Identities=35%  Similarity=0.606  Sum_probs=28.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      +..++|.||+|+|||+++..+|..++..++.++.
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds   43 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKILPVELISVDS   43 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEECCT
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhCCCcEEeccc
Confidence            4568899999999999999999999877666543

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=97.03  E-value=0.00047  Score=60.20  Aligned_cols=29  Identities=28%  Similarity=0.518  Sum_probs=25.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++..+
T Consensus       153 ~~~~g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          153 GFRKPAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             CSSSSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ecCCCeEEEEEcCCCChHHHHHHHHHhhc
Confidence            34567789999999999999999999876

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=97.02  E-value=0.00016  Score=66.31  Aligned_cols=71  Identities=20%  Similarity=0.249  Sum_probs=44.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEeccc-hhcc--------c---cChHHHHHHHHHHHhhhCCCEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSSA-IIDK--------Y---IGESARLIREMFGYARDHQPCII  129 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~~-~~~~--------~---~~~~~~~~~~~~~~~~~~~~~il  129 (292)
                      ..+.+++|.||+|+||||++++++..+..  ..+.+.... +...        .   .+.....+...+..+....|.++
T Consensus       258 ~~g~~i~I~GptGSGKTTlL~aL~~~i~~~~giitied~~E~~~~~~~~v~~~~r~~~~~~~~~~~~~l~~~LR~~PD~i  337 (511)
T 2oap_1          258 EHKFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSIEDTREIKLYHENWIAEVTRTGMGEGEIDMYDLLRAALRQRPDYI  337 (511)
T ss_dssp             HTTCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCCCSSEEEEECBCCSSSCCBCHHHHHHTTGGGCCSEE
T ss_pred             hCCCEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEEcCcccccCCCCCeEEEEeecccccCCcCHHHHHHHhhccCCCeE
Confidence            34667999999999999999999988743  344443221 1100        0   00001123344555566789999


Q ss_pred             EEccc
Q 022768          130 FMDEI  134 (292)
Q Consensus       130 ~lDe~  134 (292)
                      ++.|+
T Consensus       338 ivgEi  342 (511)
T 2oap_1          338 IVGEV  342 (511)
T ss_dssp             EESCC
T ss_pred             EeCCc
Confidence            99997

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=97.02  E-value=0.0015  Score=55.54  Aligned_cols=36  Identities=22%  Similarity=0.357  Sum_probs=28.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEecc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVSS  100 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~~  100 (292)
                      ++..++|.|++|+||||++..+|..+    |..+..+...
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D  143 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTD  143 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecC
Confidence            46789999999999999999999765    4456555543

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.01  E-value=0.0018  Score=52.05  Aligned_cols=34  Identities=9%  Similarity=-0.095  Sum_probs=24.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      ++.-.+++|+.|+||||.+-.++...   +..++.+.
T Consensus        27 ~G~l~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k   63 (214)
T 2j9r_A           27 NGWIEVICGSMFSGKSEELIRRVRRTQFAKQHAIVFK   63 (214)
T ss_dssp             SCEEEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE
Confidence            34556788999999999887777655   55555554

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=97.01  E-value=0.00021  Score=58.39  Aligned_cols=29  Identities=24%  Similarity=0.303  Sum_probs=18.8

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHH-HhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIA-SNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la-~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++ ....
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~~~L~~~~~~   53 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVANKLLEKQKN   53 (231)
T ss_dssp             EECCCEEEEECSCC----CHHHHHHC----
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhcCCC
Confidence            4667789999999999999999999 7653

>3zvl_A Bifunctional polynucleotide phosphatase/kinase; hydrolase-transferase complex, base excision repair, BER, non-homologous END-joining, NHEJ; 1.65A {Mus musculus} PDB: 3zvm_A* 3zvn_A* 1yj5_A 3u7e_B* 3u7f_B* 3u7h_B* 3u7g_A*

Probab=97.01  E-value=0.00072  Score=60.41  Aligned_cols=31  Identities=23%  Similarity=0.334  Sum_probs=26.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      .+..++|+|+||+||||+++.++..++..++
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~~~~~~~i  287 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLVSAGYVHV  287 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTGGGTCEEC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhcCcEEE
Confidence            3566889999999999999999999875544

>2f6r_A COA synthase, bifunctional coenzyme A synthase; 18044849, bifunctional coenzyme A synthase (COA synthase), S genomics; HET: ACO UNL; 1.70A {Mus musculus}

Probab=97.01  E-value=0.00036  Score=58.93  Aligned_cols=31  Identities=26%  Similarity=0.345  Sum_probs=25.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..|.|.|++|+||||+++.++ .+|.+++..
T Consensus        75 ~~iI~I~G~~GSGKSTva~~La-~lg~~~id~  105 (281)
T 2f6r_A           75 LYVLGLTGISGSGKSSVAQRLK-NLGAYIIDS  105 (281)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH-HHTCEEEEH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH-HCCCcEEeh
Confidence            4468899999999999999999 577665443

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=96.98  E-value=0.0061  Score=49.70  Aligned_cols=22  Identities=27%  Similarity=0.377  Sum_probs=18.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la   87 (292)
                      +..+++.||+|+|||+++..+.
T Consensus        76 g~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           76 NSVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCcHHhHHHHH
Confidence            6789999999999998766554

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.97  E-value=0.00062  Score=54.95  Aligned_cols=31  Identities=26%  Similarity=0.539  Sum_probs=26.9

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ..+.|.|++|+||||+++.++..++.+++..
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~   34 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDT   34 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecC
Confidence            4689999999999999999999998766543

>3exa_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2, protein structure initiative; 2.30A {Bacillus halodurans} PDB: 2qgn_A

Probab=96.97  E-value=0.00052  Score=58.51  Aligned_cols=33  Identities=27%  Similarity=0.363  Sum_probs=27.3

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      ..++|.||+|+|||+++..+|..++..++..+.
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds   36 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNGEVISGDS   36 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTEEEEECCG
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCccceeecCc
Confidence            457899999999999999999998766655443

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=96.96  E-value=0.0015  Score=63.92  Aligned_cols=26  Identities=42%  Similarity=0.654  Sum_probs=23.3

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +.++..+.|.||+|+|||||++.++.
T Consensus       458 I~~Ge~v~LiGpNGsGKSTLLk~Lag  483 (986)
T 2iw3_A          458 LKRARRYGICGPNGCGKSTLMRAIAN  483 (986)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            45677899999999999999999994

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=96.96  E-value=0.00043  Score=59.78  Aligned_cols=33  Identities=24%  Similarity=0.388  Sum_probs=27.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      ..++|.||+|+|||++++.++..++..++..+.
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~~~iis~Ds   40 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFNGEIISGDS   40 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTEEEEECCS
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcCCceecccc
Confidence            468899999999999999999999866555443

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=96.96  E-value=0.00069  Score=59.32  Aligned_cols=73  Identities=15%  Similarity=0.318  Sum_probs=45.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEecc-chh-----cc--ccC-h-------HHHHHHHHHHHhhhC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSS-AII-----DK--YIG-E-------SARLIREMFGYARDH  124 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~-~~~-----~~--~~~-~-------~~~~~~~~~~~~~~~  124 (292)
                      +.++..++|.||+|+||||++++++.....  ..+.+... ++.     ..  +.. +       ....+...+..+...
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~l~~~~~~~~g~I~ie~~~e~~~~~~~~~v~~v~~q~~~~~~~~~~t~~~~i~~~l~~  251 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKALMQEIPFDQRLITIEDVPELFLPDHPNHVHLFYPSEAKEEENAPVTAATLLRSCLRM  251 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHHHHTTSCTTSCEEEEESSSCCCCTTCSSEEEEECC----------CCHHHHHHHHTTS
T ss_pred             HhcCCEEEEECCCCCCHHHHHHHHHhcCCCCceEEEECCccccCccccCCEEEEeecCccccccccccCHHHHHHHHHhc
Confidence            456788999999999999999999987743  33444321 110     00  111 0       111234555556667


Q ss_pred             CCEEEEEcccc
Q 022768          125 QPCIIFMDEID  135 (292)
Q Consensus       125 ~~~il~lDe~d  135 (292)
                      .|..++++|+.
T Consensus       252 ~pd~~l~~e~r  262 (361)
T 2gza_A          252 KPTRILLAELR  262 (361)
T ss_dssp             CCSEEEESCCC
T ss_pred             CCCEEEEcCch
Confidence            78899999974

>2yhs_A FTSY, cell division protein FTSY; cell cycle, protein targeting, simibi class GTPase, GTP-BIND membrane, nucleotide-binding; 1.60A {Escherichia coli} PDB: 2qy9_A 2xxa_B* 1fts_A

Probab=96.93  E-value=0.00048  Score=62.37  Aligned_cols=29  Identities=31%  Similarity=0.377  Sum_probs=25.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+..+..++|.|++|+||||+++.++..+
T Consensus       289 ~i~~GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          289 EGKAPFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             CSCTTEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eccCCeEEEEECCCcccHHHHHHHHHHHh
Confidence            34567789999999999999999999876

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=96.92  E-value=0.0073  Score=48.84  Aligned_cols=57  Identities=16%  Similarity=0.155  Sum_probs=30.6

Q ss_pred             CCCCCccccccccH-HHHHHHHHHhh-ccc-CChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           25 DPGNVSYSAVGGLS-DQIRELRESIE-LPL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        25 ~~~~~~~~~l~g~~-~~~~~l~~~l~-~~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      +.|..+|.+..+.. +..+.+.+.-- .+. .+......  +..+..+++.+|+|+|||..+
T Consensus        15 p~p~~~f~~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--~~~~~~~l~~apTGsGKT~~~   74 (228)
T 3iuy_A           15 PKPTCRFKDAFQQYPDLLKSIIRVGILKPTPIQSQAWPI--ILQGIDLIVVAQTGTGKTLSY   74 (228)
T ss_dssp             CCCCCSHHHHHTTCHHHHHHHHHHTCCSCCHHHHHHHHH--HHTTCCEEEECCTTSCHHHHH
T ss_pred             CCChhhHhhhhccCHHHHHHHHHCCCCCCCHHHHHHHHH--HhCCCCEEEECCCCChHHHHH
Confidence            44556788754544 34455544321 100 01111111  123567999999999999754

>2qmh_A HPR kinase/phosphorylase; V267F mutation, ATP-binding, carbohydrate metabolism, magnesium, metal-binding, multifunctional enzyme; 2.60A {Lactobacillus casei} PDB: 1jb1_A 1kkl_A 1kkm_A*

Probab=96.92  E-value=0.00047  Score=54.73  Aligned_cols=30  Identities=27%  Similarity=0.396  Sum_probs=25.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..++|.||+|+|||+++..+++..+ .++.
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~-~iIs   63 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH-RLIA   63 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC-EEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC-eEEe
Confidence            56799999999999999999999865 4443

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=96.89  E-value=0.00049  Score=57.49  Aligned_cols=30  Identities=20%  Similarity=0.303  Sum_probs=26.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+|||||++.++....
T Consensus        28 ~i~~Ge~~~liG~nGsGKSTLlk~l~Gl~~   57 (262)
T 1b0u_A           28 QARAGDVISIIGSSGSGKSTFLRCINFLEK   57 (262)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            357788899999999999999999998764

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=96.88  E-value=0.0027  Score=52.40  Aligned_cols=54  Identities=11%  Similarity=0.008  Sum_probs=29.6

Q ss_pred             CCccccccccHHHHHHHHHHhhccc--CChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPL--MNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+|+++.-.+...+.+...-....  .+......  +..++.+++.+|+|+|||...
T Consensus        42 ~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--i~~~~~~lv~a~TGsGKT~~~   97 (249)
T 3ber_A           42 TKTFKDLGVTDVLCEACDQLGWTKPTKIQIEAIPL--ALQGRDIIGLAETGSGKTGAF   97 (249)
T ss_dssp             HCCTGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHH--HHTTCCEEEECCTTSCHHHHH
T ss_pred             cCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHH--HhCCCCEEEEcCCCCCchhHh
Confidence            3568887544555555544321000  01111111  123567999999999999864

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=96.88  E-value=0.0006  Score=57.91  Aligned_cols=29  Identities=31%  Similarity=0.401  Sum_probs=23.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc-CCcEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI-DANFL   95 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l-~~~~~   95 (292)
                      ..++|.|+||+||||+++.++..+ +..++
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i   32 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEe
Confidence            458899999999999999999864 44443

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=96.87  E-value=0.00035  Score=57.68  Aligned_cols=29  Identities=21%  Similarity=0.368  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        24 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           24 EAQPNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             EECTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            35778889999999999999999999765

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=96.86  E-value=0.00042  Score=56.02  Aligned_cols=29  Identities=34%  Similarity=0.525  Sum_probs=25.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++....
T Consensus        32 i~~Ge~~~iiG~NGsGKSTLlk~l~Gl~~   60 (214)
T 1sgw_A           32 IEKGNVVNFHGPNGIGKTTLLKTISTYLK   60 (214)
T ss_dssp             EETTCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            56688899999999999999999998663

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=96.84  E-value=0.00054  Score=57.07  Aligned_cols=28  Identities=29%  Similarity=0.533  Sum_probs=25.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        30 i~~Ge~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           30 VNKGDVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            5678889999999999999999999766

>3e70_C DPA, signal recognition particle receptor; FTSY, SRP-GTPase, protein-targeting, transport protein; HET: GDP; 1.97A {Pyrococcus furiosus} PDB: 3dmd_B 3dm9_B*

Probab=96.83  E-value=0.0034  Score=54.12  Aligned_cols=27  Identities=26%  Similarity=0.406  Sum_probs=24.2

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++..+.|.||+|+||||+++.++..+
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            457789999999999999999999866

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=96.83  E-value=0.00084  Score=52.56  Aligned_cols=33  Identities=27%  Similarity=0.437  Sum_probs=28.6

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ++|+|++|+|||++|..++.. +.+++++.....
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~~~   34 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATSQI   34 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECCCC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecCCC
Confidence            789999999999999999988 878888776543

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=96.83  E-value=0.00078  Score=57.74  Aligned_cols=29  Identities=21%  Similarity=0.210  Sum_probs=25.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++..+.
T Consensus        87 ~~~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           87 RPVPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             SCCCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            45677889999999999999999999774

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=96.83  E-value=0.00049  Score=57.64  Aligned_cols=28  Identities=29%  Similarity=0.590  Sum_probs=25.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .+.++..+.|.||+|+|||||++.++..
T Consensus        42 ~i~~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           42 DVHPGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3577888999999999999999999986

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=96.83  E-value=0.015  Score=49.32  Aligned_cols=35  Identities=29%  Similarity=0.229  Sum_probs=27.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      ++..+.+.|++|+||||++..+|..+   +..+..++.
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~  134 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecC
Confidence            46678889999999999999999765   445554443

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=96.82  E-value=0.00042  Score=57.82  Aligned_cols=29  Identities=24%  Similarity=0.285  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        42 ~i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           42 FIPSGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            35778889999999999999999999765

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=96.82  E-value=0.0005  Score=56.19  Aligned_cols=29  Identities=28%  Similarity=0.404  Sum_probs=25.8

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+||||+++.++..+.
T Consensus        31 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           31 IERGQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            56788899999999999999999998764

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=96.82  E-value=0.00057  Score=56.32  Aligned_cols=28  Identities=36%  Similarity=0.396  Sum_probs=25.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++..+.|.||+|+||||+++.++...
T Consensus        29 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           29 VPRGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            5678889999999999999999999765

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=96.81  E-value=0.0042  Score=53.79  Aligned_cols=28  Identities=29%  Similarity=0.344  Sum_probs=24.8

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..+..+.|.|+||+||||+++.++..+
T Consensus        52 ~~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           52 TGRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             CCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            5667789999999999999999999765

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=96.80  E-value=0.00044  Score=57.34  Aligned_cols=27  Identities=30%  Similarity=0.538  Sum_probs=24.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +.++..+.|.||+|+|||||++.++..
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           26 VPKGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            567888999999999999999999985

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=96.79  E-value=0.00073  Score=56.54  Aligned_cols=29  Identities=31%  Similarity=0.441  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||++.++...
T Consensus        29 ~i~~Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           29 VINEGECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35678889999999999999999999765

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=96.78  E-value=0.001  Score=54.28  Aligned_cols=28  Identities=21%  Similarity=0.336  Sum_probs=25.0

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ..+..++|.|++|+||||+++.++..++
T Consensus        24 ~~g~~i~i~G~~GsGKsT~~~~l~~~l~   51 (229)
T 4eaq_A           24 AMSAFITFEGPEGSGKTTVINEVYHRLV   51 (229)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHHT
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            3567788999999999999999999986

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=96.76  E-value=0.0008  Score=59.35  Aligned_cols=33  Identities=21%  Similarity=0.415  Sum_probs=27.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      ...++|.||+|+|||+++..++..++..++..+
T Consensus         2 ~~~i~i~GptgsGKttla~~La~~~~~~iis~D   34 (409)
T 3eph_A            2 KKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSD   34 (409)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHHHHTEEEEECC
T ss_pred             CcEEEEECcchhhHHHHHHHHHHHCCCeEeecC
Confidence            346789999999999999999999876665543

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=96.76  E-value=0.0043  Score=52.71  Aligned_cols=35  Identities=31%  Similarity=0.276  Sum_probs=27.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      +..+++.|++|+||||++..+|..+   +..+..++..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D  135 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGAD  135 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecC
Confidence            5678889999999999999999766   5566655544

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=96.75  E-value=0.0079  Score=47.66  Aligned_cols=18  Identities=39%  Similarity=0.405  Sum_probs=15.5

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      ++.+++.+|+|+|||..+
T Consensus        38 ~~~~li~~~TGsGKT~~~   55 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAF   55 (207)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEECCCCChHHHHH
Confidence            467999999999999863

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=96.75  E-value=0.0052  Score=56.06  Aligned_cols=35  Identities=17%  Similarity=0.213  Sum_probs=26.9

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      .+..|+|.|++|+||||++..++..+   +..+..+++
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            35678899999999999999999765   556665555

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=96.73  E-value=0.00069  Score=57.12  Aligned_cols=29  Identities=31%  Similarity=0.409  Sum_probs=25.7

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.++..+.|.||+|+|||||++.++..+.
T Consensus        44 i~~Ge~~~liG~NGsGKSTLlk~l~Gl~~   72 (279)
T 2ihy_A           44 IAKGDKWILYGLNGAGKTTLLNILNAYEP   72 (279)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            56788899999999999999999998663

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=96.73  E-value=0.0043  Score=58.84  Aligned_cols=21  Identities=48%  Similarity=0.563  Sum_probs=19.0

Q ss_pred             CCCCceEEEEcCCCChHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~   83 (292)
                      +.++..+.|.||+|+|||||+
T Consensus        41 i~~Ge~~~liGpNGaGKSTLl   61 (670)
T 3ux8_A           41 IPRGKLVVLTGLSGSGKSSLA   61 (670)
T ss_dssp             EETTSEEEEECSTTSSHHHHH
T ss_pred             ECCCCEEEEECCCCCCHHHHh
Confidence            567888999999999999996

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=96.71  E-value=0.0013  Score=55.74  Aligned_cols=28  Identities=29%  Similarity=0.499  Sum_probs=24.3

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ..+..+.|.|++|+||||+++.++..++
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4456788999999999999999998875

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=96.71  E-value=0.0033  Score=59.67  Aligned_cols=26  Identities=27%  Similarity=0.322  Sum_probs=21.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la   87 (292)
                      .+.++..+.|.||+|+||||+++.+.
T Consensus       344 ~I~~Ge~vaIiGpnGsGKSTLl~~i~  369 (670)
T 3ux8_A          344 KIPLGTFVAVTGVSGSGKSTLVNEVL  369 (670)
T ss_dssp             EEETTSEEEEECSTTSSHHHHHTTTH
T ss_pred             EecCCCEEEEEeeCCCCHHHHHHHHH
Confidence            35678889999999999999997543

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=96.70  E-value=0.0056  Score=48.78  Aligned_cols=23  Identities=39%  Similarity=0.609  Sum_probs=19.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.+|+|+|||.++-.++..
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~   71 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKD   71 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHH
Confidence            56999999999999988776654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=96.70  E-value=0.0072  Score=48.55  Aligned_cols=18  Identities=28%  Similarity=0.255  Sum_probs=15.5

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      +..+++.+|+|+|||..+
T Consensus        41 ~~~~lv~a~TGsGKT~~~   58 (219)
T 1q0u_A           41 GESMVGQSQTGTGKTHAY   58 (219)
T ss_dssp             TCCEEEECCSSHHHHHHH
T ss_pred             CCCEEEECCCCChHHHHH
Confidence            467999999999999864

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=96.69  E-value=0.0014  Score=52.32  Aligned_cols=30  Identities=17%  Similarity=0.236  Sum_probs=27.3

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ..|.|.|++|+|||++++.+|..+|.+++.
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~lg~~~~D   36 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHYNIPLYS   36 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHTTCCEEC
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHhCcCEEC
Confidence            368899999999999999999999999874

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=96.66  E-value=0.0013  Score=53.50  Aligned_cols=30  Identities=27%  Similarity=0.443  Sum_probs=26.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .+-|.|+||+||||+++.++..++.+++..
T Consensus        10 ~~~~~G~pGsGKsT~a~~L~~~~g~~~is~   39 (230)
T 3gmt_A           10 RLILLGAPGAGKGTQANFIKEKFGIPQIST   39 (230)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCCEECH
T ss_pred             ceeeECCCCCCHHHHHHHHHHHhCCCeeec
Confidence            478999999999999999999998877654

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=96.65  E-value=0.0017  Score=60.62  Aligned_cols=38  Identities=24%  Similarity=0.269  Sum_probs=32.2

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccch
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAI  102 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~  102 (292)
                      .+..|+|.|.+|+||||+++.+++.+   +.+++.++...+
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lDgD~i   91 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGDNI   91 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEESHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEechHHh
Confidence            45679999999999999999999998   888888764433

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=96.62  E-value=0.007  Score=47.99  Aligned_cols=19  Identities=26%  Similarity=0.260  Sum_probs=15.8

Q ss_pred             CceEEEEcCCCChHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLAR   84 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~   84 (292)
                      ++.+++.+|+|+|||..+-
T Consensus        40 ~~~~lv~apTGsGKT~~~~   58 (206)
T 1vec_A           40 GRDILARAKNGTGKSGAYL   58 (206)
T ss_dssp             TCCEEEECCSSSTTHHHHH
T ss_pred             CCCEEEECCCCCchHHHHH
Confidence            4679999999999997543

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=96.60  E-value=0.014  Score=50.75  Aligned_cols=34  Identities=21%  Similarity=0.328  Sum_probs=26.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      ....+.|.|+||+||||++..++..+   +..+..++
T Consensus        78 ~~~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~  114 (355)
T 3p32_A           78 NAHRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLA  114 (355)
T ss_dssp             CSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEe
Confidence            35578899999999999999998765   44444433

>2axn_A 6-phosphofructo-2-kinase/fructose-2,6- biphosphatase 3 (6PF-2-K/FRU- 2,6-P2ASE brain/placenta-type...; bifunctional enzyme, EDTA complex; HET: F6P EDT ADP; 2.10A {Homo sapiens} PDB: 2dwo_A* 2dwp_A* 2i1v_B* 3qpu_A* 3qpv_A* 3qpw_A*

Probab=96.60  E-value=0.0051  Score=56.47  Aligned_cols=36  Identities=17%  Similarity=0.362  Sum_probs=27.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEeccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID---ANFLKVVSSA  101 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~~~  101 (292)
                      +..|+++|.||+||||+++.+++.++   .....++...
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~~L~~~~~d~~v~s~D~   73 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGE   73 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCCeEEecccH
Confidence            45688999999999999999999884   3444455443

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=96.60  E-value=0.00057  Score=54.81  Aligned_cols=25  Identities=24%  Similarity=0.380  Sum_probs=22.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .|.|.|++|+||||+++.++..++.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            4789999999999999999998753

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=96.58  E-value=0.019  Score=46.79  Aligned_cols=55  Identities=15%  Similarity=0.060  Sum_probs=31.3

Q ss_pred             CCCccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      +..+|+++--.++..+.+...--. +. .+......  +..+..+++.+|+|+|||..+
T Consensus        28 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~ai~~--i~~~~~~li~apTGsGKT~~~   84 (237)
T 3bor_A           28 IVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIP--CIKGYDVIAQAQSGTGKTATF   84 (237)
T ss_dssp             CCCSGGGSCCCHHHHHHHHHHTCCSCCHHHHHHHHH--HHTTCCEEECCCSSHHHHHHH
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH--HhCCCCEEEECCCCCcHHHHH
Confidence            446799985555555666543211 10 01111111  122567999999999999764

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=96.58  E-value=0.00098  Score=53.62  Aligned_cols=25  Identities=44%  Similarity=0.505  Sum_probs=22.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ++..+.|.||+|+|||||++.++..
T Consensus        21 ~Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           21 TNTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             HCSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3677999999999999999999975

>2v3c_C SRP54, signal recognition 54 kDa protein; nucleotide-binding, signal recognition particle, GTP-binding, RNA-binding; 2.50A {Methanocaldococcus jannaschii} PDB: 3ndb_B

Probab=96.56  E-value=0.007  Score=54.18  Aligned_cols=35  Identities=29%  Similarity=0.338  Sum_probs=27.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      +..++|.|++|+||||++..+|..+   |..+..+++.
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D  136 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAAD  136 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecc
Confidence            4579999999999999999999866   4556555544

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=96.56  E-value=0.0015  Score=55.76  Aligned_cols=26  Identities=27%  Similarity=0.318  Sum_probs=23.4

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ++..+.|.||+|+||||+++.++..+
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            46678999999999999999999876

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=96.54  E-value=0.0008  Score=57.03  Aligned_cols=29  Identities=28%  Similarity=0.360  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        60 ~i~~Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           60 KIERGQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             EECTTCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            35678889999999999999999999865

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=96.54  E-value=0.0015  Score=50.63  Aligned_cols=24  Identities=33%  Similarity=0.497  Sum_probs=22.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +.+++|.|++|+||||++..+...
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc
Confidence            678999999999999999999885

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=96.53  E-value=0.0016  Score=55.61  Aligned_cols=28  Identities=21%  Similarity=0.338  Sum_probs=24.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ..+..+.|.||+|+||||+++.++..++
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4566788999999999999999999775

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=96.53  E-value=0.0056  Score=50.10  Aligned_cols=57  Identities=11%  Similarity=0.057  Sum_probs=30.5

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      +.|..+|.++--.++..+.+.+.--. +. .+......  +..+..+++.+|+|+|||...
T Consensus        25 p~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--~~~g~~~l~~apTGsGKT~~~   83 (242)
T 3fe2_A           25 PKPVLNFYEANFPANVMDVIARQNFTEPTAIQAQGWPV--ALSGLDMVGVAQTGSGKTLSY   83 (242)
T ss_dssp             CCCCSSTTTTTCCHHHHHHHHTTTCCSCCHHHHHHHHH--HHHTCCEEEEECTTSCHHHHH
T ss_pred             CCccCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH--HhCCCCEEEECCCcCHHHHHH
Confidence            34557788764445445555442110 00 00111111  112567999999999999864

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=96.52  E-value=0.0013  Score=55.84  Aligned_cols=37  Identities=11%  Similarity=0.214  Sum_probs=25.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEeccch
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID---ANFLKVVSSAI  102 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~~~~  102 (292)
                      ...|.|.|++|+||||+++.++..++   ..+..++...+
T Consensus         5 ~~iIgItG~sGSGKSTva~~L~~~lg~~~~~~~vI~~D~~   44 (290)
T 1a7j_A            5 HPIISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   44 (290)
T ss_dssp             SCEEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHhhcCCCeeEeecchh
Confidence            34588999999999999999999775   33444554444

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=96.52  E-value=0.024  Score=45.93  Aligned_cols=54  Identities=20%  Similarity=0.118  Sum_probs=30.0

Q ss_pred             CCccccccccHHHHHHHHHHhhcccC--ChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLM--NPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+|+++.-.+...+.+.+.-.....  +......  +..++.+++.+|+|+|||..+
T Consensus        24 ~~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~--~~~~~~~li~a~TGsGKT~~~   79 (236)
T 2pl3_A           24 ITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGL--ALQGKDVLGAAKTGSGKTLAF   79 (236)
T ss_dssp             CSBGGGSCCCHHHHHHHHHTTCCBCCHHHHHHHHH--HHTTCCEEEECCTTSCHHHHH
T ss_pred             cCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH--HhCCCCEEEEeCCCCcHHHHH
Confidence            35688875555556666543211000  0111111  123567999999999999853

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=96.50  E-value=0.0019  Score=50.41  Aligned_cols=25  Identities=24%  Similarity=0.252  Sum_probs=21.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...+.|.|++|+||||+++.++..+
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            3468899999999999999999865

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=96.48  E-value=0.00093  Score=55.79  Aligned_cols=28  Identities=39%  Similarity=0.693  Sum_probs=25.0

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+. +..+.|.||+|+||||+++.++...
T Consensus        27 ~i~-Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           27 EVN-GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             EEC-SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEC-CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            356 7789999999999999999999876

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=96.48  E-value=0.0018  Score=50.53  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=21.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ..+|+||+|+||||++++++..++
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~   51 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLG   51 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHc
Confidence            678999999999999999998775

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=96.48  E-value=0.0046  Score=53.05  Aligned_cols=26  Identities=19%  Similarity=0.314  Sum_probs=22.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +..+.|.||+|+||||+++.++..++
T Consensus        92 p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           92 PYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            44678999999999999999998875

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=96.47  E-value=0.018  Score=46.68  Aligned_cols=55  Identities=15%  Similarity=0.079  Sum_probs=30.2

Q ss_pred             CCCccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      +..+|+++.-.++..+.+.+.--. +. .+......  +..+..+++.+|+|+|||...
T Consensus        22 ~~~~f~~l~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--~~~~~~~l~~a~TGsGKT~~~   78 (230)
T 2oxc_A           22 EPADFESLLLSRPVLEGLRAAGFERPSPVQLKAIPL--GRCGLDLIVQAKSGTGKTCVF   78 (230)
T ss_dssp             --CCGGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHH--HHTTCCEEEECCTTSSHHHHH
T ss_pred             CCCCHhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH--HhCCCCEEEECCCCCcHHHHH
Confidence            346788875555555666543211 10 01111111  123567999999999999763

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=96.47  E-value=0.0029  Score=54.35  Aligned_cols=38  Identities=24%  Similarity=0.203  Sum_probs=29.4

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      ..++..++|.|++|+||||++..+|..+   +..+..+++.
T Consensus       102 ~~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D  142 (320)
T 1zu4_A          102 ENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAAD  142 (320)
T ss_dssp             TTSCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            3557789999999999999999999766   4555555543

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=96.46  E-value=0.0021  Score=51.61  Aligned_cols=32  Identities=19%  Similarity=0.131  Sum_probs=21.3

Q ss_pred             CceEEEEcCCCChHHH-HHHHHHHhc--CCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTL-LARAIASNI--DANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~-l~~~la~~l--~~~~~~~   97 (292)
                      +.-.+++|+-|+|||| +++.+.+..  +..++.+
T Consensus        28 G~I~vitG~M~sGKTT~Llr~~~r~~~~g~kvli~   62 (219)
T 3e2i_A           28 GWIECITGSMFSGKSEELIRRLRRGIYAKQKVVVF   62 (219)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCceEEE
Confidence            5567889999999999 556654433  4444433

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=96.42  E-value=0.0021  Score=59.36  Aligned_cols=39  Identities=26%  Similarity=0.345  Sum_probs=30.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEeccch
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSSAI  102 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~~~  102 (292)
                      .++..+.|+|++|+||||+++.++..++    ..+..++...+
T Consensus       367 ~~G~iI~LiG~sGSGKSTLar~La~~L~~~~G~~i~~lDgD~~  409 (552)
T 3cr8_A          367 RQGFTVFFTGLSGAGKSTLARALAARLMEMGGRCVTLLDGDIV  409 (552)
T ss_dssp             GSCEEEEEEESSCHHHHHHHHHHHHHHHTTCSSCEEEESSHHH
T ss_pred             ccceEEEEECCCCChHHHHHHHHHHhhcccCCceEEEECCcHH
Confidence            4577899999999999999999999885    23444555444

>1lw7_A Transcriptional regulator NADR; NMN, NMN adenylyl transferase, ribosylnicotinamide KINA transferase; HET: NAD; 2.90A {Haemophilus influenzae} SCOP: c.26.1.3 c.37.1.1

Probab=96.41  E-value=0.002  Score=56.49  Aligned_cols=31  Identities=26%  Similarity=0.525  Sum_probs=26.5

Q ss_pred             CCC--CceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           63 IKP--PKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        63 ~~~--~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      +.+  +..+.|.||+|+|||||++.++..+...
T Consensus       165 v~~~lg~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          165 ARPFFAKTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             TGGGTCEEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             HHHhhhCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            445  6789999999999999999999987654

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=96.41  E-value=0.011  Score=48.22  Aligned_cols=25  Identities=24%  Similarity=0.400  Sum_probs=21.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...|+|.|++|+|||+++..++...
T Consensus        29 ~~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           29 QLRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHcCCC
Confidence            4569999999999999999998643

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=96.40  E-value=0.0017  Score=54.42  Aligned_cols=23  Identities=22%  Similarity=0.489  Sum_probs=21.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ++.|.||+|+||||+++.++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            68899999999999999999865

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=96.37  E-value=0.026  Score=45.74  Aligned_cols=33  Identities=15%  Similarity=0.118  Sum_probs=21.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      +.-.+++|+-|+||||.+-..+...   +..++.+.
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~k   54 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   54 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEe
Confidence            5557788999999998665555433   44444443

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=96.37  E-value=0.011  Score=52.86  Aligned_cols=37  Identities=30%  Similarity=0.442  Sum_probs=29.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEeccc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVSSA  101 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~~~  101 (292)
                      ++..+++.|++|+||||++-.+|..+    |..+..+++..
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            45678899999999999998888655    66677666654

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=96.37  E-value=0.0015  Score=58.98  Aligned_cols=29  Identities=31%  Similarity=0.327  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+|||||+|.++...
T Consensus       134 ~i~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          134 SNFEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             HSSSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             EeCCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            35678889999999999999999999865

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=96.31  E-value=0.0034  Score=57.33  Aligned_cols=28  Identities=14%  Similarity=0.064  Sum_probs=25.2

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+..++|.|.+|+||||+++++++.++.
T Consensus       394 ~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          394 QGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            3567999999999999999999999974

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=96.30  E-value=0.0029  Score=51.37  Aligned_cols=31  Identities=13%  Similarity=0.299  Sum_probs=27.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ...|.|.|++|+|||++++.+|..++.+++.
T Consensus        14 ~~iI~i~g~~gsGk~~i~~~la~~lg~~~~d   44 (223)
T 3hdt_A           14 NLIITIEREYGSGGRIVGKKLAEELGIHFYD   44 (223)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHTCEEEC
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHcCCcEEc
Confidence            3467889999999999999999999988764

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=96.29  E-value=0.0023  Score=51.35  Aligned_cols=31  Identities=29%  Similarity=0.327  Sum_probs=26.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      ..|.|+|..||||||+++.++. +|.+++..+
T Consensus        10 ~~iglTGgigsGKStv~~~l~~-~g~~vidaD   40 (210)
T 4i1u_A           10 YAIGLTGGIGSGKTTVADLFAA-RGASLVDTD   40 (210)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH-TTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-CCCcEEECc
Confidence            3588999999999999999988 888877655

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=96.26  E-value=0.0028  Score=49.10  Aligned_cols=24  Identities=21%  Similarity=0.135  Sum_probs=21.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.|.|++|+||||++..++..+
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l   28 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAA   28 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhh
Confidence            358899999999999999999876

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=96.26  E-value=0.031  Score=48.29  Aligned_cols=28  Identities=21%  Similarity=0.313  Sum_probs=24.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...+..+.|.|++|+||||++..++..+
T Consensus        53 ~~~~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           53 CGNTLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             cCCCEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4556778999999999999999998764

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=96.26  E-value=0.035  Score=47.81  Aligned_cols=22  Identities=18%  Similarity=0.120  Sum_probs=17.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHH
Q 022768           67 KGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ..+++.+|+|+|||..+-..+.
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~   66 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLI   66 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHH
Confidence            5899999999999987654443

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=96.23  E-value=0.0017  Score=50.45  Aligned_cols=25  Identities=20%  Similarity=0.280  Sum_probs=22.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+.|.|++|+||||+++.++..+..
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~~~   28 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPILRE   28 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhhh
Confidence            5889999999999999999998743

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=96.23  E-value=0.0036  Score=54.39  Aligned_cols=33  Identities=18%  Similarity=0.321  Sum_probs=28.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      +..+..+.|.||+|+||||+++.+++.......
T Consensus        68 i~~Gq~~gIiG~nGaGKTTLl~~I~g~~~~~~g  100 (347)
T 2obl_A           68 CGIGQRIGIFAGSGVGKSTLLGMICNGASADII  100 (347)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHSCCSEE
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHhcCCCCCEE
Confidence            466888999999999999999999998866543

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=96.22  E-value=0.0058  Score=49.31  Aligned_cols=31  Identities=26%  Similarity=0.264  Sum_probs=26.6

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      .+..|.|.|++|+||||.++.++..++.++.
T Consensus         4 ~g~~i~~eG~~g~GKst~~~~l~~~l~~~~~   34 (216)
T 3tmk_A            4 RGKLILIEGLDRTGKTTQCNILYKKLQPNCK   34 (216)
T ss_dssp             CCCEEEEEECSSSSHHHHHHHHHHHHCSSEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcccce
Confidence            4667889999999999999999999986443

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=96.19  E-value=0.0048  Score=55.34  Aligned_cols=32  Identities=22%  Similarity=0.350  Sum_probs=28.1

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      +.++..+.|.||+|+|||||++.+++......
T Consensus       154 i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~~~~  185 (438)
T 2dpy_A          154 VGRGQRMGLFAGSGVGKSVLLGMMARYTRADV  185 (438)
T ss_dssp             CBTTCEEEEEECTTSSHHHHHHHHHHHSCCSE
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHhcccCCCe
Confidence            56788899999999999999999999886544

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=96.19  E-value=0.029  Score=47.73  Aligned_cols=33  Identities=24%  Similarity=0.233  Sum_probs=24.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +..+++.+|+|+|||..+-..+...+...+.+.
T Consensus        31 ~~~~lv~~~TGsGKT~~~~~~~~~~~~~~liv~   63 (337)
T 2z0m_A           31 GKNVVVRAKTGSGKTAAYAIPILELGMKSLVVT   63 (337)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEC
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHhhcCCEEEEe
Confidence            457999999999999876666555555555444

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=96.19  E-value=0.0024  Score=56.84  Aligned_cols=27  Identities=22%  Similarity=0.342  Sum_probs=23.4

Q ss_pred             CCCCce--EEEEcCCCChHHHHHHHHHHh
Q 022768           63 IKPPKG--VLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        63 ~~~~~~--vll~G~~G~GKT~l~~~la~~   89 (292)
                      +.++..  +.|.||+|+|||||++.++..
T Consensus        37 i~~Gei~~vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           37 VSQGFCFNILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             CC-CCEEEEEEECSTTSSSHHHHHHHHTS
T ss_pred             ecCCCeeEEEEECCCCCCHHHHHHHHhCc
Confidence            566777  999999999999999999875

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=96.18  E-value=0.0041  Score=57.78  Aligned_cols=36  Identities=19%  Similarity=0.312  Sum_probs=29.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEeccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSSA  101 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~~  101 (292)
                      +..|+|.|.+|+||||+++.+++.++    .+++.++...
T Consensus       396 ~~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD~D~  435 (573)
T 1m8p_A          396 GFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDT  435 (573)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEEHHH
T ss_pred             ceEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEECcHH
Confidence            45688999999999999999999986    6777776444

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=96.17  E-value=0.064  Score=50.51  Aligned_cols=35  Identities=20%  Similarity=0.170  Sum_probs=23.6

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      .+..+++.||.|+|||+.+-..+.+-+..++.+..
T Consensus       231 ~~~~vlv~ApTGSGKT~a~~l~ll~~g~~vLVl~P  265 (666)
T 3o8b_A          231 SFQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNP  265 (666)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHHTTCCEEEEES
T ss_pred             cCCeEEEEeCCchhHHHHHHHHHHHCCCeEEEEcc
Confidence            46679999999999997655444443444544443

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=96.14  E-value=0.0065  Score=54.65  Aligned_cols=26  Identities=35%  Similarity=0.561  Sum_probs=22.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+..++|.|++|+|||+|+..++...
T Consensus       150 kGq~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          150 KGGKIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             TTCEEEEECCSSSCHHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCccHHHHHHHhhh
Confidence            46679999999999999999887654

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=96.14  E-value=0.091  Score=44.44  Aligned_cols=57  Identities=14%  Similarity=0.114  Sum_probs=31.8

Q ss_pred             CCCccccccccHHHHHHHHHHhhccc--CChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPL--MNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      +..+|.++.-.+...+.|...--...  .+......+-..+++.+++++|+|+|||...
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~  148 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF  148 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHH
T ss_pred             CcCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHH
Confidence            44678888555555566554211000  0111222211123578999999999999753

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=96.14  E-value=0.0031  Score=56.09  Aligned_cols=24  Identities=21%  Similarity=0.335  Sum_probs=21.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +..+.|.||+|+||||+++.++..
T Consensus        69 ~~~valvG~nGaGKSTLln~L~Gl   92 (413)
T 1tq4_A           69 VLNVAVTGETGSGKSSFINTLRGI   92 (413)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHTC
T ss_pred             CeEEEEECCCCCcHHHHHHHHhCC
Confidence            447889999999999999999974

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=96.11  E-value=0.0045  Score=49.70  Aligned_cols=26  Identities=35%  Similarity=0.473  Sum_probs=22.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ...++|.|++|+||||++..++..+.
T Consensus        30 ~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           30 TVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            45789999999999999999998763

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=96.10  E-value=0.043  Score=52.31  Aligned_cols=23  Identities=39%  Similarity=0.528  Sum_probs=19.0

Q ss_pred             CCCceEEEEcCCCChHHHHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAI   86 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~l   86 (292)
                      ..+.++++.||+|+|||+.+-..
T Consensus        44 ~~~~~~lv~apTGsGKT~~~~l~   66 (715)
T 2va8_A           44 LEGNRLLLTSPTGSGKTLIAEMG   66 (715)
T ss_dssp             TTTCCEEEECCTTSCHHHHHHHH
T ss_pred             cCCCcEEEEcCCCCcHHHHHHHH
Confidence            44788999999999999987433

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.09  E-value=0.0049  Score=55.09  Aligned_cols=26  Identities=35%  Similarity=0.342  Sum_probs=20.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...+..++.|+||+|||+++..++..
T Consensus       159 ~~~~v~~I~G~aGsGKTt~I~~~~~~  184 (446)
T 3vkw_A          159 SSAKVVLVDGVPGCGKTKEILSRVNF  184 (446)
T ss_dssp             CCSEEEEEEECTTSCHHHHHHHHCCT
T ss_pred             ccccEEEEEcCCCCCHHHHHHHHhcc
Confidence            34455788999999999999887753

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=96.09  E-value=0.004  Score=50.71  Aligned_cols=32  Identities=25%  Similarity=0.320  Sum_probs=25.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .++..+.|.|+.|+||||+++.++.. +..+..
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~-~g~v~~   49 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY-KNDICL   49 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG-TTTEEE
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc-cCCeEE
Confidence            45667889999999999999999987 444433

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=96.09  E-value=0.0038  Score=51.18  Aligned_cols=26  Identities=19%  Similarity=0.382  Sum_probs=23.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.-|.|.|++|+||||+++.++..+
T Consensus        26 ~~~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           26 NAKFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CCCEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35678899999999999999999877

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=96.08  E-value=0.0038  Score=51.15  Aligned_cols=26  Identities=15%  Similarity=0.372  Sum_probs=23.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +..+.|.|++|+||||+++.++..++
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            45688999999999999999999984

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=96.06  E-value=0.13  Score=44.67  Aligned_cols=57  Identities=16%  Similarity=0.079  Sum_probs=30.4

Q ss_pred             CccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHH
Q 022768           29 VSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la   87 (292)
                      .+|+++.-.+...+.|...--. +. .+......  +..+..+++.+|+|+|||..+-..+
T Consensus         8 ~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--~~~~~~~lv~a~TGsGKT~~~~~~~   66 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVDCGFEHPSEVQHECIPQ--AILGMDVLCQAKSGMGKTAVFVLAT   66 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHHHSCCSCCHHHHHHHHH--HTTTCCEEEECSSCSSHHHHHHHHH
T ss_pred             CChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH--HhcCCcEEEECCCCCcHHHHHHHHH
Confidence            4577765455555555553211 00 01111111  1225679999999999998654333

>1bif_A 6-phosphofructo-2-kinase/ fructose-2,6-bisphospha; transferase (phospho), phosphatase, hydrolase (phosp glycolysis, bifunctional enzyme; HET: AGS; 2.00A {Rattus norvegicus} SCOP: c.37.1.7 c.60.1.4 PDB: 3bif_A* 2bif_A* 1k6m_A* 1c80_A* 1c7z_A* 1c81_A* 1tip_A* 1fbt_A

Probab=96.06  E-value=0.014  Score=52.82  Aligned_cols=26  Identities=23%  Similarity=0.608  Sum_probs=23.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +..|+++|.||+||||+++.+++.++
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            45689999999999999999999874

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=96.04  E-value=0.002  Score=53.61  Aligned_cols=27  Identities=15%  Similarity=0.208  Sum_probs=23.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+..|+|.|++|+||||+++.++..+.
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            356688999999999999999999984

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=96.03  E-value=0.0044  Score=49.91  Aligned_cols=26  Identities=31%  Similarity=0.354  Sum_probs=23.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.-|.|.|++|+||||+++.++..+.
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~l~   31 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAERLR   31 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            56788999999999999999998874

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=96.03  E-value=0.0095  Score=46.53  Aligned_cols=26  Identities=23%  Similarity=0.460  Sum_probs=22.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ....+++.|++|+|||+++..++...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            45579999999999999999998754

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=96.01  E-value=0.0037  Score=50.87  Aligned_cols=27  Identities=22%  Similarity=0.219  Sum_probs=20.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.-|.|.|++|+||||+++.++..+
T Consensus        23 ~~g~~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           23 ARGKFITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             CCCCEEEEECCC---CHHHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            346678899999999999999999887

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=95.99  E-value=0.056  Score=47.48  Aligned_cols=55  Identities=16%  Similarity=0.048  Sum_probs=29.7

Q ss_pred             CCccccccccHHHHHHHHHHhhccc--CChHHHHhcCCCCCceEEEEcCCCChHHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPL--MNPELFLRVGIKPPKGVLLYGPPGTGKTLLAR   84 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~   84 (292)
                      ..+|+++.-.+...+.+...-....  .+......  +..+..+++.+|+|+|||..+-
T Consensus        39 ~~~f~~~~l~~~~~~~l~~~~~~~~~~~Q~~~i~~--~~~~~~~lv~a~TGsGKT~~~~   95 (414)
T 3eiq_A           39 VDSFDDMNLSESLLRGIYAYGFEKPSAIQQRAILP--CIKGYDVIAQAQSGTGKTATFA   95 (414)
T ss_dssp             CCCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHH--HHTTCCEEECCCSCSSSHHHHH
T ss_pred             hcCHhhCCCCHHHHHHHHHcCCCCCCHHHHHHhHH--HhCCCCEEEECCCCCcccHHHH
Confidence            3567776555555555554311100  01111111  1225679999999999998743

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=95.99  E-value=0.015  Score=48.46  Aligned_cols=23  Identities=39%  Similarity=0.521  Sum_probs=20.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+.|.|++|+||||+++.+...
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999864

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=95.96  E-value=0.0038  Score=49.10  Aligned_cols=24  Identities=33%  Similarity=0.415  Sum_probs=21.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.|.|++|+||||+++.++...
T Consensus        30 ~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           30 FKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            358899999999999999999754

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=95.96  E-value=0.0044  Score=48.98  Aligned_cols=24  Identities=33%  Similarity=0.415  Sum_probs=21.2

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..++|.|++|+||||+++.++...
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECcCCCCHHHHHHHHhcCC
Confidence            358999999999999999999753

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=95.93  E-value=0.0074  Score=56.73  Aligned_cols=24  Identities=42%  Similarity=0.696  Sum_probs=19.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..++|+||||||||+++..++..+
T Consensus       196 ~~~li~GppGTGKT~~~~~~i~~l  219 (624)
T 2gk6_A          196 PLSLIQGPPGTGKTVTSATIVYHL  219 (624)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHH
Confidence            368899999999999877766543

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=95.91  E-value=0.0021  Score=51.14  Aligned_cols=29  Identities=14%  Similarity=0.189  Sum_probs=24.7

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +.+.++..+.|.|++|+||||+++.++..
T Consensus        21 ~~~~~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           21 LPSDTGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             SSCSCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCCCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            44667788999999999999999988754

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=95.90  E-value=0.09  Score=46.19  Aligned_cols=57  Identities=19%  Similarity=0.193  Sum_probs=32.5

Q ss_pred             CCCccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLARA   85 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~   85 (292)
                      +..+|+++--.++..+.|...--. +. .+......  +..+..+++.+|+|+|||..+-.
T Consensus        35 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~ai~~--i~~~~~~lv~a~TGsGKT~~~~~   93 (410)
T 2j0s_A           35 VTPTFDTMGLREDLLRGIYAYGFEKPSAIQQRAIKQ--IIKGRDVIAQSQSGTGKTATFSI   93 (410)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHH--HHTTCCEEEECCTTSSHHHHHHH
T ss_pred             CCCCHhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHH--HhCCCCEEEECCCCCCchHHHHH
Confidence            345788875556666666554211 10 11111211  12256799999999999975543

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=95.88  E-value=0.089  Score=45.70  Aligned_cols=20  Identities=30%  Similarity=0.469  Sum_probs=16.7

Q ss_pred             CceEEEEcCCCChHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARA   85 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~   85 (292)
                      +..+++.+|+|+|||..+-.
T Consensus        44 ~~~~lv~a~TGsGKT~~~~~   63 (395)
T 3pey_A           44 PRNMIAQSQSGTGKTAAFSL   63 (395)
T ss_dssp             CCCEEEECCTTSCHHHHHHH
T ss_pred             CCeEEEECCCCCcHHHHHHH
Confidence            47899999999999986543

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=95.87  E-value=0.14  Score=47.54  Aligned_cols=18  Identities=33%  Similarity=0.462  Sum_probs=15.8

Q ss_pred             CCceEEEEcCCCChHHHH
Q 022768           65 PPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l   82 (292)
                      .+..+++.+|+|+|||..
T Consensus        59 ~~~dvlv~apTGsGKTl~   76 (579)
T 3sqw_A           59 EDHDVIARAKTGTGKTFA   76 (579)
T ss_dssp             SSEEEEEECCTTSCHHHH
T ss_pred             CCCeEEEEcCCCcHHHHH
Confidence            467899999999999984

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=95.84  E-value=0.049  Score=45.06  Aligned_cols=18  Identities=33%  Similarity=0.455  Sum_probs=15.4

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      ++.+++++|+|+|||..+
T Consensus        91 ~~~~lv~a~TGsGKT~~~  108 (262)
T 3ly5_A           91 GRDLLAAAKTGSGKTLAF  108 (262)
T ss_dssp             TCCCEECCCTTSCHHHHH
T ss_pred             CCcEEEEccCCCCchHHH
Confidence            457999999999999864

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=95.84  E-value=0.024  Score=49.54  Aligned_cols=23  Identities=22%  Similarity=0.288  Sum_probs=19.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.|.|++|+||||+++.++...
T Consensus       181 ~V~lvG~~naGKSTLln~L~~~~  203 (364)
T 2qtf_A          181 SIGIVGYTNSGKTSLFNSLTGLT  203 (364)
T ss_dssp             EEEEECBTTSSHHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
Confidence            38899999999999999998643

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=95.83  E-value=0.15  Score=45.97  Aligned_cols=56  Identities=14%  Similarity=0.113  Sum_probs=31.2

Q ss_pred             CCccccccccHHHHHHHHHHhhccc--CChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPL--MNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~--~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+|.++.-.++..+.|...--...  .+......+-...+..+++.||+|+|||...
T Consensus        91 ~~~f~~~~l~~~l~~~l~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~  148 (479)
T 3fmp_B           91 VKSFEELRLKPQLLQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAF  148 (479)
T ss_dssp             CCCSGGGTCCHHHHHHHHHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHH
T ss_pred             cCCHHHcCCCHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHH
Confidence            4578887656665565554211000  0112222221123578999999999999863

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=95.81  E-value=0.0061  Score=46.09  Aligned_cols=25  Identities=32%  Similarity=0.408  Sum_probs=21.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +...+|+||.|+|||+++.+++-.+
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3457899999999999999998755

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=95.78  E-value=0.093  Score=46.80  Aligned_cols=54  Identities=15%  Similarity=0.115  Sum_probs=29.9

Q ss_pred             CCCccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l   82 (292)
                      |-.+|+++--.+...+.|...--. |. .+......  +..++.+++.+|+|+|||..
T Consensus        54 ~~~~f~~~~l~~~l~~~l~~~g~~~pt~iQ~~ai~~--i~~g~d~i~~a~TGsGKT~a  109 (434)
T 2db3_A           54 PIQHFTSADLRDIIIDNVNKSGYKIPTPIQKCSIPV--ISSGRDLMACAQTGSGKTAA  109 (434)
T ss_dssp             CCCCGGGSCCCHHHHHHHHHTTCCSCCHHHHHHHHH--HHTTCCEEEECCTTSSHHHH
T ss_pred             CcCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHH--HhcCCCEEEECCCCCCchHH
Confidence            446788875445555555443110 00 00111111  12367899999999999984

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=95.76  E-value=0.013  Score=50.20  Aligned_cols=24  Identities=42%  Similarity=0.425  Sum_probs=21.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..++|.|++|+||||+++.++...
T Consensus         5 ~v~~i~G~~GaGKTTll~~l~~~~   28 (318)
T 1nij_A            5 AVTLLTGFLGAGKTTLLRHILNEQ   28 (318)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             cEEEEEecCCCCHHHHHHHHHhhc
Confidence            357899999999999999999764

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=95.76  E-value=0.073  Score=46.54  Aligned_cols=57  Identities=16%  Similarity=0.062  Sum_probs=30.8

Q ss_pred             CCCccccccccHHHHHHHHHHhhc-cc-CChHHHHhcCCCCCceEEEEcCCCChHHHHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIEL-PL-MNPELFLRVGIKPPKGVLLYGPPGTGKTLLARA   85 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~-~~-~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~   85 (292)
                      +..+|+++.-.++..+.|...--. +. .+......  +..+..+++.+|+|+|||..+-.
T Consensus        19 ~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--i~~~~~~li~a~TGsGKT~~~~~   77 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGIFEAGFEKPSPIQEEAIPV--AITGRDILARAKNGTGKTAAFVI   77 (400)
T ss_dssp             --CCGGGGCCCHHHHHHHHHTTCCSCCHHHHHHHHH--HHHTCCEEEECCTTSCHHHHHHH
T ss_pred             ccCChhhcCCCHHHHHHHHHCCCCCCCHHHHHHHHH--HhcCCCEEEECCCCcHHHHHHHH
Confidence            345788886556666666553211 00 01111111  11245699999999999986543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=95.75  E-value=0.042  Score=49.10  Aligned_cols=18  Identities=33%  Similarity=0.302  Sum_probs=15.8

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      +..++++||+|+|||..+
T Consensus         2 g~~~lv~a~TGsGKT~~~   19 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRV   19 (431)
T ss_dssp             CCEEEEECCTTSCTTTTH
T ss_pred             CCEEEEEcCCCCCHHHHH
Confidence            467999999999999965

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=95.74  E-value=0.07  Score=42.38  Aligned_cols=23  Identities=30%  Similarity=0.405  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..|+|.|++|+|||+|++.+...
T Consensus        26 ~ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           26 IKLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEEECcCCCCHHHHHHHHhcC
Confidence            46999999999999999999863

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=95.74  E-value=0.0064  Score=45.81  Aligned_cols=22  Identities=27%  Similarity=0.495  Sum_probs=20.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .+++.|++|+|||++++.++..
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999875

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=95.73  E-value=0.019  Score=51.10  Aligned_cols=35  Identities=29%  Similarity=0.229  Sum_probs=27.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      ++..+++.|++|+||||++..+|..+   +..+..+++
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~  134 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeec
Confidence            46678889999999999999999876   445555443

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=95.71  E-value=0.012  Score=51.99  Aligned_cols=34  Identities=15%  Similarity=0.289  Sum_probs=26.7

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      .+.+++|.|++|+|||++++.++..+   +..++.++
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D   70 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIID   70 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEe
Confidence            46789999999999999999998754   44444444

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=95.69  E-value=0.0079  Score=48.76  Aligned_cols=29  Identities=21%  Similarity=0.247  Sum_probs=24.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      ..+..|.|.|++|+||||+++.++..++.
T Consensus        19 ~~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           19 PGSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34666888999999999999999987754

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=95.69  E-value=0.0059  Score=47.09  Aligned_cols=24  Identities=33%  Similarity=0.509  Sum_probs=21.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +..++|.|++|+|||+|++.++..
T Consensus         4 ~~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            4 GMKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            557999999999999999999864

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=95.68  E-value=0.014  Score=47.00  Aligned_cols=25  Identities=32%  Similarity=0.480  Sum_probs=22.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...++|.|.+|+||||++..++...
T Consensus        38 ~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           38 VVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            4678899999999999999999875

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=95.65  E-value=0.0083  Score=47.95  Aligned_cols=25  Identities=24%  Similarity=0.519  Sum_probs=22.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...++|.|++|+|||+++..++...
T Consensus        12 ~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           12 QPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4579999999999999999999764

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=95.65  E-value=0.047  Score=44.48  Aligned_cols=18  Identities=39%  Similarity=0.595  Sum_probs=15.5

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      ++.+++.+|+|+|||..+
T Consensus        66 ~~~~l~~a~TGsGKT~~~   83 (245)
T 3dkp_A           66 GRELLASAPTGSGKTLAF   83 (245)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEECCCCCcHHHHH
Confidence            567999999999999863

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=95.64  E-value=0.0068  Score=45.97  Aligned_cols=24  Identities=13%  Similarity=0.254  Sum_probs=21.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...+++.|++|+|||++++.+...
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            346899999999999999999874

>3iby_A Ferrous iron transport protein B; G protein, G domain, iron uptake, cell inner membrane, cell GTP-binding, ION transport, membrane; 2.50A {Legionella pneumophila}

Probab=95.62  E-value=0.078  Score=43.77  Aligned_cols=22  Identities=41%  Similarity=0.585  Sum_probs=20.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .++|.|.+|+||||++..+...
T Consensus         3 kI~lvG~~n~GKSTL~n~L~g~   24 (256)
T 3iby_A            3 HALLIGNPNCGKTTLFNALTNA   24 (256)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            5899999999999999999864

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=95.61  E-value=0.0071  Score=54.76  Aligned_cols=28  Identities=18%  Similarity=0.203  Sum_probs=24.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +.+ ..+.|.||+|+||||+++.++..+.
T Consensus        27 i~~-e~~~liG~nGsGKSTLl~~l~Gl~~   54 (483)
T 3euj_A           27 FDE-LVTTLSGGNGAGKSTTMAGFVTALI   54 (483)
T ss_dssp             CCS-SEEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             Ecc-ceEEEECCCCCcHHHHHHHHhcCCC
Confidence            556 7889999999999999999998763

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=95.61  E-value=0.0072  Score=52.62  Aligned_cols=27  Identities=22%  Similarity=0.319  Sum_probs=23.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+..+.|.||+|+|||||++.++....
T Consensus       214 ~G~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          214 TGRISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CCCEEEEECCCCccHHHHHHHHhcccc
Confidence            466799999999999999999997654

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=95.60  E-value=0.062  Score=45.68  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=20.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...|.|.|.||+|||||+..+...
T Consensus        10 ~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A           10 VGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCC
Confidence            445889999999999999999864

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=95.60  E-value=0.0068  Score=46.26  Aligned_cols=23  Identities=26%  Similarity=0.492  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..++|.|++|+|||++++.++..
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999999863

>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair, nucleotide excision repai hydrolase-DNA complex; HET: DNA; 2.90A {Thermotoga maritima}

Probab=95.59  E-value=0.037  Score=54.05  Aligned_cols=42  Identities=21%  Similarity=0.230  Sum_probs=28.8

Q ss_pred             CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          126 PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       126 ~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      |.+++|||-          +++-+......+.+++..+..    .+..+|+++++.
T Consensus       827 p~LLILDEP----------TsGLD~~~~~~L~~lL~~L~~----~G~TVIvI~HdL  868 (916)
T 3pih_A          827 RTLYILDEP----------TVGLHFEDVRKLVEVLHRLVD----RGNTVIVIEHNL  868 (916)
T ss_dssp             SEEEEEEST----------TTTCCHHHHHHHHHHHHHHHH----TTCEEEEECCCH
T ss_pred             CCEEEEECC----------CCCCCHHHHHHHHHHHHHHHh----cCCEEEEEeCCH
Confidence            579999995          344477777778877776642    144577777764

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=95.59  E-value=0.061  Score=43.28  Aligned_cols=24  Identities=25%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...|+|.|++|+|||+++..++..
T Consensus        29 ~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           29 KKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            456999999999999999999864

>3i8s_A Ferrous iron transport protein B; GTPase, GPCR, iron uptake, FEO, cell inner membrane, cell ME GTP-binding, ION transport, membrane; 1.80A {Escherichia coli} PDB: 3i8x_A* 3i92_A* 3hyr_A 3hyt_A* 2wic_A* 2wib_A* 2wia_A*

Probab=95.57  E-value=0.18  Score=41.91  Aligned_cols=23  Identities=30%  Similarity=0.457  Sum_probs=20.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..++|.|.+|+||||++..+...
T Consensus         4 ~~I~lvG~~n~GKSTLin~l~g~   26 (274)
T 3i8s_A            4 LTIGLIGNPNSGKTTLFNQLTGS   26 (274)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHTT
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999864

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=95.55  E-value=0.01  Score=45.18  Aligned_cols=26  Identities=23%  Similarity=0.376  Sum_probs=22.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .....+++.|++|+|||+++..+...
T Consensus         5 ~~~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            5 TREMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhcC
Confidence            34567999999999999999999763

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=95.54  E-value=0.014  Score=50.72  Aligned_cols=25  Identities=32%  Similarity=0.503  Sum_probs=22.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..+.|.|+||+||||+++.++..+
T Consensus        74 ~~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           74 AFRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            5678899999999999999999754

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=95.54  E-value=0.0058  Score=47.58  Aligned_cols=21  Identities=29%  Similarity=0.578  Sum_probs=19.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .++|.|++|+|||+|++.++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999999986

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=95.52  E-value=0.0086  Score=45.20  Aligned_cols=23  Identities=26%  Similarity=0.455  Sum_probs=20.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.|++|+|||+++..+...
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            46999999999999999998864

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=95.52  E-value=0.013  Score=56.61  Aligned_cols=24  Identities=42%  Similarity=0.696  Sum_probs=19.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..++|+||||||||+++..++..+
T Consensus       372 ~~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          372 PLSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHH
Confidence            368899999999999877776543

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=95.51  E-value=0.009  Score=48.09  Aligned_cols=25  Identities=24%  Similarity=0.426  Sum_probs=22.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.-|.|.|++|+||||.++.++..+
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568899999999999999999877

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=95.49  E-value=0.0099  Score=45.61  Aligned_cols=25  Identities=36%  Similarity=0.414  Sum_probs=21.7

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ....|++.|++|+|||++++.+...
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567999999999999999999863

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=95.48  E-value=0.089  Score=45.75  Aligned_cols=56  Identities=16%  Similarity=0.004  Sum_probs=31.2

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccC--ChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLM--NPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~--~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      .+..+|+++--.++..+.+...--..+.  +......  +..+..+++.+|+|+|||..+
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~~g~~~~~~~Q~~~i~~--i~~~~~~lv~~~TGsGKT~~~   75 (394)
T 1fuu_A           18 KVVYKFDDMELDENLLRGVFGYGFEEPSAIQQRAIMP--IIEGHDVLAQAQSGTGKTGTF   75 (394)
T ss_dssp             CCCCSSGGGCCCHHHHHHHHHHTCCSCCHHHHHHHHH--HHHTCCEEECCCSSHHHHHHH
T ss_pred             cccCChhhcCCCHHHHHHHHHcCCCCCCHHHHHHHHH--HhCCCCEEEECCCCChHHHHH
Confidence            3456788875555555666554211110  1111111  112457999999999999864

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=95.47  E-value=0.12  Score=40.01  Aligned_cols=24  Identities=25%  Similarity=0.293  Sum_probs=21.2

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..|+|.|++|+|||+|++.+...-
T Consensus        24 ~ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           24 FKLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCcCHHHHHHHHhcCC
Confidence            459999999999999999998754

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=95.47  E-value=0.0086  Score=45.09  Aligned_cols=23  Identities=26%  Similarity=0.450  Sum_probs=20.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+++.|++|+|||+++..++...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            58999999999999999998653

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=95.44  E-value=0.0095  Score=45.00  Aligned_cols=23  Identities=26%  Similarity=0.469  Sum_probs=20.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.|++|+|||++++.+...
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            46999999999999999999864

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=95.43  E-value=0.0096  Score=45.13  Aligned_cols=24  Identities=25%  Similarity=0.333  Sum_probs=20.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+++.|++|+|||++++.+...-
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            4 IKLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            358999999999999999998643

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=95.43  E-value=0.085  Score=43.15  Aligned_cols=18  Identities=22%  Similarity=0.409  Sum_probs=15.3

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      ++.+++.+|+|+|||..+
T Consensus        60 ~~~~l~~a~TGsGKT~~~   77 (253)
T 1wrb_A           60 HRDIMACAQTGSGKTAAF   77 (253)
T ss_dssp             TCCEEEECCTTSSHHHHH
T ss_pred             CCCEEEECCCCChHHHHH
Confidence            457999999999999853

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=95.41  E-value=0.0097  Score=45.15  Aligned_cols=24  Identities=25%  Similarity=0.364  Sum_probs=21.2

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+++.|++|+|||++++.+...-
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            469999999999999999998754

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=95.41  E-value=0.067  Score=53.59  Aligned_cols=23  Identities=26%  Similarity=0.346  Sum_probs=18.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +..++++||.|+|||..+-..+.
T Consensus       199 g~dvLV~ApTGSGKTlva~l~i~  221 (1108)
T 3l9o_A          199 GESVLVSAHTSAGKTVVAEYAIA  221 (1108)
T ss_dssp             TCCEEEECCSSSHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCChHHHHHHHHH
Confidence            56899999999999987655443

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=95.40  E-value=0.0095  Score=50.69  Aligned_cols=26  Identities=23%  Similarity=0.382  Sum_probs=22.6

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+..+.|.||+|+|||||++.++ ...
T Consensus       164 ~G~i~~l~G~sG~GKSTLln~l~-~~~  189 (302)
T 2yv5_A          164 EGFICILAGPSGVGKSSILSRLT-GEE  189 (302)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHH-SCC
T ss_pred             cCcEEEEECCCCCCHHHHHHHHH-Hhh
Confidence            46678999999999999999999 653

>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein phosphatase, dual activity, product, substrate, transferase, hydrolase; 1.95A {Staphylococcus xylosus} SCOP: c.98.2.1 c.91.1.2

Probab=95.40  E-value=0.012  Score=50.11  Aligned_cols=24  Identities=33%  Similarity=0.469  Sum_probs=22.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +.+++|.|++|+|||+++..+...
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~  167 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR  167 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc
Confidence            678999999999999999999875

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=95.38  E-value=0.21  Score=46.01  Aligned_cols=18  Identities=33%  Similarity=0.462  Sum_probs=15.9

Q ss_pred             CCceEEEEcCCCChHHHH
Q 022768           65 PPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l   82 (292)
                      .++.+++.+|+|+|||..
T Consensus       110 ~~~~~lv~apTGsGKTl~  127 (563)
T 3i5x_A          110 EDHDVIARAKTGTGKTFA  127 (563)
T ss_dssp             SSEEEEEECCTTSCHHHH
T ss_pred             CCCeEEEECCCCCCccHH
Confidence            467899999999999974

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=95.38  E-value=0.01  Score=45.53  Aligned_cols=23  Identities=35%  Similarity=0.488  Sum_probs=20.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.|++|+|||++++.+...
T Consensus         8 ~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            8 FKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46899999999999999999864

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=95.38  E-value=0.0089  Score=46.43  Aligned_cols=23  Identities=26%  Similarity=0.492  Sum_probs=20.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..++|.|++|+|||++++.++..
T Consensus         8 ~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            8 YEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999873

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=95.37  E-value=0.01  Score=45.08  Aligned_cols=24  Identities=33%  Similarity=0.321  Sum_probs=21.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...+++.|++|+|||++++.+...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            346999999999999999999864

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=95.36  E-value=0.01  Score=45.60  Aligned_cols=25  Identities=28%  Similarity=0.401  Sum_probs=21.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...+++.|++|+|||++++.+....
T Consensus         8 ~~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            8 ILKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCc
Confidence            4569999999999999999988643

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=95.33  E-value=0.01  Score=45.07  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.|++|+|||+++..+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35899999999999999999854

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=95.33  E-value=0.01  Score=45.38  Aligned_cols=23  Identities=48%  Similarity=0.667  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..++|.|++|+|||+|++.+...
T Consensus         5 ~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            5 YRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEECCCCccHHHHHHHHhcC
Confidence            46999999999999999999854

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=95.33  E-value=0.011  Score=44.72  Aligned_cols=23  Identities=22%  Similarity=0.413  Sum_probs=20.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.|++|+|||++++.+...
T Consensus         4 ~ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            4 YKLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            36899999999999999999864

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=95.31  E-value=0.013  Score=45.85  Aligned_cols=25  Identities=16%  Similarity=0.267  Sum_probs=21.7

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ....+++.|++|+|||+++..+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3567999999999999999999864

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=95.29  E-value=0.017  Score=55.82  Aligned_cols=22  Identities=45%  Similarity=0.699  Sum_probs=17.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHH
Q 022768           67 KGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ..++|+||||||||+++..+..
T Consensus       376 ~~~lI~GppGTGKT~~i~~~i~  397 (802)
T 2xzl_A          376 PLSLIQGPPGTGKTVTSATIVY  397 (802)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHH
Confidence            3689999999999998766554

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=95.28  E-value=0.01  Score=45.12  Aligned_cols=23  Identities=26%  Similarity=0.436  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.|++|+|||++++.+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46899999999999999999863

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=95.28  E-value=0.14  Score=46.65  Aligned_cols=23  Identities=30%  Similarity=0.579  Sum_probs=18.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +..+++.+|+|+|||..+-..+.
T Consensus        19 ~~~~l~~~~tGsGKT~~~~~~~~   41 (555)
T 3tbk_A           19 GKNTIICAPTGCGKTFVSLLICE   41 (555)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEEeCCCChHHHHHHHHHH
Confidence            45799999999999987655553

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.26  E-value=0.021  Score=50.02  Aligned_cols=28  Identities=39%  Similarity=0.585  Sum_probs=24.9

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..+..++|.||+|+|||++++.+++..
T Consensus       171 i~rGQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          171 IGRGQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             CBTTCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             ecCCcEEEEecCCCCChhHHHHHHHHHH
Confidence            5668899999999999999999998854

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=95.24  E-value=0.012  Score=44.42  Aligned_cols=22  Identities=23%  Similarity=0.359  Sum_probs=19.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .+++.|++|+|||+++..+...
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999999864

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=95.24  E-value=0.012  Score=44.57  Aligned_cols=23  Identities=22%  Similarity=0.325  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..+++.|++|+|||+++..+...
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            7 FKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            45899999999999999999863

>1knx_A Probable HPR(Ser) kinase/phosphatase; HPR kinase, HPR kinase/phosphatase, HPRK/P, P-loop, walker A BOX, catabolite repression; 2.50A {Mycoplasma pneumoniae} SCOP: c.98.2.1 c.91.1.2

Probab=95.23  E-value=0.0096  Score=50.67  Aligned_cols=23  Identities=39%  Similarity=0.504  Sum_probs=20.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +.+++|.|++|+|||+++..+..
T Consensus       147 g~gvli~G~sG~GKStlal~l~~  169 (312)
T 1knx_A          147 GVGVLLTGRSGIGKSECALDLIN  169 (312)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            67799999999999999988765

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=95.20  E-value=0.11  Score=49.56  Aligned_cols=19  Identities=42%  Similarity=0.583  Sum_probs=16.9

Q ss_pred             CCceEEEEcCCCChHHHHH
Q 022768           65 PPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~   83 (292)
                      .+.++++.||+|+|||+.+
T Consensus        38 ~~~~~lv~apTGsGKT~~~   56 (720)
T 2zj8_A           38 EGKNALISIPTASGKTLIA   56 (720)
T ss_dssp             GTCEEEEECCGGGCHHHHH
T ss_pred             CCCcEEEEcCCccHHHHHH
Confidence            3678999999999999876

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=95.20  E-value=0.012  Score=45.63  Aligned_cols=23  Identities=26%  Similarity=0.323  Sum_probs=20.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..|+|.|++|+|||+|+..+...
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            46999999999999999999863

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=95.18  E-value=0.0099  Score=50.52  Aligned_cols=28  Identities=29%  Similarity=0.328  Sum_probs=23.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+..+.|.||+|+||||+++.++.....
T Consensus       168 ~geiv~l~G~sG~GKSTll~~l~g~~~~  195 (301)
T 1u0l_A          168 KGKISTMAGLSGVGKSSLLNAINPGLKL  195 (301)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHSTTCCC
T ss_pred             cCCeEEEECCCCCcHHHHHHHhcccccc
Confidence            3567889999999999999999986643

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=95.18  E-value=0.012  Score=45.01  Aligned_cols=24  Identities=25%  Similarity=0.407  Sum_probs=20.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...+++.|++|+|||++++.+...
T Consensus         6 ~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            6 QLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             eEEEEEECcCCCCHHHHHHHHHhC
Confidence            346999999999999999999853

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=95.17  E-value=0.012  Score=44.64  Aligned_cols=21  Identities=38%  Similarity=0.620  Sum_probs=19.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .+++.|++|+|||+++..+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999974

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=95.16  E-value=0.013  Score=44.83  Aligned_cols=25  Identities=20%  Similarity=0.274  Sum_probs=21.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...+++.|++|+|||++++.+...-
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcCC
Confidence            3469999999999999999998643

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=95.14  E-value=0.015  Score=45.69  Aligned_cols=25  Identities=20%  Similarity=0.425  Sum_probs=21.8

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ....++|.|++|+|||++++.+...
T Consensus        27 ~~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           27 AEVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3457999999999999999999864

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=95.14  E-value=0.15  Score=41.82  Aligned_cols=24  Identities=29%  Similarity=0.481  Sum_probs=21.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...|+|.|++|+||||++..+...
T Consensus        22 ~~~I~lvG~~g~GKStl~n~l~~~   45 (260)
T 2xtp_A           22 ELRIILVGKTGTGKSAAGNSILRK   45 (260)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHTS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999999854

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=95.13  E-value=0.012  Score=45.08  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=21.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...+++.|++|+|||++++.+...
T Consensus         9 ~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            9 THKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346999999999999999999875

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=95.12  E-value=0.063  Score=44.41  Aligned_cols=25  Identities=24%  Similarity=0.387  Sum_probs=21.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ...|++.|.+|+|||+++.++...-
T Consensus        36 ~~~I~lvG~~g~GKSSLin~l~~~~   60 (262)
T 3def_A           36 SMTVLVLGKGGVGKSSTVNSLIGEQ   60 (262)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHTSC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            4579999999999999999998643

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=95.10  E-value=0.0039  Score=53.13  Aligned_cols=27  Identities=30%  Similarity=0.455  Sum_probs=22.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++..+.|.||+|+|||||++.++...
T Consensus       171 ~~G~~~~lvG~sG~GKSTLln~L~g~~  197 (307)
T 1t9h_A          171 FQDKTTVFAGQSGVGKSSLLNAISPEL  197 (307)
T ss_dssp             GTTSEEEEEESHHHHHHHHHHHHCC--
T ss_pred             cCCCEEEEECCCCCCHHHHHHHhcccc
Confidence            457789999999999999999998754

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=95.10  E-value=0.014  Score=45.62  Aligned_cols=23  Identities=39%  Similarity=0.489  Sum_probs=20.6

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..|+|.|++|+|||+|++.+...
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            46999999999999999999874

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=95.09  E-value=0.014  Score=46.51  Aligned_cols=27  Identities=30%  Similarity=0.299  Sum_probs=22.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      +...+|+||+|+|||+++.++.-.++.
T Consensus        23 ~~~~~I~G~NgsGKStil~ai~~~l~g   49 (203)
T 3qks_A           23 EGINLIIGQNGSGKSSLLDAILVGLYW   49 (203)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CCeEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            356789999999999999999877654

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=95.09  E-value=0.016  Score=45.39  Aligned_cols=24  Identities=17%  Similarity=0.347  Sum_probs=21.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...|+|.|++|+|||+|+..++..
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456999999999999999999875

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=95.08  E-value=0.013  Score=44.82  Aligned_cols=23  Identities=22%  Similarity=0.301  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..++|.|++|+|||+++..++..
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46899999999999999999853

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=95.08  E-value=0.014  Score=45.41  Aligned_cols=24  Identities=25%  Similarity=0.403  Sum_probs=21.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..|++.|++|+|||+++..++...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            468999999999999999998653

>3a1s_A Iron(II) transport protein B; FEOB, iron transporter, small GTPase, G protein, GDI; HET: GDP; 1.50A {Thermotoga maritima} PDB: 3a1t_A* 3a1u_A* 3a1v_A* 3a1w_A

Probab=95.07  E-value=0.04  Score=45.58  Aligned_cols=23  Identities=39%  Similarity=0.459  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..++|.|++|+|||+++..+...
T Consensus         6 ~kI~lvG~~nvGKTsL~n~l~g~   28 (258)
T 3a1s_A            6 VKVALAGCPNVGKTSLFNALTGT   28 (258)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHCC
Confidence            46899999999999999999863

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	292
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	1e-104
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	1e-101
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	1e-76
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	2e-62
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	5e-53
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	6e-36
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	2e-32
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	5e-32
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	3e-26
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	9e-26
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	7e-20
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	8e-18
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	4e-14
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	3e-11
d1um8a_	364	c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 2	2e-07
d1g41a_	443	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	2e-06
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	5e-06
d2gnoa2	198	c.37.1.20 (A:11-208) gamma subunit of DNA polymera	2e-05
d1r6bx2	268	c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, A	2e-05
d1g8pa_	333	c.37.1.20 (A:) ATPase subunit of magnesium chelata	4e-05
d1ny5a2	247	c.37.1.20 (A:138-384) Transcriptional activator si	5e-05
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	1e-04
d1jbka_	195	c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia col	2e-04
d1qvra2	387	c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus	2e-04
d1np6a_	170	c.37.1.10 (A:) Molybdopterin-guanine dinucleotide	3e-04
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	5e-04
d1lw7a2	192	c.37.1.1 (A:220-411) Transcriptional regulator Nad	7e-04
d2i3ba1	189	c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57	0.001
d1rz3a_	198	c.37.1.6 (A:) Hypothetical protein rbstp0775 {Baci	0.002
d1m8pa3	183	c.37.1.15 (A:391-573) ATP sulfurylase C-terminal d	0.003
d1n0wa_	242	c.37.1.11 (A:) DNA repair protein Rad51, catalytic	0.003
d1y63a_	174	c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishma	0.004

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

 Score =  302 bits (775), Expect = e-104
 Identities = 105/252 (41%), Positives = 152/252 (60%), Gaps = 1/252 (0%)

Query: 21  MLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKT 80
           ML ED    +++ V G  +   E+ E +E  L  P  F ++G K PKGVL+ GPPGTGKT
Sbjct: 1   MLTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKT 59

Query: 81  LLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGR 140
           LLA+AIA      F  +  S  ++ ++G  A  +R+MF  A+   PCIIF+DEIDA+G +
Sbjct: 60  LLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQ 119

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEI 200
           R +       E ++TL ++L ++DGF+    + +I ATNRPDVLDPALLRPGR DR++ +
Sbjct: 120 RGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVV 179

Query: 201 PLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDY 260
            LP+ + R +ILK+H   +    +ID   + +   GF+GADL N+  EA + A R  +  
Sbjct: 180 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRV 239

Query: 261 VIHEDFMKAVRK 272
           V   +F KA  K
Sbjct: 240 VSMVEFEKAKDK 251

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

 Score =  294 bits (754), Expect = e-101
 Identities = 102/243 (41%), Positives = 148/243 (60%), Gaps = 1/243 (0%)

Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
            V++  V G  +   EL+E +E  L NP  F  +G + PKGVLL GPPG GKT LARA+A
Sbjct: 5   KVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVA 63

Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
                 F+    S  ++ ++G  A  +R++F  A+ H PCI+F+DEIDA+G +R S    
Sbjct: 64  GEARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGG 123

Query: 148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS 207
            + E ++TL +LL ++DGF++   + ++ ATNRPD+LDPALLRPGR DR+I I  P+ + 
Sbjct: 124 GNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKG 183

Query: 208 RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFM 267
           R +IL+IHA G     ++D   + K   GF GADL N+  EA + A R  R  +  +D  
Sbjct: 184 REQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMKDLE 243

Query: 268 KAV 270
           +A 
Sbjct: 244 EAA 246

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  232 bits (592), Expect = 1e-76
 Identities = 100/245 (40%), Positives = 147/245 (60%)

Query: 28  NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIA 87
            V++  +GGL D  REL+E ++ P+ +P+ FL+ G+ P KGVL YGPPG GKTLLA+AIA
Sbjct: 3   QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIA 62

Query: 88  SNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTS 147
           +   ANF+ +    ++  + GES   +RE+F  AR   PC++F DE+D+I   R      
Sbjct: 63  NECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGD 122

Query: 148 ADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQS 207
                 R + ++L ++DG      V +I ATNRPD++DPA+LRPGRLD+ I IPLP+E+S
Sbjct: 123 GGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKS 182

Query: 208 RMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFM 267
           R+ ILK +        ++D E + K+  GF+GADL  +C  A   AIR   +  I  +  
Sbjct: 183 RVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERE 242

Query: 268 KAVRK 272
           +    
Sbjct: 243 RQTNP 247

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  196 bits (498), Expect = 2e-62
 Identities = 102/247 (41%), Positives = 148/247 (59%), Gaps = 3/247 (1%)

Query: 29  VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIAS 88
           V Y  VGG   Q+ +++E +ELPL +P LF  +G+KPP+G+LLYGPPGTGKTL+ARA+A+
Sbjct: 1   VGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN 60

Query: 89  NIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSA 148
              A F  +    I+ K  GES   +R+ F  A  + P IIF+DE+DAI  +R     + 
Sbjct: 61  ETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKR---EKTH 117

Query: 149 DREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSR 208
               +R + +LL  +DG  Q   V ++ ATNRP+ +DPAL R GR DR+++I +P+   R
Sbjct: 118 GEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGR 177

Query: 209 MEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMK 268
           +EIL+IH   +    ++D E V     G  GADL  +C+EA + AIR + D +  ED   
Sbjct: 178 LEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETI 237

Query: 269 AVRKLNE 275
               +N 
Sbjct: 238 DAEVMNS 244

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

 Score =  173 bits (440), Expect = 5e-53
 Identities = 36/255 (14%), Positives = 77/255 (30%), Gaps = 28/255 (10%)

Query: 24  EDPGNVSYSAVGGLSDQIRELRES--IELPLMNPELFLRVGIKPPKGVLL-YGPPGTGKT 80
           +   +V     G +    R        EL   +P +    G +   G+++  G   +GKT
Sbjct: 78  DGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKT 137

Query: 81  LLARAIASNI--DANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIG 138
            L  A+   +     +  V     +  Y  +    + ++       Q  +I +D +  + 
Sbjct: 138 PLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAML--QHRVIVIDSLKNVI 195

Query: 139 GRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNR---PDVLDPALLRPGRLD 195
           G      TS      R   +LL+ +          +I + N     D +   +    R +
Sbjct: 196 GAAGGNTTSGGIS--RGAFDLLSDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSN 253

Query: 196 RKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIR 255
               +   +     ++L     G+ +                    L+    E  +  I 
Sbjct: 254 STSLVISTDVDGEWQVLTRTGEGLQRL----------------THTLQTSYGEHSVLTIH 297

Query: 256 AERDYVIHEDFMKAV 270
             +     +   KA+
Sbjct: 298 TSKQSGGKQASGKAI 312

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

 Score =  130 bits (327), Expect = 6e-36
 Identities = 33/290 (11%), Positives = 69/290 (23%), Gaps = 27/290 (9%)

Query: 1   MTTLTIMRALPREVDPVVYNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLR 60
              LT  + L    + ++  M        S   +      +  L   +         FL+
Sbjct: 87  SLQLTREQMLTNRFNDLLDRMDIMFGSTGSAD-IEEWMAGVAWLHCLLPKMDSVVYDFLK 145

Query: 61  V---GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY-IGESARLIRE 116
                I   +  L  GP  +GKT LA A+        L V        + +G +      
Sbjct: 146 CMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLV 205

Query: 117 MF------GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLG 170
           +F      G      P    ++ +D +             +        +          
Sbjct: 206 VFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPP------- 258

Query: 171 KVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSR-MEILKIHAAGIAKHGEIDYEA 229
               I+  N             R  ++I+    +     +E  +          +     
Sbjct: 259 ---GIVTMNE---YSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRII--QSGIAL 310

Query: 230 VVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKL 279
           ++ L      A+         +              + K    +     +
Sbjct: 311 LLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGV 360

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

 Score =  118 bits (295), Expect = 2e-32
 Identities = 49/242 (20%), Positives = 86/242 (35%), Gaps = 17/242 (7%)

Query: 36  GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL 95
              D +  + +  EL +   +        P   VLL GPP +GKT LA  IA   +  F+
Sbjct: 13  KWGDPVTRVLDDGELLV---QQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFI 69

Query: 96  KVVSSAIIDKYIGES-ARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQR 154
           K+ S   +  +   +  + ++++F  A   Q   + +D+I+ +            R    
Sbjct: 70  KICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIG----PRFSNL 125

Query: 155 TLMELLNQLDGFDQLGKVK-MIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILK 213
            L  LL  L      G+   +I  T+R DVL    +        I +  PN  +  ++L+
Sbjct: 126 VLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQEMEML-NAFSTTIHV--PNIATGEQLLE 182

Query: 214 IHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKL 273
                    G    +    +A+   G  +     +  M  I             K +  L
Sbjct: 183 AL----ELLGNFKDKERTTIAQQVKGKKVWIGIKKLLM-LIEMSLQMDPEYRVRKFLALL 237

Query: 274 NE 275
            E
Sbjct: 238 RE 239

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

 Score =  117 bits (293), Expect = 5e-32
 Identities = 24/232 (10%), Positives = 66/232 (28%), Gaps = 16/232 (6%)

Query: 60  RVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI---IDKYIGESARLIRE 116
           +  ++ P   LL G PG+GKT L  AI      N + + +         +        ++
Sbjct: 26  KKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQHPNFDELVKLYEKD 85

Query: 117 MFGYARDHQPCIIFMDEIDAIGGRR--FSEGTSADREIQRTLMELLNQ------LDGFDQ 168
           +  +   +   +                 EGT    ++      +L        +     
Sbjct: 86  VVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATMLQAKGYETKMYVMAV 145

Query: 169 LGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYE 228
                 +    R + +        R   K    +  +     +  +H  G+     +   
Sbjct: 146 PKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLETLHKTGLFSDIRL--- 202

Query: 229 AVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAKKLE 280
              +  + ++  +  ++  +  +         V  ++    + ++ +   L 
Sbjct: 203 YNREGVKLYSSLETPSISPKETLEKEL--NRKVSGKEIQPTLERIEQKMVLN 252

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

 Score =  101 bits (251), Expect = 3e-26
 Identities = 50/243 (20%), Positives = 92/243 (37%), Gaps = 19/243 (7%)

Query: 34  VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN 93
             G     ++LR  +E              +P + +LL+GPPG GKT LA  IA  +  N
Sbjct: 11  YIGQERLKQKLRVYLEAAKARK--------EPLEHLLLFGPPGLGKTTLAHVIAHELGVN 62

Query: 94  FLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSA--DRE 151
               V+S    +  G+ A ++          +  I+F+DEI  +  +       A  D  
Sbjct: 63  L--RVTSGPAIEKPGDLAAILANSLE-----EGDILFIDEIHRLSRQAEEHLYPAMEDFV 115

Query: 152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEI 211
           +   + +         +L +  +I AT RP ++   LL    +   +E   P E ++  +
Sbjct: 116 MDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVM 175

Query: 212 LKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR 271
                 G+    E   E + + + G      + +       A  A  + +  E  ++A+ 
Sbjct: 176 RDARLLGVRITEEAALE-IGRRSRG-TMRVAKRLFRRVRDFAQVAGEEVITRERALEALA 233

Query: 272 KLN 274
            L 
Sbjct: 234 ALG 236

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

 Score =  101 bits (250), Expect = 9e-26
 Identities = 36/261 (13%), Positives = 75/261 (28%), Gaps = 30/261 (11%)

Query: 36  GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----D 91
               Q+++L   +   L NP               L G PGTGKT+  R +         
Sbjct: 20  HREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTT 72

Query: 92  ANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADRE 151
           A F+ +      +               + R       F+  +      R         +
Sbjct: 73  ARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDD 132

Query: 152 IQR------TLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPN- 204
                    +    L Q        ++ +++  +   VL+        +  K  I     
Sbjct: 133 AFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPY 192

Query: 205 -EQSRMEILKIHAAGIAKHGEIDYEAVVKLAE---GFNGADL--------RNVCTEAGMS 252
            +    +IL   A      G    + +  +A+        D          ++   +  +
Sbjct: 193 TKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYA 252

Query: 253 AIRAERDYVIHEDFMKAVRKL 273
           A +  R ++  ED  K+ +++
Sbjct: 253 AQQNGRKHIAPEDVRKSSKEV 273

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 85.3 bits (210), Expect = 7e-20
 Identities = 50/273 (18%), Positives = 85/273 (31%), Gaps = 34/273 (12%)

Query: 34  VGGLSDQIRELRESIELPLMNPELF-LRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA 92
           + G +D  R +  ++       +L         PK +L+ GP G GKT +AR +A   +A
Sbjct: 16  IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA 75

Query: 93  NF-------LKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG 145
            F          V     +                    Q  I+F+DEID I  +    G
Sbjct: 76  PFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSG 135

Query: 146 TSADREIQRTLMELLNQLDGFDQLGKVKMIMATN------------RPDVLDPALLRPGR 193
               RE      +LL  ++G     K  M+   +            RP  L P L   GR
Sbjct: 136 ADVSRE--GVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIPELQ--GR 191

Query: 194 LDRKIEIPLPNEQSRMEILKIHAAGIAKH---------GEIDYEAVVKLAEGFNGADLRN 244
           L  ++E+   +      IL    A + +            I +              +  
Sbjct: 192 LPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNE 251

Query: 245 VCTEAGMSAIRAERDYVIHEDFMKAVRKLNEAK 277
                G   +    + ++ +    +   +N   
Sbjct: 252 KTENIGARRLHTVMERLM-DKISFSASDMNGQT 283

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

 Score = 79.4 bits (194), Expect = 8e-18
 Identities = 32/276 (11%), Positives = 74/276 (26%), Gaps = 48/276 (17%)

Query: 36  GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL 95
               +   L       L++      V +         G  G GKT LA+     +     
Sbjct: 20  VRRGEAEALARIYLNRLLSGAGLSDVNM----IYGSIGRVGIGKTTLAKFTVKRVSEAAA 75

Query: 96  KVVSSAIIDKYIGESARLIREMFG---------------------------YARDHQPCI 128
           K   +         +A  +  +                                ++   +
Sbjct: 76  KEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLL 135

Query: 129 IFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPAL 188
           + +DE  ++             E   TL+ +  ++   D + ++  ++  +    L    
Sbjct: 136 VILDEFQSMLSSPRIAA-----EDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMR 190

Query: 189 LRPGRLDRKIE----IPLPNEQSRMEILKIHAAGIAKHGEIDYEA---VVKLAEGFNGA- 240
            +  +++ +I     +P    +    IL+  A    +    +      +  +     G  
Sbjct: 191 EKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVYGEDKGGD 250

Query: 241 ----DLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK 272
                       A   A    RD +  +   KAV +
Sbjct: 251 GSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSE 286

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

 Score = 68.1 bits (165), Expect = 4e-14
 Identities = 46/243 (18%), Positives = 90/243 (37%), Gaps = 20/243 (8%)

Query: 34  VGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN 93
             G  +  ++L  ++E   M  E            VLL GPPG GKT LA  IAS +  N
Sbjct: 11  FIGQENVKKKLSLALEAAKMRGE--------VLDHVLLAGPPGLGKTTLAHIIASELQTN 62

Query: 94  FLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSA--DRE 151
               V+S  +    G+ A ++  +       +  ++F+DEI  +         SA  D +
Sbjct: 63  I--HVTSGPVLVKQGDMAAILTSL------ERGDVLFIDEIHRLNKAVEELLYSAIEDFQ 114

Query: 152 IQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEI 211
           I   + +  +       +    ++ AT R  +L   L     +  +++     ++ +  I
Sbjct: 115 IDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFY-TVKELKEII 173

Query: 212 LKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVR 271
            +  +    +  +   E + K + G        +           + D +  +  +K + 
Sbjct: 174 KRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIRLTKRVRDMLTVVKADRINTDIVLKTME 232

Query: 272 KLN 274
            LN
Sbjct: 233 VLN 235

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 60.2 bits (144), Expect = 3e-11
 Identities = 35/251 (13%), Positives = 76/251 (30%), Gaps = 16/251 (6%)

Query: 30  SYSAVGGLSDQIRELRESIELPLMNPE----LFLRVGIKPPKGVLLYGPPGTGKTLLARA 85
           +   V G    + +L+  +     + +       + G    +  +LYGPPG GKT  A  
Sbjct: 12  NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHL 71

Query: 86  IASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEG 145
           +A  +  + L+  +S +  K +      +      A D+   + +    +          
Sbjct: 72  VAQELGYDILEQNASDVRSKTL------LNAGVKNALDNMSVVGYFKHNEEAQNLNGKHF 125

Query: 146 TSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNE 205
                E+          +    Q  +          +  +   +RP              
Sbjct: 126 VIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRR-- 183

Query: 206 QSRMEILKIHAAGIAKHG-EIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE 264
                I         +   ++D   + +L +   G D+R V     +S I      + HE
Sbjct: 184 PDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG-DIRQVINL--LSTISTTTKTINHE 240

Query: 265 DFMKAVRKLNE 275
           +  +  +   +
Sbjct: 241 NINEISKAWEK 251

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]} Length = 364

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

 Score = 49.1 bits (116), Expect = 2e-07
 Identities = 26/107 (24%), Positives = 48/107 (44%), Gaps = 6/107 (5%)

Query: 65  PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYI------GESARLIREMF 118
               +LL GP G+GKTL+A+ +A ++D       ++++ +             RL++   
Sbjct: 67  SKSNILLIGPTGSGKTLMAQTLAKHLDIPIAISDATSLTEAGYVGEDVENILTRLLQASD 126

Query: 119 GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG 165
              +  Q  I+F+DEID I     +   + D   +     LL  ++G
Sbjct: 127 WNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEG 173

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 443

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

 Score = 46.7 bits (110), Expect = 2e-06
 Identities = 36/160 (22%), Positives = 61/160 (38%), Gaps = 10/160 (6%)

Query: 66  PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQ 125
           PK +L+ GP G GKT +AR +A   +A F+KV   A     +G   + +  +     D  
Sbjct: 49  PKNILMIGPTGVGKTEIARRLAKLANAPFIKV--EATKFTEVGYVGKEVDSIIRDLTDSA 106

Query: 126 PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD 185
             ++   EI      R      A+  I   L+         +Q G+V+   + +      
Sbjct: 107 MKLVRQQEIAK---NRARAEDVAEERILDALLP-----PAKNQWGEVENHDSHSSTRQAF 158

Query: 186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI 225
              LR G+LD K      +    M +  +   G+ +    
Sbjct: 159 RKKLREGQLDDKEIEIDVSAGVSMGVEIMAPPGMEEMTNQ 198

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 44.7 bits (104), Expect = 5e-06
 Identities = 11/98 (11%), Positives = 33/98 (33%), Gaps = 4/98 (4%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIRE----MFGYARDH 124
            L+ G   TGK+ + +   + ++  ++ +      ++        + E    +    +  
Sbjct: 32  TLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRL 91

Query: 125 QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQ 162
              +  +  I  I         + +R+ + +   LL  
Sbjct: 92  PSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLES 129

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]} Length = 198

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 42.4 bits (99), Expect = 2e-05
 Identities = 30/211 (14%), Positives = 68/211 (32%), Gaps = 40/211 (18%)

Query: 39  DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVV 98
           DQ+  L+  IE                   +L+ G   +    ++  +   ++    K  
Sbjct: 1   DQLETLKRIIEK-------------SEGISILINGEDLSYPREVSLELPEYVEKFPPKAS 47

Query: 99  SSAIID---KYIG-ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQR 154
               ID   + IG +  R I++   Y+ +       +            +     ++   
Sbjct: 48  DVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVI----------VHDCERMTQQAAN 97

Query: 155 TLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKI 214
             ++ L +   +       +++ T R   L P +    R+  ++ + +P E   +   KI
Sbjct: 98  AFLKALEEPPEYAV-----IVLNTRRWHYLLPTIK--SRV-FRVVVNVPKEFRDLVKEKI 149

Query: 215 -----HAAGIAKHGEIDYEAVVKLAEGFNGA 240
                    + +  +   EA    AE  +G 
Sbjct: 150 GDLWEELPLLERDFKTALEAYKLGAEKLSGL 180

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 268

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 44/196 (22%), Positives = 72/196 (36%), Gaps = 34/196 (17%)

Query: 64  KPPKGVLLYGPPGTGKTLLARAIASNIDAN------------FLKVVSSAIIDKYIGESA 111
           +     LL G  G GKT +A  +A  I                L + S     KY G+  
Sbjct: 37  RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFE 96

Query: 112 RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGK 171
           +  + +          I+F+DEI  I G   + G   D           N +      GK
Sbjct: 97  KRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVD---------AANLIKPLLSSGK 147

Query: 172 VKMIMATNRPDVL-----DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEID 226
           +++I +T   +       D AL    R  +KI+I  P+ +  ++I+         H ++ 
Sbjct: 148 IRVIGSTTYQEFSNIFEKDRAL---ARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVR 204

Query: 227 Y-----EAVVKLAEGF 237
           Y      A V+LA  +
Sbjct: 205 YTAKAVRAAVELAVKY 220

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]} Length = 333

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

 Score = 42.2 bits (98), Expect = 4e-05
 Identities = 21/115 (18%), Positives = 43/115 (37%), Gaps = 14/115 (12%)

Query: 68  GVLLYGPPGTGKTLLARAIA--------------SNIDANFLKVVSSAIIDKYIGESARL 113
           GVL++G  GTGK+   RA+A              S+ +   +   ++ +    I +   +
Sbjct: 30  GVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTPV 89

Query: 114 IREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ 168
           +    G + D     + ++   + G + F  G  A        ++  N L+    
Sbjct: 90  VDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHIV 144

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 247

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 41.4 bits (97), Expect = 5e-05
 Identities = 42/204 (20%), Positives = 73/204 (35%), Gaps = 58/204 (28%)

Query: 36  GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL 95
             S +++E+ E I+          ++       VL+ G  G GK ++AR I    D +  
Sbjct: 4   FESPKMKEILEKIK----------KIS-CAECPVLITGESGVGKEVVARLIHKLSDRSKE 52

Query: 96  KVVSSAIIDKYIGESARLIREMFGYARDHQP---------------CIIFMDEIDAIGGR 140
             V    ++           E+FGY +                     +F+DEI  +   
Sbjct: 53  PFV---ALNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGEL--- 106

Query: 141 RFSEGTSADREIQRTLMELLNQLDGFDQLG-------KVKMIMATNRPDVLDPALLRPGR 193
                     E Q  L+ ++ +   F +LG        V+++ ATNR       L++ G+
Sbjct: 107 --------SLEAQAKLLRVI-ESGKFYRLGGRKEIEVNVRILAATNRN---IKELVKEGK 154

Query: 194 LDRK-------IEIPLPNEQSRME 210
                      IEI +P  + R E
Sbjct: 155 FREDLYYRLGVIEIEIPPLRERKE 178

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 40.5 bits (94), Expect = 1e-04
 Identities = 34/195 (17%), Positives = 64/195 (32%), Gaps = 40/195 (20%)

Query: 64  KPPKGVLLYGPPGTGKTLLARAIASNIDA-------------NFLKVVSSAIIDKYIGES 110
           +     L  G  G GKT +AR +A  ++              N  ++     +D    ++
Sbjct: 32  RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDA 91

Query: 111 ARL-----IREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLN 161
           A        R++    +      +  +  +DE+  +            R     L++ L 
Sbjct: 92  ASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHML-----------SRHSFNALLKTLE 140

Query: 162 QLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAK 221
                +    VK ++AT  P  L   +L      +     L  EQ R ++  I       
Sbjct: 141 -----EPPEHVKFLLATTDPQKLPVTILSRCL--QFHLKALDVEQIRHQLEHILNEEHIA 193

Query: 222 HGEIDYEAVVKLAEG 236
           H     + + + AEG
Sbjct: 194 HEPRALQLLARAAEG 208

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 195

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

 Score = 39.5 bits (92), Expect = 2e-04
 Identities = 39/171 (22%), Positives = 67/171 (39%), Gaps = 31/171 (18%)

Query: 61  VGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVSSAII--DKYIG 108
           +  +     +L G PG GKT +   +A  I              L +   A++   KY G
Sbjct: 38  LQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRG 97

Query: 109 E-SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD 167
           E   RL   +   A+     I+F+DE+  + G   ++G           M+  N L    
Sbjct: 98  EFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGA----------MDAGNMLKPAL 147

Query: 168 QLGKVKMIMATNRPDVL-----DPALLRPGRLDRKIEIPLPNEQSRMEILK 213
             G++  + AT   +       D AL R  R  +K+ +  P+ +  + IL+
Sbjct: 148 ARGELHCVGATTLDEYRQYIEKDAALER--RF-QKVFVAEPSVEDTIAILR 195

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 387

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

 Score = 40.0 bits (93), Expect = 2e-04
 Identities = 38/187 (20%), Positives = 67/187 (35%), Gaps = 34/187 (18%)

Query: 69  VLLYGPPGTGKTLLARAIASNI----------DANFLKVVSSAIIDKYIGE---SARLIR 115
            +L G PG GKT +   +A  I              + +   +++           RL  
Sbjct: 46  PVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKA 105

Query: 116 EMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMI 175
            +    +     I+F+DE+  + G   +EG           ++  N L      G++++I
Sbjct: 106 VIQEVVQSQGEVILFIDELHTVVGAGKAEGA----------VDAGNMLKPALARGELRLI 155

Query: 176 MATNRPDVL-----DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH--GEIDYE 228
            AT   D       DPAL R  R  + + +  P  +  + IL+        H    I   
Sbjct: 156 GATT-LDEYREIEKDPALER--RF-QPVYVDEPTVEETISILRGLKEKYEVHHGVRISDS 211

Query: 229 AVVKLAE 235
           A++  A 
Sbjct: 212 AIIAAAT 218

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]} Length = 170

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

 Score = 38.4 bits (88), Expect = 3e-04
 Identities = 13/132 (9%), Positives = 30/132 (22%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCI 128
           +      GTGKT L + +   + A  ++          +                    I
Sbjct: 5   LAFAAWSGTGKTTLLKKLIPALCARGIRPGLIKHTHHDMDVDKPGKDSYELRKAGAAQTI 64

Query: 129 IFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPAL 188
           +   +  A+      E     + +   +      L   +     ++       D      
Sbjct: 65  VASQQRWALMTETPDEEELDLQFLASRMDTSKLDLILVEGFKHEEIAKIVLFRDGAGHRP 124

Query: 189 LRPGRLDRKIEI 200
                    I +
Sbjct: 125 EELVIDRHVIAV 136

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

 Score = 38.2 bits (87), Expect = 5e-04
 Identities = 29/187 (15%), Positives = 55/187 (29%), Gaps = 26/187 (13%)

Query: 64  KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR- 122
           +    +L+   PG G   L  A++  +     +   S    +            +     
Sbjct: 22  RGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAP 81

Query: 123 ----------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKV 172
                       +     ++E   +GG +    T A          LL  L+      + 
Sbjct: 82  EKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPA--ET 139

Query: 173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEA--- 229
              +AT  P+ L   L    RL     +  P EQ  +  L        +   +  +A   
Sbjct: 140 WFFLATREPERLLATLRSRCRL---HYLAPPPEQYAVTWLS-------REVTMSQDALLA 189

Query: 230 VVKLAEG 236
            ++L+ G
Sbjct: 190 ALRLSAG 196

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]} Length = 192

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

 Score = 37.4 bits (85), Expect = 7e-04
 Identities = 8/69 (11%), Positives = 22/69 (31%)

Query: 67  KGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQP 126
           K V + G   +GK++L   +A+  +           + + +G   + ++           
Sbjct: 8   KTVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREFVFEKLGGDEQAMQYSDYPQMALGH 67

Query: 127 CIIFMDEID 135
                  + 
Sbjct: 68  QRYIDYAVR 76

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]} Length = 189

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.5 bits (83), Expect = 0.001
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVV 98
          + V L GPPG GKT L    +  + ++ + V 
Sbjct: 2  RHVFLTGPPGVGKTTLIHKASEVLKSSGVPVD 33

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]} Length = 198

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 36.3 bits (82), Expect = 0.002
 Identities = 9/66 (13%), Positives = 21/66 (31%)

Query: 69  VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCI 128
           + + G   +GKT LA  ++  +    + V    + D  +  + R       +   +    
Sbjct: 25  LGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMDDHIVERAKRYHTGNEEWFEYYYLQW 84

Query: 129 IFMDEI 134
                 
Sbjct: 85  DVEWLT 90

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]} Length = 183

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

 Score = 35.5 bits (80), Expect = 0.003
 Identities = 13/75 (17%), Positives = 25/75 (33%), Gaps = 5/75 (6%)

Query: 64  KPPKG--VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID---KYIGESARLIREMF 118
           +  +G  + L G   +GK  +ARA+   ++    + VS  + D     +       RE  
Sbjct: 2   RATQGFTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGDTVRHELSSELGFTREDR 61

Query: 119 GYARDHQPCIIFMDE 133
                    +     
Sbjct: 62  HTNIQRIAFVATELT 76

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]} Length = 242

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.9 bits (81), Expect = 0.003
 Identities = 11/75 (14%), Positives = 22/75 (29%)

Query: 59  LRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMF 118
           L+ GI+      ++G   TGKT +   +A        +            E       + 
Sbjct: 16  LQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLL 75

Query: 119 GYARDHQPCIIFMDE 133
             A  +      + +
Sbjct: 76  AVAERYGLSGSDVLD 90

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]} Length = 174

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

 Score = 35.0 bits (79), Expect = 0.004
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 4/76 (5%)

Query: 64  KPPKG--VLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYA 121
           + PKG  +L+ G PGTGKT +A  IA+ +  +  + +    + K          E+  + 
Sbjct: 1   EQPKGINILITGTPGTGKTSMAEMIAAEL--DGFQHLEVGKLVKENHFYTEYDTELDTHI 58

Query: 122 RDHQPCIIFMDEIDAI 137
            + +     +D ++ I
Sbjct: 59  IEEKDEDRLLDFMEPI 74

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	292
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.93
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.92
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.89
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.89
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.89
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.88
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.85
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.85
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.84
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.83
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.83
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.82
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.79
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.79
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.78
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.74
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.72
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.69
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.68
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.64
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.6
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.57
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.55
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.49
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.43
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.43
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.39
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.24
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.82
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.81
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.66
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	98.37
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	98.32
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	98.31
d1g2912	240	Maltose transport protein MalK, N-terminal domain	98.31
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.3
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	98.27
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	98.25
d2awna2	232	Maltose transport protein MalK, N-terminal domain	98.25
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	98.23
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	98.23
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.22
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	98.21
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	98.21
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	98.18
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	98.17
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	98.17
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	98.16
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	98.15
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	98.13
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	98.13
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	98.11
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	98.11
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	98.11
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	98.1
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	98.1
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.1
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	98.05
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	98.03
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	98.01
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	98.0
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	97.99
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.99
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.98
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.98
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	97.97
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.96
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.95
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.95
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.94
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.94
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	97.92
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	97.91
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.88
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.87
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	97.86
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.85
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.85
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.84
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.84
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	97.83
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.79
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.79
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.77
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.77
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.77
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	97.75
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.74
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	97.73
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.71
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.71
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	97.7
d1okkd2	207	GTPase domain of the signal recognition particle r	97.69
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.68
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.68
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	97.65
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.63
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.61
d1ls1a2	207	GTPase domain of the signal sequence recognition p	97.59
d1j8yf2	211	GTPase domain of the signal sequence recognition p	97.57
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	97.52
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.52
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	97.52
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	97.51
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	97.44
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	97.43
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	97.41
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	97.39
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	97.37
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	97.37
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	97.36
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.31
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	97.27
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	97.26
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	97.22
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	97.16
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	97.11
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	97.1
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	97.06
d2fh5b1	207	Signal recognition particle receptor beta-subunit	97.04
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	97.01
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.96
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	96.93
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.92
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	96.89
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	96.84
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	96.83
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.83
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	96.79
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	96.78
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.72
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	96.68
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.68
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.66
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	96.62
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	96.58
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	96.58
d1nrjb_	209	Signal recognition particle receptor beta-subunit	96.54
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	96.49
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	96.46
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	96.45
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	96.42
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	96.41
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	96.4
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	96.37
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	96.35
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.3
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	96.28
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	96.28
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	96.26
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.16
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	96.15
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	96.13
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.12
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	96.08
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.07
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	96.02
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.0
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	95.98
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	95.95
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	95.94
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	95.92
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	95.92
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	95.92
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.9
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	95.9
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	95.9
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	95.86
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	95.81
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.81
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.79
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	95.74
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	95.72
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	95.67
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	95.66
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	95.65
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.65
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.57
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	95.57
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	95.51
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.49
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	95.49
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	95.49
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.47
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	95.46
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	95.45
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	95.44
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	95.43
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.42
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	95.34
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	95.33
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	95.33
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	95.32
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	95.32
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	95.3
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	95.26
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	95.24
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	95.24
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	95.23
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	95.2
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	95.2
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.19
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	95.17
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	95.06
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	95.04
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	95.03
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	95.02
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	95.02
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	95.02
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	94.96
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	94.95
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	94.87
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	94.86
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	94.86
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	94.83
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	94.83
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	94.83
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	94.82
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.79
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	94.79
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.76
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	94.74
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	94.72
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	94.67
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	94.62
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	94.48
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	94.46
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	94.43
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	94.34
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	94.33
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	94.33
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	94.22
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	94.15
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	94.15
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	93.83
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	93.76
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	93.71
d1xpua3	289	Transcription termination factor Rho, ATPase domai	93.51
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	93.45
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	93.37
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	93.34
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	93.28
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	93.2
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	93.18
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	93.11
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	92.89
d1d2ea3	196	Elongation factor Tu (EF-Tu), N-terminal (G) domai	92.82
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	92.77
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	92.54
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	92.39
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	92.34
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	92.32
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	92.22
d1lkxa_	684	Myosin S1, motor domain {Dictyostelium discoideum,	92.15
d1br2a2	710	Myosin S1, motor domain {Chicken (Gallus gallus),	92.08
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	92.08
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	91.78
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	91.73
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	91.61
d2mysa2	794	Myosin S1, motor domain {Chicken (Gallus gallus),	91.4
d1d0xa2	712	Myosin S1, motor domain {Dictyostelium discoideum	91.36
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	91.22
d1w7ja2	730	Myosin S1, motor domain {Chicken (Gallus gallus),	90.74
d1kk8a2	789	Myosin S1, motor domain {Bay scallop (Aequipecten	90.41
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	90.33
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	89.85
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	89.75
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	89.66
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	89.48
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	89.42
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	89.42
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	89.38
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	89.34
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	89.25
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	88.64
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	88.29
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	87.86
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	87.84
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	87.77
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	87.55
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	86.98
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	86.78
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	85.31
d2huec1	82	Histone H4 {African clawed frog (Xenopus laevis) [	85.25
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	84.87
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	84.83
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	84.69
d1htaa_	68	Archaeal histone {Archaeon Methanothermus fervidus	84.18
d1zunb3	222	Sulfate adenylate transferase subunit cysN/C, EF-T	83.54
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	82.6
d1jnya3	224	Elongation factor eEF-1alpha, N-terminal (G) domai	81.97
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	81.71
d1puja_	273	Probable GTPase YlqF {Bacillus subtilis [TaxId: 14	80.94
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	80.7
d1ni3a1	296	YchF GTP-binding protein N-terminal domain {Fissio	80.47
d2qn6a3	205	Initiation factor eIF2 gamma subunit, N-terminal (	80.46
d1f60a3	239	Elongation factor eEF-1alpha, N-terminal (G) domai	80.3

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=7.2e-45  Score=303.01  Aligned_cols=245  Identities=42%  Similarity=0.717  Sum_probs=221.7

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      .+|+++|++|+|+++++++|.+.+.. +..+..+.++|...++++||+||||||||++|+++|++++.+++.+++..+.+
T Consensus         2 ~~p~~~~~di~G~~~~k~~l~~~i~~-l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~   80 (247)
T d1ixza_           2 EAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVE   80 (247)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHH
T ss_pred             CCCCCcHHHHccHHHHHHHHHHHHHH-HHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhh
Confidence            57889999999999999999998765 78888899999999999999999999999999999999999999999999999


Q ss_pred             cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          105 KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      .+.|.+...++.+|..++...|+||+|||+|.++.++.+.....+......+..++..++++..+.+++||+|||.++.+
T Consensus        81 ~~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tTn~~~~l  160 (247)
T d1ixza_          81 MFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDIL  160 (247)
T ss_dssp             SCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEESCGGGS
T ss_pred             ccccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCcccc
Confidence            99999999999999999999999999999999998776665555666777788888888887777899999999999999


Q ss_pred             ChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHH
Q 022768          185 DPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHE  264 (292)
Q Consensus       185 ~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~  264 (292)
                      ++++++++||+..++|++|+.++|.+||+.++.......+.+++.++..+.||+++||..+|+.|...|.+++...|+.+
T Consensus       161 d~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv~~A~l~a~~~~~~~i~~~  240 (247)
T d1ixza_         161 DPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKITMK  240 (247)
T ss_dssp             CGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSBCHH
T ss_pred             CHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHcCCCCcCHH
Confidence            99999888999999999999999999999999988888889999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q 022768          265 DFMKAV  270 (292)
Q Consensus       265 ~~~~a~  270 (292)
                      |+.+|+
T Consensus       241 d~~~A~  246 (247)
T d1ixza_         241 DLEEAA  246 (247)
T ss_dssp             HHHHHT
T ss_pred             HHHHhh
Confidence            999986

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=1.2e-44  Score=302.80  Aligned_cols=252  Identities=41%  Similarity=0.684  Sum_probs=227.2

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      +.++.+.++|+|++|+++++++|.+.+.. +.....+.++|...++++||+||||||||++++++|++++.+++.+++..
T Consensus         2 ~~~~~~~~t~~Di~Gl~~~k~~l~e~v~~-~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~   80 (256)
T d1lv7a_           2 LTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSD   80 (256)
T ss_dssp             EEECSSCCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCS
T ss_pred             CCCCCCCCCHHHHhchHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHH
Confidence            45778899999999999999999998765 67778889999999999999999999999999999999999999999999


Q ss_pred             hhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          102 IIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       102 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      +.+.+.|+++..++.+|..++...|+||+|||+|.++..++.............+..++..++......++++|+|||.+
T Consensus        81 l~~~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatTn~~  160 (256)
T d1lv7a_          81 FVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRP  160 (256)
T ss_dssp             STTSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEESCT
T ss_pred             hhhcchhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeCCCc
Confidence            99999999999999999999999999999999999988776655555555666777888888877777889999999999


Q ss_pred             CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcc
Q 022768          182 DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYV  261 (292)
Q Consensus       182 ~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i  261 (292)
                      +.+++++++++||+..+.+++|+.++|.+||+.++.+.....+.++..++..+.||+++||..++++|...|..+++..|
T Consensus       161 ~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~~A~~~a~~~~~~~i  240 (256)
T d1lv7a_         161 DVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVV  240 (256)
T ss_dssp             TTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHTTCSSB
T ss_pred             ccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHcCCCcc
Confidence            99999999989999999999999999999999999988888889999999999999999999999999999999888899


Q ss_pred             cHHHHHHHHHHHh
Q 022768          262 IHEDFMKAVRKLN  274 (292)
Q Consensus       262 ~~~~~~~a~~~~~  274 (292)
                      +.+|+.+|++++.
T Consensus       241 ~~~d~~~Al~rv~  253 (256)
T d1lv7a_         241 SMVEFEKAKDKIM  253 (256)
T ss_dssp             CHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHh
Confidence            9999999998864

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=3.2e-41  Score=283.55  Aligned_cols=240  Identities=43%  Similarity=0.746  Sum_probs=215.2

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccC
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIG  108 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~  108 (292)
                      ++|++|+|+++++++|++.+..++.+++.+.++|+.+++++||+||||||||++++++|++++.+++.+++..+.+.+.+
T Consensus         1 ~~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~~l~~~~~g   80 (258)
T d1e32a2           1 VGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG   80 (258)
T ss_dssp             CCGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHHHHTTSCTT
T ss_pred             CChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEEEEEchhhcccccc
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhh
Q 022768          109 ESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPAL  188 (292)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l  188 (292)
                      .....++.+|..+....|+||+|||+|.++.++.....+...   ..+..++..+.......++++|+|||.++.+++++
T Consensus        81 ~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~---~~~~~~~~~~~~~~~~~~vlvi~tTn~~~~ld~al  157 (258)
T d1e32a2          81 ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVER---RIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPAL  157 (258)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHH---HHHHHHHHHHHTCCCSSCEEEEEEESCGGGSCGGG
T ss_pred             cHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHH---HHHHHhccccccccccCCccEEEeCCCccccchhh
Confidence            999999999999999999999999999998776554433333   34444555555666777899999999999999999


Q ss_pred             cCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC----------
Q 022768          189 LRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER----------  258 (292)
Q Consensus       189 ~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~----------  258 (292)
                      ++++||+..+++++|+.++|.+||+.++.......+.+++.++..+.||+++||..+|++|...|.++..          
T Consensus       158 ~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv~~A~~~a~~~~~~~~~~~~~~~  237 (258)
T d1e32a2         158 RRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETI  237 (258)
T ss_dssp             TSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHHHHHHHHHHHHCCCSSCC
T ss_pred             hhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHHHHHHHHHHHhhccccchhhhhh
Confidence            9999999999999999999999999999988878888999999999999999999999999998877642          


Q ss_pred             -------CcccHHHHHHHHH
Q 022768          259 -------DYVIHEDFMKAVR  271 (292)
Q Consensus       259 -------~~i~~~~~~~a~~  271 (292)
                             ..|+++|+..|++
T Consensus       238 ~~~~~~~~~it~~Df~~AL~  257 (258)
T d1e32a2         238 DAEVMNSLAVTMDDFRWALS  257 (258)
T ss_dssp             BHHHHHHCCBCHHHHHHHHT
T ss_pred             hhhhhccCccCHHHHHHHhC
Confidence                   2488889988875

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=7.7e-41  Score=282.01  Aligned_cols=233  Identities=42%  Similarity=0.764  Sum_probs=206.2

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK  105 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~  105 (292)
                      .|..+|++++|+++++++|.+.+..++.+.+.+.++|+.+++++||+||||||||++++++|.+++.+++.+++..+.+.
T Consensus         1 ~p~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l~~~   80 (265)
T d1r7ra3           1 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTM   80 (265)
T ss_dssp             CCCCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHHHTS
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHhhhc
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCC
Q 022768          106 YIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLD  185 (292)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~  185 (292)
                      +.+.....++.+|..++...|+||+|||+|.++.+++....+........+..++..++.+....++++|+|||.++.++
T Consensus        81 ~~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld  160 (265)
T d1r7ra3          81 WFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIID  160 (265)
T ss_dssp             CTTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEECCBSCTTTS
T ss_pred             cccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEeCCCchhCC
Confidence            99999999999999999999999999999999987665555555666667777888887776777899999999999999


Q ss_pred             hhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcC
Q 022768          186 PALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAER  258 (292)
Q Consensus       186 ~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~  258 (292)
                      +++++++||+.++++++|+.++|.+||+.++.......+++++.++..+.||+++||..+|++|...|.++..
T Consensus       161 ~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv~~A~~~A~~~~~  233 (265)
T d1r7ra3         161 PAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESI  233 (265)
T ss_dssp             CGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999989999999999999999999999999887777888999999999999999999999999999987643

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.93  E-value=8.5e-25  Score=180.82  Aligned_cols=219  Identities=20%  Similarity=0.246  Sum_probs=166.6

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK  105 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~  105 (292)
                      .+|.+|++++|++++++.|..++......        -...+++||+||||||||++|+.+|++++.++..++...... 
T Consensus         3 ~RP~~~~divGqe~~~~~l~~~i~~~~~~--------~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~-   73 (238)
T d1in4a2           3 LRPKSLDEFIGQENVKKKLSLALEAAKMR--------GEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVK-   73 (238)
T ss_dssp             TSCSSGGGCCSCHHHHHHHHHHHHHHHHH--------TCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCS-
T ss_pred             CCCCcHHHcCChHHHHHHHHHHHHHHHhc--------CCCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCccccc-
Confidence            46779999999999999999998653111        234568999999999999999999999999999888766532 


Q ss_pred             ccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC-------------CCCCCe
Q 022768          106 YIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF-------------DQLGKV  172 (292)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~-------------~~~~~~  172 (292)
                           ...+...+..  ....+++++||+|.+           ....+..+...+......             ....++
T Consensus        74 -----~~~~~~~~~~--~~~~~~~~ide~~~~-----------~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (238)
T d1in4a2          74 -----QGDMAAILTS--LERGDVLFIDEIHRL-----------NKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPF  135 (238)
T ss_dssp             -----HHHHHHHHHH--CCTTCEEEEETGGGC-----------CHHHHHHHHHHHHTSCCCC---------------CCC
T ss_pred             -----HHHHHHHHHh--hccCCchHHHHHHHh-----------hhHHHhhcccceeeeeeeeeecCcccccccccCCCCe
Confidence                 1223333332  234579999999998           556666666655542110             122478


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHH
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGM  251 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~  251 (292)
                      ++|++|+.+..+++.+++  ||...+.++.|+.+++..+++......... .+..+..++..+.| +.+.+..+++.+..
T Consensus       136 ~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~g-d~R~ai~~l~~~~~  212 (238)
T d1in4a2         136 TLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIRLTKRVRD  212 (238)
T ss_dssp             EEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHHHHHHHHHHHHH
T ss_pred             EEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCC-CHHHHHHHHHHHHH
Confidence            899999999999999998  998999999999999999999887654433 22236677777776 88888888988888


Q ss_pred             HHHHhcCCcccHHHHHHHHHHHh
Q 022768          252 SAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       252 ~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      .+...+...||.+++.+++..+.
T Consensus       213 ~~~~~~~~~it~~~~~~al~~l~  235 (238)
T d1in4a2         213 MLTVVKADRINTDIVLKTMEVLN  235 (238)
T ss_dssp             HHHHHTCSSBCHHHHHHHHHHHT
T ss_pred             HHHHhcCCccCHHHHHHHHHhhC
Confidence            88788888899999999998764

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=99.92  E-value=8e-24  Score=175.03  Aligned_cols=220  Identities=21%  Similarity=0.257  Sum_probs=163.3

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK  105 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~  105 (292)
                      .+|.+|++++|+++++++|..++......        ..+..++||+||||+|||++|+++|++++.++..++.......
T Consensus         3 ~RP~~~ddivGq~~~~~~L~~~i~~~~~~--------~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~   74 (239)
T d1ixsb2           3 LRPKTLDEYIGQERLKQKLRVYLEAAKAR--------KEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKP   74 (239)
T ss_dssp             CCCCSGGGSCSCHHHHHHHHHHHHHHTTS--------SSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSH
T ss_pred             cCCCCHHHhCCHHHHHHHHHHHHHHHHhc--------CCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccc
Confidence            36889999999999999999998764221        2345689999999999999999999999999999887665321


Q ss_pred             ccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh-------------CCCCCCCe
Q 022768          106 YIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD-------------GFDQLGKV  172 (292)
Q Consensus       106 ~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-------------~~~~~~~~  172 (292)
                        +.    ......... ...++++|||+|.+           ....+..+...+....             .....+++
T Consensus        75 --~~----~~~~~~~~~-~~~~i~~iDe~~~~-----------~~~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~  136 (239)
T d1ixsb2          75 --GD----LAAILANSL-EEGDILFIDEIHRL-----------SRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRF  136 (239)
T ss_dssp             --HH----HHHHHHTTC-CTTCEEEEETGGGC-----------CHHHHHHHHHHHHHSEEEEECSCTTCCCEEEEECCCC
T ss_pred             --hh----hHHHHHhhc-cCCCeeeeeccccc-----------chhHHHhhhhhhhhhhhhhhhccchhhhhcccCCCCE
Confidence              11    111111121 23469999999998           5666677766665321             00123467


Q ss_pred             EEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCC-CCCHHHHHHHcCCCCHHHHHHHHHHHHH
Q 022768          173 KMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHG-EIDYEAVVKLAEGFNGADLRNVCTEAGM  251 (292)
Q Consensus       173 ~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~-~~~~~~l~~~~~g~~~~di~~l~~~a~~  251 (292)
                      .++++++.+.......++  ++...+.+..|+.+++..+++..+....... .-.++.++..+.| ..|.+..+++.+..
T Consensus       137 ~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~g-d~R~a~~~l~~~~~  213 (239)
T d1ixsb2         137 TLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG-TMRVAKRLFRRVRD  213 (239)
T ss_dssp             EEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTS-SHHHHHHHHHHHHH
T ss_pred             EEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCC-CHHHHHHHHHHHHH
Confidence            788888888776666666  6778899999999999999998877554332 2245667788887 78888888888888


Q ss_pred             HHHHhcCCcccHHHHHHHHHHHh
Q 022768          252 SAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       252 ~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                      +|...+...||.+++.+++..+.
T Consensus       214 ~a~~~~~~~It~~~~~~~l~~l~  236 (239)
T d1ixsb2         214 FAQVAGEEVITRERALEALAALG  236 (239)
T ss_dssp             HHTTSCCSCBCHHHHHHHHHHHT
T ss_pred             HHHHhCCCCcCHHHHHHHHhhhC
Confidence            88777888899999999997654

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.89  E-value=2.8e-22  Score=165.60  Aligned_cols=207  Identities=17%  Similarity=0.246  Sum_probs=150.9

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc--------
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN--------   93 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~--------   93 (292)
                      +++++.|.+|++++|++++++.|..++...            ..++.+||+||||+|||++|+.+++.++..        
T Consensus         2 ~~~KyrP~~~~dlig~~~~~~~L~~~i~~~------------~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~   69 (239)
T d1njfa_           2 LARKWRPQTFADVVGQEHVLTALANGLSLG------------RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPC   69 (239)
T ss_dssp             HHHHTCCSSGGGSCSCHHHHHHHHHHHHTT------------CCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCC
T ss_pred             chhhhCCCCHHHccChHHHHHHHHHHHHcC------------CCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCcc
Confidence            467899999999999999999999988652            345679999999999999999999987432        


Q ss_pred             ----------------EEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcccccccCCcCCCCCcchHHHH
Q 022768           94 ----------------FLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDEIDAIGGRRFSEGTSADREIQ  153 (292)
Q Consensus        94 ----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~  153 (292)
                                      ++.++....      .....++.+......    ....+++|||+|.+           ....+
T Consensus        70 ~~~~~~~~i~~~~~~~~~~~~~~~~------~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l-----------~~~~q  132 (239)
T d1njfa_          70 GVCDNCREIEQGRFVDLIEIDAASR------TKVEDTRDLLDNVQYAPARGRFKVYLIDEVHML-----------SRHSF  132 (239)
T ss_dssp             SCSHHHHHHHHTCCTTEEEEETTCS------SSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGS-----------CHHHH
T ss_pred             ccchHHHHHHcCCCCeEEEecchhc------CCHHHHHHHHHHHHhccccCCCEEEEEECcccC-----------CHHHH
Confidence                            334433221      112334444444322    23469999999999           67777


Q ss_pred             HHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHH
Q 022768          154 RTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVK  232 (292)
Q Consensus       154 ~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~  232 (292)
                      ..|...++.     +..++.+|++||.++.+.+++++  || ..+.+++|+.++...++...+...... .+..++.++.
T Consensus       133 ~~Llk~lE~-----~~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~  204 (239)
T d1njfa_         133 NALLKTLEE-----PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLAR  204 (239)
T ss_dssp             HHHHHHHHS-----CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHH
T ss_pred             HHHHHHHhc-----CCCCeEEEEEcCCccccChhHhh--hh-cccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHH
Confidence            777777653     34578899999999999999999  77 789999999999998888776543322 2234566777


Q ss_pred             HcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHH
Q 022768          233 LAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       233 ~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~  270 (292)
                      .+.| +.|.+..+++.    +...+...|+.+++.+++
T Consensus       205 ~s~G-d~R~ain~l~~----~~~~~~~~I~~~~v~~~l  237 (239)
T d1njfa_         205 AAEG-SLRDALSLTDQ----AIASGDGQVSTQAVSAML  237 (239)
T ss_dssp             HTTT-CHHHHHHHHHH----HHHHTTTSBCHHHHHHHH
T ss_pred             HcCC-CHHHHHHHHHH----HHHhCCCCcCHHHHHHHh
Confidence            7776 55555555544    345566789999998876

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=99.89  E-value=2.7e-23  Score=172.00  Aligned_cols=199  Identities=20%  Similarity=0.245  Sum_probs=132.3

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccC
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIG  108 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~  108 (292)
                      +=.+.++|..+.++.+..-+..+....   ......+.+++||+||||||||++|+++|++++.+++.+++.+....+.+
T Consensus         6 ~~~~~~i~~~~~i~~i~~~~~~~~~~~---~~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~   82 (246)
T d1d2na_           6 YIMNGIIKWGDPVTRVLDDGELLVQQT---KNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSE   82 (246)
T ss_dssp             TCTTCCCCCSHHHHHHHHHHHHHHHHH---HHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCH
T ss_pred             hhccCCcCcCHHHHHHHHHHHHHHHHH---hccCCCCCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccc
Confidence            334668888777777766665443221   12223457789999999999999999999999999999998776544443


Q ss_pred             h-HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC-CCCeEEEEEeCCCCCCCh
Q 022768          109 E-SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ-LGKVKMIMATNRPDVLDP  186 (292)
Q Consensus       109 ~-~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~-~~~~~vi~t~~~~~~l~~  186 (292)
                      . ....++.+|..+....|+||||||+|.++.....+.. ....   .+..++..++.... ..+++||+|||.++.+++
T Consensus        83 ~~~~~~i~~if~~A~~~~p~il~iDEid~l~~~~~~~~~-~~~~---~~~~ll~~l~~~~~~~~~v~vi~tTn~~~~ld~  158 (246)
T d1d2na_          83 TAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPR-FSNL---VLQALLVLLKKAPPQGRKLLIIGTTSRKDVLQE  158 (246)
T ss_dssp             HHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTB-CCHH---HHHHHHHHTTCCCSTTCEEEEEEEESCHHHHHH
T ss_pred             cchhhhhhhhhhhhhhcccceeehhhhhhHhhhcccccc-hhHH---HHHHHHHHhcCCCccccceeeeeccCChhhccc
Confidence            3 3467889999999999999999999999765533222 2232   33344445544332 336889999999888876


Q ss_pred             hhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCC
Q 022768          187 ALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFN  238 (292)
Q Consensus       187 ~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~  238 (292)
                      ..+. .||...+++|.++  +|.++++.... .......+...++..+.|.+
T Consensus       159 ~~~~-~rF~~~i~~P~~~--~r~~il~~l~~-~~~~~~~~~~~i~~~~~g~~  206 (246)
T d1d2na_         159 MEML-NAFSTTIHVPNIA--TGEQLLEALEL-LGNFKDKERTTIAQQVKGKK  206 (246)
T ss_dssp             TTCT-TTSSEEEECCCEE--EHHHHHHHHHH-HTCSCHHHHHHHHHHHTTSE
T ss_pred             hhhc-CccceEEecCCch--hHHHHHHHHHh-ccCCChHHHHHHHHHcCCCc
Confidence            5332 3999988885543  34444443221 11123344566777777653

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.89  E-value=5.3e-23  Score=168.66  Aligned_cols=211  Identities=19%  Similarity=0.224  Sum_probs=147.4

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc-----EEEEe
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN-----FLKVV   98 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~-----~~~~~   98 (292)
                      +.+.|.+|++++|++++++.|..++...             ...++||+||||+|||++++.+|++++..     +...+
T Consensus         6 ekyrP~~~~divg~~~~~~~L~~~i~~~-------------~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~   72 (227)
T d1sxjc2           6 EKYRPETLDEVYGQNEVITTVRKFVDEG-------------KLPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELN   72 (227)
T ss_dssp             HHTCCSSGGGCCSCHHHHHHHHHHHHTT-------------CCCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEEC
T ss_pred             hhhCCCCHHHccCcHHHHHHHHHHHHcC-------------CCCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEec
Confidence            4678999999999999999999998642             23369999999999999999999987533     45555


Q ss_pred             ccchhccccChHHHHHHHHHHH---hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEE
Q 022768           99 SSAIIDKYIGESARLIREMFGY---ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMI  175 (292)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi  175 (292)
                      .....+..   ...........   .......+++|||+|.+           ....+..|...+....     ..+.++
T Consensus        73 ~~~~~~~~---~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~-----------~~~~~~~Ll~~le~~~-----~~~~~~  133 (227)
T d1sxjc2          73 ASDDRGID---VVRNQIKDFASTRQIFSKGFKLIILDEADAM-----------TNAAQNALRRVIERYT-----KNTRFC  133 (227)
T ss_dssp             TTSCCSHH---HHHTHHHHHHHBCCSSSCSCEEEEETTGGGS-----------CHHHHHHHHHHHHHTT-----TTEEEE
T ss_pred             ccccCCee---eeecchhhccccccccCCCeEEEEEeccccc-----------hhhHHHHHHHHhhhcc-----cceeec
Confidence            44432211   01111111111   11133469999999998           6677778887777532     478889


Q ss_pred             EEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHH
Q 022768          176 MATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSAI  254 (292)
Q Consensus       176 ~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~  254 (292)
                      +++|.+..+.+.+++  || ..+.|++|+.++...++...+...... .+..++.++..+.| ..|.+..+++.+...+.
T Consensus       134 ~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~G-d~R~ain~Lq~~~~~~~  209 (227)
T d1sxjc2         134 VLANYAHKLTPALLS--QC-TRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNG-DMRRVLNVLQSCKATLD  209 (227)
T ss_dssp             EEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT-CHHHHHHHTTTTTTTTC
T ss_pred             cccCcHHHhHHHHHH--HH-hhhccccccccccccccccccccccccCCHHHHHHHHHHcCC-cHHHHHHHHHHHHHhcC
Confidence            999999999999998  77 788999999999999999887654433 22235667777776 44444444444333332


Q ss_pred             HhcCCcccHHHHHHHH
Q 022768          255 RAERDYVIHEDFMKAV  270 (292)
Q Consensus       255 ~~~~~~i~~~~~~~a~  270 (292)
                      ......|+.+++.+++
T Consensus       210 ~~~~~~It~~~v~e~~  225 (227)
T d1sxjc2         210 NPDEDEISDDVIYECC  225 (227)
T ss_dssp             SSSCCCBCHHHHHHHT
T ss_pred             CCCCCeeCHHHHHHHh
Confidence            3345679999999875

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=99.88  E-value=4.8e-22  Score=163.32  Aligned_cols=208  Identities=21%  Similarity=0.264  Sum_probs=148.3

Q ss_pred             cccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cEEE
Q 022768           22 LHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NFLK   96 (292)
Q Consensus        22 ~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~~~   96 (292)
                      ..+.+.|.+|++++|++++++.|..++...             ...++||+||||+|||++++.+|+++..     .+++
T Consensus        14 w~~ky~P~~~~diig~~~~~~~l~~~i~~~-------------~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e   80 (231)
T d1iqpa2          14 WVEKYRPQRLDDIVGQEHIVKRLKHYVKTG-------------SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLE   80 (231)
T ss_dssp             HHHHTCCCSTTTCCSCHHHHHHHHHHHHHT-------------CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEE
T ss_pred             HHHHhCCCCHHHccCcHHHHHHHHHHHHcC-------------CCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeE
Confidence            456888999999999999999999998652             3457999999999999999999998743     6777


Q ss_pred             EeccchhccccChHHHHHHHHHHH--hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEE
Q 022768           97 VVSSAIIDKYIGESARLIREMFGY--ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKM  174 (292)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~v  174 (292)
                      +++.+..+..  ............  .....+.++++||+|.+           ....+..+..++....     ..+.+
T Consensus        81 ~n~s~~~~~~--~~~~~~~~~~~~~~~~~~~~~iilide~d~~-----------~~~~~~~ll~~l~~~~-----~~~~~  142 (231)
T d1iqpa2          81 LNASDERGIN--VIREKVKEFARTKPIGGASFKIIFLDEADAL-----------TQDAQQALRRTMEMFS-----SNVRF  142 (231)
T ss_dssp             EETTCHHHHH--TTHHHHHHHHHSCCGGGCSCEEEEEETGGGS-----------CHHHHHHHHHHHHHTT-----TTEEE
T ss_pred             EecCcccchh--HHHHHHHHHHhhhhccCCCceEEeehhhhhc-----------chhHHHHHhhhcccCC-----cceEE
Confidence            7776543211  111111111111  12345689999999998           6666777777776522     47889


Q ss_pred             EEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          175 IMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       175 i~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      |+++|....+.+.+++  |+ ..+.+++|+..+...+++..+...... .+..++.++..+.|    |+|.++...... 
T Consensus       143 i~~~n~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~g----diR~ai~~Lq~~-  214 (231)
T d1iqpa2         143 ILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG----DMRRAINILQAA-  214 (231)
T ss_dssp             EEEESCGGGSCHHHHH--TE-EEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT----CHHHHHHHHHHH-
T ss_pred             EeccCChhhchHhHhC--cc-ccccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC----CHHHHHHHHHHH-
Confidence            9999999999999998  87 779999999999999999888755443 22335667777766    455544433222 


Q ss_pred             HHhcCCcccHHHHHHH
Q 022768          254 IRAERDYVIHEDFMKA  269 (292)
Q Consensus       254 ~~~~~~~i~~~~~~~a  269 (292)
                       ......++.++|.+.
T Consensus       215 -~~~~~~it~e~v~~v  229 (231)
T d1iqpa2         215 -AALDKKITDENVFMV  229 (231)
T ss_dssp             -HTTCSEECHHHHHHH
T ss_pred             -HHcCCCcCHHHHHhh
Confidence             233456888888654

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=5.9e-21  Score=156.02  Aligned_cols=203  Identities=17%  Similarity=0.195  Sum_probs=145.5

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC-----cEEEEe
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA-----NFLKVV   98 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~-----~~~~~~   98 (292)
                      +.+.|.+|++++|++++++.|..++..-             ...++||+||||+|||++|+.++++++.     .+++++
T Consensus         7 eKyrP~~~~d~ig~~~~~~~L~~~~~~~-------------~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n   73 (224)
T d1sxjb2           7 EKYRPQVLSDIVGNKETIDRLQQIAKDG-------------NMPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELN   73 (224)
T ss_dssp             HHTCCSSGGGCCSCTHHHHHHHHHHHSC-------------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEEC
T ss_pred             hHhCCCCHHHhcCCHHHHHHHHHHHHcC-------------CCCeEEEECCCCCCchhhHHHHHHHHhcccccccccccc
Confidence            4789999999999999999999998642             2346999999999999999999998864     366777


Q ss_pred             ccchhccccChHHHHHHHHHHHhh-------hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCC
Q 022768           99 SSAIIDKYIGESARLIREMFGYAR-------DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGK  171 (292)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~  171 (292)
                      ..+..+.      ..+...+....       .....++++||+|.+           ....+..+...+....     ..
T Consensus        74 ~~~~~~~------~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~-----------~~~~~~~ll~~~e~~~-----~~  131 (224)
T d1sxjb2          74 ASDDRGI------DVVRNQIKHFAQKKLHLPPGKHKIVILDEADSM-----------TAGAQQALRRTMELYS-----NS  131 (224)
T ss_dssp             TTSCCSH------HHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGS-----------CHHHHHTTHHHHHHTT-----TT
T ss_pred             ccccCCc------eehhhHHHHHHHhhccCCCcceEEEEEeccccc-----------chhHHHHHhhhccccc-----cc
Confidence            6554321      11111111111       134579999999999           6677777777766532     47


Q ss_pred             eEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHHH
Q 022768          172 VKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEAG  250 (292)
Q Consensus       172 ~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a~  250 (292)
                      +.++++++....+.+++++  || ..+.|++|+.++...++...+...... .+-.++.++..+.|    |+|.++....
T Consensus       132 ~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~G----d~R~ai~~Lq  204 (224)
T d1sxjb2         132 TRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG----DMRQAINNLQ  204 (224)
T ss_dssp             EEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT----CHHHHHHHHH
T ss_pred             eeeeeccCchhhhhhHHHH--HH-HHhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHHHcCC----cHHHHHHHHH
Confidence            7788889999999999999  77 779999999999999999887644332 12235566667766    5555555444


Q ss_pred             HHHHHhcCCcccHHHHHHHH
Q 022768          251 MSAIRAERDYVIHEDFMKAV  270 (292)
Q Consensus       251 ~~a~~~~~~~i~~~~~~~a~  270 (292)
                      ....  ....++.+++.+.+
T Consensus       205 ~~~~--~~~~i~~~~i~~~~  222 (224)
T d1sxjb2         205 STVA--GHGLVNADNVFKIV  222 (224)
T ss_dssp             HHHH--HHSSBCHHHHHHHH
T ss_pred             HHHH--cCCCcCHHHHHHHh
Confidence            3332  33468888887765

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.85  E-value=2.3e-20  Score=153.53  Aligned_cols=212  Identities=15%  Similarity=0.180  Sum_probs=148.5

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc------CCcEEEE
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI------DANFLKV   97 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l------~~~~~~~   97 (292)
                      +.+.|.+|++++|+++.++.|..++..             ....+++|+||||+|||++++.+|+++      ......+
T Consensus         4 ~ky~P~~~~diig~~~~~~~l~~~i~~-------------~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~   70 (237)
T d1sxjd2           4 EKYRPKNLDEVTAQDHAVTVLKKTLKS-------------ANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILEL   70 (237)
T ss_dssp             HHTCCSSTTTCCSCCTTHHHHHHHTTC-------------TTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEE
T ss_pred             hhhCCCCHHHccCcHHHHHHHHHHHHc-------------CCCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhhe
Confidence            468899999999999999999988764             223469999999999999999999986      4455666


Q ss_pred             eccchhccccChHHHHHHHHH------------HHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768           98 VSSAIIDKYIGESARLIREMF------------GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      +........  .....+....            .........+++|||+|.+           .......+..++.... 
T Consensus        71 ~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l-----------~~~~~~~l~~~~~~~~-  136 (237)
T d1sxjd2          71 NASDERGIS--IVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSM-----------TADAQSALRRTMETYS-  136 (237)
T ss_dssp             CSSSCCCHH--HHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGS-----------CHHHHHHHHHHHHHTT-
T ss_pred             eccccccch--HHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEeccccc-----------CHHHHHHHhhcccccc-
Confidence            654433211  1111111111            1111233469999999998           5556666666665422 


Q ss_pred             CCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHH
Q 022768          166 FDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRN  244 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~  244 (292)
                          ..+.+|.+++....+.+++++  || ..+.|++|+.++...+++..+...... .+-.++.++..+.| ..|.+..
T Consensus       137 ----~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~g-d~R~ai~  208 (237)
T d1sxjd2         137 ----GVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAG-DLRRGIT  208 (237)
T ss_dssp             ----TTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS-CHHHHHH
T ss_pred             ----ccccccccccccccccccccc--hh-hhhccccccccccchhhhhhhhhhcCcCCHHHHHHHHHHcCC-CHHHHHH
Confidence                467788888888888999998  87 788999999999999999888754432 22234666777766 6666666


Q ss_pred             HHHHHHHHHHHhc-CCcccHHHHHHHH
Q 022768          245 VCTEAGMSAIRAE-RDYVIHEDFMKAV  270 (292)
Q Consensus       245 l~~~a~~~a~~~~-~~~i~~~~~~~a~  270 (292)
                      +++.+...+.... ...|+.+++.+++
T Consensus       209 ~L~~~~~~~~~~~~~~~It~~~i~e~~  235 (237)
T d1sxjd2         209 LLQSASKGAQYLGDGKNITSTQVEELA  235 (237)
T ss_dssp             HHHHTHHHHHHHCSCCCCCHHHHHHHH
T ss_pred             HHHHHHHhchhcCCCCccCHHHHHHhh
Confidence            6666666555443 4579999999875

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.84  E-value=3.2e-20  Score=158.65  Aligned_cols=179  Identities=27%  Similarity=0.356  Sum_probs=127.2

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhc-CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchh--ccccCh
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRV-GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAII--DKYIGE  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~-~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~--~~~~~~  109 (292)
                      .++|++++++.+...+..++......... .-.++.++||+||||||||.+|+++|+.++.+++.++++++.  +.+.+.
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~   94 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE   94 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGS
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEeee
Confidence            37999999999998874432111110000 013568899999999999999999999999999999999987  446777


Q ss_pred             HHHHHHHHHHHhhh-----CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC--------CCCCeEEEE
Q 022768          110 SARLIREMFGYARD-----HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD--------QLGKVKMIM  176 (292)
Q Consensus       110 ~~~~~~~~~~~~~~-----~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~--------~~~~~~vi~  176 (292)
                      ....++.+|..+..     +.|+||||||+|.+.+.......+...  ...+..++..+++..        ...++.+|+
T Consensus        95 ~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~~~~~--~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~  172 (309)
T d1ofha_          95 VDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSR--EGVQRDLLPLVEGSTVSTKHGMVKTDHILFIA  172 (309)
T ss_dssp             TTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHH--HHHHHHHHHHHHCCEEEETTEEEECTTCEEEE
T ss_pred             ccccccccchhhhcccccccCCceEEehhhhhhhhhccCcccchhh--hHHHHHhhHHhcCCEEecCCeEEEccceeEEe
Confidence            78888888888754     247899999999997655443332211  123334444444321        123456666


Q ss_pred             E----eCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHH
Q 022768          177 A----TNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIH  215 (292)
Q Consensus       177 t----~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~  215 (292)
                      +    .+.+..+.+.++.  ||...+.+++|+..++.+|+..+
T Consensus       173 ~ga~~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~~~Il~~~  213 (309)
T d1ofha_         173 SGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEP  213 (309)
T ss_dssp             EECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             ccchhhcCcccchhhhhh--hhheeeeccCCCHHHHHHHHHHH
Confidence            6    3556678888887  99999999999999999997643

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.83  E-value=3.9e-20  Score=153.67  Aligned_cols=224  Identities=18%  Similarity=0.209  Sum_probs=139.1

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChH----HHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPE----LFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~----~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      +.+.|.+|++++|+++.+++|.+++........    .....+....++++|+||||+|||++|+++|++++.+++.++.
T Consensus         6 eky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~~~~~~   85 (253)
T d1sxja2           6 VKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNA   85 (253)
T ss_dssp             HHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECT
T ss_pred             cCcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhhhcccc
Confidence            458899999999999999999998865211110    0112233455789999999999999999999999999999988


Q ss_pred             cchhccccChHHHHHHHHH--------------HHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          100 SAIIDKYIGESARLIREMF--------------GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      ....+...  ....+....              .......+.++++||+|.+...        .......+.+.....  
T Consensus        86 ~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~--------~~~~~~~~~~~~~~~--  153 (253)
T d1sxja2          86 SDVRSKTL--LNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGG--------DRGGVGQLAQFCRKT--  153 (253)
T ss_dssp             TSCCCHHH--HHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTT--------STTHHHHHHHHHHHC--
T ss_pred             ccchhhHH--HHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccc--------hhhhhHHHhhhhccc--
Confidence            76543211  000000000              0011234679999999998322        222222333333321  


Q ss_pred             CCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHH
Q 022768          166 FDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRN  244 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~  244 (292)
                         ...++++++++....+ +.+++  | ...++|++|+.+++..+++..+...... .+-.++.++..+.|    |++.
T Consensus       154 ---~~~ii~i~~~~~~~~~-~~l~~--~-~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~G----DiR~  222 (253)
T d1sxja2         154 ---STPLILICNERNLPKM-RPFDR--V-CLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG----DIRQ  222 (253)
T ss_dssp             ---SSCEEEEESCTTSSTT-GGGTT--T-SEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT----CHHH
T ss_pred             ---cccccccccccccccc-ccccc--e-eeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCC----cHHH
Confidence               1233333333333333 45554  4 4889999999999999999887643222 22346777777765    7877


Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          245 VCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       245 l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      ++.....++  .....++.+++.+..+.
T Consensus       223 ai~~L~~~~--~~~~~i~~~~~~~~~~~  248 (253)
T d1sxja2         223 VINLLSTIS--TTTKTINHENINEISKA  248 (253)
T ss_dssp             HHHHHTHHH--HHSSCCCTTHHHHHHHH
T ss_pred             HHHHHHHHH--HcCCCCCHHHHHHHhch
Confidence            776554433  33456888887766543

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=99.83  E-value=6.3e-24  Score=180.28  Aligned_cols=160  Identities=16%  Similarity=0.215  Sum_probs=119.9

Q ss_pred             hHHHHhcCCCCCce-EEEEcCCCChHHHHHHHHHHhcC--CcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEE
Q 022768           55 PELFLRVGIKPPKG-VLLYGPPGTGKTLLARAIASNID--ANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFM  131 (292)
Q Consensus        55 ~~~~~~~~~~~~~~-vll~G~~G~GKT~l~~~la~~l~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~l  131 (292)
                      +..++.+|...+.+ +|++||||||||.+|+++|.+++  .+++.++..++.+.+.|+.+..++.+|..++.  |+||||
T Consensus       111 ~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~--~~ilf~  188 (321)
T d1w44a_         111 PVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQ--HRVIVI  188 (321)
T ss_dssp             CEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHH--CSEEEE
T ss_pred             hHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhh--ccEEEe
Confidence            34455556555555 45589999999999999999986  67899999999999999999999999999986  689999


Q ss_pred             cccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC----ChhhcCCCCcceEEEccCCCHHH
Q 022768          132 DEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL----DPALLRPGRLDRKIEIPLPNEQS  207 (292)
Q Consensus       132 De~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l----~~~l~~~~r~~~~i~l~~p~~~~  207 (292)
                      ||+|.++++++++....  ...+.+.+++.+++++....+++||++||+ ..+    ++++.+++||...+.+++|+.+.
T Consensus       189 DEid~~~~~r~~~~~~~--~~~r~v~~lL~e~dg~~~~~~v~viaatN~-~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~  265 (321)
T d1w44a_         189 DSLKNVIGAAGGNTTSG--GISRGAFDLLSDIGAMAASRGCVVIASLNP-TSNDDKIVELVKEASRSNSTSLVISTDVDG  265 (321)
T ss_dssp             ECCTTTC-------------CCHHHHHHHHHHHHHHHHHTCEEEEECCC-CCCCHHHHHHHHHHHHHSCSEEEEECSSTT
T ss_pred             ehhhhhccccccCCCCC--cchhhhhhhhhhccccccCCCeEEEEeCCC-cccccchhhhhhccCcccceeecCCCChHH
Confidence            99999998886543322  122466666666665555568999999994 444    44556677999999999999999


Q ss_pred             HHHHHHHHHcCc
Q 022768          208 RMEILKIHAAGI  219 (292)
Q Consensus       208 r~~i~~~~~~~~  219 (292)
                      |.+|++.+..+.
T Consensus       266 r~~il~~~~~~~  277 (321)
T d1w44a_         266 EWQVLTRTGEGL  277 (321)
T ss_dssp             EEEEEEECBTTC
T ss_pred             HHHHHHHhccCc
Confidence            999987665543

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.82  E-value=2.2e-19  Score=148.92  Aligned_cols=195  Identities=18%  Similarity=0.243  Sum_probs=128.7

Q ss_pred             cCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc---EEEEecc
Q 022768           24 EDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN---FLKVVSS  100 (292)
Q Consensus        24 ~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~---~~~~~~~  100 (292)
                      +.+.|.+|++++|.+++++.|..++...            ....+++|+||||+|||++++++|+.+..+   ...++..
T Consensus         3 eky~P~~~~diig~~~~~~~L~~~~~~~------------~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~   70 (252)
T d1sxje2           3 DKYRPKSLNALSHNEELTNFLKSLSDQP------------RDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVR   70 (252)
T ss_dssp             TTTCCCSGGGCCSCHHHHHHHHTTTTCT------------TCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------
T ss_pred             cccCCCCHHHccCcHHHHHHHHHHHHcC------------CCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccc
Confidence            5788999999999999999998876542            234469999999999999999999986211   1111100


Q ss_pred             chh------------------c---cccC-hHHHHHHHHHHHh--------------hhCCCEEEEEcccccccCCcCCC
Q 022768          101 AII------------------D---KYIG-ESARLIREMFGYA--------------RDHQPCIIFMDEIDAIGGRRFSE  144 (292)
Q Consensus       101 ~~~------------------~---~~~~-~~~~~~~~~~~~~--------------~~~~~~il~lDe~d~l~~~~~~~  144 (292)
                      ...                  .   ...+ .............              ......+++|||+|.+       
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l-------  143 (252)
T d1sxje2          71 QFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSL-------  143 (252)
T ss_dssp             ------------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSS-------
T ss_pred             cccccccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEecccccc-------
Confidence            000                  0   0000 0011111111111              0123469999999998       


Q ss_pred             CCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCcc--CC
Q 022768          145 GTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIA--KH  222 (292)
Q Consensus       145 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~--~~  222 (292)
                          ....+..+..+++..     ..++.+|++||..+.+.+.+++  || ..++|++|+.++..++++..+....  ..
T Consensus       144 ----~~~~~~~l~~~~e~~-----~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~i~~~e~~~~~  211 (252)
T d1sxje2         144 ----TKDAQAALRRTMEKY-----SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNERIQLE  211 (252)
T ss_dssp             ----CHHHHHHHHHHHHHS-----TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCEEC
T ss_pred             ----ccccchhhhcccccc-----cccccceeeeccccchhhhhhc--ch-heeeecccchhhHHHHHHHHHHHcCCCCC
Confidence                666677777777652     3578889999999999999998  88 6899999999999999988776432  22


Q ss_pred             CCCCHHHHHHHcCCCCHHHHHHHHHHHHHHH
Q 022768          223 GEIDYEAVVKLAEGFNGADLRNVCTEAGMSA  253 (292)
Q Consensus       223 ~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a  253 (292)
                      .+..++.++..+.|    |+|+++......+
T Consensus       212 ~~~~l~~i~~~s~G----d~R~ai~~Lq~~~  238 (252)
T d1sxje2         212 TKDILKRIAQASNG----NLRVSLLMLESMA  238 (252)
T ss_dssp             CSHHHHHHHHHHTT----CHHHHHHHHTHHH
T ss_pred             cHHHHHHHHHHcCC----cHHHHHHHHHHHH
Confidence            23335677777776    6666665444333

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=99.79  E-value=5.7e-18  Score=141.48  Aligned_cols=225  Identities=16%  Similarity=0.175  Sum_probs=148.2

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcC----CcEEEEeccchh
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNID----ANFLKVVSSAII  103 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~----~~~~~~~~~~~~  103 (292)
                      .+..+.++|++.+++.+..++...+.+      .+ ..+.+++|+||||||||++++.+++.+.    ..++.+++....
T Consensus        12 ~y~p~~l~~Re~ei~~l~~~l~~~l~~------~~-~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~   84 (276)
T d1fnna2          12 SYVPKRLPHREQQLQQLDILLGNWLRN------PG-HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYR   84 (276)
T ss_dssp             TCCCSCCTTCHHHHHHHHHHHHHHHHS------TT-SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHhC------CC-CCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhh
Confidence            334456799999999999988653221      11 3467899999999999999999999873    345555543321


Q ss_pred             cc----------------ccC-hHHHHHHHHHHHhhh-CCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhC
Q 022768          104 DK----------------YIG-ESARLIREMFGYARD-HQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDG  165 (292)
Q Consensus       104 ~~----------------~~~-~~~~~~~~~~~~~~~-~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~  165 (292)
                      ..                ..+ ........+...... ....++++|++|.+           .......+..++.....
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~-----------~~~~~~~~~~~~~~~~~  153 (276)
T d1fnna2          85 NFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL-----------APDILSTFIRLGQEADK  153 (276)
T ss_dssp             SHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS-----------CHHHHHHHHHHTTCHHH
T ss_pred             hhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHh-----------hhhhhhhHHHHHhcccc
Confidence            10                001 122223333333333 35678889999887           33333333333322211


Q ss_pred             CCCCCCeEEEEEeCCC---CCCChhhcCCCCc-ceEEEccCCCHHHHHHHHHHHHcCccCCCCCC---HHHHHHHcC---
Q 022768          166 FDQLGKVKMIMATNRP---DVLDPALLRPGRL-DRKIEIPLPNEQSRMEILKIHAAGIAKHGEID---YEAVVKLAE---  235 (292)
Q Consensus       166 ~~~~~~~~vi~t~~~~---~~l~~~l~~~~r~-~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~---~~~l~~~~~---  235 (292)
                       .....+.+|++++..   +.+++.+.+  |+ ...+.|++|+.+++.+|++.++.........+   ++.++..+.   
T Consensus       154 -~~~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia~~~~~~~  230 (276)
T d1fnna2         154 -LGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQT  230 (276)
T ss_dssp             -HSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSS
T ss_pred             -ccccceEEeecCCchhhhhhcchhhhh--hhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHHHHhhhhh
Confidence             223467788888874   357777776  44 35689999999999999998876433333333   333444431   


Q ss_pred             -----CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHH
Q 022768          236 -----GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKL  273 (292)
Q Consensus       236 -----g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~  273 (292)
                           +-+++.+..+++.|...|..++...|+.+|+.+|.+++
T Consensus       231 ~~~~~~G~~R~a~~ll~~a~~~A~~~~~~~I~~edv~~A~~~~  273 (276)
T d1fnna2         231 PLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEV  273 (276)
T ss_dssp             TTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHH
T ss_pred             hhhhcCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence                 12678888999999999999999999999999999876

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=99.79  E-value=4.4e-18  Score=142.99  Aligned_cols=229  Identities=14%  Similarity=0.100  Sum_probs=150.2

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCC---CceEEEEcCCCChHHHHHHHHHHhcC---------CcEEEE
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKP---PKGVLLYGPPGTGKTLLARAIASNID---------ANFLKV   97 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~---~~~vll~G~~G~GKT~l~~~la~~l~---------~~~~~~   97 (292)
                      ..+.+.|.+.++++|..++..+..+       |..+   ..+++|+||||||||++++++++.+.         ..+..+
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~-------~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~   86 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLS-------GAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYV   86 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHT-------SSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHc-------CCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeee
Confidence            3467889999999998887543211       1111   12366789999999999999999872         234444


Q ss_pred             eccchhcc----------------ccCh-HHHHHHHHHHHhh-hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHH
Q 022768           98 VSSAIIDK----------------YIGE-SARLIREMFGYAR-DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMEL  159 (292)
Q Consensus        98 ~~~~~~~~----------------~~~~-~~~~~~~~~~~~~-~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~  159 (292)
                      ++......                ..+. .......+..... ...+.++++||+|.+.....     ........+..+
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~-----~~~~~~~~l~~l  161 (287)
T d1w5sa2          87 NAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPR-----IAAEDLYTLLRV  161 (287)
T ss_dssp             EGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTT-----SCHHHHHHHHTH
T ss_pred             ccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccc-----cchhHHHHHHHH
Confidence            44332211                0011 1112222222222 23456889999999854331     234455556666


Q ss_pred             HHHhhCCCCCCCeEEEEEeCCCCC------CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCC---HHHH
Q 022768          160 LNQLDGFDQLGKVKMIMATNRPDV------LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEID---YEAV  230 (292)
Q Consensus       160 l~~~~~~~~~~~~~vi~t~~~~~~------l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~---~~~l  230 (292)
                      ++.+........+.+|+.++....      ..+.+.+  |+...+.|++|+.++..+|++.++........++   ++.+
T Consensus       162 ~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al~~i  239 (287)
T d1w5sa2         162 HEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELI  239 (287)
T ss_dssp             HHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHH
T ss_pred             HHhcchhhcccceeEEeecccHHHHHHHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHHHHH
Confidence            666555555567777777765542      2356666  8889999999999999999998876433333344   4455


Q ss_pred             HHHcC-----CCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          231 VKLAE-----GFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       231 ~~~~~-----g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      +..+.     ...++.+..+++.|...|..++...|+.++|.+|+++
T Consensus       240 a~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~V~~A~~e  286 (287)
T d1w5sa2         240 SDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSE  286 (287)
T ss_dssp             HHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHH
T ss_pred             HHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhc
Confidence            55542     2267888899999999999999999999999999874

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.78  E-value=2e-17  Score=136.81  Aligned_cols=220  Identities=22%  Similarity=0.298  Sum_probs=156.8

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEEec
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVS   99 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~~~   99 (292)
                      .++.++|+++.+++|...+.+             ....+++|.||||+|||++++.+|..+          +..++.++.
T Consensus        16 ~ld~~igRd~Ei~~l~~iL~r-------------~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~   82 (268)
T d1r6bx2          16 GIDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI   82 (268)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCC
T ss_pred             CCCcccChHHHHHHHHHHHhc-------------CccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeee
Confidence            456789999999999999865             335689999999999999999999865          557888888


Q ss_pred             cchhc--cccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEE
Q 022768          100 SAIID--KYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMA  177 (292)
Q Consensus       100 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t  177 (292)
                      ..+..  .+.|+.+..+..++..+....+.|+||||+|.+++.-+..  +....    +..++   ...-..+.+.+|++
T Consensus        83 ~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~--g~~~d----~a~~L---kp~L~rg~i~vIga  153 (268)
T d1r6bx2          83 GSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAAS--GGQVD----AANLI---KPLLSSGKIRVIGS  153 (268)
T ss_dssp             C---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSS--SCHHH----HHHHH---SSCSSSCCCEEEEE
T ss_pred             chHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCC--Ccccc----HHHHh---hHHHhCCCCeEEEe
Confidence            88875  5688899999999999988888999999999997543221  11121    22222   22334578999999


Q ss_pred             eCCC-----CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccC--CCCCCHHHH---HH-----HcCCCCHHHH
Q 022768          178 TNRP-----DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAK--HGEIDYEAV---VK-----LAEGFNGADL  242 (292)
Q Consensus       178 ~~~~-----~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~--~~~~~~~~l---~~-----~~~g~~~~di  242 (292)
                      |...     .+-++++.+  || ..|.+..|+.++...|++.....+..  .-.+..+.+   ..     +.+.+-|.-.
T Consensus       154 tT~eey~~~~e~d~al~r--rF-~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~~~PdKA  230 (268)
T d1r6bx2         154 TTYQEFSNIFEKDRALAR--RF-QKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKA  230 (268)
T ss_dssp             ECHHHHHCCCCCTTSSGG--GE-EEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHH
T ss_pred             CCHHHHHHHHhhcHHHHh--hh-cccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCCCCCcHH
Confidence            8653     245788888  89 88999999999999999865543211  122333332   22     2233456678


Q ss_pred             HHHHHHHHHHHHHhc----CCcccHHHHHHHHHHHh
Q 022768          243 RNVCTEAGMSAIRAE----RDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       243 ~~l~~~a~~~a~~~~----~~~i~~~~~~~a~~~~~  274 (292)
                      ..++++|...+....    ...|+.+|+...+..+.
T Consensus       231 IdllDea~a~~~~~~~~~~~~~i~~~di~~~i~~~~  266 (268)
T d1r6bx2         231 IDVIDEAGARARLMPVSKRKKTVNVADIESVVARIA  266 (268)
T ss_dssp             HHHHHHHHHHHHHSSSCCCCCSCCHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHhhccccCcccCCHHHHHHHHHHHh
Confidence            889999988776542    34688999988877653

>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase, BchI {Rhodobacter capsulatus [TaxId: 1061]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ATPase subunit of magnesium chelatase, BchI
species: Rhodobacter capsulatus [TaxId: 1061]

Probab=99.74  E-value=3.8e-17  Score=140.95  Aligned_cols=225  Identities=18%  Similarity=0.216  Sum_probs=144.5

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch----
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI----  102 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~----  102 (292)
                      |.+.|.+|+|++++|+.|.-.+..+             .++++||.||||+|||++++.++..+.. +..+....+    
T Consensus         2 ~~~~f~~I~Gq~~~kral~laa~~~-------------~~h~vLl~G~pG~GKT~lar~~~~iLp~-~~~~~~~~~~~~~   67 (333)
T d1g8pa_           2 PVFPFSAIVGQEDMKLALLLTAVDP-------------GIGGVLVFGDRGTGKSTAVRALAALLPE-IEAVEGCPVSSPN   67 (333)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHCG-------------GGCCEEEECCGGGCTTHHHHHHHHHSCC-EEEETTCTTCCSS
T ss_pred             CCCChhhccCcHHHHHHHHHHHhcc-------------CCCeEEEECCCCccHHHHHHHHHHhCCC-chhhccCccccCc
Confidence            5678999999999999887665432             1357999999999999999999987621 111110000    


Q ss_pred             ----------------------hccccChHHHHH------HHHHH---------HhhhCCCEEEEEcccccccCCcCCCC
Q 022768          103 ----------------------IDKYIGESARLI------REMFG---------YARDHQPCIIFMDEIDAIGGRRFSEG  145 (292)
Q Consensus       103 ----------------------~~~~~~~~~~~~------~~~~~---------~~~~~~~~il~lDe~d~l~~~~~~~~  145 (292)
                                            .....+.+...+      .....         .......+|++|||++.+        
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~--------  139 (333)
T d1g8pa_          68 VEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLL--------  139 (333)
T ss_dssp             GGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGS--------
T ss_pred             cccccchhhccccCcccccCceeeccCCCCcccccCcchhhhccccCcceeeccccccccccEeecccHHHH--------
Confidence                                  000000111110      00110         111123589999999998        


Q ss_pred             CcchHHHHHHHHHHHHHhhC--------CCCCCCeEEEEEeCCC-CCCChhhcCCCCcceEEEccCC-CHHHHHHHHHHH
Q 022768          146 TSADREIQRTLMELLNQLDG--------FDQLGKVKMIMATNRP-DVLDPALLRPGRLDRKIEIPLP-NEQSRMEILKIH  215 (292)
Q Consensus       146 ~~~~~~~~~~l~~~l~~~~~--------~~~~~~~~vi~t~~~~-~~l~~~l~~~~r~~~~i~l~~p-~~~~r~~i~~~~  215 (292)
                         ....+..|.+.++...-        ..-..++.+++|+|.. ..+++++++  ||...+.+..| +...+..+....
T Consensus       140 ---~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~~~~~~~~  214 (333)
T d1g8pa_         140 ---EDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRRR  214 (333)
T ss_dssp             ---CHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHHH
T ss_pred             ---HHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--hhcceeeccCcchhhHHHHHHHhh
Confidence               88899999999986421        1112268889998874 468999999  99999988776 445554443321


Q ss_pred             Hc---------------------------CccCCCCCC------HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCccc
Q 022768          216 AA---------------------------GIAKHGEID------YEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVI  262 (292)
Q Consensus       216 ~~---------------------------~~~~~~~~~------~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~  262 (292)
                      ..                           .........      ...........+.+-...+++-|...|..+++..|+
T Consensus       215 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~v~~~~~~~~~~~~~~~~~~~~S~R~~~~llrvArtiA~L~gr~~V~  294 (333)
T d1g8pa_         215 DTYDADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSDGLRGELTLLRSARALAALEGATAVG  294 (333)
T ss_dssp             HHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSCSHHHHHHHHHHHHHHHHHTTCSBCC
T ss_pred             hhcccChHHHHHHHHHHHHHHHHHHHHHhhcccceecCHHHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHcCCCCCC
Confidence            10                           000000111      112222333458889999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhhh
Q 022768          263 HEDFMKAVRKLNEAKK  278 (292)
Q Consensus       263 ~~~~~~a~~~~~~~~~  278 (292)
                      .+|+.+|+..+-.+..
T Consensus       295 ~~di~~a~~lvL~hR~  310 (333)
T d1g8pa_         295 RDHLKRVATMALSHRL  310 (333)
T ss_dssp             HHHHHHHHHHHHGGGC
T ss_pred             HHHHHHHHHHHHHhhc
Confidence            9999999887766543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.72  E-value=1.3e-16  Score=128.47  Aligned_cols=195  Identities=15%  Similarity=0.197  Sum_probs=125.5

Q ss_pred             CCCcccccc-c--cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           27 GNVSYSAVG-G--LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        27 ~~~~~~~l~-g--~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |..+|++.+ |  ++.+...+.+++..+           -.....++|+||+|+|||||++++|+++   +..+++++..
T Consensus         5 ~~~tFdnF~vg~~N~~a~~~~~~~~~~~-----------~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~   73 (213)
T d1l8qa2           5 PKYTLENFIVGEGNRLAYEVVKEALENL-----------GSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD   73 (213)
T ss_dssp             TTCCSSSCCCCTTTHHHHHHHHHHHHTT-----------TTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CCCChhhccCCCcHHHHHHHHHHHHhCc-----------CCCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechH
Confidence            567899954 5  566677777777654           1122459999999999999999999987   4567777766


Q ss_pred             chhccccChHHH-HHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeC
Q 022768          101 AIIDKYIGESAR-LIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATN  179 (292)
Q Consensus       101 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~  179 (292)
                      .+.......... ....+......  ..+|+|||+|.+.+         ....+..+..+++....   .++.+++.+..
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~--~dll~iDDi~~i~~---------~~~~~~~lf~lin~~~~---~~~~iiits~~  139 (213)
T d1l8qa2          74 DFAQAMVEHLKKGTINEFRNMYKS--VDLLLLDDVQFLSG---------KERTQIEFFHIFNTLYL---LEKQIILASDR  139 (213)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHT--CSEEEEECGGGGTT---------CHHHHHHHHHHHHHHHH---TTCEEEEEESS
T ss_pred             HHHHHHHHHHHccchhhHHHHHhh--ccchhhhhhhhhcC---------chHHHHHHHHHHHHHhh---ccceEEEecCC
Confidence            654433222111 12233333333  36999999999854         46777888888887642   13444444444


Q ss_pred             CCCC---CChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCC-CCCCHHHHHHHcCCCCHHHHHHHHHHH
Q 022768          180 RPDV---LDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKH-GEIDYEAVVKLAEGFNGADLRNVCTEA  249 (292)
Q Consensus       180 ~~~~---l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~-~~~~~~~l~~~~~g~~~~di~~l~~~a  249 (292)
                      .|..   +.++++++.+.+.++.++ |+.+++.++++.++...... .+-.++-++..+.  +.|++..+++..
T Consensus       140 ~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~~--~~R~L~~~l~~l  210 (213)
T d1l8qa2         140 HPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTK--NVREIEGKIKLI  210 (213)
T ss_dssp             CGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHCS--SHHHHHHHHHHH
T ss_pred             cchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC--cHHHHHHHHHHh
Confidence            4543   457788844456678886 67789999999988755443 1112344444543  578887777654

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.69  E-value=1.4e-16  Score=124.79  Aligned_cols=157  Identities=25%  Similarity=0.414  Sum_probs=118.1

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEEec
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVS   99 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~~~   99 (292)
                      .++.++|+++.++++...+.+             ....+++|+|+||+|||++++.+|...          +..++.++.
T Consensus        20 ~ld~~igRd~Ei~~l~~iL~r-------------~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~   86 (195)
T d1jbka_          20 KLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM   86 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECH
T ss_pred             CCCCCcCcHHHHHHHHHHHhc-------------cCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            457789999999999999876             235689999999999999999999865          567899998


Q ss_pred             cchhc--cccChHHHHHHHHHHHhhhC-CCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768          100 SAIID--KYIGESARLIREMFGYARDH-QPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus       100 ~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      ..+..  .+.|+.+..++.++..+... .+.||||||+|.+++..+...   .......|...+..       +.+.+|+
T Consensus        87 ~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g---~~d~~~~Lkp~L~r-------g~l~~Ig  156 (195)
T d1jbka_          87 GALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADG---AMDAGNMLKPALAR-------GELHCVG  156 (195)
T ss_dssp             HHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT---------CCCCHHHHHHHHHT-------TSCCEEE
T ss_pred             HHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCC---cccHHHHHHHHHhC-------CCceEEe
Confidence            88874  45678888898888887554 467999999999975432211   11233455555543       5677899


Q ss_pred             EeCCCC-----CCChhhcCCCCcceEEEccCCCHHHHHHHH
Q 022768          177 ATNRPD-----VLDPALLRPGRLDRKIEIPLPNEQSRMEIL  212 (292)
Q Consensus       177 t~~~~~-----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~  212 (292)
                      +|...+     +-++++.+  || ..|.+..|+.++...|+
T Consensus       157 atT~eey~~~~e~d~aL~r--rF-~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         157 ATTLDEYRQYIEKDAALER--RF-QKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             EECHHHHHHHTTTCHHHHT--TE-EEEECCCCCHHHHHTTC
T ss_pred             cCCHHHHHHHHHcCHHHHh--cC-CEeecCCCCHHHHHHHh
Confidence            886532     45888998  99 88999999999887664

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=99.68  E-value=7.1e-16  Score=123.77  Aligned_cols=171  Identities=16%  Similarity=0.192  Sum_probs=117.7

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc----------------------
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN----------------------   93 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~----------------------   93 (292)
                      .++++.++|...+..-            ..++++||+||+|+|||++++.+|+.+.+.                      
T Consensus         6 w~~~~~~~l~~~~~~~------------~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~   73 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAG------------RGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTH   73 (207)
T ss_dssp             GGHHHHHHHHHHHHTT------------CCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCC
T ss_pred             ccHHHHHHHHHHHHcC------------CcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccc
Confidence            4567788888877642            446679999999999999999999977321                      


Q ss_pred             --EEEEeccchhccccChHHHHHHHHHHHhh----hCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCC
Q 022768           94 --FLKVVSSAIIDKYIGESARLIREMFGYAR----DHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFD  167 (292)
Q Consensus        94 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~  167 (292)
                        +..+....-.   .......++.+.....    .....|++|||+|.+           ....+..|+.+++.     
T Consensus        74 ~~~~~~~~~~~~---~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l-----------~~~a~n~Llk~lEe-----  134 (207)
T d1a5ta2          74 PDYYTLAPEKGK---NTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL-----------TDAAANALLKTLEE-----  134 (207)
T ss_dssp             TTEEEECCCTTC---SSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGB-----------CHHHHHHHHHHHTS-----
T ss_pred             cccchhhhhhcc---cccccchhhHHhhhhhhccccCccceEEechhhhh-----------hhhhhHHHHHHHHh-----
Confidence              1222111100   0112333444444433    234679999999999           77777777777763     


Q ss_pred             CCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHH
Q 022768          168 QLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNV  245 (292)
Q Consensus       168 ~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l  245 (292)
                      +..++.+|++|+.++.+.+.+++  |+ ..+.|++|+.++...+++....   . .+.....++..++| ++|++..+
T Consensus       135 p~~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~~~~~~~~L~~~~~---~-~~~~~~~i~~~s~G-s~r~al~~  204 (207)
T d1a5ta2         135 PPAETWFFLATREPERLLATLRS--RC-RLHYLAPPPEQYAVTWLSREVT---M-SQDALLAALRLSAG-SPGAALAL  204 (207)
T ss_dssp             CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHCC---C-CHHHHHHHHHHTTT-CHHHHHHT
T ss_pred             hcccceeeeeecChhhhhhhhcc--ee-EEEecCCCCHHHHHHHHHHcCC---C-CHHHHHHHHHHcCC-CHHHHHHH
Confidence            44689999999999999999999  87 8899999999988887765331   1 22335666777776 66665544

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.64  E-value=5.8e-15  Score=128.46  Aligned_cols=201  Identities=22%  Similarity=0.331  Sum_probs=130.4

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----------CCcEEEEec
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----------DANFLKVVS   99 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----------~~~~~~~~~   99 (292)
                      .++.++|+++.++++...+.+             ....+++|.|+||+|||+++..+|..+          +..++.++.
T Consensus        20 ~ld~~~gr~~ei~~~~~~L~r-------------~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~   86 (387)
T d1qvra2          20 KLDPVIGRDEEIRRVIQILLR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQM   86 (387)
T ss_dssp             CSCCCCSCHHHHHHHHHHHHC-------------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC
T ss_pred             CCCCCcCcHHHHHHHHHHHhc-------------CCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            467789999999999999876             335568999999999999999999865          456888998


Q ss_pred             cchhc--cccChHHHHHHHHHHHhhhCC-CEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEE
Q 022768          100 SAIID--KYIGESARLIREMFGYARDHQ-PCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIM  176 (292)
Q Consensus       100 ~~~~~--~~~~~~~~~~~~~~~~~~~~~-~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~  176 (292)
                      ..+..  .+.|+.+..+..++..+.... +.||||||+|.+++..++   .+.......|.-.|..       +.+.+|+
T Consensus        87 ~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~---~g~~d~a~~Lkp~L~r-------g~~~~I~  156 (387)
T d1qvra2          87 GSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKA---EGAVDAGNMLKPALAR-------GELRLIG  156 (387)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCSSEEEEECCC----------------------HHHHHT-------TCCCEEE
T ss_pred             hhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCC---CCcccHHHHHHHHHhC-------CCcceee
Confidence            88874  467888888888888887764 678999999999753321   1223344555555543       5677899


Q ss_pred             EeCCCC----CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCC--CCHHHH---HH-----HcCCCCHHHH
Q 022768          177 ATNRPD----VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGE--IDYEAV---VK-----LAEGFNGADL  242 (292)
Q Consensus       177 t~~~~~----~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~--~~~~~l---~~-----~~~g~~~~di  242 (292)
                      +|...+    .-+++|.+  || ..|.+..|+.++...|++.....+.....  +..+.+   ..     +.+.+-|.-.
T Consensus       157 ~tT~~ey~~~e~d~al~r--rF-~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~ryi~~r~~PdKA  233 (387)
T d1qvra2         157 ATTLDEYREIEKDPALER--RF-QPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKA  233 (387)
T ss_dssp             EECHHHHHHHTTCTTTCS--CC-CCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHH
T ss_pred             ecCHHHHHHhcccHHHHH--hc-ccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcccccccccChhhH
Confidence            886421    23678887  89 88999999999999999976654322211  222222   22     3345578899


Q ss_pred             HHHHHHHHHHHHHh
Q 022768          243 RNVCTEAGMSAIRA  256 (292)
Q Consensus       243 ~~l~~~a~~~a~~~  256 (292)
                      ..++++|+......
T Consensus       234 idlld~a~a~~~i~  247 (387)
T d1qvra2         234 IDLIDEAAARLRMA  247 (387)
T ss_dssp             HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhh
Confidence            99999998776554

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.60  E-value=1.9e-14  Score=122.53  Aligned_cols=169  Identities=20%  Similarity=0.278  Sum_probs=120.8

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc-----c
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK-----Y  106 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~-----~  106 (292)
                      ..++|++++++.+...+.....+-   .+ .-.+...++|+||+|+|||.+|+.+|+.++.+++.++++++...     .
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~l---~~-~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~~l   97 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAGL---GH-EHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRL   97 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTC---SC-TTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSS
T ss_pred             CeecChHHHHHHHHHHHHHHHccC---CC-CCCCceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhhhh
Confidence            347999999999998875432110   00 01234468999999999999999999999999999999987542     1


Q ss_pred             cC----hHHHHH-HHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCCeEEE
Q 022768          107 IG----ESARLI-REMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLGKVKMI  175 (292)
Q Consensus       107 ~~----~~~~~~-~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~~~vi  175 (292)
                      .|    ...... ..+......+..+|+++||+|..           .+..+..++++++...-.      ....++++|
T Consensus        98 ~g~~~gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa-----------~~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI  166 (315)
T d1r6bx3          98 IGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKA-----------HPDVFNILLQVMDNGTLTDNNGRKADFRNVVLV  166 (315)
T ss_dssp             CCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGS-----------CHHHHHHHHHHHHHSEEEETTTEEEECTTEEEE
T ss_pred             cccCCCccccccCChhhHHHHhCccchhhhcccccc-----------cchHhhhhHHhhccceecCCCCCccCccceEEE
Confidence            22    111111 12333445566799999999998           788889999998764211      233478899


Q ss_pred             EEeCCCC-------------------------CCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          176 MATNRPD-------------------------VLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       176 ~t~~~~~-------------------------~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      +|+|...                         .+.|.+..  |++..+.|.+++.++..+|+...+.
T Consensus       167 ~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~~~~~I~~~~l~  231 (315)
T d1r6bx3         167 MTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  231 (315)
T ss_dssp             EEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             eccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhhHHHHHHHHHHH
Confidence            9998431                         14566776  9999999999999999888776554

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=99.57  E-value=1.9e-15  Score=130.78  Aligned_cols=193  Identities=15%  Similarity=0.060  Sum_probs=122.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhhhCCCEEEEEcccccccCCc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYARDHQPCIIFMDEIDAIGGRR  141 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~  141 (292)
                      |.+..++++|+||||||||++|+++|+.++.+++.+++++..+.+            .......+.+.++|+++......
T Consensus       150 ~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~------------~l~~~~~~~~~l~d~~~~~~~~~  217 (362)
T d1svma_         150 NIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNF------------ELGVAIDQFLVVFEDVKGTGGES  217 (362)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHH------------HHGGGTTCSCEEETTCCCSTTTT
T ss_pred             CCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHH------------HHHhHHHHHHHHHHHHHHhhhhc
Confidence            467778999999999999999999999999999999887754321            11112233455667666543322


Q ss_pred             CCCCCcchHHHHHHHHHHHHHhhCCCC-------CC-----CeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHH
Q 022768          142 FSEGTSADREIQRTLMELLNQLDGFDQ-------LG-----KVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRM  209 (292)
Q Consensus       142 ~~~~~~~~~~~~~~l~~~l~~~~~~~~-------~~-----~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~  209 (292)
                      ....+..   ....+..+....++...       ..     ...+|+|||..   +.++.+++||+..+.+.+|+...+.
T Consensus       218 ~~~~~~~---~~DeiD~l~~~~dg~~~~~~~~~~~~~~~~~~~p~i~ttN~~---~~~~~r~~Rf~~~i~~~~~~~~~~~  291 (362)
T d1svma_         218 RDLPSGQ---GINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEY---SVPKTLQARFVKQIDFRPKDYLKHC  291 (362)
T ss_dssp             TTCCCCS---HHHHHHTTHHHHHCSSCEEECCSSSCCEEECCCCEEEEECSC---CCCHHHHTTEEEEEECCCCHHHHHH
T ss_pred             cCCCCeE---EEehHhhcccccCCcchhhhhhhhhchhhhccCCceeecccc---cccccccccCceEEeecCCCcHHHH
Confidence            1111111   11112222222222100       00     12378899953   3333345699999999888766654


Q ss_pred             -HHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHHh
Q 022768          210 -EILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRKLN  274 (292)
Q Consensus       210 -~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~~~  274 (292)
                       .++...+.....  ..+.+.++....+++++|++++++.+...+..+....++...+.+....+.
T Consensus       292 ~~~l~~i~~~~~l--~~~~~~L~~li~~~s~~D~~~~i~~~~~~~~~~l~~ei~~~~~~~~k~~I~  355 (362)
T d1svma_         292 LERSEFLLEKRII--QSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVA  355 (362)
T ss_dssp             HHTCTHHHHTTCT--TCHHHHHHHHHHHSCGGGSCGGGHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcccCC--CCCHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHH
Confidence             344444443332  356778888888899999999999998888777777777777777766654

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.55  E-value=2.5e-14  Score=121.65  Aligned_cols=168  Identities=21%  Similarity=0.365  Sum_probs=118.0

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----  105 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----  105 (292)
                      .++|++++++.+...+......   . .-.-.|...++|+||+|+|||.+|+.+|+.+   +.+++.+++.++...    
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~---l-~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~~~   99 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAG---L-KDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVS   99 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGG---C-SCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGG
T ss_pred             eEeCHHHHHHHHHHHHHHHhcC---C-CCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchhhh
Confidence            4799999999998887653211   0 0011233468899999999999999999988   678999998877542    


Q ss_pred             -ccChHH-----HHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCC------CCCCCeE
Q 022768          106 -YIGESA-----RLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGF------DQLGKVK  173 (292)
Q Consensus       106 -~~~~~~-----~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~------~~~~~~~  173 (292)
                       ..|...     ..-..+......+..+|++|||+|..           ....+..|..+++...-.      ....+++
T Consensus       100 ~L~g~~~gyvG~~~~~~l~~~~~~~p~~Vvl~DEieK~-----------~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i  168 (315)
T d1qvra3         100 RLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKA-----------HPDVFNILLQILDDGRLTDSHGRTVDFRNTV  168 (315)
T ss_dssp             GC--------------CHHHHHHHCSSEEEEESSGGGS-----------CHHHHHHHHHHHTTTEECCSSSCCEECTTEE
T ss_pred             hhcCCCCCCcCcccCChHHHHHHhCCCcEEEEehHhhc-----------CHHHHHHHHHHhccCceeCCCCcEecCcceE
Confidence             112111     11122344455566799999999998           788888888888764211      2223788


Q ss_pred             EEEEeCCC--------------------------CCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHc
Q 022768          174 MIMATNRP--------------------------DVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAA  217 (292)
Q Consensus       174 vi~t~~~~--------------------------~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~  217 (292)
                      +|+|+|.-                          ..+.+.+..  |++..+.|.+.+.++..+|+...+.
T Consensus       169 ~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l~  236 (315)
T d1qvra3         169 IILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLS  236 (315)
T ss_dssp             EEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             EEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeeccchhhhhhHHHHHHHHH
Confidence            99999852                          347778887  9999999999999999988775544

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Transcriptional activator sigm54 (NtrC1), C-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.49  E-value=5.7e-13  Score=109.27  Aligned_cols=203  Identities=24%  Similarity=0.270  Sum_probs=123.8

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhccccCh
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDKYIGE  109 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~~~~~  109 (292)
                      +.||...+.+++.+-+...           .....+|+|+|++||||+++|+++....   ..+++.+++..+...    
T Consensus         1 ~~v~~S~~~~~~~~~~~~~-----------a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~----   65 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKI-----------SCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRD----   65 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHH-----------TTCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHH----
T ss_pred             CeEecCHHHHHHHHHHHHH-----------hCCCCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhc----
Confidence            3578888888888887764           3446679999999999999999998765   346788887665322    


Q ss_pred             HHHHHHHHHHH---------------hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCC------
Q 022768          110 SARLIREMFGY---------------ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQ------  168 (292)
Q Consensus       110 ~~~~~~~~~~~---------------~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~------  168 (292)
                        .....+|..               ......+.|||||+|.+           +...+..+..++......+.      
T Consensus        66 --~~~~~lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i~~L-----------~~~~Q~~L~~~l~~~~~~~~~~~~~~  132 (247)
T d1ny5a2          66 --IFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGEL-----------SLEAQAKLLRVIESGKFYRLGGRKEI  132 (247)
T ss_dssp             --HHHHHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGC-----------CHHHHHHHHHHHHHSEECCBTCCSBE
T ss_pred             --ccHHHhcCcccCCcCCcccccCCHHHccCCCEEEEeChHhC-----------CHHHHHHHHHHHHhCCEEECCCCCce
Confidence              111222221               11233479999999999           88889999988875331111      


Q ss_pred             CCCeEEEEEeCCC-------CCCChhhcCCCCc-ceEEEccCCC--HHHHHHHHHHHHcCc----cCC-CCCCHHHHHHH
Q 022768          169 LGKVKMIMATNRP-------DVLDPALLRPGRL-DRKIEIPLPN--EQSRMEILKIHAAGI----AKH-GEIDYEAVVKL  233 (292)
Q Consensus       169 ~~~~~vi~t~~~~-------~~l~~~l~~~~r~-~~~i~l~~p~--~~~r~~i~~~~~~~~----~~~-~~~~~~~l~~~  233 (292)
                      ..++.+|++++.+       ..+.+.+..  |+ ...+.+|+..  .++...++..++...    ... ..++.+.+..+
T Consensus       133 ~~~~RlI~~s~~~l~~l~~~~~f~~~L~~--~l~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L  210 (247)
T d1ny5a2         133 EVNVRILAATNRNIKELVKEGKFREDLYY--RLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELL  210 (247)
T ss_dssp             ECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHH
T ss_pred             ecCeEEEEecCCCHHHHHHcCCCcHHHHh--hcCeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHH
Confidence            1146788887653       124444444  33 2345555542  234444555555432    111 22455666555


Q ss_pred             cCC-C--CHHHHHHHHHHHHHHHHHhcCCcccHHHHHH
Q 022768          234 AEG-F--NGADLRNVCTEAGMSAIRAERDYVIHEDFMK  268 (292)
Q Consensus       234 ~~g-~--~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~  268 (292)
                      ... |  +.++++++++.|.   .......|+.+|+..
T Consensus       211 ~~~~WPGNl~EL~~~l~~a~---~~~~~~~I~~~dl~~  245 (247)
T d1ny5a2         211 LSYPWYGNVRELKNVIERAV---LFSEGKFIDRGELSC  245 (247)
T ss_dssp             HHSCCTTHHHHHHHHHHHHH---HHCCSSEECHHHHHH
T ss_pred             HhCCCCCHHHHHHHHHHHHH---HhCCCCeECHHHccc
Confidence            432 2  3345555555554   455667899999865

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.43  E-value=7.2e-13  Score=104.95  Aligned_cols=117  Identities=10%  Similarity=0.193  Sum_probs=88.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC------CcEEEEeccchhccccChHHHHHHHHHHHhhh----CCCEEEEEcc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID------ANFLKVVSSAIIDKYIGESARLIREMFGYARD----HQPCIIFMDE  133 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~il~lDe  133 (292)
                      ..+.+++|+||+|+|||+++..+++...      ..++.+....-   .  -..+.++.+...+..    ....|++|||
T Consensus        13 ~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~---~--I~Id~IR~i~~~~~~~~~~~~~KviIId~   87 (198)
T d2gnoa2          13 SEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGE---N--IGIDDIRTIKDFLNYSPELYTRKYVIVHD   87 (198)
T ss_dssp             CSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSS---C--BCHHHHHHHHHHHTSCCSSSSSEEEEETT
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcC---C--CCHHHHHHHHHHHhhCcccCCCEEEEEeC
Confidence            4577999999999999999999998763      24666664321   1  123444555555433    3457999999


Q ss_pred             cccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCC
Q 022768          134 IDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPN  204 (292)
Q Consensus       134 ~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~  204 (292)
                      +|.|           ....+.+|+..+++     ++.++.+|.+|+.++.+.+.+++  || ..+.++.|.
T Consensus        88 ad~l-----------~~~aqNaLLK~LEE-----Pp~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~  139 (198)
T d2gnoa2          88 CERM-----------TQQAANAFLKALEE-----PPEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPK  139 (198)
T ss_dssp             GGGB-----------CHHHHHHTHHHHHS-----CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCH
T ss_pred             cccc-----------chhhhhHHHHHHhC-----CCCCceeeeccCChhhCHHHHhc--ce-EEEeCCCch
Confidence            9999           88888888888874     45688899999999999999999  87 778888775

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=99.43  E-value=7.6e-13  Score=114.34  Aligned_cols=178  Identities=21%  Similarity=0.315  Sum_probs=106.8

Q ss_pred             cccccHHHHHHHHHHhhcccCCh------------------HHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           33 AVGGLSDQIRELRESIELPLMNP------------------ELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~------------------~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      .++|++++++.+-..+...++..                  ....+.+ .+..++||.||+|+|||.+||.+|+.++.++
T Consensus        18 ~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~-~p~~niLfiGPTGvGKTElAk~LA~~~~~~~   96 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVE-LSKSNILLIGPTGSGKTLMAQTLAKHLDIPI   96 (364)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTT-CCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             eecChHHHHHHHHHHHHHHHHHHHHHHHhhcccccccccccccccccc-CCCcceeeeCCCCccHHHHHHHHHhhcccce
Confidence            48999999999887763221110                  0111112 3567799999999999999999999999999


Q ss_pred             EEEeccchhcc-ccCh-HHHHHHHHHHH----hhhCCCEEEEEcccccccCCcCCCCCc---chHHHHHHHHHHHHHhhC
Q 022768           95 LKVVSSAIIDK-YIGE-SARLIREMFGY----ARDHQPCIIFMDEIDAIGGRRFSEGTS---ADREIQRTLMELLNQLDG  165 (292)
Q Consensus        95 ~~~~~~~~~~~-~~~~-~~~~~~~~~~~----~~~~~~~il~lDe~d~l~~~~~~~~~~---~~~~~~~~l~~~l~~~~~  165 (292)
                      +.+++..+... +.|. ....+..+...    ......+++++||++...+........   .....+..|+++++....
T Consensus        97 ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~~~V~~~lLqild~~~~  176 (364)
T d1um8a_          97 AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLV  176 (364)
T ss_dssp             EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHHHHHHHCCEE
T ss_pred             eehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhccccccccccccccchHHHHhhhhhhcCcee
Confidence            99999988652 2222 12233444333    233456899999999975433222111   345677778887773110


Q ss_pred             -C-------CCCCCeEEEEEeCC-------------------------------------------------CCCCChhh
Q 022768          166 -F-------DQLGKVKMIMATNR-------------------------------------------------PDVLDPAL  188 (292)
Q Consensus       166 -~-------~~~~~~~vi~t~~~-------------------------------------------------~~~l~~~l  188 (292)
                       .       ....+.+++.|+|.                                                 ...+.|.+
T Consensus       177 ~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEf  256 (364)
T d1um8a_         177 NIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPEL  256 (364)
T ss_dssp             C---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHH
T ss_pred             ccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHHhhhhhHHHH
Confidence             0       01112333333332                                                 01244566


Q ss_pred             cCCCCcceEEEccCCCHHHHHHHHH
Q 022768          189 LRPGRLDRKIEIPLPNEQSRMEILK  213 (292)
Q Consensus       189 ~~~~r~~~~i~l~~p~~~~r~~i~~  213 (292)
                      ..  |++..+.|.+.+.++..+|+.
T Consensus       257 ~g--Ri~~iv~f~~L~~~~l~~Il~  279 (364)
T d1um8a_         257 IG--RLPVLSTLDSISLEAMVDILQ  279 (364)
T ss_dssp             HT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             HH--HhcchhhHhhhhHHHHHHHHH
Confidence            66  999999999999999999886

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.39  E-value=1.4e-10  Score=95.88  Aligned_cols=188  Identities=15%  Similarity=0.152  Sum_probs=117.7

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccc
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKY  106 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~  106 (292)
                      |..+-++++|+++..++|.+.                 .+++++|+||+|+|||++++.+++.++..+..+++.......
T Consensus         7 p~~~~~~f~GR~~el~~l~~~-----------------~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~~~~~   69 (283)
T d2fnaa2           7 PKDNRKDFFDREKEIEKLKGL-----------------RAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERN   69 (283)
T ss_dssp             CCCSGGGSCCCHHHHHHHHHT-----------------CSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCS
T ss_pred             CCCChhhCCChHHHHHHHHhc-----------------cCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccccccc
Confidence            445679999999999888653                 245799999999999999999999999998888876554322


Q ss_pred             cChHHHHH----------------------------------------------HHHHHHhh--hCCCEEEEEccccccc
Q 022768          107 IGESARLI----------------------------------------------REMFGYAR--DHQPCIIFMDEIDAIG  138 (292)
Q Consensus       107 ~~~~~~~~----------------------------------------------~~~~~~~~--~~~~~il~lDe~d~l~  138 (292)
                      .......+                                              ..++....  ...+.++++||++.+.
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~  149 (283)
T d2fnaa2          70 YISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELV  149 (283)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGG
T ss_pred             cccHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhc
Confidence            11111111                                              11111111  1456789999999885


Q ss_pred             CCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC---------CCChhhcCCCCcceEEEccCCCHHHHH
Q 022768          139 GRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD---------VLDPALLRPGRLDRKIEIPLPNEQSRM  209 (292)
Q Consensus       139 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~---------~l~~~l~~~~r~~~~i~l~~p~~~~r~  209 (292)
                      ...       .......+......      ...+..+.++....         .....+.  +|+...+.+++.+.++..
T Consensus       150 ~~~-------~~~~~~~l~~~~~~------~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~i~L~~l~~~e~~  214 (283)
T d2fnaa2         150 KLR-------GVNLLPALAYAYDN------LKRIKFIMSGSEMGLLYDYLRVEDPESPLF--GRAFSTVELKPFSREEAI  214 (283)
T ss_dssp             GCT-------TCCCHHHHHHHHHH------CTTEEEEEEESSHHHHHHHTTTTCTTSTTT--TCCCEEEEECCCCHHHHH
T ss_pred             ccc-------hHHHHHHHHHHHHh------hhhhhhhhccccchHHHHHHHhhhhcchhc--ccceeEEeeCCCCHHHHH
Confidence            322       11222233333222      13455555543321         1111222  255578899999999999


Q ss_pred             HHHHHHHcCccCCCCCCHHHHHHHcCCCCHHHHHHHHHH
Q 022768          210 EILKIHAAGIAKHGEIDYEAVVKLAEGFNGADLRNVCTE  248 (292)
Q Consensus       210 ~i~~~~~~~~~~~~~~~~~~l~~~~~g~~~~di~~l~~~  248 (292)
                      +++...+....... -+.+.+...+.| .|..+..++..
T Consensus       215 ~~l~~~~~~~~~~~-~~~~~i~~~~~G-~P~~L~~~~~~  251 (283)
T d2fnaa2         215 EFLRRGFQEADIDF-KDYEVVYEKIGG-IPGWLTYFGFI  251 (283)
T ss_dssp             HHHHHHHHHHTCCC-CCHHHHHHHHCS-CHHHHHHHHHH
T ss_pred             HHHHhhhhhcCCCH-HHHHHHHHHhCC-CHHHHHHHHHH
Confidence            99988776544432 346788888998 67676666543

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=99.24  E-value=1.9e-10  Score=101.42  Aligned_cols=70  Identities=29%  Similarity=0.435  Sum_probs=53.3

Q ss_pred             ccccHHHHHHHHHHhhcccCChHHHHh--cCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhc
Q 022768           34 VGGLSDQIRELRESIELPLMNPELFLR--VGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIID  104 (292)
Q Consensus        34 l~g~~~~~~~l~~~l~~~~~~~~~~~~--~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~  104 (292)
                      ++|++++|+.|--.+...++....-..  ..+ .+.++|+.||+|||||.+|+.+|+.++.||+.++++.+..
T Consensus        16 VvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei-~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fTe   87 (443)
T d1g41a_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEV-TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE   87 (443)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTC-CCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC-
T ss_pred             ccCcHHHHHHHHHHHHHHHHHhhccccccccc-ccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceeee
Confidence            899999999998887544322111111  112 2568999999999999999999999999999999988764

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.82  E-value=2.2e-09  Score=88.36  Aligned_cols=68  Identities=25%  Similarity=0.340  Sum_probs=51.5

Q ss_pred             CccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhcc
Q 022768           29 VSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDK  105 (292)
Q Consensus        29 ~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~  105 (292)
                      ++|.+.-+.+...+.+.+.....         .+...+.++||+||||||||++|+++|.+++.+++.++...+...
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~---------~~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~~~~   71 (273)
T d1gvnb_           4 VNFTDKQFENRLNDNLEELIQGK---------KAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQ   71 (273)
T ss_dssp             TCCCHHHHHHHHHHHHHHHHTTC---------CCCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHHHTT
T ss_pred             cccChHHHHHHHHHHHHHHHhcc---------cCCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHHHHH
Confidence            35566555565666666655442         124567889999999999999999999999999999998777543

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.81  E-value=1.6e-08  Score=77.71  Aligned_cols=26  Identities=31%  Similarity=0.652  Sum_probs=23.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      .++|.||+|+|||||++.++..++.+
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~~   27 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGKR   27 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCCC
Confidence            48999999999999999999988554

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

Probab=98.66  E-value=3.6e-06  Score=69.19  Aligned_cols=172  Identities=16%  Similarity=0.140  Sum_probs=94.5

Q ss_pred             ccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc----CCc---EEEEeccchhc
Q 022768           32 SAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI----DAN---FLKVVSSAIID  104 (292)
Q Consensus        32 ~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~---~~~~~~~~~~~  104 (292)
                      .+++|++..+++|.+.+... .         -.....+.|+|..|+||||+|+.+++..    +..   ++-+.......
T Consensus        20 ~~~~gR~~~~~~i~~~L~~~-~---------~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~   89 (277)
T d2a5yb3          20 MTCYIREYHVDRVIKKLDEM-C---------DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAP   89 (277)
T ss_dssp             CCSCCCHHHHHHHHHHHHHH-T---------TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCST
T ss_pred             CceeCcHHHHHHHHHHHHhc-c---------CCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCC
Confidence            44789999999999988542 1         1235568899999999999999998763    211   12222111110


Q ss_pred             c--c----------------------cCh-HHHHHHHHHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHH
Q 022768          105 K--Y----------------------IGE-SARLIREMFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMEL  159 (292)
Q Consensus       105 ~--~----------------------~~~-~~~~~~~~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~  159 (292)
                      .  .                      ... ...............++.+++||++...             .   .+.. 
T Consensus        90 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~-------------~---~~~~-  152 (277)
T d2a5yb3          90 KSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQE-------------E---TIRW-  152 (277)
T ss_dssp             THHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCH-------------H---HHHH-
T ss_pred             HHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHH-------------h---hhhh-
Confidence            0  0                      000 1111112222333456789999998643             1   1111 


Q ss_pred             HHHhhCCCCCCCeEEEEEeCCCCCCChhhcCCCCcceEEEccCCCHHHHHHHHHHHHcCccCCCCC--CHHHHHHHcCCC
Q 022768          160 LNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMEILKIHAAGIAKHGEI--DYEAVVKLAEGF  237 (292)
Q Consensus       160 l~~~~~~~~~~~~~vi~t~~~~~~l~~~l~~~~r~~~~i~l~~p~~~~r~~i~~~~~~~~~~~~~~--~~~~l~~~~~g~  237 (292)
                      +..       .+..+|+||+...-. ..+..  .. ..+.+..++.++-.+++..+..........  ....+...+.| 
T Consensus       153 ~~~-------~~srilvTTR~~~v~-~~~~~--~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~G-  220 (277)
T d2a5yb3         153 AQE-------LRLRCLVTTRDVEIS-NAASQ--TC-EFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSG-  220 (277)
T ss_dssp             HHH-------TTCEEEEEESBGGGG-GGCCS--CE-EEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTT-
T ss_pred             hcc-------cCceEEEEeehHHHH-HhcCC--CC-ceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCC-
Confidence            111       244578888754221 11211  11 457899999999999998765432211110  12456677777 


Q ss_pred             CHHHH
Q 022768          238 NGADL  242 (292)
Q Consensus       238 ~~~di  242 (292)
                      .|--+
T Consensus       221 lPLAl  225 (277)
T d2a5yb3         221 NPATL  225 (277)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            45333

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=98.37  E-value=1e-06  Score=70.77  Aligned_cols=31  Identities=26%  Similarity=0.332  Sum_probs=26.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+.++..+.|.||+|+||||+++.++..+..
T Consensus        25 ~i~~Ge~vaIvG~sGsGKSTLl~ll~gl~~p   55 (241)
T d2pmka1          25 SIKQGEVIGIVGRSGSGKSTLTKLIQRFYIP   55 (241)
T ss_dssp             EEETTCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHHhcCCC
Confidence            3577889999999999999999999987643

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=98.32  E-value=1.6e-06  Score=70.24  Aligned_cols=30  Identities=37%  Similarity=0.462  Sum_probs=26.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|+||+|+||||+++.++....
T Consensus        37 ~i~~Ge~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          37 KIPAGKTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             EECTTCEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhcccC
Confidence            367788999999999999999999997663

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=98.31  E-value=2.5e-07  Score=73.58  Aligned_cols=31  Identities=29%  Similarity=0.438  Sum_probs=26.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+.++..+.|.||+|+||||+++.++.....
T Consensus        22 ~i~~Ge~~~liGpsGaGKSTll~~l~Gl~~p   52 (229)
T d3d31a2          22 KVESGEYFVILGPTGAGKTLFLELIAGFHVP   52 (229)
T ss_dssp             EECTTCEEEEECCCTHHHHHHHHHHHTSSCC
T ss_pred             EECCCCEEEEECCCCCcHHHHHHHHhcCcCC
Confidence            4677888999999999999999999976633

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=98.31  E-value=3.2e-07  Score=73.50  Aligned_cols=29  Identities=38%  Similarity=0.483  Sum_probs=25.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        25 ~i~~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          25 EVKDGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             EEETTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhcCC
Confidence            35678889999999999999999999765

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=98.30  E-value=2e-07  Score=69.97  Aligned_cols=32  Identities=28%  Similarity=0.654  Sum_probs=28.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      ++|+|.||||+||||+++.+|..++.+++...
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L~~~~id~~   34 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD   34 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            46999999999999999999999999987544

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.27  E-value=2.8e-06  Score=67.47  Aligned_cols=51  Identities=22%  Similarity=0.313  Sum_probs=35.9

Q ss_pred             HHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCC
Q 022768          118 FGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRP  181 (292)
Q Consensus       118 ~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~  181 (292)
                      ++.+....|.+|++||-          ++.-+......+.+++..+..   ..++.+|.+|++.
T Consensus       156 IAraL~~~P~lLllDEP----------Ts~LD~~~~~~i~~~l~~l~~---~~g~tii~vTHd~  206 (230)
T d1l2ta_         156 IARALANNPPIILADQP----------TGALDSKTGEKIMQLLKKLNE---EDGKTVVVVTHDI  206 (230)
T ss_dssp             HHHHHTTCCSEEEEEST----------TTTSCHHHHHHHHHHHHHHHH---TTCCEEEEECSCH
T ss_pred             HHhhhhcCCCEEEecCC----------ccccCHHHHHHHHHHHHHHHH---hhCCEEEEECCCH
Confidence            33444578999999995          455578888888888877631   1367788888854

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=98.25  E-value=1.4e-06  Score=69.61  Aligned_cols=30  Identities=40%  Similarity=0.494  Sum_probs=26.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++....
T Consensus        28 ~v~~Ge~~~liGpsGaGKSTLl~~i~Gl~~   57 (239)
T d1v43a3          28 TIKDGEFLVLLGPSGCGKTTTLRMIAGLEE   57 (239)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHHcCCC
Confidence            467788899999999999999999997663

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.25  E-value=2.5e-07  Score=73.74  Aligned_cols=29  Identities=38%  Similarity=0.499  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        22 ~i~~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          22 DIHEGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhcCC
Confidence            46778899999999999999999999755

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=98.23  E-value=3.3e-07  Score=69.71  Aligned_cols=37  Identities=30%  Similarity=0.398  Sum_probs=32.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      ++.|+|.||||+||||+++.+++.++.+++.++...+
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~d~~   40 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDDL   40 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTTHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCEEEecHHHH
Confidence            5678899999999999999999999999998876544

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=98.23  E-value=4.3e-07  Score=72.73  Aligned_cols=30  Identities=20%  Similarity=0.224  Sum_probs=26.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+..+..+.|.||+|+||||+++.++....
T Consensus        27 ~i~~Ge~~~iiG~sGsGKSTLl~~i~Gl~~   56 (240)
T d3dhwc1          27 HVPAGQIYGVIGASGAGKSTLIRCVNLLER   56 (240)
T ss_dssp             EECSSCEEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHcCCcc
Confidence            467788899999999999999999997653

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=98.22  E-value=4e-07  Score=69.78  Aligned_cols=37  Identities=19%  Similarity=0.272  Sum_probs=31.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      .+.|+|.|||||||||+|+.|++.++.+++......+
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~~~~~   43 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFNTTSAWEYGREF   43 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCEEECCTTHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCCeEeeehHHH
Confidence            5679999999999999999999999988876554443

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.21  E-value=3.9e-06  Score=67.81  Aligned_cols=30  Identities=30%  Similarity=0.379  Sum_probs=26.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.|++|+||||+++.++....
T Consensus        40 ~i~~Ge~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          40 SIEKGETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHHhcCC
Confidence            367888999999999999999999997653

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=98.21  E-value=4.1e-07  Score=68.93  Aligned_cols=29  Identities=38%  Similarity=0.730  Sum_probs=26.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .++|+|||||||||+|+.++..++.+++.
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~i~   34 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKYIN   34 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEe
Confidence            58899999999999999999999988864

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=98.18  E-value=4e-06  Score=72.57  Aligned_cols=103  Identities=17%  Similarity=0.268  Sum_probs=69.3

Q ss_pred             hhhcccCCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCC---cEE
Q 022768           19 YNMLHEDPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDA---NFL   95 (292)
Q Consensus        19 ~~~~~~~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~---~~~   95 (292)
                      ...+....+..++.+|.-.+...+.+.+.+..+              ...+||.||.|+||||++.++.+.+..   +++
T Consensus       125 lRl~~~~~~~~~l~~LG~~~~~~~~l~~l~~~~--------------~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~  190 (401)
T d1p9ra_         125 MRLLDKNATRLDLHSLGMTAHNHDNFRRLIKRP--------------HGIILVTGPTGSGKSTTLYAGLQELNSSERNIL  190 (401)
T ss_dssp             ECCEETTTTCCCGGGSCCCHHHHHHHHHHHTSS--------------SEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEE
T ss_pred             hhhhcccccchhhhhhcccHHHHHHHHHHHhhh--------------hceEEEEcCCCCCccHHHHHHhhhhcCCCceEE
Confidence            334455666778999877777888888877543              566889999999999999999998743   344


Q ss_pred             EEecc-ch-----hc-cccChHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768           96 KVVSS-AI-----ID-KYIGESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        96 ~~~~~-~~-----~~-~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      .+... +.     .. ...+.........+..+....|.+|++.|+-
T Consensus       191 tiEdPiE~~~~~~~q~~v~~~~~~~~~~~l~~~lR~dPDvi~igEiR  237 (401)
T d1p9ra_         191 TVEDPIEFDIDGIGQTQVNPRVDMTFARGLRAILRQDPDVVMVGEIR  237 (401)
T ss_dssp             EEESSCCSCCSSSEEEECBGGGTBCHHHHHHHHGGGCCSEEEESCCC
T ss_pred             EeccCcccccCCCCeeeecCCcCCCHHHHHHHHHhhcCCEEEecCcC
Confidence            33311 11     00 0011122234566677778899999999995

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=98.17  E-value=2.7e-06  Score=68.23  Aligned_cols=29  Identities=34%  Similarity=0.370  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++..+
T Consensus        28 ~i~~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          28 KVPRGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             EEETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EECCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35678889999999999999999999765

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=98.17  E-value=9.3e-06  Score=64.89  Aligned_cols=31  Identities=35%  Similarity=0.424  Sum_probs=26.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+.++..+-|.||+|+||||+++.++..+..
T Consensus        24 ~v~~Gei~glvG~nGaGKSTLl~~l~G~~~p   54 (238)
T d1vpla_          24 EIEEGEIFGLIGPNGAGKTTTLRIISTLIKP   54 (238)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            3577888999999999999999999987643

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=98.16  E-value=3.9e-07  Score=73.02  Aligned_cols=30  Identities=33%  Similarity=0.478  Sum_probs=26.2

Q ss_pred             cCCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           61 VGIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        61 ~~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.+.++..+.|.||+|+||||+++.++...
T Consensus        26 l~i~~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          26 INIENGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             EEECTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             EEECCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            346778899999999999999999999755

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=98.15  E-value=1e-06  Score=66.78  Aligned_cols=35  Identities=20%  Similarity=0.349  Sum_probs=30.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      ++.|+|+|+||+||||+++.|++.++.+++.++..
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~~d   37 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVD   37 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCCeEEeecc
Confidence            45789999999999999999999999888877643

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.13  E-value=6e-06  Score=66.60  Aligned_cols=30  Identities=27%  Similarity=0.495  Sum_probs=26.4

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++....
T Consensus        36 ~i~~Ge~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          36 TLRPGEVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhcccC
Confidence            367888999999999999999999997663

>d1e6ca_ c.37.1.2 (A:) Shikimate kinase (AroK) {Erwinia chrysanthemi [TaxId: 556]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Erwinia chrysanthemi [TaxId: 556]

Probab=98.13  E-value=5.5e-07  Score=68.53  Aligned_cols=31  Identities=23%  Similarity=0.512  Sum_probs=27.9

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .+++|.|+||+||||+++.+|..+|.+++..
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~   33 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDT   33 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEeh
Confidence            3588999999999999999999999998854

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.11  E-value=7.4e-06  Score=66.23  Aligned_cols=52  Identities=19%  Similarity=0.326  Sum_probs=36.4

Q ss_pred             HHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCCC
Q 022768          119 GYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVL  184 (292)
Q Consensus       119 ~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~l  184 (292)
                      ..+....|.+|++||-          +.+.+......+.+++..+..    .++.+|.++++.+.+
T Consensus       162 AraL~~~P~llilDEP----------t~gLD~~~~~~i~~~i~~l~~----~g~til~vsHdl~~~  213 (254)
T d1g6ha_         162 GRALMTNPKMIVMDEP----------IAGVAPGLAHDIFNHVLELKA----KGITFLIIEHRLDIV  213 (254)
T ss_dssp             HHHHHTCCSEEEEEST----------TTTCCHHHHHHHHHHHHHHHH----TTCEEEEECSCCSTT
T ss_pred             HHHHHhCcCchhhcCC----------cccCCHHHHHHHHHHHHHHHH----CCCEEEEEeCcHHHH
Confidence            3344578999999995          344577777778887777642    357788888876654

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=98.11  E-value=2.1e-06  Score=69.00  Aligned_cols=29  Identities=21%  Similarity=0.368  Sum_probs=25.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        24 ~i~~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          24 EAQPNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EECTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            36778899999999999999999999755

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=98.11  E-value=1.3e-05  Score=64.00  Aligned_cols=78  Identities=21%  Similarity=0.237  Sum_probs=52.6

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------------------ccChH
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------------------YIGES  110 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------------------~~~~~  110 (292)
                      |++++..++|+|+||+|||+++..++...   +..+.++....-...                            .....
T Consensus        22 Gi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (242)
T d1tf7a2          22 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGL  101 (242)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEESSSCHHHHHHHHHTTSCCHHHHHHTTSEEECCCCGGGSCH
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeeccCCHHHHHHHHHHcCCChHHHhhcCceEEEEeecchhhH
Confidence            36778889999999999999999999875   445555543311110                            00112


Q ss_pred             HHHHHHHHHHhhhCCCEEEEEcccccccC
Q 022768          111 ARLIREMFGYARDHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       111 ~~~~~~~~~~~~~~~~~il~lDe~d~l~~  139 (292)
                      ...+..+........+.++++|.++.+..
T Consensus       102 ~~~~~~i~~~i~~~~~~~vviDs~~~~~~  130 (242)
T d1tf7a2         102 EDHLQIIKSEINDFKPARIAIDSLSALAR  130 (242)
T ss_dssp             HHHHHHHHHHHHTTCCSEEEEECHHHHTS
T ss_pred             HHHHHHHHHHHHhcCCceeeeecchhhhc
Confidence            33344555556667889999999988853

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=98.10  E-value=6.3e-07  Score=67.62  Aligned_cols=31  Identities=39%  Similarity=0.622  Sum_probs=27.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      +++|+|+||+||||+++.+|+.++.+++..+
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~~~~~d~d   32 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLDLVFLDSD   32 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEecC
Confidence            5889999999999999999999999988543

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=98.10  E-value=7.2e-07  Score=67.49  Aligned_cols=31  Identities=29%  Similarity=0.572  Sum_probs=27.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .++|+|+||+||||+++.+|..++.+|+..+
T Consensus         3 ~IvliG~~G~GKSTig~~La~~l~~~fiD~D   33 (165)
T d2iyva1           3 KAVLVGLPGSGKSTIGRRLAKALGVGLLDTD   33 (165)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            4777799999999999999999999988543

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.10  E-value=2e-05  Score=57.17  Aligned_cols=35  Identities=23%  Similarity=0.187  Sum_probs=27.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEecc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSS  100 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~  100 (292)
                      .+..+|.+|.|+|||+++-.++...+..++.+...
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~   42 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPS   42 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESC
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcCh
Confidence            45679999999999998877777777776665544

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=98.05  E-value=1.2e-06  Score=66.19  Aligned_cols=33  Identities=30%  Similarity=0.440  Sum_probs=28.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      ++-++|.|+|||||||+++.+++.++.+++..+
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d   38 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   38 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeechh
Confidence            456788999999999999999999988776544

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=98.03  E-value=2e-06  Score=65.08  Aligned_cols=29  Identities=41%  Similarity=0.672  Sum_probs=25.9

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      +.+.+|+|.||||+||||+++.|+..++.
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            45677999999999999999999999864

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=98.01  E-value=2.2e-06  Score=66.24  Aligned_cols=32  Identities=34%  Similarity=0.482  Sum_probs=27.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +..++|.|||||||||+|+.||..++.+++.+
T Consensus         3 ~~riil~G~pGSGKsT~a~~La~~~g~~~i~~   34 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   34 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            45688899999999999999999998766543

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Escherichia coli [TaxId: 562]

Probab=98.00  E-value=9.8e-06  Score=65.80  Aligned_cols=78  Identities=19%  Similarity=0.254  Sum_probs=51.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |++.++.+.|+||||+|||++|-.++...   +..+++++...-...                .....+..+..+-....
T Consensus        50 Gi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~  129 (263)
T d1u94a1          50 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  129 (263)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHHHh
Confidence            46778889999999999999998888755   556677664432210                01123333333333344


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+++++||-+..++.
T Consensus       130 ~~~~~liViDSi~al~~  146 (263)
T d1u94a1         130 SGAVDVIVVDSVAALTP  146 (263)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEECcccccc
Confidence            46678999999988863

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.99  E-value=1.5e-05  Score=65.34  Aligned_cols=30  Identities=27%  Similarity=0.418  Sum_probs=26.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .+.++..+.|.||+|+||||+++.++..+.
T Consensus        58 ~i~~Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          58 NIEKGEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             EECTTCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhCCCc
Confidence            467888999999999999999999998763

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.99  E-value=2.7e-06  Score=65.86  Aligned_cols=33  Identities=27%  Similarity=0.438  Sum_probs=28.0

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ..+..|+|.||||+||||+|+.||..++.+++.
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~~~g~~~i~   36 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLS   36 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHCCceEc
Confidence            345678999999999999999999999876554

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.98  E-value=1.9e-06  Score=64.96  Aligned_cols=28  Identities=25%  Similarity=0.517  Sum_probs=25.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      -++|.||||+||||+++.+++.++..++
T Consensus         4 lI~i~G~~GsGKTTva~~L~~~~~~~~~   31 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLAAQLDNSAY   31 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSSEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            5889999999999999999999987654

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=97.98  E-value=3.6e-06  Score=64.82  Aligned_cols=34  Identities=21%  Similarity=0.429  Sum_probs=28.9

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      |.+...+++|+|||+||||+++.++++-++..++
T Consensus        49 ~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vi   82 (205)
T d1tuea_          49 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVI   82 (205)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEEC
T ss_pred             CCCCceEEEEECCCCccHHHHHHHHHHHhCCEEE
Confidence            3566788999999999999999999999875543

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=97.97  E-value=8.7e-06  Score=63.38  Aligned_cols=29  Identities=34%  Similarity=0.507  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++..+
T Consensus        23 ~i~~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          23 TIEKGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             EEETTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhccc
Confidence            35678889999999999999999999766

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.96  E-value=1.9e-06  Score=65.70  Aligned_cols=24  Identities=42%  Similarity=0.732  Sum_probs=22.6

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ++|+|+|||||||||+++.++..+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            579999999999999999999887

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.95  E-value=2.9e-05  Score=63.07  Aligned_cols=122  Identities=18%  Similarity=0.182  Sum_probs=68.1

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |++.++.+.|+||+|+|||++|..++...   +..+++++...-.+.                .....+..+..+-....
T Consensus        53 Gip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~  132 (268)
T d1xp8a1          53 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  132 (268)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHh
Confidence            35678889999999999999998888755   566777775432211                11123333333333334


Q ss_pred             hCCCEEEEEcccccccCCcC-CCCCcc--hHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCCC
Q 022768          123 DHQPCIIFMDEIDAIGGRRF-SEGTSA--DREIQRTLMELLNQLDGFDQLGKVKMIMATNRPDV  183 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~~~~-~~~~~~--~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~~  183 (292)
                      ...+.++++|-+..++++.. +.....  .......+..+++.+.......++.+|++.+....
T Consensus       133 ~~~~~liIiDSi~al~~r~e~~~~~~~~~~~~~a~~l~~~lr~l~~~~~~~~~~vi~tNQv~~~  196 (268)
T d1xp8a1         133 SGAIDVVVVDSVAALTPRAEIEGDMGDSLPGLQARLMSQALRKLTAILSKTGTAAIFINQVREK  196 (268)
T ss_dssp             TTCCSEEEEECTTTCCCSTTC--------CCHHHHHHHHHHHHHHHHHTTTCCEEEEEEEC---
T ss_pred             cCCCcEEEEecccccccHHHHcccccchhHHHHHHHHHHHHHHHHhhhhhcCCeEEEEeEEeec
Confidence            45678999999988874332 111110  11233444455544433333346777777654433

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.95  E-value=2.6e-06  Score=64.67  Aligned_cols=29  Identities=24%  Similarity=0.368  Sum_probs=25.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      ..|..|+|+|+||+||||+++.|++.++.
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            45778999999999999999999998853

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=97.94  E-value=2e-06  Score=66.48  Aligned_cols=31  Identities=23%  Similarity=0.441  Sum_probs=27.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      |..++|.||||+||||+|+.++..++.+++.
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~~~~~is   33 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKYQLAHIS   33 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHCCcEEe
Confidence            4569999999999999999999999877653

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.94  E-value=3.3e-06  Score=64.51  Aligned_cols=30  Identities=27%  Similarity=0.451  Sum_probs=26.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .|+|.||||+||||+++.||..++.+++..
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~~~~~i~~   31 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAYGIPHIST   31 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceech
Confidence            488999999999999999999998877654

>d2onka1 c.37.1.12 (A:1-240) Molybdate/tungstate import ATP-binding protein WtpC (ModC) {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Molybdate/tungstate import ATP-binding protein WtpC (ModC)
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.92  E-value=2.4e-05  Score=62.20  Aligned_cols=53  Identities=23%  Similarity=0.193  Sum_probs=34.8

Q ss_pred             HHHHhhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhhCCCCCCCeEEEEEeCCCC
Q 022768          117 MFGYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLDGFDQLGKVKMIMATNRPD  182 (292)
Q Consensus       117 ~~~~~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~vi~t~~~~~  182 (292)
                      .+..+....|.+|++||-          +++.+......+.+++..+..   ..++.+|.+|++.+
T Consensus       136 aiAral~~~P~illlDEP----------ts~LD~~~~~~i~~~i~~l~~---~~g~tvi~vtHd~~  188 (240)
T d2onka1         136 ALARALVIQPRLLLLDEP----------LSAVDLKTKGVLMEELRFVQR---EFDVPILHVTHDLI  188 (240)
T ss_dssp             HHHHHHTTCCSSBEEEST----------TSSCCHHHHHHHHHHHHHHHH---HHTCCEEEEESCHH
T ss_pred             HHHHHHhccCCceEecCc----------cccCCHHHHHHHHHHHHHHHH---hcCCeEEEEeCCHH
Confidence            334444578999999995          344577777777777766531   02455788887643

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.91  E-value=3.3e-05  Score=62.37  Aligned_cols=29  Identities=21%  Similarity=0.307  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        24 ~i~~GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          24 QARAGDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            35778889999999999999999999755

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.88  E-value=5.8e-06  Score=64.07  Aligned_cols=32  Identities=19%  Similarity=0.341  Sum_probs=27.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ...++|.||||+||||+|+.|++.++.+++..
T Consensus         8 ~~iI~i~GppGSGKsT~a~~La~~~g~~~is~   39 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   39 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEEeh
Confidence            45688889999999999999999998776543

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.87  E-value=5.1e-06  Score=63.56  Aligned_cols=30  Identities=37%  Similarity=0.588  Sum_probs=27.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .++|.|||||||||+++.|+..++..++.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g~~~i~~   31 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLGIPQIST   31 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            488999999999999999999998887754

>d1l7vc_ c.37.1.12 (C:) ABC transporter involved in vitamin B12 uptake, BtuD {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ABC transporter involved in vitamin B12 uptake, BtuD
species: Escherichia coli [TaxId: 562]

Probab=97.86  E-value=2.7e-05  Score=61.89  Aligned_cols=29  Identities=28%  Similarity=0.436  Sum_probs=25.2

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++..+.|.||+|+||||+++.++...
T Consensus        21 ~I~~Gei~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          21 EVRAGEILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             EEETTCEEECBCCTTSSHHHHHHHHHTSC
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            35678899999999999999999999743

>d1teva_ c.37.1.1 (A:) UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.85  E-value=5.3e-06  Score=64.11  Aligned_cols=29  Identities=28%  Similarity=0.385  Sum_probs=25.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      ..|+|.||||+||||.|+.+|+.++..++
T Consensus         2 ~iI~i~GppGSGKsT~a~~La~~~g~~~i   30 (194)
T d1teva_           2 LVVFVLGGPGAGKGTQCARIVEKYGYTHL   30 (194)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCceE
Confidence            45889999999999999999999986664

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.85  E-value=1.4e-06  Score=67.32  Aligned_cols=29  Identities=28%  Similarity=0.325  Sum_probs=25.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      .|..|+|+|+||+||||+++.|+..++.+
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            36678899999999999999999988544

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=97.84  E-value=6.1e-06  Score=63.19  Aligned_cols=30  Identities=27%  Similarity=0.473  Sum_probs=26.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .|+|.|||||||||+++.||..++.+++.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~g~~~is~   31 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKYGTPHIST   31 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceeeH
Confidence            478999999999999999999998887754

>d3adka_ c.37.1.1 (A:) Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.84  E-value=5.7e-06  Score=64.07  Aligned_cols=31  Identities=26%  Similarity=0.417  Sum_probs=27.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +..|+|.||||+||||+|+.++..++.+++.
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~is   38 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTHLS   38 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeeEe
Confidence            5678899999999999999999999876653

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=97.83  E-value=5.7e-05  Score=59.61  Aligned_cols=38  Identities=32%  Similarity=0.348  Sum_probs=28.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~   99 (292)
                      |++++..++|+|+||+|||+++..++...    +..++++..
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~   63 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   63 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCcccccc
Confidence            46788999999999999999997765422    445555543

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.79  E-value=1.8e-05  Score=59.98  Aligned_cols=37  Identities=22%  Similarity=0.309  Sum_probs=28.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      +.+.-++++|+||+||||+++.++...+..  .++...+
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~~~~~--~i~~D~~   48 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVSAGYV--HVNRDTL   48 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGGGTCE--EEEHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhcCCE--EEchHHH
Confidence            345678899999999999999998887644  4444443

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.79  E-value=8.1e-06  Score=62.38  Aligned_cols=31  Identities=32%  Similarity=0.535  Sum_probs=26.9

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      ..++|.||||+||||+++.|+..++.+++..
T Consensus         3 mrIvl~G~pGSGKtT~a~~La~~~g~~~i~~   33 (180)
T d1akya1           3 IRMVLIGPPGAGKGTQAPNLQERFHAAHLAT   33 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceEec
Confidence            3578889999999999999999998776654

>d2ak3a1 c.37.1.1 (A:0-124,A:162-225) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-3 [TaxId: 9913]

Probab=97.77  E-value=8.8e-06  Score=62.79  Aligned_cols=31  Identities=23%  Similarity=0.446  Sum_probs=26.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      ...++|.||||+||||+++.||..++.+++.
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~~~g~~~is   36 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITKHFELKHLS   36 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHBCCEEEE
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            3458889999999999999999999866653

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=97.77  E-value=0.00032  Score=54.50  Aligned_cols=92  Identities=16%  Similarity=0.250  Sum_probs=53.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc--------------------ccChHHHHHHHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK--------------------YIGESARLIREMFGY  120 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~--------------------~~~~~~~~~~~~~~~  120 (292)
                      ..+..++|.||+|+||||.+--+|..+   +..+.-+.+..+...                    ...+....+......
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~   86 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQA   86 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHHHH
Confidence            335668899999999999887777655   455555554443221                    011223334444444


Q ss_pred             hhhCCCEEEEEcccccccCCcCCCCCcchHHHHHHHHHHHHHhh
Q 022768          121 ARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQLD  164 (292)
Q Consensus       121 ~~~~~~~il~lDe~d~l~~~~~~~~~~~~~~~~~~l~~~l~~~~  164 (292)
                      ++.....+++||=.-+.         ..+....+.+..+.+.+.
T Consensus        87 a~~~~~d~ilIDTaGr~---------~~d~~~~~el~~l~~~~~  121 (211)
T d2qy9a2          87 AKARNIDVLIADTAGRL---------QNKSHLMEELKKIVRVMK  121 (211)
T ss_dssp             HHHTTCSEEEECCCCCG---------GGHHHHHHHHHHHHHHHT
T ss_pred             HHHcCCCEEEeccCCCc---------cccHHHHHHHHHHHHHHh
Confidence            54455579999976443         224455566666655554

>d1e4va1 c.37.1.1 (A:1-121,A:157-214) Adenylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.77  E-value=8.9e-06  Score=62.00  Aligned_cols=30  Identities=23%  Similarity=0.339  Sum_probs=26.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      .++|.||||+||||.++.|++.++..++.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~~~~~i~~   31 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceech
Confidence            478899999999999999999998776643

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=97.75  E-value=4.1e-05  Score=63.94  Aligned_cols=70  Identities=19%  Similarity=0.287  Sum_probs=45.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCC--cEEEEecc-chh-------ccccChHHHHHHHHHHHhhhCCCEEEEEcccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDA--NFLKVVSS-AII-------DKYIGESARLIREMFGYARDHQPCIIFMDEID  135 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~--~~~~~~~~-~~~-------~~~~~~~~~~~~~~~~~~~~~~~~il~lDe~d  135 (292)
                      +.+++|+|++|+||||++++++...+.  .++.+... ++.       .............++..+....|..+++.|+-
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~l~~~~~~~~~~~~~~~~~~~ll~~~lR~~pd~iivgEiR  245 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELR  245 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEESCCC
T ss_pred             CCCEEEEeeccccchHHHHHHhhhcccccceeeccchhhhhcccccccceeccccchhHHHHHHHHhccCCCcccCCccC
Confidence            567999999999999999999988743  23332211 110       00111112234466677778899999999983

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.74  E-value=5.4e-05  Score=61.37  Aligned_cols=78  Identities=18%  Similarity=0.213  Sum_probs=51.3

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccchhcc----------------ccChHHHHHHHHHHHhh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAIIDK----------------YIGESARLIREMFGYAR  122 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~~  122 (292)
                      |++.++.+.|+||+|+|||++|-.++...   +..+++++...-.+.                .....+..+..+-....
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~  135 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            57888899999999999999997777644   566677665442210                11123333332222334


Q ss_pred             hCCCEEEEEcccccccC
Q 022768          123 DHQPCIIFMDEIDAIGG  139 (292)
Q Consensus       123 ~~~~~il~lDe~d~l~~  139 (292)
                      ...+++++||-+..+++
T Consensus       136 ~~~~~liIiDSi~al~~  152 (269)
T d1mo6a1         136 SGALDIVVIDSVAALVP  152 (269)
T ss_dssp             TTCEEEEEEECSTTCCC
T ss_pred             cCCCCEEEEeccccccc
Confidence            45678999999988874

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=97.73  E-value=3.3e-05  Score=63.00  Aligned_cols=38  Identities=16%  Similarity=0.231  Sum_probs=30.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh----cCCcEEEEec
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN----IDANFLKVVS   99 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~----l~~~~~~~~~   99 (292)
                      |+.++..++|.|+||+|||+++..++..    .+.++..++.
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~   72 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAML   72 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEES
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeee
Confidence            5788889999999999999998888753    2667777664

>d1ckea_ c.37.1.1 (A:) CMP kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Escherichia coli [TaxId: 562]

Probab=97.71  E-value=1.2e-05  Score=63.20  Aligned_cols=28  Identities=32%  Similarity=0.589  Sum_probs=25.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      .|.|.||||+||+|.++.+++.++.+++
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~gl~~i   32 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEALQWHLL   32 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            6778899999999999999999987664

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.71  E-value=4.1e-05  Score=59.50  Aligned_cols=34  Identities=15%  Similarity=0.326  Sum_probs=26.3

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcC---CcEEEEecc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNID---ANFLKVVSS  100 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~---~~~~~~~~~  100 (292)
                      .-|+++|.||+||||+++.+++.++   ..+..++..
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~~~~~~~~~~~~D   39 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFNVG   39 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhcCCCCeEEccc
Confidence            4578899999999999999998774   344445443

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=97.70  E-value=6.6e-05  Score=63.61  Aligned_cols=23  Identities=30%  Similarity=0.468  Sum_probs=18.1

Q ss_pred             CceEEEEcCCCChHHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ++.++|+||||||||+++..+..
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~  185 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLA  185 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHH
T ss_pred             CCeEEEEcCCCCCceehHHHHHH
Confidence            34689999999999998755443

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=97.69  E-value=0.00021  Score=55.50  Aligned_cols=37  Identities=19%  Similarity=0.240  Sum_probs=26.4

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      .+..++|.||+|+||||.+--+|+.+   +..+.-+....
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt   44 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDT   44 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEecc
Confidence            35678899999999999877777655   45555444443

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.68  E-value=1.6e-05  Score=58.61  Aligned_cols=34  Identities=26%  Similarity=0.425  Sum_probs=25.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccch
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAI  102 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~  102 (292)
                      .|+|+|+||+||||+++.++.... .+..++...+
T Consensus         4 lIii~G~pGsGKTTla~~L~~~~~-~~~~~~~d~~   37 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIAKNP-GFYNINRDDY   37 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHST-TEEEECHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCC-CCEEechHHH
Confidence            578899999999999999887653 3444444433

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=97.68  E-value=0.0005  Score=53.44  Aligned_cols=39  Identities=23%  Similarity=0.388  Sum_probs=27.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccch
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAI  102 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~  102 (292)
                      ..+..++|.||+|+||||.+--+|..+   +..+.-+.+..+
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~Dt~   50 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAADTF   50 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEECTT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeeccc
Confidence            346668899999999999877777655   445544444433

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.65  E-value=0.0002  Score=56.74  Aligned_cols=25  Identities=24%  Similarity=0.300  Sum_probs=21.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.++|+||..+|||+++|.++-..
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~   65 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIA   65 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHH
Confidence            4568999999999999999998533

>d1q3ta_ c.37.1.1 (A:) CMP kinase {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: CMP kinase
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=97.63  E-value=1.6e-05  Score=62.64  Aligned_cols=28  Identities=29%  Similarity=0.619  Sum_probs=24.4

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      |.|.||||+||||.|+.||..++.+++.
T Consensus         6 IaIdGp~GsGKgT~ak~La~~lg~~~is   33 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDFGFTYLD   33 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            5577999999999999999999877653

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=97.61  E-value=9.2e-05  Score=53.19  Aligned_cols=20  Identities=35%  Similarity=0.262  Sum_probs=16.8

Q ss_pred             CCCceEEEEcCCCChHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+..++|++|+|+|||..+
T Consensus         5 ~~~~~~il~~~tGsGKT~~~   24 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRF   24 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTH
T ss_pred             HcCCcEEEEcCCCCChhHHH
Confidence            45788999999999999655

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=97.59  E-value=0.00049  Score=53.34  Aligned_cols=36  Identities=28%  Similarity=0.240  Sum_probs=25.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      +..++|.||+|+||||++.-+|..+   +..+..+.+..
T Consensus        10 ~~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt   48 (207)
T d1ls1a2          10 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADT   48 (207)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeccc
Confidence            4457889999999999887777655   55555555443

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=97.57  E-value=0.00014  Score=56.68  Aligned_cols=37  Identities=27%  Similarity=0.222  Sum_probs=22.1

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      .+..++|.||+|+||||++--+|..+   +..+..+.+..
T Consensus        11 ~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt   50 (211)
T d1j8yf2          11 IPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGADV   50 (211)
T ss_dssp             SSEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEECCC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEeec
Confidence            45668889999999999877777655   44554444443

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.52  E-value=4.4e-05  Score=58.52  Aligned_cols=25  Identities=24%  Similarity=0.320  Sum_probs=21.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .|.|.||+|+||||+|+.|+..++.
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcc
Confidence            3558999999999999999987743

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.52  E-value=2.4e-05  Score=58.53  Aligned_cols=23  Identities=26%  Similarity=0.320  Sum_probs=21.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.|+|++|||||||++.+++.+
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l   26 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPAL   26 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            58899999999999999999876

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=97.52  E-value=2.3e-05  Score=59.54  Aligned_cols=26  Identities=31%  Similarity=0.464  Sum_probs=23.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      +.|+|.|+||+||||+++.++..++.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~   27 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRK   27 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            46889999999999999999998744

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=97.51  E-value=0.00041  Score=54.51  Aligned_cols=24  Identities=33%  Similarity=0.375  Sum_probs=20.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.++|+||..+|||+++|.++-..
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~   59 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIA   59 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHHHH
Confidence            358999999999999999988533

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.44  E-value=0.00035  Score=55.13  Aligned_cols=28  Identities=29%  Similarity=0.420  Sum_probs=24.8

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      |++++..++|+||||+|||+++..++..
T Consensus        30 Gi~~G~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          30 GVETGSITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             SEESSSEEEEEESTTSSHHHHHHHHTTT
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4778899999999999999999988754

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.43  E-value=6.3e-05  Score=58.72  Aligned_cols=41  Identities=17%  Similarity=0.209  Sum_probs=33.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc----CCcEEEEeccchhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI----DANFLKVVSSAIID  104 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l----~~~~~~~~~~~~~~  104 (292)
                      ..+..|+|+|.||+||||+++.|++.+    +.+++.++...+..
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~iR~   66 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNIRF   66 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHHTT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchHHHH
Confidence            457789999999999999999999765    56777777666554

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=97.41  E-value=0.00045  Score=55.75  Aligned_cols=27  Identities=33%  Similarity=0.432  Sum_probs=22.8

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++..++|+|++|+|||+++-.+|..+
T Consensus        27 ~pg~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          27 VAGTVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            347788999999999999998888653

>d1gkya_ c.37.1.1 (A:) Guanylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.39  E-value=6.1e-05  Score=57.68  Aligned_cols=29  Identities=28%  Similarity=0.575  Sum_probs=24.7

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      +.|+|+||+|+||||+++.+++..+..+.
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~~~   30 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDSFG   30 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCccee
Confidence            35899999999999999999998765443

>d1lvga_ c.37.1.1 (A:) Guanylate kinase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.37  E-value=6.6e-05  Score=57.72  Aligned_cols=29  Identities=31%  Similarity=0.462  Sum_probs=25.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .|+|.||+|+||||+++.++...+..+..
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~~~~~   30 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSSIFGF   30 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTTTEEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCceeE
Confidence            48999999999999999999988765544

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=97.37  E-value=0.00018  Score=53.10  Aligned_cols=55  Identities=20%  Similarity=0.186  Sum_probs=37.1

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      ..+..+++..++-+.+...      ..+....++..++|.|+=|+||||++|.+++.++..
T Consensus         6 ~~l~~e~~t~~lg~~la~~------l~~~~~~~g~ii~L~G~LGaGKTtfvr~~~~~lg~~   60 (158)
T d1htwa_           6 QYIPDEFSMLRFGKKFAEI------LLKLHTEKAIMVYLNGDLGAGKTTLTRGMLQGIGHQ   60 (158)
T ss_dssp             EEECSHHHHHHHHHHHHHH------HHHHCCSSCEEEEEECSTTSSHHHHHHHHHHHTTCC
T ss_pred             eeCCCHHHHHHHHHHHHHH------HHhccCCCCeEEEEecCCCccHHHHHHHHHhhcccc
Confidence            3345555555554444332      111223556779999999999999999999999764

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=97.31  E-value=0.0002  Score=57.92  Aligned_cols=30  Identities=37%  Similarity=0.552  Sum_probs=26.0

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .+....++|+||+++|||+++.++++.+|.
T Consensus       101 ~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~  130 (267)
T d1u0ja_         101 FGKRNTIWLFGPATTGKTNIAEAIAHTVPF  130 (267)
T ss_dssp             STTCCEEEEECSTTSSHHHHHHHHHHHSSC
T ss_pred             CCccEEEEEEcCCCCCHHHHHHHHHHHhcc
Confidence            355667899999999999999999999864

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=97.27  E-value=8.8e-05  Score=56.45  Aligned_cols=27  Identities=30%  Similarity=0.532  Sum_probs=23.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      |..++|.||+|+||||+++.++.....
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~~~~~~   28 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLRERIPN   28 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhCCC
Confidence            457899999999999999999988753

>d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable tRNA modification GTPase TrmE (MnmE), G domain
species: Escherichia coli [TaxId: 562]

Probab=97.26  E-value=0.00073  Score=49.70  Aligned_cols=23  Identities=35%  Similarity=0.554  Sum_probs=20.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -.|+|.|++|+|||||++++...
T Consensus         2 ~kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           2 MKVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999999843

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.22  E-value=7.5e-05  Score=58.00  Aligned_cols=29  Identities=28%  Similarity=0.387  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      |+.++..++|+||||+|||+++..++...
T Consensus        19 Gi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          19 GIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            46788999999999999999999998754

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=97.16  E-value=9.1e-05  Score=56.29  Aligned_cols=26  Identities=23%  Similarity=0.395  Sum_probs=22.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      .++|.|++|+||||+++.++..++..
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~   28 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQ   28 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            46789999999999999999988543

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=97.11  E-value=0.00028  Score=52.58  Aligned_cols=23  Identities=22%  Similarity=0.130  Sum_probs=20.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .+.|+|.+|||||||+..++.++
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L   25 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAA   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            45699999999999999999876

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=97.10  E-value=0.00011  Score=58.70  Aligned_cols=29  Identities=34%  Similarity=0.515  Sum_probs=25.7

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      |++++..++|+||||+|||+++-.++...
T Consensus        32 Glp~G~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          32 GIETQAITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            47888999999999999999999888654

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Meiotic recombination protein DMC1/LIM15 homolog
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.06  E-value=0.00018  Score=57.26  Aligned_cols=28  Identities=29%  Similarity=0.354  Sum_probs=25.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      |++++..++|+|+||+|||+++..++..
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~   60 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVT   60 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            5788999999999999999999999864

>d2fh5b1 c.37.1.8 (B:63-269) Signal recognition particle receptor beta-subunit {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.04  E-value=0.0038  Score=47.82  Aligned_cols=23  Identities=35%  Similarity=0.482  Sum_probs=20.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ++|+|.|++|+|||+|++.+...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            36999999999999999999863

>d1wf3a1 c.37.1.8 (A:3-180) GTPase Era, N-terminal domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Thermus thermophilus [TaxId: 274]

Probab=97.01  E-value=0.0023  Score=47.88  Aligned_cols=23  Identities=26%  Similarity=0.352  Sum_probs=20.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..|.|.|.+|+|||++++.+++.
T Consensus         6 ~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           6 GFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999999864

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.96  E-value=0.00026  Score=55.11  Aligned_cols=26  Identities=15%  Similarity=0.162  Sum_probs=22.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      -.|.|.|++|+||||+++.++..++.
T Consensus         3 ~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           3 FLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhch
Confidence            45678999999999999999998864

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.93  E-value=0.00029  Score=53.33  Aligned_cols=28  Identities=21%  Similarity=0.489  Sum_probs=23.5

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      +.++|.||+|+||+|+++.++......+
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~~~~~   31 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKHPDRF   31 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCTTTE
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhCCcCe
Confidence            4689999999999999999998764444

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.92  E-value=0.00082  Score=55.25  Aligned_cols=40  Identities=15%  Similarity=0.273  Sum_probs=30.0

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhcC-----CcEEEEeccchh
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNID-----ANFLKVVSSAII  103 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l~-----~~~~~~~~~~~~  103 (292)
                      ..+..|.|.|++|+||||+++.+...+.     ..+..+....+.
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F~  122 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFL  122 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGB
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeeeE
Confidence            3455677999999999999999999873     345556655553

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.89  E-value=0.00031  Score=54.52  Aligned_cols=26  Identities=23%  Similarity=0.351  Sum_probs=23.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      |.-++|+||+|+||||+.+.++...+
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhCC
Confidence            55688999999999999999999865

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=96.84  E-value=0.003  Score=50.51  Aligned_cols=25  Identities=24%  Similarity=0.400  Sum_probs=21.9

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ....|+|.|.+|+|||+++.++...
T Consensus        31 ~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          31 NSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCcEEEEECCCCCcHHHHHHHHhCC
Confidence            3567999999999999999999864

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.83  E-value=0.0045  Score=47.56  Aligned_cols=51  Identities=25%  Similarity=0.230  Sum_probs=36.1

Q ss_pred             cccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEec
Q 022768           33 AVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVS   99 (292)
Q Consensus        33 ~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~   99 (292)
                      ++.-.+.+.+.+..++.                +...++.+|+|+|||.++-.++..++.+++.+..
T Consensus        68 ~~~Lr~yQ~eav~~~~~----------------~~~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~p  118 (206)
T d2fz4a1          68 EISLRDYQEKALERWLV----------------DKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVP  118 (206)
T ss_dssp             CCCCCHHHHHHHHHHTT----------------TSEEEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             CCCcCHHHHHHHHHHHh----------------CCCcEEEeCCCCCceehHHhHHHHhcCceeEEEc
Confidence            34455666666655432                2346788999999999998888888877766554

>d1r8sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF1 [TaxId: 9606]

Probab=96.83  E-value=0.0016  Score=47.35  Aligned_cols=22  Identities=23%  Similarity=0.359  Sum_probs=19.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .|+|.|+||+|||+|++.++..
T Consensus         2 kivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3889999999999999998854

>d1uf9a_ c.37.1.1 (A:) Dephospho-CoA kinase {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Thermus thermophilus [TaxId: 274]

Probab=96.79  E-value=0.00058  Score=51.99  Aligned_cols=30  Identities=23%  Similarity=0.307  Sum_probs=24.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      +.-+.|+|++||||||+|+.+ ...|.+++.
T Consensus         3 p~IIgitG~~gSGKstva~~l-~~~g~~~~~   32 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALL-RSWGYPVLD   32 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHH-HHTTCCEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHH-HHCCCeEEE
Confidence            344668999999999999998 567877764

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.78  E-value=0.0003  Score=55.64  Aligned_cols=29  Identities=24%  Similarity=0.360  Sum_probs=25.5

Q ss_pred             CCCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           62 GIKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        62 ~~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      |++++..++|.|+||+|||+++..+|...
T Consensus        30 Gl~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          30 GLESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            36778899999999999999999998654

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=96.72  E-value=0.0039  Score=51.56  Aligned_cols=72  Identities=22%  Similarity=0.240  Sum_probs=45.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CC--cEEEEeccchhcc----------------------------ccChHH
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DA--NFLKVVSSAIIDK----------------------------YIGESA  111 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~--~~~~~~~~~~~~~----------------------------~~~~~~  111 (292)
                      ....+-|.|+||+||||++..++..+   +.  -++.++.....+.                            ..+...
T Consensus        50 ~~~~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~~~gg~llgdr~rm~~~~~~~~~~ir~~~~~~~~gg~~  129 (323)
T d2qm8a1          50 RAIRVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSSTRTGGSILGDKTRMARLAIDRNAFIRPSPSSGTLGGVA  129 (323)
T ss_dssp             CSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGGSSCCCSSCCGGGSTTGGGCTTEEEECCCCCSSHHHHH
T ss_pred             CceEEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccHHHHhccccchhhHHHHhcccceeeccccccccccchh
Confidence            35568899999999999999999764   22  3444444332210                            112233


Q ss_pred             HHHHHHHHHhhhCCCEEEEEccccc
Q 022768          112 RLIREMFGYARDHQPCIIFMDEIDA  136 (292)
Q Consensus       112 ~~~~~~~~~~~~~~~~il~lDe~d~  136 (292)
                      .........+.....++++++-+..
T Consensus       130 ~~~~~~i~~~~~~g~d~iiiETVG~  154 (323)
T d2qm8a1         130 AKTRETMLLCEAAGFDVILVETVGV  154 (323)
T ss_dssp             HHHHHHHHHHHHTTCCEEEEEECSS
T ss_pred             HHHHHHHHhhccCCCCeEEEeehhh
Confidence            4455555555666668999988744

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=96.68  E-value=0.0007  Score=50.83  Aligned_cols=28  Identities=29%  Similarity=0.436  Sum_probs=23.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      +.+++|.|++|+|||+++-.+... |..+
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~-g~~l   41 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQR-GHRL   41 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHT-TCEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeE
Confidence            678999999999999999888875 5544

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.68  E-value=0.004  Score=51.52  Aligned_cols=72  Identities=15%  Similarity=0.260  Sum_probs=42.9

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CC--cEEEEeccchhc----------------------------cccChHH
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DA--NFLKVVSSAIID----------------------------KYIGESA  111 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~--~~~~~~~~~~~~----------------------------~~~~~~~  111 (292)
                      ....|-|.|+||+|||||+..++..+   +.  .++.++.....+                            ...+...
T Consensus        53 ~~~~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~~~ggailgdr~rm~~~~~~~~~~ir~~~~~g~lgg~~  132 (327)
T d2p67a1          53 NTLRLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSPVTGGSILGDKTRMNDLARAEAAFIRPVPSSGHLGGAS  132 (327)
T ss_dssp             CSEEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC---------------CTTTTCTTEEEEEECC-----CHH
T ss_pred             CceEEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCceeeeccccccchhHHHHhcccccccccccccccccccch
Confidence            35568899999999999999998755   22  233343322111                            0112233


Q ss_pred             HHHHHHHHHhhhCCCEEEEEccccc
Q 022768          112 RLIREMFGYARDHQPCIIFMDEIDA  136 (292)
Q Consensus       112 ~~~~~~~~~~~~~~~~il~lDe~d~  136 (292)
                      .........+.....++++++-+..
T Consensus       133 ~~~~~~~~~~~~~g~d~iliEtvG~  157 (327)
T d2p67a1         133 QRARELMLLCEAAGYDVVIVETVGV  157 (327)
T ss_dssp             HHHHHHHHHHHHTTCSEEEEEEECC
T ss_pred             hhhhHHHHHHHhcCCCeEEEeeccc
Confidence            4455555556666667888888743

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.66  E-value=0.0026  Score=48.73  Aligned_cols=19  Identities=53%  Similarity=0.667  Sum_probs=16.3

Q ss_pred             CceEEEEcCCCChHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLAR   84 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~   84 (292)
                      ++++++.+|+|+|||+.+-
T Consensus        40 ~~~~il~apTGsGKT~~a~   58 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAE   58 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHHH
Confidence            5679999999999998753

>d1mkya1 c.37.1.8 (A:2-172) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=96.62  E-value=0.0079  Score=44.40  Aligned_cols=21  Identities=33%  Similarity=0.577  Sum_probs=19.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|.|.|++|+|||||++.+..
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999975

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.58  E-value=0.0029  Score=51.22  Aligned_cols=38  Identities=18%  Similarity=0.334  Sum_probs=27.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc------CCcEEEEeccch
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI------DANFLKVVSSAI  102 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l------~~~~~~~~~~~~  102 (292)
                      .+--|-|.|++|+||||++..+...+      ...+..++..++
T Consensus        26 ~P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~Ddf   69 (286)
T d1odfa_          26 CPLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDF   69 (286)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGG
T ss_pred             CCEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCC
Confidence            34456689999999999999887665      335555665555

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.58  E-value=0.0027  Score=49.97  Aligned_cols=34  Identities=18%  Similarity=0.264  Sum_probs=22.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      ++.+++.+|+|+|||.++-..+...   +..++.+..
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~P   94 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFP   94 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEES
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEec
Confidence            6789999999999998654444322   444555443

>d1nrjb_ c.37.1.8 (B:) Signal recognition particle receptor beta-subunit {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Signal recognition particle receptor beta-subunit
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.54  E-value=0.0087  Score=45.52  Aligned_cols=23  Identities=26%  Similarity=0.593  Sum_probs=20.9

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..|+|.|+||+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            47999999999999999999865

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=96.49  E-value=0.00069  Score=51.74  Aligned_cols=31  Identities=29%  Similarity=0.334  Sum_probs=25.7

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      .+.-|.|.|+.|+||||+++.|++.++...+
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~~l~~~~~   38 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEKYKNDICL   38 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGGGTTTEEE
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            3456788899999999999999999876444

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=96.46  E-value=0.0012  Score=49.31  Aligned_cols=24  Identities=33%  Similarity=0.469  Sum_probs=21.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +.+++|.|++|+|||+++-.+...
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc
Confidence            678999999999999999887776

>d1jjva_ c.37.1.1 (A:) Dephospho-CoA kinase {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Haemophilus influenzae [TaxId: 727]

Probab=96.45  E-value=0.00074  Score=52.17  Aligned_cols=30  Identities=27%  Similarity=0.333  Sum_probs=24.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      .|.|+|++||||||+++.+. ..|.+++..+
T Consensus         4 iIgITG~igSGKStv~~~l~-~~G~~vidaD   33 (205)
T d1jjva_           4 IVGLTGGIGSGKTTIANLFT-DLGVPLVDAD   33 (205)
T ss_dssp             EEEEECSTTSCHHHHHHHHH-TTTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHH-HCCCeEEEch
Confidence            35689999999999999886 6788877543

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.42  E-value=0.0057  Score=47.50  Aligned_cols=53  Identities=17%  Similarity=0.117  Sum_probs=31.1

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcC---CCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG---IKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~---~~~~~~vll~G~~G~GKT~l~   83 (292)
                      -.+|+++.-.+...+.|.+.-   +....-.+...   +-.++.+++..|+|+|||...
T Consensus        11 i~sF~~l~L~~~l~~~L~~~g---~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlay   66 (218)
T d2g9na1          11 VDSFDDMNLSESLLRGIYAYG---FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF   66 (218)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHH
T ss_pred             cCCHHHCCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhh
Confidence            358999855555566665442   21111111111   122678999999999999743

>d1ctqa_ c.37.1.8 (A:) cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: cH-p21 Ras protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.41  E-value=0.0053  Score=45.20  Aligned_cols=22  Identities=27%  Similarity=0.504  Sum_probs=19.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .|++.|++|+|||+|+..+...
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999998864

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=96.40  E-value=0.0071  Score=45.86  Aligned_cols=32  Identities=34%  Similarity=0.489  Sum_probs=21.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHH----hcCCcEEEEec
Q 022768           68 GVLLYGPPGTGKTLLARAIAS----NIDANFLKVVS   99 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~----~l~~~~~~~~~   99 (292)
                      ++++++|.|+|||.++-.++.    ..+..++.+.+
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i~P   60 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAP   60 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEECS
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEEcC
Confidence            588999999999986554443    23444555443

>d1vhta_ c.37.1.1 (A:) Dephospho-CoA kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Dephospho-CoA kinase
species: Escherichia coli [TaxId: 562]

Probab=96.37  E-value=0.00085  Score=51.96  Aligned_cols=28  Identities=36%  Similarity=0.502  Sum_probs=22.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCcEEE
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDANFLK   96 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~~~~   96 (292)
                      .|.|+|++|+||||+++.+. .+|.+++.
T Consensus         5 iIgitG~igSGKStv~~~l~-~~G~~vid   32 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA-DLGINVID   32 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH-HTTCEEEE
T ss_pred             EEEEECCCcCCHHHHHHHHH-HCCCcEEE
Confidence            46689999999999999875 67776654

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=96.35  E-value=0.00089  Score=50.27  Aligned_cols=28  Identities=36%  Similarity=0.488  Sum_probs=23.3

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      +.+++|.|++|+|||+++-.+... |..+
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~-G~~l   42 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK-NHLF   42 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT-TCEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCce
Confidence            678999999999999999888764 4443

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.30  E-value=0.0023  Score=49.48  Aligned_cols=33  Identities=15%  Similarity=0.155  Sum_probs=26.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      |.-|.|.|+.|+||||+++.+++.+   +.+++.+.
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            4457777999999999999999877   55665543

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.28  E-value=0.014  Score=44.88  Aligned_cols=56  Identities=20%  Similarity=0.122  Sum_probs=33.0

Q ss_pred             CCCCCccccccccHHHHHHHHHHhhcccCChHHHHhcC---CCCCceEEEEcCCCChHHHHH
Q 022768           25 DPGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG---IKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        25 ~~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~---~~~~~~vll~G~~G~GKT~l~   83 (292)
                      +-+-.+|+++--.++..+.|.+.-   +....-.+...   +-.++.+++.+|+|+|||...
T Consensus         6 ~~~~~sF~~l~l~~~l~~~L~~~g---~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~   64 (212)
T d1qdea_           6 DKVVYKFDDMELDENLLRGVFGYG---FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTF   64 (212)
T ss_dssp             CCCCCCGGGGTCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             cccccChhhCCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCEEeecccccchhhhh
Confidence            334588999954455556665542   11211111111   123678999999999999843

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=96.28  E-value=0.0011  Score=52.22  Aligned_cols=23  Identities=30%  Similarity=0.494  Sum_probs=20.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .++|.|++|+|||||++.+.+.+
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Confidence            37899999999999999998755

>d1kaoa_ c.37.1.8 (A:) Rap2a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap2a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.26  E-value=0.011  Score=43.49  Aligned_cols=22  Identities=27%  Similarity=0.507  Sum_probs=19.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999998864

>d1zd9a1 c.37.1.8 (A:18-181) ADP-ribosylation factor {Human (Homo sapiens), ARL8A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL8A [TaxId: 9606]

Probab=96.16  E-value=0.0099  Score=43.52  Aligned_cols=22  Identities=36%  Similarity=0.406  Sum_probs=19.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .++|.|++|+|||+|+..+...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4889999999999999988763

>d2f7sa1 c.37.1.8 (A:5-190) Rab27b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab27b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.15  E-value=0.026  Score=41.99  Aligned_cols=21  Identities=29%  Similarity=0.417  Sum_probs=19.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -|+|.|++|+|||+|++.+.+
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            388999999999999999885

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.13  E-value=0.0086  Score=46.58  Aligned_cols=51  Identities=22%  Similarity=0.302  Sum_probs=31.1

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcC---CCCCceEEEEcCCCChHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVG---IKPPKGVLLYGPPGTGKTL   81 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~---~~~~~~vll~G~~G~GKT~   81 (292)
                      ..+|+++.-.++..+.|.+.-   +...--.+...   +-.++.+++..|+|+|||.
T Consensus        16 ~~sF~~l~L~~~l~~~L~~~g---~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          16 TPTFDTMGLREDLLRGIYAYG---FEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             CCSGGGGCCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHH
T ss_pred             CCCHHHCCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhh
Confidence            358999965666667776652   11111111100   1236789999999999996

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=96.12  E-value=0.0021  Score=47.09  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=21.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .-.++|.|.+|+|||+|++.+...
T Consensus         5 e~kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           5 EMRILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhCC
Confidence            456999999999999999998764

>d1u8za_ c.37.1.8 (A:) Ras-related protein RalA {Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein RalA
species: Cotton-top tamarin (Saguinus oedipus) [TaxId: 9490]

Probab=96.08  E-value=0.011  Score=43.63  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=19.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -++|.|.+|+|||++++.+..
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            589999999999999999875

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.07  E-value=0.0079  Score=46.11  Aligned_cols=50  Identities=16%  Similarity=0.151  Sum_probs=28.2

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcC---CCCCceEEEEcCCCChHHHH
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVG---IKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~---~~~~~~vll~G~~G~GKT~l   82 (292)
                      +|+++.-.++..+.|.+.-   +...--.+...   +-.++.+++.+|+|+|||..
T Consensus         2 sF~~l~L~~~l~~~L~~~g---~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTla   54 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAG---FEKPSPIQEEAIPVAITGRDILARAKNGTGKTAA   54 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTT---CCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHH
T ss_pred             ChHHcCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhh
Confidence            6777755555566666541   11110000000   11267799999999999963

>d2gjsa1 c.37.1.8 (A:91-258) Rad {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rad
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.02  E-value=0.0099  Score=43.78  Aligned_cols=22  Identities=50%  Similarity=0.780  Sum_probs=19.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -++|.|.+|+|||+|++.+...
T Consensus         3 Ki~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           3 KVLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCcCHHHHHHHHhCC
Confidence            3789999999999999998753

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.00  E-value=0.037  Score=43.09  Aligned_cols=57  Identities=18%  Similarity=0.156  Sum_probs=36.7

Q ss_pred             cccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           31 YSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        31 ~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |..-..+..+.+++...+..             ..+...||+|..|+|||-++-..+...   |..++.+.+.
T Consensus        54 ~~lt~~Q~~~~~~i~~~~~~-------------~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt  113 (233)
T d2eyqa3          54 FETTPDQAQAINAVLSDMCQ-------------PLAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPT  113 (233)
T ss_dssp             SCCCHHHHHHHHHHHHHHHS-------------SSCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSS
T ss_pred             cccchhHHHHHHHHHHHHhc-------------cCccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccH
Confidence            33334456666666666554             345679999999999999875555433   5555555544

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.00  E-value=0.088  Score=39.99  Aligned_cols=50  Identities=16%  Similarity=0.129  Sum_probs=28.0

Q ss_pred             ccccccccHHHHHHHHHHhhcccCChHHHHhcC---CCCCceEEEEcCCCChHHHH
Q 022768           30 SYSAVGGLSDQIRELRESIELPLMNPELFLRVG---IKPPKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        30 ~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~---~~~~~~vll~G~~G~GKT~l   82 (292)
                      +|+++--.++..+.|.+.-   +...--.+...   +-.++.+++..|+|+|||..
T Consensus         2 ~F~dl~L~~~l~~~l~~~g---~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla   54 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDCG---FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV   54 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHTT---CCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             CccccCcCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCeEEEeccccccccc
Confidence            5777754555555555431   11111111110   12367899999999999964

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=95.98  E-value=0.016  Score=46.70  Aligned_cols=18  Identities=28%  Similarity=0.410  Sum_probs=16.0

Q ss_pred             CCCceEEEEcCCCChHHH
Q 022768           64 KPPKGVLLYGPPGTGKTL   81 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~   81 (292)
                      ..++.+++.+|+|+|||+
T Consensus         7 ~~~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           7 RKKRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             STTCEEEECCCTTSSTTT
T ss_pred             hcCCcEEEEECCCCCHHH
Confidence            457889999999999996

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=95.95  E-value=0.0026  Score=47.39  Aligned_cols=24  Identities=21%  Similarity=0.375  Sum_probs=20.5

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...++|.|++|+|||||+..+...
T Consensus        13 ~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          13 TGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            455999999999999999988653

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.94  E-value=0.0023  Score=49.39  Aligned_cols=25  Identities=24%  Similarity=0.426  Sum_probs=22.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      |.-|.|.|+.|+||||+++.+++.+
T Consensus         2 gkfIviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           2 SKYIVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            4557888999999999999999877

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.92  E-value=0.0046  Score=47.85  Aligned_cols=33  Identities=24%  Similarity=0.237  Sum_probs=27.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~   98 (292)
                      |.-|.|.|+-|+||||+++.+++.+......+.
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L~~~~~~~~   35 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKLQPNCKLLK   35 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHTTTSEEEEE
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHhCCEEEE
Confidence            556888999999999999999999977665554

>d1z0fa1 c.37.1.8 (A:8-173) Rab14 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab14
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.92  E-value=0.035  Score=40.43  Aligned_cols=22  Identities=23%  Similarity=0.431  Sum_probs=19.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -++|.|.+|+|||++++.+...
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999998863

>d1deka_ c.37.1.1 (A:) Deoxynucleoside monophosphate kinase {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxynucleoside monophosphate kinase
species: Bacteriophage T4 [TaxId: 10665]

Probab=95.92  E-value=0.0017  Score=51.16  Aligned_cols=26  Identities=35%  Similarity=0.307  Sum_probs=22.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCCc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDAN   93 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~~   93 (292)
                      .|.|+|+.||||||+|+.++..+|.+
T Consensus         3 iIgiTG~igSGKsTva~~l~e~~g~~   28 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMSNYSAV   28 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHSCEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCCCe
Confidence            47799999999999999999887643

>d1fzqa_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL3 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL3 [TaxId: 10090]

Probab=95.90  E-value=0.0047  Score=45.86  Aligned_cols=23  Identities=39%  Similarity=0.525  Sum_probs=19.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ...+++.|++|+|||+|++.+..
T Consensus        16 ~~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          16 EVRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEEECCCCCCHHHHHHHHhc
Confidence            34599999999999999998865

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.90  E-value=0.0038  Score=47.75  Aligned_cols=30  Identities=17%  Similarity=0.357  Sum_probs=24.5

Q ss_pred             EEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           69 VLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      |.|.|..|+||||+++.|++.+   |.+++.+.
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~   35 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLA   35 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEe
Confidence            6788999999999999999876   55665544

>d2qtvb1 c.37.1.8 (B:24-189) SAR1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.90  E-value=0.0022  Score=46.66  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=19.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -++|.|+||+|||+|+..+...
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3889999999999999998874

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=95.86  E-value=0.023  Score=42.26  Aligned_cols=21  Identities=24%  Similarity=0.491  Sum_probs=19.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      +|-|.|.|++|||||++++.+
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            588999999999999999985

>d1c1ya_ c.37.1.8 (A:) Rap1A {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rap1A
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.81  E-value=0.013  Score=42.99  Aligned_cols=22  Identities=23%  Similarity=0.463  Sum_probs=19.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .|++.|.+|+|||+|++.+...
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4899999999999999998864

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.81  E-value=0.035  Score=39.57  Aligned_cols=33  Identities=27%  Similarity=0.341  Sum_probs=22.4

Q ss_pred             eEEEEcCCCChHHH-HHHHHHH--hcCCcEEEEecc
Q 022768           68 GVLLYGPPGTGKTL-LARAIAS--NIDANFLKVVSS  100 (292)
Q Consensus        68 ~vll~G~~G~GKT~-l~~~la~--~l~~~~~~~~~~  100 (292)
                      --+++||=.+|||+ |++.+-+  ..+..++.++..
T Consensus         4 L~~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~   39 (139)
T d2b8ta1           4 IEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPK   39 (139)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEc
Confidence            35788999999999 5555533  336666665543

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=95.79  E-value=0.0025  Score=51.88  Aligned_cols=18  Identities=28%  Similarity=0.401  Sum_probs=15.1

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      ..+++|.|+||||||+++
T Consensus        14 ~~~~lI~g~aGTGKTt~l   31 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVI   31 (306)
T ss_dssp             SSEEEECCCTTSCHHHHH
T ss_pred             CCCEEEEeeCCccHHHHH
Confidence            346899999999999864

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.74  E-value=0.007  Score=46.49  Aligned_cols=17  Identities=29%  Similarity=0.376  Sum_probs=15.2

Q ss_pred             CceEEEEcCCCChHHHH
Q 022768           66 PKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l   82 (292)
                      ++.+++..|+|+|||..
T Consensus        40 g~dvl~~a~TGsGKTla   56 (206)
T d1veca_          40 GRDILARAKNGTGKSGA   56 (206)
T ss_dssp             TCCEEEECCSSSTTHHH
T ss_pred             CCCEEeeccCccccccc
Confidence            67899999999999963

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.72  E-value=0.0044  Score=48.60  Aligned_cols=30  Identities=13%  Similarity=0.302  Sum_probs=25.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFL   95 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~   95 (292)
                      |.-|.|-|+-|+||||+++.+++.++...+
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~~~~i   31 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYPEWHV   31 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCTTSEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhhcCC
Confidence            456888999999999999999999876544

>d1z2aa1 c.37.1.8 (A:8-171) Rab23 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab23
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.67  E-value=0.0031  Score=46.44  Aligned_cols=21  Identities=14%  Similarity=0.313  Sum_probs=19.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|++.|++|+|||+|+..+..
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998885

>d2a5ja1 c.37.1.8 (A:9-181) Rab2b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab2b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.66  E-value=0.0031  Score=46.89  Aligned_cols=22  Identities=23%  Similarity=0.431  Sum_probs=19.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -+++.|++|+|||+++..+...
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3889999999999999988754

>d1x3sa1 c.37.1.8 (A:2-178) Rab18 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab18
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.65  E-value=0.044  Score=40.40  Aligned_cols=21  Identities=29%  Similarity=0.517  Sum_probs=19.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .+++.|.+|+|||+|++.+..
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998875

>d1ksha_ c.37.1.8 (A:) ADP-ribosylation factor {Mouse (Mus musculus), ARL2 [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Mouse (Mus musculus), ARL2 [TaxId: 10090]

Probab=95.65  E-value=0.003  Score=46.47  Aligned_cols=22  Identities=23%  Similarity=0.442  Sum_probs=19.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .++|.|++|+|||+|++.+...
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            5899999999999999998763

>d3raba_ c.37.1.8 (A:) Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab3a
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.57  E-value=0.0035  Score=46.41  Aligned_cols=22  Identities=27%  Similarity=0.398  Sum_probs=19.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -+++.|++|+|||+|++.+...
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3899999999999999998753

>d1u0la2 c.37.1.8 (A:69-293) Probable GTPase EngC (YjeQ), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=95.57  E-value=0.0031  Score=49.10  Aligned_cols=29  Identities=28%  Similarity=0.328  Sum_probs=23.4

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANF   94 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~   94 (292)
                      +...+|.|+||+|||||+.++........
T Consensus        95 ~kt~~~~G~SGVGKSTLiN~L~~~~~~~T  123 (225)
T d1u0la2          95 GKISTMAGLSGVGKSSLLNAINPGLKLRV  123 (225)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHSTTCCCC-
T ss_pred             CCeEEEECCCCCCHHHHHHhhcchhhhhc
Confidence            67789999999999999999976554433

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=95.51  E-value=0.043  Score=43.70  Aligned_cols=24  Identities=38%  Similarity=0.541  Sum_probs=21.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +++.|.|+.|+|||||+.++....
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~~   26 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYKT   26 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHHc
Confidence            578999999999999999997544

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.49  E-value=0.0044  Score=50.09  Aligned_cols=35  Identities=11%  Similarity=0.246  Sum_probs=23.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccch
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAI  102 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~  102 (292)
                      .|.|.|++|+||||+++.+.+.+   +.....+....+
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsf   43 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   43 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCC
Confidence            57899999999999999988866   445555555444

>d2cxxa1 c.37.1.8 (A:2-185) GTP-binding protein engB {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein engB
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.49  E-value=0.0028  Score=47.42  Aligned_cols=22  Identities=18%  Similarity=0.403  Sum_probs=19.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .|+|.|+||+|||||+.++.++
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999853

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.49  E-value=0.064  Score=40.81  Aligned_cols=21  Identities=19%  Similarity=0.154  Sum_probs=17.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHH
Q 022768           67 KGVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la   87 (292)
                      ..+++..|+|+|||...-...
T Consensus        43 ~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1          43 YNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             SEEEEECCSSSSHHHHHHHHH
T ss_pred             CCeeeechhcccccceeeccc
Confidence            479999999999998664444

>d2ew1a1 c.37.1.8 (A:4-174) Rab30 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab30
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.47  E-value=0.0037  Score=46.34  Aligned_cols=21  Identities=38%  Similarity=0.643  Sum_probs=19.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -++|.|.+|+|||+|++.++.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999986

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.46  E-value=0.004  Score=46.04  Aligned_cols=22  Identities=23%  Similarity=0.511  Sum_probs=19.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -+++.|++|+|||+|++.++..
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3889999999999999999864

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.45  E-value=0.015  Score=45.12  Aligned_cols=24  Identities=42%  Similarity=0.425  Sum_probs=20.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..++|.|.-|+||||+++.+.+..
T Consensus         4 Pv~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           4 AVTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             EEEEEEESSSSSCHHHHHHHHHSC
T ss_pred             CEEEEeeCCCCCHHHHHHHHHhcC
Confidence            357899999999999999998754

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=95.44  E-value=0.0039  Score=51.10  Aligned_cols=18  Identities=28%  Similarity=0.431  Sum_probs=15.1

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      ..+++|.|+||||||+++
T Consensus        24 ~g~~lV~g~aGSGKTt~l   41 (318)
T d1pjra1          24 EGPLLIMAGAGSGKTRVL   41 (318)
T ss_dssp             SSCEEEEECTTSCHHHHH
T ss_pred             CCCEEEEecCCccHHHHH
Confidence            345899999999999865

>d1svia_ c.37.1.8 (A:) Probable GTPase EngB {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Bacillus subtilis [TaxId: 1423]

Probab=95.43  E-value=0.0051  Score=46.57  Aligned_cols=21  Identities=19%  Similarity=0.384  Sum_probs=19.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|.|.|+||+|||||++++.+
T Consensus        25 ~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHhcC
Confidence            599999999999999999985

>d1zj6a1 c.37.1.8 (A:2-178) ADP-ribosylation factor {Human (Homo sapiens), ARL5A [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL5A [TaxId: 9606]

Probab=95.42  E-value=0.0043  Score=45.98  Aligned_cols=24  Identities=25%  Similarity=0.371  Sum_probs=21.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ...|+|.|.+|+|||+|+..+...
T Consensus        15 ~~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          15 EHKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            457999999999999999988764

>d1g16a_ c.37.1.8 (A:) Rab-related protein Sec4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein Sec4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.34  E-value=0.0044  Score=45.63  Aligned_cols=21  Identities=33%  Similarity=0.585  Sum_probs=19.2

Q ss_pred             EEEEcCCCChHHHHHHHHHHh
Q 022768           69 VLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~   89 (292)
                      +++.|.+|+|||++++.++..
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999998864

>d2erya1 c.37.1.8 (A:10-180) r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.33  E-value=0.0044  Score=45.92  Aligned_cols=21  Identities=24%  Similarity=0.411  Sum_probs=19.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -|+|.|.+|+|||+|++.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            599999999999999998876

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.33  E-value=0.0047  Score=45.84  Aligned_cols=21  Identities=33%  Similarity=0.550  Sum_probs=18.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .+++.|++|+|||+|+..+..
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHc
Confidence            388999999999999999875

>d2erxa1 c.37.1.8 (A:6-176) di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: di-Ras2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.32  E-value=0.0042  Score=45.96  Aligned_cols=21  Identities=29%  Similarity=0.504  Sum_probs=19.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -|++.|.+|+|||+|+..+..
T Consensus         4 Ki~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           4 RVAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            488999999999999998885

>d2f9la1 c.37.1.8 (A:8-182) Rab11b {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab11b
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.32  E-value=0.0048  Score=45.91  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=19.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .+++.|++|+|||+|++.+..
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998876

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.30  E-value=0.0049  Score=45.23  Aligned_cols=21  Identities=24%  Similarity=0.449  Sum_probs=19.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|++.|.+|+|||+|++.+..
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999999885

>d1r2qa_ c.37.1.8 (A:) Rab5a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab5a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.26  E-value=0.0052  Score=45.45  Aligned_cols=22  Identities=23%  Similarity=0.389  Sum_probs=19.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -+++.|.+|+|||+|+..+...
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999998853

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.24  E-value=0.0049  Score=45.40  Aligned_cols=23  Identities=17%  Similarity=0.323  Sum_probs=20.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .-|+|.|++|+|||+|++.+...
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            45899999999999999998753

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.24  E-value=0.0052  Score=45.28  Aligned_cols=21  Identities=33%  Similarity=0.352  Sum_probs=19.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -++|.|.+|+|||+|++.+..
T Consensus         5 KivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998875

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.23  E-value=0.0052  Score=46.08  Aligned_cols=21  Identities=33%  Similarity=0.551  Sum_probs=19.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -|++.|.+|+|||+|+..+.+
T Consensus         4 Kv~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           4 KVIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999998886

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.20  E-value=0.004  Score=48.72  Aligned_cols=26  Identities=15%  Similarity=0.257  Sum_probs=23.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      +-|.|-|+.|+||||+++.|++.+..
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l~~   28 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLCED   28 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            45889999999999999999998854

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=95.20  E-value=0.038  Score=44.19  Aligned_cols=25  Identities=16%  Similarity=0.090  Sum_probs=22.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      -++|.|.|..|+|||||+.++....
T Consensus         6 iRni~i~gh~~~GKTtL~e~ll~~~   30 (276)
T d2bv3a2           6 LRNIGIAAHIDAGKTTTTERILYYT   30 (276)
T ss_dssp             EEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            4689999999999999999998654

>d1e0sa_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARF6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARF6 [TaxId: 9606]

Probab=95.19  E-value=0.0036  Score=46.50  Aligned_cols=24  Identities=21%  Similarity=0.318  Sum_probs=20.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .-.+++.|++|+|||++++.+...
T Consensus        12 ~~kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          12 EMRILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTTCC
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            456999999999999999998753

>d2fn4a1 c.37.1.8 (A:24-196) r-Ras {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: r-Ras
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.17  E-value=0.0053  Score=45.61  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=19.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -|+|.|.+|+|||+|++.+...
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4999999999999999988853

>d1wmsa_ c.37.1.8 (A:) Rab9a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab9a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.06  E-value=0.0063  Score=45.13  Aligned_cols=22  Identities=36%  Similarity=0.560  Sum_probs=19.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .|+|.|++|+|||+++..+...
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999888763

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=95.04  E-value=0.008  Score=51.45  Aligned_cols=33  Identities=33%  Similarity=0.536  Sum_probs=24.9

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      .+|++|.|++|+|||++++.+...+   +.+++.++
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD   85 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVD   85 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEe
Confidence            5789999999999999987766543   44555444

>d1z0ja1 c.37.1.8 (A:2-168) Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-22a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.03  E-value=0.0066  Score=44.69  Aligned_cols=21  Identities=29%  Similarity=0.442  Sum_probs=19.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .++|.|.+|+|||+|++.+..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            488999999999999999885

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.02  E-value=0.0062  Score=45.34  Aligned_cols=22  Identities=23%  Similarity=0.311  Sum_probs=19.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -|++.|.+|+|||+|+..+...
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999988864

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=95.02  E-value=0.035  Score=43.43  Aligned_cols=16  Identities=25%  Similarity=0.532  Sum_probs=15.0

Q ss_pred             CceEEEEcCCCChHHH
Q 022768           66 PKGVLLYGPPGTGKTL   81 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~   81 (292)
                      ++.+++..|+|+|||.
T Consensus        58 g~dvvi~a~TGsGKTl   73 (238)
T d1wrba1          58 HRDIMACAQTGSGKTA   73 (238)
T ss_dssp             TCCEEEECCTTSSHHH
T ss_pred             CCCEEEECCCCCCcce
Confidence            6789999999999998

>d2bmea1 c.37.1.8 (A:6-179) Rab4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.02  E-value=0.0062  Score=45.14  Aligned_cols=21  Identities=33%  Similarity=0.518  Sum_probs=19.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -|++.|.+|+|||++++.+..
T Consensus         7 KI~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998875

>d2g6ba1 c.37.1.8 (A:58-227) Rab26 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab26
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.96  E-value=0.0071  Score=44.64  Aligned_cols=22  Identities=36%  Similarity=0.507  Sum_probs=19.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -+++.|++|+|||++++.+...
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999988763

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.95  E-value=0.0068  Score=44.42  Aligned_cols=21  Identities=24%  Similarity=0.347  Sum_probs=18.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|+|.|.+|+|||++++.+..
T Consensus         2 Kv~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           2 KLVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999999885

>d1ek0a_ c.37.1.8 (A:) Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ypt51
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.87  E-value=0.0077  Score=44.40  Aligned_cols=22  Identities=27%  Similarity=0.453  Sum_probs=19.3

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -+++.|.+|+|||+|++.+...
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999988753

>d1mh1a_ c.37.1.8 (A:) Rac {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rac
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.86  E-value=0.0074  Score=45.17  Aligned_cols=23  Identities=26%  Similarity=0.314  Sum_probs=20.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      --++|.|.+|+|||++++.+...
T Consensus         6 iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999988864

>d1mkya2 c.37.1.8 (A:173-358) Probable GTPase Der, N-terminal and middle domains {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase Der, N-terminal and middle domains
species: Thermotoga maritima [TaxId: 2336]

Probab=94.86  E-value=0.0085  Score=44.78  Aligned_cols=25  Identities=32%  Similarity=0.440  Sum_probs=21.5

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .+-.|.|.|.+|+|||||+.++.+.
T Consensus         7 ~~~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           7 DAIKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCC
Confidence            3456999999999999999999853

>d1egaa1 c.37.1.8 (A:4-182) GTPase Era, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Era, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.83  E-value=0.0064  Score=45.10  Aligned_cols=22  Identities=23%  Similarity=0.418  Sum_probs=19.7

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .|.|.|.+|+|||||++++.+.
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999853

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.83  E-value=0.26  Score=37.17  Aligned_cols=23  Identities=30%  Similarity=0.232  Sum_probs=19.9

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -++.+.|.+++|||||+.++...
T Consensus         4 ini~iiGhvd~GKSTL~~~Ll~~   26 (204)
T d2c78a3           4 VNVGTIGHVDHGKTTLTAALTYV   26 (204)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCcHHHHHHHHHHH
Confidence            46889999999999999999643

>d1moza_ c.37.1.8 (A:) ADP-ribosylation factor {Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Baker's yeast (Saccharomyces cerevisiae), ARL1 [TaxId: 4932]

Probab=94.83  E-value=0.0063  Score=45.46  Aligned_cols=26  Identities=23%  Similarity=0.341  Sum_probs=21.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHH
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      ....-.+++.|++|+|||++++.+..
T Consensus        14 ~~k~~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          14 SNKELRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             CSSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCceEEEEEECCCCCCHHHHHHHHhc
Confidence            34456799999999999999988754

>d2g3ya1 c.37.1.8 (A:73-244) GTP-binding protein GEM {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein GEM
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.82  E-value=0.0075  Score=44.68  Aligned_cols=21  Identities=43%  Similarity=0.631  Sum_probs=19.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -|+|.|.+|+|||+|++.+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998875

>d2bcgy1 c.37.1.8 (Y:3-196) GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTPase Ytp1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.79  E-value=0.0076  Score=45.62  Aligned_cols=22  Identities=32%  Similarity=0.536  Sum_probs=19.4

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -|+|.|++|+|||+|+..+...
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            3889999999999999988853

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=94.79  E-value=0.0039  Score=48.75  Aligned_cols=26  Identities=31%  Similarity=0.519  Sum_probs=20.6

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      +...+|.|+||+|||||+.++.....
T Consensus        97 ~~~~vl~G~SGVGKSSLiN~L~~~~~  122 (231)
T d1t9ha2          97 DKTTVFAGQSGVGKSSLLNAISPELG  122 (231)
T ss_dssp             TSEEEEEESHHHHHHHHHHHHCC---
T ss_pred             cceEEEECCCCccHHHHHHhhccHhH
Confidence            56788999999999999999886543

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=94.74  E-value=0.0056  Score=45.56  Aligned_cols=25  Identities=16%  Similarity=0.231  Sum_probs=21.1

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      .....|.|.|.|++|||+|++++..
T Consensus        14 ~~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          14 DTGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SCSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHhC
Confidence            3456799999999999999988854

>d1x1ra1 c.37.1.8 (A:10-178) Ras-related protein M-Ras (XRas) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-related protein M-Ras (XRas)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.72  E-value=0.0088  Score=44.14  Aligned_cols=22  Identities=23%  Similarity=0.350  Sum_probs=19.6

Q ss_pred             ceEEEEcCCCChHHHHHHHHHH
Q 022768           67 KGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~   88 (292)
                      -.+++.|.+|+|||++++.++.
T Consensus         5 ~Ki~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           5 YKLVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCcCHHHHHHHHHh
Confidence            3588999999999999999886

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.67  E-value=0.0086  Score=44.72  Aligned_cols=22  Identities=27%  Similarity=0.450  Sum_probs=19.5

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -++|.|.+|+|||++++.+...
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999988863

>d2atxa1 c.37.1.8 (A:9-193) RhoQ {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoQ
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.62  E-value=0.0089  Score=44.85  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=19.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHh
Q 022768           69 VLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~   89 (292)
                      ++|.|.+|+|||+|++.+...
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            889999999999999988863

>d2fu5c1 c.37.1.8 (C:3-175) Rab8a {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab8a
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.48  E-value=0.0058  Score=45.34  Aligned_cols=21  Identities=33%  Similarity=0.490  Sum_probs=8.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      -|+|.|.+|+|||+|++.+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999987775

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.46  E-value=0.0047  Score=45.75  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=18.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -+++.|++|+|||+|+..++..
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999887653

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=94.43  E-value=0.025  Score=45.36  Aligned_cols=36  Identities=28%  Similarity=0.363  Sum_probs=29.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      .++.+++.|.-|+||||++-.+|..+   |..++-+++.
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            46678899999999999988888766   6777777755

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=94.34  E-value=0.0038  Score=47.18  Aligned_cols=24  Identities=25%  Similarity=0.278  Sum_probs=21.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ..+|+|+.|+|||+++.++.-.+.
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhc
Confidence            467899999999999999997763

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.33  E-value=0.011  Score=44.44  Aligned_cols=22  Identities=27%  Similarity=0.360  Sum_probs=19.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      -|++.|++|+|||+|+..+...
T Consensus         5 KvvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999888753

>d1lnza2 c.37.1.8 (A:158-342) Obg GTP-binding protein middle domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Bacillus subtilis [TaxId: 1423]

Probab=94.22  E-value=0.0089  Score=44.69  Aligned_cols=21  Identities=38%  Similarity=0.507  Sum_probs=18.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|.|.|+||+|||||+.++.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            388999999999999999864

>d1xzpa2 c.37.1.8 (A:212-371) TrmE GTPase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: TrmE GTPase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.15  E-value=0.0045  Score=45.10  Aligned_cols=22  Identities=23%  Similarity=0.516  Sum_probs=19.8

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .|.|.|.||+|||+|+.++...
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999864

>d1zcba2 c.37.1.8 (A:47-75,A:202-372) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.15  E-value=0.012  Score=44.30  Aligned_cols=20  Identities=25%  Similarity=0.521  Sum_probs=18.1

Q ss_pred             eEEEEcCCCChHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la   87 (292)
                      -++|.|.+|+|||++++.+.
T Consensus         4 KivllG~~~vGKTsll~r~~   23 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQMR   23 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            48999999999999999983

>d2bmja1 c.37.1.8 (A:66-240) Centaurin gamma 1, G domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Centaurin gamma 1, G domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.83  E-value=0.018  Score=42.69  Aligned_cols=24  Identities=17%  Similarity=0.230  Sum_probs=20.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHh
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      --.+++.|.+|+|||+++..+...
T Consensus         5 ~~ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           5 ELRLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEEEECCTTTTHHHHHHHHHHS
T ss_pred             cEEEEEECCCCCCHHHHHHHHHhC
Confidence            346899999999999999988764

>d1udxa2 c.37.1.8 (A:157-336) Obg GTP-binding protein middle domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Obg GTP-binding protein middle domain
species: Thermus thermophilus [TaxId: 274]

Probab=93.76  E-value=0.012  Score=43.79  Aligned_cols=21  Identities=38%  Similarity=0.490  Sum_probs=18.9

Q ss_pred             eEEEEcCCCChHHHHHHHHHH
Q 022768           68 GVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|.|.|.||+|||||+..+.+
T Consensus         3 ~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            388999999999999999874

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=93.71  E-value=0.017  Score=44.60  Aligned_cols=23  Identities=22%  Similarity=0.405  Sum_probs=20.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHh
Q 022768           67 KGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      ..++|.|.+|+|||++++.+...
T Consensus         7 ~KilllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            46999999999999999988643

>d1xpua3 c.37.1.11 (A:129-417) Transcription termination factor Rho, ATPase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Transcription termination factor Rho, ATPase domain
species: Escherichia coli [TaxId: 562]

Probab=93.51  E-value=0.023  Score=45.69  Aligned_cols=28  Identities=39%  Similarity=0.585  Sum_probs=24.5

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +..+..++|.|++|+|||+++..+++..
T Consensus        40 igrGQr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          40 IGRGQRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             CBTTCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             ccCCCeeeEeCCCCCCHHHHHHHHHHHH
Confidence            4568889999999999999999999754

>d1byia_ c.37.1.10 (A:) Dethiobiotin synthetase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Dethiobiotin synthetase
species: Escherichia coli [TaxId: 562]

Probab=93.45  E-value=0.038  Score=42.01  Aligned_cols=33  Identities=18%  Similarity=0.156  Sum_probs=26.5

Q ss_pred             ceEEEEcC-CCChHHHHHHHHHHhc---CCcEEEEec
Q 022768           67 KGVLLYGP-PGTGKTLLARAIASNI---DANFLKVVS   99 (292)
Q Consensus        67 ~~vll~G~-~G~GKT~l~~~la~~l---~~~~~~~~~   99 (292)
                      +.++|+|. +|+||||++-.+|..+   |..+..++.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id~   38 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKP   38 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEECc
Confidence            46899999 5999999998888766   667777664

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=93.37  E-value=0.02  Score=47.25  Aligned_cols=25  Identities=32%  Similarity=0.428  Sum_probs=22.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .|.|-|+-|+||||+++.+++.++.
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEEECCccCCHHHHHHHHHHHhcc
Confidence            4778899999999999999998853

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=93.34  E-value=0.4  Score=40.29  Aligned_cols=51  Identities=22%  Similarity=0.324  Sum_probs=40.0

Q ss_pred             cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           37 LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        37 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      +.+++++|.+-+..-              .+..+|.|-+|+|||.++..+++..+.|++.+....
T Consensus        16 QP~aI~~l~~~l~~g--------------~~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~   66 (413)
T d1t5la1          16 QPQAIAKLVDGLRRG--------------VKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNK   66 (413)
T ss_dssp             HHHHHHHHHHHHHHT--------------CSEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSH
T ss_pred             CHHHHHHHHHHHhcC--------------CCcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCH
Confidence            455677777766431              356889999999999999999999999988777554

>d1ihua2 c.37.1.10 (A:308-586) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.28  E-value=0.052  Score=43.10  Aligned_cols=35  Identities=31%  Similarity=0.377  Sum_probs=26.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      .+.++++|.-|+||||++-.+|..+   |..++.+++.
T Consensus        20 ~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~D   57 (279)
T d1ihua2          20 HGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSD   57 (279)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCC
Confidence            3456677999999999877777655   7778777765

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.20  E-value=0.029  Score=47.33  Aligned_cols=25  Identities=28%  Similarity=0.438  Sum_probs=20.7

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.-.+|+|+.|+|||+++.+++=.+
T Consensus        25 ~~l~~i~G~NGsGKS~ileAi~~~l   49 (427)
T d1w1wa_          25 SNFTSIIGPNGSGKSNMMDAISFVL   49 (427)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4456899999999999999997544

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.18  E-value=0.024  Score=42.42  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=20.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      -+++.|..|+|||++++.+...-
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48999999999999999997654

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=93.11  E-value=0.13  Score=40.58  Aligned_cols=54  Identities=24%  Similarity=0.309  Sum_probs=34.9

Q ss_pred             ccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccch
Q 022768           36 GLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSAI  102 (292)
Q Consensus        36 g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~~  102 (292)
                      .+..+.+++...+..             ..+...||+|..|+|||-++-..+...   |..+..+.....
T Consensus        87 ~Q~~ai~ei~~d~~~-------------~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~  143 (264)
T d1gm5a3          87 AQKRAHQEIRNDMIS-------------EKPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSI  143 (264)
T ss_dssp             HHHHHHHHHHHHHHS-------------SSCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHH
T ss_pred             hHHHHHHHHHHHhhc-------------cCcceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHh
Confidence            345555555555443             445678999999999999875555432   666666665544

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.89  E-value=0.024  Score=45.81  Aligned_cols=25  Identities=28%  Similarity=0.440  Sum_probs=20.9

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .-.+|+||.|+|||+++++++-.++
T Consensus        25 ~lnvlvG~NgsGKS~iL~Ai~~~lg   49 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNIIDAIKWVFG   49 (308)
T ss_dssp             SEEEEECCTTTCSTHHHHHHHHTSC
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHhC
Confidence            3568999999999999999976553

>d1d2ea3 c.37.1.8 (A:55-250) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Cow (Bos taurus), mitochondrial [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Cow (Bos taurus), mitochondrial [TaxId: 9913]

Probab=92.82  E-value=0.47  Score=35.43  Aligned_cols=22  Identities=36%  Similarity=0.324  Sum_probs=19.8

Q ss_pred             ceEEEEcCCCChHHHHHHHHHH
Q 022768           67 KGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~   88 (292)
                      -++.+.|....|||||+.++..
T Consensus         4 ini~iiGHvd~GKSTL~~~l~~   25 (196)
T d1d2ea3           4 VNVGTIGHVDHGKTTLTAAITK   25 (196)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCcHHHHHHHHHH
Confidence            4689999999999999998875

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.77  E-value=0.037  Score=38.12  Aligned_cols=27  Identities=19%  Similarity=0.158  Sum_probs=23.4

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+..++|.|-+|+||+++++++...+
T Consensus         4 kqgf~i~~tg~~~~gk~~ia~al~~~l   30 (122)
T d1g8fa3           4 KQGFSIVLGNSLTVSREQLSIALLSTF   30 (122)
T ss_dssp             GCCEEEEECTTCCSCHHHHHHHHHHHH
T ss_pred             ccceEEEEeCCCCCCHHHHHHHHHHHH
Confidence            346789999999999999999997765

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=92.54  E-value=0.032  Score=41.52  Aligned_cols=22  Identities=23%  Similarity=0.419  Sum_probs=19.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHh
Q 022768           68 GVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .+++.|..|+|||++++.+...
T Consensus         4 KivllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4899999999999999988653

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=92.39  E-value=0.066  Score=42.31  Aligned_cols=33  Identities=24%  Similarity=0.451  Sum_probs=27.0

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      .|.|+|.=|+||||++-.+|..+   |..++-+++.
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID~D   38 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVGCD   38 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEEEC
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEecC
Confidence            57789999999999998877655   7788888765

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=92.34  E-value=0.071  Score=43.98  Aligned_cols=46  Identities=20%  Similarity=0.328  Sum_probs=31.4

Q ss_pred             CCccccccc----cHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGG----LSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g----~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+|+.+.+    ++++.+.+...+...+.          ..+.+++-||..|+|||+.+
T Consensus        51 ~f~FD~vf~~~~~q~~vy~~v~~~v~~~l~----------G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          51 EFKFDKIFDQQDTNVDVFKEVGQLVQSSLD----------GYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             EEEESEEECTTCCHHHHHHHHHHHHGGGGG----------TCCEEEEEECCTTSSHHHHH
T ss_pred             EeecCeEeCCCCCHHHHHHHhhhhhcchhc----------ccccceeeeeccCCcccccc
Confidence            367888877    45556655554444321          33567888999999999976

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=92.32  E-value=0.029  Score=46.17  Aligned_cols=24  Identities=29%  Similarity=0.382  Sum_probs=21.6

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCC
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      |.|-|+-|+||||+++.+++.+..
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~~   31 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhh
Confidence            778899999999999999998754

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.22  E-value=0.046  Score=46.24  Aligned_cols=23  Identities=22%  Similarity=0.390  Sum_probs=21.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      +.+|.|.|.||+|||+++.++..
T Consensus        56 ~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          56 VLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            56799999999999999999974

>d1lkxa_ c.37.1.9 (A:) Myosin S1, motor domain {Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum, class-I myosin MyoE [TaxId: 44689]

Probab=92.15  E-value=0.082  Score=47.88  Aligned_cols=27  Identities=26%  Similarity=0.437  Sum_probs=23.6

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.+|++.|.+|+|||..+|.+.+.+
T Consensus        84 ~~~QsIiisGeSGsGKTe~~k~il~yL  110 (684)
T d1lkxa_          84 QENQCVIISGESGAGKTEASKKIMQFL  110 (684)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            346789999999999999999998865

>d1br2a2 c.37.1.9 (A:80-789) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=92.08  E-value=0.083  Score=48.07  Aligned_cols=27  Identities=22%  Similarity=0.422  Sum_probs=23.5

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.+|++.|.+|+|||..+|.+.+.+
T Consensus        89 ~~~Q~IiisGeSGaGKTe~~k~il~yL  115 (710)
T d1br2a2          89 REDQSILCTGESGAGKTENTKKVIQYL  115 (710)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            346789999999999999998888766

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=92.08  E-value=0.032  Score=45.82  Aligned_cols=25  Identities=28%  Similarity=0.381  Sum_probs=19.1

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhcCC
Q 022768           68 GVLLYGPPGTGKTLLARAIASNIDA   92 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l~~   92 (292)
                      .|.|-|+-|+||||+++.+++.++.
T Consensus         6 rI~IEG~iGsGKTTl~~~La~~l~~   30 (329)
T d1e2ka_           6 RVYIDGPHGMGKTTTTQLLVALGSR   30 (329)
T ss_dssp             EEEECSCTTSSHHHHHHHHTC----
T ss_pred             EEEEECCcCCCHHHHHHHHHHHhCC
Confidence            3677899999999999999988754

>d1c4oa1 c.37.1.19 (A:2-409) Nucleotide excision repair enzyme UvrB {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Thermus thermophilus [TaxId: 274]

Probab=91.78  E-value=1.2  Score=37.25  Aligned_cols=50  Identities=24%  Similarity=0.297  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           38 SDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        38 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      .+++++|.+.+..              ..+...|.|.+|+||+.++..+++..+.|++.+....
T Consensus        14 p~aI~~l~~~L~~--------------g~~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~~~   63 (408)
T d1c4oa1          14 PKAIAGLVEALRD--------------GERFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNK   63 (408)
T ss_dssp             HHHHHHHHHHHHT--------------TCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESSH
T ss_pred             HHHHHHHHHHHhc--------------CCCcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeCCH
Confidence            4556777666643              1345799999999999999999999999988776544

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.73  E-value=0.54  Score=38.41  Aligned_cols=25  Identities=12%  Similarity=0.232  Sum_probs=21.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      -++|.|.|..|.|||||+.++....
T Consensus        17 IRNI~iiGhvd~GKTTL~d~Ll~~~   41 (341)
T d1n0ua2          17 VRNMSVIAHVDHGKSTLTDSLVQRA   41 (341)
T ss_dssp             EEEEEEECCGGGTHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCcHHHHHHHHHHHC
Confidence            4679999999999999999997544

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=91.61  E-value=0.44  Score=34.23  Aligned_cols=19  Identities=32%  Similarity=0.478  Sum_probs=15.2

Q ss_pred             EEEEcCCCChHHHHHHHHH
Q 022768           69 VLLYGPPGTGKTLLARAIA   87 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la   87 (292)
                      +.+|-.+|=||||.|--+|
T Consensus         5 i~vytG~GKGKTTAAlG~a   23 (157)
T d1g5ta_           5 IIVFTGNGKGKTTAAFGTA   23 (157)
T ss_dssp             EEEEESSSSCHHHHHHHHH
T ss_pred             EEEEeCCCCCcHHHHHHHH
Confidence            6677778999999876665

>d2mysa2 c.37.1.9 (A:4-33,A:80-843) Myosin S1, motor domain {Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), pectoral muscle [TaxId: 9031]

Probab=91.40  E-value=0.1  Score=48.13  Aligned_cols=27  Identities=22%  Similarity=0.504  Sum_probs=22.7

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.+|++.|.+|+|||..+|.+.+.+
T Consensus       121 ~~~QsIiisGeSGaGKTe~~K~il~yL  147 (794)
T d2mysa2         121 RENQSILITGESGAGKTVNTKRVIQYF  147 (794)
T ss_dssp             TCCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            346789999999999999888777655

>d1d0xa2 c.37.1.9 (A:2-33,A:80-759) Myosin S1, motor domain {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Dictyostelium discoideum [TaxId: 44689]

Probab=91.36  E-value=0.063  Score=48.85  Aligned_cols=27  Identities=22%  Similarity=0.460  Sum_probs=23.2

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.+|++.|.+|+|||..+|.+.+.+
T Consensus       123 ~~nQsIiisGeSGaGKTe~~k~il~yL  149 (712)
T d1d0xa2         123 RQNQSLLITGESGAGKTENTKKVIQYL  149 (712)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCceEEEeCCCCCCHHHHHHHHHHHH
Confidence            346789999999999999998888765

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=91.22  E-value=0.1  Score=41.61  Aligned_cols=34  Identities=18%  Similarity=0.375  Sum_probs=26.6

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc---CCcEEEEeccc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI---DANFLKVVSSA  101 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~~~~  101 (292)
                      .|.++|.=|+||||++-.+|..+   |..++-+++..
T Consensus         4 ~IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID~Dp   40 (289)
T d2afhe1           4 QCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDP   40 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEECS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEecCC
Confidence            46779999999999887776544   77888888653

>d1w7ja2 c.37.1.9 (A:63-792) Myosin S1, motor domain {Chicken (Gallus gallus), Va isoform [TaxId: 9031]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Chicken (Gallus gallus), Va isoform [TaxId: 9031]

Probab=90.74  E-value=0.14  Score=46.76  Aligned_cols=27  Identities=22%  Similarity=0.416  Sum_probs=23.2

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.+|+|.|.+|+|||..++.+.+.+
T Consensus        92 ~~~Q~IiisGeSGsGKTe~~k~il~~l  118 (730)
T d1w7ja2          92 ERNQSIIVSGESGAGKTVSAKYAMRYF  118 (730)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            346789999999999999998888765

>d1kk8a2 c.37.1.9 (A:1-28,A:77-837) Myosin S1, motor domain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Myosin S1, motor domain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=90.41  E-value=0.12  Score=47.66  Aligned_cols=27  Identities=22%  Similarity=0.415  Sum_probs=22.9

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+.+|+|.|.+|+|||..+|.+.+.+
T Consensus       119 ~~nQ~IiisGESGaGKTe~~K~il~yL  145 (789)
T d1kk8a2         119 RENQSCLITGESGAGKTENTKKVIMYL  145 (789)
T ss_dssp             TSEEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            346789999999999999988888765

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.33  E-value=0.05  Score=44.56  Aligned_cols=53  Identities=13%  Similarity=0.162  Sum_probs=30.8

Q ss_pred             CCCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           26 PGNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        26 ~~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ....+|+.+.+.+..-+.+-+.+..++-.. .+    -..+..++-||+.|+|||+.+
T Consensus        41 ~~~f~FD~vf~~~~~q~~vf~~~~~~lv~~-~l----~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          41 SKPYAFDRVFQSSTSQEQVYNDCAKKIVKD-VL----EGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             TEEEECSEEECTTCCHHHHHHHHTHHHHHH-HH----TTCCEEEEEECSTTSSHHHHH
T ss_pred             CceeECCEEECCCCCHHHHHHHHHHHHHHH-HH----cCCCcceeeecccCCCCceec
Confidence            345778888776443333333222211110 01    134678999999999999985

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=89.85  E-value=0.1  Score=41.43  Aligned_cols=27  Identities=30%  Similarity=0.498  Sum_probs=23.2

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHHhc
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      ..+..++|.|++|+|||+++..+++..
T Consensus        66 gkGQr~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          66 AKGGKIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             ETTCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             cCCCEEEeeCCCCCCHHHHHHHHHHHH
Confidence            447779999999999999999998663

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=89.75  E-value=0.12  Score=42.86  Aligned_cols=46  Identities=22%  Similarity=0.296  Sum_probs=28.6

Q ss_pred             CCccccccccH----HHHHHH-HHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGGLS----DQIREL-RESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g~~----~~~~~l-~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+|+.+.+.+    ++.+.+ ...+...+.          ..+.+++-||.+|+|||+++
T Consensus        47 ~f~FD~vf~~~~~q~~vy~~~~~plv~~~l~----------G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          47 SFTFDRVFDMSCKQSDIFDFSIKPTVDDILN----------GYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHHHTT----------TCCEEEEEECSTTSSHHHHH
T ss_pred             eEECCeEcCCCCCHHHHHHHHHHHHHHHhhc----------cCceeEEecccCCCCcceee
Confidence            47888887654    333332 222322211          34567899999999999875

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=89.66  E-value=0.06  Score=44.23  Aligned_cols=53  Identities=21%  Similarity=0.140  Sum_probs=29.8

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLAR   84 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~~   84 (292)
                      ..+|+.+.+.+..-+.+-+.+..|+-.. .+.   -..+..++-||..|+|||+.+-
T Consensus        51 ~F~fD~Vf~~~~~q~~vy~~~~~plv~~-~~~---~G~n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          51 EFIVDKVFDDTVDNFTVYENTIKPLIID-LYE---NGCVCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             EEECSEEECTTCCHHHHHHHHTHHHHHH-HHH---HCCEEEEEEECCTTSSHHHHHH
T ss_pred             eEeCCeecCCCCCHHHHHHHHHHHHHHH-HHh---cCCCeEEEeeeccccccceeee
Confidence            4567777765544444433322221110 010   0235678899999999999863

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=89.48  E-value=0.5  Score=33.27  Aligned_cols=34  Identities=12%  Similarity=-0.035  Sum_probs=22.4

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh---cCCcEEEEe
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN---IDANFLKVV   98 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~---l~~~~~~~~   98 (292)
                      .|.--+++||=.+|||+-+-..++.   .+..++.++
T Consensus         6 ~G~l~lI~GpMfSGKTteLi~~~~~~~~~g~~vl~i~   42 (141)
T d1xx6a1           6 HGWVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFK   42 (141)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             ceeEEEEEeccccHHHHHHHHHHHHhhhcCCcEEEEE
Confidence            3455678999999999955444433   366665555

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=89.42  E-value=0.59  Score=36.93  Aligned_cols=27  Identities=30%  Similarity=0.320  Sum_probs=21.6

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +..+..++|.|++|+|||+++..+...
T Consensus        64 ig~GQr~~Ifg~~g~GKt~l~~~~~~~   90 (276)
T d1fx0a3          64 VGRGQRELIIGDRQTGKTAVATDTILN   90 (276)
T ss_dssp             CBTTCBCBEEESSSSSHHHHHHHHHHT
T ss_pred             ccCCceEeeccCCCCChHHHHHHHHhh
Confidence            345777999999999999999776543

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=89.42  E-value=0.1  Score=38.74  Aligned_cols=32  Identities=25%  Similarity=0.404  Sum_probs=25.0

Q ss_pred             EEEEcCCCChHHHHHHHHHHhcCCcEEEEeccc
Q 022768           69 VLLYGPPGTGKTLLARAIASNIDANFLKVVSSA  101 (292)
Q Consensus        69 vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~  101 (292)
                      +||.|+.++|||..|..++... .+++++-...
T Consensus         2 iLVtGGarSGKS~~AE~l~~~~-~~~~YiAT~~   33 (180)
T d1c9ka_           2 ILVTGGARSGKSRHAEALIGDA-PQVLYIATSQ   33 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCSC-SSEEEEECCC
T ss_pred             EEEECCCCccHHHHHHHHHhcC-CCcEEEEccC
Confidence            6899999999999999998654 4566655544

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=89.38  E-value=0.23  Score=37.85  Aligned_cols=34  Identities=24%  Similarity=0.371  Sum_probs=26.2

Q ss_pred             ceEEEE-cCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           67 KGVLLY-GPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        67 ~~vll~-G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      +.|.++ +..|+||||++-.+|..+   |.++..+++.
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~la~~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            346566 669999999998888765   7788888754

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=89.34  E-value=0.12  Score=39.82  Aligned_cols=23  Identities=30%  Similarity=0.273  Sum_probs=20.2

Q ss_pred             eEEEEcCCCChHHHHHHHHHHhc
Q 022768           68 GVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        68 ~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      .|.|.|.+++|||||+.++....
T Consensus         7 ~IaIiGh~d~GKSTL~~~L~~~~   29 (227)
T d1g7sa4           7 IVSVLGHVDHGKTTLLDHIRGSA   29 (227)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCccHHHHHHHHHhhc
Confidence            38899999999999999998653

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=89.25  E-value=0.08  Score=42.91  Aligned_cols=19  Identities=37%  Similarity=0.602  Sum_probs=16.0

Q ss_pred             CceEEEEcCCCChHHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLAR   84 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~   84 (292)
                      +...+|.|.+|||||||..
T Consensus        14 ~~valffGLSGTGKTTLs~   32 (318)
T d1j3ba1          14 GDVAVFFGLSGTGKTTLST   32 (318)
T ss_dssp             CCEEEEEECTTSCHHHHTC
T ss_pred             CCEEEEEccCCCCcccccc
Confidence            4568999999999999753

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=88.64  E-value=0.097  Score=43.56  Aligned_cols=46  Identities=20%  Similarity=0.257  Sum_probs=28.9

Q ss_pred             CCccccccccH----HHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGGLS----DQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g~~----~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+|+.+.+.+    ++.+.+...+...+.          ..+.+++-||..|+|||+.+
T Consensus        43 ~f~FD~vf~~~~~q~~vy~~v~~lv~~~l~----------G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          43 QHMYDRVFDGNATQDDVFEDTKYLVQSAVD----------GYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             EEECSEEECTTCCHHHHHHTTTHHHHHHHT----------TCEEEEEEECSTTSSHHHHH
T ss_pred             EEECCeecCCCCCHHHHHHHHHHHHHHHhc----------CCceeeeccccCCCCccccc
Confidence            35688876654    444444333332211          33567889999999999985

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=87.86  E-value=0.13  Score=41.42  Aligned_cols=18  Identities=39%  Similarity=0.639  Sum_probs=15.6

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      +...+|.|.+|||||||.
T Consensus        14 ~~~alfFGLSGTGKTTLs   31 (313)
T d2olra1          14 GDVAVFFGLSGTGKTTLS   31 (313)
T ss_dssp             SCEEEEECSTTSSHHHHH
T ss_pred             CCEEEEEccCCCCcccce
Confidence            456789999999999976

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=87.84  E-value=0.29  Score=37.14  Aligned_cols=32  Identities=22%  Similarity=0.350  Sum_probs=24.7

Q ss_pred             EEEE-cCCCChHHHHHHHHHHhc---CCcEEEEecc
Q 022768           69 VLLY-GPPGTGKTLLARAIASNI---DANFLKVVSS  100 (292)
Q Consensus        69 vll~-G~~G~GKT~l~~~la~~l---~~~~~~~~~~  100 (292)
                      |.|+ |..|+||||++..+|..+   +..+..+++.
T Consensus         4 Iav~s~KGGvGKTtia~nlA~~la~~g~~VlliD~D   39 (232)
T d1hyqa_           4 ITVASGKGGTGKTTITANLGVALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEECCCCCChHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            4455 889999999998888766   6777777754

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.77  E-value=0.12  Score=43.07  Aligned_cols=51  Identities=22%  Similarity=0.277  Sum_probs=29.0

Q ss_pred             CCCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           27 GNVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        27 ~~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ...+|+.+.+.+..-+.+-+.+. ++-. ..+    -..+.+++-||..|+|||+.+
T Consensus        92 ~~F~FD~vf~~~~~Q~~Vy~~v~-plv~-~vl----~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_          92 QIFSFDQVFHPLSSQSDIFEMVS-PLIQ-SAL----DGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             CEEECSEEECTTCCHHHHHTTTH-HHHH-HHH----TTCEEEEEEECSTTSSHHHHH
T ss_pred             eeeECCeEECCCCCccchHHHHH-HHHH-HHh----cccceeEEeeccCCCccceEe
Confidence            34678888775433333333221 1110 011    134567899999999999875

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=87.55  E-value=0.079  Score=44.10  Aligned_cols=51  Identities=18%  Similarity=0.230  Sum_probs=28.4

Q ss_pred             CCccccccccHHHHHHHHHHhhcccCChHHHHhcCCCCCceEEEEcCCCChHHHHH
Q 022768           28 NVSYSAVGGLSDQIRELRESIELPLMNPELFLRVGIKPPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        28 ~~~~~~l~g~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~vll~G~~G~GKT~l~   83 (292)
                      ..+|+.+.+.+..-+.+-+.+..++-. ..+    -..+.+++-||..|+|||+.+
T Consensus        81 ~f~FD~vf~~~~~Q~~Vy~~~~~plv~-~~l----~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_          81 AFCFDFAFDETASNEVVYRFTARPLVQ-TIF----EGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             EEECSEEECTTCCHHHHHHHTTHHHHH-HHH----TTCEEEEEEEESTTSSHHHHH
T ss_pred             eEeCCeecCCCCCHHHHHHHHHHHHHH-HHH----hccCceEEeeccCCCCCceee
Confidence            357888877543333333222221110 011    133567888999999999985

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=86.98  E-value=0.17  Score=40.92  Aligned_cols=18  Identities=39%  Similarity=0.637  Sum_probs=15.8

Q ss_pred             CceEEEEcCCCChHHHHH
Q 022768           66 PKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~   83 (292)
                      +...+|.|.+|||||||.
T Consensus        14 gd~alfFGLSGTGKTTLs   31 (323)
T d1ii2a1          14 GDVTVFFGLSGTGKTTLS   31 (323)
T ss_dssp             CCEEEEECCTTSSHHHHH
T ss_pred             CCEEEEEccCCCCcccce
Confidence            456789999999999987

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=86.78  E-value=0.12  Score=39.11  Aligned_cols=17  Identities=29%  Similarity=0.313  Sum_probs=15.2

Q ss_pred             CceEEEEcCCCChHHHH
Q 022768           66 PKGVLLYGPPGTGKTLL   82 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l   82 (292)
                      +..+++..|+|||||..
T Consensus        38 G~dvii~a~TGSGKTla   54 (209)
T d1q0ua_          38 GESMVGQSQTGTGKTHA   54 (209)
T ss_dssp             TCCEEEECCSSHHHHHH
T ss_pred             CCCeEeeccccccccee
Confidence            67899999999999974

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=85.31  E-value=0.24  Score=39.51  Aligned_cols=27  Identities=33%  Similarity=0.309  Sum_probs=22.2

Q ss_pred             CCCCceEEEEcCCCChHHHHHHHHHHh
Q 022768           63 IKPPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        63 ~~~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      +..+..++|.|++|+|||+++..++..
T Consensus        65 ig~GQr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          65 IGRGQRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             CBTTCBCEEEESTTSSHHHHHHHHHHH
T ss_pred             ccCCCEEEeecCCCCChHHHHHHHHHh
Confidence            355778999999999999998877643

>d2huec1 a.22.1.1 (C:20-101) Histone H4 {African clawed frog (Xenopus laevis) [TaxId: 8355]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Nucleosome core histones
domain: Histone H4
species: African clawed frog (Xenopus laevis) [TaxId: 8355]

Probab=85.25  E-value=0.25  Score=31.38  Aligned_cols=42  Identities=26%  Similarity=0.276  Sum_probs=33.2

Q ss_pred             HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          227 YEAVVKLAEGFNGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       227 ~~~l~~~~~g~~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      ++.+.....    ..+.+++++|..++.-..+.+|+.+|+.-|++.
T Consensus        32 ~~~l~~~l~----~~l~~i~~~a~~~~~hakRKTvt~~DV~~Alkr   73 (82)
T d2huec1          32 YEETRGVLK----VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR   73 (82)
T ss_dssp             HHHHHHHHH----HHHHHHHHHHHHHHHHTTCSEECHHHHHHHTTT
T ss_pred             HHHHHHHHH----HHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            444554433    377899999999998889999999999998864

>d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecQ helicase domain
species: Escherichia coli [TaxId: 562]

Probab=84.87  E-value=0.31  Score=36.44  Aligned_cols=32  Identities=25%  Similarity=0.277  Sum_probs=22.0

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcCCcEEEE
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNIDANFLKV   97 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~   97 (292)
                      +.++++.-|+|+|||..............+.+
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~~~~~~~~~~v   71 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPALLLNGLTVVV   71 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHSSSEEEEE
T ss_pred             CCCEEEEcCCCCCCcchhhhhhhhccCceEEe
Confidence            56799999999999987655444433333333

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=84.83  E-value=0.3  Score=40.03  Aligned_cols=19  Identities=37%  Similarity=0.557  Sum_probs=16.2

Q ss_pred             CCceEEEEcCCCChHHHHH
Q 022768           65 PPKGVLLYGPPGTGKTLLA   83 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~   83 (292)
                      .+..++-||..|+|||+.+
T Consensus        80 ~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          80 YNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             CEEEEEEEECTTSSHHHHH
T ss_pred             CCceEEeeeeccccceEEe
Confidence            3567889999999999875

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=84.69  E-value=0.39  Score=39.42  Aligned_cols=43  Identities=19%  Similarity=0.330  Sum_probs=28.0

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHhcCCcEEEEeccchhccccChHHHHHHHHHHHhh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASNIDANFLKVVSSAIIDKYIGESARLIREMFGYAR  122 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (292)
                      .+..++-||..|+|||+.+      +|.+         .....|-....+..+|....
T Consensus        86 ~n~ti~aYGqTgSGKT~Tm------~G~~---------~~~~~Glipr~l~~lf~~~~  128 (349)
T d2zfia1          86 YNVCIFAYGQTGAGKSYTM------MGKQ---------EKDQQGIIPQLCEDLFSRIN  128 (349)
T ss_dssp             CCEEEEEECSTTSSHHHHH------TBCS---------GGGCBCHHHHHHHHHHHHHH
T ss_pred             cCceeeeeccCCCCCceee------ccCc---------cccccCchHHHHhhhhhhcc
Confidence            3578999999999999985      1211         01224556666777776654

>d1htaa_ a.22.1.2 (A:) Archaeal histone {Archaeon Methanothermus fervidus, histone A [TaxId: 2180]}

class: All alpha proteins
fold: Histone-fold
superfamily: Histone-fold
family: Archaeal histone
domain: Archaeal histone
species: Archaeon Methanothermus fervidus, histone A [TaxId: 2180]

Probab=84.18  E-value=0.57  Score=28.29  Aligned_cols=35  Identities=23%  Similarity=0.072  Sum_probs=30.7

Q ss_pred             CHHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHH
Q 022768          238 NGADLRNVCTEAGMSAIRAERDYVIHEDFMKAVRK  272 (292)
Q Consensus       238 ~~~di~~l~~~a~~~a~~~~~~~i~~~~~~~a~~~  272 (292)
                      .---+..++..|...+...++.+|+.+|+..|++.
T Consensus        33 ~e~fi~~l~~~a~~~a~~~kRkTi~~~DV~~Alk~   67 (68)
T d1htaa_          33 LEEMGEEIASEAVKLAKHAGRKTIKAEDIELARKM   67 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHh
Confidence            33478899999999999999999999999999874

>d1zunb3 c.37.1.8 (B:16-237) Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain {Pseudomonas syringae pv. tomato [TaxId: 323]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Sulfate adenylate transferase subunit cysN/C, EF-Tu domain G-like domain
species: Pseudomonas syringae pv. tomato [TaxId: 323]

Probab=83.54  E-value=0.44  Score=36.38  Aligned_cols=25  Identities=20%  Similarity=0.230  Sum_probs=21.4

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      ..+++.|...+|||||+.++....+
T Consensus        10 ~~i~viGHVd~GKSTL~~~Ll~~~g   34 (222)
T d1zunb3          10 LRFLTCGNVDDGKSTLIGRLLHDSK   34 (222)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3478999999999999999986654

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.60  E-value=0.32  Score=41.21  Aligned_cols=26  Identities=23%  Similarity=0.165  Sum_probs=19.1

Q ss_pred             CCCceEEEEcCCCChHHHHH-HHHHHh
Q 022768           64 KPPKGVLLYGPPGTGKTLLA-RAIASN   89 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~-~~la~~   89 (292)
                      +....+||.+.+|||||+++ ..++..
T Consensus        14 p~~g~~lv~A~AGsGKT~~l~~r~~~l   40 (485)
T d1w36b1          14 PLQGERLIEASAGTGKTFTIAALYLRL   40 (485)
T ss_dssp             CCSSCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEcCchHHHHHHHHHHHHH
Confidence            45667999999999999864 434443

>d1jnya3 c.37.1.8 (A:4-227) Elongation factor eEF-1alpha, N-terminal (G) domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=81.97  E-value=0.46  Score=36.17  Aligned_cols=25  Identities=16%  Similarity=0.270  Sum_probs=21.0

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      -+|.+.|.-++|||||+.++....+
T Consensus         4 iNi~viGHVd~GKTTL~~~Ll~~~g   28 (224)
T d1jnya3           4 LNLIVIGHVDHGKSTLVGRLLMDRG   28 (224)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHB
T ss_pred             cEEEEEecCCCCHHHHHHHHHHHcC
Confidence            4689999999999999998875443

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.71  E-value=5.9  Score=26.98  Aligned_cols=32  Identities=16%  Similarity=0.138  Sum_probs=21.1

Q ss_pred             ceEEEEcCCCChHHHHHHHHHHhc---CCcEEEEe
Q 022768           67 KGVLLYGPPGTGKTLLARAIASNI---DANFLKVV   98 (292)
Q Consensus        67 ~~vll~G~~G~GKT~l~~~la~~l---~~~~~~~~   98 (292)
                      .--+++||=.+|||+-+=..++..   +..++.++
T Consensus         3 ~L~li~GpMfsGKTt~Li~~~~~~~~~g~~v~~ik   37 (133)
T d1xbta1           3 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIK   37 (133)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEEEecccCHHHHHHHHHHHHHHHcCCcEEEEe
Confidence            345788999999999554444332   55565555

>d1puja_ c.37.1.8 (A:) Probable GTPase YlqF {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase YlqF
species: Bacillus subtilis [TaxId: 1423]

Probab=80.94  E-value=0.47  Score=37.37  Aligned_cols=25  Identities=28%  Similarity=0.448  Sum_probs=21.6

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .+-.+++.|-|.+||||++.++.+.
T Consensus       111 ~~~~v~vvG~PNvGKSsliN~L~~~  135 (273)
T d1puja_         111 RAIRALIIGIPNVGKSTLINRLAKK  135 (273)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CceEEEEEecCccchhhhhhhhhcc
Confidence            3455899999999999999999874

>d1z63a1 c.37.1.19 (A:432-661) Helicase of the SNF2/Rad54 hamily {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Helicase of the SNF2/Rad54 hamily
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=80.70  E-value=2.2  Score=32.07  Aligned_cols=25  Identities=36%  Similarity=0.363  Sum_probs=19.2

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhc
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNI   90 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l   90 (292)
                      +.+.+|.=+.|.|||..+-+++..+
T Consensus        31 ~~g~iLaDe~GlGKT~~~i~~~~~~   55 (230)
T d1z63a1          31 GFGICLADDMGLGKTLQTIAVFSDA   55 (230)
T ss_dssp             TCCEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCChHHHHHHhhhhh
Confidence            4568888899999999876666544

>d1ni3a1 c.37.1.8 (A:11-306) YchF GTP-binding protein N-terminal domain {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: YchF GTP-binding protein N-terminal domain
species: Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]

Probab=80.47  E-value=0.62  Score=37.11  Aligned_cols=25  Identities=28%  Similarity=0.360  Sum_probs=21.3

Q ss_pred             CCceEEEEcCCCChHHHHHHHHHHh
Q 022768           65 PPKGVLLYGPPGTGKTLLARAIASN   89 (292)
Q Consensus        65 ~~~~vll~G~~G~GKT~l~~~la~~   89 (292)
                      .+..+-|.|.|.+||||+..++.+.
T Consensus         9 ~~~kiGivG~Pn~GKSTlfnalT~~   33 (296)
T d1ni3a1           9 NNLKTGIVGMPNVGKSTFFRAITKS   33 (296)
T ss_dssp             SCCEEEEEECSSSSHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHCC
Confidence            3455889999999999999999854

>d2qn6a3 c.37.1.8 (A:2-206) Initiation factor eIF2 gamma subunit, N-terminal (G) domain {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor eIF2 gamma subunit, N-terminal (G) domain
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=80.46  E-value=0.64  Score=34.70  Aligned_cols=25  Identities=32%  Similarity=0.457  Sum_probs=21.3

Q ss_pred             CCCceEEEEcCCCChHHHHHHHHHH
Q 022768           64 KPPKGVLLYGPPGTGKTLLARAIAS   88 (292)
Q Consensus        64 ~~~~~vll~G~~G~GKT~l~~~la~   88 (292)
                      .|.-++.+.|...+|||||+..+..
T Consensus         6 ~p~ini~iiGhVd~GKSTL~~~L~~   30 (205)
T d2qn6a3           6 QPEVNIGVVGHVDHGKTTLVQAITG   30 (205)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHS
T ss_pred             CCCeEEEEEEccCCcHHHHHHHHHh
Confidence            3445799999999999999999974

>d1f60a3 c.37.1.8 (A:2-240) Elongation factor eEF-1alpha, N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor eEF-1alpha, N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=80.30  E-value=0.6  Score=36.01  Aligned_cols=26  Identities=15%  Similarity=0.210  Sum_probs=21.8

Q ss_pred             CceEEEEcCCCChHHHHHHHHHHhcC
Q 022768           66 PKGVLLYGPPGTGKTLLARAIASNID   91 (292)
Q Consensus        66 ~~~vll~G~~G~GKT~l~~~la~~l~   91 (292)
                      .-++.+.|..++|||||+..++..++
T Consensus         6 ~iNi~iiGHvD~GKsTl~~~ll~~~g   31 (239)
T d1f60a3           6 HINVVVIGHVDSGKSTTTGHLIYKCG   31 (239)
T ss_dssp             EEEEEEEECTTSCHHHHHHHHHHHHS
T ss_pred             ccEEEEEeCCCCCHHHHHHHHHHHcC
Confidence            34799999999999999999975543