Citrus Sinensis ID: 012016

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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-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470---
Protein Sequence
MDTSATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEESTESQ
Secondary Structure (PSIPRED)
cccccccHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHcccccEEEEEEccccccccHHHHHHHHHHcccccccccEEEEEEccccccEEEEccccccEEEEEccEEEEEEEEEEEccccccccccccccccEEEEEEEEEcccccHHHcccHHHHHHHHHHHHHHcccEEEEEEEcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcHHHHHHHcccccccEEEEccccccHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHccccEEEEEEcccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccccccccccccccccccEEEcccccHHHHHHHHHHHccccccccHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHccccEEEEEEEccccccHHHHHHHHHHHHHHHccHHHcEEEEccccccccEEEEEccccEEEEEEccEEEEEEEEEEccccccccccccccccccEEEEEEEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEcccccccccccccccEEcccccccHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccEEEEccccccHHHHHHHHHHHccccEEEEEccEccccHHHHHHHHcccccEEEEEEEccEEEEccccccccccccccccccccEEEEHHHHHHHcccHccccccEEEEEEcccHHcccHHHccccccccEEEEccccHHHHHHHHHHHcccccccHHHHHHHHHHHccccHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Coil and Loop (DISEMBL)
MDTSATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVylgkktspsvqriKVSKlekenhvnismesdEQVVDVFNGIKLKWVLVCRQvesrsfnhsstnIQAQVRYFELtfpkkykdvvigSYLPCVEKEAKSVQQESKTIKILTVNYnnlycnwtdawipvnldhpatFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRgyllygppgtgkSSLIAAMANYLNfdvydleltelrsnSDLRTLLVATANRSILVVEDIDctidlqdrlpadiagegegpiqqnkVTLSGFLNFIDglwsscgderiIVFTTnhkekldpallrpgrmdvhvhmsyctpsGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQlmrnddpeLVLNGLIEFLKVkrkededakprkiheestesq
Flexible Loop (DISEMBL)
mdtsatsaeNKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVylgkktspsvqrikvsklekenhvnismesdeqvvDVFNGIKLKWVLVCRQVESrsfnhsstniqaQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDlerfvkrkdyyrrvgkawkrgyllygpPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTtnhkekldpalLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQlmrnddpelVLNGLIEFlkvkrkededakprkiheestesq
Low Complexity Region (SEG)
MDTSATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGikehilfeeieeliSTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEESTESQ
Disordered region (IsUnstruct)
**************AKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKK**************************EQVVDVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKV*********************
Disordered Region (DISOPRED)
*****************ILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSP*****************ISMESDEQVVDVFNGIKLKWVLV*******************VRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCT*************************LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLI**************************
Disordered Region (DISEMBL)
**********KLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVE*********SKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRK******************
Disordered Region (DISPRO)
**********KLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQD***************QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDA*************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDTSATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEESTESQ
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	473	2.2.26 [Sep-21-2011]
Q9P6Q3	449	Probable mitochondrial ch	yes	no	0.420	0.443	0.372	2e-32
Q7ZTL7	419	Mitochondrial chaperone B	N/A	no	0.397	0.448	0.362	5e-28
Q54DY9	458	Probable mitochondrial ch	no	no	0.435	0.449	0.338	4e-27
Q7ZV60	420	Mitochondrial chaperone B	yes	no	0.348	0.392	0.384	5e-27
Q9Y276	419	Mitochondrial chaperone B	yes	no	0.513	0.579	0.307	2e-26
Q5E9H5	419	Mitochondrial chaperone B	yes	no	0.524	0.591	0.308	2e-26
Q9CZP5	418	Mitochondrial chaperone B	yes	no	0.545	0.617	0.313	1e-25
P32839	456	Mitochondrial chaperone B	yes	no	0.346	0.359	0.394	1e-25
Q54HY8	421	Probable mitochondrial ch	no	no	0.365	0.410	0.357	5e-22
Q7URM7	728	ATP-dependent zinc metall	yes	no	0.443	0.288	0.295	1e-15

>sp|Q9P6Q3|BCS1_SCHPO Probable mitochondrial chaperone bcs1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC644.07 PE=2 SV=1

 Score =  140 bits (354), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 80/215 (37%), Positives = 116/215 (53%), Gaps = 16/215 (7%)

Query: 195 NYNNLYCNWTDAWIPVNLDHPAT---FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA 251
           N   +Y  W   W P    HP +     ++ +E   K  I  D+  F++   +Y   G  
Sbjct: 183 NKTTIYTAWATEWKP--FGHPRSKRMLSSVVLESNVKKMITDDVHDFLRNSQWYDTRGIP 240

Query: 252 WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSD-LRTLLVATANRSILVV 310
           ++RGYLLYGPPG+GK+S + A+A  L++D+  L L E     D L  LL     ++++++
Sbjct: 241 YRRGYLLYGPPGSGKTSFLYALAGELDYDICVLNLAEKGLTDDRLNHLLSNVPPKAVVLL 300

Query: 311 EDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE 370
           ED+D     ++R        GE     N VT SG LN +DG+ SS  DERII  TTNH E
Sbjct: 301 EDVDSAFQGRER-------SGEVGFHAN-VTFSGLLNALDGVTSS--DERIIFMTTNHPE 350

Query: 371 KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG 405
           KLDPAL+RPGR+DV  ++   TP   + +   + G
Sbjct: 351 KLDPALVRPGRVDVKAYLGNATPEQVREMFTRFYG 385

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q7ZTL7|BCS1_XENLA Mitochondrial chaperone BCS1 OS=Xenopus laevis GN=bcs1l PE=2 SV=1

 Score =  125 bits (315), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 74/204 (36%), Positives = 110/204 (53%), Gaps = 16/204 (7%)

Query: 193 TVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAW 252
           TV YN +   W     P          ++ +EQ    KI+QD++ F++   +Y   G  +
Sbjct: 166 TVMYNAVGAEWRQFGFP---RRRRPLSSVVLEQGISEKIVQDVKGFIENPKWYSDRGIPY 222

Query: 253 KRGYLLYGPPGTGKSSLIAAMANYLNFDV-YDLELTELRSNSDLRTLLVATANRSILVVE 311
           +RGYLLYGPPG GKSS I A+A  L + +          S+  L  LL     +SI+++E
Sbjct: 223 RRGYLLYGPPGCGKSSFITALAGELEYSICLMSLSDSSLSDDRLNHLLSVAPQQSIILLE 282

Query: 312 DIDCTI---DLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH 368
           D+D      DL  + P    G G       ++T SG LN +DG+ S+  + RI+  TTNH
Sbjct: 283 DVDAAFVSRDLNKQNPTAYQGMG-------RLTFSGLLNALDGVAST--EARIVFMTTNH 333

Query: 369 KEKLDPALLRPGRMDVHVHMSYCT 392
            ++LDPAL+RPGR+DV  ++ +CT
Sbjct: 334 IDRLDPALIRPGRVDVKQYVGHCT 357

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Xenopus laevis (taxid: 8355)

>sp|Q54DY9|BCS1B_DICDI Probable mitochondrial chaperone BCS1-B OS=Dictyostelium discoideum GN=bcsl1b PE=3 SV=1

 Score =  123 bits (308), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 81/239 (33%), Positives = 124/239 (51%), Gaps = 33/239 (13%)

Query: 177 KEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPA---TFETLAMEQEQKTKIMQ 233
           +EAK +  E +  K L   Y ++  +W          HP       ++ +++ +   I+Q
Sbjct: 170 EEAKEMALEKEEGKTLI--YTSMGTDWR------RFGHPRRKRPISSVILDKGKSELIIQ 221

Query: 234 DLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT-ELRSN 292
           D+++F+   D+Y   G  ++RGYLLYGPPGTGKSS I A+A  L   +  L L  +  S+
Sbjct: 222 DVKKFLNNSDWYNDRGIPYRRGYLLYGPPGTGKSSFITALAGELQLSICILNLAGKSVSD 281

Query: 293 SDLRTLLVATANRSILVVEDIDCTI-----DLQDRL-PADIAGEGEGPIQ---------- 336
           + L  LL     RSI+++EDID  I     DL  +   A+      G +Q          
Sbjct: 282 TSLNQLLATAPQRSIILLEDIDSAIQTGNHDLSAKSNSANAPSISSGGLQYQGYYGNPSV 341

Query: 337 ---QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCT 392
               + +T SG LN +DG+ +S G  RI+  TTNH EKLD  L+RPGR+D+ + +  C+
Sbjct: 342 SSGGSALTFSGLLNALDGVAASEG--RILFMTTNHLEKLDKVLIRPGRVDLQIEIGLCS 398

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Dictyostelium discoideum (taxid: 44689)

>sp|Q7ZV60|BCS1_DANRE Mitochondrial chaperone BCS1 OS=Danio rerio GN=bcs1l PE=2 SV=2

 Score =  122 bits (307), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 68/177 (38%), Positives = 109/177 (61%), Gaps = 12/177 (6%)

Query: 220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF 279
           ++ +E     +I+ D++ F+    +Y   G  ++RGYLLYGPPG GKSS I A+A  L +
Sbjct: 190 SVVLESGVAERIVDDVKEFIGNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELGY 249

Query: 280 DVYDLELTELRSNSD--LRTLLVATANRSILVVEDIDCTIDLQDRLPAD--IAGEGEGPI 335
            +  + L++ RS SD  L  LL     +SI+++ED+D     ++ LP +  +A +G G  
Sbjct: 250 SICLMSLSD-RSLSDDRLNHLLSVAPQQSIILLEDVDAAFVSRELLPTENPLAYQGMG-- 306

Query: 336 QQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCT 392
              ++T SG LN +DG+ SS  + RI+  TTN  E+LDPAL+RPGR+D+  ++ +C+
Sbjct: 307 ---RLTFSGLLNALDGVASS--EARIVFMTTNFIERLDPALVRPGRVDLKQYVGHCS 358

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Danio rerio (taxid: 7955)

>sp|Q9Y276|BCS1_HUMAN Mitochondrial chaperone BCS1 OS=Homo sapiens GN=BCS1L PE=1 SV=1

 Score =  120 bits (302), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 134/273 (49%), Gaps = 30/273 (10%)

Query: 177 KEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPA---TFETLAMEQEQKTKIMQ 233
           +E    Q+E KT+         +Y      W P    +P       ++ ++Q    +I++
Sbjct: 155 RELALQQEEGKTV---------MYTAVGSEWRP--FGYPRRRRPLNSVVLQQGLADRIVR 203

Query: 234 DLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV-YDLELTELRSN 292
           D++ F+    +Y   G  ++RGYLLYGPPG GKSS I A+A  L   +          S+
Sbjct: 204 DVQEFIDNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSSLSD 263

Query: 293 SDLRTLLVATANRSILVVEDIDCTI---DLQDRLPADIAGEGEGPIQQNKVTLSGFLNFI 349
             L  LL     +S++++ED+D      DL    P    G G       ++T SG LN +
Sbjct: 264 DRLNHLLSVAPQQSLVLLEDVDAAFLSRDLAVENPVKYQGLG-------RLTFSGLLNAL 316

Query: 350 DGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH 409
           DG+ S+  + RI+  TTNH ++LDPAL+RPGR+D+  ++ YC+      +   +   +  
Sbjct: 317 DGVAST--EARIVFMTTNHVDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQRFYPGQAP 374

Query: 410 ILFEEIEE--LISTTQVTPAEVAEQLM-RNDDP 439
            L E   E  L +T Q++PA+V    M   +DP
Sbjct: 375 SLAENFAEHVLRATNQISPAQVQGYFMLYKNDP 407

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Homo sapiens (taxid: 9606)

>sp|Q5E9H5|BCS1_BOVIN Mitochondrial chaperone BCS1 OS=Bos taurus GN=BCS1L PE=2 SV=1

 Score =  120 bits (302), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 139/279 (49%), Gaps = 31/279 (11%)

Query: 177 KEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPA---TFETLAMEQEQKTKIMQ 233
           +E    Q+E KT+         +Y      W P    +P       ++ +EQ    +I++
Sbjct: 155 RELALQQEEGKTV---------MYTAVGSEWRP--FGYPRRRRPLNSVVLEQGVTERIVR 203

Query: 234 DLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV-YDLELTELRSN 292
           D+  F+    +Y   G  ++RGYLLYGPPG GKSS I A+A  L   +          S+
Sbjct: 204 DIREFIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELQHSICLLSLTDSSLSD 263

Query: 293 SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQ---NKVTLSGFLNFI 349
             L  LL     +S++++ED+D        L  D+A   E PI+     ++T SG LN +
Sbjct: 264 DRLNHLLSVAPQQSLVLLEDVDAAF-----LSRDLA--AENPIKYQGLGRLTFSGLLNAL 316

Query: 350 DGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH 409
           DG+ S+  + RI+  TTNH ++LDPAL+RPGR+D+  ++ +C+      +   +   +  
Sbjct: 317 DGVAST--EARIVFMTTNHIDRLDPALIRPGRVDMKEYVGHCSRWQLTQMFQRFYPGQAT 374

Query: 410 ILFEEIEE--LISTTQVTPAEVAEQLM--RNDDPELVLN 444
            L E   +  L +TTQ++PA+V    M  +ND    + N
Sbjct: 375 SLAENFADRVLQATTQISPAQVQGYFMLYKNDPAGAIQN 413

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Bos taurus (taxid: 9913)

>sp|Q9CZP5|BCS1_MOUSE Mitochondrial chaperone BCS1 OS=Mus musculus GN=Bcs1l PE=1 SV=1

 Score =  118 bits (295), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/284 (31%), Positives = 143/284 (50%), Gaps = 26/284 (9%)

Query: 176 EKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDL 235
           E  A ++QQE       TV Y  +   W     P         +++ ++Q    +I++D+
Sbjct: 153 EARALALQQEEGK----TVMYTAVGSEWRTFGYP---RRRRPLDSVVLQQGLADRIVKDI 205

Query: 236 ERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV-YDLELTELRSNSD 294
             F+    +Y   G  ++RGYLLYGPPG GKSS I A+A  L   +          S+  
Sbjct: 206 REFIDNPKWYIDRGIPYRRGYLLYGPPGCGKSSFITALAGELEHSICLLSLTDSSLSDDR 265

Query: 295 LRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQ---NKVTLSGFLNFIDG 351
           L  LL     +S++++ED+D        L  D+A   E PI+     ++T SG LN +DG
Sbjct: 266 LNHLLSVAPQQSLVLLEDVDAAF-----LSRDLA--VENPIKYQGLGRLTFSGLLNALDG 318

Query: 352 LWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL 411
           + S+  + RI+  TTN+ ++LDPAL+RPGR+D+  ++ YC+      +   +   +   L
Sbjct: 319 VAST--EARIVFMTTNYIDRLDPALIRPGRVDLKEYVGYCSHWQLTQMFQRFYPGQAPSL 376

Query: 412 FEEIEE--LISTTQVTPAEVAEQLM--RNDDPELVLNGLIEFLK 451
            E   E  L +T++++PA+V    M  +ND    V N  IE L+
Sbjct: 377 AENFAEHVLKATSEISPAQVQGYFMLYKNDPMGAVHN--IESLR 418

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Mus musculus (taxid: 10090)

>sp|P32839|BCS1_YEAST Mitochondrial chaperone BCS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=BCS1 PE=1 SV=2

 Score =  118 bits (295), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/175 (39%), Positives = 101/175 (57%), Gaps = 11/175 (6%)

Query: 220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF 279
           ++ ++   K  I+ D+  F+K   +Y   G  ++RGYLLYGPPG+GK+S I A+A  L++
Sbjct: 227 SVILDSGIKEGILDDVYDFMKNGKWYSDRGIPYRRGYLLYGPPGSGKTSFIQALAGELDY 286

Query: 280 DVYDLELTELRSNSD-LRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQN 338
           ++  L L+E     D L  L+     RSIL++EDID   + + +        GE     +
Sbjct: 287 NICILNLSENNLTDDRLNHLMNNMPERSILLLEDIDAAFNKRSQ-------TGEQGFHSS 339

Query: 339 KVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTP 393
            VT SG LN +DG+ SS  +E I   TTNH EKLD A++RPGR+D  V +   TP
Sbjct: 340 -VTFSGLLNALDGVTSS--EETITFMTTNHPEKLDAAIMRPGRIDYKVFVGNATP 391

Essential for the expression of the Rieske iron-sulfur protein.

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

>sp|Q54HY8|BCS1A_DICDI Probable mitochondrial chaperone BCS1-A OS=Dictyostelium discoideum GN=bcs1la PE=3 SV=1

 Score =  106 bits (264), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 64/179 (35%), Positives = 100/179 (55%), Gaps = 6/179 (3%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           +  ++ +  + K+K+++D++ F+  + +YR  G  ++RGYLLYG PG GKSSLI A+A  
Sbjct: 185 SLSSVILADDLKSKLIEDIKSFITNESWYRNRGIPYRRGYLLYGEPGNGKSSLINAIAGE 244

Query: 277 LNFDVYDLELTELR-SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPI 335
           LN D+  + L+     +  +  LL     +SIL++EDID           ++        
Sbjct: 245 LNLDICIVSLSSKDIDDKQINHLLNNAPPKSILLIEDIDAAFKSH---RDNVDSNNNNSN 301

Query: 336 QQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPS 394
             N +T SG LN +DG+ S  G  RI+  TTN  E LD AL+R GR+D+ + +S  T S
Sbjct: 302 NNNSLTYSGLLNALDGVASQEG--RILFMTTNKIELLDSALIREGRIDLKIKVSNATKS 358

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Dictyostelium discoideum (taxid: 44689)

>sp|Q7URM7|FTSH2_RHOBA ATP-dependent zinc metalloprotease FtsH 2 OS=Rhodopirellula baltica (strain SH1) GN=ftsH2 PE=3 SV=1

 Score = 85.1 bits (209), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 108/227 (47%), Gaps = 17/227 (7%)

Query: 213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAA 272
           D P TFE +A  +E   ++ + ++ F+K  + Y+ +G    +G LL GPPGTGK+ L  A
Sbjct: 245 DLPTTFEDVAGIEEAVDEVREVVD-FLKNSEKYQSLGGRIPKGVLLVGPPGTGKTLLAKA 303

Query: 273 MANYLNFDVYDLELTELR------SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPAD 326
           +A       + L  ++          + +R +     NR+  ++      ID  D L   
Sbjct: 304 IAGEAGVPFFSLSGSDFVEMFVGVGAARVRDMFTQAVNRAPCII-----FIDELDALGKS 358

Query: 327 IAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHV 386
            +G   G   + + TL+  L  +DG  S+ G   I+V  TN  E LDPALLRPGR D HV
Sbjct: 359 RSGSVVGGHDEREQTLNALLVEMDGFDSNSG--VIVVAATNRPETLDPALLRPGRFDRHV 416

Query: 387 HMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQL 433
            +     +G + + A ++   +++  +E  EL     +T   V   L
Sbjct: 417 LVDRPDVAGREEILAVHV---KNVKLDETVELKGIASITSGFVGADL 460

Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins.

Rhodopirellula baltica (strain SH1) (taxid: 243090)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 4

EC: .

EC: -

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	473
255561048	528	ATP binding protein, putative [Ricinus c	0.945	0.846	0.677	0.0
224094843	461	predicted protein [Populus trichocarpa]	0.940	0.965	0.686	1e-180
225431310	522	PREDICTED: uncharacterized protein LOC10	0.947	0.858	0.612	1e-165
13877697	534	putative mitochondrial protein [Arabidop	0.955	0.846	0.620	1e-164
21592769	534	BCS1 protein-like protein [Arabidopsis t	0.955	0.846	0.620	1e-163
30693378	576	cytochrome BC1 synthesis [Arabidopsis th	0.955	0.784	0.620	1e-163
449464576	489	PREDICTED: ATP-dependent zinc metallopro	0.989	0.957	0.590	1e-163
449520948	480	PREDICTED: uncharacterized protein LOC10	0.942	0.929	0.618	1e-163
449520946	501	PREDICTED: uncharacterized protein LOC10	0.942	0.890	0.618	1e-163
449464546	480	PREDICTED: uncharacterized protein LOC10	0.942	0.929	0.616	1e-162

>gi|255561048|ref|XP_002521536.1| ATP binding protein, putative [Ricinus communis] gi|223539214|gb|EEF40807.1| ATP binding protein, putative [Ricinus communis]

 Score =  650 bits (1678), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 307/453 (67%), Positives = 376/453 (83%), Gaps = 6/453 (1%)

Query: 9   ENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVID 68
           E  LATAKT+LSTAASVAATVMLAR+VA+D+LPYE  DYF F +RK   RFSSQ+T+V+D
Sbjct: 7   ETNLATAKTVLSTAASVAATVMLARSVAQDILPYEFHDYFLFNIRKILGRFSSQITMVVD 66

Query: 69  EHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLK 128
           E DG   NQIY+AA+ YL    SPS +R KVSK EKE ++ + ME +E+++DV+ G+K K
Sbjct: 67  EFDGFVHNQIYEAAETYLASNISPSTRRFKVSKPEKEKNLTVKMEGNEEIIDVYRGVKFK 126

Query: 129 WVLVCRQVESRS----FNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQ 184
           W+ VC QVESR+    F+H++T ++++VR FE++FPKK+K++ + SYLP + +EA+S+ Q
Sbjct: 127 WIFVCSQVESRNLHHPFDHNAT-LRSEVRSFEVSFPKKHKEMALESYLPHIVREAESMVQ 185

Query: 185 ESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDY 244
           E KT++I +V+Y+N+Y N  DAW PVNLDHPATF+TLA++ + K  I++DLERFVKRKDY
Sbjct: 186 EKKTLRIFSVDYDNIYGNLADAWKPVNLDHPATFQTLALDAQLKGTILEDLERFVKRKDY 245

Query: 245 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATAN 304
           YR+VGKAWKRGYLLYGPPGTGKSSLIAAMANYL FD+YDLELTELR NS+LR LL+ATAN
Sbjct: 246 YRKVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDIYDLELTELRCNSELRKLLIATAN 305

Query: 305 RSILVVEDIDCTIDLQDRLPADIAGEGEGPI-QQNKVTLSGFLNFIDGLWSSCGDERIIV 363
           RSILVVEDIDCTI+ QDRL    A E       Q +VTLSG LNFIDGLWSSCGDERII+
Sbjct: 306 RSILVVEDIDCTIEFQDRLAEANAAEFHAHYPPQKQVTLSGLLNFIDGLWSSCGDERIII 365

Query: 364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQ 423
           FTTNHKEKLDPALLRPGRMDVHVHMSYCTP GF+LLAANYLGIK+H LF  IE+LI T Q
Sbjct: 366 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPCGFRLLAANYLGIKDHHLFGRIEDLILTAQ 425

Query: 424 VTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKE 456
           VTPAEVAEQL+R+D+ E VL+ LI+FL+V++KE
Sbjct: 426 VTPAEVAEQLLRSDELETVLSELIQFLEVRKKE 458

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224094843|ref|XP_002310261.1| predicted protein [Populus trichocarpa] gi|222853164|gb|EEE90711.1| predicted protein [Populus trichocarpa]

 Score =  639 bits (1647), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 309/450 (68%), Positives = 375/450 (83%), Gaps = 5/450 (1%)

Query: 5   ATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLT 64
           ++S E KLATAK +LSTAASVAAT MLAR++A+D +P+E Q YF++++R F  RFSSQLT
Sbjct: 2   SSSTETKLATAKIVLSTAASVAATAMLARSIAQDFMPHEFQAYFFYKIRNFFGRFSSQLT 61

Query: 65  IVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNG 124
           +V+DE DG   N+IY AA+ YLG K SPS QR+KVSK EKEN   + M+ +E++VD+F  
Sbjct: 62  MVVDEFDGYTYNEIYGAAETYLGSKISPSTQRLKVSKPEKENEFTVKMDRNEEIVDIFQD 121

Query: 125 IKLKWVLVCRQVESR----SFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAK 180
           +K KW LVC  V+S+    SFNH++T ++++VR FE++FPK++K++V+ SY P + K AK
Sbjct: 122 VKFKWALVCTHVDSKDHYNSFNHTAT-LRSEVRSFEVSFPKEHKEMVLESYFPYIVKVAK 180

Query: 181 SVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVK 240
           S+ QE KT+KI TV+Y ++Y N  DAW PVNLDHPATF+TLA++ + K KI++DLERFVK
Sbjct: 181 SMVQEKKTLKIFTVDYEHMYGNLADAWKPVNLDHPATFDTLALDTKDKDKILEDLERFVK 240

Query: 241 RKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLV 300
           R+DYYR+VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD+YDLELTE+R NSDLR +L+
Sbjct: 241 RRDYYRKVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDIYDLELTEVRCNSDLRKVLI 300

Query: 301 ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER 360
           ATANRSILVVEDIDCTI+LQDR+  + A  G G   Q +VTLSG LNFIDGLWSSCGDER
Sbjct: 301 ATANRSILVVEDIDCTIELQDRIAEERATPGLGYPPQKQVTLSGLLNFIDGLWSSCGDER 360

Query: 361 IIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIS 420
           IIVFTTNH EKLDPALLRPGRMDVHVHMSYCTP GFK LAANYLGIK+H+LFEEIEELI 
Sbjct: 361 IIVFTTNHIEKLDPALLRPGRMDVHVHMSYCTPCGFKFLAANYLGIKDHVLFEEIEELIK 420

Query: 421 TTQVTPAEVAEQLMRNDDPELVLNGLIEFL 450
           T +VTPAEVAEQLMR+D+ E VL  LIEFL
Sbjct: 421 TAEVTPAEVAEQLMRSDELETVLKELIEFL 450

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225431310|ref|XP_002269184.1| PREDICTED: uncharacterized protein LOC100241950 [Vitis vinifera] gi|147815615|emb|CAN63838.1| hypothetical protein VITISV_041357 [Vitis vinifera]

 Score =  587 bits (1512), Expect = e-165,   Method: Compositional matrix adjust.
 Identities = 277/452 (61%), Positives = 359/452 (79%), Gaps = 4/452 (0%)

Query: 8   AENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVI 67
           +E KLA+AKT+ STAAS+ AT M+ R+V +D LPYE Q  F   +R+  NRFS Q+T+VI
Sbjct: 9   SETKLASAKTVFSTAASLLATAMVFRSVLQDFLPYEAQQIFCSGIRRLFNRFSPQMTMVI 68

Query: 68  DEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKL 127
           DE DG+A NQI++AA+ YLG K   S QR++VS+  KE   NI++E D+++VDVF G+K 
Sbjct: 69  DEFDGIAYNQIFEAAETYLGSKVCSS-QRLRVSRPAKERKFNINVERDQEIVDVFRGVKF 127

Query: 128 KWVLVCRQVESRSFNHS---STNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQ 184
           +W+L+C + ESRS  +    ++ I+++VR FEL+F KK+ D+V+ SY P + KE+ S+ Q
Sbjct: 128 RWLLICIKTESRSIYNPRDFNSTIRSEVRSFELSFHKKHLDMVLNSYFPYILKESVSLIQ 187

Query: 185 ESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDY 244
           E KT+K+ TV++  ++   +DAW  ++LDHP+TF+T+AM+ E K+KI++DL+RFV+R+DY
Sbjct: 188 EKKTLKLFTVDFEKMFGKMSDAWSSISLDHPSTFDTIAMDSELKSKILEDLKRFVRRRDY 247

Query: 245 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATAN 304
           Y++VGKAWKRGYLLYGPPGTGKSSLIAA+ANYLNFD+YDLELTELR NS+LR LL+ATAN
Sbjct: 248 YKKVGKAWKRGYLLYGPPGTGKSSLIAAIANYLNFDIYDLELTELRCNSELRRLLLATAN 307

Query: 305 RSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF 364
           RSILVVEDIDCTI LQDR              + +VTLSG LNFIDGLWSSCGDERII+F
Sbjct: 308 RSILVVEDIDCTIQLQDRSAESQVMNPRSFQFEKQVTLSGLLNFIDGLWSSCGDERIIIF 367

Query: 365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQV 424
           TTNHK+KLDPALLRPGRMD+H+HMSYCTP GFK+LAANYLGI  H LF  IE LI TT+V
Sbjct: 368 TTNHKDKLDPALLRPGRMDMHIHMSYCTPYGFKILAANYLGIINHYLFSYIENLIQTTEV 427

Query: 425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRKE 456
           TPAEVAE L+++D+PE  L  LI+FL+VK++E
Sbjct: 428 TPAEVAEHLLQSDEPEKALRDLIKFLEVKKEE 459

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|13877697|gb|AAK43926.1|AF370607_1 putative mitochondrial protein [Arabidopsis thaliana] gi|4835244|emb|CAB42922.1| putative mitochondrial protein [Arabidopsis thaliana] gi|20856863|gb|AAM26687.1| AT3g50930/F18B3_210 [Arabidopsis thaliana]

 Score =  583 bits (1502), Expect = e-164,   Method: Compositional matrix adjust.
 Identities = 285/459 (62%), Positives = 367/459 (79%), Gaps = 7/459 (1%)

Query: 11  KLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEH 70
           +LATAKT+L+TAASVAAT MLAR++ +D LP E+  Y  +  R     FSSQ+TI+I+E 
Sbjct: 12  RLATAKTVLTTAASVAATAMLARSLVQDYLPDEVHHYISYGFRSIFGYFSSQMTIIIEEF 71

Query: 71  DGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWV 130
           +G A N++++AA+ YL  K SPS +RIKVSK EKEN+ N+++E DE+VVD +NG+K +W+
Sbjct: 72  EGFAHNEVFEAAEAYLATKISPSNKRIKVSKHEKENNYNVTVERDEEVVDTYNGVKFQWI 131

Query: 131 LVCRQVESRSFNHS---STNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
           L CR VES+ F++    ++ ++++VR FEL F KK+KDV + SYLP + K A  ++QE K
Sbjct: 132 LHCRHVESKHFHNPRDLNSTLRSEVRSFELNFHKKFKDVALESYLPFMVKRATLMKQEKK 191

Query: 188 TIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRR 247
           T+KI T++  N+Y N++DAW  V LDHP+TF+TLAM+ + KT +M+DL++FVKR+D+Y+R
Sbjct: 192 TLKIFTLSPENMYGNYSDAWTSVTLDHPSTFKTLAMDSDVKTSVMEDLDKFVKRRDFYKR 251

Query: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSI 307
           VGKAWKRGYLLYGPPGTGKSSLIAAMAN+LNFD+YDLELT + +NS+LR LL+ATANRSI
Sbjct: 252 VGKAWKRGYLLYGPPGTGKSSLIAAMANHLNFDIYDLELTAVNNNSELRRLLIATANRSI 311

Query: 308 LVVEDIDCTIDLQDRL---PADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF 364
           L+VEDIDC+++L+DR    P   + + E P +  KVTLSG LNFIDGLWSSCGDERII+F
Sbjct: 312 LIVEDIDCSLELKDRTSDEPPRESDDIEDP-RYKKVTLSGLLNFIDGLWSSCGDERIIIF 370

Query: 365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQV 424
           TTN+KEKLD ALLRPGRMD+H+HMSYCTPS FK LA NYL IKEH LF +IEE I  T+V
Sbjct: 371 TTNYKEKLDAALLRPGRMDMHIHMSYCTPSTFKALALNYLEIKEHRLFSKIEEGIEATEV 430

Query: 425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPR 463
           TPAEVAEQLMRND  + VL GLIEFLKVK+ E+E  K +
Sbjct: 431 TPAEVAEQLMRNDSVDKVLEGLIEFLKVKKIENEQDKAK 469

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21592769|gb|AAM64718.1| BCS1 protein-like protein [Arabidopsis thaliana]

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 285/459 (62%), Positives = 367/459 (79%), Gaps = 7/459 (1%)

Query: 11  KLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEH 70
           +LATAKT+L+TAASVAAT MLAR++ +D LP E+  Y  +  R     FSSQ+TI+I+E 
Sbjct: 12  RLATAKTVLTTAASVAATAMLARSLVQDYLPDEVHHYISYGFRSIFGYFSSQMTIIIEEF 71

Query: 71  DGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWV 130
           +G A N++++AA+ YL  K SPS +RIKVSK EKEN+ N+++E DE+VVD +NG+K +W+
Sbjct: 72  EGFAHNEVFEAAEAYLATKISPSNKRIKVSKHEKENNYNVTVERDEEVVDTYNGVKFQWI 131

Query: 131 LVCRQVESRSFNHS---STNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
           L CR VES+ F++    ++ ++++VR FEL F KK+KDV + SYLP + K A  ++QE K
Sbjct: 132 LHCRHVESKHFHNPRDLNSTLRSEVRSFELNFHKKFKDVALESYLPFMVKRATLMKQEKK 191

Query: 188 TIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRR 247
           T+KI T++  N+Y N++DAW  V LDHP+TF+TLAM+ + KT +M+DL++FVKR+D+Y+R
Sbjct: 192 TLKIFTLSPENMYGNYSDAWTSVTLDHPSTFKTLAMDSDVKTSVMEDLDKFVKRRDFYKR 251

Query: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSI 307
           VGKAWKRGYLLYGPPGTGKSSLIAAMAN+LNFD+YDLELT + +NS+LR LL+ATANRSI
Sbjct: 252 VGKAWKRGYLLYGPPGTGKSSLIAAMANHLNFDIYDLELTAVNNNSELRRLLIATANRSI 311

Query: 308 LVVEDIDCTIDLQDRL---PADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF 364
           L+VEDIDC+++L+DR    P   + + E P +  KVTLSG LNFIDGLWSSCGDERII+F
Sbjct: 312 LIVEDIDCSLELKDRTSDEPPRESDDIEDP-RYKKVTLSGLLNFIDGLWSSCGDERIIIF 370

Query: 365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQV 424
           TTN+KEKLD ALLRPGRMD+H+HMSYCTPS FK LA NYL IKEH LF +IEE I  T+V
Sbjct: 371 TTNYKEKLDAALLRPGRMDMHIHMSYCTPSTFKALALNYLEIKEHRLFSKIEEGIEATEV 430

Query: 425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPR 463
           TPAEVAEQLMRND  + VL GLIEFLKVK+ E+E  K +
Sbjct: 431 TPAEVAEQLMRNDSVDKVLEGLIEFLKVKKIENEQDKAK 469

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30693378|ref|NP_190662.2| cytochrome BC1 synthesis [Arabidopsis thaliana] gi|18086343|gb|AAL57634.1| AT3g50930/F18B3_210 [Arabidopsis thaliana] gi|27363216|gb|AAO11527.1| At3g50930/F18B3_210 [Arabidopsis thaliana] gi|332645207|gb|AEE78728.1| cytochrome BC1 synthesis [Arabidopsis thaliana]

 Score =  582 bits (1501), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 285/459 (62%), Positives = 367/459 (79%), Gaps = 7/459 (1%)

Query: 11  KLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEH 70
           +LATAKT+L+TAASVAAT MLAR++ +D LP E+  Y  +  R     FSSQ+TI+I+E 
Sbjct: 54  RLATAKTVLTTAASVAATAMLARSLVQDYLPDEVHHYISYGFRSIFGYFSSQMTIIIEEF 113

Query: 71  DGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWV 130
           +G A N++++AA+ YL  K SPS +RIKVSK EKEN+ N+++E DE+VVD +NG+K +W+
Sbjct: 114 EGFAHNEVFEAAEAYLATKISPSNKRIKVSKHEKENNYNVTVERDEEVVDTYNGVKFQWI 173

Query: 131 LVCRQVESRSFNHS---STNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
           L CR VES+ F++    ++ ++++VR FEL F KK+KDV + SYLP + K A  ++QE K
Sbjct: 174 LHCRHVESKHFHNPRDLNSTLRSEVRSFELNFHKKFKDVALESYLPFMVKRATLMKQEKK 233

Query: 188 TIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRR 247
           T+KI T++  N+Y N++DAW  V LDHP+TF+TLAM+ + KT +M+DL++FVKR+D+Y+R
Sbjct: 234 TLKIFTLSPENMYGNYSDAWTSVTLDHPSTFKTLAMDSDVKTSVMEDLDKFVKRRDFYKR 293

Query: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSI 307
           VGKAWKRGYLLYGPPGTGKSSLIAAMAN+LNFD+YDLELT + +NS+LR LL+ATANRSI
Sbjct: 294 VGKAWKRGYLLYGPPGTGKSSLIAAMANHLNFDIYDLELTAVNNNSELRRLLIATANRSI 353

Query: 308 LVVEDIDCTIDLQDRL---PADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF 364
           L+VEDIDC+++L+DR    P   + + E P +  KVTLSG LNFIDGLWSSCGDERII+F
Sbjct: 354 LIVEDIDCSLELKDRTSDEPPRESDDIEDP-RYKKVTLSGLLNFIDGLWSSCGDERIIIF 412

Query: 365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQV 424
           TTN+KEKLD ALLRPGRMD+H+HMSYCTPS FK LA NYL IKEH LF +IEE I  T+V
Sbjct: 413 TTNYKEKLDAALLRPGRMDMHIHMSYCTPSTFKALALNYLEIKEHRLFSKIEEGIEATEV 472

Query: 425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPR 463
           TPAEVAEQLMRND  + VL GLIEFLKVK+ E+E  K +
Sbjct: 473 TPAEVAEQLMRNDSVDKVLEGLIEFLKVKKIENEQDKAK 511

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464576|ref|XP_004150005.1| PREDICTED: ATP-dependent zinc metalloprotease FtsH-like [Cucumis sativus] gi|449520958|ref|XP_004167499.1| PREDICTED: ATP-dependent zinc metalloprotease FtsH-like [Cucumis sativus]

 Score =  581 bits (1498), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 278/471 (59%), Positives = 360/471 (76%), Gaps = 3/471 (0%)

Query: 1   MDTSATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFS 60
           M ++ +S+    A  K +L+ AAS AAT++LAR+VA DLLP  ++ Y Y   R   NRFS
Sbjct: 1   MPSNPSSSHPNFANVKPLLTAAASFAATLVLARSVANDLLPPHLRSYLYHGCRDIFNRFS 60

Query: 61  SQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVD 120
           SQLT++IDE DGL  NQIYDAA  YL  K SPS  R+KV+K EKE+++  +MES++Q+ D
Sbjct: 61  SQLTMIIDERDGLGPNQIYDAADTYLATKVSPSTHRLKVTKPEKEDNITTTMESNQQITD 120

Query: 121 VFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAK 180
           +F+G++  WVLVC Q+E ++  +     ++ VR F+L F +K++D+V+ SYLP +  +AK
Sbjct: 121 IFDGVQFHWVLVCSQIEEQNLYNPRLPFRSTVRSFKLCFHRKHRDMVLKSYLPHILHQAK 180

Query: 181 SVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVK 240
            ++Q++KT+KI T ++ ++Y N ++ WIP NLDHPATFE LAM+ E K  I++DLERFVK
Sbjct: 181 ELKQQTKTLKIYTFDFRHMYGNNSNLWIPTNLDHPATFEKLAMDSEIKDFILRDLERFVK 240

Query: 241 RKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLV 300
           RK+YYR+VGKAWKRGYLLYGPPGTGKSSLIAAMANYL F VYDLELTE++ NSDLR LL+
Sbjct: 241 RKEYYRKVGKAWKRGYLLYGPPGTGKSSLIAAMANYLRFAVYDLELTEIQCNSDLRKLLI 300

Query: 301 ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQ--NKVTLSGFLNFIDGLWSSCGD 358
              NRSILVVEDIDC+I  QDR  ++ A E   P ++   +VTLSG LNFIDGLWSSCGD
Sbjct: 301 GMGNRSILVVEDIDCSIQFQDR-ESESAEEENIPFRRRTTQVTLSGLLNFIDGLWSSCGD 359

Query: 359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEEL 418
           ERII+FTTN KEKLD ALLRPGRMDVHVHMSYC+P GF+LLA+NYLGI+ H LF EIEEL
Sbjct: 360 ERIIIFTTNRKEKLDGALLRPGRMDVHVHMSYCSPCGFRLLASNYLGIENHQLFGEIEEL 419

Query: 419 ISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEES 469
           I   +VTPAEVAEQL++ +D +  L  L+EFL+ K+  +E+ +  KI +ES
Sbjct: 420 ILKAKVTPAEVAEQLLKGEDGDTALRELMEFLEDKKMRNEEERKGKIDDES 470

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520948|ref|XP_004167494.1| PREDICTED: uncharacterized protein LOC101229933 isoform 2 [Cucumis sativus]

 Score =  581 bits (1497), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 279/451 (61%), Positives = 350/451 (77%), Gaps = 5/451 (1%)

Query: 8   AENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVI 67
           A++ L  AK IL+ AAS AATV+L R++A DLLP E ++YFY  +R   +RFSSQLT+V+
Sbjct: 8   AQSNLPNAKAILTAAASFAATVLLLRSIANDLLPSEFREYFYDGIRTIFSRFSSQLTMVV 67

Query: 68  DEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKL 127
           DE DGL  NQIY+AA++YL  K SPS  R+KVSK EKE+++  ++E +E+VVD FNG+K 
Sbjct: 68  DEMDGLGPNQIYEAAEIYLATKISPSTARLKVSKPEKEDNITTAVERNEEVVDTFNGVKF 127

Query: 128 KWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
            WVLVC QV+  +F++  +  ++ +R FEL F KK++++V+ SYLP +  +AK ++Q++K
Sbjct: 128 HWVLVCEQVQRENFHNPRSPYRSVIRSFELCFHKKHREMVLKSYLPHILHQAKELKQQTK 187

Query: 188 TIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRR 247
           T+KI T +Y N+Y + +D WIP NLDHP+TFE LAM+ E K  I+ DLERFVKRK YY +
Sbjct: 188 TLKIYTFDYQNMYGSISDLWIPTNLDHPSTFEKLAMDSEIKHFILNDLERFVKRKKYYEK 247

Query: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSI 307
           VGKAWKRGYLLYGPPGTGKSSLIAAMANYL FDVYDLELT +  NSDLR LL+  ANRSI
Sbjct: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELTGVECNSDLRKLLMGIANRSI 307

Query: 308 LVVEDIDCTIDLQDRLPADIAGEGEGPIQQNK---VTLSGFLNFIDGLWSSCGDERIIVF 364
           LVVEDIDC+++ QDR       E E P    +   VTLSG LNFIDGLWSSCGDERII+F
Sbjct: 308 LVVEDIDCSVEFQDR--DSEKDEEEDPSTSRRRRLVTLSGLLNFIDGLWSSCGDERIIIF 365

Query: 365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQV 424
           TTNHKEKLDPALLRPGRMDVH+HMSYCTP GF++LA+NYLGI+ H LF EIE LI   +V
Sbjct: 366 TTNHKEKLDPALLRPGRMDVHIHMSYCTPCGFRVLASNYLGIENHRLFGEIEGLIPGAKV 425

Query: 425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRK 455
           TPAEVAEQL++ ++ +  L  LIEFLKVK +
Sbjct: 426 TPAEVAEQLLKGEESDNSLMDLIEFLKVKTR 456

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449520946|ref|XP_004167493.1| PREDICTED: uncharacterized protein LOC101229933 isoform 1 [Cucumis sativus]

 Score =  581 bits (1497), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 279/451 (61%), Positives = 350/451 (77%), Gaps = 5/451 (1%)

Query: 8   AENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVI 67
           A++ L  AK IL+ AAS AATV+L R++A DLLP E ++YFY  +R   +RFSSQLT+V+
Sbjct: 8   AQSNLPNAKAILTAAASFAATVLLLRSIANDLLPSEFREYFYDGIRTIFSRFSSQLTMVV 67

Query: 68  DEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKL 127
           DE DGL  NQIY+AA++YL  K SPS  R+KVSK EKE+++  ++E +E+VVD FNG+K 
Sbjct: 68  DEMDGLGPNQIYEAAEIYLATKISPSTARLKVSKPEKEDNITTAVERNEEVVDTFNGVKF 127

Query: 128 KWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
            WVLVC QV+  +F++  +  ++ +R FEL F KK++++V+ SYLP +  +AK ++Q++K
Sbjct: 128 HWVLVCEQVQRENFHNPRSPYRSVIRSFELCFHKKHREMVLKSYLPHILHQAKELKQQTK 187

Query: 188 TIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRR 247
           T+KI T +Y N+Y + +D WIP NLDHP+TFE LAM+ E K  I+ DLERFVKRK YY +
Sbjct: 188 TLKIYTFDYQNMYGSISDLWIPTNLDHPSTFEKLAMDSEIKHFILNDLERFVKRKKYYEK 247

Query: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSI 307
           VGKAWKRGYLLYGPPGTGKSSLIAAMANYL FDVYDLELT +  NSDLR LL+  ANRSI
Sbjct: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELTGVECNSDLRKLLMGIANRSI 307

Query: 308 LVVEDIDCTIDLQDRLPADIAGEGEGPIQQNK---VTLSGFLNFIDGLWSSCGDERIIVF 364
           LVVEDIDC+++ QDR       E E P    +   VTLSG LNFIDGLWSSCGDERII+F
Sbjct: 308 LVVEDIDCSVEFQDR--DSEKDEEEDPSTSRRRRLVTLSGLLNFIDGLWSSCGDERIIIF 365

Query: 365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQV 424
           TTNHKEKLDPALLRPGRMDVH+HMSYCTP GF++LA+NYLGI+ H LF EIE LI   +V
Sbjct: 366 TTNHKEKLDPALLRPGRMDVHIHMSYCTPCGFRVLASNYLGIENHRLFGEIEGLIPGAKV 425

Query: 425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRK 455
           TPAEVAEQL++ ++ +  L  LIEFLKVK +
Sbjct: 426 TPAEVAEQLLKGEESDNSLMDLIEFLKVKTR 456

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464546|ref|XP_004149990.1| PREDICTED: uncharacterized protein LOC101205613 isoform 2 [Cucumis sativus]

 Score =  578 bits (1490), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 278/451 (61%), Positives = 349/451 (77%), Gaps = 5/451 (1%)

Query: 8   AENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVI 67
           A++ L  AK IL+ AAS AATV+L R++A DLLP E ++YFY  +R   +RFSSQLT+V+
Sbjct: 8   AQSNLPNAKAILTAAASFAATVLLLRSIANDLLPSEFREYFYDGIRTIFSRFSSQLTMVV 67

Query: 68  DEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKL 127
           DE DGL  NQIY+AA++YL  K SPS  R+KVSK EKE+++  ++E +E+VVD FNG+K 
Sbjct: 68  DEMDGLGPNQIYEAAEIYLATKISPSTARLKVSKPEKEDNITTAVERNEEVVDTFNGVKF 127

Query: 128 KWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
            WVLVC QV+  +F++  +  ++ +R FEL F KK++++V+ SYLP +  +AK ++Q++K
Sbjct: 128 HWVLVCEQVQRENFHNPRSPYRSVIRSFELCFHKKHREMVLKSYLPHILHQAKELKQQTK 187

Query: 188 TIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRR 247
           T+KI T +Y N+Y + +D WIP NLDHP+TFE LAM+ E K  I+ DLERFVKRK YY +
Sbjct: 188 TLKIYTFDYQNMYGSISDLWIPTNLDHPSTFEKLAMDSEIKHFILNDLERFVKRKKYYEK 247

Query: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSI 307
           VGKAWKRGYLLYGPPGTGKSSLIAAMANYL FDVYDLELT +  NSDLR LL+  ANRSI
Sbjct: 248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVYDLELTGVECNSDLRKLLMGIANRSI 307

Query: 308 LVVEDIDCTIDLQDRLPADIAGEGEGPIQQNK---VTLSGFLNFIDGLWSSCGDERIIVF 364
           LVVEDIDC+++ QDR       E E P    +   VTLSG LNFIDGLWSSCGDERII+F
Sbjct: 308 LVVEDIDCSVEFQDR--DSEKDEEEDPSTSRRRRLVTLSGLLNFIDGLWSSCGDERIIIF 365

Query: 365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQV 424
           TTNHKEKLDPALLRPGRMDVH+HMSYCTP GF++LA+NY GI+ H LF EIE LI   +V
Sbjct: 366 TTNHKEKLDPALLRPGRMDVHIHMSYCTPCGFRVLASNYHGIENHRLFGEIEGLIPGAKV 425

Query: 425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRK 455
           TPAEVAEQL++ ++ +  L  LIEFLKVK +
Sbjct: 426 TPAEVAEQLLKGEESDNSLMDLIEFLKVKTR 456

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	473
TAIR|locus:2077997	576	BCS1 "cytochrome BC1 synthesis	0.983	0.807	0.591	1.4e-157
TAIR|locus:2078007	451	AT3G50940 [Arabidopsis thalian	0.936	0.982	0.550	1e-132
TAIR|locus:1005716649	495	AT2G18193 [Arabidopsis thalian	0.909	0.868	0.484	1.6e-109
TAIR|locus:2175986	505	AT5G17760 [Arabidopsis thalian	0.934	0.875	0.450	7.2e-107
TAIR|locus:2053109	494	AT2G18190 [Arabidopsis thalian	0.951	0.910	0.470	8.3e-106
TAIR|locus:2175956	533	AT5G17740 [Arabidopsis thalian	0.940	0.834	0.445	2.9e-103
TAIR|locus:2175946	470	AT5G17730 [Arabidopsis thalian	0.923	0.929	0.447	1.4e-101
TAIR|locus:2175976	392	AT5G17750 [Arabidopsis thalian	0.668	0.806	0.5	1.5e-89
TAIR|locus:2098648	510	AT3G28540 [Arabidopsis thalian	0.604	0.560	0.414	7.2e-88
TAIR|locus:2098658	530	AT3G28510 [Arabidopsis thalian	0.955	0.852	0.395	9.2e-86

TAIR|locus:2077997 BCS1 "cytochrome BC1 synthesis" [Arabidopsis thaliana (taxid:3702)]

 Score = 1453 (516.5 bits), Expect = 1.4e-157, Sum P(2) = 1.4e-157
 Identities = 279/472 (59%), Positives = 365/472 (77%)

Query:     3 TSATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQ 62
             + ++SAE++LATAKT+L+TAASVAAT MLAR++ +D LP E+  Y  +  R     FSSQ
Sbjct:    46 SDSSSAESRLATAKTVLTTAASVAATAMLARSLVQDYLPDEVHHYISYGFRSIFGYFSSQ 105

Query:    63 LTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVF 122
             +TI+I+E +G A N++++AA+ YL  K SPS +RIKVSK EKEN+ N+++E DE+VVD +
Sbjct:   106 MTIIIEEFEGFAHNEVFEAAEAYLATKISPSNKRIKVSKHEKENNYNVTVERDEEVVDTY 165

Query:   123 NGIKLKWVLVCRQVESRSFNHS---STNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEA 179
             NG+K +W+L CR VES+ F++    ++ ++++VR FEL F KK+KDV + SYLP + K A
Sbjct:   166 NGVKFQWILHCRHVESKHFHNPRDLNSTLRSEVRSFELNFHKKFKDVALESYLPFMVKRA 225

Query:   180 KSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFV 239
               ++QE KT+KI T++  N+Y N++DAW  V LDHP+TF+TLAM+ + KT +M+DL++FV
Sbjct:   226 TLMKQEKKTLKIFTLSPENMYGNYSDAWTSVTLDHPSTFKTLAMDSDVKTSVMEDLDKFV 285

Query:   240 KRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLL 299
             KR+D+Y+RVGKAWKRGYLLYGPPGTGKSSLIAAMAN+LNFD+YDLELT + +NS+LR LL
Sbjct:   286 KRRDFYKRVGKAWKRGYLLYGPPGTGKSSLIAAMANHLNFDIYDLELTAVNNNSELRRLL 345

Query:   300 VATANRSILVVEDIDCTIDLQDRL---PADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSC 356
             +ATANRSIL+VEDIDC+++L+DR    P   + + E P +  KVTLSG LNFIDGLWSSC
Sbjct:   346 IATANRSILIVEDIDCSLELKDRTSDEPPRESDDIEDP-RYKKVTLSGLLNFIDGLWSSC 404

Query:   357 GDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXXXXX 416
             GDERII+FTTN+KEKLD ALLRPGRMD+H+HMSYCTPS FK LA NYL            
Sbjct:   405 GDERIIIFTTNYKEKLDAALLRPGRMDMHIHMSYCTPSTFKALALNYLEIKEHRLFSKIE 464

Query:   417 XXXSTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEE 468
                  T+VTPAEVAEQLMRND  + VL GLIEFLKVK+ E+E  K +   +E
Sbjct:   465 EGIEATEVTPAEVAEQLMRNDSVDKVLEGLIEFLKVKKIENEQDKAKTEKQE 516

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

GO:0052542 "defense response by callose deposition" evidence=RCA

TAIR|locus:2078007 AT3G50940 [Arabidopsis thaliana (taxid:3702)]

 Score = 1301 (463.0 bits), Expect = 1.0e-132, P = 1.0e-132
 Identities = 251/456 (55%), Positives = 347/456 (76%)

Query:     5 ATSAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLT 64
             ++S+E+ LATAKT L+  ASVAA  +LAR+V +D +P E+ +Y     R+F + FS Q+T
Sbjct:     2 SSSSESHLATAKTALTAVASVAAAAILARSVVQDYMPNEVHEYISHGFRRFFSYFSYQMT 61

Query:    65 IVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNG 124
              VI+E  G   NQ+++AA+ YL  K S S +RIKV+KLEK+++ ++++E DE+VVD+F+G
Sbjct:    62 AVIEEFGGFEHNQVFEAAEAYLSTKISNSTRRIKVNKLEKQSNYSVTVERDEEVVDIFDG 121

Query:   125 IKLKWVLVCRQVESRSFNHS---STNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKS 181
             +KL W+LVCR V+ + F +    ++ ++++VR +EL+F KK+K++V+ SYLP V ++A S
Sbjct:   122 VKLSWILVCRHVDKKDFRNPRDLNSTLKSEVRSYELSFRKKFKNMVLESYLPFVVEQAAS 181

Query:   182 VQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKR 241
             ++Q+ KT+KI TV+      +++  W  V LDHP+TF TLA++ E K  +++DL+RFV+R
Sbjct:   182 IKQKFKTLKIFTVD------SYSVEWTSVTLDHPSTFRTLALDPEVKKNLVEDLDRFVQR 235

Query:   242 KDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVA 301
             K +Y RVGKAWKRGYLLYGPPGTGKSSLIAA+AN+LNFD+YDL+LT L +N++LR LL++
Sbjct:   236 KGFYGRVGKAWKRGYLLYGPPGTGKSSLIAAIANHLNFDIYDLDLTSLNNNAELRRLLMS 295

Query:   302 TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI 361
             TANRSILVVEDIDC+I+L+DR   D   E   P+ +  VTLSG LNF+DGLWSSCG+ERI
Sbjct:   296 TANRSILVVEDIDCSIELKDR-STD--QENNDPLHKT-VTLSGLLNFVDGLWSSCGNERI 351

Query:   362 IVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXXXXXXXXST 421
             IVFTTN++EKLDPALLRPGRMD+H+HMSYCTP+ FK+LA+NYL                 
Sbjct:   352 IVFTTNYREKLDPALLRPGRMDMHIHMSYCTPAAFKVLASNYLEIQDHILFEQIEEFIRE 411

Query:   422 TQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKED 457
              +VTPAEVAEQLMR+D  + VL GL+EFLK K++ D
Sbjct:   412 IEVTPAEVAEQLMRSDSVDKVLQGLVEFLKAKKQID 447

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:1005716649 AT2G18193 [Arabidopsis thaliana (taxid:3702)]

 Score = 1082 (385.9 bits), Expect = 1.6e-109, P = 1.6e-109
 Identities = 221/456 (48%), Positives = 313/456 (68%)

Query:    17 TILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKN 76
             ++ S  AS+   +ML R++  D +P +++ YF   L +F    S  LT++IDE+ GL +N
Sbjct:    13 SLFSAYASLTGFLMLFRSMLHDFVPEKLRSYFSSLLDRFFTPKSKYLTVIIDENFGLNRN 72

Query:    77 QIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQV 136
             Q++DAA++YL  K  P  +R++V K+ K+ H  IS+E  E+++D F   ++KW  V    
Sbjct:    73 QVFDAAEMYLRSKIGPETERLRVGKIPKQKHFTISIERGEEILDTFEESEVKWSYV---- 128

Query:   137 ESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNY 196
               +S N     ++   RY+ELTF KK +D V+ SYL  V  E++ +++  + +K+ +   
Sbjct:   129 --QSENEKGDKVK---RYYELTFEKKLRDKVLNSYLTHVVAESEEIKRNLRVVKLYS--- 180

Query:   197 NNLYCNWTDA------WIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGK 250
              ++Y +  D       W  +NL+HP+TF+TLAM+   K KI+ DLERF+KRK++Y+RVGK
Sbjct:   181 RDVYASDDDDGMAGGNWGCINLEHPSTFDTLAMDPNAKKKIIDDLERFLKRKEFYKRVGK 240

Query:   251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVV 310
             AWKRGYLLYGPPGTGKSSLIAAMANYL FDV+DLEL+ +  N +L+ +L++T NRSILV+
Sbjct:   241 AWKRGYLLYGPPGTGKSSLIAAMANYLKFDVFDLELSSIYDNGELKRVLLSTTNRSILVI 300

Query:   311 EDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE 370
             EDIDC  +++DR   +   + +  I+  KVTLSG LNFIDGLWSS GDERIIVFTTNHKE
Sbjct:   301 EDIDCNAEVRDR---EAENQEDEQIK-GKVTLSGILNFIDGLWSSFGDERIIVFTTNHKE 356

Query:   371 KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXX--XXXXXXSTTQVTPAE 428
             +LDPALLRPGRMDVH++MSYCT  GF+ L +NYLG                 +T+VTPAE
Sbjct:   357 RLDPALLRPGRMDVHINMSYCTGLGFRTLVSNYLGLDGLNHPLCEEIEALVDSTEVTPAE 416

Query:   429 VAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRK 464
             +AE+LM++DD ++VL G+I F++ KRK  E +K +K
Sbjct:   417 LAEELMQDDDTDVVLRGVISFVE-KRKV-ERSKTKK 450

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:2175986 AT5G17760 [Arabidopsis thaliana (taxid:3702)]

 Score = 1057 (377.1 bits), Expect = 7.2e-107, P = 7.2e-107
 Identities = 211/468 (45%), Positives = 306/468 (65%)

Query:    12 LATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRK-FCNRFSSQLTIVIDEH 70
             L +  ++ +  AS+A  +M+ R++A +L+P  +QD+ Y  LR  F    SS LT+ ID+ 
Sbjct:     7 LPSPTSVFTAYASMAGYMMMIRSMAHELIPAPLQDFIYRTLRSLFFRSSSSTLTLTIDDD 66

Query:    71 DGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWV 130
             +    N+IY AA+ YL  K SP   R+++SK  K+ HVN+ +   E V DV+  ++L W 
Sbjct:    67 NMGMNNEIYRAAQTYLSTKISPDAVRLRISKGHKDKHVNLYLSDGEIVNDVYEDVQLVWR 126

Query:   131 LVCRQVESRSFN------------HSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKE 178
              V    + +                   +   +  YFEL+F KK+KD+++ SY+P +E +
Sbjct:   127 FVTDGGDKKGGGGGVGGRGGGGGRRGGMDDDGKSEYFELSFDKKHKDLILNSYVPYIESK 186

Query:   179 AKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERF 238
             AK ++ E + + + ++N  +L       W  V L+HP+TFET+AME + K  +++DL+RF
Sbjct:   187 AKEIRDERRILMLHSLN--SL------RWESVILEHPSTFETMAMEDDLKRDVIEDLDRF 238

Query:   239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTL 298
             ++RK++Y+RVGKAWKRGYLLYGPPGTGKSSL+AAMANYL FDVYDL+L  +  +SDLR L
Sbjct:   239 IRRKEFYKRVGKAWKRGYLLYGPPGTGKSSLVAAMANYLKFDVYDLQLASVMRDSDLRRL 298

Query:   299 LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD 358
             L+AT NRSILV+EDIDC +DL +R+   + G+  G   Q  +TLSG LNFIDGLWSSCGD
Sbjct:   299 LLATRNRSILVIEDIDCAVDLPNRIEQPVEGKNRGE-SQGPLTLSGLLNFIDGLWSSCGD 357

Query:   359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXXXXXXX 418
             ERII+FTTNHK++LDPALLRPGRMD+H++M +C+  GFK LA+NYLG             
Sbjct:   358 ERIIIFTTNHKDRLDPALLRPGRMDMHIYMGHCSFQGFKTLASNYLGLSDAAMPHRLFPE 417

Query:   419 XSTT----QVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKP 462
                      +TPA+VAE+LM+++D ++ L GL+  L+  R + +++ P
Sbjct:   418 IERLIDGEVMTPAQVAEELMKSEDADVALEGLVNVLEKMRLKSKESNP 465

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM;IDA

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

GO:0009627 "systemic acquired resistance" evidence=RCA

GO:0009697 "salicylic acid biosynthetic process" evidence=RCA

TAIR|locus:2053109 AT2G18190 [Arabidopsis thaliana (taxid:3702)]

 Score = 1047 (373.6 bits), Expect = 8.3e-106, P = 8.3e-106
 Identities = 221/470 (47%), Positives = 311/470 (66%)

Query:     7 SAENKLATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIV 66
             S  N   +  ++ +  AS+   +ML R++  D +P  ++ Y    L +F    S  LT+V
Sbjct:     4 SISNISLSPSSLFTAYASLTGFLMLFRSLFNDEVPERLRSYITDLLNRFFTPKSKNLTMV 63

Query:    67 IDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIK 126
             IDE  G  +NQ++DAA+VYL  K  P   R++V KL K+ H  I +E  E+++D F   +
Sbjct:    64 IDEIIGFKRNQVFDAAEVYLRNKIGPETARLRVGKLPKQKHFTIYIEKGEEILDTFENSE 123

Query:   127 LKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQES 186
             L+W  V    ES   N +S   Q + RY+ELTF KK +D V+ SYL  V  E++  +++ 
Sbjct:   124 LRWTYV----ESE--NEAS---QKEKRYYELTFEKKLRDKVMNSYLSHVVAESEETKRDL 174

Query:   187 KTIKILT--VNYNNLYCNWTDA-WIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKD 243
             + +K+ +  V  +        A W  +NL+HP+TFETLAM+   K KI+ D+ERF+KR++
Sbjct:   175 RAVKLYSRDVRASKDDDGMAGAGWGCINLEHPSTFETLAMDPGAKKKIIDDMERFLKRRE 234

Query:   244 YYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATA 303
             +Y+RVGKAWKRGYLLYGPPGTGKSSLIAAMANYL FDV+DLEL+ +  N+ L+++L++T 
Sbjct:   235 FYKRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLKFDVFDLELSSIYENAQLKSILLSTT 294

Query:   304 NRSILVVEDIDCT-IDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII 362
             NRSILV+EDIDC+  ++ DR   +     EG     +VTLSG LNF+DGLWSS GDERII
Sbjct:   295 NRSILVIEDIDCSSAEVVDREADEYQEYEEG--YYGRVTLSGLLNFVDGLWSSFGDERII 352

Query:   363 VFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXX--XXXXXXS 420
             VFTTNHKE+LDPALLRPGRMD+H++MSYCT  GF+ L +NYLG                 
Sbjct:   353 VFTTNHKERLDPALLRPGRMDMHINMSYCTGLGFRTLVSNYLGLGGLNHPLCEEIEALID 412

Query:   421 TTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEEST 470
             +T+VTPAE+AE+LM+ DD ++VL G++ F  V+ ++ E +K +++ E ST
Sbjct:   413 STEVTPAELAEELMQEDDTDVVLRGVVSF--VENRKVEISKTKEL-EGST 459

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175956 AT5G17740 [Arabidopsis thaliana (taxid:3702)]

 Score = 1023 (365.2 bits), Expect = 2.9e-103, P = 2.9e-103
 Identities = 207/465 (44%), Positives = 303/465 (65%)

Query:    17 TILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGL-AK 75
             ++ ST AS+   VM+ + +   ++P  +Q++ +  L+ F    SS LT+ ID+   +   
Sbjct:    12 SMFSTYASMMGYVMIIKPMINTIIPRPVQNFVFSYLKSFAGSRSSTLTLTIDQMSSMYIP 71

Query:    76 NQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQ 135
             +++Y AA+ YL  K SP+  R+ +++   E  V + +   E V DV+NGIKLKW  + R 
Sbjct:    72 DELYAAAQAYLSTKISPNSVRLIMARDPAEKKVKLYLSDGEVVSDVYNGIKLKWRFLARN 131

Query:   136 VESRSFNHSSTNIQAQVRY--FELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILT 193
               +        + Q  ++    EL+F KK++D+V+ SY+P VE +AK V  + + +K+  
Sbjct:   132 KNNTMVEEYGQSYQGNIQRESLELSFDKKHRDLVVNSYIPYVESKAKEVNNKRRILKM-- 189

Query:   194 VNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWK 253
                 + Y +    W  VN  HP+TF+T+AM  + K  +++DL+RFV RKD+Y+RVGKAWK
Sbjct:   190 ----HCYSHMAQTWQSVNFKHPSTFDTMAMNDDLKRSMIEDLDRFVGRKDFYKRVGKAWK 245

Query:   254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDI 313
             RGYLLYGPPGTGKSSL+AAMANYL FD+YDL+L  ++ ++ LR+LL+AT N SIL++EDI
Sbjct:   246 RGYLLYGPPGTGKSSLVAAMANYLKFDIYDLQLASVQGDAHLRSLLLATNNSSILLIEDI 305

Query:   314 DCTIDLQDRL-PADIAGEGEGPIQQNK-VTLSGFLNFIDGLWSSCGDERIIVFTTNHKEK 371
             DC++DL  RL P     +  G +Q +K +TLSG LN IDGLWSSCG+ERII+FTTN+KEK
Sbjct:   306 DCSVDLPTRLQPPTETSQPLGAVQVSKPLTLSGLLNCIDGLWSSCGNERIIIFTTNNKEK 365

Query:   372 LDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXXX-----XXXXXSTTQVTP 426
             LDPALLRPGRMD+H++M +C+  GFK LA+NYLG                       +TP
Sbjct:   366 LDPALLRPGRMDMHIYMGHCSFQGFKTLASNYLGLSDENDDTHPLCPDIKHLIDGHVLTP 425

Query:   427 AEVAEQLMRNDDPELVLNGLIEFLKVKRKE----DEDAKPRKIHE 467
             A+VAE+LM+++D +  L GL++ LK KR E    D+++K +K+ E
Sbjct:   426 AQVAEELMKDEDADAALEGLVKVLKRKRLEPKKCDDESKMKKLKE 470

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175946 AT5G17730 [Arabidopsis thaliana (taxid:3702)]

 Score = 1007 (359.5 bits), Expect = 1.4e-101, P = 1.4e-101
 Identities = 203/454 (44%), Positives = 292/454 (64%)

Query:    12 LATAKTILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEH- 70
             L +    +S  AS+   VM+ +      +P  +Q+Y    L  F +   S LT++ID+H 
Sbjct:     7 LPSLAPFVSAYASLTGYVMMIKPFLEMTIPPPLQNYMISYLNSFLHSTPSTLTLIIDDHI 66

Query:    71 -DGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKW 129
              +G+  N++Y AA+VY+  K + + +R+++S+   E +VNI     E V D++ GI++KW
Sbjct:    67 KNGMY-NELYGAAQVYISTKVNHNAERLRISRDRSEKNVNIHFSVGEVVSDIYQGIEVKW 125

Query:   130 VLVCRQVESRSFNHSSTNIQAQV--RYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
                    +S   ++   + +        EL+F KK+ ++V+ SY+P VE +AK +  E K
Sbjct:   126 RFCVDSNKSNMVHYFGEHFKLNPDRECVELSFEKKHTELVLNSYIPYVESKAKVINNERK 185

Query:   188 TIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRR 247
              +K+    Y+  YC     W  VNL+HP+TF+T+AM +E K  +M DL+RF++RKD+Y+R
Sbjct:   186 ILKM----YS--YCCMYLKWQSVNLEHPSTFDTMAMNEELKRSVMGDLDRFIRRKDFYKR 239

Query:   248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSI 307
             VGK WKRGYLLYGPPGTGK+SL+AA+ANYL FD+YDL+L  +R ++DLR LL+ T N SI
Sbjct:   240 VGKPWKRGYLLYGPPGTGKTSLVAAIANYLKFDIYDLQLASVREDADLRRLLLGTTNSSI 299

Query:   308 LVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTN 367
             L+VEDIDC +DL  RL      + +G    + +TLSG L  IDGLWSSCGDERI++FTT 
Sbjct:   300 LLVEDIDCAVDLHTRLQPKTQDDTKG---SSMLTLSGLLTCIDGLWSSCGDERIVIFTTT 356

Query:   368 HKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXXXXXXXXSTTQ---V 424
             HKE+LDPALLRPGRMD+H+HM +C    FK LA+NYLG                 +   +
Sbjct:   357 HKERLDPALLRPGRMDMHIHMGHCCFDVFKTLASNYLGLSHDDPHHLYPEIERLIKGEVL 416

Query:   425 TPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDE 458
             TPA+VAE+LM+N+DP++ L GL++ LK KR E E
Sbjct:   417 TPAQVAEELMKNEDPDVALEGLVKVLKRKRLELE 450

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2175976 AT5G17750 [Arabidopsis thaliana (taxid:3702)]

 Score = 849 (303.9 bits), Expect = 1.5e-89, Sum P(2) = 1.5e-89
 Identities = 162/324 (50%), Positives = 227/324 (70%)

Query:    83 KVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKW-VLVCRQVESRSF 141
             + YL  K SP   ++++++     +VN+ +   E V DV+ GI+LKW  L  R  ++   
Sbjct:    55 QAYLSSKISPDASKLRMTRDPNNKNVNLHLSQGEVVSDVYKGIELKWRYLEGRNKKTTVV 114

Query:   142 NHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYC 201
                +       + FEL+F KK+KD+V+ SY+  VE++AK +++E + IK+      + Y 
Sbjct:   115 GEETEEAIVNWQCFELSFDKKHKDLVVKSYIAYVERKAKVIKEERRIIKM------HSYS 168

Query:   202 NWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGP 261
             ++T  W  V  +HP+TF T+AM  + K+ +M+DL+RF+KRKDYY+RVGKAWKR Y LYGP
Sbjct:   169 SYTLRWQSVKFEHPSTFHTMAMTPKLKSSVMEDLDRFIKRKDYYKRVGKAWKRSYFLYGP 228

Query:   262 PGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQD 321
             PGTGKSSL+AAMANYL FD+YDL+L  ++ ++ LR+LL+AT N SIL+VEDIDC++DL  
Sbjct:   229 PGTGKSSLVAAMANYLKFDIYDLQLANVQGDAQLRSLLLATNNSSILLVEDIDCSVDLPT 288

Query:   322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGR 381
             RL       G  P     +TLSG LN IDGLWSSCGDERI++FTTN+KE LDPALLRPG 
Sbjct:   289 RLQPATTTLG-APKGSTPLTLSGLLNCIDGLWSSCGDERIVIFTTNNKEVLDPALLRPGC 347

Query:   382 MDVHVHMSYCTPSGFKLLAANYLG 405
             MD+H+++ +C+  GFK+LA+NYLG
Sbjct:   348 MDMHIYLGHCSFEGFKILASNYLG 371

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2098648 AT3G28540 [Arabidopsis thaliana (taxid:3702)]

 Score = 598 (215.6 bits), Expect = 7.2e-88, Sum P(2) = 7.2e-88
 Identities = 123/297 (41%), Positives = 189/297 (63%)

Query:    27 ATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHD---GLAKNQIYDAAK 83
             A++M   +V R  +PY+I+DY      K     S+ + I   E+    GL K+Q YD  +
Sbjct:    16 ASLMFFWSVYRQFVPYQIRDYLEKCFYKMFGLVSNSVHIKFTEYTEDKGLKKSQAYDLIR 75

Query:    84 VYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQVESRSFNH 143
              YL  K++   QR+K ++ +    + +S+++ E V DVF G+K+ W L   +   ++   
Sbjct:    76 NYLSSKSTARAQRLKANESKNSKSLVLSLDNHEAVEDVFQGVKVVWSLSVWKSNDQA--D 133

Query:   144 SSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNW 203
             SS     + RY  L+F  +Y++++  +YL  V +E K +  +++  K+ T N +  Y  W
Sbjct:   134 SS-----EKRYLTLSFHNRYREMITTTYLDHVLREGKEIGLKNRERKLYTNNSSQDYSAW 188

Query:   204 TDA-WIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPP 262
              +  W  V  DHPATFETLAM+ E+K  + +DL +F K KDYYR+VGK WKRGYLL+GPP
Sbjct:   189 REGRWSNVPFDHPATFETLAMDLEKKEGMKKDLIKFTKGKDYYRKVGKPWKRGYLLFGPP 248

Query:   263 GTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDL 319
             GTGKS++I+AMAN+L +DVYDLELT ++ NS+L+ L++ T  +SI+V+EDIDC++DL
Sbjct:   249 GTGKSTMISAMANFLEYDVYDLELTTVKDNSELKKLMLDTKGKSIVVIEDIDCSLDL 305

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2098658 AT3G28510 [Arabidopsis thaliana (taxid:3702)]

 Score = 839 (300.4 bits), Expect = 9.2e-86, Sum P(2) = 9.2e-86
 Identities = 187/473 (39%), Positives = 282/473 (59%)

Query:    18 ILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEH--DGLAK 75
             I     +   + M    + +  +P   + Y      K     S  + I   E+  +GL +
Sbjct:     7 IWGITGTTVTSFMFFWAIYKQYVPAHFRAYVERYFHKMIGWISYYVDIKFTEYTDEGLKR 66

Query:    76 NQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQ 135
             +Q YD+ + YL  K++   +R+K ++ +    +  SM+  E++ D F G+K+KW    + 
Sbjct:    67 SQAYDSIRNYLASKSTALAKRLKANETKNSKSLVFSMDDHEEIEDEFEGVKVKWYSNVKV 126

Query:   136 VESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVN 195
             ++ +S N+   + + + R+F L+F ++++ ++I +YL  V +E K++   ++  K+ T N
Sbjct:   127 IQPQS-NYGQRSSEER-RHFTLSFHRRHRGMIIETYLDHVLREGKAIGLMNRERKLYTNN 184

Query:   196 YNNLYCNWTDA-WIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKR 254
              +  +  W    W  V   HPATFETLAM+ E+K  I +DL +F K KDYY++VGK WKR
Sbjct:   185 SSQEWYPWRSGKWSNVPFHHPATFETLAMDPEKKEGIKKDLIKFSKGKDYYKKVGKPWKR 244

Query:   255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDID 314
             GYLL+GPPGTGKS++IAA+AN+L++DVYDLELT ++ NS+L+ LL+ T ++SI+V+EDID
Sbjct:   245 GYLLFGPPGTGKSTMIAAIANFLDYDVYDLELTTVKDNSELKKLLLDTTSKSIIVIEDID 304

Query:   315 CTIDL----QDRLPADIAGEGE----G---PI---QQNKVTLSGFLNFIDGLWSSCGDER 360
             C++DL    + +   D   +GE    G   P    +Q+KVTLSG LN IDGLWS+C  E+
Sbjct:   305 CSLDLTGQRKKKKEEDEEEDGEEKKEGEKKPKVDDKQSKVTLSGLLNSIDGLWSACSGEK 364

Query:   361 IIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGXXXXXXXXXXXXXXS 420
             IIVFTTN  +KLDPAL+R GRMD H+ MSYC    FK+LA NYL                
Sbjct:   365 IIVFTTNFVDKLDPALIRRGRMDNHIEMSYCKFEAFKVLAKNYLEIETHDLYGEIERKLE 424

Query:   421 TTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEESTESQ 473
              T ++PA+VAE LM   D E   +  I+ L VK  E+E  K RK+ EE  + +
Sbjct:   425 ETDMSPADVAETLMPKSDEEDA-DICIKRL-VKTLEEEKEKARKLAEEEEKKK 475

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0001666 "response to hypoxia" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0005783 "endoplasmic reticulum" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

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

Fail to connect to STRING server

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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	473
pfam14363	100	pfam14363, AAA_assoc, Domain associated at C-termi	3e-34
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	1e-20
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	2e-13
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	1e-12
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	2e-12
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	1e-11
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	8e-11
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	4e-10
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	6e-10
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	1e-09
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	5e-09
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	2e-08
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	2e-08
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	5e-08
smart00382	148	smart00382, AAA, ATPases associated with a variety	1e-07
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	4e-06
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	4e-06
PRK08939	306	PRK08939, PRK08939, primosomal protein DnaI; Revie	8e-06
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	6e-05
pfam05673	248	pfam05673, DUF815, Protein of unknown function (DU	3e-04
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	6e-04
PRK08116	268	PRK08116, PRK08116, hypothetical protein; Validate	0.001
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	0.002
PRK06851	367	PRK06851, PRK06851, hypothetical protein; Provisio	0.002
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	0.002
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	0.003
pfam13207	114	pfam13207, AAA_17, AAA domain	0.003

>gnl|CDD|222710 pfam14363, AAA_assoc, Domain associated at C-terminal with AAA

 Score =  123 bits (312), Expect = 3e-34
 Identities = 47/100 (47%), Positives = 70/100 (70%), Gaps = 3/100 (3%)

Query: 39  LLPYEIQDYFYFRLRK-FCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRI 97
           LLP+E+++Y    LR+ F +RFS  LTIVIDE+DG ++NQ+YDAA+ YL  K SPS +R+
Sbjct: 1   LLPHELREYLSSLLRRLFGSRFSPYLTIVIDEYDGFSRNQLYDAAEAYLSTKISPSARRL 60

Query: 98  KVSKLEKENH--VNISMESDEQVVDVFNGIKLKWVLVCRQ 135
           K SK +K  +  + +S++  E+V DVF G+K+ W  V  +
Sbjct: 61  KASKAKKSKNSSLVLSLDDGEEVTDVFEGVKVWWTSVVTE 100

This domain is found in association with the AAA family, pfam00004. Length = 100

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

 Score = 86.9 bits (216), Expect = 1e-20
 Identities = 44/144 (30%), Positives = 68/144 (47%), Gaps = 22/144 (15%)

Query: 256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN------SDLRTLL--VATANRSI 307
            LLYGPPGTGK++L  A+A  L     ++  +EL S         LR L          +
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60

Query: 308 LVVEDIDCTIDLQDRLPADIAG-EGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT 366
           + +++ID            +AG  G G   +++  ++  L  +DG  +S   + I++  T
Sbjct: 61  IFIDEIDA-----------LAGSRGSGGDSESRRVVNQLLTELDGF-TSSLSKVIVIAAT 108

Query: 367 NHKEKLDPALLRPGRMDVHVHMSY 390
           N  +KLDPALLR GR D  +    
Sbjct: 109 NRPDKLDPALLR-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|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score = 72.2 bits (177), Expect = 2e-13
 Identities = 48/180 (26%), Positives = 81/180 (45%), Gaps = 22/180 (12%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           T + +   +E K ++ + +E  +KR + +R++G    +G LLYGPPGTGK+ L  A+A  
Sbjct: 240 TLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALE 299

Query: 277 LN--------FDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIA 328
                      ++    + E   N             SI+ +++ID          +  +
Sbjct: 300 SRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEID----------SLAS 349

Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVH 387
           G G       +  +   L  +DG+      E ++V   TN  + LDPALLRPGR D  ++
Sbjct: 350 GRGPSEDGSGRRVVGQLLTELDGI---EKAEGVLVIAATNRPDDLDPALLRPGRFDRLIY 406

Length = 494

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

 Score = 69.9 bits (171), Expect = 1e-12
 Identities = 58/176 (32%), Positives = 86/176 (48%), Gaps = 22/176 (12%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           T+E +   +E K KI + +E  +K  + +  +G    +G LLYGPPGTGK+ L  A+AN 
Sbjct: 176 TYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE 235

Query: 277 LNFDVYDLELTEL------RSNSDLRTLLV-ATANR-SILVVEDIDCTIDLQDRLPADIA 328
                  +   E+       S   LR +   A  N  SI+ +++ID     ++    ++ 
Sbjct: 236 AGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKRE----EVT 291

Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMD 383
           GE E      K  ++  L  +DGL    G  R+IV   TN  + LDPAL RPGR D
Sbjct: 292 GEVE------KRVVAQLLTLMDGLK---GRGRVIVIGATNRPDALDPALRRPGRFD 338

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

 Score = 68.3 bits (167), Expect = 2e-12
 Identities = 60/167 (35%), Positives = 88/167 (52%), Gaps = 17/167 (10%)

Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDV 281
           ++Q  +I + +E  +   + Y  +G    +G +LYGPPGTGK+ L  A+AN  +     V
Sbjct: 189 EQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRV 248

Query: 282 YDLELTELRSNSD---LRTLL-VATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
              EL +         +R L  VA  N  SI+ +++ID       R  A   GE E  IQ
Sbjct: 249 VGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAI--GTKRYDATSGGEKE--IQ 304

Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           +   T+   LN +DG + S GD ++I+  TN  E LDPAL+RPGR+D
Sbjct: 305 R---TMLELLNQLDG-FDSRGDVKVIM-ATNRIESLDPALIRPGRID 346

Length = 438

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

 Score = 66.2 bits (162), Expect = 1e-11
 Identities = 53/175 (30%), Positives = 84/175 (48%), Gaps = 18/175 (10%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF  +A  +E K +  +++  F+K+ + +  VG    +G LL GPPGTGK+ L  A+A  
Sbjct: 181 TFRDIAGIEEAKEE-FEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE 239

Query: 277 LNFDVYDLELTELR------SNSDLRTLLVATANRS--ILVVEDIDCTIDLQDRLPADIA 328
                + +  +E          + +R L       S  I+ +++ID    +  +  A I 
Sbjct: 240 AEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDA---VGRQRGAGIG 296

Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           G G    +Q   TL+  L  +DG   + G   I++  TN  + LD ALLRPGR D
Sbjct: 297 G-GNDEREQ---TLNQLLTEMDGFKGNKG--VIVIAATNRVDILDAALLRPGRFD 345

Length = 638

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

 Score = 62.9 bits (153), Expect = 8e-11
 Identities = 56/176 (31%), Positives = 89/176 (50%), Gaps = 19/176 (10%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           ++E +   +EQ  +I + +E  +K  + +  VG    +G LLYGPPGTGK+ L  A+A+ 
Sbjct: 120 SYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE 179

Query: 277 LNFDVYDLELTEL---------RSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADI 327
            N     +  +EL         R   ++  L    A  SI+ +++ID       R  +  
Sbjct: 180 TNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAP-SIIFIDEIDAIA--AKRTDSGT 236

Query: 328 AGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           +G+ E  +Q+   TL   L  +DG +   G+ ++I   TN  + LDPALLRPGR D
Sbjct: 237 SGDRE--VQR---TLMQLLAELDG-FDPRGNVKVIA-ATNRPDILDPALLRPGRFD 285

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

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

 Score = 61.1 bits (149), Expect = 4e-10
 Identities = 56/177 (31%), Positives = 88/177 (49%), Gaps = 31/177 (17%)

Query: 226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE 285
           EQ  +I + +E  +K  + +  +G    +G LLYGPPGTGK+ L  A+AN  +       
Sbjct: 158 EQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTD------- 210

Query: 286 LTELR-SNSDL------------RTLLVATANR--SILVVEDIDCTIDLQDRLPADIAGE 330
            T +R   S+L            R L      +  SI+ +++ID  I  + R  +  +G+
Sbjct: 211 ATFIRVVGSELVQKYIGEGARLVRELFELAREKAPSIIFIDEID-AIGAK-RFDSGTSGD 268

Query: 331 GEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVH 387
            E  +Q+   T+   LN +DG +   G+ ++I   TN  + LDPALLRPGR D  + 
Sbjct: 269 RE--VQR---TMLELLNQLDG-FDPRGNVKVI-MATNRPDILDPALLRPGRFDRKIE 318

Length = 406

>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 = 57.2 bits (138), Expect = 6e-10
 Identities = 31/154 (20%), Positives = 51/154 (33%), Gaps = 37/154 (24%)

Query: 253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS-----------NSDLRTL 298
            +  LLYGPPGTGK++L  A+AN L         L  ++L                L   
Sbjct: 19  PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFE 78

Query: 299 LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL--WSSC 356
           L   A   +L +++I       D L                   +  L  ++ L      
Sbjct: 79  LAEKAKPGVLFIDEI-------DSLSRG--------------AQNALLRVLETLNDLRID 117

Query: 357 GDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSY 390
            +   ++  TN     D       R+D+ + +  
Sbjct: 118 RENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 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|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH

 Score = 59.6 bits (145), Expect = 1e-09
 Identities = 57/190 (30%), Positives = 87/190 (45%), Gaps = 36/190 (18%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSL---IAAM 273
           TF+ +A   E K ++M+ ++ F+K    + ++G    +G LL GPPGTGK+ L   +A  
Sbjct: 53  TFKDVAGIDEAKEELMEIVD-FLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE 111

Query: 274 ANYLNFDVYDLELTELRSNSDLRTLLVAT-ANR-------------SILVVEDIDCTIDL 319
           A    F +         S SD   + V   A+R              I+ +++ID     
Sbjct: 112 AGVPFFSI---------SGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAV--- 159

Query: 320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRP 379
             R      G G    +Q   TL+  L  +DG  ++ G   I++  TN  + LDPALLRP
Sbjct: 160 -GRQRGAGLGGGNDEREQ---TLNQLLVEMDGFGTNTG--VIVIAATNRPDVLDPALLRP 213

Query: 380 GRMDVHVHMS 389
           GR D  V + 
Sbjct: 214 GRFDRQVVVD 223

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|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed

 Score = 58.1 bits (140), Expect = 5e-09
 Identities = 55/185 (29%), Positives = 85/185 (45%), Gaps = 32/185 (17%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF  +A   E K ++  +L  +++    ++++G    +G L+ GPPGTGK+ L  A+A  
Sbjct: 150 TFADVAGCDEAKEEV-AELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 208

Query: 277 LNFDVYDLELTELRSNSDLRTLLVAT--------------ANRSILVVEDIDCTIDLQDR 322
                + +      S SD   + V                A   I+ +++ID     +  
Sbjct: 209 AKVPFFTI------SGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG- 261

Query: 323 LPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT-TNHKEKLDPALLRPGR 381
                AG G G  ++ + TL+  L  +DG     G+E IIV   TN  + LDPALLRPGR
Sbjct: 262 -----AGLGGGHDEREQ-TLNQMLVEMDGFE---GNEGIIVIAATNRPDVLDPALLRPGR 312

Query: 382 MDVHV 386
            D  V
Sbjct: 313 FDRQV 317

Length = 644

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

 Score = 55.9 bits (135), Expect = 2e-08
 Identities = 53/167 (31%), Positives = 82/167 (49%), Gaps = 21/167 (12%)

Query: 227 QKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL 286
           QK +I + +E  +   + Y ++G    RG LLYGPPGTGK+ L  A+A++       +  
Sbjct: 153 QKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVG 212

Query: 287 TEL---------RSNSDLRTLLVATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
           +E          R   D+  L  A  N  SI+ ++++D       R  A    + E  +Q
Sbjct: 213 SEFVQKYLGEGPRMVRDVFRL--ARENAPSIIFIDEVDSIA--TKRFDAQTGADRE--VQ 266

Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           +  + L   LN +DG   +   + I+   TN  + LDPALLRPGR+D
Sbjct: 267 RILLEL---LNQMDGFDQTTNVKVIM--ATNRADTLDPALLRPGRLD 308

Length = 398

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

 Score = 56.2 bits (136), Expect = 2e-08
 Identities = 61/182 (33%), Positives = 86/182 (47%), Gaps = 26/182 (14%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF  +A   E K ++ + ++ F+K    Y+ +G    +G LL GPPGTGK+ L  A+A  
Sbjct: 148 TFADVAGVDEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGE 206

Query: 277 LN---FDVYDLELTEL---RSNSDLRTLLVATANR---SILVVEDIDCTIDLQDRLPADI 327
                F +   +  E+      S +R L    A +    I+    ID  ID   R     
Sbjct: 207 AGVPFFSISGSDFVEMFVGVGASRVRDL-FEQAKKNAPCIIF---IDE-IDAVGR--QRG 259

Query: 328 AGEGEGP--IQQNKVTLSGFLNFIDGLWSSCGDERIIVFT-TNHKEKLDPALLRPGRMDV 384
           AG G G    +Q   TL+  L  +DG     G+E +IV   TN  + LDPALLRPGR D 
Sbjct: 260 AGLGGGNDEREQ---TLNQLLVEMDG---FGGNEGVIVIAATNRPDVLDPALLRPGRFDR 313

Query: 385 HV 386
            +
Sbjct: 314 QI 315

Length = 596

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

 Score = 54.9 bits (132), Expect = 5e-08
 Identities = 46/170 (27%), Positives = 77/170 (45%), Gaps = 25/170 (14%)

Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL 284
           +E K ++ + +E  +K  + + ++G    +G LL+GPPGTGK+ L  A+A     +   +
Sbjct: 459 EEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAV 518

Query: 285 ELTEL------RSNSDLRTLL--VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
              E+       S   +R +      A  +I+  ++ID         PA  A        
Sbjct: 519 RGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIA------PARGARFDT---- 568

Query: 337 QNKVT---LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
              VT   ++  L  +DG+        +++  TN  + LDPALLRPGR D
Sbjct: 569 --SVTDRIVNQLLTEMDGIQELSN--VVVIAATNRPDILDPALLRPGRFD 614

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

 Score = 50.8 bits (121), Expect = 1e-07
 Identities = 35/146 (23%), Positives = 55/146 (37%), Gaps = 13/146 (8%)

Query: 253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY-----DLELTELRSNSDLRTLLVATANRSI 307
               L+ GPPG+GK++L  A+A  L          D E         L  ++V     S 
Sbjct: 2   GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61

Query: 308 LVVEDIDCTIDLQDRLPADI-----AGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII 362
                +   + L  +L  D+             Q+  + L   L  +  L S       +
Sbjct: 62  SGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKN--LTV 119

Query: 363 VFTTNHKEKLDPALLRPGRMDVHVHM 388
           + TTN ++ L PALLR  R D  + +
Sbjct: 120 ILTTNDEKDLGPALLRR-RFDRRIVL 144

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|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score = 48.7 bits (117), Expect = 4e-06
 Identities = 54/159 (33%), Positives = 79/159 (49%), Gaps = 31/159 (19%)

Query: 240 KRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-SNSDL--- 295
           K+ + +  VG    +G LLYGPPGTGK+ L  A+A+  N        T +R   S+L   
Sbjct: 152 KKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETN-------ATFIRVVGSELVQK 204

Query: 296 ---------RTL--LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSG 344
                    R L  L      SI+ +++ID  I  + R  +  +G+ E  +Q+   TL  
Sbjct: 205 FIGEGARLVRELFELAREKAPSIIFIDEID-AIAAK-RTDSGTSGDRE--VQR---TLMQ 257

Query: 345 FLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
            L  +DG +   G+ +II   TN  + LDPA+LRPGR D
Sbjct: 258 LLAEMDG-FDPRGNVKIIA-ATNRIDILDPAILRPGRFD 294

Length = 389

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

 Score = 48.8 bits (117), Expect = 4e-06
 Identities = 29/84 (34%), Positives = 44/84 (52%), Gaps = 17/84 (20%)

Query: 215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMA 274
           P T   +   ++ K ++ + +E ++K K          K+  LLYGPPG GK+SL  A+A
Sbjct: 10  PKTLSDVVGNEKAKEQLREWIESWLKGKP---------KKALLLYGPPGVGKTSLAHALA 60

Query: 275 NYLNFDVYDLELTELRSN-SDLRT 297
           N   ++V  +EL     N SD RT
Sbjct: 61  NDYGWEV--IEL-----NASDQRT 77

Length = 482

>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed

 Score = 47.2 bits (113), Expect = 8e-06
 Identities = 33/117 (28%), Positives = 51/117 (43%), Gaps = 24/117 (20%)

Query: 162 KYKDVVIGSYLPCVEK-EAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFET 220
            Y DV   SYLP  EK EA   +   K I+ +              ++P +L   A+   
Sbjct: 87  GYIDV---SYLPTPEKIEADEEKAIKKRIQSI--------------YMPKDLLQ-ASLAD 128

Query: 221 LAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL 277
           + ++   +   +     F++   Y    G+   +G  LYG  G GKS L+AA+AN L
Sbjct: 129 IDLDDRDRLDALMAALDFLE--AY--PPGE-KVKGLYLYGDFGVGKSYLLAAIANEL 180

Length = 306

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

 Score = 45.2 bits (107), Expect = 6e-05
 Identities = 51/226 (22%), Positives = 91/226 (40%), Gaps = 32/226 (14%)

Query: 254 RGYLLYGPPGTGKSSLIAAMAN----YLNFDVYDLELTELRSNSDLRTLLVAT----ANR 305
           +G LL+GPPGTGK+ L  A+AN    +L+ +  ++ L++    S+LR   +         
Sbjct: 19  KGVLLHGPPGTGKTLLARALANEGAEFLSINGPEI-LSKYVGESELRLRELFEEAEKLAP 77

Query: 306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT 365
           SI+ +++ID     +               +  +  ++  L  +DGL      + I++  
Sbjct: 78  SIIFIDEIDALAPKR----------SSDQGEVERRVVAQLLALMDGL---KRGQVIVIGA 124

Query: 366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVT 425
           TN  + LDPA  RPGR D  + ++    +G        L I   ++F        T    
Sbjct: 125 TNRPDGLDPAKRRPGRFDREIEVNLPDEAGRL----EILQIHTRLMFLGPPGTGKTL--- 177

Query: 426 PAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEESTE 471
            A         D   L     +   +++R  D   +   + E+  E
Sbjct: 178 -AARTVGKSGADLGALAKEAALR--ELRRAIDLVGEYIGVTEDDFE 220

Length = 494

>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815)

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 19/79 (24%)

Query: 202 NWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGY----- 256
             + A  PV    P   + L     QK  ++++ E+F+               G      
Sbjct: 11  GESGALEPVPHPDPVDLDDLVGIDRQKEALLRNTEQFL--------------AGLPANNV 56

Query: 257 LLYGPPGTGKSSLIAAMAN 275
           LL+G  GTGKSSL+ A+ N
Sbjct: 57  LLWGARGTGKSSLVKALLN 75

This family consists of several bacterial proteins of unknown function. Length = 248

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

 Score = 41.6 bits (99), Expect = 6e-04
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 257 LLYGPPGTGKSSLIAAMANYLNFDVY 282
           +L+GPPGTGK++L   +A   +    
Sbjct: 40  ILWGPPGTGKTTLARIIAGATDAPFE 65

Length = 413

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

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 11/64 (17%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKR---GYLLYGPPGTGKSSLIAAM 273
           TFE    ++  + K  +   ++VK+        +  K+   G LL+G  GTGK+ L A +
Sbjct: 83  TFENFLFDKGSE-KAYKIARKYVKK-------FEEMKKENVGLLLWGSVGTGKTYLAACI 134

Query: 274 ANYL 277
           AN L
Sbjct: 135 ANEL 138

Length = 268

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

 Score = 38.3 bits (89), Expect = 0.002
 Identities = 28/105 (26%), Positives = 37/105 (35%), Gaps = 17/105 (16%)

Query: 242 KDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD---VYDLELTELRSNSD-LRT 297
            D  RR         LL GP GTGK+SL+  +   L          E     + S  LR 
Sbjct: 13  LDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRE 72

Query: 298 LL-------------VATANRSILVVEDIDCTIDLQDRLPADIAG 329
           LL             +  A  + L  E I+   DL + L   +A 
Sbjct: 73  LLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLAR 117

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

>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional

 Score = 39.9 bits (94), Expect = 0.002
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 2/51 (3%)

Query: 244 YYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSD 294
            Y  +     R ++L G PGTGKS+L+  +        YD+E   L  +SD
Sbjct: 21  LYDSIIDGANRIFILKGGPGTGKSTLMKKIGEEFLEKGYDVEF--LHCSSD 69

Length = 367

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

 Score = 40.1 bits (94), Expect = 0.002
 Identities = 20/37 (54%), Positives = 24/37 (64%), Gaps = 2/37 (5%)

Query: 242 KDYYRRVGKAWKRGYLLYGPPGTGKSSLIA-AMANYL 277
            + YR  G    +G LLYGPPG GK +LIA A+AN L
Sbjct: 205 PELYREYGLKPPKGVLLYGPPGCGK-TLIAKAVANSL 240

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|200312 TIGR03689, pup_AAA, proteasome ATPase

 Score = 39.7 bits (93), Expect = 0.003
 Identities = 18/42 (42%), Positives = 28/42 (66%), Gaps = 2/42 (4%)

Query: 345 FLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHV 386
            L  IDG+ S   D  I++  +N ++ +DPA+LRPGR+DV +
Sbjct: 321 LLAEIDGVESL--DNVIVIGASNREDMIDPAILRPGRLDVKI 360

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|221983 pfam13207, AAA_17, AAA domain

 Score = 37.3 bits (86), Expect = 0.003
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE 285
            L+ GPPG+GKS+L   +A  L   V  L+
Sbjct: 2   ILITGPPGSGKSTLAKKLAEKLGIPVISLD 31

Length = 114

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	473
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	100.0
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.98
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.97
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.97
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.97
CHL00176	638	ftsH cell division protein; Validated	99.97
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.97
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.97
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.97
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.97
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.97
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.97
CHL00195	489	ycf46 Ycf46; Provisional	99.97
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.96
CHL00206	2281	ycf2 Ycf2; Provisional	99.96
PF14363	98	AAA_assoc: Domain associated at C-terminal with AA	99.96
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.96
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.95
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.95
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.95
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.95
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.95
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.93
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.93
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.92
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.92
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.9
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.88
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.83
PF00004	132	AAA: ATPase family associated with various cellula	99.82
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.77
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.76
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.75
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.75
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.74
CHL00181	287	cbbX CbbX; Provisional	99.74
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.73
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.71
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.69
PRK04195	482	replication factor C large subunit; Provisional	99.68
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.68
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.68
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.67
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.66
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.65
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.65
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.65
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.63
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.63
PHA02544	316	44 clamp loader, small subunit; Provisional	99.62
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.62
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.62
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.62
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.62
PLN03025	319	replication factor C subunit; Provisional	99.62
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.61
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.61
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.61
PRK13342	413	recombination factor protein RarA; Reviewed	99.61
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.6
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.6
PRK06893	229	DNA replication initiation factor; Validated	99.6
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.6
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.59
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.58
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.58
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.57
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.57
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.57
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.56
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.56
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.56
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.56
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.56
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.54
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.54
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.53
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.53
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.53
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.53
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.52
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.52
PRK08727	233	hypothetical protein; Validated	99.52
PRK08084	235	DNA replication initiation factor; Provisional	99.52
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.52
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.52
PRK12402	337	replication factor C small subunit 2; Reviewed	99.5
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.5
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.5
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.49
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.49
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.49
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.49
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.49
PRK13341	725	recombination factor protein RarA/unknown domain f	99.48
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.48
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.47
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.47
PRK05642	234	DNA replication initiation factor; Validated	99.46
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.46
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.45
PRK10865	857	protein disaggregation chaperone; Provisional	99.45
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.45
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.45
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.45
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.44
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.44
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.43
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.43
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.43
PRK12422	445	chromosomal replication initiation protein; Provis	99.43
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.43
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.42
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.41
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.41
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.37
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.37
PRK06620	214	hypothetical protein; Validated	99.36
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.36
CHL00095	821	clpC Clp protease ATP binding subunit	99.35
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.35
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.35
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.35
PHA02244	383	ATPase-like protein	99.34
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.34
KOG2028	554	consensus ATPase related to the helicase subunit o	99.32
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.32
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.3
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.3
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.29
PRK07952	244	DNA replication protein DnaC; Validated	99.27
COG0714	329	MoxR-like ATPases [General function prediction onl	99.27
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.27
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.27
PRK10865	857	protein disaggregation chaperone; Provisional	99.26
PRK09087	226	hypothetical protein; Validated	99.26
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.25
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.25
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.24
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.23
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.23
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.22
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.21
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.21
PRK08116	268	hypothetical protein; Validated	99.21
PRK08181	269	transposase; Validated	99.19
PRK08939	306	primosomal protein DnaI; Reviewed	99.18
CHL00095	821	clpC Clp protease ATP binding subunit	99.18
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.16
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.14
PRK12377	248	putative replication protein; Provisional	99.13
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.12
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.12
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.1
PRK06526	254	transposase; Provisional	99.1
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.1
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.1
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.07
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.06
smart00382	148	AAA ATPases associated with a variety of cellular	99.06
PRK13531	498	regulatory ATPase RavA; Provisional	99.06
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.06
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.06
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.05
PRK04132	846	replication factor C small subunit; Provisional	99.04
smart00350	509	MCM minichromosome maintenance proteins.	99.04
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.04
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.04
PF07726	131	AAA_3: ATPase family associated with various cellu	99.03
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.02
PRK06835	329	DNA replication protein DnaC; Validated	98.98
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.96
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.94
PRK11608	326	pspF phage shock protein operon transcriptional ac	98.93
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	98.92
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.91
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.9
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	98.9
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	98.9
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	98.89
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	98.88
PRK09183	259	transposase/IS protein; Provisional	98.88
PRK06921	266	hypothetical protein; Provisional	98.87
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.86
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.85
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.85
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.84
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.82
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.75
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.74
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.74
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	98.73
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.73
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	98.72
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.71
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.71
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.68
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	98.68
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.67
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.66
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.65
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.65
PRK09862	506	putative ATP-dependent protease; Provisional	98.63
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.62
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.62
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.61
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.61
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	98.59
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.59
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.59
PF13173	128	AAA_14: AAA domain	98.58
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.54
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.54
PHA02624	647	large T antigen; Provisional	98.47
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.46
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.45
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.45
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.43
KOG1514	767	consensus Origin recognition complex, subunit 1, a	98.41
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.4
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.4
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.36
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.36
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.36
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.35
PF05729	166	NACHT: NACHT domain	98.33
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.32
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.31
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.3
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	98.28
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.26
PHA02774	613	E1; Provisional	98.22
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	98.2
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.2
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.18
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.17
PRK13765	637	ATP-dependent protease Lon; Provisional	98.16
PHA00729	226	NTP-binding motif containing protein	98.14
PRK15115	444	response regulator GlrR; Provisional	98.13
COG2204	464	AtoC Response regulator containing CheY-like recei	98.06
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.03
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	98.02
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	98.0
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.98
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.95
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.93
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.93
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.92
PRK15455	644	PrkA family serine protein kinase; Provisional	97.91
PRK06581	263	DNA polymerase III subunit delta'; Validated	97.89
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.88
PRK10365	441	transcriptional regulatory protein ZraR; Provision	97.87
COG1485	367	Predicted ATPase [General function prediction only	97.87
PRK00131	175	aroK shikimate kinase; Reviewed	97.85
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.83
PRK07261	171	topology modulation protein; Provisional	97.8
PRK08118	167	topology modulation protein; Reviewed	97.8
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	97.8
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.79
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	97.79
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.74
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.74
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.71
PF14516	331	AAA_35: AAA-like domain	97.7
) 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	97.7
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.7
PRK14737	186	gmk guanylate kinase; Provisional	97.7
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	97.69
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	97.68
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	97.68
COG1241	682	MCM2 Predicted ATPase involved in replication cont	97.66
PRK13947	171	shikimate kinase; Provisional	97.64
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.62
PRK06067	234	flagellar accessory protein FlaH; Validated	97.61
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.6
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.59
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.59
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.58
PRK03839	180	putative kinase; Provisional	97.58
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.58
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.58
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	97.57
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.57
PRK00625	173	shikimate kinase; Provisional	97.57
PRK13949	169	shikimate kinase; Provisional	97.56
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.54
PF08740	187	BCS1_N: BCS1 N terminal; InterPro: IPR014851 AAA A	97.53
PRK13948	182	shikimate kinase; Provisional	97.52
PRK05973	237	replicative DNA helicase; Provisional	97.52
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	97.49
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	97.49
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.48
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.47
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.47
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.45
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.43
PRK06217	183	hypothetical protein; Validated	97.43
PRK04040	188	adenylate kinase; Provisional	97.43
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.42
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.41
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.41
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.4
PRK13946	184	shikimate kinase; Provisional	97.4
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.38
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.38
PRK14532	188	adenylate kinase; Provisional	97.37
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.37
PRK05057	172	aroK shikimate kinase I; Reviewed	97.36
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.36
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.35
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.35
PRK14531	183	adenylate kinase; Provisional	97.35
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.35
PRK11823	446	DNA repair protein RadA; Provisional	97.35
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.34
smart00072	184	GuKc Guanylate kinase homologues. Active enzymes c	97.33
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.33
PRK04841	903	transcriptional regulator MalT; Provisional	97.31
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.3
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	97.3
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.3
PTZ00202	550	tuzin; Provisional	97.29
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.29
PRK03731	171	aroL shikimate kinase II; Reviewed	97.28
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.25
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	97.24
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.24
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.24
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.24
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.23
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	97.22
PRK06547	172	hypothetical protein; Provisional	97.22
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.21
PLN02674	244	adenylate kinase	97.21
PRK06762	166	hypothetical protein; Provisional	97.21
PRK14530	215	adenylate kinase; Provisional	97.2
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	97.19
KOG2383	467	consensus Predicted ATPase [General function predi	97.19
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	97.19
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.18
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	97.17
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	97.17
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.17
PRK08233	182	hypothetical protein; Provisional	97.17
PRK09376	416	rho transcription termination factor Rho; Provisio	97.16
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.16
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.15
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.15
COG1855	604	ATPase (PilT family) [General function prediction	97.14
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.14
PRK04296	190	thymidine kinase; Provisional	97.14
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.14
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	97.13
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.12
PRK14528	186	adenylate kinase; Provisional	97.11
PF13479	213	AAA_24: AAA domain	97.1
PRK02496	184	adk adenylate kinase; Provisional	97.1
PF13245	76	AAA_19: Part of AAA domain	97.09
PRK13808	333	adenylate kinase; Provisional	97.09
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	97.08
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	97.08
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.08
COG4133	209	CcmA ABC-type transport system involved in cytochr	97.07
PF00519	432	PPV_E1_C: Papillomavirus helicase; InterPro: IPR00	97.07
PLN02199	303	shikimate kinase	97.06
PRK00300	205	gmk guanylate kinase; Provisional	97.04
PTZ00088	229	adenylate kinase 1; Provisional	97.04
PLN02200	234	adenylate kinase family protein	97.02
PRK00409	782	recombination and DNA strand exchange inhibitor pr	97.02
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	97.0
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	97.0
PRK00279	215	adk adenylate kinase; Reviewed	96.98
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.97
PRK06696	223	uridine kinase; Validated	96.97
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.97
PRK13695	174	putative NTPase; Provisional	96.94
PRK04182	180	cytidylate kinase; Provisional	96.93
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.93
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.93
PRK14527	191	adenylate kinase; Provisional	96.93
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.93
PRK09354	349	recA recombinase A; Provisional	96.92
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.92
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.9
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.89
cd03246	173	ABCC_Protease_Secretion This family represents the	96.89
PRK01184	184	hypothetical protein; Provisional	96.89
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	96.89
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.87
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.87
PLN02459	261	probable adenylate kinase	96.86
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.86
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.85
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	96.84
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	96.84
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	96.83
PRK10416	318	signal recognition particle-docking protein FtsY;	96.82
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.82
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	96.82
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	96.81
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	96.8
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	96.8
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	96.79
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	96.79
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.78
PRK04328	249	hypothetical protein; Provisional	96.78
cd01128	249	rho_factor Transcription termination factor rho is	96.77
PHA02530	300	pseT polynucleotide kinase; Provisional	96.76
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.76
TIGR00767	415	rho transcription termination factor Rho. Members	96.76
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	96.75
PRK14526	211	adenylate kinase; Provisional	96.74
COG4650	531	RtcR Sigma54-dependent transcription regulator con	96.74
PHA00350	399	putative assembly protein	96.73
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	96.73
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.72
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	96.71
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	96.71
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	96.71
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.71
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	96.69
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.68
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.67
COG4178	604	ABC-type uncharacterized transport system, permeas	96.67
PRK10646	153	ADP-binding protein; Provisional	96.65
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.65
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.64
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.63
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.63
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	96.63
COG3378	517	Phage associated DNA primase [General function pre	96.62
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.62
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	96.61
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	96.6
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	96.6
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.6
PRK13546	264	teichoic acids export protein ATP-binding subunit;	96.58
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.58
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.58
PRK14529	223	adenylate kinase; Provisional	96.57
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	96.56
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.56
PRK00889	175	adenylylsulfate kinase; Provisional	96.55
PRK12608	380	transcription termination factor Rho; Provisional	96.55
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	96.55
PRK14021	542	bifunctional shikimate kinase/3-dehydroquinate syn	96.54
smart00487	201	DEXDc DEAD-like helicases superfamily.	96.53
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.52
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.51
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.49
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.48
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.48
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	96.48
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.48
PRK13889	988	conjugal transfer relaxase TraA; Provisional	96.47
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.47
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.46
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.46
PRK09302	509	circadian clock protein KaiC; Reviewed	96.46
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.45
PRK13764	602	ATPase; Provisional	96.44
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	96.43
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	96.41
PRK05541	176	adenylylsulfate kinase; Provisional	96.39
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.39
PRK12338	319	hypothetical protein; Provisional	96.39
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.39
PRK09825	176	idnK D-gluconate kinase; Provisional	96.38
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.38
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	96.36
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.36
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	96.36
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.35
cd03239	178	ABC_SMC_head The structural maintenance of chromos	96.33
PRK11545	163	gntK gluconate kinase 1; Provisional	96.32
TIGR00959	428	ffh signal recognition particle protein. This mode	96.32
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.31
KOG0479	818	consensus DNA replication licensing factor, MCM3 c	96.31
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	96.31
cd04177	168	RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the	96.3
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	96.3
PLN02165	334	adenylate isopentenyltransferase	96.29
PRK14730	195	coaE dephospho-CoA kinase; Provisional	96.29
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.28

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

Probab=100.00  E-value=9.7e-101  Score=768.33  Aligned_cols=436  Identities=50%  Similarity=0.857  Sum_probs=407.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHhhhccCCCceEEEEecCCCCccchhHHHHHHHhccCCCccccc
Q 012016           17 TILSTAASVAATVMLARTVARDLLPYEIQDYFYFRLRKFCNRFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQR   96 (473)
Q Consensus        17 ~~~~~~~S~~a~~~~~~~~~~~~~P~~l~~~~~~~~~~l~~~~~~~~ti~i~e~~~~~~n~ly~a~~~YL~~~~~~~~~r   96 (473)
                      ++|+.+||++|++|++|+|+++++|.+++.|+.+++++|++.++++.++.|.|++|+.+|++|.|+|.||++++++.+.|
T Consensus         2 ~~~~~~~s~~~~~~~~~~~~~~~~p~~~~~y~~~~~~~l~g~~s~~~~~~~~e~~g~~~n~~~~aie~yl~~k~~~~~~r   81 (457)
T KOG0743|consen    2 SVFTAYASLLGSLMFIKSMLQDIIPPSINPYFISALRGLFGVFSSYALIRIGEQDGVFRNQLYVAIEVYLSSKSSAIAKR   81 (457)
T ss_pred             CccchhHHHHHHHHHHHHHHHHhcchhHHHHHHHHHHHhhccCcccEEEEeehhccchHHHHHHHHHHhhhccchhhhhh
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             eEEeeccCCCceEEecCCCceEEEeecCeeeEEEEEEeeccCCccCCCCCCcccceeEEEEEecCCchhHHHHhhhHHHH
Q 012016           97 IKVSKLEKENHVNISMESDEQVVDVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVE  176 (473)
Q Consensus        97 l~~~~~~~~~~~~~~~~~~~~v~D~f~G~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~l~f~~~~~~~~l~~yl~~v~  176 (473)
                      ++.+.+.+++++++.++++++|.|+|+||+++|.+++...+...+.  ..  ..+.|+|+|+|++++|+.|+++|++++.
T Consensus        82 l~~~~~~~s~~~~l~~~~~~~i~d~f~gv~~~w~~~~~~~~~~~~~--~~--~~~~r~~~L~f~k~~~e~V~~syl~~v~  157 (457)
T KOG0743|consen   82 LTQNLSKNSKSLVLGLDDNEEISDEFEGVPVKWRHFVDYNEKWIFV--ER--EREKRYFELTFHKKPRELVTLSYLPYVV  157 (457)
T ss_pred             hhhhhccccccceEEecCCcEEEEEEeceEEEEEEEEEecCccccc--cc--CCcceEEEEEecCccHHHhHHhHHHHHH
Confidence            9999999999999999999999999999999999998876655332  11  4678999999999999999999999999


Q ss_pred             HHHHHHHhhcceeeEeeecccc-cccCCCCcceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCce
Q 012016          177 KEAKSVQQESKTIKILTVNYNN-LYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRG  255 (473)
Q Consensus       177 ~~~~~~~~~~~~~~i~~~~~~~-~~~~~~~~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg  255 (473)
                      ..+++|+++++.+++|+++... ++...+..|+++.++||.+|++|+|++++|++|++|+..|+++++||+++|+||+||
T Consensus       158 ~~~k~I~~~~r~~kl~t~~~~~~~~~~~~~~W~~v~f~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRG  237 (457)
T KOG0743|consen  158 SKAKEILEENRELKLYTNSGKTVIYTAKGGEWRSVGFPHPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRG  237 (457)
T ss_pred             HHHHHHHHHHHHHHHhhcCCCcccccccCCcceecCCCCCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcchhcc
Confidence            9999999999999999997654 344357899999999999999999999999999999999999999999999999999


Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPI  335 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~  335 (473)
                      ||||||||||||++++||||+|++++|+++++++..+.+|++++..++++|||+||||||.+..++|.+.......   .
T Consensus       238 YLLYGPPGTGKSS~IaAmAn~L~ydIydLeLt~v~~n~dLr~LL~~t~~kSIivIEDIDcs~~l~~~~~~~~~~~~---~  314 (457)
T KOG0743|consen  238 YLLYGPPGTGKSSFIAAMANYLNYDIYDLELTEVKLDSDLRHLLLATPNKSILLIEDIDCSFDLRERRKKKKENFE---G  314 (457)
T ss_pred             ceeeCCCCCCHHHHHHHHHhhcCCceEEeeeccccCcHHHHHHHHhCCCCcEEEEeeccccccccccccccccccc---C
Confidence            9999999999999999999999999999999999999999999999999999999999999998877665432211   1


Q ss_pred             cchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc-cCCHHH
Q 012016          336 QQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE-HILFEE  414 (473)
Q Consensus       336 ~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~-~~l~~~  414 (473)
                      ..++.++|+|||++||+||+||+++|||+||||+++|||||+||||||+||+|++|++++++.|+.|||+.++ |.++++
T Consensus       315 ~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h~L~~e  394 (457)
T KOG0743|consen  315 DLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDHRLFDE  394 (457)
T ss_pred             CcceeehHHhhhhhccccccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCcchhHH
Confidence            3467999999999999999999999999999999999999999999999999999999999999999999985 999999


Q ss_pred             HHHHHhcCCCCHHHHHHHHhcCC-CHHHHHHHHHHHHHHhhhcccc
Q 012016          415 IEELISTTQVTPAEVAEQLMRND-DPELVLNGLIEFLKVKRKEDED  459 (473)
Q Consensus       415 i~~l~~~~~~t~a~i~~~l~~~~-~~~~al~~l~~~l~~~~~~~~~  459 (473)
                      |++++.++.+|||||++.||.+. |++.|+++|+++|+.++.+..+
T Consensus       395 ie~l~~~~~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~~~~~~~~~  440 (457)
T KOG0743|consen  395 IERLIEETEVTPAQVAEELMKNKNDADVALKGLVEALESKKEKRNK  440 (457)
T ss_pred             HHHHhhcCccCHHHHHHHHhhccccHHHHHHHHHHHHHhhhhhhcc
Confidence            99999999999999999999987 8999999999999998875444

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

Probab=100.00  E-value=1.4e-41  Score=331.43  Aligned_cols=234  Identities=24%  Similarity=0.352  Sum_probs=196.4

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +.-.+..++++|+|.++++++|.+.++.++.+++.|.++|+.||+|+|||||||||||.||+|+|++.+..|+.+..+++
T Consensus       142 v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSEl  221 (406)
T COG1222         142 VEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSEL  221 (406)
T ss_pred             eccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceEEEeccHHH
Confidence            33455689999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             ------cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceE
Q 012016          290 ------RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI  361 (473)
Q Consensus       290 ------~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  361 (473)
                            .+..-++++|.-+.  .||||||||||+++.  .|...     ..+++.+.++++-+||++|||+.+.  +++-
T Consensus       222 VqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~--kR~d~-----~t~gDrEVQRTmleLL~qlDGFD~~--~nvK  292 (406)
T COG1222         222 VQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGA--KRFDS-----GTSGDREVQRTMLELLNQLDGFDPR--GNVK  292 (406)
T ss_pred             HHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhc--ccccC-----CCCchHHHHHHHHHHHHhccCCCCC--CCeE
Confidence                  24456778887664  789999999999986  33222     1245677899999999999999664  6799


Q ss_pred             EEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc---cccCCHHHHHHHHhcCCCCHHHHHHHHhcC--
Q 012016          362 IVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI---KEHILFEEIEELISTTQVTPAEVAEQLMRN--  436 (473)
Q Consensus       362 iI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~---~~~~l~~~i~~l~~~~~~t~a~i~~~l~~~--  436 (473)
                      ||++||+++.|||||+||||||+.|+||+|+.++|.+|++.+.+.   .+...++.++.+.+  ++|+||+...|...  
T Consensus       293 VI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~--g~sGAdlkaictEAGm  370 (406)
T COG1222         293 VIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTE--GFSGADLKAICTEAGM  370 (406)
T ss_pred             EEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcC--CCchHHHHHHHHHHhH
Confidence            999999999999999999999999999999999999999987654   35566777777665  49999999998643  


Q ss_pred             -----CCHHHHHHHHHHHHHHhh
Q 012016          437 -----DDPELVLNGLIEFLKVKR  454 (473)
Q Consensus       437 -----~~~~~al~~l~~~l~~~~  454 (473)
                           +......+++.++.++.-
T Consensus       371 ~AiR~~R~~Vt~~DF~~Av~KV~  393 (406)
T COG1222         371 FAIRERRDEVTMEDFLKAVEKVV  393 (406)
T ss_pred             HHHHhccCeecHHHHHHHHHHHH
Confidence                 333445566666665443

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

Probab=100.00  E-value=1.5e-38  Score=321.47  Aligned_cols=206  Identities=28%  Similarity=0.376  Sum_probs=177.5

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc-----
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL-----  289 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~-----  289 (473)
                      ..+|+++.|-++.|+++.+ +..|++.|+.|.++|...|+|+||.||||||||.||+|+|.+.++|||....++.     
T Consensus       300 nv~F~dVkG~DEAK~ELeE-iVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdEm~V  378 (752)
T KOG0734|consen  300 NVTFEDVKGVDEAKQELEE-IVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMFV  378 (752)
T ss_pred             ccccccccChHHHHHHHHH-HHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhhhhh
Confidence            3689999999999999866 6669999999999999999999999999999999999999999999999998886     


Q ss_pred             -cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          290 -RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       290 -~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                       .+...+|.+|..+.  .||||||||||+++..  |...        +....+.++++||..|||+..+  +++|||++|
T Consensus       379 GvGArRVRdLF~aAk~~APcIIFIDEiDavG~k--R~~~--------~~~y~kqTlNQLLvEmDGF~qN--eGiIvigAT  446 (752)
T KOG0734|consen  379 GVGARRVRDLFAAAKARAPCIIFIDEIDAVGGK--RNPS--------DQHYAKQTLNQLLVEMDGFKQN--EGIIVIGAT  446 (752)
T ss_pred             cccHHHHHHHHHHHHhcCCeEEEEechhhhccc--CCcc--------HHHHHHHHHHHHHHHhcCcCcC--CceEEEecc
Confidence             25688999998875  7899999999999763  3222        1236789999999999999765  569999999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHH
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQL  433 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l  433 (473)
                      |.|+.||+||+||||||+||.+|.|+...|.+|+..|+..-.+.-.-+..-++.++ ++++||+++++
T Consensus       447 Nfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlV  514 (752)
T KOG0734|consen  447 NFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLV  514 (752)
T ss_pred             CChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHH
Confidence            99999999999999999999999999999999999999865333333444445543 79999998876

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

Probab=100.00  E-value=7.5e-37  Score=317.76  Aligned_cols=210  Identities=25%  Similarity=0.351  Sum_probs=184.1

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc----
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL----  289 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~----  289 (473)
                      ++.+|++|+|.+++|+++.+.+..+++.++.|.++|+.+++|||||||||||||++|+|+|++.+.+|+.+.+.++    
T Consensus       429 p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~sk~  508 (693)
T KOG0730|consen  429 PNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFSKY  508 (693)
T ss_pred             CCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHHHHh
Confidence            4589999999999999999999999999999999999999999999999999999999999999999999998887    


Q ss_pred             --cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          290 --RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       290 --~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                        .++..++++|.++.  .||||||||||++...|+  +.        ......+.+++||+.|||+...  .+++||++
T Consensus       509 vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~--g~--------~~~v~~RVlsqLLtEmDG~e~~--k~V~ViAA  576 (693)
T KOG0730|consen  509 VGESERAIREVFRKARQVAPCIIFFDEIDALAGSRG--GS--------SSGVTDRVLSQLLTEMDGLEAL--KNVLVIAA  576 (693)
T ss_pred             cCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccC--CC--------ccchHHHHHHHHHHHccccccc--CcEEEEec
Confidence              35788999999886  689999999999987332  11        1245789999999999999654  56999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHhc
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLMR  435 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~~  435 (473)
                      ||+|+.||+||+||||||..|++|+|+.+.|.+|++.++..-.....-+++.|++.+ +||+|||.+.|.+
T Consensus       577 TNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq~  647 (693)
T KOG0730|consen  577 TNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQE  647 (693)
T ss_pred             cCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHHH
Confidence            999999999999999999999999999999999999998765444444556666543 6999999999854

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

Probab=100.00  E-value=4.3e-36  Score=320.67  Aligned_cols=250  Identities=27%  Similarity=0.380  Sum_probs=203.8

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc---
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL---  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~---  289 (473)
                      +.+.+|.|++|.++.|++|++.+ .|+++++.|.++|...|+|+||+||||||||.||+|+|.+.++||+.++.++.   
T Consensus       305 ~t~V~FkDVAG~deAK~El~E~V-~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE~  383 (774)
T KOG0731|consen  305 NTGVKFKDVAGVDEAKEELMEFV-KFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEM  383 (774)
T ss_pred             CCCCccccccCcHHHHHHHHHHH-HHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHHHH
Confidence            44589999999999999998855 59999999999999999999999999999999999999999999999999986   


Q ss_pred             ---cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          290 ---RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       290 ---~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                         ...+.++.+|..+.  .|||+||||||++...+. ....     .+.+.+...++++||..|||..+.  .++|+++
T Consensus       384 ~~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~-G~~~-----~~~~~e~e~tlnQll~emDgf~~~--~~vi~~a  455 (774)
T KOG0731|consen  384 FVGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRG-GKGT-----GGGQDEREQTLNQLLVEMDGFETS--KGVIVLA  455 (774)
T ss_pred             hcccchHHHHHHHHHhhccCCeEEEeccccccccccc-cccc-----CCCChHHHHHHHHHHHHhcCCcCC--CcEEEEe
Confidence               24788999998876  689999999999976332 1011     244566789999999999999765  5699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccC-CHHHHHHHHh-cCCCCHHHHHHHHhc-------
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHI-LFEEIEELIS-TTQVTPAEVAEQLMR-------  435 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~-l~~~i~~l~~-~~~~t~a~i~~~l~~-------  435 (473)
                      +||+++.||+||+||||||++|+++.|+..+|..|+..+++..... ...++.++.. ..++++|||+++|..       
T Consensus       456 ~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r  535 (774)
T KOG0731|consen  456 ATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCNEAALLAAR  535 (774)
T ss_pred             ccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHH
Confidence            9999999999999999999999999999999999999998765332 3344444444 347999999998752       


Q ss_pred             C-------CCHHHHHHHHHHHHHHhhh--cccccCcccccccccc
Q 012016          436 N-------DDPELVLNGLIEFLKVKRK--EDEDAKPRKIHEESTE  471 (473)
Q Consensus       436 ~-------~~~~~al~~l~~~l~~~~~--~~~~~~~~~~~e~~~~  471 (473)
                      +       .+.+.|++.++..++.+..  ..++.+..++||+.|.
T Consensus       536 ~~~~~i~~~~~~~a~~Rvi~G~~~~~~~~~~~~~~~~a~~eagha  580 (774)
T KOG0731|consen  536 KGLREIGTKDLEYAIERVIAGMEKKSRVLSLEEKKTVAYHEAGHA  580 (774)
T ss_pred             hccCccchhhHHHHHHHHhccccccchhcCHhhhhhhhhhhccch
Confidence            1       3556666666665544332  3446778899998873

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

Probab=100.00  E-value=3.7e-35  Score=301.20  Aligned_cols=208  Identities=22%  Similarity=0.332  Sum_probs=182.8

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc----
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL----  289 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~----  289 (473)
                      +..+|++|++.++++.++...+..++++++.|+++|+..|.|+|||||||||||.||+|+||+.|.+|+.+...++    
T Consensus       506 PdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPELlNkY  585 (802)
T KOG0733|consen  506 PDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPELLNKY  585 (802)
T ss_pred             CCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHHHHHHH
Confidence            4579999999999999999999999999999999999999999999999999999999999999999999998887    


Q ss_pred             --cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          290 --RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       290 --~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                        .++..+|.+|..+.  .||||||||||++.+.|+.          +....+.+.+++||..|||+...  .++.||++
T Consensus       586 VGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~----------~~s~~s~RvvNqLLtElDGl~~R--~gV~viaA  653 (802)
T KOG0733|consen  586 VGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSD----------EGSSVSSRVVNQLLTELDGLEER--RGVYVIAA  653 (802)
T ss_pred             hhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCC----------CCchhHHHHHHHHHHHhcccccc--cceEEEee
Confidence              35678999998875  7999999999999874332          22445789999999999999665  45999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc-----ccCCHHHHHHHHhcCCCCHHHHHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK-----EHILFEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~-----~~~l~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      ||+|+.+|||++||||||..+++++|+.++|..|++......     ....+++|++...-.+||+||++.++
T Consensus       654 TNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLv  726 (802)
T KOG0733|consen  654 TNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALV  726 (802)
T ss_pred             cCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHH
Confidence            999999999999999999999999999999999999988743     33445666665554579999998886

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

Probab=100.00  E-value=1.7e-35  Score=303.70  Aligned_cols=218  Identities=20%  Similarity=0.340  Sum_probs=185.2

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc------
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL------  289 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~------  289 (473)
                      .+|.+|+|.++...++.+.+.. +++++.|..+|..|+||+|||||||||||+||+|+|+++++|++.++..++      
T Consensus       187 v~f~diGG~d~~~~el~~li~~-i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApeivSGvSG  265 (802)
T KOG0733|consen  187 VSFSDIGGLDKTLAELCELIIH-IKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVSGVSG  265 (802)
T ss_pred             cchhhccChHHHHHHHHHHHHH-hcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchhhhcccCc
Confidence            5899999999999999887765 999999999999999999999999999999999999999999999999887      


Q ss_pred             cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC--CCCceEEEEe
Q 012016          290 RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS--CGDERIIVFT  365 (473)
Q Consensus       290 ~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~--~~~~~iiI~t  365 (473)
                      .++..++++|..+.  .|||+||||||++.+.|.-.          .....++++++||+.||++...  .|..++||++
T Consensus       266 ESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~a----------qreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgA  335 (802)
T KOG0733|consen  266 ESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEA----------QREMERRIVAQLLTSMDELSNEKTKGDPVLVIGA  335 (802)
T ss_pred             ccHHHHHHHHHHHhccCCeEEEeecccccccchhhH----------HHHHHHHHHHHHHHhhhcccccccCCCCeEEEec
Confidence            35789999999986  69999999999998744321          1344689999999999998654  3577999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc---cccCCHHHHHHHHhcCCCCHHHHHHHHhcCCCHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI---KEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELV  442 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~---~~~~l~~~i~~l~~~~~~t~a~i~~~l~~~~~~~~a  442 (473)
                      ||+|+.|||||+|+||||..|.+..|+..+|..|++..+..   .....+..++.+..  +|.+||+..+|..  ....|
T Consensus       336 TnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTP--GfVGADL~AL~~~--Aa~vA  411 (802)
T KOG0733|consen  336 TNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTP--GFVGADLMALCRE--AAFVA  411 (802)
T ss_pred             CCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCC--CccchhHHHHHHH--HHHHH
Confidence            99999999999999999999999999999999999987763   34445666666655  5999999888744  24456


Q ss_pred             HHHHHH
Q 012016          443 LNGLIE  448 (473)
Q Consensus       443 l~~l~~  448 (473)
                      ++.+.+
T Consensus       412 ikR~ld  417 (802)
T KOG0733|consen  412 IKRILD  417 (802)
T ss_pred             HHHHhh
Confidence            666444

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

Probab=100.00  E-value=2.9e-34  Score=267.75  Aligned_cols=215  Identities=25%  Similarity=0.395  Sum_probs=181.7

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc---
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL---  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~---  289 (473)
                      .+..++.+++|.+-+|++|.+.++.++...+.|+++|+.||||+|||||||||||+|++|+|++....|+.+..+++   
T Consensus       149 kpdvsy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~firvvgsefvqk  228 (408)
T KOG0727|consen  149 KPDVSYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQK  228 (408)
T ss_pred             CCCccccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHHHHHH
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999998886   


Q ss_pred             ---cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          290 ---RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       290 ---~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                         .+...++.+|.-+.  .|+||||||||++..  .|.+.     ..|.+.+.++.+-.|||.|||+...  .++-+|+
T Consensus       229 ylgegprmvrdvfrlakenapsiifideidaiat--krfda-----qtgadrevqril~ellnqmdgfdq~--~nvkvim  299 (408)
T KOG0727|consen  229 YLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIAT--KRFDA-----QTGADREVQRILIELLNQMDGFDQT--TNVKVIM  299 (408)
T ss_pred             HhccCcHHHHHHHHHHhccCCcEEEeehhhhHhh--hhccc-----cccccHHHHHHHHHHHHhccCcCcc--cceEEEE
Confidence               24566788877654  789999999999975  34322     2355677889999999999999654  6799999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHh-cCCCCHHHHHHHHhcC
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIS-TTQVTPAEVAEQLMRN  436 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~-~~~~t~a~i~~~l~~~  436 (473)
                      +||+.+.|||||+||||+|+.|+||+|+..+++-++......-.....-+++.++. ...+|.|+|...|...
T Consensus       300 atnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicqea  372 (408)
T KOG0727|consen  300 ATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQEA  372 (408)
T ss_pred             ecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHHHH
Confidence            99999999999999999999999999999999888887665443333445555554 4469999998888653

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

Probab=100.00  E-value=5.8e-34  Score=299.84  Aligned_cols=246  Identities=25%  Similarity=0.350  Sum_probs=206.5

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc---
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL---  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~---  289 (473)
                      ....+|.+++|.++.|+++.+ +..|++.+..|..+|...|+|+||+||||||||.||+|+|.+.+.|++.++.++.   
T Consensus       144 ~~~v~F~DVAG~dEakeel~E-iVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FVem  222 (596)
T COG0465         144 QVKVTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM  222 (596)
T ss_pred             ccCcChhhhcCcHHHHHHHHH-HHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCceeccchhhhhh
Confidence            344799999999999999987 5559999999999999999999999999999999999999999999999999986   


Q ss_pred             ---cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          290 ---RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       290 ---~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                         ...+.+|.+|.++.  .|||+||||||++...|+..       ..+.+.....++++||.+|||+..+  +++|+++
T Consensus       223 fVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g-------~GggnderEQTLNQlLvEmDGF~~~--~gvivia  293 (596)
T COG0465         223 FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAG-------LGGGNDEREQTLNQLLVEMDGFGGN--EGVIVIA  293 (596)
T ss_pred             hcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCC-------CCCCchHHHHHHHHHHhhhccCCCC--CceEEEe
Confidence               36789999999986  59999999999996533222       1244566778999999999999754  5699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc---CCHHHHHHHHhcCCCCHHHHHHHHh-------
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH---ILFEEIEELISTTQVTPAEVAEQLM-------  434 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~---~l~~~i~~l~~~~~~t~a~i~~~l~-------  434 (473)
                      +||+|+-|||||+||||||++|.++.|+...|.+|++-++.....   .....+++...  +++.|++++.+.       
T Consensus       294 aTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tp--GfsGAdL~nl~NEAal~aa  371 (596)
T COG0465         294 ATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTP--GFSGADLANLLNEAALLAA  371 (596)
T ss_pred             cCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCC--CcccchHhhhHHHHHHHHH
Confidence            999999999999999999999999999999999999976654422   33334443333  699999988873       


Q ss_pred             -------cCCCHHHHHHHHHHHHHHhhh--cccccCccccccccc
Q 012016          435 -------RNDDPELVLNGLIEFLKVKRK--EDEDAKPRKIHEEST  470 (473)
Q Consensus       435 -------~~~~~~~al~~l~~~l~~~~~--~~~~~~~~~~~e~~~  470 (473)
                             ...+.+.|.+.++...+++.+  .+++++.++|||.+|
T Consensus       372 r~n~~~i~~~~i~ea~drv~~G~erks~vise~ek~~~AYhEagh  416 (596)
T COG0465         372 RRNKKEITMRDIEEAIDRVIAGPERKSRVISEAEKKITAYHEAGH  416 (596)
T ss_pred             HhcCeeEeccchHHHHHHHhcCcCcCCcccChhhhcchHHHHHHH
Confidence                   236889999999998887765  556788899999865

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

Probab=100.00  E-value=6.3e-33  Score=291.06  Aligned_cols=231  Identities=23%  Similarity=0.314  Sum_probs=187.8

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc-
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL-  289 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~-  289 (473)
                      +.-+..+|+||+|.+++|.+|++.+..++++++.|.. |...+.|+|||||||||||.+|+|+|.++.+.|+.+...++ 
T Consensus       664 PKIPnV~WdDVGGLeevK~eIldTIqlPL~hpeLfss-glrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGPELL  742 (953)
T KOG0736|consen  664 PKIPNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGPELL  742 (953)
T ss_pred             CCCCccchhcccCHHHHHHHHHHHhcCcccChhhhhc-cccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCHHHH
Confidence            3456679999999999999999999999999997765 66667899999999999999999999999999999998887 


Q ss_pred             -----cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE
Q 012016          290 -----RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII  362 (473)
Q Consensus       290 -----~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  362 (473)
                           +++.++|++|.++.  .|||||+||+|.+.+.|++.+..        .+-..+.+++||.+|||+.......+.|
T Consensus       743 NMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~sGDS--------GGVMDRVVSQLLAELDgls~~~s~~VFV  814 (953)
T KOG0736|consen  743 NMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGRSGDS--------GGVMDRVVSQLLAELDGLSDSSSQDVFV  814 (953)
T ss_pred             HHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCCCCCc--------cccHHHHHHHHHHHhhcccCCCCCceEE
Confidence                 46789999999986  79999999999999977664322        2457899999999999998656678999


Q ss_pred             EEecCCCCCCCccccCCCceeeEEEeCCCCHHH-HHHHHHHH---hCccccCCHHHHHHHHhcCCCCHHHHHHHHhcCCC
Q 012016          363 VFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSG-FKLLAANY---LGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDD  438 (473)
Q Consensus       363 I~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~-r~~l~~~~---l~~~~~~l~~~i~~l~~~~~~t~a~i~~~l~~~~~  438 (473)
                      |++||+|+-|||||+||||||.-++++.+..++ +..+++..   +..++.....+|+..+.. .+|+||+-.+|-.  .
T Consensus       815 iGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~-~~TGADlYsLCSd--A  891 (953)
T KOG0736|consen  815 IGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPP-NMTGADLYSLCSD--A  891 (953)
T ss_pred             EecCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCc-CCchhHHHHHHHH--H
Confidence            999999999999999999999999999986655 45555543   344455556666666553 6999999888732  2


Q ss_pred             HHHHHHHHHHHHHHh
Q 012016          439 PELVLNGLIEFLKVK  453 (473)
Q Consensus       439 ~~~al~~l~~~l~~~  453 (473)
                      .-.|+++-+..++..
T Consensus       892 ~l~AikR~i~~ie~g  906 (953)
T KOG0736|consen  892 MLAAIKRTIHDIESG  906 (953)
T ss_pred             HHHHHHHHHHHhhhc
Confidence            344555555555444

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

Probab=100.00  E-value=1.9e-33  Score=266.89  Aligned_cols=217  Identities=26%  Similarity=0.356  Sum_probs=178.6

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +...+..++.+++|.+.+.++|.+.++.++.++++|...|+.+|+|++|||+||||||.||+|+||.....|+.+-.+++
T Consensus       176 ~eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvGseL  255 (440)
T KOG0726|consen  176 VEKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSEL  255 (440)
T ss_pred             cccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhhhHHH
Confidence            34455579999999999999999999999999999999999999999999999999999999999999999998888876


Q ss_pred             c------CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceE
Q 012016          290 R------SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI  361 (473)
Q Consensus       290 ~------~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  361 (473)
                      .      +..-++++|.-+.  .|||+||||||++..  .|-+..     ++.....++++-.|||.+||+.+.  +.+-
T Consensus       256 iQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGt--KRyds~-----SggerEiQrtmLELLNQldGFdsr--gDvK  326 (440)
T KOG0726|consen  256 IQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGT--KRYDSN-----SGGEREIQRTMLELLNQLDGFDSR--GDVK  326 (440)
T ss_pred             HHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhcc--ccccCC-----CccHHHHHHHHHHHHHhccCcccc--CCeE
Confidence            2      3345677777654  799999999999975  332222     355667788999999999999774  5699


Q ss_pred             EEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHh-cCCCCHHHHHHHHhc
Q 012016          362 IVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIS-TTQVTPAEVAEQLMR  435 (473)
Q Consensus       362 iI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~-~~~~t~a~i~~~l~~  435 (473)
                      ||++||+.+.|||||+||||+|+.|+||.|+...++.||...-..-...-.-.++.++. ...+|+|||...|..
T Consensus       327 vimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAictE  401 (440)
T KOG0726|consen  327 VIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAICTE  401 (440)
T ss_pred             EEEecccccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHHHH
Confidence            99999999999999999999999999999999999998875544322112223444443 456999999888754

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

Probab=100.00  E-value=9e-32  Score=276.90  Aligned_cols=232  Identities=23%  Similarity=0.345  Sum_probs=183.1

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .++.+|++|+|.+.+|++|.+.+..++.+++.|.++|.++++|+|||||||||||++++++|++++.+++.+..+.+.  
T Consensus       139 ~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l~~k  218 (398)
T PTZ00454        139 KPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQK  218 (398)
T ss_pred             CCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHHHH
Confidence            455799999999999999999999999999999999999999999999999999999999999999999998876642  


Q ss_pred             ----CchHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          +...++++|..+  .+|+||||||||.++..+  ....     .+.+....+.+..||+.+|++...  .+++||+
T Consensus       219 ~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r--~~~~-----~~~d~~~~r~l~~LL~~ld~~~~~--~~v~VI~  289 (398)
T PTZ00454        219 YLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKR--FDAQ-----TGADREVQRILLELLNQMDGFDQT--TNVKVIM  289 (398)
T ss_pred             hcchhHHHHHHHHHHHHhcCCeEEEEECHhhhcccc--cccc-----CCccHHHHHHHHHHHHHhhccCCC--CCEEEEE
Confidence                234567777655  478999999999997522  1111     122334567889999999998654  4589999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHHhc-------C
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQLMR-------N  436 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l~~-------~  436 (473)
                      |||+++.||||++||||||.+|+|++|+.++|..|++.++........-++..++.. .++|+|||..+|..       .
T Consensus       290 aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~eA~~~A~r~  369 (398)
T PTZ00454        290 ATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRK  369 (398)
T ss_pred             ecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999999999999999988765432222234444432 36999999888753       2


Q ss_pred             CCHHHHHHHHHHHHHHh
Q 012016          437 DDPELVLNGLIEFLKVK  453 (473)
Q Consensus       437 ~~~~~al~~l~~~l~~~  453 (473)
                      +......+++.+++++.
T Consensus       370 ~~~~i~~~df~~A~~~v  386 (398)
T PTZ00454        370 NRYVILPKDFEKGYKTV  386 (398)
T ss_pred             CCCccCHHHHHHHHHHH
Confidence            23344455666666543

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

Probab=100.00  E-value=1.3e-32  Score=256.33  Aligned_cols=214  Identities=28%  Similarity=0.370  Sum_probs=179.1

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc--
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL--  289 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~--  289 (473)
                      .-+..+++-++|.+.+.++|.+.++.++++++.|..+|++-|+|+|||||||||||.||+|+|++....|+.++.+++  
T Consensus       140 KvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht~c~firvsgselvq  219 (404)
T KOG0728|consen  140 KVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQ  219 (404)
T ss_pred             hCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhcceEEEEechHHHHH
Confidence            344578899999999999999999999999999999999999999999999999999999999999999999999987  


Q ss_pred             ----cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          290 ----RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       290 ----~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                          .+...++++|..+.  .|+|||+||||.+...  |...     ..|++...++++-.|||.+||+...  .++-+|
T Consensus       220 k~igegsrmvrelfvmarehapsiifmdeidsigs~--r~e~-----~~ggdsevqrtmlellnqldgfeat--knikvi  290 (404)
T KOG0728|consen  220 KYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSS--RVES-----GSGGDSEVQRTMLELLNQLDGFEAT--KNIKVI  290 (404)
T ss_pred             HHhhhhHHHHHHHHHHHHhcCCceEeeecccccccc--cccC-----CCCccHHHHHHHHHHHHhccccccc--cceEEE
Confidence                23456788887765  7999999999999763  2221     2345667889999999999999765  569999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc---ccCCHHHHHHHHhcCCCCHHHHHHHHhcC
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK---EHILFEEIEELISTTQVTPAEVAEQLMRN  436 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~t~a~i~~~l~~~  436 (473)
                      ++||+.+-|||||+||||+|+.|+||.|+.++|.+|++..-+.-   .......|++-+.  +.|+|++...|...
T Consensus       291 matnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~--gasgaevk~vctea  364 (404)
T KOG0728|consen  291 MATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMP--GASGAEVKGVCTEA  364 (404)
T ss_pred             EeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCC--CCccchhhhhhhhh
Confidence            99999999999999999999999999999999999998654432   2333445554443  47888888877543

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

Probab=99.98  E-value=5e-32  Score=254.49  Aligned_cols=219  Identities=26%  Similarity=0.364  Sum_probs=187.8

Q ss_pred             ceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          207 WIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       207 w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ...+.-.+..++.+++|-.++.+.+.+.++.++.+++.|-++|+.||+|+|||||||||||.+|+|+||..+.-|+.+-.
T Consensus       165 mm~veekpdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdacfirvig  244 (435)
T KOG0729|consen  165 MMQVEEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIG  244 (435)
T ss_pred             EEEeecCCCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCceEEeehh
Confidence            34566677789999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             ccc------cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          287 TEL------RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       287 ~~~------~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      +++      .+...++++|..+.  ..||||+||||++.+  .|.     .++.+++++.++++-.|++.+||+...  +
T Consensus       245 selvqkyvgegarmvrelf~martkkaciiffdeidaigg--arf-----ddg~ggdnevqrtmleli~qldgfdpr--g  315 (435)
T KOG0729|consen  245 SELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGG--ARF-----DDGAGGDNEVQRTMLELINQLDGFDPR--G  315 (435)
T ss_pred             HHHHHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccC--ccc-----cCCCCCcHHHHHHHHHHHHhccCCCCC--C
Confidence            876      24567788888775  469999999999975  232     223355677889999999999999653  6


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh---CccccCCHHHHHHHHhcCCCCHHHHHHHHhc
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL---GIKEHILFEEIEELISTTQVTPAEVAEQLMR  435 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l---~~~~~~l~~~i~~l~~~~~~t~a~i~~~l~~  435 (473)
                      ++-++++||+|+.|||||+||||+|+.++|.+|+.+.|..|++.+.   ..+...-++-+++|+.+  -|+|++...|..
T Consensus       316 nikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcpn--stgaeirsvcte  393 (435)
T KOG0729|consen  316 NIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPN--STGAEIRSVCTE  393 (435)
T ss_pred             CeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCCC--CcchHHHHHHHH
Confidence            7899999999999999999999999999999999999998887544   34455668888888886  789999888865


Q ss_pred             C
Q 012016          436 N  436 (473)
Q Consensus       436 ~  436 (473)
                      .
T Consensus       394 a  394 (435)
T KOG0729|consen  394 A  394 (435)
T ss_pred             h
Confidence            4

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.97  E-value=2.7e-31  Score=282.79  Aligned_cols=248  Identities=25%  Similarity=0.355  Sum_probs=192.0

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .+..+|++++|.+++|+++.+.+ .+++.++.|...|..+++|+|||||||||||++++++|++++.+++.++++++.  
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~-~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~~  127 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIV-DFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM  127 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHH-HHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHHHH
Confidence            45679999999999999988654 578999999999999999999999999999999999999999999999987652  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          +...++.+|..+.  .|+||||||||.++..+...  .     .+.+.....++++||+.||++.+.  ++++||+
T Consensus       128 ~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~--~-----~~~~~~~~~~~~~lL~~~d~~~~~--~~v~vI~  198 (495)
T TIGR01241       128 FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAG--L-----GGGNDEREQTLNQLLVEMDGFGTN--TGVIVIA  198 (495)
T ss_pred             HhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccC--c-----CCccHHHHHHHHHHHhhhccccCC--CCeEEEE
Confidence                3467888888764  68999999999997632211  0     112334567899999999998654  4599999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHhc-------C
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLMR-------N  436 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~~-------~  436 (473)
                      |||+++.|||+++||||||.+|+++.|+.++|.+|++.++.........++..++..+ ++|++|+..++-+       .
T Consensus       199 aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA~~~a~~~  278 (495)
T TIGR01241       199 ATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARK  278 (495)
T ss_pred             ecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999999999999999999998765333334455555543 6999999877642       2


Q ss_pred             CCHHHHHHHHHHHHHHhhh---------cccccCccccccccc
Q 012016          437 DDPELVLNGLIEFLKVKRK---------EDEDAKPRKIHEEST  470 (473)
Q Consensus       437 ~~~~~al~~l~~~l~~~~~---------~~~~~~~~~~~e~~~  470 (473)
                      +......+++..++++...         ...+.+..++||++|
T Consensus       279 ~~~~i~~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~A~hEaGh  321 (495)
T TIGR01241       279 NKTEITMNDIEEAIDRVIAGPEKKSRVISEKEKKLVAYHEAGH  321 (495)
T ss_pred             CCCCCCHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHhH
Confidence            2333445566666654321         123345668888875

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.

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

Probab=99.97  E-value=1.9e-31  Score=249.98  Aligned_cols=212  Identities=21%  Similarity=0.336  Sum_probs=175.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc---
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL---  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~---  289 (473)
                      .+..++++++|.+.+.+++++.+..++.+++.|..+|+.||+|+|+|||||||||.+|+|+|...+..|..+-...+   
T Consensus       165 kPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQLVQM  244 (424)
T KOG0652|consen  165 KPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQM  244 (424)
T ss_pred             CCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcchHHHhh
Confidence            34468999999999999999999999999999999999999999999999999999999999999988887776665   


Q ss_pred             --cC-chHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          290 --RS-NSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       290 --~~-~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                        .+ ..-++..|.-+  ..|+||||||+|+++.  .|.....     .++...++++-.|||.+||+.+.  +.+-||+
T Consensus       245 fIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGt--KRfDSek-----~GDREVQRTMLELLNQLDGFss~--~~vKviA  315 (424)
T KOG0652|consen  245 FIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGT--KRFDSEK-----AGDREVQRTMLELLNQLDGFSSD--DRVKVIA  315 (424)
T ss_pred             hhcchHHHHHHHHHHhhccCCeEEEEechhhhcc--ccccccc-----cccHHHHHHHHHHHHhhcCCCCc--cceEEEe
Confidence              22 33455555544  4799999999999975  4433322     33556789999999999999665  6799999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC---ccccCCHHHHHHHHhcCCCCHHHHHHHHhc
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG---IKEHILFEEIEELISTTQVTPAEVAEQLMR  435 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~---~~~~~l~~~i~~l~~~~~~t~a~i~~~l~~  435 (473)
                      +||+.+-|||||+|.||+|+.|+||.|+.+.|..|++..-+   ......++++++-.+  .+.+|+....|+.
T Consensus       316 ATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTd--dFNGAQcKAVcVE  387 (424)
T KOG0652|consen  316 ATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTD--DFNGAQCKAVCVE  387 (424)
T ss_pred             ecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhccc--ccCchhheeeehh
Confidence            99999999999999999999999999999999988876544   445666777776555  4888887776653

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

Probab=99.97  E-value=8e-31  Score=257.65  Aligned_cols=205  Identities=20%  Similarity=0.323  Sum_probs=171.7

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc----
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR----  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~----  290 (473)
                      ...|++|+|..+.|+-|.+.+..++.-+++|+.+-.||+ |+|++||||||||+||+|+|.+.+..|+.++.+.+.    
T Consensus       208 ~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWk-gvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstltSKwR  286 (491)
T KOG0738|consen  208 NIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWK-GVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKWR  286 (491)
T ss_pred             CcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccc-eeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhhhhhc
Confidence            368999999999999999999999999999998877775 999999999999999999999999999999988873    


Q ss_pred             -CchHHHHHHHHhc---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC--ceEEEE
Q 012016          291 -SNSDLRTLLVATA---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD--ERIIVF  364 (473)
Q Consensus       291 -~~~~l~~l~~~~~---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~--~~iiI~  364 (473)
                       ..+.+.++|..+.   .|++|||||||.|+..|++         ++++..+++.-+.||.+|||+......  -++|++
T Consensus       287 GeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~---------s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLA  357 (491)
T KOG0738|consen  287 GESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGG---------SSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLA  357 (491)
T ss_pred             cchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCC---------ccchhHHHHHHHHHHHHhhccccccccceeEEEEe
Confidence             3355666665554   7999999999999874433         245677899999999999998654322  266778


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc---ccCCHHHHHHHHhcCCCCHHHHHHHH
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK---EHILFEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      +||.|++||.||+|  ||...|++|+|+.++|..|++..++.-   +....+++.+.++  +||++||..+|
T Consensus       358 ATN~PWdiDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~e--GySGaDI~nvC  425 (491)
T KOG0738|consen  358 ATNFPWDIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSE--GYSGADITNVC  425 (491)
T ss_pred             ccCCCcchHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhc--CCChHHHHHHH
Confidence            99999999999999  999999999999999999999998754   2334455555444  59999999888

>CHL00176 ftsH cell division protein; Validated

Probab=99.97  E-value=1e-30  Score=282.55  Aligned_cols=248  Identities=24%  Similarity=0.339  Sum_probs=193.3

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      ....+|++++|.++.|+++.+ +..+++.++.|...|..+++|+||+||||||||++|+++|++++.|++.++++++.  
T Consensus       177 ~~~~~f~dv~G~~~~k~~l~e-iv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~~~  255 (638)
T CHL00176        177 DTGITFRDIAGIEEAKEEFEE-VVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEM  255 (638)
T ss_pred             CCCCCHHhccChHHHHHHHHH-HHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHHHH
Confidence            445799999999999988865 55688999999999999999999999999999999999999999999999988752  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....++.+|..+.  .||||||||||+++..++  ...     .+.+.....+++.||..||++...  .+++||+
T Consensus       256 ~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~--~~~-----~~~~~e~~~~L~~LL~~~dg~~~~--~~ViVIa  326 (638)
T CHL00176        256 FVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRG--AGI-----GGGNDEREQTLNQLLTEMDGFKGN--KGVIVIA  326 (638)
T ss_pred             hhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhccc--CCC-----CCCcHHHHHHHHHHHhhhccccCC--CCeeEEE
Confidence                3456778887764  689999999999975221  111     122344567899999999998654  4599999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHhc-------C
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLMR-------N  436 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~~-------~  436 (473)
                      |||+++.+||||+||||||.+|+++.|+.++|..|++.++..........+..++..+ +++++|+..++-+       .
T Consensus       327 aTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~  406 (638)
T CHL00176        327 ATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARR  406 (638)
T ss_pred             ecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHh
Confidence            9999999999999999999999999999999999999998765433444556666544 6999999877632       1


Q ss_pred             -------CCHHHHHHHHHHHHHHhhh-cccccCccccccccc
Q 012016          437 -------DDPELVLNGLIEFLKVKRK-EDEDAKPRKIHEEST  470 (473)
Q Consensus       437 -------~~~~~al~~l~~~l~~~~~-~~~~~~~~~~~e~~~  470 (473)
                             .+.+.|++.++..++.+.. ...+.+..++||++|
T Consensus       407 ~~~~It~~dl~~Ai~rv~~g~~~~~~~~~~~~~~vA~hEaGh  448 (638)
T CHL00176        407 KKATITMKEIDTAIDRVIAGLEGTPLEDSKNKRLIAYHEVGH  448 (638)
T ss_pred             CCCCcCHHHHHHHHHHHHhhhccCccccHHHHHHHHHHhhhh
Confidence                   2345555555544443322 233456679999876

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.97  E-value=2.2e-30  Score=271.74  Aligned_cols=205  Identities=23%  Similarity=0.349  Sum_probs=160.5

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc----------eE
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD----------VY  282 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~----------~~  282 (473)
                      .++.+|++|+|.++++++|.+.+..++.+++.|+..|.++++|+|||||||||||++++++|++++.+          ++
T Consensus       176 ~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl  255 (512)
T TIGR03689       176 VPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFL  255 (512)
T ss_pred             CCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEE
Confidence            35679999999999999999999999999999999999999999999999999999999999999765          23


Q ss_pred             Eccccccc------CchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhc
Q 012016          283 DLELTELR------SNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID  350 (473)
Q Consensus       283 ~l~~~~~~------~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld  350 (473)
                      .+..+++.      ....++.+|..+.      .++||||||+|+++..++  ..       ..+...+..+++||+.||
T Consensus       256 ~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~--~~-------~s~d~e~~il~~LL~~LD  326 (512)
T TIGR03689       256 NIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRG--SG-------VSSDVETTVVPQLLSELD  326 (512)
T ss_pred             eccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccC--CC-------ccchHHHHHHHHHHHHhc
Confidence            33333321      2345666666543      589999999999986322  11       112234678899999999


Q ss_pred             ccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHH
Q 012016          351 GLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVA  430 (473)
Q Consensus       351 g~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~  430 (473)
                      |+.+.  ++++||+|||+++.|||||+||||||.+|+|++|+.++|++|+++|+... .++.+++..   ..+.+.+++.
T Consensus       327 gl~~~--~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~~-l~l~~~l~~---~~g~~~a~~~  400 (512)
T TIGR03689       327 GVESL--DNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTDS-LPLDADLAE---FDGDREATAA  400 (512)
T ss_pred             ccccC--CceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhcc-CCchHHHHH---hcCCCHHHHH
Confidence            99764  46999999999999999999999999999999999999999999998743 233333332   2345555544


Q ss_pred             HH
Q 012016          431 EQ  432 (473)
Q Consensus       431 ~~  432 (473)
                      .+
T Consensus       401 al  402 (512)
T TIGR03689       401 AL  402 (512)
T ss_pred             HH
Confidence            43

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.

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.97  E-value=4.8e-30  Score=264.82  Aligned_cols=232  Identities=25%  Similarity=0.336  Sum_probs=183.7

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-  290 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-  290 (473)
                      ..+..+|++|+|.+++++++.+.+..++.+++.|+.+|..+++|+|||||||||||++|+++|++++.+++.++++++. 
T Consensus       124 ~~p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~~l~~  203 (389)
T PRK03992        124 ESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQ  203 (389)
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCCEEEeehHHHhH
Confidence            3445789999999999999999999999999999999999999999999999999999999999999999999988762 


Q ss_pred             -----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          291 -----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       291 -----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                           ....++.+|..+.  .|+||||||||.++..+.  ...     ...+.....++..|++.+|++...  .+++||
T Consensus       204 ~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~--~~~-----~~~~~~~~~~l~~lL~~ld~~~~~--~~v~VI  274 (389)
T PRK03992        204 KFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRT--DSG-----TSGDREVQRTLMQLLAEMDGFDPR--GNVKII  274 (389)
T ss_pred             hhccchHHHHHHHHHHHHhcCCeEEEEechhhhhcccc--cCC-----CCccHHHHHHHHHHHHhccccCCC--CCEEEE
Confidence                 2345667776654  689999999999975321  111     111234467788899999987543  468999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc---CCHHHHHHHHhcCCCCHHHHHHHHhc-----
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH---ILFEEIEELISTTQVTPAEVAEQLMR-----  435 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~---~l~~~i~~l~~~~~~t~a~i~~~l~~-----  435 (473)
                      +|||+++.+|++++||||||..|+|+.|+.++|.+|++.++.....   .....++...  .+++++|+..+|..     
T Consensus       275 ~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t--~g~sgadl~~l~~eA~~~a  352 (389)
T PRK03992        275 AATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELT--EGASGADLKAICTEAGMFA  352 (389)
T ss_pred             EecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHc--CCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999998865422   3344444443  36999999887753     


Q ss_pred             --CCCHHHHHHHHHHHHHHhh
Q 012016          436 --NDDPELVLNGLIEFLKVKR  454 (473)
Q Consensus       436 --~~~~~~al~~l~~~l~~~~  454 (473)
                        .+......+++.++++..+
T Consensus       353 ~~~~~~~i~~~d~~~A~~~~~  373 (389)
T PRK03992        353 IRDDRTEVTMEDFLKAIEKVM  373 (389)
T ss_pred             HHcCCCCcCHHHHHHHHHHHh
Confidence              2333345666776666543

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

Probab=99.97  E-value=5.6e-30  Score=266.75  Aligned_cols=232  Identities=24%  Similarity=0.269  Sum_probs=190.6

Q ss_pred             CcceeccCCCC--CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          205 DAWIPVNLDHP--ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       205 ~~w~~~~~~~p--~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      ...+.+.+..+  ..|++++|..++|+.+.+.+..+.+.+..|...+.+.+.|+|||||||||||.||.|+|...++.++
T Consensus       651 ~aLR~ik~~k~tgi~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fi  730 (952)
T KOG0735|consen  651 LALRGIKLVKSTGIRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFI  730 (952)
T ss_pred             HHhhhccccccCCCCceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEE
Confidence            35566666554  4799999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Ecccccc------cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc
Q 012016          283 DLELTEL------RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS  354 (473)
Q Consensus       283 ~l~~~~~------~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~  354 (473)
                      .+...++      .++..+|.+|..+.  .|||||+||+|.+.+.|+..          ..+...+.+++||..|||...
T Consensus       731 svKGPElL~KyIGaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhD----------sTGVTDRVVNQlLTelDG~Eg  800 (952)
T KOG0735|consen  731 SVKGPELLSKYIGASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHD----------STGVTDRVVNQLLTELDGAEG  800 (952)
T ss_pred             EecCHHHHHHHhcccHHHHHHHHHHhhccCCeEEEeccccccCcccCCC----------CCCchHHHHHHHHHhhccccc
Confidence            9998876      35788999998875  79999999999998843321          123467899999999999865


Q ss_pred             CCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHH
Q 012016          355 SCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQL  433 (473)
Q Consensus       355 ~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l  433 (473)
                      -  .++.|+++|.+|+.+||||+||||+|+.|+.+.|+..+|.+|+...-.........+++.++.. .++|+||++.+|
T Consensus       801 l--~GV~i~aaTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll  878 (952)
T KOG0735|consen  801 L--DGVYILAATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLL  878 (952)
T ss_pred             c--ceEEEEEecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHH
Confidence            4  5699999999999999999999999999999999999999999876654434444455555543 369999999888


Q ss_pred             hcCCCHHHHHHHHHHHHHHh
Q 012016          434 MRNDDPELVLNGLIEFLKVK  453 (473)
Q Consensus       434 ~~~~~~~~al~~l~~~l~~~  453 (473)
                      ..     .-+..+-+++.+.
T Consensus       879 ~~-----A~l~avh~~l~~~  893 (952)
T KOG0735|consen  879 YN-----AQLAAVHEILKRE  893 (952)
T ss_pred             HH-----HHHHHHHHHHHhc
Confidence            43     3344444555433

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

Probab=99.97  E-value=5.2e-30  Score=265.58  Aligned_cols=233  Identities=23%  Similarity=0.305  Sum_probs=181.4

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-  290 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-  290 (473)
                      ..++.+|++|+|.++++++|.+.+..++.+++.|..+|..+++|+|||||||||||++|+++|++++.+++.+..+++. 
T Consensus       176 ~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~seL~~  255 (438)
T PTZ00361        176 KAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQ  255 (438)
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEecchhhh
Confidence            4455899999999999999999999999999999999999999999999999999999999999999999998877652 


Q ss_pred             -----CchHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          291 -----SNSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       291 -----~~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                           +...++.+|..+  ..|+||||||||.++..  |....     .+.......++..||+.+|++...  .++.||
T Consensus       256 k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~k--R~~~~-----sgg~~e~qr~ll~LL~~Ldg~~~~--~~V~VI  326 (438)
T PTZ00361        256 KYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTK--RYDAT-----SGGEKEIQRTMLELLNQLDGFDSR--GDVKVI  326 (438)
T ss_pred             hhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhcc--CCCCC-----CcccHHHHHHHHHHHHHHhhhccc--CCeEEE
Confidence                 233466677655  36899999999999752  21111     122334567788999999998543  458999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHh-cCCCCHHHHHHHHhc-------
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIS-TTQVTPAEVAEQLMR-------  435 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~-~~~~t~a~i~~~l~~-------  435 (473)
                      +|||+++.|||+++||||||.+|+|+.|+.++|..|++.++.........++..++. ..++|+|++..+|..       
T Consensus       327 ~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~eA~~~Alr  406 (438)
T PTZ00361        327 MATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALR  406 (438)
T ss_pred             EecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999886543222223444443 336999999887742       


Q ss_pred             CCCHHHHHHHHHHHHHHh
Q 012016          436 NDDPELVLNGLIEFLKVK  453 (473)
Q Consensus       436 ~~~~~~al~~l~~~l~~~  453 (473)
                      .+......+++.+++++.
T Consensus       407 ~~r~~Vt~~D~~~A~~~v  424 (438)
T PTZ00361        407 ERRMKVTQADFRKAKEKV  424 (438)
T ss_pred             hcCCccCHHHHHHHHHHH
Confidence            223334455555555543

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

Probab=99.97  E-value=2.6e-30  Score=242.23  Aligned_cols=223  Identities=19%  Similarity=0.294  Sum_probs=179.4

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      ....+|++++|+++.|+... .+..|+.+++.|..|.   |+++|||||||||||++|+|+|++++.|++.+..+++.  
T Consensus       115 ~~~it~ddViGqEeAK~kcr-li~~yLenPe~Fg~WA---PknVLFyGppGTGKTm~Akalane~kvp~l~vkat~liGe  190 (368)
T COG1223         115 ISDITLDDVIGQEEAKRKCR-LIMEYLENPERFGDWA---PKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGE  190 (368)
T ss_pred             hccccHhhhhchHHHHHHHH-HHHHHhhChHHhcccC---cceeEEECCCCccHHHHHHHHhcccCCceEEechHHHHHH
Confidence            34579999999999998874 4667999999887753   78999999999999999999999999999999998874  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....+++++..+.  .|||+||||+|++.-  +|+-+..       .+.....++.||..|||+.+.  ++++.|+
T Consensus       191 hVGdgar~Ihely~rA~~~aPcivFiDE~DAiaL--dRryQel-------RGDVsEiVNALLTelDgi~en--eGVvtIa  259 (368)
T COG1223         191 HVGDGARRIHELYERARKAAPCIVFIDELDAIAL--DRRYQEL-------RGDVSEIVNALLTELDGIKEN--EGVVTIA  259 (368)
T ss_pred             HhhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhh--hhhHHHh-------cccHHHHHHHHHHhccCcccC--CceEEEe
Confidence                2467888888775  799999999999975  2321111       234567899999999999754  6699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHhcC-------
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLMRN-------  436 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~~~-------  436 (473)
                      +||+|+.||||++.  ||...|+|.+|+.++|..|++.|...-..+....+..+...+ ++|+.||.+-+++.       
T Consensus       260 aTN~p~~LD~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikekvlK~aLh~Ai~  337 (368)
T COG1223         260 ATNRPELLDPAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVLKTALHRAIA  337 (368)
T ss_pred             ecCChhhcCHHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHHHHHHHHHHHHH
Confidence            99999999999999  999999999999999999999998866555555566665543 69999998877642       


Q ss_pred             CCH-HHHHHHHHHHHHH
Q 012016          437 DDP-ELVLNGLIEFLKV  452 (473)
Q Consensus       437 ~~~-~~al~~l~~~l~~  452 (473)
                      +|. ...-+++..++++
T Consensus       338 ed~e~v~~edie~al~k  354 (368)
T COG1223         338 EDREKVEREDIEKALKK  354 (368)
T ss_pred             hchhhhhHHHHHHHHHh
Confidence            222 2334556666654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.97  E-value=2.4e-29  Score=279.36  Aligned_cols=209  Identities=22%  Similarity=0.306  Sum_probs=175.0

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc---
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR---  290 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~---  290 (473)
                      +..+|++++|.+++|+.|.+.+..++..++.|.++|..+++|+|||||||||||++|+++|++++.+++.++.+++.   
T Consensus       448 ~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~~~  527 (733)
T TIGR01243       448 PNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKW  527 (733)
T ss_pred             cccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhhcc
Confidence            34689999999999999999999999999999999999999999999999999999999999999999999987752   


Q ss_pred             ---CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          291 ---SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       291 ---~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                         ++..++.+|..+.  .||||||||||.+++.++.  .       .......+.+++||..|||+...  .+++||+|
T Consensus       528 vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~--~-------~~~~~~~~~~~~lL~~ldg~~~~--~~v~vI~a  596 (733)
T TIGR01243       528 VGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGA--R-------FDTSVTDRIVNQLLTEMDGIQEL--SNVVVIAA  596 (733)
T ss_pred             cCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCC--C-------CCccHHHHHHHHHHHHhhcccCC--CCEEEEEe
Confidence               3567888888764  6899999999999863321  1       11223567899999999998653  56999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQL  433 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l  433 (473)
                      ||+|+.||||++||||||.+|++|+|+.++|.+||+.+..........++..++..+ ++|++||..+|
T Consensus       597 Tn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~  665 (733)
T TIGR01243       597 TNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVC  665 (733)
T ss_pred             CCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999999999999999999999999887654332233344444433 69999998876

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.97  E-value=1.7e-29  Score=265.38  Aligned_cols=222  Identities=20%  Similarity=0.260  Sum_probs=171.1

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc----
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR----  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~----  290 (473)
                      +.+|++|+|.+.+|+.+.+....|.   ......|.++++|+|||||||||||++|+++|++++.+++.++++.+.    
T Consensus       224 ~~~~~dvgGl~~lK~~l~~~~~~~~---~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~l~~~~v  300 (489)
T CHL00195        224 NEKISDIGGLDNLKDWLKKRSTSFS---KQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIV  300 (489)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHhh---HHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHHhccccc
Confidence            4689999999999998877665553   335667999999999999999999999999999999999999987652    


Q ss_pred             --CchHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          291 --SNSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       291 --~~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                        ++..++++|..+  ..||||||||||.++..+..         .+......+.++.|+..|+..    ...++||+||
T Consensus       301 Gese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~---------~~d~~~~~rvl~~lL~~l~~~----~~~V~vIaTT  367 (489)
T CHL00195        301 GESESRMRQMIRIAEALSPCILWIDEIDKAFSNSES---------KGDSGTTNRVLATFITWLSEK----KSPVFVVATA  367 (489)
T ss_pred             ChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccC---------CCCchHHHHHHHHHHHHHhcC----CCceEEEEec
Confidence              356788888754  47999999999998752111         122344678889999988853    2468999999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccC--CHHHHHHHHhcC-CCCHHHHHHHHhcC------C
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHI--LFEEIEELISTT-QVTPAEVAEQLMRN------D  437 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~--l~~~i~~l~~~~-~~t~a~i~~~l~~~------~  437 (473)
                      |+++.|||+++||||||..|+++.|+.++|.+|++.++......  ...++..++..+ ++|+|||...+...      .
T Consensus       368 N~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~~~A~~~  447 (489)
T CHL00195        368 NNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAMYIAFYE  447 (489)
T ss_pred             CChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999999999999999999998764221  123455555533 79999998876431      1


Q ss_pred             CHHHHHHHHHHHHHH
Q 012016          438 DPELVLNGLIEFLKV  452 (473)
Q Consensus       438 ~~~~al~~l~~~l~~  452 (473)
                      ......+++..+++.
T Consensus       448 ~~~lt~~dl~~a~~~  462 (489)
T CHL00195        448 KREFTTDDILLALKQ  462 (489)
T ss_pred             CCCcCHHHHHHHHHh
Confidence            223344555555543

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

Probab=99.96  E-value=4e-28  Score=258.82  Aligned_cols=228  Identities=27%  Similarity=0.390  Sum_probs=186.3

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .+..+|++++|.++.|+.+.+.+..++..++.|.+.|..+++|+|||||||||||+||+|+|++++.+|+.++.+++.  
T Consensus       236 ~~~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~sk  315 (494)
T COG0464         236 DEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSK  315 (494)
T ss_pred             CCCcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHHHhcc
Confidence            445799999999999999999999999999999999999999999999999999999999999999999999988763  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ++..++++|..+.  .||||||||+|.++..++.          ..+....+.+++||..|||+...  .++++|+
T Consensus       316 ~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~----------~~~~~~~r~~~~lL~~~d~~e~~--~~v~vi~  383 (494)
T COG0464         316 WVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGP----------SEDGSGRRVVGQLLTELDGIEKA--EGVLVIA  383 (494)
T ss_pred             ccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCC----------CCchHHHHHHHHHHHHhcCCCcc--CceEEEe
Confidence                4678899998876  7999999999999873321          11222368999999999998654  5599999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCH--HHHHHHHh-cCCCCHHHHHHHHhcC-----
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILF--EEIEELIS-TTQVTPAEVAEQLMRN-----  436 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~--~~i~~l~~-~~~~t~a~i~~~l~~~-----  436 (473)
                      |||+|+.+|||++||||||..|++|.|+.++|..++..++......+.  -++..+++ ..+++++||...|...     
T Consensus       384 aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~  463 (494)
T COG0464         384 ATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEAL  463 (494)
T ss_pred             cCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999985443221  23333333 3359999998887531     


Q ss_pred             --C-CHHHHHHHHHHHHHH
Q 012016          437 --D-DPELVLNGLIEFLKV  452 (473)
Q Consensus       437 --~-~~~~al~~l~~~l~~  452 (473)
                        . ..+..++++.++++.
T Consensus       464 ~~~~~~~~~~~~~~~a~~~  482 (494)
T COG0464         464 REARRREVTLDDFLDALKK  482 (494)
T ss_pred             HHhccCCccHHHHHHHHHh
Confidence              1 224556666666654

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.96  E-value=8.9e-29  Score=280.85  Aligned_cols=213  Identities=14%  Similarity=0.122  Sum_probs=156.0

Q ss_pred             chhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc----------------------------
Q 012016          241 RKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN----------------------------  292 (473)
Q Consensus       241 ~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~----------------------------  292 (473)
                      ++..+.++|..+++|+||+||||||||+||+|+|.+.++|++.++++++...                            
T Consensus      1618 ~kP~slrLGl~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~ 1697 (2281)
T CHL00206       1618 GKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDL 1697 (2281)
T ss_pred             CcCHHHHcCCCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhccccccccccccccccccccccccccccc
Confidence            4567788899999999999999999999999999999999999988765310                            


Q ss_pred             ---------------------hHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHh
Q 012016          293 ---------------------SDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFI  349 (473)
Q Consensus       293 ---------------------~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~l  349 (473)
                                           ..++.+|..+.  +||||+|||||++...                .....+++.||+.|
T Consensus      1698 ~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~~----------------ds~~ltL~qLLneL 1761 (2281)
T CHL00206       1698 DTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVN----------------ESNYLSLGLLVNSL 1761 (2281)
T ss_pred             chhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCCC----------------ccceehHHHHHHHh
Confidence                                 12566676654  7999999999999641                11234689999999


Q ss_pred             cccccC-CCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC---HHHHHHHHhc-CCC
Q 012016          350 DGLWSS-CGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL---FEEIEELIST-TQV  424 (473)
Q Consensus       350 dg~~~~-~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l---~~~i~~l~~~-~~~  424 (473)
                      ||.... ...+++||+|||+|+.|||||+||||||++|+++.|+..+|.+++...+......+   ..++..++.. .|+
T Consensus      1762 Dg~~~~~s~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~Gf 1841 (2281)
T CHL00206       1762 SRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGS 1841 (2281)
T ss_pred             ccccccCCCCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCC
Confidence            986432 23569999999999999999999999999999999999999988775432211111   1123444443 379


Q ss_pred             CHHHHHHHHhc--------------CCCHHHHHHHHHHHHHHhhhcccccCccccccccc
Q 012016          425 TPAEVAEQLMR--------------NDDPELVLNGLIEFLKVKRKEDEDAKPRKIHEEST  470 (473)
Q Consensus       425 t~a~i~~~l~~--------------~~~~~~al~~l~~~l~~~~~~~~~~~~~~~~e~~~  470 (473)
                      |+||++.++-.              ..+.+.|+...+..++.+-... +.+..++||.+|
T Consensus      1842 SGADLanLvNEAaliAirq~ks~Id~~~I~~Al~Rq~~g~~~~~~~~-~~~~ia~yEiGh 1900 (2281)
T CHL00206       1842 NARDLVALTNEALSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSV-QDHGILFYQIGR 1900 (2281)
T ss_pred             CHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHHhhhhhcccCc-chhhhhhhHHhH
Confidence            99999887631              1356777777776665432222 333457776654

>PF14363 AAA_assoc: Domain associated at C-terminal with AAA

Probab=99.96  E-value=9.6e-29  Score=205.42  Aligned_cols=97  Identities=47%  Similarity=0.832  Sum_probs=93.6

Q ss_pred             hCCHHHHHHHHHHHHhhhc-cCCCceEEEEecCCCCccchhHHHHHHHhccCCCccccceEEeeccCCCceEEecCCCce
Q 012016           39 LLPYEIQDYFYFRLRKFCN-RFSSQLTIVIDEHDGLAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQ  117 (473)
Q Consensus        39 ~~P~~l~~~~~~~~~~l~~-~~~~~~ti~i~e~~~~~~n~ly~a~~~YL~~~~~~~~~rl~~~~~~~~~~~~~~~~~~~~  117 (473)
                      |||++||+++.+++++++. +++||+||+|+|++|+.+|++|+||++||+++++++++||++++++++++++++|++||+
T Consensus         1 ~~P~~lr~~~~~~~~~~~~~~~s~~~ti~I~E~~g~~~N~ly~a~~~YL~s~~s~~a~rL~~~~~~~~~~~~l~l~~~e~   80 (98)
T PF14363_consen    1 LLPHELRSYLRSLLRRLFSSRFSPYLTIVIPEFDGLSRNELYDAAQAYLSSKISPSARRLKASKSKNSKNLVLSLDDGEE   80 (98)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCCcEEEEEEeCCCccccHHHHHHHHHHhhccCcccceeeecccCCCCceEEecCCCCE
Confidence            6899999999999988776 899999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEeecCeeeEEEEEEee
Q 012016          118 VVDVFNGIKLKWVLVCRQ  135 (473)
Q Consensus       118 v~D~f~G~~~~W~~~~~~  135 (473)
                      |+|+|+||++||.+++.+
T Consensus        81 V~D~F~Gv~v~W~~~~~e   98 (98)
T PF14363_consen   81 VVDVFEGVKVWWSSVCTE   98 (98)
T ss_pred             EEEEECCEEEEEEEEccC
Confidence            999999999999999863

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

Probab=99.96  E-value=5.7e-29  Score=237.11  Aligned_cols=202  Identities=24%  Similarity=0.347  Sum_probs=169.7

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc----
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR----  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~----  290 (473)
                      ...|++++|.+..|+.|.+.+..+++-++.|..--+|| +|+|||||||||||+||+|+|.+.+-.|+.++.+++.    
T Consensus       129 NVkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~Pw-rgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLvSKWm  207 (439)
T KOG0739|consen  129 NVKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPW-RGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWM  207 (439)
T ss_pred             CCchhhhccchhHHHHHHhheeecccchhhhcCCCCcc-eeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHHHHHHh
Confidence            36789999999999999999999999999888655554 6999999999999999999999999999999998872    


Q ss_pred             --CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          291 --SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       291 --~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                        ++.-+..+|..+.  .|+||||||||.++..+.          ++++...+++-..||.+|.|+-. ..++++|+++|
T Consensus       208 GESEkLVknLFemARe~kPSIIFiDEiDslcg~r~----------enEseasRRIKTEfLVQMqGVG~-d~~gvLVLgAT  276 (439)
T KOG0739|consen  208 GESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRS----------ENESEASRRIKTEFLVQMQGVGN-DNDGVLVLGAT  276 (439)
T ss_pred             ccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCC----------CCchHHHHHHHHHHHHhhhcccc-CCCceEEEecC
Confidence              3444567776664  689999999998876322          23455678899999999999854 34579999999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcC-CCCHHHHH
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTT-QVTPAEVA  430 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~t~a~i~  430 (473)
                      |-|+.||.|++|  ||+..|++|+|...+|..+++..++...|.+ ..++..|...+ ++|++||.
T Consensus       277 NiPw~LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDis  340 (439)
T KOG0739|consen  277 NIPWVLDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDIS  340 (439)
T ss_pred             CCchhHHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceE
Confidence            999999999999  9999999999999999999999999887766 44666666544 68888873

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.95  E-value=3.4e-28  Score=265.38  Aligned_cols=246  Identities=20%  Similarity=0.303  Sum_probs=185.6

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc----
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR----  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~----  290 (473)
                      ..+|+++.|.+..++++.+. ..++..++.|...|...++|+||+||||||||++++++|++++.+++.++++++.    
T Consensus       148 ~~~~~di~g~~~~~~~l~~i-~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~~~~  226 (644)
T PRK10733        148 KTTFADVAGCDEAKEEVAEL-VEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFV  226 (644)
T ss_pred             hCcHHHHcCHHHHHHHHHHH-HHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHHhhh
Confidence            46799999999999888664 4567778888888988899999999999999999999999999999999987652    


Q ss_pred             --CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          291 --SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       291 --~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                        ....++.+|..+.  .||||||||||.++..+.  ...     .+.+.....++++||..|||+.+.  ..+++|+||
T Consensus       227 g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~--~~~-----~g~~~~~~~~ln~lL~~mdg~~~~--~~vivIaaT  297 (644)
T PRK10733        227 GVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG--AGL-----GGGHDEREQTLNQMLVEMDGFEGN--EGIIVIAAT  297 (644)
T ss_pred             cccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccC--CCC-----CCCchHHHHHHHHHHHhhhcccCC--CCeeEEEec
Confidence              3456777787664  689999999999975221  110     122344567999999999998664  459999999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHHhc-------CCC
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQLMR-------NDD  438 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l~~-------~~~  438 (473)
                      |+|+.||||++||||||++|++++|+.++|.+|++.++.........++..+... .++|+||+.+++-.       .+.
T Consensus       298 N~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~eAa~~a~r~~~  377 (644)
T PRK10733        298 NRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNK  377 (644)
T ss_pred             CChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence            9999999999999999999999999999999999999875433222334445543 37999999888742       222


Q ss_pred             HHHHHHHHHHHHHHh-------h--hcccccCccccccccc
Q 012016          439 PELVLNGLIEFLKVK-------R--KEDEDAKPRKIHEEST  470 (473)
Q Consensus       439 ~~~al~~l~~~l~~~-------~--~~~~~~~~~~~~e~~~  470 (473)
                      ......++.+++.+.       .  ..+.+....++||.+|
T Consensus       378 ~~i~~~d~~~a~~~v~~g~~~~~~~~~~~~~~~~a~he~gh  418 (644)
T PRK10733        378 RVVSMVEFEKAKDKIMMGAERRSMVMTEAQKESTAYHEAGH  418 (644)
T ss_pred             CcccHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHHH
Confidence            223334444443322       1  1233456678888765

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

Probab=99.95  E-value=1.7e-28  Score=235.25  Aligned_cols=210  Identities=26%  Similarity=0.348  Sum_probs=176.1

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-----
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-----  290 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-----  290 (473)
                      .+|+.+.|.-++..++++-+..++.+++.+.++|+.+|.|++||||||||||.+++++|..+|.+++.+..+.+.     
T Consensus       129 ~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~lv~kyiG  208 (388)
T KOG0651|consen  129 ISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKYIG  208 (388)
T ss_pred             cCHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhcCCceEEeeHhhhhhhhcc
Confidence            589999999999999999999999999999999999999999999999999999999999999999999988873     


Q ss_pred             -CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecC
Q 012016          291 -SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTN  367 (473)
Q Consensus       291 -~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  367 (473)
                       +..-+++.|..+.  .|||||+||||++++-+  ..     +....+...+++|..|+|.|||+..-  ..+-+|+|||
T Consensus       209 EsaRlIRemf~yA~~~~pciifmdeiDAigGRr--~s-----e~Ts~dreiqrTLMeLlnqmdgfd~l--~rVk~ImatN  279 (388)
T KOG0651|consen  209 ESARLIRDMFRYAREVIPCIIFMDEIDAIGGRR--FS-----EGTSSDREIQRTLMELLNQMDGFDTL--HRVKTIMATN  279 (388)
T ss_pred             cHHHHHHHHHHHHhhhCceEEeehhhhhhccEE--ec-----cccchhHHHHHHHHHHHHhhccchhc--ccccEEEecC
Confidence             2355777787775  68999999999997522  11     11233567789999999999998665  4589999999


Q ss_pred             CCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC---ccccCCHHHHHHHHhcCCCCHHHHHHHHhcC
Q 012016          368 HKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG---IKEHILFEEIEELISTTQVTPAEVAEQLMRN  436 (473)
Q Consensus       368 ~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~---~~~~~l~~~i~~l~~~~~~t~a~i~~~l~~~  436 (473)
                      +|+.|||+|+||||+|+.+++|.|+...|..+++-.-.   ..+...++++..+.++  +..+++...|...
T Consensus       280 rpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~--f~gad~rn~~tEa  349 (388)
T KOG0651|consen  280 RPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDG--FNGADLRNVCTEA  349 (388)
T ss_pred             CccccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhc--cChHHHhhhcccc
Confidence            99999999999999999999999999999887664322   2234457778777775  8888888877654

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

Probab=99.95  E-value=1.4e-27  Score=237.02  Aligned_cols=194  Identities=18%  Similarity=0.169  Sum_probs=143.7

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-----
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-----  290 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-----  290 (473)
                      .+|+++.+.-.+-...++.+...+ .+++....|+.+|++++||||||||||++++++|+++|.+++.++.+++.     
T Consensus       112 ~~f~~~~g~~~~~p~f~dk~~~hi-~kn~l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk~vG  190 (413)
T PLN00020        112 RSFDNLVGGYYIAPAFMDKVAVHI-AKNFLALPNIKVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESENAG  190 (413)
T ss_pred             cchhhhcCccccCHHHHHHHHHHH-HhhhhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcCcCC
Confidence            566666443333333333222111 23445557889999999999999999999999999999999999999873     


Q ss_pred             -CchHHHHHHHHhc-------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc--------c-
Q 012016          291 -SNSDLRTLLVATA-------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL--------W-  353 (473)
Q Consensus       291 -~~~~l~~l~~~~~-------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--------~-  353 (473)
                       ++..++++|..+.       +||||||||||++++.++  ..       ......+....+||+.||+.        | 
T Consensus       191 EsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~--~~-------~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~  261 (413)
T PLN00020        191 EPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFG--TT-------QYTVNNQMVNGTLMNIADNPTNVSLGGDWR  261 (413)
T ss_pred             cHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCC--CC-------CcchHHHHHHHHHHHHhcCCcccccccccc
Confidence             4578999998764       599999999999986322  10       01112344458999998863        3 


Q ss_pred             -cCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC
Q 012016          354 -SSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT  422 (473)
Q Consensus       354 -~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~  422 (473)
                       ......++||+|||+|+.|||+|+||||||..+  ..|+.++|..|++.++.... ....++..+++..
T Consensus       262 ~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~-l~~~dv~~Lv~~f  328 (413)
T PLN00020        262 EKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDG-VSREDVVKLVDTF  328 (413)
T ss_pred             ccccCCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCC-CCHHHHHHHHHcC
Confidence             122356899999999999999999999999865  58999999999999887653 3367788877654

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.95  E-value=2.1e-27  Score=243.78  Aligned_cols=212  Identities=25%  Similarity=0.320  Sum_probs=169.8

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-  290 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-  290 (473)
                      ..+..+|++++|.++++++|.+.+..++.+++.|..+|..+++|+|||||||||||++++++|++++.+++.+....+. 
T Consensus       115 ~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~~~~l~~  194 (364)
T TIGR01242       115 ERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVR  194 (364)
T ss_pred             cCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEecchHHHHH
Confidence            3455789999999999999999999999999999999999999999999999999999999999999999988766542 


Q ss_pred             -----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          291 -----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       291 -----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                           ....++.+|..+.  .|+||||||+|.++..+  ....     .+.+......+..+++.+|++...  .++.||
T Consensus       195 ~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~--~~~~-----~~~~~~~~~~l~~ll~~ld~~~~~--~~v~vI  265 (364)
T TIGR01242       195 KYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKR--TDSG-----TSGDREVQRTLMQLLAELDGFDPR--GNVKVI  265 (364)
T ss_pred             HhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhcccc--ccCC-----CCccHHHHHHHHHHHHHhhCCCCC--CCEEEE
Confidence                 1234556665543  68999999999987522  1111     112334467788899999987443  468999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc---CCHHHHHHHHhcCCCCHHHHHHHHh
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH---ILFEEIEELISTTQVTPAEVAEQLM  434 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~---~l~~~i~~l~~~~~~t~a~i~~~l~  434 (473)
                      +|||+++.+|++++||||||..|+|+.|+.++|..|++.++.....   ....++....+  +++++|+..+|.
T Consensus       266 ~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~--g~sg~dl~~l~~  337 (364)
T TIGR01242       266 AATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTE--GASGADLKAICT  337 (364)
T ss_pred             EecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcC--CCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999988754322   33455555443  599999987764

Many proteins may score above the trusted cutoff because an internal

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

Probab=99.95  E-value=1.8e-27  Score=234.10  Aligned_cols=218  Identities=20%  Similarity=0.337  Sum_probs=177.8

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhc-CCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC---
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVG-KAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS---  291 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g-~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~---  291 (473)
                      .+|++|+|.+.+++.+.+.+..++++++.|...+ ..+++|+|||||||||||.+|+|+|++.|.+++.++.+.+.+   
T Consensus        89 v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~KWf  168 (386)
T KOG0737|consen   89 VSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTSKWF  168 (386)
T ss_pred             eehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccchhhH
Confidence            6899999999999999999999999999997433 256789999999999999999999999999999999988742   


Q ss_pred             --chH-HHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          292 --NSD-LRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       292 --~~~-l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                        ... +..+|.-+.  +|+||||||+|..+..| +         ..++......-++|...-||+.+..+..++|+++|
T Consensus       169 gE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R-~---------s~dHEa~a~mK~eFM~~WDGl~s~~~~rVlVlgAT  238 (386)
T KOG0737|consen  169 GEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQR-R---------STDHEATAMMKNEFMALWDGLSSKDSERVLVLGAT  238 (386)
T ss_pred             HHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhc-c---------cchHHHHHHHHHHHHHHhccccCCCCceEEEEeCC
Confidence              233 344444443  79999999999997633 1         13355566777888888999998877778999999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc---ccCCHHHHHHHHhcCCCCHHHHHHHHhcCCCHHHHH
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK---EHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVL  443 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~t~a~i~~~l~~~~~~~~al  443 (473)
                      |+|.+||.|++|  ||...++++.|+.++|.+|++-+|..+   .+....+++.+.+  +||+.|+.++|..     .|+
T Consensus       239 NRP~DlDeAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~--GySGSDLkelC~~-----Aa~  309 (386)
T KOG0737|consen  239 NRPFDLDEAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTE--GYSGSDLKELCRL-----AAL  309 (386)
T ss_pred             CCCccHHHHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcC--CCcHHHHHHHHHH-----HhH
Confidence            999999999999  999999999999999999999999865   3455566666655  5999999999854     344


Q ss_pred             HHHHHHHHH
Q 012016          444 NGLIEFLKV  452 (473)
Q Consensus       444 ~~l~~~l~~  452 (473)
                      ..+.+.++.
T Consensus       310 ~~ire~~~~  318 (386)
T KOG0737|consen  310 RPIRELLVS  318 (386)
T ss_pred             hHHHHHHHh
Confidence            444444444

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

Probab=99.93  E-value=3.5e-25  Score=242.88  Aligned_cols=214  Identities=21%  Similarity=0.285  Sum_probs=174.1

Q ss_pred             eccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEE
Q 012016          209 PVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYD  283 (473)
Q Consensus       209 ~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~  283 (473)
                      +...+...+|++++|.+.++..+.+.+-.++.+++.|..+++.++||+|||||||||||++++|+|..+     +..++.
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            344455578999999999999999999999999999999999999999999999999999999999988     344444


Q ss_pred             cccccc------cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC
Q 012016          284 LELTEL------RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS  355 (473)
Q Consensus       284 l~~~~~------~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~  355 (473)
                      -...+.      ..+..++-+|..+.  +|+|+|+||||-+.+.+...          .........+.||..|||+.+.
T Consensus       335 rkgaD~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSsk----------qEqih~SIvSTLLaLmdGldsR  404 (1080)
T KOG0732|consen  335 RKGADCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSSK----------QEQIHASIVSTLLALMDGLDSR  404 (1080)
T ss_pred             hcCchhhccccCcHHHHHHHHHHHHhccCceEEeccccccccccccch----------HHHhhhhHHHHHHHhccCCCCC
Confidence            333332      24677888888775  79999999999998755332          1234567889999999999775


Q ss_pred             CCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHH-HHHHh-cCCCCHHHHHHHH
Q 012016          356 CGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEI-EELIS-TTQVTPAEVAEQL  433 (473)
Q Consensus       356 ~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i-~~l~~-~~~~t~a~i~~~l  433 (473)
                        +.++||++||+++.+||||+||||||+.++||+|+.+.|..|+...-.....+..... ..+.+ ..++-+|++..+|
T Consensus       405 --gqVvvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLC  482 (1080)
T KOG0732|consen  405 --GQVVVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALC  482 (1080)
T ss_pred             --CceEEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHH
Confidence              4599999999999999999999999999999999999999999987766555554433 33433 2368889987776


Q ss_pred             h
Q 012016          434 M  434 (473)
Q Consensus       434 ~  434 (473)
                      .
T Consensus       483 T  483 (1080)
T KOG0732|consen  483 T  483 (1080)
T ss_pred             H
Confidence            3

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.93  E-value=6.5e-25  Score=244.03  Aligned_cols=208  Identities=26%  Similarity=0.350  Sum_probs=168.8

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc---
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR---  290 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~---  290 (473)
                      +..+|++|+|.+++++.|.+.+..++..++.|..+|..+++|+|||||||||||++++++|++++.+++.+++.++.   
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~~~~  252 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKY  252 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHhccc
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999887652   


Q ss_pred             ---CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          291 ---SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       291 ---~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                         ....++.+|..+.  .++||||||||.+...++.          .........++.|++.||++...  ..++||+|
T Consensus       253 ~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~----------~~~~~~~~~~~~Ll~~ld~l~~~--~~vivI~a  320 (733)
T TIGR01243       253 YGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREE----------VTGEVEKRVVAQLLTLMDGLKGR--GRVIVIGA  320 (733)
T ss_pred             ccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccC----------CcchHHHHHHHHHHHHhhccccC--CCEEEEee
Confidence               2356777887654  6799999999999753211          11123467889999999998654  45889999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQL  433 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l  433 (473)
                      ||+++.+|++++|||||+..|+++.|+.++|.+|++.+...........+..+++. .+++++++..++
T Consensus       321 tn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~  389 (733)
T TIGR01243       321 TNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALA  389 (733)
T ss_pred             cCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999977654322112233334432 369999887764

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.

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

Probab=99.92  E-value=1.7e-24  Score=225.98  Aligned_cols=207  Identities=25%  Similarity=0.349  Sum_probs=178.9

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc----
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL----  289 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~----  289 (473)
                      ++.+ ++++|.......+.+.+..++..+..+...|.++++|+|+|||||||||.+++|+|++.+..++.++..++    
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            6667 88899999999999999999999999999999999999999999999999999999999999999999887    


Q ss_pred             --cCchHHHHHHHHhc--c-CceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          290 --RSNSDLRTLLVATA--N-RSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       290 --~~~~~l~~l~~~~~--~-~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                        .+++.|++.|..+.  + |+||+|||+|.+.+.+..           .+....++.++|+..|||...  ..++|+|+
T Consensus       259 ~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~-----------~~~~e~Rv~sqlltL~dg~~~--~~~vivl~  325 (693)
T KOG0730|consen  259 PGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREG-----------ADDVESRVVSQLLTLLDGLKP--DAKVIVLA  325 (693)
T ss_pred             ccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccc-----------cchHHHHHHHHHHHHHhhCcC--cCcEEEEE
Confidence              35788999998875  4 899999999999873321           122367899999999999864  35699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHh-cCCCCHHHHHHHHhc
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIS-TTQVTPAEVAEQLMR  435 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~-~~~~t~a~i~~~l~~  435 (473)
                      +||+|+.|||+++| ||||..+++..|+..+|.+|++.+.....+....++..+.. ..++++||+...|-.
T Consensus       326 atnrp~sld~alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~~e  396 (693)
T KOG0730|consen  326 ATNRPDSLDPALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALCRE  396 (693)
T ss_pred             ecCCccccChhhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHHHH
Confidence            99999999999999 99999999999999999999999888766654455555554 458999999988853

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

Probab=99.92  E-value=9.5e-25  Score=221.89  Aligned_cols=210  Identities=21%  Similarity=0.274  Sum_probs=177.8

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      ..+..|++++|.+..|+.+.+.+..++.+++.|..+ .++.+|+||.||||||||+|++|+|.+.+..++.++.+++.  
T Consensus       147 ~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~gl-r~p~rglLLfGPpgtGKtmL~~aiAsE~~atff~iSassLtsK  225 (428)
T KOG0740|consen  147 LRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGL-REPVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSLTSK  225 (428)
T ss_pred             CCcccccCCcchhhHHHHhhhhhhhcccchHhhhcc-ccccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHhhhh
Confidence            344789999999999999999999999988888765 45678999999999999999999999999999999999883  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ++.-++.+|.-+.  +|+|+||||||.++..+  .        ++.+..+.+...++|...++..+...+.++||+
T Consensus       226 ~~Ge~eK~vralf~vAr~~qPsvifidEidslls~R--s--------~~e~e~srr~ktefLiq~~~~~s~~~drvlvig  295 (428)
T KOG0740|consen  226 YVGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKR--S--------DNEHESSRRLKTEFLLQFDGKNSAPDDRVLVIG  295 (428)
T ss_pred             ccChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhc--C--------CcccccchhhhhHHHhhhccccCCCCCeEEEEe
Confidence                2244555665443  89999999999998733  1        234566788999999999999988888899999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcC-CCCHHHHHHHHhc
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTT-QVTPAEVAEQLMR  435 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~t~a~i~~~l~~  435 (473)
                      |||.|+.+|.|++|  ||...+++|.|+.++|..+|.+++....+.+ ..+++.+++.+ +++..||.++|-.
T Consensus       296 aTN~P~e~Dea~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~ke  366 (428)
T KOG0740|consen  296 ATNRPWELDEAARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCKE  366 (428)
T ss_pred             cCCCchHHHHHHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHHH
Confidence            99999999999999  9999999999999999999999998775555 36777776643 6999999888853

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

Probab=99.90  E-value=1.1e-23  Score=213.87  Aligned_cols=209  Identities=22%  Similarity=0.387  Sum_probs=156.4

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHh----chhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-ceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVK----RKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-DVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~----~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-~~~~l~~  286 (473)
                      ..+.-.|++++- ..+.++.-..+.+.+.    -++.-.++|++.-+|+|||||||||||.+|+-|..-|+. +--.++.
T Consensus       212 i~Pdf~Fe~mGI-GGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNG  290 (744)
T KOG0741|consen  212 INPDFNFESMGI-GGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNG  290 (744)
T ss_pred             cCCCCChhhccc-ccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCc
Confidence            344456777631 1223333332332222    367788899999999999999999999999999999965 4455666


Q ss_pred             ccc------cCchHHHHHHHHhc----------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhc
Q 012016          287 TEL------RSNSDLRTLLVATA----------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID  350 (473)
Q Consensus       287 ~~~------~~~~~l~~l~~~~~----------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld  350 (473)
                      .++      .+++.+|++|..+.          .--||++||||+++..|+..        .+........+++||.-||
T Consensus       291 PeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~--------~g~TGVhD~VVNQLLsKmD  362 (744)
T KOG0741|consen  291 PEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSM--------AGSTGVHDTVVNQLLSKMD  362 (744)
T ss_pred             HHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCC--------CCCCCccHHHHHHHHHhcc
Confidence            654      46788999998774          22699999999998633221        1234456788999999999


Q ss_pred             ccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc-------cccCCHHHHHHHHhcCC
Q 012016          351 GLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI-------KEHILFEEIEELISTTQ  423 (473)
Q Consensus       351 g~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~-------~~~~l~~~i~~l~~~~~  423 (473)
                      |+..-  ++++||+-||+++.+|+||+||||+..++++++|+.+.|.+|++.+-..       ......++++.+..+  
T Consensus       363 GVeqL--NNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKN--  438 (744)
T KOG0741|consen  363 GVEQL--NNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKN--  438 (744)
T ss_pred             cHHhh--hcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcC--
Confidence            98664  5699999999999999999999999999999999999999988765432       234556677777665  


Q ss_pred             CCHHHHHHHH
Q 012016          424 VTPAEVAEQL  433 (473)
Q Consensus       424 ~t~a~i~~~l  433 (473)
                      +|+||+..++
T Consensus       439 fSGAEleglV  448 (744)
T KOG0741|consen  439 FSGAELEGLV  448 (744)
T ss_pred             CchhHHHHHH
Confidence            9999996654

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.88  E-value=1.7e-22  Score=199.96  Aligned_cols=227  Identities=18%  Similarity=0.184  Sum_probs=168.7

Q ss_pred             ecCCchhHHHHhhhHHHHHHHHHHHhhcceeeEeeecccccccCCCCcceeccCCCCCCccccccchHHHHHHHHHHHHH
Q 012016          159 FPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERF  238 (473)
Q Consensus       159 f~~~~~~~~l~~yl~~v~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~f  238 (473)
                      |.++.-.+|.++|+..++-....+++..+...-|....+.....-.+ -..........|+++++.+.+++.|.+....-
T Consensus       296 YTtkeg~~V~w~yi~r~LGqPSLiREsSrg~~pw~gsls~~k~~i~~-~~~~s~~gk~pl~~ViL~psLe~Rie~lA~aT  374 (630)
T KOG0742|consen  296 YTTKEGTLVTWRYIERRLGQPSLIRESSRGRFPWIGSLSALKHPIQG-SRSASSRGKDPLEGVILHPSLEKRIEDLAIAT  374 (630)
T ss_pred             eeccccchhHHHHHHHHcCCchhhhhhccccCCCcccHHHHhchhhh-hHhhhhcCCCCcCCeecCHHHHHHHHHHHHHh
Confidence            45666778999999999999988888877665555543321110000 11122233456999999999999886543322


Q ss_pred             HhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-----CchHHHHHHHHhc---cCceEEE
Q 012016          239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-----SNSDLRTLLVATA---NRSILVV  310 (473)
Q Consensus       239 l~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-----~~~~l~~l~~~~~---~~sIL~i  310 (473)
                      -     ..+....+-|++|||||||||||++++.||.+.|+++-.+...++.     ....++++|..+.   ++-+|||
T Consensus       375 a-----NTK~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTkiH~lFDWakkS~rGLllFI  449 (630)
T KOG0742|consen  375 A-----NTKKHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKIHKLFDWAKKSRRGLLLFI  449 (630)
T ss_pred             c-----ccccccchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCccccchHHHHHHHHHHHHHhhcccceEEEe
Confidence            2     2233456778999999999999999999999999999988888873     3467888988764   4578899


Q ss_pred             eccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCC
Q 012016          311 EDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       311 DdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~  390 (473)
                      ||.|+.+.  .|.+..+       +...+..|+.||-- .|-.+   ..+++|++||+|++||.|+-.  |||..|+||+
T Consensus       450 DEADAFLc--eRnktym-------SEaqRsaLNAlLfR-TGdqS---rdivLvlAtNrpgdlDsAV~D--Ride~veFpL  514 (630)
T KOG0742|consen  450 DEADAFLC--ERNKTYM-------SEAQRSALNALLFR-TGDQS---RDIVLVLATNRPGDLDSAVND--RIDEVVEFPL  514 (630)
T ss_pred             hhhHHHHH--Hhchhhh-------cHHHHHHHHHHHHH-hcccc---cceEEEeccCCccchhHHHHh--hhhheeecCC
Confidence            99999987  4444333       23456778887733 33222   468999999999999999999  9999999999


Q ss_pred             CCHHHHHHHHHHHhCc
Q 012016          391 CTPSGFKLLAANYLGI  406 (473)
Q Consensus       391 p~~~~r~~l~~~~l~~  406 (473)
                      |..++|..|+..|+..
T Consensus       515 PGeEERfkll~lYlnk  530 (630)
T KOG0742|consen  515 PGEEERFKLLNLYLNK  530 (630)
T ss_pred             CChHHHHHHHHHHHHH
Confidence            9999999999998863

>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=99.83  E-value=3.4e-19  Score=167.01  Aligned_cols=190  Identities=19%  Similarity=0.239  Sum_probs=126.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN  292 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~  292 (473)
                      -.|.+|++++|+++++..+.-.+.....+.        ..-.++|||||||+||||||..||++++.++..++...+...
T Consensus        18 lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~--------~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i~k~   89 (233)
T PF05496_consen   18 LRPKSLDEFIGQEHLKGNLKILIRAAKKRG--------EALDHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAIEKA   89 (233)
T ss_dssp             TS-SSCCCS-S-HHHHHHHHHHHHHHHCTT--------S---EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC--SC
T ss_pred             cCCCCHHHccCcHHHHhhhHHHHHHHHhcC--------CCcceEEEECCCccchhHHHHHHHhccCCCeEeccchhhhhH
Confidence            457899999999998887644443332211        123479999999999999999999999999999988777777


Q ss_pred             hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-----cCCC---------C
Q 012016          293 SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-----SSCG---------D  358 (473)
Q Consensus       293 ~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-----~~~~---------~  358 (473)
                      .++..++.....+.|||||||+.+                     ++.....|+..|+...     ..+.         .
T Consensus        90 ~dl~~il~~l~~~~ILFIDEIHRl---------------------nk~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~  148 (233)
T PF05496_consen   90 GDLAAILTNLKEGDILFIDEIHRL---------------------NKAQQEILLPAMEDGKIDIIIGKGPNARSIRINLP  148 (233)
T ss_dssp             HHHHHHHHT--TT-EEEECTCCC-----------------------HHHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE--
T ss_pred             HHHHHHHHhcCCCcEEEEechhhc---------------------cHHHHHHHHHHhccCeEEEEeccccccceeeccCC
Confidence            889999988889999999999987                     2344455777776432     1111         1


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHH-HHHHhcCCCCHHHHHHHH
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEI-EELISTTQVTPAEVAEQL  433 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i-~~l~~~~~~t~a~i~~~l  433 (473)
                      ..-+|++|++...|.+.|+.  ||....++.+.+.++..+|+.+........+.++. ..++....-||.-.-++|
T Consensus       149 ~FTligATTr~g~ls~pLrd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrGtPRiAnrll  222 (233)
T PF05496_consen  149 PFTLIGATTRAGLLSSPLRD--RFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRGTPRIANRLL  222 (233)
T ss_dssp             --EEEEEESSGCCTSHCCCT--TSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTTSHHHHHHHH
T ss_pred             CceEeeeeccccccchhHHh--hcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            35689999999999999999  99999999999999999999987666555554443 334444556666444443

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.

>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=99.82  E-value=6.5e-20  Score=159.79  Aligned_cols=123  Identities=32%  Similarity=0.538  Sum_probs=100.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc------CchHHHHHHHHhc--c-CceEEEeccccccccccCCccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR------SNSDLRTLLVATA--N-RSILVVEDIDCTIDLQDRLPAD  326 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~------~~~~l~~l~~~~~--~-~sIL~iDdiD~l~~~~~r~~~~  326 (473)
                      +||+||||||||++++++|+.++.+++.+++..+.      ....+..++..+.  . ++||+|||+|.+....   .  
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~---~--   75 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKS---Q--   75 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHC---S--
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccc---c--
Confidence            69999999999999999999999999999998875      2356777777653  4 7999999999997632   0  


Q ss_pred             cCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCC
Q 012016          327 IAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       327 ~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~  390 (473)
                           ..........+..|++.++..... ..+++||+|||.++.++|+++| |||+..|++|.
T Consensus        76 -----~~~~~~~~~~~~~L~~~l~~~~~~-~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   76 -----PSSSSFEQRLLNQLLSLLDNPSSK-NSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             -----TSSSHHHHHHHHHHHHHHHTTTTT-SSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             -----cccccccccccceeeecccccccc-cccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence                 112345677889999999987553 3469999999999999999998 89999999974

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 ....

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.77  E-value=9.1e-18  Score=170.08  Aligned_cols=189  Identities=18%  Similarity=0.219  Sum_probs=139.1

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS  293 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~  293 (473)
                      .|.+|++++|.++.++.+...+......        ..+++++|||||||||||++++++|++++.++...+...+....
T Consensus        20 rP~~~~~~vG~~~~~~~l~~~l~~~~~~--------~~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~~~~~   91 (328)
T PRK00080         20 RPKSLDEFIGQEKVKENLKIFIEAAKKR--------GEALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPG   91 (328)
T ss_pred             CcCCHHHhcCcHHHHHHHHHHHHHHHhc--------CCCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccccChH
Confidence            4689999999999988876665533221        23356899999999999999999999999998887776666667


Q ss_pred             HHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-----cC---------CCCc
Q 012016          294 DLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-----SS---------CGDE  359 (473)
Q Consensus       294 ~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-----~~---------~~~~  359 (473)
                      .+..++.....+.||||||||.+..                  ...   ..|.+.|+...     ..         .-..
T Consensus        92 ~l~~~l~~l~~~~vl~IDEi~~l~~------------------~~~---e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~  150 (328)
T PRK00080         92 DLAAILTNLEEGDVLFIDEIHRLSP------------------VVE---EILYPAMEDFRLDIMIGKGPAARSIRLDLPP  150 (328)
T ss_pred             HHHHHHHhcccCCEEEEecHhhcch------------------HHH---HHHHHHHHhcceeeeeccCccccceeecCCC
Confidence            7888888888899999999998732                  011   12333333221     00         0123


Q ss_pred             eEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCH-HHHHHHHhcCCCCHHHHHHHH
Q 012016          360 RIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILF-EEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       360 ~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      ..+|++||++..++++|++  ||+..++|+.|+.+++.+++.+.......... +.+..++...+-+|..+...|
T Consensus       151 ~~li~at~~~~~l~~~L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l  223 (328)
T PRK00080        151 FTLIGATTRAGLLTSPLRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLL  223 (328)
T ss_pred             ceEEeecCCcccCCHHHHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHH
Confidence            6789999999999999988  99999999999999999999988776544443 345555655566665554444

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.76  E-value=3.1e-17  Score=160.90  Aligned_cols=177  Identities=16%  Similarity=0.254  Sum_probs=124.3

Q ss_pred             ccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCC---ceeEEeCCCCCCHHHHHHHHHHhc-------CCceEEcccc
Q 012016          218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWK---RGYLLYGPPGTGKSSLIAAMANYL-------NFDVYDLELT  287 (473)
Q Consensus       218 f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~---rg~LL~GPpGtGKT~la~alA~~l-------~~~~~~l~~~  287 (473)
                      +++++|.+++|+.|.+.+. ++.......+.|....   .++||+||||||||++|+++|+.+       ..+++.++++
T Consensus         5 l~~~~Gl~~vk~~i~~~~~-~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~   83 (261)
T TIGR02881         5 LSRMVGLDEVKALIKEIYA-WIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERA   83 (261)
T ss_pred             HHHhcChHHHHHHHHHHHH-HHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHH
Confidence            6789999999999977654 3333344445665432   468999999999999999999875       2356666666


Q ss_pred             cccC------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceE
Q 012016          288 ELRS------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI  361 (473)
Q Consensus       288 ~~~~------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  361 (473)
                      ++.+      ...++.+|..+ .++||||||+|.+..  +           +........+..|++.|+..    ....+
T Consensus        84 ~l~~~~~g~~~~~~~~~~~~a-~~~VL~IDE~~~L~~--~-----------~~~~~~~~~i~~Ll~~~e~~----~~~~~  145 (261)
T TIGR02881        84 DLVGEYIGHTAQKTREVIKKA-LGGVLFIDEAYSLAR--G-----------GEKDFGKEAIDTLVKGMEDN----RNEFV  145 (261)
T ss_pred             HhhhhhccchHHHHHHHHHhc-cCCEEEEechhhhcc--C-----------CccchHHHHHHHHHHHHhcc----CCCEE
Confidence            5521      34456666554 468999999999842  0           11122355677888888764    23456


Q ss_pred             EEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHH
Q 012016          362 IVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEI  415 (473)
Q Consensus       362 iI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i  415 (473)
                      +|++++..+     .++|+|.+  ||+.+|+||.++.+++..|+.+++......+.++.
T Consensus       146 vila~~~~~~~~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a  202 (261)
T TIGR02881       146 LILAGYSDEMDYFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEEA  202 (261)
T ss_pred             EEecCCcchhHHHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHH
Confidence            666554332     47899998  99999999999999999999999876544444443

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.

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=99.75  E-value=4.6e-17  Score=154.64  Aligned_cols=180  Identities=19%  Similarity=0.319  Sum_probs=148.2

Q ss_pred             CCcceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCc
Q 012016          204 TDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFD  280 (473)
Q Consensus       204 ~~~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~  280 (473)
                      ++...+|....|..+++|+|.+.+|+.|++....|+.+.         +..++||||++|||||++++|+.+++   |+.
T Consensus        12 ~~~l~~i~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~---------pannvLL~G~rGtGKSSlVkall~~y~~~GLR   82 (249)
T PF05673_consen   12 SGYLEPIKHPDPIRLDDLIGIERQKEALIENTEQFLQGL---------PANNVLLWGARGTGKSSLVKALLNEYADQGLR   82 (249)
T ss_pred             CCcEEecCCCCCCCHHHhcCHHHHHHHHHHHHHHHHcCC---------CCcceEEecCCCCCHHHHHHHHHHHHhhcCce
Confidence            345788988999999999999999999999999999743         36789999999999999999999977   788


Q ss_pred             eEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCce
Q 012016          281 VYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER  360 (473)
Q Consensus       281 ~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~  360 (473)
                      ++.++-.++..-..+...+...+.+-|||+||+.  +.                  ........|-..|||--...++++
T Consensus        83 lIev~k~~L~~l~~l~~~l~~~~~kFIlf~DDLs--Fe------------------~~d~~yk~LKs~LeGgle~~P~Nv  142 (249)
T PF05673_consen   83 LIEVSKEDLGDLPELLDLLRDRPYKFILFCDDLS--FE------------------EGDTEYKALKSVLEGGLEARPDNV  142 (249)
T ss_pred             EEEECHHHhccHHHHHHHHhcCCCCEEEEecCCC--CC------------------CCcHHHHHHHHHhcCccccCCCcE
Confidence            9999998888878888888878889999999974  22                  123456778888899888888999


Q ss_pred             EEEEecCCCCCCCccc----------cCC-----------CceeeEEEeCCCCHHHHHHHHHHHhCccccCCH
Q 012016          361 IIVFTTNHKEKLDPAL----------LRP-----------GRMDVHVHMSYCTPSGFKLLAANYLGIKEHILF  412 (473)
Q Consensus       361 iiI~tTN~~~~ld~aL----------lrp-----------gRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~  412 (473)
                      +|.+|+|+..-+....          +.|           .||...|.|..|+.++..+|+.+++...+..+.
T Consensus       143 liyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~  215 (249)
T PF05673_consen  143 LIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELD  215 (249)
T ss_pred             EEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCC
Confidence            9999999854433221          111           299999999999999999999999976554443

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

Probab=99.75  E-value=2.8e-18  Score=166.07  Aligned_cols=179  Identities=18%  Similarity=0.268  Sum_probs=135.8

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhh-cCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRV-GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLEL  286 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~-g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~  286 (473)
                      -|++|+-+..+|++++.+...-+.-.+..... =+.|.|-+|||||||||||+|++|+|+.|         .-.++.+++
T Consensus       140 lWEsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins  219 (423)
T KOG0744|consen  140 LWESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS  219 (423)
T ss_pred             hHHHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh
Confidence            47788999999999999877666533322211 25788899999999999999999999998         234567777


Q ss_pred             cccc------CchHHHHHHHHhc-------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc
Q 012016          287 TELR------SNSDLRTLLVATA-------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW  353 (473)
Q Consensus       287 ~~~~------~~~~l~~l~~~~~-------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  353 (473)
                      .++.      +..-+..+|.+..       .-..++|||++.+...|.....      ..+....-+.++.+|.+||.+.
T Consensus       220 hsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S------~~EpsDaIRvVNalLTQlDrlK  293 (423)
T KOG0744|consen  220 HSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASS------RNEPSDAIRVVNALLTQLDRLK  293 (423)
T ss_pred             hHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhc------CCCCchHHHHHHHHHHHHHHhc
Confidence            6662      3344555555542       2356789999999864322111      1234456789999999999996


Q ss_pred             cCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          354 SSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       354 ~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ..  .+++|.+|+|-.+.+|.|+..  |-|.+.++++|+.+++..|++..+.
T Consensus       294 ~~--~NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~Ilkscie  341 (423)
T KOG0744|consen  294 RY--PNVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCIE  341 (423)
T ss_pred             cC--CCEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHHH
Confidence            65  569999999999999999999  9999999999999999999988764

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.74  E-value=3.7e-17  Score=163.75  Aligned_cols=182  Identities=18%  Similarity=0.214  Sum_probs=130.5

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHH
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLR  296 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~  296 (473)
                      +|++++|.++.++.+...+......+        ..+.+++||||||||||++++++|++++.++..+..........+.
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~~--------~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~~~~l~   73 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMRQ--------EALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLA   73 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhcC--------CCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcCchhHH
Confidence            68999999998888776664433221        2245799999999999999999999999988877766555566777


Q ss_pred             HHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--------------cCCCCceEE
Q 012016          297 TLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--------------SSCGDERII  362 (473)
Q Consensus       297 ~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--------------~~~~~~~ii  362 (473)
                      ..+.....+.+|||||+|.+..                     .....|++.|+...              .......++
T Consensus        74 ~~l~~~~~~~vl~iDEi~~l~~---------------------~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~l  132 (305)
T TIGR00635        74 AILTNLEEGDVLFIDEIHRLSP---------------------AVEELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTL  132 (305)
T ss_pred             HHHHhcccCCEEEEehHhhhCH---------------------HHHHHhhHHHhhhheeeeeccCccccceeecCCCeEE
Confidence            7777778889999999998842                     11222444443211              001123788


Q ss_pred             EEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcCCCCHHHH
Q 012016          363 VFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTTQVTPAEV  429 (473)
Q Consensus       363 I~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~~~t~a~i  429 (473)
                      |++||++..+++++++  ||...++++.++.++..+++....+...... .+.+..++...+-.|..+
T Consensus       133 i~~t~~~~~l~~~l~s--R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~  198 (305)
T TIGR00635       133 VGATTRAGMLTSPLRD--RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIA  198 (305)
T ss_pred             EEecCCccccCHHHHh--hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchH
Confidence            9999999999999998  9999999999999999999988776443333 233444444444444433

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.

>CHL00181 cbbX CbbX; Provisional

Probab=99.74  E-value=4.4e-17  Score=161.59  Aligned_cols=175  Identities=18%  Similarity=0.244  Sum_probs=126.6

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCc---eeEEeCCCCCCHHHHHHHHHHhcC-------CceEEccccc
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKR---GYLLYGPPGTGKSSLIAAMANYLN-------FDVYDLELTE  288 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~r---g~LL~GPpGtGKT~la~alA~~l~-------~~~~~l~~~~  288 (473)
                      ++++|.+++|++|.+.+. ++.....+.+.|..++.   ++||+||||||||++|+++|+.+.       -+++.++.++
T Consensus        23 ~~l~Gl~~vK~~i~e~~~-~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~  101 (287)
T CHL00181         23 EELVGLAPVKTRIREIAA-LLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDD  101 (287)
T ss_pred             HhcCCcHHHHHHHHHHHH-HHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHH
Confidence            379999999999988654 45555666777875542   489999999999999999999762       2577777665


Q ss_pred             cc------CchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE
Q 012016          289 LR------SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII  362 (473)
Q Consensus       289 ~~------~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  362 (473)
                      +.      +......++..+ .++||||||+|.+...  +          +...........|+..|+...    .+++|
T Consensus       102 l~~~~~g~~~~~~~~~l~~a-~ggVLfIDE~~~l~~~--~----------~~~~~~~e~~~~L~~~me~~~----~~~~v  164 (287)
T CHL00181        102 LVGQYIGHTAPKTKEVLKKA-MGGVLFIDEAYYLYKP--D----------NERDYGSEAIEILLQVMENQR----DDLVV  164 (287)
T ss_pred             HHHHHhccchHHHHHHHHHc-cCCEEEEEccchhccC--C----------CccchHHHHHHHHHHHHhcCC----CCEEE
Confidence            42      223345555553 5689999999988531  0          112234667788888887532    45777


Q ss_pred             EEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHH
Q 012016          363 VFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFE  413 (473)
Q Consensus       363 I~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~  413 (473)
                      |++++...     .++|+|.+  ||+.+|+|+.++.+++.+|+..++......+.+
T Consensus       165 I~ag~~~~~~~~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~  218 (287)
T CHL00181        165 IFAGYKDRMDKFYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQYQLTP  218 (287)
T ss_pred             EEeCCcHHHHHHHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhcCCCCh
Confidence            77775421     34699999  999999999999999999999998765444433

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.73  E-value=5.7e-17  Score=160.77  Aligned_cols=174  Identities=16%  Similarity=0.240  Sum_probs=128.1

Q ss_pred             cc-ccccchHHHHHHHHHHHHHHhchhHHhhhcCCC---CceeEEeCCCCCCHHHHHHHHHHhcC-------CceEEccc
Q 012016          218 FE-TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAW---KRGYLLYGPPGTGKSSLIAAMANYLN-------FDVYDLEL  286 (473)
Q Consensus       218 f~-~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~---~rg~LL~GPpGtGKT~la~alA~~l~-------~~~~~l~~  286 (473)
                      ++ +++|.+++|+.|.+.+. ++..++.+.+.|...   ..++||+||||||||++|+++|+.+.       -+++.+++
T Consensus        20 l~~~l~Gl~~vk~~i~e~~~-~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~   98 (284)
T TIGR02880        20 LDRELIGLKPVKTRIREIAA-LLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR   98 (284)
T ss_pred             HHHhccCHHHHHHHHHHHHH-HHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH
Confidence            44 68999999999877554 466667777788764   44899999999999999999998873       26777776


Q ss_pred             cccc------CchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCce
Q 012016          287 TELR------SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER  360 (473)
Q Consensus       287 ~~~~------~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~  360 (473)
                      .++.      +...+..+|..+ .+++|||||++.+...  +          ............|++.|+..    ..++
T Consensus        99 ~~l~~~~~g~~~~~~~~~~~~a-~~gvL~iDEi~~L~~~--~----------~~~~~~~~~~~~Ll~~le~~----~~~~  161 (284)
T TIGR02880        99 DDLVGQYIGHTAPKTKEILKRA-MGGVLFIDEAYYLYRP--D----------NERDYGQEAIEILLQVMENQ----RDDL  161 (284)
T ss_pred             HHHhHhhcccchHHHHHHHHHc-cCcEEEEechhhhccC--C----------CccchHHHHHHHHHHHHhcC----CCCE
Confidence            6542      224455666554 5699999999988431  0          11123456778888988753    2457


Q ss_pred             EEEEecCCC--C---CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC
Q 012016          361 IIVFTTNHK--E---KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL  411 (473)
Q Consensus       361 iiI~tTN~~--~---~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l  411 (473)
                      +||++++..  +   .++|+|.+  ||+.+|+||.++.+++..|+.+++......+
T Consensus       162 ~vI~a~~~~~~~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~l  215 (284)
T TIGR02880       162 VVILAGYKDRMDSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQYRF  215 (284)
T ss_pred             EEEEeCCcHHHHHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhcccc
Confidence            777776543  2   35899999  9999999999999999999999987654333

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.

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

Probab=99.71  E-value=1.9e-16  Score=151.43  Aligned_cols=184  Identities=18%  Similarity=0.225  Sum_probs=140.6

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS  293 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~  293 (473)
                      .|.+|++++|++++|+.+.-.+.....+.+        ...++|||||||.|||+||..||+++|.++-..+...+....
T Consensus        21 RP~~l~efiGQ~~vk~~L~ifI~AAk~r~e--------~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK~g   92 (332)
T COG2255          21 RPKTLDEFIGQEKVKEQLQIFIKAAKKRGE--------ALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPG   92 (332)
T ss_pred             CcccHHHhcChHHHHHHHHHHHHHHHhcCC--------CcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccccChh
Confidence            478999999999888887555554433322        245799999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-----cCCC---------Cc
Q 012016          294 DLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-----SSCG---------DE  359 (473)
Q Consensus       294 ~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-----~~~~---------~~  359 (473)
                      ++..++.....+.|||||||+.+.+                     ..-.-|-..|+.+.     ...+         ..
T Consensus        93 DlaaiLt~Le~~DVLFIDEIHrl~~---------------------~vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLpp  151 (332)
T COG2255          93 DLAAILTNLEEGDVLFIDEIHRLSP---------------------AVEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPP  151 (332)
T ss_pred             hHHHHHhcCCcCCeEEEehhhhcCh---------------------hHHHHhhhhhhheeEEEEEccCCccceEeccCCC
Confidence            9999999999999999999999843                     12222334443321     0111         23


Q ss_pred             eEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCH-HHHHHHHhcCCCCHHH
Q 012016          360 RIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILF-EEIEELISTTQVTPAE  428 (473)
Q Consensus       360 ~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~~~t~a~  428 (473)
                      .-+|++|.+...|...|+.  ||....++.+.+.++...|+.+.-..-+..+. +....++....-||.-
T Consensus       152 FTLIGATTr~G~lt~PLrd--RFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPRI  219 (332)
T COG2255         152 FTLIGATTRAGMLTNPLRD--RFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRGTPRI  219 (332)
T ss_pred             eeEeeeccccccccchhHH--hcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccCCcHH
Confidence            5689999999999999998  99999999999999999999987765544443 3444445555677763

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.69  E-value=8.9e-16  Score=165.45  Aligned_cols=156  Identities=16%  Similarity=0.292  Sum_probs=120.8

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.|.+.+.    .        ...++.|||+||+|||||++++++|+.++.             
T Consensus        10 YRPqtFdEVIGQe~Vv~~L~~aL~----~--------gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~   77 (830)
T PRK07003         10 WRPKDFASLVGQEHVVRALTHALD----G--------GRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCR   77 (830)
T ss_pred             hCCCcHHHHcCcHHHHHHHHHHHh----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccH
Confidence            456899999999988877655432    1        223568999999999999999999998853             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++..+-.+...+++++....      ...|+||||+|.+.                     ....
T Consensus        78 sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT---------------------~~A~  136 (830)
T PRK07003         78 ACREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLT---------------------NHAF  136 (830)
T ss_pred             HHHHHhcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCC---------------------HHHH
Confidence                       455665554344456777776542      35799999999873                     3457


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      +.||+.|+..    ...++||++||.+++|.+.|++  || .++.|..++.++....+...+..+.
T Consensus       137 NALLKtLEEP----P~~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~Eg  195 (830)
T PRK07003        137 NAMLKTLEEP----PPHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAGHIVSHLERILGEER  195 (830)
T ss_pred             HHHHHHHHhc----CCCeEEEEEECChhhccchhhh--he-EEEecCCcCHHHHHHHHHHHHHHcC
Confidence            8889888853    3468999999999999999998  88 6899999999999888888776553

>PRK04195 replication factor C large subunit; Provisional

Probab=99.68  E-value=8.6e-16  Score=163.37  Aligned_cols=162  Identities=21%  Similarity=0.360  Sum_probs=123.5

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS  291 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~  291 (473)
                      ...|.+|++|+|+++.++.+.+.+..+.+        |. +++++|||||||||||++|+++|++++++++.++.++...
T Consensus         7 KyrP~~l~dlvg~~~~~~~l~~~l~~~~~--------g~-~~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~r~   77 (482)
T PRK04195          7 KYRPKTLSDVVGNEKAKEQLREWIESWLK--------GK-PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRT   77 (482)
T ss_pred             hcCCCCHHHhcCCHHHHHHHHHHHHHHhc--------CC-CCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEccccccc
Confidence            56789999999999999998888776653        22 2679999999999999999999999999999999988766


Q ss_pred             chHHHHHHHHhc--------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          292 NSDLRTLLVATA--------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       292 ~~~l~~l~~~~~--------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                      ...+..++....        .+.||+|||+|.+..                 ......+..|++.++.      ....+|
T Consensus        78 ~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~-----------------~~d~~~~~aL~~~l~~------~~~~iI  134 (482)
T PRK04195         78 ADVIERVAGEAATSGSLFGARRKLILLDEVDGIHG-----------------NEDRGGARAILELIKK------AKQPII  134 (482)
T ss_pred             HHHHHHHHHHhhccCcccCCCCeEEEEecCccccc-----------------ccchhHHHHHHHHHHc------CCCCEE
Confidence            555665554332        467999999998843                 0122345667777663      124577


Q ss_pred             EecCCCCCCCc-cccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          364 FTTNHKEKLDP-ALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       364 ~tTN~~~~ld~-aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      +++|.+..+++ .|.+  |+ ..|+|+.|+..+...++...+..++
T Consensus       135 li~n~~~~~~~k~Lrs--r~-~~I~f~~~~~~~i~~~L~~i~~~eg  177 (482)
T PRK04195        135 LTANDPYDPSLRELRN--AC-LMIEFKRLSTRSIVPVLKRICRKEG  177 (482)
T ss_pred             EeccCccccchhhHhc--cc-eEEEecCCCHHHHHHHHHHHHHHcC
Confidence            78898888877 5544  44 6799999999999988888775443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.68  E-value=8.4e-16  Score=159.96  Aligned_cols=157  Identities=16%  Similarity=0.311  Sum_probs=117.0

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++++|++.+...|...+.    .       | ..+..|||+||||||||++|+++|+.++.            
T Consensus        11 KyRP~~f~dvVGQe~iv~~L~~~i~----~-------~-ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C   78 (484)
T PRK14956         11 KYRPQFFRDVIHQDLAIGALQNALK----S-------G-KIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNEC   78 (484)
T ss_pred             HhCCCCHHHHhChHHHHHHHHHHHH----c-------C-CCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCC
Confidence            3457899999999888776554433    1       1 13457999999999999999999999865            


Q ss_pred             ------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 ------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                                  +++.++...-.+...++++.....      ...|+||||+|.+.                     ...
T Consensus        79 ~sC~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls---------------------~~A  137 (484)
T PRK14956         79 TSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLT---------------------DQS  137 (484)
T ss_pred             cHHHHHHccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcC---------------------HHH
Confidence                        355555543333455665554332      34699999999872                     456


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      ++.||..|+.    ++..+++|++|+.++.|.+++++  |+ .+++|..++.++....+.+.+..++
T Consensus       138 ~NALLKtLEE----Pp~~viFILaTte~~kI~~TI~S--RC-q~~~f~~ls~~~i~~~L~~i~~~Eg  197 (484)
T PRK14956        138 FNALLKTLEE----PPAHIVFILATTEFHKIPETILS--RC-QDFIFKKVPLSVLQDYSEKLCKIEN  197 (484)
T ss_pred             HHHHHHHhhc----CCCceEEEeecCChhhccHHHHh--hh-heeeecCCCHHHHHHHHHHHHHHcC
Confidence            7888988875    34568999999999999999998  88 4789999999888887777765543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.68  E-value=3.6e-16  Score=166.47  Aligned_cols=156  Identities=18%  Similarity=0.321  Sum_probs=121.4

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ..+|.+|++|+|++.+++.|.+.+.    .        ...++.|||+||+|||||++++++|+.++.            
T Consensus         9 KYRPqtFddVIGQe~vv~~L~~al~----~--------gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~   76 (700)
T PRK12323          9 KWRPRDFTTLVGQEHVVRALTHALE----Q--------QRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQ   76 (700)
T ss_pred             HhCCCcHHHHcCcHHHHHHHHHHHH----h--------CCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCC
Confidence            3467999999999988887665443    1        123568999999999999999999999865            


Q ss_pred             -----------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCcc
Q 012016          280 -----------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQ  336 (473)
Q Consensus       280 -----------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~  336 (473)
                                       +++.++..+-.+...+++++....      ...|+||||+|.+.                   
T Consensus        77 PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls-------------------  137 (700)
T PRK12323         77 PCGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLT-------------------  137 (700)
T ss_pred             CCcccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcC-------------------
Confidence                             455565554344566777766542      35799999999872                   


Q ss_pred             chhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       337 ~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                        ....+.||+.|+.    ...+++||++||.+++|.+.+++  |+ .++.|..++.++....+...+..+
T Consensus       138 --~~AaNALLKTLEE----PP~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~E  199 (700)
T PRK12323        138 --NHAFNAMLKTLEE----PPEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEE  199 (700)
T ss_pred             --HHHHHHHHHhhcc----CCCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHc
Confidence              4567889998885    34568999999999999999998  87 689999999999888888776544

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.67  E-value=1.9e-15  Score=159.12  Aligned_cols=154  Identities=19%  Similarity=0.351  Sum_probs=113.9

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++++|++.+++.+..    .+...        ..+.++|||||||||||++|+++|+.++.            
T Consensus         7 kyRP~~~~divGq~~i~~~L~~----~i~~~--------~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c   74 (472)
T PRK14962          7 KYRPKTFSEVVGQDHVKKLIIN----ALKKN--------SISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNEC   74 (472)
T ss_pred             HHCCCCHHHccCcHHHHHHHHH----HHHcC--------CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCccc
Confidence            3467999999999887665544    33321        23567999999999999999999999864            


Q ss_pred             ------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 ------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                                  +++.++.+.-.+...++++.....      ...||||||+|.+.                     ...
T Consensus        75 ~~c~~i~~g~~~dv~el~aa~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt---------------------~~a  133 (472)
T PRK14962         75 RACRSIDEGTFMDVIELDAASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLT---------------------KEA  133 (472)
T ss_pred             HHHHHHhcCCCCccEEEeCcccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhH---------------------HHH
Confidence                        466666654334455665554432      45799999999873                     334


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      +..||..++..    +..+++|++|+.+..+++++++  |+. .++|..++.++...++...+.
T Consensus       134 ~~~LLk~LE~p----~~~vv~Ilattn~~kl~~~L~S--R~~-vv~f~~l~~~el~~~L~~i~~  190 (472)
T PRK14962        134 FNALLKTLEEP----PSHVVFVLATTNLEKVPPTIIS--RCQ-VIEFRNISDELIIKRLQEVAE  190 (472)
T ss_pred             HHHHHHHHHhC----CCcEEEEEEeCChHhhhHHHhc--CcE-EEEECCccHHHHHHHHHHHHH
Confidence            67788888753    3457778888788899999998  874 799999999998888777654

>TIGR00763 lon ATP-dependent protease La

Probab=99.66  E-value=1.2e-15  Score=170.63  Aligned_cols=159  Identities=25%  Similarity=0.249  Sum_probs=115.3

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--------
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--------  291 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--------  291 (473)
                      ++.|.+++|+.|.+.+......       +...+..+||+||||||||++++++|+.++.+++.++++.+.+        
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            4778888998888766533221       2223347999999999999999999999999999887665422        


Q ss_pred             -------chHHHHHHHHhc-cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc----ccC----
Q 012016          292 -------NSDLRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL----WSS----  355 (473)
Q Consensus       292 -------~~~l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~----~~~----  355 (473)
                             ...+.+.|..+. .+.||||||||.+...              .+.   ...+.||..||..    ...    
T Consensus       394 ~~~~g~~~g~i~~~l~~~~~~~~villDEidk~~~~--------------~~~---~~~~aLl~~ld~~~~~~f~d~~~~  456 (775)
T TIGR00763       394 RTYVGAMPGRIIQGLKKAKTKNPLFLLDEIDKIGSS--------------FRG---DPASALLEVLDPEQNNAFSDHYLD  456 (775)
T ss_pred             CceeCCCCchHHHHHHHhCcCCCEEEEechhhcCCc--------------cCC---CHHHHHHHhcCHHhcCccccccCC
Confidence                   234445555433 4569999999998531              011   1245677766631    000    


Q ss_pred             ---CCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          356 ---CGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       356 ---~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                         .-.++++|+|||.++.++|+|++  ||+ .|+|+.|+.+++..|+++|+.
T Consensus       457 ~~~d~s~v~~I~TtN~~~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l~  506 (775)
T TIGR00763       457 VPFDLSKVIFIATANSIDTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYLI  506 (775)
T ss_pred             ceeccCCEEEEEecCCchhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHHH
Confidence               01358899999999999999999  996 789999999999999998873

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.

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

Probab=99.65  E-value=1.1e-15  Score=152.53  Aligned_cols=151  Identities=25%  Similarity=0.349  Sum_probs=110.6

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS  293 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~  293 (473)
                      .|.+|++++|++.+.-+ -.-+.+.+..         ..-.+.+|||||||||||+|+.||+..+.+|..++.... +..
T Consensus        19 RP~~lde~vGQ~HLlg~-~~~lrr~v~~---------~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~~-gvk   87 (436)
T COG2256          19 RPKSLDEVVGQEHLLGE-GKPLRRAVEA---------GHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTS-GVK   87 (436)
T ss_pred             CCCCHHHhcChHhhhCC-CchHHHHHhc---------CCCceeEEECCCCCCHHHHHHHHHHhhCCceEEeccccc-cHH
Confidence            57899999998765422 0112222221         113479999999999999999999999999999987654 557


Q ss_pred             HHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE-ec
Q 012016          294 DLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF-TT  366 (473)
Q Consensus       294 ~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~-tT  366 (473)
                      +++.++..+.      ++.|||||||+.+-                     +.-...||-.|+.      +.+++|+ ||
T Consensus        88 dlr~i~e~a~~~~~~gr~tiLflDEIHRfn---------------------K~QQD~lLp~vE~------G~iilIGATT  140 (436)
T COG2256          88 DLREIIEEARKNRLLGRRTILFLDEIHRFN---------------------KAQQDALLPHVEN------GTIILIGATT  140 (436)
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEehhhhcC---------------------hhhhhhhhhhhcC------CeEEEEeccC
Confidence            8888887763      47999999999872                     2223446666653      3467776 55


Q ss_pred             CCC-CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          367 NHK-EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       367 N~~-~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ..| -.|.+||+.  |. ++.++...+.++.++++.+-+.
T Consensus       141 ENPsF~ln~ALlS--R~-~vf~lk~L~~~di~~~l~ra~~  177 (436)
T COG2256         141 ENPSFELNPALLS--RA-RVFELKPLSSEDIKKLLKRALL  177 (436)
T ss_pred             CCCCeeecHHHhh--hh-heeeeecCCHHHHHHHHHHHHh
Confidence            555 689999998  76 5788999999999999988443

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=2.8e-15  Score=160.08  Aligned_cols=155  Identities=17%  Similarity=0.307  Sum_probs=118.9

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.|...+.    +        ...+..|||+||||||||++|+++|+.++.             
T Consensus         9 yRPktFddVIGQe~vv~~L~~aI~----~--------grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~   76 (702)
T PRK14960          9 YRPRNFNELVGQNHVSRALSSALE----R--------GRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCA   76 (702)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCH
Confidence            456899999999988777655443    1        123578999999999999999999999864             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++.++-.+...+++++....      ...|+||||+|.+.                     ....
T Consensus        77 sC~~I~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS---------------------~~A~  135 (702)
T PRK14960         77 TCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLS---------------------THSF  135 (702)
T ss_pred             HHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcC---------------------HHHH
Confidence                       566666654445566777776542      45799999999872                     3467


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    +..+.+|++|+.+..+.+.+++  |+ .+++|..++.++....+...+..+
T Consensus       136 NALLKtLEEP----P~~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs~eEI~k~L~~Il~kE  193 (702)
T PRK14960        136 NALLKTLEEP----PEHVKFLFATTDPQKLPITVIS--RC-LQFTLRPLAVDEITKHLGAILEKE  193 (702)
T ss_pred             HHHHHHHhcC----CCCcEEEEEECChHhhhHHHHH--hh-heeeccCCCHHHHHHHHHHHHHHc
Confidence            7888888753    3457888888889999989887  87 578999999999888887776554

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=4.8e-15  Score=152.14  Aligned_cols=156  Identities=15%  Similarity=0.262  Sum_probs=113.7

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++++|++..++.+.+.+.    .        ...++.|||+||||||||++|+++|+.+..             
T Consensus        10 yrP~~~~~iiGq~~~~~~l~~~~~----~--------~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~   77 (363)
T PRK14961         10 WRPQYFRDIIGQKHIVTAISNGLS----L--------GRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCI   77 (363)
T ss_pred             hCCCchhhccChHHHHHHHHHHHH----c--------CCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCH
Confidence            356899999999988877654332    1        123568999999999999999999999852             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++.++-.....+++++....      ...|++|||+|.+.                     ....
T Consensus        78 ~c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~---------------------~~a~  136 (363)
T PRK14961         78 ICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLS---------------------RHSF  136 (363)
T ss_pred             HHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcC---------------------HHHH
Confidence                       344444433223355666665432      34699999999872                     3455


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      +.||..++..    +....+|++|+.++.+.+++..  |+ ..++|+.++.++....+...+...+
T Consensus       137 naLLk~lEe~----~~~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g  195 (363)
T PRK14961        137 NALLKTLEEP----PQHIKFILATTDVEKIPKTILS--RC-LQFKLKIISEEKIFNFLKYILIKES  195 (363)
T ss_pred             HHHHHHHhcC----CCCeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcC
Confidence            6788888753    3457788888888899999987  77 5789999999999888887665443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.63  E-value=6.1e-15  Score=154.99  Aligned_cols=155  Identities=12%  Similarity=0.231  Sum_probs=120.0

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---------------  277 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---------------  277 (473)
                      ..|.+|++|+|++.+++.+.+.+.    .        ...+++|||+||||+|||++|+++|+.+               
T Consensus         7 yRP~~f~dliGQe~vv~~L~~a~~----~--------~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~   74 (491)
T PRK14964          7 YRPSSFKDLVGQDVLVRILRNAFT----L--------NKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCH   74 (491)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHH----c--------CCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccH
Confidence            456899999999987776543322    1        1236789999999999999999999865               


Q ss_pred             ---------CCceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          278 ---------NFDVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       278 ---------~~~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                               +.+++.++.++-.+...+++++....      +..|++|||+|.+.                     ...+
T Consensus        75 ~C~~i~~~~~~Dv~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls---------------------~~A~  133 (491)
T PRK14964         75 NCISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLS---------------------NSAF  133 (491)
T ss_pred             HHHHHhccCCCCEEEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCC---------------------HHHH
Confidence                     35677788776556677888776653      45799999999772                     3467


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    ++.+++|++|+.++++.++++.  |+ ..++|..++.++....+...+..+
T Consensus       134 NaLLK~LEeP----p~~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~~el~~~L~~ia~~E  191 (491)
T PRK14964        134 NALLKTLEEP----APHVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPTDKLVEHLVDIAKKE  191 (491)
T ss_pred             HHHHHHHhCC----CCCeEEEEEeCChHHHHHHHHH--hh-eeeecccccHHHHHHHHHHHHHHc
Confidence            8899998853    3568888889999999999998  77 568999999999888877766544

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.63  E-value=8.6e-15  Score=154.92  Aligned_cols=156  Identities=17%  Similarity=0.281  Sum_probs=117.5

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++++|++.+.+.+...+.    .        ...+.+|||+||||||||++|+++|+.++.            
T Consensus        14 kyRP~~f~dliGq~~vv~~L~~ai~----~--------~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~   81 (507)
T PRK06645         14 KYRPSNFAELQGQEVLVKVLSYTIL----N--------DRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKT   81 (507)
T ss_pred             hhCCCCHHHhcCcHHHHHHHHHHHH----c--------CCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCC
Confidence            3567999999999988776544332    1        123568999999999999999999999854            


Q ss_pred             ----------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccc
Q 012016          280 ----------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQ  337 (473)
Q Consensus       280 ----------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~  337 (473)
                                      +++.++..+-.+...+++++..+.      ...|++|||+|.+.                    
T Consensus        82 C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls--------------------  141 (507)
T PRK06645         82 CEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLS--------------------  141 (507)
T ss_pred             CCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcC--------------------
Confidence                            344444443334567777776653      45799999999772                    


Q ss_pred             hhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          338 NKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       338 ~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                       ...++.|+..|+.    ++..+++|++|+.++++++++++  |+ ..++|..++.++...++...+..+
T Consensus       142 -~~a~naLLk~LEe----pp~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~e  203 (507)
T PRK06645        142 -KGAFNALLKTLEE----PPPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQE  203 (507)
T ss_pred             -HHHHHHHHHHHhh----cCCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHc
Confidence             3457788888874    34568888888889999999988  77 578999999999888888777544

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.62  E-value=1.2e-14  Score=146.46  Aligned_cols=157  Identities=15%  Similarity=0.218  Sum_probs=113.3

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .|..  ...|.+|++++|+++.++.+...+.    .       | ..+..+||+||||+|||++++++|++++.+++.++
T Consensus        10 ~w~~--kyrP~~~~~~~~~~~~~~~l~~~~~----~-------~-~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~   75 (316)
T PHA02544         10 MWEQ--KYRPSTIDECILPAADKETFKSIVK----K-------G-RIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVN   75 (316)
T ss_pred             ccee--ccCCCcHHHhcCcHHHHHHHHHHHh----c-------C-CCCeEEEeeCcCCCCHHHHHHHHHHHhCccceEec
Confidence            4543  5667999999999988887665443    1       1 23557788999999999999999999999999999


Q ss_pred             cccccCchHHHHHHH----Hh---ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          286 LTELRSNSDLRTLLV----AT---ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       286 ~~~~~~~~~l~~l~~----~~---~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ++. .....++..+.    ..   ..+.+|+|||+|.+..                    ......|...++..    ..
T Consensus        76 ~~~-~~~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~--------------------~~~~~~L~~~le~~----~~  130 (316)
T PHA02544         76 GSD-CRIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGL--------------------ADAQRHLRSFMEAY----SK  130 (316)
T ss_pred             cCc-ccHHHHHHHHHHHHHhhcccCCCeEEEEECcccccC--------------------HHHHHHHHHHHHhc----CC
Confidence            887 22233333221    11   3578999999997721                    11223344445543    23


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      ...+|+|||.+..+++++++  ||. .+.|+.|+.+++..++..++
T Consensus       131 ~~~~Ilt~n~~~~l~~~l~s--R~~-~i~~~~p~~~~~~~il~~~~  173 (316)
T PHA02544        131 NCSFIITANNKNGIIEPLRS--RCR-VIDFGVPTKEEQIEMMKQMI  173 (316)
T ss_pred             CceEEEEcCChhhchHHHHh--hce-EEEeCCCCHHHHHHHHHHHH
Confidence            46788999999999999998  885 78999999999887776543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.62  E-value=6.3e-15  Score=156.73  Aligned_cols=155  Identities=17%  Similarity=0.315  Sum_probs=117.7

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.|.+.+.    .        ...+..|||+||||||||++|+++|+.++.             
T Consensus        10 yRP~~f~divGq~~v~~~L~~~~~----~--------~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~   77 (509)
T PRK14958         10 WRPRCFQEVIGQAPVVRALSNALD----Q--------QYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCE   77 (509)
T ss_pred             HCCCCHHHhcCCHHHHHHHHHHHH----h--------CCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCH
Confidence            456899999999988887765543    1        123568999999999999999999999853             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++..+-.+-..+++++....      +..|++|||+|.+.                     ....
T Consensus        78 ~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls---------------------~~a~  136 (509)
T PRK14958         78 NCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLS---------------------GHSF  136 (509)
T ss_pred             HHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcC---------------------HHHH
Confidence                       366677665455567777776543      34699999999873                     3457


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    ++.+++|++|+.+.++.+.++.  |+ ..++|..++.++....+...+..+
T Consensus       137 naLLk~LEep----p~~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~l~~il~~e  194 (509)
T PRK14958        137 NALLKTLEEP----PSHVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPPLQIAAHCQHLLKEE  194 (509)
T ss_pred             HHHHHHHhcc----CCCeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCHHHHHHHHHHHHHHc
Confidence            8899888853    3568888888889999989887  77 578899988888776666665443

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.62  E-value=1e-14  Score=157.55  Aligned_cols=154  Identities=18%  Similarity=0.324  Sum_probs=117.6

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC--------------
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF--------------  279 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~--------------  279 (473)
                      .|.+|++|+|++.+++.|.+.+.    .        ...+..|||+||+|||||++|+++|+.++.              
T Consensus        11 RP~~f~divGQe~vv~~L~~~l~----~--------~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~   78 (647)
T PRK07994         11 RPQTFAEVVGQEHVLTALANALD----L--------GRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDN   78 (647)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHH
Confidence            56899999999988876654333    1        123567999999999999999999999855              


Q ss_pred             ----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHH
Q 012016          280 ----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLS  343 (473)
Q Consensus       280 ----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls  343 (473)
                                +++.++..+-.+...+++++....      ...|+||||+|.+                     +....+
T Consensus        79 C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~L---------------------s~~a~N  137 (647)
T PRK07994         79 CREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHML---------------------SRHSFN  137 (647)
T ss_pred             HHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhC---------------------CHHHHH
Confidence                      345555543233456676665542      3469999999987                     345788


Q ss_pred             HHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          344 GFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       344 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .||..|+.    +++.+++|++|+.+..|.+.++.  |+ .+++|..++.++....+.+.+..+
T Consensus       138 ALLKtLEE----Pp~~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e  194 (647)
T PRK07994        138 ALLKTLEE----PPEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRQQLEHILQAE  194 (647)
T ss_pred             HHHHHHHc----CCCCeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHHHHHHHHHHHHHc
Confidence            99999985    34568888888899999999998  86 789999999999888888776443

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=99.62  E-value=6.7e-15  Score=155.89  Aligned_cols=159  Identities=21%  Similarity=0.210  Sum_probs=117.1

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHH---
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLR---  296 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~---  296 (473)
                      +=.|.+++|++|++++.--...+       .--..-++|.||||+|||||+++||+.+|..|+.+++..+.++.+++   
T Consensus       324 dHYGLekVKeRIlEyLAV~~l~~-------~~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRGHR  396 (782)
T COG0466         324 DHYGLEKVKERILEYLAVQKLTK-------KLKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRGHR  396 (782)
T ss_pred             cccCchhHHHHHHHHHHHHHHhc-------cCCCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhcccc
Confidence            34577889999998775332221       11123588999999999999999999999999999999997766553   


Q ss_pred             ------------HHHHHh-ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc---------
Q 012016          297 ------------TLLVAT-ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS---------  354 (473)
Q Consensus       297 ------------~l~~~~-~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~---------  354 (473)
                                  +-+..+ ....+++|||||.+...              ..+   .-.+.||..+|--..         
T Consensus       397 RTYIGamPGrIiQ~mkka~~~NPv~LLDEIDKm~ss--------------~rG---DPaSALLEVLDPEQN~~F~DhYLe  459 (782)
T COG0466         397 RTYIGAMPGKIIQGMKKAGVKNPVFLLDEIDKMGSS--------------FRG---DPASALLEVLDPEQNNTFSDHYLE  459 (782)
T ss_pred             ccccccCChHHHHHHHHhCCcCCeEEeechhhccCC--------------CCC---ChHHHHHhhcCHhhcCchhhcccc
Confidence                        222222 25689999999998541              011   112456655542110         


Q ss_pred             CC--CCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          355 SC--GDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       355 ~~--~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      -+  =.++++|+|+|..+.++..|+.  ||. .|+++-.+.++...|+++||=
T Consensus       460 v~yDLS~VmFiaTANsl~tIP~PLlD--RME-iI~lsgYt~~EKl~IAk~~Li  509 (782)
T COG0466         460 VPYDLSKVMFIATANSLDTIPAPLLD--RME-VIRLSGYTEDEKLEIAKRHLI  509 (782)
T ss_pred             CccchhheEEEeecCccccCChHHhc--cee-eeeecCCChHHHHHHHHHhcc
Confidence            00  0359999999999999999999  996 799999999999999999984

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.62  E-value=2.5e-14  Score=133.93  Aligned_cols=178  Identities=20%  Similarity=0.296  Sum_probs=146.8

Q ss_pred             CcceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCce
Q 012016          205 DAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDV  281 (473)
Q Consensus       205 ~~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~  281 (473)
                      +...+++-.+|..+.+|+|.+.+|+.+++....|+.+.         +..++||+|..|||||+|++|+-++.   +..+
T Consensus        46 ~~L~pv~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~---------pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrL  116 (287)
T COG2607          46 GYLEPVPDPDPIDLADLVGVDRQKEALVRNTEQFAEGL---------PANNVLLWGARGTGKSSLVKALLNEYADEGLRL  116 (287)
T ss_pred             CcccCCCCCCCcCHHHHhCchHHHHHHHHHHHHHHcCC---------cccceEEecCCCCChHHHHHHHHHHHHhcCCeE
Confidence            34568888888999999999999999999999999743         36789999999999999999999988   6789


Q ss_pred             EEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceE
Q 012016          282 YDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI  361 (473)
Q Consensus       282 ~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  361 (473)
                      +.++-.++.+-..|.+.+...+.+-|||+||+--  .                  ........|-..+||-.+..+.+|+
T Consensus       117 VEV~k~dl~~Lp~l~~~Lr~~~~kFIlFcDDLSF--e------------------~gd~~yK~LKs~LeG~ve~rP~NVl  176 (287)
T COG2607         117 VEVDKEDLATLPDLVELLRARPEKFILFCDDLSF--E------------------EGDDAYKALKSALEGGVEGRPANVL  176 (287)
T ss_pred             EEEcHHHHhhHHHHHHHHhcCCceEEEEecCCCC--C------------------CCchHHHHHHHHhcCCcccCCCeEE
Confidence            9999999888888889999899999999999842  1                  1234556677888998888888999


Q ss_pred             EEEecCCCCCCCcccc--------------------CCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC
Q 012016          362 IVFTTNHKEKLDPALL--------------------RPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL  411 (473)
Q Consensus       362 iI~tTN~~~~ld~aLl--------------------rpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l  411 (473)
                      |.+|+|+...|+....                    -..||...+.|..|+.++..+|+.+|........
T Consensus       177 ~YATSNRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~  246 (287)
T COG2607         177 FYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDI  246 (287)
T ss_pred             EEEecCCcccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCC
Confidence            9999998655542221                    1239999999999999999999999986554433

>PLN03025 replication factor C subunit; Provisional

Probab=99.62  E-value=1.2e-14  Score=146.78  Aligned_cols=155  Identities=15%  Similarity=0.230  Sum_probs=111.0

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----CceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----FDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~l~~  286 (473)
                      ...|.+|++++|++++.+.|..    ++...       .  ..++|||||||||||++|.++|+++.     ..++.++.
T Consensus         6 kyrP~~l~~~~g~~~~~~~L~~----~~~~~-------~--~~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln~   72 (319)
T PLN03025          6 KYRPTKLDDIVGNEDAVSRLQV----IARDG-------N--MPNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELNA   72 (319)
T ss_pred             hcCCCCHHHhcCcHHHHHHHHH----HHhcC-------C--CceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeecc
Confidence            5678999999999887766543    33221       1  23699999999999999999999982     34666776


Q ss_pred             ccccCchHHHHHHHHh---------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          287 TELRSNSDLRTLLVAT---------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~---------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      ++..+...++..+...         ....|++|||+|.+..                     ...+.|+..|+..    +
T Consensus        73 sd~~~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~---------------------~aq~aL~~~lE~~----~  127 (319)
T PLN03025         73 SDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTS---------------------GAQQALRRTMEIY----S  127 (319)
T ss_pred             cccccHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCH---------------------HHHHHHHHHHhcc----c
Confidence            6654444555554321         2357999999998832                     2345566666643    2


Q ss_pred             CceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          358 DERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       358 ~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ....+|++||....+.++|+.  |+ ..++|+.|+.++....+...+..+
T Consensus       128 ~~t~~il~~n~~~~i~~~L~S--Rc-~~i~f~~l~~~~l~~~L~~i~~~e  174 (319)
T PLN03025        128 NTTRFALACNTSSKIIEPIQS--RC-AIVRFSRLSDQEILGRLMKVVEAE  174 (319)
T ss_pred             CCceEEEEeCCccccchhHHH--hh-hcccCCCCCHHHHHHHHHHHHHHc
Confidence            335677889988999999998  76 479999999999888877766544

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.61  E-value=1.4e-14  Score=158.89  Aligned_cols=155  Identities=18%  Similarity=0.308  Sum_probs=114.8

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD------------  280 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~------------  280 (473)
                      ..|.+|++|+|++.+++.|.+.    +...        ..+..|||+||||||||++|+++|+.++..            
T Consensus        10 yRP~tFddIIGQe~Iv~~Lkna----I~~~--------rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~   77 (944)
T PRK14949         10 WRPATFEQMVGQSHVLHALTNA----LTQQ--------RLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCS   77 (944)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHH----HHhC--------CCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCch
Confidence            3568999999999888775443    3221        235679999999999999999999998653            


Q ss_pred             ------------eEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          281 ------------VYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       281 ------------~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                  ++.++..+..+...++++.....      ...|+||||+|.+                     ....+
T Consensus        78 sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~L---------------------T~eAq  136 (944)
T PRK14949         78 SCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHML---------------------SRSSF  136 (944)
T ss_pred             HHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhc---------------------CHHHH
Confidence                        23333332223345666654432      3579999999987                     35678


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    +..+++|++|+.+.+|.++++.  |+ .+++|..++.++....+.+.+..+
T Consensus       137 NALLKtLEEP----P~~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~eEI~~~L~~il~~E  194 (944)
T PRK14949        137 NALLKTLEEP----PEHVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQDEIGTQLNHILTQE  194 (944)
T ss_pred             HHHHHHHhcc----CCCeEEEEECCCchhchHHHHH--hh-eEEeCCCCCHHHHHHHHHHHHHHc
Confidence            8999999853    3457788888889999999998  87 689999999999888888776544

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=99.61  E-value=1.4e-14  Score=152.64  Aligned_cols=162  Identities=20%  Similarity=0.289  Sum_probs=114.8

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch------
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS------  293 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~------  293 (473)
                      +=.|..++|++|++.+.--.       -.|-.-..-+.|+||||+|||+++++||..||..|+.++...+.+..      
T Consensus       412 DHYgm~dVKeRILEfiAV~k-------Lrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGHR  484 (906)
T KOG2004|consen  412 DHYGMEDVKERILEFIAVGK-------LRGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGHR  484 (906)
T ss_pred             cccchHHHHHHHHHHHHHHh-------hcccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhcccc
Confidence            44567889999988654111       11223344689999999999999999999999999999988875433      


Q ss_pred             ---------HHHHHHHHh-ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHH------HHhcccccCC-
Q 012016          294 ---------DLRTLLVAT-ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL------NFIDGLWSSC-  356 (473)
Q Consensus       294 ---------~l~~l~~~~-~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL------~~ldg~~~~~-  356 (473)
                               .+.+.+... ....+++|||||.+..              +.++.....+-.+|      ||+|..-.-+ 
T Consensus       485 RTYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~--------------g~qGDPasALLElLDPEQNanFlDHYLdVp~  550 (906)
T KOG2004|consen  485 RTYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGS--------------GHQGDPASALLELLDPEQNANFLDHYLDVPV  550 (906)
T ss_pred             eeeeccCChHHHHHHHhhCCCCceEEeehhhhhCC--------------CCCCChHHHHHHhcChhhccchhhhcccccc
Confidence                     333444444 3678999999999952              22222232222222      2222221100 


Q ss_pred             -CCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          357 -GDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       357 -~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                       =..+++|+|.|..+.++|+|+.  ||. .|+++-...++...|+.+||-
T Consensus       551 DLSkVLFicTAN~idtIP~pLlD--RME-vIelsGYv~eEKv~IA~~yLi  597 (906)
T KOG2004|consen  551 DLSKVLFICTANVIDTIPPPLLD--RME-VIELSGYVAEEKVKIAERYLI  597 (906)
T ss_pred             chhheEEEEeccccccCChhhhh--hhh-eeeccCccHHHHHHHHHHhhh
Confidence             0358999999999999999999  996 699999999999999999985

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.61  E-value=3e-14  Score=146.92  Aligned_cols=177  Identities=17%  Similarity=0.209  Sum_probs=122.5

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc---------------
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD---------------  280 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~---------------  280 (473)
                      ..|++|+|++.+++.+.+.+....   ..+...+...+++|||+||||+|||++|+++|+.+...               
T Consensus         2 ~~f~~IiGq~~~~~~L~~~i~~~~---~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~   78 (394)
T PRK07940          2 SVWDDLVGQEAVVAELRAAARAAR---ADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRT   78 (394)
T ss_pred             ChhhhccChHHHHHHHHHHHHhcc---ccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHH
Confidence            358999999999998877665332   23444555668899999999999999999999977432               


Q ss_pred             --------eEEccccc-ccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHH
Q 012016          281 --------VYDLELTE-LRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGF  345 (473)
Q Consensus       281 --------~~~l~~~~-~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~L  345 (473)
                              ++.+.... ...-..+++++....      ...|+||||+|.+.                     ....+.|
T Consensus        79 ~~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~---------------------~~aanaL  137 (394)
T PRK07940         79 VLAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLT---------------------ERAANAL  137 (394)
T ss_pred             HhcCCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcC---------------------HHHHHHH
Confidence                    23333221 123456777776553      34699999999883                     2345778


Q ss_pred             HHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCC
Q 012016          346 LNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVT  425 (473)
Q Consensus       346 L~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t  425 (473)
                      |..|+..    +.+.++|++|+.++.+.|++++  |+ ..++|+.|+.++....+....+.    ..+.+..++.-.+-+
T Consensus       138 Lk~LEep----~~~~~fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~~~i~~~L~~~~~~----~~~~a~~la~~s~G~  206 (394)
T PRK07940        138 LKAVEEP----PPRTVWLLCAPSPEDVLPTIRS--RC-RHVALRTPSVEAVAEVLVRRDGV----DPETARRAARASQGH  206 (394)
T ss_pred             HHHhhcC----CCCCeEEEEECChHHChHHHHh--hC-eEEECCCCCHHHHHHHHHHhcCC----CHHHHHHHHHHcCCC
Confidence            9888753    3457777777779999999998  87 68999999999987777643322    233344444444444


Q ss_pred             HH
Q 012016          426 PA  427 (473)
Q Consensus       426 ~a  427 (473)
                      +.
T Consensus       207 ~~  208 (394)
T PRK07940        207 IG  208 (394)
T ss_pred             HH
Confidence            44

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.61  E-value=1.4e-14  Score=151.17  Aligned_cols=153  Identities=22%  Similarity=0.313  Sum_probs=110.6

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN  292 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~  292 (473)
                      -.|.+|++++|++..... ...+...+.+.         ...+++|+||||||||++|+++|+.++.+++.++.... +.
T Consensus         6 ~RP~~l~d~vGq~~~v~~-~~~L~~~i~~~---------~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~~-~~   74 (413)
T PRK13342          6 MRPKTLDEVVGQEHLLGP-GKPLRRMIEAG---------RLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTS-GV   74 (413)
T ss_pred             hCCCCHHHhcCcHHHhCc-chHHHHHHHcC---------CCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEecccc-cH
Confidence            457899999998876544 11122233221         13489999999999999999999999999999887653 34


Q ss_pred             hHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          293 SDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       293 ~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                      ..++.++....      .+.||||||+|.+.                     ......|+..++.      ..+++|++|
T Consensus        75 ~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~---------------------~~~q~~LL~~le~------~~iilI~at  127 (413)
T PRK13342         75 KDLREVIEEARQRRSAGRRTILFIDEIHRFN---------------------KAQQDALLPHVED------GTITLIGAT  127 (413)
T ss_pred             HHHHHHHHHHHHhhhcCCceEEEEechhhhC---------------------HHHHHHHHHHhhc------CcEEEEEeC
Confidence            45666665542      56899999999873                     2234556766653      235666544


Q ss_pred             --CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          367 --NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       367 --N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                        |....++++|++  |+ ..+.|+.++.++...++...+..
T Consensus       128 t~n~~~~l~~aL~S--R~-~~~~~~~ls~e~i~~lL~~~l~~  166 (413)
T PRK13342        128 TENPSFEVNPALLS--RA-QVFELKPLSEEDIEQLLKRALED  166 (413)
T ss_pred             CCChhhhccHHHhc--cc-eeeEeCCCCHHHHHHHHHHHHHH
Confidence              334689999998  88 67999999999999999887653

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.60  E-value=2.3e-14  Score=154.40  Aligned_cols=154  Identities=16%  Similarity=0.309  Sum_probs=117.6

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---------------
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---------------  278 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---------------  278 (473)
                      .|.+|++++|++.+.+.+.+.+..            ...++.||||||+|||||++|+++|+.++               
T Consensus        11 rP~~f~~viGq~~v~~~L~~~i~~------------~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~   78 (559)
T PRK05563         11 RPQTFEDVVGQEHITKTLKNAIKQ------------GKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEI   78 (559)
T ss_pred             CCCcHHhccCcHHHHHHHHHHHHc------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHH
Confidence            468999999999888776655441            12467899999999999999999999874               


Q ss_pred             ---------CceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHH
Q 012016          279 ---------FDVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLS  343 (473)
Q Consensus       279 ---------~~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls  343 (473)
                               .+++.++.++..+-..++++.....      ..-|++|||+|.+.                     ....+
T Consensus        79 C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt---------------------~~a~n  137 (559)
T PRK05563         79 CKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLS---------------------TGAFN  137 (559)
T ss_pred             HHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC---------------------HHHHH
Confidence                     4566666654444456777666543      45799999999873                     34677


Q ss_pred             HHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          344 GFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       344 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .||..++..    +..+++|++|+.++.+++++++  |+. .++|+.|+.++....+...+...
T Consensus       138 aLLKtLEep----p~~~ifIlatt~~~ki~~tI~S--Rc~-~~~f~~~~~~ei~~~L~~i~~~e  194 (559)
T PRK05563        138 ALLKTLEEP----PAHVIFILATTEPHKIPATILS--RCQ-RFDFKRISVEDIVERLKYILDKE  194 (559)
T ss_pred             HHHHHhcCC----CCCeEEEEEeCChhhCcHHHHh--Hhe-EEecCCCCHHHHHHHHHHHHHHc
Confidence            889888753    3568888888889999999988  874 68999999999888777766544

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.60  E-value=3.4e-14  Score=145.19  Aligned_cols=156  Identities=18%  Similarity=0.324  Sum_probs=115.1

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++++|++..++.+.+.+.    .        ...++.||||||||+|||++++++|+.+..             
T Consensus         8 ~rp~~~~~iig~~~~~~~l~~~~~----~--------~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~   75 (355)
T TIGR02397         8 YRPQTFEDVIGQEHIVQTLKNAIK----N--------GRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECE   75 (355)
T ss_pred             hCCCcHhhccCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCH
Confidence            457899999999988887766443    1        123568999999999999999999998742             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++.....+...+++++..+.      .+.|++|||+|.+.                     ....
T Consensus        76 ~c~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~---------------------~~~~  134 (355)
T TIGR02397        76 SCKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLS---------------------KSAF  134 (355)
T ss_pred             HHHHHhcCCCCCEEEeeccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcC---------------------HHHH
Confidence                       344444432223345666666543      34699999999772                     2356


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      +.|+..++..    +...++|++||.++.+.+++.+  |+ ..++|+.|+.++...++..++...+
T Consensus       135 ~~Ll~~le~~----~~~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g  193 (355)
T TIGR02397       135 NALLKTLEEP----PEHVVFILATTEPHKIPATILS--RC-QRFDFKRIPLEDIVERLKKILDKEG  193 (355)
T ss_pred             HHHHHHHhCC----ccceeEEEEeCCHHHHHHHHHh--he-eEEEcCCCCHHHHHHHHHHHHHHcC
Confidence            7788888753    3457888888999999999988  87 4789999999999888888776544

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=99.60  E-value=2.2e-14  Score=138.05  Aligned_cols=165  Identities=11%  Similarity=0.183  Sum_probs=103.0

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +....+.+||++++.+..  .+...+..-      +   .....+.++||||||||||+|++|+|+++   +..+.++++
T Consensus         7 ~~~~~~~~fd~f~~~~~~--~~~~~~~~~------~---~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~   75 (229)
T PRK06893          7 IHQIDDETLDNFYADNNL--LLLDSLRKN------F---IDLQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPL   75 (229)
T ss_pred             CCCCCcccccccccCChH--HHHHHHHHH------h---hccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeH
Confidence            445667899999976532  222222111      1   11123468999999999999999999986   455555555


Q ss_pred             ccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          287 TELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                      ....  ....+.+....+..+|+|||++.+..                .......+..+++   .....  +..++|.|+
T Consensus        76 ~~~~--~~~~~~~~~~~~~dlLilDDi~~~~~----------------~~~~~~~l~~l~n---~~~~~--~~~illits  132 (229)
T PRK06893         76 SKSQ--YFSPAVLENLEQQDLVCLDDLQAVIG----------------NEEWELAIFDLFN---RIKEQ--GKTLLLISA  132 (229)
T ss_pred             HHhh--hhhHHHHhhcccCCEEEEeChhhhcC----------------ChHHHHHHHHHHH---HHHHc--CCcEEEEeC
Confidence            4321  12234455566778999999998742                1112233444444   33222  234555555


Q ss_pred             C-CCCCCC---ccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          367 N-HKEKLD---PALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       367 N-~~~~ld---~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      | .|..++   |+|.+..+.+..++++.|+.+.+..++++.....+
T Consensus       133 ~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~  178 (229)
T PRK06893        133 DCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQRG  178 (229)
T ss_pred             CCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHcC
Confidence            4 565554   88888444567899999999999999997765443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.60  E-value=1.4e-14  Score=156.04  Aligned_cols=156  Identities=17%  Similarity=0.311  Sum_probs=117.5

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.|.+.+.    .        ...+++|||+||+|||||++|+++|+.++.             
T Consensus        10 YRP~tFddIIGQe~vv~~L~~ai~----~--------~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~   77 (709)
T PRK08691         10 WRPKTFADLVGQEHVVKALQNALD----E--------GRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQ   77 (709)
T ss_pred             hCCCCHHHHcCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccH
Confidence            456899999999988887666544    1        133578999999999999999999998753             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++..+-.+...+++++...      ....|+||||+|.+.                     ...+
T Consensus        78 sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls---------------------~~A~  136 (709)
T PRK08691         78 SCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLS---------------------KSAF  136 (709)
T ss_pred             HHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccC---------------------HHHH
Confidence                       33444444333445677777643      245799999999762                     3456


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      +.||..|+..    .+.+++|++|+.+.++.+.++.  |+ ..+.|+.++.++....+...+..++
T Consensus       137 NALLKtLEEP----p~~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEg  195 (709)
T PRK08691        137 NAMLKTLEEP----PEHVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTAQQVADHLAHVLDSEK  195 (709)
T ss_pred             HHHHHHHHhC----CCCcEEEEEeCCccccchHHHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcC
Confidence            7889888853    3457888899999999999886  87 5788999999998888887776543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=2.6e-14  Score=154.09  Aligned_cols=155  Identities=16%  Similarity=0.310  Sum_probs=116.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++++|++.+.+.|.+.+    ...        ..+..|||+||+|||||++++++|+.++.             
T Consensus        10 yRP~~f~dviGQe~vv~~L~~~l----~~~--------rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~p   77 (618)
T PRK14951         10 YRPRSFSEMVGQEHVVQALTNAL----TQQ--------RLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATP   77 (618)
T ss_pred             HCCCCHHHhcCcHHHHHHHHHHH----HcC--------CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCC
Confidence            45689999999888777655533    321        23568999999999999999999999853             


Q ss_pred             ----------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccc
Q 012016          280 ----------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQ  337 (473)
Q Consensus       280 ----------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~  337 (473)
                                      +++.++..+-.+...+++++....      ...|++|||+|.+.                    
T Consensus        78 Cg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls--------------------  137 (618)
T PRK14951         78 CGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLT--------------------  137 (618)
T ss_pred             CCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCC--------------------
Confidence                            355555544334456777776543      34699999999873                    


Q ss_pred             hhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          338 NKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       338 ~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                       ....+.||..|+..    ++..++|++|+.+.++.+.++.  |+ .+++|..++.++....+...+..+
T Consensus       138 -~~a~NaLLKtLEEP----P~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~e  199 (618)
T PRK14951        138 -NTAFNAMLKTLEEP----PEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAE  199 (618)
T ss_pred             -HHHHHHHHHhcccC----CCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHc
Confidence             34577888888753    3567888888889999989887  77 689999999999888887766544

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=4.6e-14  Score=149.86  Aligned_cols=155  Identities=21%  Similarity=0.378  Sum_probs=114.9

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.|...+.    .        ...+..+|||||||||||++|+++|+.+..             
T Consensus         8 yRP~~~~dvvGq~~v~~~L~~~i~----~--------~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~s   75 (504)
T PRK14963          8 ARPITFDEVVGQEHVKEVLLAALR----Q--------GRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECES   75 (504)
T ss_pred             hCCCCHHHhcChHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChh
Confidence            456899999999988777655443    2        123567899999999999999999998842             


Q ss_pred             ----------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHH
Q 012016          280 ----------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLS  343 (473)
Q Consensus       280 ----------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls  343 (473)
                                +++.++.....+...++++....      ..+.||||||+|.+                     ....++
T Consensus        76 c~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~l---------------------s~~a~n  134 (504)
T PRK14963         76 CLAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMM---------------------SKSAFN  134 (504)
T ss_pred             hHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECcccc---------------------CHHHHH
Confidence                      25555554333344555554332      24679999999866                     235677


Q ss_pred             HHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          344 GFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       344 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .|+..|+..    +...++|++||.+..+.+++.+  |+. +++|..++.++....+...+..+
T Consensus       135 aLLk~LEep----~~~t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls~~el~~~L~~i~~~e  191 (504)
T PRK14963        135 ALLKTLEEP----PEHVIFILATTEPEKMPPTILS--RTQ-HFRFRRLTEEEIAGKLRRLLEAE  191 (504)
T ss_pred             HHHHHHHhC----CCCEEEEEEcCChhhCChHHhc--ceE-EEEecCCCHHHHHHHHHHHHHHc
Confidence            888888753    3457888889999999999988  774 79999999999888888766544

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.59  E-value=2.5e-14  Score=152.71  Aligned_cols=155  Identities=14%  Similarity=0.301  Sum_probs=115.3

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC--------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN--------------  278 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~--------------  278 (473)
                      ..|.+|++++|++.+++.+.+.+.    .        ...+++|||+||||+|||++|+++|+.+.              
T Consensus        10 yRP~~F~dIIGQe~iv~~L~~aI~----~--------~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~   77 (605)
T PRK05896         10 YRPHNFKQIIGQELIKKILVNAIL----N--------NKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCS   77 (605)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHH----c--------CCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccH
Confidence            467899999999988877655432    1        12357899999999999999999999874              


Q ss_pred             ----------CceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          279 ----------FDVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       279 ----------~~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                .+++.++..+..+...++.+.....      ...|++|||+|.+.                     ....
T Consensus        78 sCr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt---------------------~~A~  136 (605)
T PRK05896         78 VCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLS---------------------TSAW  136 (605)
T ss_pred             HHHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCC---------------------HHHH
Confidence                      2455555544334455676665432      35699999999872                     2345


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    ++..++|++|+.+..+.+++++  |+. .++|+.++.++....+...+...
T Consensus       137 NaLLKtLEEP----p~~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~eL~~~L~~il~ke  194 (605)
T PRK05896        137 NALLKTLEEP----PKHVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNSELQELLKSIAKKE  194 (605)
T ss_pred             HHHHHHHHhC----CCcEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHHHHHHHHHHHHHHc
Confidence            7888888853    3468888888999999999998  875 79999999999887777765443

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=3.6e-14  Score=157.86  Aligned_cols=156  Identities=19%  Similarity=0.298  Sum_probs=116.8

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++|+|++.+++.|...+.    .        ....+.||||||+|||||++++++|+.|..            
T Consensus         8 KyRP~~f~eiiGqe~v~~~L~~~i~----~--------~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C   75 (824)
T PRK07764          8 RYRPATFAEVIGQEHVTEPLSTALD----S--------GRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGEC   75 (824)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHH----h--------CCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCccc
Confidence            4567999999999988877655443    1        123467999999999999999999999952            


Q ss_pred             --------------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchh
Q 012016          280 --------------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNK  339 (473)
Q Consensus       280 --------------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~  339 (473)
                                    +++.++..+......++++....      ....|+||||+|.|.                     .
T Consensus        76 ~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt---------------------~  134 (824)
T PRK07764         76 DSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVT---------------------P  134 (824)
T ss_pred             HHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcC---------------------H
Confidence                          34555544433445566654332      245799999999883                     4


Q ss_pred             HHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          340 VTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       340 ~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ...+.||+.|+..    ....+||++|+.+++|.++|+.  |+ .+++|..++.++...++...+..+
T Consensus       135 ~a~NaLLK~LEEp----P~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~E  195 (824)
T PRK07764        135 QGFNALLKIVEEP----PEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPEVMRGYLERICAQE  195 (824)
T ss_pred             HHHHHHHHHHhCC----CCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHc
Confidence            5678899999864    3568888888999999999987  77 589999999999888888776443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=3.5e-14  Score=154.33  Aligned_cols=155  Identities=17%  Similarity=0.312  Sum_probs=114.8

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc-----------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD-----------  280 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~-----------  280 (473)
                      ...|.+|++|+|++.+++.+...+.    .        ...++.||||||+|+|||++|+++|+.+...           
T Consensus        11 KyRP~~f~dIiGQe~~v~~L~~aI~----~--------~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~   78 (725)
T PRK07133         11 KYRPKTFDDIVGQDHIVQTLKNIIK----S--------NKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQE   78 (725)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhH
Confidence            3467899999999988877665543    1        1246789999999999999999999988432           


Q ss_pred             ----------eEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHH
Q 012016          281 ----------VYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSG  344 (473)
Q Consensus       281 ----------~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~  344 (473)
                                ++.++...-.+...++++...+.      ...|++|||+|.+.                     ....+.
T Consensus        79 C~~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT---------------------~~A~NA  137 (725)
T PRK07133         79 CIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLS---------------------KSAFNA  137 (725)
T ss_pred             HHHhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCC---------------------HHHHHH
Confidence                      23333322123345666665543      45799999999873                     346788


Q ss_pred             HHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          345 FLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       345 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      ||..|+..    ++.+++|++|+.++.|.+++++  |+. +++|..++.++....+...+..
T Consensus       138 LLKtLEEP----P~~tifILaTte~~KLl~TI~S--Rcq-~ieF~~L~~eeI~~~L~~il~k  192 (725)
T PRK07133        138 LLKTLEEP----PKHVIFILATTEVHKIPLTILS--RVQ-RFNFRRISEDEIVSRLEFILEK  192 (725)
T ss_pred             HHHHhhcC----CCceEEEEEcCChhhhhHHHHh--hce-eEEccCCCHHHHHHHHHHHHHH
Confidence            99988853    4568888888999999999998  884 8999999999988777765543

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=4.6e-14  Score=151.59  Aligned_cols=156  Identities=23%  Similarity=0.366  Sum_probs=116.7

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC--------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN--------------  278 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~--------------  278 (473)
                      ..|.+|++|+|++.+++.|...+.    .        ...+..|||+||+|||||++|+++|+.++              
T Consensus         7 yRP~~f~eivGq~~i~~~L~~~i~----~--------~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~   74 (584)
T PRK14952          7 YRPATFAEVVGQEHVTEPLSSALD----A--------GRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCE   74 (584)
T ss_pred             hCCCcHHHhcCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccH
Confidence            456899999999888777655433    2        12356799999999999999999999875              


Q ss_pred             ------------CceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhH
Q 012016          279 ------------FDVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKV  340 (473)
Q Consensus       279 ------------~~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~  340 (473)
                                  .+++.++.++..+-..++++....      ...-|+||||+|.+.                     ..
T Consensus        75 ~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt---------------------~~  133 (584)
T PRK14952         75 SCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVT---------------------TA  133 (584)
T ss_pred             HHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCC---------------------HH
Confidence                        245555554443445566554433      245799999999872                     34


Q ss_pred             HHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          341 TLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       341 ~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      ..+.||..|+..    +..+++|++|+.++++.++++.  |+ .+++|..++.++....+..++..++
T Consensus       134 A~NALLK~LEEp----p~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~eg  194 (584)
T PRK14952        134 GFNALLKIVEEP----PEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPRTMRALIARICEQEG  194 (584)
T ss_pred             HHHHHHHHHhcC----CCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcC
Confidence            678899998853    3568889988999999999998  75 6899999999998888877666543

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=5.5e-14  Score=149.78  Aligned_cols=155  Identities=17%  Similarity=0.319  Sum_probs=113.4

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++++|++.+++.+...+.    .        ...+..|||+||||||||++|+++|+.+..             
T Consensus        10 yRP~~f~diiGq~~~v~~L~~~i~----~--------~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~   77 (546)
T PRK14957         10 YRPQSFAEVAGQQHALNSLVHALE----T--------QKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCE   77 (546)
T ss_pred             HCcCcHHHhcCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccH
Confidence            356899999999988877655433    1        123567999999999999999999998853             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++.....+...+++++....      ...|++|||+|.+.                     ....
T Consensus        78 sC~~i~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls---------------------~~a~  136 (546)
T PRK14957         78 NCVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLS---------------------KQSF  136 (546)
T ss_pred             HHHHHhcCCCCceEEeecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhcc---------------------HHHH
Confidence                       455555433333345555554432      45799999999872                     3467


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    ++.+++|++|+.+..+.++++.  |+ ..++|..++.++....+...+..+
T Consensus       137 naLLK~LEep----p~~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls~~eI~~~L~~il~~e  194 (546)
T PRK14957        137 NALLKTLEEP----PEYVKFILATTDYHKIPVTILS--RC-IQLHLKHISQADIKDQLKIILAKE  194 (546)
T ss_pred             HHHHHHHhcC----CCCceEEEEECChhhhhhhHHH--he-eeEEeCCCCHHHHHHHHHHHHHHc
Confidence            7899988853    3457778777778889888887  77 689999999999877777665443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=3e-14  Score=152.47  Aligned_cols=154  Identities=18%  Similarity=0.331  Sum_probs=115.4

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC--------------
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF--------------  279 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~--------------  279 (473)
                      .|.+|++|+|++.+++.+.+.+.    .        ...+..|||+||||+|||++|+++|+.++.              
T Consensus        11 rP~~f~divGq~~v~~~L~~~i~----~--------~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~   78 (527)
T PRK14969         11 RPKSFSELVGQEHVVRALTNALE----Q--------QRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSA   78 (527)
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHH----c--------CCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHH
Confidence            56899999999988887655443    1        123568999999999999999999999854              


Q ss_pred             ----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHH
Q 012016          280 ----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLS  343 (473)
Q Consensus       280 ----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls  343 (473)
                                +++.++.+.-.....+++++....      ...|+||||+|.+.                     ....+
T Consensus        79 C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls---------------------~~a~n  137 (527)
T PRK14969         79 CLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLS---------------------KSAFN  137 (527)
T ss_pred             HHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCC---------------------HHHHH
Confidence                      344455443334456777766542      35799999999872                     34677


Q ss_pred             HHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          344 GFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       344 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .||..|+..    ++.+++|++|+.++.+.+.++.  |+ .+++|..++.++....+...+..+
T Consensus       138 aLLK~LEep----p~~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~i~~~L~~il~~e  194 (527)
T PRK14969        138 AMLKTLEEP----PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPLIVSHLQHILEQE  194 (527)
T ss_pred             HHHHHHhCC----CCCEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHHHHHHHHHHHHHc
Confidence            899998863    3567888888889899888887  77 689999999999887777766443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=9.6e-14  Score=142.84  Aligned_cols=156  Identities=19%  Similarity=0.350  Sum_probs=112.8

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++++|++..++.+.+.+.    .        ...+++||||||||+|||++++++|+.+..            
T Consensus        10 k~rP~~~~~iig~~~~~~~l~~~i~----~--------~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~   77 (367)
T PRK14970         10 KYRPQTFDDVVGQSHITNTLLNAIE----N--------NHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSF   77 (367)
T ss_pred             HHCCCcHHhcCCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCc
Confidence            3567899999999988776655443    1        123578999999999999999999998743            


Q ss_pred             ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc
Q 012016          280 DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW  353 (473)
Q Consensus       280 ~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  353 (473)
                      .++.++.....+...+++++..+.      .+.||+|||+|.+.                     ...++.|+..++.. 
T Consensus        78 ~~~~l~~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~---------------------~~~~~~ll~~le~~-  135 (367)
T PRK14970         78 NIFELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLS---------------------SAAFNAFLKTLEEP-  135 (367)
T ss_pred             ceEEeccccCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcC---------------------HHHHHHHHHHHhCC-
Confidence            233444333333456777766432      45799999999763                     23467788887752 


Q ss_pred             cCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          354 SSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       354 ~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                         +...++|++|+.+..+.+++.+  |+. .++++.|+.++...++...+...
T Consensus       136 ---~~~~~~Il~~~~~~kl~~~l~s--r~~-~v~~~~~~~~~l~~~l~~~~~~~  183 (367)
T PRK14970        136 ---PAHAIFILATTEKHKIIPTILS--RCQ-IFDFKRITIKDIKEHLAGIAVKE  183 (367)
T ss_pred             ---CCceEEEEEeCCcccCCHHHHh--cce-eEecCCccHHHHHHHHHHHHHHc
Confidence               3456778888888999999987  664 68999999999887777665543

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.57  E-value=3.9e-14  Score=157.73  Aligned_cols=158  Identities=18%  Similarity=0.268  Sum_probs=114.8

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEE
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYD  283 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~  283 (473)
                      .|..++.++|.++....+++.+    .++         -+.+++|+||||||||++++++|+.+          +..++.
T Consensus       177 r~~~l~~~igr~~ei~~~~~~L----~~~---------~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~  243 (731)
T TIGR02639       177 KNGKIDPLIGREDELERTIQVL----CRR---------KKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS  243 (731)
T ss_pred             hcCCCCcccCcHHHHHHHHHHH----hcC---------CCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE
Confidence            4567899999887777655433    222         25689999999999999999999987          788999


Q ss_pred             cccccccC--------chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc
Q 012016          284 LELTELRS--------NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW  353 (473)
Q Consensus       284 l~~~~~~~--------~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  353 (473)
                      ++++.+..        +..++.++..+.  .++||||||||.+.+.....         +   ......+-|+..+.   
T Consensus       244 ~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~---------~---~~~~~~~~L~~~l~---  308 (731)
T TIGR02639       244 LDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATS---------G---GSMDASNLLKPALS---  308 (731)
T ss_pred             ecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCC---------C---ccHHHHHHHHHHHh---
Confidence            99877642        257788887764  47899999999997521100         0   01112223334332   


Q ss_pred             cCCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          354 SSCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       354 ~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                         .+++.+|++||..+     ..|+||.|  ||. .|+++.|+.+++..|++....
T Consensus       309 ---~g~i~~IgaTt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~  359 (731)
T TIGR02639       309 ---SGKLRCIGSTTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKILKGLKE  359 (731)
T ss_pred             ---CCCeEEEEecCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHHHHHHH
Confidence               14688888888643     57999999  997 799999999999999996554

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.56  E-value=4e-14  Score=135.42  Aligned_cols=159  Identities=15%  Similarity=0.229  Sum_probs=102.8

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE  288 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~  288 (473)
                      ...+.+|++++..  ..+.+++.+..++..         ..++.++|+||||||||++++++++++   +.+++.+++..
T Consensus         8 ~~~~~~~~~~~~~--~~~~~~~~l~~~~~~---------~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~   76 (226)
T TIGR03420         8 LPDDPTFDNFYAG--GNAELLAALRQLAAG---------KGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAE   76 (226)
T ss_pred             CCCchhhcCcCcC--CcHHHHHHHHHHHhc---------CCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHH
Confidence            4455789998832  344555555555431         225689999999999999999999987   46788888887


Q ss_pred             ccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecC-
Q 012016          289 LRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTN-  367 (473)
Q Consensus       289 ~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN-  367 (473)
                      +..  .....+.......+|+|||+|.+..                .   ......|...++.....  +.. +|+|++ 
T Consensus        77 ~~~--~~~~~~~~~~~~~lLvIDdi~~l~~----------------~---~~~~~~L~~~l~~~~~~--~~~-iIits~~  132 (226)
T TIGR03420        77 LAQ--ADPEVLEGLEQADLVCLDDVEAIAG----------------Q---PEWQEALFHLYNRVREA--GGR-LLIAGRA  132 (226)
T ss_pred             HHH--hHHHHHhhcccCCEEEEeChhhhcC----------------C---hHHHHHHHHHHHHHHHc--CCe-EEEECCC
Confidence            642  2234444455667999999998732                1   11123344444433222  123 445554 


Q ss_pred             CCCCCC---ccccCCCce--eeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          368 HKEKLD---PALLRPGRM--DVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       368 ~~~~ld---~aLlrpgRf--d~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .+..++   +.|.+  |+  ..+|.+|.|+.+++..+++.+....
T Consensus       133 ~~~~~~~~~~~L~~--r~~~~~~i~l~~l~~~e~~~~l~~~~~~~  175 (226)
T TIGR03420       133 APAQLPLRLPDLRT--RLAWGLVFQLPPLSDEEKIAALQSRAARR  175 (226)
T ss_pred             ChHHCCcccHHHHH--HHhcCeeEecCCCCHHHHHHHHHHHHHHc
Confidence            444432   66776  65  4789999999999999988765433

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.

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

Probab=99.56  E-value=2.5e-14  Score=150.62  Aligned_cols=192  Identities=18%  Similarity=0.259  Sum_probs=131.6

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC----CceEEcccccccCc--
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN----FDVYDLELTELRSN--  292 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~----~~~~~l~~~~~~~~--  292 (473)
                      .+++..+..|++..++...+           +.-..++||+||+|||||.|++++++++.    +.+..++|+.+...  
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            46666666777665533322           22345899999999999999999999983    55667888887532  


Q ss_pred             hHHHHHHH----Hh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          293 SDLRTLLV----AT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       293 ~~l~~l~~----~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                      ..+++.+.    .+  -.|+||++||+|+++...        +...+........+..+|+.+-......+..+.+|+|.
T Consensus       477 e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~s--------~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~  548 (952)
T KOG0735|consen  477 EKIQKFLNNVFSEALWYAPSIIVLDDLDCLASAS--------SNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATG  548 (952)
T ss_pred             HHHHHHHHHHHHHHHhhCCcEEEEcchhhhhccC--------cccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEec
Confidence            33444333    33  379999999999998511        11112233344556666655433333444456889999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc-cCCHHHHHHHHhcC-CCCHHHH
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE-HILFEEIEELISTT-QVTPAEV  429 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~-~~l~~~i~~l~~~~-~~t~a~i  429 (473)
                      +....|+|-|..|++|+.++.++.|...+|.+|+.+.+.... .....+++-+..++ |+.+.|+
T Consensus       549 qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL  613 (952)
T KOG0735|consen  549 QELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDL  613 (952)
T ss_pred             hhhhhcChhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhH
Confidence            999999999999999999999999999999999999886542 23344444443333 4666555

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=4.9e-14  Score=152.43  Aligned_cols=155  Identities=16%  Similarity=0.255  Sum_probs=116.0

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.+.+.+.    .        ...++.||||||+|+|||++++++|+.++.             
T Consensus        10 ~RP~~f~~iiGq~~v~~~L~~~i~----~--------~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~   77 (576)
T PRK14965         10 YRPQTFSDLTGQEHVSRTLQNAID----T--------GRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCP   77 (576)
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccH
Confidence            356899999999988877766543    1        124678999999999999999999999853             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++..+......++++.....      ...|++|||+|.+.                     ....
T Consensus        78 ~c~~i~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt---------------------~~a~  136 (576)
T PRK14965         78 PCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLS---------------------TNAF  136 (576)
T ss_pred             HHHHHhcCCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCC---------------------HHHH
Confidence                       244555443334456666665442      34699999999872                     3467


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    ++.+++|++|+.+++|.++++.  |+ .+++|..++.++....+...+..+
T Consensus       137 naLLk~LEep----p~~~~fIl~t~~~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~L~~i~~~e  194 (576)
T PRK14965        137 NALLKTLEEP----PPHVKFIFATTEPHKVPITILS--RC-QRFDFRRIPLQKIVDRLRYIADQE  194 (576)
T ss_pred             HHHHHHHHcC----CCCeEEEEEeCChhhhhHHHHH--hh-hhhhcCCCCHHHHHHHHHHHHHHh
Confidence            8899999853    3568899999999999999997  77 478999999988777776655443

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=6.3e-14  Score=150.29  Aligned_cols=156  Identities=19%  Similarity=0.315  Sum_probs=113.1

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++|+|++.+++.|.+.+.    .        ...+..|||+||||||||++|+++|+.+..            
T Consensus         9 KyRP~sf~dIiGQe~v~~~L~~ai~----~--------~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C   76 (624)
T PRK14959          9 RYRPQTFAEVAGQETVKAILSRAAQ----E--------NRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTC   76 (624)
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHH----c--------CCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCccc
Confidence            3467999999999988766655433    1        122468999999999999999999999964            


Q ss_pred             ------------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 ------------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ------------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                                  +++.++...-.....++.+....      ....||||||+|.+.                     ...
T Consensus        77 ~sC~~i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt---------------------~~a  135 (624)
T PRK14959         77 EQCRKVTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLT---------------------REA  135 (624)
T ss_pred             HHHHHHhcCCCCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCC---------------------HHH
Confidence                        24555543222334445443222      245799999999872                     345


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .+.||..|+..    ....++|++||.+..+.+.+++  |+ .+|+|+.++.++...++...+..+
T Consensus       136 ~naLLk~LEEP----~~~~ifILaTt~~~kll~TI~S--Rc-q~i~F~pLs~~eL~~~L~~il~~e  194 (624)
T PRK14959        136 FNALLKTLEEP----PARVTFVLATTEPHKFPVTIVS--RC-QHFTFTRLSEAGLEAHLTKVLGRE  194 (624)
T ss_pred             HHHHHHHhhcc----CCCEEEEEecCChhhhhHHHHh--hh-hccccCCCCHHHHHHHHHHHHHHc
Confidence            68888888753    2458889999999999999887  87 478999999999887777655443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.56  E-value=2e-13  Score=143.58  Aligned_cols=154  Identities=19%  Similarity=0.265  Sum_probs=111.0

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.+...+.    .        ...+..||||||||+|||++|+++|+.+..             
T Consensus        11 yRP~~~~diiGq~~~v~~L~~~i~----~--------~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c   78 (451)
T PRK06305         11 YRPQTFSEILGQDAVVAVLKNALR----F--------NRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQC   78 (451)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHH----c--------CCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCccc
Confidence            456899999999988776655443    1        124678999999999999999999998742             


Q ss_pred             ------------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 ------------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ------------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                                  +++.++.....+...++.+....      ..+.|+||||+|.+.                     ...
T Consensus        79 ~~C~~i~~~~~~d~~~i~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt---------------------~~~  137 (451)
T PRK06305         79 ASCKEISSGTSLDVLEIDGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLT---------------------KEA  137 (451)
T ss_pred             HHHHHHhcCCCCceEEeeccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhC---------------------HHH
Confidence                        34444432222234454433322      356899999999873                     234


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      .+.|+..|+..    ++..++|++||.+..|.+++.+  |+. .++|+.++.++....+...+..
T Consensus       138 ~n~LLk~lEep----~~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~l~~~el~~~L~~~~~~  195 (451)
T PRK06305        138 FNSLLKTLEEP----PQHVKFFLATTEIHKIPGTILS--RCQ-KMHLKRIPEETIIDKLALIAKQ  195 (451)
T ss_pred             HHHHHHHhhcC----CCCceEEEEeCChHhcchHHHH--hce-EEeCCCCCHHHHHHHHHHHHHH
Confidence            67788888863    3457888888989999999998  774 7899999999987777765543

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.54  E-value=1.6e-13  Score=145.23  Aligned_cols=156  Identities=19%  Similarity=0.316  Sum_probs=112.4

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++++|++.+.+.+.+.+.    .        ...++.||||||||+|||++|+++|..++.             
T Consensus        10 yRP~~f~diiGq~~i~~~L~~~i~----~--------~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~   77 (486)
T PRK14953         10 YRPKFFKEVIGQEIVVRILKNAVK----L--------QRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCE   77 (486)
T ss_pred             hCCCcHHHccChHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccH
Confidence            456899999999988876655443    1        224568999999999999999999998852             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++.++..+...++.+....      ....|++|||+|.+.                     ....
T Consensus        78 nc~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt---------------------~~a~  136 (486)
T PRK14953         78 NCVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLT---------------------KEAF  136 (486)
T ss_pred             HHHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcC---------------------HHHH
Confidence                       23444443323334455544433      245799999999773                     3356


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      +.||..++..    +...++|++|+.++.+.+++.+  |+. .+.|+.++.++....+...+...+
T Consensus       137 naLLk~LEep----p~~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~ls~~el~~~L~~i~k~eg  195 (486)
T PRK14953        137 NALLKTLEEP----PPRTIFILCTTEYDKIPPTILS--RCQ-RFIFSKPTKEQIKEYLKRICNEEK  195 (486)
T ss_pred             HHHHHHHhcC----CCCeEEEEEECCHHHHHHHHHH--hce-EEEcCCCCHHHHHHHHHHHHHHcC
Confidence            7788888753    3457788888888889999887  774 799999999999888887665443

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=2.5e-13  Score=144.15  Aligned_cols=155  Identities=19%  Similarity=0.302  Sum_probs=116.6

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC--------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN--------------  278 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~--------------  278 (473)
                      ..|.+|++++|++.+++.+...+.    .        ...++.||||||||+|||++|+++|+.+.              
T Consensus         8 yRP~~fdeiiGqe~v~~~L~~~I~----~--------grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~   75 (535)
T PRK08451          8 YRPKHFDELIGQESVSKTLSLALD----N--------NRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCI   75 (535)
T ss_pred             HCCCCHHHccCcHHHHHHHHHHHH----c--------CCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccH
Confidence            457899999999988877665443    1        13467899999999999999999999872              


Q ss_pred             ----------CceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          279 ----------FDVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       279 ----------~~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                .+++.++..+-.+-..+++++....      ..-|++|||+|.+.                     ....
T Consensus        76 ~C~~~~~~~h~dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt---------------------~~A~  134 (535)
T PRK08451         76 QCQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLT---------------------KEAF  134 (535)
T ss_pred             HHHHHhhcCCCeEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC---------------------HHHH
Confidence                      2455555443333466777765532      34699999999872                     4567


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..|+..    +....+|++|+.+..+.++++.  |+ .+++|..++.++....+...+..+
T Consensus       135 NALLK~LEEp----p~~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~E  192 (535)
T PRK08451        135 NALLKTLEEP----PSYVKFILATTDPLKLPATILS--RT-QHFRFKQIPQNSIISHLKTILEKE  192 (535)
T ss_pred             HHHHHHHhhc----CCceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHHHHHHHHHHHHHHc
Confidence            8889988864    3457778888888999999998  86 589999999999877777666544

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.53  E-value=1.1e-13  Score=148.46  Aligned_cols=185  Identities=21%  Similarity=0.256  Sum_probs=121.2

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCce
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDV  281 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~  281 (473)
                      ...|.+|++++|.+...+.+...+    ..         +.+..+||+||||||||++|+++++++          +.++
T Consensus        58 ~~rp~~f~~iiGqs~~i~~l~~al----~~---------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~f  124 (531)
T TIGR02902        58 KTRPKSFDEIIGQEEGIKALKAAL----CG---------PNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAF  124 (531)
T ss_pred             hhCcCCHHHeeCcHHHHHHHHHHH----hC---------CCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCE
Confidence            356789999999988877765432    11         124689999999999999999998753          3678


Q ss_pred             EEccccccc-CchHHH-HH--------------------------HHHhccCceEEEeccccccccccCCccccCCCCCC
Q 012016          282 YDLELTELR-SNSDLR-TL--------------------------LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEG  333 (473)
Q Consensus       282 ~~l~~~~~~-~~~~l~-~l--------------------------~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~  333 (473)
                      +.++|+... ++..+. .+                          ......+++|||||||.+.                
T Consensus       125 i~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~----------------  188 (531)
T TIGR02902       125 VEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELH----------------  188 (531)
T ss_pred             EEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCC----------------
Confidence            888876421 111111 00                          0112346899999999883                


Q ss_pred             CccchhHHHHHHHHHhcccc-------------------------cCCCCceEEEEecCCCCCCCccccCCCceeeEEEe
Q 012016          334 PIQQNKVTLSGFLNFIDGLW-------------------------SSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM  388 (473)
Q Consensus       334 ~~~~~~~~ls~LL~~ldg~~-------------------------~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~  388 (473)
                           ....+.||..|+.-.                         ..+.+-++|++|||.|+.++|++++  |+. .|.|
T Consensus       189 -----~~~q~~LL~~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrs--R~~-~I~f  260 (531)
T TIGR02902       189 -----PVQMNKLLKVLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRS--RCV-EIFF  260 (531)
T ss_pred             -----HHHHHHHHHHHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhh--hhh-eeeC
Confidence                 234455665553210                         0011236677788999999999998  884 7899


Q ss_pred             CCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHHHHH
Q 012016          389 SYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       389 ~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      +.++.+++..|+++.+......+.++...++.....+.+++.+.+
T Consensus       261 ~pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll  305 (531)
T TIGR02902       261 RPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV  305 (531)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH
Confidence            999999999999998876554444444444443333445554443

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.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.53  E-value=3.3e-13  Score=132.48  Aligned_cols=145  Identities=21%  Similarity=0.225  Sum_probs=102.0

Q ss_pred             HHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHH----------
Q 012016          227 QKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLR----------  296 (473)
Q Consensus       227 ~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~----------  296 (473)
                      ..+.+++.+..++..           .+.+||+||||||||++|+++|+.+|.+++.+++..-....++.          
T Consensus         6 ~~~~l~~~~l~~l~~-----------g~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~   74 (262)
T TIGR02640         6 AVKRVTSRALRYLKS-----------GYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKK   74 (262)
T ss_pred             HHHHHHHHHHHHHhc-----------CCeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhh
Confidence            345555666655542           35799999999999999999999999999988776532211110          


Q ss_pred             -----------------------HHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc
Q 012016          297 -----------------------TLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW  353 (473)
Q Consensus       297 -----------------------~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  353 (473)
                                             .++....++.+|+||||+.+-                     ..+.+.|+..|+.-.
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~g~l~~A~~~g~~lllDEi~r~~---------------------~~~q~~Ll~~Le~~~  133 (262)
T TIGR02640        75 VHDQFIHNVVKLEDIVRQNWVDNRLTLAVREGFTLVYDEFTRSK---------------------PETNNVLLSVFEEGV  133 (262)
T ss_pred             HHHHHHHHhhhhhcccceeecCchHHHHHHcCCEEEEcchhhCC---------------------HHHHHHHHHHhcCCe
Confidence                                   112223467899999999762                     345666777775321


Q ss_pred             -cC-----------CCCceEEEEecCCC-----CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          354 -SS-----------CGDERIIVFTTNHK-----EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       354 -~~-----------~~~~~iiI~tTN~~-----~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                       .-           ...+..||+|+|..     ..++++|++  || ..+++++|+.++..+|+....+.
T Consensus       134 ~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~--R~-~~i~i~~P~~~~e~~Il~~~~~~  200 (262)
T TIGR02640       134 LELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLD--RL-ITIFMDYPDIDTETAILRAKTDV  200 (262)
T ss_pred             EEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHHh--hc-EEEECCCCCHHHHHHHHHHhhCC
Confidence             00           11245689999976     356899999  98 68999999999999999887653

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).

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.53  E-value=2.1e-13  Score=147.33  Aligned_cols=156  Identities=15%  Similarity=0.299  Sum_probs=116.5

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc-----------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD-----------  280 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~-----------  280 (473)
                      ...|.+|++|+|++.+++.|.+.+.    .       | ..+.++||+||+|+|||++|+++|+.++..           
T Consensus        17 KyRP~~f~dliGq~~~v~~L~~~~~----~-------g-ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~   84 (598)
T PRK09111         17 KYRPQTFDDLIGQEAMVRTLTNAFE----T-------G-RIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTID   84 (598)
T ss_pred             hhCCCCHHHhcCcHHHHHHHHHHHH----c-------C-CCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccc
Confidence            3567999999999988877665443    1       1 235689999999999999999999998542           


Q ss_pred             ------------------eEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCcc
Q 012016          281 ------------------VYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQ  336 (473)
Q Consensus       281 ------------------~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~  336 (473)
                                        ++.++..+..+...+++++..+.      ...|+||||+|.+.                   
T Consensus        85 ~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls-------------------  145 (598)
T PRK09111         85 LCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLS-------------------  145 (598)
T ss_pred             cCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCC-------------------
Confidence                              23333333233456777765543      45799999999872                   


Q ss_pred             chhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       337 ~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                        ....+.||..|+..    ++..++|++|+.++++.+.++.  |+ ..++|..++.++....+...+..+
T Consensus       146 --~~a~naLLKtLEeP----p~~~~fIl~tte~~kll~tI~S--Rc-q~~~f~~l~~~el~~~L~~i~~ke  207 (598)
T PRK09111        146 --TAAFNALLKTLEEP----PPHVKFIFATTEIRKVPVTVLS--RC-QRFDLRRIEADVLAAHLSRIAAKE  207 (598)
T ss_pred             --HHHHHHHHHHHHhC----CCCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHc
Confidence              34578889888753    3568888888888889889887  77 579999999999888888776544

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.53  E-value=2.3e-13  Score=146.29  Aligned_cols=155  Identities=18%  Similarity=0.290  Sum_probs=114.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.+...+.    .        ...++.||||||||+|||++|+++|+.++.             
T Consensus        10 yRP~~f~diiGqe~iv~~L~~~i~----~--------~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~   77 (563)
T PRK06647         10 RRPRDFNSLEGQDFVVETLKHSIE----S--------NKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECS   77 (563)
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHH----c--------CCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccch
Confidence            356899999999988887665543    1        123568999999999999999999999853             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++...-..-..++++...+      ....|++|||+|.+.                     ....
T Consensus        78 ~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls---------------------~~a~  136 (563)
T PRK06647         78 SCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLS---------------------NSAF  136 (563)
T ss_pred             HHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcC---------------------HHHH
Confidence                       34444433222334566655332      245799999999872                     3467


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.||..++.    ++...++|++|+.+..+.++|+.  |+. .++|..++.++....+...+...
T Consensus       137 naLLK~LEe----pp~~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~~el~~~L~~i~~~e  194 (563)
T PRK06647        137 NALLKTIEE----PPPYIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSLEKIYNMLKKVCLED  194 (563)
T ss_pred             HHHHHhhcc----CCCCEEEEEecCChHHhHHHHHH--hce-EEEecCCCHHHHHHHHHHHHHHc
Confidence            888888885    34568888888888999999988  875 68999999999888777766433

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=1.3e-13  Score=143.21  Aligned_cols=154  Identities=15%  Similarity=0.279  Sum_probs=110.0

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.+...+.    +        ...+.+||||||||+|||++|+++|+.+..             
T Consensus        10 ~RP~~~~eiiGq~~~~~~L~~~~~----~--------~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~   77 (397)
T PRK14955         10 YRPKKFADITAQEHITRTIQNSLR----M--------GRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEV   77 (397)
T ss_pred             cCCCcHhhccChHHHHHHHHHHHH----h--------CCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccC
Confidence            467899999999988876655433    1        123567999999999999999999999854             


Q ss_pred             -------------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCC
Q 012016          280 -------------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGP  334 (473)
Q Consensus       280 -------------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~  334 (473)
                                         +++.++......-..++++.....      ...|+||||+|.+.                 
T Consensus        78 ~~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~-----------------  140 (397)
T PRK14955         78 TEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLS-----------------  140 (397)
T ss_pred             CCCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCC-----------------
Confidence                               223333322223356666655542      45799999999873                 


Q ss_pred             ccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          335 IQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       335 ~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                          ....+.|+..++..    ++..++|++|+.+..+-+++.+  |+. +++|..++.++....+...+..
T Consensus       141 ----~~~~~~LLk~LEep----~~~t~~Il~t~~~~kl~~tl~s--R~~-~v~f~~l~~~ei~~~l~~~~~~  201 (397)
T PRK14955        141 ----IAAFNAFLKTLEEP----PPHAIFIFATTELHKIPATIAS--RCQ-RFNFKRIPLEEIQQQLQGICEA  201 (397)
T ss_pred             ----HHHHHHHHHHHhcC----CCCeEEEEEeCChHHhHHHHHH--HHH-HhhcCCCCHHHHHHHHHHHHHH
Confidence                23456788887743    3457777777778888888887  774 7899999998887777766543

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.52  E-value=3.1e-13  Score=146.19  Aligned_cols=154  Identities=15%  Similarity=0.288  Sum_probs=111.5

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++++|++.+++.+...+    .+        ...+.+|||+||||||||++|+++|+.+..             
T Consensus        10 yRP~~f~eivGQe~i~~~L~~~i----~~--------~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~   77 (620)
T PRK14954         10 YRPSKFADITAQEHITHTIQNSL----RM--------DRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEV   77 (620)
T ss_pred             HCCCCHHHhcCcHHHHHHHHHHH----Hc--------CCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCcccccccc
Confidence            35689999999998877654433    21        234668999999999999999999999855             


Q ss_pred             -------------------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCC
Q 012016          280 -------------------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGP  334 (473)
Q Consensus       280 -------------------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~  334 (473)
                                         +++.++.....+...++.+....      ...-|+||||+|.+.                 
T Consensus        78 ~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt-----------------  140 (620)
T PRK14954         78 TEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLS-----------------  140 (620)
T ss_pred             CCCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcC-----------------
Confidence                               22223332222345666666554      246799999999873                 


Q ss_pred             ccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          335 IQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       335 ~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                          ....+.||..|+..    ++..++|++|+.+.+|.+++..  |+ ..++|..++.++....+...+..
T Consensus       141 ----~~a~naLLK~LEeP----p~~tv~IL~t~~~~kLl~TI~S--Rc-~~vef~~l~~~ei~~~L~~i~~~  201 (620)
T PRK14954        141 ----TAAFNAFLKTLEEP----PPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPLDEIQSQLQMICRA  201 (620)
T ss_pred             ----HHHHHHHHHHHhCC----CCCeEEEEEeCChhhhhHHHHh--hc-eEEecCCCCHHHHHHHHHHHHHH
Confidence                23467888888853    3457777777888999999987  76 58999999999877777665543

>PRK08727 hypothetical protein; Validated

Probab=99.52  E-value=2.8e-13  Score=130.67  Aligned_cols=159  Identities=18%  Similarity=0.267  Sum_probs=104.5

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +......+|+++++.+.-   ....+.....        | .+...++|+||+|||||+|++|+|+++   +..+.+++.
T Consensus        10 ~~~~~~~~f~~f~~~~~n---~~~~~~~~~~--------~-~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~   77 (233)
T PRK08727         10 LRYPSDQRFDSYIAAPDG---LLAQLQALAA--------G-QSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPL   77 (233)
T ss_pred             CCCCCcCChhhccCCcHH---HHHHHHHHHh--------c-cCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeH
Confidence            344556789999866542   2222222111        1 123569999999999999999998876   667777776


Q ss_pred             ccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          287 TELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                      .+..  ..+...+....+..+|+|||++.+..                .......+..++|.+.   ..   +.-+|+|+
T Consensus        78 ~~~~--~~~~~~~~~l~~~dlLiIDDi~~l~~----------------~~~~~~~lf~l~n~~~---~~---~~~vI~ts  133 (233)
T PRK08727         78 QAAA--GRLRDALEALEGRSLVALDGLESIAG----------------QREDEVALFDFHNRAR---AA---GITLLYTA  133 (233)
T ss_pred             HHhh--hhHHHHHHHHhcCCEEEEeCcccccC----------------ChHHHHHHHHHHHHHH---Hc---CCeEEEEC
Confidence            5543  34556666777888999999998742                1112334444544432   21   23355555


Q ss_pred             C-CCCCC---CccccCCCce--eeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          367 N-HKEKL---DPALLRPGRM--DVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       367 N-~~~~l---d~aLlrpgRf--d~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      | .|..+   +|+|.+  ||  ..+++++.|+.+++..+++.....
T Consensus       134 ~~~p~~l~~~~~dL~S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~  177 (233)
T PRK08727        134 RQMPDGLALVLPDLRS--RLAQCIRIGLPVLDDVARAAVLRERAQR  177 (233)
T ss_pred             CCChhhhhhhhHHHHH--HHhcCceEEecCCCHHHHHHHHHHHHHH
Confidence            4 66654   789988  86  578999999999999999975543

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.52  E-value=2.4e-13  Score=131.29  Aligned_cols=160  Identities=16%  Similarity=0.195  Sum_probs=99.9

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT  287 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~  287 (473)
                      .+.++.+|++++-..  ...++..+..+....         ..+.++||||||||||+|++++|+++.   ..+.++++.
T Consensus        14 ~~~~~~~fd~f~~~~--n~~a~~~l~~~~~~~---------~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~   82 (235)
T PRK08084         14 YLPDDETFASFYPGD--NDSLLAALQNALRQE---------HSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLD   82 (235)
T ss_pred             CCCCcCCccccccCc--cHHHHHHHHHHHhCC---------CCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHH
Confidence            345567899987431  233445555443211         135899999999999999999999863   445555554


Q ss_pred             cccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecC
Q 012016          288 ELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTN  367 (473)
Q Consensus       288 ~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  367 (473)
                      ....  ...+++....+-.+|+|||++.+..                .......+..++|.+   ... +...+|+.+++
T Consensus        83 ~~~~--~~~~~~~~~~~~dlliiDdi~~~~~----------------~~~~~~~lf~l~n~~---~e~-g~~~li~ts~~  140 (235)
T PRK08084         83 KRAW--FVPEVLEGMEQLSLVCIDNIECIAG----------------DELWEMAIFDLYNRI---LES-GRTRLLITGDR  140 (235)
T ss_pred             HHhh--hhHHHHHHhhhCCEEEEeChhhhcC----------------CHHHHHHHHHHHHHH---HHc-CCCeEEEeCCC
Confidence            4321  1223333344457999999998742                112233344444433   221 22245555555


Q ss_pred             CCCC---CCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhC
Q 012016          368 HKEK---LDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       368 ~~~~---ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      .|..   +.|+|+.  |+.  .++++..|+.+++.++++....
T Consensus       141 ~p~~l~~~~~~L~S--Rl~~g~~~~l~~~~~~~~~~~l~~~a~  181 (235)
T PRK08084        141 PPRQLNLGLPDLAS--RLDWGQIYKLQPLSDEEKLQALQLRAR  181 (235)
T ss_pred             ChHHcCcccHHHHH--HHhCCceeeecCCCHHHHHHHHHHHHH
Confidence            6655   5789998  885  7899999999999999876443

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.52  E-value=5e-14  Score=136.25  Aligned_cols=155  Identities=22%  Similarity=0.294  Sum_probs=107.2

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------ceEEcc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------DVYDLE  285 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------~~~~l~  285 (473)
                      ...|.+|+++++++.+.+.+.+.+..  +           --..||||||||||||+.|.++|.+|.-      .+..++
T Consensus        29 KYrPkt~de~~gQe~vV~~L~~a~~~--~-----------~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~ln   95 (346)
T KOG0989|consen   29 KYRPKTFDELAGQEHVVQVLKNALLR--R-----------ILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELN   95 (346)
T ss_pred             HhCCCcHHhhcchHHHHHHHHHHHhh--c-----------CCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhc
Confidence            57789999999999888887776653  1           1247999999999999999999999954      233444


Q ss_pred             cccccCchHHH-------HHHHHh--------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhc
Q 012016          286 LTELRSNSDLR-------TLLVAT--------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID  350 (473)
Q Consensus       286 ~~~~~~~~~l~-------~l~~~~--------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld  350 (473)
                      .++-.+.+-.+       .+....        +..-|++|||.|.+.                     ..+.+.|.+.||
T Consensus        96 aSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmt---------------------sdaq~aLrr~mE  154 (346)
T KOG0989|consen   96 ASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMT---------------------SDAQAALRRTME  154 (346)
T ss_pred             ccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhh---------------------HHHHHHHHHHHh
Confidence            44432222111       111111        012699999999883                     456788889998


Q ss_pred             ccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          351 GLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       351 g~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ...    ....+|+.||.++.|.+.+..  |+. ..+|+....+....-++.....+
T Consensus       155 ~~s----~~trFiLIcnylsrii~pi~S--RC~-KfrFk~L~d~~iv~rL~~Ia~~E  204 (346)
T KOG0989|consen  155 DFS----RTTRFILICNYLSRIIRPLVS--RCQ-KFRFKKLKDEDIVDRLEKIASKE  204 (346)
T ss_pred             ccc----cceEEEEEcCChhhCChHHHh--hHH-HhcCCCcchHHHHHHHHHHHHHh
Confidence            742    458899999999999999988  875 56777766554444444444333

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.52  E-value=5.5e-13  Score=136.87  Aligned_cols=159  Identities=14%  Similarity=0.186  Sum_probs=108.3

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---------CceEEcccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---------FDVYDLELT  287 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---------~~~~~l~~~  287 (473)
                      ..+.+++.++..+.|...+...+.+         ..+.+++|+||||||||++++++++.+.         ..++.++|.
T Consensus        13 ~p~~l~gRe~e~~~l~~~l~~~~~~---------~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~   83 (365)
T TIGR02928        13 VPDRIVHRDEQIEELAKALRPILRG---------SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQ   83 (365)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECC
Confidence            3467899888888888777655542         1245799999999999999999998763         567778876


Q ss_pred             cccCch--------------------------HHHHHHHH---hccCceEEEeccccccccccCCccccCCCCCCCccch
Q 012016          288 ELRSNS--------------------------DLRTLLVA---TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQN  338 (473)
Q Consensus       288 ~~~~~~--------------------------~l~~l~~~---~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~  338 (473)
                      ...+..                          .+..++..   ..++.||+|||+|.+..                  ..
T Consensus        84 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~------------------~~  145 (365)
T TIGR02928        84 ILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVG------------------DD  145 (365)
T ss_pred             CCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhcc------------------CC
Confidence            543211                          01112221   23467999999999852                  01


Q ss_pred             hHHHHHHHHHhcccccCCCCceEEEEecCCCC---CCCccccCCCcee-eEEEeCCCCHHHHHHHHHHHhC
Q 012016          339 KVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE---KLDPALLRPGRMD-VHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       339 ~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~---~ld~aLlrpgRfd-~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ...+..|+...+. ....+..+++|+++|.++   .+++.+.+  ||. ..|+|+.++.++...++...+.
T Consensus       146 ~~~L~~l~~~~~~-~~~~~~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       146 DDLLYQLSRARSN-GDLDNAKVGVIGISNDLKFRENLDPRVKS--SLCEEEIIFPPYDAEELRDILENRAE  213 (365)
T ss_pred             cHHHHhHhccccc-cCCCCCeEEEEEEECCcchHhhcCHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHH
Confidence            2244455543211 111224588899999875   57888877  774 6799999999999999998775

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.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.50  E-value=6.8e-13  Score=134.53  Aligned_cols=155  Identities=14%  Similarity=0.242  Sum_probs=103.4

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----CceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----FDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~l~~  286 (473)
                      ...|.+|++++|.+++++.+...+    ..       +.  ..++|||||||||||++++++|+++.     .++..+++
T Consensus         8 ky~P~~~~~~~g~~~~~~~L~~~~----~~-------~~--~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~   74 (337)
T PRK12402          8 KYRPALLEDILGQDEVVERLSRAV----DS-------PN--LPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNV   74 (337)
T ss_pred             hhCCCcHHHhcCCHHHHHHHHHHH----hC-------CC--CceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEech
Confidence            456789999999888776654433    22       11  23699999999999999999999984     34566666


Q ss_pred             ccccC--------------------------chHHHHHHHHh-------ccCceEEEeccccccccccCCccccCCCCCC
Q 012016          287 TELRS--------------------------NSDLRTLLVAT-------ANRSILVVEDIDCTIDLQDRLPADIAGEGEG  333 (473)
Q Consensus       287 ~~~~~--------------------------~~~l~~l~~~~-------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~  333 (473)
                      .++..                          ...+++++...       ..+.+|+|||+|.+..               
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~---------------  139 (337)
T PRK12402         75 ADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALRE---------------  139 (337)
T ss_pred             hhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCH---------------
Confidence            54310                          01122222221       2356999999997731               


Q ss_pred             CccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          334 PIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       334 ~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                            .....|+..++...    ....+|++|+.+..+.++|..  |+ ..++|..|+.++...++...+...
T Consensus       140 ------~~~~~L~~~le~~~----~~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~~~~~~~l~~~~~~~  200 (337)
T PRK12402        140 ------DAQQALRRIMEQYS----RTCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTDDELVDVLESIAEAE  200 (337)
T ss_pred             ------HHHHHHHHHHHhcc----CCCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCHHHHHHHHHHHHHHc
Confidence                  12334555555432    234566677777778888887  76 578999999999988888876544

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=5.1e-13  Score=145.15  Aligned_cols=154  Identities=18%  Similarity=0.297  Sum_probs=113.2

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++++|++.+++.|...+..           | ....+||||||||||||++|+++|+.++.            
T Consensus         9 kyRP~~f~~liGq~~i~~~L~~~l~~-----------~-rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg   76 (620)
T PRK14948          9 KYRPQRFDELVGQEAIATTLKNALIS-----------N-RIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCG   76 (620)
T ss_pred             HhCCCcHhhccChHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCc
Confidence            34678999999998888776554431           1 12458999999999999999999999854            


Q ss_pred             --------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchh
Q 012016          280 --------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNK  339 (473)
Q Consensus       280 --------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~  339 (473)
                                    +++.++.........+++++..+.      ...|+||||+|.+.                     .
T Consensus        77 ~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt---------------------~  135 (620)
T PRK14948         77 KCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLS---------------------T  135 (620)
T ss_pred             ccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccC---------------------H
Confidence                          344444433234457777776543      34799999999872                     3


Q ss_pred             HHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          340 VTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       340 ~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ...+.||..|+..    ....++|++|+.++.+.++|+.  |+ ..++|+.++.++....+.....
T Consensus       136 ~a~naLLK~LEeP----p~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~~ei~~~L~~ia~  194 (620)
T PRK14948        136 AAFNALLKTLEEP----PPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPLEAMVQHLSEIAE  194 (620)
T ss_pred             HHHHHHHHHHhcC----CcCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHH
Confidence            4678899999853    3558888888889999999987  77 5689999988876665555443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.50  E-value=2.4e-13  Score=143.58  Aligned_cols=192  Identities=18%  Similarity=0.263  Sum_probs=119.3

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLE  285 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~  285 (473)
                      .+.+..+|++++..+.-+ .....+..+...+      |.. .+.++||||||||||+|++|+|+++     +..+++++
T Consensus       114 ~l~~~~tfd~fv~g~~n~-~a~~~~~~~~~~~------~~~-~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~  185 (450)
T PRK00149        114 PLNPKYTFDNFVVGKSNR-LAHAAALAVAENP------GKA-YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVT  185 (450)
T ss_pred             CCCCCCcccccccCCCcH-HHHHHHHHHHhCc------Ccc-CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEE
Confidence            355567899976433222 2333333333321      222 3579999999999999999999998     56688888


Q ss_pred             cccccC-------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          286 LTELRS-------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       286 ~~~~~~-------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      +.++..       ......+.....+..+|+|||||.+..                .   ..+...|+..++.+...  .
T Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~----------------~---~~~~~~l~~~~n~l~~~--~  244 (450)
T PRK00149        186 SEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAG----------------K---ERTQEEFFHTFNALHEA--G  244 (450)
T ss_pred             HHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcC----------------C---HHHHHHHHHHHHHHHHC--C
Confidence            766421       112223333445678999999998742                1   11233455555544333  2


Q ss_pred             ceEEEEecCCCCC---CCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHH-HHhcCCCCHHHHHHH
Q 012016          359 ERIIVFTTNHKEK---LDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEE-LISTTQVTPAEVAEQ  432 (473)
Q Consensus       359 ~~iiI~tTN~~~~---ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~-l~~~~~~t~a~i~~~  432 (473)
                      ..+||.++..|..   ++++|..  ||.  ..+++..|+.++|..|++..+...+..+.+++.. +++...-+..++...
T Consensus       245 ~~iiits~~~p~~l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~R~l~~~  322 (450)
T PRK00149        245 KQIVLTSDRPPKELPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVRELEGA  322 (450)
T ss_pred             CcEEEECCCCHHHHHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCcCCCHHHHHHH
Confidence            2455555555544   6788887  885  6899999999999999999887655445444444 444445555555444


Q ss_pred             H
Q 012016          433 L  433 (473)
Q Consensus       433 l  433 (473)
                      +
T Consensus       323 l  323 (450)
T PRK00149        323 L  323 (450)
T ss_pred             H
Confidence            3

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.49  E-value=3.9e-13  Score=140.10  Aligned_cols=190  Identities=17%  Similarity=0.225  Sum_probs=117.1

Q ss_pred             CCCCCCccccc-cchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcc
Q 012016          212 LDHPATFETLA-MEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLE  285 (473)
Q Consensus       212 ~~~p~~f~~l~-~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~  285 (473)
                      +.+..+|++++ |...  ......+..+...+      |. ....++||||||||||+|++|+|+++     +..++.++
T Consensus       103 l~~~~tfd~fi~g~~n--~~a~~~~~~~~~~~------~~-~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~  173 (405)
T TIGR00362       103 LNPKYTFDNFVVGKSN--RLAHAAALAVAENP------GK-AYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVS  173 (405)
T ss_pred             CCCCCcccccccCCcH--HHHHHHHHHHHhCc------Cc-cCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEE
Confidence            44557899954 4332  22333333333321      11 23569999999999999999999987     57788888


Q ss_pred             cccccC-------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          286 LTELRS-------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       286 ~~~~~~-------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      +.++..       ...+........+..+|+|||+|.+..                .   ..+...|++.++.+...  +
T Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~----------------~---~~~~~~l~~~~n~~~~~--~  232 (405)
T TIGR00362       174 SEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAG----------------K---ERTQEEFFHTFNALHEN--G  232 (405)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcC----------------C---HHHHHHHHHHHHHHHHC--C
Confidence            765421       111222233344578999999998742                1   11223344544444332  2


Q ss_pred             ceEEEEecCCCC---CCCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHH-HHhcCCCCHHHHHHH
Q 012016          359 ERIIVFTTNHKE---KLDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEE-LISTTQVTPAEVAEQ  432 (473)
Q Consensus       359 ~~iiI~tTN~~~---~ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~-l~~~~~~t~a~i~~~  432 (473)
                      ..+||.++..|.   .+++.|..  ||.  ..++++.|+.++|..|++..+...+..+.+++.. +++...-+..++...
T Consensus       233 ~~iiits~~~p~~l~~l~~~l~S--Rl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~~~~~r~l~~~  310 (405)
T TIGR00362       233 KQIVLTSDRPPKELPGLEERLRS--RFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVRELEGA  310 (405)
T ss_pred             CCEEEecCCCHHHHhhhhhhhhh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHHH
Confidence            345555555554   46688887  886  5899999999999999999887665555454443 444445556655444


Q ss_pred             H
Q 012016          433 L  433 (473)
Q Consensus       433 l  433 (473)
                      +
T Consensus       311 l  311 (405)
T TIGR00362       311 L  311 (405)
T ss_pred             H
Confidence            3

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).

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.49  E-value=4.9e-13  Score=128.35  Aligned_cols=157  Identities=13%  Similarity=0.234  Sum_probs=99.3

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      .+...|.+|+++.+..  .+.++..+..+..        +....++++|+||||||||+|++++++++   +.+++.+++
T Consensus         9 ~~~~~~~~~d~f~~~~--~~~~~~~l~~~~~--------~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~   78 (227)
T PRK08903          9 LGPPPPPTFDNFVAGE--NAELVARLRELAA--------GPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDA   78 (227)
T ss_pred             CCCCChhhhcccccCC--cHHHHHHHHHHHh--------ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeh
Confidence            3455668899987332  1233343443332        22335689999999999999999999976   667888887


Q ss_pred             ccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          287 TELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                      .....      .+.......+|+|||+|.+..                  ....   .|+..++.....  ...++|+|+
T Consensus        79 ~~~~~------~~~~~~~~~~liiDdi~~l~~------------------~~~~---~L~~~~~~~~~~--~~~~vl~~~  129 (227)
T PRK08903         79 ASPLL------AFDFDPEAELYAVDDVERLDD------------------AQQI---ALFNLFNRVRAH--GQGALLVAG  129 (227)
T ss_pred             HHhHH------HHhhcccCCEEEEeChhhcCc------------------hHHH---HHHHHHHHHHHc--CCcEEEEeC
Confidence            66421      123344678999999998731                  1222   344444433222  234455555


Q ss_pred             CCCC---CCCccccCCCce--eeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          367 NHKE---KLDPALLRPGRM--DVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       367 N~~~---~ld~aLlrpgRf--d~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.+.   .+.+.|..  ||  ...|+++.|+.+++..++..+....
T Consensus       130 ~~~~~~~~l~~~L~s--r~~~~~~i~l~pl~~~~~~~~l~~~~~~~  173 (227)
T PRK08903        130 PAAPLALPLREDLRT--RLGWGLVYELKPLSDADKIAALKAAAAER  173 (227)
T ss_pred             CCCHHhCCCCHHHHH--HHhcCeEEEecCCCHHHHHHHHHHHHHHc
Confidence            5432   34566776  66  5799999999998888777654433

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.49  E-value=7.5e-13  Score=143.81  Aligned_cols=155  Identities=16%  Similarity=0.286  Sum_probs=111.8

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++|+|++.+++.|...+.    .        ...+..||||||||+|||++++++|+.++.             
T Consensus        10 yRP~~~~eiiGq~~~~~~L~~~i~----~--------~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c   77 (585)
T PRK14950         10 WRSQTFAELVGQEHVVQTLRNAIA----E--------GRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTC   77 (585)
T ss_pred             hCCCCHHHhcCCHHHHHHHHHHHH----h--------CCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccC
Confidence            457899999999998887655443    1        123557999999999999999999998742             


Q ss_pred             ------------ceEEcccccccCchHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 ------------DVYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ------------~~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                                  +++.++.+...+...++++....      ....|+||||+|.+.                     ...
T Consensus        78 ~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~---------------------~~a  136 (585)
T PRK14950         78 EMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLS---------------------TAA  136 (585)
T ss_pred             HHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCC---------------------HHH
Confidence                        23444443333345566655433      245799999999772                     345


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ++.||..|+..    ....++|++|+.++.+.+.+..  |+. .++|..++..+...++...+...
T Consensus       137 ~naLLk~LEep----p~~tv~Il~t~~~~kll~tI~S--R~~-~i~f~~l~~~el~~~L~~~a~~e  195 (585)
T PRK14950        137 FNALLKTLEEP----PPHAIFILATTEVHKVPATILS--RCQ-RFDFHRHSVADMAAHLRKIAAAE  195 (585)
T ss_pred             HHHHHHHHhcC----CCCeEEEEEeCChhhhhHHHHh--ccc-eeeCCCCCHHHHHHHHHHHHHHc
Confidence            77888888864    2457888888888888888887  764 68999999998887777665443

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

Probab=99.49  E-value=7.2e-13  Score=140.89  Aligned_cols=168  Identities=17%  Similarity=0.220  Sum_probs=121.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc------CchHHHHHHHHhc--cCceEEEeccccccccccCC
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR------SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRL  323 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~------~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~  323 (473)
                      ....+||+|+||||||+++++.|.++|.+++.++|.++.      ++..+...|..+.  +|+|||+-++|.+.-.++  
T Consensus       430 ~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~d--  507 (953)
T KOG0736|consen  430 LNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQD--  507 (953)
T ss_pred             cceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCC--
Confidence            345699999999999999999999999999999998873      3456777777664  799999999998863111  


Q ss_pred             ccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          324 PADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                              .+.+-.....+..++. +|... .....+|+|+||+..+.+++.+.+  -|-..|.++.|+.++|.+|++.|
T Consensus       508 --------gged~rl~~~i~~~ls-~e~~~-~~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y  575 (953)
T KOG0736|consen  508 --------GGEDARLLKVIRHLLS-NEDFK-FSCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWY  575 (953)
T ss_pred             --------CchhHHHHHHHHHHHh-ccccc-CCCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHH
Confidence                    1222222333444443 23222 233569999999999999999998  88889999999999999999999


Q ss_pred             hCccccCCHHHHHHHHhc-CCCCHHHHHHHH
Q 012016          404 LGIKEHILFEEIEELIST-TQVTPAEVAEQL  433 (473)
Q Consensus       404 l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l  433 (473)
                      +.....--......++.. .+++.+++..+.
T Consensus       576 ~~~~~~n~~v~~k~~a~~t~gfs~~~L~~l~  606 (953)
T KOG0736|consen  576 LNHLPLNQDVNLKQLARKTSGFSFGDLEALV  606 (953)
T ss_pred             HhccccchHHHHHHHHHhcCCCCHHHHHHHh
Confidence            875432222233344443 368888875543

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.49  E-value=7.9e-13  Score=143.64  Aligned_cols=156  Identities=19%  Similarity=0.344  Sum_probs=118.3

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-------------  278 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-------------  278 (473)
                      ...|.+|++|+|++.+++.+...+.    .        ...++.||||||+|+|||++++++|+.+.             
T Consensus        10 kyRP~~f~~viGq~~~~~~L~~~i~----~--------~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~   77 (614)
T PRK14971         10 KYRPSTFESVVGQEALTTTLKNAIA----T--------NKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNE   77 (614)
T ss_pred             HHCCCCHHHhcCcHHHHHHHHHHHH----c--------CCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCc
Confidence            4567999999999988887766543    1        22467899999999999999999999874             


Q ss_pred             ------------CceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhH
Q 012016          279 ------------FDVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKV  340 (473)
Q Consensus       279 ------------~~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~  340 (473)
                                  .+++.++..+......++.++..+.      ..-|++|||+|.+.                     ..
T Consensus        78 C~sC~~~~~~~~~n~~~ld~~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls---------------------~~  136 (614)
T PRK14971         78 CESCVAFNEQRSYNIHELDAASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLS---------------------QA  136 (614)
T ss_pred             chHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCC---------------------HH
Confidence                        4556666654444466777775543      35699999999872                     34


Q ss_pred             HHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          341 TLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       341 ~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ..+.||..|+..    +...++|++|+.+.++-++|+.  |+ ..++|..++.++....+...+..+
T Consensus       137 a~naLLK~LEep----p~~tifIL~tt~~~kIl~tI~S--Rc-~iv~f~~ls~~ei~~~L~~ia~~e  196 (614)
T PRK14971        137 AFNAFLKTLEEP----PSYAIFILATTEKHKILPTILS--RC-QIFDFNRIQVADIVNHLQYVASKE  196 (614)
T ss_pred             HHHHHHHHHhCC----CCCeEEEEEeCCchhchHHHHh--hh-heeecCCCCHHHHHHHHHHHHHHc
Confidence            577899988863    3457888888888999999998  77 469999999999887777665544

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.48  E-value=2.7e-13  Score=149.21  Aligned_cols=152  Identities=21%  Similarity=0.292  Sum_probs=105.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN  292 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~  292 (473)
                      ..|.+|++++|++..... ...+...+....         ..++|||||||||||++|+++|+.++.+++.+++... ..
T Consensus        22 ~RP~tldd~vGQe~ii~~-~~~L~~~i~~~~---------~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~~~-~i   90 (725)
T PRK13341         22 LRPRTLEEFVGQDHILGE-GRLLRRAIKADR---------VGSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVLA-GV   90 (725)
T ss_pred             cCCCcHHHhcCcHHHhhh-hHHHHHHHhcCC---------CceEEEECCCCCCHHHHHHHHHHHhcCcceeehhhhh-hh
Confidence            457999999998876643 112222332211         2479999999999999999999999999888887642 22


Q ss_pred             hHHHHHHHHh-------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          293 SDLRTLLVAT-------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       293 ~~l~~l~~~~-------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                      ..++..+...       ....+|||||||.+..                     .....|+..++.      ..+++|++
T Consensus        91 ~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~---------------------~qQdaLL~~lE~------g~IiLI~a  143 (725)
T PRK13341         91 KDLRAEVDRAKERLERHGKRTILFIDEVHRFNK---------------------AQQDALLPWVEN------GTITLIGA  143 (725)
T ss_pred             HHHHHHHHHHHHHhhhcCCceEEEEeChhhCCH---------------------HHHHHHHHHhcC------ceEEEEEe
Confidence            3344333322       3467999999998731                     223456666653      23566664


Q ss_pred             c--CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          366 T--NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       366 T--N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      |  |....+++++++  |+ ..++|+.++.+++..++.+++.
T Consensus       144 TTenp~~~l~~aL~S--R~-~v~~l~pLs~edi~~IL~~~l~  182 (725)
T PRK13341        144 TTENPYFEVNKALVS--RS-RLFRLKSLSDEDLHQLLKRALQ  182 (725)
T ss_pred             cCCChHhhhhhHhhc--cc-cceecCCCCHHHHHHHHHHHHH
Confidence            4  333578899998  65 4689999999999999998875

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.48  E-value=7.9e-13  Score=148.63  Aligned_cols=157  Identities=17%  Similarity=0.255  Sum_probs=110.2

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEE
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYD  283 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~  283 (473)
                      .|..++.++|.++....+++.+.    ++         .+.+.+|+||||||||++++.+|..+          +..++.
T Consensus       182 r~~~ld~~iGr~~ei~~~i~~l~----r~---------~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~  248 (852)
T TIGR03345       182 REGKIDPVLGRDDEIRQMIDILL----RR---------RQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLS  248 (852)
T ss_pred             cCCCCCcccCCHHHHHHHHHHHh----cC---------CcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEE
Confidence            45689999998876555554332    21         24689999999999999999999986          356787


Q ss_pred             cccccccC--------chHHHHHHHHhc---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc
Q 012016          284 LELTELRS--------NSDLRTLLVATA---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       284 l~~~~~~~--------~~~l~~l~~~~~---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  352 (473)
                      ++++.+..        ...++.++....   .++|||||||+.+....+.         .+    .....+-|+..+.  
T Consensus       249 l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~---------~~----~~d~~n~Lkp~l~--  313 (852)
T TIGR03345       249 LDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQ---------AG----QGDAANLLKPALA--  313 (852)
T ss_pred             eehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCc---------cc----cccHHHHhhHHhh--
Confidence            87776531        256777887653   5789999999999752110         00    0111122333332  


Q ss_pred             ccCCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          353 WSSCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       353 ~~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                          .+++.+|+||+..+     .+||||.|  ||. .|.++.|+.++...|++.+..
T Consensus       314 ----~G~l~~IgaTT~~e~~~~~~~d~AL~r--Rf~-~i~v~eps~~~~~~iL~~~~~  364 (852)
T TIGR03345       314 ----RGELRTIAATTWAEYKKYFEKDPALTR--RFQ-VVKVEEPDEETAIRMLRGLAP  364 (852)
T ss_pred             ----CCCeEEEEecCHHHHhhhhhccHHHHH--hCe-EEEeCCCCHHHHHHHHHHHHH
Confidence                24688888888643     48999999  996 799999999999999765443

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.

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.47  E-value=8.1e-13  Score=136.97  Aligned_cols=177  Identities=21%  Similarity=0.226  Sum_probs=114.1

Q ss_pred             Cccc-cccchHHHHHHHHHHHHHHhchhHHhhh--cC-CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-
Q 012016          217 TFET-LAMEQEQKTKIMQDLERFVKRKDYYRRV--GK-AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-  291 (473)
Q Consensus       217 ~f~~-l~~~~~~k~~l~~~l~~fl~~~~~y~~~--g~-~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-  291 (473)
                      .++. |+|+++.|+.+...+.+..++-......  +. .++.++||+||||||||++|+++|+.++.|++.++++.+.. 
T Consensus        68 ~L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~  147 (412)
T PRK05342         68 HLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEA  147 (412)
T ss_pred             HHhhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccC
Confidence            3543 7999999998877665544332111000  11 23578999999999999999999999999999999887632 


Q ss_pred             -------chHHHHHHHH------hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc----
Q 012016          292 -------NSDLRTLLVA------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS----  354 (473)
Q Consensus       292 -------~~~l~~l~~~------~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~----  354 (473)
                             ...+..++..      ...++||||||||.+.....  .  .   ....+.........||+.|||-..    
T Consensus       148 gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~--~--~---~~~~d~s~~~vQ~~LL~~Leg~~~~v~~  220 (412)
T PRK05342        148 GYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSE--N--P---SITRDVSGEGVQQALLKILEGTVASVPP  220 (412)
T ss_pred             CcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccC--C--C---CcCCCcccHHHHHHHHHHHhcCeEEeCC
Confidence                   1223333322      23679999999999964210  0  0   001111223577889999987421    


Q ss_pred             CC-----CCceEEEEecCCCC----------------------------------------------------CCCcccc
Q 012016          355 SC-----GDERIIVFTTNHKE----------------------------------------------------KLDPALL  377 (473)
Q Consensus       355 ~~-----~~~~iiI~tTN~~~----------------------------------------------------~ld~aLl  377 (473)
                      ..     ..+.++|.|+|-..                                                    .+.|+|+
T Consensus       221 ~gg~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEfl  300 (412)
T PRK05342        221 QGGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFI  300 (412)
T ss_pred             CCCcCcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHh
Confidence            11     12346777777510                                                    0233344


Q ss_pred             CCCceeeEEEeCCCCHHHHHHHHHH
Q 012016          378 RPGRMDVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       378 rpgRfd~~I~~~~p~~~~r~~l~~~  402 (473)
                        ||+|..+.|...+.+....|+..
T Consensus       301 --gRld~iv~f~~L~~~~L~~Il~~  323 (412)
T PRK05342        301 --GRLPVVATLEELDEEALVRILTE  323 (412)
T ss_pred             --CCCCeeeecCCCCHHHHHHHHHH
Confidence              59999999999999999888874

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.47  E-value=5.4e-13  Score=148.48  Aligned_cols=158  Identities=22%  Similarity=0.224  Sum_probs=114.9

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchH-----
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSD-----  294 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~-----  294 (473)
                      +..|.+++|+.|++.+......       +......++|+||||||||++++++|+.++.+++.++++.+.+...     
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~~-------~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~  395 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSRV-------NKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHR  395 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHhc-------ccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccch
Confidence            4788999999998877643321       1223446999999999999999999999999999988877643322     


Q ss_pred             ----------HHHHHHHhc-cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc----cc-----
Q 012016          295 ----------LRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL----WS-----  354 (473)
Q Consensus       295 ----------l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~----~~-----  354 (473)
                                +.+.+.... ...||+|||||.+....                 .....+.|+..+|.-    +.     
T Consensus       396 ~~~~g~~~G~~~~~l~~~~~~~~villDEidk~~~~~-----------------~g~~~~aLlevld~~~~~~~~d~~~~  458 (784)
T PRK10787        396 RTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSDM-----------------RGDPASALLEVLDPEQNVAFSDHYLE  458 (784)
T ss_pred             hccCCCCCcHHHHHHHhcCCCCCEEEEEChhhccccc-----------------CCCHHHHHHHHhccccEEEEeccccc
Confidence                      223333332 45699999999885310                 112356777777631    00     


Q ss_pred             --CCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          355 --SCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       355 --~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                        ..-.++++|+|+|.. .++|+|+.  ||. .|.++.++.++..+|+++++.
T Consensus       459 ~~~dls~v~~i~TaN~~-~i~~aLl~--R~~-ii~~~~~t~eek~~Ia~~~L~  507 (784)
T PRK10787        459 VDYDLSDVMFVATSNSM-NIPAPLLD--RME-VIRLSGYTEDEKLNIAKRHLL  507 (784)
T ss_pred             ccccCCceEEEEcCCCC-CCCHHHhc--cee-eeecCCCCHHHHHHHHHHhhh
Confidence              011458999999987 59999999  996 689999999999999999984

>PRK05642 DNA replication initiation factor; Validated

Probab=99.46  E-value=1.8e-12  Score=125.08  Aligned_cols=162  Identities=18%  Similarity=0.197  Sum_probs=102.5

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +...+..+|++++...  ....+..+..+.....      ....+.++||||+|||||+|++|+|+++   +..+++++.
T Consensus        10 ~~~~~~~tfdnF~~~~--~~~a~~~~~~~~~~~~------~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~   81 (234)
T PRK05642         10 VRLRDDATFANYYPGA--NAAALGYVERLCEADA------GWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL   81 (234)
T ss_pred             CCCCCcccccccCcCC--hHHHHHHHHHHhhccc------cCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH
Confidence            4455667999987332  2344444444432111      1113679999999999999999999875   577888887


Q ss_pred             ccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          287 TELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                      .++...  ...++....+..+|+|||++.+..                .....   ..|++.++.....  +..+||.++
T Consensus        82 ~~~~~~--~~~~~~~~~~~d~LiiDDi~~~~~----------------~~~~~---~~Lf~l~n~~~~~--g~~ilits~  138 (234)
T PRK05642         82 AELLDR--GPELLDNLEQYELVCLDDLDVIAG----------------KADWE---EALFHLFNRLRDS--GRRLLLAAS  138 (234)
T ss_pred             HHHHhh--hHHHHHhhhhCCEEEEechhhhcC----------------ChHHH---HHHHHHHHHHHhc--CCEEEEeCC
Confidence            765421  223344444557999999997732                11122   3344444443322  235555555


Q ss_pred             CCCCC---CCccccCCCce--eeEEEeCCCCHHHHHHHHHHHh
Q 012016          367 NHKEK---LDPALLRPGRM--DVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       367 N~~~~---ld~aLlrpgRf--d~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      ..|..   ..|+|+.  ||  ...+.+..|+.+.+..+++...
T Consensus       139 ~~p~~l~~~~~~L~S--Rl~~gl~~~l~~~~~e~~~~il~~ka  179 (234)
T PRK05642        139 KSPRELPIKLPDLKS--RLTLALVFQMRGLSDEDKLRALQLRA  179 (234)
T ss_pred             CCHHHcCccCccHHH--HHhcCeeeecCCCCHHHHHHHHHHHH
Confidence            55533   3688888  87  4778889999999999988543

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.46  E-value=4.7e-13  Score=147.97  Aligned_cols=154  Identities=19%  Similarity=0.317  Sum_probs=106.3

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLEL  286 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~  286 (473)
                      .++.++|.++....+++.+..    +         -+.++||+||||||||++++++|..+          +..++.++.
T Consensus       184 ~~~~liGR~~ei~~~i~iL~r----~---------~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~  250 (758)
T PRK11034        184 GIDPLIGREKELERAIQVLCR----R---------RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI  250 (758)
T ss_pred             CCCcCcCCCHHHHHHHHHHhc----c---------CCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccH
Confidence            466788877777766654442    1         24688999999999999999999874          566777766


Q ss_pred             ccccC--------chHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHH-HhcccccC
Q 012016          287 TELRS--------NSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN-FIDGLWSS  355 (473)
Q Consensus       287 ~~~~~--------~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~-~ldg~~~~  355 (473)
                      ..+..        +..++.++...  ..++||||||||.+++....            .. ....+..+|. .+.     
T Consensus       251 ~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~------------~~-g~~d~~nlLkp~L~-----  312 (758)
T PRK11034        251 GSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAA------------SG-GQVDAANLIKPLLS-----  312 (758)
T ss_pred             HHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCC------------CC-cHHHHHHHHHHHHh-----
Confidence            55421        23456666544  35789999999999752110            00 1111222222 221     


Q ss_pred             CCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          356 CGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       356 ~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                       .+++.+|++||.++     ..||+|.|  ||+ .|+++.|+.+++..|++.+..
T Consensus       313 -~g~i~vIgATt~~E~~~~~~~D~AL~r--RFq-~I~v~ePs~~~~~~IL~~~~~  363 (758)
T PRK11034        313 -SGKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKP  363 (758)
T ss_pred             -CCCeEEEecCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHH
Confidence             24688999998865     57999999  996 799999999999999986543

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.45  E-value=2.9e-12  Score=132.96  Aligned_cols=158  Identities=17%  Similarity=0.212  Sum_probs=106.5

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcccccccC
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTELRS  291 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~~~~  291 (473)
                      ..+.+++.++..++|...+...+.+.         .+.+++||||||||||++++.+++.+     +..++.+++....+
T Consensus        28 ~P~~l~~Re~e~~~l~~~l~~~~~~~---------~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~   98 (394)
T PRK00411         28 VPENLPHREEQIEELAFALRPALRGS---------RPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRT   98 (394)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHhCCC---------CCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCC
Confidence            44678887777777776665554321         14579999999999999999999987     57788888754321


Q ss_pred             c-----------------------hHH-HHHH---HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHH
Q 012016          292 N-----------------------SDL-RTLL---VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSG  344 (473)
Q Consensus       292 ~-----------------------~~l-~~l~---~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~  344 (473)
                      .                       ..+ ..+.   .....+.||+|||+|.+..                 ......+..
T Consensus        99 ~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~-----------------~~~~~~l~~  161 (394)
T PRK00411         99 RYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFE-----------------KEGNDVLYS  161 (394)
T ss_pred             HHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhc-----------------cCCchHHHH
Confidence            1                       111 1111   1122457999999998851                 012345666


Q ss_pred             HHHHhcccccCCCCceEEEEecCCC---CCCCccccCCCce-eeEEEeCCCCHHHHHHHHHHHhC
Q 012016          345 FLNFIDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRM-DVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       345 LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRf-d~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      |++.++...   +.++.+|+++|..   +.+++.+.+  |+ ...|+|+.++.++...++...+.
T Consensus       162 l~~~~~~~~---~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~  221 (394)
T PRK00411        162 LLRAHEEYP---GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVE  221 (394)
T ss_pred             HHHhhhccC---CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHH
Confidence            666655432   2357788888876   456777765  55 36789999999999999988764

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.45  E-value=4.8e-13  Score=150.75  Aligned_cols=157  Identities=19%  Similarity=0.267  Sum_probs=111.9

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEE
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYD  283 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~  283 (473)
                      .|-.++.++|.+.....+++.|.    ++         .+.+++|+||||||||++++++|..+          +.+++.
T Consensus       173 r~~~l~~vigr~~ei~~~i~iL~----r~---------~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~  239 (857)
T PRK10865        173 EQGKLDPVIGRDEEIRRTIQVLQ----RR---------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA  239 (857)
T ss_pred             hcCCCCcCCCCHHHHHHHHHHHh----cC---------CcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEE
Confidence            35678999998876665555443    22         24689999999999999999999988          789999


Q ss_pred             cccccccC--------chHHHHHHHHh---ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc
Q 012016          284 LELTELRS--------NSDLRTLLVAT---ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       284 l~~~~~~~--------~~~l~~l~~~~---~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  352 (473)
                      ++++.+..        +..++.+|...   ..++||||||+|.+.+....         .+.    ....+-|...+.  
T Consensus       240 l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~---------~~~----~d~~~~lkp~l~--  304 (857)
T PRK10865        240 LDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKA---------DGA----MDAGNMLKPALA--  304 (857)
T ss_pred             EehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCC---------ccc----hhHHHHhcchhh--
Confidence            88877532        23577777654   35789999999999752110         011    111111222221  


Q ss_pred             ccCCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          353 WSSCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       353 ~~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                          .+++.+|++|+..+     .+|+||.|  ||+ .|.++.|+.+++..|++....
T Consensus       305 ----~g~l~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~~iL~~l~~  355 (857)
T PRK10865        305 ----RGELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAILRGLKE  355 (857)
T ss_pred             ----cCCCeEEEcCCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHHHHHHHHhh
Confidence                24688999888876     48999999  997 589999999999998876543

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.45  E-value=1.1e-12  Score=140.20  Aligned_cols=192  Identities=18%  Similarity=0.216  Sum_probs=119.5

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLE  285 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~  285 (473)
                      .+....+|++++..+.-. .....+......      .+. +.+.++|||++|||||+|++|||+++     ++.+++++
T Consensus       280 ~L~~~~TFDnFvvG~sN~-~A~aaa~avae~------~~~-~~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yit  351 (617)
T PRK14086        280 RLNPKYTFDTFVIGASNR-FAHAAAVAVAEA------PAK-AYNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVS  351 (617)
T ss_pred             CCCCCCCHhhhcCCCccH-HHHHHHHHHHhC------ccc-cCCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee
Confidence            345556899987544322 122222222221      121 23459999999999999999999987     57888888


Q ss_pred             cccccC-------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          286 LTELRS-------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       286 ~~~~~~-------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      +.++..       +..+..+.....+..+|+||||+.+..                ..   .+...|++.++.+...   
T Consensus       352 aeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~g----------------ke---~tqeeLF~l~N~l~e~---  409 (617)
T PRK14086        352 SEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLED----------------KE---STQEEFFHTFNTLHNA---  409 (617)
T ss_pred             HHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccC----------------CH---HHHHHHHHHHHHHHhc---
Confidence            766521       111222223345678999999998843                11   1223344444444332   


Q ss_pred             ceEEEEecCCC----CCCCccccCCCce--eeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHH-hcCCCCHHHHHH
Q 012016          359 ERIIVFTTNHK----EKLDPALLRPGRM--DVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELI-STTQVTPAEVAE  431 (473)
Q Consensus       359 ~~iiI~tTN~~----~~ld~aLlrpgRf--d~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~-~~~~~t~a~i~~  431 (473)
                      +.-||+|+|.+    ..+++.|.+  ||  ...+++..|+.+.|..|++.........+.+++...+ ....-+..++..
T Consensus       410 gk~IIITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~PD~EtR~aIL~kka~~r~l~l~~eVi~yLa~r~~rnvR~Leg  487 (617)
T PRK14086        410 NKQIVLSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPPELETRIAILRKKAVQEQLNAPPEVLEFIASRISRNIRELEG  487 (617)
T ss_pred             CCCEEEecCCChHhhhhccHHHHh--hhhcCceEEcCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhccCCHHHHHH
Confidence            13344566654    357888988  88  5677999999999999999988776666666665554 344455566655


Q ss_pred             HHh
Q 012016          432 QLM  434 (473)
Q Consensus       432 ~l~  434 (473)
                      .|.
T Consensus       488 aL~  490 (617)
T PRK14086        488 ALI  490 (617)
T ss_pred             HHH
Confidence            443

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.45  E-value=1.3e-12  Score=144.45  Aligned_cols=159  Identities=13%  Similarity=0.277  Sum_probs=111.5

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHH
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLL  299 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~  299 (473)
                      .|+|+++.++.|.+.+.....+-.   .. ..|...+||+||||||||.+|+++|..++.+++.+++++......+.+++
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~---~~-~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~Li  534 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLG---HE-HKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLI  534 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhcccc---CC-CCCcceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHc
Confidence            367888888877776654432110   00 12234699999999999999999999999999999988764322222221


Q ss_pred             ---------------HH---hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcc-ccc-CCC--
Q 012016          300 ---------------VA---TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDG-LWS-SCG--  357 (473)
Q Consensus       300 ---------------~~---~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~~-~~~--  357 (473)
                                     ..   ....+||+|||||.+-                     ....+.||..||. ... ..|  
T Consensus       535 G~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~---------------------~~v~~~LLq~ld~G~ltd~~g~~  593 (758)
T PRK11034        535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAH---------------------PDVFNLLLQVMDNGTLTDNNGRK  593 (758)
T ss_pred             CCCCCcccccccchHHHHHHhCCCcEEEeccHhhhh---------------------HHHHHHHHHHHhcCeeecCCCce
Confidence                           11   1245899999999872                     3467788888873 211 111  


Q ss_pred             ---CceEEEEecCCC-------------------------CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          358 ---DERIIVFTTNHK-------------------------EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       358 ---~~~iiI~tTN~~-------------------------~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                         .+.+||+|||.-                         ..+.|.|+.  |+|.+|.|+..+.++..+|+..++.
T Consensus       594 vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~~~~l~~I~~~~l~  667 (758)
T PRK11034        594 ADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_pred             ecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCCHHHHHHHHHHHHH
Confidence               357899999932                         125577777  9999999999999999999987775

>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=99.45  E-value=1.5e-12  Score=124.41  Aligned_cols=175  Identities=18%  Similarity=0.271  Sum_probs=105.6

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccccc
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTE  288 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~  288 (473)
                      +.-||++++-.+. .+.....+......+.      . ....++||||+|+|||+|++|+++++     +..+++++..+
T Consensus         3 ~~~tFdnfv~g~~-N~~a~~~~~~ia~~~~------~-~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~   74 (219)
T PF00308_consen    3 PKYTFDNFVVGES-NELAYAAAKAIAENPG------E-RYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEE   74 (219)
T ss_dssp             TT-SCCCS--TTT-THHHHHHHHHHHHSTT------T-SSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHH
T ss_pred             CCCccccCCcCCc-HHHHHHHHHHHHhcCC------C-CCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHH
Confidence            3468999864332 2223333443333221      1 22358999999999999999999986     56788887665


Q ss_pred             cc-------CchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceE
Q 012016          289 LR-------SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI  361 (473)
Q Consensus       289 ~~-------~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  361 (473)
                      +.       ....+.++........+|+|||++.+..                   ...+...|.+.++.+...  +..+
T Consensus        75 f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~-------------------~~~~q~~lf~l~n~~~~~--~k~l  133 (219)
T PF00308_consen   75 FIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAG-------------------KQRTQEELFHLFNRLIES--GKQL  133 (219)
T ss_dssp             HHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTT-------------------HHHHHHHHHHHHHHHHHT--TSEE
T ss_pred             HHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcC-------------------chHHHHHHHHHHHHHHhh--CCeE
Confidence            42       1233445555667889999999998843                   123444555555554433  3356


Q ss_pred             EEEecCCCCC---CCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHH
Q 012016          362 IVFTTNHKEK---LDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELI  419 (473)
Q Consensus       362 iI~tTN~~~~---ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~  419 (473)
                      |+.+...|..   ++|.|..  ||.  ..+++..|+.+.|..++..........+.+++...+
T Consensus       134 i~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l  194 (219)
T PF00308_consen  134 ILTSDRPPSELSGLLPDLRS--RLSWGLVVELQPPDDEDRRRILQKKAKERGIELPEEVIEYL  194 (219)
T ss_dssp             EEEESS-TTTTTTS-HHHHH--HHHCSEEEEE----HHHHHHHHHHHHHHTT--S-HHHHHHH
T ss_pred             EEEeCCCCccccccChhhhh--hHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHH
Confidence            6555566654   4677776  764  589999999999999999988776666666655544

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.

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.44  E-value=8.5e-13  Score=138.62  Aligned_cols=155  Identities=17%  Similarity=0.331  Sum_probs=123.0

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---------------
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---------------  278 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---------------  278 (473)
                      .|.+|++++|++.+.+.|.+.+..            .....+|||.||.|||||++|+.+|+.++               
T Consensus        11 RP~~F~evvGQe~v~~~L~nal~~------------~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~   78 (515)
T COG2812          11 RPKTFDDVVGQEHVVKTLSNALEN------------GRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCIS   78 (515)
T ss_pred             CcccHHHhcccHHHHHHHHHHHHh------------CcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhh
Confidence            458999999999888887665541            12256899999999999999999999884               


Q ss_pred             ---------CceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHH
Q 012016          279 ---------FDVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLS  343 (473)
Q Consensus       279 ---------~~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls  343 (473)
                               .+++.+|..+-.+-+++|++.....      +.-|++|||++.+                     ++..++
T Consensus        79 Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHML---------------------S~~afN  137 (515)
T COG2812          79 CKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHML---------------------SKQAFN  137 (515)
T ss_pred             hHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhh---------------------hHHHHH
Confidence                     3444555554455677888887763      4579999999977                     467889


Q ss_pred             HHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          344 GFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       344 ~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      .||..++.    ++..+++|++|..++++++.++.  |+ .+..|...+.++....+..++..++
T Consensus       138 ALLKTLEE----PP~hV~FIlATTe~~Kip~TIlS--Rc-q~f~fkri~~~~I~~~L~~i~~~E~  195 (515)
T COG2812         138 ALLKTLEE----PPSHVKFILATTEPQKIPNTILS--RC-QRFDFKRLDLEEIAKHLAAILDKEG  195 (515)
T ss_pred             HHhccccc----CccCeEEEEecCCcCcCchhhhh--cc-ccccccCCCHHHHHHHHHHHHHhcC
Confidence            99998874    56779999999999999999997  77 4678889999998888888887553

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.44  E-value=3.3e-12  Score=131.88  Aligned_cols=175  Identities=23%  Similarity=0.279  Sum_probs=111.7

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhh----hcCC-CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC---
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRR----VGKA-WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS---  291 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~----~g~~-~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~---  291 (473)
                      .++|+++.++.+...+.+..++-.....    .+.+ .+.++||+||||||||++|+++|..++.++..++++.+..   
T Consensus        78 ~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L~~~gy  157 (413)
T TIGR00382        78 YVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGY  157 (413)
T ss_pred             eecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhcccccc
Confidence            3589999998887766544433111000    0111 1458999999999999999999999999999888776531   


Q ss_pred             -----chHHHHHHHH------hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC----C
Q 012016          292 -----NSDLRTLLVA------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS----C  356 (473)
Q Consensus       292 -----~~~l~~l~~~------~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~----~  356 (473)
                           ...+..++..      ...++||||||||.+......  ...     ..+.......+.||+.|+|....    .
T Consensus       158 vG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~--~s~-----~~dvsg~~vq~~LL~iLeG~~~~v~~~~  230 (413)
T TIGR00382       158 VGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSEN--PSI-----TRDVSGEGVQQALLKIIEGTVANVPPQG  230 (413)
T ss_pred             ccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhcc--ccc-----cccccchhHHHHHHHHhhccceecccCC
Confidence                 1223333332      235789999999988642110  000     00111235677888888875321    1


Q ss_pred             -----CCceEEEEecCCC---------------------------C-----------------------CCCccccCCCc
Q 012016          357 -----GDERIIVFTTNHK---------------------------E-----------------------KLDPALLRPGR  381 (473)
Q Consensus       357 -----~~~~iiI~tTN~~---------------------------~-----------------------~ld~aLlrpgR  381 (473)
                           ..+.++|.|+|-.                           +                       .+.|+|+  ||
T Consensus       231 gr~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEfl--gR  308 (413)
T TIGR00382       231 GRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFI--GR  308 (413)
T ss_pred             CccccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHh--CC
Confidence                 1346888898861                           0                       0224444  49


Q ss_pred             eeeEEEeCCCCHHHHHHHHHHH
Q 012016          382 MDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       382 fd~~I~~~~p~~~~r~~l~~~~  403 (473)
                      +|..+.|...+.+....|+...
T Consensus       309 ld~Iv~f~pL~~~~L~~Il~~~  330 (413)
T TIGR00382       309 LPVIATLEKLDEEALIAILTKP  330 (413)
T ss_pred             CCeEeecCCCCHHHHHHHHHHH
Confidence            9999999999999988887753

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.

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.43  E-value=1.2e-11  Score=124.68  Aligned_cols=148  Identities=14%  Similarity=0.245  Sum_probs=109.5

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC--------CceEEcccc-
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN--------FDVYDLELT-  287 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~--------~~~~~l~~~-  287 (473)
                      +|++++|++.+++.+...+.            ....++.|||+||+|+|||++|+++|+.+-        .+++.+... 
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~------------~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~   69 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSII------------KNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN   69 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHH------------cCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecccc
Confidence            68999999988888766542            123467899999999999999999999762        234344331 


Q ss_pred             -cccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCce
Q 012016          288 -ELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER  360 (473)
Q Consensus       288 -~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~  360 (473)
                       ...+...++++.....      ..-|++|||+|.+                     +....+.||..++.    ++++.
T Consensus        70 ~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m---------------------~~~a~naLLK~LEe----pp~~t  124 (313)
T PRK05564         70 KKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKM---------------------TEQAQNAFLKTIEE----PPKGV  124 (313)
T ss_pred             CCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhc---------------------CHHHHHHHHHHhcC----CCCCe
Confidence             1123456777666432      4579999999977                     24467789999885    34568


Q ss_pred             EEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          361 IIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       361 iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      ++|++|+.++.+.|+++.  |+ .+++|+.|+.++....+...+
T Consensus       125 ~~il~~~~~~~ll~TI~S--Rc-~~~~~~~~~~~~~~~~l~~~~  165 (313)
T PRK05564        125 FIILLCENLEQILDTIKS--RC-QIYKLNRLSKEEIEKFISYKY  165 (313)
T ss_pred             EEEEEeCChHhCcHHHHh--hc-eeeeCCCcCHHHHHHHHHHHh
Confidence            888888889999999998  77 489999999999877666543

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.43  E-value=4.5e-12  Score=137.74  Aligned_cols=193  Identities=18%  Similarity=0.238  Sum_probs=124.9

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEccccc
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLELTE  288 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~~~  288 (473)
                      +.|.+.++..++|...|...+.+        ..+...++|+||||||||.+++.+.++|          .+.++.++|..
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            56777777777777766655542        2223346799999999999999998877          25678888865


Q ss_pred             ccCc-----------------------hHHHHHHHHhc----cCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          289 LRSN-----------------------SDLRTLLVATA----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       289 ~~~~-----------------------~~l~~l~~~~~----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                      +.+.                       ..+..+|....    ...||+|||||.+..                  ..+..
T Consensus       827 Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~k------------------K~QDV  888 (1164)
T PTZ00112        827 VVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLIT------------------KTQKV  888 (1164)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCc------------------cHHHH
Confidence            4221                       12333443321    246999999999853                  12334


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCC---CCCCCccccCCCceee-EEEeCCCCHHHHHHHHHHHhCccccCCHHHHHH
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNH---KEKLDPALLRPGRMDV-HVHMSYCTPSGFKLLAANYLGIKEHILFEEIEE  417 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~---~~~ld~aLlrpgRfd~-~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~  417 (473)
                      |-.|++...    ..+..++||+++|.   ++.|+|.+..  ||.. .|.|++++.+++..|+...+......+.+++..
T Consensus       889 LYnLFR~~~----~s~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIE  962 (1164)
T PTZ00112        889 LFTLFDWPT----KINSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQ  962 (1164)
T ss_pred             HHHHHHHhh----ccCCeEEEEEecCchhcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHH
Confidence            444444322    12346888899986   5677888877  6653 488999999999999998776432223333333


Q ss_pred             HHhcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 012016          418 LISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKV  452 (473)
Q Consensus       418 l~~~~~~t~a~i~~~l~~~~~~~~al~~l~~~l~~  452 (473)
                      ++..         .....+||++.||+-|..+++.
T Consensus       963 LIAr---------kVAq~SGDARKALDILRrAgEi  988 (1164)
T PTZ00112        963 LCAR---------KVANVSGDIRKALQICRKAFEN  988 (1164)
T ss_pred             HHHH---------hhhhcCCHHHHHHHHHHHHHhh
Confidence            3321         0112358999999888888875

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.43  E-value=5.3e-12  Score=126.93  Aligned_cols=156  Identities=17%  Similarity=0.196  Sum_probs=105.9

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----CceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----FDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~l~~  286 (473)
                      ...|.+|++++|.+++++.+...+    ...       .  ..++|||||||||||++++++++.+.     .+++.++.
T Consensus        10 kyrP~~~~~~~g~~~~~~~l~~~i----~~~-------~--~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~~   76 (319)
T PRK00440         10 KYRPRTLDEIVGQEEIVERLKSYV----KEK-------N--MPHLLFAGPPGTGKTTAALALARELYGEDWRENFLELNA   76 (319)
T ss_pred             hhCCCcHHHhcCcHHHHHHHHHHH----hCC-------C--CCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEEecc
Confidence            567799999999988777665543    221       1  22589999999999999999999873     34455544


Q ss_pred             ccccCchHHHHHHHH----h----ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          287 TELRSNSDLRTLLVA----T----ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~----~----~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ++......++..+..    .    ..+.+|+|||+|.+..                     .....|+..++...    .
T Consensus        77 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~---------------------~~~~~L~~~le~~~----~  131 (319)
T PRK00440         77 SDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS---------------------DAQQALRRTMEMYS----Q  131 (319)
T ss_pred             ccccchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH---------------------HHHHHHHHHHhcCC----C
Confidence            433222223222221    1    1346999999998732                     12345666666432    3


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      ...+|+++|.+..+.+++.+  |+. .++|+.++.++...++..++...+
T Consensus       132 ~~~lIl~~~~~~~l~~~l~s--r~~-~~~~~~l~~~ei~~~l~~~~~~~~  178 (319)
T PRK00440        132 NTRFILSCNYSSKIIDPIQS--RCA-VFRFSPLKKEAVAERLRYIAENEG  178 (319)
T ss_pred             CCeEEEEeCCccccchhHHH--Hhh-eeeeCCCCHHHHHHHHHHHHHHcC
Confidence            35677788888888888887  765 589999999999888888776543

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.43  E-value=2.1e-12  Score=135.45  Aligned_cols=152  Identities=16%  Similarity=0.252  Sum_probs=98.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC-------chHHHHHHHHhccCceEEEeccccccccccCC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS-------NSDLRTLLVATANRSILVVEDIDCTIDLQDRL  323 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~-------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~  323 (473)
                      ++++||||||+|||+|++|+|+++   +..+++++...+..       ............+..+|+||||+.+.+     
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~-----  216 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSG-----  216 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcC-----
Confidence            579999999999999999999987   67888887755421       111212222235678999999998742     


Q ss_pred             ccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC-C---CCCCccccCCCcee--eEEEeCCCCHHHHH
Q 012016          324 PADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH-K---EKLDPALLRPGRMD--VHVHMSYCTPSGFK  397 (473)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~-~---~~ld~aLlrpgRfd--~~I~~~~p~~~~r~  397 (473)
                                 ....+..+..++|.+   ...   +..+|+|+|. |   ..++++|.+  ||.  ..+.++.|+.+.+.
T Consensus       217 -----------k~~~qeelf~l~N~l---~~~---~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~  277 (445)
T PRK12422        217 -----------KGATQEEFFHTFNSL---HTE---GKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLR  277 (445)
T ss_pred             -----------ChhhHHHHHHHHHHH---HHC---CCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHH
Confidence                       111233333444433   221   2345555554 4   356789988  885  88999999999999


Q ss_pred             HHHHHHhCccccCCHHHHHH-HHhcCCCCHHHH
Q 012016          398 LLAANYLGIKEHILFEEIEE-LISTTQVTPAEV  429 (473)
Q Consensus       398 ~l~~~~l~~~~~~l~~~i~~-l~~~~~~t~a~i  429 (473)
                      .+++......+..+.+++.. ++....-...++
T Consensus       278 ~iL~~k~~~~~~~l~~evl~~la~~~~~dir~L  310 (445)
T PRK12422        278 SFLERKAEALSIRIEETALDFLIEALSSNVKSL  310 (445)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHH
Confidence            99998887665555555555 444433334333

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.43  E-value=1.5e-11  Score=125.87  Aligned_cols=152  Identities=18%  Similarity=0.287  Sum_probs=111.6

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      .+|.++++|+|+++.++.+.+.+..            ...+.++||+||+|+||+++|.++|+.+-.             
T Consensus        13 ~~P~~~~~iiGq~~~~~~L~~~~~~------------~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~   80 (365)
T PRK07471         13 PHPRETTALFGHAAAEAALLDAYRS------------GRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPP   80 (365)
T ss_pred             CCCCchhhccChHHHHHHHHHHHHc------------CCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCcccccc
Confidence            5889999999999888887654431            234678999999999999999999998721             


Q ss_pred             ---------------------ceEEcccc--c-------ccCchHHHHHHHHhc------cCceEEEeccccccccccCC
Q 012016          280 ---------------------DVYDLELT--E-------LRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRL  323 (473)
Q Consensus       280 ---------------------~~~~l~~~--~-------~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~  323 (473)
                                           +++.+...  +       ...-..++++.....      .+.|++|||+|.+       
T Consensus        81 ~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m-------  153 (365)
T PRK07471         81 TSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEM-------  153 (365)
T ss_pred             ccccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhc-------
Confidence                                 11222110  1       012244555554432      4679999999977       


Q ss_pred             ccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          324 PADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                                    +....+.||..++..    +...++|++|+.++.+.|.+++  |+ .+|.|+.|+.++...++...
T Consensus       154 --------------~~~aanaLLK~LEep----p~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~i~~~L~~~  212 (365)
T PRK07471        154 --------------NANAANALLKVLEEP----PARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPEDVIDALAAA  212 (365)
T ss_pred             --------------CHHHHHHHHHHHhcC----CCCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHHHHHHHHHh
Confidence                          346678899888753    3457888999999999999887  87 58999999999988888765


Q ss_pred             h
Q 012016          404 L  404 (473)
Q Consensus       404 l  404 (473)
                      .
T Consensus       213 ~  213 (365)
T PRK07471        213 G  213 (365)
T ss_pred             c
Confidence            4

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.42  E-value=2e-12  Score=135.73  Aligned_cols=190  Identities=17%  Similarity=0.281  Sum_probs=114.3

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~  286 (473)
                      +.+..+|++++..+.-. .....+..+...+      |  +...++||||||||||+|++|+|+++     +..++++++
T Consensus        98 l~~~~tFdnFv~g~~n~-~a~~~~~~~~~~~------~--~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~  168 (440)
T PRK14088         98 LNPDYTFENFVVGPGNS-FAYHAALEVAKNP------G--RYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITS  168 (440)
T ss_pred             CCCCCcccccccCCchH-HHHHHHHHHHhCc------C--CCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEH
Confidence            45557899987433322 2233333333221      1  23469999999999999999999986     457788776


Q ss_pred             ccccC-------chHHHHHHHHhc-cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          287 TELRS-------NSDLRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       287 ~~~~~-------~~~l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      .++..       ...+........ ++.+|+|||++.+.+                .   ..+...|+..++.+...  .
T Consensus       169 ~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~----------------~---~~~q~elf~~~n~l~~~--~  227 (440)
T PRK14088        169 EKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIG----------------K---TGVQTELFHTFNELHDS--G  227 (440)
T ss_pred             HHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcC----------------c---HHHHHHHHHHHHHHHHc--C
Confidence            65421       111222222222 578999999998753                0   11122344444444332  2


Q ss_pred             ceEEEEecCCCCC---CCccccCCCce--eeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHH-hcCCCCHHHHHHH
Q 012016          359 ERIIVFTTNHKEK---LDPALLRPGRM--DVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELI-STTQVTPAEVAEQ  432 (473)
Q Consensus       359 ~~iiI~tTN~~~~---ld~aLlrpgRf--d~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~-~~~~~t~a~i~~~  432 (473)
                      ..+||.+.+.|..   +++.+..  ||  ...+.+..|+.+.|..|++..+......+.+++...+ +...-+..++...
T Consensus       228 k~iIitsd~~p~~l~~l~~rL~S--R~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~~~~~R~L~g~  305 (440)
T PRK14088        228 KQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRGA  305 (440)
T ss_pred             CeEEEECCCCHHHHHHHHHHHhh--HHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhccccCHHHHHHH
Confidence            2444444455544   5567777  66  4678999999999999999988765555555554444 3334455555444


Q ss_pred             H
Q 012016          433 L  433 (473)
Q Consensus       433 l  433 (473)
                      +
T Consensus       306 l  306 (440)
T PRK14088        306 I  306 (440)
T ss_pred             H
Confidence            4

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.41  E-value=2.1e-12  Score=145.98  Aligned_cols=157  Identities=18%  Similarity=0.252  Sum_probs=109.7

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEE
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYD  283 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~  283 (473)
                      .|..++.++|.++....+++.+.    ++         .+.+.+|+||||||||++++++|..+          +.+++.
T Consensus       168 ~~~~~~~~igr~~ei~~~~~~l~----r~---------~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~  234 (852)
T TIGR03346       168 REGKLDPVIGRDEEIRRTIQVLS----RR---------TKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLA  234 (852)
T ss_pred             hCCCCCcCCCcHHHHHHHHHHHh----cC---------CCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEE
Confidence            44678899998876555554432    21         25689999999999999999999986          678888


Q ss_pred             cccccccC--------chHHHHHHHHhc---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc
Q 012016          284 LELTELRS--------NSDLRTLLVATA---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       284 l~~~~~~~--------~~~l~~l~~~~~---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  352 (473)
                      ++++.+..        +..+..++....   .++||||||||.+.....             ........+-|...+   
T Consensus       235 l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~-------------~~~~~d~~~~Lk~~l---  298 (852)
T TIGR03346       235 LDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGK-------------AEGAMDAGNMLKPAL---  298 (852)
T ss_pred             eeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCC-------------CcchhHHHHHhchhh---
Confidence            88776521        235677776553   579999999999864110             000111222222222   


Q ss_pred             ccCCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          353 WSSCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       353 ~~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                        . .+++.+|++|+..+     .+|+++.|  ||. .|.++.|+.+++..|++.+..
T Consensus       299 --~-~g~i~~IgaTt~~e~r~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~iL~~~~~  350 (852)
T TIGR03346       299 --A-RGELHCIGATTLDEYRKYIEKDAALER--RFQ-PVFVDEPTVEDTISILRGLKE  350 (852)
T ss_pred             --h-cCceEEEEeCcHHHHHHHhhcCHHHHh--cCC-EEEeCCCCHHHHHHHHHHHHH
Confidence              1 24588888888764     47999999  996 589999999999999886543

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.

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.41  E-value=1.3e-11  Score=125.80  Aligned_cols=180  Identities=15%  Similarity=0.172  Sum_probs=120.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------ce----
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------DV----  281 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------~~----  281 (473)
                      .||..|+.|+|+++.+..+...+.    +        ...+..+||+||+|+|||+++..+|+.+..       +.    
T Consensus        17 ~~P~~~~~l~Gh~~a~~~L~~a~~----~--------grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~   84 (351)
T PRK09112         17 PSPSENTRLFGHEEAEAFLAQAYR----E--------GKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLAD   84 (351)
T ss_pred             CCCCchhhccCcHHHHHHHHHHHH----c--------CCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCC
Confidence            689999999999988877655433    1        123568999999999999999999998843       11    


Q ss_pred             -------------------EEcccc---------cccCchHHHHHHHHhc------cCceEEEeccccccccccCCcccc
Q 012016          282 -------------------YDLELT---------ELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADI  327 (473)
Q Consensus       282 -------------------~~l~~~---------~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~  327 (473)
                                         +.+...         ...+...++++.....      ..-|++|||+|.+           
T Consensus        85 ~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l-----------  153 (351)
T PRK09112         85 PDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDM-----------  153 (351)
T ss_pred             CCCCCHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhc-----------
Confidence                               111100         0011233444333221      4579999999987           


Q ss_pred             CCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          328 AGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       328 ~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                                +....+.||..++..    +...++|+.|+.++.+.|.++.  |+ .+++|+.|+.++...++.......
T Consensus       154 ----------~~~aanaLLk~LEEp----p~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~~~~~L~~~~~~~  216 (351)
T PRK09112        154 ----------NRNAANAILKTLEEP----PARALFILISHSSGRLLPTIRS--RC-QPISLKPLDDDELKKALSHLGSSQ  216 (351)
T ss_pred             ----------CHHHHHHHHHHHhcC----CCCceEEEEECChhhccHHHHh--hc-cEEEecCCCHHHHHHHHHHhhccc
Confidence                      245567799988763    3456777778889999999987  88 699999999999988888742221


Q ss_pred             ccCCHHHHHHHHhcCCCCHHHHHHHH
Q 012016          408 EHILFEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       408 ~~~l~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      . ...+.+..++...+-+|....+++
T Consensus       217 ~-~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        217 G-SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             C-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence            1 223344455555555665444443

>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=99.37  E-value=5.8e-12  Score=110.18  Aligned_cols=115  Identities=28%  Similarity=0.420  Sum_probs=80.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHHH-----------HHHHhccCceEEEeccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLRT-----------LLVATANRSILVVEDIDCTID  318 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~~-----------l~~~~~~~sIL~iDdiD~l~~  318 (473)
                      .++++++||||||||++++.+++.+   +.+++.+++...........           .......+.+|+|||++.+..
T Consensus        19 ~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~~~   98 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSR   98 (151)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhhhH
Confidence            5689999999999999999999999   89999999887643322221           112234679999999997621


Q ss_pred             cccCCccccCCCCCCCccchhHHHHHHHHHhcccccC--CCCceEEEEecCCCC--CCCccccCCCceeeEEEeCC
Q 012016          319 LQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS--CGDERIIVFTTNHKE--KLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       319 ~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~--~~~~~iiI~tTN~~~--~ld~aLlrpgRfd~~I~~~~  390 (473)
                                           .....++..+......  ...+..+|+++|...  .+++.+..  ||+.+|++++
T Consensus        99 ---------------------~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~~~~  151 (151)
T cd00009          99 ---------------------GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIVIPL  151 (151)
T ss_pred             ---------------------HHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccEeecCC
Confidence                                 2233444444443221  124578888888876  67788887  9998888763

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.37  E-value=8.9e-12  Score=131.11  Aligned_cols=187  Identities=15%  Similarity=0.282  Sum_probs=115.9

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcccccc
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTEL  289 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~~  289 (473)
                      +.+|++++..+.- +.....+..+...+      |.. .++++||||+|||||+|++|+++++     +..++++++.++
T Consensus       111 ~~tFdnFv~g~~n-~~A~~aa~~~a~~~------~~~-~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f  182 (450)
T PRK14087        111 ENTFENFVIGSSN-EQAFIAVQTVSKNP------GIS-YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEF  182 (450)
T ss_pred             ccchhcccCCCcH-HHHHHHHHHHHhCc------Ccc-cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHH
Confidence            4688888744432 22333343333221      222 3479999999999999999999965     467788877664


Q ss_pred             cCc---------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCce
Q 012016          290 RSN---------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER  360 (473)
Q Consensus       290 ~~~---------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~  360 (473)
                      ...         ..+.+......+..+|+|||++.+..                .......+..++|.+.   ..  + .
T Consensus       183 ~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~----------------k~~~~e~lf~l~N~~~---~~--~-k  240 (450)
T PRK14087        183 ARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLSY----------------KEKTNEIFFTIFNNFI---EN--D-K  240 (450)
T ss_pred             HHHHHHHHHHhhhHHHHHHHHhccCCEEEEeccccccC----------------CHHHHHHHHHHHHHHH---Hc--C-C
Confidence            211         22333334445678999999997742                1122334444454443   22  1 2


Q ss_pred             EEEEecCC-CC---CCCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCcccc--CCHHH-HHHHHhcCCCCHHHHHH
Q 012016          361 IIVFTTNH-KE---KLDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEH--ILFEE-IEELISTTQVTPAEVAE  431 (473)
Q Consensus       361 iiI~tTN~-~~---~ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~--~l~~~-i~~l~~~~~~t~a~i~~  431 (473)
                      .+|+|+|. |+   .+++.|..  ||.  ..+.+..|+.+++..++++.+...+.  .+.++ +.-++....-.+..+..
T Consensus       241 ~iIltsd~~P~~l~~l~~rL~S--R~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~~gd~R~L~g  318 (450)
T PRK14087        241 QLFFSSDKSPELLNGFDNRLIT--RFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYYSDDVRKIKG  318 (450)
T ss_pred             cEEEECCCCHHHHhhccHHHHH--HHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHccCCCHHHHHH
Confidence            45566654 43   45788888  884  77889999999999999998865432  34344 44444455566666655


Q ss_pred             HH
Q 012016          432 QL  433 (473)
Q Consensus       432 ~l  433 (473)
                      .|
T Consensus       319 aL  320 (450)
T PRK14087        319 SV  320 (450)
T ss_pred             HH
Confidence            55

>PRK06620 hypothetical protein; Validated

Probab=99.36  E-value=1.8e-11  Score=116.50  Aligned_cols=150  Identities=16%  Similarity=0.238  Sum_probs=95.0

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCC-CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAW-KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR  290 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~-~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~  290 (473)
                      ..++-+|++++..+.- +.....+..+..      .++..+ .+.++||||||||||+|++++|+..+..++  +.... 
T Consensus         9 ~~~~~tfd~Fvvg~~N-~~a~~~~~~~~~------~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~--~~~~~-   78 (214)
T PRK06620          9 TSSKYHPDEFIVSSSN-DQAYNIIKNWQC------GFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYII--KDIFF-   78 (214)
T ss_pred             CCCCCCchhhEecccH-HHHHHHHHHHHH------ccccCCCcceEEEECCCCCCHHHHHHHHHhccCCEEc--chhhh-
Confidence            3445689998765422 223444443332      122222 478999999999999999999999876332  21111 


Q ss_pred             CchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCC
Q 012016          291 SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE  370 (473)
Q Consensus       291 ~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~  370 (473)
                       ..   ..   ..+..+|+|||||.+                     ....+..++|.+..   .  +..++|.++..|.
T Consensus        79 -~~---~~---~~~~d~lliDdi~~~---------------------~~~~lf~l~N~~~e---~--g~~ilits~~~p~  125 (214)
T PRK06620         79 -NE---EI---LEKYNAFIIEDIENW---------------------QEPALLHIFNIINE---K--QKYLLLTSSDKSR  125 (214)
T ss_pred             -ch---hH---HhcCCEEEEeccccc---------------------hHHHHHHHHHHHHh---c--CCEEEEEcCCCcc
Confidence             11   11   234579999999843                     12345556655542   2  2366666665554


Q ss_pred             C--CCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          371 K--LDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       371 ~--ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .  + |+|+.  |+.  ..+++..|+.+.+..++.......
T Consensus       126 ~l~l-~~L~S--Rl~~gl~~~l~~pd~~~~~~~l~k~~~~~  163 (214)
T PRK06620        126 NFTL-PDLSS--RIKSVLSILLNSPDDELIKILIFKHFSIS  163 (214)
T ss_pred             ccch-HHHHH--HHhCCceEeeCCCCHHHHHHHHHHHHHHc
Confidence            4  5 78887  875  468999999999999998776543

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.36  E-value=1.1e-11  Score=138.14  Aligned_cols=155  Identities=17%  Similarity=0.315  Sum_probs=108.2

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCC----CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch--
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA----WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS--  293 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~----~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~--  293 (473)
                      .|+|+++.++.|.+.+...        +.|..    |...+||+||||||||+||+++|..++.+++.+++++.....  
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~--------~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~~  526 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRS--------RAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTV  526 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHH--------hcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhcccH
Confidence            4566666666665544321        22321    223589999999999999999999999999999987753211  


Q ss_pred             -----------------HHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--c
Q 012016          294 -----------------DLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--S  354 (473)
Q Consensus       294 -----------------~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--~  354 (473)
                                       .+.+.+. ....+||+|||||.+-                     ....+.||+.||.-.  .
T Consensus       527 ~~lig~~~gyvg~~~~~~l~~~~~-~~p~~VvllDEieka~---------------------~~~~~~Ll~~ld~g~~~d  584 (731)
T TIGR02639       527 SRLIGAPPGYVGFEQGGLLTEAVR-KHPHCVLLLDEIEKAH---------------------PDIYNILLQVMDYATLTD  584 (731)
T ss_pred             HHHhcCCCCCcccchhhHHHHHHH-hCCCeEEEEechhhcC---------------------HHHHHHHHHhhccCeeec
Confidence                             1222222 2356899999999762                     346677888887531  1


Q ss_pred             CCC-----CceEEEEecCCCC-------------------------CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          355 SCG-----DERIIVFTTNHKE-------------------------KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       355 ~~~-----~~~iiI~tTN~~~-------------------------~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      ..|     .+.+||+|||...                         .+.|.|+.  |||.+|.|...+.++...|+.+.+
T Consensus       585 ~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs~e~l~~Iv~~~L  662 (731)
T TIGR02639       585 NNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLSEEVLEKIVQKFV  662 (731)
T ss_pred             CCCcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCCHHHHHHHHHHHH
Confidence            111     3578999998631                         24566766  999999999999999999999887


Q ss_pred             Cc
Q 012016          405 GI  406 (473)
Q Consensus       405 ~~  406 (473)
                      ..
T Consensus       663 ~~  664 (731)
T TIGR02639       663 DE  664 (731)
T ss_pred             HH
Confidence            53

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.35  E-value=1.6e-11  Score=138.36  Aligned_cols=152  Identities=22%  Similarity=0.307  Sum_probs=108.1

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEcc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLE  285 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~  285 (473)
                      ..++.++|.++..+.+++.+.    +         ..+++++|+||||||||++++++|..+          +.+++.++
T Consensus       176 ~~~~~~igr~~ei~~~~~~L~----r---------~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~  242 (821)
T CHL00095        176 GNLDPVIGREKEIERVIQILG----R---------RTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLD  242 (821)
T ss_pred             CCCCCCCCcHHHHHHHHHHHc----c---------cccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEee
Confidence            357788888877777766543    2         125689999999999999999999987          47899999


Q ss_pred             cccccC--------chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHH-HHhccccc
Q 012016          286 LTELRS--------NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL-NFIDGLWS  354 (473)
Q Consensus       286 ~~~~~~--------~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL-~~ldg~~~  354 (473)
                      ++.+..        +..++.++..+.  .++||||||||.+++....         .+     ....+.+| ..+.    
T Consensus       243 ~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~---------~g-----~~~~a~lLkp~l~----  304 (821)
T CHL00095        243 IGLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAA---------EG-----AIDAANILKPALA----  304 (821)
T ss_pred             HHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCC---------CC-----cccHHHHhHHHHh----
Confidence            876531        246777877654  4789999999999752110         01     11122233 2222    


Q ss_pred             CCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          355 SCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       355 ~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                        .+++.+|++|+..+     ..||+|.+  ||. .|.++.|+.++...|++..
T Consensus       305 --rg~l~~IgaTt~~ey~~~ie~D~aL~r--Rf~-~I~v~ep~~~e~~aILr~l  353 (821)
T CHL00095        305 --RGELQCIGATTLDEYRKHIEKDPALER--RFQ-PVYVGEPSVEETIEILFGL  353 (821)
T ss_pred             --CCCcEEEEeCCHHHHHHHHhcCHHHHh--cce-EEecCCCCHHHHHHHHHHH
Confidence              24578888888664     47999999  996 5899999999988887754

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.35  E-value=1.7e-11  Score=123.62  Aligned_cols=156  Identities=22%  Similarity=0.263  Sum_probs=103.9

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-------CCceEEc--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-------NFDVYDL--  284 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-------~~~~~~l--  284 (473)
                      .|.+|++++|+++.++.+.-.+..             +-..++||+||||||||++++++|+.+       +.++-..  
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~~-------------~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~   69 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAID-------------PGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARP   69 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHhc-------------cCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcc
Confidence            467899999999988876542211             112479999999999999999999998       3221110  


Q ss_pred             c----c--------------------c----cccCchHHHHHHH-----------HhccCceEEEeccccccccccCCcc
Q 012016          285 E----L--------------------T----ELRSNSDLRTLLV-----------ATANRSILVVEDIDCTIDLQDRLPA  325 (473)
Q Consensus       285 ~----~--------------------~----~~~~~~~l~~l~~-----------~~~~~sIL~iDdiD~l~~~~~r~~~  325 (473)
                      .    +                    +    .+.+.-.+...+.           ...++.+|++|||+.+         
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            0    0                    0    0111111111111           1124579999999977         


Q ss_pred             ccCCCCCCCccchhHHHHHHHHHhcccc---------cCCCCceEEEEecCCCC-CCCccccCCCceeeEEEeCCCCH-H
Q 012016          326 DIAGEGEGPIQQNKVTLSGFLNFIDGLW---------SSCGDERIIVFTTNHKE-KLDPALLRPGRMDVHVHMSYCTP-S  394 (473)
Q Consensus       326 ~~~~~~~~~~~~~~~~ls~LL~~ldg~~---------~~~~~~~iiI~tTN~~~-~ld~aLlrpgRfd~~I~~~~p~~-~  394 (473)
                                  ...+.+.|++.|+.-.         ...+...++|+|+|..+ .++++|+.  ||...|.+++|.. +
T Consensus       141 ------------~~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~~~  206 (334)
T PRK13407        141 ------------EDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRDVE  206 (334)
T ss_pred             ------------CHHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCcHH
Confidence                        2456777888775321         11234577888888654 68999999  9999999999988 8


Q ss_pred             HHHHHHHHHhC
Q 012016          395 GFKLLAANYLG  405 (473)
Q Consensus       395 ~r~~l~~~~l~  405 (473)
                      ++.+++.+...
T Consensus       207 e~~~il~~~~~  217 (334)
T PRK13407        207 TRVEVIRRRDA  217 (334)
T ss_pred             HHHHHHHHhhc
Confidence            88999987544

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.35  E-value=4.6e-12  Score=126.35  Aligned_cols=129  Identities=19%  Similarity=0.198  Sum_probs=91.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHH--------------H-----HHHHhccCceEEEecc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLR--------------T-----LLVATANRSILVVEDI  313 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~--------------~-----l~~~~~~~sIL~iDdi  313 (473)
                      .+.+||.||||||||++++.+|..++.+++.+++.......++.              .     +......+.+|++||+
T Consensus        64 ~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~~g~illlDEi  143 (327)
T TIGR01650        64 DRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQHNVALCFDEY  143 (327)
T ss_pred             CCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHhCCeEEEechh
Confidence            56899999999999999999999999999998876642211110              0     1112246788999999


Q ss_pred             ccccccccCCccccCCCCCCCccchhHHHHHHHHHhcc--cc---c-----CCCCceEEEEecCCCC------------C
Q 012016          314 DCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDG--LW---S-----SCGDERIIVFTTNHKE------------K  371 (473)
Q Consensus       314 D~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg--~~---~-----~~~~~~iiI~tTN~~~------------~  371 (473)
                      |..-                     ..+++.|...+|.  ..   .     .+.....+|+|.|..+            .
T Consensus       144 n~a~---------------------p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~  202 (327)
T TIGR01650       144 DAGR---------------------PDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQ  202 (327)
T ss_pred             hccC---------------------HHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeec
Confidence            9762                     2344444444441  10   0     1223467899999864            4


Q ss_pred             CCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          372 LDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       372 ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      +++|++.  ||-..+.++||+.+.-..|+....
T Consensus       203 l~~A~lD--RF~i~~~~~Yp~~e~E~~Il~~~~  233 (327)
T TIGR01650       203 INQAQMD--RWSIVTTLNYLEHDNEAAIVLAKA  233 (327)
T ss_pred             CCHHHHh--heeeEeeCCCCCHHHHHHHHHhhc
Confidence            6889999  998889999999999999887654

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.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.35  E-value=1.6e-11  Score=133.84  Aligned_cols=173  Identities=20%  Similarity=0.333  Sum_probs=111.4

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceE
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVY  282 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~  282 (473)
                      ..|.+|++++|.+...+.++..+.             .+.+..++|+||||||||++|+++++..          +.+++
T Consensus       148 ~rp~~~~~iiGqs~~~~~l~~~ia-------------~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv  214 (615)
T TIGR02903       148 LRPRAFSEIVGQERAIKALLAKVA-------------SPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFV  214 (615)
T ss_pred             cCcCcHHhceeCcHHHHHHHHHHh-------------cCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeE
Confidence            347899999999887777654331             1224579999999999999999998766          35678


Q ss_pred             EcccccccCc-hHHH----------------HHHHH------------hccCceEEEeccccccccccCCccccCCCCCC
Q 012016          283 DLELTELRSN-SDLR----------------TLLVA------------TANRSILVVEDIDCTIDLQDRLPADIAGEGEG  333 (473)
Q Consensus       283 ~l~~~~~~~~-~~l~----------------~l~~~------------~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~  333 (473)
                      .+++..+..+ ..+.                +.+..            ..++++|||||++.+-.               
T Consensus       215 ~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~---------------  279 (615)
T TIGR02903       215 EVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDP---------------  279 (615)
T ss_pred             EEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCH---------------
Confidence            8887654211 1110                11111            12467999999987732               


Q ss_pred             CccchhHHHHHHHHHhccc--------c----------------cCCCCceEEEE-ecCCCCCCCccccCCCceeeEEEe
Q 012016          334 PIQQNKVTLSGFLNFIDGL--------W----------------SSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHM  388 (473)
Q Consensus       334 ~~~~~~~~ls~LL~~ldg~--------~----------------~~~~~~~iiI~-tTN~~~~ld~aLlrpgRfd~~I~~  388 (473)
                            .....|+..|+.-        +                ...+..+++|+ ||+.++.++++|++  ||. .++|
T Consensus       280 ------~~Q~~Ll~~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrS--R~~-~i~~  350 (615)
T TIGR02903       280 ------LLQNKLLKVLEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRS--RCA-EVFF  350 (615)
T ss_pred             ------HHHHHHHHHHhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHh--cee-EEEe
Confidence                  2233344444221        0                01122345554 66778899999988  986 5789


Q ss_pred             CCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC
Q 012016          389 SYCTPSGFKLLAANYLGIKEHILFEEIEELISTT  422 (473)
Q Consensus       389 ~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~  422 (473)
                      +.++.++...|+++++......+.+++..++...
T Consensus       351 ~pls~edi~~Il~~~a~~~~v~ls~eal~~L~~y  384 (615)
T TIGR02903       351 EPLTPEDIALIVLNAAEKINVHLAAGVEELIARY  384 (615)
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHC
Confidence            9999999999999987654333444555555443

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.

>PHA02244 ATPase-like protein

Probab=99.34  E-value=1.4e-11  Score=124.14  Aligned_cols=119  Identities=20%  Similarity=0.316  Sum_probs=82.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc----c----cCchHHH--HHHHHhccCceEEEeccccccccccCC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE----L----RSNSDLR--TLLVATANRSILVVEDIDCTIDLQDRL  323 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~----~----~~~~~l~--~l~~~~~~~sIL~iDdiD~l~~~~~r~  323 (473)
                      ..+||+||||||||++|++||..++.+++.++...    +    .....+.  .++....++.+|+|||++.+.      
T Consensus       120 ~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~~~GgvLiLDEId~a~------  193 (383)
T PHA02244        120 IPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAFKKGGLFFIDEIDASI------  193 (383)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHhhcCCEEEEeCcCcCC------
Confidence            47999999999999999999999999999876321    1    0111111  334445688999999999763      


Q ss_pred             ccccCCCCCCCccchhHHHHHHHHHhcc-c------ccCCCCceEEEEecCCC-----------CCCCccccCCCceeeE
Q 012016          324 PADIAGEGEGPIQQNKVTLSGFLNFIDG-L------WSSCGDERIIVFTTNHK-----------EKLDPALLRPGRMDVH  385 (473)
Q Consensus       324 ~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~------~~~~~~~~iiI~tTN~~-----------~~ld~aLlrpgRfd~~  385 (473)
                                     ..++..|...++. .      .-....+..+|+|+|.+           ..|++|++.  || .+
T Consensus       194 ---------------p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllD--RF-v~  255 (383)
T PHA02244        194 ---------------PEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLD--RF-AP  255 (383)
T ss_pred             ---------------HHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHh--hc-EE
Confidence                           2334444444431 1      01122457899999973           578999999  99 57


Q ss_pred             EEeCCCCHHHH
Q 012016          386 VHMSYCTPSGF  396 (473)
Q Consensus       386 I~~~~p~~~~r  396 (473)
                      |+|++|+..+.
T Consensus       256 I~~dyp~~~E~  266 (383)
T PHA02244        256 IEFDYDEKIEH  266 (383)
T ss_pred             eeCCCCcHHHH
Confidence            99999984443

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.34  E-value=4.4e-11  Score=127.00  Aligned_cols=164  Identities=18%  Similarity=0.284  Sum_probs=115.5

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHh---c--------------hhHH----hhhcCCCCceeEEeCCCCCCHHHH
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVK---R--------------KDYY----RRVGKAWKRGYLLYGPPGTGKSSL  269 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~---~--------------~~~y----~~~g~~~~rg~LL~GPpGtGKT~l  269 (473)
                      ....|..|.+|.+++.+...++..|+.|--   +              ++.+    ...+.|.++-+||+||||-|||||
T Consensus       263 dky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGKTTL  342 (877)
T KOG1969|consen  263 DKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGKTTL  342 (877)
T ss_pred             cccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCChhHH
Confidence            356778999999999999999998876521   1              1111    112566777899999999999999


Q ss_pred             HHHHHHhcCCceEEcccccccCchHHHHHHHHh----------ccCceEEEeccccccccccCCccccCCCCCCCccchh
Q 012016          270 IAAMANYLNFDVYDLELTELRSNSDLRTLLVAT----------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNK  339 (473)
Q Consensus       270 a~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~----------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~  339 (473)
                      |+.+|+..||.+++++.++-.+...+++.+..+          .+|..|||||||-..                     .
T Consensus       343 AHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~---------------------~  401 (877)
T KOG1969|consen  343 AHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAP---------------------R  401 (877)
T ss_pred             HHHHHHhcCceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCc---------------------H
Confidence            999999999999999999988877777666543          368899999998432                     2


Q ss_pred             HHHHHHHHHhc--ccccCCC---------------CceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHH
Q 012016          340 VTLSGFLNFID--GLWSSCG---------------DERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFK  397 (473)
Q Consensus       340 ~~ls~LL~~ld--g~~~~~~---------------~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~  397 (473)
                      ..+..++..+.  +....+.               =.+-||+.+|..  .-|||+.---+...|+|..|......
T Consensus       402 ~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdL--YaPaLR~Lr~~A~ii~f~~p~~s~Lv  474 (877)
T KOG1969|consen  402 AAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDL--YAPALRPLRPFAEIIAFVPPSQSRLV  474 (877)
T ss_pred             HHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCc--cchhhhhcccceEEEEecCCChhHHH
Confidence            23333333332  1100000               126799999964  45787521157788999998887644

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=99.32  E-value=5.7e-12  Score=124.23  Aligned_cols=150  Identities=19%  Similarity=0.308  Sum_probs=98.3

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc---eEEccccccc
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD---VYDLELTELR  290 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~---~~~l~~~~~~  290 (473)
                      .|.++++++|++.+.-+ -..+...+....         -.+++||||||||||+||+.|++-..-+   ++.++.... 
T Consensus       133 RPktL~dyvGQ~hlv~q-~gllrs~ieq~~---------ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a-  201 (554)
T KOG2028|consen  133 RPKTLDDYVGQSHLVGQ-DGLLRSLIEQNR---------IPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNA-  201 (554)
T ss_pred             CcchHHHhcchhhhcCc-chHHHHHHHcCC---------CCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEecccc-
Confidence            46788888887654433 112222222111         3479999999999999999999988655   555554443 


Q ss_pred             CchHHHHHHHHhc-------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          291 SNSDLRTLLVATA-------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       291 ~~~~l~~l~~~~~-------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                      +..+++.+|....       ++.|||||||+..-.                     .-...||-.++     + +.+++|
T Consensus       202 ~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNk---------------------sQQD~fLP~VE-----~-G~I~lI  254 (554)
T KOG2028|consen  202 KTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNK---------------------SQQDTFLPHVE-----N-GDITLI  254 (554)
T ss_pred             chHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhh---------------------hhhhcccceec-----c-CceEEE
Confidence            3467888887653       689999999987621                     11122343332     2 246666


Q ss_pred             E-ecCCC-CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          364 F-TTNHK-EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       364 ~-tTN~~-~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      + ||..| -.|..||+.  |+ .++-+...+.+....|+.+-+
T Consensus       255 GATTENPSFqln~aLlS--RC-~VfvLekL~~n~v~~iL~rai  294 (554)
T KOG2028|consen  255 GATTENPSFQLNAALLS--RC-RVFVLEKLPVNAVVTILMRAI  294 (554)
T ss_pred             ecccCCCccchhHHHHh--cc-ceeEeccCCHHHHHHHHHHHH
Confidence            5 55555 578899998  76 456777788888888887633

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.32  E-value=3.2e-11  Score=112.37  Aligned_cols=124  Identities=21%  Similarity=0.288  Sum_probs=90.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCC------------------------ceEEcccccc-cCchHHHHHHHHhc---
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNF------------------------DVYDLELTEL-RSNSDLRTLLVATA---  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~------------------------~~~~l~~~~~-~~~~~l~~l~~~~~---  303 (473)
                      .+..||||||+|+|||++++++++.+..                        ++..++.... .+.+.++.++....   
T Consensus        13 ~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~~   92 (188)
T TIGR00678        13 LAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTP   92 (188)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccCc
Confidence            4568999999999999999999998732                        2333322211 12345655555442   


Q ss_pred             ---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCC
Q 012016          304 ---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPG  380 (473)
Q Consensus       304 ---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpg  380 (473)
                         ...|+||||+|.+.                     ....+.||..|+..    +...++|++||.+..+.+++.+  
T Consensus        93 ~~~~~kviiide~~~l~---------------------~~~~~~Ll~~le~~----~~~~~~il~~~~~~~l~~~i~s--  145 (188)
T TIGR00678        93 QESGRRVVIIEDAERMN---------------------EAAANALLKTLEEP----PPNTLFILITPSPEKLLPTIRS--  145 (188)
T ss_pred             ccCCeEEEEEechhhhC---------------------HHHHHHHHHHhcCC----CCCeEEEEEECChHhChHHHHh--
Confidence               45799999999873                     23466788888753    3457788888888999999998  


Q ss_pred             ceeeEEEeCCCCHHHHHHHHHHH
Q 012016          381 RMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       381 Rfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                      |+ ..++|+.|+.++...++...
T Consensus       146 r~-~~~~~~~~~~~~~~~~l~~~  167 (188)
T TIGR00678       146 RC-QVLPFPPLSEEALLQWLIRQ  167 (188)
T ss_pred             hc-EEeeCCCCCHHHHHHHHHHc
Confidence            77 48999999999988777765

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.

>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=99.30  E-value=2.1e-12  Score=114.20  Aligned_cols=105  Identities=30%  Similarity=0.427  Sum_probs=73.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHH---------------HhccCceEEEecccccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLV---------------ATANRSILVVEDIDCTIDL  319 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~---------------~~~~~sIL~iDdiD~l~~~  319 (473)
                      ++||+||||||||++++.+|..++.+++.+.++...+..+|.....               ...++.|++||||+..   
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~a---   77 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINRA---   77 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG----
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcccC---
Confidence            5899999999999999999999999999998887644443321111               1126799999999865   


Q ss_pred             ccCCccccCCCCCCCccchhHHHHHHHHHhcccccC----------CCC-----ceEEEEecCCCC----CCCccccCCC
Q 012016          320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS----------CGD-----ERIIVFTTNHKE----KLDPALLRPG  380 (473)
Q Consensus       320 ~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~----------~~~-----~~iiI~tTN~~~----~ld~aLlrpg  380 (473)
                                        ...++..|++.++.-.-.          ...     +..||+|+|..+    .+++||++  
T Consensus        78 ------------------~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~--  137 (139)
T PF07728_consen   78 ------------------PPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLD--  137 (139)
T ss_dssp             -------------------HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHT--
T ss_pred             ------------------CHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHh--
Confidence                              234555566665532110          111     378999999988    89999999  


Q ss_pred             ce
Q 012016          381 RM  382 (473)
Q Consensus       381 Rf  382 (473)
                      ||
T Consensus       138 Rf  139 (139)
T PF07728_consen  138 RF  139 (139)
T ss_dssp             T-
T ss_pred             hC
Confidence            87

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.

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

Probab=99.30  E-value=6.3e-11  Score=121.18  Aligned_cols=198  Identities=17%  Similarity=0.261  Sum_probs=132.1

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc-----eEEcccccccCch
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD-----VYDLELTELRSNS  293 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~-----~~~l~~~~~~~~~  293 (473)
                      +.+..-++..+.+...+..++.+..         |.++++|||||||||..++-++.++.-+     ++++||....+..
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~~---------p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~   87 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGER---------PSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPY   87 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCCC---------CccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHH
Confidence            3477888888888887776665422         4569999999999999999999998443     8889988764322


Q ss_pred             H-HHHH------------------------HHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHH
Q 012016          294 D-LRTL------------------------LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF  348 (473)
Q Consensus       294 ~-l~~l------------------------~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~  348 (473)
                      . +.++                        +.......||++||+|.+..                .  ....+-.|+..
T Consensus        88 ~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~----------------~--~~~~LY~L~r~  149 (366)
T COG1474          88 QVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVD----------------K--DGEVLYSLLRA  149 (366)
T ss_pred             HHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhcc----------------c--cchHHHHHHhh
Confidence            1 1111                        22222457999999999964                0  11445555544


Q ss_pred             hcccccCCCCceEEEEecCCC---CCCCccccCCCce-eeEEEeCCCCHHHHHHHHHHHhCc--cccCCHHHHHHHHhcC
Q 012016          349 IDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRM-DVHVHMSYCTPSGFKLLAANYLGI--KEHILFEEIEELISTT  422 (473)
Q Consensus       349 ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRf-d~~I~~~~p~~~~r~~l~~~~l~~--~~~~l~~~i~~l~~~~  422 (473)
                      .+..    ...+++|+.+|..   +.+||.+..  ++ ..+|.||+.+.+|...|+......  ......+.+-.++.. 
T Consensus       150 ~~~~----~~~v~vi~i~n~~~~~~~ld~rv~s--~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~-  222 (366)
T COG1474         150 PGEN----KVKVSIIAVSNDDKFLDYLDPRVKS--SLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAA-  222 (366)
T ss_pred             cccc----ceeEEEEEEeccHHHHHHhhhhhhh--ccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHH-
Confidence            3332    3457888988876   578888875  44 356999999999999999987652  233344444433321 


Q ss_pred             CCCHHHHHHHHhcCCCHHHHHHHHHHHHHHhhhccc
Q 012016          423 QVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRKEDE  458 (473)
Q Consensus       423 ~~t~a~i~~~l~~~~~~~~al~~l~~~l~~~~~~~~  458 (473)
                              -....+||+..|++-+-.+.+...+...
T Consensus       223 --------~~a~~~GDAR~aidilr~A~eiAe~~~~  250 (366)
T COG1474         223 --------LVAAESGDARKAIDILRRAGEIAEREGS  250 (366)
T ss_pred             --------HHHHcCccHHHHHHHHHHHHHHHHhhCC
Confidence                    1112346888888888877776665433

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.29  E-value=1.9e-11  Score=123.75  Aligned_cols=154  Identities=21%  Similarity=0.301  Sum_probs=103.6

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------ceE------
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------DVY------  282 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------~~~------  282 (473)
                      -+|.+|+|+++.|..++..+..+             ...|+||.||+|||||++++++++.+..       |+.      
T Consensus        14 ~pf~~ivGq~~~k~al~~~~~~p-------------~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~~p   80 (350)
T CHL00081         14 FPFTAIVGQEEMKLALILNVIDP-------------KIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPSDP   80 (350)
T ss_pred             CCHHHHhChHHHHHHHHHhccCC-------------CCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCCCh
Confidence            47999999999999987765532             2358999999999999999999888731       111      


Q ss_pred             ----------------------Ecccccc---cCch------HHHHHHHH-----------hccCceEEEeccccccccc
Q 012016          283 ----------------------DLELTEL---RSNS------DLRTLLVA-----------TANRSILVVEDIDCTIDLQ  320 (473)
Q Consensus       283 ----------------------~l~~~~~---~~~~------~l~~l~~~-----------~~~~sIL~iDdiD~l~~~~  320 (473)
                                            .+.+..+   .++.      ++.+.+..           ..++++|++|||+.+.   
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~---  157 (350)
T CHL00081         81 ELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLD---  157 (350)
T ss_pred             hhhchhhhhhhcccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCC---
Confidence                                  0000000   0111      12222211           2246899999999873   


Q ss_pred             cCCccccCCCCCCCccchhHHHHHHHHHhcc---------cccCCCCceEEEEecCCCC-CCCccccCCCceeeEEEeCC
Q 012016          321 DRLPADIAGEGEGPIQQNKVTLSGFLNFIDG---------LWSSCGDERIIVFTTNHKE-KLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       321 ~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~~-~ld~aLlrpgRfd~~I~~~~  390 (473)
                                        ..+.+.|++.|+.         .....+...++|+|.|..+ .+.++|+.  ||.++|.+.+
T Consensus       158 ------------------~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~Lld--Rf~l~i~l~~  217 (350)
T CHL00081        158 ------------------DHLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGMHAEIRT  217 (350)
T ss_pred             ------------------HHHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHH--HhCceeecCC
Confidence                              3456667777743         1111223466667777554 69999999  9999999999


Q ss_pred             CC-HHHHHHHHHHHhC
Q 012016          391 CT-PSGFKLLAANYLG  405 (473)
Q Consensus       391 p~-~~~r~~l~~~~l~  405 (473)
                      |+ .+.+.+|+++...
T Consensus       218 ~~~~~~e~~il~~~~~  233 (350)
T CHL00081        218 VKDPELRVKIVEQRTS  233 (350)
T ss_pred             CCChHHHHHHHHhhhc
Confidence            98 5889999987644

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.27  E-value=1.9e-11  Score=118.20  Aligned_cols=129  Identities=25%  Similarity=0.373  Sum_probs=86.2

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE  288 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~  288 (473)
                      ..++.+|+++....+..+.++..+..|.....   .    ...+++|+||||||||+|+.|||+++   +..++.++..+
T Consensus        65 ~~~~~tFdnf~~~~~~q~~al~~a~~~~~~~~---~----~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~~  137 (244)
T PRK07952         65 LHQNCSFENYRVECEGQMNALSKARQYVEEFD---G----NIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVAD  137 (244)
T ss_pred             cccCCccccccCCCchHHHHHHHHHHHHHhhc---c----CCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHHH
Confidence            34567999997665555556666666664211   1    13489999999999999999999998   77888887766


Q ss_pred             ccC---------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCc
Q 012016          289 LRS---------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDE  359 (473)
Q Consensus       289 ~~~---------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~  359 (473)
                      +..         +....+++....+..+|+|||+++...                .......+..+++.-   ..   ..
T Consensus       138 l~~~l~~~~~~~~~~~~~~l~~l~~~dlLvIDDig~~~~----------------s~~~~~~l~~Ii~~R---y~---~~  195 (244)
T PRK07952        138 IMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEIGVQTE----------------SRYEKVIINQIVDRR---SS---SK  195 (244)
T ss_pred             HHHHHHHHHhhccccHHHHHHHhccCCEEEEeCCCCCCC----------------CHHHHHHHHHHHHHH---Hh---CC
Confidence            531         123345666677889999999987521                122334555555432   11   24


Q ss_pred             eEEEEecCCC
Q 012016          360 RIIVFTTNHK  369 (473)
Q Consensus       360 ~iiI~tTN~~  369 (473)
                      ..+|+|||..
T Consensus       196 ~~tiitSNl~  205 (244)
T PRK07952        196 RPTGMLTNSN  205 (244)
T ss_pred             CCEEEeCCCC
Confidence            6788899864

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.27  E-value=6.6e-11  Score=120.05  Aligned_cols=130  Identities=25%  Similarity=0.296  Sum_probs=90.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHH------HHHH------HHhcc---C---ceEEEeccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDL------RTLL------VATAN---R---SILVVEDID  314 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l------~~l~------~~~~~---~---sIL~iDdiD  314 (473)
                      .+.+||-||||||||++++++|..++.+++.++|..-...+++      ....      .-...   .   +|+++|||+
T Consensus        43 ~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEIn  122 (329)
T COG0714          43 GGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEIN  122 (329)
T ss_pred             CCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEeccc
Confidence            4579999999999999999999999999999998865332222      1111      00111   1   399999998


Q ss_pred             cccccccCCccccCCCCCCCccchhHHHHHHHHHhccc-------c-cCCCCceEEEEecC-----CCCCCCccccCCCc
Q 012016          315 CTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL-------W-SSCGDERIIVFTTN-----HKEKLDPALLRPGR  381 (473)
Q Consensus       315 ~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-------~-~~~~~~~iiI~tTN-----~~~~ld~aLlrpgR  381 (473)
                      ..                     ...+.+.||..|+.-       . -.-....++|+|+|     ....|++|+++  |
T Consensus       123 ra---------------------~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld--R  179 (329)
T COG0714         123 RA---------------------PPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD--R  179 (329)
T ss_pred             cC---------------------CHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh--h
Confidence            65                     245677788777651       1 11224467888889     34568999999  9


Q ss_pred             eeeEEEeCCC-CHHHHHHHHHHHhC
Q 012016          382 MDVHVHMSYC-TPSGFKLLAANYLG  405 (473)
Q Consensus       382 fd~~I~~~~p-~~~~r~~l~~~~l~  405 (473)
                      |...++++|| ..++...+......
T Consensus       180 f~~~~~v~yp~~~~e~~~i~~~~~~  204 (329)
T COG0714         180 FLLRIYVDYPDSEEEERIILARVGG  204 (329)
T ss_pred             EEEEEecCCCCchHHHHHHHHhCcc
Confidence            9999999999 55555555554443

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

Probab=99.27  E-value=5.7e-11  Score=127.06  Aligned_cols=180  Identities=26%  Similarity=0.353  Sum_probs=132.1

Q ss_pred             hchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc------CchHHHHHHHHhc--cCceEEEe
Q 012016          240 KRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR------SNSDLRTLLVATA--NRSILVVE  311 (473)
Q Consensus       240 ~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~------~~~~l~~l~~~~~--~~sIL~iD  311 (473)
                      ..++.++..+..++++++++||||||||.+++++|+. +.....++.....      ....++.++..+.  .++++++|
T Consensus         5 ~~~~~~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~d   83 (494)
T COG0464           5 KEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFID   83 (494)
T ss_pred             cCHHHHHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEeec
Confidence            3456678889999999999999999999999999999 5444555554432      2455666666654  56999999


Q ss_pred             ccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCC
Q 012016          312 DIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYC  391 (473)
Q Consensus       312 diD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p  391 (473)
                      ++|.+.+.+.-          ..........++++..+|++.  .+. ++++..||.+..+|+++++||||+..+.++.|
T Consensus        84 ~~~~~~~~~~~----------~~~~~~~~v~~~l~~~~d~~~--~~~-v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~  150 (494)
T COG0464          84 EIDALAPKRSS----------DQGEVERRVVAQLLALMDGLK--RGQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNLP  150 (494)
T ss_pred             hhhhcccCccc----------cccchhhHHHHHHHHhccccc--CCc-eEEEeecCCccccChhHhCccccceeeecCCC
Confidence            99999763321          112345678999999999987  455 88888999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHhCccccCCHHHHHHHHh-cCCCCHHHHHHHH
Q 012016          392 TPSGFKLLAANYLGIKEHILFEEIEELIS-TTQVTPAEVAEQL  433 (473)
Q Consensus       392 ~~~~r~~l~~~~l~~~~~~l~~~i~~l~~-~~~~t~a~i~~~l  433 (473)
                      +...+.++..................++. ..+++.+++..++
T Consensus       151 ~~~~~~ei~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~  193 (494)
T COG0464         151 DEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALA  193 (494)
T ss_pred             CHHHHHHHHHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHH
Confidence            99999877776543321111222222322 2347777776555

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=2.2e-10  Score=115.76  Aligned_cols=124  Identities=19%  Similarity=0.314  Sum_probs=95.7

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCC------------------------ceEEccccc---ccCchHHHHHHHHhc-
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNF------------------------DVYDLELTE---LRSNSDLRTLLVATA-  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~------------------------~~~~l~~~~---~~~~~~l~~l~~~~~-  303 (473)
                      .+.+|||+||+|+||+++|.++|+.+..                        +++.+....   ..+-+.++++..... 
T Consensus        21 ~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~~~~  100 (328)
T PRK05707         21 HPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSFVVQ  100 (328)
T ss_pred             cceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHHHhh
Confidence            3678999999999999999999998832                        455554321   224466777665543 


Q ss_pred             -----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          304 -----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       304 -----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                           ..-|++||++|.+                     +....+.||+.++..    +++.++|++|+.++.|.|+++.
T Consensus       101 ~~~~~~~kv~iI~~a~~m---------------------~~~aaNaLLK~LEEP----p~~~~fiL~t~~~~~ll~TI~S  155 (328)
T PRK05707        101 TAQLGGRKVVLIEPAEAM---------------------NRNAANALLKSLEEP----SGDTVLLLISHQPSRLLPTIKS  155 (328)
T ss_pred             ccccCCCeEEEECChhhC---------------------CHHHHHHHHHHHhCC----CCCeEEEEEECChhhCcHHHHh
Confidence                 3568899999987                     356778899999863    4568999999999999999998


Q ss_pred             CCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          379 PGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       379 pgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                        |+. .+.|+.|+.++....+...
T Consensus       156 --Rc~-~~~~~~~~~~~~~~~L~~~  177 (328)
T PRK05707        156 --RCQ-QQACPLPSNEESLQWLQQA  177 (328)
T ss_pred             --hce-eeeCCCcCHHHHHHHHHHh
Confidence              885 5999999999877666654

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.26  E-value=1.5e-10  Score=130.81  Aligned_cols=162  Identities=15%  Similarity=0.255  Sum_probs=109.0

Q ss_pred             ccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchH
Q 012016          218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSD  294 (473)
Q Consensus       218 f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~  294 (473)
                      +..|+|++...+.|...+.....+-.   .. ..|...+||+||+|||||++|++||+.+   +.+++.++++.+.....
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~---~~-~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~~~~  642 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLS---DP-NRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHS  642 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhccc---CC-CCCCceEEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhhhhh
Confidence            34678888887777776654322100   00 0112368999999999999999999988   45788888877643222


Q ss_pred             HHHHH---------------HH---hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc--cc
Q 012016          295 LRTLL---------------VA---TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL--WS  354 (473)
Q Consensus       295 l~~l~---------------~~---~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--~~  354 (473)
                      ..+++               ..   ....++|+|||++.+-                     ....+.|++.++.-  ..
T Consensus       643 ~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~---------------------~~v~~~Ll~ile~g~l~d  701 (857)
T PRK10865        643 VSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAH---------------------PDVFNILLQVLDDGRLTD  701 (857)
T ss_pred             HHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCC---------------------HHHHHHHHHHHhhCceec
Confidence            22222               11   1234899999998762                     34567777777531  11


Q ss_pred             CC-----CCceEEEEecCCC-------------------------CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          355 SC-----GDERIIVFTTNHK-------------------------EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       355 ~~-----~~~~iiI~tTN~~-------------------------~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      ..     -.+.+||+|||..                         ..+.|+|+.  |+|.++.|.+++.+....|+..++
T Consensus       702 ~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELln--Rld~iivF~PL~~edl~~Iv~~~L  779 (857)
T PRK10865        702 GQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHPLGEQHIASIAQIQL  779 (857)
T ss_pred             CCceEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHH--hCCeeEecCCCCHHHHHHHHHHHH
Confidence            11     1246899999972                         134577887  999999999999999999999887


Q ss_pred             Cc
Q 012016          405 GI  406 (473)
Q Consensus       405 ~~  406 (473)
                      ..
T Consensus       780 ~~  781 (857)
T PRK10865        780 QR  781 (857)
T ss_pred             HH
Confidence            53

>PRK09087 hypothetical protein; Validated

Probab=99.26  E-value=1.5e-10  Score=111.09  Aligned_cols=161  Identities=13%  Similarity=0.131  Sum_probs=96.4

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR  290 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~  290 (473)
                      ...++.+|++++..+.- ..+...+..+.         + ...+.++||||+|+|||+|++++|+..+..++...  .+.
T Consensus        13 ~~~~~~~~~~Fi~~~~N-~~a~~~l~~~~---------~-~~~~~l~l~G~~GsGKThLl~~~~~~~~~~~i~~~--~~~   79 (226)
T PRK09087         13 SHDPAYGRDDLLVTESN-RAAVSLVDHWP---------N-WPSPVVVLAGPVGSGKTHLASIWREKSDALLIHPN--EIG   79 (226)
T ss_pred             CCCCCCChhceeecCch-HHHHHHHHhcc---------c-CCCCeEEEECCCCCCHHHHHHHHHHhcCCEEecHH--Hcc
Confidence            34455689998853211 11333222211         1 11335999999999999999999998776654442  221


Q ss_pred             CchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCC
Q 012016          291 SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE  370 (473)
Q Consensus       291 ~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~  370 (473)
                       ...+    ... ...+|+|||+|.+..                   .+..+..++|.+.   ..  +..+||.++..|.
T Consensus        80 -~~~~----~~~-~~~~l~iDDi~~~~~-------------------~~~~lf~l~n~~~---~~--g~~ilits~~~p~  129 (226)
T PRK09087         80 -SDAA----NAA-AEGPVLIEDIDAGGF-------------------DETGLFHLINSVR---QA--GTSLLMTSRLWPS  129 (226)
T ss_pred             -hHHH----Hhh-hcCeEEEECCCCCCC-------------------CHHHHHHHHHHHH---hC--CCeEEEECCCChH
Confidence             1111    111 225899999997521                   1233444444443   22  2344544444443


Q ss_pred             C---CCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHH
Q 012016          371 K---LDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIE  416 (473)
Q Consensus       371 ~---ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~  416 (473)
                      .   ..|+|+.  |+.  ..+++..|+.+.+..++++.+...+..+.+++.
T Consensus       130 ~~~~~~~dL~S--Rl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~  178 (226)
T PRK09087        130 SWNVKLPDLKS--RLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVV  178 (226)
T ss_pred             HhccccccHHH--HHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            2   3678887  875  789999999999999999988765444444443

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.25  E-value=2.2e-10  Score=115.21  Aligned_cols=174  Identities=17%  Similarity=0.230  Sum_probs=117.9

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-----------------
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-----------------  279 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-----------------  279 (473)
                      .|++|+|++.+++.+...+..            ...+.+|||+||+|+||+++|.++|+.+-.                 
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~------------~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~h   69 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQ------------NRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNH   69 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHh------------CCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCC
Confidence            488999999988877665431            123569999999999999999999998721                 


Q ss_pred             -ceEEcccccc-----------------------cCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCC
Q 012016          280 -DVYDLELTEL-----------------------RSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAG  329 (473)
Q Consensus       280 -~~~~l~~~~~-----------------------~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~  329 (473)
                       +++.+.....                       ..-+.++++.....      ...|++||++|.+             
T Consensus        70 PDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m-------------  136 (314)
T PRK07399         70 PDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETM-------------  136 (314)
T ss_pred             CCEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhc-------------
Confidence             2232222100                       01124555544432      4589999999987             


Q ss_pred             CCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc
Q 012016          330 EGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH  409 (473)
Q Consensus       330 ~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~  409 (473)
                              +....+.||..|+..    + +.++|++|+.++.|-|+++.  |+ ..|+|+.++.++...++......+. 
T Consensus       137 --------~~~aaNaLLK~LEEP----p-~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~~~~~~~L~~~~~~~~-  199 (314)
T PRK07399        137 --------NEAAANALLKTLEEP----G-NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLSDEQLEQVLKRLGDEEI-  199 (314)
T ss_pred             --------CHHHHHHHHHHHhCC----C-CCeEEEEECChHhCcHHHHh--hc-eEEecCCCCHHHHHHHHHHhhcccc-
Confidence                    245678899999864    3 45788888899999999998  87 5899999999998888886543221 


Q ss_pred             CCHHHHHHHHhcCCCCHHHHHHHH
Q 012016          410 ILFEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       410 ~l~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                       ...+...++..++-+|....+.+
T Consensus       200 -~~~~~~~l~~~a~Gs~~~al~~l  222 (314)
T PRK07399        200 -LNINFPELLALAQGSPGAAIANI  222 (314)
T ss_pred             -chhHHHHHHHHcCCCHHHHHHHH
Confidence             11123444544455665554433

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.25  E-value=5.5e-11  Score=121.67  Aligned_cols=70  Identities=19%  Similarity=0.299  Sum_probs=50.7

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcC-CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGK-AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~-~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      .|+|+++.|+.+...+....++......... -.+.++||+||||||||+++++||..++.+++.++++.+
T Consensus        16 ~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~f   86 (443)
T PRK05201         16 YIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKF   86 (443)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchhh
Confidence            3789999999987766543322111001111 125789999999999999999999999999999987644

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.24  E-value=4e-10  Score=114.26  Aligned_cols=146  Identities=19%  Similarity=0.279  Sum_probs=104.2

Q ss_pred             Ccccccc-chHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC----------------
Q 012016          217 TFETLAM-EQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF----------------  279 (473)
Q Consensus       217 ~f~~l~~-~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~----------------  279 (473)
                      .|++|.| ++.+.+.+...+.    .        ...+..||||||+|+||+++|.++|+.+-.                
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~----~--------~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~   70 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIA----K--------NRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCK   70 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHH----c--------CCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHH
Confidence            4677877 6666665544332    1        234678999999999999999999998721                


Q ss_pred             --------ceEEcccccc-cCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHH
Q 012016          280 --------DVYDLELTEL-RSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSG  344 (473)
Q Consensus       280 --------~~~~l~~~~~-~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~  344 (473)
                              ++..+....- ...+.++++.....      ..-|++|||+|.+                     +....+.
T Consensus        71 ~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~---------------------~~~a~Na  129 (329)
T PRK08058         71 RIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKM---------------------TASAANS  129 (329)
T ss_pred             HHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhh---------------------CHHHHHH
Confidence                    2333322211 12346666655433      4579999999987                     2456788


Q ss_pred             HHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHH
Q 012016          345 FLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       345 LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~  402 (473)
                      ||..|+.    +++..++|++|+.++.|.|+++.  |+ .+++|+.|+.++....+..
T Consensus       130 LLK~LEE----Pp~~~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        130 LLKFLEE----PSGGTTAILLTENKHQILPTILS--RC-QVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             HHHHhcC----CCCCceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCHHHHHHHHHH
Confidence            9999985    34568888999999999999998  77 5799999999987666653

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.23  E-value=7.1e-11  Score=120.81  Aligned_cols=70  Identities=19%  Similarity=0.319  Sum_probs=51.1

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhc-CCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVG-KAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g-~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      -++|+++.|+.+...+....++...-...+ -..|+++||+||||||||++++++|..++.+++.++.+.+
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~~   83 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKF   83 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeEEEeeccee
Confidence            478889999988776664433221111111 1235899999999999999999999999999999986543

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.

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.23  E-value=3.1e-10  Score=114.78  Aligned_cols=153  Identities=22%  Similarity=0.293  Sum_probs=102.2

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-------CCceE-------
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-------NFDVY-------  282 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-------~~~~~-------  282 (473)
                      +|..|+|+++.|..++-.+..+             ...+++|.||||||||++++++++.+       +.++-       
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            5889999999998875544421             13479999999999999999999877       22111       


Q ss_pred             --------------------------Ecccc----cccCchHHHHHHH-----------HhccCceEEEecccccccccc
Q 012016          283 --------------------------DLELT----ELRSNSDLRTLLV-----------ATANRSILVVEDIDCTIDLQD  321 (473)
Q Consensus       283 --------------------------~l~~~----~~~~~~~l~~l~~-----------~~~~~sIL~iDdiD~l~~~~~  321 (473)
                                                ++...    .+.+.-.+...+.           ...++.+|+||||+.+.    
T Consensus        69 ~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~----  144 (337)
T TIGR02030        69 MMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLE----  144 (337)
T ss_pred             ccChHHhhhhhcccccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCC----
Confidence                                      11100    1111112222221           12356899999999872    


Q ss_pred             CCccccCCCCCCCccchhHHHHHHHHHhcc---------cccCCCCceEEEEecCCCC-CCCccccCCCceeeEEEeCCC
Q 012016          322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDG---------LWSSCGDERIIVFTTNHKE-KLDPALLRPGRMDVHVHMSYC  391 (473)
Q Consensus       322 r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~~-~ld~aLlrpgRfd~~I~~~~p  391 (473)
                                       ..+.+.|++.|+.         .........++|+|+|..+ .+.++|+.  ||.+++.+++|
T Consensus       145 -----------------~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p  205 (337)
T TIGR02030       145 -----------------DHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTV  205 (337)
T ss_pred             -----------------HHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHh--hcceEEECCCC
Confidence                             3566777777742         2112223467777777554 68999999  99999999999


Q ss_pred             CH-HHHHHHHHHHhC
Q 012016          392 TP-SGFKLLAANYLG  405 (473)
Q Consensus       392 ~~-~~r~~l~~~~l~  405 (473)
                      .. +++.+|+.+...
T Consensus       206 ~~~eer~eIL~~~~~  220 (337)
T TIGR02030       206 RDVELRVEIVERRTE  220 (337)
T ss_pred             CCHHHHHHHHHhhhh
Confidence            86 888889887543

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.22  E-value=2.6e-10  Score=129.12  Aligned_cols=160  Identities=18%  Similarity=0.285  Sum_probs=108.4

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHH
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDL  295 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l  295 (473)
                      ..|+|++...+.+.+.+.....+-.   . ...|...+||+||+|||||++|++||..+   +.+++.++++.......+
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~---~-~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~  640 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLS---D-PNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSV  640 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCC---C-CCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchH
Confidence            3577888877777776654321100   0 01123469999999999999999999988   568888888776332222


Q ss_pred             HHH---------------H-H--HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--cC
Q 012016          296 RTL---------------L-V--ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--SS  355 (473)
Q Consensus       296 ~~l---------------~-~--~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--~~  355 (473)
                      ..+               + .  .....+||+|||||.+                     .....+.||+.+|.-.  ..
T Consensus       641 ~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka---------------------~~~v~~~Ll~~l~~g~l~d~  699 (852)
T TIGR03346       641 ARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKA---------------------HPDVFNVLLQVLDDGRLTDG  699 (852)
T ss_pred             HHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccC---------------------CHHHHHHHHHHHhcCceecC
Confidence            221               1 1  1124589999999976                     2456677888775321  11


Q ss_pred             C-----CCceEEEEecCCCC-------------------------CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          356 C-----GDERIIVFTTNHKE-------------------------KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       356 ~-----~~~~iiI~tTN~~~-------------------------~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      .     -.+.+||+|||...                         .+.|.|+.  |+|.+|.|.+++.+....|+...+.
T Consensus       700 ~g~~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL~~e~l~~I~~l~L~  777 (852)
T TIGR03346       700 QGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPLGREQIARIVEIQLG  777 (852)
T ss_pred             CCeEEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCcCHHHHHHHHHHHHH
Confidence            1     13578999999731                         13466666  9999999999999999999988765

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.21  E-value=1.9e-10  Score=129.53  Aligned_cols=156  Identities=17%  Similarity=0.252  Sum_probs=106.3

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCc-eeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc---
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKR-GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN---  292 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~r-g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~---  292 (473)
                      .|+|+++..+.+.+.+.....+-.   .  ...|. .+||+||||||||.+|+++|..+   ...++.++++++...   
T Consensus       567 ~v~GQ~~Av~~v~~~i~~~~~gl~---~--~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~~~  641 (852)
T TIGR03345       567 RVIGQDHALEAIAERIRTARAGLE---D--PRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAHTV  641 (852)
T ss_pred             eEcChHHHHHHHHHHHHHHhcCCC---C--CCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhhhh
Confidence            577888888887777654432110   0  01133 48999999999999999999998   457788887765221   


Q ss_pred             ----------------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--c
Q 012016          293 ----------------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--S  354 (473)
Q Consensus       293 ----------------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--~  354 (473)
                                      ..|.+.+.. ...+||+|||||.+                     .....+.|+..+|.-.  .
T Consensus       642 ~~l~g~~~gyvg~~~~g~L~~~v~~-~p~svvllDEieka---------------------~~~v~~~Llq~ld~g~l~d  699 (852)
T TIGR03345       642 SRLKGSPPGYVGYGEGGVLTEAVRR-KPYSVVLLDEVEKA---------------------HPDVLELFYQVFDKGVMED  699 (852)
T ss_pred             ccccCCCCCcccccccchHHHHHHh-CCCcEEEEechhhc---------------------CHHHHHHHHHHhhcceeec
Confidence                            123333332 45699999999865                     2345666777776321  1


Q ss_pred             CCC-----CceEEEEecCCCC-----------------------------CCCccccCCCceeeEEEeCCCCHHHHHHHH
Q 012016          355 SCG-----DERIIVFTTNHKE-----------------------------KLDPALLRPGRMDVHVHMSYCTPSGFKLLA  400 (473)
Q Consensus       355 ~~~-----~~~iiI~tTN~~~-----------------------------~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~  400 (473)
                      ..|     .+.+||+|||...                             .+.|+|+.  |++ .|.|...+.+....|+
T Consensus       700 ~~Gr~vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv  776 (852)
T TIGR03345       700 GEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIPYLPLDDDVLAAIV  776 (852)
T ss_pred             CCCcEEeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEEeCCCCHHHHHHHH
Confidence            111     3579999999521                             14566777  998 7899999999999999


Q ss_pred             HHHhC
Q 012016          401 ANYLG  405 (473)
Q Consensus       401 ~~~l~  405 (473)
                      ...+.
T Consensus       777 ~~~L~  781 (852)
T TIGR03345       777 RLKLD  781 (852)
T ss_pred             HHHHH
Confidence            88775

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.

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.21  E-value=7.5e-10  Score=112.07  Aligned_cols=125  Identities=18%  Similarity=0.211  Sum_probs=94.6

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------------------ceEEcccc------------------
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------------------DVYDLELT------------------  287 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------------------~~~~l~~~------------------  287 (473)
                      ..+.+|||+||+|+||+++|.++|+.+..                         +++.+...                  
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            44679999999999999999999998832                         12222211                  


Q ss_pred             -----------cccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhc
Q 012016          288 -----------ELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID  350 (473)
Q Consensus       288 -----------~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld  350 (473)
                                 ....-+.++++.....      ..-|++||++|.+                     +....+.||+.++
T Consensus        99 ~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m---------------------~~~AaNaLLKtLE  157 (342)
T PRK06964         99 DEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEAL---------------------NVAAANALLKTLE  157 (342)
T ss_pred             hcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhc---------------------CHHHHHHHHHHhc
Confidence                       0112345666655543      3469999999987                     3567789999998


Q ss_pred             ccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          351 GLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       351 g~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                      .    +++++++|++|++++.|.|++++  |+ ..|.|+.|+.++..+.+...
T Consensus       158 E----Pp~~t~fiL~t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        158 E----PPPGTVFLLVSARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             C----CCcCcEEEEEECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            5    45679999999999999999998  88 68999999999888776653

>PRK08116 hypothetical protein; Validated

Probab=99.21  E-value=1.1e-10  Score=114.76  Aligned_cols=149  Identities=23%  Similarity=0.354  Sum_probs=91.0

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC-
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS-  291 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~-  291 (473)
                      .+|+++...++. ..+...+..+...   +... .....|++|+||||||||+|+.|+|+++   +.+++.++..++.. 
T Consensus        82 ~tFdnf~~~~~~-~~a~~~a~~y~~~---~~~~-~~~~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~  156 (268)
T PRK08116         82 STFENFLFDKGS-EKAYKIARKYVKK---FEEM-KKENVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNR  156 (268)
T ss_pred             cchhcccCChHH-HHHHHHHHHHHHH---HHhh-ccCCceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHH
Confidence            467777644433 3334444444432   1111 1224689999999999999999999987   78888888765421 


Q ss_pred             ---------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE
Q 012016          292 ---------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII  362 (473)
Q Consensus       292 ---------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  362 (473)
                               .....+++....+..+|+|||+...-                   ........|.+.+|....   .+..+
T Consensus       157 i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~-------------------~t~~~~~~l~~iin~r~~---~~~~~  214 (268)
T PRK08116        157 IKSTYKSSGKEDENEIIRSLVNADLLILDDLGAER-------------------DTEWAREKVYNIIDSRYR---KGLPT  214 (268)
T ss_pred             HHHHHhccccccHHHHHHHhcCCCEEEEecccCCC-------------------CCHHHHHHHHHHHHHHHH---CCCCE
Confidence                     11223455556677899999996421                   112334455666665432   23568


Q ss_pred             EEecCCC-CC----CCccccCCCce---eeEEEeCCCCH
Q 012016          363 VFTTNHK-EK----LDPALLRPGRM---DVHVHMSYCTP  393 (473)
Q Consensus       363 I~tTN~~-~~----ld~aLlrpgRf---d~~I~~~~p~~  393 (473)
                      |+|||.+ +.    +++.+..  |+   ...|.|+-++.
T Consensus       215 IiTsN~~~~eL~~~~~~ri~s--Rl~e~~~~v~~~g~d~  251 (268)
T PRK08116        215 IVTTNLSLEELKNQYGKRIYD--RILEMCTPVENEGKSY  251 (268)
T ss_pred             EEECCCCHHHHHHHHhHHHHH--HHHHcCEEEEeeCcCh
Confidence            8888875 33    5666766  64   44567766664

>PRK08181 transposase; Validated

Probab=99.19  E-value=1.1e-10  Score=114.52  Aligned_cols=64  Identities=30%  Similarity=0.485  Sum_probs=51.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC-------chHHHHHHHHhccCceEEEeccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS-------NSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~-------~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      ..+++|+||||||||+|+.|+|+++   |+.++.++..++..       +..+.+.+....+..+|+|||++..
T Consensus       106 ~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~  179 (269)
T PRK08181        106 GANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYV  179 (269)
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEeccccc
Confidence            4689999999999999999999866   77888877766521       2345566677778899999999876

>PRK08939 primosomal protein DnaI; Reviewed

Probab=99.18  E-value=8.3e-11  Score=117.70  Aligned_cols=96  Identities=24%  Similarity=0.388  Sum_probs=70.0

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc--
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR--  290 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~--  290 (473)
                      .+|+++...+..+..+......|+...   ..  .+..+|++|+||+|||||+|+.|||+++   |.++..+...++.  
T Consensus       124 atf~~~~~~~~~~~~~~~~~~~fi~~~---~~--~~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~~  198 (306)
T PRK08939        124 ASLADIDLDDRDRLDALMAALDFLEAY---PP--GEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIRE  198 (306)
T ss_pred             CcHHHhcCCChHHHHHHHHHHHHHHHh---hc--cCCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHHH
Confidence            678888766555556666666666532   11  1245799999999999999999999998   7777777665541  


Q ss_pred             -----CchHHHHHHHHhccCceEEEeccccc
Q 012016          291 -----SNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       291 -----~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                           .+..+.+.+....+..+|+|||+..-
T Consensus       199 lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e  229 (306)
T PRK08939        199 LKNSISDGSVKEKIDAVKEAPVLMLDDIGAE  229 (306)
T ss_pred             HHHHHhcCcHHHHHHHhcCCCEEEEecCCCc
Confidence                 22345666777788999999999754

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.18  E-value=4.1e-10  Score=127.16  Aligned_cols=159  Identities=19%  Similarity=0.288  Sum_probs=105.9

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCch--
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNS--  293 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~--  293 (473)
                      +.|+|+++..+.|...+.....+-   .. ...|...+||+||+|||||+||++||+.+   +.+++.+++++.....  
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl---~~-~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGL---KN-PNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTV  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcc---cC-CCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccH
Confidence            357787777777766554322110   00 01122358999999999999999999988   4678888877653211  


Q ss_pred             -----------------HHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--c
Q 012016          294 -----------------DLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--S  354 (473)
Q Consensus       294 -----------------~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--~  354 (473)
                                       .|.+.+. ....+||+|||+|.+                     .....+.|+..+|.-.  .
T Consensus       585 ~~l~g~~~gyvg~~~~~~l~~~~~-~~p~~VvllDeieka---------------------~~~v~~~Llq~le~g~~~d  642 (821)
T CHL00095        585 SKLIGSPPGYVGYNEGGQLTEAVR-KKPYTVVLFDEIEKA---------------------HPDIFNLLLQILDDGRLTD  642 (821)
T ss_pred             HHhcCCCCcccCcCccchHHHHHH-hCCCeEEEECChhhC---------------------CHHHHHHHHHHhccCceec
Confidence                             1222222 123489999999976                     2456777888887421  1


Q ss_pred             CC-----CCceEEEEecCCCCC-------------------------------------CCccccCCCceeeEEEeCCCC
Q 012016          355 SC-----GDERIIVFTTNHKEK-------------------------------------LDPALLRPGRMDVHVHMSYCT  392 (473)
Q Consensus       355 ~~-----~~~~iiI~tTN~~~~-------------------------------------ld~aLlrpgRfd~~I~~~~p~  392 (473)
                      ..     -.+.+||+|||....                                     +.|.|+.  |+|.+|.|...+
T Consensus       643 ~~g~~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln--Rid~ii~F~pL~  720 (821)
T CHL00095        643 SKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN--RLDEIIVFRQLT  720 (821)
T ss_pred             CCCcEEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhc--cCCeEEEeCCCC
Confidence            11     145899999995311                                     2245566  999999999999


Q ss_pred             HHHHHHHHHHHhC
Q 012016          393 PSGFKLLAANYLG  405 (473)
Q Consensus       393 ~~~r~~l~~~~l~  405 (473)
                      .++..+|+...+.
T Consensus       721 ~~~l~~Iv~~~l~  733 (821)
T CHL00095        721 KNDVWEIAEIMLK  733 (821)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999988775

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.16  E-value=4.5e-10  Score=122.55  Aligned_cols=159  Identities=18%  Similarity=0.293  Sum_probs=114.1

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccccccCchHHH
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELTELRSNSDLR  296 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~~~~~~~~l~  296 (473)
                      .|+|+++....+.+.+..-..+   ... ...|-..+||.||.|+|||.||+++|..|.   -.++.+|+++......+.
T Consensus       492 rViGQd~AV~avs~aIrraRaG---L~d-p~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~EkHsVS  567 (786)
T COG0542         492 RVIGQDEAVEAVSDAIRRARAG---LGD-PNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHSVS  567 (786)
T ss_pred             ceeChHHHHHHHHHHHHHHhcC---CCC-CCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHHHHHHH
Confidence            4778777777766655533221   000 012234689999999999999999999996   889999999986655555


Q ss_pred             HHHHHhc------------------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc--ccCC
Q 012016          297 TLLVATA------------------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL--WSSC  356 (473)
Q Consensus       297 ~l~~~~~------------------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--~~~~  356 (473)
                      +++-.-+                  ..|||++|||+..                     ....++-||+.||.-  ....
T Consensus       568 rLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKA---------------------HpdV~nilLQVlDdGrLTD~~  626 (786)
T COG0542         568 RLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKA---------------------HPDVFNLLLQVLDDGRLTDGQ  626 (786)
T ss_pred             HHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhc---------------------CHHHHHHHHHHhcCCeeecCC
Confidence            5543221                  2489999999864                     456888899999742  2222


Q ss_pred             C-----CceEEEEecCCC----------------------------CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          357 G-----DERIIVFTTNHK----------------------------EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       357 ~-----~~~iiI~tTN~~----------------------------~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                      |     .+.|||+|||--                            ..+.|+++.  |+|..|.|...+.+...+|+...
T Consensus       627 Gr~VdFrNtiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~  704 (786)
T COG0542         627 GRTVDFRNTIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQ  704 (786)
T ss_pred             CCEEecceeEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHH
Confidence            2     257899999942                            013456666  99999999999999999999988


Q ss_pred             hC
Q 012016          404 LG  405 (473)
Q Consensus       404 l~  405 (473)
                      +.
T Consensus       705 L~  706 (786)
T COG0542         705 LN  706 (786)
T ss_pred             HH
Confidence            75

>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=99.14  E-value=8.6e-10  Score=100.42  Aligned_cols=112  Identities=17%  Similarity=0.300  Sum_probs=81.6

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc-----------------------CCceEEcccccc---cCchHHHHHHHHhc--
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL-----------------------NFDVYDLELTEL---RSNSDLRTLLVATA--  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l-----------------------~~~~~~l~~~~~---~~~~~l~~l~~~~~--  303 (473)
                      .+..|||+||+|+||+++|.++|+.+                       ..+++.++....   ...+.++++.....  
T Consensus        18 l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~   97 (162)
T PF13177_consen   18 LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLS   97 (162)
T ss_dssp             --SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHHHHHHHHHHH
Confidence            46789999999999999999999987                       134455544432   24467777766553  


Q ss_pred             ----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCC
Q 012016          304 ----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRP  379 (473)
Q Consensus       304 ----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrp  379 (473)
                          ..-|++|||+|.+                     .....+.||..|+..    +...++|++|+.++.|.|.++. 
T Consensus        98 ~~~~~~KviiI~~ad~l---------------------~~~a~NaLLK~LEep----p~~~~fiL~t~~~~~il~TI~S-  151 (162)
T PF13177_consen   98 PSEGKYKVIIIDEADKL---------------------TEEAQNALLKTLEEP----PENTYFILITNNPSKILPTIRS-  151 (162)
T ss_dssp             -TTSSSEEEEEETGGGS----------------------HHHHHHHHHHHHST----TTTEEEEEEES-GGGS-HHHHT-
T ss_pred             HhcCCceEEEeehHhhh---------------------hHHHHHHHHHHhcCC----CCCEEEEEEECChHHChHHHHh-
Confidence                3579999999987                     356789999999854    4679999999999999999998 


Q ss_pred             CceeeEEEeCCC
Q 012016          380 GRMDVHVHMSYC  391 (473)
Q Consensus       380 gRfd~~I~~~~p  391 (473)
                       |+ ..|.|+..
T Consensus       152 -Rc-~~i~~~~l  161 (162)
T PF13177_consen  152 -RC-QVIRFRPL  161 (162)
T ss_dssp             -TS-EEEEE---
T ss_pred             -hc-eEEecCCC
Confidence             87 46777653

...

>PRK12377 putative replication protein; Provisional

Probab=99.13  E-value=4.3e-10  Score=109.11  Aligned_cols=94  Identities=19%  Similarity=0.329  Sum_probs=64.3

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC-
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS-  291 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~-  291 (473)
                      .+|+++....+..+.++..+..+...-   ..    ...+++|+||||||||+|+.|||+++   +..++.++..++.. 
T Consensus        71 ~tFdnf~~~~~~~~~a~~~a~~~a~~~---~~----~~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~~~  143 (248)
T PRK12377         71 CSFANYQVQNDGQRYALSQAKSIADEL---MT----GCTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVMSR  143 (248)
T ss_pred             CCcCCcccCChhHHHHHHHHHHHHHHH---Hh----cCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHHHH
Confidence            578887654433434445454444321   11    13589999999999999999999998   67777777666521 


Q ss_pred             -------chHHHHHHHHhccCceEEEeccccc
Q 012016          292 -------NSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       292 -------~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                             .....+++....+..+|+|||++..
T Consensus       144 l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~  175 (248)
T PRK12377        144 LHESYDNGQSGEKFLQELCKVDLLVLDEIGIQ  175 (248)
T ss_pred             HHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence                   1123456667778899999999764

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.12  E-value=6.6e-10  Score=111.82  Aligned_cols=117  Identities=21%  Similarity=0.336  Sum_probs=89.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC------------------------CceEEcccccccC----chHHHHHHHHhc-
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN------------------------FDVYDLELTELRS----NSDLRTLLVATA-  303 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~------------------------~~~~~l~~~~~~~----~~~l~~l~~~~~-  303 (473)
                      +..+||+||||||||++|.++|+.+.                        .+++.++.++...    .+.++++..... 
T Consensus        24 ~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~  103 (325)
T COG0470          24 PHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSE  103 (325)
T ss_pred             CceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHHhcc
Confidence            34799999999999999999999986                        5888888888754    234555544432 


Q ss_pred             -----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          304 -----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       304 -----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                           ..-|++|||+|.+.                     ....+.|+..++..    +.+..+|++||.+..+-|.+..
T Consensus       104 ~~~~~~~kviiidead~mt---------------------~~A~nallk~lEep----~~~~~~il~~n~~~~il~tI~S  158 (325)
T COG0470         104 SPLEGGYKVVIIDEADKLT---------------------EDAANALLKTLEEP----PKNTRFILITNDPSKILPTIRS  158 (325)
T ss_pred             CCCCCCceEEEeCcHHHHh---------------------HHHHHHHHHHhccC----CCCeEEEEEcCChhhccchhhh
Confidence                 35799999999883                     35667788877743    4568899999999999998887


Q ss_pred             CCceeeEEEeCCCCHHHHH
Q 012016          379 PGRMDVHVHMSYCTPSGFK  397 (473)
Q Consensus       379 pgRfd~~I~~~~p~~~~r~  397 (473)
                        |+ ..+.|+.|+...+.
T Consensus       159 --Rc-~~i~f~~~~~~~~i  174 (325)
T COG0470         159 --RC-QRIRFKPPSRLEAI  174 (325)
T ss_pred             --cc-eeeecCCchHHHHH
Confidence              77 47888876655543

>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=99.12  E-value=1.6e-10  Score=106.14  Aligned_cols=108  Identities=24%  Similarity=0.417  Sum_probs=76.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC----ceEEcccccccC----chHHHHHHHHhc------cCceEEEeccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF----DVYDLELTELRS----NSDLRTLLVATA------NRSILVVEDIDCTID  318 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~----~~~~l~~~~~~~----~~~l~~l~~~~~------~~sIL~iDdiD~l~~  318 (473)
                      ...+||.||+|||||.|++++|..+..    +++.+|++.+..    ...+..++....      ...||+|||||.+..
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            457999999999999999999999996    999999999876    444555554432      457999999999854


Q ss_pred             cccCCccccCCCCCCCccchhHHHHHHHHHhccccc--CCC-----CceEEEEecCCCC
Q 012016          319 LQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS--SCG-----DERIIVFTTNHKE  370 (473)
Q Consensus       319 ~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~--~~~-----~~~iiI~tTN~~~  370 (473)
                      .          ...+.+.......+.||..||+-.-  ..+     .+.+||+|+|--.
T Consensus        83 ~----------~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~  131 (171)
T PF07724_consen   83 S----------NSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGA  131 (171)
T ss_dssp             T----------TTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSST
T ss_pred             c----------ccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccccc
Confidence            1          0012223344667888888875321  112     3579999999743

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 ....

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.10  E-value=4.4e-09  Score=105.80  Aligned_cols=124  Identities=13%  Similarity=0.128  Sum_probs=95.0

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC------------------------CceEEccc--ccccCchHHHHHHHHhc--
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN------------------------FDVYDLEL--TELRSNSDLRTLLVATA--  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~------------------------~~~~~l~~--~~~~~~~~l~~l~~~~~--  303 (473)
                      .+.+|||+||+|+||+++|.++|+.+-                        -+++.+..  +...+.+.+|++.....  
T Consensus        23 l~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~I~id~iR~l~~~~~~~  102 (325)
T PRK06871         23 GHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKDIGVDQVREINEKVSQH  102 (325)
T ss_pred             cceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCCCCHHHHHHHHHHHhhc
Confidence            367999999999999999999999872                        23444432  11224456776655442  


Q ss_pred             ----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCC
Q 012016          304 ----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRP  379 (473)
Q Consensus       304 ----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrp  379 (473)
                          ..-|++||++|.+                     +....+.||+.++.    +++..++|++|+.++.|.|++++ 
T Consensus       103 ~~~g~~KV~iI~~a~~m---------------------~~~AaNaLLKtLEE----Pp~~~~fiL~t~~~~~llpTI~S-  156 (325)
T PRK06871        103 AQQGGNKVVYIQGAERL---------------------TEAAANALLKTLEE----PRPNTYFLLQADLSAALLPTIYS-  156 (325)
T ss_pred             cccCCceEEEEechhhh---------------------CHHHHHHHHHHhcC----CCCCeEEEEEECChHhCchHHHh-
Confidence                3469999999987                     35678899999985    45679999999999999999998 


Q ss_pred             CceeeEEEeCCCCHHHHHHHHHHH
Q 012016          380 GRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       380 gRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                       |+ .++.|+.|+.++..+.+...
T Consensus       157 -RC-~~~~~~~~~~~~~~~~L~~~  178 (325)
T PRK06871        157 -RC-QTWLIHPPEEQQALDWLQAQ  178 (325)
T ss_pred             -hc-eEEeCCCCCHHHHHHHHHHH
Confidence             87 57899999999877666543

>PRK06526 transposase; Provisional

Probab=99.10  E-value=1.1e-10  Score=113.72  Aligned_cols=64  Identities=23%  Similarity=0.386  Sum_probs=48.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc-------CchHHHHHHHHhccCceEEEeccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR-------SNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~-------~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      +.+++|+||||||||+|+.+|+.++   |+.++.....++.       ....+...+.......+|+|||++.+
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~  171 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYI  171 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccC
Confidence            4589999999999999999999986   7777776665441       12234455556667899999999876

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.10  E-value=2.9e-09  Score=107.88  Aligned_cols=123  Identities=14%  Similarity=0.142  Sum_probs=95.5

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC------------------------CceEEcccc---cccCchHHHHHHHHhc-
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN------------------------FDVYDLELT---ELRSNSDLRTLLVATA-  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~------------------------~~~~~l~~~---~~~~~~~l~~l~~~~~-  303 (473)
                      .+.+|||+||+|+||+++|.++|..+-                        -+++.+...   ...+-+.+|++..... 
T Consensus        23 l~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~  102 (334)
T PRK07993         23 GHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKSSLGVDAVREVTEKLYE  102 (334)
T ss_pred             cceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccCCHHHHHHHHHHHhh
Confidence            467999999999999999999999882                        234444322   1234456777665543 


Q ss_pred             -----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          304 -----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       304 -----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                           ..-|++||++|.+                     +....+.||+.|+.    ++++.++|++|++++.|.|.+++
T Consensus       103 ~~~~g~~kV~iI~~ae~m---------------------~~~AaNaLLKtLEE----Pp~~t~fiL~t~~~~~lLpTIrS  157 (334)
T PRK07993        103 HARLGGAKVVWLPDAALL---------------------TDAAANALLKTLEE----PPENTWFFLACREPARLLATLRS  157 (334)
T ss_pred             ccccCCceEEEEcchHhh---------------------CHHHHHHHHHHhcC----CCCCeEEEEEECChhhChHHHHh
Confidence                 4579999999988                     35678899999985    45679999999999999999998


Q ss_pred             CCceeeEEEeCCCCHHHHHHHHHH
Q 012016          379 PGRMDVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       379 pgRfd~~I~~~~p~~~~r~~l~~~  402 (473)
                        |+. .+.|+.|+.++....+..
T Consensus       158 --RCq-~~~~~~~~~~~~~~~L~~  178 (334)
T PRK07993        158 --RCR-LHYLAPPPEQYALTWLSR  178 (334)
T ss_pred             --ccc-cccCCCCCHHHHHHHHHH
Confidence              885 689999999887766643

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.10  E-value=1.3e-09  Score=118.26  Aligned_cols=202  Identities=22%  Similarity=0.287  Sum_probs=119.5

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEE-c
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYD-L  284 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~-l  284 (473)
                      .|.  ....|.++++|+++++..+++...+....        .+..+.+.++|+||||||||++++++|+.++..++. .
T Consensus        73 pW~--eKyrP~~ldel~~~~~ki~~l~~~l~~~~--------~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~  142 (637)
T TIGR00602        73 PWV--EKYKPETQHELAVHKKKIEEVETWLKAQV--------LENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWS  142 (637)
T ss_pred             chH--HHhCCCCHHHhcCcHHHHHHHHHHHHhcc--------cccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHh
Confidence            463  36778999999999988777655444221        122334569999999999999999999999876544 1


Q ss_pred             ccc---c------------------ccCchHHHHHHHHh------------ccCceEEEeccccccccccCCccccCCCC
Q 012016          285 ELT---E------------------LRSNSDLRTLLVAT------------ANRSILVVEDIDCTIDLQDRLPADIAGEG  331 (473)
Q Consensus       285 ~~~---~------------------~~~~~~l~~l~~~~------------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~  331 (473)
                      +..   .                  ......+..++..+            .++.||||||++.++.             
T Consensus       143 npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~-------------  209 (637)
T TIGR00602       143 NPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFY-------------  209 (637)
T ss_pred             hhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhch-------------
Confidence            111   0                  01123344444432            2457999999998753             


Q ss_pred             CCCccchhHHHHHHHH--HhcccccCCCCceEEEE-ecCCCC--------------CCCccccCCCceeeEEEeCCCCHH
Q 012016          332 EGPIQQNKVTLSGFLN--FIDGLWSSCGDERIIVF-TTNHKE--------------KLDPALLRPGRMDVHVHMSYCTPS  394 (473)
Q Consensus       332 ~~~~~~~~~~ls~LL~--~ldg~~~~~~~~~iiI~-tTN~~~--------------~ld~aLlrpgRfd~~I~~~~p~~~  394 (473)
                          . ....+..+|.  ..+    . + ...+|+ +|..+.              .|.++++.--|+ .+|.|+..+..
T Consensus       210 ----r-~~~~lq~lLr~~~~e----~-~-~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv-~~I~FnPia~t  277 (637)
T TIGR00602       210 ----R-DTRALHEILRWKYVS----I-G-RCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRV-SNISFNPIAPT  277 (637)
T ss_pred             ----h-hHHHHHHHHHHHhhc----C-C-CceEEEEecCCccccccccccccchhcccCHhHhcccce-eEEEeCCCCHH
Confidence                1 1223444444  222    1 1 233333 332221              133677732245 37999999999


Q ss_pred             HHHHHHHHHhCccccCCHHHHHHHHhcCCC-CHHHHHHHH-hcCCCHHHHHHHHHHH
Q 012016          395 GFKLLAANYLGIKEHILFEEIEELISTTQV-TPAEVAEQL-MRNDDPELVLNGLIEF  449 (473)
Q Consensus       395 ~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~-t~a~i~~~l-~~~~~~~~al~~l~~~  449 (473)
                      +.++.+.+.+..+......       ...+ ++..+..++ ...||...|+..|.-+
T Consensus       278 ~l~K~L~rIl~~E~~~~~~-------~~~~p~~~~l~~I~~~s~GDiRsAIn~LQf~  327 (637)
T TIGR00602       278 IMKKFLNRIVTIEAKKNGE-------KIKVPKKTSVELLCQGCSGDIRSAINSLQFS  327 (637)
T ss_pred             HHHHHHHHHHHhhhhcccc-------ccccCCHHHHHHHHHhCCChHHHHHHHHHHH
Confidence            9888888777644211111       1112 233333333 3568999999888765

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.07  E-value=8.6e-10  Score=103.21  Aligned_cols=187  Identities=18%  Similarity=0.258  Sum_probs=110.8

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-C----CceEEc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-N----FDVYDL  284 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-~----~~~~~l  284 (473)
                      ++...|..+.+++|.++..+.+    .-+.+.       |-  -.+++|.||||||||+-+.++|++| |    --+..+
T Consensus        18 VeKYrP~~l~dIVGNe~tv~rl----~via~~-------gn--mP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLEL   84 (333)
T KOG0991|consen   18 VEKYRPSVLQDIVGNEDTVERL----SVIAKE-------GN--MPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLEL   84 (333)
T ss_pred             HHhhCchHHHHhhCCHHHHHHH----HHHHHc-------CC--CCceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhhc
Confidence            4567889999999998776654    223322       21  2379999999999999999999998 3    346677


Q ss_pred             ccccccCchHHHHHHHHhc---------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC
Q 012016          285 ELTELRSNSDLRTLLVATA---------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS  355 (473)
Q Consensus       285 ~~~~~~~~~~l~~l~~~~~---------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~  355 (473)
                      +.++-.+-.-++.-+..-.         +..|+++||.|.+..              +.    ++.+   -..|+-..+ 
T Consensus        85 NASdeRGIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~--------------gA----QQAl---RRtMEiyS~-  142 (333)
T KOG0991|consen   85 NASDERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTA--------------GA----QQAL---RRTMEIYSN-  142 (333)
T ss_pred             cCccccccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhh--------------HH----HHHH---HHHHHHHcc-
Confidence            8777666555555443322         347999999998853              21    2222   222332222 


Q ss_pred             CCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHHHHHhc
Q 012016          356 CGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMR  435 (473)
Q Consensus       356 ~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~~~l~~  435 (473)
                         ..-+.+++|..+++=+.+-.  |+. .+.++..+..+...-+.....             .+...+|+.-+...+..
T Consensus       143 ---ttRFalaCN~s~KIiEPIQS--RCA-iLRysklsd~qiL~Rl~~v~k-------------~Ekv~yt~dgLeaiift  203 (333)
T KOG0991|consen  143 ---TTRFALACNQSEKIIEPIQS--RCA-ILRYSKLSDQQILKRLLEVAK-------------AEKVNYTDDGLEAIIFT  203 (333)
T ss_pred             ---cchhhhhhcchhhhhhhHHh--hhH-hhhhcccCHHHHHHHHHHHHH-------------HhCCCCCcchHHHhhhh
Confidence               23466778877776555555  553 455666666654322222221             12334454444333332


Q ss_pred             -CCCHHHHHHHHHHHH
Q 012016          436 -NDDPELVLNGLIEFL  450 (473)
Q Consensus       436 -~~~~~~al~~l~~~l  450 (473)
                       .+|...|++.|..-.
T Consensus       204 a~GDMRQalNnLQst~  219 (333)
T KOG0991|consen  204 AQGDMRQALNNLQSTV  219 (333)
T ss_pred             ccchHHHHHHHHHHHh
Confidence             356666666655443

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.06  E-value=7.3e-10  Score=121.58  Aligned_cols=152  Identities=21%  Similarity=0.235  Sum_probs=102.8

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-------------------
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-------------------  277 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-------------------  277 (473)
                      .|..|+|++..+..+.-.+...             -..||||.||||||||+++++|++.+                   
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            4789999988887664333211             12479999999999999999999988                   


Q ss_pred             ----------------CCceEEcccccc----cCchHHHHHHH-----------HhccCceEEEeccccccccccCCccc
Q 012016          278 ----------------NFDVYDLELTEL----RSNSDLRTLLV-----------ATANRSILVVEDIDCTIDLQDRLPAD  326 (473)
Q Consensus       278 ----------------~~~~~~l~~~~~----~~~~~l~~l~~-----------~~~~~sIL~iDdiD~l~~~~~r~~~~  326 (473)
                                      ..+++.+.++..    .+.-++...+.           ......|||||||+.+-         
T Consensus        69 ~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~---------  139 (633)
T TIGR02442        69 EWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLD---------  139 (633)
T ss_pred             ccChhhhhcccccccCCCCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCC---------
Confidence                            245666554422    12222333221           11255799999999873         


Q ss_pred             cCCCCCCCccchhHHHHHHHHHhccc---------ccCCCCceEEEEecCCC-CCCCccccCCCceeeEEEeCCCC-HHH
Q 012016          327 IAGEGEGPIQQNKVTLSGFLNFIDGL---------WSSCGDERIIVFTTNHK-EKLDPALLRPGRMDVHVHMSYCT-PSG  395 (473)
Q Consensus       327 ~~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~-~~ld~aLlrpgRfd~~I~~~~p~-~~~  395 (473)
                                  ....+.|++.|+.-         ........++|+|+|.. ..|.++|+.  ||+.+|.++++. .++
T Consensus       140 ------------~~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~~l~i~v~~~~~~~~  205 (633)
T TIGR02442       140 ------------DHLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RFGLCVDVAAPRDPEE  205 (633)
T ss_pred             ------------HHHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--hcceEEEccCCCchHH
Confidence                        45677788887521         11112347888888864 468899999  999999999985 566


Q ss_pred             HHHHHHHHh
Q 012016          396 FKLLAANYL  404 (473)
Q Consensus       396 r~~l~~~~l  404 (473)
                      +.+++.+.+
T Consensus       206 ~~~il~~~~  214 (633)
T TIGR02442       206 RVEIIRRRL  214 (633)
T ss_pred             HHHHHHHHH
Confidence            777776544

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.06  E-value=1.1e-09  Score=94.74  Aligned_cols=118  Identities=24%  Similarity=0.354  Sum_probs=71.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc---eEEcccccccC--------------------chHHHHHHHHhc--cCce
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD---VYDLELTELRS--------------------NSDLRTLLVATA--NRSI  307 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~---~~~l~~~~~~~--------------------~~~l~~l~~~~~--~~sI  307 (473)
                      +..++|+||||||||++++++|..+...   ++.+++.....                    .......+..+.  .+.+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            4579999999999999999999999775   88888775421                    123333333333  2499


Q ss_pred             EEEeccccccccccCCccccCCCCCCCccchhHHHHHH--HHHhcccccCCCCceEEEEecCCC-CCCCccccCCCceee
Q 012016          308 LVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGF--LNFIDGLWSSCGDERIIVFTTNHK-EKLDPALLRPGRMDV  384 (473)
Q Consensus       308 L~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~L--L~~ldg~~~~~~~~~iiI~tTN~~-~~ld~aLlrpgRfd~  384 (473)
                      |+|||++.+...                . ........  .......  .......+|+++|.. ...+..+.+  |++.
T Consensus        82 iiiDei~~~~~~----------------~-~~~~~~~~~~~~~~~~~--~~~~~~~~i~~~~~~~~~~~~~~~~--~~~~  140 (148)
T smart00382       82 LILDEITSLLDA----------------E-QEALLLLLEELRLLLLL--KSEKNLTVILTTNDEKDLGPALLRR--RFDR  140 (148)
T ss_pred             EEEECCcccCCH----------------H-HHHHHHhhhhhHHHHHH--HhcCCCEEEEEeCCCccCchhhhhh--ccce
Confidence            999999987531                0 01100000  0000000  112347888888863 333444444  8888


Q ss_pred             EEEeCCC
Q 012016          385 HVHMSYC  391 (473)
Q Consensus       385 ~I~~~~p  391 (473)
                      ++.++.+
T Consensus       141 ~~~~~~~  147 (148)
T smart00382      141 RIVLLLI  147 (148)
T ss_pred             EEEecCC
Confidence            8887665

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.06  E-value=8.7e-10  Score=115.02  Aligned_cols=128  Identities=18%  Similarity=0.238  Sum_probs=81.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC--ceEEcccc-----cccCchHHHHH-----HHH-----hccCceEEEecccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF--DVYDLELT-----ELRSNSDLRTL-----LVA-----TANRSILVVEDIDC  315 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~--~~~~l~~~-----~~~~~~~l~~l-----~~~-----~~~~sIL~iDdiD~  315 (473)
                      ..++||+||||||||++|++++...+.  ++..+.+.     ++.+...+...     |..     .....+||+|||..
T Consensus        39 g~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~r  118 (498)
T PRK13531         39 GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWK  118 (498)
T ss_pred             CCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcCcHHHhhhhhcCchhhhcCCccccccEEeeccccc
Confidence            457999999999999999999998743  33322221     22111111111     111     11234899999975


Q ss_pred             ccccccCCccccCCCCCCCccchhHHHHHHHHHhc-ccccCCC-----CceEEEEecCCCC---CCCccccCCCceeeEE
Q 012016          316 TIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID-GLWSSCG-----DERIIVFTTNHKE---KLDPALLRPGRMDVHV  386 (473)
Q Consensus       316 l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld-g~~~~~~-----~~~iiI~tTN~~~---~ld~aLlrpgRfd~~I  386 (473)
                      +                     +..+.+.||..|. +.....+     +.+++|+|||...   ...+|+..  ||-+.|
T Consensus       119 a---------------------sp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~D--RFliri  175 (498)
T PRK13531        119 A---------------------GPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYD--RMLIRL  175 (498)
T ss_pred             C---------------------CHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHh--hEEEEE
Confidence            5                     4578888999983 3222111     2367777888532   23358999  999999


Q ss_pred             EeCCCC-HHHHHHHHHHH
Q 012016          387 HMSYCT-PSGFKLLAANY  403 (473)
Q Consensus       387 ~~~~p~-~~~r~~l~~~~  403 (473)
                      .+|+|+ .+++..|+...
T Consensus       176 ~vp~l~~~~~e~~lL~~~  193 (498)
T PRK13531        176 WLDKVQDKANFRSMLTSQ  193 (498)
T ss_pred             ECCCCCchHHHHHHHHcc
Confidence            999997 56667777653

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.06  E-value=1.7e-09  Score=112.02  Aligned_cols=115  Identities=17%  Similarity=0.288  Sum_probs=70.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc-----eEEcccc------cc------c------CchHHHHHHHHhc----cC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD-----VYDLELT------EL------R------SNSDLRTLLVATA----NR  305 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~-----~~~l~~~------~~------~------~~~~l~~l~~~~~----~~  305 (473)
                      +++++|+||||||||++|+++|+.+...     +..+...      ++      .      ....+.+++..+.    .+
T Consensus       194 ~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~  273 (459)
T PRK11331        194 KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKK  273 (459)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccCC
Confidence            4689999999999999999999988421     1111111      10      0      0122333444432    57


Q ss_pred             ceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc------------------ccCCCCceEEEEecC
Q 012016          306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL------------------WSSCGDERIIVFTTN  367 (473)
Q Consensus       306 sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~------------------~~~~~~~~iiI~tTN  367 (473)
                      .+||||||+..-.                    ...+..++..|+.-                  .-.-+.++.||+|+|
T Consensus       274 ~vliIDEINRani--------------------~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMN  333 (459)
T PRK11331        274 YVFIIDEINRANL--------------------SKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYIIGLMN  333 (459)
T ss_pred             cEEEEehhhccCH--------------------HHhhhhhhhhccccccccccceeeeccccccccccCCCCeEEEEecC
Confidence            9999999986521                    11222222222200                  002246789999999


Q ss_pred             CCC----CCCccccCCCceeeEEEeCC
Q 012016          368 HKE----KLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       368 ~~~----~ld~aLlrpgRfd~~I~~~~  390 (473)
                      ..+    .+|.||+|  ||. .|++..
T Consensus       334 t~Drs~~~lD~AlrR--RF~-fi~i~p  357 (459)
T PRK11331        334 TADRSLAVVDYALRR--RFS-FIDIEP  357 (459)
T ss_pred             ccccchhhccHHHHh--hhh-eEEecC
Confidence            987    79999999  996 466654

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.06  E-value=6.7e-09  Score=104.24  Aligned_cols=123  Identities=15%  Similarity=0.179  Sum_probs=94.9

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC-----------------------CceEEcccc---cccCchHHHHHHHHhc--
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN-----------------------FDVYDLELT---ELRSNSDLRTLLVATA--  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~-----------------------~~~~~l~~~---~~~~~~~l~~l~~~~~--  303 (473)
                      .+.+|||+||.|+||+++|.++|..+-                       -+++.+...   ...+.+.++++.....  
T Consensus        24 l~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~vdqiR~l~~~~~~~  103 (319)
T PRK06090         24 IPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGKSITVEQIRQCNRLAQES  103 (319)
T ss_pred             cceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCCcCCHHHHHHHHHHHhhC
Confidence            467899999999999999999999871                       345555432   1234456666554432  


Q ss_pred             ----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCC
Q 012016          304 ----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRP  379 (473)
Q Consensus       304 ----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrp  379 (473)
                          ..-|++||++|.+                     +....+.||+.++.    ++++.++|++|+.++.|.|.+++ 
T Consensus       104 ~~~~~~kV~iI~~ae~m---------------------~~~AaNaLLKtLEE----Pp~~t~fiL~t~~~~~lLpTI~S-  157 (319)
T PRK06090        104 SQLNGYRLFVIEPADAM---------------------NESASNALLKTLEE----PAPNCLFLLVTHNQKRLLPTIVS-  157 (319)
T ss_pred             cccCCceEEEecchhhh---------------------CHHHHHHHHHHhcC----CCCCeEEEEEECChhhChHHHHh-
Confidence                3479999999987                     35677899999985    45679999999999999999998 


Q ss_pred             CceeeEEEeCCCCHHHHHHHHHH
Q 012016          380 GRMDVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       380 gRfd~~I~~~~p~~~~r~~l~~~  402 (473)
                       |+ ..+.|+.|+.++..+.+..
T Consensus       158 -RC-q~~~~~~~~~~~~~~~L~~  178 (319)
T PRK06090        158 -RC-QQWVVTPPSTAQAMQWLKG  178 (319)
T ss_pred             -cc-eeEeCCCCCHHHHHHHHHH
Confidence             88 4789999999987766654

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.05  E-value=3.6e-09  Score=106.90  Aligned_cols=64  Identities=22%  Similarity=0.290  Sum_probs=50.6

Q ss_pred             CCcc-ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------ceEEccc
Q 012016          216 ATFE-TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------DVYDLEL  286 (473)
Q Consensus       216 ~~f~-~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------~~~~l~~  286 (473)
                      .-|+ ++.|.++.++++++.+.....+       +...++.++|+||||||||+|+++||+.++.       ++|.+..
T Consensus        47 ~~F~~~~~G~~~~i~~lv~~l~~~a~g-------~~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~  118 (361)
T smart00763       47 RFFDHDFFGMEEAIERFVNYFKSAAQG-------LEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKW  118 (361)
T ss_pred             cccchhccCcHHHHHHHHHHHHHHHhc-------CCCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEe
Confidence            4567 8999999988888766654421       1223578999999999999999999999976       8888876

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK04132 replication factor C small subunit; Provisional

Probab=99.04  E-value=2.5e-09  Score=118.84  Aligned_cols=124  Identities=11%  Similarity=0.123  Sum_probs=99.7

Q ss_pred             eEEeC--CCCCCHHHHHHHHHHhc-----CCceEEcccccccCchHHHHHHHHhc--------cCceEEEeccccccccc
Q 012016          256 YLLYG--PPGTGKSSLIAAMANYL-----NFDVYDLELTELRSNSDLRTLLVATA--------NRSILVVEDIDCTIDLQ  320 (473)
Q Consensus       256 ~LL~G--PpGtGKT~la~alA~~l-----~~~~~~l~~~~~~~~~~l~~l~~~~~--------~~sIL~iDdiD~l~~~~  320 (473)
                      .+..|  |++.||||+|.|+|+++     +.+++.+|+++..+...+++++....        +..|++|||+|.+.   
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt---  643 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALT---  643 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCC---
Confidence            46679  99999999999999998     67899999998767778887775432        12599999999883   


Q ss_pred             cCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHH
Q 012016          321 DRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLA  400 (473)
Q Consensus       321 ~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~  400 (473)
                                        ....+.|+..|+..    +....+|++||.++.+.++|++  |+ ..+.|+.|+.++....+
T Consensus       644 ------------------~~AQnALLk~lEep----~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~~i~~~L  698 (846)
T PRK04132        644 ------------------QDAQQALRRTMEMF----SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRL  698 (846)
T ss_pred             ------------------HHHHHHHHHHhhCC----CCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHHHHHHHH
Confidence                              34567788888853    3458899999999999999998  87 68999999998887777


Q ss_pred             HHHhCcc
Q 012016          401 ANYLGIK  407 (473)
Q Consensus       401 ~~~l~~~  407 (473)
                      ......+
T Consensus       699 ~~I~~~E  705 (846)
T PRK04132        699 RYIAENE  705 (846)
T ss_pred             HHHHHhc
Confidence            7665443

>smart00350 MCM minichromosome maintenance proteins

Probab=99.04  E-value=1.5e-09  Score=116.32  Aligned_cols=128  Identities=17%  Similarity=0.208  Sum_probs=85.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc----ccccccC---------chHHHHHHHHhccCceEEEecccccccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL----ELTELRS---------NSDLRTLLVATANRSILVVEDIDCTIDLQD  321 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l----~~~~~~~---------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~  321 (473)
                      ++||+|+||||||.+++++++......+..    ++..+..         ...++.-.....++.+++|||+|.+-    
T Consensus       238 ~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~----  313 (509)
T smart00350      238 NILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTAAVTRDPETREFTLEGGALVLADNGVCCIDEFDKMD----  313 (509)
T ss_pred             eEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcCCccccceEccCcceEEecCccEEecCCCEEEEechhhCC----
Confidence            599999999999999999999886544432    2111210         00011101112467899999999873    


Q ss_pred             CCccccCCCCCCCccchhHHHHHHHHHhccc---------ccCCCCceEEEEecCCCC-------------CCCccccCC
Q 012016          322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGL---------WSSCGDERIIVFTTNHKE-------------KLDPALLRP  379 (473)
Q Consensus       322 r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~~-------------~ld~aLlrp  379 (473)
                                       ....+.|+..|+.-         ...-.....||+|+|..+             .|++++++ 
T Consensus       314 -----------------~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLs-  375 (509)
T smart00350      314 -----------------DSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAAANPIGGRYDPKLTPEENIDLPAPILS-  375 (509)
T ss_pred             -----------------HHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEEeCCCCcccCCCcChhhccCCChHHhC-
Confidence                             34456666666432         111224567889999763             58999999 


Q ss_pred             CceeeEE-EeCCCCHHHHHHHHHHHhC
Q 012016          380 GRMDVHV-HMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       380 gRfd~~I-~~~~p~~~~r~~l~~~~l~  405 (473)
                       |||... -+++|+.+....|+.+.+.
T Consensus       376 -RFdLi~~~~d~~~~~~d~~i~~~i~~  401 (509)
T smart00350      376 -RFDLLFVVLDEVDEERDRELAKHVVD  401 (509)
T ss_pred             -ceeeEEEecCCCChHHHHHHHHHHHH
Confidence             999754 4578999999999988654

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=99.04  E-value=3.6e-09  Score=108.52  Aligned_cols=177  Identities=16%  Similarity=0.256  Sum_probs=107.8

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLE  285 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~  285 (473)
                      .+.+.-+|++++..+.-+.. ......+-..+      |. ...-++||||.|.|||+|++|++++.     +..+++++
T Consensus        79 ~l~~~ytFdnFv~g~~N~~A-~aa~~~va~~~------g~-~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~  150 (408)
T COG0593          79 GLNPKYTFDNFVVGPSNRLA-YAAAKAVAENP------GG-AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLT  150 (408)
T ss_pred             cCCCCCchhheeeCCchHHH-HHHHHHHHhcc------CC-cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEecc
Confidence            35556799998765543322 22222222211      22 24469999999999999999999988     34466666


Q ss_pred             cccccC-------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          286 LTELRS-------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       286 ~~~~~~-------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ......       +..+.+.-... +-.+|+||||+.+..                .   ..+...|.+.+..+...  +
T Consensus       151 se~f~~~~v~a~~~~~~~~Fk~~y-~~dlllIDDiq~l~g----------------k---~~~qeefFh~FN~l~~~--~  208 (408)
T COG0593         151 SEDFTNDFVKALRDNEMEKFKEKY-SLDLLLIDDIQFLAG----------------K---ERTQEEFFHTFNALLEN--G  208 (408)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHhh-ccCeeeechHhHhcC----------------C---hhHHHHHHHHHHHHHhc--C
Confidence            544310       11111222222 567999999999853                1   12233344433333333  2


Q ss_pred             ceEEEEecCCCCC---CCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHH
Q 012016          359 ERIIVFTTNHKEK---LDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELI  419 (473)
Q Consensus       359 ~~iiI~tTN~~~~---ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~  419 (473)
                      +.||+.+...|..   +.|.|.+  ||.  ..+.+..|+.+.|..++.......+..+.+++...+
T Consensus       209 kqIvltsdr~P~~l~~~~~rL~S--R~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~l  272 (408)
T COG0593         209 KQIVLTSDRPPKELNGLEDRLRS--RLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFL  272 (408)
T ss_pred             CEEEEEcCCCchhhccccHHHHH--HHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            3555555555654   4588887  875  677899999999999999877666655655555544

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.04  E-value=1e-08  Score=102.95  Aligned_cols=123  Identities=15%  Similarity=0.215  Sum_probs=91.2

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC---------------------CceEEcc--cccc-------cCchHHHHHHHH
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN---------------------FDVYDLE--LTEL-------RSNSDLRTLLVA  301 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~---------------------~~~~~l~--~~~~-------~~~~~l~~l~~~  301 (473)
                      .+.+|||+||+|+||+++|.++|+.+-                     -+++.++  ...-       ..-+.++++...
T Consensus        25 l~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~~  104 (319)
T PRK08769         25 LGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQK  104 (319)
T ss_pred             cceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHHHH
Confidence            466899999999999999999998772                     2334342  1110       123455655554


Q ss_pred             hc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCcc
Q 012016          302 TA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPA  375 (473)
Q Consensus       302 ~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~a  375 (473)
                      ..      ..-|++||++|.+                     +....+.||+.|+.    ++++.++|++|+.++.|.|.
T Consensus       105 ~~~~p~~g~~kV~iI~~ae~m---------------------~~~AaNaLLKtLEE----Pp~~~~fiL~~~~~~~lLpT  159 (319)
T PRK08769        105 LALTPQYGIAQVVIVDPADAI---------------------NRAACNALLKTLEE----PSPGRYLWLISAQPARLPAT  159 (319)
T ss_pred             HhhCcccCCcEEEEeccHhhh---------------------CHHHHHHHHHHhhC----CCCCCeEEEEECChhhCchH
Confidence            32      3469999999988                     35677899999885    34568899999999999999


Q ss_pred             ccCCCceeeEEEeCCCCHHHHHHHHHH
Q 012016          376 LLRPGRMDVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       376 LlrpgRfd~~I~~~~p~~~~r~~l~~~  402 (473)
                      +++  |+ ..|.|+.|+.++....+..
T Consensus       160 IrS--RC-q~i~~~~~~~~~~~~~L~~  183 (319)
T PRK08769        160 IRS--RC-QRLEFKLPPAHEALAWLLA  183 (319)
T ss_pred             HHh--hh-eEeeCCCcCHHHHHHHHHH
Confidence            998  88 4789999999887666553

>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=99.03  E-value=1.5e-10  Score=99.72  Aligned_cols=106  Identities=26%  Similarity=0.294  Sum_probs=61.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHH--HHH-------hc---cCceEEEeccccccccccC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTL--LVA-------TA---NRSILVVEDIDCTIDLQDR  322 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l--~~~-------~~---~~sIL~iDdiD~l~~~~~r  322 (473)
                      ++||.|+||+|||++++++|..++..+..+.++.-...+++.-.  +..       ..   -..|+++|||...      
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNra------   74 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRA------   74 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS------
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccC------
Confidence            48999999999999999999999999998887532111121100  000       01   1369999999765      


Q ss_pred             CccccCCCCCCCccchhHHHHHHHHHhcc-------cccCCCCceEEEEecCCCC-----CCCccccCCCcee
Q 012016          323 LPADIAGEGEGPIQQNKVTLSGFLNFIDG-------LWSSCGDERIIVFTTNHKE-----KLDPALLRPGRMD  383 (473)
Q Consensus       323 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-------~~~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd  383 (473)
                                     ..++.+.||..|..       ..-..++..+||+|-|..+     .|+.|++.  ||-
T Consensus        75 ---------------ppktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~D--RF~  130 (131)
T PF07726_consen   75 ---------------PPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLD--RFM  130 (131)
T ss_dssp             ----------------HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHT--TSS
T ss_pred             ---------------CHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhc--ccc
Confidence                           35678999988843       2223445678888999876     68888888  873

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.

>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=99.02  E-value=1.2e-09  Score=102.11  Aligned_cols=46  Identities=33%  Similarity=0.553  Sum_probs=35.6

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .|.+|.|++..|..+.-...            |   ..++||+||||||||++|+++...|
T Consensus         1 Df~dI~GQe~aKrAL~iAAa------------G---~h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAA------------G---GHHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHH------------C---C--EEEES-CCCTHHHHHHHHHHCS
T ss_pred             ChhhhcCcHHHHHHHHHHHc------------C---CCCeEEECCCCCCHHHHHHHHHHhC
Confidence            48899999999988744332            2   3699999999999999999999987

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.98  E-value=2.1e-09  Score=108.51  Aligned_cols=103  Identities=22%  Similarity=0.333  Sum_probs=67.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC---------chHHHHHHHHhccCceEEEecccccccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS---------NSDLRTLLVATANRSILVVEDIDCTIDLQD  321 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~---------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~  321 (473)
                      .+++||||+|||||+|+.|||+++   |..++.++..++..         .......+....+..+|+|||+.....   
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e~~---  260 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTEKI---  260 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCCCC---
Confidence            689999999999999999999997   78888887766521         112222345556779999999976521   


Q ss_pred             CCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC-CC----CCccccC
Q 012016          322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK-EK----LDPALLR  378 (473)
Q Consensus       322 r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-~~----ld~aLlr  378 (473)
                                      .....+.|.+.++.....   +.-+|+|||.+ +.    +++.+..
T Consensus       261 ----------------t~~~~~~Lf~iin~R~~~---~k~tIiTSNl~~~el~~~~~eri~S  303 (329)
T PRK06835        261 ----------------TEFSKSELFNLINKRLLR---QKKMIISTNLSLEELLKTYSERISS  303 (329)
T ss_pred             ----------------CHHHHHHHHHHHHHHHHC---CCCEEEECCCCHHHHHHHHhHHHHH
Confidence                            123334555555543321   24577888864 22    4455554

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.96  E-value=4.4e-09  Score=102.63  Aligned_cols=93  Identities=26%  Similarity=0.445  Sum_probs=65.7

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC-
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS-  291 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~-  291 (473)
                      ..+.++-+.+...+.....+..+..   +|.     -+.+++|+||||||||+|+.|||+++   |.+++.+...++.. 
T Consensus        76 ~~~~d~~~~~~~~~~~l~~~~~~~~---~~~-----~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~~  147 (254)
T COG1484          76 FEEFDFEFQPGIDKKALEDLASLVE---FFE-----RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSK  147 (254)
T ss_pred             cccccccCCcchhHHHHHHHHHHHH---Hhc-----cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHHH
Confidence            3445566666666666666655542   333     25699999999999999999999998   78888888877621 


Q ss_pred             ------chHHH-HHHHHhccCceEEEeccccc
Q 012016          292 ------NSDLR-TLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       292 ------~~~l~-~l~~~~~~~sIL~iDdiD~l  316 (473)
                            +.... ++.....+-.+|||||+...
T Consensus       148 Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~  179 (254)
T COG1484         148 LKAAFDEGRLEEKLLRELKKVDLLIIDDIGYE  179 (254)
T ss_pred             HHHHHhcCchHHHHHHHhhcCCEEEEecccCc
Confidence                  11222 23333678899999999765

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.94  E-value=1e-09  Score=101.48  Aligned_cols=64  Identities=31%  Similarity=0.568  Sum_probs=49.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc-------CchHHHHHHHHhccCceEEEeccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR-------SNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~-------~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      +.|++|+||||||||+||.|||+++   |++++.++..++.       ......+.+....+..+|||||+...
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~  120 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYE  120 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCccccccEeccccccee
Confidence            4699999999999999999999987   8888888877762       23345566777778899999999643

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.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=98.93  E-value=1e-08  Score=103.78  Aligned_cols=154  Identities=19%  Similarity=0.215  Sum_probs=102.0

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCch
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNS  293 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~  293 (473)
                      .+++++|.....+.+++.+......           ...|||+|++||||+++|++|....   +.|++.++|..+.. .
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~-----------~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~-~   71 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPL-----------DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-N   71 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCH-H
Confidence            3678899888888888887766542           3479999999999999999998765   46999999998742 3


Q ss_pred             HHHHHH------------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-c
Q 012016          294 DLRTLL------------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-S  354 (473)
Q Consensus       294 ~l~~l~------------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~  354 (473)
                      .+...+                  ....+++.|||||||.+.                     ......|++.++.-. .
T Consensus        72 ~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L~---------------------~~~Q~~L~~~l~~~~~~  130 (326)
T PRK11608         72 LLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAP---------------------MLVQEKLLRVIEYGELE  130 (326)
T ss_pred             HHHHHHccccccccCCcccccCCchhccCCCeEEeCChhhCC---------------------HHHHHHHHHHHhcCcEE
Confidence            333322                  123456889999999883                     334555666664321 1


Q ss_pred             CCC------CceEEEEecCCC-------CCCCccccCCCce-eeEEEeCCCCH--HHHHHHHHHHhC
Q 012016          355 SCG------DERIIVFTTNHK-------EKLDPALLRPGRM-DVHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       355 ~~~------~~~iiI~tTN~~-------~~ld~aLlrpgRf-d~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                      ..+      .++-||+||+..       ..+.+.|..  || ..+|++|....  +....|+.+|+.
T Consensus       131 ~~g~~~~~~~~~RiI~~s~~~l~~l~~~g~f~~dL~~--~l~~~~i~lPpLReR~eDI~~L~~~fl~  195 (326)
T PRK11608        131 RVGGSQPLQVNVRLVCATNADLPAMVAEGKFRADLLD--RLAFDVVQLPPLRERQSDIMLMAEHFAI  195 (326)
T ss_pred             eCCCCceeeccEEEEEeCchhHHHHHHcCCchHHHHH--hcCCCEEECCChhhhhhhHHHHHHHHHH
Confidence            111      135677777653       345566776  77 44666666433  335567776653

>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=98.92  E-value=3e-08  Score=99.55  Aligned_cols=65  Identities=28%  Similarity=0.427  Sum_probs=44.0

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC--CceEEcccccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN--FDVYDLELTEL  289 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~--~~~~~l~~~~~  289 (473)
                      ..+.++|+.+.++..-- +...++.       |+--.|++||.||||||||.||-+||++||  .||..++.+++
T Consensus        22 ~~~GlVGQ~~AReAagi-iv~mIk~-------~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~isgSEi   88 (398)
T PF06068_consen   22 IADGLVGQEKAREAAGI-IVDMIKE-------GKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVSISGSEI   88 (398)
T ss_dssp             EETTEES-HHHHHHHHH-HHHHHHT-------T--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEEEEGGGG
T ss_pred             ccccccChHHHHHHHHH-HHHHHhc-------ccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeEccccee
Confidence            35789999988887643 3334432       233368999999999999999999999995  56666665554

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.

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=98.91  E-value=9.7e-09  Score=111.67  Aligned_cols=128  Identities=21%  Similarity=0.176  Sum_probs=90.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC--ceEEcccccc----cCchHHHHHHH-----------HhccCceEEEeccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF--DVYDLELTEL----RSNSDLRTLLV-----------ATANRSILVVEDIDCT  316 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~--~~~~l~~~~~----~~~~~l~~l~~-----------~~~~~sIL~iDdiD~l  316 (473)
                      .++||.|+||||||+++++++..++.  +++.+.+...    .+.-.+...+.           ...++++||||||+.+
T Consensus        17 g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~lDEi~rl   96 (589)
T TIGR02031        17 GGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYVDMANLL   96 (589)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcEeccchhhC
Confidence            47999999999999999999998864  5777765221    11111221111           1235679999999987


Q ss_pred             cccccCCccccCCCCCCCccchhHHHHHHHHHhccc---------ccCCCCceEEEEecCCCC---CCCccccCCCceee
Q 012016          317 IDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL---------WSSCGDERIIVFTTNHKE---KLDPALLRPGRMDV  384 (473)
Q Consensus       317 ~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~~---~ld~aLlrpgRfd~  384 (473)
                      .                     ..+.+.|++.|+.-         .........||+|+|..+   .|.++|+.  ||+.
T Consensus        97 ~---------------------~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~Lld--Rf~l  153 (589)
T TIGR02031        97 D---------------------DGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLD--RLAL  153 (589)
T ss_pred             C---------------------HHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHH--hccC
Confidence            3                     45677788888531         111123467888999765   78999999  9999


Q ss_pred             EEEeCCC-CHHHHHHHHHHHh
Q 012016          385 HVHMSYC-TPSGFKLLAANYL  404 (473)
Q Consensus       385 ~I~~~~p-~~~~r~~l~~~~l  404 (473)
                      +|.+.++ ..++|.+|+++++
T Consensus       154 ~v~~~~~~~~~er~eil~~~~  174 (589)
T TIGR02031       154 HVSLEDVASQDLRVEIVRRER  174 (589)
T ss_pred             eeecCCCCCHHHHHHHHHHHH
Confidence            9998874 6666889988876

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.

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

Probab=98.90  E-value=7.4e-09  Score=101.07  Aligned_cols=93  Identities=28%  Similarity=0.357  Sum_probs=66.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--------chHHHHHHHHh------ccCceEEEeccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--------NSDLRTLLVAT------ANRSILVVEDIDCTID  318 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--------~~~l~~l~~~~------~~~sIL~iDdiD~l~~  318 (473)
                      +.++||.||.|||||.||+.+|+.|+.||...|++.+..        ++-+.+++..+      +++.|++|||||.+..
T Consensus        97 KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIar  176 (408)
T COG1219          97 KSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIAR  176 (408)
T ss_pred             eccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhc
Confidence            457999999999999999999999999999999988732        23455666554      3789999999999954


Q ss_pred             cccCCccccCCCCCCCccchhHHHHHHHHHhccc
Q 012016          319 LQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       319 ~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  352 (473)
                      ..    ...+.   ..+-...-....||..|+|-
T Consensus       177 kS----eN~SI---TRDVSGEGVQQALLKiiEGT  203 (408)
T COG1219         177 KS----ENPSI---TRDVSGEGVQQALLKIIEGT  203 (408)
T ss_pred             cC----CCCCc---ccccCchHHHHHHHHHHcCc
Confidence            21    11110   00112234556788888875

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=98.90  E-value=8.9e-09  Score=104.36  Aligned_cols=149  Identities=18%  Similarity=0.218  Sum_probs=93.5

Q ss_pred             ccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHHHH
Q 012016          222 AMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLRTL  298 (473)
Q Consensus       222 ~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~~l  298 (473)
                      +|.....+.+++.+......           ...|||+|++||||+++|++|....   +.|++.++|..+.. ..+...
T Consensus         2 iG~S~~m~~~~~~~~~~a~~-----------~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~-~~l~~~   69 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAPL-----------DRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSE-NLLDSE   69 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCCh-HHHHHH
Confidence            44555556666666554432           3579999999999999999998766   47999999997642 233322


Q ss_pred             H------------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-c-----
Q 012016          299 L------------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-S-----  354 (473)
Q Consensus       299 ~------------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~-----  354 (473)
                      +                  ....+++.|||||||.+.                     ......|+..++.-. .     
T Consensus        70 lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L~---------------------~~~Q~~Ll~~l~~~~~~~~g~~  128 (329)
T TIGR02974        70 LFGHEAGAFTGAQKRHQGRFERADGGTLFLDELATAS---------------------LLVQEKLLRVIEYGEFERVGGS  128 (329)
T ss_pred             HhccccccccCcccccCCchhhCCCCEEEeCChHhCC---------------------HHHHHHHHHHHHcCcEEecCCC
Confidence            2                  123357899999999883                     334555666664321 0     


Q ss_pred             -CCCCceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCC--HHHHHHHHHHHhC
Q 012016          355 -SCGDERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCT--PSGFKLLAANYLG  405 (473)
Q Consensus       355 -~~~~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~--~~~r~~l~~~~l~  405 (473)
                       ....++-||++||..       ..+.+.|..  |+. ..|++|...  .+....|+..|+.
T Consensus       129 ~~~~~~~RiI~at~~~l~~~~~~g~fr~dL~~--rl~~~~i~lPpLReR~eDI~~L~~~fl~  188 (329)
T TIGR02974       129 QTLQVDVRLVCATNADLPALAAEGRFRADLLD--RLAFDVITLPPLRERQEDIMLLAEHFAI  188 (329)
T ss_pred             ceeccceEEEEechhhHHHHhhcCchHHHHHH--HhcchhcCCCchhhhhhhHHHHHHHHHH
Confidence             011235677777653       244566666  774 456666554  3445667776664

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

>TIGR01817 nifA Nif-specific regulatory protein

Probab=98.90  E-value=1.3e-08  Score=109.99  Aligned_cols=155  Identities=17%  Similarity=0.214  Sum_probs=103.2

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN  292 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~  292 (473)
                      .+|+.++|.....+.+++.+......           ...+||+|++||||+++|++|....   +.|++.++|..+.. 
T Consensus       193 ~~~~~liG~s~~~~~~~~~~~~~a~~-----------~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~~-  260 (534)
T TIGR01817       193 GKEDGIIGKSPAMRQVVDQARVVARS-----------NSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSE-  260 (534)
T ss_pred             CccCceEECCHHHHHHHHHHHHHhCc-----------CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCCH-
Confidence            57899999999888888887766532           3479999999999999999999875   57999999998733 


Q ss_pred             hHHHHHH------------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-
Q 012016          293 SDLRTLL------------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-  353 (473)
Q Consensus       293 ~~l~~l~------------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-  353 (473)
                      ..+...+                  ....+++.|||||||.+.                     ......|++.++.-. 
T Consensus       261 ~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~---------------------~~~Q~~Ll~~l~~~~~  319 (534)
T TIGR01817       261 TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEIS---------------------PAFQAKLLRVLQEGEF  319 (534)
T ss_pred             HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCC---------------------HHHHHHHHHHHhcCcE
Confidence            3333222                  112356899999999883                     234456666664321 


Q ss_pred             cCCC------CceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCC--HHHHHHHHHHHhC
Q 012016          354 SSCG------DERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCT--PSGFKLLAANYLG  405 (473)
Q Consensus       354 ~~~~------~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~--~~~r~~l~~~~l~  405 (473)
                      ...+      .++-+|+||+..       ..+.+.|..  |+. ..|++|...  .+....|+..|+.
T Consensus       320 ~~~~~~~~~~~~~riI~~s~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLreR~eDi~~L~~~~l~  385 (534)
T TIGR01817       320 ERVGGNRTLKVDVRLVAATNRDLEEAVAKGEFRADLYY--RINVVPIFLPPLRERREDIPLLAEAFLE  385 (534)
T ss_pred             EECCCCceEeecEEEEEeCCCCHHHHHHcCCCCHHHHH--HhcCCeeeCCCcccccccHHHHHHHHHH
Confidence            1111      135677777653       233344444  553 467777654  3556677777765

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.

>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=98.89  E-value=7.1e-09  Score=94.93  Aligned_cols=115  Identities=21%  Similarity=0.213  Sum_probs=74.1

Q ss_pred             cccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHH-
Q 012016          221 LAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLR-  296 (473)
Q Consensus       221 l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~-  296 (473)
                      |+|.....+++++.+......           +..|||+|++||||+.+|++|.+..   +.|++.++|+.+.. +.+. 
T Consensus         1 liG~s~~m~~~~~~~~~~a~~-----------~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~-~~~e~   68 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASS-----------DLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPE-ELLES   68 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTS-----------TS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-H-HHHHH
T ss_pred             CEeCCHHHHHHHHHHHHHhCC-----------CCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhc-chhhh
Confidence            355566666777766655432           4579999999999999999999976   47999999998743 2333 


Q ss_pred             HHHH-----------------HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-cCCC-
Q 012016          297 TLLV-----------------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-SSCG-  357 (473)
Q Consensus       297 ~l~~-----------------~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~~~-  357 (473)
                      ++|-                 ...+...||||||+.+.                     ......|++.|+.-. ...| 
T Consensus        69 ~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~---------------------~~~Q~~Ll~~l~~~~~~~~g~  127 (168)
T PF00158_consen   69 ELFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDLP---------------------PELQAKLLRVLEEGKFTRLGS  127 (168)
T ss_dssp             HHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS----------------------HHHHHHHHHHHHHSEEECCTS
T ss_pred             hhhccccccccccccccCCceeeccceEEeecchhhhH---------------------HHHHHHHHHHHhhchhccccc
Confidence            3331                 22367899999999983                     345566777776321 1111 


Q ss_pred             -----CceEEEEecCC
Q 012016          358 -----DERIIVFTTNH  368 (473)
Q Consensus       358 -----~~~iiI~tTN~  368 (473)
                           -++-||+||+.
T Consensus       128 ~~~~~~~~RiI~st~~  143 (168)
T PF00158_consen  128 DKPVPVDVRIIASTSK  143 (168)
T ss_dssp             SSEEE--EEEEEEESS
T ss_pred             cccccccceEEeecCc
Confidence                 14667777775

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 ....

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.88  E-value=2.1e-07  Score=92.27  Aligned_cols=64  Identities=30%  Similarity=0.471  Sum_probs=47.6

Q ss_pred             ccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC--CceEEcccccc
Q 012016          218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN--FDVYDLELTEL  289 (473)
Q Consensus       218 f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~--~~~~~l~~~~~  289 (473)
                      =+-++|+.+.++..= .+...++.       |+--.+|+|+.||||||||.||-+||++||  .||..++.+++
T Consensus        38 ~dG~VGQ~~AReAaG-vIv~mik~-------gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~isgsEi  103 (450)
T COG1224          38 GDGLVGQEEAREAAG-VIVKMIKQ-------GKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEI  103 (450)
T ss_pred             CCcccchHHHHHhhh-HHHHHHHh-------CcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCceeecccee
Confidence            367889888777542 22223332       444578999999999999999999999995  67777777765

>PRK09183 transposase/IS protein; Provisional

Probab=98.88  E-value=3.1e-09  Score=104.12  Aligned_cols=64  Identities=22%  Similarity=0.357  Sum_probs=47.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc-------CchHHHHHHHH-hccCceEEEeccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR-------SNSDLRTLLVA-TANRSILVVEDIDCT  316 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~-------~~~~l~~l~~~-~~~~sIL~iDdiD~l  316 (473)
                      ..+++|+||||||||+|+.++|+.+   |..+..++..++.       ....+...+.. ...+.+|+|||++..
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~~dlLiiDdlg~~  176 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYL  176 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcCCCEEEEcccccC
Confidence            4589999999999999999998765   7778777765542       11224444544 456789999999865

>PRK06921 hypothetical protein; Provisional

Probab=98.87  E-value=1.6e-08  Score=99.53  Aligned_cols=63  Identities=29%  Similarity=0.372  Sum_probs=46.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccccccCc-----hHHHHHHHHhccCceEEEecccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTELRSN-----SDLRTLLVATANRSILVVEDIDC  315 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~~~~~-----~~l~~l~~~~~~~sIL~iDdiD~  315 (473)
                      ..+++|+||||||||+|+.|||+++    +..++.++..++...     ..+...+....+..+|+|||++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~~~~~~~~~~~~~~~~dlLiIDDl~~  188 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKVEVLFIDDLFK  188 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHHHHHHHHHHHHHhcCCCEEEEecccc
Confidence            4689999999999999999999987    567777776553211     12233444556789999999954

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.86  E-value=1.3e-08  Score=102.92  Aligned_cols=123  Identities=12%  Similarity=0.187  Sum_probs=90.5

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcC-------------------------CceEEccccc----------ccCchHH
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLN-------------------------FDVYDLELTE----------LRSNSDL  295 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~-------------------------~~~~~l~~~~----------~~~~~~l  295 (473)
                      ..+.+|||+||+|+|||++|.++|+.+.                         -+++.++...          ..+-+.+
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            3467899999999999999999999872                         3455555421          1234566


Q ss_pred             HHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC
Q 012016          296 RTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK  369 (473)
Q Consensus       296 ~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  369 (473)
                      |++...+.      ..-|++||+++.+                     +....+.|+..|+...    .+..+|++|+.+
T Consensus        99 R~l~~~~~~~p~~~~~kV~iiEp~~~L---------------------d~~a~naLLk~LEep~----~~~~~Ilvth~~  153 (325)
T PRK08699         99 REIIDNVYLTSVRGGLRVILIHPAESM---------------------NLQAANSLLKVLEEPP----PQVVFLLVSHAA  153 (325)
T ss_pred             HHHHHHHhhCcccCCceEEEEechhhC---------------------CHHHHHHHHHHHHhCc----CCCEEEEEeCCh
Confidence            76665543      3468999999987                     2455677888887652    347788899999


Q ss_pred             CCCCccccCCCceeeEEEeCCCCHHHHHHHHH
Q 012016          370 EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAA  401 (473)
Q Consensus       370 ~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~  401 (473)
                      +.+.|++.+  |+ .++.|+.|+.++....+.
T Consensus       154 ~~ll~ti~S--Rc-~~~~~~~~~~~~~~~~L~  182 (325)
T PRK08699        154 DKVLPTIKS--RC-RKMVLPAPSHEEALAYLR  182 (325)
T ss_pred             HhChHHHHH--Hh-hhhcCCCCCHHHHHHHHH
Confidence            999999887  77 578999999988765554

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.85  E-value=4e-08  Score=104.83  Aligned_cols=209  Identities=19%  Similarity=0.320  Sum_probs=121.1

Q ss_pred             CCcceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          204 TDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       204 ~~~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      ...|..  ...|.+.++|+.+++..++|...+...+.        +..+.+-+||+||||||||++++++|+++++.+..
T Consensus         6 ~~~W~~--ky~P~~~~eLavhkkKv~eV~~wl~~~~~--------~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~E   75 (519)
T PF03215_consen    6 SEPWVE--KYAPKTLDELAVHKKKVEEVRSWLEEMFS--------GSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQE   75 (519)
T ss_pred             cCccch--hcCCCCHHHhhccHHHHHHHHHHHHHHhc--------cCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEE
Confidence            345644  57789999999998777777776664432        33445678999999999999999999999988775


Q ss_pred             c-ccccc----------cC-----------chHHHHH-HHHh-------------ccCceEEEeccccccccccCCcccc
Q 012016          284 L-ELTEL----------RS-----------NSDLRTL-LVAT-------------ANRSILVVEDIDCTIDLQDRLPADI  327 (473)
Q Consensus       284 l-~~~~~----------~~-----------~~~l~~l-~~~~-------------~~~sIL~iDdiD~l~~~~~r~~~~~  327 (473)
                      - +....          .+           ...+..+ +...             .++.||+|||+-.++.         
T Consensus        76 w~np~~~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~---------  146 (519)
T PF03215_consen   76 WINPVSFRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFH---------  146 (519)
T ss_pred             ecCCCCccccccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccc---------
Confidence            3 22111          00           0111222 1111             2467999999976543         


Q ss_pred             CCCCCCCccchhHHHHHHHHHhcccccCCCC-ceEEEEe-c------CCCC--------CCCccccCCCceeeEEEeCCC
Q 012016          328 AGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD-ERIIVFT-T------NHKE--------KLDPALLRPGRMDVHVHMSYC  391 (473)
Q Consensus       328 ~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~-~~iiI~t-T------N~~~--------~ld~aLlrpgRfd~~I~~~~p  391 (473)
                              ......-..|...+..    .+. .+|||+| +      |...        .+++.++.-.++ .+|.|..-
T Consensus       147 --------~~~~~f~~~L~~~l~~----~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i-~~I~FNpI  213 (519)
T PF03215_consen  147 --------RDTSRFREALRQYLRS----SRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGI-TRIKFNPI  213 (519)
T ss_pred             --------hhHHHHHHHHHHHHHc----CCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCc-eEEEecCC
Confidence                    1112233333334432    122 4777776 1      1111        356666643344 47999998


Q ss_pred             CHHHHHHHHHHHhCccccCCHHHHHHHHhcCC-CCHHHHHHHHhc--CCCHHHHHHHHHHHHH
Q 012016          392 TPSGFKLLAANYLGIKEHILFEEIEELISTTQ-VTPAEVAEQLMR--NDDPELVLNGLIEFLK  451 (473)
Q Consensus       392 ~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~-~t~a~i~~~l~~--~~~~~~al~~l~~~l~  451 (473)
                      .....+.-+.+.+..+       ......... -...++.+.+..  +||...|+..|.-+..
T Consensus       214 a~T~mkKaL~rI~~~E-------~~~~~~~~~~p~~~~~l~~I~~~s~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  214 APTFMKKALKRILKKE-------ARSSSGKNKVPDKQSVLDSIAESSNGDIRSAINNLQFWCL  269 (519)
T ss_pred             CHHHHHHHHHHHHHHH-------hhhhcCCccCCChHHHHHHHHHhcCchHHHHHHHHHHHhc
Confidence            8887777777665433       111111111 122443344432  4888889888875554

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.85  E-value=3.7e-08  Score=108.69  Aligned_cols=155  Identities=17%  Similarity=0.174  Sum_probs=98.0

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN  292 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~  292 (473)
                      .+|++++|.....+++++.+......           ...+||+|++||||+++|++|.+..   +.|++.+||..+.. 
T Consensus       322 ~~~~~l~g~s~~~~~~~~~~~~~a~~-----------~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~-  389 (638)
T PRK11388        322 HTFDHMPQDSPQMRRLIHFGRQAAKS-----------SFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPD-  389 (638)
T ss_pred             ccccceEECCHHHHHHHHHHHHHhCc-----------CCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCCh-
Confidence            46888999888888887777766542           3469999999999999999999876   46999999998743 


Q ss_pred             hHH-HHHHH--------------HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC-C
Q 012016          293 SDL-RTLLV--------------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS-C  356 (473)
Q Consensus       293 ~~l-~~l~~--------------~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-~  356 (473)
                      +.+ .++|.              ...+++.||||||+.+.                     ......|+..++.-.-. .
T Consensus       390 ~~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l~---------------------~~~Q~~Ll~~l~~~~~~~~  448 (638)
T PRK11388        390 EALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYLS---------------------PELQSALLQVLKTGVITRL  448 (638)
T ss_pred             HHHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhCC---------------------HHHHHHHHHHHhcCcEEeC
Confidence            222 23332              12356899999999883                     23445566666532111 1


Q ss_pred             CC------ceEEEEecCCC-------CCCCccccCCCce-eeEEEeCCCCH--HHHHHHHHHHhC
Q 012016          357 GD------ERIIVFTTNHK-------EKLDPALLRPGRM-DVHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       357 ~~------~~iiI~tTN~~-------~~ld~aLlrpgRf-d~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                      +.      .+-||+|||..       ..+.+.|.-  |+ ...|++|....  +....|+..|+.
T Consensus       449 ~~~~~~~~~~riI~~t~~~l~~~~~~~~f~~dL~~--~l~~~~i~lPpLreR~~Di~~L~~~~l~  511 (638)
T PRK11388        449 DSRRLIPVDVRVIATTTADLAMLVEQNRFSRQLYY--ALHAFEITIPPLRMRREDIPALVNNKLR  511 (638)
T ss_pred             CCCceEEeeEEEEEeccCCHHHHHhcCCChHHHhh--hhceeEEeCCChhhhhhHHHHHHHHHHH
Confidence            11      35577877753       122233332  33 34455555432  234566666664

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

Probab=98.84  E-value=3.4e-08  Score=101.95  Aligned_cols=137  Identities=22%  Similarity=0.300  Sum_probs=94.1

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEc-cccccc------CchHHHHHHHHhc--cCceEEEeccccccccccC
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL-ELTELR------SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDR  322 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l-~~~~~~------~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r  322 (473)
                      +-..+||+||||+|||.||+-+|...++|++.+ +..++.      ....+...|..+-  .-+||++|||+.+++... 
T Consensus       537 ~lvSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD~vp-  615 (744)
T KOG0741|consen  537 PLVSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYVP-  615 (744)
T ss_pred             cceEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhcccc-
Confidence            345799999999999999999999999999864 333332      2345677777763  459999999999976321 


Q ss_pred             CccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCC-ccccCCCceeeEEEeCCCCH-HHHHHHH
Q 012016          323 LPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLD-PALLRPGRMDVHVHMSYCTP-SGFKLLA  400 (473)
Q Consensus       323 ~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld-~aLlrpgRfd~~I~~~~p~~-~~r~~l~  400 (473)
                                -+...++.++..|+-++...... |...+|++||...+-|. -.++.  .|+..|++|..+. ++...++
T Consensus       616 ----------IGPRfSN~vlQaL~VllK~~ppk-g~kLli~~TTS~~~vL~~m~i~~--~F~~~i~Vpnl~~~~~~~~vl  682 (744)
T KOG0741|consen  616 ----------IGPRFSNLVLQALLVLLKKQPPK-GRKLLIFGTTSRREVLQEMGILD--CFSSTIHVPNLTTGEQLLEVL  682 (744)
T ss_pred             ----------cCchhhHHHHHHHHHHhccCCCC-CceEEEEecccHHHHHHHcCHHH--hhhheeecCccCchHHHHHHH
Confidence                      22345667777777777765322 22345555666655443 24556  8899999998776 5555555


Q ss_pred             HH
Q 012016          401 AN  402 (473)
Q Consensus       401 ~~  402 (473)
                      ..
T Consensus       683 ~~  684 (744)
T KOG0741|consen  683 EE  684 (744)
T ss_pred             HH
Confidence            53

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=98.82  E-value=1.3e-08  Score=111.29  Aligned_cols=153  Identities=22%  Similarity=0.335  Sum_probs=105.2

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLEL  286 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~  286 (473)
                      .+|-++|.++..+.+++.|.+..             +.+-+|.|+||+|||.++..+|...          +..++.+|+
T Consensus       168 klDPvIGRd~EI~r~iqIL~RR~-------------KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~  234 (786)
T COG0542         168 KLDPVIGRDEEIRRTIQILSRRT-------------KNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDL  234 (786)
T ss_pred             CCCCCcChHHHHHHHHHHHhccC-------------CCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEecH
Confidence            57788998888888877665332             4577999999999999999999876          678899999


Q ss_pred             ccccC--------chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCC
Q 012016          287 TELRS--------NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSC  356 (473)
Q Consensus       287 ~~~~~--------~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~  356 (473)
                      +.+..        +..++.++....  .+.|||||||+.+.+...-         .|   . ..-.+.+|.-+-    ..
T Consensus       235 g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~---------~G---~-a~DAaNiLKPaL----AR  297 (786)
T COG0542         235 GSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGAT---------EG---G-AMDAANLLKPAL----AR  297 (786)
T ss_pred             HHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcc---------cc---c-ccchhhhhHHHH----hc
Confidence            88742        456677776654  3799999999999751110         01   0 111222332221    22


Q ss_pred             CCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          357 GDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       357 ~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                      | +.-+|++|..-+     .=|+||-|  ||. .|.+..|+.++-..|++..
T Consensus       298 G-eL~~IGATT~~EYRk~iEKD~AL~R--RFQ-~V~V~EPs~e~ti~ILrGl  345 (786)
T COG0542         298 G-ELRCIGATTLDEYRKYIEKDAALER--RFQ-KVLVDEPSVEDTIAILRGL  345 (786)
T ss_pred             C-CeEEEEeccHHHHHHHhhhchHHHh--cCc-eeeCCCCCHHHHHHHHHHH
Confidence            3 344555443221     23899999  996 7899999999988777753

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.75  E-value=7.4e-07  Score=86.30  Aligned_cols=51  Identities=29%  Similarity=0.448  Sum_probs=37.2

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..++|+...++.. ..+.+.++.+.       --.|++||.||||||||.||-+|+.+|
T Consensus        38 ~g~vGQ~~AReAa-giivdlik~Kk-------maGravLlaGppgtGKTAlAlaisqEL   88 (456)
T KOG1942|consen   38 AGFVGQENAREAA-GIIVDLIKSKK-------MAGRAVLLAGPPGTGKTALALAISQEL   88 (456)
T ss_pred             cccccchhhhhhh-hHHHHHHHhhh-------ccCcEEEEecCCCCchhHHHHHHHHHh
Confidence            4577887777653 23333444332       125799999999999999999999999

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.74  E-value=1.8e-08  Score=101.80  Aligned_cols=130  Identities=22%  Similarity=0.311  Sum_probs=85.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--------chHHHHHHHHh------ccCceEEEeccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--------NSDLRTLLVAT------ANRSILVVEDIDCTID  318 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--------~~~l~~l~~~~------~~~sIL~iDdiD~l~~  318 (473)
                      +.++||.||.|+|||.|++-||+.+++||...||+.+..        ++-+.+++..+      .+..|+||||+|.+..
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~  305 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITK  305 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcc
Confidence            458999999999999999999999999999999998832        24466666655      3789999999999963


Q ss_pred             cccCCccccCCCCCCCccchhHHHHHHHHHhcccc---------cCCCCceEEEEecCCC-------CCCCccccCCCce
Q 012016          319 LQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW---------SSCGDERIIVFTTNHK-------EKLDPALLRPGRM  382 (473)
Q Consensus       319 ~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~---------~~~~~~~iiI~tTN~~-------~~ld~aLlrpgRf  382 (473)
                      ....-..       ..+-...-....||..++|-.         ....++.+.|=|||-.       ..||.-+.|  |+
T Consensus       306 ~~~~i~~-------~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~Ldk~I~r--R~  376 (564)
T KOG0745|consen  306 KAESIHT-------SRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGLDKIISR--RL  376 (564)
T ss_pred             cCccccc-------cccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccchHHHHHH--hh
Confidence            2111000       001122345567888887641         1223345555566542       345555555  44


Q ss_pred             e-eEEEeCCC
Q 012016          383 D-VHVHMSYC  391 (473)
Q Consensus       383 d-~~I~~~~p  391 (473)
                      + ..+-|..|
T Consensus       377 ~d~slGFg~~  386 (564)
T KOG0745|consen  377 DDKSLGFGAP  386 (564)
T ss_pred             cchhcccCCC
Confidence            3 44555555

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.74  E-value=3.2e-08  Score=87.52  Aligned_cols=78  Identities=28%  Similarity=0.371  Sum_probs=54.1

Q ss_pred             cchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC---ceEEcccccccCchHHHHHH
Q 012016          223 MEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF---DVYDLELTELRSNSDLRTLL  299 (473)
Q Consensus       223 ~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~---~~~~l~~~~~~~~~~l~~l~  299 (473)
                      |.....+++.+.+......           ...+||+|+|||||+++|++|....+.   +++.+++....     .+++
T Consensus         2 G~S~~~~~l~~~l~~~a~~-----------~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-----~~~l   65 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERLAKS-----------SSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-----AELL   65 (138)
T ss_dssp             -SCHHHHHHHHHHHHHHCS-----------SS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-----HHHH
T ss_pred             CCCHHHHHHHHHHHHHhCC-----------CCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-----HHHH
Confidence            3344556666666655432           357999999999999999999998753   56666776643     3444


Q ss_pred             HHhccCceEEEecccccc
Q 012016          300 VATANRSILVVEDIDCTI  317 (473)
Q Consensus       300 ~~~~~~sIL~iDdiD~l~  317 (473)
                      .. ..+..|+|+|||.+.
T Consensus        66 ~~-a~~gtL~l~~i~~L~   82 (138)
T PF14532_consen   66 EQ-AKGGTLYLKNIDRLS   82 (138)
T ss_dssp             HH-CTTSEEEEECGCCS-
T ss_pred             HH-cCCCEEEECChHHCC
Confidence            44 488899999999983

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=98.73  E-value=7.4e-08  Score=103.18  Aligned_cols=157  Identities=17%  Similarity=0.226  Sum_probs=100.3

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS  291 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~  291 (473)
                      ..+|++++|.....+.+.+.+..+-..           ...+||+|++||||+++|++|.+..   +.|++.++|..+..
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 RYRLDDLLGASAPMEQVRALVRLYARS-----------DATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAE  276 (526)
T ss_pred             ccchhheeeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCCh
Confidence            357999999998888888877765442           3479999999999999999999765   67999999998743


Q ss_pred             chHHHHHHH-------------------HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc
Q 012016          292 NSDLRTLLV-------------------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       292 ~~~l~~l~~-------------------~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  352 (473)
                       ..+...+.                   ....++.||||||+.+.                     ......|+..++.-
T Consensus       277 -~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp---------------------~~~Q~~Ll~~L~~~  334 (526)
T TIGR02329       277 -SLLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMP---------------------LPLQTRLLRVLEER  334 (526)
T ss_pred             -hHHHHHhcCCcccccccccccccccchhhcCCceEEecChHhCC---------------------HHHHHHHHHHHhcC
Confidence             22332221                   22356889999999883                     33455566666431


Q ss_pred             c--cCCC-----CceEEEEecCCC-C------CCCccccCCCcee-eEEEeCCCCH--HHHHHHHHHHhCc
Q 012016          353 W--SSCG-----DERIIVFTTNHK-E------KLDPALLRPGRMD-VHVHMSYCTP--SGFKLLAANYLGI  406 (473)
Q Consensus       353 ~--~~~~-----~~~iiI~tTN~~-~------~ld~aLlrpgRfd-~~I~~~~p~~--~~r~~l~~~~l~~  406 (473)
                      .  .-.+     -++-+|++||.. .      .+.+.|..  |+. ..|++|+...  +....|+..|+..
T Consensus       335 ~~~r~g~~~~~~~dvRiIaat~~~l~~~v~~g~fr~dL~~--rL~~~~I~lPPLReR~eDI~~L~~~fl~~  403 (526)
T TIGR02329       335 EVVRVGGTEPVPVDVRVVAATHCALTTAVQQGRFRRDLFY--RLSILRIALPPLRERPGDILPLAAEYLVQ  403 (526)
T ss_pred             cEEecCCCceeeecceEEeccCCCHHHHhhhcchhHHHHH--hcCCcEEeCCCchhchhHHHHHHHHHHHH
Confidence            1  0001     123467777653 1      22233333  443 4566665433  3456677777653

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.

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.73  E-value=4.5e-07  Score=87.87  Aligned_cols=113  Identities=15%  Similarity=0.147  Sum_probs=83.0

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcC----------------------CceEEccccc-ccCchHHHHHHHHhc----
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLN----------------------FDVYDLELTE-LRSNSDLRTLLVATA----  303 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~----------------------~~~~~l~~~~-~~~~~~l~~l~~~~~----  303 (473)
                      .++.++||+||+|+||..+|.++|..+-                      -+++.+.... ....+.++++.....    
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            3567999999999999999999998871                      2333322111 123345555554332    


Q ss_pred             ---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCC
Q 012016          304 ---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPG  380 (473)
Q Consensus       304 ---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpg  380 (473)
                         ..-|++|+++|.+                     .....+.||..++.    ++.+.++|++|+.++.+.|.+++  
T Consensus        85 e~~~~KV~II~~ae~m---------------------~~~AaNaLLK~LEE----Pp~~t~fiLit~~~~~lLpTI~S--  137 (261)
T PRK05818         85 ESNGKKIYIIYGIEKL---------------------NKQSANSLLKLIEE----PPKNTYGIFTTRNENNILNTILS--  137 (261)
T ss_pred             hcCCCEEEEeccHhhh---------------------CHHHHHHHHHhhcC----CCCCeEEEEEECChHhCchHhhh--
Confidence               2479999999987                     35678899999985    45679999999999999999998  


Q ss_pred             ceeeEEEeCCC
Q 012016          381 RMDVHVHMSYC  391 (473)
Q Consensus       381 Rfd~~I~~~~p  391 (473)
                      |+. .+.++.+
T Consensus       138 RCq-~~~~~~~  147 (261)
T PRK05818        138 RCV-QYVVLSK  147 (261)
T ss_pred             hee-eeecCCh
Confidence            874 4667666

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=98.72  E-value=9.9e-08  Score=97.07  Aligned_cols=155  Identities=23%  Similarity=0.274  Sum_probs=104.6

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-------Cc--------
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-------FD--------  280 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-------~~--------  280 (473)
                      -.|.-++|++..|..|......             |--.|+|+-|+.|||||++++|||.-|.       .+        
T Consensus        14 ~pf~aivGqd~lk~aL~l~av~-------------P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~P   80 (423)
T COG1239          14 LPFTAIVGQDPLKLALGLNAVD-------------PQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDDP   80 (423)
T ss_pred             cchhhhcCchHHHHHHhhhhcc-------------cccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCCh
Confidence            4688899999999887654332             2235899999999999999999999882       11        


Q ss_pred             -------------------------eEEcccccc----cCchHHHHHHH-----------HhccCceEEEeccccccccc
Q 012016          281 -------------------------VYDLELTEL----RSNSDLRTLLV-----------ATANRSILVVEDIDCTIDLQ  320 (473)
Q Consensus       281 -------------------------~~~l~~~~~----~~~~~l~~l~~-----------~~~~~sIL~iDdiD~l~~~~  320 (473)
                                               ++.+.+...    .+.=++.+.+.           ...++.||+|||+..|-   
T Consensus        81 ~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~---  157 (423)
T COG1239          81 EEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLD---  157 (423)
T ss_pred             hhhhHHHHhhccccccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEecccccc---
Confidence                                     111111111    01111222222           12367999999998762   


Q ss_pred             cCCccccCCCCCCCccchhHHHHHHHHHhc---------ccccCCCCceEEEEecCCC-CCCCccccCCCceeeEEEeCC
Q 012016          321 DRLPADIAGEGEGPIQQNKVTLSGFLNFID---------GLWSSCGDERIIVFTTNHK-EKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       321 ~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld---------g~~~~~~~~~iiI~tTN~~-~~ld~aLlrpgRfd~~I~~~~  390 (473)
                                        ......||+.+.         |+.-..+-+.++|+|+|.- ..|-|-|+.  ||..+|...+
T Consensus       158 ------------------d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqLlD--Rfg~~v~~~~  217 (423)
T COG1239         158 ------------------DHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQLLD--RFGLEVDTHY  217 (423)
T ss_pred             ------------------HHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhhHh--hhcceeeccC
Confidence                              356666776663         3333334568999999976 578889999  9999999988


Q ss_pred             C-CHHHHHHHHHHHhCc
Q 012016          391 C-TPSGFKLLAANYLGI  406 (473)
Q Consensus       391 p-~~~~r~~l~~~~l~~  406 (473)
                      | +.++|.+|..+-+..
T Consensus       218 ~~~~~~rv~Ii~r~~~f  234 (423)
T COG1239         218 PLDLEERVEIIRRRLAF  234 (423)
T ss_pred             CCCHHHHHHHHHHHHHh
Confidence            7 456677887776554

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.71  E-value=7.3e-08  Score=103.25  Aligned_cols=90  Identities=18%  Similarity=0.200  Sum_probs=68.4

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHh-----------cCCceEEc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY-----------LNFDVYDL  284 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~-----------l~~~~~~l  284 (473)
                      .+|++++|.....+.+.+.+..+-..           ...+||+|++||||+++|++|.+.           -+.|++.+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~A~s-----------~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~i  284 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLYARS-----------SAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAV  284 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEe
Confidence            46899999988888887777655432           347999999999999999999987           46799999


Q ss_pred             ccccccCchHHHHHH-------------------HHhccCceEEEecccccc
Q 012016          285 ELTELRSNSDLRTLL-------------------VATANRSILVVEDIDCTI  317 (473)
Q Consensus       285 ~~~~~~~~~~l~~l~-------------------~~~~~~sIL~iDdiD~l~  317 (473)
                      +|..+.. ..+...+                   .....++.||||||+.+.
T Consensus       285 nCaal~e-~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp  335 (538)
T PRK15424        285 NCGAIAE-SLLEAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMP  335 (538)
T ss_pred             ecccCCh-hhHHHHhcCCccccccCccccccCCchhccCCCEEEEcChHhCC
Confidence            9998743 2233222                   123356899999999883

>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=98.71  E-value=4.6e-08  Score=96.48  Aligned_cols=137  Identities=21%  Similarity=0.405  Sum_probs=78.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc---eEEcccccccCchHHHHHHHHh-------------ccCceEEEeccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD---VYDLELTELRSNSDLRTLLVAT-------------ANRSILVVEDIDCT  316 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~---~~~l~~~~~~~~~~l~~l~~~~-------------~~~sIL~iDdiD~l  316 (473)
                      .+.+||.||+|||||++++.+-..+.-.   +..+.++...+...+++++...             .++.|+||||+..-
T Consensus        33 ~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDDlN~p  112 (272)
T PF12775_consen   33 GRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDDLNMP  112 (272)
T ss_dssp             TEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEETTT-S
T ss_pred             CCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecccCCC
Confidence            4689999999999999998877766432   3344555443444455444322             13479999999864


Q ss_pred             cccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC------CceEEEEecCCCC---CCCccccCCCceeeEEE
Q 012016          317 IDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG------DERIIVFTTNHKE---KLDPALLRPGRMDVHVH  387 (473)
Q Consensus       317 ~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~~~iiI~tTN~~~---~ld~aLlrpgRfd~~I~  387 (473)
                      ..  +          ..+....-..+.++++. .|.+....      .++.+|++.|...   .+++.|+|  .| ..+.
T Consensus       113 ~~--d----------~ygtq~~iElLRQ~i~~-~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r--~f-~i~~  176 (272)
T PF12775_consen  113 QP--D----------KYGTQPPIELLRQLIDY-GGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR--HF-NILN  176 (272)
T ss_dssp             ---------------TTS--HHHHHHHHHHHC-SEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT--TE-EEEE
T ss_pred             CC--C----------CCCCcCHHHHHHHHHHh-cCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh--he-EEEE
Confidence            32  0          00111112333333321 23333211      2467788887542   47888888  77 4789


Q ss_pred             eCCCCHHHHHHHHHHHhC
Q 012016          388 MSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       388 ~~~p~~~~r~~l~~~~l~  405 (473)
                      +++|+.++...|+..++.
T Consensus       177 ~~~p~~~sl~~If~~il~  194 (272)
T PF12775_consen  177 IPYPSDESLNTIFSSILQ  194 (272)
T ss_dssp             ----TCCHHHHHHHHHHH
T ss_pred             ecCCChHHHHHHHHHHHh
Confidence            999999998888877665

>TIGR00368 Mg chelatase-related protein

Probab=98.68  E-value=8.3e-08  Score=102.07  Aligned_cols=142  Identities=18%  Similarity=0.217  Sum_probs=87.9

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC----------------
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF----------------  279 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~----------------  279 (473)
                      ..|+++.|+...++.+.-.    .           .....++|.||||||||+++++++..+.-                
T Consensus       189 ~d~~dv~Gq~~~~~al~~a----a-----------~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~le~~~i~s~~  253 (499)
T TIGR00368       189 LDLKDIKGQQHAKRALEIA----A-----------AGGHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSLV  253 (499)
T ss_pred             CCHHHhcCcHHHHhhhhhh----c-----------cCCCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEEeccccccch
Confidence            4789999987776554221    1           12357999999999999999999975521                


Q ss_pred             ------------ceEEcccccc-----cCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 ------------DVYDLELTEL-----RSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 ------------~~~~l~~~~~-----~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                  |+.....+..     .+....+.-......+.+|||||++.+                     ....+
T Consensus       254 g~~~~~~~~~~~Pf~~p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~---------------------~~~~~  312 (499)
T TIGR00368       254 GKLIDRKQIKQRPFRSPHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEF---------------------KRSVL  312 (499)
T ss_pred             hhhccccccccCCccccccccchhhhhCCccccchhhhhccCCCeEecCChhhC---------------------CHHHH
Confidence                        1111111100     000001111223446789999999876                     24556


Q ss_pred             HHHHHHhcccc---------cCCCCceEEEEecCCC------C-----------------CCCccccCCCceeeEEEeCC
Q 012016          343 SGFLNFIDGLW---------SSCGDERIIVFTTNHK------E-----------------KLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       343 s~LL~~ldg~~---------~~~~~~~iiI~tTN~~------~-----------------~ld~aLlrpgRfd~~I~~~~  390 (473)
                      ..|+..|+.-.         ..-..+..+|+++|..      +                 ++...|+.  |||.+++++.
T Consensus       313 ~~L~~~LE~~~v~i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllD--R~dl~~~~~~  390 (499)
T TIGR00368       313 DALREPIEDGSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLD--RIDLSVEVPL  390 (499)
T ss_pred             HHHHHHHHcCcEEEEecCcceeccCCeEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHh--hCCEEEEEcC
Confidence            66666664321         0112357888888852      1                 57778888  9999999999


Q ss_pred             CCHHH
Q 012016          391 CTPSG  395 (473)
Q Consensus       391 p~~~~  395 (473)
                      ++.++
T Consensus       391 ~~~~~  395 (499)
T TIGR00368       391 LPPEK  395 (499)
T ss_pred             CCHHH
Confidence            87764

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=98.68  E-value=1.6e-07  Score=104.46  Aligned_cols=89  Identities=19%  Similarity=0.315  Sum_probs=67.8

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN  292 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~  292 (473)
                      ..|++++|.....+.+.+.+......           ...+||+|++|||||++|++|....   +.+++.++|..+.. 
T Consensus       373 ~~~~~liG~S~~~~~~~~~~~~~a~~-----------~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~-  440 (686)
T PRK15429        373 SEFGEIIGRSEAMYSVLKQVEMVAQS-----------DSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPA-  440 (686)
T ss_pred             ccccceeecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCCh-
Confidence            57889999999888888888765432           3479999999999999999999865   57999999987632 


Q ss_pred             hHHHH-H-----------------HHHhccCceEEEeccccc
Q 012016          293 SDLRT-L-----------------LVATANRSILVVEDIDCT  316 (473)
Q Consensus       293 ~~l~~-l-----------------~~~~~~~sIL~iDdiD~l  316 (473)
                      ..+.. +                 ......++.|||||||.+
T Consensus       441 ~~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L  482 (686)
T PRK15429        441 GLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDM  482 (686)
T ss_pred             hHhhhhhcCcccccccccccchhhHHHhcCCCeEEEechhhC
Confidence            11111 1                 112345789999999987

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.67  E-value=1.7e-07  Score=100.85  Aligned_cols=156  Identities=13%  Similarity=0.235  Sum_probs=96.8

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS  291 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~  291 (473)
                      ..+|++++|.....+.+++.+......           ...+||+|++||||+++|+++....   +.|++.++|..+..
T Consensus       200 ~~~f~~~ig~s~~~~~~~~~~~~~A~~-----------~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~~  268 (520)
T PRK10820        200 DSAFSQIVAVSPKMRQVVEQARKLAML-----------DAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPD  268 (520)
T ss_pred             cccccceeECCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCCH
Confidence            368999999888777777777654332           3469999999999999999987654   46899999998743


Q ss_pred             chHHHH-HH-----------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc-
Q 012016          292 NSDLRT-LL-----------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL-  352 (473)
Q Consensus       292 ~~~l~~-l~-----------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-  352 (473)
                       ..+.. +|                 ....+++.|||||||.+..                     .....|++++..- 
T Consensus       269 -~~~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~---------------------~~Q~~Ll~~l~~~~  326 (520)
T PRK10820        269 -DVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSP---------------------RMQAKLLRFLNDGT  326 (520)
T ss_pred             -HHHHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEEeChhhCCH---------------------HHHHHHHHHHhcCC
Confidence             22222 22                 1123568899999998832                     3335566666431 


Q ss_pred             ccCCC------CceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCCH--HHHHHHHHHHhC
Q 012016          353 WSSCG------DERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       353 ~~~~~------~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                      ....|      .++-||+||+.+       ..+.+.|..  |+. ..|++|....  +....|+..|+.
T Consensus       327 ~~~~g~~~~~~~~vRiI~st~~~l~~l~~~g~f~~dL~~--rL~~~~i~lPpLreR~~Di~~L~~~fl~  393 (520)
T PRK10820        327 FRRVGEDHEVHVDVRVICATQKNLVELVQKGEFREDLYY--RLNVLTLNLPPLRDRPQDIMPLTELFVA  393 (520)
T ss_pred             cccCCCCcceeeeeEEEEecCCCHHHHHHcCCccHHHHh--hcCeeEEeCCCcccChhHHHHHHHHHHH
Confidence            11111      124567766653       234455555  654 4455555432  234455555554

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.66  E-value=1.8e-06  Score=85.63  Aligned_cols=119  Identities=19%  Similarity=0.249  Sum_probs=85.7

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC------------------------CceEEccccc-ccCchHHHHHHHHhc---
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN------------------------FDVYDLELTE-LRSNSDLRTLLVATA---  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~------------------------~~~~~l~~~~-~~~~~~l~~l~~~~~---  303 (473)
                      .+.+|||+||  +||+.+|.++|..+-                        -+++.+.... ....+.++++.....   
T Consensus        23 l~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~~p  100 (290)
T PRK07276         23 LNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSG  100 (290)
T ss_pred             cceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhhCc
Confidence            4678999996  689999999998761                        2333333221 123456776665543   


Q ss_pred             ---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCC
Q 012016          304 ---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPG  380 (473)
Q Consensus       304 ---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpg  380 (473)
                         ...|++||++|.+                     .....+.||+.++.    ++.+.++|++|+.++.+-|.+++  
T Consensus       101 ~~~~~kV~II~~ad~m---------------------~~~AaNaLLKtLEE----Pp~~t~~iL~t~~~~~lLpTI~S--  153 (290)
T PRK07276        101 YEGKQQVFIIKDADKM---------------------HVNAANSLLKVIEE----PQSEIYIFLLTNDENKVLPTIKS--  153 (290)
T ss_pred             ccCCcEEEEeehhhhc---------------------CHHHHHHHHHHhcC----CCCCeEEEEEECChhhCchHHHH--
Confidence               3579999999987                     34677899999985    45668999999999999999998  


Q ss_pred             ceeeEEEeCCCCHHHHHHHHH
Q 012016          381 RMDVHVHMSYCTPSGFKLLAA  401 (473)
Q Consensus       381 Rfd~~I~~~~p~~~~r~~l~~  401 (473)
                      |+ .+|.|+. +.+...+++.
T Consensus       154 Rc-q~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        154 RT-QIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             cc-eeeeCCC-cHHHHHHHHH
Confidence            87 5788876 5555444443

>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=98.65  E-value=2.7e-07  Score=87.63  Aligned_cols=158  Identities=25%  Similarity=0.333  Sum_probs=84.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC---ceEEccccccc---------------------------------------
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF---DVYDLELTELR---------------------------------------  290 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~---~~~~l~~~~~~---------------------------------------  290 (473)
                      ...++|+||.|+|||+|++.+.+.+.-   ..+.++.....                                       
T Consensus        20 ~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   99 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDLS   99 (234)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-
T ss_pred             CcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcch
Confidence            468999999999999999999998832   11111110000                                       


Q ss_pred             --CchHHHHHHHHh---ccCceEEEecccccc-ccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 --SNSDLRTLLVAT---ANRSILVVEDIDCTI-DLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 --~~~~l~~l~~~~---~~~sIL~iDdiD~l~-~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                        ....+..++...   ..+.||+|||++.+. .                .......+..|.+.++.....  .++.+|+
T Consensus       100 ~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~----------------~~~~~~~~~~l~~~~~~~~~~--~~~~~v~  161 (234)
T PF01637_consen  100 EDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIA----------------SEEDKDFLKSLRSLLDSLLSQ--QNVSIVI  161 (234)
T ss_dssp             GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBC----------------TTTTHHHHHHHHHHHHH------TTEEEEE
T ss_pred             hhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhc----------------ccchHHHHHHHHHHHhhcccc--CCceEEE
Confidence              011222333322   245899999999986 2                112355667777777764332  3344444


Q ss_pred             ecCCC----C--CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc--CCHHHHHHHHhcCCCCHHHHHH
Q 012016          365 TTNHK----E--KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH--ILFEEIEELISTTQVTPAEVAE  431 (473)
Q Consensus       365 tTN~~----~--~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~--~l~~~i~~l~~~~~~t~a~i~~  431 (473)
                      ++...    +  .-.+.+..  |+.. +.++..+.++..+++...+.....  ...++++.+..-++-.|.-|..
T Consensus       162 ~~S~~~~~~~~~~~~~~~~~--~~~~-~~l~~l~~~e~~~~~~~~~~~~~~~~~~~~~~~~i~~~~gG~P~~l~~  233 (234)
T PF01637_consen  162 TGSSDSLMEEFLDDKSPLFG--RFSH-IELKPLSKEEAREFLKELFKELIKLPFSDEDIEEIYSLTGGNPRYLQE  233 (234)
T ss_dssp             EESSHHHHHHTT-TTSTTTT-----E-EEE----HHHHHHHHHHHHHCC------HHHHHHHHHHHTT-HHHHHH
T ss_pred             ECCchHHHHHhhcccCcccc--ccce-EEEeeCCHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHhCCCHHHHhc
Confidence            44332    1  11223333  8876 999999999999999886543311  2456666666666677766643

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.65  E-value=1.1e-06  Score=86.31  Aligned_cols=155  Identities=17%  Similarity=0.210  Sum_probs=83.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC-ceEEcc-----cc--cc------------cCc------hHHHHHHHH---hcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF-DVYDLE-----LT--EL------------RSN------SDLRTLLVA---TAN  304 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~-~~~~l~-----~~--~~------------~~~------~~l~~l~~~---~~~  304 (473)
                      ..++|+||+|+|||++++.+++.+.. .+....     .+  ++            ...      ..+...+..   ..+
T Consensus        44 ~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~~  123 (269)
T TIGR03015        44 GFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAGK  123 (269)
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCCC
Confidence            35899999999999999999999862 222111     10  00            000      112222211   235


Q ss_pred             CceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC--CCCCC----ccccC
Q 012016          305 RSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH--KEKLD----PALLR  378 (473)
Q Consensus       305 ~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~--~~~ld----~aLlr  378 (473)
                      +.+|+|||++.+..                  .....+..|.+...    ..+..+.||++...  .+.+.    ..+.+
T Consensus       124 ~~vliiDe~~~l~~------------------~~~~~l~~l~~~~~----~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~  181 (269)
T TIGR03015       124 RALLVVDEAQNLTP------------------ELLEELRMLSNFQT----DNAKLLQIFLVGQPEFRETLQSPQLQQLRQ  181 (269)
T ss_pred             CeEEEEECcccCCH------------------HHHHHHHHHhCccc----CCCCeEEEEEcCCHHHHHHHcCchhHHHHh
Confidence            68999999997631                  11222333332211    11122333333321  12221    13445


Q ss_pred             CCceeeEEEeCCCCHHHHHHHHHHHhCccc-----cCCHHHHHHHHhcCCCCHHHHHHH
Q 012016          379 PGRMDVHVHMSYCTPSGFKLLAANYLGIKE-----HILFEEIEELISTTQVTPAEVAEQ  432 (473)
Q Consensus       379 pgRfd~~I~~~~p~~~~r~~l~~~~l~~~~-----~~l~~~i~~l~~~~~~t~a~i~~~  432 (473)
                        |+...++++..+.++...++...+....     ....+.++.+.+.++-.|..|...
T Consensus       182 --r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l  238 (269)
T TIGR03015       182 --RIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINIL  238 (269)
T ss_pred             --heeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHH
Confidence              8888999999999999888887765321     122355555555555555555443

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.

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.63  E-value=1.5e-07  Score=99.91  Aligned_cols=119  Identities=21%  Similarity=0.307  Sum_probs=77.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC----------ceEEcccc-----cc------------------cCchHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF----------DVYDLELT-----EL------------------RSNSDLRTLL  299 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~----------~~~~l~~~-----~~------------------~~~~~l~~l~  299 (473)
                      ...++|.||||||||++++.|+..+.-          .++.+...     .+                  .+....+.-.
T Consensus       210 G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG~  289 (506)
T PRK09862        210 GHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGE  289 (506)
T ss_pred             CcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhhccccccCCcCCCCccCCCccchHHHHhCCCceehhhH
Confidence            457999999999999999999987631          11111000     00                  0001112222


Q ss_pred             HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcc-cc--c------CCCCceEEEEecCCCC
Q 012016          300 VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDG-LW--S------SCGDERIIVFTTNHKE  370 (473)
Q Consensus       300 ~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg-~~--~------~~~~~~iiI~tTN~~~  370 (473)
                      .....+.+|||||++.+                     ....+..|++.|+. ..  +      ....+..+|+|+|...
T Consensus       290 l~~A~gGvLfLDEi~e~---------------------~~~~~~~L~~~LE~g~v~I~r~g~~~~~pa~f~lIAa~NP~p  348 (506)
T PRK09862        290 ISLAHNGVLFLDELPEF---------------------ERRTLDALREPIESGQIHLSRTRAKITYPARFQLVAAMNPSP  348 (506)
T ss_pred             hhhccCCEEecCCchhC---------------------CHHHHHHHHHHHHcCcEEEecCCcceeccCCEEEEEeecCcc
Confidence            33456799999999865                     34667777877743 21  0      1124578899999752


Q ss_pred             ---------------------CCCccccCCCceeeEEEeCCCCHH
Q 012016          371 ---------------------KLDPALLRPGRMDVHVHMSYCTPS  394 (473)
Q Consensus       371 ---------------------~ld~aLlrpgRfd~~I~~~~p~~~  394 (473)
                                           ++..+++.  |||.++.+++|+.+
T Consensus       349 cG~~~~~~c~c~~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~  391 (506)
T PRK09862        349 TGHYQGNHNRCTPEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPG  391 (506)
T ss_pred             ceecCCCCCCcCHHHHHHHHhhCCHhHHh--hccEEEEeCCCCHH
Confidence                                 46778888  99999999999876

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.62  E-value=1.5e-06  Score=86.79  Aligned_cols=122  Identities=16%  Similarity=0.209  Sum_probs=90.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc--------C---C--ceEEcc--cccccCchHHHHHHHHhc-------cCceEE
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL--------N---F--DVYDLE--LTELRSNSDLRTLLVATA-------NRSILV  309 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l--------~---~--~~~~l~--~~~~~~~~~l~~l~~~~~-------~~sIL~  309 (473)
                      .++.|||+|+.|.||+.++.++++.+        +   .  ++..++  ... .+...++++....+       .+-|++
T Consensus        17 l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~-i~vd~Ir~l~~~~~~~~~~~~~~KvvI   95 (299)
T PRK07132         17 ISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKD-LSKSEFLSAINKLYFSSFVQSQKKILI   95 (299)
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCc-CCHHHHHHHHHHhccCCcccCCceEEE
Confidence            45789999999999999999999987        1   1  233343  222 23356666665542       567999


Q ss_pred             EeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeC
Q 012016          310 VEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMS  389 (473)
Q Consensus       310 iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~  389 (473)
                      ||++|.+                     .....+.||..|+.    +++..++|++|+.++.+-|+++.  |+ .+++|+
T Consensus        96 I~~~e~m---------------------~~~a~NaLLK~LEE----Pp~~t~~il~~~~~~kll~TI~S--Rc-~~~~f~  147 (299)
T PRK07132         96 IKNIEKT---------------------SNSLLNALLKTIEE----PPKDTYFLLTTKNINKVLPTIVS--RC-QVFNVK  147 (299)
T ss_pred             Eeccccc---------------------CHHHHHHHHHHhhC----CCCCeEEEEEeCChHhChHHHHh--Ce-EEEECC
Confidence            9999876                     24567789999986    45668888888888999999987  76 579999


Q ss_pred             CCCHHHHHHHHHH
Q 012016          390 YCTPSGFKLLAAN  402 (473)
Q Consensus       390 ~p~~~~r~~l~~~  402 (473)
                      .++.++....+..
T Consensus       148 ~l~~~~l~~~l~~  160 (299)
T PRK07132        148 EPDQQKILAKLLS  160 (299)
T ss_pred             CCCHHHHHHHHHH
Confidence            9998887755543

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.62  E-value=4.2e-07  Score=89.83  Aligned_cols=112  Identities=17%  Similarity=0.234  Sum_probs=83.0

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC----------------CceEEccccc---ccCchHHHHHHHHhc------cCc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN----------------FDVYDLELTE---LRSNSDLRTLLVATA------NRS  306 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~----------------~~~~~l~~~~---~~~~~~l~~l~~~~~------~~s  306 (473)
                      .+.+|||+||+|+||+.+|.++|..+-                -+++.+....   ..+-+.++++.....      ..-
T Consensus        18 l~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~k   97 (290)
T PRK05917         18 VPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYK   97 (290)
T ss_pred             cCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCce
Confidence            467899999999999999999999872                2344342211   123455666555443      346


Q ss_pred             eEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEE
Q 012016          307 ILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHV  386 (473)
Q Consensus       307 IL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I  386 (473)
                      |++||++|.+                     .....+.||+.++.    ++++.++|+.|+.++.|.|.+++  |+. .+
T Consensus        98 v~ii~~ad~m---------------------t~~AaNaLLK~LEE----Pp~~~~fiL~~~~~~~ll~TI~S--Rcq-~~  149 (290)
T PRK05917         98 IYIIHEADRM---------------------TLDAISAFLKVLED----PPQHGVIILTSAKPQRLPPTIRS--RSL-SI  149 (290)
T ss_pred             EEEEechhhc---------------------CHHHHHHHHHHhhc----CCCCeEEEEEeCChhhCcHHHHh--cce-EE
Confidence            9999999988                     34677889999985    45679999999999999999998  874 67


Q ss_pred             EeCCC
Q 012016          387 HMSYC  391 (473)
Q Consensus       387 ~~~~p  391 (473)
                      .|+.+
T Consensus       150 ~~~~~  154 (290)
T PRK05917        150 HIPME  154 (290)
T ss_pred             Eccch
Confidence            77754

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.61  E-value=7.3e-08  Score=81.49  Aligned_cols=61  Identities=20%  Similarity=0.361  Sum_probs=39.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      |.||||||+|||++++.||..+.-.+-......+-....-.+.+..-....++++||+...
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~~q~vvi~DD~~~~   61 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQGQPVVIIDDFGQD   61 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccCCCcEEEEeecCcc
Confidence            5799999999999999999887533311111111111122334555667899999999865

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

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.61  E-value=4.6e-07  Score=97.34  Aligned_cols=154  Identities=15%  Similarity=0.166  Sum_probs=98.0

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCch
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNS  293 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~  293 (473)
                      .+++++|.....+.+.+.+...-..           ...+||+|++||||+++|++|....   +.+++.++|..+.. .
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~-----------~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~-~  252 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAAS-----------DLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPE-S  252 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCCh-H
Confidence            5688999988888888877765432           4579999999999999999999875   57999999998743 2


Q ss_pred             HHHH-HH-----------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-c
Q 012016          294 DLRT-LL-----------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-S  354 (473)
Q Consensus       294 ~l~~-l~-----------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~  354 (473)
                      .+.. +|                 ....+++.|||||||.+.                     ......|++.++.-. .
T Consensus       253 ~~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~---------------------~~~Q~~Ll~~l~~~~~~  311 (509)
T PRK05022        253 LAESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGELP---------------------LALQAKLLRVLQYGEIQ  311 (509)
T ss_pred             HHHHHhcCccccccCCCcccCCcchhhcCCCEEEecChhhCC---------------------HHHHHHHHHHHhcCCEe
Confidence            2222 22                 123456889999999883                     234455666664321 0


Q ss_pred             C------CCCceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCCH--HHHHHHHHHHhC
Q 012016          355 S------CGDERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       355 ~------~~~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                      .      ...++-||+|||..       ..+.+.|..  |+. ..|++|....  +....|+..|+.
T Consensus       312 ~~g~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~dL~~--rl~~~~i~lPpLreR~eDI~~L~~~fl~  376 (509)
T PRK05022        312 RVGSDRSLRVDVRVIAATNRDLREEVRAGRFRADLYH--RLSVFPLSVPPLRERGDDVLLLAGYFLE  376 (509)
T ss_pred             eCCCCcceecceEEEEecCCCHHHHHHcCCccHHHHh--cccccEeeCCCchhchhhHHHHHHHHHH
Confidence            0      01135677777653       234445544  553 3355555432  234456666654

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.59  E-value=6.8e-07  Score=86.04  Aligned_cols=164  Identities=15%  Similarity=0.208  Sum_probs=110.4

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-CCc----------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-NFD----------  280 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-~~~----------  280 (473)
                      ...|.+|+.+....+....+.....    ..+         -.++|+|||+|+||-+.+.|+-+++ |.-          
T Consensus         6 kyrpksl~~l~~~~e~~~~Lksl~~----~~d---------~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t   72 (351)
T KOG2035|consen    6 KYRPKSLDELIYHEELANLLKSLSS----TGD---------FPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRT   72 (351)
T ss_pred             hcCcchhhhcccHHHHHHHHHHhcc----cCC---------CCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEE
Confidence            3456788888887766665533221    011         1379999999999999999999988 111          


Q ss_pred             ------------------eEEcccccccCc--hHHHHHHHHhcc-----------CceEEEeccccccccccCCccccCC
Q 012016          281 ------------------VYDLELTELRSN--SDLRTLLVATAN-----------RSILVVEDIDCTIDLQDRLPADIAG  329 (473)
Q Consensus       281 ------------------~~~l~~~~~~~~--~~l~~l~~~~~~-----------~sIL~iDdiD~l~~~~~r~~~~~~~  329 (473)
                                        .+.++.++.+..  --+++++...++           -.+++|.|+|.+.            
T Consensus        73 ~~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT------------  140 (351)
T KOG2035|consen   73 FTTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELT------------  140 (351)
T ss_pred             EecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhh------------
Confidence                              122333333322  234566655431           2689999999883            


Q ss_pred             CCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc
Q 012016          330 EGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH  409 (473)
Q Consensus       330 ~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~  409 (473)
                               +....+|-..|+...+.    .-+|+.+|....+=+++..  |+ ..|.+|.|+.++...++.+.+..++.
T Consensus       141 ---------~dAQ~aLRRTMEkYs~~----~RlIl~cns~SriIepIrS--RC-l~iRvpaps~eeI~~vl~~v~~kE~l  204 (351)
T KOG2035|consen  141 ---------RDAQHALRRTMEKYSSN----CRLILVCNSTSRIIEPIRS--RC-LFIRVPAPSDEEITSVLSKVLKKEGL  204 (351)
T ss_pred             ---------HHHHHHHHHHHHHHhcC----ceEEEEecCcccchhHHhh--he-eEEeCCCCCHHHHHHHHHHHHHHhcc
Confidence                     33445566666655443    4477788888888888987  76 57999999999999999998887766


Q ss_pred             CCHHHHH
Q 012016          410 ILFEEIE  416 (473)
Q Consensus       410 ~l~~~i~  416 (473)
                      .+..++.
T Consensus       205 ~lp~~~l  211 (351)
T KOG2035|consen  205 QLPKELL  211 (351)
T ss_pred             cCcHHHH
Confidence            6655443

>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=98.59  E-value=8.4e-07  Score=85.33  Aligned_cols=133  Identities=23%  Similarity=0.200  Sum_probs=82.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhc-cCceEEEeccccccccccCCccccCCCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEG  331 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~  331 (473)
                      ..|-.++||+|||||.+++++|+.+|.+++.++|++..+-..+.+++..+. .++-+++||++.+-.             
T Consensus        32 ~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~~~~l~ril~G~~~~GaW~cfdefnrl~~-------------   98 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMDYQSLSRILKGLAQSGAWLCFDEFNRLSE-------------   98 (231)
T ss_dssp             TTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-HHHHHHHHHHHHHHT-EEEEETCCCSSH-------------
T ss_pred             CCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccccHHHHHHHHHHHhhcCchhhhhhhhhhhH-------------
Confidence            457789999999999999999999999999999999888889999998775 689999999998731             


Q ss_pred             CCCccchhHHHHHHHHHh-cccccCC------C------CceEEEEecCC----CCCCCccccCCCceeeEEEeCCCCHH
Q 012016          332 EGPIQQNKVTLSGFLNFI-DGLWSSC------G------DERIIVFTTNH----KEKLDPALLRPGRMDVHVHMSYCTPS  394 (473)
Q Consensus       332 ~~~~~~~~~~ls~LL~~l-dg~~~~~------~------~~~iiI~tTN~----~~~ld~aLlrpgRfd~~I~~~~p~~~  394 (473)
                           ..-..+++.+..+ +.+....      +      ...-+++|.|.    ...||+.|..   +-+.|.|..||..
T Consensus        99 -----~vLS~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~---lFRpvam~~PD~~  170 (231)
T PF12774_consen   99 -----EVLSVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKA---LFRPVAMMVPDLS  170 (231)
T ss_dssp             -----HHHHHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCT---TEEEEE--S--HH
T ss_pred             -----HHHHHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHH---HhheeEEeCCCHH
Confidence                 1122222222222 1111110      0      11234556663    3567777764   3478999999999


Q ss_pred             HHHHHHHHHhCc
Q 012016          395 GFKLLAANYLGI  406 (473)
Q Consensus       395 ~r~~l~~~~l~~  406 (473)
                      ...++.-.-.+.
T Consensus       171 ~I~ei~L~s~GF  182 (231)
T PF12774_consen  171 LIAEILLLSQGF  182 (231)
T ss_dssp             HHHHHHHHCCCT
T ss_pred             HHHHHHHHHcCc
Confidence            877666544443

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.59  E-value=2.4e-07  Score=90.83  Aligned_cols=157  Identities=17%  Similarity=0.215  Sum_probs=100.5

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc------eEE
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD------VYD  283 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~------~~~  283 (473)
                      ++...|..++++++..+....+.+    |..       .+.  -.+.|+|||||||||+.+.|.|+.+-.+      +..
T Consensus        32 vekyrP~~l~dv~~~~ei~st~~~----~~~-------~~~--lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~le   98 (360)
T KOG0990|consen   32 VEKYRPPFLGIVIKQEPIWSTENR----YSG-------MPG--LPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLE   98 (360)
T ss_pred             ccCCCCchhhhHhcCCchhhHHHH----hcc-------CCC--CCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHH
Confidence            346788999999998766554433    321       111  2289999999999999999999988442      233


Q ss_pred             cccccccCchHH---HHHHHHhc---------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcc
Q 012016          284 LELTELRSNSDL---RTLLVATA---------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDG  351 (473)
Q Consensus       284 l~~~~~~~~~~l---~~l~~~~~---------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg  351 (473)
                      ++.++-.+-.-.   ...|..+.         ....+++||.|++.                     +...++|-..+..
T Consensus        99 lnaSd~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT---------------------~~AQnALRRviek  157 (360)
T KOG0990|consen   99 LNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMT---------------------RDAQNALRRVIEK  157 (360)
T ss_pred             hhccCccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHhh---------------------HHHHHHHHHHHHH
Confidence            444443222112   22333333         34689999999884                     2333444444444


Q ss_pred             cccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          352 LWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       352 ~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ..    .+.-+...+|++..+.|++..  ||. ...|...+..+-.....+....+
T Consensus       158 ~t----~n~rF~ii~n~~~ki~pa~qs--Rct-rfrf~pl~~~~~~~r~shi~e~e  206 (360)
T KOG0990|consen  158 YT----ANTRFATISNPPQKIHPAQQS--RCT-RFRFAPLTMAQQTERQSHIRESE  206 (360)
T ss_pred             hc----cceEEEEeccChhhcCchhhc--ccc-cCCCCCCChhhhhhHHHHHHhcc
Confidence            32    346666889999999999997  664 35666667666666666665544

>PF13173 AAA_14: AAA domain

Probab=98.58  E-value=2.9e-07  Score=80.28  Aligned_cols=115  Identities=18%  Similarity=0.284  Sum_probs=71.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC--CceEEcccccccCch----HHHHHHHHh--ccCceEEEeccccccccccCCcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN--FDVYDLELTELRSNS----DLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPA  325 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~--~~~~~l~~~~~~~~~----~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~  325 (473)
                      +.++|+||.|+|||++++.++..+.  ..++.+++.+.....    .+.+.+...  ..+.+||||||..+..       
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEiq~~~~-------   75 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLADPDLLEYFLELIKPGKKYIFIDEIQYLPD-------   75 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHhhhhhHHHHHHhhccCCcEEEEehhhhhcc-------
Confidence            4689999999999999999999886  788888877653211    133444333  3679999999987621       


Q ss_pred             ccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCcc--ccCCCceeeEEEeCCCCHHHH
Q 012016          326 DIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPA--LLRPGRMDVHVHMSYCTPSGF  396 (473)
Q Consensus       326 ~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~a--LlrpgRfd~~I~~~~p~~~~r  396 (473)
                                  ....+..+.+   .    . .+.-||+|+.....+...  -.-+||.. .+++.+.+..++
T Consensus        76 ------------~~~~lk~l~d---~----~-~~~~ii~tgS~~~~l~~~~~~~l~gr~~-~~~l~Plsf~E~  127 (128)
T PF13173_consen   76 ------------WEDALKFLVD---N----G-PNIKIILTGSSSSLLSKDIAESLAGRVI-EIELYPLSFREF  127 (128)
T ss_pred             ------------HHHHHHHHHH---h----c-cCceEEEEccchHHHhhcccccCCCeEE-EEEECCCCHHHh
Confidence                        2233333333   1    1 223444444433322111  11246885 789998888764

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.54  E-value=3.7e-07  Score=101.55  Aligned_cols=128  Identities=19%  Similarity=0.226  Sum_probs=81.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC-------ceEEcccccccC-c----h--HHHHHHHHhccCceEEEecccccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF-------DVYDLELTELRS-N----S--DLRTLLVATANRSILVVEDIDCTIDL  319 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~-------~~~~l~~~~~~~-~----~--~l~~l~~~~~~~sIL~iDdiD~l~~~  319 (473)
                      ..+||.|+||||||.+++++++....       +...+.+..... .    .  .+..-....+.+++++|||+|.+.  
T Consensus       493 ihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~vgLTa~~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkms--  570 (915)
T PTZ00111        493 INVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSVGLTASIKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCH--  570 (915)
T ss_pred             ceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccccccchhhhcccccCcccccCCcEEEcCCCeEEecchhhCC--
Confidence            36999999999999999999986533       333333332210 0    0  000000112357899999999873  


Q ss_pred             ccCCccccCCCCCCCccchhHHHHHHHHHhccc---------ccCCCCceEEEEecCCCC-------------CCCcccc
Q 012016          320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL---------WSSCGDERIIVFTTNHKE-------------KLDPALL  377 (473)
Q Consensus       320 ~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~~-------------~ld~aLl  377 (473)
                                         ......|+..|+.-         ...-....-||+|+|..+             .|+++|+
T Consensus       571 -------------------~~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LL  631 (915)
T PTZ00111        571 -------------------NESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIENINISPSLF  631 (915)
T ss_pred             -------------------HHHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCcccccCCChHHh
Confidence                               33456667777432         111224577899999752             4678999


Q ss_pred             CCCceeeE-EEeCCCCHHHHHHHHHHHh
Q 012016          378 RPGRMDVH-VHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       378 rpgRfd~~-I~~~~p~~~~r~~l~~~~l  404 (473)
                      .  |||.. +-++.|+.+.=..|+.+.+
T Consensus       632 S--RFDLIf~l~D~~d~~~D~~lA~hI~  657 (915)
T PTZ00111        632 T--RFDLIYLVLDHIDQDTDQLISLSIA  657 (915)
T ss_pred             h--hhcEEEEecCCCChHHHHHHHHHHH
Confidence            9  99865 5667788877666666554

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.54  E-value=7.9e-07  Score=97.09  Aligned_cols=50  Identities=34%  Similarity=0.448  Sum_probs=38.7

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      .-+++++|+++.++.+...+.    .           +++++|+||||||||++++++|+.++..
T Consensus        15 ~~~~~viG~~~a~~~l~~a~~----~-----------~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        15 RLIDQVIGQEEAVEIIKKAAK----Q-----------KRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             hhHhhccCHHHHHHHHHHHHH----c-----------CCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            467888998877765543332    1           2489999999999999999999999644

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PHA02624 large T antigen; Provisional

Probab=98.47  E-value=6.2e-07  Score=95.56  Aligned_cols=125  Identities=18%  Similarity=0.229  Sum_probs=81.2

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccC
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIA  328 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~  328 (473)
                      |+|.++.++||||||||||+++.+|++.|+-.+..++.+.    +.++-.+.-+....+.+|||+-.-.-.    .... 
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt----~ks~FwL~pl~D~~~~l~dD~t~~~~~----~~~L-  497 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQPAD----NKDL-  497 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCc----chhHHHhhhhhhceEEEeeeccccccc----cccC-
Confidence            6777889999999999999999999999966666665332    345555666677889999999632110    0000 


Q ss_pred             CCCCCCccchhHHHHHHHHHhcccccCC-----CCc-----eEEEEecCCCCCCCccccCCCceeeEEEeCC
Q 012016          329 GEGEGPIQQNKVTLSGFLNFIDGLWSSC-----GDE-----RIIVFTTNHKEKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       329 ~~~~~~~~~~~~~ls~LL~~ldg~~~~~-----~~~-----~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~  390 (473)
                           ..+..-..+..|-|.+||-..-+     ...     --.|.|||. ..|+..+.-  ||-.++.|..
T Consensus       498 -----p~G~~~dNl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlliT~Ne-y~iP~T~~~--Rf~~~~~F~~  561 (647)
T PHA02624        498 -----PSGQGMNNLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIVTMNE-YLIPQTVKA--RFAKVLDFKP  561 (647)
T ss_pred             -----CcccccchhhHHHhhcCCCCccccchhccCchhccCCCeEEeecC-cccchhHHH--HHHHhccccc
Confidence                 00111223456778888861100     001     135678886 456777777  8988888864

>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=98.46  E-value=3.7e-07  Score=93.39  Aligned_cols=100  Identities=24%  Similarity=0.382  Sum_probs=64.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------ceEE--cc----ccccc-CchHHHHHHHHhccCc-eEEEeccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------DVYD--LE----LTELR-SNSDLRTLLVATANRS-ILVVEDID  314 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------~~~~--l~----~~~~~-~~~~l~~l~~~~~~~s-IL~iDdiD  314 (473)
                      ..+.++|++||||+|+|||+|+-...+.+..      ++..  .+    +..+. ....+..+.....+.+ +|+|||+.
T Consensus        58 ~~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~~~~~lLcfDEF~  137 (362)
T PF03969_consen   58 PPPPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELAKESRLLCFDEFQ  137 (362)
T ss_pred             cCCCCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHHhcCCEEEEeeee
Confidence            3457899999999999999999999988843      1111  11    01111 2234444555555554 99999997


Q ss_pred             cccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC-CCC
Q 012016          315 CTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK-EKL  372 (473)
Q Consensus       315 ~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-~~l  372 (473)
                      .-                  +-.....+..|++.+=   .   .++++|+|+|++ +.|
T Consensus       138 V~------------------DiaDAmil~rLf~~l~---~---~gvvlVaTSN~~P~~L  172 (362)
T PF03969_consen  138 VT------------------DIADAMILKRLFEALF---K---RGVVLVATSNRPPEDL  172 (362)
T ss_pred             cc------------------chhHHHHHHHHHHHHH---H---CCCEEEecCCCChHHH
Confidence            43                  2223556677776552   2   458999999974 443

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

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.45  E-value=2.7e-06  Score=84.04  Aligned_cols=69  Identities=19%  Similarity=0.293  Sum_probs=48.8

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhh-cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRV-GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE  288 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~-g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~  288 (473)
                      -++|+++.|+.+--.+.+-.++...-..+ .--.|+++|..||.|+|||.+|+-||+..+.||+.+..+.
T Consensus        16 yIIGQ~~AKkaVAIALRNR~RR~qL~~~lr~EV~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATK   85 (444)
T COG1220          16 YIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATK   85 (444)
T ss_pred             HhcCcHHHHHHHHHHHHHHHHHHhcCHHHhhccCccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeee
Confidence            36788888888765555443332211111 1123789999999999999999999999998888766544

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.45  E-value=6.4e-07  Score=91.84  Aligned_cols=158  Identities=15%  Similarity=0.147  Sum_probs=103.6

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHh----cCCceEEcccccccC
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY----LNFDVYDLELTELRS  291 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~----l~~~~~~l~~~~~~~  291 (473)
                      ..+++|+|....-+++++.+..+-           +-...+|++|++||||+.+|++|...    .+.|++.+||..+..
T Consensus        75 ~~~~~LIG~~~~~~~~~eqik~~a-----------p~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~~e  143 (403)
T COG1221          75 EALDDLIGESPSLQELREQIKAYA-----------PSGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAYSE  143 (403)
T ss_pred             hhhhhhhccCHHHHHHHHHHHhhC-----------CCCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHhCc
Confidence            468899999888888888777521           12346999999999999999998854    367999999999976


Q ss_pred             chHHHHHHHHh-----------------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc--
Q 012016          292 NSDLRTLLVAT-----------------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL--  352 (473)
Q Consensus       292 ~~~l~~l~~~~-----------------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--  352 (473)
                      +-...++|-..                 .+...||+|||..+..                     .....|+.+||.-  
T Consensus       144 n~~~~eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~---------------------~~Q~kLl~~le~g~~  202 (403)
T COG1221         144 NLQEAELFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPP---------------------EGQEKLLRVLEEGEY  202 (403)
T ss_pred             CHHHHHHhccccceeecccCCcCchheecCCCEEehhhhhhCCH---------------------hHHHHHHHHHHcCce
Confidence            65555554321                 2568999999998843                     2334566666641  


Q ss_pred             ---cc--CCCCceEEEEecCC-C-CCCCc--cccCCCceeeEEEeCCCCH--HHHHHHHHHHhCc
Q 012016          353 ---WS--SCGDERIIVFTTNH-K-EKLDP--ALLRPGRMDVHVHMSYCTP--SGFKLLAANYLGI  406 (473)
Q Consensus       353 ---~~--~~~~~~iiI~tTN~-~-~~ld~--aLlrpgRfd~~I~~~~p~~--~~r~~l~~~~l~~  406 (473)
                         -+  .....+-+|++||- + +.+-.  .|.+ -|+...|++|....  +++..|+..|+..
T Consensus       203 ~rvG~~~~~~~dVRli~AT~~~l~~~~~~g~dl~~-rl~~~~I~LPpLrER~~Di~~L~e~Fl~~  266 (403)
T COG1221         203 RRVGGSQPRPVDVRLICATTEDLEEAVLAGADLTR-RLNILTITLPPLRERKEDILLLAEHFLKS  266 (403)
T ss_pred             EecCCCCCcCCCceeeeccccCHHHHHHhhcchhh-hhcCceecCCChhhchhhHHHHHHHHHHH
Confidence               11  11234667776663 2 22222  4443 16666777666433  3355677777653

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.43  E-value=8.1e-06  Score=90.92  Aligned_cols=122  Identities=23%  Similarity=0.354  Sum_probs=80.3

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCC-CCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc-----
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA-WKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR-----  290 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~-~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~-----  290 (473)
                      .|+|+++....|-+.+.....      .++.+ +.-.+||.||.|+|||-||+|+|.++   .-.++.+|+++..     
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~------gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evskl  636 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRA------GLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSKL  636 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhc------ccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhhc
Confidence            467777777776666554332      12222 45579999999999999999999998   4568888888621     


Q ss_pred             --------CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--cCCC-
Q 012016          291 --------SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--SSCG-  357 (473)
Q Consensus       291 --------~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--~~~~-  357 (473)
                              +....-.+.....  ..+||+|||||..                     ....++.|+..+|.-.  ...| 
T Consensus       637 igsp~gyvG~e~gg~LteavrrrP~sVVLfdeIEkA---------------------h~~v~n~llq~lD~GrltDs~Gr  695 (898)
T KOG1051|consen  637 IGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKA---------------------HPDVLNILLQLLDRGRLTDSHGR  695 (898)
T ss_pred             cCCCcccccchhHHHHHHHHhcCCceEEEEechhhc---------------------CHHHHHHHHHHHhcCccccCCCc
Confidence                    1122333333333  3499999999964                     2446677777776421  1222 


Q ss_pred             ----CceEEEEecCC
Q 012016          358 ----DERIIVFTTNH  368 (473)
Q Consensus       358 ----~~~iiI~tTN~  368 (473)
                          .+.|||+|+|.
T Consensus       696 ~Vd~kN~I~IMTsn~  710 (898)
T KOG1051|consen  696 EVDFKNAIFIMTSNV  710 (898)
T ss_pred             EeeccceEEEEeccc
Confidence                35799999885

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=98.41  E-value=9.4e-06  Score=87.01  Aligned_cols=170  Identities=15%  Similarity=0.232  Sum_probs=104.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEcccccccCchHH----------------------HHHHH-
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLELTELRSNSDL----------------------RTLLV-  300 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~~~~~~~~~l----------------------~~l~~-  300 (473)
                      ..+++.|-||||||.++..+-+.|          .++++.++...+.+...+                      ..-|. 
T Consensus       423 ~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~  502 (767)
T KOG1514|consen  423 SCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFTV  502 (767)
T ss_pred             eeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhcc
Confidence            368999999999999999999976          477778887766432222                      22222 


Q ss_pred             --HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          301 --ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       301 --~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                        ....++||+|||+|.|..                  ..+   .-|-|+.|.... .+...+||+..|+.+ |+..++-
T Consensus       503 ~k~~~~~~VvLiDElD~Lvt------------------r~Q---dVlYn~fdWpt~-~~sKLvvi~IaNTmd-lPEr~l~  559 (767)
T KOG1514|consen  503 PKPKRSTTVVLIDELDILVT------------------RSQ---DVLYNIFDWPTL-KNSKLVVIAIANTMD-LPERLLM  559 (767)
T ss_pred             CCCCCCCEEEEeccHHHHhc------------------ccH---HHHHHHhcCCcC-CCCceEEEEeccccc-CHHHHhc
Confidence              112468999999999863                  112   335566664332 234566666666543 3333331


Q ss_pred             ---CCcee-eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHHhh
Q 012016          379 ---PGRMD-VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKR  454 (473)
Q Consensus       379 ---pgRfd-~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~~~l~~~~~~~~al~~l~~~l~~~~  454 (473)
                         ..|++ ..|.|...+.+|..+|+...|....+. ..++.+|+..         ....-+||+..|++-...+.+.+.
T Consensus       560 nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~~~f-~~~aielvar---------kVAavSGDaRraldic~RA~Eia~  629 (767)
T KOG1514|consen  560 NRVSSRLGLTRICFQPYTHEQLQEIISARLKGLDAF-ENKAIELVAR---------KVAAVSGDARRALDICRRAAEIAE  629 (767)
T ss_pred             cchhhhccceeeecCCCCHHHHHHHHHHhhcchhhc-chhHHHHHHH---------HHHhccccHHHHHHHHHHHHHHhh
Confidence               12554 568899999999999999887655332 2233333321         122235777777777666666554


Q ss_pred             hc
Q 012016          455 KE  456 (473)
Q Consensus       455 ~~  456 (473)
                      ..
T Consensus       630 ~~  631 (767)
T KOG1514|consen  630 ER  631 (767)
T ss_pred             hh
Confidence            43

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.40  E-value=1e-06  Score=76.48  Aligned_cols=38  Identities=37%  Similarity=0.597  Sum_probs=29.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc--------CCceEEccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL--------NFDVYDLELTELR  290 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l--------~~~~~~l~~~~~~  290 (473)
                      .+.++++||||+|||++++.+++.+        +.+++.+++....
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   49 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSR   49 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHS
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCC
Confidence            4579999999999999999999988        7788887776653

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=98.40  E-value=2.7e-07  Score=95.27  Aligned_cols=48  Identities=27%  Similarity=0.462  Sum_probs=39.7

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...|.||.|++..|+.+.-...               -.+++|++||||||||++++-|..-|
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAAA---------------GgHnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAAA---------------GGHNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHHh---------------cCCcEEEecCCCCchHHhhhhhcccC
Confidence            4689999999999988743222               25689999999999999999998877

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=98.36  E-value=2.2e-06  Score=89.68  Aligned_cols=157  Identities=19%  Similarity=0.224  Sum_probs=101.7

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~  289 (473)
                      ..+.+|++|+|......++++.+..+-.           -.-.+||.|.+||||..+|++|.+..   +-||+.+||..+
T Consensus       239 ~a~y~f~~Iig~S~~m~~~~~~akr~A~-----------tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAi  307 (560)
T COG3829         239 KAKYTFDDIIGESPAMLRVLELAKRIAK-----------TDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAI  307 (560)
T ss_pred             ccccchhhhccCCHHHHHHHHHHHhhcC-----------CCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccC
Confidence            3446899999998887777776654433           24589999999999999999999977   679999999987


Q ss_pred             cCchHHHHHH-------------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhc
Q 012016          290 RSNSDLRTLL-------------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID  350 (473)
Q Consensus       290 ~~~~~l~~l~-------------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld  350 (473)
                      - +.-|...|                   ...++.+-||+|||..+                     .......||..+.
T Consensus       308 P-e~LlESELFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgem---------------------pl~LQaKLLRVLQ  365 (560)
T COG3829         308 P-ETLLESELFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEM---------------------PLPLQAKLLRVLQ  365 (560)
T ss_pred             C-HHHHHHHHhCcCCccccccccCCCCcceeeccCCeEEehhhccC---------------------CHHHHHHHHHHHh
Confidence            2 22222222                   12235689999999876                     2456667777764


Q ss_pred             c--cccCC-----CCceEEEEecCCC-------CCCCccccCCCceeeEEEeCCCCHHHH----HHHHHHHhC
Q 012016          351 G--LWSSC-----GDERIIVFTTNHK-------EKLDPALLRPGRMDVHVHMSYCTPSGF----KLLAANYLG  405 (473)
Q Consensus       351 g--~~~~~-----~~~~iiI~tTN~~-------~~ld~aLlrpgRfd~~I~~~~p~~~~r----~~l~~~~l~  405 (473)
                      .  ++.-+     .-.+-||++||..       ..+-..|.-  |+. ++.+..|.-.+|    ..|+..|+.
T Consensus       366 Ekei~rvG~t~~~~vDVRIIAATN~nL~~~i~~G~FReDLYY--RLN-V~~i~iPPLReR~eDI~~L~~~Fl~  435 (560)
T COG3829         366 EKEIERVGGTKPIPVDVRIIAATNRNLEKMIAEGTFREDLYY--RLN-VIPITIPPLRERKEDIPLLAEYFLD  435 (560)
T ss_pred             hceEEecCCCCceeeEEEEEeccCcCHHHHHhcCcchhhhee--eec-eeeecCCCcccCcchHHHHHHHHHH
Confidence            2  11111     1246789999974       223333443  444 345555555444    455555554

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.36  E-value=3.3e-06  Score=89.79  Aligned_cols=154  Identities=17%  Similarity=0.223  Sum_probs=94.9

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCch
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNS  293 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~  293 (473)
                      .+.+++|.....+.+.+.+.....           ....+|+.|++||||+++|+++....   +.+++.++|..+. ..
T Consensus       136 ~~~~lig~s~~~~~l~~~~~~~~~-----------~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~-~~  203 (469)
T PRK10923        136 PTTDIIGEAPAMQDVFRIIGRLSR-----------SSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIP-KD  203 (469)
T ss_pred             ccccceecCHHHHHHHHHHHHHhc-----------cCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCC-HH
Confidence            355677776666666555543322           23579999999999999999999986   4799999998873 23


Q ss_pred             HHHHHHHH------------------hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--
Q 012016          294 DLRTLLVA------------------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--  353 (473)
Q Consensus       294 ~l~~l~~~------------------~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--  353 (473)
                      .+...+..                  ...++.|||||||.+.                     ......|+.+++.-.  
T Consensus       204 ~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~---------------------~~~q~~L~~~l~~~~~~  262 (469)
T PRK10923        204 LIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMP---------------------LDVQTRLLRVLADGQFY  262 (469)
T ss_pred             HHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCC---------------------HHHHHHHHHHHhcCcEE
Confidence            33333311                  2346789999999883                     233455666665321  


Q ss_pred             cCCC-----CceEEEEecCCC-------CCCCccccCCCce-eeEEEeCCCCH--HHHHHHHHHHhC
Q 012016          354 SSCG-----DERIIVFTTNHK-------EKLDPALLRPGRM-DVHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       354 ~~~~-----~~~iiI~tTN~~-------~~ld~aLlrpgRf-d~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                      ...+     -++-||+||+..       ..+.+.|..  |+ ...|++|....  +....|+..|+.
T Consensus       263 ~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~--~l~~~~i~~PpLreR~~Di~~l~~~~l~  327 (469)
T PRK10923        263 RVGGYAPVKVDVRIIAATHQNLEQRVQEGKFREDLFH--RLNVIRVHLPPLRERREDIPRLARHFLQ  327 (469)
T ss_pred             eCCCCCeEEeeEEEEEeCCCCHHHHHHcCCchHHHHH--HhcceeecCCCcccchhhHHHHHHHHHH
Confidence            1011     124567777643       245566666  66 35566655432  345567777764

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.36  E-value=2.9e-06  Score=89.56  Aligned_cols=153  Identities=20%  Similarity=0.231  Sum_probs=90.4

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCch
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNS  293 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~  293 (473)
                      .+..+++.....+.+...+.....           ....++|+|++||||+++|+++....   +.+++.++|..+.. .
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~a~-----------~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~-~  204 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKIAP-----------SDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPE-N  204 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHHhC-----------CCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCCh-H
Confidence            345566665555555554443221           23579999999999999999998876   46899999998732 3


Q ss_pred             HHHHHHHH------------------hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-c
Q 012016          294 DLRTLLVA------------------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-S  354 (473)
Q Consensus       294 ~l~~l~~~------------------~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~  354 (473)
                      .+...+..                  ...++.|||||||.+.                     ......|+..++.-. .
T Consensus       205 ~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~---------------------~~~q~~l~~~l~~~~~~  263 (445)
T TIGR02915       205 LLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLP---------------------LNLQAKLLRFLQERVIE  263 (445)
T ss_pred             HHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhCC---------------------HHHHHHHHHHHhhCeEE
Confidence            33333211                  1356899999999883                     234455666664321 0


Q ss_pred             C-C-----CCceEEEEecCCC-------CCCCccccCCCceeeEEEeCCCCHHHHH----HHHHHHhC
Q 012016          355 S-C-----GDERIIVFTTNHK-------EKLDPALLRPGRMDVHVHMSYCTPSGFK----LLAANYLG  405 (473)
Q Consensus       355 ~-~-----~~~~iiI~tTN~~-------~~ld~aLlrpgRfd~~I~~~~p~~~~r~----~l~~~~l~  405 (473)
                      . .     ..++-+|+||+..       ..+.+.|..  |+. .+.+..|.-.+|.    .|+..|+.
T Consensus       264 ~~~~~~~~~~~~rii~~~~~~l~~~~~~~~~~~~L~~--~l~-~~~i~lPpLr~R~~Di~~l~~~~l~  328 (445)
T TIGR02915       264 RLGGREEIPVDVRIVCATNQDLKRMIAEGTFREDLFY--RIA-EISITIPPLRSRDGDAVLLANAFLE  328 (445)
T ss_pred             eCCCCceeeeceEEEEecCCCHHHHHHcCCccHHHHH--Hhc-cceecCCCchhchhhHHHHHHHHHH
Confidence            0 0     1135667777654       234444543  443 2444455555543    45665554

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).

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.35  E-value=1.3e-05  Score=83.82  Aligned_cols=208  Identities=21%  Similarity=0.307  Sum_probs=113.4

Q ss_pred             CcceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          205 DAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       205 ~~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ..|..  ...|.+.++|+-+.....++.+.+..+....      .....+-+||+||+|||||+.++.||.++|+.+..-
T Consensus        70 elW~e--Ky~P~t~eeLAVHkkKI~eVk~WL~~~~~~~------~~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew  141 (634)
T KOG1970|consen   70 ELWVE--KYKPRTLEELAVHKKKISEVKQWLKQVAEFT------PKLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIEW  141 (634)
T ss_pred             chhHH--hcCcccHHHHhhhHHhHHHHHHHHHHHHHhc------cCCCceEEEEeCCCCCCchhHHHHHHHhhCceeeee
Confidence            45643  5668999999998877777766665222111      122346789999999999999999999999988764


Q ss_pred             c-------cccccCc---------hHHHH---HHHHh--------------ccCceEEEeccccccccccCCccccCCCC
Q 012016          285 E-------LTELRSN---------SDLRT---LLVAT--------------ANRSILVVEDIDCTIDLQDRLPADIAGEG  331 (473)
Q Consensus       285 ~-------~~~~~~~---------~~l~~---l~~~~--------------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~  331 (473)
                      .       ...+.+.         +.|..   .+..+              ..+.+|+|||+=..+.             
T Consensus       142 ~Npi~~~~~~~~h~~t~~~~~~~~s~L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~-------------  208 (634)
T KOG1970|consen  142 SNPINLKEPENLHNETSFLMFPYQSQLAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFY-------------  208 (634)
T ss_pred             cCCccccccccccccchhcccchhhHHHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhh-------------
Confidence            3       1111111         11211   11111              1346899999976643             


Q ss_pred             CCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC--CCCCCccccCC------CceeeEEEeCCCCHHHHHHHHHHH
Q 012016          332 EGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH--KEKLDPALLRP------GRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       332 ~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~--~~~ld~aLlrp------gRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                          ......+...|...-.   . |.--+||+.|+.  ++..++..+.|      .|++ +|.|.+-...-.++.+.++
T Consensus       209 ----~d~~~~f~evL~~y~s---~-g~~PlIf~iTd~~~~g~nnq~rlf~~d~q~~~ri~-~IsFNPIa~T~MKK~L~ri  279 (634)
T KOG1970|consen  209 ----RDDSETFREVLRLYVS---I-GRCPLIFIITDSLSNGNNNQDRLFPKDIQEEPRIS-NISFNPIAPTIMKKFLKRI  279 (634)
T ss_pred             ----hhhHHHHHHHHHHHHh---c-CCCcEEEEEeccccCCCcchhhhchhhhhhccCcc-eEeecCCcHHHHHHHHHHH
Confidence                1123334444432211   1 111244444433  24444433322      2553 6788877777777777666


Q ss_pred             hCccccCCHHHHHHHHhcCCCCHHHHHHHHhc-CCCHHHHHHHHHHH
Q 012016          404 LGIKEHILFEEIEELISTTQVTPAEVAEQLMR-NDDPELVLNGLIEF  449 (473)
Q Consensus       404 l~~~~~~l~~~i~~l~~~~~~t~a~i~~~l~~-~~~~~~al~~l~~~  449 (473)
                      +......+.+ +.      --.-++|-.+|.. .||.+.|+..|.=+
T Consensus       280 c~~e~~~~s~-~k------~~~~~~v~~i~~~s~GDIRsAInsLQls  319 (634)
T KOG1970|consen  280 CRIEANKKSG-IK------VPDTAEVELICQGSGGDIRSAINSLQLS  319 (634)
T ss_pred             HHHhcccccC-Cc------CchhHHHHHHHHhcCccHHHHHhHhhhh
Confidence            6544322221 00      0012333334432 46888888877755

>PF05729 NACHT: NACHT domain

Probab=98.33  E-value=4.3e-06  Score=75.11  Aligned_cols=133  Identities=19%  Similarity=0.309  Sum_probs=71.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC--------Cc-eEEcccccccCc---hHHHHHH------------------HHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN--------FD-VYDLELTELRSN---SDLRTLL------------------VATA  303 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~--------~~-~~~l~~~~~~~~---~~l~~l~------------------~~~~  303 (473)
                      |-++|+|+||+|||++++.++..+.        .+ ++.+.+.+....   ..+.+.+                  ....
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKN   80 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcC
Confidence            3579999999999999999998771        11 223333333211   1222222                  1223


Q ss_pred             cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCC-CCCccccCCCce
Q 012016          304 NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE-KLDPALLRPGRM  382 (473)
Q Consensus       304 ~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~-~ld~aLlrpgRf  382 (473)
                      .+.+|+||.+|.+.....             ..........|.+.+...  ..+.-.++|.+..... .+...+-.    
T Consensus        81 ~~~llilDglDE~~~~~~-------------~~~~~~~~~~l~~l~~~~--~~~~~~liit~r~~~~~~~~~~~~~----  141 (166)
T PF05729_consen   81 KRVLLILDGLDELEEQDQ-------------SQERQRLLDLLSQLLPQA--LPPGVKLIITSRPRAFPDLRRRLKQ----  141 (166)
T ss_pred             CceEEEEechHhcccchh-------------hhHHHHHHHHHHHHhhhc--cCCCCeEEEEEcCChHHHHHHhcCC----
Confidence            568999999998853100             000111222222333321  1112233333332221 22222222    


Q ss_pred             eeEEEeCCCCHHHHHHHHHHHhC
Q 012016          383 DVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       383 d~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ...+++...+.++..++++.|+.
T Consensus       142 ~~~~~l~~~~~~~~~~~~~~~f~  164 (166)
T PF05729_consen  142 AQILELEPFSEEDIKQYLRKYFS  164 (166)
T ss_pred             CcEEEECCCCHHHHHHHHHHHhh
Confidence            15689999999999999999875

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.32  E-value=3.7e-06  Score=88.98  Aligned_cols=152  Identities=20%  Similarity=0.240  Sum_probs=89.4

Q ss_pred             ccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchH
Q 012016          218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSD  294 (473)
Q Consensus       218 f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~  294 (473)
                      +..+++.......+.+.+.....           ....+|++|++||||+++++++....   +.+++.++|..+.. ..
T Consensus       142 ~~~ii~~S~~~~~~~~~~~~~a~-----------~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~-~~  209 (457)
T PRK11361        142 WGHILTNSPAMMDICKDTAKIAL-----------SQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPE-SL  209 (457)
T ss_pred             ccceecccHHHhHHHHHHHHHcC-----------CCcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCH-HH
Confidence            34456655555555555443332           13479999999999999999998765   57999999998742 23


Q ss_pred             HHHHHHH------------------hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-cC
Q 012016          295 LRTLLVA------------------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-SS  355 (473)
Q Consensus       295 l~~l~~~------------------~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~  355 (473)
                      +...+..                  ...+++|||||||.+.                     ......|++.++.-. ..
T Consensus       210 ~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~---------------------~~~q~~L~~~l~~~~~~~  268 (457)
T PRK11361        210 LESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMP---------------------LVLQAKLLRILQEREFER  268 (457)
T ss_pred             HHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhCC---------------------HHHHHHHHHHHhcCcEEe
Confidence            3322211                  1346799999999883                     234556666665321 00


Q ss_pred             -CC-----CceEEEEecCCC-------CCCCccccCCCceeeEEEeCCCCHHHH----HHHHHHHhC
Q 012016          356 -CG-----DERIIVFTTNHK-------EKLDPALLRPGRMDVHVHMSYCTPSGF----KLLAANYLG  405 (473)
Q Consensus       356 -~~-----~~~iiI~tTN~~-------~~ld~aLlrpgRfd~~I~~~~p~~~~r----~~l~~~~l~  405 (473)
                       .+     .++-||+|||..       ..+.+.|..  |+. .+.+..|.-.+|    ..|+..|+.
T Consensus       269 ~~~~~~~~~~~rii~~t~~~l~~~~~~g~~~~~l~~--~l~-~~~i~~ppLreR~~di~~l~~~~l~  332 (457)
T PRK11361        269 IGGHQTIKVDIRIIAATNRDLQAMVKEGTFREDLFY--RLN-VIHLILPPLRDRREDISLLANHFLQ  332 (457)
T ss_pred             CCCCceeeeceEEEEeCCCCHHHHHHcCCchHHHHH--Hhc-cceecCCChhhchhhHHHHHHHHHH
Confidence             01     135677888753       123333433  332 345555555554    345555554

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.31  E-value=9e-06  Score=83.58  Aligned_cols=159  Identities=16%  Similarity=0.098  Sum_probs=101.0

Q ss_pred             ccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcccccccCc
Q 012016          218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTELRSN  292 (473)
Q Consensus       218 f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~~~~~  292 (473)
                      -+++.|.+.....+.+.+...+....         +..+++.|-||||||.+..-+-..+     ....++++|.++...
T Consensus       149 p~~l~gRe~e~~~v~~F~~~hle~~t---------~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~  219 (529)
T KOG2227|consen  149 PGTLKGRELEMDIVREFFSLHLELNT---------SGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEA  219 (529)
T ss_pred             CCCccchHHHHHHHHHHHHhhhhccc---------CcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccch
Confidence            35677777666666555554444322         5689999999999999888665554     335578888876322


Q ss_pred             hH---------------------HHHHHHH----hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHH
Q 012016          293 SD---------------------LRTLLVA----TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN  347 (473)
Q Consensus       293 ~~---------------------l~~l~~~----~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~  347 (473)
                      ..                     ..+.|..    ....-++|+||+|.++.   |               .+.++-    
T Consensus       220 ~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~t---r---------------~~~vLy----  277 (529)
T KOG2227|consen  220 SAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLIT---R---------------SQTVLY----  277 (529)
T ss_pred             HHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhh---c---------------ccceee----
Confidence            11                     1122221    12357999999999963   1               112222    


Q ss_pred             HhcccccCCCCceEEEEecCCCCCCCcccc----CCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          348 FIDGLWSSCGDERIIVFTTNHKEKLDPALL----RPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       348 ~ldg~~~~~~~~~iiI~tTN~~~~ld~aLl----rpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .+..+..-++..+|+|+..|..+.-|..|-    |-+--...+.|++++.++..+|+...+...
T Consensus       278 ~lFewp~lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~  341 (529)
T KOG2227|consen  278 TLFEWPKLPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEE  341 (529)
T ss_pred             eehhcccCCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcc
Confidence            222222234456888999998765554442    233445678999999999999999888655

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.30  E-value=5.1e-06  Score=88.14  Aligned_cols=152  Identities=18%  Similarity=0.233  Sum_probs=94.0

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHH
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDL  295 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l  295 (473)
                      ..+++......++...+.....           ....+++.|.+||||+++++++....   +.+++.++|..+. ...+
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~-----------~~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~-~~~~  201 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSR-----------SDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIP-KDLI  201 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhC-----------cCCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCC-HHHH
Confidence            3466666666666665544221           13479999999999999999998875   5689999998873 2333


Q ss_pred             HHHHHH------------------hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-cC-
Q 012016          296 RTLLVA------------------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-SS-  355 (473)
Q Consensus       296 ~~l~~~------------------~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~~-  355 (473)
                      ...+..                  ...++.|||||||.+.                     ......|++.++.-. .. 
T Consensus       202 ~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~---------------------~~~q~~ll~~l~~~~~~~~  260 (463)
T TIGR01818       202 ESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMP---------------------LDAQTRLLRVLADGEFYRV  260 (463)
T ss_pred             HHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCC---------------------HHHHHHHHHHHhcCcEEEC
Confidence            333211                  2246889999999883                     233455666664311 00 


Q ss_pred             C-----CCceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCC--HHHHHHHHHHHhC
Q 012016          356 C-----GDERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCT--PSGFKLLAANYLG  405 (473)
Q Consensus       356 ~-----~~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~--~~~r~~l~~~~l~  405 (473)
                      .     ..++-||+||+..       ..+.+.|..  |+. .+|++|...  .+....|+..|+.
T Consensus       261 ~~~~~~~~~~rii~~~~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLr~R~~Di~~l~~~~l~  323 (463)
T TIGR01818       261 GGRTPIKVDVRIVAATHQNLEALVRQGKFREDLFH--RLNVIRIHLPPLRERREDIPRLARHFLA  323 (463)
T ss_pred             CCCceeeeeeEEEEeCCCCHHHHHHcCCcHHHHHH--HhCcceecCCCcccchhhHHHHHHHHHH
Confidence            0     1134566666643       233444544  554 477777766  5667777777764

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.

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=98.28  E-value=7e-06  Score=87.54  Aligned_cols=161  Identities=22%  Similarity=0.294  Sum_probs=95.9

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhc-CCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc--c------c
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVG-KAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE--L------R  290 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g-~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~--~------~  290 (473)
                      +|.+.+++|+.++-.|  |=.....+.+.| ..-.-++||+|.||||||.|.+.+++.+..-+|.---.+  +      .
T Consensus       430 sIye~edvKkglLLqL--fGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVt  507 (804)
T KOG0478|consen  430 SIYELEDVKKGLLLQL--FGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVT  507 (804)
T ss_pred             hhhcccchhhhHHHHH--hcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEE
Confidence            4667778888775433  322223333333 112246999999999999999999999866555322111  0      0


Q ss_pred             CchHHHHHHHH-----hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhc---------ccccCC
Q 012016          291 SNSDLRTLLVA-----TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID---------GLWSSC  356 (473)
Q Consensus       291 ~~~~l~~l~~~-----~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ld---------g~~~~~  356 (473)
                      .+.+-++++.+     ++..+|..|||+|.+-.                     .+-+.|+..|+         |+..+-
T Consensus       508 rd~dtkqlVLesGALVLSD~GiCCIDEFDKM~d---------------------StrSvLhEvMEQQTvSIAKAGII~sL  566 (804)
T KOG0478|consen  508 KDPDTRQLVLESGALVLSDNGICCIDEFDKMSD---------------------STRSVLHEVMEQQTLSIAKAGIIASL  566 (804)
T ss_pred             ecCccceeeeecCcEEEcCCceEEchhhhhhhH---------------------HHHHHHHHHHHHhhhhHhhcceeeec
Confidence            11122222222     24789999999998832                     23344555543         333333


Q ss_pred             CCceEEEEecCCCC-------------CCCccccCCCceeeE-EEeCCCCHHHHHHHHHHHhC
Q 012016          357 GDERIIVFTTNHKE-------------KLDPALLRPGRMDVH-VHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       357 ~~~~iiI~tTN~~~-------------~ld~aLlrpgRfd~~-I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ....-|+++.|..+             .|+|.|++  |||.+ +-+..|+...=+.|..+..+
T Consensus       567 NAR~SVLAaANP~~skynp~k~i~eNI~LpptLLS--RFDLIylllD~~DE~~Dr~La~Hivs  627 (804)
T KOG0478|consen  567 NARCSVLAAANPIRSKYNPNKSIIENINLPPTLLS--RFDLIFLLLDKPDERSDRRLADHIVA  627 (804)
T ss_pred             cccceeeeeeccccccCCCCCchhhccCCChhhhh--hhcEEEEEecCcchhHHHHHHHHHHH
Confidence            34556888888532             47899999  99964 34566766644555555443

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.26  E-value=9.4e-06  Score=87.98  Aligned_cols=119  Identities=20%  Similarity=0.164  Sum_probs=85.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC--ceEEccccc----ccCchHHHHHHH-----------HhccCceEEEeccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF--DVYDLELTE----LRSNSDLRTLLV-----------ATANRSILVVEDIDCT  316 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~--~~~~l~~~~----~~~~~~l~~l~~-----------~~~~~sIL~iDdiD~l  316 (473)
                      .|++|-|++|||||+++++++..+..  |+..+..+.    +.+.-+|...+.           ....+.||||||+..+
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            58999999999999999999999854  776655432    223333433332           2235689999999765


Q ss_pred             cccccCCccccCCCCCCCccchhHHHHHHHHHhcc---------cccCCCCceEEEEecCCC---CCCCccccCCCceee
Q 012016          317 IDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDG---------LWSSCGDERIIVFTTNHK---EKLDPALLRPGRMDV  384 (473)
Q Consensus       317 ~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRfd~  384 (473)
                                           ...+++.|+..|+.         .....+...++|+|-|..   +.|.++++.  ||++
T Consensus       106 ---------------------~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLD--Rf~l  162 (584)
T PRK13406        106 ---------------------EPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALAD--RLAF  162 (584)
T ss_pred             ---------------------CHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHh--heEE
Confidence                                 36788999988853         222223456777774432   468999999  9999


Q ss_pred             EEEeCCCCHHH
Q 012016          385 HVHMSYCTPSG  395 (473)
Q Consensus       385 ~I~~~~p~~~~  395 (473)
                      +|.+++|+..+
T Consensus       163 ~v~v~~~~~~~  173 (584)
T PRK13406        163 HLDLDGLALRD  173 (584)
T ss_pred             EEEcCCCChHH
Confidence            99999998765

>PHA02774 E1; Provisional

Probab=98.22  E-value=1.1e-05  Score=86.02  Aligned_cols=58  Identities=28%  Similarity=0.460  Sum_probs=43.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEE-cccccccCchHHHHHHHHhccCceEEEecc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYD-LELTELRSNSDLRTLLVATANRSILVVEDI  313 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~-l~~~~~~~~~~l~~l~~~~~~~sIL~iDdi  313 (473)
                      |.|.+++++||||||||||+++.+|++.++..++. ++..+       .-.+..+....|++|||+
T Consensus       430 ~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s-------~FwLqpl~d~ki~vlDD~  488 (613)
T PHA02774        430 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKS-------HFWLQPLADAKIALLDDA  488 (613)
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECcc-------ccccchhccCCEEEEecC
Confidence            45556799999999999999999999999755543 54321       112444556779999999

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=98.20  E-value=6.9e-06  Score=91.99  Aligned_cols=182  Identities=21%  Similarity=0.275  Sum_probs=113.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhc-hhHHhhhcCCC-Cc-eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKR-KDYYRRVGKAW-KR-GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~-~~~y~~~g~~~-~r-g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      ..|.....+.+....-..+.+.+..+-+. +.-|...+... .. ..|++||||.|||+.+.+.|..+|+.++..|.+..
T Consensus       314 ~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g~~v~E~Nas~~  393 (871)
T KOG1968|consen  314 YQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELGFKVVEKNASDV  393 (871)
T ss_pred             cccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhcccceeecCcccc
Confidence            44556677777766666666666554211 11122211111 11 36999999999999999999999999999999988


Q ss_pred             cCchHHHHHHHHhc--------------------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHh
Q 012016          290 RSNSDLRTLLVATA--------------------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFI  349 (473)
Q Consensus       290 ~~~~~l~~l~~~~~--------------------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~l  349 (473)
                      .+...+.+.+..+.                    ...||++||+|.++. .+|              ..-..++.+.+. 
T Consensus       394 RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~-~dR--------------g~v~~l~~l~~k-  457 (871)
T KOG1968|consen  394 RSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG-EDR--------------GGVSKLSSLCKK-  457 (871)
T ss_pred             ccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc-hhh--------------hhHHHHHHHHHh-
Confidence            77666655443321                    124999999998864 111              122334444431 


Q ss_pred             cccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc-CCHHHHHHHHh
Q 012016          350 DGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH-ILFEEIEELIS  420 (473)
Q Consensus       350 dg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~-~l~~~i~~l~~  420 (473)
                              ..+-+|+|+|.........+.  |-+.-|+|+.|+.+++..-+..++..+.. .....++.++.
T Consensus       458 --------s~~Piv~~cndr~~p~sr~~~--~~~~~l~f~kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~  519 (871)
T KOG1968|consen  458 --------SSRPLVCTCNDRNLPKSRALS--RACSDLRFSKPSSELIRSRIMSICKSEGIKISDDVLEEISK  519 (871)
T ss_pred             --------ccCCeEEEecCCCCccccchh--hhcceeeecCCcHHHHHhhhhhhhcccceecCcHHHHHHHH
Confidence                    236688888877665553333  44467999999999977666665554422 22344444443

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.20  E-value=1.8e-05  Score=78.11  Aligned_cols=178  Identities=15%  Similarity=0.234  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEcccccccCchHHHH-H
Q 012016          229 TKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLELTELRSNSDLRT-L  298 (473)
Q Consensus       229 ~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~~~~~~~~~l~~-l  298 (473)
                      +++++.+...+..+.      ..-..++||+|++|.|||++++..+...         ..|++.++....-+...+-. +
T Consensus        43 ~~~L~~L~~Ll~~P~------~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~I  116 (302)
T PF05621_consen   43 KEALDRLEELLEYPK------RHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAI  116 (302)
T ss_pred             HHHHHHHHHHHhCCc------ccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHH
Confidence            345566666555443      1223589999999999999999999755         35677766554423222211 1


Q ss_pred             HH-----------------------HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC
Q 012016          299 LV-----------------------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS  355 (473)
Q Consensus       299 ~~-----------------------~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~  355 (473)
                      +.                       ..-+.-+|+|||++.++.              |.....+.    +||.+..+...
T Consensus       117 L~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLa--------------Gs~~~qr~----~Ln~LK~L~Ne  178 (302)
T PF05621_consen  117 LEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLA--------------GSYRKQRE----FLNALKFLGNE  178 (302)
T ss_pred             HHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhc--------------ccHHHHHH----HHHHHHHHhhc
Confidence            11                       122557999999999864              11222222    33333333222


Q ss_pred             CCCceEEEEecCCCC--CCCccccCCCceeeEEEeCC-CCHHHHHHHHHHHhCc-----cccCCHHHH-HHHHhcCCCCH
Q 012016          356 CGDERIIVFTTNHKE--KLDPALLRPGRMDVHVHMSY-CTPSGFKLLAANYLGI-----KEHILFEEI-EELISTTQVTP  426 (473)
Q Consensus       356 ~~~~~iiI~tTN~~~--~ld~aLlrpgRfd~~I~~~~-p~~~~r~~l~~~~l~~-----~~~~l~~~i-~~l~~~~~~t~  426 (473)
                      ..-.++.|+|-.-..  .-|+-+-+  ||+. +.+|. -.-+++..|+..+-..     .+.....++ ..+....+-+.
T Consensus       179 L~ipiV~vGt~~A~~al~~D~QLa~--RF~~-~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~i  255 (302)
T PF05621_consen  179 LQIPIVGVGTREAYRALRTDPQLAS--RFEP-FELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLI  255 (302)
T ss_pred             cCCCeEEeccHHHHHHhccCHHHHh--ccCC-ccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCch
Confidence            222244444443222  23677777  9974 45555 2334456666655432     122222333 34445555555


Q ss_pred             HHHHHHH
Q 012016          427 AEVAEQL  433 (473)
Q Consensus       427 a~i~~~l  433 (473)
                      +++..++
T Consensus       256 G~l~~ll  262 (302)
T PF05621_consen  256 GELSRLL  262 (302)
T ss_pred             HHHHHHH
Confidence            6665554

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PLN03210 Resistant to P

Probab=98.18  E-value=4.6e-05  Score=89.75  Aligned_cols=154  Identities=18%  Similarity=0.220  Sum_probs=88.4

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCce---EEccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV---YDLEL  286 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~---~~l~~  286 (473)
                      ....++..+++++|.++..+++...+.           .+....+-+-|+||+|+|||+||+++++.+...+   +.++.
T Consensus       175 l~~~~~~~~~~~vG~~~~l~~l~~lL~-----------l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~g~vfv~~  243 (1153)
T PLN03210        175 LNLTPSNDFEDFVGIEDHIAKMSSLLH-----------LESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDR  243 (1153)
T ss_pred             hccccCcccccccchHHHHHHHHHHHc-----------cccCceEEEEEEcCCCCchHHHHHHHHHHHhhcCCeEEEeec
Confidence            344455678899998877777655442           1122356789999999999999999998874321   11111


Q ss_pred             ccc-------c-----C-c--hHH-----HHHHH--------------H-hccCceEEEeccccccccccCCccccCCCC
Q 012016          287 TEL-------R-----S-N--SDL-----RTLLV--------------A-TANRSILVVEDIDCTIDLQDRLPADIAGEG  331 (473)
Q Consensus       287 ~~~-------~-----~-~--~~l-----~~l~~--------------~-~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~  331 (473)
                      ..+       .     . +  ..+     .+++.              . ..++.+|||||+|..               
T Consensus       244 ~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~---------------  308 (1153)
T PLN03210        244 AFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQ---------------  308 (1153)
T ss_pred             cccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCH---------------
Confidence            000       0     0 0  001     11110              0 124678999998742               


Q ss_pred             CCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          332 EGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       332 ~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                              ..+..|....+  |.  +.+.-||+||...     .+++....+..++++.|+.++-.+|+..+...
T Consensus       309 --------~~l~~L~~~~~--~~--~~GsrIIiTTrd~-----~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~  366 (1153)
T PLN03210        309 --------DVLDALAGQTQ--WF--GSGSRIIVITKDK-----HFLRAHGIDHIYEVCLPSNELALEMFCRSAFK  366 (1153)
T ss_pred             --------HHHHHHHhhCc--cC--CCCcEEEEEeCcH-----HHHHhcCCCeEEEecCCCHHHHHHHHHHHhcC
Confidence                    12233332222  11  1223455566643     33333346778999999999999999887643

syringae 6; Provisional

>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=98.17  E-value=4.3e-05  Score=75.48  Aligned_cols=144  Identities=22%  Similarity=0.214  Sum_probs=75.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh--c--CCc-eEEcccccccCc------------------------hHHHHHHHHh-
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY--L--NFD-VYDLELTELRSN------------------------SDLRTLLVAT-  302 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~--l--~~~-~~~l~~~~~~~~------------------------~~l~~l~~~~-  302 (473)
                      .+-+.|+|++|+|||+||..+++.  .  .++ ++.++++...+.                        ..+...+... 
T Consensus        19 ~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L   98 (287)
T PF00931_consen   19 VRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRELL   98 (287)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHH
T ss_pred             eEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhhh
Confidence            567999999999999999999987  3  232 223333322111                        1111222211 


Q ss_pred             -ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCc
Q 012016          303 -ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGR  381 (473)
Q Consensus       303 -~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgR  381 (473)
                       ..+++|||||++...                       .+..+...+...    ..+.-||+||....... .+-   .
T Consensus        99 ~~~~~LlVlDdv~~~~-----------------------~~~~l~~~~~~~----~~~~kilvTTR~~~v~~-~~~---~  147 (287)
T PF00931_consen   99 KDKRCLLVLDDVWDEE-----------------------DLEELREPLPSF----SSGSKILVTTRDRSVAG-SLG---G  147 (287)
T ss_dssp             CCTSEEEEEEEE-SHH-----------------------HH-------HCH----HSS-EEEEEESCGGGGT-THH---S
T ss_pred             ccccceeeeeeecccc-----------------------cccccccccccc----ccccccccccccccccc-ccc---c
Confidence             248999999997531                       222222222111    11245566776533211 111   1


Q ss_pred             eeeEEEeCCCCHHHHHHHHHHHhCccc----cCCHHHHHHHHhcCCCCHH
Q 012016          382 MDVHVHMSYCTPSGFKLLAANYLGIKE----HILFEEIEELISTTQVTPA  427 (473)
Q Consensus       382 fd~~I~~~~p~~~~r~~l~~~~l~~~~----~~l~~~i~~l~~~~~~t~a  427 (473)
                      -+..++++..+.++-.+|+..+.....    ..+.+...++++..+..|-
T Consensus       148 ~~~~~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~glPL  197 (287)
T PF00931_consen  148 TDKVIELEPLSEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGGLPL  197 (287)
T ss_dssp             CEEEEECSS--HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT-HH
T ss_pred             cccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence            157899999999999999999876543    2223344455555555554

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.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=98.16  E-value=1.3e-05  Score=87.49  Aligned_cols=50  Identities=28%  Similarity=0.422  Sum_probs=40.0

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +|..|++++|+++.++.+...+.    .           ++.++|+||||||||+++++++..+.
T Consensus        26 ~~~~~~~vigq~~a~~~L~~~~~----~-----------~~~~l~~G~~G~GKttla~~l~~~l~   75 (637)
T PRK13765         26 PERLIDQVIGQEHAVEVIKKAAK----Q-----------RRHVMMIGSPGTGKSMLAKAMAELLP   75 (637)
T ss_pred             CcccHHHcCChHHHHHHHHHHHH----h-----------CCeEEEECCCCCcHHHHHHHHHHHcC
Confidence            46789999998888776544332    1           24799999999999999999999874

>PHA00729 NTP-binding motif containing protein

Probab=98.14  E-value=2.9e-06  Score=80.75  Aligned_cols=62  Identities=13%  Similarity=0.240  Sum_probs=38.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc----------cCchHHHHHHHHh----ccCceEEEecccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL----------RSNSDLRTLLVAT----ANRSILVVEDIDC  315 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~----------~~~~~l~~l~~~~----~~~sIL~iDdiD~  315 (473)
                      ..++|+||||||||+||.+||+.++..+..+.....          .+...+.+.+..+    .+..+|+|||+..
T Consensus        18 ~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~   93 (226)
T PHA00729         18 VSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGI   93 (226)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCch
Confidence            379999999999999999999998643333211110          1222333333222    2336899999754

>PRK15115 response regulator GlrR; Provisional

Probab=98.13  E-value=1.3e-05  Score=84.65  Aligned_cols=64  Identities=23%  Similarity=0.262  Sum_probs=48.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHHHHHH------------------HhccCceEEEe
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLRTLLV------------------ATANRSILVVE  311 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~~l~~------------------~~~~~sIL~iD  311 (473)
                      ...++++|++||||+++|+++.+..   +.+++.++|..+. ...+...+.                  ....++.||||
T Consensus       157 ~~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~-~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~  235 (444)
T PRK15115        157 DVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALP-EQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLD  235 (444)
T ss_pred             CCeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCC-HHHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEE
Confidence            3469999999999999999998875   5799999999873 233332221                  12346899999


Q ss_pred             cccccc
Q 012016          312 DIDCTI  317 (473)
Q Consensus       312 diD~l~  317 (473)
                      |||.+.
T Consensus       236 ~i~~l~  241 (444)
T PRK15115        236 EIGDMP  241 (444)
T ss_pred             ccccCC
Confidence            999883

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=98.06  E-value=2.9e-05  Score=81.21  Aligned_cols=153  Identities=18%  Similarity=0.197  Sum_probs=99.3

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCch
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNS  293 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~  293 (473)
                      .+..++|.....+++.+.+...-..           ...||++|++||||..+|++|...-   +-||+.+||..+-. +
T Consensus       139 ~~~~liG~S~am~~l~~~i~kvA~s-----------~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~-~  206 (464)
T COG2204         139 LGGELVGESPAMQQLRRLIAKVAPS-----------DASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPE-N  206 (464)
T ss_pred             ccCCceecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCH-H
Confidence            4667888887777777766544332           3579999999999999999999987   46999999998832 2


Q ss_pred             HHHH-HHH-----------------HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc-cc
Q 012016          294 DLRT-LLV-----------------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL-WS  354 (473)
Q Consensus       294 ~l~~-l~~-----------------~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-~~  354 (473)
                      -+.. +|-                 ...+++.||||||..+.                     ......||..+..- ..
T Consensus       207 l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mp---------------------l~~Q~kLLRvLqe~~~~  265 (464)
T COG2204         207 LLESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMP---------------------LELQVKLLRVLQEREFE  265 (464)
T ss_pred             HHHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccCC---------------------HHHHHHHHHHHHcCeeE
Confidence            2322 332                 12357899999998763                     34556677666421 11


Q ss_pred             CCC------CceEEEEecCCC-------CCCCccccCCCceeeEEEeCCCCHHHH----HHHHHHHhC
Q 012016          355 SCG------DERIIVFTTNHK-------EKLDPALLRPGRMDVHVHMSYCTPSGF----KLLAANYLG  405 (473)
Q Consensus       355 ~~~------~~~iiI~tTN~~-------~~ld~aLlrpgRfd~~I~~~~p~~~~r----~~l~~~~l~  405 (473)
                      .-|      -++-||++||..       ..+-+.|.-  |+. ++.+..|.-.+|    .-|+.+|+.
T Consensus       266 rvG~~~~i~vdvRiIaaT~~dL~~~v~~G~FReDLyy--RLn-V~~i~iPpLRER~EDIp~L~~hfl~  330 (464)
T COG2204         266 RVGGNKPIKVDVRIIAATNRDLEEEVAAGRFREDLYY--RLN-VVPLRLPPLRERKEDIPLLAEHFLK  330 (464)
T ss_pred             ecCCCcccceeeEEEeecCcCHHHHHHcCCcHHHHHh--hhc-cceecCCcccccchhHHHHHHHHHH
Confidence            111      135588999874       223344444  554 456666655554    466666664

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.03  E-value=3.8e-06  Score=85.32  Aligned_cols=130  Identities=22%  Similarity=0.229  Sum_probs=74.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc----c---------cCchHHHHHHHHhccCceEEEeccccccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE----L---------RSNSDLRTLLVATANRSILVVEDIDCTIDLQ  320 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~----~---------~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~  320 (473)
                      -++||.|.||||||.|.+.+++.....+|..-...    +         .++..+..-..-..+++|++|||+|.+-   
T Consensus        58 ihiLlvGdpg~gKS~ll~~~~~~~pr~v~~~g~~~s~~gLta~~~~d~~~~~~~leaGalvlad~GiccIDe~dk~~---  134 (331)
T PF00493_consen   58 IHILLVGDPGTGKSQLLKYVAKLAPRSVYTSGKGSSAAGLTASVSRDPVTGEWVLEAGALVLADGGICCIDEFDKMK---  134 (331)
T ss_dssp             --EEEECSCHHCHHHHHHCCCCT-SSEEEEECCGSTCCCCCEEECCCGGTSSECEEE-HHHHCTTSEEEECTTTT-----
T ss_pred             cceeeccchhhhHHHHHHHHHhhCCceEEECCCCcccCCccceeccccccceeEEeCCchhcccCceeeeccccccc---
Confidence            36999999999999999998877766655321111    1         1111111111224578999999999872   


Q ss_pred             cCCccccCCCCCCCccchhHHHHHHHHHhcccc---------cCCCCceEEEEecCCCC-------------CCCccccC
Q 012016          321 DRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW---------SSCGDERIIVFTTNHKE-------------KLDPALLR  378 (473)
Q Consensus       321 ~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~---------~~~~~~~iiI~tTN~~~-------------~ld~aLlr  378 (473)
                                        ......|+..|+...         ..-+.+.-|++++|...             .+++.|+.
T Consensus       135 ------------------~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~ni~l~~~LLS  196 (331)
T PF00493_consen  135 ------------------EDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSENINLPPPLLS  196 (331)
T ss_dssp             ------------------CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCCT-S-CCCHC
T ss_pred             ------------------chHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHhcccchhhHh
Confidence                              234566777776421         11123456888988765             47889999


Q ss_pred             CCceeeEEEe-CCCCHHHHHHHHHHHhCc
Q 012016          379 PGRMDVHVHM-SYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       379 pgRfd~~I~~-~~p~~~~r~~l~~~~l~~  406 (473)
                        |||..+.+ ..|+.+.=..|+.+.+..
T Consensus       197 --RFDLif~l~D~~d~~~D~~la~~il~~  223 (331)
T PF00493_consen  197 --RFDLIFLLRDKPDEEEDERLAEHILDS  223 (331)
T ss_dssp             --C-SEEECC--TTT-HHHHHHHHHHHTT
T ss_pred             --hcCEEEEeccccccccccccceEEEec
Confidence              99987665 557766666777766654

; 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.

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=98.02  E-value=5.6e-05  Score=77.96  Aligned_cols=63  Identities=16%  Similarity=0.280  Sum_probs=40.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc-CCceEEcccccccCchHHHHHHHHhccCceEEEeccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      ..++++.||+|||||+++.+++.+. -..-.......+..+-. ...+.......+|+|||+..+
T Consensus       209 ~~Nli~lGp~GTGKThla~~l~~~~a~~sG~f~T~a~Lf~~L~-~~~lg~v~~~DlLI~DEvgyl  272 (449)
T TIGR02688       209 NYNLIELGPKGTGKSYIYNNLSPYVILISGGTITVAKLFYNIS-TRQIGLVGRWDVVAFDEVATL  272 (449)
T ss_pred             CCcEEEECCCCCCHHHHHHHHhHHHHHHcCCcCcHHHHHHHHH-HHHHhhhccCCEEEEEcCCCC
Confidence            3589999999999999999998872 11102223333221111 134445567899999999875

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.

>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=98.00  E-value=2.5e-05  Score=73.14  Aligned_cols=114  Identities=18%  Similarity=0.242  Sum_probs=60.0

Q ss_pred             eEEeCCCCCCHHHHHHHH-HHh-c--CCceEEccccccc-----C---------------------chHHHHHHHHhccC
Q 012016          256 YLLYGPPGTGKSSLIAAM-ANY-L--NFDVYDLELTELR-----S---------------------NSDLRTLLVATANR  305 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~al-A~~-l--~~~~~~l~~~~~~-----~---------------------~~~l~~l~~~~~~~  305 (473)
                      ++++|.||+|||+.|-.. ... +  |.+++. +...+.     .                     ...+ ......+.+
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t-ni~gL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT-NIPGLNIEKIQPVLGYDIPTRLIDLSDPDFEEDWDDP-DDWRKLPKG   80 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE---TTB-S--EEEE--TTT-S-----S--SSSEEGGGH-HHHTTSGTT
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE-ccCCcchhhhhhhccccccccccccccccchhhhhhh-hhhcccCCC
Confidence            689999999999977655 332 2  666654 333221     0                     0111 112223368


Q ss_pred             ceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeE
Q 012016          306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVH  385 (473)
Q Consensus       306 sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~  385 (473)
                      ++|||||+...++.+....               ......++++...   ...+.-||++|.++..+|+.+++  .++.+
T Consensus        81 ~liviDEa~~~~~~r~~~~---------------~~~~~~~~~l~~h---Rh~g~diiliTQ~~~~id~~ir~--lve~~  140 (193)
T PF05707_consen   81 SLIVIDEAQNFFPSRSWKG---------------KKVPEIIEFLAQH---RHYGWDIILITQSPSQIDKFIRD--LVEYH  140 (193)
T ss_dssp             -EEEETTGGGTSB---T-T-------------------HHHHGGGGC---CCTT-EEEEEES-GGGB-HHHHC--CEEEE
T ss_pred             cEEEEECChhhcCCCcccc---------------ccchHHHHHHHHh---CcCCcEEEEEeCCHHHHhHHHHH--HHheE
Confidence            9999999999887332100               0112233443322   22457899999999999999987  88988


Q ss_pred             EEeCCC
Q 012016          386 VHMSYC  391 (473)
Q Consensus       386 I~~~~p  391 (473)
                      +++..+
T Consensus       141 ~~~~k~  146 (193)
T PF05707_consen  141 YHCRKL  146 (193)
T ss_dssp             EEEEE-
T ss_pred             EEEEee
Confidence            887654

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.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.98  E-value=4.3e-05  Score=68.10  Aligned_cols=31  Identities=29%  Similarity=0.574  Sum_probs=25.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      ++++||||+|||+++..++..+   +.+++.++.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~   35 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDI   35 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEEC
Confidence            6899999999999999999887   455555443

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.

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.95  E-value=3.8e-05  Score=75.04  Aligned_cols=92  Identities=16%  Similarity=0.191  Sum_probs=60.1

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-----ceEE-----cccccc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-----DVYD-----LELTEL  289 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-----~~~~-----l~~~~~  289 (473)
                      .|.|+.-+++.|+..+..++.++.      -..|--+=|||++||||++.++.||+.+-.     +++.     .++..-
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            577888999999999998887654      011335678999999999999999998722     2111     111111


Q ss_pred             cCc----hHHHHHHHH---hccCceEEEecccccc
Q 012016          290 RSN----SDLRTLLVA---TANRSILVVEDIDCTI  317 (473)
Q Consensus       290 ~~~----~~l~~l~~~---~~~~sIL~iDdiD~l~  317 (473)
                      ...    .+|+..+..   ...++|+++||+|.+-
T Consensus       157 ~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKmp  191 (344)
T KOG2170|consen  157 SKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKLP  191 (344)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCceEEechhhhcC
Confidence            111    222222222   2378999999999883

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.93  E-value=1.4e-05  Score=76.22  Aligned_cols=23  Identities=48%  Similarity=0.846  Sum_probs=20.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      +..+||||+||+|||++|+.+++
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcCC
Confidence            35699999999999999999974

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.

>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=97.93  E-value=6.8e-06  Score=70.36  Aligned_cols=31  Identities=39%  Similarity=0.741  Sum_probs=28.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      |+|.||||+||||+++.||+.+|++++.++.
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            7899999999999999999999988876664

...

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.92  E-value=4.5e-05  Score=72.00  Aligned_cols=40  Identities=25%  Similarity=0.399  Sum_probs=32.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~  288 (473)
                      |.+...-++++||||||||+++..+|...   +..++.++...
T Consensus         8 Gi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~   50 (209)
T TIGR02237         8 GVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG   50 (209)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            66777789999999999999999888644   66777777754

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.91  E-value=1.5e-05  Score=84.82  Aligned_cols=67  Identities=24%  Similarity=0.331  Sum_probs=52.1

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-CCceEEccc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLEL  286 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~~  286 (473)
                      ....-|+++.|.++.++.|++.+.....+-+       ..++-++|.||||+|||+|+++||+.+ .+++|.+..
T Consensus        70 ~ry~fF~d~yGlee~ieriv~~l~~Aa~gl~-------~~~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~kg  137 (644)
T PRK15455         70 KRYPAFEEFYGMEEAIEQIVSYFRHAAQGLE-------EKKQILYLLGPVGGGKSSLAERLKSLMERVPIYVLKA  137 (644)
T ss_pred             ccccchhcccCcHHHHHHHHHHHHHHHHhcC-------CCCceEEEecCCCCCchHHHHHHHHHHHhCcceeecC
Confidence            3345689999999999999887765544321       234679999999999999999999988 467777654

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=97.89  E-value=0.00022  Score=68.26  Aligned_cols=125  Identities=11%  Similarity=0.110  Sum_probs=94.2

Q ss_pred             CceeEEeCCCC-CCHHHHHHHHHHhc---------CCceEEcccc-------cccCchHHHHHHHHhc------cCceEE
Q 012016          253 KRGYLLYGPPG-TGKSSLIAAMANYL---------NFDVYDLELT-------ELRSNSDLRTLLVATA------NRSILV  309 (473)
Q Consensus       253 ~rg~LL~GPpG-tGKT~la~alA~~l---------~~~~~~l~~~-------~~~~~~~l~~l~~~~~------~~sIL~  309 (473)
                      ...|||.|..+ +||..++.-++..+         +-+++.+...       ...+...+|++.....      ..-|++
T Consensus        15 shAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~~~p~~g~~KViI   94 (263)
T PRK06581         15 YNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLSKTSAISGYKVAI   94 (263)
T ss_pred             hheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHhhCcccCCcEEEE
Confidence            46899999998 99999988887766         2455555432       1234456666655442      457999


Q ss_pred             EeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeC
Q 012016          310 VEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMS  389 (473)
Q Consensus       310 iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~  389 (473)
                      |+++|.+                     .....+.||..++.    ++.+.++|++|..++.+.|.++.  |+ .++.|+
T Consensus        95 I~~ae~m---------------------t~~AANALLKtLEE----PP~~t~fILit~~~~~LLpTIrS--RC-q~i~~~  146 (263)
T PRK06581         95 IYSAELM---------------------NLNAANSCLKILED----APKNSYIFLITSRAASIISTIRS--RC-FKINVR  146 (263)
T ss_pred             EechHHh---------------------CHHHHHHHHHhhcC----CCCCeEEEEEeCChhhCchhHhh--ce-EEEeCC
Confidence            9999988                     34677899999885    45678999999999999999998  87 578999


Q ss_pred             CCCHHHHHHHHHHHhC
Q 012016          390 YCTPSGFKLLAANYLG  405 (473)
Q Consensus       390 ~p~~~~r~~l~~~~l~  405 (473)
                      .|....-.++...++.
T Consensus       147 ~p~~~~~~e~~~~~~~  162 (263)
T PRK06581        147 SSILHAYNELYSQFIQ  162 (263)
T ss_pred             CCCHHHHHHHHHHhcc
Confidence            9999777766665554

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.88  E-value=8.9e-05  Score=85.36  Aligned_cols=129  Identities=22%  Similarity=0.329  Sum_probs=92.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-------c------hHH----HHHHHHhccCceEEEecccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-------N------SDL----RTLLVATANRSILVVEDIDC  315 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-------~------~~l----~~l~~~~~~~sIL~iDdiD~  315 (473)
                      .+++||-|.||.|||+|+.|+|+..|-.++.+++++-.+       .      .++    ...+..+.++.-+++||+.-
T Consensus      1543 ~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVlLDEiNL 1622 (4600)
T COG5271        1543 GKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVLLDEINL 1622 (4600)
T ss_pred             CCceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhhcCCEEEeehhhh
Confidence            467999999999999999999999999999999886411       0      111    12344556788999999964


Q ss_pred             ccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc----------CCCCceEEEEecCCC------CCCCccccCC
Q 012016          316 TIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS----------SCGDERIIVFTTNHK------EKLDPALLRP  379 (473)
Q Consensus       316 l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~----------~~~~~~iiI~tTN~~------~~ld~aLlrp  379 (473)
                      .                     ++..+.+|-.++|.-..          .+.++..|++|-|.-      ..|+..++. 
T Consensus      1623 a---------------------SQSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qggGRKgLPkSF~n- 1680 (4600)
T COG5271        1623 A---------------------SQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGGGRKGLPKSFLN- 1680 (4600)
T ss_pred             h---------------------HHHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCCCcccCCHHHhh-
Confidence            3                     46677788777764321          122344555555543      358889998 


Q ss_pred             CceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          380 GRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       380 gRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                       ||- +|.|...+.+....|+...+.
T Consensus      1681 -RFs-vV~~d~lt~dDi~~Ia~~~yp 1704 (4600)
T COG5271        1681 -RFS-VVKMDGLTTDDITHIANKMYP 1704 (4600)
T ss_pred             -hhh-eEEecccccchHHHHHHhhCC
Confidence             995 688998888888888877665

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=97.87  E-value=6.7e-05  Score=79.01  Aligned_cols=64  Identities=23%  Similarity=0.274  Sum_probs=48.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHHHHHHH------------------hccCceEEEe
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLRTLLVA------------------TANRSILVVE  311 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~~l~~~------------------~~~~sIL~iD  311 (473)
                      ...++++|.+||||+++++++....   +.+++.++|..+. ...+...+..                  ..+++.||||
T Consensus       162 ~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~-~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld  240 (441)
T PRK10365        162 EATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALN-ESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLD  240 (441)
T ss_pred             CCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCC-HHHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEe
Confidence            4579999999999999999998765   5789999999864 2334333311                  2246889999


Q ss_pred             cccccc
Q 012016          312 DIDCTI  317 (473)
Q Consensus       312 diD~l~  317 (473)
                      |||.+.
T Consensus       241 ei~~l~  246 (441)
T PRK10365        241 EIGDIS  246 (441)
T ss_pred             ccccCC
Confidence            999884

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.87  E-value=4.2e-05  Score=76.52  Aligned_cols=98  Identities=21%  Similarity=0.312  Sum_probs=59.2

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCce-EEcccc-----------cccCc-hHHHHHHHH-hccCceEEEeccccc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDV-YDLELT-----------ELRSN-SDLRTLLVA-TANRSILVVEDIDCT  316 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~-~~l~~~-----------~~~~~-~~l~~l~~~-~~~~sIL~iDdiD~l  316 (473)
                      .+++|++||||-|+|||+|.-..-..+..+- ..+-..           .+.+. ..+..+-.. +.+--||+|||+.--
T Consensus        63 ~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~FM~~vH~~l~~l~g~~dpl~~iA~~~~~~~~vLCfDEF~Vt  142 (367)
T COG1485          63 GPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQGQTDPLPPIADELAAETRVLCFDEFEVT  142 (367)
T ss_pred             CCCceEEEECCCCccHHHHHHHHHhhCCccccccccHHHHHHHHHHHHHHHcCCCCccHHHHHHHHhcCCEEEeeeeeec
Confidence            4678999999999999999999888774322 111100           00111 111111111 124579999998642


Q ss_pred             cccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC-CCC
Q 012016          317 IDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK-EKL  372 (473)
Q Consensus       317 ~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-~~l  372 (473)
                                        +-....+++.|++.+=.      .++++|+|+|.+ +.|
T Consensus       143 ------------------DI~DAMiL~rL~~~Lf~------~GV~lvaTSN~~P~~L  175 (367)
T COG1485         143 ------------------DIADAMILGRLLEALFA------RGVVLVATSNTAPDNL  175 (367)
T ss_pred             ------------------ChHHHHHHHHHHHHHHH------CCcEEEEeCCCChHHh
Confidence                              22245677777776642      459999999963 443

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.85  E-value=1.7e-05  Score=72.19  Aligned_cols=35  Identities=29%  Similarity=0.378  Sum_probs=31.5

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.+..++|+||||||||++++++|..+++++++.+
T Consensus         2 ~~~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d   36 (175)
T PRK00131          2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD   36 (175)
T ss_pred             CCCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            34678999999999999999999999999998765

>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=97.83  E-value=0.00066  Score=70.05  Aligned_cols=88  Identities=19%  Similarity=0.258  Sum_probs=57.4

Q ss_pred             eEEEEecCCC--CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc---------------------cCCHHHHH
Q 012016          360 RIIVFTTNHK--EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE---------------------HILFEEIE  416 (473)
Q Consensus       360 ~iiI~tTN~~--~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~---------------------~~l~~~i~  416 (473)
                      .+|+.|++.-  ..|..||  |+|.-..|.++.++++.-+..+...|....                     .....++.
T Consensus       185 HVIFlT~dv~~~k~LskaL--Pn~vf~tI~L~Das~~~Ak~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld  262 (431)
T PF10443_consen  185 HVIFLTDDVSYSKPLSKAL--PNRVFKTISLSDASPESAKQYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELD  262 (431)
T ss_pred             EEEEECCCCchhhhHHHhC--CCCceeEEeecCCCHHHHHHHHHHHhcccccccccccccccccccccccccccchHHHH
Confidence            3444444421  3455565  457778999999999998888888886531                     13556777


Q ss_pred             HHHhcCCCCHHHHHHHH---hcCCCHHHHHHHHHHH
Q 012016          417 ELISTTQVTPAEVAEQL---MRNDDPELVLNGLIEF  449 (473)
Q Consensus       417 ~l~~~~~~t~a~i~~~l---~~~~~~~~al~~l~~~  449 (473)
                      ..++..|--.-|+.-+.   .....+..|+++++.-
T Consensus       263 ~~i~~LGGRltDLe~lvrRiksGe~p~~Av~~iI~q  298 (431)
T PF10443_consen  263 ECIEPLGGRLTDLEFLVRRIKSGESPEEAVEEIISQ  298 (431)
T ss_pred             HHHHHcCCcHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            77776555555553332   2356899999988753

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 [].

>PRK07261 topology modulation protein; Provisional

Probab=97.80  E-value=8.5e-05  Score=68.18  Aligned_cols=100  Identities=17%  Similarity=0.252  Sum_probs=61.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPI  335 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~  335 (473)
                      +++.|+||+|||||++.|+..++.+++.+|.-.....              .   .+                       
T Consensus         3 i~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~--------------~---~~-----------------------   42 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPN--------------W---QE-----------------------   42 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccc--------------c---cc-----------------------
Confidence            7899999999999999999999998877664322100              0   00                       


Q ss_pred             cchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          336 QQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       336 ~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ......+..+.+.+.+      + . +|+-.|....+-+..+.  ++|..|.+.+|.......++++.+.
T Consensus        43 ~~~~~~~~~~~~~~~~------~-~-wIidg~~~~~~~~~~l~--~ad~vI~Ld~p~~~~~~R~lkR~~~  102 (171)
T PRK07261         43 RDDDDMIADISNFLLK------H-D-WIIDGNYSWCLYEERMQ--EADQIIFLNFSRFNCLYRAFKRYLK  102 (171)
T ss_pred             CCHHHHHHHHHHHHhC------C-C-EEEcCcchhhhHHHHHH--HCCEEEEEcCCHHHHHHHHHHHHHH
Confidence            0001111112222211      2 3 44444444433234444  7899999999988888888888764

>PRK08118 topology modulation protein; Reviewed

Probab=97.80  E-value=4.1e-05  Score=70.00  Aligned_cols=32  Identities=34%  Similarity=0.532  Sum_probs=29.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .+++.||||+||||+++.|++.++.+++.+|.
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~   34 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDA   34 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecch
Confidence            58999999999999999999999999998884

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=97.80  E-value=4.4e-05  Score=81.04  Aligned_cols=163  Identities=15%  Similarity=0.224  Sum_probs=99.7

Q ss_pred             ccccccchHHHHHHHHHHHHHHhchhHHhhhcCCC--CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc------
Q 012016          218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAW--KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL------  289 (473)
Q Consensus       218 f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~--~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~------  289 (473)
                      |-.|.|++.+|..|.-.+   +.+-..+..-|.+.  .-++++.|.||||||-+.++.++.+...+|..--.+-      
T Consensus       344 ~PsIyGhe~VK~GilL~L---fGGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsPR~vYtsGkaSSaAGLTa  420 (764)
T KOG0480|consen  344 FPSIYGHELVKAGILLSL---FGGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSPRSVYTSGKASSAAGLTA  420 (764)
T ss_pred             CccccchHHHHhhHHHHH---hCCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccCCcceEecCcccccccceE
Confidence            456778888888775433   22222222222222  2359999999999999999999999888875432211      


Q ss_pred             ---cCch----HHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcc---------cc
Q 012016          290 ---RSNS----DLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDG---------LW  353 (473)
Q Consensus       290 ---~~~~----~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg---------~~  353 (473)
                         .++.    .+..--...+..+|..|||+|.+-.                     .-.-.++.+|+.         +.
T Consensus       421 aVvkD~esgdf~iEAGALmLADnGICCIDEFDKMd~---------------------~dqvAihEAMEQQtISIaKAGv~  479 (764)
T KOG0480|consen  421 AVVKDEESGDFTIEAGALMLADNGICCIDEFDKMDV---------------------KDQVAIHEAMEQQTISIAKAGVV  479 (764)
T ss_pred             EEEecCCCCceeeecCcEEEccCceEEechhcccCh---------------------HhHHHHHHHHHhheehheecceE
Confidence               1110    0000001124789999999998731                     111234455542         22


Q ss_pred             cCCCCceEEEEecCCCC-------------CCCccccCCCceee-EEEeCCCCHHHHHHHHHHHhCc
Q 012016          354 SSCGDERIIVFTTNHKE-------------KLDPALLRPGRMDV-HVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       354 ~~~~~~~iiI~tTN~~~-------------~ld~aLlrpgRfd~-~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      .+-+...-|++++|...             .++++++.  |||. .|-+..|++..=..|.++.+..
T Consensus       480 aTLnARtSIlAAANPv~GhYdR~ktl~eNi~msApimS--RFDL~FiLlD~~nE~~D~~ia~hIld~  544 (764)
T KOG0480|consen  480 ATLNARTSILAAANPVGGHYDRKKTLRENINMSAPIMS--RFDLFFILLDDCNEVVDYAIARHILDL  544 (764)
T ss_pred             EeecchhhhhhhcCCcCCccccccchhhhcCCCchhhh--hhcEEEEEecCCchHHHHHHHHHHHHH
Confidence            22223455788888653             46788999  9994 4677889988877777777654

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.79  E-value=0.00013  Score=65.31  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-.+.+.||||+|||+++.-+|+.|
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHHH
Confidence            3468999999999999999999888

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=97.79  E-value=0.00011  Score=83.96  Aligned_cols=138  Identities=20%  Similarity=0.224  Sum_probs=89.0

Q ss_pred             CCceeEEeCCCCCCHHHH-HHHHHHhcCCceEEcccccccCchHHHHHHHHhc-----------------cCceEEEecc
Q 012016          252 WKRGYLLYGPPGTGKSSL-IAAMANYLNFDVYDLELTELRSNSDLRTLLVATA-----------------NRSILVVEDI  313 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~l-a~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~-----------------~~sIL~iDdi  313 (473)
                      -.|+|+++||||+|||+| ..++-+++.+.+..++.+.-.........+....                 ..-|||.|||
T Consensus      1493 t~R~~i~cGppGSgK~mlM~~sLrs~~~~ev~~~Nfs~~t~T~s~ls~Ler~t~yy~~tg~~~l~PK~~vK~lVLFcDeI 1572 (3164)
T COG5245        1493 TLRSYIYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMTPSKLSVLERETEYYPNTGVVRLYPKPVVKDLVLFCDEI 1572 (3164)
T ss_pred             ccceEEEECCCCCccchhcchhhhhhhheeeeEEeeccccCCHHHHHHHHhhceeeccCCeEEEccCcchhheEEEeecc
Confidence            368999999999999995 5689999999999999877654443444443321                 2369999999


Q ss_pred             ccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC------CceEEEEecCCCCCC-----CccccCCCce
Q 012016          314 DCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG------DERIIVFTTNHKEKL-----DPALLRPGRM  382 (473)
Q Consensus       314 D~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~~~iiI~tTN~~~~l-----d~aLlrpgRf  382 (473)
                      . +..  .+  .       ...+..-..+..|+ +-.|+|+...      .++++.+++|.+.+.     ...++|  | 
T Consensus      1573 n-Lp~--~~--~-------y~~~~vI~FlR~l~-e~QGfw~s~~~~wvTI~~i~l~Gacnp~td~gRv~~~eRf~r--~- 1636 (3164)
T COG5245        1573 N-LPY--GF--E-------YYPPTVIVFLRPLV-ERQGFWSSIAVSWVTICGIILYGACNPGTDEGRVKYYERFIR--K- 1636 (3164)
T ss_pred             C-Ccc--cc--c-------cCCCceEEeeHHHH-HhcccccchhhhHhhhcceEEEccCCCCCCcccCccHHHHhc--C-
Confidence            8 422  11  0       00111111222232 3356666432      247788899987543     234554  2 


Q ss_pred             eeEEEeCCCCHHHHHHHHHHHhC
Q 012016          383 DVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       383 d~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ...|++.||.......|...++.
T Consensus      1637 ~v~vf~~ype~~SL~~Iyea~l~ 1659 (3164)
T COG5245        1637 PVFVFCCYPELASLRNIYEAVLM 1659 (3164)
T ss_pred             ceEEEecCcchhhHHHHHHHHHH
Confidence            46789999999998888887765

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.74  E-value=0.0001  Score=75.56  Aligned_cols=102  Identities=21%  Similarity=0.318  Sum_probs=62.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----C-CceEEcccccc----------------------cCchHHHHHHHHhccC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----N-FDVYDLELTEL----------------------RSNSDLRTLLVATANR  305 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----~-~~~~~l~~~~~----------------------~~~~~l~~l~~~~~~~  305 (473)
                      +..++|.||+|+|||+++..||..+    | ..+..+.....                      .+...+...+....+.
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~~  216 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELRNK  216 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhcCC
Confidence            4569999999999999999999864    3 24443333322                      2234556666666778


Q ss_pred             ceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCcc
Q 012016          306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPA  375 (473)
Q Consensus       306 sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~a  375 (473)
                      .+|+||......                    ....+...+..+.+... +-...+|+-+|+..+.++..
T Consensus       217 DlVLIDTaG~~~--------------------~d~~l~e~La~L~~~~~-~~~~lLVLsAts~~~~l~ev  265 (374)
T PRK14722        217 HMVLIDTIGMSQ--------------------RDRTVSDQIAMLHGADT-PVQRLLLLNATSHGDTLNEV  265 (374)
T ss_pred             CEEEEcCCCCCc--------------------ccHHHHHHHHHHhccCC-CCeEEEEecCccChHHHHHH
Confidence            999999986431                    12345556666654322 11224444566666666544

>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=97.74  E-value=0.00021  Score=65.90  Aligned_cols=30  Identities=27%  Similarity=0.249  Sum_probs=23.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      +|++||||||||+++..++.+.   |.+++.++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s   34 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVT   34 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEE
Confidence            7899999999999998877654   55555444

A related protein is found in archaea.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.71  E-value=0.00039  Score=65.28  Aligned_cols=90  Identities=27%  Similarity=0.435  Sum_probs=53.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccC----------chHHHHHHHHh-----------ccCceEE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRS----------NSDLRTLLVAT-----------ANRSILV  309 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~----------~~~l~~l~~~~-----------~~~sIL~  309 (473)
                      +..++.||||||||++++.++..+   +..++.+..+.-..          ...+..++...           ....+||
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~~~~~~~~~~~vli   98 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKTGIEAQTIHSFLYRIPNGDDEGRPELPKKDVLI   98 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHTS-EEEHHHHTTEECCEECCSSCC-TSTSEEE
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhhCcchhhHHHHHhcCCcccccccccCCcccEEE
Confidence            568899999999999999988766   66777666554311          12222222211           2347999


Q ss_pred             EeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC
Q 012016          310 VEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH  368 (473)
Q Consensus       310 iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  368 (473)
                      |||+..+                     ....+..|+..+..    .+..+|+|+=.+.
T Consensus        99 VDEasmv---------------------~~~~~~~ll~~~~~----~~~klilvGD~~Q  132 (196)
T PF13604_consen   99 VDEASMV---------------------DSRQLARLLRLAKK----SGAKLILVGDPNQ  132 (196)
T ss_dssp             ESSGGG----------------------BHHHHHHHHHHS-T-----T-EEEEEE-TTS
T ss_pred             Eeccccc---------------------CHHHHHHHHHHHHh----cCCEEEEECCcch
Confidence            9999765                     24456666766553    2345666665553

>PF14516 AAA_35: AAA-like domain

Probab=97.70  E-value=0.00063  Score=69.20  Aligned_cols=37  Identities=22%  Similarity=0.342  Sum_probs=31.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~  289 (473)
                      +.-+.++||..+|||||+..+.+.+   |+..+.+|+..+
T Consensus        31 G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~   70 (331)
T PF14516_consen   31 GSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQL   70 (331)
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecC
Confidence            4568999999999999999888776   788888887765

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.70  E-value=6.2e-05  Score=65.00  Aligned_cols=52  Identities=15%  Similarity=0.116  Sum_probs=41.9

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .|.|++-+++.|++.+..++..+.      -.-|--+-|+||||||||++++.||+.+
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~------p~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPN------PRKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCC------CCCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            678999999999999999987542      1112345699999999999999999986

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

>cd01394 radB RadB

Probab=97.70  E-value=0.00024  Score=67.52  Aligned_cols=38  Identities=29%  Similarity=0.423  Sum_probs=30.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      |++...-++++||||+|||+++..+|...   +.+++.++.
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~   55 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDT   55 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEC
Confidence            56666779999999999999999988765   566666654

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>PRK14737 gmk guanylate kinase; Provisional

Probab=97.70  E-value=0.00016  Score=67.29  Aligned_cols=168  Identities=15%  Similarity=0.124  Sum_probs=82.7

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc---Cc---h--H--HHHHHHH-hccCceEEEeccccccccc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR---SN---S--D--LRTLLVA-TANRSILVVEDIDCTIDLQ  320 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~---~~---~--~--l~~l~~~-~~~~sIL~iDdiD~l~~~~  320 (473)
                      .++-++|.||+|+|||+|++.|.....--++.++.+.-.   .+   .  .  =++-|.. ..++..+--.+.+.-    
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~~~~~~~v~~TTR~~r~gE~~G~dY~fvs~~~F~~~i~~~~f~e~~~~~g~----   78 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEHPDFLFSISCTTRAPRPGDEEGKTYFFLTIEEFKKGIADGEFLEWAEVHDN----   78 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcCCccccccCccCCCCCCCCCCCceeEeCCHHHHHHHHHcCCeEEEEEECCe----
Confidence            456799999999999999999988763222333332210   00   0  0  0112222 123333333333211    


Q ss_pred             cCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC--CCceeeEEEeCCCCHHHHHH
Q 012016          321 DRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR--PGRMDVHVHMSYCTPSGFKL  398 (473)
Q Consensus       321 ~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr--pgRfd~~I~~~~p~~~~r~~  398 (473)
                                   ..+.+...+...++          .+.++|+..+.. .+ ..+..  |.+. ..|++..|+.+.+.+
T Consensus        79 -------------~YGt~~~~i~~~~~----------~g~~~i~d~~~~-g~-~~l~~~~~~~~-~~Ifi~pps~e~l~~  132 (186)
T PRK14737         79 -------------YYGTPKAFIEDAFK----------EGRSAIMDIDVQ-GA-KIIKEKFPERI-VTIFIEPPSEEEWEE  132 (186)
T ss_pred             -------------eecCcHHHHHHHHH----------cCCeEEEEcCHH-HH-HHHHHhCCCCe-EEEEEECCCHHHHHH
Confidence                         12334444444442          224444433321 11 11222  2221 578999999777554


Q ss_pred             HHHHHhCccccCCHHHHHHHHhcCC--CCHHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 012016          399 LAANYLGIKEHILFEEIEELISTTQ--VTPAEVAEQLMRNDDPELVLNGLIEFLKVK  453 (473)
Q Consensus       399 l~~~~l~~~~~~l~~~i~~l~~~~~--~t~a~i~~~l~~~~~~~~al~~l~~~l~~~  453 (473)
                      -+...    .....+++...+....  ..-....+.++.+++.+.+.+.+...+..+
T Consensus       133 RL~~R----~~~s~e~i~~Rl~~~~~e~~~~~~~D~vI~N~dle~a~~ql~~ii~~~  185 (186)
T PRK14737        133 RLIHR----GTDSEESIEKRIENGIIELDEANEFDYKIINDDLEDAIADLEAIICGK  185 (186)
T ss_pred             HHHhc----CCCCHHHHHHHHHHHHHHHhhhccCCEEEECcCHHHHHHHHHHHHhcC
Confidence            33321    2223455655554311  111222334456779999999998887654

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.69  E-value=0.00063  Score=66.61  Aligned_cols=57  Identities=19%  Similarity=0.207  Sum_probs=40.6

Q ss_pred             eEEEEecCC------------CCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHH
Q 012016          360 RIIVFTTNH------------KEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELI  419 (473)
Q Consensus       360 ~iiI~tTN~------------~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~  419 (473)
                      -++|++||+            |..++-.|+.  |+ ..|...+.+.++.+.|++.....++..+.++...++
T Consensus       318 PiiimaTNrgit~iRGTn~~SphGiP~D~lD--R~-lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~L  386 (454)
T KOG2680|consen  318 PIIIMATNRGITRIRGTNYRSPHGIPIDLLD--RM-LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLL  386 (454)
T ss_pred             cEEEEEcCCceEEeecCCCCCCCCCcHHHhh--hh-heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHH
Confidence            467777775            5677888887  77 466777777888888888877777666666555554

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=97.68  E-value=9.5e-05  Score=67.70  Aligned_cols=23  Identities=35%  Similarity=0.739  Sum_probs=20.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++|.|+||+||||+++.+++.+
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHH
T ss_pred             CEEEECcCCCCHHHHHHHHHHHh
Confidence            37999999999999999999988

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=97.68  E-value=0.0002  Score=74.54  Aligned_cols=89  Identities=19%  Similarity=0.247  Sum_probs=67.6

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN  292 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~  292 (473)
                      ..+..++|.......+++.++.-..+           .-.|||.|..||||..+|++|-+..   +.|++.+||..+-. 
T Consensus       220 ~~~~~iIG~S~am~~ll~~i~~VA~S-----------d~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPe-  287 (550)
T COG3604         220 LEVGGIIGRSPAMRQLLKEIEVVAKS-----------DSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPE-  287 (550)
T ss_pred             cccccceecCHHHHHHHHHHHHHhcC-----------CCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccch-
Confidence            56789999998888888877754432           3479999999999999999999877   67999999998732 


Q ss_pred             hHHH-HHHH-----------------HhccCceEEEeccccc
Q 012016          293 SDLR-TLLV-----------------ATANRSILVVEDIDCT  316 (473)
Q Consensus       293 ~~l~-~l~~-----------------~~~~~sIL~iDdiD~l  316 (473)
                      +-+. ++|-                 +..+++-||+|||..+
T Consensus       288 sLlESELFGHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGel  329 (550)
T COG3604         288 SLLESELFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGEL  329 (550)
T ss_pred             HHHHHHHhcccccccccchhccCcceeecCCCeEechhhccC
Confidence            1111 2221                 1236789999999876

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=97.66  E-value=6.9e-05  Score=81.77  Aligned_cols=125  Identities=18%  Similarity=0.184  Sum_probs=74.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccc-ccc--C-----chHHHHHHHH-----hccCceEEEecccccccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT-ELR--S-----NSDLRTLLVA-----TANRSILVVEDIDCTIDLQD  321 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~-~~~--~-----~~~l~~l~~~-----~~~~sIL~iDdiD~l~~~~~  321 (473)
                      ++||.|.||||||.|.+.+++.+...+|.---+ +..  +     +...-+....     .+.++|.+|||+|.+-    
T Consensus       321 nILLvGDPgtaKSqlLk~v~~~aPr~vytsgkgss~~GLTAav~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm~----  396 (682)
T COG1241         321 HILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSSAAGLTAAVVRDKVTGEWVLEAGALVLADGGVCCIDEFDKMN----  396 (682)
T ss_pred             eEEEcCCCchhHHHHHHHHHhhCCceEEEccccccccCceeEEEEccCCCeEEEeCCEEEEecCCEEEEEeccCCC----
Confidence            599999999999999999999997777643211 110  0     0000011111     2478999999999772    


Q ss_pred             CCccccCCCCCCCccchhHHHHHHHHHhccc---------ccCCCCceEEEEecCCCC-------------CCCccccCC
Q 012016          322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGL---------WSSCGDERIIVFTTNHKE-------------KLDPALLRP  379 (473)
Q Consensus       322 r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~~-------------~ld~aLlrp  379 (473)
                                       ....+.+...|+..         ...-+...-|++++|.+.             .|+++|+. 
T Consensus       397 -----------------~~dr~aihEaMEQQtIsIaKAGI~atLnARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLS-  458 (682)
T COG1241         397 -----------------EEDRVAIHEAMEQQTISIAKAGITATLNARCSVLAAANPKFGRYDPKKTVAENINLPAPLLS-  458 (682)
T ss_pred             -----------------hHHHHHHHHHHHhcEeeecccceeeecchhhhhhhhhCCCCCcCCCCCCHHHhcCCChhHHh-
Confidence                             22334455555421         111112344677788653             47888999 


Q ss_pred             CceeeEEEeC-CCCHHHHHHHHHH
Q 012016          380 GRMDVHVHMS-YCTPSGFKLLAAN  402 (473)
Q Consensus       380 gRfd~~I~~~-~p~~~~r~~l~~~  402 (473)
                       |||...-+. .|+.+.=..|+.+
T Consensus       459 -RFDLifvl~D~~d~~~D~~ia~h  481 (682)
T COG1241         459 -RFDLIFVLKDDPDEEKDEEIAEH  481 (682)
T ss_pred             -hCCeeEEecCCCCccchHHHHHH
Confidence             999765443 3666543333333

>PRK13947 shikimate kinase; Provisional

Probab=97.64  E-value=5.1e-05  Score=69.17  Aligned_cols=32  Identities=31%  Similarity=0.432  Sum_probs=30.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      +++|.|+||||||++++.+|+.+++++++.+.
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d~   34 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTDK   34 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECch
Confidence            58999999999999999999999999998774

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.62  E-value=0.00024  Score=67.64  Aligned_cols=21  Identities=29%  Similarity=0.480  Sum_probs=19.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMA  274 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA  274 (473)
                      +.++|.||.|+|||++.+.++
T Consensus        30 ~~~~itGpNg~GKStlLk~i~   50 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVA   50 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            679999999999999999998

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

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.61  E-value=0.00034  Score=67.41  Aligned_cols=38  Identities=29%  Similarity=0.315  Sum_probs=29.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      |.|.+..++++||||||||+++..++...   +.+++.++.
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            67777889999999999999999987543   555555443

>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=97.60  E-value=5.9e-05  Score=67.26  Aligned_cols=31  Identities=29%  Similarity=0.452  Sum_probs=28.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++|+||||+|||++++.+|..+++++++.+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d   31 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD   31 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            4799999999999999999999999998776

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.

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.59  E-value=0.00026  Score=66.54  Aligned_cols=113  Identities=22%  Similarity=0.267  Sum_probs=65.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccC
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIA  328 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~  328 (473)
                      |....-.++|.|+.|+|||++++.|+.+     +..+......+.+   ....+...-|+.|||++.+..          
T Consensus        48 g~k~d~~lvl~G~QG~GKStf~~~L~~~-----~~~d~~~~~~~kd---~~~~l~~~~iveldEl~~~~k----------  109 (198)
T PF05272_consen   48 GCKNDTVLVLVGKQGIGKSTFFRKLGPE-----YFSDSINDFDDKD---FLEQLQGKWIVELDELDGLSK----------  109 (198)
T ss_pred             CCcCceeeeEecCCcccHHHHHHHHhHH-----hccCccccCCCcH---HHHHHHHhHheeHHHHhhcch----------
Confidence            4444556899999999999999999766     2222222112222   223445668999999987631          


Q ss_pred             CCCCCCccchhHHHHHHHHHh-cccc-------cCCCCceEEEEecCCCCCC-CccccCCCceeeEEEeCC
Q 012016          329 GEGEGPIQQNKVTLSGFLNFI-DGLW-------SSCGDERIIVFTTNHKEKL-DPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       329 ~~~~~~~~~~~~~ls~LL~~l-dg~~-------~~~~~~~iiI~tTN~~~~l-d~aLlrpgRfd~~I~~~~  390 (473)
                              .....+..++..- +...       ...+...++|+|||..+-| |+.=-|  || ..|+++.
T Consensus       110 --------~~~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnR--Rf-~~v~v~~  169 (198)
T PF05272_consen  110 --------KDVEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNR--RF-WPVEVSK  169 (198)
T ss_pred             --------hhHHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCe--EE-EEEEEcC
Confidence                    1122333333221 1111       1112235789999998755 455556  77 4566554

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.59  E-value=0.00025  Score=67.85  Aligned_cols=39  Identities=26%  Similarity=0.395  Sum_probs=31.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      |.+...-++++||||+|||+++..+|...   +.+++.+++.
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            56666779999999999999999998754   6777777766

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.58  E-value=0.00087  Score=69.33  Aligned_cols=65  Identities=25%  Similarity=0.462  Sum_probs=43.4

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc-------CCceEEcccccc----------------------cCchHHHHHHHHh
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL-------NFDVYDLELTEL----------------------RSNSDLRTLLVAT  302 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l-------~~~~~~l~~~~~----------------------~~~~~l~~l~~~~  302 (473)
                      .++.++|+||+|+|||+.+.-+|..+       +..+..+++...                      .....+...+...
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~~  252 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQS  252 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHHh
Confidence            35679999999999999999999865       234433333221                      1123445555555


Q ss_pred             ccCceEEEeccccc
Q 012016          303 ANRSILVVEDIDCT  316 (473)
Q Consensus       303 ~~~sIL~iDdiD~l  316 (473)
                      ....+|+||.+..+
T Consensus       253 ~~~DlVLIDTaGr~  266 (388)
T PRK12723        253 KDFDLVLVDTIGKS  266 (388)
T ss_pred             CCCCEEEEcCCCCC
Confidence            56788999998754

>PRK03839 putative kinase; Provisional

Probab=97.58  E-value=6.1e-05  Score=69.47  Aligned_cols=30  Identities=30%  Similarity=0.597  Sum_probs=28.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++|.|+||+||||+++.+|+.+++++++++
T Consensus         3 I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            789999999999999999999999998765

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.58  E-value=0.00019  Score=65.81  Aligned_cols=63  Identities=22%  Similarity=0.255  Sum_probs=46.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch-----------------------HHHHHHHH-hccCceEEE
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS-----------------------DLRTLLVA-TANRSILVV  310 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~-----------------------~l~~l~~~-~~~~sIL~i  310 (473)
                      -+|+.||||+|||+++..++..++.+++.+.......++                       ++.+++.. ..++.+++|
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~~~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~~~~VlI   82 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATAQPFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAPGRCVLV   82 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCCCCChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCCCCEEEe
Confidence            479999999999999999999998888777765543221                       34444444 345668899


Q ss_pred             ecccccc
Q 012016          311 EDIDCTI  317 (473)
Q Consensus       311 DdiD~l~  317 (473)
                      |-+..+.
T Consensus        83 D~Lt~~~   89 (170)
T PRK05800         83 DCLTTWV   89 (170)
T ss_pred             hhHHHHH
Confidence            9888764

>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=97.58  E-value=4.5e-05  Score=67.15  Aligned_cols=30  Identities=40%  Similarity=0.655  Sum_probs=25.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +++.||||+||||+++.++..++..++..|
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~~~i~~D   31 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGAVVISQD   31 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCEEEeHH
Confidence            689999999999999999999995555443

...

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=97.57  E-value=0.00019  Score=66.29  Aligned_cols=29  Identities=41%  Similarity=0.716  Sum_probs=24.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      .++|.||||+||||+|+.||+.++++-++
T Consensus         2 riiilG~pGaGK~T~A~~La~~~~i~hls   30 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKLGLPHLD   30 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEc
Confidence            47999999999999999999996555443

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.57  E-value=5.7e-05  Score=68.78  Aligned_cols=33  Identities=33%  Similarity=0.416  Sum_probs=31.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      +.+.|.|++|+||||+.+++|+.|+++|++.|-
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D~   35 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTDQ   35 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccchH
Confidence            579999999999999999999999999999884

>PRK00625 shikimate kinase; Provisional

Probab=97.57  E-value=7e-05  Score=68.91  Aligned_cols=32  Identities=31%  Similarity=0.544  Sum_probs=29.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .++|.|+||+|||++++.+|+.++++++++|.
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D~   33 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTDD   33 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhhH
Confidence            48999999999999999999999999998873

>PRK13949 shikimate kinase; Provisional

Probab=97.56  E-value=7.2e-05  Score=68.54  Aligned_cols=32  Identities=34%  Similarity=0.504  Sum_probs=29.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .++|.||||+|||++++.+|+.++++++++|.
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~~id~D~   34 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLSFIDLDF   34 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCeecccH
Confidence            68999999999999999999999999998773

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.54  E-value=0.0012  Score=68.79  Aligned_cols=116  Identities=16%  Similarity=0.173  Sum_probs=69.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc-cccccCchHHHHH---HHHhc--cCceEEEeccccccccccCCccccC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE-LTELRSNSDLRTL---LVATA--NRSILVVEDIDCTIDLQDRLPADIA  328 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~-~~~~~~~~~l~~l---~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~  328 (473)
                      -++++||.+||||++++-+...+.-.++.++ +........+.+.   +....  ....+|||||.++-+          
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~~~l~d~~~~~~~~~~~~~~yifLDEIq~v~~----------  108 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLDEIQNVPD----------  108 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcchhhHHHHHHHHHHhhccCCceEEEecccCchh----------
Confidence            8999999999999999888888755433333 3333333333222   22222  348999999998621          


Q ss_pred             CCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCC-CccccCCCceeeEEEeCCCCHHHHHH
Q 012016          329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKL-DPALLRPGRMDVHVHMSYCTPSGFKL  398 (473)
Q Consensus       329 ~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l-d~aLlrpgRfd~~I~~~~p~~~~r~~  398 (473)
                               ....+..|.   |.     +...++|.++|..-.+ ..+-.=|||. ..+++.+.+..++..
T Consensus       109 ---------W~~~lk~l~---d~-----~~~~v~itgsss~ll~~~~~~~L~GR~-~~~~l~PlSF~Efl~  161 (398)
T COG1373         109 ---------WERALKYLY---DR-----GNLDVLITGSSSSLLSKEISESLAGRG-KDLELYPLSFREFLK  161 (398)
T ss_pred             ---------HHHHHHHHH---cc-----ccceEEEECCchhhhccchhhhcCCCc-eeEEECCCCHHHHHh
Confidence                     233333333   32     1114566655554222 2233346794 688999999999854

>PF08740 BCS1_N: BCS1 N terminal; InterPro: IPR014851 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=97.53  E-value=0.0062  Score=56.54  Aligned_cols=138  Identities=17%  Similarity=0.224  Sum_probs=94.1

Q ss_pred             eEEEEecCCCCccchhHHHHHHHhccCC-CccccceEEeecc----------------------CCCceEEecCCCceEE
Q 012016           63 LTIVIDEHDGLAKNQIYDAAKVYLGKKT-SPSVQRIKVSKLE----------------------KENHVNISMESDEQVV  119 (473)
Q Consensus        63 ~ti~i~e~~~~~~n~ly~a~~~YL~~~~-~~~~~rl~~~~~~----------------------~~~~~~~~~~~~~~v~  119 (473)
                      .|+.|+.     .+++|+.+-.+|+... ...++++.+....                      +.+.+.+.+..| ...
T Consensus        27 ~sv~I~~-----~D~~Y~~lm~Wls~q~~~~~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~G-~h~  100 (187)
T PF08740_consen   27 SSVEIPS-----DDEAYDWLMRWLSSQPFSKRSRHLSATTRSNSSWDDDESDDEDSWDTNTSDDKKKPIRFTPSPG-THW  100 (187)
T ss_pred             EEEEECC-----CCHHHHHHHHHHhhCCcccccceeEEEeecccccccccccccchhccccccCCcCCeEEEeCCC-CEE
Confidence            4667765     4578999999999775 4446777776522                      356788999999 777


Q ss_pred             EeecCeeeEEEEEEeeccCCccCCCCCCcccceeEEEEEecCCchhHHHHhhhHHHHHHHHHHHhhcceeeEeeeccccc
Q 012016          120 DVFNGIKLKWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNL  199 (473)
Q Consensus       120 D~f~G~~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~l~f~~~~~~~~l~~yl~~v~~~~~~~~~~~~~~~i~~~~~~~~  199 (473)
                      ..|+|   .|..+.+..+....+.+.   ..+.+.++|++..+.++ +|..+|.+..+... .+++++ ..||.....  
T Consensus       101 F~y~G---~~~~~~R~~~~~~~~~~~---~~~~e~l~l~~lg~s~~-~l~~ll~ear~~~~-~~~~~~-t~Iy~~~~~--  169 (187)
T PF08740_consen  101 FWYKG---RWFWFSRQRESNSYNSWT---GAPDETLTLSCLGRSPK-PLKDLLEEAREYYL-KKQKGK-TTIYRADGS--  169 (187)
T ss_pred             EEECC---EEEEEEEEeccccccccC---CCCceEEEEEEecCCHH-HHHHHHHHHHHHHH-HhcCCc-EEEEeCCCC--
Confidence            88998   688888887544433222   23578999999988765 56666555544432 233344 458887432  


Q ss_pred             ccCCCCcceeccCCCCCCcccc
Q 012016          200 YCNWTDAWIPVNLDHPATFETL  221 (473)
Q Consensus       200 ~~~~~~~w~~~~~~~p~~f~~l  221 (473)
                          +..|..+.-.++.++++|
T Consensus       170 ----~~~W~~~~~r~~RplsTV  187 (187)
T PF08740_consen  170 ----EYRWRRVASRPKRPLSTV  187 (187)
T ss_pred             ----CCCCcCCCCcCCCCCCCC
Confidence                126999888888888875

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) []. This domain is found at the N terminus of the mitochondrial BSC1 subfamily, belonging to the AAA ATPase family. At2g21640 and BCS1 are both highly stress responsive genes which encode mitochondrial proteins. The promoter of BCS1 was not responsive to H2O2 or rotenone, but highly responsive to salicylic acid (SA). The SA dependent pathway represented by BCS1 is one of at least three distinctive pathways to regulate mitochondrial stress response at a transcriptional level []. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III []. BCS1, a component of the inner membrane of mitochondria, belongs to the group of proteins with internal, noncleavable import signals. It has a transmembrane domain (amino acid residues 51 to 68), a presequence type helix (residues 69 to 83), and an import auxiliary region (residues 84 to 126) [].

>PRK13948 shikimate kinase; Provisional

Probab=97.52  E-value=0.00011  Score=68.10  Aligned_cols=35  Identities=26%  Similarity=0.151  Sum_probs=32.4

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++++.++|.|++|+|||++++.+|+.++.++++.|
T Consensus         8 ~~~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D   42 (182)
T PRK13948          8 RPVTWVALAGFMGTGKSRIGWELSRALMLHFIDTD   42 (182)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEECC
Confidence            34678999999999999999999999999999888

>PRK05973 replicative DNA helicase; Provisional

Probab=97.52  E-value=0.00049  Score=66.40  Aligned_cols=38  Identities=24%  Similarity=0.028  Sum_probs=28.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      |.++..-+++.|+||+|||+++..+|...   |.+++++++
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSl  100 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTL  100 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEE
Confidence            56666779999999999999888776644   666655443

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=97.49  E-value=0.00078  Score=67.46  Aligned_cols=132  Identities=17%  Similarity=0.262  Sum_probs=90.6

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceE
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVY  282 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~  282 (473)
                      ....+..++...|+.+++.....+.+++....+-.           ...-+|+.|..||||-.+|+|.....   ..||+
T Consensus       191 ~~~~~~~~~~~~F~~~v~~S~~mk~~v~qA~k~Am-----------lDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFl  259 (511)
T COG3283         191 QLQNVAAQDVSGFEQIVAVSPKMKHVVEQAQKLAM-----------LDAPLLITGETGTGKDLLAKACHLASPRHSKPFL  259 (511)
T ss_pred             HHhhcccccccchHHHhhccHHHHHHHHHHHHhhc-----------cCCCeEEecCCCchHHHHHHHHhhcCcccCCCee
Confidence            34455666778999999988777777665554432           12358999999999999999977655   68999


Q ss_pred             EcccccccCchHHHHHHH------------HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHh-
Q 012016          283 DLELTELRSNSDLRTLLV------------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFI-  349 (473)
Q Consensus       283 ~l~~~~~~~~~~l~~l~~------------~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~l-  349 (473)
                      .++|..+-.+..=.++|-            +.+++.-+++|||..+.                     ......||.++ 
T Consensus       260 alNCA~lPe~~aEsElFG~apg~~gk~GffE~AngGTVlLDeIgEmS---------------------p~lQaKLLRFL~  318 (511)
T COG3283         260 ALNCASLPEDAAESELFGHAPGDEGKKGFFEQANGGTVLLDEIGEMS---------------------PRLQAKLLRFLN  318 (511)
T ss_pred             EeecCCCchhHhHHHHhcCCCCCCCccchhhhccCCeEEeehhhhcC---------------------HHHHHHHHHHhc
Confidence            999999844332333333            33467888999997662                     45566677777 


Q ss_pred             cccccCCCC------ceEEEEecCCC
Q 012016          350 DGLWSSCGD------ERIIVFTTNHK  369 (473)
Q Consensus       350 dg~~~~~~~------~~iiI~tTN~~  369 (473)
                      ||....-|+      ++-||+||..+
T Consensus       319 DGtFRRVGee~Ev~vdVRVIcatq~n  344 (511)
T COG3283         319 DGTFRRVGEDHEVHVDVRVICATQVN  344 (511)
T ss_pred             CCceeecCCcceEEEEEEEEeccccc
Confidence            443222222      36788888765

>PF06431 Polyoma_lg_T_C: Polyomavirus large T antigen C-terminus; InterPro: IPR010932 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []

Probab=97.49  E-value=0.0008  Score=67.72  Aligned_cols=125  Identities=20%  Similarity=0.250  Sum_probs=69.7

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccC
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIA  328 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~  328 (473)
                      ++|.+|.+||-||-.||||+||+|+-+.+|-....+++..    +.|.--+--+-..-.+++||+---..          
T Consensus       151 N~PKkRy~lFkGPvNsGKTTlAAAlLdL~gG~~LNvN~p~----dkl~FELG~AiDQfmVvFEDVKGq~~----------  216 (417)
T PF06431_consen  151 NIPKKRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQPS----------  216 (417)
T ss_dssp             TBTTB-EEEEE-STTSSHHHHHHHHHHHH-EEEE-TSS-T----TTHHHHHCCCTT-SEEEEEEE--SST----------
T ss_pred             CCCcceeEEEecCcCCchHHHHHHHHHhcCCceeecCCCh----hhcchhhheeeceEEEEEEecCCCcC----------
Confidence            4566889999999999999999999999998888888764    34444444445778899999842210          


Q ss_pred             CCCCCCccchhHHHHHHHHHhccccc-----CCCCce-----EEEEecCCCCCCCccccCCCceeeEEEeCC
Q 012016          329 GEGEGPIQQNKVTLSGFLNFIDGLWS-----SCGDER-----IIVFTTNHKEKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       329 ~~~~~~~~~~~~~ls~LL~~ldg~~~-----~~~~~~-----iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~  390 (473)
                      ...+-..+..-..+..|-..+||...     ..-+.+     --|.|.|. -.++..+.-  ||...+.|..
T Consensus       217 ~~~~Lp~G~G~~NLDNLRD~LDG~V~VNLErKH~NK~sQiFPPgIvTmNe-Y~iP~Tv~v--Rf~~~~~F~~  285 (417)
T PF06431_consen  217 DNKDLPPGQGMNNLDNLRDYLDGAVKVNLERKHQNKRSQIFPPGIVTMNE-YKIPQTVKV--RFCKVLDFRP  285 (417)
T ss_dssp             TTTT----SHHHHHHTTHHHHH-SS-EEEECSSSEEEEE----EEEEESS--B--HHHHT--TEEEEEE---
T ss_pred             CCCCCCCCCCcccchhhhhhccCceeechhhhhcccccccCCCceEeecc-ccCCcceee--eeEeeEeccc
Confidence            00011122233455556667776421     000111     24668876 467788877  9998888864

Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA []. ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA []. These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 2H1L_H 1SVO_A 1SVM_E 1SVL_B 1N25_A 4E2I_K.

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.48  E-value=0.00044  Score=65.09  Aligned_cols=63  Identities=19%  Similarity=0.366  Sum_probs=41.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh-----cCCceE-------------Ecccc-ccc--------CchHHHHHHHHhc--
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY-----LNFDVY-------------DLELT-ELR--------SNSDLRTLLVATA--  303 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~-----l~~~~~-------------~l~~~-~~~--------~~~~l~~l~~~~~--  303 (473)
                      .+.++|.||+|+|||++++.++..     .|.++-             .+... ++.        ....+.+++....  
T Consensus        25 g~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~l~~~~s~~~~e~~~~~~iL~~~~~~  104 (199)
T cd03283          25 KNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKG  104 (199)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcccceEEEeccchhccccccChHHHHHHHHHHHHHhccCC
Confidence            357899999999999999999853     344331             11000 000        1134566777777  


Q ss_pred             cCceEEEecccc
Q 012016          304 NRSILVVEDIDC  315 (473)
Q Consensus       304 ~~sIL~iDdiD~  315 (473)
                      .+.++++||.-.
T Consensus       105 ~p~llllDEp~~  116 (199)
T cd03283         105 EPVLFLLDEIFK  116 (199)
T ss_pred             CCeEEEEecccC
Confidence            899999999854

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

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.47  E-value=0.0011  Score=69.69  Aligned_cols=62  Identities=16%  Similarity=0.220  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc
Q 012016          226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE  288 (473)
Q Consensus       226 ~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~  288 (473)
                      ...+.+.+.+...+.......... ..|..++|+||+|+|||+++..+|..+   |..+..+++..
T Consensus        69 ~~~~~v~~~L~~~l~~~~~~~~~~-~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~  133 (437)
T PRK00771         69 HVIKIVYEELVKLLGEETEPLVLP-LKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADT  133 (437)
T ss_pred             HHHHHHHHHHHHHhCCCccccccC-CCCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCC
Confidence            334555555555443321111111 236689999999999999999999887   55565555443

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.47  E-value=0.00063  Score=65.51  Aligned_cols=37  Identities=27%  Similarity=0.322  Sum_probs=25.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHH-HHhc--CCceEEcc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAM-ANYL--NFDVYDLE  285 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~al-A~~l--~~~~~~l~  285 (473)
                      |.+...-+++.||||||||+++..+ ++.+  +..+..++
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~   59 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVS   59 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEe
Confidence            4566678999999999999997544 4332  44554444

>TIGR02012 tigrfam_recA protein RecA

Probab=97.45  E-value=0.00065  Score=68.38  Aligned_cols=70  Identities=16%  Similarity=0.207  Sum_probs=44.1

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHH---H
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLV---A  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~---~  301 (473)
                      |.|..+-++++||||||||+|+..++...   +.++..++.....                     ..+.....+.   .
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            56667789999999999999977655443   5555555443210                     1111112221   2


Q ss_pred             hccCceEEEeccccccc
Q 012016          302 TANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~  318 (473)
                      .....+||||-+.++.+
T Consensus       131 ~~~~~lIVIDSv~al~~  147 (321)
T TIGR02012       131 SGAVDIIVVDSVAALVP  147 (321)
T ss_pred             ccCCcEEEEcchhhhcc
Confidence            23678999999998864

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.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.43  E-value=6.3e-05  Score=68.98  Aligned_cols=37  Identities=32%  Similarity=0.494  Sum_probs=26.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc---eEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD---VYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~---~~~l~~~~~  289 (473)
                      ++.++|+||+|+|||++++++...+..+   ++.+++...
T Consensus        24 ~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen   24 PRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             ---EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            5789999999999999999998887444   666666655

>PRK06217 hypothetical protein; Validated

Probab=97.43  E-value=0.00014  Score=67.40  Aligned_cols=32  Identities=28%  Similarity=0.393  Sum_probs=29.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .|+|.|+||+||||++++|+..++++++++|.
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D~   34 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTDD   34 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcCc
Confidence            48999999999999999999999999887763

>PRK04040 adenylate kinase; Provisional

Probab=97.43  E-value=0.0012  Score=61.61  Aligned_cols=30  Identities=20%  Similarity=0.501  Sum_probs=26.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc--CCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL--NFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l--~~~~~  282 (473)
                      +.-++++|+||||||++++.++..+  +++++
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~~   33 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLKEDYKIV   33 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhccCCeEE
Confidence            3468999999999999999999999  66654

>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=97.42  E-value=0.00037  Score=68.55  Aligned_cols=90  Identities=23%  Similarity=0.411  Sum_probs=56.7

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC---ceEEccc-ccc
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF---DVYDLEL-TEL  289 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~---~~~~l~~-~~~  289 (473)
                      .+.+++++...+...+.+.+.+...++           ...++++.||+|+|||++++++..++..   .++.++- .++
T Consensus        99 ~~~sle~l~~~~~~~~~~~~~l~~~v~-----------~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~  167 (270)
T PF00437_consen   99 KPFSLEDLGESGSIPEEIAEFLRSAVR-----------GRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPEL  167 (270)
T ss_dssp             S--CHCCCCHTHHCHHHHHHHHHHCHH-----------TTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S
T ss_pred             ccccHhhccCchhhHHHHHHHHhhccc-----------cceEEEEECCCccccchHHHHHhhhccccccceEEeccccce
Confidence            445889998776666655554443332           1458999999999999999999998833   3333321 111


Q ss_pred             -------------cCchHHHHHHHHh--ccCceEEEeccc
Q 012016          290 -------------RSNSDLRTLLVAT--ANRSILVVEDID  314 (473)
Q Consensus       290 -------------~~~~~l~~l~~~~--~~~sIL~iDdiD  314 (473)
                                   .....+.+++..+  .+|.+|++.||-
T Consensus       168 ~l~~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR  207 (270)
T PF00437_consen  168 RLPGPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIGEIR  207 (270)
T ss_dssp             --SCSSEEEEEEETTTBSHHHHHHHHTTS--SEEEESCE-
T ss_pred             eecccceEEEEeecCcccHHHHHHHHhcCCCCcccccccC
Confidence                         1234566666654  478999999995

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 ....

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.41  E-value=0.00033  Score=70.54  Aligned_cols=57  Identities=25%  Similarity=0.308  Sum_probs=41.6

Q ss_pred             chHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          224 EQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       224 ~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++.++.+.+.++..+....     -..++..+.|.|+||||||++++.+|..+|+++++++
T Consensus       109 ~~~~~~~~~~~l~~~~~~~~-----~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~id~D  165 (309)
T PRK08154        109 SPAQLARVRDALSGMLGAGR-----RAARRRRIALIGLRGAGKSTLGRMLAARLGVPFVELN  165 (309)
T ss_pred             CHHHHHHHHHHHHHHHhhhh-----hccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEeHH
Confidence            34555555555554443211     2345678999999999999999999999999999766

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.41  E-value=0.00066  Score=65.18  Aligned_cols=23  Identities=35%  Similarity=0.537  Sum_probs=21.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+-|.||+|||||||.+.+|...
T Consensus        31 fvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          31 FVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48899999999999999999876

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.40  E-value=0.00016  Score=64.46  Aligned_cols=30  Identities=30%  Similarity=0.411  Sum_probs=26.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++|.||||+|||++++.++..++..+++.|
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~~D   31 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFIDGD   31 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEeCc
Confidence            689999999999999999999988776543

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>PRK13946 shikimate kinase; Provisional

Probab=97.40  E-value=0.00016  Score=67.18  Aligned_cols=34  Identities=32%  Similarity=0.445  Sum_probs=31.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ++.|+|.|+||||||++++.+|+.||+++++.|.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D~   43 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDADT   43 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcCH
Confidence            5689999999999999999999999999998884

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.38  E-value=0.00017  Score=66.49  Aligned_cols=29  Identities=24%  Similarity=0.497  Sum_probs=26.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +++.||||+|||++++.||..+++..+..
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is~   30 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLSA   30 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            68999999999999999999999766654

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.

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.38  E-value=0.00016  Score=65.50  Aligned_cols=29  Identities=31%  Similarity=0.550  Sum_probs=25.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ++|.||||+|||++++.+++.++..+++.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v~~   29 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFIEG   29 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEEeC
Confidence            57899999999999999999998776544

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK14532 adenylate kinase; Provisional

Probab=97.37  E-value=0.00018  Score=66.72  Aligned_cols=30  Identities=20%  Similarity=0.437  Sum_probs=27.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .++|.||||+|||++++.||..+|++.+..
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            489999999999999999999999877655

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=97.37  E-value=0.00017  Score=63.63  Aligned_cols=30  Identities=30%  Similarity=0.497  Sum_probs=28.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.+.|+||||||++++.||..++++++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            689999999999999999999999999887

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.36  E-value=0.00021  Score=65.61  Aligned_cols=34  Identities=41%  Similarity=0.690  Sum_probs=31.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      +..++|.||+|+|||++++.+|+.+++++++.|.
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~~~~vd~D~   37 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQ   37 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcCCcEEECCc
Confidence            4579999999999999999999999999988875

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.36  E-value=0.0007  Score=69.80  Aligned_cols=69  Identities=23%  Similarity=0.341  Sum_probs=46.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc--------------------CchHHHHHHHHh--c
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR--------------------SNSDLRTLLVAT--A  303 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~--------------------~~~~l~~l~~~~--~  303 (473)
                      |.++..-++|+||||+|||+|+..+|..+   +.++++++..+..                    ....+..++...  .
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            56666779999999999999999888765   3466665543210                    112233333322  3


Q ss_pred             cCceEEEecccccc
Q 012016          304 NRSILVVEDIDCTI  317 (473)
Q Consensus       304 ~~sIL~iDdiD~l~  317 (473)
                      ++.+|+||.|..+.
T Consensus       158 ~~~lVVIDSIq~l~  171 (372)
T cd01121         158 KPDLVIIDSIQTVY  171 (372)
T ss_pred             CCcEEEEcchHHhh
Confidence            78999999998875

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.35  E-value=0.00079  Score=66.88  Aligned_cols=61  Identities=21%  Similarity=0.357  Sum_probs=41.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----C-CceEEcccccc----------------------cCchHHHHHHHHhccC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----N-FDVYDLELTEL----------------------RSNSDLRTLLVATANR  305 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----~-~~~~~l~~~~~----------------------~~~~~l~~l~~~~~~~  305 (473)
                      ++.++|.||+|+|||+++..||.++    + ..+..+++...                      .....+...+......
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~r~~a~eql~~~~~~~~~p~~~~~~~~~l~~~l~~~~~~  273 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILGVPVKVARDPKELRKALDRLRDK  273 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCccchhHHHHHHHHHHHhCCceeccCCHHHHHHHHHHccCC
Confidence            3468999999999999999999876    3 56665555442                      1223455555555556


Q ss_pred             ceEEEecc
Q 012016          306 SILVVEDI  313 (473)
Q Consensus       306 sIL~iDdi  313 (473)
                      .+|+||..
T Consensus       274 d~vliDt~  281 (282)
T TIGR03499       274 DLILIDTA  281 (282)
T ss_pred             CEEEEeCC
Confidence            77777753

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.35  E-value=0.00081  Score=60.78  Aligned_cols=24  Identities=33%  Similarity=0.580  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+++.||+|||||+|.+++|+..
T Consensus        30 e~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhcc
Confidence            358999999999999999999865

>PRK14531 adenylate kinase; Provisional

Probab=97.35  E-value=0.00021  Score=66.20  Aligned_cols=31  Identities=26%  Similarity=0.483  Sum_probs=27.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +-+++.||||+|||++++.+|..+|++.+..
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            4699999999999999999999999887654

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.35  E-value=0.0009  Score=67.46  Aligned_cols=70  Identities=16%  Similarity=0.212  Sum_probs=45.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc---------------------cCchHHHHHHH---H
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL---------------------RSNSDLRTLLV---A  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~---------------------~~~~~l~~l~~---~  301 (473)
                      |.|..+-+.+|||||||||+|+..++...   +..+..++....                     .+.+.+..++.   .
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            56666779999999999999998776443   556666554321                     01112222222   2


Q ss_pred             hccCceEEEeccccccc
Q 012016          302 TANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~  318 (473)
                      .....+||||-+-++.+
T Consensus       131 s~~~~lIVIDSvaal~~  147 (325)
T cd00983         131 SGAVDLIVVDSVAALVP  147 (325)
T ss_pred             ccCCCEEEEcchHhhcc
Confidence            23578999999998864

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.35  E-value=0.00076  Score=71.30  Aligned_cols=70  Identities=24%  Similarity=0.342  Sum_probs=48.1

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc--------------------CchHHHHHHHHh--c
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR--------------------SNSDLRTLLVAT--A  303 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~--------------------~~~~l~~l~~~~--~  303 (473)
                      |.+...-+||+||||+|||+|+..+|..+   +.++++++..+..                    ....+.+++...  .
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            56666779999999999999999988765   5677766654320                    112233333332  3


Q ss_pred             cCceEEEeccccccc
Q 012016          304 NRSILVVEDIDCTID  318 (473)
Q Consensus       304 ~~sIL~iDdiD~l~~  318 (473)
                      ++.+||||.|..+..
T Consensus       156 ~~~lVVIDSIq~l~~  170 (446)
T PRK11823        156 KPDLVVIDSIQTMYS  170 (446)
T ss_pred             CCCEEEEechhhhcc
Confidence            678999999988753

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.34  E-value=0.0014  Score=65.34  Aligned_cols=156  Identities=19%  Similarity=0.267  Sum_probs=93.1

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHH-HHH--hcCCceEEcccccc-cC----
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAA-MAN--YLNFDVYDLELTEL-RS----  291 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~a-lA~--~l~~~~~~l~~~~~-~~----  291 (473)
                      .+.|..+..+.+-+.+..-.-..+         ...+++.||.|+|||.++.. ++.  +.|-+++.+-+... ..    
T Consensus        25 ~l~g~~~~~~~l~~~lkqt~~~gE---------snsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~a   95 (408)
T KOG2228|consen   25 NLFGVQDEQKHLSELLKQTILHGE---------SNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIA   95 (408)
T ss_pred             ceeehHHHHHHHHHHHHHHHHhcC---------CCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHH
Confidence            345556666666666655444333         56899999999999997763 333  56767665554332 11    


Q ss_pred             ----------------------chHHHHHHHHhc-------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          292 ----------------------NSDLRTLLVATA-------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       292 ----------------------~~~l~~l~~~~~-------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                            .+.+..++....       .+.|.++||+|-..+                  ..++++
T Consensus        96 l~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~------------------h~rQtl  157 (408)
T KOG2228|consen   96 LKGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAP------------------HSRQTL  157 (408)
T ss_pred             HHHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhcccc------------------chhhHH
Confidence                                  122233332221       235667788997643                  223333


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCC---CCCccccCCCceeeE-EEeCC-CCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKE---KLDPALLRPGRMDVH-VHMSY-CTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~---~ld~aLlrpgRfd~~-I~~~~-p~~~~r~~l~~~~l~~~  407 (473)
                        |-|..|-..+. ...+.||+.|.+.+   .|...+..  ||... |+|+. ...++...+.+..+...
T Consensus       158 --lYnlfDisqs~-r~Piciig~Ttrld~lE~LEKRVKS--RFshr~I~m~~~~~l~~yv~l~r~ll~v~  222 (408)
T KOG2228|consen  158 --LYNLFDISQSA-RAPICIIGVTTRLDILELLEKRVKS--RFSHRVIFMLPSLPLGDYVDLYRKLLSVP  222 (408)
T ss_pred             --HHHHHHHHhhc-CCCeEEEEeeccccHHHHHHHHHHh--hcccceeeccCCCChHHHHHHHHHHhcCC
Confidence              44666654432 34578888777654   44456666  88644 77765 46788889999888543

>smart00072 GuKc Guanylate kinase homologues

Probab=97.33  E-value=0.0011  Score=61.56  Aligned_cols=24  Identities=38%  Similarity=0.711  Sum_probs=22.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +-++|.||+|+||+++++.|+...
T Consensus         3 r~ivl~Gpsg~GK~tl~~~L~~~~   26 (184)
T smart00072        3 RPIVLSGPSGVGKGTLLAELIQEI   26 (184)
T ss_pred             cEEEEECCCCCCHHHHHHHHHhcC
Confidence            568999999999999999999986

Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=97.33  E-value=0.00073  Score=64.45  Aligned_cols=40  Identities=23%  Similarity=0.207  Sum_probs=30.2

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---C------CceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---N------FDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~------~~~~~l~~~~  288 (473)
                      |.+...-+.|+||||+|||+++..+|...   +      ..++.++...
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            56667779999999999999999887653   2      5556655543

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.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.31  E-value=0.006  Score=70.07  Aligned_cols=150  Identities=17%  Similarity=0.134  Sum_probs=84.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc--------------------------------h----HHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN--------------------------------S----DLR  296 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~--------------------------------~----~l~  296 (473)
                      .+-++++||+|.|||+++...+...+ ++.-+++..-.++                                .    -+.
T Consensus        32 ~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  110 (903)
T PRK04841         32 YRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFA  110 (903)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHH
Confidence            45689999999999999999887766 5544443211000                                0    011


Q ss_pred             HHHHH---hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCC
Q 012016          297 TLLVA---TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLD  373 (473)
Q Consensus       297 ~l~~~---~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld  373 (473)
                      .++..   ...|.+|||||++.+-+                 ......+..|+..+       +.+..+|+|+.....++
T Consensus       111 ~~~~~l~~~~~~~~lvlDD~h~~~~-----------------~~~~~~l~~l~~~~-------~~~~~lv~~sR~~~~~~  166 (903)
T PRK04841        111 QLFIELADWHQPLYLVIDDYHLITN-----------------PEIHEAMRFFLRHQ-------PENLTLVVLSRNLPPLG  166 (903)
T ss_pred             HHHHHHhcCCCCEEEEEeCcCcCCC-----------------hHHHHHHHHHHHhC-------CCCeEEEEEeCCCCCCc
Confidence            22222   24678999999997621                 11233444444432       23355555665422222


Q ss_pred             c-cccCCCceeeEEEeC----CCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHHHH
Q 012016          374 P-ALLRPGRMDVHVHMS----YCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQ  432 (473)
Q Consensus       374 ~-aLlrpgRfd~~I~~~----~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~~~  432 (473)
                      - .+...   +..+++.    ..+.++-..++...++..  ...++++.+.+.++--|.-+...
T Consensus       167 ~~~l~~~---~~~~~l~~~~l~f~~~e~~~ll~~~~~~~--~~~~~~~~l~~~t~Gwp~~l~l~  225 (903)
T PRK04841        167 IANLRVR---DQLLEIGSQQLAFDHQEAQQFFDQRLSSP--IEAAESSRLCDDVEGWATALQLI  225 (903)
T ss_pred             hHhHHhc---CcceecCHHhCCCCHHHHHHHHHhccCCC--CCHHHHHHHHHHhCChHHHHHHH
Confidence            1 11111   2234444    568888888887766543  34567777777776666655433

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.30  E-value=0.00022  Score=62.94  Aligned_cols=43  Identities=28%  Similarity=0.524  Sum_probs=33.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRT  297 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~  297 (473)
                      ..++|+.|-||||||+++..+|..++++.+.++  ++..+.++..
T Consensus         7 ~PNILvtGTPG~GKstl~~~lae~~~~~~i~is--d~vkEn~l~~   49 (176)
T KOG3347|consen    7 RPNILVTGTPGTGKSTLAERLAEKTGLEYIEIS--DLVKENNLYE   49 (176)
T ss_pred             CCCEEEeCCCCCCchhHHHHHHHHhCCceEehh--hHHhhhcchh
Confidence            458999999999999999999999999887654  4433444433

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=97.30  E-value=0.0013  Score=57.63  Aligned_cols=28  Identities=29%  Similarity=0.427  Sum_probs=24.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      ..-++|.|+.|+|||++++++++.++.+
T Consensus        22 ~~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        22 GTVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            4568999999999999999999999643

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.30  E-value=0.0035  Score=65.81  Aligned_cols=63  Identities=21%  Similarity=0.307  Sum_probs=41.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccccccc----------------------CchHHHHHHHHhccC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTELR----------------------SNSDLRTLLVATANR  305 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~~~----------------------~~~~l~~l~~~~~~~  305 (473)
                      ++.++|.||+|+|||+++..||..+     +..+..+++....                      +..++...+......
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~~~  300 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLRDC  300 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhCCC
Confidence            4568999999999999999888754     3456655554321                      123344444444556


Q ss_pred             ceEEEecccc
Q 012016          306 SILVVEDIDC  315 (473)
Q Consensus       306 sIL~iDdiD~  315 (473)
                      .+|+||....
T Consensus       301 DlVlIDt~G~  310 (424)
T PRK05703        301 DVILIDTAGR  310 (424)
T ss_pred             CEEEEeCCCC
Confidence            7788887643

>PTZ00202 tuzin; Provisional

Probab=97.29  E-value=0.017  Score=60.12  Aligned_cols=76  Identities=22%  Similarity=0.298  Sum_probs=52.1

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS  293 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~  293 (473)
                      -|....+++|.+.....+...+..          .....++-+.|.||+|||||++++.+...++.+.+.+|...  ...
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~----------~d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNprg--~eE  324 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRR----------LDTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVRG--TED  324 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhc----------cCCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCCC--HHH
Confidence            345566788877666665444331          12223457899999999999999999999998888888773  233


Q ss_pred             HHHHHHHH
Q 012016          294 DLRTLLVA  301 (473)
Q Consensus       294 ~l~~l~~~  301 (473)
                      -++.++..
T Consensus       325 lLr~LL~A  332 (550)
T PTZ00202        325 TLRSVVKA  332 (550)
T ss_pred             HHHHHHHH
Confidence            44444443

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=97.29  E-value=0.00025  Score=65.84  Aligned_cols=30  Identities=30%  Similarity=0.525  Sum_probs=27.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++|.||||+|||++++.||..+++.++.++
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~~   31 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHISTG   31 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEECc
Confidence            799999999999999999999998877653

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.28  E-value=0.00028  Score=64.37  Aligned_cols=33  Identities=27%  Similarity=0.457  Sum_probs=30.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ..++|.|+||+|||++++.+|..+|+++++.|.
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~lg~~~~d~D~   35 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQALGYRFVDTDQ   35 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEEccH
Confidence            358999999999999999999999999998764

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.25  E-value=0.00025  Score=63.52  Aligned_cols=28  Identities=25%  Similarity=0.526  Sum_probs=26.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      +-+.|||||||||+++-||+++|++++.
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vs   30 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVS   30 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceee
Confidence            5688999999999999999999999985

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=97.24  E-value=0.0015  Score=62.51  Aligned_cols=37  Identities=27%  Similarity=0.342  Sum_probs=26.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLE  285 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~  285 (473)
                      |.|....+|+.||||||||+|+..++...    |.+++.++
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs   55 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVS   55 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEE
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEE
Confidence            67777889999999999999988655322    55555444

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 ....

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.24  E-value=0.0013  Score=60.28  Aligned_cols=63  Identities=19%  Similarity=0.203  Sum_probs=44.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-----------------------chHHHHHHHHhccCceEEEec
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-----------------------NSDLRTLLVATANRSILVVED  312 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-----------------------~~~l~~l~~~~~~~sIL~iDd  312 (473)
                      +|+.||||+|||+++..++...+.+++++......+                       ...+.+.+...+.+.+|+||-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~~~~d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLIDc   81 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATAEAFDDEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLIDC   81 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEccCcCCHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEEc
Confidence            689999999999999999988777777766554321                       123444443333466899998


Q ss_pred             cccccc
Q 012016          313 IDCTID  318 (473)
Q Consensus       313 iD~l~~  318 (473)
                      +.....
T Consensus        82 lt~~~~   87 (169)
T cd00544          82 LTLWVT   87 (169)
T ss_pred             HhHHHH
Confidence            887653

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.

>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=97.24  E-value=0.00083  Score=60.40  Aligned_cols=26  Identities=42%  Similarity=0.629  Sum_probs=23.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||+|+|||+|+++|+..+.
T Consensus        25 g~~~~i~G~nGsGKStll~~l~g~~~   50 (157)
T cd00267          25 GEIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45789999999999999999999874

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.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.24  E-value=0.0042  Score=63.96  Aligned_cols=58  Identities=22%  Similarity=0.316  Sum_probs=37.2

Q ss_pred             hHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       225 ~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      .+.++.+.+.+...+.....+    ...++-++|.||+|+|||+++..||..+   +..+..+++
T Consensus       217 ~~~~~~l~~~l~~~l~~~~~~----~~~~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~a  277 (436)
T PRK11889        217 EEVIEYILEDMRSHFNTENVF----EKEVQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITT  277 (436)
T ss_pred             HHHHHHHHHHHHHHhcccccc----ccCCcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEec
Confidence            345556666655555432211    1124679999999999999999999877   344444443

>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=97.23  E-value=0.0077  Score=58.16  Aligned_cols=125  Identities=17%  Similarity=0.283  Sum_probs=75.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC---ceEEcccccc---------------cCchHHH-----------HHHHHh-
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF---DVYDLELTEL---------------RSNSDLR-----------TLLVAT-  302 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~---~~~~l~~~~~---------------~~~~~l~-----------~l~~~~-  302 (473)
                      +-.+.+.||+|||||+++..+-..+..   .++.+....-               .....+.           +..... 
T Consensus        13 ~fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~~k~~   92 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYIKKSP   92 (241)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHhhhhc
Confidence            346899999999999999998887732   2222211000               0111111           111111 


Q ss_pred             ----ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          303 ----ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       303 ----~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                          ..+.+|+|||+..-                   ......+..+++.  |-    --++.+|+++...-.|||.++.
T Consensus        93 ~~k~~~~~LiIlDD~~~~-------------------~~k~~~l~~~~~~--gR----H~~is~i~l~Q~~~~lp~~iR~  147 (241)
T PF04665_consen   93 QKKNNPRFLIILDDLGDK-------------------KLKSKILRQFFNN--GR----HYNISIIFLSQSYFHLPPNIRS  147 (241)
T ss_pred             ccCCCCCeEEEEeCCCCc-------------------hhhhHHHHHHHhc--cc----ccceEEEEEeeecccCCHHHhh
Confidence                12689999997421                   1113345666642  21    1247788888888999999876


Q ss_pred             CCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          379 PGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       379 pgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                        =++.++-++ -+......|++.+..
T Consensus       148 --n~~y~i~~~-~s~~dl~~i~~~~~~  171 (241)
T PF04665_consen  148 --NIDYFIIFN-NSKRDLENIYRNMNI  171 (241)
T ss_pred             --cceEEEEec-CcHHHHHHHHHhccc
Confidence              677777776 467777777777643

This is thought to be an ATPase involved in viral DNA packaging [].

>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=97.22  E-value=0.0014  Score=61.60  Aligned_cols=25  Identities=40%  Similarity=0.604  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |+-++|.||+|+|||+.+.-||.++
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~   25 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARL   25 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHH
Confidence            4568999999999999999999877

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 ....

>PRK06547 hypothetical protein; Provisional

Probab=97.22  E-value=0.00048  Score=63.32  Aligned_cols=33  Identities=30%  Similarity=0.496  Sum_probs=29.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-|++.||+|+|||++++.+++.++.+++.++
T Consensus        15 ~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         15 MITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            567899999999999999999999998877655

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.21  E-value=0.0016  Score=64.21  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=23.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .++++.||+|+|||+|+++++..+.
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccC
Confidence            5899999999999999999999883

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.

>PLN02674 adenylate kinase

Probab=97.21  E-value=0.0014  Score=63.51  Aligned_cols=31  Identities=23%  Similarity=0.456  Sum_probs=27.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      ...++|.||||+||+++++.||..+++..+.
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~~~~his   61 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEYCLCHLA   61 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHcCCcEEc
Confidence            4569999999999999999999999876554

>PRK06762 hypothetical protein; Provisional

Probab=97.21  E-value=0.00032  Score=63.64  Aligned_cols=34  Identities=15%  Similarity=0.260  Sum_probs=28.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      +.-++|.|+||+|||++++.+++.++..++.++.
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~~   35 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERLGRGTLLVSQ   35 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEecH
Confidence            3568999999999999999999999655655553

>PRK14530 adenylate kinase; Provisional

Probab=97.20  E-value=0.00036  Score=66.34  Aligned_cols=31  Identities=26%  Similarity=0.435  Sum_probs=27.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ..++|.||||+|||++++.||..++++++..
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            3589999999999999999999999887754

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=97.19  E-value=0.0012  Score=64.87  Aligned_cols=39  Identities=21%  Similarity=0.117  Sum_probs=31.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      |.+....++++||||||||+++..+|...   |.++++++..
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            56767779999999999999998776543   6677777765

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=97.19  E-value=0.0014  Score=66.67  Aligned_cols=26  Identities=35%  Similarity=0.579  Sum_probs=22.2

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +|+|++|||.-|||||+|.-..-..+
T Consensus       113 ~PkGlYlYG~VGcGKTmLMDlFy~~~  138 (467)
T KOG2383|consen  113 PPKGLYLYGSVGCGKTMLMDLFYDAL  138 (467)
T ss_pred             CCceEEEecccCcchhHHHHHHhhcC
Confidence            48999999999999999998766443

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=97.19  E-value=0.0018  Score=72.59  Aligned_cols=126  Identities=20%  Similarity=0.307  Sum_probs=80.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEcccccccC--------chHHHHHHHHh---ccCceEEEe
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLELTELRS--------NSDLRTLLVAT---ANRSILVVE  311 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~~~~~~--------~~~l~~l~~~~---~~~sIL~iD  311 (473)
                      +++-+|.|.||+|||.++.-+|+..          +..++.++...+..        +..+..++...   ..+.||+||
T Consensus       208 k~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfig  287 (898)
T KOG1051|consen  208 KNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLG  287 (898)
T ss_pred             CCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEec
Confidence            4688999999999999999999876          34556666654421        34555666543   367899999


Q ss_pred             ccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC-----CCCCccccCCCceeeEE
Q 012016          312 DIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK-----EKLDPALLRPGRMDVHV  386 (473)
Q Consensus       312 diD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-----~~ld~aLlrpgRfd~~I  386 (473)
                      |++.+....             .. ........+|..+-.   .  ++.-+|+||..-     -.=||+|-|  ||+. +
T Consensus       288 elh~lvg~g-------------~~-~~~~d~~nlLkp~L~---r--g~l~~IGatT~e~Y~k~iekdPalEr--rw~l-~  345 (898)
T KOG1051|consen  288 ELHWLVGSG-------------SN-YGAIDAANLLKPLLA---R--GGLWCIGATTLETYRKCIEKDPALER--RWQL-V  345 (898)
T ss_pred             ceeeeecCC-------------Cc-chHHHHHHhhHHHHh---c--CCeEEEecccHHHHHHHHhhCcchhh--Ccce-e
Confidence            999987511             11 112233334443322   1  236677755432     234899999  9984 6


Q ss_pred             EeCCCCHHHHHHHH
Q 012016          387 HMSYCTPSGFKLLA  400 (473)
Q Consensus       387 ~~~~p~~~~r~~l~  400 (473)
                      .++.|+.+.-..++
T Consensus       346 ~v~~pS~~~~~~iL  359 (898)
T KOG1051|consen  346 LVPIPSVENLSLIL  359 (898)
T ss_pred             EeccCcccchhhhh
Confidence            78899876533333

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.18  E-value=0.00081  Score=61.09  Aligned_cols=26  Identities=27%  Similarity=0.392  Sum_probs=23.1

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +...+.|.||+|+|||+|++.|+..+
T Consensus        25 ~Ge~~~l~G~nGsGKSTLl~~i~G~~   50 (163)
T cd03216          25 RGEVHALLGENGAGKSTLMKILSGLY   50 (163)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            34568999999999999999999876

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.

>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=97.17  E-value=0.0014  Score=60.58  Aligned_cols=65  Identities=17%  Similarity=0.213  Sum_probs=38.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc--eEEccc---ccc-----cCchHHHHHH---HHhccCceEEEecccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD--VYDLEL---TEL-----RSNSDLRTLL---VATANRSILVVEDIDCTI  317 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~--~~~l~~---~~~-----~~~~~l~~l~---~~~~~~sIL~iDdiD~l~  317 (473)
                      ..-+.|.||.|+|||||++.|+..+...  -+.++.   ..+     .+...-+++-   .-+.+|.++++||--.-+
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~~~p~lllLDEPts~L  102 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAYL  102 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHhcCCCEEEEECCcccC
Confidence            4468899999999999999999976211  011111   101     1112222221   123489999999986544

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.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=97.17  E-value=0.00036  Score=66.04  Aligned_cols=22  Identities=45%  Similarity=0.842  Sum_probs=17.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++.||||||||+++.+++..+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHh
Confidence            8999999999998777777666

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=97.17  E-value=0.00089  Score=67.62  Aligned_cols=66  Identities=27%  Similarity=0.388  Sum_probs=48.7

Q ss_pred             Ccc-ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-CCceEEcccccc
Q 012016          217 TFE-TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLELTEL  289 (473)
Q Consensus       217 ~f~-~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~~~~~  289 (473)
                      .|+ ++.|.++..+++++++...-.+.       -.-++-+||.||+|+|||++++.|.+.+ .+++|.+..+.+
T Consensus        58 ~f~~~~~G~~~~i~~lV~~fk~AA~g~-------~~~krIl~L~GPvg~GKSsl~~~Lk~~le~y~~Y~l~~~Pm  125 (358)
T PF08298_consen   58 FFEDEFYGMEETIERLVNYFKSAAQGL-------EERKRILLLLGPVGGGKSSLAELLKRGLEEYPIYTLKGCPM  125 (358)
T ss_pred             CccccccCcHHHHHHHHHHHHHHHhcc-------CccceEEEEECCCCCCHHHHHHHHHHHhheEEEEEecCCcc
Confidence            355 78898888888877665443321       2335689999999999999999999988 457777654444

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK08233 hypothetical protein; Provisional

Probab=97.17  E-value=0.0018  Score=59.36  Aligned_cols=34  Identities=15%  Similarity=0.197  Sum_probs=26.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC-CceEEcccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN-FDVYDLELT  287 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~-~~~~~l~~~  287 (473)
                      .-+.+.|+||+||||+++.|+..++ ..++..+..
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~~l~~~~~~~~d~~   38 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKLKNSKALYFDRY   38 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCCCCceEEECCE
Confidence            3477889999999999999999985 445544443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.16  E-value=0.002  Score=66.19  Aligned_cols=23  Identities=35%  Similarity=0.632  Sum_probs=21.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcC
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .+|.||||+|||+|++.|++...
T Consensus       172 ~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        172 GLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             EEEeCCCCCChhHHHHHHHHHHH
Confidence            78999999999999999999774

>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=97.16  E-value=0.0016  Score=57.97  Aligned_cols=62  Identities=24%  Similarity=0.321  Sum_probs=40.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC-----------ceEEcccccccCchHHHHHHH---HhccCceEEEecccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF-----------DVYDLELTELRSNSDLRTLLV---ATANRSILVVEDIDCTI  317 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~-----------~~~~l~~~~~~~~~~l~~l~~---~~~~~sIL~iDdiD~l~  317 (473)
                      ...+.|.||+|+|||+|+++|+..+..           .+..+.  .+ +....+++..   -+.+|.++++||-..-+
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~~i~~~~--~l-S~G~~~rv~laral~~~p~illlDEP~~~L  101 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFE--QL-SGGEKMRLALAKLLLENPNLLLLDEPTNHL  101 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCeEEEEEEc--cC-CHHHHHHHHHHHHHhcCCCEEEEeCCccCC
Confidence            456899999999999999999998731           111111  01 2223333322   23589999999987544

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.15  E-value=0.0022  Score=62.04  Aligned_cols=37  Identities=30%  Similarity=0.246  Sum_probs=27.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh-c--CCceEEcc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY-L--NFDVYDLE  285 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~-l--~~~~~~l~  285 (473)
                      |.+....+|++||||||||+++..++.+ +  |.+++.++
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs   56 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVA   56 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEE
Confidence            6777888999999999999998765543 2  44554444

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.

>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=97.15  E-value=0.002  Score=60.59  Aligned_cols=63  Identities=21%  Similarity=0.320  Sum_probs=39.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh-c----CCce--------------EEcccccc---------cCchHHHHHHHHhccC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY-L----NFDV--------------YDLELTEL---------RSNSDLRTLLVATANR  305 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~-l----~~~~--------------~~l~~~~~---------~~~~~l~~l~~~~~~~  305 (473)
                      .-++|.||.|+|||++++.++.- +    |..+              ..+...+.         .....+..++.....+
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~~~~~~~~g~~~~~~~~~i~~~dqi~~~~~~~d~i~~~~s~~~~e~~~l~~i~~~~~~~  109 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPR  109 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHHHHHHHHcCCCccccccccCCcCEEEEEecCcccccCCceeHHHHHHHHHHHHHhccCC
Confidence            46999999999999999999932 1    2111              11111110         0112344555555689


Q ss_pred             ceEEEeccccc
Q 012016          306 SILVVEDIDCT  316 (473)
Q Consensus       306 sIL~iDdiD~l  316 (473)
                      .++++||.-.-
T Consensus       110 ~llllDEp~~g  120 (202)
T cd03243         110 SLVLIDELGRG  120 (202)
T ss_pred             eEEEEecCCCC
Confidence            99999999654

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

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=97.14  E-value=0.00041  Score=71.25  Aligned_cols=44  Identities=27%  Similarity=0.593  Sum_probs=38.3

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++++..+++.+++.|.+.                  .+|+|+.||||.|||++|+|+|.++
T Consensus       244 ~~ledY~L~dkl~eRL~er------------------aeGILIAG~PGaGKsTFaqAlAefy  287 (604)
T COG1855         244 LSLEDYGLSDKLKERLEER------------------AEGILIAGAPGAGKSTFAQALAEFY  287 (604)
T ss_pred             echhhcCCCHHHHHHHHhh------------------hcceEEecCCCCChhHHHHHHHHHH
Confidence            4789999999888887542                  3599999999999999999999988

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.14  E-value=0.00039  Score=63.85  Aligned_cols=34  Identities=26%  Similarity=0.301  Sum_probs=28.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .+-++|.||||+|||+++++++..++.+++.++.
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~~~~~~~~~~   35 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVLAEPWLHFGV   35 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhhCCCccccCc
Confidence            3568999999999999999999998877665443

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>PRK04296 thymidine kinase; Provisional

Probab=97.14  E-value=0.0027  Score=59.28  Aligned_cols=30  Identities=23%  Similarity=0.300  Sum_probs=23.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l  284 (473)
                      -.+++||||+|||+++..++..+   +..++.+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            47899999999999888877765   5555544

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.14  E-value=0.0025  Score=62.68  Aligned_cols=85  Identities=21%  Similarity=0.288  Sum_probs=51.7

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccc-cc--
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT-EL--  289 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~-~~--  289 (473)
                      .+++++...++..+.+.+.    +..          ....+++.||+|+|||++++++..++.   ..++.++-. ++  
T Consensus        57 ~~l~~lg~~~~~~~~l~~~----~~~----------~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~~  122 (264)
T cd01129          57 LDLEKLGLKPENLEIFRKL----LEK----------PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQI  122 (264)
T ss_pred             CCHHHcCCCHHHHHHHHHH----Hhc----------CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceecC
Confidence            5688888777665554222    211          123589999999999999999988773   334443211 11  


Q ss_pred             --------cC--chHHHHHHHHh--ccCceEEEeccc
Q 012016          290 --------RS--NSDLRTLLVAT--ANRSILVVEDID  314 (473)
Q Consensus       290 --------~~--~~~l~~l~~~~--~~~sIL~iDdiD  314 (473)
                              ..  ...+.+.+..+  .+|.+|++.|+.
T Consensus       123 ~~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR  159 (264)
T cd01129         123 PGINQVQVNEKAGLTFARGLRAILRQDPDIIMVGEIR  159 (264)
T ss_pred             CCceEEEeCCcCCcCHHHHHHHHhccCCCEEEeccCC
Confidence                    10  11233444333  378999999994

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.

>TIGR03263 guanyl_kin guanylate kinase

Probab=97.13  E-value=0.0021  Score=59.01  Aligned_cols=25  Identities=32%  Similarity=0.444  Sum_probs=22.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      -++|.||+|+|||++++.|++.+..
T Consensus         3 ii~l~G~~GsGKsTl~~~L~~~~~~   27 (180)
T TIGR03263         3 LIVISGPSGVGKSTLVKALLEEDPN   27 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHccCcc
Confidence            4899999999999999999997754

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.12  E-value=0.0015  Score=62.73  Aligned_cols=53  Identities=15%  Similarity=0.104  Sum_probs=37.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEcccccccCchHHHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLELTELRSNSDLRTLLVA  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~~~~~~~~~l~~l~~~  301 (473)
                      |.+...-+.|+||||||||+++..+|...         +..++.++...-.....+.++...
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~~~~~   76 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQIAER   76 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHHHHHH
Confidence            56666779999999999999999887442         256777776654344555555443

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 .

>PRK14528 adenylate kinase; Provisional

Probab=97.11  E-value=0.00049  Score=63.98  Aligned_cols=30  Identities=23%  Similarity=0.512  Sum_probs=27.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .+++.||||+|||++++.+|..++++.+.+
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~~~~~is~   32 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERLSIPQIST   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCeeeC
Confidence            489999999999999999999999887654

>PF13479 AAA_24: AAA domain

Probab=97.10  E-value=0.0012  Score=62.85  Aligned_cols=60  Identities=32%  Similarity=0.495  Sum_probs=38.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc-------------ccCchHHHHHHHHh----ccCceEEEeccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE-------------LRSNSDLRTLLVAT----ANRSILVVEDIDCT  316 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~-------------~~~~~~l~~l~~~~----~~~sIL~iDdiD~l  316 (473)
                      -.++||||||+|||+++..+-+-+   +++++.+.             +.+-..+.+.+...    ..-..||||-++.+
T Consensus         4 ~~~lIyG~~G~GKTt~a~~~~k~l---~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y~tiVIDsis~~   80 (213)
T PF13479_consen    4 IKILIYGPPGSGKTTLAASLPKPL---FIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEEDEADYDTIVIDSISWL   80 (213)
T ss_pred             eEEEEECCCCCCHHHHHHhCCCeE---EEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhccCCCCEEEEECHHHH
Confidence            368999999999999999883322   22333321             12334555655443    24579999988866

>PRK02496 adk adenylate kinase; Provisional

Probab=97.10  E-value=0.00046  Score=63.83  Aligned_cols=29  Identities=28%  Similarity=0.566  Sum_probs=26.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +++.||||+|||++++.||..++++.+..
T Consensus         4 i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          4 LIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            88999999999999999999999887654

>PF13245 AAA_19: Part of AAA domain

Probab=97.09  E-value=0.00075  Score=53.31  Aligned_cols=33  Identities=42%  Similarity=0.633  Sum_probs=22.3

Q ss_pred             eeEEeCCCCCCHH-HHHHHHHHhc------CCceEEcccc
Q 012016          255 GYLLYGPPGTGKS-SLIAAMANYL------NFDVYDLELT  287 (473)
Q Consensus       255 g~LL~GPpGtGKT-~la~alA~~l------~~~~~~l~~~  287 (473)
                      -+++.|||||||| ++++.++..+      +..+..+..+
T Consensus        12 ~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t   51 (76)
T PF13245_consen   12 LFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPT   51 (76)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCC
Confidence            4566999999999 4555666555      4456665544

>PRK13808 adenylate kinase; Provisional

Probab=97.09  E-value=0.0021  Score=64.94  Aligned_cols=29  Identities=24%  Similarity=0.488  Sum_probs=26.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      |+|.||||+|||+++..||..++++.+.+
T Consensus         3 Iiv~GpPGSGK~T~a~~LA~~ygl~~is~   31 (333)
T PRK13808          3 LILLGPPGAGKGTQAQRLVQQYGIVQLST   31 (333)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceecc
Confidence            89999999999999999999998866654

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=97.08  E-value=0.0028  Score=60.66  Aligned_cols=63  Identities=19%  Similarity=0.330  Sum_probs=41.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH-hc----CCc---------eE-----Ecccc-ccc--------CchHHHHHHHHhcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN-YL----NFD---------VY-----DLELT-ELR--------SNSDLRTLLVATAN  304 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~-~l----~~~---------~~-----~l~~~-~~~--------~~~~l~~l~~~~~~  304 (473)
                      .+.++|.||.|+|||++.+.++. .+    |..         ++     .+... ++.        .-.++..++..+.+
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~  110 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTS  110 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCccccccccchHHHHHHHHHHHHHhCCC
Confidence            35689999999999999999988 22    211         11     11111 111        11345666777788


Q ss_pred             CceEEEecccc
Q 012016          305 RSILVVEDIDC  315 (473)
Q Consensus       305 ~sIL~iDdiD~  315 (473)
                      +++++|||+..
T Consensus       111 ~sLvllDE~~~  121 (222)
T cd03287         111 RSLVILDELGR  121 (222)
T ss_pred             CeEEEEccCCC
Confidence            99999999964

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

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=97.08  E-value=0.002  Score=60.54  Aligned_cols=21  Identities=24%  Similarity=0.510  Sum_probs=19.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMA  274 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA  274 (473)
                      +.++|.||.|+|||++.+.++
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            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

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.08  E-value=0.00046  Score=63.64  Aligned_cols=30  Identities=20%  Similarity=0.377  Sum_probs=26.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -+++.||||+||||+++.++..+|+..+..
T Consensus         5 ii~i~G~~GsGKsTl~~~l~~~~g~~~~~~   34 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQCEKIVEKYGFTHLST   34 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            588999999999999999999998776544

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=97.07  E-value=0.0029  Score=58.29  Aligned_cols=25  Identities=32%  Similarity=0.632  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-.+.+.||.|+|||||.+.+|.-+
T Consensus        28 Ge~~~i~G~NG~GKTtLLRilaGLl   52 (209)
T COG4133          28 GEALQITGPNGAGKTTLLRILAGLL   52 (209)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHccc
Confidence            3458999999999999999999877

>PF00519 PPV_E1_C: Papillomavirus helicase; InterPro: IPR001177 Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species

Probab=97.07  E-value=0.00083  Score=68.30  Aligned_cols=113  Identities=23%  Similarity=0.256  Sum_probs=66.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccC
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIA  328 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~  328 (473)
                      |+|.+..++|||||+||||+++-.+-+.++-.++..--+.    +  +-.+.-....-|-+|||+-.-.           
T Consensus       258 g~PKKnClvi~GPPdTGKS~F~~SLi~Fl~GkViSf~Ns~----S--hFWLqPL~d~Ki~llDDAT~~c-----------  320 (432)
T PF00519_consen  258 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSK----S--HFWLQPLADAKIALLDDATYPC-----------  320 (432)
T ss_dssp             TBTTSSEEEEESSCCCSHHHHHHHHHHHHTSEEE-GGGTT----S--CGGGGGGCT-SSEEEEEE-HHH-----------
T ss_pred             CCCcccEEEEECCCCCchhHHHHHHHHHhCCEEEEecCCC----C--cccccchhcCcEEEEcCCcccH-----------
Confidence            7788899999999999999999999999988877532211    1  1123344566789999985321           


Q ss_pred             CCCCCCccchhHHH-HHHHHHhcccccC----CCC-----ceEEEEecCCCCCCCccc---cCCCceeeEEEeCCC
Q 012016          329 GEGEGPIQQNKVTL-SGFLNFIDGLWSS----CGD-----ERIIVFTTNHKEKLDPAL---LRPGRMDVHVHMSYC  391 (473)
Q Consensus       329 ~~~~~~~~~~~~~l-s~LL~~ldg~~~~----~~~-----~~iiI~tTN~~~~ld~aL---lrpgRfd~~I~~~~p  391 (473)
                                -.-+ ..|-|.+||-.-+    ...     ---++.|||.-=.-++.+   .+  |+ ..++|+.|
T Consensus       321 ----------W~Y~D~ylRNaLDGN~vsiD~KHkap~Qik~PPLlITsN~dv~~~~~~~YLhS--Ri-~~f~F~n~  383 (432)
T PF00519_consen  321 ----------WDYIDTYLRNALDGNPVSIDCKHKAPVQIKCPPLLITSNIDVKKDDRWKYLHS--RI-TCFEFPNP  383 (432)
T ss_dssp             ----------HHHHHHHTHHHHCTSEEEEEESSSEEEEEE---EEEEESS-TTTSCCCHHHCT--TE-EEEE--S-
T ss_pred             ----------HHHHHHHHHhccCCCeeeeeccCCCceEeecCceEEecCCCCCcchhhhhhhh--eE-EEEEcCCc
Confidence                      1222 3355888874110    000     013677888654444443   35  77 46777765

The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication []. It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins []. The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase []. In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other []. Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity []. The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1TUE_K 1R9W_A 2V9P_B 2GXA_I 1KSX_J 1KSY_A 1F08_B.

>PLN02199 shikimate kinase

Probab=97.06  E-value=0.0011  Score=65.55  Aligned_cols=34  Identities=26%  Similarity=0.486  Sum_probs=31.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .++++|.|++|+|||++++.+|+.+++++++.|.
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD~  135 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCDT  135 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEehHH
Confidence            4689999999999999999999999999998873

>PRK00300 gmk guanylate kinase; Provisional

Probab=97.04  E-value=0.007  Score=56.77  Aligned_cols=27  Identities=33%  Similarity=0.422  Sum_probs=24.3

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ++.-+.|.||+|+|||+|++.|+..++
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            456799999999999999999999876

>PTZ00088 adenylate kinase 1; Provisional

Probab=97.04  E-value=0.00061  Score=65.55  Aligned_cols=31  Identities=23%  Similarity=0.537  Sum_probs=28.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++|.||||+|||++++.+|+.++++++.++
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g~~~is~g   38 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKENLKHINMG   38 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEECC
Confidence            3999999999999999999999998887665

>PLN02200 adenylate kinase family protein

Probab=97.02  E-value=0.00073  Score=65.26  Aligned_cols=30  Identities=20%  Similarity=0.361  Sum_probs=26.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      +.-+++.||||+|||++++.||..+|++.+
T Consensus        43 ~~ii~I~G~PGSGKsT~a~~La~~~g~~hi   72 (234)
T PLN02200         43 PFITFVLGGPGSGKGTQCEKIVETFGFKHL   72 (234)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCeEE
Confidence            456899999999999999999999987653

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=97.02  E-value=0.0028  Score=71.54  Aligned_cols=63  Identities=13%  Similarity=0.323  Sum_probs=39.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc-----CCc----------eEEcccccccC--------------chHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL-----NFD----------VYDLELTELRS--------------NSDLRTLLVATA  303 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l-----~~~----------~~~l~~~~~~~--------------~~~l~~l~~~~~  303 (473)
                      .+.++|.||.+.|||++++.++-..     |.+          +++--...+.+              ...+..++..+.
T Consensus       327 ~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~Il~~~~  406 (782)
T PRK00409        327 KTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKAD  406 (782)
T ss_pred             ceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccceEEEecCCccchhhchhHHHHHHHHHHHHHHhCC
Confidence            3578999999999999999887432     322          22111111111              122334455556


Q ss_pred             cCceEEEecccc
Q 012016          304 NRSILVVEDIDC  315 (473)
Q Consensus       304 ~~sIL~iDdiD~  315 (473)
                      .+++++|||+..
T Consensus       407 ~~sLvLlDE~~~  418 (782)
T PRK00409        407 KNSLVLFDELGA  418 (782)
T ss_pred             cCcEEEecCCCC
Confidence            899999999964

>TIGR01351 adk adenylate kinases

Probab=97.00  E-value=0.00065  Score=64.34  Aligned_cols=29  Identities=28%  Similarity=0.528  Sum_probs=26.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +++.||||+|||++++.||..+|++.+..
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            78999999999999999999999877654

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>TIGR01069 mutS2 MutS2 family protein

Probab=97.00  E-value=0.0027  Score=71.47  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=21.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      +.++|.||.|+|||++.+.++..
T Consensus       323 ~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       323 RVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             eEEEEECCCCCCchHHHHHHHHH
Confidence            57999999999999999999876

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.98  E-value=0.00076  Score=64.12  Aligned_cols=29  Identities=28%  Similarity=0.498  Sum_probs=26.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      |+++||||+|||++++.||..++++.+.+
T Consensus         3 I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            89999999999999999999999887765

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.97  E-value=0.0026  Score=58.14  Aligned_cols=26  Identities=27%  Similarity=0.461  Sum_probs=23.3

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +..-+.|.||+|+|||+|+++|+..+
T Consensus        27 ~G~~~~l~G~nGsGKstLl~~i~G~~   52 (171)
T cd03228          27 PGEKVAIVGPSGSGKSTLLKLLLRLY   52 (171)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            34569999999999999999999986

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.

>PRK06696 uridine kinase; Validated

Probab=96.97  E-value=0.0022  Score=61.33  Aligned_cols=38  Identities=13%  Similarity=0.229  Sum_probs=32.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR  290 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~  290 (473)
                      +.-|.+.|++|+||||+++.|+..|   |.+++.+.+.++.
T Consensus        22 ~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~   62 (223)
T PRK06696         22 PLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFH   62 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecccccc
Confidence            4568999999999999999999999   6778777766654

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.97  E-value=0.001  Score=51.41  Aligned_cols=22  Identities=32%  Similarity=0.525  Sum_probs=20.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +.+.|+||+|||++++++++.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999996

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK13695 putative NTPase; Provisional

Probab=96.94  E-value=0.0063  Score=55.71  Aligned_cols=23  Identities=39%  Similarity=0.742  Sum_probs=20.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++|.|++|+|||++++.+++.+
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999988775

>PRK04182 cytidylate kinase; Provisional

Probab=96.93  E-value=0.0008  Score=61.47  Aligned_cols=30  Identities=27%  Similarity=0.483  Sum_probs=27.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -+.|.|+||||||++++.+|..+|+++++.
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg~~~id~   31 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLGLKHVSA   31 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEecH
Confidence            378999999999999999999999998863

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.93  E-value=0.00071  Score=61.35  Aligned_cols=30  Identities=27%  Similarity=0.525  Sum_probs=27.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      -+++.|.|||||||+++.|+ .+|++++.++
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~lg~~~i~l~   31 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-ELGYKVIELN   31 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-HhCCceeeHH
Confidence            37899999999999999999 9999988765

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.93  E-value=0.0028  Score=58.87  Aligned_cols=61  Identities=13%  Similarity=0.284  Sum_probs=38.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHH-h----cCCce---------E-----Eccccccc---------CchHHHHHHHHhccCce
Q 012016          256 YLLYGPPGTGKSSLIAAMAN-Y----LNFDV---------Y-----DLELTELR---------SNSDLRTLLVATANRSI  307 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~-~----l~~~~---------~-----~l~~~~~~---------~~~~l~~l~~~~~~~sI  307 (473)
                      ++|.||.|+|||++++.++- .    .|..+         +     .+...+..         .-..+..++..+..+++
T Consensus         2 ~~ltG~N~~GKst~l~~i~~~~~la~~G~~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~~l   81 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGLIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATENSL   81 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHHHhCCCeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCCeE
Confidence            68999999999999999983 2    23222         1     11111110         11234455555568999


Q ss_pred             EEEeccccc
Q 012016          308 LVVEDIDCT  316 (473)
Q Consensus       308 L~iDdiD~l  316 (473)
                      +++||...-
T Consensus        82 lllDEp~~g   90 (185)
T smart00534       82 VLLDELGRG   90 (185)
T ss_pred             EEEecCCCC
Confidence            999999754

>PRK14527 adenylate kinase; Provisional

Probab=96.93  E-value=0.00078  Score=62.79  Aligned_cols=32  Identities=25%  Similarity=0.513  Sum_probs=27.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +.-+++.||||+|||++++.+|..+++..+..
T Consensus         6 ~~~i~i~G~pGsGKsT~a~~La~~~~~~~is~   37 (191)
T PRK14527          6 NKVVIFLGPPGAGKGTQAERLAQELGLKKLST   37 (191)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCCCCCc
Confidence            34699999999999999999999998766543

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.93  E-value=0.036  Score=55.79  Aligned_cols=99  Identities=12%  Similarity=0.076  Sum_probs=52.6

Q ss_pred             CceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE-EEecCC---CC--CCCccccC
Q 012016          305 RSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII-VFTTNH---KE--KLDPALLR  378 (473)
Q Consensus       305 ~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii-I~tTN~---~~--~ld~aLlr  378 (473)
                      |.++.||++.+++....-....    ...-+...-.....|++++.|-.+-..+.+++ +.+|..   +.  .++.+|..
T Consensus       157 PVL~avD~~n~l~~~S~Y~~~~----~~~I~~~~L~l~~~f~~~~s~~~~~~nG~~v~~l~~t~~~~~~~~~~l~~~L~~  232 (309)
T PF10236_consen  157 PVLVAVDGFNALFGPSAYRDPD----FKPIHPHDLTLVRLFLDLLSGKRDFKNGAVVTALAATSVSNAPKSPTLPVALGG  232 (309)
T ss_pred             ceEEEehhhHHhhCCccccCCC----CccccHHHhhHHHHHHHHhcCccccCCCeEEEEEeccccccccCCccchhhhcc
Confidence            6788999999998632211110    01112223344555666655443322222332 444332   22  45555553


Q ss_pred             -CCc-----ee-------------eEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          379 -PGR-----MD-------------VHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       379 -pgR-----fd-------------~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                       +++     |.             ..|+++..+.++...++..|....
T Consensus       233 ~~~~~~~dPy~~~d~~~~~~l~~~~~i~v~~~s~~E~~~ll~yy~~~~  280 (309)
T PF10236_consen  233 KEGFPHLDPYVKRDPRVAESLKGVKPIEVPRLSKEEARSLLEYYADSG  280 (309)
T ss_pred             ccCCCCCCCcccccHHHHHHhcCCceEEeCCCCHHHHHHHHHHHHHCC
Confidence             111     11             167899999999999999887643

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).

>PRK09354 recA recombinase A; Provisional

Probab=96.92  E-value=0.0038  Score=63.52  Aligned_cols=70  Identities=14%  Similarity=0.195  Sum_probs=43.7

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHH---H
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLV---A  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~---~  301 (473)
                      |.|..+-+++|||||||||+|+..++...   |...++++...-.                     +.+....++.   .
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            56666779999999999999988665432   5555555543310                     1111111221   2


Q ss_pred             hccCceEEEeccccccc
Q 012016          302 TANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~  318 (473)
                      .....+||||-+-++.+
T Consensus       136 s~~~~lIVIDSvaaL~~  152 (349)
T PRK09354        136 SGAVDLIVVDSVAALVP  152 (349)
T ss_pred             cCCCCEEEEeChhhhcc
Confidence            23578999999998864

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.92  E-value=0.0035  Score=59.28  Aligned_cols=22  Identities=32%  Similarity=0.454  Sum_probs=19.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      +-++|.||.|+|||++++.++.
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5699999999999999999874

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

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.90  E-value=0.00083  Score=60.90  Aligned_cols=30  Identities=27%  Similarity=0.583  Sum_probs=27.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.+.|++|+|||++++.+|+.++++++..+
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~~~~   32 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLISAG   32 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCceecHH
Confidence            789999999999999999999999987653

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.89  E-value=0.0045  Score=63.78  Aligned_cols=24  Identities=33%  Similarity=0.400  Sum_probs=21.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+|+.||+|+|||++++++.+++
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i  173 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHC  173 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            358999999999999999999877

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).

>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=96.89  E-value=0.0038  Score=57.18  Aligned_cols=25  Identities=32%  Similarity=0.586  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||+|+|||+|+++|+..+
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcc
Confidence            3458999999999999999999976

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

>PRK01184 hypothetical protein; Provisional

Probab=96.89  E-value=0.00094  Score=61.69  Aligned_cols=29  Identities=24%  Similarity=0.339  Sum_probs=25.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -++|.||||+||||+++ ++..+|++++..
T Consensus         3 ~i~l~G~~GsGKsT~a~-~~~~~g~~~i~~   31 (184)
T PRK01184          3 IIGVVGMPGSGKGEFSK-IAREMGIPVVVM   31 (184)
T ss_pred             EEEEECCCCCCHHHHHH-HHHHcCCcEEEh
Confidence            47899999999999887 889999888765

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=96.89  E-value=0.024  Score=54.76  Aligned_cols=126  Identities=22%  Similarity=0.219  Sum_probs=70.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCc---eEEccccccc-------------C-------------chHHHHHHHHhccC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFD---VYDLELTELR-------------S-------------NSDLRTLLVATANR  305 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~---~~~l~~~~~~-------------~-------------~~~l~~l~~~~~~~  305 (473)
                      -+.++|+.|||||.+.+|+..-++-+   ++.++...+.             .             ...|.+++..-.++
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            36889999999999999887776422   2233322221             0             12233333344467


Q ss_pred             ceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCcc--------cc
Q 012016          306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPA--------LL  377 (473)
Q Consensus       306 sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~a--------Ll  377 (473)
                      .++++||.+.+..                  ..-..+.-|.|.-++..  ..-.+++|+=.    +|.|.        +.
T Consensus       133 v~l~vdEah~L~~------------------~~le~Lrll~nl~~~~~--~~l~ivL~Gqp----~L~~~lr~~~l~e~~  188 (269)
T COG3267         133 VVLMVDEAHDLND------------------SALEALRLLTNLEEDSS--KLLSIVLIGQP----KLRPRLRLPVLRELE  188 (269)
T ss_pred             eEEeehhHhhhCh------------------hHHHHHHHHHhhccccc--CceeeeecCCc----ccchhhchHHHHhhh
Confidence            9999999998742                  11222222233222211  11123344322    12222        23


Q ss_pred             CCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          378 RPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       378 rpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      .  |++..|++++.+.++-...++..++.
T Consensus       189 ~--R~~ir~~l~P~~~~~t~~yl~~~Le~  215 (269)
T COG3267         189 Q--RIDIRIELPPLTEAETGLYLRHRLEG  215 (269)
T ss_pred             h--eEEEEEecCCcChHHHHHHHHHHHhc
Confidence            4  99988999999999777777766653

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.87  E-value=0.0045  Score=56.89  Aligned_cols=25  Identities=32%  Similarity=0.513  Sum_probs=22.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...+.|.||+|+|||+|+++|+..+
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~   52 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGDL   52 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccC
Confidence            4568999999999999999999976

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.

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.87  E-value=0.00067  Score=58.09  Aligned_cols=22  Identities=32%  Similarity=0.579  Sum_probs=21.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |+|.|+||+||||+++.|+..+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999998

...

>PLN02459 probable adenylate kinase

Probab=96.86  E-value=0.0035  Score=61.21  Aligned_cols=30  Identities=20%  Similarity=0.463  Sum_probs=26.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .++|.||||+|||++++.+|..++++.+..
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~~~~is~   60 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLGVPHIAT   60 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeC
Confidence            488899999999999999999998766543

>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=96.86  E-value=0.01  Score=59.65  Aligned_cols=28  Identities=32%  Similarity=0.319  Sum_probs=24.7

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..+..+-|+||=|+|||++++.+-+.+.
T Consensus        18 ~~~~~IgL~G~WGsGKSs~l~~l~~~L~   45 (325)
T PF07693_consen   18 DDPFVIGLYGEWGSGKSSFLNMLKEELK   45 (325)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4567899999999999999999988874

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 [].

>TIGR00416 sms DNA repair protein RadA

Probab=96.85  E-value=0.0057  Score=64.83  Aligned_cols=69  Identities=25%  Similarity=0.287  Sum_probs=45.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc--------------------CchHHHHHHHHh--c
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR--------------------SNSDLRTLLVAT--A  303 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~--------------------~~~~l~~l~~~~--~  303 (473)
                      |.++..-+||+|+||+|||+|+..+|..+   +.++++++..+-.                    ....+..+....  .
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            56666779999999999999999887755   3466555543210                    111222222222  3


Q ss_pred             cCceEEEecccccc
Q 012016          304 NRSILVVEDIDCTI  317 (473)
Q Consensus       304 ~~sIL~iDdiD~l~  317 (473)
                      ++.+||||.|..+.
T Consensus       170 ~~~~vVIDSIq~l~  183 (454)
T TIGR00416       170 NPQACVIDSIQTLY  183 (454)
T ss_pred             CCcEEEEecchhhc
Confidence            67899999998764

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)).

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=96.84  E-value=0.0028  Score=57.72  Aligned_cols=37  Identities=27%  Similarity=0.432  Sum_probs=33.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~  289 (473)
                      +..+.|.|.+|+|||++|.|+...|   |+.+|.+|...+
T Consensus        23 ~~viW~TGLSGsGKSTiA~ale~~L~~~G~~~y~LDGDnv   62 (197)
T COG0529          23 GAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLDGDNV   62 (197)
T ss_pred             CeEEEeecCCCCCHHHHHHHHHHHHHHcCCeEEEecChhH
Confidence            4568899999999999999999988   899999998776

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.84  E-value=0.0042  Score=58.29  Aligned_cols=121  Identities=21%  Similarity=0.326  Sum_probs=67.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc--------------------------C-----------CceEEcccccccC
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL--------------------------N-----------FDVYDLELTELRS  291 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l--------------------------~-----------~~~~~l~~~~~~~  291 (473)
                      |+|.+.=+++.|+.|||||.|.+-+|-=+                          +           +.++.++...+..
T Consensus        24 GiP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~~~~~~~~~~~~  103 (235)
T COG2874          24 GIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNW  103 (235)
T ss_pred             CCccCeEEEEECCCCccHHHHHHHHHHHHHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeEEEEeccccccc
Confidence            35666668999999999999999888533                          1           2233343333322


Q ss_pred             chH-----HHHHHHH--hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          292 NSD-----LRTLLVA--TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       292 ~~~-----l~~l~~~--~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                      +..     |..++..  ..+..|++||-+..+..                . ........+++.+..+.+   .+.+||+
T Consensus       104 ~~~~~~~~L~~l~~~~k~~~~dViIIDSls~~~~----------------~-~~~~~vl~fm~~~r~l~d---~gKvIil  163 (235)
T COG2874         104 GRRSARKLLDLLLEFIKRWEKDVIIIDSLSAFAT----------------Y-DSEDAVLNFMTFLRKLSD---LGKVIIL  163 (235)
T ss_pred             ChHHHHHHHHHHHhhHHhhcCCEEEEecccHHhh----------------c-ccHHHHHHHHHHHHHHHh---CCCEEEE
Confidence            222     2222222  23678999999987753                1 122333444444444432   3455555


Q ss_pred             ecCCCCCCCccccCC--CceeeEEEeCC
Q 012016          365 TTNHKEKLDPALLRP--GRMDVHVHMSY  390 (473)
Q Consensus       365 tTN~~~~ld~aLlrp--gRfd~~I~~~~  390 (473)
                      |. ||..++++++-+  .-+|.++++..
T Consensus       164 Tv-hp~~l~e~~~~rirs~~d~~l~L~~  190 (235)
T COG2874         164 TV-HPSALDEDVLTRIRSACDVYLRLRL  190 (235)
T ss_pred             Ee-ChhhcCHHHHHHHHHhhheeEEEEh
Confidence            55 567788776530  13455555543

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=96.83  E-value=0.00099  Score=70.81  Aligned_cols=63  Identities=19%  Similarity=0.293  Sum_probs=43.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc--cc------CchHHHHHHHH-----hccCceEEEecccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE--LR------SNSDLRTLLVA-----TANRSILVVEDIDCTI  317 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~--~~------~~~~l~~l~~~-----~~~~sIL~iDdiD~l~  317 (473)
                      ++||+|.||||||-+.+.+++-....++..-...  ++      .+.--++.-..     .+.++|.+|||+|.+-
T Consensus       484 nvLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGASavGLTa~v~KdPvtrEWTLEaGALVLADkGvClIDEFDKMn  559 (854)
T KOG0477|consen  484 NVLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGASAVGLTAYVRKDPVTREWTLEAGALVLADKGVCLIDEFDKMN  559 (854)
T ss_pred             eEEEecCCCccHHHHHHHHHhcCcceeEeccCCccccceeEEEeeCCccceeeeccCeEEEccCceEEeehhhhhc
Confidence            4999999999999999999999887777543222  11      11101111111     2478999999999984

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.82  E-value=0.015  Score=58.80  Aligned_cols=34  Identities=24%  Similarity=0.185  Sum_probs=27.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +.-++|.||+|+||||++..||..+   +..+..+++
T Consensus       114 ~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~  150 (318)
T PRK10416        114 PFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAG  150 (318)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEec
Confidence            4568999999999999999999987   445554444

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.82  E-value=0.0019  Score=63.75  Aligned_cols=61  Identities=21%  Similarity=0.371  Sum_probs=34.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc----------CchHHHHHHHH-----hccCceEEEeccccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR----------SNSDLRTLLVA-----TANRSILVVEDIDCT  316 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~----------~~~~l~~l~~~-----~~~~sIL~iDdiD~l  316 (473)
                      ++|+|.||+|||++++.|+.++   +..+..++...+.          .+..++..+..     .....||++||.-.+
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls~~~iVI~Dd~nYi   82 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALSKDTIVILDDNNYI   82 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHTT-SEEEE-S---S
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhccCeEEEEeCCchH
Confidence            7999999999999999999986   5666666543331          12333333322     245689999998755

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=96.82  E-value=0.0015  Score=56.44  Aligned_cols=64  Identities=25%  Similarity=0.336  Sum_probs=40.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC--------------------ceEEcccccccCchHHHHH--HHHhccCceEEE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF--------------------DVYDLELTELRSNSDLRTL--LVATANRSILVV  310 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~--------------------~~~~l~~~~~~~~~~l~~l--~~~~~~~sIL~i  310 (473)
                      ..-++|+|+=|+|||++++++|..+|.                    +++.+|+=.+.+..++..+  +......+|.+|
T Consensus        15 g~vi~L~GdLGaGKTtf~r~l~~~lg~~~~V~SPTF~l~~~Y~~~~~~l~H~DLYRl~~~~e~~~~g~~e~~~~~~i~~I   94 (123)
T PF02367_consen   15 GDVILLSGDLGAGKTTFVRGLARALGIDEEVTSPTFSLVNEYEGGNIPLYHFDLYRLEDPEELEDLGLEEYLFEDGICVI   94 (123)
T ss_dssp             -EEEEEEESTTSSHHHHHHHHHHHTT--S----TTTTSEEEEEETTEEEEEEE-TT-SSTHHHHHCTTTTCSSSSEEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHcCCCCCcCCCCeEEEEEecCCCceEEEeeccccCCHHHHHHCCchhhhCCCCEEEE
Confidence            456999999999999999999999953                    3344444444444443332  122345778887


Q ss_pred             eccccc
Q 012016          311 EDIDCT  316 (473)
Q Consensus       311 DdiD~l  316 (473)
                      |=.+.+
T Consensus        95 EW~e~~  100 (123)
T PF02367_consen   95 EWPERL  100 (123)
T ss_dssp             ESGGGG
T ss_pred             ECcccc
Confidence            755544

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=96.81  E-value=0.0069  Score=61.41  Aligned_cols=127  Identities=22%  Similarity=0.342  Sum_probs=76.0

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC----------------------------chHHHHHHHHh-
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS----------------------------NSDLRTLLVAT-  302 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~----------------------------~~~l~~l~~~~-  302 (473)
                      .|..+.|||-.|||||.+++.+-+.++.+...+++-+.-+                            -..+..+|... 
T Consensus        29 ~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~  108 (438)
T KOG2543|consen   29 IPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWP  108 (438)
T ss_pred             cceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhH
Confidence            3567899999999999999999999988877766543211                            01222333331 


Q ss_pred             --c---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC-CCCCCccc
Q 012016          303 --A---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH-KEKLDPAL  376 (473)
Q Consensus       303 --~---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~-~~~ld~aL  376 (473)
                        +   +...|++|.+|.+-+                  .....+..|+..-.-+ .   ...+.|...-. .++  --+
T Consensus       109 ~~t~~d~~~~liLDnad~lrD------------------~~a~ll~~l~~L~el~-~---~~~i~iils~~~~e~--~y~  164 (438)
T KOG2543|consen  109 AATNRDQKVFLILDNADALRD------------------MDAILLQCLFRLYELL-N---EPTIVIILSAPSCEK--QYL  164 (438)
T ss_pred             HhhccCceEEEEEcCHHhhhc------------------cchHHHHHHHHHHHHh-C---CCceEEEEeccccHH--Hhh
Confidence              1   346889999998842                  2345556555432222 1   12333333322 111  112


Q ss_pred             cCCCcee-eEEEeCCCCHHHHHHHHHH
Q 012016          377 LRPGRMD-VHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       377 lrpgRfd-~~I~~~~p~~~~r~~l~~~  402 (473)
                      .+-|-++ ..++||.++.++..+|+.+
T Consensus       165 ~n~g~~~i~~l~fP~Ys~~e~~~Il~~  191 (438)
T KOG2543|consen  165 INTGTLEIVVLHFPQYSVEETQVILSR  191 (438)
T ss_pred             cccCCCCceEEecCCCCHHHHHHHHhc
Confidence            2234443 5789999999998888764

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=96.80  E-value=0.0041  Score=59.29  Aligned_cols=22  Identities=32%  Similarity=0.437  Sum_probs=19.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      +-++|.||.|+|||++.+.+|.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            4689999999999999999874

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 clam

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=96.80  E-value=0.0021  Score=54.90  Aligned_cols=24  Identities=33%  Similarity=0.358  Sum_probs=20.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++++++||+|+|||.++.+.+..+
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~   24 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILEL   24 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHH
Confidence            368999999999999888777665

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=96.79  E-value=0.0061  Score=61.19  Aligned_cols=62  Identities=19%  Similarity=0.345  Sum_probs=41.0

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEE----cccccccCchHHHHHHHHhccCceEEEecccc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYD----LELTELRSNSDLRTLLVATANRSILVVEDIDC  315 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~----l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~  315 (473)
                      +....++|+|+.|+|||+++..|...+|-....    +.+.++.+. .  ..+.....+-+++.+|++.
T Consensus        74 ~~~~~~~l~G~g~nGKStl~~~l~~l~G~~~~~~~~~~~~~~~~~~-~--f~~a~l~gk~l~~~~E~~~  139 (304)
T TIGR01613        74 TEQKLFFLYGNGGNGKSTFQNLLSNLLGDYATTAVASLKMNEFQEH-R--FGLARLEGKRAVIGDEVQK  139 (304)
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHhChhhccCCcchhhhhccCC-C--chhhhhcCCEEEEecCCCC
Confidence            445679999999999999999999988754322    222222111 1  1223345678889999863

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=96.79  E-value=0.00094  Score=60.46  Aligned_cols=26  Identities=38%  Similarity=0.653  Sum_probs=21.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      |.|.|+||||||+|+++|+.. |++++
T Consensus         2 I~i~G~~stGKTTL~~~L~~~-g~~~v   27 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR-GYPVV   27 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH-T-EEE
T ss_pred             EEEECCCCCCHHHHHHHHHHc-CCeEE
Confidence            689999999999999999999 88876

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.78  E-value=0.0015  Score=60.67  Aligned_cols=32  Identities=31%  Similarity=0.452  Sum_probs=27.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..+.|.||+|+||||+++.|+..++.+++..+
T Consensus         3 ~~i~l~G~sGsGKsTl~~~l~~~~~~~~~~~~   34 (186)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQTQLLVAH   34 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHhccCCCeEEEcC
Confidence            36899999999999999999999887665433

>PRK04328 hypothetical protein; Provisional

Probab=96.78  E-value=0.0075  Score=58.78  Aligned_cols=40  Identities=30%  Similarity=0.277  Sum_probs=31.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh---cCCceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY---LNFDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~---l~~~~~~l~~~~  288 (473)
                      |.|....+|++||||||||.|+..++.+   -|.+.+.++..+
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~ee   61 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVALEE   61 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEeeC
Confidence            5677778999999999999998865543   267788887655

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=96.77  E-value=0.0058  Score=59.56  Aligned_cols=27  Identities=30%  Similarity=0.535  Sum_probs=23.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      ..-++|.||+|+|||+|++.+++.+..
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            345899999999999999999998864

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.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.76  E-value=0.0013  Score=65.58  Aligned_cols=31  Identities=26%  Similarity=0.237  Sum_probs=26.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-CCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-NFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l  284 (473)
                      .-+++.||||||||++++.++..+ +..++..
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l~~   34 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVNR   34 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEEec
Confidence            468999999999999999999999 6655554

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=96.76  E-value=0.00098  Score=59.56  Aligned_cols=27  Identities=26%  Similarity=0.548  Sum_probs=23.5

Q ss_pred             EeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          258 LYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       258 L~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      |.||||+|||++++.||..+|+..+.+
T Consensus         1 i~G~PgsGK~t~~~~la~~~~~~~is~   27 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYGLVHISV   27 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHTSEEEEH
T ss_pred             CcCCCCCChHHHHHHHHHhcCcceech
Confidence            579999999999999999998765543

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>TIGR00767 rho transcription termination factor Rho

Probab=96.76  E-value=0.0041  Score=64.15  Aligned_cols=25  Identities=28%  Similarity=0.542  Sum_probs=22.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .-++|.||||+|||+|++.+++.+.
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhc
Confidence            3489999999999999999999863

Members of this family differ in the specificity of RNA binding.

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.75  E-value=0.012  Score=68.93  Aligned_cols=130  Identities=17%  Similarity=0.207  Sum_probs=81.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC------------chHH--H--HHHHHhccCceEEEeccccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS------------NSDL--R--TLLVATANRSILVVEDIDCTID  318 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~------------~~~l--~--~l~~~~~~~sIL~iDdiD~l~~  318 (473)
                      .+|+.||..+|||+++..+|.+.|..++.++-.+..+            +..|  +  -+.....++--|++||+.-.. 
T Consensus       890 P~LiQGpTSSGKTSMI~yla~~tghkfVRINNHEHTdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~GyWIVLDELNLAp-  968 (4600)
T COG5271         890 PLLIQGPTSSGKTSMILYLARETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEGVLVEALRRGYWIVLDELNLAP-  968 (4600)
T ss_pred             cEEEecCCCCCcchHHHHHHHHhCccEEEecCcccchHHHHhhceeecCCCceeeehhHHHHHHhcCcEEEeeccccCc-
Confidence            3899999999999999999999999999988654311            1111  1  123344577899999996432 


Q ss_pred             cccCCccccCCCCCCCccchhHHHHHHHHHhcccc-------cCCCCceEEEEecCCCC------CCCccccCCCceeeE
Q 012016          319 LQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-------SSCGDERIIVFTTNHKE------KLDPALLRPGRMDVH  385 (473)
Q Consensus       319 ~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-------~~~~~~~iiI~tTN~~~------~ld~aLlrpgRfd~~  385 (473)
                                       ...-..++.||.--..+.       -.+.++..+++|-|.|.      .|..|++.  || ..
T Consensus       969 -----------------TDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRN--RF-lE 1028 (4600)
T COG5271         969 -----------------TDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRN--RF-LE 1028 (4600)
T ss_pred             -----------------HHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHh--hh-Hh
Confidence                             122334444442111110       01223456667777764      46678877  88 45


Q ss_pred             EEeCCCCHHHHHHHHHHHhC
Q 012016          386 VHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       386 I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ++|..-..++...|+.....
T Consensus      1029 ~hFddipedEle~ILh~rc~ 1048 (4600)
T COG5271        1029 MHFDDIPEDELEEILHGRCE 1048 (4600)
T ss_pred             hhcccCcHHHHHHHHhccCc
Confidence            67776667777777764443

>PRK14526 adenylate kinase; Provisional

Probab=96.74  E-value=0.0015  Score=62.13  Aligned_cols=28  Identities=32%  Similarity=0.704  Sum_probs=25.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      ++|.||||+|||++++.+|..++++.+.
T Consensus         3 i~l~G~pGsGKsT~a~~La~~~~~~~is   30 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNELNYYHIS   30 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            7899999999999999999999877654

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=96.74  E-value=0.0035  Score=61.33  Aligned_cols=65  Identities=23%  Similarity=0.361  Sum_probs=53.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH------hcCCceEEcccccccCchHHHHHHHHh-----------------ccCceEE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN------YLNFDVYDLELTELRSNSDLRTLLVAT-----------------ANRSILV  309 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~------~l~~~~~~l~~~~~~~~~~l~~l~~~~-----------------~~~sIL~  309 (473)
                      ...+||.||.|.|||.|++-+-.      .+.-+++.++|..+.++..+..+|-..                 ..+..||
T Consensus       208 r~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadggmlf  287 (531)
T COG4650         208 RAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGMLF  287 (531)
T ss_pred             cCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCceEe
Confidence            34699999999999999998764      457789999999998887777776543                 2568999


Q ss_pred             Eecccccc
Q 012016          310 VEDIDCTI  317 (473)
Q Consensus       310 iDdiD~l~  317 (473)
                      +|||..+.
T Consensus       288 ldeigelg  295 (531)
T COG4650         288 LDEIGELG  295 (531)
T ss_pred             hHhhhhcC
Confidence            99998874

>PHA00350 putative assembly protein

Probab=96.73  E-value=0.0048  Score=63.79  Aligned_cols=120  Identities=13%  Similarity=0.108  Sum_probs=61.6

Q ss_pred             eeEEeCCCCCCHHHHHHH--HHHhc--CCceEEccccccc--------------------Cc------hHHHHHHHHhcc
Q 012016          255 GYLLYGPPGTGKSSLIAA--MANYL--NFDVYDLELTELR--------------------SN------SDLRTLLVATAN  304 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~a--lA~~l--~~~~~~l~~~~~~--------------------~~------~~l~~l~~~~~~  304 (473)
                      -++++|+||+|||..+-.  |-.++  |.+++. +...+.                    ..      ......+...+.
T Consensus         3 I~l~tG~pGSGKT~~aV~~~i~palk~GR~V~T-NI~Gl~le~i~~~~~~~p~~~~li~i~~~~~~~~~~~~~~~~w~p~   81 (399)
T PHA00350          3 IYAIVGRPGSYKSYEAVVYHIIPALKDGRKVIT-NIPGLNLDVFEKVFGEFPSTARLIRIVDRNLEGFESMNRPFSWRPR   81 (399)
T ss_pred             eEEEecCCCCchhHHHHHHHHHHHHHCCCEEEE-CCCCCCHHHHHhhcccCcccceeEEeccccccchhhhccccccCCC
Confidence            368999999999997664  43333  665552 322111                    00      011111222457


Q ss_pred             CceEEEeccccccccccCCccccCCC-CCCC-----ccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          305 RSILVVEDIDCTIDLQDRLPADIAGE-GEGP-----IQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       305 ~sIL~iDdiD~l~~~~~r~~~~~~~~-~~~~-----~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                      .++|||||+..+++.+...+....-. ..+.     .......+..|. ..      ...+.=||++|.++..||..++.
T Consensus        82 gaLIViDEaq~~~p~r~~~~~~~~~~~p~~~~~~~~~~~p~~~i~~l~-~H------RH~G~DIiliTQ~~~~Id~~iR~  154 (399)
T PHA00350         82 GALYVIDEAQMIFPKRLGFKMANIFKRPFTDFEPHLPEGPENFLEAFM-RH------RHYNWDIILLTPNIRKIHSDIRA  154 (399)
T ss_pred             CCEEEEECchhhcCCCccccccccccccccccccccccCCHHHHHHHH-Hh------cccCceEEEEeCCHHHhhHHHHH
Confidence            89999999999987432211100000 0000     001112222222 11      11234588899999999988765


Q ss_pred             CCceee
Q 012016          379 PGRMDV  384 (473)
Q Consensus       379 pgRfd~  384 (473)
                        ++++
T Consensus       155 --lvE~  158 (399)
T PHA00350        155 --MIEM  158 (399)
T ss_pred             --hhhh
Confidence              5554

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=96.73  E-value=0.0024  Score=66.55  Aligned_cols=169  Identities=18%  Similarity=0.140  Sum_probs=93.8

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCC--CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc--c-CchH
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA--WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL--R-SNSD  294 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~--~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~--~-~~~~  294 (473)
                      +|.|..++|+.++-.|.   .+...-..-|..  -.-+++|.|.||..||-|.+.+.+.....+|..--.+-  . +..-
T Consensus       343 EIyGheDVKKaLLLlLV---Ggvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlapRgvYTTGrGSSGVGLTAAV  419 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLV---GGVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAPRGVYTTGRGSSGVGLTAAV  419 (721)
T ss_pred             hhccchHHHHHHHHHhh---CCCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcCcccceecCCCCCccccchhh
Confidence            57788888988765544   221111111111  12358999999999999999999988777776443321  1 1111


Q ss_pred             HHHHH------H----HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          295 LRTLL------V----ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       295 l~~l~------~----~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                      ++.-+      .    -....+|.+|||+|.+.. .+|..-...        ..++++|---   .|+..+-....-|++
T Consensus       420 mkDpvTgEM~LEGGALVLAD~GICCIDEfDKM~e-~DRtAIHEV--------MEQQTISIaK---AGI~TtLNAR~sILa  487 (721)
T KOG0482|consen  420 MKDPVTGEMVLEGGALVLADGGICCIDEFDKMDE-SDRTAIHEV--------MEQQTISIAK---AGINTTLNARTSILA  487 (721)
T ss_pred             hcCCCCCeeEeccceEEEccCceEeehhhhhhhh-hhhHHHHHH--------HHhhhhhhhh---hccccchhhhHHhhh
Confidence            11100      0    123678999999998853 122111000        0111111000   122222223355777


Q ss_pred             ecCCCC-------------CCCccccCCCceeeEEE-eCCCCHHHHHHHHHHHhC
Q 012016          365 TTNHKE-------------KLDPALLRPGRMDVHVH-MSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       365 tTN~~~-------------~ld~aLlrpgRfd~~I~-~~~p~~~~r~~l~~~~l~  405 (473)
                      +.|...             .|++||+.  |||...- ...|+.+.=..|+++..-
T Consensus       488 AANPayGRYnprrs~e~NI~LPaALLS--RFDll~Li~D~pdrd~D~~LA~HiTy  540 (721)
T KOG0482|consen  488 AANPAYGRYNPRRSPEQNINLPAALLS--RFDLLWLIQDRPDRDNDLRLAQHITY  540 (721)
T ss_pred             hcCccccccCcccChhHhcCCcHHHHH--hhhhhhhhccCCcccchHHHHHHhHh
Confidence            777531             57899999  9996544 355888877778877543

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.72  E-value=0.0015  Score=58.49  Aligned_cols=30  Identities=37%  Similarity=0.533  Sum_probs=25.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      +++.|+||+|||++++.++..+   +.+.+.++
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~   34 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLD   34 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEc
Confidence            6899999999999999999998   66666554

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>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=96.71  E-value=0.0014  Score=61.52  Aligned_cols=35  Identities=37%  Similarity=0.553  Sum_probs=27.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      -++|+||+|||||.++-++|+.+|.|++..|--..
T Consensus         3 v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Driq~   37 (233)
T PF01745_consen    3 VYLIVGPTGTGKTALAIALAQKTGAPVISLDRIQC   37 (233)
T ss_dssp             EEEEE-STTSSHHHHHHHHHHHH--EEEEE-SGGG
T ss_pred             EEEEECCCCCChhHHHHHHHHHhCCCEEEecceec
Confidence            47999999999999999999999999999885543

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=96.71  E-value=0.0016  Score=60.15  Aligned_cols=28  Identities=32%  Similarity=0.540  Sum_probs=24.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      +|-++|.||+|+|||+|++.|+....-.
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~~~~~~   29 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQEFPDK   29 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHSTTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcccc
Confidence            4679999999999999999999987543

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=96.71  E-value=0.0014  Score=58.24  Aligned_cols=44  Identities=23%  Similarity=0.422  Sum_probs=34.3

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHH
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLR  296 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~  296 (473)
                      +.+-.+++-|++|||||+++++++.+|+.+|++-|  ++...++..
T Consensus        10 ~~k~~i~vmGvsGsGKSTigk~L~~~l~~~F~dgD--d~Hp~~Nve   53 (191)
T KOG3354|consen   10 PFKYVIVVMGVSGSGKSTIGKALSEELGLKFIDGD--DLHPPANVE   53 (191)
T ss_pred             CCceeEEEEecCCCChhhHHHHHHHHhCCcccccc--cCCCHHHHH
Confidence            44557899999999999999999999999887644  444444443

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.71  E-value=0.011  Score=66.30  Aligned_cols=63  Identities=24%  Similarity=0.306  Sum_probs=40.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---C--CceEEcccccc----------cCchHHHHHHHHh------------ccCc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---N--FDVYDLELTEL----------RSNSDLRTLLVAT------------ANRS  306 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~--~~~~~l~~~~~----------~~~~~l~~l~~~~------------~~~s  306 (473)
                      +-.+|.|+||||||++++++...+   +  .+++.+..+..          .....+++++...            ....
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~~~~~~~~~v~l~ApTg~AA~~L~e~~g~~a~Tih~lL~~~~~~~~~~~~~~~~~~~  418 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELAEELGGLLPVGLAAPTGRAAKRLGEVTGLTASTIHRLLGYGPDTFRHNHLEDPIDCD  418 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCceEEEEeCchHHHHHHHHhcCCccccHHHHhhccCCccchhhhhccccCC
Confidence            468999999999999999987765   4  45554433221          0123445555321            1347


Q ss_pred             eEEEeccccc
Q 012016          307 ILVVEDIDCT  316 (473)
Q Consensus       307 IL~iDdiD~l  316 (473)
                      +|+|||+-.+
T Consensus       419 llIvDEaSMv  428 (720)
T TIGR01448       419 LLIVDESSMM  428 (720)
T ss_pred             EEEEeccccC
Confidence            9999999755

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.69  E-value=0.002  Score=60.09  Aligned_cols=23  Identities=35%  Similarity=0.579  Sum_probs=21.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -++|.|+||+|||++++-+|++|
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L   25 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKEL   25 (261)
T ss_pred             eEEEecCCCCCchHHHHHHHHHH
Confidence            37899999999999999999999

>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=96.68  E-value=0.01  Score=54.76  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=20.5

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHH
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ...-+.|.||.|+|||||.+++..
T Consensus        20 ~G~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          20 LNVLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhh
Confidence            345689999999999999999964

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.

>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=96.67  E-value=0.0089  Score=54.68  Aligned_cols=25  Identities=40%  Similarity=0.640  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...+.|.||+|+|||+|++.||..+
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~   50 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLL   50 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3468999999999999999999976

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.

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=96.67  E-value=0.0041  Score=67.16  Aligned_cols=28  Identities=32%  Similarity=0.437  Sum_probs=24.1

Q ss_pred             CCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          250 KAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       250 ~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+++..+|+.||+|||||+|.+|||.-.
T Consensus       416 v~~G~~llI~G~SG~GKTsLlRaiaGLW  443 (604)
T COG4178         416 VRPGERLLITGESGAGKTSLLRALAGLW  443 (604)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            3445569999999999999999999865

>PRK10646 ADP-binding protein; Provisional

Probab=96.65  E-value=0.011  Score=53.11  Aligned_cols=27  Identities=26%  Similarity=0.422  Sum_probs=24.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      ..-++|.|+=|+|||++++++++.+|.
T Consensus        28 g~vi~L~GdLGaGKTtf~rgl~~~Lg~   54 (153)
T PRK10646         28 ATVIYLYGDLGAGKTTFSRGFLQALGH   54 (153)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            346899999999999999999999964

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.65  E-value=0.0067  Score=64.97  Aligned_cols=29  Identities=28%  Similarity=0.292  Sum_probs=24.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.+....+|+.||||||||+|+..++...
T Consensus       259 G~~~gs~~li~G~~G~GKt~l~~~f~~~~  287 (484)
T TIGR02655       259 GFFKDSIILATGATGTGKTLLVSKFLENA  287 (484)
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            56667779999999999999998877755

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.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.64  E-value=0.0016  Score=63.33  Aligned_cols=32  Identities=41%  Similarity=0.565  Sum_probs=26.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      ++|.|+||+|||+++++++..+   +.+++.++..
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~~D   36 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTD   36 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEccH
Confidence            6899999999999999999988   4666666543

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.63  E-value=0.0023  Score=64.08  Aligned_cols=25  Identities=28%  Similarity=0.567  Sum_probs=23.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++++++.||+|+|||++++++++++
T Consensus       132 ~~~ilI~G~tGSGKTTll~al~~~i  156 (299)
T TIGR02782       132 RKNILVVGGTGSGKTTLANALLAEI  156 (299)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999999886

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.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.63  E-value=0.03  Score=58.37  Aligned_cols=36  Identities=25%  Similarity=0.375  Sum_probs=27.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----CCceEEccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTE  288 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~  288 (473)
                      +.-++|.||+|+|||+++..||..+    |..+..+++..
T Consensus       223 ~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt  262 (432)
T PRK12724        223 RKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDN  262 (432)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccc
Confidence            3458899999999999999999754    45565555444

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=96.63  E-value=0.0048  Score=58.55  Aligned_cols=24  Identities=38%  Similarity=0.710  Sum_probs=21.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+.|+.||||||||++.+-+|+-+
T Consensus       138 lntLiigpP~~GKTTlLRdiaR~~  161 (308)
T COG3854         138 LNTLIIGPPQVGKTTLLRDIARLL  161 (308)
T ss_pred             eeeEEecCCCCChHHHHHHHHHHh
Confidence            368999999999999999999876

>COG3378 Phage associated DNA primase [General function prediction only]

Probab=96.62  E-value=0.0078  Score=64.24  Aligned_cols=65  Identities=26%  Similarity=0.446  Sum_probs=42.4

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCC-ceEEcccccccCchHHHHHHHHhccCceEEEecccc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNF-DVYDLELTELRSNSDLRTLLVATANRSILVVEDIDC  315 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~-~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~  315 (473)
                      .|...+.|+||-|+|||+++..|.+.+|. .+..+....+.....=+..+...-...++..+|.+.
T Consensus       228 ~~~k~~~l~G~G~nGKstf~~li~~llG~~n~~s~~~~~~~~~~~~~~~~A~Lvg~~~v~~~E~~k  293 (517)
T COG3378         228 SEQKLFWLYGPGGNGKSTFVDLISNLLGRYNVTSAPLTDLEADDRHPFGLAALVGKRLVTVSETEK  293 (517)
T ss_pred             cceeEEEEEcCCCCChHHHHHHHHHHhccchhccccHHHhhhhccCcchHHHhhCceEEEecCccc
Confidence            46678999999999999999999999974 444555554432111112222334566777777654

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.62  E-value=0.0063  Score=61.46  Aligned_cols=53  Identities=15%  Similarity=0.154  Sum_probs=38.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEcccccccCchHHHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLELTELRSNSDLRTLLVA  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~~~~~~~~~l~~l~~~  301 (473)
                      |++...-++++||||||||.++..+|-..         +..+++++...-.....+.+....
T Consensus        98 Gi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~~~~  159 (317)
T PRK04301         98 GIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAEA  159 (317)
T ss_pred             CccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHHHHH
Confidence            56666778999999999999999888552         347788887664445566655543

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=96.61  E-value=0.0085  Score=66.72  Aligned_cols=28  Identities=21%  Similarity=0.307  Sum_probs=24.0

Q ss_pred             CCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          250 KAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       250 ~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +++..-+-+.|++|||||||++.|.+.+
T Consensus       496 I~~Ge~vaIvG~SGsGKSTL~KLL~gly  523 (709)
T COG2274         496 IPPGEKVAIVGRSGSGKSTLLKLLLGLY  523 (709)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3444459999999999999999999977

>PF00488 MutS_V: MutS domain V C-terminus

Probab=96.60  E-value=0.011  Score=57.02  Aligned_cols=97  Identities=13%  Similarity=0.297  Sum_probs=54.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-----CCce---------E-----Ecccc-ccc--------CchHHHHHHHHhccC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-----NFDV---------Y-----DLELT-ELR--------SNSDLRTLLVATANR  305 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-----~~~~---------~-----~l~~~-~~~--------~~~~l~~l~~~~~~~  305 (473)
                      +.++|.||..+|||++++.+|-..     |..+         +     .+... ++.        .-..+..++..+.++
T Consensus        44 ~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~  123 (235)
T PF00488_consen   44 RIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAESAEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNATEK  123 (235)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSEEEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH--TT
T ss_pred             eEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecccccccccEEEeecccccccccccccHHHhHHHHHhhhhhcccc
Confidence            578999999999999999988643     3211         1     11111 111        124566777777889


Q ss_pred             ceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCC
Q 012016          306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEK  371 (473)
Q Consensus       306 sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~  371 (473)
                      ++|+|||+-.-..                ..+.......+++.+-.   .  .+..+|+||+..+-
T Consensus       124 sLvliDE~g~gT~----------------~~eg~ai~~aile~l~~---~--~~~~~i~~TH~~~l  168 (235)
T PF00488_consen  124 SLVLIDELGRGTN----------------PEEGIAIAIAILEYLLE---K--SGCFVIIATHFHEL  168 (235)
T ss_dssp             EEEEEESTTTTSS----------------HHHHHHHHHHHHHHHHH---T--TT-EEEEEES-GGG
T ss_pred             eeeecccccCCCC----------------hhHHHHHHHHHHHHHHH---h--ccccEEEEeccchh
Confidence            9999999964211                12223333444444432   1  12567888887653

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=96.60  E-value=0.0086  Score=57.17  Aligned_cols=63  Identities=17%  Similarity=0.324  Sum_probs=41.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc-----CC---------ceE-----Eccccc-cc--------CchHHHHHHHHhcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL-----NF---------DVY-----DLELTE-LR--------SNSDLRTLLVATAN  304 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l-----~~---------~~~-----~l~~~~-~~--------~~~~l~~l~~~~~~  304 (473)
                      .+.++|.||.|.|||++.+.++...     |.         +++     .+...+ +.        .-.++..++..+..
T Consensus        30 ~~~~~itG~n~~gKs~~l~~i~~~~~la~~G~~vpa~~~~i~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~  109 (218)
T cd03286          30 PRILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATP  109 (218)
T ss_pred             CcEEEEECCCCCchHHHHHHHHHHHHHHHcCCccCccccEeccccEEEEecCcccccccCcchHHHHHHHHHHHHHhCCC
Confidence            4578999999999999999887643     21         111     111111 11        11345567777789


Q ss_pred             CceEEEecccc
Q 012016          305 RSILVVEDIDC  315 (473)
Q Consensus       305 ~sIL~iDdiD~  315 (473)
                      +++++|||+..
T Consensus       110 ~sLvLlDE~~~  120 (218)
T cd03286         110 DSLVILDELGR  120 (218)
T ss_pred             CeEEEEecccC
Confidence            99999999864

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

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.60  E-value=0.0072  Score=62.29  Aligned_cols=27  Identities=44%  Similarity=0.742  Sum_probs=24.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      +..+++.||.|||||+++++|.+.+..
T Consensus        22 ~~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   22 GLNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             CcEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            568899999999999999999998843

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=96.58  E-value=0.011  Score=58.12  Aligned_cols=25  Identities=32%  Similarity=0.327  Sum_probs=22.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...+.|.||+|+|||+|+++|+..+
T Consensus        50 Ge~~~liG~NGsGKSTLlk~L~Gl~   74 (264)
T PRK13546         50 GDVIGLVGINGSGKSTLSNIIGGSL   74 (264)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCc
Confidence            4458999999999999999999976

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.58  E-value=0.013  Score=62.51  Aligned_cols=64  Identities=23%  Similarity=0.303  Sum_probs=42.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccccc--c--------------------cCchHHHHHHHHhcc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTE--L--------------------RSNSDLRTLLVATAN  304 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~--~--------------------~~~~~l~~l~~~~~~  304 (473)
                      +...+.|.||+|+|||+++..||..+     +..+..++...  .                    .....+...+....+
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~~  428 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLRD  428 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhcc
Confidence            35678999999999999999998754     23343333221  1                    122456666666667


Q ss_pred             CceEEEecccc
Q 012016          305 RSILVVEDIDC  315 (473)
Q Consensus       305 ~sIL~iDdiD~  315 (473)
                      ..+||||....
T Consensus       429 ~DLVLIDTaG~  439 (559)
T PRK12727        429 YKLVLIDTAGM  439 (559)
T ss_pred             CCEEEecCCCc
Confidence            78889888854

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.58  E-value=0.002  Score=59.87  Aligned_cols=26  Identities=27%  Similarity=0.682  Sum_probs=23.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ...+++.||+|+|||+++++++..+.
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            45799999999999999999998873

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.

>PRK14529 adenylate kinase; Provisional

Probab=96.57  E-value=0.0022  Score=61.35  Aligned_cols=28  Identities=25%  Similarity=0.488  Sum_probs=25.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .++|.||||+|||++++.||..++++.+
T Consensus         2 ~I~l~G~PGsGK~T~a~~La~~~~~~~i   29 (223)
T PRK14529          2 NILIFGPNGSGKGTQGALVKKKYDLAHI   29 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCCCc
Confidence            3789999999999999999999998765

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=96.56  E-value=0.0025  Score=58.85  Aligned_cols=30  Identities=30%  Similarity=0.392  Sum_probs=27.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      +.|+|+||+|||++++.+++ +|+++++.|.
T Consensus         2 i~itG~~gsGKst~~~~l~~-~g~~~i~~D~   31 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE-LGIPVIDADK   31 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH-CCCCEEecCH
Confidence            67999999999999999999 8998887763

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>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=96.56  E-value=0.013  Score=57.62  Aligned_cols=62  Identities=26%  Similarity=0.415  Sum_probs=46.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc----hHHHHHHHHhc---cCceEEEeccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN----SDLRTLLVATA---NRSILVVEDID  314 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~----~~l~~l~~~~~---~~sIL~iDdiD  314 (473)
                      ..+.||.|.+|+||.++++..|.-.++.++.++.+.--+.    ++|+.++..+.   .+.+++|+|-+
T Consensus        31 ~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~y~~~~f~~dLk~~~~~ag~~~~~~vfll~d~q   99 (268)
T PF12780_consen   31 RGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITKGYSIKDFKEDLKKALQKAGIKGKPTVFLLTDSQ   99 (268)
T ss_dssp             TEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTSTTTHHHHHHHHHHHHHHHHHCS-S-EEEEEECCC
T ss_pred             CCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeCCcCHHHHHHHHHHHHHHHhccCCCeEEEecCcc
Confidence            3568999999999999999999999999999987654222    45666665553   57888888754

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.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.55  E-value=0.0029  Score=57.95  Aligned_cols=34  Identities=26%  Similarity=0.349  Sum_probs=27.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +.-+.|.|+||+|||+++++++..+   +.++..++.
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id~   40 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDG   40 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEcC
Confidence            4578999999999999999999988   444555554

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.55  E-value=0.01  Score=60.88  Aligned_cols=23  Identities=30%  Similarity=0.535  Sum_probs=21.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+|.||||||||+|++.+|+.+
T Consensus       135 R~LIvG~pGtGKTTLl~~la~~i  157 (380)
T PRK12608        135 RGLIVAPPRAGKTVLLQQIAAAV  157 (380)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            36999999999999999999977

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=96.55  E-value=0.011  Score=64.75  Aligned_cols=27  Identities=22%  Similarity=0.431  Sum_probs=24.0

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++...+.+.||+|+|||||++.|+..+
T Consensus       367 ~~G~~~aIvG~sGsGKSTLl~ll~gl~  393 (582)
T PRK11176        367 PAGKTVALVGRSGSGKSTIANLLTRFY  393 (582)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            345569999999999999999999987

>PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional

Probab=96.54  E-value=0.0024  Score=69.18  Aligned_cols=32  Identities=19%  Similarity=0.340  Sum_probs=30.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      -++|.|+||+|||++.+.+|+.|+++++++|.
T Consensus         8 ~i~LiG~~GaGKttvg~~LA~~L~~~fiD~D~   39 (542)
T PRK14021          8 QAVIIGMMGAGKTRVGKEVAQMMRLPFADADV   39 (542)
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEEchH
Confidence            48999999999999999999999999999884

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=96.53  E-value=0.0071  Score=54.97  Aligned_cols=24  Identities=29%  Similarity=0.491  Sum_probs=19.3

Q ss_pred             ceeEEeCCCCCCHHH-HHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSS-LIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~-la~alA~~l  277 (473)
                      +.+++.||+|||||. ++..+...+
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~   49 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEAL   49 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHh
Confidence            589999999999999 555655554

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.52  E-value=0.0028  Score=59.58  Aligned_cols=29  Identities=28%  Similarity=0.395  Sum_probs=25.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      +.-+++.|+||+|||++++.+|..++..+
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~~~~~   31 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHRAIDI   31 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            34689999999999999999999998754

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.51  E-value=0.13  Score=57.26  Aligned_cols=65  Identities=25%  Similarity=0.304  Sum_probs=41.7

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc--CCceEE
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL--NFDVYD  283 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l--~~~~~~  283 (473)
                      .|.+.++-+|......+..+.+...+    .    +        ..-.|-+||+-|.|.|||+++...+..+  +..+.-
T Consensus         6 ~~~~sk~~~P~~~~~~v~R~rL~~~L----~----~--------~~~~RL~li~APAGfGKttl~aq~~~~~~~~~~v~W   69 (894)
T COG2909           6 MLIPSKLVRPVRPDNYVVRPRLLDRL----R----R--------ANDYRLILISAPAGFGKTTLLAQWRELAADGAAVAW   69 (894)
T ss_pred             CCCccccCCCCCcccccccHHHHHHH----h----c--------CCCceEEEEeCCCCCcHHHHHHHHHHhcCcccceeE
Confidence            56666777777777766654443332    2    1        1114579999999999999999998633  444443


Q ss_pred             ccc
Q 012016          284 LEL  286 (473)
Q Consensus       284 l~~  286 (473)
                      +++
T Consensus        70 lsl   72 (894)
T COG2909          70 LSL   72 (894)
T ss_pred             eec
Confidence            333

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.49  E-value=0.0083  Score=67.50  Aligned_cols=63  Identities=22%  Similarity=0.362  Sum_probs=41.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc----------CchHHHHHHHH-------hccCceEEEecc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR----------SNSDLRTLLVA-------TANRSILVVEDI  313 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~----------~~~~l~~l~~~-------~~~~sIL~iDdi  313 (473)
                      +-++|.|+||||||++++++...+   |+.+..+-.+...          ....+..++..       .....+|||||+
T Consensus       369 ~~~il~G~aGTGKTtll~~i~~~~~~~g~~V~~~ApTg~Aa~~L~~~~g~~a~Ti~~~~~~~~~~~~~~~~~~llIvDEa  448 (744)
T TIGR02768       369 DIAVVVGRAGTGKSTMLKAAREAWEAAGYRVIGAALSGKAAEGLQAESGIESRTLASLEYAWANGRDLLSDKDVLVIDEA  448 (744)
T ss_pred             CEEEEEecCCCCHHHHHHHHHHHHHhCCCeEEEEeCcHHHHHHHHhccCCceeeHHHHHhhhccCcccCCCCcEEEEECc
Confidence            457999999999999999987654   6677665444320          11233343321       124589999999


Q ss_pred             ccc
Q 012016          314 DCT  316 (473)
Q Consensus       314 D~l  316 (473)
                      -.+
T Consensus       449 sMv  451 (744)
T TIGR02768       449 GMV  451 (744)
T ss_pred             ccC
Confidence            655

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>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=96.48  E-value=0.01  Score=54.70  Aligned_cols=25  Identities=36%  Similarity=0.570  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||+|+|||+|++.|+..+
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~~   49 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGLL   49 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4468999999999999999999976

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.48  E-value=0.009  Score=60.73  Aligned_cols=26  Identities=23%  Similarity=0.401  Sum_probs=23.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.++++.||+|+|||++++|+..++.
T Consensus       160 ~~nili~G~tgSGKTTll~aL~~~ip  185 (332)
T PRK13900        160 KKNIIISGGTSTGKTTFTNAALREIP  185 (332)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHhhCC
Confidence            46899999999999999999999884

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=96.48  E-value=0.0096  Score=53.94  Aligned_cols=24  Identities=33%  Similarity=0.578  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +..++.||.|+|||+++++++-.+
T Consensus        22 ~~~~i~G~NgsGKS~~l~~i~~~~   45 (162)
T cd03227          22 SLTIITGPNGSGKSTILDAIGLAL   45 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH
Confidence            478999999999999999986544

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.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.48  E-value=0.0083  Score=61.52  Aligned_cols=24  Identities=38%  Similarity=0.502  Sum_probs=22.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+++.|.||||||.|+-.++..+
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            458999999999999999999998

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=96.47  E-value=0.0089  Score=68.63  Aligned_cols=89  Identities=18%  Similarity=0.317  Sum_probs=55.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc----------CchHHHHHHHH-------hccCceEEEeccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR----------SNSDLRTLLVA-------TANRSILVVEDID  314 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~----------~~~~l~~l~~~-------~~~~sIL~iDdiD  314 (473)
                      -++|.|+||||||++++++...+   |+.++.+-++...          ....+..++..       .....+|||||+-
T Consensus       364 v~vv~G~AGTGKTT~l~~~~~~~e~~G~~V~~~ApTGkAA~~L~e~tGi~a~TI~sll~~~~~~~~~l~~~~vlIVDEAS  443 (988)
T PRK13889        364 LGVVVGYAGTGKSAMLGVAREAWEAAGYEVRGAALSGIAAENLEGGSGIASRTIASLEHGWGQGRDLLTSRDVLVIDEAG  443 (988)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEecCcHHHHHHHhhccCcchhhHHHHHhhhcccccccccCcEEEEECcc
Confidence            46899999999999988776544   7777766544320          12344444432       1245799999997


Q ss_pred             cccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC
Q 012016          315 CTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH  368 (473)
Q Consensus       315 ~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  368 (473)
                      -+                     ....+..||.....    .+..+|+|+=++.
T Consensus       444 Mv---------------------~~~~m~~LL~~a~~----~garvVLVGD~~Q  472 (988)
T PRK13889        444 MV---------------------GTRQLERVLSHAAD----AGAKVVLVGDPQQ  472 (988)
T ss_pred             cC---------------------CHHHHHHHHHhhhh----CCCEEEEECCHHH
Confidence            55                     23455666655432    2345677665543

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.47  E-value=0.011  Score=63.36  Aligned_cols=49  Identities=22%  Similarity=0.217  Sum_probs=36.1

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh----cCCceEEcccccccCchHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY----LNFDVYDLELTELRSNSDLRTLL  299 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~----l~~~~~~l~~~~~~~~~~l~~l~  299 (473)
                      |.+..+.+|+.||||||||+|+..++.+    .|-+.+++.+.+  +...+.+-.
T Consensus        17 Glp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~eE--~~~~l~~~~   69 (484)
T TIGR02655        17 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFEE--SPQDIIKNA   69 (484)
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEec--CHHHHHHHH
Confidence            6777889999999999999999977443    267888888753  334444433

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.46  E-value=0.0082  Score=60.50  Aligned_cols=53  Identities=15%  Similarity=0.059  Sum_probs=37.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh---------cCCceEEcccccccCchHHHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY---------LNFDVYDLELTELRSNSDLRTLLVA  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~---------l~~~~~~l~~~~~~~~~~l~~l~~~  301 (473)
                      |++...-+.++||||+|||.|+..+|-.         .+..+++++...-...+.+.+....
T Consensus        92 Gi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~  153 (313)
T TIGR02238        92 GIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAER  153 (313)
T ss_pred             CCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHH
Confidence            5666677899999999999999877632         2457778887654455666665543

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.

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=96.46  E-value=0.0033  Score=61.55  Aligned_cols=40  Identities=28%  Similarity=0.294  Sum_probs=31.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~  288 (473)
                      |.|..+.+|++|+||||||.++...+...   |.+++.++..+
T Consensus        19 G~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e   61 (260)
T COG0467          19 GLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEE   61 (260)
T ss_pred             CCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence            56777889999999999999988777654   66677666554

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.46  E-value=0.019  Score=61.97  Aligned_cols=119  Identities=19%  Similarity=0.275  Sum_probs=0.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc------------------------------------eEEcccccc---
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD------------------------------------VYDLELTEL---  289 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~------------------------------------~~~l~~~~~---  289 (473)
                      |.+...-+|++|+||||||+|+..++.+.-..                                    ++.++....   
T Consensus        27 G~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~ee~~~~i~~~~~~~g~d~~~~~~~g~l~~~~~~~~~~~  106 (509)
T PRK09302         27 GLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSE  106 (509)
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEccCCHHHHHHHHHHcCCCHHHHhhCCeEEEEecCccccc


Q ss_pred             ---cCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccch--hHHHHHHHHHhcccccCCCC
Q 012016          290 ---RSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQN--KVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       290 ---~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~--~~~ls~LL~~ldg~~~~~~~  358 (473)
                         .....+..++....      .+..++||.+..+..              +.+...  +..+..|++.+..      .
T Consensus       107 ~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls~l~~--------------~~d~~~~~r~~l~~L~~~Lk~------~  166 (509)
T PRK09302        107 QEEAGEYDLEALFIRIEYAIDKIGAKRVVLDSIEALFS--------------GFSNEAVVRRELRRLFAWLKQ------K  166 (509)
T ss_pred             ccccccccHHHHHHHHHHHHHhhCCCEEEECCHHHHHh--------------hccCHHHHHHHHHHHHHHHHh------C


Q ss_pred             ceEEEEecCCCCCCCccccCCC----ceeeEEEe
Q 012016          359 ERIIVFTTNHKEKLDPALLRPG----RMDVHVHM  388 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpg----Rfd~~I~~  388 (473)
                      +..+|+|++.....++ +-+.|    .+|.+|.+
T Consensus       167 g~TvLlt~~~~~~~~~-~~~~~~~~~laDgVI~L  199 (509)
T PRK09302        167 GVTAVITGERGDEYGP-LTRYGVEEFVSDCVIIL  199 (509)
T ss_pred             CCEEEEEECCccCcCC-ccccCceEEEeeEEEEE

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.45  E-value=0.0081  Score=60.44  Aligned_cols=26  Identities=15%  Similarity=0.542  Sum_probs=23.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+.++++.||+|+|||++++++++.+
T Consensus       143 ~~~~ili~G~tGsGKTTll~al~~~~  168 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTFLKSLVDEI  168 (308)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHccC
Confidence            35689999999999999999999887

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.

>PRK13764 ATPase; Provisional

Probab=96.44  E-value=0.0031  Score=68.53  Aligned_cols=26  Identities=38%  Similarity=0.769  Sum_probs=23.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..++|++||||+||||+++|+++++.
T Consensus       257 ~~~ILIsG~TGSGKTTll~AL~~~i~  282 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFAQALAEFYA  282 (602)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            46899999999999999999999884

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=96.43  E-value=0.01  Score=65.09  Aligned_cols=27  Identities=30%  Similarity=0.477  Sum_probs=23.8

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++..-+.+.||+|+|||||++.|++.+
T Consensus       359 ~~G~~v~IvG~sGsGKSTLl~lL~gl~  385 (588)
T PRK13657        359 KPGQTVAIVGPTGAGKSTLINLLQRVF  385 (588)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCc
Confidence            345569999999999999999999876

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=96.41  E-value=0.031  Score=51.55  Aligned_cols=66  Identities=15%  Similarity=0.116  Sum_probs=41.3

Q ss_pred             eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC--CCCHHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 012016          384 VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT--QVTPAEVAEQLMRNDDPELVLNGLIEFLKVK  453 (473)
Q Consensus       384 ~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~--~~t~a~i~~~l~~~~~~~~al~~l~~~l~~~  453 (473)
                      ..|.+-+|+.++.+.-+.    ..+....+.|+.-+..+  ++...+--+.++-|+|.+.|++++...+...
T Consensus       116 v~IFi~pPs~eeL~~RL~----~Rgtds~e~I~~Rl~~a~~Ei~~~~~fdyvivNdd~e~a~~~l~~ii~ae  183 (191)
T COG0194         116 VSIFILPPSLEELERRLK----GRGTDSEEVIARRLENAKKEISHADEFDYVIVNDDLEKALEELKSIILAE  183 (191)
T ss_pred             EEEEEcCCCHHHHHHHHH----ccCCCCHHHHHHHHHHHHHHHHHHHhCCEEEECccHHHHHHHHHHHHHHH
Confidence            457888899888654443    22334455555544422  2333333444566899999999998877655

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.39  E-value=0.003  Score=57.86  Aligned_cols=26  Identities=23%  Similarity=0.351  Sum_probs=23.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.-++|.|+||+|||++++++++.+.
T Consensus         7 ~~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            45789999999999999999999885

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.39  E-value=0.023  Score=58.34  Aligned_cols=37  Identities=24%  Similarity=0.265  Sum_probs=28.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~  289 (473)
                      ++.++|.||+|+|||+++..+|..+   +..+..+++...
T Consensus       206 ~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDty  245 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTF  245 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCcc
Confidence            5568999999999999999999876   555655555443

>PRK12338 hypothetical protein; Provisional

Probab=96.39  E-value=0.0033  Score=63.17  Aligned_cols=30  Identities=27%  Similarity=0.346  Sum_probs=26.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      |.-+++.|+||||||++++++|..++...+
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l~~~~~   33 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTLNIKHL   33 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHCCCeEE
Confidence            457899999999999999999999997653

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.39  E-value=0.0029  Score=57.09  Aligned_cols=37  Identities=35%  Similarity=0.461  Sum_probs=30.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR  290 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~  290 (473)
                      .-+.|.|.||+|||++|+++...|   +.+++.+|...+.
T Consensus         3 ~vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD~lR   42 (156)
T PF01583_consen    3 FVIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGDNLR   42 (156)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHHHHC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCcchh
Confidence            358899999999999999999988   7888888877653

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=96.38  E-value=0.0034  Score=57.90  Aligned_cols=29  Identities=28%  Similarity=0.489  Sum_probs=25.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .-+.+.||+|+|||+++++++..++...+
T Consensus         4 e~i~l~G~sGsGKSTl~~~la~~l~~~~i   32 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFSAKFI   32 (176)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCEEE
Confidence            35899999999999999999999987543

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.38  E-value=0.0028  Score=58.15  Aligned_cols=25  Identities=28%  Similarity=0.382  Sum_probs=22.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      -++|.||||+|||+++++|+..++.
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCc
Confidence            4789999999999999999998754

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=96.36  E-value=0.016  Score=55.53  Aligned_cols=27  Identities=22%  Similarity=0.450  Sum_probs=23.7

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+.-...++||.|+|||||++.++.+.
T Consensus        55 ~~ge~W~I~G~NGsGKTTLL~ll~~~~   81 (257)
T COG1119          55 NPGEHWAIVGPNGAGKTTLLSLLTGEH   81 (257)
T ss_pred             cCCCcEEEECCCCCCHHHHHHHHhccc
Confidence            445578999999999999999999876

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.36  E-value=0.017  Score=52.29  Aligned_cols=29  Identities=21%  Similarity=0.197  Sum_probs=23.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEE
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYD  283 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~  283 (473)
                      -+.+|+++|+|||++|-++|-..   |..+..
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~~g~~v~~   35 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALGHGYRVGV   35 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence            37889999999999999888765   555554

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=96.36  E-value=0.013  Score=64.25  Aligned_cols=28  Identities=36%  Similarity=0.599  Sum_probs=24.4

Q ss_pred             CCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          250 KAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       250 ~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +++..-+.+.||+|+|||||++.|++.+
T Consensus       373 i~~G~~vaIvG~SGsGKSTL~~lL~g~~  400 (588)
T PRK11174        373 LPAGQRIALVGPSGAGKTSLLNALLGFL  400 (588)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3445679999999999999999999976

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.35  E-value=0.011  Score=60.33  Aligned_cols=53  Identities=13%  Similarity=0.026  Sum_probs=37.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh---------cCCceEEcccccccCchHHHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY---------LNFDVYDLELTELRSNSDLRTLLVA  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~---------l~~~~~~l~~~~~~~~~~l~~l~~~  301 (473)
                      |++...-+.|+||||||||.|+..+|-.         ++-.+++++...-.....+.+....
T Consensus       122 Gi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~  183 (344)
T PLN03187        122 GIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAER  183 (344)
T ss_pred             CCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            5666666899999999999999877632         1356777877654455666665543

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms

Probab=96.33  E-value=0.025  Score=52.24  Aligned_cols=24  Identities=33%  Similarity=0.548  Sum_probs=21.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -..++||.|+|||++..||+-.++
T Consensus        24 ~~~i~G~NGsGKSnil~Ai~~~~~   47 (178)
T cd03239          24 FNAIVGPNGSGKSNIVDAICFVLG   47 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcC
Confidence            467999999999999999987763

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>PRK11545 gntK gluconate kinase 1; Provisional

Probab=96.32  E-value=0.0031  Score=57.36  Aligned_cols=27  Identities=30%  Similarity=0.464  Sum_probs=23.4

Q ss_pred             eCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          259 YGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       259 ~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .||||||||+++++++..++..+++-|
T Consensus         1 ~G~sGsGKSTla~~la~~l~~~~~~~d   27 (163)
T PRK11545          1 MGVSGSGKSAVASEVAHQLHAAFLDGD   27 (163)
T ss_pred             CCCCCCcHHHHHHHHHHHhCCeEEeCc
Confidence            399999999999999999987666554

>TIGR00959 ffh signal recognition particle protein

Probab=96.32  E-value=0.25  Score=52.02  Aligned_cols=37  Identities=24%  Similarity=0.305  Sum_probs=29.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~~  289 (473)
                      +.-+++.||+|+|||+++..+|.++    |..+..+++...
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l~~~~g~kV~lV~~D~~  139 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYLKKKQGKKVLLVACDLY  139 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHhCCCeEEEEecccc
Confidence            5679999999999999999888774    566766666544

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.31  E-value=0.0078  Score=60.54  Aligned_cols=40  Identities=15%  Similarity=0.189  Sum_probs=30.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~~~  288 (473)
                      |.+...-++++||||||||+++..+|-..         +-.+++++...
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            56666678999999999999999887653         23667776554

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.

>KOG0479 consensus DNA replication licensing factor, MCM3 component [Replication, recombination and repair]

Probab=96.31  E-value=0.011  Score=62.63  Aligned_cols=112  Identities=20%  Similarity=0.290  Sum_probs=66.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc--c-----------cCchHHHHHHHHhccCceEEEecccccccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE--L-----------RSNSDLRTLLVATANRSILVVEDIDCTIDLQD  321 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~--~-----------~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~  321 (473)
                      ++||.|.|.+.||-|.+.+-|.....+-..--.+  +           .++..|..--.-...++|++|||+|.+.+   
T Consensus       336 NiLlvGDPSvAKSQLLRyVLntAplAI~TTGRGSSGVGLTAAVTtD~eTGERRLEAGAMVLADRGVVCIDEFDKMsD---  412 (818)
T KOG0479|consen  336 NILLVGDPSVAKSQLLRYVLNTAPLAIATTGRGSSGVGLTAAVTTDQETGERRLEAGAMVLADRGVVCIDEFDKMSD---  412 (818)
T ss_pred             eEEEecCchHHHHHHHHHHHhcccccccccCCCCCCccceeEEeeccccchhhhhcCceEEccCceEEehhcccccc---
Confidence            5999999999999999999987744332211111  0           12223322111235789999999998843   


Q ss_pred             CCccccCCCCCCCccchhHHHHHHHHHh------cccccCCCCceEEEEecCCCC-------------CCCccccCCCce
Q 012016          322 RLPADIAGEGEGPIQQNKVTLSGFLNFI------DGLWSSCGDERIIVFTTNHKE-------------KLDPALLRPGRM  382 (473)
Q Consensus       322 r~~~~~~~~~~~~~~~~~~~ls~LL~~l------dg~~~~~~~~~iiI~tTN~~~-------------~ld~aLlrpgRf  382 (473)
                                     ..+..+.....+=      .|+..+-....-|+++.|...             .|+..|+.  ||
T Consensus       413 ---------------iDRvAIHEVMEQqtVTIaKAGIHasLNARCSVlAAANPvyG~Yd~~k~P~eNIgLpDSLLS--RF  475 (818)
T KOG0479|consen  413 ---------------IDRVAIHEVMEQQTVTIAKAGIHASLNARCSVLAAANPVYGQYDQSKTPMENIGLPDSLLS--RF  475 (818)
T ss_pred             ---------------hhHHHHHHHHhcceEEeEeccchhhhccceeeeeecCccccccCCCCChhhccCCcHHHHh--hh
Confidence                           1233333333221      133333334456888888652             35677888  99


Q ss_pred             eeEE
Q 012016          383 DVHV  386 (473)
Q Consensus       383 d~~I  386 (473)
                      |...
T Consensus       476 DLlF  479 (818)
T KOG0479|consen  476 DLLF  479 (818)
T ss_pred             cEEE
Confidence            8543

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=96.31  E-value=0.017  Score=62.94  Aligned_cols=26  Identities=27%  Similarity=0.454  Sum_probs=23.2

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++..+.+.||+|+|||||++.|++.+
T Consensus       357 ~G~~v~IvG~sGsGKSTLl~lL~gl~  382 (571)
T TIGR02203       357 PGETVALVGRSGSGKSTLVNLIPRFY  382 (571)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            34569999999999999999999887

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.

>cd04177 RSR1 RSR1 subgroup

Probab=96.30  E-value=0.02  Score=51.68  Aligned_cols=23  Identities=26%  Similarity=0.478  Sum_probs=20.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++|.|+||+|||+++.++++..
T Consensus         3 ki~liG~~~~GKTsli~~~~~~~   25 (168)
T cd04177           3 KIVVLGAGGVGKSALTVQFVQNV   25 (168)
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            48999999999999999988544

RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=96.30  E-value=0.01  Score=64.10  Aligned_cols=27  Identities=30%  Similarity=0.532  Sum_probs=23.8

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++..-+.+.||+|+|||||++.+++..
T Consensus       359 ~~G~~vaIvG~SGsGKSTLl~lL~g~~  385 (529)
T TIGR02868       359 PPGERVAILGPSGSGKSTLLMLLTGLL  385 (529)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            345569999999999999999999877

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.

>PLN02165 adenylate isopentenyltransferase

Probab=96.29  E-value=0.0045  Score=62.50  Aligned_cols=37  Identities=19%  Similarity=0.389  Sum_probs=31.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +.-+.|.||+|+|||+|+..||..++..++..|.-.+
T Consensus        43 g~iivIiGPTGSGKStLA~~LA~~l~~eIIsaDs~Qv   79 (334)
T PLN02165         43 DKVVVIMGATGSGKSRLSVDLATRFPSEIINSDKMQV   79 (334)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHcCCceecCChhee
Confidence            3468999999999999999999999988777665433

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=96.29  E-value=0.0042  Score=58.27  Aligned_cols=32  Identities=22%  Similarity=0.248  Sum_probs=28.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      -+.++||+|+|||++++.+++.+|+++++.|.
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~~g~~~i~~D~   34 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQKGIPILDADI   34 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCeEeeCcH
Confidence            47899999999999999999998999987653

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.28  E-value=0.014  Score=63.71  Aligned_cols=85  Identities=21%  Similarity=0.344  Sum_probs=53.0

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccc-----
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT-----  287 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~-----  287 (473)
                      .+|+++.+.++..+.+.+.+.    .          +...+|++||.|+|||+++.++.++++   .+++.++-.     
T Consensus       293 ~~l~~lg~~~~~~~~l~~~~~----~----------~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~tiEdpvE~~~  358 (564)
T TIGR02538       293 LDIDKLGFEPDQKALFLEAIH----K----------PQGMVLVTGPTGSGKTVSLYTALNILNTEEVNISTAEDPVEINL  358 (564)
T ss_pred             CCHHHcCCCHHHHHHHHHHHH----h----------cCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEEEecCCceecC
Confidence            578999988876665543322    1          123478999999999999988888874   234432211     


Q ss_pred             -cc-----c--CchHHHHHHHHh--ccCceEEEeccc
Q 012016          288 -EL-----R--SNSDLRTLLVAT--ANRSILVVEDID  314 (473)
Q Consensus       288 -~~-----~--~~~~l~~l~~~~--~~~sIL~iDdiD  314 (473)
                       .+     .  ....+...+...  .+|.||++.||-
T Consensus       359 ~~~~q~~v~~~~g~~~~~~l~~~LR~dPDvI~vGEiR  395 (564)
T TIGR02538       359 PGINQVNVNPKIGLTFAAALRSFLRQDPDIIMVGEIR  395 (564)
T ss_pred             CCceEEEeccccCCCHHHHHHHHhccCCCEEEeCCCC
Confidence             11     1  112344444433  378999999995

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	473
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		4e-13
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-11
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		3e-11
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		3e-11
2ce7_A	476	Edta Treated Length = 476		4e-11
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		1e-10
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-10
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		3e-10
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		1e-09
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		3e-09
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		2e-08
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		2e-08
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		2e-08
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		4e-08
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		4e-08
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		5e-08
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		5e-08
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		5e-08
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		7e-08
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		4e-07
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		5e-07
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		6e-07
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		7e-07
3vfd_A	389	Human Spastin Aaa Domain Length = 389		8e-07
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		9e-07
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		7e-05

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score = 72.8 bits (177), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 91/176 (51%), Gaps = 17/176 (9%)
Query: 216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 275
           +T++ +    +Q  +I + +E  VK  + +  +G A  +G +LYGPPGTGK+ L  A+A+
Sbjct: 145 STYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAH 204
Query: 276 YLNFDVYDLELTEL------RSNSDLRTLLVATANR--SILVVEDIDCTIDLQDRLPADI 327
           + +     +   EL        +  +R L V       SI+ +++ID     +     + 
Sbjct: 205 HTDCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTR----VEG 260
Query: 328 AGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           +G G+  +Q+   T+   LN +DG  +S   +  I+  TN  + LDPALLRPGR+D
Sbjct: 261 SGGGDSEVQR---TMLELLNQLDGFETSKNIK--IIMATNRLDILDPALLRPGRID 311

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 67.8 bits (164), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/187 (29%), Positives = 90/187 (48%), Gaps = 17/187 (9%)
Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF+ +    EQ  ++ + +E  +K  + ++RVG    +G LLYGPPGTGK+ L  A+A  
Sbjct: 179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT 238
Query: 277 L--NF------DVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIA 328
           +  NF       + D  + E  S   +R +          ++      +D  D +     
Sbjct: 239 IGANFIFSPASGIVDKYIGE--SARIIREMFAYAKEHEPCII-----FMDEVDAIGGRRF 291
Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
            EG    ++ + TL   L  +DG + + G  +II+  TN  + LDPALLRPGR+D  V +
Sbjct: 292 SEGTSADREIQRTLMELLTQMDG-FDNLGQTKIIM-ATNRPDTLDPALLRPGRLDRKVEI 349
Query: 389 SYCTPSG 395
                +G
Sbjct: 350 PLPNEAG 356

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/166 (31%), Positives = 80/166 (48%), Gaps = 19/166 (11%)
Query: 227 QKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL 286
           QK +I + +E  + + D Y ++G    RG LLYGPPGTGK+ L+ A+AN        +  
Sbjct: 180 QKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNG 239
Query: 287 TEL---------RSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQ 337
           +E          R   D+  L    A  SI+ ++++D       R  A    + E  +Q+
Sbjct: 240 SEFVHKYLGEGPRMVRDVFRLARENAP-SIIFIDEVDSIA--TKRFDAQTGSDRE--VQR 294
Query: 338 NKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
               L   L  +DG   S   +  ++  TN  + LDPALLRPGR+D
Sbjct: 295 ---ILIELLTQMDGFDQSTNVK--VIMATNRADTLDPALLRPGRLD 335

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 57/187 (30%), Positives = 92/187 (49%), Gaps = 19/187 (10%)
Query: 210 VNLDHP-ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSS 268
           +N + P   F+ +A  +E K ++++ ++ F+K  + Y  +G    +G LL GPPGTGK+ 
Sbjct: 1   INAEKPNVRFKDMAGNEEAKEEVVEIVD-FLKYPERYANLGAKIPKGVLLVGPPGTGKTL 59
Query: 269 LIAAMANYLNFDVYDL------ELTELRSNSDLRTLLVATANR---SILVVEDIDCTIDL 319
           L  A+A   +   + +      E+      S +R L   TA +   SI+ +++ID  I  
Sbjct: 60  LAKAVAGEAHVPFFSMGGSSFIEMFVGLGASRVRDLF-ETAKKQAPSIIFIDEIDA-IGK 117
Query: 320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRP 379
                  ++G  E      + TL+  L  +DG  S      I++  TN  E LDPAL+RP
Sbjct: 118 SRAAGGVVSGNDE-----REQTLNQLLAEMDGFGSENA-PVIVLAATNRPEILDPALMRP 171
Query: 380 GRMDVHV 386
           GR D  V
Sbjct: 172 GRFDRQV 178

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 66.2 bits (160), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 52/172 (30%), Positives = 79/172 (45%), Gaps = 29/172 (16%)
Query: 226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE 285
           E+  + ++++  F+K    + R+G    +G LL GPPGTGK+ L  A+A   N   + + 
Sbjct: 22  EEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHI- 80
Query: 286 LTELRSNSDLRTLLVATANRS--------------ILVVEDIDCTIDLQDRLPADIAGEG 331
                S SD   L V                    I+ +++ID     +       AG G
Sbjct: 81  -----SGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRG------AGLG 129
Query: 332 EGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
            G  ++ + TL+  L  +DG  S  G   I++  TN  + LDPALLRPGR D
Sbjct: 130 GGHDEREQ-TLNQLLVEMDGFDSKEGI--IVMAATNRPDILDPALLRPGRFD 178

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 56/174 (32%), Positives = 88/174 (50%), Gaps = 17/174 (9%)
Query: 218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL 277
           +E +   ++Q  +I + +E  +K  + + +VG    +G LLYGPPGTGK+ L  A+A   
Sbjct: 16  YEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET 75
Query: 278 NFDVYDLELTEL------RSNSDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIAG 329
           N     +  +EL         S ++ +  L      SI+ +++ID       R  A   G
Sbjct: 76  NATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIA--AKRTDALTGG 133
Query: 330 EGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           + E  +Q+   TL   L  +DG + + GD +II   TN  + LDPA+LRPGR D
Sbjct: 134 DRE--VQR---TLMQLLAEMDG-FDARGDVKII-GATNRPDILDPAILRPGRFD 180

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 64.3 bits (155), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 51/172 (29%), Positives = 78/172 (45%), Gaps = 29/172 (16%)
Query: 226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE 285
           E+  + ++++  F+K    + R+G    +G LL GPPGTG + L  A+A   N   + + 
Sbjct: 22  EEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGATLLARAVAGEANVPFFHI- 80
Query: 286 LTELRSNSDLRTLLVATANRS--------------ILVVEDIDCTIDLQDRLPADIAGEG 331
                S SD   L V                    I+ +++ID     +       AG G
Sbjct: 81  -----SGSDFVELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRG------AGLG 129
Query: 332 EGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
            G  ++ + TL+  L  +DG  S  G   I++  TN  + LDPALLRPGR D
Sbjct: 130 GGHDEREQ-TLNQLLVEMDGFDSKEGI--IVMAATNRPDILDPALLRPGRFD 178

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 63.2 bits (152), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 86/185 (46%), Gaps = 32/185 (17%)
Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF  +A   E K ++ + +E +++    ++++G    +G L+ GPPGTGK+ L  A+A  
Sbjct: 10  TFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68
Query: 277 LNFDVYDLELTELRSNSDLRTLLVAT--------------ANRSILVVEDIDCTIDLQDR 322
                + +      S SD   + V                A   I+ +++ID     +  
Sbjct: 69  AKVPFFTI------SGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG- 121
Query: 323 LPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGR 381
                AG G G  ++ + TL+  L  +DG     G+E IIV   TN  + LDPALLRPGR
Sbjct: 122 -----AGLGGGHDEREQ-TLNQMLVEMDGFE---GNEGIIVIAATNRPDVLDPALLRPGR 172
Query: 382 MDVHV 386
            D  V
Sbjct: 173 FDRQV 177

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 61.6 bits (148), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/167 (33%), Positives = 85/167 (50%), Gaps = 17/167 (10%)
Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN-----YLNF 279
           + Q  +I + +E  +   + Y  +G    +G +LYG PGTGK+ L  A+AN     +L  
Sbjct: 188 ESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRI 247
Query: 280 DVYDLELTELRSNSDL--RTLLVATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
              +L    L     L  +   VA  N  SI+ +++ID       R  ++  GE E  IQ
Sbjct: 248 VGSELIQKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAI--GTKRYDSNSGGERE--IQ 303
Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           +   T+   LN +DG +   GD ++I+  TN  E LDPAL+RPGR+D
Sbjct: 304 R---TMLELLNQLDG-FDDRGDVKVIM-ATNKIETLDPALIRPGRID 345

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score = 59.7 bits (143), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 82/165 (49%), Gaps = 21/165 (12%)
Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL---ELTELRSNSDL 295
           +KR D ++ +G    +G L+YGPPGTGK+ L  A A   N     L   +L ++      
Sbjct: 201 MKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLVQMYIGEGA 260
Query: 296 RTL-----LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID 350
           + +     L      +I+ ++++D       R  ++ +G+ E  +Q+   T+   LN +D
Sbjct: 261 KLVRDAFALAKEKAPTIIFIDELDAIG--TKRFDSEKSGDRE--VQR---TMLELLNQLD 313
Query: 351 GLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHMSYCTPS 394
           G  S   D+R+ V   TN  + LDPALLR GR+D  +   +  PS
Sbjct: 314 GFSS---DDRVKVLAATNRVDVLDPALLRSGRLDRKIE--FPLPS 353

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 48/184 (26%), Positives = 91/184 (49%), Gaps = 17/184 (9%)
Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           +F+ +A   E K ++ + ++ ++K  + + ++G    +G LL GPPG GK+ L  A+A  
Sbjct: 4   SFKDVAGMHEAKLEVREFVD-YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE 62
Query: 277 LNFDVYDLELTEL------RSNSDLRTLLVATANRS--ILVVEDIDCTIDLQDRLPADIA 328
                  +   E          + +R+L      R+  I+ +++ID    +  +    ++
Sbjct: 63  AQVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDA---VGKKRSTTMS 119
Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
           G      +Q   TL+  L  +DG+ ++  D  I++ +TN  + LD AL+RPGR+D HV +
Sbjct: 120 GFSNTEEEQ---TLNQLLVEMDGMGTT--DHVIVLASTNRADILDGALMRPGRLDRHVFI 174
Query: 389 SYCT 392
              T
Sbjct: 175 DLPT 178

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 84/180 (46%), Gaps = 17/180 (9%)
Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           T+E +   ++ K ++ + ++  V+  D + + G    +G L YGPPG GK+ L  A+AN 
Sbjct: 13  TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 72
Query: 277 LNFDVYDLELTEL------RSNSDLRTLL--VATANRSILVVEDIDCTIDLQDRLPADIA 328
              +   ++  EL       S +++R +      A   +L  +++D     +     D  
Sbjct: 73  CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGG 132
Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
           G  +  I Q        L  +DG+  S      I+  TN  + +DPA+LRPGR+D  +++
Sbjct: 133 GAADRVINQ-------ILTEMDGM--STKKNVFIIGATNRPDIIDPAILRPGRLDQLIYI 183

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score = 57.4 bits (137), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 84/181 (46%), Gaps = 17/181 (9%)
Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           T+  +   ++Q  K+ + +E  +   + +  +G    +G LLYGPPGTGK+    A+AN 
Sbjct: 207 TYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANR 266
Query: 277 LN---FDVYDLELTELRSNSDLRTL-----LVATANRSILVVEDIDCTIDLQDRLPADIA 328
            +     V   EL +       R +     +  T    I+  ++ID     +     D  
Sbjct: 267 TDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGAR----FDDG 322
Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
             G+  +Q+  + L   +  +DG +   G+ +++ F TN    LDPALLRPGR+D  V  
Sbjct: 323 AGGDNEVQRTMLEL---ITQLDG-FDPRGNIKVM-FATNRPNTLDPALLRPGRIDRKVEF 377
Query: 389 S 389
           S
Sbjct: 378 S 378

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 84/180 (46%), Gaps = 17/180 (9%)
Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           T+E +   ++ K ++ + ++  V+  D + + G    +G L YGPPG GK+ L  A+AN 
Sbjct: 475 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 534
Query: 277 LNFDVYDLELTEL------RSNSDLRTLL--VATANRSILVVEDIDCTIDLQDRLPADIA 328
              +   ++  EL       S +++R +      A   +L  +++D     +     D  
Sbjct: 535 CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGG 594
Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
           G  +  I Q        L  +DG+  S      I+  TN  + +DPA+LRPGR+D  +++
Sbjct: 595 GAADRVINQ-------ILTEMDGM--STKKNVFIIGATNRPDIIDPAILRPGRLDQLIYI 645

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 84/180 (46%), Gaps = 17/180 (9%)
Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           T+E +   ++ K ++ + ++  V+  D + + G    +G L YGPPG GK+ L  A+AN 
Sbjct: 475 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 534
Query: 277 LNFDVYDLELTEL------RSNSDLRTLL--VATANRSILVVEDIDCTIDLQDRLPADIA 328
              +   ++  EL       S +++R +      A   +L  +++D     +     D  
Sbjct: 535 CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGG 594
Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
           G  +  I Q        L  +DG+  S      I+  TN  + +DPA+LRPGR+D  +++
Sbjct: 595 GAADRVINQ-------ILTEMDGM--STKKNVFIIGATNRPDIIDPAILRPGRLDQLIYI 645

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 80/179 (44%), Gaps = 20/179 (11%)
Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL 284
           ++Q  +I + +E  ++    ++ +G    RG LLYGPPGTGK+ +  A+AN      + +
Sbjct: 210 RKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLI 269
Query: 285 ELTEL------RSNSDLRTLLVATANR--SILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
              E+       S S+LR           +I+ ++++D     +++   ++         
Sbjct: 270 NGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV--------- 320
Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSG 395
             +  +S  L  +DGL        I++  TN    +DPAL R GR D  V +     +G
Sbjct: 321 -ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 80/179 (44%), Gaps = 20/179 (11%)
Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL 284
           ++Q  +I + +E  ++    ++ +G    RG LLYGPPGTGK+ +  A+AN      + +
Sbjct: 210 RKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLI 269
Query: 285 ELTEL------RSNSDLRTLLVATANR--SILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
              E+       S S+LR           +I+ ++++D     +++   ++         
Sbjct: 270 NGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV--------- 320
Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSG 395
             +  +S  L  +DGL        I++  TN    +DPAL R GR D  V +     +G
Sbjct: 321 -ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 44/186 (23%), Positives = 83/186 (44%), Gaps = 20/186 (10%)
Query: 218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL 277
           ++ +   ++Q  +I + +E  ++    ++ +G    RG LLYGPPGTGK+ +  A+AN  
Sbjct: 203 YDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET 262
Query: 278 NFDVYDLELTEL------RSNSDLRTLLVATANR--SILVVEDIDCTIDLQDRLPADIAG 329
               + +   E+       S S+LR           +I+ ++++D     +++   ++  
Sbjct: 263 GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV-- 320
Query: 330 EGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMS 389
                    +  +S  L  +DGL        I++  TN    +DPAL R GR D  V + 
Sbjct: 321 --------ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIG 370
Query: 390 YCTPSG 395
               +G
Sbjct: 371 IPDATG 376

>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 = 55.5 bits (132), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 80/179 (44%), Gaps = 20/179 (11%)
Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL 284
           ++Q  +I + +E  ++    ++ +G    RG LLYGPPGTGK+ +  A+AN      + +
Sbjct: 210 RKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLI 269
Query: 285 ELTEL------RSNSDLRTLLVATANR--SILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
              E+       S S+LR           +I+ ++++D     +++   ++         
Sbjct: 270 NGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEV--------- 320
Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSG 395
             +  +S  L  +DGL        I++  TN    +DPAL R GR D  V +     +G
Sbjct: 321 -ERRIVSQLLTLMDGLKQRA--HVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATG 376

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score = 52.8 bits (125), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 65/161 (40%), Gaps = 25/161 (15%)
Query: 238 FVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRT 297
           F+K    +  +G    +G LL GPPG GK+ L  A+A                S SD   
Sbjct: 49  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITA------SGSDFVE 102
Query: 298 LLVA-----------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL 346
           + V            TA R    +  ID  ID   R      G G    +Q   TL+  L
Sbjct: 103 MFVGVGAARVRDLFETAKRHAPCIVFID-EIDAVGRKRGSGVGGGNDEREQ---TLNQLL 158
Query: 347 NFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHV 386
             +DG      D  I+V   TN  + LDPALLRPGR D  +
Sbjct: 159 VEMDGFEK---DTAIVVMAATNRPDILDPALLRPGRFDRQI 196

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 65/161 (40%), Gaps = 25/161 (15%)
Query: 238 FVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRT 297
           F+K    +  +G    +G LL GPPG GK+ L  A+A                S SD   
Sbjct: 58  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITA------SGSDFVE 111
Query: 298 LLVA-----------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL 346
           + V            TA R    +  ID  ID   R      G G    +Q   TL+  L
Sbjct: 112 MFVGVGAARVRDLFETAKRHAPCIVFID-EIDAVGRKRGSGVGGGNDEREQ---TLNQLL 167
Query: 347 NFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHV 386
             +DG      D  I+V   TN  + LDPALLRPGR D  +
Sbjct: 168 VEMDGFEK---DTAIVVMAATNRPDILDPALLRPGRFDRQI 205

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 50/163 (30%), Positives = 66/163 (40%), Gaps = 25/163 (15%)
Query: 238 FVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRT 297
           F+K    +  +G    +G LL GPPG GK+ L  A+A                S SD   
Sbjct: 34  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITA------SGSDFVE 87
Query: 298 LLVA-----------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL 346
           + V            TA R    +  ID  ID   R      G G     + + TL+  L
Sbjct: 88  MFVGVGAARVRDLFETAKRHAPCIVFID-EIDAVGRKRGSGVGGGN---DEREQTLNQLL 143
Query: 347 NFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHM 388
             +DG      D  I+V   TN  + LDPALLRPGR D  + +
Sbjct: 144 VEMDGFEK---DTAIVVMAATNRPDILDPALLRPGRFDRQIAI 183

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 52.0 bits (123), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 50/163 (30%), Positives = 66/163 (40%), Gaps = 25/163 (15%)
Query: 238 FVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRT 297
           F+K    +  +G    +G LL GPPG GK+ L  A+A                S SD   
Sbjct: 58  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITA------SGSDFVE 111
Query: 298 LLVA-----------TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL 346
           + V            TA R    +  ID  ID   R      G G     + + TL+  L
Sbjct: 112 MFVGVGAARVRDLFETAKRHAPCIVFID-EIDAVGRKRGSGVGGGN---DEREQTLNQLL 167
Query: 347 NFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHM 388
             +DG      D  I+V   TN  + LDPALLRPGR D  + +
Sbjct: 168 VEMDGFEK---DTAIVVMAATNRPDILDPALLRPGRFDRQIAI 207

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score = 52.0 bits (123), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 57/210 (27%), Positives = 95/210 (45%), Gaps = 16/210 (7%)
Query: 173 PCVEKEAKSVQQESKTIKILTVNYNNLYCN-WTDAWIPVNLDHPATFETLAMEQEQKTKI 231
           P     A   +++ K  + +  N  NL  N   D    V  D  A  + LA +  Q+  I
Sbjct: 74  PSTPTTATRKKKDLKNFRNVDSNLANLIMNEIVDNGTAVKFDDIAG-QDLAKQALQEIVI 132
Query: 232 MQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS 291
           +  L     R + +  + +A  RG LL+GPPG GK+ L  A+A   N   +++    L S
Sbjct: 133 LPSL-----RPELFTGL-RAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTS 186
Query: 292 N--SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFI 349
               +   L+ A       V  ++  +I   D++ + +    EG    ++   + FL   
Sbjct: 187 KYVGEGEKLVRAL----FAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEF 242
Query: 350 DGLWSSCGDERIIVF-TTNHKEKLDPALLR 378
           DG+  S GD+R++V   TN  ++LD A+LR
Sbjct: 243 DGVQ-SAGDDRVLVMGATNRPQELDEAVLR 271

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score = 51.6 bits (122), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 42/161 (26%), Positives = 72/161 (44%), Gaps = 14/161 (8%)
Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTL 298
           V+  D ++ +G     G LL GPPG GK+ L  A+AN    +   ++  EL +      +
Sbjct: 30  VRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLN------M 83
Query: 299 LVATANRSILVV-----EDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW 353
            V  + R++  V         C I   D + A      +     +   ++  L  +DGL 
Sbjct: 84  YVGESERAVRQVFQRAKNSAPCVI-FFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLE 142
Query: 354 SSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPS 394
           +    +  I+  TN  + +DPA+LRPGR+D  + +    P+
Sbjct: 143 AR--QQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPA 181

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score = 45.4 bits (106), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 41/177 (23%), Positives = 81/177 (45%), Gaps = 21/177 (11%)
Query: 212 LDH--PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSL 269
           +DH  P  +E +A  +  K  I + +   + R D +  + +   +G LL+GPPGTGK+ +
Sbjct: 75  MDHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGL-RGPPKGILLFGPPGTGKTLI 133
Query: 270 IAAMANYLNFDVYDLELTELRS-----NSDLRTLLVATA---NRSILVVEDIDCTIDLQD 321
              +A+      + +  + L S        +   L A A     +++ +++ID  +  + 
Sbjct: 134 GKCIASQSGATFFSISASSLTSKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQR- 192
Query: 322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR 378
                    G+G  + ++   + FL  +DG  +S  D  ++V  TN  +++D A  R
Sbjct: 193 ---------GDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARR 240

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	473
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	9e-19
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	5e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	3e-13
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	4e-13
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	3e-11
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	8e-11
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	1e-10
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	1e-10
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	2e-10
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	3e-10
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	3e-10
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	4e-10
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	8e-10
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	4e-09
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	2e-08
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	4e-08
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	2e-07
2qgz_A	308	Helicase loader, putative primosome component; str	2e-07
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	4e-07
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	6e-07
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-06
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	2e-04
2fna_A	357	Conserved hypothetical protein; structural genomic	4e-06
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	6e-06
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	6e-06
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	7e-04
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	2e-05
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	4e-05
2chg_A	226	Replication factor C small subunit; DNA-binding pr	1e-04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	1e-04
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	2e-04

>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 = 76.0 bits (186), Expect = 9e-15
 Identities = 71/474 (14%), Positives = 142/474 (29%), Gaps = 160/474 (33%)

Query: 106 NHVNISMESDEQ------VVDVFNGIKLKWVLVCRQVE--------SRSFNH---SSTNI 148
           +H ++  E+ E       ++ VF          C+ V+            +H   S   +
Sbjct: 3   HHHHMDFETGEHQYQYKDILSVFED-AFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAV 61

Query: 149 QAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWI 208
              +R F                   + K+ + VQ+  + +  L +NY  L         
Sbjct: 62  SGTLRLFWTL----------------LSKQEEMVQKFVEEV--LRINYKFLM----SPIK 99

Query: 209 PVNLDHPATFETLAMEQEQKTKIMQDLERF----VKRKDYYRRVGKAWKR-----GYLLY 259
                 P+      M  EQ+ ++  D + F    V R   Y ++ +A          L+ 
Sbjct: 100 TEQRQ-PSMMTR--MYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLID 156

Query: 260 GPPGTGKSSLIAAMAN------YLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDI 313
           G  G+GK+ +   +         ++F ++ L L    S   +           + +++ +
Sbjct: 157 GVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV-----------LEMLQKL 205

Query: 314 DCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF---------IDGLWSS--------- 355
              ID      +D +   +  I   +  L   L           +  + ++         
Sbjct: 206 LYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLS 265

Query: 356 CGDERIIVFTTNHK---EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK----- 407
           C   +I++ TT  K   + L  A      +D H  M+        LL   YL  +     
Sbjct: 266 C---KILL-TTRFKQVTDFLSAATTTHISLD-HHSMTLTPDEVKSLL-LKYLDCRPQDLP 319

Query: 408 ----------------------------EHILFEEIEELI--STTQVTPAE--------- 428
                                       +H+  +++  +I  S   + PAE         
Sbjct: 320 REVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379

Query: 429 -------VAEQL-------MRNDDPELVLNGLIEFLKVKRKEDEDAKPRK--IH 466
                  +   L       +   D  +V+N L ++  V++      K     I 
Sbjct: 380 VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK----QPKESTISIP 429

>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 = 51.8 bits (123), Expect = 4e-07
 Identities = 72/486 (14%), Positives = 139/486 (28%), Gaps = 158/486 (32%)

Query: 28  TVMLARTVARDLLPYEIQDYFYFR------------------LRKFCNRFSSQLTIVIDE 69
           T  +A  V      Y++Q    F+                  L+K   +     T   D 
Sbjct: 164 TW-VALDVCLS---YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH 219

Query: 70  HDG--LAKNQIYDAAKVYLGKKTSPSVQRIKVSKLEKENHVNISMESDEQVVDVFNGIKL 127
                L  + I    +  L  K   +   +    L    +V      + +  + FN +  
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPYENCLLV----LL---NV-----QNAKAWNAFN-LSC 266

Query: 128 KWVLVCRQVESRSFNHSSTNIQAQVRYFELTFPKKYKDVVIGSYLPCVEKEAKSVQQESK 187
           K +L  R  +   F  ++T     + +  +T        ++  YL C     + + +E  
Sbjct: 267 KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC---RPQDLPREVL 323

Query: 188 TIKILTVNYNNLYCNWTDAWIPVNL-DHPATFETLA-MEQEQKTKIMQ----DLERFVKR 241
           T     +           + I  ++ D  AT++    +  ++ T I++     LE    R
Sbjct: 324 TTNPRRL-----------SIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYR 372

Query: 242 KDYYRRVG--------------KAWKRGYLLYGPPGT-----GKSSLIAAMANYLNFDVY 282
           K  + R+                 W    ++            K SL+          + 
Sbjct: 373 K-MFDRLSVFPPSAHIPTILLSLIW--FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIP 429

Query: 283 DLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL 342
            + L       +   L     +RSI+   +I  T D  D +P                  
Sbjct: 430 SIYLELKVKLENEYAL-----HRSIVDHYNIPKTFDSDDLIP------------------ 466

Query: 343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHV--HMSYCTPSG-FKLL 399
                ++D  + S                             H+  H+          L 
Sbjct: 467 ----PYLDQYFYS-----------------------------HIGHHLKNIEHPERMTLF 493

Query: 400 AANYLGIKEHILFEEIEELI---STTQVTPAEVAEQL---------MRNDDP--ELVLNG 445
              +L       F  +E+ I   ST       +   L         + ++DP  E ++N 
Sbjct: 494 RMVFLD------FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNA 547

Query: 446 LIEFLK 451
           +++FL 
Sbjct: 548 ILDFLP 553

>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 = 70.6 bits (173), Expect = 3e-13
 Identities = 47/175 (26%), Positives = 81/175 (46%), Gaps = 20/175 (11%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
            ++ +   ++Q  +I + +E  ++    ++ +G    RG LLYGPPGTGK+ +  A+AN 
Sbjct: 202 GYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 261

Query: 277 LNFDVYDLELTEL------RSNSDLRTLL-VATANR-SILVVEDIDCTIDLQDRLPADIA 328
                + +   E+       S S+LR     A  N  +I+ ++++D     ++       
Sbjct: 262 TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKRE----KTH 317

Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
           GE E      +  +S  L  +DGL        I++  TN    +DPAL R GR D
Sbjct: 318 GEVE------RRIVSQLLTLMDGL--KQRAHVIVMAATNRPNSIDPALRRFGRFD 364

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score = 68.4 bits (168), Expect = 4e-13
 Identities = 56/166 (33%), Positives = 86/166 (51%), Gaps = 17/166 (10%)

Query: 226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE 285
           +Q  +I + +E  +K  + + +VG    +G LLYGPPGTGK+ L  A+A   N     + 
Sbjct: 24  KQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVV 83

Query: 286 LTEL------RSNSDLRTLL-VATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQ 337
            +EL         S ++ +  +A     SI+ +++ID  I  + R  A   G+ E  +Q+
Sbjct: 84  GSELVKKFIGEGASLVKDIFKLAKEKAPSIIFIDEID-AIAAK-RTDALTGGDRE--VQR 139

Query: 338 NKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMD 383
              TL   L  +DG   + GD +II   TN  + LDPA+LRPGR D
Sbjct: 140 ---TLMQLLAEMDGF-DARGDVKIIG-ATNRPDILDPAILRPGRFD 180

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score = 62.9 bits (153), Expect = 3e-11
 Identities = 26/164 (15%), Positives = 50/164 (30%), Gaps = 23/164 (14%)

Query: 242 KDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL------------ 289
           K++ +           ++G  G GKS     +   +  +   +   EL            
Sbjct: 25  KNFLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLI 84

Query: 290 RSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF- 348
           R        ++   N   L + D+D                    +     TL    +  
Sbjct: 85  RQRYREAAEIIRKGNMCCLFINDLDAGA--GRMGGTTQYTVNNQMVNA---TLMNIADNP 139

Query: 349 ----IDGLWSSCGDERI-IVFTTNHKEKLDPALLRPGRMDVHVH 387
               + G+++   + R+ I+ T N    L   L+R GRM+    
Sbjct: 140 TNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW 183

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score = 61.6 bits (150), Expect = 8e-11
 Identities = 54/189 (28%), Positives = 80/189 (42%), Gaps = 32/189 (16%)

Query: 213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAA 272
               TF+ +A  +E K ++ +++  F+K    +  +G    +G LL GPPG GK+ L  A
Sbjct: 34  APKVTFKDVAGAEEAKEEL-KEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARA 92

Query: 273 MANYLNFDVYDLELTELRSNSDLRTLLVAT-ANRSILVVED--------------IDCTI 317
           +A                S SD   + V   A R    V D              ID  I
Sbjct: 93  VAGEARVPFITA------SGSDFVEMFVGVGAAR----VRDLFETAKRHAPCIVFID-EI 141

Query: 318 DLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALL 377
           D   R     +G G G  ++ + TL+  L  +DG         +++  TN  + LDPALL
Sbjct: 142 DAVGRKRG--SGVGGGNDEREQ-TLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALL 196

Query: 378 RPGRMDVHV 386
           RPGR D  +
Sbjct: 197 RPGRFDRQI 205

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score = 61.2 bits (149), Expect = 1e-10
 Identities = 57/185 (30%), Positives = 85/185 (45%), Gaps = 32/185 (17%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF  +A   E K + + +L  +++    ++++G    +G L+ GPPGTGK+ L  A+A  
Sbjct: 10  TFADVAGCDEAKEE-VAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68

Query: 277 LNFDVYDLELTELRSNSDLRTLLVAT-ANRSILVVED--------------IDCTIDLQD 321
                + +      S SD   + V   A+R    V D              ID  ID   
Sbjct: 69  AKVPFFTI------SGSDFVEMFVGVGASR----VRDMFEQAKKAAPCIIFID-EIDAVG 117

Query: 322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGR 381
           R     AG G G  ++ + TL+  L  +DG   + G   I++  TN  + LDPALLRPGR
Sbjct: 118 RQRG--AGLGGGHDEREQ-TLNQMLVEMDGFEGNEG--IIVIAATNRPDVLDPALLRPGR 172

Query: 382 MDVHV 386
            D  V
Sbjct: 173 FDRQV 177

>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 = 60.8 bits (148), Expect = 1e-10
 Identities = 54/185 (29%), Positives = 80/185 (43%), Gaps = 32/185 (17%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF+ +A  +E K + ++++  F+K    +  +G    +G LL GPPG GK+ L  A+A  
Sbjct: 14  TFKDVAGAEEAKEE-LKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 72

Query: 277 LNFDVYDLELTELRSNSDLRTLLVAT-ANRSILVVED--------------IDCTIDLQD 321
                         S SD   + V   A R    V D              ID  ID   
Sbjct: 73  ARVPFITA------SGSDFVEMFVGVGAAR----VRDLFETAKRHAPCIVFID-EIDAVG 121

Query: 322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGR 381
           R     +G G G  ++ + TL+  L  +DG         +++  TN  + LDPALLRPGR
Sbjct: 122 RKRG--SGVGGGNDEREQ-TLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGR 176

Query: 382 MDVHV 386
            D  +
Sbjct: 177 FDRQI 181

>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 = 60.3 bits (147), Expect = 2e-10
 Identities = 50/187 (26%), Positives = 83/187 (44%), Gaps = 34/187 (18%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
            F+ +A  +E K ++++ ++ F+K  + Y  +G    +G LL GPPGTGK+ L  A+A  
Sbjct: 9   RFKDMAGNEEAKEEVVEIVD-FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGE 67

Query: 277 LNFDVYDLELTELRSNSDLRTLLVAT-ANR-------------SILVVEDIDCTIDLQDR 322
            +   + +        S    + V   A+R             SI+ +++ID     + R
Sbjct: 68  AHVPFFSM------GGSSFIEMFVGLGASRVRDLFETAKKQAPSIIFIDEIDAI--GKSR 119

Query: 323 LPADIAG---EGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRP 379
               +     E E  + Q    + GF +    +        I++  TN  E LDPAL+RP
Sbjct: 120 AAGGVVSGNDEREQTLNQLLAEMDGFGSENAPV--------IVLAATNRPEILDPALMRP 171

Query: 380 GRMDVHV 386
           GR D  V
Sbjct: 172 GRFDRQV 178

>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 = 60.1 bits (146), Expect = 3e-10
 Identities = 33/172 (19%), Positives = 64/172 (37%), Gaps = 27/172 (15%)

Query: 226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL- 284
           +  T+++ D E  V++     R         LL GPP +GK++L A +A   NF    + 
Sbjct: 40  DPVTRVLDDGELLVQQTKNSDRTPL---VSVLLEGPPHSGKTALAAKIAEESNFPFIKIC 96

Query: 285 ------ELTELRSNSDLRTLLV-ATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
                   +E      ++ +   A  ++ S +VV+DI+  +D        I         
Sbjct: 97  SPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYV-----PIGPRFS---- 147

Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVH 387
              + L   L  +          ++++  TT+ K+ L   +         +H
Sbjct: 148 --NLVLQALLVLLKKAPPQ--GRKLLIIGTTSRKDVLQ-EMEMLNAFSTTIH 194

>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 = 59.6 bits (145), Expect = 3e-10
 Identities = 45/186 (24%), Positives = 87/186 (46%), Gaps = 31/186 (16%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           +F+ +A   E K ++ + ++ ++K  + + ++G    +G LL GPPG GK+ L  A+A  
Sbjct: 4   SFKDVAGMHEAKLEVREFVD-YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE 62

Query: 277 LNFDVYDLELTELRSNSDLRTLLVAT-ANR-------------SILVVEDIDCTIDLQDR 322
                  +      + ++   ++    A R              I+ +++ID    +  +
Sbjct: 63  AQVPFLAM------AGAEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDA---VGKK 113

Query: 323 LPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGR 381
               ++G      +Q   TL+  L  +DG+ +    + +IV  +TN  + LD AL+RPGR
Sbjct: 114 RSTTMSGFSNTEEEQ---TLNQLLVEMDGMGT---TDHVIVLASTNRADILDGALMRPGR 167

Query: 382 MDVHVH 387
           +D HV 
Sbjct: 168 LDRHVF 173

>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 = 60.2 bits (146), Expect = 4e-10
 Identities = 52/196 (26%), Positives = 91/196 (46%), Gaps = 28/196 (14%)

Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT-----ELR 290
           + R D +  +    K G LL+GPPGTGK+ +   +A+      F +    LT     E  
Sbjct: 104 MLRPDIFTGLRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGE-- 160

Query: 291 SNSDLRTL-LVATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF 348
               +R L  VA   + +++ +++ID    L  R      G+GE    +   T   FL  
Sbjct: 161 GEKMVRALFAVARCQQPAVIFIDEIDSL--LSQR------GDGEHESSRRIKT--EFLVQ 210

Query: 349 IDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK 407
           +DG  +S  ++RI+V   TN  +++D A  R  R+   +++     S  K +  N +  +
Sbjct: 211 LDGATTS-SEDRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKE 267

Query: 408 EHILFE-EIEELISTT 422
           +  L E EIE+++  +
Sbjct: 268 QCCLSEEEIEQIVQQS 283

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score = 58.9 bits (143), Expect = 8e-10
 Identities = 51/196 (26%), Positives = 82/196 (41%), Gaps = 27/196 (13%)

Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT-----ELR 290
             R + +  +    K G LL+GPPG GK+ L  A+A   +    ++    LT     +  
Sbjct: 41  SVRPELFTGLRAPAK-GLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSKYVGD-- 97

Query: 291 SNSDLRTL-LVATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF 348
               +R L  VA   + SI+ ++++D        L    + E E     ++   + FL  
Sbjct: 98  GEKLVRALFAVARHMQPSIIFIDEVDSL------LSERSSSEHEA----SRRLKTEFLVE 147

Query: 349 IDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK 407
            DGL  +   +RI+V   TN  ++LD A LR  R    V++S       +LL    L  +
Sbjct: 148 FDGLPGNPDGDRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQ 205

Query: 408 EHIL-FEEIEELISTT 422
              L  E +  L   T
Sbjct: 206 GSPLDTEALRRLAKIT 221

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score = 57.5 bits (139), Expect = 4e-09
 Identities = 55/196 (28%), Positives = 87/196 (44%), Gaps = 28/196 (14%)

Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT-----ELR 290
             R + +  +    + G LL+GPPG GK+ L  A+A   N   F++    LT     E  
Sbjct: 135 SLRPELFTGLRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGE-- 191

Query: 291 SNSDLRTL-LVATANR-SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF 348
               +R L  VA   + SI+ ++ +D        L     GE +     ++   + FL  
Sbjct: 192 GEKLVRALFAVARELQPSIIFIDQVDSL------LCERREGEHDA----SRRLKTEFLIE 241

Query: 349 IDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK 407
            DG+  S GD+R++V   TN  ++LD A+LR  R    V++S        LL  N L  +
Sbjct: 242 FDGV-QSAGDDRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQ 298

Query: 408 EHILFE-EIEELISTT 422
              L + E+ +L   T
Sbjct: 299 GSPLTQKELAQLARMT 314

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426} Length = 202

 Score = 53.5 bits (129), Expect = 2e-08
 Identities = 25/108 (23%), Positives = 48/108 (44%), Gaps = 15/108 (13%)

Query: 216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 275
           A+   + +  + + K ++  ERFV   +  ++      +G  L+G  G GK+ L+AA+AN
Sbjct: 22  ASLSDVDLNDDGRIKAIRFAERFVAEYEPGKK-----MKGLYLHGSFGVGKTYLLAAIAN 76

Query: 276 YL---NFDVY-----DL--ELTELRSNSDLRTLLVATANRSILVVEDI 313
            L   N         +L  EL     +  +   L       +L+++D+
Sbjct: 77  ELAKRNVSSLIVYVPELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDL 124

>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 = 54.5 bits (131), Expect = 4e-08
 Identities = 23/104 (22%), Positives = 37/104 (35%), Gaps = 21/104 (20%)

Query: 215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGY----LLYGPPGTGKSSLI 270
           P   + +   +    K+   L  +   K    +       G     +LYGPPG GK++  
Sbjct: 35  PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA 94

Query: 271 AAMANYLNFDVYDLELTELRSN-SDLRTLLVATANRSILVVEDI 313
             +A  L +D+  LE      N SD          RS  ++   
Sbjct: 95  HLVAQELGYDI--LEQ-----NASD---------VRSKTLLNAG 122

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 51.6 bits (124), Expect = 2e-07
 Identities = 43/157 (27%), Positives = 64/157 (40%), Gaps = 29/157 (18%)

Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN----FDVYDLELT-----EL 289
           +K    +      W+ G LL+GPPGTGKS L  A+A   N    F +   +L      E 
Sbjct: 32  IKFPHLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGE- 89

Query: 290 RSNSDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN 347
            S   ++ L  L      SI+ +++ID       R       E E    +   T   FL 
Sbjct: 90  -SEKLVKNLFQLARENKPSIIFIDEIDSL--CGSR------SENESEAARRIKT--EFLV 138

Query: 348 FIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMD 383
            + G+     ++ I+V   TN    LD A+ R  R +
Sbjct: 139 QMQGV--GVDNDGILVLGATNIPWVLDSAIRR--RFE 171

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3} Length = 308

 Score = 51.4 bits (123), Expect = 2e-07
 Identities = 33/168 (19%), Positives = 59/168 (35%), Gaps = 33/168 (19%)

Query: 159 FPKKYKD--VVIGSYLPCVEKEAKSVQQESKTIKILTVNYNNLYCNWTDAWIPVNLDHPA 216
            P    +      SYL   E       Q+   I       +          +P +  H  
Sbjct: 76  QPILAMNEGYADVSYLETKELVE---AQKQAAISERIQLVS----------LPKSYRH-I 121

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
               + +    + +    +  FV++         A ++G  LYG  G GKS L+AAMA+ 
Sbjct: 122 HLSDIDVNNASRMEAFSAILDFVEQYP------SAEQKGLYLYGDMGIGKSYLLAAMAHE 175

Query: 277 LN---------FDVYDL--ELTELRSNSDLRTLLVATANRSILVVEDI 313
           L+                 ++    SN  ++  + A  N  +L+++DI
Sbjct: 176 LSEKKGVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDI 223

>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 = 50.8 bits (122), Expect = 4e-07
 Identities = 44/160 (27%), Positives = 67/160 (41%), Gaps = 28/160 (17%)

Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT-----ELR 290
           VK    ++   K    G LLYGPPGTGKS L  A+A   N   F V   +L      E  
Sbjct: 38  VKFPHLFKGNRKPTS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGE-- 94

Query: 291 SNSDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF 348
           S   ++ L  +      SI+ ++ +D       R      GEGE    +   T    L  
Sbjct: 95  SEKLVKQLFAMARENKPSIIFIDQVDAL--TGTR------GEGESEASRRIKT--ELLVQ 144

Query: 349 IDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVH 387
           ++G+      + ++V   TN   +LD A+ R  R +  ++
Sbjct: 145 MNGV--GNDSQGVLVLGATNIPWQLDSAIRR--RFERRIY 180

>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 = 48.5 bits (116), Expect = 6e-07
 Identities = 23/109 (21%), Positives = 37/109 (33%), Gaps = 17/109 (15%)

Query: 216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN 275
           A  +T   +   + + +  +  FV   +          +G    G PG GK+ L  A   
Sbjct: 7   ANLDTYHPKNVSQNRALLTIRVFVHNFN------PEEGKGLTFVGSPGVGKTHLAVATLK 60

Query: 276 YLN---------FDVYDL--ELTELRSNSDLRTLLVATANRSILVVEDI 313
            +          FD  DL   L  L         L    N  +LV++D+
Sbjct: 61  AIYEKKGIRGYFFDTKDLIFRLKHLMDEGKDTKFLKTVLNSPVLVLDDL 109

>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 = 48.4 bits (116), Expect = 2e-06
 Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 2/57 (3%)

Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN--YLNF 279
           ++ K ++ + ++  V+  D + + G    +G L YGPPG GK+ L  A+AN    NF
Sbjct: 21  EDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANF 77

>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 = 42.2 bits (100), Expect = 2e-04
 Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)

Query: 342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVH 387
           ++  L  +DG+  S      I+  TN  + +DPA+LRPGR+D  ++
Sbjct: 139 INQILTEMDGM--STKKNVFIIGATNRPDIIDPAILRPGRLDQLIY 182

>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 Length = 357

 Score = 47.8 bits (113), Expect = 4e-06
 Identities = 27/134 (20%), Positives = 47/134 (35%), Gaps = 2/134 (1%)

Query: 233 QDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV--YDLELTELR 290
            + + F  R+    ++        L+ G   TGKSS+I    N LN      DL   E R
Sbjct: 10  DNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEER 69

Query: 291 SNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID 350
           +    +  L+        +V+ +   +     +   +    E     N+     F N ++
Sbjct: 70  NYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLE 129

Query: 351 GLWSSCGDERIIVF 364
               +  D  IIV 
Sbjct: 130 SFEQASKDNVIIVL 143

>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 = 47.6 bits (113), Expect = 6e-06
 Identities = 48/197 (24%), Positives = 79/197 (40%), Gaps = 30/197 (15%)

Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN----FDVYDLELT-----EL 289
           +K    +      W+ G LL+GPPGTGKS L  A+A   N    F +   +L      E 
Sbjct: 154 IKFPHLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGE- 211

Query: 290 RSNSDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN 347
            S   ++ L  L      SI+ +++ID          +    E E   +      + FL 
Sbjct: 212 -SEKLVKNLFQLARENKPSIIFIDEIDSL------CGSRSENESEAARR----IKTEFLV 260

Query: 348 FIDGLWSSCGDERIIVF-TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI 406
            + G+     ++ I+V   TN    LD A+ R  R +  +++          +   +LG 
Sbjct: 261 QMQGVGVD--NDGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGS 316

Query: 407 KEHILFEE-IEELISTT 422
            ++ L E   +EL   T
Sbjct: 317 TQNSLTEADFQELGRKT 333

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score = 46.8 bits (112), Expect = 6e-06
 Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN--YLNF 279
           ++ + ++   +   V+  D ++ +G     G LL GPPG GK+ L  A+AN   LNF
Sbjct: 16  EDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNF 72

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score = 40.2 bits (95), Expect = 7e-04
 Identities = 30/131 (22%), Positives = 56/131 (42%), Gaps = 19/131 (14%)

Query: 342 LSGFLNFIDGLWSSCGDERIIVF---TTNHKEKLDPALLRPGRMDVHVHMSYCTPSG--- 395
           ++  L  +DGL     + R  VF    TN  + +DPA+LRPGR+D  + +    P+    
Sbjct: 131 VNQLLTEMDGL-----EARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLA 185

Query: 396 -FKLLAANYLGIK--EHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKV 452
             K +  N         +  E I   +     T A+++  L+R    E  +  L + +  
Sbjct: 186 ILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSA-LVR----EASICALRQEMAR 240

Query: 453 KRKEDEDAKPR 463
           ++  +E  + +
Sbjct: 241 QKSGNEKGELK 251

>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 = 45.6 bits (108), Expect = 2e-05
 Identities = 43/158 (27%), Positives = 66/158 (41%), Gaps = 24/158 (15%)

Query: 239 VKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELTEL---RSN 292
           VK    ++   K    G LLYGPPGTGKS L  A+A   N   F V   +L       S 
Sbjct: 71  VKFPHLFKGNRKPTS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMGESE 129

Query: 293 SDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFID 350
             ++ L  +      SI+ ++ +D       R      GEGE    +   T    L  ++
Sbjct: 130 KLVKQLFAMARENKPSIIFIDQVDAL--TGTR------GEGESEASRRIKT--ELLVQMN 179

Query: 351 GLWSSCGDERIIVFT-TNHKEKLDPALLRPGRMDVHVH 387
           G+      + ++V   TN   +LD A+ R  R +  ++
Sbjct: 180 GV--GNDSQGVLVLGATNIPWQLDSAIRR--RFERRIY 213

>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 Length = 377

 Score = 44.6 bits (105), Expect = 4e-05
 Identities = 21/108 (19%), Positives = 40/108 (37%), Gaps = 14/108 (12%)

Query: 253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVED 312
           KR +L  GP  +GK++L AA+         ++ L   R N +L                 
Sbjct: 169 KRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVA-------------- 214

Query: 313 IDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER 360
           ID  + + + +        + P  Q    L    +++DG      +++
Sbjct: 215 IDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKK 262

>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} Length = 226

 Score = 42.6 bits (101), Expect = 1e-04
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 257 LLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL 289
           L  GPPGTGK++   A+A  L  + +     E+
Sbjct: 42  LFSGPPGTGKTATAIALARDLFGENWRDNFIEM 74

>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 Length = 319

 Score = 43.1 bits (102), Expect = 1e-04
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 257 LLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL 289
           L  GPPGTGK++   A+A  L  + +     E+
Sbjct: 42  LFSGPPGTGKTATAIALARDLFGENWRDNFIEM 74

>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 Length = 327

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 3/41 (7%)

Query: 257 LLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN-SDLR 296
           L  GPPG GK++   A+A  L  + +     EL  N SD R
Sbjct: 50  LFAGPPGVGKTTAALALARELFGENWRHNFLEL--NASDER 88

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	473
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	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
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.96
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.96
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.96
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.95
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.95
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.95
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.95
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.95
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.94
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.94
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.94
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.93
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.92
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.92
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.92
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.92
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.91
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.91
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.91
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.9
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.87
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.82
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.8
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.79
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.77
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.77
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.74
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.73
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.71
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.71
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.71
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.68
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.68
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.68
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.67
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.65
3pvs_A	447	Replication-associated recombination protein A; ma	99.65
3bos_A	242	Putative DNA replication factor; P-loop containing	99.65
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.63
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.63
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.62
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.62
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.62
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.61
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.6
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.6
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.6
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.59
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.59
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.58
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.58
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.58
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.57
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.56
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.55
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.55
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.55
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.54
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.52
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.51
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.51
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.51
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.51
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.5
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.47
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.46
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.44
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.39
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.39
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.38
3co5_A	143	Putative two-component system transcriptional RES	99.37
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.34
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.34
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.3
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.24
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.23
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.21
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	99.11
2qgz_A	308	Helicase loader, putative primosome component; str	99.07
1tue_A	212	Replication protein E1; helicase, replication, E1E	99.07
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	98.96
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.9
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.88
2fna_A	357	Conserved hypothetical protein; structural genomic	98.83
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.83
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.8
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.8
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.74
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.71
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.63
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.53
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.51
3f8t_A	506	Predicted ATPase involved in replication control,	98.5
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.39
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.21
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.19
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.15
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.79
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.76
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.71
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.69
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.69
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.65
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.62
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.61
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.59
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.58
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.58
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.55
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.53
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.51
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.49
1via_A	175	Shikimate kinase; structural genomics, transferase	97.49
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.48
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.48
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.48
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.47
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.46
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.45
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.45
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.45
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.43
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.42
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.38
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.37
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.35
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.34
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.33
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.32
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.31
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.29
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.29
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.28
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.28
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.28
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.27
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.27
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.26
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.26
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.23
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.22
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.22
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.21
3io5_A	333	Recombination and repair protein; storage dimer, i	97.21
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.2
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.2
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.2
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.2
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	97.19
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.18
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.18
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.16
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.16
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.14
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	97.13
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.12
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	97.11
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	97.1
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.07
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.07
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	97.05
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.05
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	97.04
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.01
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	97.0
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.97
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.96
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.95
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.95
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.9
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.9
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.89
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.89
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.88
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.88
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.87
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.86
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.84
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.84
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.83
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.82
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	96.82
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.8
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.79
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.79
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.78
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.77
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.77
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.75
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.67
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	96.65
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.65
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.61
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	96.58
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.56
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.55
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.55
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	96.54
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.54
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.54
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	96.51
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.51
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	96.5
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.48
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.48
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.46
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.45
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.43
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.43
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	96.41
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.41
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.38
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.37
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.35
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	96.34
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.34
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.34
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.33
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	96.32
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.3
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.28
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	96.28
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.25
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.25
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	96.24
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	96.23
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	96.21
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	96.21
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	96.21
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.2
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	96.19
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.17
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	96.16
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.15
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	96.14
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	96.12
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	96.09
1nrj_B	218	SR-beta, signal recognition particle receptor beta	96.08
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	96.07
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	96.04
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	96.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	95.98
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.96
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	95.96
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.95
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	95.93
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.92
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.91
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.9
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.9
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	95.88
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	95.86
3b6e_A	216	Interferon-induced helicase C domain-containing P;	95.84
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	95.83
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.82
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	95.81
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.8
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	95.8
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	95.79
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	95.79
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	95.77
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.77
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.76
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	95.75
3kw6_A	78	26S protease regulatory subunit 8; structural geno	95.74
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	95.74
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	95.74
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.71
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	95.71
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	95.7
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	95.66
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	95.66
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.65
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	95.64
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.63
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.62
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	95.61
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	95.55
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.55
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	95.52
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.52
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	95.51
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	95.51
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	95.5
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	95.48
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	95.48
2og2_A	359	Putative signal recognition particle receptor; nuc	95.47
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.47
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.47
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.4
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	95.38
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.35
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.35
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	95.32
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	95.3
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.3
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	95.28
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	95.21
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	95.2
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.2
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	95.17
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	95.16
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	95.15
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	95.14
1p9r_A	418	General secretion pathway protein E; bacterial typ	95.13
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	95.13
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.13
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.11
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	95.11
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	95.11
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.11
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	95.1
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	95.1
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	95.09
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.06
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.05
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	95.04
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.03
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	95.01
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.01
2ewv_A	372	Twitching motility protein PILT; pilus retraction	95.01
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.94
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.94
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	94.93
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.91
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	94.91
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	94.9
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	94.88
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	94.88
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	94.87
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	94.87
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.84
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	94.83
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	94.79
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	94.73
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	94.73
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	94.71
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	94.69
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.69
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	94.64
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.62
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.61
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	94.6
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.6
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.59
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	94.59
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.58
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	94.57
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.56
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	94.55
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	94.54
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.53
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.53
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	94.53
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	94.51
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	94.5
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	94.47
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	94.46
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.46
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	94.43
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.42
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.41
2xxa_A	433	Signal recognition particle protein; protein trans	94.4
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	94.4
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	94.38
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.37
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	94.36
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.36
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	94.32
2krk_A	86	26S protease regulatory subunit 8; structural geno	94.29
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	94.28
3llu_A	196	RAS-related GTP-binding protein C; structural geno	94.28
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.27
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	94.27
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.26
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.25
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.24
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	94.23
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.21
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.18
1b0u_A	262	Histidine permease; ABC transporter, transport pro	94.16
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	94.15
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	94.15
1sgw_A	214	Putative ABC transporter; structural genomics, P p	94.11
2fh5_B	214	SR-beta, signal recognition particle receptor beta	94.1
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.08
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	94.08
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.08
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	94.05
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	94.04
2ghi_A	260	Transport protein; multidrug resistance protein, M	94.03
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	94.03
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	94.01
1g6h_A	257	High-affinity branched-chain amino acid transport	94.0
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	93.99
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.98
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	93.96
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.94
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.92
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	93.91
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	93.9
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.89
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.87
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	93.85
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	93.83
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	93.82
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.82
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.81
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	93.81
1ji0_A	240	ABC transporter; ATP binding protein, structural g	93.8
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.78
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	93.78
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.77
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.7
2wji_A	165	Ferrous iron transport protein B homolog; membrane	93.7
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.69
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.69
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	93.67
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.67
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.63
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.62
3def_A	262	T7I23.11 protein; chloroplast, TOC33, GTPase, hydr	93.61
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.59
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	93.58
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	93.57
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	93.55
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	93.53
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.52
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.51
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.51
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.48
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.46
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.43
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.38
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.38
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.37
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	93.36
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	93.35
3cpj_B	223	GTP-binding protein YPT31/YPT8; RAB GTPase, prenyl	93.32
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	93.27
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	93.23
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.22
3ice_A	422	Transcription termination factor RHO; transcriptio	93.18
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.17
3iby_A	256	Ferrous iron transport protein B; G protein, G dom	93.15
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	93.12
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.1
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	93.09
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.0
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	92.99
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	92.98
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	92.98
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	92.98
3gj0_A	221	GTP-binding nuclear protein RAN; G protein, GDP, a	92.97
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	92.96
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	92.91
4djt_A	218	GTP-binding nuclear protein GSP1; structural genom	92.9
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	92.85
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	92.84
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	92.84
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	92.81
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.8
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	92.8
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	92.78
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	92.74
3r7w_A	307	Gtpase1, GTP-binding protein GTR1; RAG gtpases, GT	92.67
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	92.66
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.65
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.65
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	92.65
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	92.61
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	92.61
2hf9_A	226	Probable hydrogenase nickel incorporation protein	92.57
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	92.54
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	92.53
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	92.45
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	92.42
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	92.41
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	92.39
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	92.37
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.34
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.33
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	92.3
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.29
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.27
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	92.27
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	92.25
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.23
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	92.23
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	92.22
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.16
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	92.14

>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=1.8e-40  Score=338.77  Aligned_cols=213  Identities=25%  Similarity=0.315  Sum_probs=180.1

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .+..+|++|+|.+++|++|.+.+..++.+++.|++.|.++++|+|||||||||||+||+|+|++++.+++.++++++.  
T Consensus       142 ~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l~sk  221 (405)
T 4b4t_J          142 VPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELVQK  221 (405)
T ss_dssp             SCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGGSCS
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHhhcc
Confidence            455899999999999999999999999999999999999999999999999999999999999999999999999874  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ++..++.+|..+.  .||||||||||+++..+....       .+.+.....++++||+.|||+.+.  .+++||+
T Consensus       222 ~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~-------~~~~~~~~~~l~~lL~~lDg~~~~--~~V~vIa  292 (405)
T 4b4t_J          222 YIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGS-------GGGDSEVQRTMLELLNQLDGFETS--KNIKIIM  292 (405)
T ss_dssp             STTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSS-------SGGGGHHHHHHHHHHHHHHTTTCC--CCEEEEE
T ss_pred             ccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCC-------CCCcHHHHHHHHHHHHhhhccCCC--CCeEEEe
Confidence                3467888888774  799999999999986332211       122345678899999999999765  4599999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      |||+|+.|||||+||||||++|+|++|+.++|.+||+.++.........++..++..+ ++|+|||..+|.
T Consensus       293 ATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~  363 (405)
T 4b4t_J          293 ATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCT  363 (405)
T ss_dssp             EESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             ccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999998754322222344444433 699999988773

>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=5.7e-40  Score=336.04  Aligned_cols=215  Identities=23%  Similarity=0.325  Sum_probs=180.1

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR  290 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~  290 (473)
                      .-.+..+|++|+|.+++|++|.+.+..|+.+++.|.+.|.+|++|||||||||||||+||+|+|++++.+++.++.+++.
T Consensus       174 ~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s~l~  253 (437)
T 4b4t_I          174 DKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELI  253 (437)
T ss_dssp             ESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESGGGC
T ss_pred             ccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHHHhh
Confidence            34566899999999999999999999999999999999999999999999999999999999999999999999998874


Q ss_pred             ------CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE
Q 012016          291 ------SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII  362 (473)
Q Consensus       291 ------~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  362 (473)
                            ++..++.+|..+.  .||||||||||+++..+.  ...     .+.+.....++++||+.|||+...  ++++|
T Consensus       254 sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~--~~~-----~~~~~~~~~~l~~LL~~lDg~~~~--~~ViV  324 (437)
T 4b4t_I          254 QKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRY--DSN-----SGGEREIQRTMLELLNQLDGFDDR--GDVKV  324 (437)
T ss_dssp             CSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCS--CSS-----CSSCCHHHHHHHHHHHHHHHCCCS--SSEEE
T ss_pred             hccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCC--CCC-----CCccHHHHHHHHHHHHHhhCcCCC--CCEEE
Confidence                  3456788887764  789999999999986332  211     122345678999999999998654  56999


Q ss_pred             EEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHHh
Q 012016          363 VFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQLM  434 (473)
Q Consensus       363 I~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l~  434 (473)
                      |+|||+|+.|||||+||||||++|+|++|+.++|.+||+.++.........+++.++.. .++|+|||..+|.
T Consensus       325 IaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~  397 (437)
T 4b4t_I          325 IMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCT  397 (437)
T ss_dssp             EEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             EEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999999875432222233444433 3699999988774

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.9e-39  Score=334.62  Aligned_cols=231  Identities=23%  Similarity=0.317  Sum_probs=186.7

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .+..+|++|+|.+++|++|.+.+..++.+++.|.+.|.+|++|+|||||||||||++|+|+|++++.+++.++++++.  
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s~l~sk  254 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDK  254 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGTCCS
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehhhhccc
Confidence            456899999999999999999999999999999999999999999999999999999999999999999999999874  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          +...++.+|..+.  .||||||||||+++..+.  ...     ...+.....++++||+.|||+.+.  ++++||+
T Consensus       255 ~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~--~~~-----~~~~~~~~~~l~~lL~~lDg~~~~--~~vivI~  325 (437)
T 4b4t_L          255 YIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRF--SEG-----TSADREIQRTLMELLTQMDGFDNL--GQTKIIM  325 (437)
T ss_dssp             SSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCS--SSC-----CSSTTHHHHHHHHHHHHHHSSSCT--TSSEEEE
T ss_pred             cchHHHHHHHHHHHHHHhcCCceeeeecccccccccc--cCC-----CCcchHHHHHHHHHHHHhhcccCC--CCeEEEE
Confidence                2456788887664  799999999999986332  111     122344577899999999999765  4699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHhc-------C
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLMR-------N  436 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~~-------~  436 (473)
                      |||+|+.|||||+||||||.+|+||+|+.++|..||+.++.........++..++..+ ++|+|||..+|..       .
T Consensus       326 ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~eA~~~air~  405 (437)
T 4b4t_L          326 ATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGFFAIRD  405 (437)
T ss_dssp             EESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHHHHHHHHHHT
T ss_pred             ecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHHHHHHHHHHc
Confidence            9999999999999999999999999999999999999998654322222344444433 6999999887742       2


Q ss_pred             CCHHHHHHHHHHHHHH
Q 012016          437 DDPELVLNGLIEFLKV  452 (473)
Q Consensus       437 ~~~~~al~~l~~~l~~  452 (473)
                      +......+++..++++
T Consensus       406 ~~~~i~~~d~~~Al~~  421 (437)
T 4b4t_L          406 DRDHINPDDLMKAVRK  421 (437)
T ss_dssp             TCSSBCHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHH
Confidence            2222334555555543

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.4e-39  Score=336.77  Aligned_cols=213  Identities=23%  Similarity=0.336  Sum_probs=179.6

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR  290 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~  290 (473)
                      .-.++.+|++|+|.+++|++|.+.+..|+.+++.|++.|.++++|||||||||||||++|+|+|++++.+++.++++++.
T Consensus       173 ~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s~l~  252 (434)
T 4b4t_M          173 DEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLV  252 (434)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGGC
T ss_pred             CCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehhhhh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999999874


Q ss_pred             ------CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE
Q 012016          291 ------SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII  362 (473)
Q Consensus       291 ------~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  362 (473)
                            +...++.+|..+.  .||||||||+|+++..  |.....     +.......++++||+.|||+.+.  ++++|
T Consensus       253 ~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~--R~~~~~-----~~~~~~~~~~~~lL~~ldg~~~~--~~ViV  323 (434)
T 4b4t_M          253 QMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTK--RFDSEK-----SGDREVQRTMLELLNQLDGFSSD--DRVKV  323 (434)
T ss_dssp             SSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCC--CSSGGG-----GTTHHHHHHHHHHHHHHTTSCSS--CSSEE
T ss_pred             hcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhc--cCCCCC-----CCchHHHHHHHHHHHHhhccCCC--CCEEE
Confidence                  2456788887664  7999999999999863  322111     12334567899999999999765  46999


Q ss_pred             EEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc---cCCHHHHHHHHhcCCCCHHHHHHHHh
Q 012016          363 VFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE---HILFEEIEELISTTQVTPAEVAEQLM  434 (473)
Q Consensus       363 I~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~---~~l~~~i~~l~~~~~~t~a~i~~~l~  434 (473)
                      |+|||+|+.|||||+||||||.+|+||+|+.++|.+||+.++....   ....++++...+  ++|+|||..+|.
T Consensus       324 IaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~--G~sGADi~~l~~  396 (434)
T 4b4t_M          324 LAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTD--EFNGAQLKAVTV  396 (434)
T ss_dssp             EEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCS--SCCHHHHHHHHH
T ss_pred             EEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCC--CCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999998886432   233445544433  699999988874

>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=4.3e-39  Score=332.84  Aligned_cols=214  Identities=25%  Similarity=0.372  Sum_probs=179.6

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-  290 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-  290 (473)
                      -.+..+|++|+|.+++|++|.+.+..|+.+++.|.+.|++|++|+|||||||||||++|+|+|++++.+++.++++++. 
T Consensus       165 ~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l~~  244 (428)
T 4b4t_K          165 EKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFVH  244 (428)
T ss_dssp             SSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGTCC
T ss_pred             CCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchhhc
Confidence            3556899999999999999999999999999999999999999999999999999999999999999999999999873 


Q ss_pred             -----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          291 -----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       291 -----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                           +...++.+|..+.  .||||||||+|+++..+.  ...     .+.+....+++++||+.|||+.+.  .+++||
T Consensus       245 ~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~--~~~-----~~~~~~~~r~l~~lL~~ldg~~~~--~~v~vI  315 (428)
T 4b4t_K          245 KYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRF--DAQ-----TGSDREVQRILIELLTQMDGFDQS--TNVKVI  315 (428)
T ss_dssp             SSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCS--SSC-----SCCCCHHHHHHHHHHHHHHHSCSS--CSEEEE
T ss_pred             cccchhHHHHHHHHHHHHHcCCCeeechhhhhhhcccc--CCC-----CCCChHHHHHHHHHHHHhhCCCCC--CCEEEE
Confidence                 3467888888764  789999999999986332  111     122345678999999999999776  459999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeC-CCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHHh
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMS-YCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQLM  434 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~-~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l~  434 (473)
                      +|||+|+.|||||+||||||++|+|| +|+.++|..|++.++.........++..++.. .++|+|||..+|.
T Consensus       316 ~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~  388 (428)
T 4b4t_K          316 MATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQ  388 (428)
T ss_dssp             EEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHH
T ss_pred             EecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHH
Confidence            99999999999999999999999997 89999999999998865432222234444443 3699999988874

>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=1.1e-38  Score=329.45  Aligned_cols=214  Identities=26%  Similarity=0.315  Sum_probs=180.6

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +.-.+..+|++|+|.+++|++|.+.+..++.+++.|.++|+++++|+|||||||||||+||+|+|++++.+++.++++++
T Consensus       200 v~e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s~L  279 (467)
T 4b4t_H          200 VEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSEL  279 (467)
T ss_dssp             EESSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGGGG
T ss_pred             ecCCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhHHh
Confidence            33456689999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             c------CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceE
Q 012016          290 R------SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI  361 (473)
Q Consensus       290 ~------~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  361 (473)
                      .      ++..++.+|..+.  .||||||||+|.++..+..  ..     .+.......+++.||+.|||....  .+++
T Consensus       280 ~sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~--~~-----~~~~~~~~~~l~~lL~~lDg~~~~--~~Vi  350 (467)
T 4b4t_H          280 VQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFD--DG-----AGGDNEVQRTMLELITQLDGFDPR--GNIK  350 (467)
T ss_dssp             CCCSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSS--SS-----CGGGGHHHHHHHHHHHHHHSSCCT--TTEE
T ss_pred             hcccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccC--cC-----CCccHHHHHHHHHHHHHhhccCCC--CcEE
Confidence            4      3467888888764  7899999999999863321  11     122345567899999999998654  5699


Q ss_pred             EEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc---CCHHHHHHHHhcCCCCHHHHHHHHh
Q 012016          362 IVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH---ILFEEIEELISTTQVTPAEVAEQLM  434 (473)
Q Consensus       362 iI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~---~l~~~i~~l~~~~~~t~a~i~~~l~  434 (473)
                      ||+|||+|+.|||||+||||||++|+|++|+.++|.+||+.++.....   ...+.++...+  ++|+|||..+|.
T Consensus       351 VIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~--GfSGADI~~l~~  424 (467)
T 4b4t_H          351 VMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCP--NSTGAELRSVCT  424 (467)
T ss_dssp             EEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCC--SCCHHHHHHHHH
T ss_pred             EEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCC--CCCHHHHHHHHH
Confidence            999999999999999999999999999999999999999999875432   33445554443  699999988774

>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=3.8e-34  Score=315.39  Aligned_cols=213  Identities=22%  Similarity=0.308  Sum_probs=160.4

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc---
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL---  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~---  289 (473)
                      .++.+|++++|.+++|++|.+.+..++++++.|.+.|..+++|+|||||||||||++|+|+|++++.+++.++.+++   
T Consensus       471 ~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~l~s~  550 (806)
T 3cf2_A          471 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTM  550 (806)
T ss_dssp             CCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHHHHTT
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccchhhcc
Confidence            34578999999999999999999999999999999999999999999999999999999999999999999998886   


Q ss_pred             ---cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          290 ---RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       290 ---~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                         .++..++++|..+.  .||||||||||+++..|+....       .......+++++||.+|||+.+.  .+++||+
T Consensus       551 ~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~-------~~~~~~~rv~~~lL~~mdg~~~~--~~V~vi~  621 (806)
T 3cf2_A          551 WFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIG-------DGGGAADRVINQILTEMDGMSTK--KNVFIIG  621 (806)
T ss_dssp             TCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC---------------------CHHHHHHHHHHHSSCSS--SSEEEEC
T ss_pred             ccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCC-------CCchHHHHHHHHHHHHHhCCCCC--CCEEEEE
Confidence               35678999998875  6899999999999873321111       12334578999999999999665  4599999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      |||+|+.||||++||||||.+|++++|+.++|.+||+.++.........++..+++.+ ++|+|||.++|.
T Consensus       622 aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~  692 (806)
T 3cf2_A          622 ATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQ  692 (806)
T ss_dssp             C-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHH
T ss_pred             eCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999998765333333455555543 699999998874

>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=2.4e-32  Score=301.14  Aligned_cols=209  Identities=22%  Similarity=0.317  Sum_probs=178.3

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc---
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR---  290 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~---  290 (473)
                      +..+|++|+|.++++++|.+.+..++.+++.|..+|..+++|+|||||||||||+||+++|++++.+++.++++++.   
T Consensus       199 ~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l~sk~  278 (806)
T 3cf2_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (806)
T ss_dssp             SSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHHHSSC
T ss_pred             CCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHhhccc
Confidence            44789999999999999999999999999999999999999999999999999999999999999999999988863   


Q ss_pred             ---CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          291 ---SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       291 ---~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                         ++..++.+|..+.  .||||||||||.+++.++  .        ......++++++||..||++.+.  .+++||+|
T Consensus       279 ~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~--~--------~~~~~~~riv~~LL~~mdg~~~~--~~V~VIaa  346 (806)
T 3cf2_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKRE--K--------THGEVERRIVSQLLTLMDGLKQR--AHVIVMAA  346 (806)
T ss_dssp             TTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTT--T--------CCCTTHHHHHHHHHTHHHHCCGG--GCEEEEEE
T ss_pred             chHHHHHHHHHHHHHHHcCCeEEEEehhcccccccC--C--------CCChHHHHHHHHHHHHHhccccc--CCEEEEEe
Confidence               3467888998775  689999999999986322  1        12334578999999999999765  45999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHHh
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQLM  434 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l~  434 (473)
                      ||+++.|||||+||||||.+|+++.|+.++|.+|++.++.........++..++.. .+++++|+..+|-
T Consensus       347 TN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~  416 (806)
T 3cf2_A          347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  416 (806)
T ss_dssp             CSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHHH
T ss_pred             cCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHHH
Confidence            99999999999999999999999999999999999999875533333344445443 3699999988763

>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=99.96  E-value=1.2e-28  Score=244.98  Aligned_cols=211  Identities=21%  Similarity=0.322  Sum_probs=172.3

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .++.+|++|+|.+++++.|.+.+..++..++.|...|.++++++|||||||||||++++++|++++.+++.+++.++.  
T Consensus         9 ~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~~~   88 (301)
T 3cf0_A            9 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTM   88 (301)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHHhh
Confidence            345789999999999999999999999999999999999999999999999999999999999999999999987762  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....++.+|..+.  .++||||||||.+...+.....       .........++.||..||++...  .+++||+
T Consensus        89 ~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~-------~~~~~~~~~~~~lL~~l~~~~~~--~~v~vi~  159 (301)
T 3cf0_A           89 WFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIG-------DGGGAADRVINQILTEMDGMSTK--KNVFIIG  159 (301)
T ss_dssp             HHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTC-------CSSCSCCHHHHHHHHHHHSSCTT--SSEEEEE
T ss_pred             hcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcC-------CcchHHHHHHHHHHHHhhcccCC--CCEEEEE
Confidence                3456777787664  5799999999998763321110       11123456788999999987543  4699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc---CCHHHHHHHHhcCCCCHHHHHHHHh
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH---ILFEEIEELISTTQVTPAEVAEQLM  434 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~---~l~~~i~~l~~~~~~t~a~i~~~l~  434 (473)
                      |||+++.+|++++|||||+..|+++.|+.++|..|++.++.....   ...+.++..  ..+++++|+..+|-
T Consensus       160 atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~--~~g~sg~dl~~l~~  230 (301)
T 3cf0_A          160 ATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKM--TNGFSGADLTEICQ  230 (301)
T ss_dssp             EESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHT--CSSCCHHHHHHHHH
T ss_pred             ecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHH--cCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999999875432   223344432  34699999988763

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.96  E-value=1.9e-28  Score=240.51  Aligned_cols=209  Identities=20%  Similarity=0.308  Sum_probs=162.3

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--  291 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--  291 (473)
                      +..+|++|+|.+++|+.|.+.+..++.+++.++.+|..+++|++|+||||||||+|++++|+.++.+++.++..++..  
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~~~~   84 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLNMY   84 (274)
T ss_dssp             -------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTCSST
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHHhhh
Confidence            347899999999999999999999999999999999999999999999999999999999999999999998877632  


Q ss_pred             ----chHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          292 ----NSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       292 ----~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                          ...+..+|..+  ..++++|+||+|.+...+.  ..        ........++.++..|+|....  ..++++++
T Consensus        85 ~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~--~~--------~~~~~~~~~~~~l~~Lsgg~~~--~~~i~ia~  152 (274)
T 2x8a_A           85 VGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRS--DR--------ETGASVRVVNQLLTEMDGLEAR--QQVFIMAA  152 (274)
T ss_dssp             THHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC-------------------CTTHHHHHHHHHHTCCST--TCEEEEEE
T ss_pred             hhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccC--CC--------cchHHHHHHHHHHHhhhccccc--CCEEEEee
Confidence                23566777764  3689999999999864221  11        0112345788999999997543  45889999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc---cCCHHHHHHHHhc---CCCCHHHHHHHHh
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE---HILFEEIEELIST---TQVTPAEVAEQLM  434 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~---~~l~~~i~~l~~~---~~~t~a~i~~~l~  434 (473)
                      ||+|+.|||+++||||||.+|++++|+.++|..|++.++....   .....+++.++..   .++|+|||..+|-
T Consensus       153 tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~  227 (274)
T 2x8a_A          153 TNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVR  227 (274)
T ss_dssp             ESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHH
T ss_pred             cCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHH
Confidence            9999999999999999999999999999999999999885321   1112234444443   3899999988773

>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=99.96  E-value=1e-28  Score=259.11  Aligned_cols=211  Identities=25%  Similarity=0.361  Sum_probs=166.9

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--  291 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--  291 (473)
                      .+.+|++|+|.++.++++.+.+. ++..+..|..+|...++|+||+||||||||+|++++|++++.+++.++++++..  
T Consensus        11 ~~~~f~di~G~~~~~~~l~e~v~-~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~~~   89 (476)
T 2ce7_A           11 KRVTFKDVGGAEEAIEELKEVVE-FLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVELF   89 (476)
T ss_dssp             CCCCGGGCCSCHHHHHHHHHHHH-HHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTTCC
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHH-HhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHHHH
Confidence            34689999999999999987654 678889999999999999999999999999999999999999999999887632  


Q ss_pred             ----chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          292 ----NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       292 ----~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                          ...++.+|..+.  .|+||||||||.+...+.  ..     ..+.+.....+++.||..||++...  .+++||+|
T Consensus        90 ~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~--~~-----~~g~~~~~~~~l~~LL~~ld~~~~~--~~viVIaa  160 (476)
T 2ce7_A           90 VGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRG--AG-----LGGGHDEREQTLNQLLVEMDGFDSK--EGIIVMAA  160 (476)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC----------------CHHHHHHHHHHHHHHHSCGG--GTEEEEEE
T ss_pred             hcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcc--cc-----cCcCcHHHHHHHHHHHHHHhccCCC--CCEEEEEe
Confidence                345677777664  689999999999965221  11     0122344567899999999987543  45999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHHh
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQLM  434 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l~  434 (473)
                      ||+++.|||+++||||||..|.++.|+.++|..|++.++.........++..+... .+++++|+.++|-
T Consensus       161 Tn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~  230 (476)
T 2ce7_A          161 TNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVN  230 (476)
T ss_dssp             ESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             cCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHH
Confidence            99999999999999999999999999999999999998875422211223334443 3689999977653

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.95  E-value=5.7e-27  Score=235.27  Aligned_cols=206  Identities=21%  Similarity=0.281  Sum_probs=169.8

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-CCceEEccccccc--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLELTELR--  290 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~~~~~~--  290 (473)
                      ++.+|++|+|.+++|+.|.+.+..+++.++.|.. +..+++|+|||||||||||++|+++|+++ +.+++.++++++.  
T Consensus         7 ~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~~~   85 (322)
T 1xwi_A            7 PNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSK   85 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCT-TCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSCCS
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhC-CCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHHhh
Confidence            4578999999999999999999999999888874 35667899999999999999999999999 8999999988763  


Q ss_pred             ----CchHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....++.+|..+  .+++||||||||.+...+.  .        .........+++||..||++... ..+++||+
T Consensus        86 ~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~--~--------~~~~~~~~~~~~ll~~ld~~~~~-~~~v~vI~  154 (322)
T 1xwi_A           86 WLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRS--E--------NESEAARRIKTEFLVQMQGVGVD-NDGILVLG  154 (322)
T ss_dssp             SCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSS--S--------CCTTHHHHHHHHHHHHHHCSSSC-CTTEEEEE
T ss_pred             hhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccc--c--------ccchHHHHHHHHHHHHHhccccc-CCCEEEEE
Confidence                235677777665  3689999999999975221  1        11234567889999999997532 35699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccC-CHHHHHHHHhcC-CCCHHHHHHHH
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHI-LFEEIEELISTT-QVTPAEVAEQL  433 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~-l~~~i~~l~~~~-~~t~a~i~~~l  433 (473)
                      |||+++.+|++++|  ||+..|+++.|+.++|..|++.++...... ...++..++..+ +++++++..+|
T Consensus       155 atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~  223 (322)
T 1xwi_A          155 ATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIV  223 (322)
T ss_dssp             EESCTTTSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHH
T ss_pred             ecCCcccCCHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            99999999999999  999999999999999999999998765443 355667777654 69999998877

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.95  E-value=4.4e-27  Score=230.90  Aligned_cols=214  Identities=25%  Similarity=0.300  Sum_probs=170.6

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS  291 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~  291 (473)
                      ..++.+|++|+|.+++++.|.+.+..++..++.|...|...++++||+||||||||++++++|+.++.+++.+++..+..
T Consensus        10 ~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~   89 (285)
T 3h4m_A           10 ERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVK   89 (285)
T ss_dssp             SSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGGCC
T ss_pred             CCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHHHH
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999887632


Q ss_pred             ------chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          292 ------NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       292 ------~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                            ...+..++..+.  .++||||||+|.+...+  ....     .+........+..+++.+++....  .+++||
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~--~~~~-----~~~~~~~~~~l~~ll~~~~~~~~~--~~~~vI  160 (285)
T 3h4m_A           90 KFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKR--TDAL-----TGGDREVQRTLMQLLAEMDGFDAR--GDVKII  160 (285)
T ss_dssp             CSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCC--SSSC-----CGGGGHHHHHHHHHHHHHHTTCSS--SSEEEE
T ss_pred             hccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccC--cccc-----CCccHHHHHHHHHHHHHhhCCCCC--CCEEEE
Confidence                  234555665543  57899999999997522  1110     112334567888889988876443  469999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHHh
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQLM  434 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l~  434 (473)
                      +|||.++.+|++++|||||+..++++.|+.++|.+|++.++.........++..+... .+++++++..++.
T Consensus       161 ~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~  232 (285)
T 3h4m_A          161 GATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICT  232 (285)
T ss_dssp             EECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             EeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999998875433222234444432 3589999877653

>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=99.95  E-value=6e-27  Score=226.61  Aligned_cols=211  Identities=23%  Similarity=0.328  Sum_probs=153.1

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC---
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS---  291 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~---  291 (473)
                      +.+|++++|.+++++.+.+.+. ++..++.|...|...++++|||||||||||++++++|++++.+++.++++.+..   
T Consensus         2 ~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~   80 (262)
T 2qz4_A            2 GVSFKDVAGMHEAKLEVREFVD-YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIG   80 (262)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHH-HHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSST
T ss_pred             CCCHHHhCCHHHHHHHHHHHHH-HHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhcc
Confidence            4789999999999999977654 578888899999999999999999999999999999999999999999887632   


Q ss_pred             ---chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          292 ---NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       292 ---~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                         ...++.+|..+.  .++||||||+|.+...+.....      ..........+..|++.+++...  ...+++|+||
T Consensus        81 ~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~------~~~~~~~~~~l~~ll~~~~~~~~--~~~~~vi~~t  152 (262)
T 2qz4_A           81 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMS------GFSNTEEEQTLNQLLVEMDGMGT--TDHVIVLAST  152 (262)
T ss_dssp             THHHHHHHHHHHHHHHTCSEEEEEECC-------------------------CHHHHHHHHHHHTCCT--TCCEEEEEEE
T ss_pred             ChhHHHHHHHHHHHHhcCCeEEEEeCcchhhcccccccc------CccchhHHHHHHHHHHHhhCcCC--CCCEEEEecC
Confidence               245666666554  5899999999998652211000      01123345678899999998643  3469999999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHH--HHHHHhc-CCCCHHHHHHHHh
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEE--IEELIST-TQVTPAEVAEQLM  434 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~--i~~l~~~-~~~t~a~i~~~l~  434 (473)
                      |.++.+|++++|||||+..++++.|+.++|..|++.++.........+  +..+... .+++++++..++-
T Consensus       153 n~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~  223 (262)
T 2qz4_A          153 NRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICN  223 (262)
T ss_dssp             SCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999987543333322  2344443 3689999877653

>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=99.95  E-value=8.7e-27  Score=233.76  Aligned_cols=209  Identities=20%  Similarity=0.274  Sum_probs=169.8

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-  290 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-  290 (473)
                      ..++.+|++|+|.+++|+.|.+.+..++..++.+.. +..+++|+|||||||||||++|+++|++++.+++.++++++. 
T Consensus        11 ~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l~~   89 (322)
T 3eie_A           11 EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS   89 (322)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCT-TCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHHHT
T ss_pred             cCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhc-CCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHHhh
Confidence            456689999999999999999999999988888776 455678999999999999999999999999999999988763 


Q ss_pred             -----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          291 -----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       291 -----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                           ....++.+|..+.  +++||||||||.+...+..          +.........+.|+..|+++... ...++||
T Consensus        90 ~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~----------~~~~~~~~~~~~ll~~l~~~~~~-~~~v~vi  158 (322)
T 3eie_A           90 KWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGE----------GESEASRRIKTELLVQMNGVGND-SQGVLVL  158 (322)
T ss_dssp             TTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC----------------CCTHHHHHHHHHHHGGGGTS-CCCEEEE
T ss_pred             cccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCC----------CcchHHHHHHHHHHHHhcccccc-CCceEEE
Confidence                 2345666666553  6799999999999752211          12234577889999999998543 3469999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccC-CHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHI-LFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~-l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      +|||+++.||++++|  ||+..|+++.|+.++|..|++.++...... ....+..+...+ ++++++|..+|-
T Consensus       159 ~atn~~~~ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~  229 (322)
T 3eie_A          159 GATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVK  229 (322)
T ss_dssp             EEESCGGGSCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHH
T ss_pred             EecCChhhCCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999  999999999999999999999998865443 345667676654 699999987763

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.95  E-value=2.6e-26  Score=222.40  Aligned_cols=212  Identities=23%  Similarity=0.350  Sum_probs=161.5

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .++.+|++++|.+++++.+.+.+ .++..++.|+..|...++|+||+||||||||++++++|+.++.+++.++++++.  
T Consensus         6 ~~~~~~~~i~G~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~~~~   84 (257)
T 1lv7_A            6 QIKTTFADVAGCDEAKEEVAELV-EYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM   84 (257)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHH-HHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTS
T ss_pred             CCCCCHHHhcCcHHHHHHHHHHH-HHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHHHHH
Confidence            45679999999999999998765 467788889999999999999999999999999999999999999999988763  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....++.+|..+.  .++++||||+|.+...+.  ...     .+........++.+|..++++...  ..++||+
T Consensus        85 ~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~--~~~-----~~~~~~~~~~~~~ll~~l~~~~~~--~~~~vI~  155 (257)
T 1lv7_A           85 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG--AGL-----GGGHDEREQTLNQMLVEMDGFEGN--EGIIVIA  155 (257)
T ss_dssp             CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCS--TTS-----CCTTCHHHHHHHHHHHHHHTCCSS--SCEEEEE
T ss_pred             hhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCC--CCc-----CCCchHHHHHHHHHHHHhhCcccC--CCEEEEE
Confidence                2355777777664  468999999999865211  110     112233457889999999987543  4599999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      |||+++.+|++++|||||+..++++.|+.++|.+|++.++..........+..+.... +++++|+...+.
T Consensus       156 ~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~  226 (257)
T 1lv7_A          156 ATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVN  226 (257)
T ss_dssp             EESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             eeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999988643221112233333333 579999987653

>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=99.94  E-value=3.6e-26  Score=232.46  Aligned_cols=207  Identities=20%  Similarity=0.284  Sum_probs=166.3

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .++.+|++|+|.+++++.|.+.+..++..++.|.. +..+++|+|||||||||||++|+++|++++.+++.++++++.  
T Consensus        45 ~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~~~l~~~  123 (355)
T 2qp9_X           45 KPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSK  123 (355)
T ss_dssp             --CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCS-SCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEHHHHHSC
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhc-CCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeHHHHhhh
Confidence            34578999999999999999999999998888876 566778999999999999999999999999999999988762  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....++.+|..+.  .++||||||||.+...+.  .        +.........+.||..|+++... ...++||+
T Consensus       124 ~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~--~--------~~~~~~~~~~~~ll~~l~~~~~~-~~~v~vI~  192 (355)
T 2qp9_X          124 WMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRG--E--------GESEASRRIKTELLVQMNGVGND-SQGVLVLG  192 (355)
T ss_dssp             C---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC----------------CTHHHHHHHHHHHHHHHCC----CCEEEEE
T ss_pred             hcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCC--C--------CcchHHHHHHHHHHHHhhccccc-CCCeEEEe
Confidence                2345666776553  789999999999865221  1        12234567889999999987532 34699999


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccC-CHHHHHHHHhcC-CCCHHHHHHHH
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHI-LFEEIEELISTT-QVTPAEVAEQL  433 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~-l~~~i~~l~~~~-~~t~a~i~~~l  433 (473)
                      |||+++.||++++|  ||+..++++.|+.++|..|+..++...... ...++..++..+ ++++++|..+|
T Consensus       193 atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          193 ATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             EESCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             ecCCcccCCHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            99999999999999  999999999999999999999998765433 345666666544 68999998876

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.94  E-value=1.9e-26  Score=243.21  Aligned_cols=211  Identities=24%  Similarity=0.335  Sum_probs=165.6

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--  291 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--  291 (473)
                      ++.+|++|+|.++.++++.+.+ .++..+..|..+|...++|+||+||||||||+|++++|++++.+++.++++++..  
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv-~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~  104 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIV-EFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF  104 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHH-HHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSC
T ss_pred             CCCCHHHcCCcHHHHHHHHHHH-HHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhh
Confidence            5679999999999999987755 4677888899999999999999999999999999999999999999999887632  


Q ss_pred             ----chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          292 ----NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       292 ----~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                          ...++.+|..+.  .++|+||||||.+...+.  ...     .+.......+++.||..|+|....  ..+++|++
T Consensus       105 ~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~--~~~-----~~~~~e~~~~l~~LL~~Ldg~~~~--~~viviAa  175 (499)
T 2dhr_A          105 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRG--SGV-----GGGNDEREQTLNQLLVEMDGFEKD--TAIVVMAA  175 (499)
T ss_dssp             TTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSS--SST-----TTSSHHHHHHHHHHHHHGGGCCSS--CCCEEEEC
T ss_pred             hhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhc--cCc-----CCCcHHHHHHHHHHHHHhcccccC--ccEEEEEe
Confidence                234666776654  579999999999864221  100     112334467889999999987543  45899999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      ||+|+.|||+++||||||.+|+++.|+.++|.+|++.++.........++..+.... +++++|+.++|-
T Consensus       176 tn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~  245 (499)
T 2dhr_A          176 TNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  245 (499)
T ss_dssp             CSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHH
T ss_pred             cCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHH
Confidence            999999999999999999999999999999999999887643221122233344433 688899877753

>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=99.94  E-value=7.5e-26  Score=238.85  Aligned_cols=208  Identities=23%  Similarity=0.326  Sum_probs=171.7

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--  291 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--  291 (473)
                      .+.+|++|+|.+..++.|.+.+..++..++.|..+|.++++++|||||||||||++|+++|++++.+++.++++.+.+  
T Consensus       199 ~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~~~~  278 (489)
T 3hu3_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (489)
T ss_dssp             TCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHHTSC
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhhhhh
Confidence            456899999999999999999999999999999999999999999999999999999999999999999999887632  


Q ss_pred             ----chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          292 ----NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       292 ----~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                          ...++.+|..+.  .++||||||||.+...+..          .........++.||..|++....  ..++||+|
T Consensus       279 ~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~----------~~~~~~~~~~~~LL~~ld~~~~~--~~v~vIaa  346 (489)
T 3hu3_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK----------THGEVERRIVSQLLTLMDGLKQR--AHVIVMAA  346 (489)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTS----------CCCHHHHHHHHHHHHHHHHSCTT--SCEEEEEE
T ss_pred             cchhHHHHHHHHHHHHhcCCcEEEecchhhhcccccc----------ccchHHHHHHHHHHHHhhccccC--CceEEEEe
Confidence                345677777664  5689999999999762211          11234567889999999987543  46999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQL  433 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l  433 (473)
                      ||+++.||++++|+|||+..|+++.|+.++|..|++.++.........++..++.. .+++++++..+|
T Consensus       347 Tn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~  415 (489)
T 3hu3_A          347 TNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALC  415 (489)
T ss_dssp             ESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             cCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHH
Confidence            99999999999999999999999999999999999998875433222234444443 369999998775

>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=99.93  E-value=2.3e-25  Score=232.97  Aligned_cols=208  Identities=21%  Similarity=0.262  Sum_probs=167.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-CCceEEccccccc-
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLELTELR-  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~~~~~~-  290 (473)
                      .++.+|++|+|.+++++.|.+.+..++..++.|.. +..+++++|||||||||||++|+++|+++ +.+++.++++++. 
T Consensus       128 ~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~l~~  206 (444)
T 2zan_A          128 RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVS  206 (444)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSG-GGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC----
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhc-cCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHHHHh
Confidence            45679999999999999999999989988887764 34567899999999999999999999999 8999999988763 


Q ss_pred             -----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          291 -----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       291 -----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                           ....++.+|..+.  .++||||||||.+...+.  .        .........++.||..|+++... ..+++||
T Consensus       207 ~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~--~--------~~~~~~~~~~~~lL~~l~~~~~~-~~~v~vI  275 (444)
T 2zan_A          207 KWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRS--E--------NESEAARRIKTEFLVQMQGVGVD-NDGILVL  275 (444)
T ss_dssp             -----CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSS--C--------CCCGGGHHHHHHHHTTTTCSSCC-CSSCEEE
T ss_pred             hhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCCC--C--------ccccHHHHHHHHHHHHHhCcccC-CCCEEEE
Confidence                 2345677776553  689999999999875221  1        12334567889999999997532 3569999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccC-CHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHI-LFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~-l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      +|||.++.||++++|  ||+..|+++.|+.++|..|++.++...... ...++..++..+ ++++++|..+|-
T Consensus       276 ~atn~~~~ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~  346 (444)
T 2zan_A          276 GATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVR  346 (444)
T ss_dssp             EEESCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ecCCCccccCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            999999999999999  999999999999999999999998765432 345666666544 699999988763

>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=99.92  E-value=3e-26  Score=223.15  Aligned_cols=212  Identities=25%  Similarity=0.353  Sum_probs=158.4

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--  291 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--  291 (473)
                      ++.+|++++|.++.++.+.+.+. ++..++.|...|...++|+||+||||||||++|+++|++++.+++.++++.+..  
T Consensus         6 ~~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~~~   84 (268)
T 2r62_A            6 PNVRFKDMAGNEEAKEEVVEIVD-FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMF   84 (268)
T ss_dssp             CCCCSTTSSSCTTTHHHHHHHHH-HHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTTTTSC
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHH-HHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHHHHhh
Confidence            45789999999999999988655 688889999999999999999999999999999999999999999998877531  


Q ss_pred             ----chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          292 ----NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       292 ----~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                          ...++.+|..+.  .++||||||+|.+...+.....      ...+......++.|++.+++.... ...++||+|
T Consensus        85 ~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~------~~~~~~~~~~~~~ll~~l~~~~~~-~~~v~vi~t  157 (268)
T 2r62_A           85 VGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGV------VSGNDEREQTLNQLLAEMDGFGSE-NAPVIVLAA  157 (268)
T ss_dssp             SSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC----------------CCCSCSSTTTTTTTTTCSSCS-CSCCEEEEC
T ss_pred             cchHHHHHHHHHHHHHhcCCeEEEEeChhhhccccccccc------CCCchhHHHHHHHHHHHhhCcccC-CCCEEEEEe
Confidence                233444554443  5799999999999652211000      011122344667788888876432 345899999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQL  433 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l  433 (473)
                      ||.++.+|++++|+|||+..|+++.|+.++|..+++.++..........+..+... .+++++++..++
T Consensus       158 tn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~  226 (268)
T 2r62_A          158 TNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANII  226 (268)
T ss_dssp             BSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHH
T ss_pred             cCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHH
Confidence            99999999999999999999999999999999999998864322111122333332 258888887765

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.92  E-value=1.4e-24  Score=223.26  Aligned_cols=211  Identities=25%  Similarity=0.333  Sum_probs=165.2

Q ss_pred             ccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          210 VNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       210 ~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +...++.+|++|+|.+.+++.|.+.+..+...++.|...+. +++++|||||||||||++|+++|++++.+++.++++.+
T Consensus       106 ~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l  184 (389)
T 3vfd_A          106 VDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRA-PARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASL  184 (389)
T ss_dssp             BCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGC-CCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC
T ss_pred             hccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCC-CCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHh
Confidence            33567789999999999999999999999888888887764 47899999999999999999999999999999999886


Q ss_pred             cC------chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceE
Q 012016          290 RS------NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERI  361 (473)
Q Consensus       290 ~~------~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~i  361 (473)
                      ..      ...++.+|..+.  +++||||||||.++..+.          .+........+..|+..+++........++
T Consensus       185 ~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~----------~~~~~~~~~~~~~ll~~l~~~~~~~~~~v~  254 (389)
T 3vfd_A          185 TSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERR----------EGEHDASRRLKTEFLIEFDGVQSAGDDRVL  254 (389)
T ss_dssp             -------CHHHHHHHHHHHHHSSSEEEEEETGGGGC------------------CTHHHHHHHHHHHHHHHC-----CEE
T ss_pred             hccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCC----------CccchHHHHHHHHHHHHhhcccccCCCCEE
Confidence            32      344566665543  579999999999975221          112234577888999999998765556799


Q ss_pred             EEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcC-CCCHHHHHHHH
Q 012016          362 IVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTT-QVTPAEVAEQL  433 (473)
Q Consensus       362 iI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~t~a~i~~~l  433 (473)
                      ||+|||.++.||++++|  ||+.+|+++.|+.++|..|+..++......+ ...+..+.... +++++++..++
T Consensus       255 vI~atn~~~~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~  326 (389)
T 3vfd_A          255 VMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALA  326 (389)
T ss_dssp             EEEEESCGGGCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             EEEecCCchhcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            99999999999999999  9999999999999999999999987654443 44555555533 68998887765

>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=99.92  E-value=2.5e-24  Score=208.15  Aligned_cols=212  Identities=24%  Similarity=0.338  Sum_probs=159.9

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .++.+|++++|.++.+.++.+... ++..+..+...+...++|++|+||||||||+|++++|+.++.+++.++..++.  
T Consensus        10 ~~~~~~~~i~g~~~~~~~l~~l~~-~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~~~~   88 (254)
T 1ixz_A           10 APKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM   88 (254)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHHHH-HHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHS
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHH-HHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHHHHH
Confidence            445799999999999998876544 56677888999999999999999999999999999999999999988876542  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....+..+|....  .++++++||+|.+...+..  ..     ..........++.+++.|+|....  ..+++++
T Consensus        89 ~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~--~~-----~~~~~~~~~~~~~ll~~l~g~~~~--~~~i~~a  159 (254)
T 1ixz_A           89 FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGS--GV-----GGGNDEREQTLNQLLVEMDGFEKD--TAIVVMA  159 (254)
T ss_dssp             CTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC----------------CHHHHHHHHHHHHHHHTCCTT--CCEEEEE
T ss_pred             HhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCc--cc-----cccchHHHHHHHHHHHHHhCCCCC--CCEEEEE
Confidence                1234666777654  5799999999988642211  00     011233456788999999987443  3478889


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      +||+|+.+|++++|||||+.+|+++.|+.++|.+|++.+..........++..+.... +++++|+..+|-
T Consensus       160 ~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~  230 (254)
T 1ixz_A          160 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLN  230 (254)
T ss_dssp             EESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             ccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999887543222122233444433 688899877763

>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=99.92  E-value=3.2e-24  Score=218.22  Aligned_cols=208  Identities=23%  Similarity=0.362  Sum_probs=164.3

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC--
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS--  291 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~--  291 (473)
                      ++.+|++|+|.++.++.|.+.+..++..++.|...+ .+++++||+||||||||++|+++|++++.+++.++++++..  
T Consensus        79 ~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~~  157 (357)
T 3d8b_A           79 PPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKW  157 (357)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-SCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGCCSS
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhcc-CCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhhccc
Confidence            467899999999999999999998888888877665 45789999999999999999999999999999999988743  


Q ss_pred             ----chHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          292 ----NSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       292 ----~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                          ...++.++..+  .+++||||||||.+...+.          .+........++.||..+++.....+..++||+|
T Consensus       158 ~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~----------~~~~~~~~~~~~~lL~~l~~~~~~~~~~v~vI~a  227 (357)
T 3d8b_A          158 VGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRG----------DGEHESSRRIKTEFLVQLDGATTSSEDRILVVGA  227 (357)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC----------------CHHHHHHHHHHHHHHC----CCCCEEEEEE
T ss_pred             cchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCC----------CCcchHHHHHHHHHHHHHhcccccCCCCEEEEEe
Confidence                23455566544  3679999999999975221          1123345678899999999876555567999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      ||.++.+|++++|  ||+..++++.|+.++|..++..++......+ ...+..++..+ +++++++..+|-
T Consensus       228 tn~~~~l~~~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          228 TNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             ESCGGGBCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             cCChhhCCHHHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            9999999999999  9999999999999999999999886543333 45566666544 689999987763

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.91  E-value=6.7e-24  Score=209.54  Aligned_cols=208  Identities=22%  Similarity=0.315  Sum_probs=160.8

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-  291 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-  291 (473)
                      .++.+|++++|.++.++.+.+.+..+...++.|...+ .+++++||+||||||||++++++|++++.+++.++++.+.. 
T Consensus        15 ~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l~~~   93 (297)
T 3b9p_A           15 GAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSK   93 (297)
T ss_dssp             SSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGG-CCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTTSSS
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCC-CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHHhhc
Confidence            3568999999999999999999988888888777665 44689999999999999999999999999999999887632 


Q ss_pred             -----chHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC-CCCceEEE
Q 012016          292 -----NSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS-CGDERIIV  363 (473)
Q Consensus       292 -----~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-~~~~~iiI  363 (473)
                           ...++.++..+  .+++||||||+|.+...+..          ..........+.||..+++.... .+..++||
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~----------~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi  163 (297)
T 3b9p_A           94 YVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSS----------SEHEASRRLKTEFLVEFDGLPGNPDGDRIVVL  163 (297)
T ss_dssp             SCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC---------------CCSHHHHHHHHHHHHHCC------CEEEE
T ss_pred             ccchHHHHHHHHHHHHHHcCCcEEEeccHHHhcccccc----------CcchHHHHHHHHHHHHHhcccccCCCCcEEEE
Confidence                 23345555544  36899999999999762211          11223456778899999987543 23468999


Q ss_pred             EecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhc-CCCCHHHHHHHH
Q 012016          364 FTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELIST-TQVTPAEVAEQL  433 (473)
Q Consensus       364 ~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~-~~~t~a~i~~~l  433 (473)
                      +|||.++.+|++++|  ||+..++++.|+.++|..|+..++......+ ...+..+... .+++++++..++
T Consensus       164 ~~tn~~~~l~~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~  233 (297)
T 3b9p_A          164 AATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALA  233 (297)
T ss_dssp             EEESCGGGBCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHH
T ss_pred             eecCChhhCCHHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999  9999999999999999999999887554333 3445555543 368888887765

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.91  E-value=3.1e-23  Score=203.37  Aligned_cols=211  Identities=24%  Similarity=0.339  Sum_probs=158.7

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--  290 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--  290 (473)
                      .++.+|++++|.++.++++.+... ++..+..+..++...++|++|+||||||||+|++++|+.++.+++.+++.++.  
T Consensus        34 ~~~~~~~~i~g~~~~~~~l~~l~~-~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~~~~  112 (278)
T 1iy2_A           34 APKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM  112 (278)
T ss_dssp             CCCCCGGGSSSCHHHHHHHHHHHH-HHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHS
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHH-HHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHHHHH
Confidence            466899999999999998876544 56677888899999999999999999999999999999999999988876542  


Q ss_pred             ----CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEE
Q 012016          291 ----SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVF  364 (473)
Q Consensus       291 ----~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~  364 (473)
                          ....+..+|....  .++++++||+|.+...+..  ..     ..........+..+++.++|....  ..+++++
T Consensus       113 ~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~--~~-----~~~~~~~~~~~~~ll~~lsgg~~~--~~~i~~a  183 (278)
T 1iy2_A          113 FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGS--GV-----GGGNDEREQTLNQLLVEMDGFEKD--TAIVVMA  183 (278)
T ss_dssp             TTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC---------------CHHHHHHHHHHHHHHTTCCTT--CCEEEEE
T ss_pred             HhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhccccc--cc-----CCcchHHHHHHHHHHHHHhCCCCC--CCEEEEE
Confidence                1234566676653  5799999999988642111  00     011223456788899999886432  3478889


Q ss_pred             ecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhc-CCCCHHHHHHHH
Q 012016          365 TTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELIST-TQVTPAEVAEQL  433 (473)
Q Consensus       365 tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~-~~~t~a~i~~~l  433 (473)
                      +||+|+.|||+++|||||+.+|+++.|+.++|.+|++.++.........++..+... .+++++|+..+|
T Consensus       184 ~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~  253 (278)
T 1iy2_A          184 ATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLL  253 (278)
T ss_dssp             EESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             ecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHH
Confidence            999999999999999999999999999999999999988754322111223334333 358888887665

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.91  E-value=1.3e-24  Score=215.22  Aligned_cols=172  Identities=16%  Similarity=0.147  Sum_probs=123.5

Q ss_pred             HhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC------chHHHHHHHHhc------cCceEEEec
Q 012016          245 YRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS------NSDLRTLLVATA------NRSILVVED  312 (473)
Q Consensus       245 y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~------~~~l~~l~~~~~------~~sIL~iDd  312 (473)
                      ....+..+++|+|||||||||||++|+++|++++.+++.++++++.+      ...++.+|..+.      .++||||||
T Consensus        28 l~~~~~~~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDE  107 (293)
T 3t15_A           28 LKLPNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFIND  107 (293)
T ss_dssp             SCCTTCCCCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEEC
T ss_pred             HhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEec
Confidence            33456778899999999999999999999999999999999888632      345667776652      689999999


Q ss_pred             cccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc---------CCCCceEEEEecCCCCCCCccccCCCcee
Q 012016          313 IDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS---------SCGDERIIVFTTNHKEKLDPALLRPGRMD  383 (473)
Q Consensus       313 iD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~---------~~~~~~iiI~tTN~~~~ld~aLlrpgRfd  383 (473)
                      ||.+...  +. ...     ......+...+.|++.||+...         ....+++||+|||+++.+|++++||||||
T Consensus       108 iD~~~~~--~~-~~~-----~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d  179 (293)
T 3t15_A          108 LDAGAGR--MG-GTT-----QYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRME  179 (293)
T ss_dssp             CC----------------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEE
T ss_pred             hhhhcCC--CC-CCc-----cccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCc
Confidence            9998751  11 000     1112345677889999985431         12346899999999999999999999999


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHH
Q 012016          384 VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEV  429 (473)
Q Consensus       384 ~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i  429 (473)
                      .+|++  |+.++|..|++.++... ....+.++.+...  ++++++
T Consensus       180 ~~i~~--P~~~~r~~Il~~~~~~~-~~~~~~l~~~~~~--~~~~~l  220 (293)
T 3t15_A          180 KFYWA--PTREDRIGVCTGIFRTD-NVPAEDVVKIVDN--FPGQSI  220 (293)
T ss_dssp             EEEEC--CCHHHHHHHHHHHHGGG-CCCHHHHHHHHHH--SCSCCH
T ss_pred             eeEeC--cCHHHHHHHHHHhccCC-CCCHHHHHHHhCC--CCcccH
Confidence            99974  69999999999888644 3446677777665  555444

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.82  E-value=5.7e-19  Score=177.31  Aligned_cols=195  Identities=14%  Similarity=0.169  Sum_probs=146.3

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .|..  ...|.+|++++|.+..++.+...+......        .....++||+||||||||++|+++|+.++.+++.++
T Consensus        18 ~~~~--~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~--------~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~   87 (338)
T 3pfi_A           18 TYET--SLRPSNFDGYIGQESIKKNLNVFIAAAKKR--------NECLDHILFSGPAGLGKTTLANIISYEMSANIKTTA   87 (338)
T ss_dssp             -------CCCCSGGGCCSCHHHHHHHHHHHHHHHHT--------TSCCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEE
T ss_pred             hhhh--ccCCCCHHHhCChHHHHHHHHHHHHHHHhc--------CCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEec
Confidence            4543  345679999999999999887776654321        224568999999999999999999999999999999


Q ss_pred             cccccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc-----------
Q 012016          286 LTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS-----------  354 (473)
Q Consensus       286 ~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~-----------  354 (473)
                      +..+.....+...+.....+++|||||||.+.                     ......|+..++...-           
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~---------------------~~~~~~Ll~~l~~~~~~~~~~~~~~~~  146 (338)
T 3pfi_A           88 APMIEKSGDLAAILTNLSEGDILFIDEIHRLS---------------------PAIEEVLYPAMEDYRLDIIIGSGPAAQ  146 (338)
T ss_dssp             GGGCCSHHHHHHHHHTCCTTCEEEEETGGGCC---------------------HHHHHHHHHHHHTSCC---------CC
T ss_pred             chhccchhHHHHHHHhccCCCEEEEechhhcC---------------------HHHHHHHHHHHHhccchhhcccCcccc
Confidence            98887777888888888899999999999873                     3345666766664320           


Q ss_pred             ---CCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcCCCCHHHHH
Q 012016          355 ---SCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTTQVTPAEVA  430 (473)
Q Consensus       355 ---~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~~~t~a~i~  430 (473)
                         .....+++|++||....++++|++  ||+.+++|+.|+.+++..++..++......+ .+.+..++......+.++.
T Consensus       147 ~~~~~~~~~~~i~atn~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~  224 (338)
T 3pfi_A          147 TIKIDLPKFTLIGATTRAGMLSNPLRD--RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRSRSTPRIAL  224 (338)
T ss_dssp             CCCCCCCCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTTTTCHHHHH
T ss_pred             ceecCCCCeEEEEeCCCccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHH
Confidence               000137899999999999999999  9999999999999999999998876543332 3344445554455665554


Q ss_pred             HHH
Q 012016          431 EQL  433 (473)
Q Consensus       431 ~~l  433 (473)
                      +.+
T Consensus       225 ~~l  227 (338)
T 3pfi_A          225 RLL  227 (338)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=99.80  E-value=5.3e-20  Score=193.06  Aligned_cols=172  Identities=15%  Similarity=0.086  Sum_probs=118.5

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC--CceEEcccccccC
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN--FDVYDLELTELRS  291 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~--~~~~~l~~~~~~~  291 (473)
                      +...|++++|.++.++.+...+..+.        .|..+++++|||||||||||++|+++|++++  .+++.++++.+.+
T Consensus        32 ~~~~~~~iiG~~~~~~~l~~~~~~~~--------~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~~  103 (456)
T 2c9o_A           32 AKQAASGLVGQENAREACGVIVELIK--------SKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYS  103 (456)
T ss_dssp             BCSEETTEESCHHHHHHHHHHHHHHH--------TTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGCC
T ss_pred             hhhchhhccCHHHHHHHHHHHHHHHH--------hCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHHH
Confidence            33568999999999998876554332        3566778999999999999999999999999  9999999888742


Q ss_pred             -----chHHHHHHHHh-----ccCceEEEeccccccccccCCccccCCCCC---------CCccchhHHHHHHHHHhccc
Q 012016          292 -----NSDLRTLLVAT-----ANRSILVVEDIDCTIDLQDRLPADIAGEGE---------GPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       292 -----~~~l~~l~~~~-----~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~---------~~~~~~~~~ls~LL~~ldg~  352 (473)
                           ...+++.|..+     ..++||||||+|.++..+............         .+........+.++..++..
T Consensus       104 ~~~~~~~~~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~~~  183 (456)
T 2c9o_A          104 TEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKE  183 (456)
T ss_dssp             SSSCHHHHHHHHHHHTEEEEEEEEEEEEEEEEEEEEEC--------------CEEEEEEETTEEEEEEECHHHHHHHHHT
T ss_pred             HhhhhhHHHHHHHHHHHhhhhcCCcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccchhHhhhHHHHHHHhhc
Confidence                 23477888776     378999999999998733221100000000         00011123344566666532


Q ss_pred             ccCCCCceEEEEecCCCCCCCccccCCCceee--EEEeCCCCH
Q 012016          353 WSSCGDERIIVFTTNHKEKLDPALLRPGRMDV--HVHMSYCTP  393 (473)
Q Consensus       353 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~--~I~~~~p~~  393 (473)
                      ....++.++|++|||+++.+|++++||||||.  .+.+|.|+.
T Consensus       184 ~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~  226 (456)
T 2c9o_A          184 RVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKG  226 (456)
T ss_dssp             TCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCS
T ss_pred             cCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCch
Confidence            22334445566899999999999999999998  567777754

>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=99.79  E-value=3.2e-18  Score=170.42  Aligned_cols=190  Identities=19%  Similarity=0.209  Sum_probs=143.9

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN  292 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~  292 (473)
                      ..|.+|++++|.+..++.+...+......        ...+.++||+||||||||++|+++++.++.+++.+++..+...
T Consensus         6 ~~p~~~~~~ig~~~~~~~l~~~l~~~~~~--------~~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~   77 (324)
T 1hqc_A            6 LRPKTLDEYIGQERLKQKLRVYLEAAKAR--------KEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKP   77 (324)
T ss_dssp             CCCCSTTTCCSCHHHHHHHHHHHHHHHHH--------CSCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCCSH
T ss_pred             cCcccHHHhhCHHHHHHHHHHHHHHHHcc--------CCCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccCCh
Confidence            35679999999998888887766544321        1235689999999999999999999999999999999888777


Q ss_pred             hHHHHHHHH-hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc-----C---------CC
Q 012016          293 SDLRTLLVA-TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS-----S---------CG  357 (473)
Q Consensus       293 ~~l~~l~~~-~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~-----~---------~~  357 (473)
                      ..+...+.. ...+++|||||+|.+..                     .....|+..++...-     .         ..
T Consensus        78 ~~l~~~l~~~~~~~~~l~lDEi~~l~~---------------------~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~  136 (324)
T 1hqc_A           78 GDLAAILANSLEEGDILFIDEIHRLSR---------------------QAEEHLYPAMEDFVMDIVIGQGPAARTIRLEL  136 (324)
T ss_dssp             HHHHHHHTTTCCTTCEEEETTTTSCCH---------------------HHHHHHHHHHHHSEEEECCSSSSSCCCEEEEC
T ss_pred             HHHHHHHHHhccCCCEEEEECCccccc---------------------chHHHHHHHHHhhhhHHhccccccccccccCC
Confidence            777777766 56889999999998732                     234455555553210     0         01


Q ss_pred             CceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcCCCCHHHHHHHH
Q 012016          358 DERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       358 ~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      ..+++|++||.+..++++|++  ||+.++.++.|+.+++..++..++......+ .+.++.++....-.|.++.+.+
T Consensus       137 ~~~~~i~~t~~~~~~~~~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G~~r~l~~~l  211 (324)
T 1hqc_A          137 PRFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLF  211 (324)
T ss_dssp             CCCEEEEEESCCSSCSCSTTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCSCHHHHHHHH
T ss_pred             CCEEEEEeCCCcccCCHHHHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccCCHHHHHHHH
Confidence            247899999999999999998  9998999999999999999998876543333 3445555555556777766654

>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=99.77  E-value=1.5e-19  Score=187.27  Aligned_cols=162  Identities=14%  Similarity=0.161  Sum_probs=72.5

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcC-CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-------
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGK-AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-------  291 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~-~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-------  291 (473)
                      .|+|+++.|+.+...+....++...+...+. .+++++||+||||||||++++++|+.++.+++.++++.+..       
T Consensus        16 ~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~~~~~g~vG~d   95 (444)
T 1g41_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE   95 (444)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC----CCCC
T ss_pred             HhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchhhcccceeecc
Confidence            6899999999998888776665554444433 35789999999999999999999999999999999866522       


Q ss_pred             -chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe-cCCC
Q 012016          292 -NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT-TNHK  369 (473)
Q Consensus       292 -~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t-TN~~  369 (473)
                       ...++.++..+.  .++++||+|.+...             .......++++.||+.|||+.+..   .+ +++ ||++
T Consensus        96 ~e~~lr~lf~~a~--~~~~~De~d~~~~~-------------~~~~~e~rvl~~LL~~~dg~~~~~---~v-~a~~TN~~  156 (444)
T 1g41_A           96 VDSIIRDLTDSAM--KLVRQQEIAKNRAR-------------AEDVAEERILDALLPPAKNQWGEV---EN-HDSHSSTR  156 (444)
T ss_dssp             THHHHHHHHHHHH--HHHHHHHHHSCC-----------------------------------------------------
T ss_pred             HHHHHHHHHHHHH--hcchhhhhhhhhcc-------------chhhHHHHHHHHHHHHhhcccccc---cc-ccccccCH
Confidence             345566665442  24458888866421             112345789999999999996542   23 444 9999


Q ss_pred             CCCCccccCCCceeeEEEeCCCCHH-HHHHHH
Q 012016          370 EKLDPALLRPGRMDVHVHMSYCTPS-GFKLLA  400 (473)
Q Consensus       370 ~~ld~aLlrpgRfd~~I~~~~p~~~-~r~~l~  400 (473)
                      +.|||||+||||||++|+++.|+.. .+.+|+
T Consensus       157 ~~ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          157 QAFRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             --------------------------------
T ss_pred             HHHHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            9999999999999999999999987 565554

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.77  E-value=2.7e-18  Score=169.92  Aligned_cols=174  Identities=14%  Similarity=0.229  Sum_probs=131.5

Q ss_pred             cc-ccccchHHHHHHHHHHHHHHhchhHHhhhcCCC---CceeEEeCCCCCCHHHHHHHHHHhc-------CCceEEccc
Q 012016          218 FE-TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAW---KRGYLLYGPPGTGKSSLIAAMANYL-------NFDVYDLEL  286 (473)
Q Consensus       218 f~-~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~---~rg~LL~GPpGtGKT~la~alA~~l-------~~~~~~l~~  286 (473)
                      ++ +++|.+++++.|.+.+..+.. +..+.+.|...   ..++||+||||||||++|+++|+.+       ..+++.+++
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 699999999999888776543 45566666544   3469999999999999999999998       348889888


Q ss_pred             ccccC------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCce
Q 012016          287 TELRS------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER  360 (473)
Q Consensus       287 ~~~~~------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~  360 (473)
                      +.+..      ...+..+|... .++||||||+|.+...+.            ........+..|++.|+..    ..++
T Consensus       108 ~~l~~~~~g~~~~~~~~~~~~~-~~~vl~iDEid~l~~~~~------------~~~~~~~~~~~Ll~~l~~~----~~~~  170 (309)
T 3syl_A          108 DDLVGQYIGHTAPKTKEVLKRA-MGGVLFIDEAYYLYRPDN------------ERDYGQEAIEILLQVMENN----RDDL  170 (309)
T ss_dssp             GGTCCSSTTCHHHHHHHHHHHH-TTSEEEEETGGGSCCCC---------------CCTHHHHHHHHHHHHHC----TTTC
T ss_pred             HHhhhhcccccHHHHHHHHHhc-CCCEEEEEChhhhccCCC------------cccccHHHHHHHHHHHhcC----CCCE
Confidence            87632      23455555544 678999999999864111            1123467788899988853    2457


Q ss_pred             EEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC
Q 012016          361 IIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL  411 (473)
Q Consensus       361 iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l  411 (473)
                      ++|+|||.++     .++|+|++  ||+.+|+|+.|+.+++..|+..++......+
T Consensus       171 ~~i~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~  224 (309)
T 3syl_A          171 VVILAGYADRMENFFQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQM  224 (309)
T ss_dssp             EEEEEECHHHHHHHHHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEE
T ss_pred             EEEEeCChHHHHHHHhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCC
Confidence            8889998653     35799999  9999999999999999999999987554333

>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=99.74  E-value=3.3e-17  Score=161.65  Aligned_cols=173  Identities=17%  Similarity=0.271  Sum_probs=122.4

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhh-cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-------
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRV-GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-------  291 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~-g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-------  291 (473)
                      .++|.++.++.+...+...+......... +...+.++||+||||||||++++++|+.++.+++.++++.+..       
T Consensus        16 ~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~~~~~~~   95 (310)
T 1ofh_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKE   95 (310)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGS
T ss_pred             hcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccCCccCcc
Confidence            58899999999888776543322111111 1134578999999999999999999999999999999887642       


Q ss_pred             -chHHHHHHHHh-------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc------CCC
Q 012016          292 -NSDLRTLLVAT-------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS------SCG  357 (473)
Q Consensus       292 -~~~l~~l~~~~-------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~------~~~  357 (473)
                       ...+..++...       ..++||||||+|.+......         .+.........+.|+..+++...      ...
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~---------~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~  166 (310)
T 1ofh_A           96 VDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEY---------SGADVSREGVQRDLLPLVEGSTVSTKHGMVKT  166 (310)
T ss_dssp             TTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSC---------CSSHHHHHHHHHHHHHHHHCCEEEETTEEEEC
T ss_pred             HHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccc---------cccchhHHHHHHHHHHHhcCCeEecccccccC
Confidence             23355555432       35799999999998642110         01122223346778888886411      012


Q ss_pred             CceEEEEe----cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          358 DERIIVFT----TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       358 ~~~iiI~t----TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                      ..+++|++    ++.+..++|+|++  ||+.+|+|+.|+.+++..|+...
T Consensus       167 ~~~~~i~~~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~~  214 (310)
T 1ofh_A          167 DHILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEP  214 (310)
T ss_dssp             TTCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             CcEEEEEcCCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHhh
Confidence            35788887    5678899999998  99999999999999999999853

>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=99.73  E-value=3.3e-17  Score=163.57  Aligned_cols=158  Identities=15%  Similarity=0.156  Sum_probs=121.0

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .|..  ...|.+|++++|.++.++.+.+.+.    .        ...+..+|++||||||||++++++|+.++.+++.++
T Consensus        15 ~~~~--k~rP~~~~~ivg~~~~~~~l~~~l~----~--------~~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~   80 (324)
T 3u61_B           15 ILEQ--KYRPSTIDECILPAFDKETFKSITS----K--------GKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVN   80 (324)
T ss_dssp             SHHH--HSCCCSTTTSCCCHHHHHHHHHHHH----T--------TCCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEE
T ss_pred             hHHH--hhCCCCHHHHhCcHHHHHHHHHHHH----c--------CCCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEc
Confidence            4543  4567899999999988777665443    1        233567899999999999999999999999999999


Q ss_pred             cccccCchHHHHHHHHhc-------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          286 LTELRSNSDLRTLLVATA-------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       286 ~~~~~~~~~l~~l~~~~~-------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ++... ...++..+....       .+.||||||+|.+..                    ......|+..++...    .
T Consensus        81 ~~~~~-~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~--------------------~~~~~~L~~~le~~~----~  135 (324)
T 3u61_B           81 GSDCK-IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGL--------------------AESQRHLRSFMEAYS----S  135 (324)
T ss_dssp             TTTCC-HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGG--------------------HHHHHHHHHHHHHHG----G
T ss_pred             ccccC-HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCc--------------------HHHHHHHHHHHHhCC----C
Confidence            87754 455555444321       568999999998841                    234556777776542    3


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      .+.+|+|||.+..++++|++  ||. .++|+.|+.+++..++..++.
T Consensus       136 ~~~iI~~~n~~~~l~~~l~s--R~~-~i~~~~~~~~e~~~il~~~~~  179 (324)
T 3u61_B          136 NCSIIITANNIDGIIKPLQS--RCR-VITFGQPTDEDKIEMMKQMIR  179 (324)
T ss_dssp             GCEEEEEESSGGGSCTTHHH--HSE-EEECCCCCHHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCccccCHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHH
Confidence            47889999999999999999  985 799999999998887776543

>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=99.71  E-value=2.7e-16  Score=146.24  Aligned_cols=155  Identities=16%  Similarity=0.198  Sum_probs=115.1

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~  286 (473)
                      ...|.+|++++|.++.++.+.+.+.    ..         ...+++|+||||||||++++++++.+     ...++.+++
T Consensus        10 ~~~p~~~~~~~g~~~~~~~l~~~l~----~~---------~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~   76 (226)
T 2chg_A           10 KYRPRTLDEVVGQDEVIQRLKGYVE----RK---------NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNA   76 (226)
T ss_dssp             HTSCSSGGGCCSCHHHHHHHHHHHH----TT---------CCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEET
T ss_pred             hcCCCCHHHHcCcHHHHHHHHHHHh----CC---------CCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEecc
Confidence            3467899999998887777655443    21         12359999999999999999999986     456777777


Q ss_pred             ccccCchHHHHHHHHh--------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          287 TELRSNSDLRTLLVAT--------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~--------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ........+...+...        ..+.+|+|||+|.+..                     .....|+..++..    ..
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~---------------------~~~~~l~~~l~~~----~~  131 (226)
T 2chg_A           77 SDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA---------------------DAQAALRRTMEMY----SK  131 (226)
T ss_dssp             TCTTCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCH---------------------HHHHHHHHHHHHT----TT
T ss_pred             ccccChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCH---------------------HHHHHHHHHHHhc----CC
Confidence            6655444444444332        4578999999998732                     2345566666543    24


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +..+|+|||.++.+++++.+  |+. .++++.|+.++...++..++...
T Consensus       132 ~~~~i~~~~~~~~~~~~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~  177 (226)
T 2chg_A          132 SCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKE  177 (226)
T ss_dssp             TEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHH
T ss_pred             CCeEEEEeCChhhcCHHHHH--hCc-eeecCCCCHHHHHHHHHHHHHHc
Confidence            57889999999999999999  887 89999999999999998876543

>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=99.71  E-value=1.5e-16  Score=155.05  Aligned_cols=167  Identities=19%  Similarity=0.249  Sum_probs=114.3

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc-C------
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR-S------  291 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~-~------  291 (473)
                      +.+++.....+.++.....+.   ......+..+++++||+||||||||++|+++|+.++.+++.+++++.. .      
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~---~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~~~g~~~~~~  109 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLV---QQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAK  109 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHH---HHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHH---HHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHHhcCCchHHH
Confidence            345666666566655422222   222333456678999999999999999999999999999998876521 1      


Q ss_pred             chHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC
Q 012016          292 NSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK  369 (473)
Q Consensus       292 ~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  369 (473)
                      ...++.++..+  ..+++|||||||.++..+.           .........+..|+..+++... .+..++||+|||.+
T Consensus       110 ~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~-----------~~~~~~~~~l~~L~~~~~~~~~-~~~~~~ii~ttn~~  177 (272)
T 1d2n_A          110 CQAMKKIFDDAYKSQLSCVVVDDIERLLDYVP-----------IGPRFSNLVLQALLVLLKKAPP-QGRKLLIIGTTSRK  177 (272)
T ss_dssp             HHHHHHHHHHHHTSSEEEEEECCHHHHTTCBT-----------TTTBCCHHHHHHHHHHTTCCCS-TTCEEEEEEEESCH
T ss_pred             HHHHHHHHHHHHhcCCcEEEEEChhhhhccCC-----------CChhHHHHHHHHHHHHhcCccC-CCCCEEEEEecCCh
Confidence            13456666654  3579999999999864211           1122345566777777776532 34467899999999


Q ss_pred             CCCCc-cccCCCceeeEEEeCCCCH-HHHHHHHHH
Q 012016          370 EKLDP-ALLRPGRMDVHVHMSYCTP-SGFKLLAAN  402 (473)
Q Consensus       370 ~~ld~-aLlrpgRfd~~I~~~~p~~-~~r~~l~~~  402 (473)
                      +.+++ .+.+  ||+..|++|.++. ++...++..
T Consensus       178 ~~l~~~~l~~--rf~~~i~~p~l~~r~~i~~i~~~  210 (272)
T 1d2n_A          178 DVLQEMEMLN--AFSTTIHVPNIATGEQLLEALEL  210 (272)
T ss_dssp             HHHHHTTCTT--TSSEEEECCCEEEHHHHHHHHHH
T ss_pred             hhcchhhhhc--ccceEEcCCCccHHHHHHHHHHh
Confidence            98988 5555  9999999987766 555555554

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.71  E-value=2.2e-16  Score=160.11  Aligned_cols=182  Identities=16%  Similarity=0.158  Sum_probs=122.8

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC--ceEEccccccc---
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF--DVYDLELTELR---  290 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~--~~~~l~~~~~~---  290 (473)
                      .+|++++|.+..++.+..... .+.       .|..+++++||+||||||||++++++|+.++.  +++.+++..+.   
T Consensus        41 ~~~~~ivG~~~~~~~l~~l~~-~~~-------~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~  112 (368)
T 3uk6_A           41 QASQGMVGQLAARRAAGVVLE-MIR-------EGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFSLE  112 (368)
T ss_dssp             SEETTEESCHHHHHHHHHHHH-HHH-------TTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGGGSCSS
T ss_pred             cchhhccChHHHHHHHHHHHH-HHH-------cCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchhhhhcc
Confidence            449999999988887644332 222       24455689999999999999999999999974  66666644310   


Q ss_pred             -----------------------------------------------C-----chHHHHHHHHhc-----------cCce
Q 012016          291 -----------------------------------------------S-----NSDLRTLLVATA-----------NRSI  307 (473)
Q Consensus       291 -----------------------------------------------~-----~~~l~~l~~~~~-----------~~sI  307 (473)
                                                                     .     ...++..+....           .++|
T Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~~v  192 (368)
T 3uk6_A          113 MSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIPGV  192 (368)
T ss_dssp             SCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CBCE
T ss_pred             cchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccCce
Confidence                                                           0     233444443321           1579


Q ss_pred             EEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec-----------CCCCCCCccc
Q 012016          308 LVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT-----------NHKEKLDPAL  376 (473)
Q Consensus       308 L~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT-----------N~~~~ld~aL  376 (473)
                      |||||+|.+.                     ...++.|+..++..    ...+++++|.           |.+..++++|
T Consensus       193 l~IDEi~~l~---------------------~~~~~~L~~~le~~----~~~~~ii~t~~~~~~i~~t~~~~~~~l~~~l  247 (368)
T 3uk6_A          193 LFIDEVHMLD---------------------IESFSFLNRALESD----MAPVLIMATNRGITRIRGTSYQSPHGIPIDL  247 (368)
T ss_dssp             EEEESGGGSB---------------------HHHHHHHHHHTTCT----TCCEEEEEESCSEEECBTSSCEEETTCCHHH
T ss_pred             EEEhhccccC---------------------hHHHHHHHHHhhCc----CCCeeeeecccceeeeeccCCCCcccCCHHH
Confidence            9999999873                     34566777777643    2234444443           3578899999


Q ss_pred             cCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCH-HHHHHHHhcCC-CCHHHHHHHH
Q 012016          377 LRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILF-EEIEELISTTQ-VTPAEVAEQL  433 (473)
Q Consensus       377 lrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~~-~t~a~i~~~l  433 (473)
                      ++  ||.. |+|+.|+.+++..++..++......+. +.++.++.... .++.++...|
T Consensus       248 ~s--R~~~-i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll  303 (368)
T 3uk6_A          248 LD--RLLI-VSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLI  303 (368)
T ss_dssp             HT--TEEE-EEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             Hh--hccE-EEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHH
Confidence            99  9976 899999999999999988765444333 33444444433 5666655544

>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=99.68  E-value=2.1e-17  Score=168.07  Aligned_cols=173  Identities=19%  Similarity=0.240  Sum_probs=118.2

Q ss_pred             cccchHHHHHHHHHHHHHHhchhHHhh-hcC-CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-------
Q 012016          221 LAMEQEQKTKIMQDLERFVKRKDYYRR-VGK-AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-------  291 (473)
Q Consensus       221 l~~~~~~k~~l~~~l~~fl~~~~~y~~-~g~-~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-------  291 (473)
                      |+|++..++.+...+.....+...... .+. .++.++||+||||||||++|+++|+.++.+++.++++.+..       
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l~~~~~~g~~   96 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGED   96 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHTTCHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHhccccccccc
Confidence            689999999988877655433221100 111 24678999999999999999999999999999999987642       


Q ss_pred             -chHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC---------
Q 012016          292 -NSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS---------  355 (473)
Q Consensus       292 -~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~---------  355 (473)
                       ...+..++...      ..++||||||||.+...+..  ..     .+.+.......+.||..|||....         
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~--~~-----~~~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~  169 (363)
T 3hws_A           97 VENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDN--PS-----ITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKH  169 (363)
T ss_dssp             HTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSC--C--------CHHHHHHHHHHHHHHHHCC------------
T ss_pred             HHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccc--cc-----cccccchHHHHHHHHHHhcCceeeccCcccccc
Confidence             23445555543      36789999999998652211  10     011222344889999999953210         


Q ss_pred             --------CCCceEEEEecCCC----------CC-----------------------------------CCccccCCCce
Q 012016          356 --------CGDERIIVFTTNHK----------EK-----------------------------------LDPALLRPGRM  382 (473)
Q Consensus       356 --------~~~~~iiI~tTN~~----------~~-----------------------------------ld~aLlrpgRf  382 (473)
                              ...++++|+|+|..          ..                                   +.|+|+.  ||
T Consensus       170 ~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~--R~  247 (363)
T 3hws_A          170 PQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG--RL  247 (363)
T ss_dssp             ----CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT--TC
T ss_pred             CCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc--cc
Confidence                    11234555555532          11                                   6788887  99


Q ss_pred             eeEEEeCCCCHHHHHHHHHH
Q 012016          383 DVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       383 d~~I~~~~p~~~~r~~l~~~  402 (473)
                      +..+.|+.|+.+.+..|+..
T Consensus       248 ~~~~~~~pl~~~~~~~I~~~  267 (363)
T 3hws_A          248 PVVATLNELSEEALIQILKE  267 (363)
T ss_dssp             CEEEECCCCCHHHHHHHHHS
T ss_pred             CeeeecCCCCHHHHHHHHHH
Confidence            99999999999999999886

>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=99.68  E-value=1.6e-15  Score=142.55  Aligned_cols=156  Identities=19%  Similarity=0.310  Sum_probs=113.3

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|..|++++|.+..++.+...+..           + ..++.++|+||||||||++++++++.++.            
T Consensus        16 ~~~p~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~   83 (250)
T 1njg_A           16 KWRPQTFADVVGQEHVLTALANGLSL-----------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVC   83 (250)
T ss_dssp             HTCCCSGGGCCSCHHHHHHHHHHHHH-----------T-CCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCS
T ss_pred             ccCCccHHHHhCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCccc
Confidence            35668899999998887776655431           1 12457999999999999999999998743            


Q ss_pred             ------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 ------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                                  +++.++.........++.++....      .+.+|+|||+|.+.                     ...
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~---------------------~~~  142 (250)
T 1njg_A           84 DNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS---------------------RHS  142 (250)
T ss_dssp             HHHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC---------------------HHH
T ss_pred             HHHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECccccc---------------------HHH
Confidence                        223333222222344566665532      46899999999862                     235


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +..|+..++..    +...++|++||.+..+++++.+  |+ ..++++.++.++...++..++...
T Consensus       143 ~~~l~~~l~~~----~~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~  201 (250)
T 1njg_A          143 FNALLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEE  201 (250)
T ss_dssp             HHHHHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHhcC----CCceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCCHHHHHHHHHHHHHhc
Confidence            56677777643    3468899999999999999988  75 689999999999999999887543

>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=99.68  E-value=7.1e-16  Score=164.09  Aligned_cols=196  Identities=18%  Similarity=0.300  Sum_probs=126.6

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhch-hHHhhhcC---CCCceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRK-DYYRRVGK---AWKRGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~-~~y~~~g~---~~~rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      .|..  ...|.+|++++|.++.++.+.+.+..+.... ..+...|.   ++++++||+||||||||++|+++|++++.++
T Consensus        28 lW~e--kyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~~~  105 (516)
T 1sxj_A           28 LWTV--KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI  105 (516)
T ss_dssp             CHHH--HTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEE
T ss_pred             Cccc--ccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCCCE
Confidence            5644  4577899999999999999888877654322 22333333   3568999999999999999999999999999


Q ss_pred             EEcccccccCchHHHHHHH-------------Hh-------ccCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          282 YDLELTELRSNSDLRTLLV-------------AT-------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       282 ~~l~~~~~~~~~~l~~l~~-------------~~-------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                      +.+++++......+...+.             ..       ..+.||||||+|.+..                  ..+..
T Consensus       106 i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~------------------~~~~~  167 (516)
T 1sxj_A          106 LEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSG------------------GDRGG  167 (516)
T ss_dssp             EEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCT------------------TSTTH
T ss_pred             EEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccch------------------hhHHH
Confidence            9999988755433333222             11       3578999999999853                  01223


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHh
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELIS  420 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~  420 (473)
                      +..|++.++..    ...+|+|+++.....++ .+.|   +...|.|+.|+.+++..++...+......+ .+.+..+++
T Consensus       168 l~~L~~~l~~~----~~~iIli~~~~~~~~l~-~l~~---r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~  239 (516)
T 1sxj_A          168 VGQLAQFCRKT----STPLILICNERNLPKMR-PFDR---VCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQ  239 (516)
T ss_dssp             HHHHHHHHHHC----SSCEEEEESCTTSSTTG-GGTT---TSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHH
T ss_pred             HHHHHHHHHhc----CCCEEEEEcCCCCccch-hhHh---ceEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            55566666542    12233333333334443 3544   456899999999999988887665433222 233444444


Q ss_pred             cCCCCHHHH
Q 012016          421 TTQVTPAEV  429 (473)
Q Consensus       421 ~~~~t~a~i  429 (473)
                      ..+-...++
T Consensus       240 ~s~GdiR~~  248 (516)
T 1sxj_A          240 TTRGDIRQV  248 (516)
T ss_dssp             HTTTCHHHH
T ss_pred             HcCCcHHHH
Confidence            333334333

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.67  E-value=8e-17  Score=146.37  Aligned_cols=151  Identities=19%  Similarity=0.265  Sum_probs=104.9

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEc
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDL  284 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l  284 (473)
                      |.+|++++|.++..+.+.+.+.    .         ..+++++|+||||||||++++++++.+          +.+++.+
T Consensus        18 ~~~~~~~~g~~~~~~~l~~~l~----~---------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~   84 (195)
T 1jbk_A           18 QGKLDPVIGRDEEIRRTIQVLQ----R---------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLAL   84 (195)
T ss_dssp             TTCSCCCCSCHHHHHHHHHHHT----S---------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEE
T ss_pred             hccccccccchHHHHHHHHHHh----c---------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEe
Confidence            5689999998887777655432    1         225689999999999999999999997          7888888


Q ss_pred             ccccccC--------chHHHHHHHHh---ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc
Q 012016          285 ELTELRS--------NSDLRTLLVAT---ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW  353 (473)
Q Consensus       285 ~~~~~~~--------~~~l~~l~~~~---~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  353 (473)
                      ++..+..        ...+..++...   ..+.||+|||+|.+......          .........   |...++.  
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~----------~~~~~~~~~---l~~~~~~--  149 (195)
T 1jbk_A           85 DMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKA----------DGAMDAGNM---LKPALAR--  149 (195)
T ss_dssp             CHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT----------------CCCCHHH---HHHHHHT--
T ss_pred             eHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcc----------cchHHHHHH---HHHhhcc--
Confidence            8776531        12344454433   35779999999998642110          001111222   2333321  


Q ss_pred             cCCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHH
Q 012016          354 SSCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLA  400 (473)
Q Consensus       354 ~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~  400 (473)
                          .++.+|++||.++     .+++++++  ||+ .|+++.|+.+++.+|+
T Consensus       150 ----~~~~~i~~~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          150 ----GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             ----TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             ----CCeEEEEeCCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHHh
Confidence                3477888888876     78999999  998 6999999999988764

>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=99.65  E-value=7.9e-16  Score=152.19  Aligned_cols=155  Identities=15%  Similarity=0.198  Sum_probs=114.1

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~  286 (473)
                      ...|.+|++++|.++.++.+.+.+.    .       |.  ..++|||||||||||++++++|+.+     +.+++.+++
T Consensus        10 k~~p~~~~~~~g~~~~~~~l~~~l~----~-------~~--~~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~   76 (319)
T 2chq_A           10 KYRPRTLDEVVGQDEVIQRLKGYVE----R-------KN--IPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNA   76 (319)
T ss_dssp             TTSCSSGGGSCSCHHHHHHHHTTTT----T-------TC--CCCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEET
T ss_pred             hcCCCCHHHHhCCHHHHHHHHHHHh----C-------CC--CCeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeC
Confidence            4567899999999888776654332    1       11  2249999999999999999999987     456777887


Q ss_pred             ccccCchHHHHHHHHh--------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          287 TELRSNSDLRTLLVAT--------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~--------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ++..+...+++.+...        ..+.||+|||+|.+.                     ....+.|+..++..    +.
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~---------------------~~~~~~L~~~le~~----~~  131 (319)
T 2chq_A           77 SDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALT---------------------ADAQAALRRTMEMY----SK  131 (319)
T ss_dssp             TSTTCTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSC---------------------HHHHHTTGGGTSSS----SS
T ss_pred             ccccChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCC---------------------HHHHHHHHHHHHhc----CC
Confidence            7654333333332221        347899999999873                     22345566666542    34


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ..++|++||.+..+++++.+  |+. .++|+.|+.+++..++..++...
T Consensus       132 ~~~~i~~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~  177 (319)
T 2chq_A          132 SCRFILSCNYVSRIIEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKE  177 (319)
T ss_dssp             SEEEEEEESCGGGSCHHHHT--TCE-EEECCCCCHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEeCChhhcchHHHh--hCe-EEEecCCCHHHHHHHHHHHHHHc
Confidence            68899999999999999998  886 89999999999999998877544

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.65  E-value=1.4e-15  Score=158.85  Aligned_cols=150  Identities=21%  Similarity=0.314  Sum_probs=110.2

Q ss_pred             CCCCCccccccchHHH---HHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          213 DHPATFETLAMEQEQK---TKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k---~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      -.|.+|++++|++..+   +.+...+    ...       .  ..++|||||||||||+++++||+.++.+++.+++...
T Consensus        20 ~rP~~l~~ivGq~~~~~~~~~L~~~i----~~~-------~--~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~~~   86 (447)
T 3pvs_A           20 MRPENLAQYIGQQHLLAAGKPLPRAI----EAG-------H--LHSMILWGPPGTGKTTLAEVIARYANADVERISAVTS   86 (447)
T ss_dssp             TCCCSTTTCCSCHHHHSTTSHHHHHH----HHT-------C--CCEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETTTC
T ss_pred             hCCCCHHHhCCcHHHHhchHHHHHHH----HcC-------C--CcEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEeccC
Confidence            4578999999998777   4443332    221       1  2589999999999999999999999999999887654


Q ss_pred             cCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEE
Q 012016          290 RSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV  363 (473)
Q Consensus       290 ~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI  363 (473)
                       +...++.++..+.      +++||||||||.+..                     .....||..++.      ..+++|
T Consensus        87 -~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~---------------------~~q~~LL~~le~------~~v~lI  138 (447)
T 3pvs_A           87 -GVKEIREAIERARQNRNAGRRTILFVDEVHRFNK---------------------SQQDAFLPHIED------GTITFI  138 (447)
T ss_dssp             -CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC---------------------------CCHHHHHT------TSCEEE
T ss_pred             -CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCH---------------------HHHHHHHHHHhc------CceEEE
Confidence             3455666665543      679999999998732                     123446666664      235666


Q ss_pred             Eec--CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          364 FTT--NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       364 ~tT--N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      ++|  |....++++|++  |+. .+.|+.|+.+++..++.+++..
T Consensus       139 ~att~n~~~~l~~aL~s--R~~-v~~l~~l~~edi~~il~~~l~~  180 (447)
T 3pvs_A          139 GATTENPSFELNSALLS--RAR-VYLLKSLSTEDIEQVLTQAMED  180 (447)
T ss_dssp             EEESSCGGGSSCHHHHT--TEE-EEECCCCCHHHHHHHHHHHHHC
T ss_pred             ecCCCCcccccCHHHhC--cee-EEeeCCcCHHHHHHHHHHHHHH
Confidence            544  444689999999  886 6889999999999999998764

>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=99.65  E-value=6.3e-16  Score=146.26  Aligned_cols=161  Identities=15%  Similarity=0.197  Sum_probs=106.7

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEccccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELTE  288 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~~  288 (473)
                      +.++.+|+++++.+ ..+.+++.+..+...         +.+++++|+||||||||++++++++.+.   .+++.+++..
T Consensus        21 ~~~~~~~~~~~~~~-~~~~~~~~l~~~~~~---------~~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~   90 (242)
T 3bos_A           21 LPDDETFTSYYPAA-GNDELIGALKSAASG---------DGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGI   90 (242)
T ss_dssp             CCTTCSTTTSCC---CCHHHHHHHHHHHHT---------CSCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGG
T ss_pred             CCCCCChhhccCCC-CCHHHHHHHHHHHhC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHH
Confidence            44557999998732 223444555555432         1357899999999999999999999874   7888888876


Q ss_pred             ccCchHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCce-EEEEecC
Q 012016          289 LRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER-IIVFTTN  367 (473)
Q Consensus       289 ~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~-iiI~tTN  367 (473)
                      +...  +.+.+....++.+|+|||+|.+..                   .......|+..++.....  ... +|+.+++
T Consensus        91 ~~~~--~~~~~~~~~~~~vliiDe~~~~~~-------------------~~~~~~~l~~~l~~~~~~--~~~~ii~~~~~  147 (242)
T 3bos_A           91 HASI--STALLEGLEQFDLICIDDVDAVAG-------------------HPLWEEAIFDLYNRVAEQ--KRGSLIVSASA  147 (242)
T ss_dssp             GGGS--CGGGGTTGGGSSEEEEETGGGGTT-------------------CHHHHHHHHHHHHHHHHH--CSCEEEEEESS
T ss_pred             HHHH--HHHHHHhccCCCEEEEeccccccC-------------------CHHHHHHHHHHHHHHHHc--CCCeEEEEcCC
Confidence            5321  222333446789999999998742                   111233455554443322  123 4444444


Q ss_pred             CCC---CCCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          368 HKE---KLDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       368 ~~~---~ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .+.   .+++++.+  ||.  ..++++.|+.+++..++..++...
T Consensus       148 ~~~~~~~~~~~l~~--r~~~~~~i~l~~~~~~~~~~~l~~~~~~~  190 (242)
T 3bos_A          148 SPMEAGFVLPDLVS--RMHWGLTYQLQPMMDDEKLAALQRRAAMR  190 (242)
T ss_dssp             CTTTTTCCCHHHHH--HHHHSEEEECCCCCGGGHHHHHHHHHHHT
T ss_pred             CHHHHHHhhhhhhh--HhhcCceEEeCCCCHHHHHHHHHHHHHHc
Confidence            444   45688888  886  899999999999999999887543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.63  E-value=2.6e-15  Score=148.41  Aligned_cols=161  Identities=17%  Similarity=0.270  Sum_probs=115.3

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHH
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDL  295 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l  295 (473)
                      +.++|.+..++.+...+......-.   . ...+...+||+||||||||++|+++|+.+   +.+++.++++.+......
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~~---~-~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~   92 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGLK---D-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV   92 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTCS---C-TTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHH
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCCC---C-CCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccH
Confidence            3577888888888777665432110   0 11223479999999999999999999998   567899988876443222


Q ss_pred             HHHH---------------H---HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          296 RTLL---------------V---ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       296 ~~l~---------------~---~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      ..++               .   ....++||||||+|.+.                     ....+.|+..|+...-..+
T Consensus        93 ~~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~---------------------~~~~~~Ll~~le~~~~~~~  151 (311)
T 4fcw_A           93 SRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAH---------------------PDVFNILLQMLDDGRLTDS  151 (311)
T ss_dssp             HHHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSC---------------------HHHHHHHHHHHHHSEEECT
T ss_pred             HHhcCCCCccccccccchHHHHHHhCCCeEEEEeChhhcC---------------------HHHHHHHHHHHhcCEEEcC
Confidence            2221               1   11245899999999873                     3456777777765321111


Q ss_pred             -------CceEEEEecCC--------------------------CCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          358 -------DERIIVFTTNH--------------------------KEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       358 -------~~~iiI~tTN~--------------------------~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                             .+.++|+|||.                          ...++|+|+.  ||+..+.+++|+.+++..|+..++
T Consensus       152 ~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p~~~~~~~~i~~~~l  229 (311)
T 4fcw_A          152 HGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQM  229 (311)
T ss_dssp             TSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHT
T ss_pred             CCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCCCCHHHHHHHHHHHH
Confidence                   25789999998                          5578899998  999999999999999999999887


Q ss_pred             Cc
Q 012016          405 GI  406 (473)
Q Consensus       405 ~~  406 (473)
                      ..
T Consensus       230 ~~  231 (311)
T 4fcw_A          230 SY  231 (311)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>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=99.63  E-value=2.8e-15  Score=149.74  Aligned_cols=187  Identities=17%  Similarity=0.241  Sum_probs=118.5

Q ss_pred             CCCCCCccccc-cchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          212 LDHPATFETLA-MEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       212 ~~~p~~f~~l~-~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      +.+..+|++++ |... .. ....+......+       .....+++||||||||||++++++++.+   +.+++.+++.
T Consensus         4 l~~~~~f~~fv~g~~~-~~-a~~~~~~~~~~~-------~~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~   74 (324)
T 1l8q_A            4 LNPKYTLENFIVGEGN-RL-AYEVVKEALENL-------GSLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSAD   74 (324)
T ss_dssp             CCTTCCSSSCCCCTTT-HH-HHHHHHHHHHTT-------TTSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CCCCCCcccCCCCCcH-HH-HHHHHHHHHhCc-------CCCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHH
Confidence            44557899997 4332 22 223333333321       1234689999999999999999999999   8999999887


Q ss_pred             cccCc-------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCce
Q 012016          288 ELRSN-------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDER  360 (473)
Q Consensus       288 ~~~~~-------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~  360 (473)
                      .+...       ..+........++.+|||||+|.+..                .   ......++..++.....  +.+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~vL~iDEi~~l~~----------------~---~~~~~~l~~~l~~~~~~--~~~  133 (324)
T 1l8q_A           75 DFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSG----------------K---ERTQIEFFHIFNTLYLL--EKQ  133 (324)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTT----------------C---HHHHHHHHHHHHHHHHT--TCE
T ss_pred             HHHHHHHHHHHcCcHHHHHHHhcCCCEEEEcCcccccC----------------C---hHHHHHHHHHHHHHHHC--CCe
Confidence            65210       11112222234589999999998742                0   12233444444443322  236


Q ss_pred             EEEEecCCCC---CCCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCHH-HHHHHHhcCCCCHHHHHHH
Q 012016          361 IIVFTTNHKE---KLDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILFE-EIEELISTTQVTPAEVAEQ  432 (473)
Q Consensus       361 iiI~tTN~~~---~ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~-~i~~l~~~~~~t~a~i~~~  432 (473)
                      +|+++++.+.   .++++|++  ||+  ..++++. +.+++..++..++......+.+ .++.++... ....++...
T Consensus       134 iii~~~~~~~~l~~l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~-g~~r~l~~~  207 (324)
T 1l8q_A          134 IILASDRHPQKLDGVSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT-KNVREIEGK  207 (324)
T ss_dssp             EEEEESSCGGGCTTSCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC-SSHHHHHHH
T ss_pred             EEEEecCChHHHHHhhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC-CCHHHHHHH
Confidence            6667777765   68999998  886  7899999 9999999999988654443433 344444444 445554443

>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=99.62  E-value=4.8e-15  Score=146.78  Aligned_cols=154  Identities=14%  Similarity=0.210  Sum_probs=115.1

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~  286 (473)
                      ...|.+|++++|.++.++.+.+.+.    .       | ..+ ++||+||||||||++++++|+.+     +.+++.+++
T Consensus        14 ~~~p~~~~~~~g~~~~~~~l~~~l~----~-------~-~~~-~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~   80 (323)
T 1sxj_B           14 KYRPQVLSDIVGNKETIDRLQQIAK----D-------G-NMP-HMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNA   80 (323)
T ss_dssp             HTCCSSGGGCCSCTHHHHHHHHHHH----S-------C-CCC-CEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECT
T ss_pred             hcCCCCHHHHHCCHHHHHHHHHHHH----c-------C-CCC-eEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecC
Confidence            3567899999999988877655432    1       1 123 39999999999999999999986     456788887


Q ss_pred             ccccCchHHHHHHHHh--------c-cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          287 TELRSNSDLRTLLVAT--------A-NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~--------~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      ++..+...+++++...        . .+.||+|||+|.+..                     .....|+..++..    +
T Consensus        81 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~---------------------~~~~~L~~~le~~----~  135 (323)
T 1sxj_B           81 SDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA---------------------GAQQALRRTMELY----S  135 (323)
T ss_dssp             TSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH---------------------HHHHTTHHHHHHT----T
T ss_pred             ccccChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCH---------------------HHHHHHHHHHhcc----C
Confidence            7654445565555432        1 378999999998732                     2345566666542    2


Q ss_pred             CceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          358 DERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       358 ~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      ...++|++||.+..+++++.+  |+. .++|+.|+.++...++...+..
T Consensus       136 ~~~~~il~~~~~~~l~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~  181 (323)
T 1sxj_B          136 NSTRFAFACNQSNKIIEPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKL  181 (323)
T ss_dssp             TTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHH
T ss_pred             CCceEEEEeCChhhchhHHHh--hce-EEeecCCCHHHHHHHHHHHHHH
Confidence            457888899999999999998  775 8999999999999999887653

>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=99.62  E-value=1.3e-14  Score=146.94  Aligned_cols=156  Identities=19%  Similarity=0.310  Sum_probs=115.6

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC------------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF------------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~------------  279 (473)
                      ...|.+|++++|.++.++.+...+.    .       | ..++.|||+||||||||++++++|+.++.            
T Consensus         9 k~rp~~~~~~vg~~~~~~~L~~~l~----~-------~-~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~   76 (373)
T 1jr3_A            9 KWRPQTFADVVGQEHVLTALANGLS----L-------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVC   76 (373)
T ss_dssp             HTCCCSTTTSCSCHHHHHHHHHHHH----H-------T-CCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSS
T ss_pred             hhCCCchhhccCcHHHHHHHHHHHH----h-------C-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCccc
Confidence            3466889999999888877666543    1       1 23457999999999999999999998854            


Q ss_pred             ------------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 ------------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ------------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                                  +++.++.........++.++....      .+.||+|||+|.+.                     ...
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~---------------------~~~  135 (373)
T 1jr3_A           77 DNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS---------------------RHS  135 (373)
T ss_dssp             HHHHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSC---------------------HHH
T ss_pred             HHHHHHhccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhc---------------------HHH
Confidence                        233344332223345666666543      46799999999872                     235


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .+.|+..++..    +..+++|++|+.+..+++++.+  |+ ..++|+.|+.++...++..++...
T Consensus       136 ~~~Ll~~le~~----~~~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~~~~~~~~l~~~~~~~  194 (373)
T 1jr3_A          136 FNALLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEE  194 (373)
T ss_dssp             HHHHHHHHHSC----CSSEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcC----CCceEEEEEeCChHhCcHHHHh--he-eEeeCCCCCHHHHHHHHHHHHHHc
Confidence            66777777653    3468899999999999999998  77 689999999999999998877543

>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=99.62  E-value=9.3e-16  Score=164.04  Aligned_cols=160  Identities=19%  Similarity=0.177  Sum_probs=111.5

Q ss_pred             ccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc-----
Q 012016          218 FETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN-----  292 (473)
Q Consensus       218 f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~-----  292 (473)
                      .++++|.+++++.+.+.+........       ..+..++|+||||||||+++++||+.++.++..+++..+...     
T Consensus        80 ~~di~G~~~vk~~i~~~~~l~~~~~~-------~~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~g  152 (543)
T 3m6a_A           80 DEEHHGLEKVKERILEYLAVQKLTKS-------LKGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRG  152 (543)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHHHHSSS-------CCSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC---------
T ss_pred             HHHhccHHHHHHHHHHHHHHHHhccc-------CCCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhhh
Confidence            34588888888887654432221111       135579999999999999999999999999999988765321     


Q ss_pred             ----------hHHHHHHHHhc-cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC------
Q 012016          293 ----------SDLRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS------  355 (473)
Q Consensus       293 ----------~~l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~------  355 (473)
                                ..+...|..+. ...||||||||.+....                 .....+.||..||.....      
T Consensus       153 ~~~~~ig~~~~~~~~~~~~a~~~~~vl~lDEid~l~~~~-----------------~~~~~~~LL~~ld~~~~~~~~~~~  215 (543)
T 3m6a_A          153 HRRTYVGAMPGRIIQGMKKAGKLNPVFLLDEIDKMSSDF-----------------RGDPSSAMLEVLDPEQNSSFSDHY  215 (543)
T ss_dssp             -----------CHHHHHHTTCSSSEEEEEEESSSCC--------------------------CCGGGTCTTTTTBCCCSS
T ss_pred             HHHHHhccCchHHHHHHHHhhccCCEEEEhhhhhhhhhh-----------------ccCHHHHHHHHHhhhhcceeeccc
Confidence                      12333444442 45699999999986411                 112345677777643211      


Q ss_pred             -----CCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          356 -----CGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       356 -----~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                           .-.+++||+|||.++.+||+|++  ||+ .|+|+.|+.+++..|+.+++
T Consensus       216 ~~~~~~~~~v~iI~ttN~~~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l  266 (543)
T 3m6a_A          216 IEETFDLSKVLFIATANNLATIPGPLRD--RME-IINIAGYTEIEKLEIVKDHL  266 (543)
T ss_dssp             SCCCCBCSSCEEEEECSSTTTSCHHHHH--HEE-EEECCCCCHHHHHHHHHHTH
T ss_pred             CCeeecccceEEEeccCccccCCHHHHh--hcc-eeeeCCCCHHHHHHHHHHHH
Confidence                 00357999999999999999999  996 69999999999999999887

>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=99.61  E-value=6.5e-15  Score=146.07  Aligned_cols=155  Identities=14%  Similarity=0.196  Sum_probs=112.9

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----CceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----FDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~l~~  286 (473)
                      ...|.+|++++|.++.++.+...+.    .       |.  ..++||+||||||||++++++|+.+.     .+++.+++
T Consensus        18 k~~p~~~~~~~g~~~~~~~l~~~l~----~-------~~--~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~   84 (327)
T 1iqp_A           18 KYRPQRLDDIVGQEHIVKRLKHYVK----T-------GS--MPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNA   84 (327)
T ss_dssp             HTCCCSTTTCCSCHHHHHHHHHHHH----H-------TC--CCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEET
T ss_pred             ccCCCCHHHhhCCHHHHHHHHHHHH----c-------CC--CCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeec
Confidence            3567899999999888877665443    1       11  23599999999999999999999873     34677776


Q ss_pred             ccccCchHHHHHHHHh--------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          287 TELRSNSDLRTLLVAT--------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~--------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ++..+...++..+...        ..+.||+|||+|.+.                     ....+.|+..++..    +.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~---------------------~~~~~~L~~~le~~----~~  139 (327)
T 1iqp_A           85 SDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALT---------------------QDAQQALRRTMEMF----SS  139 (327)
T ss_dssp             TCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSC---------------------HHHHHHHHHHHHHT----TT
T ss_pred             cccCchHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCC---------------------HHHHHHHHHHHHhc----CC
Confidence            6542222333322221        347899999999873                     23456677777643    24


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      ...+|++||.+..+++++.+  |+. .++|+.++.++...++...+...
T Consensus       140 ~~~~i~~~~~~~~l~~~l~s--r~~-~~~~~~l~~~~~~~~l~~~~~~~  185 (327)
T 1iqp_A          140 NVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENE  185 (327)
T ss_dssp             TEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTT
T ss_pred             CCeEEEEeCCccccCHHHHh--hCc-EEEecCCCHHHHHHHHHHHHHhc
Confidence            57888899999999999998  886 79999999999999888776543

>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=99.60  E-value=5.7e-15  Score=148.40  Aligned_cols=158  Identities=18%  Similarity=0.234  Sum_probs=113.8

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC------C
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN------F  279 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~------~  279 (473)
                      .|..  ...|.+|++++|.++.++.+...+    ..       |.  ..++||+||||||||++++++|+.++      .
T Consensus        26 ~~~~--k~~p~~~~~i~g~~~~~~~l~~~l----~~-------~~--~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~   90 (353)
T 1sxj_D           26 PWVE--KYRPKNLDEVTAQDHAVTVLKKTL----KS-------AN--LPHMLFYGPPGTGKTSTILALTKELYGPDLMKS   90 (353)
T ss_dssp             CHHH--HTCCSSTTTCCSCCTTHHHHHHHT----TC-------TT--CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTT
T ss_pred             cHHH--hcCCCCHHHhhCCHHHHHHHHHHH----hc-------CC--CCEEEEECCCCCCHHHHHHHHHHHhCCCccccc
Confidence            4543  346789999999998877665433    22       11  23499999999999999999999874      4


Q ss_pred             ceEEcccccccCchHHHHHHHHh------------------ccCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          280 DVYDLELTELRSNSDLRTLLVAT------------------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       280 ~~~~l~~~~~~~~~~l~~l~~~~------------------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                      .+..+++++......+++.+...                  ..+.||+|||+|.+.                     ...
T Consensus        91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~---------------------~~~  149 (353)
T 1sxj_D           91 RILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMT---------------------ADA  149 (353)
T ss_dssp             SEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSC---------------------HHH
T ss_pred             ceEEEccccccchHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccC---------------------HHH
Confidence            57778877654333333322211                  234699999999873                     234


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      .+.|+..|+...    ....+|++||++..+++++++  |+. .++|+.|+.++...++...+..
T Consensus       150 ~~~Ll~~le~~~----~~~~~il~~~~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~  207 (353)
T 1sxj_D          150 QSALRRTMETYS----GVTRFCLICNYVTRIIDPLAS--QCS-KFRFKALDASNAIDRLRFISEQ  207 (353)
T ss_dssp             HHHHHHHHHHTT----TTEEEEEEESCGGGSCHHHHH--HSE-EEECCCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhcC----CCceEEEEeCchhhCcchhhc--cCc-eEEeCCCCHHHHHHHHHHHHHH
Confidence            466777776532    346777889999999999998  886 8999999999998888877643

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.60  E-value=8.4e-15  Score=145.80  Aligned_cols=151  Identities=13%  Similarity=0.199  Sum_probs=106.1

Q ss_pred             cccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEccccccc
Q 012016          221 LAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLELTELR  290 (473)
Q Consensus       221 l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~~~~~  290 (473)
                      |.+.++..+.|...+...+..         ..+.++|||||||||||++++++++++          ++.++.++|..+.
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            444445555555555544432         236789999999999999999999998          4577888876642


Q ss_pred             C----------------------chHHHHHHHHh----ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHH
Q 012016          291 S----------------------NSDLRTLLVAT----ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSG  344 (473)
Q Consensus       291 ~----------------------~~~l~~l~~~~----~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~  344 (473)
                      +                      ...+.+.|...    ..+.||+|||+|.+.                    .+..+-.
T Consensus        93 t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~--------------------~q~~L~~  152 (318)
T 3te6_A           93 GMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL--------------------SEKILQY  152 (318)
T ss_dssp             --HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC--------------------CTHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh--------------------cchHHHH
Confidence            2                      23456666653    346899999999884                    1345555


Q ss_pred             HHHHhcccccCCCCceEEEEecCCCCC----CCccccCCCcee-eEEEeCCCCHHHHHHHHHHHhCc
Q 012016          345 FLNFIDGLWSSCGDERIIVFTTNHKEK----LDPALLRPGRMD-VHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       345 LL~~ldg~~~~~~~~~iiI~tTN~~~~----ld~aLlrpgRfd-~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      |++...    .....++||+++|..+.    |++++.+  ||. ..|+|+.++.++...|+.+.+..
T Consensus       153 l~~~~~----~~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          153 FEKWIS----SKNSKLSIICVGGHNVTIREQINIMPSL--KAHFTEIKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             HHHHHH----CSSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             HHhccc----ccCCcEEEEEEecCcccchhhcchhhhc--cCCceEEEeCCCCHHHHHHHHHHHHHh
Confidence            655432    12245889999998764    4556666  886 68999999999999999988754

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.60  E-value=3.4e-15  Score=149.41  Aligned_cols=152  Identities=14%  Similarity=0.191  Sum_probs=107.4

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHH
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLR  296 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~  296 (473)
                      .+++++|.++.++.+...+..               ++++||+||||||||++++++|+.++.+++.+++..-.....+.
T Consensus        25 ~~~~i~g~~~~~~~l~~~l~~---------------~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~~~l~   89 (331)
T 2r44_A           25 VGKVVVGQKYMINRLLIGICT---------------GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLPSDLI   89 (331)
T ss_dssp             HTTTCCSCHHHHHHHHHHHHH---------------TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCHHHHH
T ss_pred             hccceeCcHHHHHHHHHHHHc---------------CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCChhhcC
Confidence            457888888887776554431               25899999999999999999999999999888874221111111


Q ss_pred             HH---------HHHhcc---CceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc-------ccCCC
Q 012016          297 TL---------LVATAN---RSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL-------WSSCG  357 (473)
Q Consensus       297 ~l---------~~~~~~---~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-------~~~~~  357 (473)
                      ..         +.....   .+||||||+|.+.                     ....+.|+..|+..       ....+
T Consensus        90 g~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~---------------------~~~~~~Ll~~l~~~~~~~~g~~~~~~  148 (331)
T 2r44_A           90 GTMIYNQHKGNFEVKKGPVFSNFILADEVNRSP---------------------AKVQSALLECMQEKQVTIGDTTYPLD  148 (331)
T ss_dssp             EEEEEETTTTEEEEEECTTCSSEEEEETGGGSC---------------------HHHHHHHHHHHHHSEEEETTEEEECC
T ss_pred             CceeecCCCCceEeccCcccccEEEEEccccCC---------------------HHHHHHHHHHHhcCceeeCCEEEECC
Confidence            00         000011   3799999999762                     34556666666532       11123


Q ss_pred             CceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          358 DERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       358 ~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      ...++|+|+|..+     .++++|++  ||+.++++++|+.+++..|+...+..
T Consensus       149 ~~~~viat~np~~~~~~~~l~~~l~~--Rf~~~i~i~~p~~~~~~~il~~~~~~  200 (331)
T 2r44_A          149 NPFLVLATQNPVEQEGTYPLPEAQVD--RFMMKIHLTYLDKESELEVMRRVSNM  200 (331)
T ss_dssp             SSCEEEEEECTTCCSCCCCCCHHHHT--TSSEEEECCCCCHHHHHHHHHHHHCT
T ss_pred             CCEEEEEecCCCcccCcccCCHHHHh--heeEEEEcCCCCHHHHHHHHHhcccc
Confidence            3577888888553     38999999  99999999999999999999988764

>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=99.59  E-value=6.5e-14  Score=140.75  Aligned_cols=191  Identities=17%  Similarity=0.204  Sum_probs=128.0

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS  291 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~  291 (473)
                      .-.|.+|++++|.+.+++.+...+..-.       ..|. ++..++|+||||||||+|++++|+.++.++...+......
T Consensus        18 ~lr~~~l~~~~g~~~~~~~l~~~i~~~~-------~~~~-~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~~~   89 (334)
T 1in4_A           18 FLRPKSLDEFIGQENVKKKLSLALEAAK-------MRGE-VLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVK   89 (334)
T ss_dssp             TTSCSSGGGCCSCHHHHHHHHHHHHHHH-------HHTC-CCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCS
T ss_pred             HcCCccHHHccCcHHHHHHHHHHHHHHH-------hcCC-CCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHhcC
Confidence            3456799999998766665543332211       1122 2457999999999999999999999998887666555545


Q ss_pred             chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc------cCC--------C
Q 012016          292 NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW------SSC--------G  357 (473)
Q Consensus       292 ~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~------~~~--------~  357 (473)
                      ...+..++.....+.|++|||++.+..                     .....|+..++...      ...        -
T Consensus        90 ~~~l~~~~~~~~~~~v~~iDE~~~l~~---------------------~~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l  148 (334)
T 1in4_A           90 QGDMAAILTSLERGDVLFIDEIHRLNK---------------------AVEELLYSAIEDFQIDIMIGKGPSAKSIRIDI  148 (334)
T ss_dssp             HHHHHHHHHHCCTTCEEEEETGGGCCH---------------------HHHHHHHHHHHTSCCCC---------------
T ss_pred             HHHHHHHHHHccCCCEEEEcchhhcCH---------------------HHHHHHHHHHHhcccceeeccCcccccccccC
Confidence            556666666556788999999998742                     11222333332110      000        0


Q ss_pred             CceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC-HHHHHHHHhcCCCCHHHHHHHH
Q 012016          358 DERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL-FEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       358 ~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l-~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      ..+.++++|+.+..|++++++  ||...+.|++++.+++..++++......... .+.+..++....-+|..+...|
T Consensus       149 ~~~~li~at~~~~~Ls~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G~~R~a~~ll  223 (334)
T 1in4_A          149 QPFTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLT  223 (334)
T ss_dssp             CCCEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHHHHHH
T ss_pred             CCeEEEEecCCcccCCHHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCCChHHHHHHH
Confidence            235677899999999999999  9998999999999999999988765332222 3445555555556666554443

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.59  E-value=2.7e-15  Score=152.13  Aligned_cols=161  Identities=16%  Similarity=0.141  Sum_probs=113.2

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEccc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLEL  286 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~  286 (473)
                      ..+++++|.++..+.+...+...+.         ...+++++|+||||||||++++++++.+         +.+++.+++
T Consensus        16 ~~p~~~~gr~~~~~~l~~~l~~~~~---------~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~   86 (387)
T 2v1u_A           16 YVPDVLPHREAELRRLAEVLAPALR---------GEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNA   86 (387)
T ss_dssp             CCCSCCTTCHHHHHHHHHTTGGGTS---------SCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEET
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHc---------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEEC
Confidence            3458899988887777665443221         1235689999999999999999999998         888888887


Q ss_pred             ccccCc----------------------hH-HHHHHHHh---ccCceEEEeccccccccccCCccccCCCCCCCccchhH
Q 012016          287 TELRSN----------------------SD-LRTLLVAT---ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKV  340 (473)
Q Consensus       287 ~~~~~~----------------------~~-l~~l~~~~---~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~  340 (473)
                      ....+.                      .. +..++...   ..+.||||||+|.+...                .....
T Consensus        87 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~----------------~~~~~  150 (387)
T 2v1u_A           87 RHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKR----------------PGGQD  150 (387)
T ss_dssp             TTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHS----------------TTHHH
T ss_pred             CcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhccc----------------CCCCh
Confidence            654221                      12 22222222   23679999999998530                01345


Q ss_pred             HHHHHHHHhcccccCCCCceEEEEecCCC---CCCCccccCCCceee-EEEeCCCCHHHHHHHHHHHhC
Q 012016          341 TLSGFLNFIDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRMDV-HVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       341 ~ls~LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRfd~-~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      .+..+++.++....  +..+++|++||.+   +.+++++.+  ||.. .|+|+.++.++...++...+.
T Consensus       151 ~l~~l~~~~~~~~~--~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~  215 (387)
T 2v1u_A          151 LLYRITRINQELGD--RVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAE  215 (387)
T ss_dssp             HHHHHHHGGGCC-------CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHH
T ss_pred             HHHhHhhchhhcCC--CceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHH
Confidence            66666666554310  2458899999987   788999998  8875 899999999999999998765

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.58  E-value=1.9e-15  Score=137.05  Aligned_cols=144  Identities=17%  Similarity=0.268  Sum_probs=99.1

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEc
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDL  284 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l  284 (473)
                      |.+|++++|.++..+.+.+.+.    .         ..++++||+||||||||++++++++.+          +.+++.+
T Consensus        18 ~~~~~~~~g~~~~~~~l~~~l~----~---------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~   84 (187)
T 2p65_A           18 AGKLDPVIGRDTEIRRAIQILS----R---------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSL   84 (187)
T ss_dssp             TTCSCCCCSCHHHHHHHHHHHT----S---------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEE
T ss_pred             ccccchhhcchHHHHHHHHHHh----C---------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEE
Confidence            5689999998877666655432    1         235689999999999999999999997          7888888


Q ss_pred             ccccccC--------chHHHHHHHHh---ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc
Q 012016          285 ELTELRS--------NSDLRTLLVAT---ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW  353 (473)
Q Consensus       285 ~~~~~~~--------~~~l~~l~~~~---~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  353 (473)
                      ++..+..        ...+..++...   ..+.+|+|||+|.+...+..            ..........|+..++.  
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~------------~~~~~~~~~~l~~~~~~--  150 (187)
T 2p65_A           85 DLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAV------------AEGALDAGNILKPMLAR--  150 (187)
T ss_dssp             CHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSS------------CTTSCCTHHHHHHHHHT--
T ss_pred             eHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhcccccc------------cccchHHHHHHHHHHhc--
Confidence            8766421        12344444433   35689999999998631110            00012233334444432  


Q ss_pred             cCCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCC
Q 012016          354 SSCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCT  392 (473)
Q Consensus       354 ~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~  392 (473)
                          ..+++|++||.++     .+|+++++  ||+. |+++.|+
T Consensus       151 ----~~~~ii~~~~~~~~~~~~~~~~~l~~--R~~~-i~i~~p~  187 (187)
T 2p65_A          151 ----GELRCIGATTVSEYRQFIEKDKALER--RFQQ-ILVEQPS  187 (187)
T ss_dssp             ----TCSCEEEEECHHHHHHHTTTCHHHHH--HEEE-EECCSCC
T ss_pred             ----CCeeEEEecCHHHHHHHHhccHHHHH--hcCc-ccCCCCC
Confidence                3478889998775     68999999  9984 9999986

>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=99.58  E-value=1.2e-14  Score=147.68  Aligned_cols=151  Identities=17%  Similarity=0.274  Sum_probs=111.6

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----------CCceEEcccc
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----------NFDVYDLELT  287 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----------~~~~~~l~~~  287 (473)
                      ++++|.++..+.+.+.+..++..         ..+++++|+||||||||++++++++.+           +.+++.+++.
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~---------~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~   90 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKN---------EVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCR   90 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTT---------CCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECc
Confidence            78999999888888877665542         225689999999999999999999998           8999999876


Q ss_pred             ccc-Cc-----------------------hH-HHHHHHHhcc-CceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          288 ELR-SN-----------------------SD-LRTLLVATAN-RSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       288 ~~~-~~-----------------------~~-l~~l~~~~~~-~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                      ... +.                       .. +..++..... +.||+|||+|.+...                 .....
T Consensus        91 ~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~-----------------~~~~~  153 (384)
T 2qby_B           91 EVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKR-----------------RGGDI  153 (384)
T ss_dssp             HHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHS-----------------TTSHH
T ss_pred             cCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccC-----------------CCCce
Confidence            543 11                       11 2222222222 339999999998530                 01223


Q ss_pred             -HHHHHHHhcccccCCCCceEEEEecCCC---CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          342 -LSGFLNFIDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       342 -ls~LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                       +..|+...        .++.+|+|||.+   +.+++++++  ||+..|+|+.++.++...++..++.
T Consensus       154 ~l~~l~~~~--------~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~  211 (384)
T 2qby_B          154 VLYQLLRSD--------ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAE  211 (384)
T ss_dssp             HHHHHHTSS--------SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHH
T ss_pred             eHHHHhcCC--------cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHH
Confidence             44444332        358899999987   788999988  8877999999999999999998764

>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=99.58  E-value=4.1e-14  Score=144.30  Aligned_cols=174  Identities=18%  Similarity=0.245  Sum_probs=113.3

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHh-----------------hhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYR-----------------RVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~-----------------~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .|+|+++.|+.|...+...+.+.....                 ......+.++||+||||||||++|+++|+.++.+++
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            478999999999887754443322100                 011234568999999999999999999999999999


Q ss_pred             EcccccccC--------chHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHH
Q 012016          283 DLELTELRS--------NSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNF  348 (473)
Q Consensus       283 ~l~~~~~~~--------~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~  348 (473)
                      .+++..+..        ...+..++...      ..++||||||+|.+...+.  ....     ..+.......+.|+..
T Consensus       102 ~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~--~~~~-----~~~~~~~~~~~~Ll~~  174 (376)
T 1um8_A          102 ISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSE--NRSI-----TRDVSGEGVQQALLKI  174 (376)
T ss_dssp             EEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC---------------------CHHHHHHHHHH
T ss_pred             EecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcC--CCce-----ecccchHHHHHHHHHH
Confidence            999887631        22344444432      2679999999999864211  1000     1111223477888998


Q ss_pred             hccccc----C-------------CCCceEEEEecCCC-----------------------------------------C
Q 012016          349 IDGLWS----S-------------CGDERIIVFTTNHK-----------------------------------------E  370 (473)
Q Consensus       349 ldg~~~----~-------------~~~~~iiI~tTN~~-----------------------------------------~  370 (473)
                      |++..-    .             ...++++|+|||..                                         .
T Consensus       175 le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~  254 (376)
T 1um8_A          175 VEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTY  254 (376)
T ss_dssp             HHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHT
T ss_pred             hhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhc
Confidence            886410    0             01345777777621                                         1


Q ss_pred             CCCccccCCCceeeEEEeCCCCHHHHHHHHHH
Q 012016          371 KLDPALLRPGRMDVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       371 ~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~  402 (473)
                      .+.|+|+.  ||+..+.|+.++.++...|+..
T Consensus       255 ~~~p~l~~--R~~~~i~~~~l~~~~l~~i~~~  284 (376)
T 1um8_A          255 GLIPELIG--RLPVLSTLDSISLEAMVDILQK  284 (376)
T ss_dssp             TCCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             CCChHHhc--CCCceeeccCCCHHHHHHHHhh
Confidence            24566777  9999999999999999888874

>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=99.57  E-value=1.1e-14  Score=151.87  Aligned_cols=189  Identities=17%  Similarity=0.274  Sum_probs=117.9

Q ss_pred             CCCCCCccccc-cchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcc
Q 012016          212 LDHPATFETLA-MEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLE  285 (473)
Q Consensus       212 ~~~p~~f~~l~-~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~  285 (473)
                      +.+..+|++++ |.....  ....+..+...+      +.  ..+++||||||||||+|++++|+++     +.+++.++
T Consensus        98 l~~~~tfd~fv~g~~n~~--a~~~~~~~a~~~------~~--~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~  167 (440)
T 2z4s_A           98 LNPDYTFENFVVGPGNSF--AYHAALEVAKHP------GR--YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYIT  167 (440)
T ss_dssp             CCTTCSGGGCCCCTTTHH--HHHHHHHHHHST------TS--SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEE
T ss_pred             CCCCCChhhcCCCCchHH--HHHHHHHHHhCC------CC--CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEee
Confidence            44456899987 533222  223333333321      11  5689999999999999999999998     88899888


Q ss_pred             cccccCc-------hHHHHHHHHhc-cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          286 LTELRSN-------SDLRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       286 ~~~~~~~-------~~l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      +..+...       .....+..... ++.||||||+|.+..                   .......|+..++.+...  
T Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~-------------------~~~~q~~l~~~l~~l~~~--  226 (440)
T 2z4s_A          168 SEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIG-------------------KTGVQTELFHTFNELHDS--  226 (440)
T ss_dssp             HHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSS-------------------CHHHHHHHHHHHHHHHTT--
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccC-------------------ChHHHHHHHHHHHHHHHC--
Confidence            7765210       11112222334 689999999998843                   012334455555444322  


Q ss_pred             CceEEEEecCCCCC---CCccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCH-HHHHHHHhcCCCCHHHHHH
Q 012016          358 DERIIVFTTNHKEK---LDPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILF-EEIEELISTTQVTPAEVAE  431 (473)
Q Consensus       358 ~~~iiI~tTN~~~~---ld~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~-~~i~~l~~~~~~t~a~i~~  431 (473)
                      +..+||.|.+.+..   ++++|++  ||.  ..++++.|+.+++..++...+......+. +.+..++.....++.++..
T Consensus       227 ~~~iIitt~~~~~~l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~~gn~R~l~~  304 (440)
T 2z4s_A          227 GKQIVICSDREPQKLSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENVDDNLRRLRG  304 (440)
T ss_dssp             TCEEEEEESSCGGGCSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHCCSCHHHHHH
T ss_pred             CCeEEEEECCCHHHHHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcCCCHHHHHH
Confidence            23555555555554   8899998  886  78999999999999999988754332222 2233344444455555544


Q ss_pred             HH
Q 012016          432 QL  433 (473)
Q Consensus       432 ~l  433 (473)
                      .|
T Consensus       305 ~L  306 (440)
T 2z4s_A          305 AI  306 (440)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>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=99.56  E-value=2.1e-14  Score=144.10  Aligned_cols=156  Identities=21%  Similarity=0.214  Sum_probs=100.6

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------c-----
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------D-----  280 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------~-----  280 (473)
                      .+|.+|++++|.+..++.+...    ...+         ...++||+||||||||++|+++|+.++.       +     
T Consensus        18 ~~~~~f~~i~G~~~~~~~l~~~----~~~~---------~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~   84 (350)
T 1g8p_A           18 RPVFPFSAIVGQEDMKLALLLT----AVDP---------GIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPN   84 (350)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHH----HHCG---------GGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSS
T ss_pred             CCCCCchhccChHHHHHHHHHH----hhCC---------CCceEEEECCCCccHHHHHHHHHHhCccccccccccccccc
Confidence            3567899999998866543221    1111         1346999999999999999999999863       2     


Q ss_pred             ---------------------eEEccccc----ccCchHHHHHHHHh-----------ccCceEEEeccccccccccCCc
Q 012016          281 ---------------------VYDLELTE----LRSNSDLRTLLVAT-----------ANRSILVVEDIDCTIDLQDRLP  324 (473)
Q Consensus       281 ---------------------~~~l~~~~----~~~~~~l~~l~~~~-----------~~~sIL~iDdiD~l~~~~~r~~  324 (473)
                                           ++.+....    +.+...+...+...           ..+++|||||||.+.       
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~-------  157 (350)
T 1g8p_A           85 VEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLE-------  157 (350)
T ss_dssp             GGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSC-------
T ss_pred             cccccchhhhhccccccCCCcccccCCCcchhhheeechhhhhhcCCceeecCceeeecCCCEEEEeChhhCC-------
Confidence                                 11111100    00111112222211           247899999999873       


Q ss_pred             cccCCCCCCCccchhHHHHHHHHHhccc----ccCC-----CCceEEEEecCCCC-CCCccccCCCceeeEEEeCCC-CH
Q 012016          325 ADIAGEGEGPIQQNKVTLSGFLNFIDGL----WSSC-----GDERIIVFTTNHKE-KLDPALLRPGRMDVHVHMSYC-TP  393 (473)
Q Consensus       325 ~~~~~~~~~~~~~~~~~ls~LL~~ldg~----~~~~-----~~~~iiI~tTN~~~-~ld~aLlrpgRfd~~I~~~~p-~~  393 (473)
                                    ......|+..++.-    ....     +..+++|+|||..+ .++++|++  ||+.+++++.| +.
T Consensus       158 --------------~~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~  221 (350)
T 1g8p_A          158 --------------DHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDV  221 (350)
T ss_dssp             --------------HHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSH
T ss_pred             --------------HHHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCCcH
Confidence                          23455666666531    1111     12578899999754 89999999  99999999999 67


Q ss_pred             HHHHHHHHHHh
Q 012016          394 SGFKLLAANYL  404 (473)
Q Consensus       394 ~~r~~l~~~~l  404 (473)
                      +.+..|+...+
T Consensus       222 ~~~~~il~~~~  232 (350)
T 1g8p_A          222 ETRVEVIRRRD  232 (350)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            77778887643

>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=99.55  E-value=4.9e-14  Score=141.90  Aligned_cols=180  Identities=11%  Similarity=0.156  Sum_probs=115.9

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc-CC-----------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL-NF-----------  279 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l-~~-----------  279 (473)
                      ...|.+|++++|+++..+.+...+.   .       .| ..+. ++|+||||||||++++++|+.+ +.           
T Consensus         7 kyrP~~~~~~vg~~~~~~~l~~~~~---~-------~~-~~~~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~   74 (354)
T 1sxj_E            7 KYRPKSLNALSHNEELTNFLKSLSD---Q-------PR-DLPH-LLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQ   74 (354)
T ss_dssp             TTCCCSGGGCCSCHHHHHHHHTTTT---C-------TT-CCCC-EEEECSTTSSHHHHHHTHHHHHSCTTCCC-------
T ss_pred             ccCCCCHHHhcCCHHHHHHHHHHHh---h-------CC-CCCe-EEEECCCCCCHHHHHHHHHHHHcCCCCCeEEeccee
Confidence            4578999999998877665543320   1       12 2233 9999999999999999999964 21           


Q ss_pred             -----------------ceEEcccccccCch--HHHHHHHHh----------------ccCceEEEeccccccccccCCc
Q 012016          280 -----------------DVYDLELTELRSNS--DLRTLLVAT----------------ANRSILVVEDIDCTIDLQDRLP  324 (473)
Q Consensus       280 -----------------~~~~l~~~~~~~~~--~l~~l~~~~----------------~~~sIL~iDdiD~l~~~~~r~~  324 (473)
                                       +++.++........  .+++.+...                .++.||+|||++.+.       
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~-------  147 (354)
T 1sxj_E           75 FVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLT-------  147 (354)
T ss_dssp             -----------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSC-------
T ss_pred             ecccccccceeeeecccceEEecHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccC-------
Confidence                             12333333221111  345544432                246699999999852       


Q ss_pred             cccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          325 ADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       325 ~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                                    ....+.|++.|+...    .+..+|++||.++.+.+++.+  |+ ..++|+.|+.++...++...+
T Consensus       148 --------------~~~~~~L~~~le~~~----~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~~~~~l~~~~  206 (354)
T 1sxj_E          148 --------------KDAQAALRRTMEKYS----KNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVV  206 (354)
T ss_dssp             --------------HHHHHHHHHHHHHST----TTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHH
T ss_pred             --------------HHHHHHHHHHHHhhc----CCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcCHHHHHHHHHHHH
Confidence                          234566777776532    357888999999999999998  88 789999999999999998877


Q ss_pred             CccccCC--HHHHHHHHhcCCCCHHHHHH
Q 012016          405 GIKEHIL--FEEIEELISTTQVTPAEVAE  431 (473)
Q Consensus       405 ~~~~~~l--~~~i~~l~~~~~~t~a~i~~  431 (473)
                      ..++...  .+.++.++...+-++.++..
T Consensus       207 ~~~~~~~~~~~~l~~i~~~~~G~~r~a~~  235 (354)
T 1sxj_E          207 TNERIQLETKDILKRIAQASNGNLRVSLL  235 (354)
T ss_dssp             HHHTCEECCSHHHHHHHHHHTTCHHHHHH
T ss_pred             HHcCCCCCcHHHHHHHHHHcCCCHHHHHH
Confidence            5443222  23334444333344444433

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.55  E-value=3.5e-14  Score=157.80  Aligned_cols=160  Identities=14%  Similarity=0.221  Sum_probs=113.5

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc---
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN---  292 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~---  292 (473)
                      +.++|.+..++.+...+........   . ...+..++||+||||||||++|+++|+.+   +.+++.++++.+...   
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~---~-~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~  566 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLK---D-PKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHST  566 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCS---C-TTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCC
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccC---C-CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhccccccc
Confidence            4578888888887776654332100   0 01112269999999999999999999998   789999999987432   


Q ss_pred             --hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC-------CCCceEEE
Q 012016          293 --SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS-------CGDERIIV  363 (473)
Q Consensus       293 --~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-------~~~~~iiI  363 (473)
                        ..+...+. ...++||||||||.+                     ....++.|+..||.-.-.       ...+++||
T Consensus       567 ~~~~l~~~~~-~~~~~vl~lDEi~~~---------------------~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI  624 (758)
T 3pxi_A          567 SGGQLTEKVR-RKPYSVVLLDAIEKA---------------------HPDVFNILLQVLEDGRLTDSKGRTVDFRNTILI  624 (758)
T ss_dssp             C---CHHHHH-HCSSSEEEEECGGGS---------------------CHHHHHHHHHHHHHSBCC-----CCBCTTCEEE
T ss_pred             ccchhhHHHH-hCCCeEEEEeCcccc---------------------CHHHHHHHHHHhccCeEEcCCCCEeccCCeEEE
Confidence              23333332 245789999999976                     245677888888752111       11357999


Q ss_pred             EecCCCCC------------CCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          364 FTTNHKEK------------LDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       364 ~tTN~~~~------------ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      +|||.+..            ++|+|+.  |||..|.|+.|+.+++..|+..++..
T Consensus       625 ~ttn~~~~~~~~~~~~~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l~~  677 (758)
T 3pxi_A          625 MTSNVGASEKDKVMGELKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMSDQ  677 (758)
T ss_dssp             EEESSSTTCCHHHHHHHHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHHHH
T ss_pred             EeCCCChhhHHHHHHHHHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHHHH
Confidence            99997544            7888888  99999999999999999999988753

>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=99.55  E-value=9.3e-14  Score=141.10  Aligned_cols=160  Identities=16%  Similarity=0.104  Sum_probs=114.6

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccccccCc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTELRSN  292 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~~~~~  292 (473)
                      .+++++|.++..+.+...+...+.+..       +..+.++|+||||||||++++++++.+    +.+++.+++....+.
T Consensus        15 ~p~~l~gr~~~~~~l~~~l~~~~~~~~-------~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~~   87 (389)
T 1fnn_A           15 VPKRLPHREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNF   87 (389)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTT-------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSH
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHcCCC-------CCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCCH
Confidence            347899999988888887776554311       112389999999999999999999998    678888887654321


Q ss_pred             h----------------------H----HHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHH
Q 012016          293 S----------------------D----LRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL  346 (473)
Q Consensus       293 ~----------------------~----l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL  346 (473)
                      .                      .    +...+.....+.||+|||+|.+                     ....+..|+
T Consensus        88 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l---------------------~~~~~~~L~  146 (389)
T 1fnn_A           88 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL---------------------APDILSTFI  146 (389)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS---------------------CHHHHHHHH
T ss_pred             HHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc---------------------chHHHHHHH
Confidence            1                      1    1112222245789999999976                     134566777


Q ss_pred             HHhcccccCCCCceEEEEecCCC---CCCCccccCCCceee-EEEeCCCCHHHHHHHHHHHhCc
Q 012016          347 NFIDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRMDV-HVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       347 ~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRfd~-~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      ..++........++.+|++||.+   +.+++.+.+  ||.. .|+|+.++.++...++...+..
T Consensus       147 ~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~~  208 (389)
T 1fnn_A          147 RLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKA  208 (389)
T ss_dssp             HHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHHHHHHHHHHHHh
Confidence            77765422111357888999988   678888887  8875 8999999999999999887653

>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=99.54  E-value=3.6e-14  Score=143.59  Aligned_cols=159  Identities=16%  Similarity=0.235  Sum_probs=111.5

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc------CCceEEcccccc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL------NFDVYDLELTEL  289 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l------~~~~~~l~~~~~  289 (473)
                      ..+++++|.++..+.+.+.+...+..         ..++.++|+||||||||+|++++++.+      +.+++.+++...
T Consensus        17 ~~p~~~~gr~~e~~~l~~~l~~~~~~---------~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~~   87 (386)
T 2qby_A           17 YIPDELPHREDQIRKIASILAPLYRE---------EKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQI   87 (386)
T ss_dssp             CCCSCCTTCHHHHHHHHHSSGGGGGT---------CCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHHH
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHcC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCCC
Confidence            44588999888777766544432221         235689999999999999999999998      888988886542


Q ss_pred             cC----------------------chH-HHHH---HHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHH
Q 012016          290 RS----------------------NSD-LRTL---LVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLS  343 (473)
Q Consensus       290 ~~----------------------~~~-l~~l---~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls  343 (473)
                      .+                      ... +..+   +.....+.||+|||+|.+...                 .....+.
T Consensus        88 ~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~-----------------~~~~~l~  150 (386)
T 2qby_A           88 DTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKK-----------------YNDDILY  150 (386)
T ss_dssp             CSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHS-----------------SCSTHHH
T ss_pred             CCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhcc-----------------CcCHHHH
Confidence            11                      112 2222   222234789999999998531                 0134567


Q ss_pred             HHHHHhcccccCCCCceEEEEecCCC---CCCCccccCCCcee-eEEEeCCCCHHHHHHHHHHHhC
Q 012016          344 GFLNFIDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRMD-VHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       344 ~LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRfd-~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      .|+..++..   .+.++.+|++||.+   +.+++.+.+  ||. ..|+|+.++.++...++...+.
T Consensus       151 ~l~~~~~~~---~~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~  211 (386)
T 2qby_A          151 KLSRINSEV---NKSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYNAEELEDILTKRAQ  211 (386)
T ss_dssp             HHHHHHHSC---CC--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECCCCHHHHHHHHHHHHH
T ss_pred             HHhhchhhc---CCCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHH
Confidence            777777654   22458888999877   567888887  665 5899999999999999998764

>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=99.52  E-value=1e-13  Score=154.01  Aligned_cols=154  Identities=15%  Similarity=0.285  Sum_probs=113.2

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCC----CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc---
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA----WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN---  292 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~----~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~---  292 (473)
                      .++|.++.++.+...+...        +.|..    +..++||+||||||||++|+++|+.++.+++.++++.+...   
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            4667777777666554422        22321    23369999999999999999999999999999998876321   


Q ss_pred             ----------------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc--
Q 012016          293 ----------------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS--  354 (473)
Q Consensus       293 ----------------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~--  354 (473)
                                      ..+...+.. ..++||||||||.+.                     ...++.|+..||.-.-  
T Consensus       531 ~~l~g~~~g~~g~~~~~~l~~~~~~-~~~~vl~lDEi~~~~---------------------~~~~~~Ll~~le~~~~~~  588 (758)
T 1r6b_X          531 SRLIGAPPGYVGFDQGGLLTDAVIK-HPHAVLLLDEIEKAH---------------------PDVFNILLQVMDNGTLTD  588 (758)
T ss_dssp             SSSCCCCSCSHHHHHTTHHHHHHHH-CSSEEEEEETGGGSC---------------------HHHHHHHHHHHHHSEEEE
T ss_pred             hhhcCCCCCCcCccccchHHHHHHh-CCCcEEEEeCccccC---------------------HHHHHHHHHHhcCcEEEc
Confidence                            123333332 457999999999762                     3577888888874211  


Q ss_pred             CCC-----CceEEEEecCCCC-------------------------CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          355 SCG-----DERIIVFTTNHKE-------------------------KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       355 ~~~-----~~~iiI~tTN~~~-------------------------~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      ..|     .+++||+|||...                         .++|+|+.  |||..|.|+.|+.+++..|+..++
T Consensus       589 ~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l~~~~~~~i~~~~l  666 (758)
T 1r6b_X          589 NNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFI  666 (758)
T ss_dssp             TTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHH
T ss_pred             CCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCCCHHHHHHHHHHHH
Confidence            111     3578999999753                         67888998  999999999999999999999887


Q ss_pred             C
Q 012016          405 G  405 (473)
Q Consensus       405 ~  405 (473)
                      .
T Consensus       667 ~  667 (758)
T 1r6b_X          667 V  667 (758)
T ss_dssp             H
T ss_pred             H
Confidence            5

>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=99.51  E-value=2.1e-13  Score=137.15  Aligned_cols=157  Identities=24%  Similarity=0.350  Sum_probs=111.8

Q ss_pred             cceeccCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----Cc
Q 012016          206 AWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----FD  280 (473)
Q Consensus       206 ~w~~~~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----~~  280 (473)
                      .|..  ...|.+|++++|++.+++.+...    +..       |. .+ ++||+||||||||++++++|+.+.     ..
T Consensus        14 ~~~~--k~rp~~~~~~~g~~~~~~~L~~~----i~~-------g~-~~-~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~   78 (340)
T 1sxj_C           14 PWVE--KYRPETLDEVYGQNEVITTVRKF----VDE-------GK-LP-HLLFYGPPGTGKTSTIVALAREIYGKNYSNM   78 (340)
T ss_dssp             CHHH--HTCCSSGGGCCSCHHHHHHHHHH----HHT-------TC-CC-CEEEECSSSSSHHHHHHHHHHHHHTTSHHHH
T ss_pred             chHH--HhCCCcHHHhcCcHHHHHHHHHH----Hhc-------CC-Cc-eEEEECCCCCCHHHHHHHHHHHHcCCCccce
Confidence            4543  35778999999988776655443    332       21 22 399999999999999999999873     34


Q ss_pred             eEEcccccccCchHHHHHHHHh--------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc
Q 012016          281 VYDLELTELRSNSDLRTLLVAT--------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       281 ~~~l~~~~~~~~~~l~~l~~~~--------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  352 (473)
                      +..++.++..+...+++.+...        ..+.|++|||+|.+.                     ....+.|+..++..
T Consensus        79 ~~~~~~~~~~~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~---------------------~~~~~~L~~~le~~  137 (340)
T 1sxj_C           79 VLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMT---------------------NAAQNALRRVIERY  137 (340)
T ss_dssp             EEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSC---------------------HHHHHHHHHHHHHT
T ss_pred             EEEEcCcccccHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCC---------------------HHHHHHHHHHHhcC
Confidence            6666666543444455444322        136899999999873                     23455677777653


Q ss_pred             ccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          353 WSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       353 ~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                          .....+|++||.+..+.|++++  |+. .+.|+.++.++....+...+.
T Consensus       138 ----~~~~~~il~~n~~~~i~~~i~s--R~~-~~~~~~l~~~~~~~~l~~~~~  183 (340)
T 1sxj_C          138 ----TKNTRFCVLANYAHKLTPALLS--QCT-RFRFQPLPQEAIERRIANVLV  183 (340)
T ss_dssp             ----TTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCHHHHHHHHHHHHH
T ss_pred             ----CCCeEEEEEecCccccchhHHh--hce-eEeccCCCHHHHHHHHHHHHH
Confidence                2457788889999999999998  886 789999999988887776663

>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=99.51  E-value=4.6e-13  Score=134.54  Aligned_cols=146  Identities=16%  Similarity=0.166  Sum_probs=105.9

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC------------------------CceEEcccc---cccCchHHHHHHHHhc-
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN------------------------FDVYDLELT---ELRSNSDLRTLLVATA-  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~------------------------~~~~~l~~~---~~~~~~~l~~l~~~~~-  303 (473)
                      .+++|||+||||||||++++++|+.+.                        .+++.++..   .-.+...+++++.... 
T Consensus        23 ~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~~~i~~ir~l~~~~~~  102 (334)
T 1a5t_A           23 GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNE  102 (334)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTS
T ss_pred             cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccccCCCCCHHHHHHHHHHHhh
Confidence            466899999999999999999999874                        245555543   2223456777766543 


Q ss_pred             -----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          304 -----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       304 -----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                           .+.|++|||+|.+.                     ....+.||+.++.    ++...++|++||.++.+.|++++
T Consensus       103 ~~~~~~~kvviIdead~l~---------------------~~a~naLLk~lEe----p~~~~~~Il~t~~~~~l~~ti~S  157 (334)
T 1a5t_A          103 HARLGGAKVVWVTDAALLT---------------------DAAANALLKTLEE----PPAETWFFLATREPERLLATLRS  157 (334)
T ss_dssp             CCTTSSCEEEEESCGGGBC---------------------HHHHHHHHHHHTS----CCTTEEEEEEESCGGGSCHHHHT
T ss_pred             ccccCCcEEEEECchhhcC---------------------HHHHHHHHHHhcC----CCCCeEEEEEeCChHhCcHHHhh
Confidence                 46899999999873                     3456788888875    34568899999999999999998


Q ss_pred             CCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHH
Q 012016          379 PGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEV  429 (473)
Q Consensus       379 pgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i  429 (473)
                        |+. .++|+.|+.++...++......    ..+.+..++..++-++..+
T Consensus       158 --Rc~-~~~~~~~~~~~~~~~L~~~~~~----~~~~~~~l~~~s~G~~r~a  201 (334)
T 1a5t_A          158 --RCR-LHYLAPPPEQYAVTWLSREVTM----SQDALLAALRLSAGSPGAA  201 (334)
T ss_dssp             --TSE-EEECCCCCHHHHHHHHHHHCCC----CHHHHHHHHHHTTTCHHHH
T ss_pred             --cce-eeeCCCCCHHHHHHHHHHhcCC----CHHHHHHHHHHcCCCHHHH
Confidence              874 7999999999998888876522    2233444444444444443

>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=99.51  E-value=4.7e-14  Score=158.69  Aligned_cols=157  Identities=18%  Similarity=0.248  Sum_probs=104.2

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEE
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYD  283 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~  283 (473)
                      .|..|+.++|.++..+.+++.+.    +         ..++++||+||||||||++++++|+.+          +.+++.
T Consensus       165 r~~~ld~viGr~~~i~~l~~~l~----~---------~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~  231 (854)
T 1qvr_A          165 AEGKLDPVIGRDEEIRRVIQILL----R---------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVS  231 (854)
T ss_dssp             HTTCSCCCCSCHHHHHHHHHHHH----C---------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEE
T ss_pred             hcCCCcccCCcHHHHHHHHHHHh----c---------CCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEE
Confidence            35789999999877777665442    2         225689999999999999999999998          889999


Q ss_pred             cccccccC--------chHHHHHHHHhc---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc
Q 012016          284 LELTELRS--------NSDLRTLLVATA---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL  352 (473)
Q Consensus       284 l~~~~~~~--------~~~l~~l~~~~~---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~  352 (473)
                      ++++.+..        ...+..++..+.   .++||||||+|.+.+....             .......+.|...++. 
T Consensus       232 l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~-------------~g~~~~~~~L~~~l~~-  297 (854)
T 1qvr_A          232 LQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKA-------------EGAVDAGNMLKPALAR-  297 (854)
T ss_dssp             ECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC--------------------------------HHHHHT-
T ss_pred             eehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCc-------------cchHHHHHHHHHHHhC-
Confidence            99887632        134666666553   5689999999998642110             0011222333333332 


Q ss_pred             ccCCCCceEEEEecCCCC----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          353 WSSCGDERIIVFTTNHKE----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       353 ~~~~~~~~iiI~tTN~~~----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                           .++.+|++||.++    .+|++|+|  ||+. |.++.|+.+++..|++.++.
T Consensus       298 -----~~i~~I~at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~iL~~~~~  346 (854)
T 1qvr_A          298 -----GELRLIGATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLKE  346 (854)
T ss_dssp             -----TCCCEEEEECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHHH
T ss_pred             -----CCeEEEEecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHHHHhhhh
Confidence                 3477888888775    47999999  9986 99999999999999986654

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.51  E-value=1e-13  Score=145.66  Aligned_cols=147  Identities=16%  Similarity=0.217  Sum_probs=105.2

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceE
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVY  282 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~  282 (473)
                      ..|..|+.++|.++..+.+++.+.    +         ..+.++||+||||||||++++++|+.+          +.+++
T Consensus       174 ~r~~~ld~iiGr~~~i~~l~~~l~----r---------~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~  240 (468)
T 3pxg_A          174 AKEDSLDPVIGRSKEIQRVIEVLS----R---------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVM  240 (468)
T ss_dssp             TTSSCSCCCCCCHHHHHHHHHHHH----C---------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEE
T ss_pred             HhcCCCCCccCcHHHHHHHHHHHh----c---------cCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEE
Confidence            345789999999888877766443    1         225689999999999999999999997          78899


Q ss_pred             Ecccccc-c--CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          283 DLELTEL-R--SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       283 ~l~~~~~-~--~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      .++++.. .  ....+..++....  .++|||||     ..                    ....+.|+..|+      .
T Consensus       241 ~l~~~~~~~g~~e~~~~~~~~~~~~~~~~iLfiD-----~~--------------------~~a~~~L~~~L~------~  289 (468)
T 3pxg_A          241 TLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID-----AA--------------------IDASNILKPSLA------R  289 (468)
T ss_dssp             CC----------CTTHHHHHHHHHTCCCCEEEEC-----C----------------------------CCCTT------S
T ss_pred             EeeCCccccchHHHHHHHHHHHHHhcCCeEEEEe-----Cc--------------------hhHHHHHHHhhc------C
Confidence            9888721 1  1245667776554  57899999     11                    112233444443      1


Q ss_pred             CceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          358 DERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       358 ~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      ..+.+|++||.++     .+|++|+|  ||. .|.|+.|+.+++..|++.++..
T Consensus       290 g~v~vI~at~~~e~~~~~~~~~al~~--Rf~-~i~v~~p~~e~~~~iL~~~~~~  340 (468)
T 3pxg_A          290 GELQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDR  340 (468)
T ss_dssp             SSCEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTT
T ss_pred             CCEEEEecCCHHHHHHHhhcCHHHHH--hCc-cceeCCCCHHHHHHHHHHHHHH
Confidence            3588999999987     69999999  998 5999999999999999987764

>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=99.50  E-value=7.5e-14  Score=135.23  Aligned_cols=155  Identities=16%  Similarity=0.182  Sum_probs=99.9

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccccccCc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELTELRSN  292 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~~~~~~  292 (473)
                      .+|++++|.....+.+.+.+.....           .+.++||+||||||||++|+++++.+.   .+++.++++.+.. 
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~~~-----------~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~-   70 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHLAP-----------LDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-   70 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHHTT-----------SCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCH-
T ss_pred             cccccceeCCHHHHHHHHHHHHHhC-----------CCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCCh-
Confidence            4789999998888888777765432           246899999999999999999999985   6899999987632 


Q ss_pred             hHHHH-HH-----------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-
Q 012016          293 SDLRT-LL-----------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-  353 (473)
Q Consensus       293 ~~l~~-l~-----------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-  353 (473)
                      ..+.. +|                 .....+++|||||||.+..                     .....|+..++... 
T Consensus        71 ~~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~---------------------~~q~~Ll~~l~~~~~  129 (265)
T 2bjv_A           71 NLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPM---------------------MVQEKLLRVIEYGEL  129 (265)
T ss_dssp             HHHHHHHHCCC---------CCCCHHHHTTTSEEEEESGGGSCH---------------------HHHHHHHHHHHHCEE
T ss_pred             hHHHHHhcCCcccccccccccccchhhhcCCcEEEEechHhcCH---------------------HHHHHHHHHHHhCCe
Confidence            22221 11                 1113468999999998732                     33455666665321 


Q ss_pred             c------CCCCceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCCH--HHHHHHHHHHhC
Q 012016          354 S------SCGDERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       354 ~------~~~~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                      .      .....+.||+|||.+       ..++++|..  ||+ ..|.+|....  +....|+..++.
T Consensus       130 ~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~--Rl~~~~i~lp~L~~R~~di~~l~~~~l~  195 (265)
T 2bjv_A          130 ERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLD--ALAFDVVQLPPLRERESDIMLMAEYFAI  195 (265)
T ss_dssp             CCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHH--HHCSEEEECCCGGGCHHHHHHHHHHHHH
T ss_pred             ecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHH--hhcCcEEeCCChhhhhHHHHHHHHHHHH
Confidence            0      001246788899874       357888888  886 4566666544  456666666653

>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=99.47  E-value=3e-13  Score=150.23  Aligned_cols=158  Identities=22%  Similarity=0.290  Sum_probs=110.5

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEE
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYD  283 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~  283 (473)
                      .|..|+.++|.++..+.+++.+.    .         ..+.++||+||||||||++++++|+.+          +..++.
T Consensus       181 ~~~~~d~~iGr~~~i~~l~~~l~----~---------~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~  247 (758)
T 1r6b_X          181 RVGGIDPLIGREKELERAIQVLC----R---------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYS  247 (758)
T ss_dssp             HTTCSCCCCSCHHHHHHHHHHHT----S---------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEE
T ss_pred             hcCCCCCccCCHHHHHHHHHHHh----c---------cCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEE
Confidence            34689999999887777655432    1         236789999999999999999999987          677888


Q ss_pred             cccccccC--------chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc
Q 012016          284 LELTELRS--------NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW  353 (473)
Q Consensus       284 l~~~~~~~--------~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~  353 (473)
                      +++..+..        ...++.++....  .++||||||+|.+.+...            .........    +.+..+.
T Consensus       248 ~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~------------~~~~~~~~~----~~L~~~l  311 (758)
T 1r6b_X          248 LDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGA------------ASGGQVDAA----NLIKPLL  311 (758)
T ss_dssp             CCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCC------------SSSCHHHHH----HHHSSCS
T ss_pred             EcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCC------------CCcchHHHH----HHHHHHH
Confidence            88766532        245667776665  379999999999864110            001112222    2222222


Q ss_pred             cCCCCceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          354 SSCGDERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       354 ~~~~~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ..  .++.+|++||.++     .+|++|.|  ||+ .|.|+.|+.+++..++..+..
T Consensus       312 ~~--~~~~~I~at~~~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~il~~l~~  363 (758)
T 1r6b_X          312 SS--GKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKP  363 (758)
T ss_dssp             SS--CCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHH
T ss_pred             hC--CCeEEEEEeCchHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHHHHHHHH
Confidence            22  3578888888653     57899999  998 699999999999999887653

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.46  E-value=9.4e-14  Score=122.51  Aligned_cols=131  Identities=11%  Similarity=0.104  Sum_probs=88.9

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHH
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLR  296 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~  296 (473)
                      +++|.....+.+.+.+.....           ....+||+||||||||++|+++++..   +.+++ +++..+.....+.
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~-----------~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~~~~~   69 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSE-----------TDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNAPQLN   69 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTT-----------CCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTSSCHH
T ss_pred             CceeCCHHHHHHHHHHHHHhC-----------CCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcchhhh
Confidence            466777777777776664432           24579999999999999999999987   77899 9999876655565


Q ss_pred             HHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC-------
Q 012016          297 TLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK-------  369 (473)
Q Consensus       297 ~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-------  369 (473)
                      ..+..+ .+++|||||||.+.                     ......|+..|...    ...+.+|+|||.+       
T Consensus        70 ~~~~~a-~~g~l~ldei~~l~---------------------~~~q~~Ll~~l~~~----~~~~~~I~~t~~~~~~~~~~  123 (145)
T 3n70_A           70 DFIALA-QGGTLVLSHPEHLT---------------------REQQYHLVQLQSQE----HRPFRLIGIGDTSLVELAAS  123 (145)
T ss_dssp             HHHHHH-TTSCEEEECGGGSC---------------------HHHHHHHHHHHHSS----SCSSCEEEEESSCHHHHHHH
T ss_pred             cHHHHc-CCcEEEEcChHHCC---------------------HHHHHHHHHHHhhc----CCCEEEEEECCcCHHHHHHc
Confidence            655543 66899999999873                     23345566666432    2345678888864       


Q ss_pred             CCCCccccCCCcee-eEEEeCC
Q 012016          370 EKLDPALLRPGRMD-VHVHMSY  390 (473)
Q Consensus       370 ~~ld~aLlrpgRfd-~~I~~~~  390 (473)
                      ..+++.|..  |+. ..|++|.
T Consensus       124 ~~~~~~L~~--rl~~~~i~lPp  143 (145)
T 3n70_A          124 NHIIAELYY--CFAMTQIACLP  143 (145)
T ss_dssp             SCCCHHHHH--HHHHHEEECCC
T ss_pred             CCCCHHHHH--HhcCCEEeCCC
Confidence            234455544  442 3466654

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.44  E-value=4.6e-13  Score=148.73  Aligned_cols=147  Identities=16%  Similarity=0.207  Sum_probs=106.0

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceE
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVY  282 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~  282 (473)
                      ..|..|+.++|.++.++.+++.+.    +         ..+.++||+||||||||++|+++|+.+          +.+++
T Consensus       174 ~~~~~ld~iiG~~~~i~~l~~~l~----~---------~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~  240 (758)
T 3pxi_A          174 AKEDSLDPVIGRSKEIQRVIEVLS----R---------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVM  240 (758)
T ss_dssp             TTSSCSCCCCCCHHHHHHHHHHHH----C---------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEE
T ss_pred             HhhCCCCCccCchHHHHHHHHHHh----C---------CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEE
Confidence            345689999999988887766543    1         235689999999999999999999997          88888


Q ss_pred             Ecccccc---cCchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          283 DLELTEL---RSNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       283 ~l~~~~~---~~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      .+++..-   .....++.++..+.  .++|||||     ..                    ....+.|+..|+      .
T Consensus       241 ~~~~g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD-----~~--------------------~~~~~~L~~~l~------~  289 (758)
T 3pxi_A          241 TLDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID-----AA--------------------IDASNILKPSLA------R  289 (758)
T ss_dssp             CC----------CTTHHHHHHHHHTCCCCEEEEC-----C----------------------------CCCTT------S
T ss_pred             EecccccccchHHHHHHHHHHHHHhcCCEEEEEc-----Cc--------------------hhHHHHHHHHHh------c
Confidence            8887221   12346777776654  57999999     10                    112233443433      1


Q ss_pred             CceEEEEecCCCC-----CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          358 DERIIVFTTNHKE-----KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       358 ~~~iiI~tTN~~~-----~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      .++.+|+|||..+     .+||+|+|  ||. .|.|+.|+.+++..|++.+...
T Consensus       290 ~~v~~I~at~~~~~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~  340 (758)
T 3pxi_A          290 GELQCIGATTLDEYRKYIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDR  340 (758)
T ss_dssp             SSCEEEEECCTTTTHHHHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTT
T ss_pred             CCEEEEeCCChHHHHHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHH
Confidence            4588999999988     79999999  995 5999999999999999987654

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.39  E-value=2.4e-12  Score=127.72  Aligned_cols=151  Identities=17%  Similarity=0.231  Sum_probs=99.8

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHH
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLR  296 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~  296 (473)
                      +++|.....+.+.+.+....           +.+.++||+||||||||++|+++++..   +.+++.++|+.+... .+.
T Consensus         3 ~iig~s~~~~~~~~~~~~~a-----------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~-l~~   70 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVA-----------PSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNES-LLE   70 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHC-----------STTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHH-HHH
T ss_pred             CcEECCHHHHHHHHHHHHHh-----------CCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChH-HHH
Confidence            56777777777777666443           124689999999999999999999976   678999998876321 111


Q ss_pred             -HHH-----------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccccc----
Q 012016          297 -TLL-----------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWS----  354 (473)
Q Consensus       297 -~l~-----------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~----  354 (473)
                       ++|                 .....+++|||||||.+..                     .....|+..++...-    
T Consensus        71 ~~lfg~~~g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~~---------------------~~q~~Ll~~l~~~~~~~~g  129 (304)
T 1ojl_A           71 SELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISP---------------------LMQVRLLRAIQEREVQRVG  129 (304)
T ss_dssp             HHHTCCCSSCCC---CCCCCHHHHHTTSEEEEESCTTCCH---------------------HHHHHHHHHHHSSBCCBTT
T ss_pred             HHhcCccccccCchhhhhcCHHHhcCCCEEEEeccccCCH---------------------HHHHHHHHHHhcCEeeecC
Confidence             111                 1123468999999998732                     345567777664320    


Q ss_pred             ---CCCCceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCC--HHHHHHHHHHHhC
Q 012016          355 ---SCGDERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCT--PSGFKLLAANYLG  405 (473)
Q Consensus       355 ---~~~~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~--~~~r~~l~~~~l~  405 (473)
                         .....+.||+|||..       ..++++|..  ||. ..|++|...  .+....|+..|+.
T Consensus       130 ~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~--Rl~~~~i~lPpL~eR~edi~~l~~~~l~  191 (304)
T 1ojl_A          130 SNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYY--RLNVVAIEMPSLRQRREDIPLLADHFLR  191 (304)
T ss_dssp             BCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHH--HHSSEEEECCCSGGGGGGHHHHHHHHHH
T ss_pred             CcccccCCeEEEEecCccHHHHHHhCCcHHHHHh--hcCeeEEeccCHHHhHhhHHHHHHHHHH
Confidence               011347788899875       346677777  774 446666655  4556667777664

>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=99.39  E-value=1.4e-12  Score=129.37  Aligned_cols=123  Identities=19%  Similarity=0.258  Sum_probs=97.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc------CCceEEccccc-ccCchHHHHHHHHhc------cCceEEEecccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL------NFDVYDLELTE-LRSNSDLRTLLVATA------NRSILVVEDIDCTIDL  319 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l------~~~~~~l~~~~-~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~  319 (473)
                      ...||||||||||||++++++|+.+      +.+++.++.+. -.+...+++++..+.      ...|+||||+|.+.  
T Consensus        18 ~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt--   95 (305)
T 2gno_A           18 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMT--   95 (305)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBC--
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccccCCceEEEeccHHHhC--
Confidence            3589999999999999999999863      45788887653 234456777776653      35799999999873  


Q ss_pred             ccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHH
Q 012016          320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLL  399 (473)
Q Consensus       320 ~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l  399 (473)
                                         ....+.||..|+.    +++..++|++||.+.++.|++++  |   .++|+.|+.++....
T Consensus        96 -------------------~~a~naLLk~LEe----p~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~~~i~~~  147 (305)
T 2gno_A           96 -------------------QQAANAFLKALEE----PPEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVPKEFRDL  147 (305)
T ss_dssp             -------------------HHHHHHTHHHHHS----CCTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCCHHHHHH
T ss_pred             -------------------HHHHHHHHHHHhC----CCCCeEEEEEECChHhChHHHHc--e---eEeCCCCCHHHHHHH
Confidence                               3456788988885    34568888889999999999999  7   789999999998888


Q ss_pred             HHHHhC
Q 012016          400 AANYLG  405 (473)
Q Consensus       400 ~~~~l~  405 (473)
                      +...++
T Consensus       148 L~~~~~  153 (305)
T 2gno_A          148 VKEKIG  153 (305)
T ss_dssp             HHHHHT
T ss_pred             HHHHhC
Confidence            877653

>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=99.38  E-value=1.8e-12  Score=145.88  Aligned_cols=159  Identities=18%  Similarity=0.293  Sum_probs=111.9

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc---
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN---  292 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~---  292 (473)
                      +.++|.+..++.+...+.....+..   . ...+..++||+||||||||++|+++|+.+   +.+++.++++.+...   
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~---~-~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~  633 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLK---D-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV  633 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCS---C-SSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGG
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccC---C-CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHH
Confidence            4567777777777666553321100   0 01122479999999999999999999999   789999999876432   


Q ss_pred             ----------------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC-
Q 012016          293 ----------------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS-  355 (473)
Q Consensus       293 ----------------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~-  355 (473)
                                      ..+...+.. ...+||||||||.+                     ....++.|+..||.-.-. 
T Consensus       634 s~l~g~~~~~~G~~~~g~l~~~~~~-~~~~vl~lDEi~~l---------------------~~~~~~~Ll~~l~~~~~~~  691 (854)
T 1qvr_A          634 SRLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKA---------------------HPDVFNILLQILDDGRLTD  691 (854)
T ss_dssp             GGC--------------CHHHHHHH-CSSEEEEESSGGGS---------------------CHHHHHHHHHHHTTTEECC
T ss_pred             HHHcCCCCCCcCccccchHHHHHHh-CCCeEEEEeccccc---------------------CHHHHHHHHHHhccCceEC
Confidence                            112222222 34689999999976                     245778888888743211 


Q ss_pred             -CC-----CceEEEEecCCC--------------------------CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          356 -CG-----DERIIVFTTNHK--------------------------EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       356 -~~-----~~~iiI~tTN~~--------------------------~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                       .+     .+.+||+|||..                          ..+.|+|+.  |||..+.|.+|+.+++..|+..+
T Consensus       692 ~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~pl~~edi~~i~~~~  769 (854)
T 1qvr_A          692 SHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQ  769 (854)
T ss_dssp             SSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHH
T ss_pred             CCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCCCCCHHHHHHHHHHH
Confidence             11     357899999972                          346777777  99999999999999999999988


Q ss_pred             hC
Q 012016          404 LG  405 (473)
Q Consensus       404 l~  405 (473)
                      +.
T Consensus       770 l~  771 (854)
T 1qvr_A          770 LS  771 (854)
T ss_dssp             HH
T ss_pred             HH
Confidence            75

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.37  E-value=3.5e-13  Score=118.61  Aligned_cols=131  Identities=13%  Similarity=0.032  Sum_probs=86.5

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHH
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLL  299 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~  299 (473)
                      +++|.+...+.+.+.+..+..           ...++||+||||||||++|+++++..+ +++.++++.+.. .....++
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~-----------~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~-~~~~~~~   71 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAK-----------RTSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLI-DMPMELL   71 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHT-----------CSSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHH-HCHHHHH
T ss_pred             CceeCCHHHHHHHHHHHHHhC-----------CCCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCCh-HhhhhHH
Confidence            466777777888777775543           245799999999999999999999998 999999987632 1234444


Q ss_pred             HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC-CC----CCc
Q 012016          300 VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK-EK----LDP  374 (473)
Q Consensus       300 ~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-~~----ld~  374 (473)
                      . ...+++|||||||.+..                     .....|+..++...   ..++.+|+|||.+ +.    +++
T Consensus        72 ~-~a~~~~l~lDei~~l~~---------------------~~q~~Ll~~l~~~~---~~~~~iI~~tn~~~~~~~~~~~~  126 (143)
T 3co5_A           72 Q-KAEGGVLYVGDIAQYSR---------------------NIQTGITFIIGKAE---RCRVRVIASCSYAAGSDGISCEE  126 (143)
T ss_dssp             H-HTTTSEEEEEECTTCCH---------------------HHHHHHHHHHHHHT---TTTCEEEEEEEECTTTC--CHHH
T ss_pred             H-hCCCCeEEEeChHHCCH---------------------HHHHHHHHHHHhCC---CCCEEEEEecCCCHHHHHhCccH
Confidence            4 34578999999998732                     23344566665432   2346778888754 33    333


Q ss_pred             cccCCCce-eeEEEeCC
Q 012016          375 ALLRPGRM-DVHVHMSY  390 (473)
Q Consensus       375 aLlrpgRf-d~~I~~~~  390 (473)
                      .|..  |+ ...|++|.
T Consensus       127 ~L~~--rl~~~~i~lPp  141 (143)
T 3co5_A          127 KLAG--LFSESVVRIPP  141 (143)
T ss_dssp             HHHH--HSSSEEEEECC
T ss_pred             HHHH--HhcCcEEeCCC
Confidence            4443  43 34667665

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.34  E-value=3.2e-13  Score=145.78  Aligned_cols=128  Identities=20%  Similarity=0.259  Sum_probs=89.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc----cccccC---chH------HHHHHHHhccCceEEEecccccccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE----LTELRS---NSD------LRTLLVATANRSILVVEDIDCTIDLQD  321 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~----~~~~~~---~~~------l~~l~~~~~~~sIL~iDdiD~l~~~~~  321 (473)
                      ++||+||||||||+||+++|+.++..++...    +..+..   ...      +..-....+.++||||||||.+.    
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~~~~~~g~~~~~~G~l~~A~~gil~IDEid~l~----  404 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGEYYLEAGALVLADGGIAVIDEIDKMR----  404 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECSSGGGTSSCSEEECHHHHHSSSEECCTTTTCCC----
T ss_pred             ceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceeeeccccccccccCCeeEecCCCcEEeehhhhCC----
Confidence            7999999999999999999999987766532    222210   000      00001112357999999999873    


Q ss_pred             CCccccCCCCCCCccchhHHHHHHHHHhcccc---------cCCCCceEEEEecCCCC-------------CCCccccCC
Q 012016          322 RLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW---------SSCGDERIIVFTTNHKE-------------KLDPALLRP  379 (473)
Q Consensus       322 r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~---------~~~~~~~iiI~tTN~~~-------------~ld~aLlrp  379 (473)
                                       ....+.|+..|+.-.         ........||+|||.+.             .|+++|++ 
T Consensus       405 -----------------~~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~-  466 (595)
T 3f9v_A          405 -----------------DEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIAAGNPKFGRYISERPVSDNINLPPTILS-  466 (595)
T ss_dssp             -----------------SHHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGG-
T ss_pred             -----------------HhHhhhhHHHHhCCEEEEecCCcEEEecCceEEEEEcCCcCCccCcccCchhccCCCHHHHh-
Confidence                             234566777776321         11224578999999986             89999999 


Q ss_pred             Ccee-eEEEeCCCCHHHHHHHHHHHhCc
Q 012016          380 GRMD-VHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       380 gRfd-~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                       ||| ..+..++|+.+ ...|+.+.+..
T Consensus       467 -RFDl~~~~~~~~~~e-~~~i~~~il~~  492 (595)
T 3f9v_A          467 -RFDLIFILKDQPGEQ-DRELANYILDV  492 (595)
T ss_dssp             -GCSCCEEECCTTHHH-HHHHHHHHHTT
T ss_pred             -hCeEEEEeCCCCCHH-HHHHHHHHHHH
Confidence             998 46667778888 88888887764

>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=99.34  E-value=1.9e-12  Score=117.84  Aligned_cols=128  Identities=18%  Similarity=0.291  Sum_probs=82.8

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccccc
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTEL  289 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~~  289 (473)
                      .+.+|++++......+.+++.+..++..      ...+.+.+++|+||||||||+|++++++.+    |..++.++..++
T Consensus         5 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~------~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~   78 (180)
T 3ec2_A            5 WNANLDTYHPKNVSQNRALLTIRVFVHN------FNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDL   78 (180)
T ss_dssp             TTCCSSSCCCCSHHHHHHHHHHHHHHHS------CCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHH
T ss_pred             hhCccccccCCCHHHHHHHHHHHHHHHh------ccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHH
Confidence            3478999988655566666777766653      223346789999999999999999999987    667776666554


Q ss_pred             cCc-------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE
Q 012016          290 RSN-------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII  362 (473)
Q Consensus       290 ~~~-------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  362 (473)
                      ...       ......+....++.+|+|||++....                +......+..+++..   ..   .+..+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~~~~----------------~~~~~~~l~~ll~~~---~~---~~~~i  136 (180)
T 3ec2_A           79 IFRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGSERL----------------SDWQRELISYIITYR---YN---NLKST  136 (180)
T ss_dssp             HHHHHHHHHHTCCSHHHHHHHTCSEEEEETCSSSCC----------------CHHHHHHHHHHHHHH---HH---TTCEE
T ss_pred             HHHHHHHhcCchHHHHHHHhcCCCEEEEeCCCCCcC----------------CHHHHHHHHHHHHHH---HH---cCCCE
Confidence            210       01113444556789999999985421                222334444444433   21   23677


Q ss_pred             EEecCCC
Q 012016          363 VFTTNHK  369 (473)
Q Consensus       363 I~tTN~~  369 (473)
                      |+|||.+
T Consensus       137 i~tsn~~  143 (180)
T 3ec2_A          137 IITTNYS  143 (180)
T ss_dssp             EEECCCC
T ss_pred             EEEcCCC
Confidence            8888875

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.30  E-value=6.7e-12  Score=132.40  Aligned_cols=146  Identities=15%  Similarity=0.132  Sum_probs=92.5

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC--ceEEccccc-----ccCc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF--DVYDLELTE-----LRSN  292 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~--~~~~l~~~~-----~~~~  292 (473)
                      .++|.+++++.+...+.    .           ..++||+||||||||++|+++|+.++.  ++..+.+..     +.+.
T Consensus        23 ~ivGq~~~i~~l~~al~----~-----------~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~~t~~dL~G~   87 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAAL----S-----------GESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGP   87 (500)
T ss_dssp             TCSSCHHHHHHHHHHHH----H-----------TCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTTCCHHHHHCC
T ss_pred             hhHHHHHHHHHHHHHHh----c-----------CCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhcCCHHHhcCc
Confidence            45677766665543321    1           358999999999999999999999853  444433321     1110


Q ss_pred             hHH-----HHHHHHhc-----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc-------ccC
Q 012016          293 SDL-----RTLLVATA-----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL-------WSS  355 (473)
Q Consensus       293 ~~l-----~~l~~~~~-----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~-------~~~  355 (473)
                      ...     ...+....     .++|||||||+.+                     ...+.+.|+..|+.-       ...
T Consensus        88 ~~~~~~~~~g~~~~~~~g~l~~~~IL~IDEI~r~---------------------~~~~q~~LL~~lee~~v~i~G~~~~  146 (500)
T 3nbx_X           88 LSIQALKDEGRYERLTSGYLPEAEIVFLDEIWKA---------------------GPAILNTLLTAINERQFRNGAHVEK  146 (500)
T ss_dssp             BC----------CBCCTTSGGGCSEEEEESGGGC---------------------CHHHHHHHHHHHHSSEEECSSSEEE
T ss_pred             ccHHHHhhchhHHhhhccCCCcceeeeHHhHhhh---------------------cHHHHHHHHHHHHHHhccCCCCcCC
Confidence            000     11121111     4568999999865                     245677788888531       111


Q ss_pred             CCCceEEEEecCCCC---CCCccccCCCceeeEEEeCCCCH-HHHHHHHHHHh
Q 012016          356 CGDERIIVFTTNHKE---KLDPALLRPGRMDVHVHMSYCTP-SGFKLLAANYL  404 (473)
Q Consensus       356 ~~~~~iiI~tTN~~~---~ld~aLlrpgRfd~~I~~~~p~~-~~r~~l~~~~l  404 (473)
                      . +.+++|+|||.+.   .+.+++++  ||..+|++++|+. +++..|+....
T Consensus       147 ~-~~~~iI~ATN~lpe~~~~~~aLld--RF~~~i~v~~p~~~ee~~~IL~~~~  196 (500)
T 3nbx_X          147 I-PMRLLVAASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQQ  196 (500)
T ss_dssp             C-CCCEEEEEESSCCCTTCTTHHHHT--TCCEEEECCSCCCHHHHHHHHTCCC
T ss_pred             c-chhhhhhccccCCCccccHHHHHH--HHHHHHHHHHhhhhhhHHHHHhccc
Confidence            1 2346788888632   24459999  9999999999997 67888887654

>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=99.24  E-value=5.8e-11  Score=121.45  Aligned_cols=164  Identities=9%  Similarity=0.114  Sum_probs=105.7

Q ss_pred             CccccccchHHHHHHHHHH-HHHHhchhHHhhhcCCCCceeEE--eCCCCCCHHHHHHHHHHhc---------CCceEEc
Q 012016          217 TFETLAMEQEQKTKIMQDL-ERFVKRKDYYRRVGKAWKRGYLL--YGPPGTGKSSLIAAMANYL---------NFDVYDL  284 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l-~~fl~~~~~y~~~g~~~~rg~LL--~GPpGtGKT~la~alA~~l---------~~~~~~l  284 (473)
                      ..+.++|.++..+.+.+.+ .....+.       ...++.++|  +||||+|||+|++++++.+         +.+++.+
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~~-------~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~   92 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSGA-------GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYV   92 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSS-------CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcCC-------CCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEE
Confidence            3477899888888877766 5443220       012457999  9999999999999999887         5567777


Q ss_pred             ccccccCc----------------------hH----HHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccch
Q 012016          285 ELTELRSN----------------------SD----LRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQN  338 (473)
Q Consensus       285 ~~~~~~~~----------------------~~----l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~  338 (473)
                      ++....+.                      ..    +...+.....+.||+|||+|.+...               ....
T Consensus        93 ~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~---------------~~~~  157 (412)
T 1w5s_A           93 NAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSS---------------PRIA  157 (412)
T ss_dssp             EGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSC---------------TTSC
T ss_pred             ECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhc---------------cCcc
Confidence            76432111                      11    1222222235789999999988420               0012


Q ss_pred             hHHHHHHHHHhcccccCCC--CceEEEEecCCCC---CCC---ccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          339 KVTLSGFLNFIDGLWSSCG--DERIIVFTTNHKE---KLD---PALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       339 ~~~ls~LL~~ldg~~~~~~--~~~iiI~tTN~~~---~ld---~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ...+..|+..++.... .+  ..+.+|+|||.++   .++   +.+.+  |+...++++.++.++..+++...+.
T Consensus       158 ~~~l~~l~~~~~~~~~-~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~~~~i~l~~l~~~e~~~ll~~~~~  229 (412)
T 1w5s_A          158 AEDLYTLLRVHEEIPS-RDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAE  229 (412)
T ss_dssp             HHHHHHHHTHHHHSCC-TTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhccc-CCCCceEEEEEEeccccHHHHHhhhcchhhh--hcCCeeeeCCCCHHHHHHHHHHHHH
Confidence            3455556655554321 12  4578888887664   344   66666  5655699999999999999987654

>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=99.23  E-value=2.9e-11  Score=147.61  Aligned_cols=137  Identities=20%  Similarity=0.352  Sum_probs=99.5

Q ss_pred             CceeEEeCCCCCCHHHHH-HHHHHhcCCceEEcccccccCchHHHHHHHHh-----------------ccCceEEEeccc
Q 012016          253 KRGYLLYGPPGTGKSSLI-AAMANYLNFDVYDLELTELRSNSDLRTLLVAT-----------------ANRSILVVEDID  314 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la-~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~-----------------~~~sIL~iDdiD  314 (473)
                      ++++||+||||||||++| +++++..+++++.++++...+...+++.+...                 ..++|||||||+
T Consensus      1267 ~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEin 1346 (2695)
T 4akg_A         1267 KRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEIN 1346 (2695)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETTT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEecccc
Confidence            469999999999999999 56666668899999998877777777776642                 123699999998


Q ss_pred             cccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC------CceEEEEecCCCC-----CCCccccCCCcee
Q 012016          315 CTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG------DERIIVFTTNHKE-----KLDPALLRPGRMD  383 (473)
Q Consensus       315 ~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~~~iiI~tTN~~~-----~ld~aLlrpgRfd  383 (473)
                      ....  ++          .+.......+.+++. ..|++....      .++.+|+|||++.     .|+|+|+|  || 
T Consensus      1347 mp~~--d~----------yg~q~~lelLRq~le-~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllR--rf- 1410 (2695)
T 4akg_A         1347 LPKL--DK----------YGSQNVVLFLRQLME-KQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTR--HA- 1410 (2695)
T ss_dssp             CSCC--CS----------SSCCHHHHHHHHHHH-TSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHT--TE-
T ss_pred             cccc--cc----------cCchhHHHHHHHHHh-cCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhh--ee-
Confidence            6321  11          111223344555542 234443211      2478999999995     79999999  99 


Q ss_pred             eEEEeCCCCHHHHHHHHHHHhC
Q 012016          384 VHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       384 ~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      ..|.++.|+.+++..|+..++.
T Consensus      1411 ~vi~i~~P~~~~l~~I~~~il~ 1432 (2695)
T 4akg_A         1411 AILYLGYPSGKSLSQIYEIYYK 1432 (2695)
T ss_dssp             EEEECCCCTTTHHHHHHHHHHH
T ss_pred             eEEEeCCCCHHHHHHHHHHHHH
Confidence            6899999999999999988764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.21  E-value=3.9e-11  Score=111.00  Aligned_cols=96  Identities=25%  Similarity=0.378  Sum_probs=66.4

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCC-CCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA-WKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~-~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~  290 (473)
                      +.+|+++++.....+.+++.+..++....      .. .+++++|+||||||||+|++++++.+   +.+++.+++..+.
T Consensus        21 ~~~f~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~   94 (202)
T 2w58_A           21 RASLSDVDLNDDGRIKAIRFAERFVAEYE------PGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPELF   94 (202)
T ss_dssp             CCCTTSSCCSSHHHHHHHHHHHHHHHHCC------SSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHHH
T ss_pred             cCCHhhccCCChhHHHHHHHHHHHHHHhh------hccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHHH
Confidence            46899998876555666666666665321      11 12799999999999999999999988   6778777766531


Q ss_pred             C-------chHHHHHHHHhccCceEEEeccccc
Q 012016          291 S-------NSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       291 ~-------~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      .       ...+...+....+..+|+|||++..
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~lilDei~~~  127 (202)
T 2w58_A           95 RELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAE  127 (202)
T ss_dssp             HHHHHC---CCCHHHHHHHHHSSEEEEEEECCC
T ss_pred             HHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            1       1112333444456679999999765

>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=99.11  E-value=8.5e-11  Score=119.67  Aligned_cols=121  Identities=21%  Similarity=0.270  Sum_probs=87.3

Q ss_pred             hcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCcccc
Q 012016          248 VGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADI  327 (473)
Q Consensus       248 ~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~  327 (473)
                      .++++++.++|+||||+|||+|++++++.++..++.++...    ......+....+..++++||++.+.....+. .  
T Consensus       164 ~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~~~~----~~~~~~lg~~~q~~~~l~dd~~~~~~~~r~l-~--  236 (377)
T 1svm_A          164 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPL----DRLNFELGVAIDQFLVVFEDVKGTGGESRDL-P--  236 (377)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCT----TTHHHHHGGGTTCSCEEETTCCCSTTTTTTC-C--
T ss_pred             cccCCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEeccc----hhHHHHHHHhcchhHHHHHHHHHHHHHHhhc-c--
Confidence            37788889999999999999999999999988776644332    1223234455678889999999875421110 0  


Q ss_pred             CCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCC
Q 012016          328 AGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       328 ~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~  390 (473)
                             ..........+.+.+||.       +.++++||+++.+ +++++|||++..+...+
T Consensus       237 -------~~~~~~~~~~l~~~ldG~-------v~v~~~tn~~~~l-~alf~pg~ld~~~~~l~  284 (377)
T 1svm_A          237 -------SGQGINNLDNLRDYLDGS-------VKVNLEKKHLNKR-TQIFPPGIVTMNEYSVP  284 (377)
T ss_dssp             -------CCSHHHHHHTTHHHHHCS-------SCEEECCSSSCCE-EECCCCEEEEECSCCCC
T ss_pred             -------ccCcchHHHHHHHHhcCC-------CeEeeccCchhhH-HHhhcCcccChhHHhhc
Confidence                   001112456677888863       5678899999999 89999999999888766

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=99.07  E-value=1.2e-10  Score=115.57  Aligned_cols=96  Identities=26%  Similarity=0.419  Sum_probs=63.1

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC----CceEEccccccc
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN----FDVYDLELTELR  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~----~~~~~l~~~~~~  290 (473)
                      +.+|+++......+..+.+.+..|+...      +..+..+++||||||||||+|+.++|+++.    .+++.+.+..+.
T Consensus       120 ~~tfd~f~~~~~~~~~~~~~~~~~i~~~------~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l~  193 (308)
T 2qgz_A          120 HIHLSDIDVNNASRMEAFSAILDFVEQY------PSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFA  193 (308)
T ss_dssp             SCCGGGSCCCSHHHHHHHHHHHHHHHHC------SCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHHH
T ss_pred             hCCHhhCcCCChHHHHHHHHHHHHHHhc------cccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHHH
Confidence            3689999876544555666666666532      111357999999999999999999999764    777777665431


Q ss_pred             -------CchHHHHHHHHhccCceEEEeccccc
Q 012016          291 -------SNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       291 -------~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                             ....+...+....+..+|||||++..
T Consensus       194 ~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~  226 (308)
T 2qgz_A          194 IDVKNAISNGSVKEEIDAVKNVPVLILDDIGAE  226 (308)
T ss_dssp             HHHHCCCC----CCTTHHHHTSSEEEEETCCC-
T ss_pred             HHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence                   11112222333446689999999754

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=99.07  E-value=3.6e-10  Score=104.77  Aligned_cols=114  Identities=20%  Similarity=0.196  Sum_probs=69.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccccccccCCccccC
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIA  328 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~  328 (473)
                      +.|.++++|||||||||||+++.++|+.++-.++....+.  ...    .+.......|++|||+|.-.           
T Consensus        54 ~iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~fans~--s~f----~l~~l~~~kIiiLDEad~~~-----------  116 (212)
T 1tue_A           54 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNST--SHF----WLEPLTDTKVAMLDDATTTC-----------  116 (212)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCSS--SCG----GGGGGTTCSSEEEEEECHHH-----------
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeEEecc--chh----hhcccCCCCEEEEECCCchh-----------
Confidence            4666778999999999999999999999976654432111  110    12233456799999998421           


Q ss_pred             CCCCCCccchhHHHHHHHHHhcccc----cCCC-----CceEEEEecCCC---CCCCccccCCCceeeEEEeCCC
Q 012016          329 GEGEGPIQQNKVTLSGFLNFIDGLW----SSCG-----DERIIVFTTNHK---EKLDPALLRPGRMDVHVHMSYC  391 (473)
Q Consensus       329 ~~~~~~~~~~~~~ls~LL~~ldg~~----~~~~-----~~~iiI~tTN~~---~~ld~aLlrpgRfd~~I~~~~p  391 (473)
                               .......+-+.+||..    ....     ....+|.|||..   +.--+.|..  |+- .+.|+.|
T Consensus       117 ---------~~~~d~~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~S--Ri~-~f~F~~~  179 (212)
T 1tue_A          117 ---------WTYFDTYMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLES--RIT-VFEFPNA  179 (212)
T ss_dssp             ---------HHHHHHHCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHT--SCE-EEECCSC
T ss_pred             ---------HHHHHHHHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhh--hEE-EEEcCCC
Confidence                     1222234556777741    1110     124688899974   222245666  774 6777754

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=98.96  E-value=1.5e-09  Score=117.41  Aligned_cols=52  Identities=33%  Similarity=0.357  Sum_probs=40.6

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ...|..|++++|.+.+++.+...    +..           ...++|+||||||||+|+++||+.+.
T Consensus        34 ~~rp~~l~~i~G~~~~l~~l~~~----i~~-----------g~~vll~Gp~GtGKTtlar~ia~~l~   85 (604)
T 3k1j_A           34 EVPEKLIDQVIGQEHAVEVIKTA----ANQ-----------KRHVLLIGEPGTGKSMLGQAMAELLP   85 (604)
T ss_dssp             CCCSSHHHHCCSCHHHHHHHHHH----HHT-----------TCCEEEECCTTSSHHHHHHHHHHTSC
T ss_pred             cccccccceEECchhhHhhcccc----ccC-----------CCEEEEEeCCCCCHHHHHHHHhccCC
Confidence            34567899999988776554333    321           35899999999999999999999885

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.90  E-value=2.1e-09  Score=95.15  Aligned_cols=57  Identities=18%  Similarity=0.236  Sum_probs=46.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHHHHHHHhccCceEEEeccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      ...++|+||+|+|||+|++++++.+   |..++.++..++...       ....++.+|+|||++.+
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~-------~~~~~~~lLilDE~~~~   95 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLT-------DAAFEAEYLAVDQVEKL   95 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCC-------GGGGGCSEEEEESTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHH-------HHHhCCCEEEEeCcccc
Confidence            5689999999999999999999988   777888877766443       11346899999999875

>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=98.88  E-value=2.5e-09  Score=125.77  Aligned_cols=147  Identities=13%  Similarity=0.170  Sum_probs=90.3

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhc----------hhHHhh------hc------------CCCCceeEEeCCCCCCHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKR----------KDYYRR------VG------------KAWKRGYLLYGPPGTGKS  267 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~----------~~~y~~------~g------------~~~~rg~LL~GPpGtGKT  267 (473)
                      .+|+++.+.++.|+.+++.+..++..          ++.++.      .|            .|..+.+|+|||||||||
T Consensus      1017 ~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tG~~glD~~lg~GG~p~g~~~l~~G~~g~GKT 1096 (1706)
T 3cmw_A         1017 SSTGSMSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKT 1096 (1706)
T ss_dssp             -------CTTHHHHHHHHHHHHHHHHHHCGGGSEEGGGCGGGSCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHH
T ss_pred             ceeeecCCccHHHHHHHHHHHHHHhhccCcccchhchhhhhccccccccCchhHHHHhccCCCCCCCEEEEEcCCCCChH
Confidence            68999999999999999999988854          345555      22            233344999999999999


Q ss_pred             HHHHHHHHhc---CCceEEccccc----------------cc------CchHHHHHHHHh--ccCceEEEeccccccccc
Q 012016          268 SLIAAMANYL---NFDVYDLELTE----------------LR------SNSDLRTLLVAT--ANRSILVVEDIDCTIDLQ  320 (473)
Q Consensus       268 ~la~alA~~l---~~~~~~l~~~~----------------~~------~~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~  320 (473)
                      .|+.++|.+.   +-+...++...                +.      ++..++.++..+  ..+++|++|++|++.+.+
T Consensus      1097 ~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~~~~~~i~~d~~~al~~~~ 1176 (1706)
T 3cmw_A         1097 TLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTPKA 1176 (1706)
T ss_dssp             HHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCCHH
T ss_pred             HHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHhcCCeEEEeCchHhcCccc
Confidence            9999999876   34444443332                11      234555555433  368999999999998732


Q ss_pred             cCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC
Q 012016          321 DRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK  369 (473)
Q Consensus       321 ~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  369 (473)
                      .-.+ ...   +.......+.++++|..|+++...  .+++|| +||+.
T Consensus      1177 ~~~g-~~~---~~~~~~~~r~~~q~l~~~~~~~~~--~~v~v~-~~n~~ 1218 (1706)
T 3cmw_A         1177 EIEG-EIG---DSHMGLAARMMSQAMRKLAGNLKQ--SNTLLI-FINQI 1218 (1706)
T ss_dssp             HHHS-CTT---CCCTTHHHHHHHHHHHHHHHHHHH--TTCEEE-EEECE
T ss_pred             cccc-ccc---cccccHHHHHHHHHHHHHHhhhcc--CCeEEE-Eeccc
Confidence            2100 000   011133456799999999997554  235555 77765

>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=98.83  E-value=5e-08  Score=97.09  Aligned_cols=174  Identities=18%  Similarity=0.139  Sum_probs=99.2

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc-----c
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL-----R  290 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~-----~  290 (473)
                      ...+.++|.++..+.+.+ +    ..            +.++++||+|+|||+|++.+++.++.+++.+++...     .
T Consensus        10 ~~~~~~~gR~~el~~L~~-l----~~------------~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (357)
T 2fna_A           10 DNRKDFFDREKEIEKLKG-L----RA------------PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYI   72 (357)
T ss_dssp             CSGGGSCCCHHHHHHHHH-T----CS------------SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCC
T ss_pred             CCHHHhcChHHHHHHHHH-h----cC------------CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchhhccccCC
Confidence            345677887655555433 2    21            489999999999999999999998776666665432     0


Q ss_pred             C-----------------------------------------------chHHHHHHH---Hhc-cCceEEEecccccccc
Q 012016          291 S-----------------------------------------------NSDLRTLLV---ATA-NRSILVVEDIDCTIDL  319 (473)
Q Consensus       291 ~-----------------------------------------------~~~l~~l~~---~~~-~~sIL~iDdiD~l~~~  319 (473)
                      +                                               ...+..++.   ... .+.+|+|||++.+...
T Consensus        73 ~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~  152 (357)
T 2fna_A           73 SYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKL  152 (357)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGC
T ss_pred             CHHHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhcc
Confidence            0                                               112233332   222 3789999999987420


Q ss_pred             ccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCC---------CccccCCCceeeEEEeCC
Q 012016          320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKL---------DPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       320 ~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l---------d~aLlrpgRfd~~I~~~~  390 (473)
                                    ........+..+.   +..     .++.+|+|+.....+         ...+  .||+...|+++.
T Consensus       153 --------------~~~~~~~~l~~~~---~~~-----~~~~~i~~g~~~~~l~~~l~~~~~~~~l--~~r~~~~i~l~~  208 (357)
T 2fna_A          153 --------------RGVNLLPALAYAY---DNL-----KRIKFIMSGSEMGLLYDYLRVEDPESPL--FGRAFSTVELKP  208 (357)
T ss_dssp             --------------TTCCCHHHHHHHH---HHC-----TTEEEEEEESSHHHHHHHTTTTCTTSTT--TTCCCEEEEECC
T ss_pred             --------------CchhHHHHHHHHH---HcC-----CCeEEEEEcCchHHHHHHHhccCCCCcc--ccCccceeecCC
Confidence                          0011122233332   221     235666666543211         1112  247777899999


Q ss_pred             CCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHHH
Q 012016          391 CTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAE  431 (473)
Q Consensus       391 p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~~  431 (473)
                      .+.++..+++...+........+ ...+...++-.|.-+..
T Consensus       209 l~~~e~~~~l~~~~~~~~~~~~~-~~~i~~~t~G~P~~l~~  248 (357)
T 2fna_A          209 FSREEAIEFLRRGFQEADIDFKD-YEVVYEKIGGIPGWLTY  248 (357)
T ss_dssp             CCHHHHHHHHHHHHHHHTCCCCC-HHHHHHHHCSCHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHcCCCCCc-HHHHHHHhCCCHHHHHH
Confidence            99999999998765321111111 14444545556654433

>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=98.83  E-value=3e-09  Score=105.30  Aligned_cols=116  Identities=14%  Similarity=0.124  Sum_probs=66.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc--cc----cc-C-chHHHHHHHHhccCceEEEeccccccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL--TE----LR-S-NSDLRTLLVATANRSILVVEDIDCTIDLQ  320 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~--~~----~~-~-~~~l~~l~~~~~~~sIL~iDdiD~l~~~~  320 (473)
                      |.+..+.++|+||||||||+|+.++|...+.++..++.  .+    .. + +..+..+.....+..+||||+++.+....
T Consensus       119 Gi~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~LLVIDsI~aL~~~~  198 (331)
T 2vhj_A          119 HRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAA  198 (331)
T ss_dssp             EEEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEECCTTTC---
T ss_pred             CCCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCCEEEEeccccccccc
Confidence            44556678999999999999999999876655444444  11    11 1 12222333333332399999999885411


Q ss_pred             cCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccc
Q 012016          321 DRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPAL  376 (473)
Q Consensus       321 ~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aL  376 (473)
                      ..  .       .......+.+.+++..|+++...  .++.+|++|| +...|+++
T Consensus       199 ~~--~-------s~~G~v~~~lrqlL~~L~~~~k~--~gvtVIlttn-p~s~deal  242 (331)
T 2vhj_A          199 GG--N-------TTSGGISRGAFDLLSDIGAMAAS--RGCVVIASLN-PTSNDDKI  242 (331)
T ss_dssp             -----------------CCHHHHHHHHHHHHHHHH--HTCEEEEECC-CSSCSSSH
T ss_pred             cc--c-------cccchHHHHHHHHHHHHHHHHhh--CCCEEEEEeC-CcccchhH
Confidence            10  0       00111234566666666655433  2367888888 56666664

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.80  E-value=5.9e-07  Score=89.09  Aligned_cols=179  Identities=20%  Similarity=0.149  Sum_probs=102.6

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc----
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR----  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~----  290 (473)
                      +..-+.++|.++..+.+.+.+..           |    +.++++||+|+|||+|++.+++.++  .+.+++....    
T Consensus         8 ~~~~~~~~gR~~el~~L~~~l~~-----------~----~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~~~~~~~~   70 (350)
T 2qen_A            8 KTRREDIFDREEESRKLEESLEN-----------Y----PLTLLLGIRRVGKSSLLRAFLNERP--GILIDCRELYAERG   70 (350)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHH-----------C----SEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHHHHHHTTT
T ss_pred             CCChHhcCChHHHHHHHHHHHhc-----------C----CeEEEECCCcCCHHHHHHHHHHHcC--cEEEEeeccccccc
Confidence            34556788877766666554321           1    5899999999999999999999886  4444433210    


Q ss_pred             --C------------------------------------chHHHHHH---HHh---ccCceEEEeccccccccccCCccc
Q 012016          291 --S------------------------------------NSDLRTLL---VAT---ANRSILVVEDIDCTIDLQDRLPAD  326 (473)
Q Consensus       291 --~------------------------------------~~~l~~l~---~~~---~~~sIL~iDdiD~l~~~~~r~~~~  326 (473)
                        +                                    ...+..++   ...   ..+.+|+|||++.+....      
T Consensus        71 ~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~------  144 (350)
T 2qen_A           71 HITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYG------  144 (350)
T ss_dssp             CBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBT------
T ss_pred             CCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccC------
Confidence              0                                    01122222   221   138899999999874200      


Q ss_pred             cCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCC---C------CCccccCCCceeeEEEeCCCCHHHHH
Q 012016          327 IAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE---K------LDPALLRPGRMDVHVHMSYCTPSGFK  397 (473)
Q Consensus       327 ~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~---~------ld~aLlrpgRfd~~I~~~~p~~~~r~  397 (473)
                              .......+..|-..++..     .++.+|+|+....   .      ....+.  ||+...++++..+.++..
T Consensus       145 --------~~~~~~~~~~L~~~~~~~-----~~~~~il~g~~~~~l~~~l~~~~~~~~l~--~~~~~~i~l~pl~~~e~~  209 (350)
T 2qen_A          145 --------SRGGKELLALFAYAYDSL-----PNLKIILTGSEVGLLHDFLKITDYESPLY--GRIAGEVLVKPFDKDTSV  209 (350)
T ss_dssp             --------TTTTHHHHHHHHHHHHHC-----TTEEEEEEESSHHHHHHHHCTTCTTSTTT--TCCCEEEECCCCCHHHHH
T ss_pred             --------ccchhhHHHHHHHHHHhc-----CCeEEEEECCcHHHHHHHHhhcCCCCccc--cCccceeeCCCCCHHHHH
Confidence                    001122333333333321     2355666654321   1      111222  476678999999999999


Q ss_pred             HHHHHHhCcccc-CCHHHHHHHHhcCCCCHHHHHH
Q 012016          398 LLAANYLGIKEH-ILFEEIEELISTTQVTPAEVAE  431 (473)
Q Consensus       398 ~l~~~~l~~~~~-~l~~~i~~l~~~~~~t~a~i~~  431 (473)
                      +++...+..... ...+.+..+...++-.|.-+..
T Consensus       210 ~~l~~~~~~~~~~~~~~~~~~i~~~tgG~P~~l~~  244 (350)
T 2qen_A          210 EFLKRGFREVNLDVPENEIEEAVELLDGIPGWLVV  244 (350)
T ss_dssp             HHHHHHHHTTTCCCCHHHHHHHHHHHTTCHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            998876543222 2344555666656666664443

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.80  E-value=5e-09  Score=97.32  Aligned_cols=121  Identities=16%  Similarity=0.141  Sum_probs=77.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh--------cC-CceEEcccccccC---------------------chHHHHHHH-Hh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY--------LN-FDVYDLELTELRS---------------------NSDLRTLLV-AT  302 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~--------l~-~~~~~l~~~~~~~---------------------~~~l~~l~~-~~  302 (473)
                      --+|++|+||||||+++.+++..        .| .+++..++..+.-                     ...+.+.+. ..
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~   85 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIKKPE   85 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTTSGG
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhhccc
Confidence            36899999999999998886543        34 6776555443310                     022222211 12


Q ss_pred             ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCce
Q 012016          303 ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRM  382 (473)
Q Consensus       303 ~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRf  382 (473)
                      ..++||||||++.+++.+..            ..+..    .++..+..   ......-||++|+.++.|+.+++.  |+
T Consensus        86 ~~~~vliIDEAq~l~~~~~~------------~~e~~----rll~~l~~---~r~~~~~iil~tq~~~~l~~~lr~--ri  144 (199)
T 2r2a_A           86 NIGSIVIVDEAQDVWPARSA------------GSKIP----ENVQWLNT---HRHQGIDIFVLTQGPKLLDQNLRT--LV  144 (199)
T ss_dssp             GTTCEEEETTGGGTSBCCCT------------TCCCC----HHHHGGGG---TTTTTCEEEEEESCGGGBCHHHHT--TE
T ss_pred             cCceEEEEEChhhhccCccc------------cchhH----HHHHHHHh---cCcCCeEEEEECCCHHHHhHHHHH--Hh
Confidence            34899999999998652110            00011    24444443   222346788889889999999988  99


Q ss_pred             eeEEEeCCCCHHH
Q 012016          383 DVHVHMSYCTPSG  395 (473)
Q Consensus       383 d~~I~~~~p~~~~  395 (473)
                      +.+++++.|....
T Consensus       145 ~~~~~l~~~~~~~  157 (199)
T 2r2a_A          145 RKHYHIASNKMGM  157 (199)
T ss_dssp             EEEEEEEECSSCC
T ss_pred             heEEEEcCcccCc
Confidence            9999998865443

>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=98.74  E-value=4.9e-08  Score=94.24  Aligned_cols=59  Identities=20%  Similarity=0.266  Sum_probs=39.9

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEeccccc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCT  316 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~l  316 (473)
                      +++++++||||||||||+++.|||+.++.- -.++.+..      ...+.....+.|+++||....
T Consensus       102 ~~~n~~~l~GppgtGKt~~a~ala~~~~l~-G~vn~~~~------~f~l~~~~~k~i~l~Ee~~~~  160 (267)
T 1u0j_A          102 GKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWTNE------NFPFNDCVDKMVIWWEEGKMT  160 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTTCS------SCTTGGGSSCSEEEECSCCEE
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHhhhccc-ceeecccc------ccccccccccEEEEeccccch
Confidence            446789999999999999999999987552 22233211      112344456677777777644

>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=98.71  E-value=5.8e-08  Score=118.96  Aligned_cols=129  Identities=17%  Similarity=0.171  Sum_probs=94.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhc-cCceEEEeccccccccccCCccccCCCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEG  331 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~  331 (473)
                      ..|.+++||+|||||++++++|+.+|.+++.++|++-.+...+.++|..+. .++++++||++.+-.             
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~~~lg~~~~g~~~~Gaw~~~DE~nr~~~-------------  711 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDE-------------  711 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCHHHHHHHHHHHHHHTCEEEEETTTSSCH-------------
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCChhHhhHHHHHHHhcCCEeeehhhhhcCh-------------
Confidence            458999999999999999999999999999999998878888888887765 589999999997632             


Q ss_pred             CCCccchhHHHHHHH----HHhc---------ccccCCCCceEEEEecC----CCCCCCccccCCCceeeEEEeCCCCHH
Q 012016          332 EGPIQQNKVTLSGFL----NFID---------GLWSSCGDERIIVFTTN----HKEKLDPALLRPGRMDVHVHMSYCTPS  394 (473)
Q Consensus       332 ~~~~~~~~~~ls~LL----~~ld---------g~~~~~~~~~iiI~tTN----~~~~ld~aLlrpgRfd~~I~~~~p~~~  394 (473)
                           .....+++.+    +.+.         |-.-.......|++|.|    ....|+++|.+  || +.|.|.+|+.+
T Consensus       712 -----evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~--~F-r~v~m~~Pd~~  783 (2695)
T 4akg_A          712 -----KVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKK--SF-REFSMKSPQSG  783 (2695)
T ss_dssp             -----HHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHT--TE-EEEECCCCCHH
T ss_pred             -----HHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHh--he-EEEEeeCCCHH
Confidence                 1122222222    2221         10001112345778888    34578999998  88 68999999999


Q ss_pred             HHHHHHHH
Q 012016          395 GFKLLAAN  402 (473)
Q Consensus       395 ~r~~l~~~  402 (473)
                      ...++...
T Consensus       784 ~i~ei~l~  791 (2695)
T 4akg_A          784 TIAEMILQ  791 (2695)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            88777543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.63  E-value=1.7e-07  Score=115.51  Aligned_cols=137  Identities=18%  Similarity=0.333  Sum_probs=92.2

Q ss_pred             CceeEEeCCCCCCHHHHHHH-HHHhcCCceEEcccccccCchHHHHHHHHh------------------ccCceEEEecc
Q 012016          253 KRGYLLYGPPGTGKSSLIAA-MANYLNFDVYDLELTELRSNSDLRTLLVAT------------------ANRSILVVEDI  313 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~a-lA~~l~~~~~~l~~~~~~~~~~l~~l~~~~------------------~~~sIL~iDdi  313 (473)
                      .+.+||+||||||||++++. +++..+.+++.++++.-.+...+...+...                  .++.|+||||+
T Consensus      1304 ~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiDDi 1383 (3245)
T 3vkg_A         1304 HRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEI 1383 (3245)
T ss_dssp             TCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEETTT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEeccc
Confidence            45799999999999988765 444457788899998877777777777531                  11259999999


Q ss_pred             ccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC------CceEEEEecCCCC-----CCCccccCCCce
Q 012016          314 DCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG------DERIIVFTTNHKE-----KLDPALLRPGRM  382 (473)
Q Consensus       314 D~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~~~iiI~tTN~~~-----~ld~aLlrpgRf  382 (473)
                      +.-..  +          ..+....-..+.+++.. .|.+....      .++.+|+|.|.|.     .|+|+++|  ||
T Consensus      1384 Nmp~~--D----------~yGtQ~~ielLrqlld~-~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r--~F 1448 (3245)
T 3vkg_A         1384 NLPST--D----------KYGTQRVITFIRQMVEK-GGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLR--HA 1448 (3245)
T ss_dssp             TCCCC--C----------TTSCCHHHHHHHHHHHH-SEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHT--TC
T ss_pred             CCCCc--c----------ccccccHHHHHHHHHHc-CCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHh--hc
Confidence            84311  0          01111222333333322 12222111      3467899999883     58999999  99


Q ss_pred             eeEEEeCCCCHHHHHHHHHHHhC
Q 012016          383 DVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       383 d~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                      . .+.+++|+.++...|+..++.
T Consensus      1449 ~-vi~i~~ps~esL~~If~til~ 1470 (3245)
T 3vkg_A         1449 P-ILLVDFPSTSSLTQIYGTFNR 1470 (3245)
T ss_dssp             C-EEECCCCCHHHHHHHHHHHHH
T ss_pred             e-EEEeCCCCHHHHHHHHHHHHH
Confidence            6 599999999999999876653

>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=98.53  E-value=4.5e-07  Score=92.65  Aligned_cols=153  Identities=16%  Similarity=0.227  Sum_probs=93.9

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccccccCchHH
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELTELRSNSDL  295 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~~~~~~~~l  295 (473)
                      +.+++.....+.+.+.+....           +....+||+|++||||+++++++....+   .+++.++|+.+..+---
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~a-----------~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~~  205 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKIS-----------CAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFE  205 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHT-----------TCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHH
T ss_pred             hhhhhccHHhhHHHHHHHHhc-----------CCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHHHH
Confidence            445666555666655555422           1235689999999999999999998764   68999999886322111


Q ss_pred             HHHHH-----------------HhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhccc--ccCC
Q 012016          296 RTLLV-----------------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGL--WSSC  356 (473)
Q Consensus       296 ~~l~~-----------------~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~--~~~~  356 (473)
                      .++|.                 ...++++||||||+.+.                     ......||..++.-  ..-+
T Consensus       206 ~elfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~---------------------~~~q~~Ll~~l~~~~~~~~g  264 (387)
T 1ny5_A          206 AELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELS---------------------LEAQAKLLRVIESGKFYRLG  264 (387)
T ss_dssp             HHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCC---------------------HHHHHHHHHHHHHSEECCBT
T ss_pred             HHhcCCCCCCCCCcccccCCceeeCCCcEEEEcChhhCC---------------------HHHHHHHHHHHhcCcEEeCC
Confidence            12221                 22356899999999873                     34555666666531  1001


Q ss_pred             C-----CceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCCH--HHHHHHHHHHhC
Q 012016          357 G-----DERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       357 ~-----~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                      +     .++.||+|||..       ..+.+.|..  |+. ..|++|....  +....|+..|+.
T Consensus       265 ~~~~~~~~~rii~at~~~l~~~~~~g~fr~dl~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~  326 (387)
T 1ny5_A          265 GRKEIEVNVRILAATNRNIKELVKEGKFREDLYY--RLGVIEIEIPPLRERKEDIIPLANHFLK  326 (387)
T ss_dssp             CCSBEECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHHH
T ss_pred             CCceeeccEEEEEeCCCCHHHHHHcCCccHHHHH--hhcCCeecCCcchhccccHHHHHHHHHH
Confidence            1     235688888863       334445543  443 4566666432  556677777764

>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=98.51  E-value=6.8e-07  Score=90.69  Aligned_cols=152  Identities=17%  Similarity=0.229  Sum_probs=94.7

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc--eEEcccccccCchHHHH
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD--VYDLELTELRSNSDLRT  297 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~--~~~l~~~~~~~~~~l~~  297 (473)
                      .+++......++...+...-.           ....+|++|++||||+.+++++....+..  ++.++|..+..+.--.+
T Consensus       130 ~~ig~s~~~~~~~~~~~~~a~-----------~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~~  198 (368)
T 3dzd_A          130 EFVGEHPKILEIKRLIPKIAK-----------SKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAESE  198 (368)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHT-----------SCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHHH
T ss_pred             cccccchHHHHHHhhhhhhhc-----------cchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHHH
Confidence            456666555555554443221           13469999999999999999999887543  99999998743322223


Q ss_pred             HH-----------------HHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-c-CCC-
Q 012016          298 LL-----------------VATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-S-SCG-  357 (473)
Q Consensus       298 l~-----------------~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~-~~~-  357 (473)
                      +|                 ....+++.||||||+.+.                     ......||..++.-. . -++ 
T Consensus       199 lfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~---------------------~~~Q~~Ll~~l~~~~~~~~g~~  257 (368)
T 3dzd_A          199 LFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELD---------------------QRVQAKLLRVLETGSFTRLGGN  257 (368)
T ss_dssp             HHEECSCSSSSCCCCEECHHHHTTTSEEEEETGGGSC---------------------HHHHHHHHHHHHHSEECCBTCC
T ss_pred             hcCccccccCCcccccCChHhhcCCCeEEecChhhCC---------------------HHHHHHHHHHHHhCCcccCCCC
Confidence            32                 122356789999999883                     345566777775311 1 111 


Q ss_pred             ----CceEEEEecCCC-------CCCCccccCCCcee-eEEEeCCCCH--HHHHHHHHHHhC
Q 012016          358 ----DERIIVFTTNHK-------EKLDPALLRPGRMD-VHVHMSYCTP--SGFKLLAANYLG  405 (473)
Q Consensus       358 ----~~~iiI~tTN~~-------~~ld~aLlrpgRfd-~~I~~~~p~~--~~r~~l~~~~l~  405 (473)
                          -.+-+|++||..       ..+.+.|..  |+. ..|++|....  +....|+.+|+.
T Consensus       258 ~~~~~~~rii~at~~~l~~~v~~g~fr~dL~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~  317 (368)
T 3dzd_A          258 QKIEVDIRVISATNKNLEEEIKKGNFREDLYY--RLSVFQIYLPPLRERGKDVILLAEYFLK  317 (368)
T ss_dssp             CBEECCCEEEEEESSCHHHHHHTTSSCHHHHH--HHTSEEEECCCGGGSTTHHHHHHHHHHH
T ss_pred             cceeeeeEEEEecCCCHHHHHHcCCccHHHHH--HhCCeEEeCCChhhchhhHHHHHHHHHH
Confidence                134577877753       233444544  443 3577777655  667777777764

>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=98.50  E-value=7.7e-08  Score=99.47  Aligned_cols=143  Identities=17%  Similarity=0.115  Sum_probs=84.2

Q ss_pred             cccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHH-HHhcCCceEEccccc----ccCc---
Q 012016          221 LAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAM-ANYLNFDVYDLELTE----LRSN---  292 (473)
Q Consensus       221 l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~al-A~~l~~~~~~l~~~~----~~~~---  292 (473)
                      |.|++.+|+.|.-.+.   .+...     ..-.-++||.|+||| ||.|++++ ++.+....|......    +...   
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 LPGAEEVGKMLALQLF---SCVGK-----NSERLHVLLAGYPVV-CSEILHHVLDHLAPRGVYVDLRRTELTDLTAVLKE  285 (506)
T ss_dssp             STTCHHHHHHHHHHHT---TCCSS-----GGGCCCEEEESCHHH-HHHHHHHHHHHTCSSEEEEEGGGCCHHHHSEEEEE
T ss_pred             cCCCHHHHHHHHHHHc---CCccc-----cCCceeEEEECCCCh-HHHHHHHHHHHhCCCeEEecCCCCCccCceEEEEc
Confidence            7788887776644332   11000     011226999999999 99999999 887765554322111    0000   


Q ss_pred             ---hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc-c----CCCCceEEEE
Q 012016          293 ---SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW-S----SCGDERIIVF  364 (473)
Q Consensus       293 ---~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~-~----~~~~~~iiI~  364 (473)
                         ..++.-....+...|+|||||+.+                     ...+.+.|+..|+.-. +    .-+....||+
T Consensus       286 ~tG~~~~~G~l~LAdgGvl~lDEIn~~---------------------~~~~qsaLlEaMEe~~VtI~G~~lparf~VIA  344 (506)
T 3f8t_A          286 DRGWALRAGAAVLADGGILAVDHLEGA---------------------PEPHRWALMEAMDKGTVTVDGIALNARCAVLA  344 (506)
T ss_dssp             SSSEEEEECHHHHTTTSEEEEECCTTC---------------------CHHHHHHHHHHHHHSEEEETTEEEECCCEEEE
T ss_pred             CCCcccCCCeeEEcCCCeeehHhhhhC---------------------CHHHHHHHHHHHhCCcEEECCEEcCCCeEEEE
Confidence               000000112346799999999876                     3567778888876311 0    1123578999


Q ss_pred             ecCCCC-----------CCCccccCCCceeeEE-EeCCCCHHH
Q 012016          365 TTNHKE-----------KLDPALLRPGRMDVHV-HMSYCTPSG  395 (473)
Q Consensus       365 tTN~~~-----------~ld~aLlrpgRfd~~I-~~~~p~~~~  395 (473)
                      |+|..+           .|+++++.  |||..+ .+++|+.+.
T Consensus       345 A~NP~~~yd~~~s~~~~~Lp~alLD--RFDLi~i~~d~pd~e~  385 (506)
T 3f8t_A          345 AINPGEQWPSDPPIARIDLDQDFLS--HFDLIAFLGVDPRPGE  385 (506)
T ss_dssp             EECCCC--CCSCGGGGCCSCHHHHT--TCSEEEETTC------
T ss_pred             EeCcccccCCCCCccccCCChHHhh--heeeEEEecCCCChhH
Confidence            999875           78899999  998754 456666543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.39  E-value=1.4e-06  Score=107.77  Aligned_cols=129  Identities=19%  Similarity=0.134  Sum_probs=95.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhc-cCceEEEeccccccccccCCccccCCCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATA-NRSILVVEDIDCTIDLQDRLPADIAGEG  331 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~-~~sIL~iDdiD~l~~~~~r~~~~~~~~~  331 (473)
                      ..|..+.||+|||||.+++.+|+.+|.+++.++|++-.+...+.++|..+. .++..++||++.+-              
T Consensus       604 ~~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~~~~g~i~~G~~~~GaW~cfDEfNrl~--------------  669 (3245)
T 3vkg_A          604 RMGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLE--------------  669 (3245)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCHHHHHHHHHHHHHHTCEEEEETTTSSC--------------
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCHHHHHHHHhhHhhcCcEEEehhhhcCC--------------
Confidence            346789999999999999999999999999999998777777888887765 68999999998762              


Q ss_pred             CCCccchhHHHHHHHHHhc-----------------ccccCCCCceEEEEecCC----CCCCCccccCCCceeeEEEeCC
Q 012016          332 EGPIQQNKVTLSGFLNFID-----------------GLWSSCGDERIIVFTTNH----KEKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       332 ~~~~~~~~~~ls~LL~~ld-----------------g~~~~~~~~~iiI~tTN~----~~~ld~aLlrpgRfd~~I~~~~  390 (473)
                             ..+++.+...|.                 |-.-.-....-|++|.|.    ...|+++|..  || +.|.|++
T Consensus       670 -------~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~--lF-r~v~m~~  739 (3245)
T 3vkg_A          670 -------ERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKK--LF-RSMAMIK  739 (3245)
T ss_dssp             -------HHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHT--TE-EEEECCS
T ss_pred             -------HHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHh--hc-EEEEEeC
Confidence                   233333333221                 210011123567788883    3689999998  88 6799999


Q ss_pred             CCHHHHHHHHHHHhC
Q 012016          391 CTPSGFKLLAANYLG  405 (473)
Q Consensus       391 p~~~~r~~l~~~~l~  405 (473)
                      |+.+...++.-.-.+
T Consensus       740 Pd~~~i~ei~L~s~G  754 (3245)
T 3vkg_A          740 PDREMIAQVMLYSQG  754 (3245)
T ss_dssp             CCHHHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHHcc
Confidence            999998877654444

>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=98.21  E-value=8e-06  Score=81.55  Aligned_cols=122  Identities=17%  Similarity=0.181  Sum_probs=82.6

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc---CC-c--eEEcccccccCchHHHHHHHHh------ccCceEEEecccc-ccc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL---NF-D--VYDLELTELRSNSDLRTLLVAT------ANRSILVVEDIDC-TID  318 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l---~~-~--~~~l~~~~~~~~~~l~~l~~~~------~~~sIL~iDdiD~-l~~  318 (473)
                      ....||||||+|+||++.++++++.+   +. +  ++.++     .+..+++++..+      ..+-|++|||++. +. 
T Consensus        17 ~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~-----~~~~~~~l~~~~~~~plf~~~kvvii~~~~~kl~-   90 (343)
T 1jr3_D           17 LRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSID-----PNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPN-   90 (343)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECC-----TTCCHHHHHHHHHHHHHCCSCEEEEEECCSSCCC-
T ss_pred             CCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEec-----CCCCHHHHHHHhcCcCCccCCeEEEEECCCCCCC-
Confidence            35689999999999999999998876   33 2  23333     123455555443      2568999999986 52 


Q ss_pred             cccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC------CCCCccccCCCceeeEEEeCCCC
Q 012016          319 LQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK------EKLDPALLRPGRMDVHVHMSYCT  392 (473)
Q Consensus       319 ~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~------~~ld~aLlrpgRfd~~I~~~~p~  392 (473)
                                          ....+.|+..++..    ++..++|++|+.+      .++.+++..  |+ .+++|..++
T Consensus        91 --------------------~~~~~aLl~~le~p----~~~~~~il~~~~~~~~~~~~k~~~~i~s--r~-~~~~~~~l~  143 (343)
T 1jr3_D           91 --------------------AAINEQLLTLTGLL----HDDLLLIVRGNKLSKAQENAAWFTALAN--RS-VQVTCQTPE  143 (343)
T ss_dssp             --------------------TTHHHHHHHHHTTC----BTTEEEEEEESCCCTTTTTSHHHHHHTT--TC-EEEEECCCC
T ss_pred             --------------------hHHHHHHHHHHhcC----CCCeEEEEEcCCCChhhHhhHHHHHHHh--Cc-eEEEeeCCC
Confidence                                23456677777753    2346666655543      346677776  65 578999999


Q ss_pred             HHHHHHHHHHHhCc
Q 012016          393 PSGFKLLAANYLGI  406 (473)
Q Consensus       393 ~~~r~~l~~~~l~~  406 (473)
                      ..+....+...+..
T Consensus       144 ~~~l~~~l~~~~~~  157 (343)
T 1jr3_D          144 QAQLPRWVAARAKQ  157 (343)
T ss_dssp             TTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            98888777776643

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.19  E-value=2.5e-06  Score=101.74  Aligned_cols=114  Identities=13%  Similarity=0.163  Sum_probs=69.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHHHh--
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLVAT--  302 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~~~--  302 (473)
                      |++.+++++||||||||||+|+.++|.+.   |..+..++.....                     ..+.+.+.+...  
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            37778899999999999999999998775   4555555544321                     112233333333  


Q ss_pred             -ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC
Q 012016          303 -ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK  369 (473)
Q Consensus       303 -~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~  369 (473)
                       ..+++||||+++.+.+...... .+.   +.......+.++++|..|++.....   .++|++||..
T Consensus      1503 ~~~~~lVVIDsi~al~p~~~~~g-~~~---~~~~~~~~R~lsqlL~~L~~~~~~~---~v~VI~tNq~ 1563 (2050)
T 3cmu_A         1503 SGAVDVIVVDSVAALTPKAEIEG-EIG---DSHMGLAARMMSQAMRKLAGNLKQS---NTLLIFINQI 1563 (2050)
T ss_dssp             HTCCSEEEESCGGGCCCHHHHHS-CTT---CCCTTHHHHHHHHHHHHHHHHHHTT---TCEEEEEECE
T ss_pred             cCCCCEEEEcChhHhcccccccc-ccc---ccccchHHHHHHHHHHHHHHHHHhC---CcEEEEEccc
Confidence             5789999999998875211000 000   0011113567788888888876543   3455555543

>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=98.15  E-value=7e-06  Score=74.51  Aligned_cols=27  Identities=26%  Similarity=0.543  Sum_probs=23.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      .+.|.||+|+|||||++.|++.++..+
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            478999999999999999999886443

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.79  E-value=0.00027  Score=75.48  Aligned_cols=51  Identities=24%  Similarity=0.198  Sum_probs=35.0

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      |.....++|-+...+.|.+.+.    ..       ....+-++|+||+|+|||+||..+++.
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~----~~-------~~~~~~v~I~G~~GiGKTtLa~~~~~~  170 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLS----KL-------KGEPGWVTIHGMAGCGKSVLAAEAVRD  170 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHT----TS-------TTSCEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CCCCCeecccHHHHHHHHHHHh----cc-------cCCCceEEEEcCCCCCHHHHHHHHHhc
Confidence            3445668887777666655432    11       112457999999999999999998753

>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=97.76  E-value=9.3e-05  Score=68.25  Aligned_cols=40  Identities=23%  Similarity=0.169  Sum_probs=31.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~  288 (473)
                      |.+...-++|+||||+|||+|+..+|...+.+++.++...
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            4566667999999999999999999985566666665543

>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=97.71  E-value=0.00013  Score=75.88  Aligned_cols=53  Identities=28%  Similarity=0.417  Sum_probs=34.8

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...|.+|++|  .+++++.+ ..+..++...          .+.++|.||||||||+++.+++..+
T Consensus        17 ~~~p~~~~~L--n~~Q~~av-~~~~~~i~~~----------~~~~li~G~aGTGKT~ll~~~~~~l   69 (459)
T 3upu_A           17 RGSHMTFDDL--TEGQKNAF-NIVMKAIKEK----------KHHVTINGPAGTGATTLTKFIIEAL   69 (459)
T ss_dssp             ----CCSSCC--CHHHHHHH-HHHHHHHHSS----------SCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             ccCCCccccC--CHHHHHHH-HHHHHHHhcC----------CCEEEEEeCCCCCHHHHHHHHHHHH
Confidence            4566788887  34444443 3344444431          2379999999999999999999887

>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=97.69  E-value=4.8e-05  Score=67.33  Aligned_cols=32  Identities=22%  Similarity=0.236  Sum_probs=29.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      -++|.||||+||||+++.|+..+++++++.+.
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~~~~i~~d~   34 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELKYPIIKGSS   34 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHCCCEEECCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeeecCcc
Confidence            57899999999999999999999999987764

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.69  E-value=2.3e-05  Score=70.64  Aligned_cols=34  Identities=26%  Similarity=0.323  Sum_probs=30.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ++.++|.||||||||++++.+|..+++++++.|.
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~~~~i~~d~   38 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTKRILYDSDK   38 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCCEEEHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEEChH
Confidence            4579999999999999999999999999987653

>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=97.65  E-value=0.00016  Score=67.73  Aligned_cols=28  Identities=21%  Similarity=0.196  Sum_probs=24.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      |++...-++|+||||+|||+|+..+|..
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~   47 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVT   47 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHH
Confidence            4566667999999999999999999984

>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=97.62  E-value=3.1e-05  Score=69.25  Aligned_cols=35  Identities=20%  Similarity=0.302  Sum_probs=30.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~  287 (473)
                      +.-++|.||||+||||++++++..++.+++.++..
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~~D   37 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGVD   37 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCCeEEeccc
Confidence            35689999999999999999999999988876644

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.61  E-value=3.5e-05  Score=70.69  Aligned_cols=33  Identities=36%  Similarity=0.423  Sum_probs=30.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ...++|.||||+||||++++||..+++++++.+
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~d   57 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFARKLNVPFIDLD   57 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHcCCCEEcch
Confidence            457999999999999999999999999988765

>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=97.59  E-value=3.4e-05  Score=69.77  Aligned_cols=34  Identities=26%  Similarity=0.330  Sum_probs=29.9

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +.+.-++|.||||+||||+++.++..++++++..
T Consensus         3 ~~~~~I~l~G~~GsGKST~~~~L~~~l~~~~i~~   36 (193)
T 2rhm_A            3 QTPALIIVTGHPATGKTTLSQALATGLRLPLLSK   36 (193)
T ss_dssp             SCCEEEEEEESTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHcCCeEecH
Confidence            3456799999999999999999999999888764

>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=97.58  E-value=0.00022  Score=71.67  Aligned_cols=70  Identities=11%  Similarity=0.131  Sum_probs=46.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHHH---
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLVA---  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~~---  301 (473)
                      |++...-++|+||||+|||+|+..+|..+   +.+++.++.....                     +...+...+..   
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            45666679999999999999999999875   5566555544321                     11122222222   


Q ss_pred             hccCceEEEeccccccc
Q 012016          302 TANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~  318 (473)
                      ...+.+++||.+..+.+
T Consensus       137 ~~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          137 SGVVDLIVVDSVAALVP  153 (356)
T ss_dssp             TSCCSEEEEECTTTCCC
T ss_pred             hcCCCeEEehHhhhhcC
Confidence            24578999999988763

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.58  E-value=0.00034  Score=64.75  Aligned_cols=29  Identities=28%  Similarity=0.201  Sum_probs=24.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.+....++|+||||+|||+|++.+|..+
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~   47 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHFIAKG   47 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            35556679999999999999999999654

>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=97.55  E-value=0.00097  Score=76.93  Aligned_cols=164  Identities=18%  Similarity=0.187  Sum_probs=92.0

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---C--C--ceEEccc
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---N--F--DVYDLEL  286 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~--~--~~~~l~~  286 (473)
                      .|.....++|.++..++|.+.+..    ..       ...+-+.|+|++|+|||+||+.+++..   .  +  .++.++.
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~----~~-------~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~  187 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWK----LN-------GEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSI  187 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHT----TT-------TSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEEC
T ss_pred             CCCCCceeccHHHHHHHHHHHHhh----cc-------CCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEE
Confidence            455667788988777776665431    11       124568999999999999999988762   1  2  2334443


Q ss_pred             cccc---------------------------CchHHHHHHHHh----ccCceEEEeccccccccccCCccccCCCCCCCc
Q 012016          287 TELR---------------------------SNSDLRTLLVAT----ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPI  335 (473)
Q Consensus       287 ~~~~---------------------------~~~~l~~l~~~~----~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~  335 (473)
                      +...                           ....+...+...    .++.+|||||++...                  
T Consensus       188 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~------------------  249 (1249)
T 3sfz_A          188 GKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPW------------------  249 (1249)
T ss_dssp             CSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHH------------------
T ss_pred             CCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHH------------------
Confidence            3210                           011222222211    237899999997431                  


Q ss_pred             cchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCC-CCHHHHHHHHHHHhCccccCCHHH
Q 012016          336 QQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSY-CTPSGFKLLAANYLGIKEHILFEE  414 (473)
Q Consensus       336 ~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~-p~~~~r~~l~~~~l~~~~~~l~~~  414 (473)
                                  .++.+    +.+.-||+||..+...... .   .....+.++. .+.++-.+|+..+.......+.+.
T Consensus       250 ------------~~~~~----~~~~~ilvTtR~~~~~~~~-~---~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~  309 (1249)
T 3sfz_A          250 ------------VLKAF----DNQCQILLTTRDKSVTDSV-M---GPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAE  309 (1249)
T ss_dssp             ------------HHTTT----CSSCEEEEEESSTTTTTTC-C---SCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTH
T ss_pred             ------------HHHhh----cCCCEEEEEcCCHHHHHhh-c---CCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHH
Confidence                        01111    1234566777655433211 1   1234577775 888888888887775443333344


Q ss_pred             HHHHHhcCCCCH
Q 012016          415 IEELISTTQVTP  426 (473)
Q Consensus       415 i~~l~~~~~~t~  426 (473)
                      ..++++..+.-|
T Consensus       310 ~~~i~~~~~glP  321 (1249)
T 3sfz_A          310 AHSIIKECKGSP  321 (1249)
T ss_dssp             HHHHHHHTTTCH
T ss_pred             HHHHHHHhCCCH
Confidence            555555554444

>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=97.53  E-value=0.00017  Score=72.56  Aligned_cols=70  Identities=16%  Similarity=0.220  Sum_probs=48.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHHH---
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLVA---  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~~---  301 (473)
                      |.+..+.++|+||||+|||+|+..+|..+   +.+++.++.....                     +...+.+++..   
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            56667789999999999999999888764   5667666653211                     11223333332   


Q ss_pred             hccCceEEEeccccccc
Q 012016          302 TANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~  318 (473)
                      .....+||||.+..+..
T Consensus       139 ~~~~~lVVIDsl~~l~~  155 (356)
T 1u94_A          139 SGAVDVIVVDSVAALTP  155 (356)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             ccCCCEEEEcCHHHhcc
Confidence            24678999999998863

>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=97.51  E-value=8.3e-05  Score=73.80  Aligned_cols=40  Identities=15%  Similarity=0.202  Sum_probs=31.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~~~  288 (473)
                      |.+...-++|+||||+|||+|+..+|...         +..+++++...
T Consensus       103 Gl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          103 GIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            56666779999999999999999998764         45666666543

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.49  E-value=4.2e-05  Score=69.64  Aligned_cols=30  Identities=17%  Similarity=0.216  Sum_probs=22.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYD  283 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~  283 (473)
                      .-++++||||+|||+++..++..+   +..++.
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~   36 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIYKLGKKKVAV   36 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHTTCEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEE
Confidence            357899999999999986666543   555543

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.49  E-value=5.7e-05  Score=67.58  Aligned_cols=31  Identities=32%  Similarity=0.471  Sum_probs=28.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++|.||||+|||+++++||..+++++++.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d~d   36 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLDSD   36 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEccc
Confidence            5899999999999999999999999988754

>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=97.48  E-value=6.1e-05  Score=67.82  Aligned_cols=32  Identities=31%  Similarity=0.495  Sum_probs=29.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..++|.|+||+|||++++.||..+|+++++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~D   34 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKALGVGLLDTD   34 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHcCCCEEeCc
Confidence            35899999999999999999999999988765

>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=97.48  E-value=6.2e-05  Score=67.57  Aligned_cols=33  Identities=27%  Similarity=0.423  Sum_probs=29.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++.++|.||||+|||++++++|..+++++++.+
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~d   43 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSGLKYINVG   43 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhCCeEEEHH
Confidence            456999999999999999999999999887654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.48  E-value=6.5e-05  Score=66.66  Aligned_cols=32  Identities=34%  Similarity=0.501  Sum_probs=29.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..++|.|+||||||++++.||..+|+++++.+
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~id~D   39 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVLDTD   39 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            47999999999999999999999999998765

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.47  E-value=7.4e-05  Score=66.39  Aligned_cols=32  Identities=41%  Similarity=0.717  Sum_probs=28.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..+.|.||||+||||+++.||..++.++++.+
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id~d   36 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD   36 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEEHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEecc
Confidence            46899999999999999999999998777643

>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=97.46  E-value=0.00037  Score=70.39  Aligned_cols=69  Identities=16%  Similarity=0.206  Sum_probs=47.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHHHh--
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLVAT--  302 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~~~--  302 (473)
                      |.+..+.++|+||||+|||+|+..+|..+   +.+++.+++....                     +...+...+...  
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            56667779999999999999999888764   5566666544321                     112233333322  


Q ss_pred             -ccCceEEEecccccc
Q 012016          303 -ANRSILVVEDIDCTI  317 (473)
Q Consensus       303 -~~~sIL~iDdiD~l~  317 (473)
                       ....+||||.+..+.
T Consensus       150 ~~~~~lVVIDsl~~l~  165 (366)
T 1xp8_A          150 SGAIDVVVVDSVAALT  165 (366)
T ss_dssp             TTCCSEEEEECTTTCC
T ss_pred             cCCCCEEEEeChHHhc
Confidence             357899999999886

>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=97.45  E-value=0.00022  Score=71.63  Aligned_cols=69  Identities=13%  Similarity=0.193  Sum_probs=45.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHHH---
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLVA---  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~~---  301 (473)
                      |.+..+-++|+||||+|||+|+..+|..+   +..+..++.....                     +...+..++..   
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            55666779999999999999999888654   4555555543211                     11122222222   


Q ss_pred             hccCceEEEecccccc
Q 012016          302 TANRSILVVEDIDCTI  317 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~  317 (473)
                      ...+.+||||++..+.
T Consensus       137 ~~~~~lIVIDsl~~l~  152 (349)
T 2zr9_A          137 SGALDIIVIDSVAALV  152 (349)
T ss_dssp             TTCCSEEEEECGGGCC
T ss_pred             cCCCCEEEEcChHhhc
Confidence            2358999999999886

>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=97.45  E-value=7.9e-05  Score=67.43  Aligned_cols=33  Identities=30%  Similarity=0.478  Sum_probs=29.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh-cCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY-LNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~-l~~~~~~l~  285 (473)
                      +..++|.|+||||||++++.+|.. +|+++++++
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~l~g~~~id~d   43 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAELDGFQHLEVG   43 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTTEEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCCEEeeHH
Confidence            346999999999999999999999 798888765

>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=97.43  E-value=0.00031  Score=70.31  Aligned_cols=40  Identities=15%  Similarity=0.067  Sum_probs=30.7

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---------CCceEEccccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---------NFDVYDLELTE  288 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---------~~~~~~l~~~~  288 (473)
                      |.+...-++|+||||+|||+|+..+|...         +..+++++...
T Consensus       118 Gl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          118 GIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            55666679999999999999999998862         45666665543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.42  E-value=0.00025  Score=84.85  Aligned_cols=70  Identities=16%  Similarity=0.233  Sum_probs=52.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc------------------------hHHHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN------------------------SDLRTLLVA  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~------------------------~~l~~l~~~  301 (473)
                      |.+..+.++|+||||||||+|+.+++.+.   |.+.+.+++......                        ..+.+.+..
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            46778889999999999999999988754   677777776654211                        122334444


Q ss_pred             hccCceEEEeccccccc
Q 012016          302 TANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~  318 (473)
                      ...+.+||||++..+.+
T Consensus      1157 ~~~~dlvVIDsl~~L~~ 1173 (2050)
T 3cmu_A         1157 SGAVDVIVVDSVAALTP 1173 (2050)
T ss_dssp             HTCCSEEEESCGGGCCC
T ss_pred             hCCCCEEEECCcccccc
Confidence            56799999999999854

>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=97.38  E-value=0.0004  Score=74.31  Aligned_cols=64  Identities=30%  Similarity=0.371  Sum_probs=41.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc----------cCchHHHHHHHHhc-----------cCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL----------RSNSDLRTLLVATA-----------NRSIL  308 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~----------~~~~~l~~l~~~~~-----------~~sIL  308 (473)
                      .+.+++.||||||||+++.+++..+   +.++..+..+..          .....+..++....           ...+|
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e~~~~~a~Tih~ll~~~~~~~~~~~~~~~~~dvl  283 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLL  283 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTSCEEEHHHHTTEETTEESCSSSSCCSCSEE
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHHHHHhHhhhcccHHHHHHHHcCCcchhhhhhcccccCCEE
Confidence            3578999999999999999999865   666665533321          01223344432111           34799


Q ss_pred             EEeccccc
Q 012016          309 VVEDIDCT  316 (473)
Q Consensus       309 ~iDdiD~l  316 (473)
                      +|||+..+
T Consensus       284 IIDEasml  291 (574)
T 3e1s_A          284 IVDEVSMM  291 (574)
T ss_dssp             EECCGGGC
T ss_pred             EEcCccCC
Confidence            99999755

>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=97.37  E-value=9.7e-05  Score=65.55  Aligned_cols=32  Identities=19%  Similarity=0.412  Sum_probs=28.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..++|.|+||+|||++++.+|..+++++++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~lg~~~id~d   34 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCcEEccc
Confidence            35899999999999999999999999988755

>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=97.35  E-value=0.00045  Score=66.72  Aligned_cols=29  Identities=28%  Similarity=0.239  Sum_probs=23.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.+...-++|+||||+|||+|+..+|..+
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            44455679999999999999999998644

>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=97.34  E-value=0.00014  Score=66.44  Aligned_cols=33  Identities=30%  Similarity=0.483  Sum_probs=29.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +..++|.||||+||||+++.|+..+++++++++
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l~~~~i~~d   52 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKLGIPQISTG   52 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            346899999999999999999999999988764

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.33  E-value=0.00013  Score=69.78  Aligned_cols=33  Identities=27%  Similarity=0.466  Sum_probs=29.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT  287 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~  287 (473)
                      -++|.||||||||+++++||..++.+++..|.-
T Consensus         3 li~I~G~~GSGKSTla~~La~~~~~~~i~~D~~   35 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQETGWPVVALDRV   35 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCCEEECCSG
T ss_pred             EEEEECCCCcCHHHHHHHHHhcCCCeEEeccHH
Confidence            478999999999999999999999999887753

>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=97.32  E-value=0.00013  Score=64.21  Aligned_cols=30  Identities=27%  Similarity=0.365  Sum_probs=27.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      -++|.||||+||||+++.+ ..+|++++.++
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~g~~~i~~~   32 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KERGAKVIVMS   32 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHTTCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCcEEEHh
Confidence            5889999999999999999 99999988753

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.31  E-value=0.00013  Score=65.82  Aligned_cols=33  Identities=18%  Similarity=0.311  Sum_probs=28.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-++|.|+||+||||+++.++..+++++++.+
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~d   35 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKYGYTHLSAG   35 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCeEEeHH
Confidence            346899999999999999999999999887654

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.29  E-value=0.00075  Score=63.33  Aligned_cols=61  Identities=26%  Similarity=0.335  Sum_probs=42.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc---------cc-----------------CchHHHHHHHHhcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE---------LR-----------------SNSDLRTLLVATAN  304 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~---------~~-----------------~~~~l~~l~~~~~~  304 (473)
                      -.+++.|+||+|||+++-.+|..+   |+++..++...         +.                 .+..+..++.  ..
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D~q~~~~~~al~~gl~~~~~~~~~~~~~~~~e~~l~~~L~--~~   84 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVETHGRAETEALLNGLPQQPLLRTEYRGMTLEEMDLDALLK--AA   84 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCTTCHHHHHHHTTSCBCCCEEEEETTEEEEECCHHHHHH--HC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeCCCCChhHHHHhcCccccCcceeecCCcccccccHHHHHh--cC
Confidence            469999999999999999999876   77766444321         11                 1123444443  36


Q ss_pred             CceEEEeccccc
Q 012016          305 RSILVVEDIDCT  316 (473)
Q Consensus       305 ~sIL~iDdiD~l  316 (473)
                      +.+++|||+-..
T Consensus        85 pdlvIVDElG~~   96 (228)
T 2r8r_A           85 PSLVLVDELAHT   96 (228)
T ss_dssp             CSEEEESCTTCB
T ss_pred             CCEEEEeCCCCC
Confidence            889999998754

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.29  E-value=0.00017  Score=65.98  Aligned_cols=33  Identities=24%  Similarity=0.365  Sum_probs=29.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-++|.||||+||||+++.|+..+|+.+++.+
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~d   50 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEACGYPFIEGD   50 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHHTCCEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCEEEeCC
Confidence            346999999999999999999999998887655

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.28  E-value=0.00011  Score=65.38  Aligned_cols=32  Identities=28%  Similarity=0.333  Sum_probs=26.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH-hcCCceEEc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN-YLNFDVYDL  284 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~-~l~~~~~~l  284 (473)
                      +.-++|.||||+||||+++.++. .+++.++..
T Consensus         2 ~~~I~i~G~~GsGKST~a~~L~~~~~~~~~i~~   34 (181)
T 1ly1_A            2 KKIILTIGCPGSGKSTWAREFIAKNPGFYNINR   34 (181)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHSTTEEEECH
T ss_pred             CeEEEEecCCCCCHHHHHHHHHhhcCCcEEecH
Confidence            34689999999999999999999 677665543

>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=97.28  E-value=0.00014  Score=65.41  Aligned_cols=33  Identities=18%  Similarity=0.311  Sum_probs=29.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-++|.|+||+|||++++.++..+++++++.+
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~d   38 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAG   38 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEeeHH
Confidence            457999999999999999999999998888764

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.28  E-value=0.00013  Score=65.66  Aligned_cols=32  Identities=28%  Similarity=0.587  Sum_probs=28.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..++|.||||+||||+++.+|..+++++++.+
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l~~~~i~~d   36 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQELGFKKLSTG   36 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTCEEECHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEecHH
Confidence            35899999999999999999999998887654

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.27  E-value=0.00015  Score=65.62  Aligned_cols=33  Identities=15%  Similarity=0.308  Sum_probs=29.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-++|.||||+||||+++.+|..+++++++.+
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~d   41 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTG   41 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            357999999999999999999999999888765

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.27  E-value=0.00015  Score=64.11  Aligned_cols=31  Identities=29%  Similarity=0.428  Sum_probs=28.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++|.|+||+|||++++.++..+++++++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d   32 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDVD   32 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            4789999999999999999999999988755

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.26  E-value=0.00013  Score=67.71  Aligned_cols=32  Identities=19%  Similarity=0.367  Sum_probs=28.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..++|.||||+||||+++.||..++++++..+
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~d   37 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEYGLAHLSTG   37 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCceEEehh
Confidence            46899999999999999999999999888763

>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=97.26  E-value=0.00037  Score=69.93  Aligned_cols=29  Identities=24%  Similarity=0.336  Sum_probs=25.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |++...-+.|+||||+|||+|+..+|...
T Consensus       127 gi~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          127 GIETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            56666679999999999999999999876

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.23  E-value=0.00016  Score=65.51  Aligned_cols=33  Identities=18%  Similarity=0.341  Sum_probs=29.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-++|.||||+||||+++.++..+++++++.+
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d   44 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYGFTHLSTG   44 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            457999999999999999999999998887664

>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=97.22  E-value=0.00019  Score=66.39  Aligned_cols=31  Identities=19%  Similarity=0.301  Sum_probs=28.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++|.||||+||||+++.||..++++++..+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~d   32 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKYGIPHISTG   32 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeHH
Confidence            3789999999999999999999999888764

>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=97.22  E-value=0.00016  Score=65.02  Aligned_cols=30  Identities=17%  Similarity=0.376  Sum_probs=26.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC-----CceEE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN-----FDVYD  283 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~  283 (473)
                      .-++|.||||+||||+++.|+..++     ++++.
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~i~   38 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLRKEGVNYKMVS   38 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTTTCCCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcCcceEEEe
Confidence            4689999999999999999999987     66664

>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=97.21  E-value=0.00021  Score=66.35  Aligned_cols=31  Identities=23%  Similarity=0.415  Sum_probs=28.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ..++|.||||+||||+++.||..++++++..
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   35 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQERFHAAHLAT   35 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeh
Confidence            4689999999999999999999999988776

>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=97.21  E-value=0.001  Score=65.63  Aligned_cols=69  Identities=13%  Similarity=0.080  Sum_probs=42.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc-----CCceEEccccccc---------------------CchHH-HHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTELR---------------------SNSDL-RTLLVA  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~~~---------------------~~~~l-~~l~~~  301 (473)
                      |.+.. -++++||||+|||+|+..++...     +..+.+++...-.                     +.+.+ ..++..
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            45555 58999999999999976555433     4556666543320                     11222 222222


Q ss_pred             h-----ccCceEEEeccccccc
Q 012016          302 T-----ANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~-----~~~sIL~iDdiD~l~~  318 (473)
                      .     ..+.+||||-|..+..
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            2     3689999999999863

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.20  E-value=0.00018  Score=67.19  Aligned_cols=33  Identities=15%  Similarity=0.346  Sum_probs=29.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-++|.||||+||||+++.||..+++++++.+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~d   39 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHFELKHLSSG   39 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHSSSEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCeEEech
Confidence            456999999999999999999999999887653

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.20  E-value=0.00042  Score=67.52  Aligned_cols=34  Identities=32%  Similarity=0.458  Sum_probs=27.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      +..++|.||||+||||+++.++..++...+.++.
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~   66 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN   66 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEec
Confidence            4569999999999999999999998444445554

>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=97.20  E-value=0.00026  Score=63.04  Aligned_cols=33  Identities=30%  Similarity=0.484  Sum_probs=28.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ...+.|.||||+|||++++.++..+|..+++.+
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~~d   40 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   40 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHhhCcEEEeCc
Confidence            346899999999999999999999988777654

>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=97.20  E-value=0.00019  Score=64.84  Aligned_cols=36  Identities=31%  Similarity=0.363  Sum_probs=28.9

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ..+.-+.|.||||+||||++++|+..++...+.++.
T Consensus         7 ~~g~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~   42 (191)
T 1zp6_A            7 LGGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   42 (191)
T ss_dssp             CTTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHhccCCCeEEEcc
Confidence            345569999999999999999999987666555553

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=97.19  E-value=0.0014  Score=61.23  Aligned_cols=28  Identities=32%  Similarity=0.378  Sum_probs=23.1

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      |.+...-++|+||||+|||+++..+|..
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~   46 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWN   46 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            4566667999999999999998877654

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.18  E-value=0.0002  Score=66.09  Aligned_cols=30  Identities=20%  Similarity=0.340  Sum_probs=27.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++|.||||+||||+++.++..++++++..+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~~~~~i~~d   32 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIEKYEIPHISTG   32 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEeeHH
Confidence            789999999999999999999999888764

>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=97.18  E-value=0.00043  Score=68.38  Aligned_cols=28  Identities=18%  Similarity=0.177  Sum_probs=24.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      |.+...-++|+||||+|||+++..+|..
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            5566667999999999999999998865

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.16  E-value=0.00043  Score=66.00  Aligned_cols=38  Identities=16%  Similarity=0.193  Sum_probs=30.7

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      .+..++|.||||+|||++++.|+..++...+.++...+
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            34579999999999999999999999865555555544

>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=97.16  E-value=0.01  Score=62.99  Aligned_cols=43  Identities=16%  Similarity=0.250  Sum_probs=32.2

Q ss_pred             cchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHH
Q 012016          223 MEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       223 ~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      |.++.+++|.+.+..    .      +....+.+.|+|++|+|||+||+.+++
T Consensus       132 GR~~~~~~l~~~L~~----~------~~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          132 IREYHVDRVIKKLDE----M------CDLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCHHHHHHHHHHHHH----H------TTSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHhc----c------cCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            777777777766532    1      111246789999999999999999997

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.14  E-value=0.00028  Score=64.43  Aligned_cols=32  Identities=19%  Similarity=0.318  Sum_probs=28.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .-|+|.||||+|||++++.|++.+++++++.+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~d   47 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG   47 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeHH
Confidence            45899999999999999999999999887765

>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=97.13  E-value=0.00029  Score=66.15  Aligned_cols=32  Identities=25%  Similarity=0.377  Sum_probs=28.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..++|.|+||+||||+++.||..++++++..+
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~d   48 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNFCVCHLATG   48 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceecHH
Confidence            46999999999999999999999998887763

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.12  E-value=0.00019  Score=66.73  Aligned_cols=32  Identities=13%  Similarity=0.236  Sum_probs=28.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +..++|.||||+||||+++.||..++.+++++
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   36 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQLAHISA   36 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            45699999999999999999999999877654

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=97.11  E-value=0.00037  Score=63.77  Aligned_cols=32  Identities=19%  Similarity=0.420  Sum_probs=27.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      +.-+.|.||+|+||||++++|+..+|..+++-
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~~g~~~i~~   60 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADETGLEFAEA   60 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHCCEEEEG
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCCeEEcc
Confidence            45689999999999999999999998766654

>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=97.10  E-value=0.00034  Score=62.65  Aligned_cols=35  Identities=29%  Similarity=0.464  Sum_probs=30.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      +.-+.|.|++|+||||+++.++..+   |++++.++..
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d~~   42 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGD   42 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEECCh
Confidence            4468899999999999999999998   8888877643

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.07  E-value=0.00026  Score=63.36  Aligned_cols=29  Identities=21%  Similarity=0.219  Sum_probs=23.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .-++|.|+||+||||+++.++..++.+++
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~l~~~~i   34 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHERLPGSFV   34 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHHSTTCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCEE
Confidence            46899999999999999999999999887

>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=97.07  E-value=0.001  Score=67.94  Aligned_cols=27  Identities=33%  Similarity=0.270  Sum_probs=22.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      |++...-++|+||||+|||+|+..+|-
T Consensus       174 GI~~Gei~~I~G~sGsGKTTLl~~la~  200 (400)
T 3lda_A          174 GVETGSITELFGEFRTGKSQLCHTLAV  200 (400)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcCCCcEEEEEcCCCCChHHHHHHHHH
Confidence            556666799999999999999997763

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=97.05  E-value=0.00021  Score=71.62  Aligned_cols=50  Identities=20%  Similarity=0.375  Sum_probs=36.5

Q ss_pred             hHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       225 ~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      +.+.+.+++.+..++...+         ...++|.||||+|||+++++||+.++++++.
T Consensus         5 ~~L~~~il~~l~~~i~~g~---------~~~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A            5 HKLADDVLQLLDNRIEDNY---------RVCVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             HHHHHHHHHHHHHTTTTCS---------CEEEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCC---------eeEEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            4455666665554443211         2469999999999999999999999988844

>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=97.05  E-value=0.00072  Score=80.04  Aligned_cols=70  Identities=16%  Similarity=0.194  Sum_probs=51.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh---cCCceEEcccccccC---------------------chHHHHHHHHh--
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY---LNFDVYDLELTELRS---------------------NSDLRTLLVAT--  302 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~---l~~~~~~l~~~~~~~---------------------~~~l~~l~~~~--  302 (473)
                      |++..+.++|+||||||||+|+.++|..   .|..+++++......                     ...+.+++...  
T Consensus        30 Gi~~G~i~lI~G~pGsGKT~LAlqla~~~~~~G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L~~  109 (1706)
T 3cmw_A           30 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  109 (1706)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCeEEEEECCCCCCHHHHHHHHHHHHhhCCCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHHHh
Confidence            6777889999999999999999998875   367777777655311                     22334444333  


Q ss_pred             -ccCceEEEeccccccc
Q 012016          303 -ANRSILVVEDIDCTID  318 (473)
Q Consensus       303 -~~~sIL~iDdiD~l~~  318 (473)
                       ..+.+||||++..+..
T Consensus       110 ~~~~~LVVIDSLt~L~~  126 (1706)
T 3cmw_A          110 SGAVDVIVVDSVAALTP  126 (1706)
T ss_dssp             HTCCSEEEESCSTTCCC
T ss_pred             ccCCCEEEEcchhhhcc
Confidence             4688999999998865

>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=97.04  E-value=0.00039  Score=65.92  Aligned_cols=33  Identities=18%  Similarity=0.369  Sum_probs=29.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.-++|.||||+||||+++.|++.++++++..+
T Consensus        29 ~~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~~   61 (243)
T 3tlx_A           29 DGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTG   61 (243)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEEecH
Confidence            457999999999999999999999999888664

>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=97.01  E-value=0.0017  Score=67.33  Aligned_cols=74  Identities=15%  Similarity=0.226  Sum_probs=57.0

Q ss_pred             CceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC-------------CCC
Q 012016          305 RSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH-------------KEK  371 (473)
Q Consensus       305 ~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~-------------~~~  371 (473)
                      +.|++|||+|.+.                     ....+.|+..|+..    ... ++|++||.             ++.
T Consensus       296 ~~VliIDEa~~l~---------------------~~a~~aLlk~lEe~----~~~-~~il~tn~~~~~i~~~~~~~~~~~  349 (456)
T 2c9o_A          296 PGVLFVDEVHMLD---------------------IECFTYLHRALESS----IAP-IVIFASNRGNCVIRGTEDITSPHG  349 (456)
T ss_dssp             ECEEEEESGGGCB---------------------HHHHHHHHHHTTST----TCC-EEEEEECCSEEECBTTSSCEEETT
T ss_pred             ceEEEEechhhcC---------------------HHHHHHHHHHhhcc----CCC-EEEEecCCcccccccccccccccc
Confidence            4799999999872                     46788899888853    233 45544433             678


Q ss_pred             CCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          372 LDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       372 ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      |+|+++.  ||.. +.|+.++.++...++...+...
T Consensus       350 l~~~i~s--R~~~-~~~~~~~~~e~~~iL~~~~~~~  382 (456)
T 2c9o_A          350 IPLDLLD--RVMI-IRTMLYTPQEMKQIIKIRAQTE  382 (456)
T ss_dssp             CCHHHHT--TEEE-EECCCCCHHHHHHHHHHHHHHH
T ss_pred             CChhHHh--hcce-eeCCCCCHHHHHHHHHHHHHHh
Confidence            9999999  9976 6999999999999998776533

>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=97.00  E-value=0.00032  Score=64.84  Aligned_cols=30  Identities=17%  Similarity=0.246  Sum_probs=27.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .++|.||||+||||+++.|+..++++++..
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            378999999999999999999999988776

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.97  E-value=0.00047  Score=68.27  Aligned_cols=34  Identities=26%  Similarity=0.495  Sum_probs=30.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ++.++|.||+|+|||+++..||..++..++.+|.
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds   38 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADALPCELISVDS   38 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEEECT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCcEEeccc
Confidence            4579999999999999999999999988888764

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.96  E-value=0.00048  Score=61.98  Aligned_cols=31  Identities=23%  Similarity=0.283  Sum_probs=28.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      -+.|.|+||+||||+++.+++.+   |++++..+
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            37899999999999999999998   89988775

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.95  E-value=0.00044  Score=64.56  Aligned_cols=30  Identities=20%  Similarity=0.433  Sum_probs=27.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -++|.||||+||||+++.|+..++++++..
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            378999999999999999999999887765

>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=96.95  E-value=0.00041  Score=63.39  Aligned_cols=31  Identities=29%  Similarity=0.297  Sum_probs=27.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      -+.|.||+|+||||+++.||+ +|+++++.+.
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~i~~d~   33 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYVLDADK   33 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEEEEHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEEEEccH
Confidence            478999999999999999999 9998887764

>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=96.90  E-value=0.0017  Score=59.50  Aligned_cols=110  Identities=9%  Similarity=0.132  Sum_probs=66.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc------------cC--------------------chHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL------------RS--------------------NSDLRTL  298 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~------------~~--------------------~~~l~~l  298 (473)
                      ..+++|+++|.|||++|-++|-..   |..++.+....-            ..                    .......
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~  108 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAV  108 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHH
Confidence            468999999999999999998776   777776643220            00                    0111222


Q ss_pred             HHH----h--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCC
Q 012016          299 LVA----T--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKL  372 (473)
Q Consensus       299 ~~~----~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~l  372 (473)
                      +..    .  ....+|||||+-.....                  .-.....+++.+..    .++..-||+|+|.+   
T Consensus       109 l~~a~~~l~~~~yDlvILDEi~~al~~------------------g~l~~~ev~~~l~~----Rp~~~~vIlTGr~a---  163 (196)
T 1g5t_A          109 WQHGKRMLADPLLDMVVLDELTYMVAY------------------DYLPLEEVISALNA----RPGHQTVIITGRGC---  163 (196)
T ss_dssp             HHHHHHHTTCTTCSEEEEETHHHHHHT------------------TSSCHHHHHHHHHT----SCTTCEEEEECSSC---
T ss_pred             HHHHHHHHhcCCCCEEEEeCCCccccC------------------CCCCHHHHHHHHHh----CcCCCEEEEECCCC---
Confidence            222    2  24589999999664320                  01122335555542    34568899999874   


Q ss_pred             CccccCCCceeeEEEeCC
Q 012016          373 DPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       373 d~aLlrpgRfd~~I~~~~  390 (473)
                      ++.|+.  .-|.+=+|..
T Consensus       164 p~~l~e--~AD~VTem~~  179 (196)
T 1g5t_A          164 HRDILD--LADTVSELRP  179 (196)
T ss_dssp             CHHHHH--HCSEEEECCC
T ss_pred             cHHHHH--hCcceeeecc
Confidence            566665  5566655543

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.90  E-value=0.00054  Score=65.45  Aligned_cols=33  Identities=30%  Similarity=0.518  Sum_probs=30.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ...+.|.||+|+||||+++.||..+++++++.+
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            357999999999999999999999999998865

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.89  E-value=0.00062  Score=63.64  Aligned_cols=31  Identities=19%  Similarity=0.472  Sum_probs=27.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      ++-++|.||||+||+|.++.||..++++.+.
T Consensus        29 ~kiI~llGpPGsGKgTqa~~L~~~~g~~hIs   59 (217)
T 3umf_A           29 AKVIFVLGGPGSGKGTQCEKLVQKFHFNHLS   59 (217)
T ss_dssp             CEEEEEECCTTCCHHHHHHHHHHHHCCEEEC
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHCCceEc
Confidence            4678899999999999999999999887653

>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=96.89  E-value=0.00061  Score=63.16  Aligned_cols=32  Identities=34%  Similarity=0.521  Sum_probs=28.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .-+.|.||+|+||||+++.+++.+|+++++.+
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g~~~~d~g   37 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQWHLLDSG   37 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCcccCc
Confidence            36899999999999999999999998877643

>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=96.88  E-value=0.00053  Score=62.80  Aligned_cols=30  Identities=23%  Similarity=0.346  Sum_probs=26.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      -+.|.||+|+||||+++.+|. +|+++++.+
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~id~d   33 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPLVDAD   33 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcccchH
Confidence            578999999999999999998 899888765

>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=96.88  E-value=0.00066  Score=64.18  Aligned_cols=31  Identities=23%  Similarity=0.502  Sum_probs=27.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      +.-+.|.||||+||||+++.|+..+|+..+.
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg~~~~~   57 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFGLQHLS   57 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCCCEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEec
Confidence            4579999999999999999999999876554

>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=96.87  E-value=0.0034  Score=63.04  Aligned_cols=23  Identities=52%  Similarity=0.836  Sum_probs=21.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+++.||+|+||||++++|++.+
T Consensus       125 ~i~I~GptGSGKTTlL~~l~g~~  147 (356)
T 3jvv_A          125 LVLVTGPTGSGKSTTLAAMLDYL  147 (356)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhcc
Confidence            58999999999999999999877

>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=96.86  E-value=0.00059  Score=62.21  Aligned_cols=31  Identities=26%  Similarity=0.276  Sum_probs=28.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      -+.|.||+|+|||++++.+|..+|+++++.+
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            6889999999999999999999999998765

>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=96.84  E-value=0.00063  Score=62.29  Aligned_cols=32  Identities=25%  Similarity=0.281  Sum_probs=29.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      -+.|.|++|||||++++.++..+|+++++.|.
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vid~D~   45 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVVNVDR   45 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEEECcH
Confidence            57899999999999999999999999988663

>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=96.84  E-value=0.00071  Score=61.53  Aligned_cols=33  Identities=12%  Similarity=0.141  Sum_probs=28.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-CCceEEccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLEL  286 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~~  286 (473)
                      .-+.|.||||+||||+++.++..+ |++++.++.
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~~   38 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNF   38 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTSCGGGEEEEES
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHCCCceEEEec
Confidence            468999999999999999999999 588877653

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.83  E-value=0.00069  Score=61.45  Aligned_cols=29  Identities=24%  Similarity=0.657  Sum_probs=26.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      -+.|.|+||+||||+++.||+.++.+++.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~~~   30 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEIFK   30 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEEEC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcEEc
Confidence            37899999999999999999999987664

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.82  E-value=0.00038  Score=62.55  Aligned_cols=24  Identities=33%  Similarity=0.558  Sum_probs=22.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -++|.||||+||||+++.|+..++
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            488999999999999999999886

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=96.82  E-value=0.0019  Score=60.32  Aligned_cols=38  Identities=26%  Similarity=0.197  Sum_probs=27.8

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh----cCCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY----LNFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~----l~~~~~~l~~  286 (473)
                      |.++..-++++|+||+|||+++..+|..    .+.+++.+++
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            5566677999999999999998876543    2556655443

>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=96.80  E-value=0.0008  Score=62.33  Aligned_cols=28  Identities=29%  Similarity=0.532  Sum_probs=25.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      ++|.||||+||+|.++.||..+|++.+.
T Consensus         3 Iil~GpPGsGKgTqa~~La~~~g~~~is   30 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKEKGFVHIS   30 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            7889999999999999999999987754

>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=96.79  E-value=0.0028  Score=59.44  Aligned_cols=62  Identities=10%  Similarity=0.239  Sum_probs=38.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc-------ccc-------------CchHHHHHHHHh---ccCceE
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT-------ELR-------------SNSDLRTLLVAT---ANRSIL  308 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~-------~~~-------------~~~~l~~l~~~~---~~~sIL  308 (473)
                      -++++||||+|||+++..++..+   +..++.+...       .+.             ....+.+.+...   ..+.+|
T Consensus        14 i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvV   93 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVI   93 (223)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEE
Confidence            47889999999999888777665   5555554211       110             112333333322   236899


Q ss_pred             EEeccccc
Q 012016          309 VVEDIDCT  316 (473)
Q Consensus       309 ~iDdiD~l  316 (473)
                      +|||+..+
T Consensus        94 iIDEaQ~l  101 (223)
T 2b8t_A           94 GIDEVQFF  101 (223)
T ss_dssp             EECSGGGS
T ss_pred             EEecCccC
Confidence            99999865

>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=96.79  E-value=0.00081  Score=63.54  Aligned_cols=33  Identities=33%  Similarity=0.361  Sum_probs=29.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +..+.|.||||+|||++++.||..+++++++.+
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~lg~~~~d~g   41 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARALGARYLDTG   41 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCcccCC
Confidence            346899999999999999999999999887654

>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=96.78  E-value=0.0008  Score=64.39  Aligned_cols=33  Identities=36%  Similarity=0.428  Sum_probs=28.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh---cCCceEEccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY---LNFDVYDLEL  286 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~---l~~~~~~l~~  286 (473)
                      .-++|.|+||+|||++++.++..   +|++++.++.
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~   40 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGS   40 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECc
Confidence            46899999999999999999998   7888874443

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.77  E-value=0.0014  Score=59.73  Aligned_cols=27  Identities=22%  Similarity=0.353  Sum_probs=24.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      .-++|.||||+||||+++.|+..++..
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~   31 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELK   31 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhc
Confidence            458999999999999999999998763

>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=96.75  E-value=0.00087  Score=61.24  Aligned_cols=33  Identities=30%  Similarity=0.356  Sum_probs=26.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      +.-+.|.||+|+||||++++||..+   |...+.++
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d   60 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILD   60 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEec
Confidence            4568999999999999999999998   54433444

>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=96.67  E-value=0.00092  Score=60.64  Aligned_cols=31  Identities=29%  Similarity=0.459  Sum_probs=28.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .-+.|.|++|+|||++++.||.. |+++++.+
T Consensus         9 ~~I~i~G~~GsGKST~~~~La~~-g~~~id~d   39 (203)
T 1uf9_A            9 IIIGITGNIGSGKSTVAALLRSW-GYPVLDLD   39 (203)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHT-TCCEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHC-CCEEEccc
Confidence            46899999999999999999998 99888766

>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=96.65  E-value=0.0018  Score=66.48  Aligned_cols=59  Identities=19%  Similarity=0.177  Sum_probs=38.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHH-hccCceEEEecc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVA-TANRSILVVEDI  313 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~-~~~~sIL~iDdi  313 (473)
                      +.-++|.||||+||||+++.++..+++.++..+  .+..-..+...... ...+..++||..
T Consensus       258 ~~lIil~G~pGSGKSTla~~L~~~~~~~~i~~D--~~~~~~~~~~~~~~~l~~g~~vIiD~~  317 (416)
T 3zvl_A          258 PEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNRD--TLGSWQRCVSSCQAALRQGKRVVIDNT  317 (416)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHTGGGTCEECCGG--GSCSHHHHHHHHHHHHHTTCCEEEESC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhcCcEEEccc--hHHHHHHHHHHHHHHHhcCCcEEEeCC
Confidence            456899999999999999999999987766544  33332333333222 234444556543

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.65  E-value=0.0012  Score=60.82  Aligned_cols=32  Identities=28%  Similarity=0.342  Sum_probs=29.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..+.|.|++|+|||++++.++..+|+++++.+
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~d   35 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDTG   35 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecCC
Confidence            46899999999999999999999999988765

>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=96.61  E-value=0.0013  Score=60.80  Aligned_cols=31  Identities=35%  Similarity=0.467  Sum_probs=27.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .-+.|.|++|+||||+++.++. +|+++++.|
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-lg~~~id~D   35 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-LGINVIDAD   35 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-TTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-cCCEEEEcc
Confidence            4689999999999999999998 899888765

>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=96.58  E-value=0.0091  Score=51.36  Aligned_cols=24  Identities=25%  Similarity=0.347  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            358999999999999999998643

>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=96.56  E-value=0.0083  Score=61.82  Aligned_cols=61  Identities=20%  Similarity=0.315  Sum_probs=38.5

Q ss_pred             hHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       225 ~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +.+++.+.+.+...+......... ...+.-+++.||+|+||||++..||.++   |..+..+++
T Consensus        73 ~~v~~~l~~eL~~~L~~~~~~~~~-~~~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~  136 (443)
T 3dm5_A           73 EHIIKIVYEELTKFLGTEAKPIEI-KEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCS  136 (443)
T ss_dssp             HHHHHHHHHHHHHHTTSSCCCCCC-CSSSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEC
T ss_pred             HHHHHHHHHHHHHHhcCccccccc-CCCCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            345556666666665431111111 1235678999999999999999999877   555554443

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.55  E-value=0.0019  Score=61.45  Aligned_cols=31  Identities=35%  Similarity=0.548  Sum_probs=27.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .-+.|.||+|+||||+++.||..||+.+++.
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~Lg~~~~d~   58 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESLNWRLLDS   58 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCCcCCC
Confidence            4689999999999999999999999988763

>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=96.55  E-value=0.0013  Score=60.28  Aligned_cols=32  Identities=22%  Similarity=0.243  Sum_probs=27.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-CCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~  285 (473)
                      .-+.|.||+|+||||+++.|+..+ ++.++..+
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~~D   54 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKHLPNCSVISQD   54 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTSTTEEEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCcEEEeCC
Confidence            457899999999999999999988 67766655

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=96.54  E-value=0.0016  Score=61.12  Aligned_cols=32  Identities=25%  Similarity=0.399  Sum_probs=28.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..+.|.||+|+|||++++.+|..+|+++++.+
T Consensus        17 ~~i~i~G~~gsGKst~~~~l~~~lg~~~~d~d   48 (236)
T 1q3t_A           17 IQIAIDGPASSGKSTVAKIIAKDFGFTYLDTG   48 (236)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCceecCC
Confidence            45889999999999999999999999887754

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.54  E-value=0.0039  Score=55.48  Aligned_cols=20  Identities=30%  Similarity=0.446  Sum_probs=17.5

Q ss_pred             CceeEEeCCCCCCHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAA  272 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~a  272 (473)
                      +.-+.|.||+|+|||||+++
T Consensus         9 gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHH
Confidence            44589999999999999994

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.54  E-value=0.00058  Score=62.54  Aligned_cols=30  Identities=20%  Similarity=0.242  Sum_probs=25.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      +.-|.|.|+||+||||+++.++..++.+.+
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~~~   39 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNNNV   39 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHTTC
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHcCC
Confidence            346899999999999999999998765433

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=96.51  E-value=0.014  Score=66.09  Aligned_cols=43  Identities=19%  Similarity=0.135  Sum_probs=30.8

Q ss_pred             ccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          222 AMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       222 ~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      +|.++..+.|.+.+.    ..        ...+-+.|+||+|.|||+||+.+++.
T Consensus       131 VGRe~eLeeL~elL~----~~--------d~~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALL----EL--------RPAKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CCCHHHHHHHHHHHH----HC--------CSSCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHh----cc--------CCCeEEEEEcCCCccHHHHHHHHHHh
Confidence            666666666655443    11        11467899999999999999999864

>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=96.51  E-value=0.0025  Score=58.87  Aligned_cols=29  Identities=24%  Similarity=0.336  Sum_probs=24.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |++...-+.|.||+|+|||+|++.|+..+
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            45556679999999999999999999854

>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=96.50  E-value=0.0013  Score=63.97  Aligned_cols=32  Identities=25%  Similarity=0.313  Sum_probs=26.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-CCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-NFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-~~~~~~l~  285 (473)
                      .-++|.||||+||||+++.++..+ ++.++..+
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i~~D   35 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNINRD   35 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEECHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEeccc
Confidence            468999999999999999999974 77666543

>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=96.48  E-value=0.0018  Score=61.46  Aligned_cols=29  Identities=24%  Similarity=0.186  Sum_probs=25.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      +.-+.|.||+|+|||++++.|+..+++++
T Consensus        22 ~~iI~I~G~~GSGKST~a~~L~~~lg~~~   50 (252)
T 1uj2_A           22 PFLIGVSGGTASGKSSVCAKIVQLLGQNE   50 (252)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTGGG
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHhhhhc
Confidence            34689999999999999999999999873

>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=96.48  E-value=0.016  Score=61.52  Aligned_cols=74  Identities=4%  Similarity=0.073  Sum_probs=48.4

Q ss_pred             ceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCC--CCCccccCCCcee
Q 012016          306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE--KLDPALLRPGRMD  383 (473)
Q Consensus       306 sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~--~ld~aLlrpgRfd  383 (473)
                      -+|||||+..++...              .......+..+...  |    ..-++-+|++|.+|.  .++..++.  -|.
T Consensus       345 ivvVIDE~~~L~~~~--------------~~~~~~~L~~Iar~--G----Ra~GIhLIlaTQRPs~d~I~~~Ira--n~~  402 (574)
T 2iut_A          345 IVVVVDEFADMMMIV--------------GKKVEELIARIAQK--A----RAAGIHLILATQRPSVDVITGLIKA--NIP  402 (574)
T ss_dssp             EEEEESCCTTHHHHT--------------CHHHHHHHHHHHHH--C----TTTTEEEEEEESCCCTTTSCHHHHH--TCC
T ss_pred             EEEEEeCHHHHhhhh--------------hHHHHHHHHHHHHH--H----hhCCeEEEEEecCcccccccHHHHh--hhc
Confidence            489999999876410              01112223333321  1    124588999999987  78877765  677


Q ss_pred             eEEEeCCCCHHHHHHHHH
Q 012016          384 VHVHMSYCTPSGFKLLAA  401 (473)
Q Consensus       384 ~~I~~~~p~~~~r~~l~~  401 (473)
                      ..|.|...+..+-..++.
T Consensus       403 ~RI~lrv~s~~Dsr~ILd  420 (574)
T 2iut_A          403 TRIAFQVSSKIDSRTILD  420 (574)
T ss_dssp             EEEEECCSCHHHHHHHHS
T ss_pred             cEEEEEcCCHHHHHHhcC
Confidence            888899988888776663

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.46  E-value=0.0018  Score=59.27  Aligned_cols=29  Identities=28%  Similarity=0.434  Sum_probs=25.3

Q ss_pred             CCCCceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          250 KAWKRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       250 ~~~~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .+.++-++|.||||+||||+++.|+..++
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            34566799999999999999999999885

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.45  E-value=0.0017  Score=64.57  Aligned_cols=36  Identities=28%  Similarity=0.443  Sum_probs=32.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +-++|.||+|+|||+|+..||..++..++..|.-.+
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~qv   76 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKMQV   76 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSSTT
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCcEEccccccc
Confidence            468999999999999999999999999988876654

>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=96.43  E-value=0.0051  Score=57.88  Aligned_cols=31  Identities=23%  Similarity=0.196  Sum_probs=26.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++++||+|+|||.++.+++..++.+++.+-
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~  140 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINELSTPTLIVV  140 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEE
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCEEEEe
Confidence            4899999999999999999988876665544

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.43  E-value=0.002  Score=57.88  Aligned_cols=26  Identities=15%  Similarity=0.386  Sum_probs=22.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ++-+.|.||+|+|||||++.|+..+.
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            34689999999999999999999764

>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=96.41  E-value=0.0021  Score=59.10  Aligned_cols=36  Identities=19%  Similarity=0.270  Sum_probs=29.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      .++++|.||+|+|||+|+.+++...+ .++..|.-.+
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~-~iIsdDs~~v   69 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH-RLIADDRVDV   69 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC-EEEESSEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC-eEEecchhhe
Confidence            46899999999999999999999877 6666554443

>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=96.41  E-value=0.013  Score=61.40  Aligned_cols=41  Identities=5%  Similarity=0.095  Sum_probs=32.5

Q ss_pred             ceEEEEecCCCC--CCCccccCCCceeeEEEeCCCCHHHHHHHHH
Q 012016          359 ERIIVFTTNHKE--KLDPALLRPGRMDVHVHMSYCTPSGFKLLAA  401 (473)
Q Consensus       359 ~~iiI~tTN~~~--~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~  401 (473)
                      ++-+|++|.+|.  .++..++.  -|...|.|...+..+.+.++.
T Consensus       332 GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lrv~s~~dsr~ilg  374 (512)
T 2ius_A          332 GIHLVLATQRPSVDVITGLIKA--NIPTRIAFTVSSKIDSRTILD  374 (512)
T ss_dssp             TEEEEEEESCCCTTTSCHHHHH--HCCEEEEECCSSHHHHHHHHS
T ss_pred             CcEEEEEecCCccccccHHHHh--hcCCeEEEEcCCHHHHHHhcC
Confidence            478889999986  57776766  677888999999888887765

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.38  E-value=0.0053  Score=66.56  Aligned_cols=58  Identities=24%  Similarity=0.389  Sum_probs=36.2

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE  288 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~  288 (473)
                      ..|-+-.+++.+++.|...+.    .           +.-.|++||||||||+++..+...+   +..+..+..+.
T Consensus       183 ~~~~~~~LN~~Q~~AV~~al~----~-----------~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN  243 (646)
T 4b3f_X          183 LTFFNTCLDTSQKEAVLFALS----Q-----------KELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSN  243 (646)
T ss_dssp             CCCSSTTCCHHHHHHHHHHHH----C-----------SSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             ccccCCCCCHHHHHHHHHHhc----C-----------CCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCch
Confidence            344344567788877655432    1           1246999999999998766655544   55565555443

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.37  E-value=0.0022  Score=57.61  Aligned_cols=33  Identities=30%  Similarity=0.503  Sum_probs=26.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLE  285 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~  285 (473)
                      +.-++|.|+||+|||++++.+|..++   .++..++
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~   48 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLD   48 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEee
Confidence            45689999999999999999999874   4444443

>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=96.35  E-value=0.019  Score=56.02  Aligned_cols=59  Identities=15%  Similarity=0.279  Sum_probs=39.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----CCceEEccccccc----------------------CchHHHHHHHHhccCc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTELR----------------------SNSDLRTLLVATANRS  306 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~~~----------------------~~~~l~~l~~~~~~~s  306 (473)
                      +..++|.||+|+||||++..||..+    |..+..+++....                      ....++..+....++.
T Consensus       105 g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~r~~a~eqL~~~~~~~gl~~~~~~~~~~l~~al~~~~~~d  184 (296)
T 2px0_A          105 SKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRIAAVEQLKTYAELLQAPLEVCYTKEEFQQAKELFSEYD  184 (296)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCSSTTHHHHHHHHHTTTTCCCCBCSSHHHHHHHHHHGGGSS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcccchHHHHHHHHHHhcCCCeEecCCHHHHHHHHHHhcCCC
Confidence            4578999999999999999999765    4455554433211                      1123444444456678


Q ss_pred             eEEEe
Q 012016          307 ILVVE  311 (473)
Q Consensus       307 IL~iD  311 (473)
                      +|+||
T Consensus       185 lvIiD  189 (296)
T 2px0_A          185 HVFVD  189 (296)
T ss_dssp             EEEEE
T ss_pred             EEEEe
Confidence            88888

>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=96.34  E-value=0.0026  Score=62.44  Aligned_cols=34  Identities=21%  Similarity=0.501  Sum_probs=29.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ++-++|.||+|+|||+|+..+|..++..++..|.
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            4568999999999999999999999877776654

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.34  E-value=0.0082  Score=62.16  Aligned_cols=37  Identities=19%  Similarity=0.236  Sum_probs=29.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLE  285 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~  285 (473)
                      |.++..-++|.||||+|||+|+..+|..+    |.++..++
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s  239 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFS  239 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEE
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEE
Confidence            56666679999999999999999888754    55666554

>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=96.34  E-value=0.0024  Score=57.46  Aligned_cols=25  Identities=36%  Similarity=0.595  Sum_probs=22.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      -+.|.||+|+||||+++.|+..++.
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~~g   28 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQLDN   28 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSS
T ss_pred             EEEEECCCCCcHHHHHHHHhcccCC
Confidence            5789999999999999999987654

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.33  E-value=0.0058  Score=55.77  Aligned_cols=35  Identities=17%  Similarity=0.262  Sum_probs=27.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      +.-+.|.||+|+|||++++.++..+   +.+++.++..
T Consensus        22 ~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d   59 (201)
T 1rz3_A           22 RLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMD   59 (201)
T ss_dssp             SEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccC
Confidence            3458899999999999999999976   6666655433

>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=96.32  E-value=0.012  Score=50.53  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=20.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+++.|++|+|||+|+.++.+..
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            58999999999999999998753

>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=96.30  E-value=0.001  Score=60.88  Aligned_cols=27  Identities=22%  Similarity=0.133  Sum_probs=23.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      +.-|+|.|+||+||||+++.++..++.
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            346899999999999999999998743

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.28  E-value=0.0024  Score=57.98  Aligned_cols=25  Identities=24%  Similarity=0.305  Sum_probs=22.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +.-+.|.||+|+||||+++.|+..+
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            4568999999999999999999987

>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=96.28  E-value=0.0054  Score=63.29  Aligned_cols=95  Identities=16%  Similarity=0.262  Sum_probs=64.4

Q ss_pred             HHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC------CCCceEEEEec---
Q 012016          296 RTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS------CGDERIIVFTT---  366 (473)
Q Consensus       296 ~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~------~~~~~iiI~tT---  366 (473)
                      ++.+..+.+.+||++||||.+....+.         .+.+....-....||..||+-..+      ...++++|+|.   
T Consensus       242 ~~ai~~ae~~~il~~DEidki~~~~~~---------~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~  312 (444)
T 1g41_A          242 QKAIDAVEQNGIVFIDEIDKICKKGEY---------SGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQ  312 (444)
T ss_dssp             HHHHHHHHHHCEEEEETGGGGSCCSSC---------SSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCS
T ss_pred             HHHHHHhccCCeeeHHHHHHHhhccCC---------CCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccc
Confidence            344445557889999999999641110         011222233556899999973211      12468888886   


Q ss_pred             -CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHH
Q 012016          367 -NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAA  401 (473)
Q Consensus       367 -N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~  401 (473)
                       +.+.++-|.|+.  ||+.+|+|+.++.+++..|+.
T Consensus       313 ~~~~~dlipel~~--R~~i~i~l~~lt~~e~~~Il~  346 (444)
T 1g41_A          313 VARPSDLIPELQG--RLPIRVELTALSAADFERILT  346 (444)
T ss_dssp             SCCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHH
T ss_pred             cCChhhcchHHhc--ccceeeeCCCCCHHHHHHHHH
Confidence             344556688887  999999999999999999884

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.25  E-value=0.0051  Score=56.27  Aligned_cols=63  Identities=13%  Similarity=0.249  Sum_probs=40.4

Q ss_pred             ceeEEeCCCCCCHH-HHHHHHHHhc--CCceEEcccc-------cccC----------chHHHHHHHHhccCceEEEecc
Q 012016          254 RGYLLYGPPGTGKS-SLIAAMANYL--NFDVYDLELT-------ELRS----------NSDLRTLLVATANRSILVVEDI  313 (473)
Q Consensus       254 rg~LL~GPpGtGKT-~la~alA~~l--~~~~~~l~~~-------~~~~----------~~~l~~l~~~~~~~sIL~iDdi  313 (473)
                      .-+++|||.|+||| .|++++.++.  +..++.+...       .+.+          ...+.+++....+-.+|+|||+
T Consensus        21 ~l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlIDEa  100 (195)
T 1w4r_A           21 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEG  100 (195)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEESSG
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccccCccchhhhhhccCCcccceecCCHHHHHHhccCCCEEEEEch
Confidence            35899999999999 8999999876  5566655422       0100          0111122222334579999999


Q ss_pred             ccc
Q 012016          314 DCT  316 (473)
Q Consensus       314 D~l  316 (473)
                      .-+
T Consensus       101 QFf  103 (195)
T 1w4r_A          101 QFF  103 (195)
T ss_dssp             GGC
T ss_pred             hhh
Confidence            876

>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=96.25  E-value=0.0061  Score=62.80  Aligned_cols=34  Identities=26%  Similarity=0.412  Sum_probs=27.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      ++.+++.||||+||||++..||..+   |..+..+++
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~  135 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAA  135 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEec
Confidence            4579999999999999999999987   355554443

>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=96.24  E-value=0.022  Score=52.25  Aligned_cols=57  Identities=12%  Similarity=0.127  Sum_probs=32.1

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhc---CCCCceeEEeCCCCCCHHHH-HHHHHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVG---KAWKRGYLLYGPPGTGKSSL-IAAMAN  275 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g---~~~~rg~LL~GPpGtGKT~l-a~alA~  275 (473)
                      .+|+++...+...+.+.+.-   +..+..++...   .--.+.+++.+|+|+|||.. +-.+..
T Consensus        14 ~~f~~l~l~~~l~~~l~~~g---~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~   74 (224)
T 1qde_A           14 YKFDDMELDENLLRGVFGYG---FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ   74 (224)
T ss_dssp             CCGGGGTCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CChhhcCCCHHHHHHHHHCC---CCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHH
Confidence            57888888777666554320   11111111110   01135799999999999986 334443

>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=96.23  E-value=0.0072  Score=52.38  Aligned_cols=24  Identities=29%  Similarity=0.331  Sum_probs=21.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+++.|++|+|||+|+.++.+.-
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            368999999999999999998754

>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=96.21  E-value=0.0024  Score=61.93  Aligned_cols=31  Identities=29%  Similarity=0.297  Sum_probs=27.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .-+.|.|++|+||||+++.++ .+|+++++.+
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~lg~~~id~D  106 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NLGAYIIDSD  106 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HHTCEEEEHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HCCCcEEehh
Confidence            458999999999999999999 6898887765

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=96.21  E-value=0.0027  Score=63.22  Aligned_cols=33  Identities=21%  Similarity=0.299  Sum_probs=28.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .-++|.||+|+|||+++..||..++..++..|.
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            468999999999999999999999877666553

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=96.21  E-value=0.0026  Score=58.51  Aligned_cols=30  Identities=17%  Similarity=0.161  Sum_probs=28.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      .-|.|.||+|||||++++.+|..||+++++
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            368999999999999999999999999996

>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=96.20  E-value=0.0029  Score=58.23  Aligned_cols=27  Identities=26%  Similarity=0.297  Sum_probs=23.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      +.-+.|.||+|+|||++++.|+..+..
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            456899999999999999999998753

>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=96.19  E-value=0.017  Score=49.70  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
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            46899999999999999999864

>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=96.17  E-value=0.0032  Score=57.92  Aligned_cols=34  Identities=26%  Similarity=0.338  Sum_probs=27.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC----CceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN----FDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~----~~~~~l~~  286 (473)
                      +.-++|.|+||+||||+++.|+..++    .+++.++.
T Consensus        25 ~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~~   62 (211)
T 1m7g_A           25 GLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDG   62 (211)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEECC
Confidence            45689999999999999999999875    44555553

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=96.16  E-value=0.013  Score=51.65  Aligned_cols=24  Identities=25%  Similarity=0.380  Sum_probs=21.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            358999999999999999998753

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.15  E-value=0.0045  Score=56.83  Aligned_cols=26  Identities=38%  Similarity=0.584  Sum_probs=23.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.-+.|.||+|+|||||+++|+..+.
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            44588999999999999999999885

>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=96.14  E-value=0.0085  Score=51.82  Aligned_cols=23  Identities=26%  Similarity=0.394  Sum_probs=20.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+++.|++|+|||+|+.++.+.-
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999999998643

>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=96.12  E-value=0.017  Score=49.82  Aligned_cols=22  Identities=27%  Similarity=0.445  Sum_probs=20.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+.++.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999874

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=96.09  E-value=0.021  Score=50.16  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhhC
Confidence            46999999999999999999864

>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=96.08  E-value=0.018  Score=52.60  Aligned_cols=25  Identities=24%  Similarity=0.511  Sum_probs=22.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...++|.|++|+|||+|+.++++..
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            3579999999999999999999865

>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=96.07  E-value=0.0042  Score=61.11  Aligned_cols=34  Identities=24%  Similarity=0.281  Sum_probs=28.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT  287 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~  287 (473)
                      +-++|.||+|+|||+|+..+|..++..++..|.-
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds~   37 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNGEVISGDSM   37 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTEEEEECCGG
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCccceeecCcc
Confidence            3578999999999999999999998766655543

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=96.04  E-value=0.0041  Score=56.42  Aligned_cols=26  Identities=31%  Similarity=0.611  Sum_probs=22.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.-+.|.||+|+||||+++.|+..+.
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~~~~   32 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVKALA   32 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHSS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            34588999999999999999999864

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=96.00  E-value=0.025  Score=50.75  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        15 ~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           15 HKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999999864

>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=95.98  E-value=0.021  Score=51.64  Aligned_cols=23  Identities=22%  Similarity=0.271  Sum_probs=17.5

Q ss_pred             ceeEEeCCCCCCHHHH-HHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSL-IAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~l-a~alA~~  276 (473)
                      +.+++.+|+|+|||.. +..+...
T Consensus        39 ~~~li~~~TGsGKT~~~~~~~~~~   62 (207)
T 2gxq_A           39 KDLIGQARTGTGKTLAFALPIAER   62 (207)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHHHH
Confidence            5799999999999986 3344443

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.96  E-value=0.0035  Score=57.39  Aligned_cols=32  Identities=22%  Similarity=0.300  Sum_probs=26.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC--CceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN--FDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~--~~~~~l~  285 (473)
                      .-+.|.||+|+|||||++.|+..++  ..++..+
T Consensus         7 ~~i~i~G~~GsGKSTl~~~l~~~~~~~i~~v~~d   40 (211)
T 3asz_A            7 FVIGIAGGTASGKTTLAQALARTLGERVALLPMD   40 (211)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHGGGEEEEEGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCeEEEecC
Confidence            4588999999999999999999987  5555443

>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=95.96  E-value=0.012  Score=50.85  Aligned_cols=23  Identities=30%  Similarity=0.385  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
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            36899999999999999999863

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.95  E-value=0.0029  Score=59.55  Aligned_cols=30  Identities=20%  Similarity=0.388  Sum_probs=26.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -+-|.||||+|||++++.|+..++++.+..
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            366899999999999999999999888755

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=95.93  E-value=0.014  Score=51.16  Aligned_cols=23  Identities=35%  Similarity=0.502  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        13 ~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           13 AKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46899999999999999999864

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.91  E-value=0.0041  Score=56.81  Aligned_cols=26  Identities=35%  Similarity=0.566  Sum_probs=22.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ++-+.|.||+|+|||||++.|+..+.
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            45789999999999999999998763

>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=95.90  E-value=0.023  Score=59.93  Aligned_cols=29  Identities=28%  Similarity=0.305  Sum_probs=24.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |++...-++|.||||+|||+|++.++..+
T Consensus       277 ~i~~G~i~~i~G~~GsGKSTLl~~l~g~~  305 (525)
T 1tf7_A          277 GFFKDSIILATGATGTGKTLLVSRFVENA  305 (525)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            45556679999999999999999999765

>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=95.90  E-value=0.0064  Score=55.25  Aligned_cols=25  Identities=36%  Similarity=0.599  Sum_probs=22.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      |-++|.||+|+|||+|++.|.....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            4589999999999999999988764

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=95.88  E-value=0.0091  Score=51.65  Aligned_cols=21  Identities=43%  Similarity=0.703  Sum_probs=19.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      .+++.|++|+|||+|+.++.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            589999999999999999865

>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=95.86  E-value=0.027  Score=50.49  Aligned_cols=24  Identities=25%  Similarity=0.499  Sum_probs=21.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ...+++.|++|+|||+|+..+.+.
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346999999999999999999875

>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=95.84  E-value=0.014  Score=52.89  Aligned_cols=23  Identities=22%  Similarity=0.462  Sum_probs=19.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      +.+++.+|+|+|||.++..++..
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~   71 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKD   71 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHH
Confidence            57999999999999988777664

>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=95.83  E-value=0.05  Score=46.68  Aligned_cols=22  Identities=18%  Similarity=0.303  Sum_probs=19.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+.++.+.
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            3789999999999999999763

>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=95.82  E-value=0.0076  Score=62.03  Aligned_cols=61  Identities=13%  Similarity=0.147  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       225 ~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      +.+.+.+.+.+...+.....-.......++-+++.||+|+||||++..||..+   |..+..++
T Consensus        69 ~~v~~~v~~eL~~~L~~~~~~~~~~~~~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~  132 (433)
T 3kl4_A           69 EWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVA  132 (433)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCCCCSCCSSSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             HHHHHHHHHHHHHhcCccccccccccCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEe
Confidence            33455555556655543110000011235678999999999999999999877   55555444

>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=95.81  E-value=0.028  Score=51.49  Aligned_cols=58  Identities=14%  Similarity=0.161  Sum_probs=32.1

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCC---CCceeEEeCCCCCCHHHHHHHHH
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA---WKRGYLLYGPPGTGKSSLIAAMA  274 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~---~~rg~LL~GPpGtGKT~la~alA  274 (473)
                      +..+|+++...+.+.+.+.+.-   +..+..++....+   -.+.+++.+|+|+|||..+...+
T Consensus        12 ~~~~f~~~~l~~~l~~~l~~~g---~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~   72 (220)
T 1t6n_A           12 HSSGFRDFLLKPELLRAIVDCG---FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLAT   72 (220)
T ss_dssp             --CCSTTSCCCHHHHHHHHHTT---CCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHH
T ss_pred             cCCCHhhcCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHH
Confidence            3356888887777766654310   1111111111110   13579999999999998655443

>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=95.80  E-value=0.0067  Score=53.56  Aligned_cols=27  Identities=26%  Similarity=0.263  Sum_probs=23.6

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +...-+.|.||.|+|||+|+++|+..+
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            334458999999999999999999988

>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=95.80  E-value=0.015  Score=50.64  Aligned_cols=23  Identities=39%  Similarity=0.593  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|+||+|||+|+.++.+.
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            36899999999999999999864

>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=95.79  E-value=0.014  Score=52.14  Aligned_cols=23  Identities=26%  Similarity=0.485  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
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            46899999999999999999874

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=95.79  E-value=0.014  Score=52.02  Aligned_cols=24  Identities=38%  Similarity=0.488  Sum_probs=21.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            469999999999999999998743

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=95.77  E-value=0.021  Score=50.73  Aligned_cols=23  Identities=35%  Similarity=0.522  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            36999999999999999999875

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.77  E-value=0.008  Score=58.90  Aligned_cols=53  Identities=17%  Similarity=0.249  Sum_probs=33.7

Q ss_pred             hHHHHHHHHHHHHHHhchhHHhhhc--CCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          225 QEQKTKIMQDLERFVKRKDYYRRVG--KAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       225 ~~~k~~l~~~l~~fl~~~~~y~~~g--~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +.+++.+.+.+...+........+.  ...+.-+.|.||+|+||||+++.||..+
T Consensus        70 ~~~~~~~~~~l~~~l~~~~~~~~l~~~~~~g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A           70 SEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             HHHHHHHHHHHHHHHCC--CCCSCCCCSSSCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcccccccccccCCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3455566666665554221001111  2334568999999999999999999987

>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=95.76  E-value=0.0058  Score=59.96  Aligned_cols=33  Identities=36%  Similarity=0.539  Sum_probs=27.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      .++++..+.|.||+|+|||||+++|+..+.-.+
T Consensus       122 ~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~~G~I  154 (305)
T 2v9p_A          122 GIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSV  154 (305)
T ss_dssp             TCTTCSEEEEECSSSSSHHHHHHHHHHHHTCEE
T ss_pred             EecCCCEEEEECCCCCcHHHHHHHHhhhcCceE
Confidence            456667799999999999999999999884333

>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=95.75  E-value=0.0083  Score=54.22  Aligned_cols=33  Identities=21%  Similarity=0.254  Sum_probs=28.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +|++|++|+|||++|..+|.. +.+++++.....
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            689999999999999999988 888888776553

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=95.74  E-value=0.0094  Score=45.86  Aligned_cols=46  Identities=7%  Similarity=-0.195  Sum_probs=33.5

Q ss_pred             CCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          389 SYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       389 ~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      |.|+.++|.+||+.++.........++..++..+ ++|+|||..+|.
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~   47 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCT   47 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHH
Confidence            6899999999999999865332223444555433 699999988773

>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=95.74  E-value=0.015  Score=65.40  Aligned_cols=24  Identities=38%  Similarity=0.419  Sum_probs=20.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHH
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ...-+.|.||.|+||||+++.+|.
T Consensus       672 ~g~i~~ItGPNGaGKSTlLr~i~~  695 (918)
T 3thx_B          672 SERVMIITGPNMGGKSSYIKQVAL  695 (918)
T ss_dssp             SCCEEEEESCCCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCchHHHHHHHHH
Confidence            345689999999999999999874

>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=95.74  E-value=0.02  Score=49.97  Aligned_cols=24  Identities=29%  Similarity=0.491  Sum_probs=21.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            469999999999999999998754

>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=95.71  E-value=0.0073  Score=64.94  Aligned_cols=35  Identities=29%  Similarity=0.464  Sum_probs=30.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      +.-|+|.|+||+||||++++|+..|   |.+++.++..
T Consensus        52 g~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lDgD   89 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLDGD   89 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEESHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEechH
Confidence            4568999999999999999999999   9999888643

>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=95.71  E-value=0.016  Score=51.46  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=20.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+++.|++|+|||+|+.++++..
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            58999999999999999998753

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=95.70  E-value=0.021  Score=50.27  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=21.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|+.++.+..
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCC
Confidence            468999999999999999998653

>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=95.66  E-value=0.035  Score=62.43  Aligned_cols=23  Identities=26%  Similarity=0.280  Sum_probs=20.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ..-++|.||.|+|||++++.+|.
T Consensus       662 g~i~~ItGpNGsGKSTlLr~ial  684 (934)
T 3thx_A          662 QMFHIITGPNMGGKSTYIRQTGV  684 (934)
T ss_dssp             BCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            45689999999999999999853

>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=95.66  E-value=0.023  Score=50.24  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
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            46899999999999999999863

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.65  E-value=0.0067  Score=56.26  Aligned_cols=25  Identities=32%  Similarity=0.579  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +.-+.|.||+|+|||||++.|+..+
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4468999999999999999999977

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=95.64  E-value=0.041  Score=48.74  Aligned_cols=24  Identities=21%  Similarity=0.332  Sum_probs=21.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|++.+.+..
T Consensus        15 ~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           15 FKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhc
Confidence            368999999999999999988754

>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=95.63  E-value=0.0073  Score=55.34  Aligned_cols=26  Identities=27%  Similarity=0.510  Sum_probs=23.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||+|+|||||+++|+..+.
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            44588999999999999999999874

>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=95.62  E-value=0.0076  Score=55.29  Aligned_cols=26  Identities=23%  Similarity=0.441  Sum_probs=22.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ++-+.|.||+|+|||+|+++|+....
T Consensus        19 g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           19 RKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            34588999999999999999998864

>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=95.61  E-value=0.0063  Score=61.87  Aligned_cols=34  Identities=29%  Similarity=0.409  Sum_probs=28.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      +.-++|.||+|+|||+|+..||..++..++..|.
T Consensus         2 ~~~i~i~GptgsGKttla~~La~~~~~~iis~Ds   35 (409)
T 3eph_A            2 KKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSDS   35 (409)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHHHHTEEEEECCT
T ss_pred             CcEEEEECcchhhHHHHHHHHHHHCCCeEeecCc
Confidence            3468899999999999999999999876665543

>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=95.55  E-value=0.039  Score=51.41  Aligned_cols=24  Identities=25%  Similarity=0.279  Sum_probs=21.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..++|.|++|+|||+|+.++.+..
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHcCCC
Confidence            469999999999999999998754

>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=95.55  E-value=0.0081  Score=55.99  Aligned_cols=29  Identities=38%  Similarity=0.474  Sum_probs=24.1

Q ss_pred             CCCCceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          250 KAWKRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       250 ~~~~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .+...-+.|.||+|+|||||+++|+..+.
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            34456689999999999999999999875

>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=95.52  E-value=0.037  Score=61.36  Aligned_cols=24  Identities=29%  Similarity=0.412  Sum_probs=21.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..-+.|.||.|+|||++++.+|..
T Consensus       607 g~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          607 RRMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHHH
Confidence            456899999999999999999874

>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=95.52  E-value=0.012  Score=61.50  Aligned_cols=25  Identities=28%  Similarity=0.398  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +.-+.|.||+|+|||||++.||..+
T Consensus       293 GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          293 PFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCcccHHHHHHHHHHHh
Confidence            4458899999999999999999987

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=95.51  E-value=0.0069  Score=56.69  Aligned_cols=32  Identities=19%  Similarity=0.162  Sum_probs=28.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .-+.+.|++|||||++++.+|..+|+++++-+
T Consensus        15 ~iI~i~g~~gsGk~~i~~~la~~lg~~~~d~~   46 (223)
T 3hdt_A           15 LIITIEREYGSGGRIVGKKLAEELGIHFYDDD   46 (223)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTCEEECHH
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHcCCcEEcHH
Confidence            36889999999999999999999999998743

>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=95.51  E-value=0.027  Score=52.16  Aligned_cols=53  Identities=21%  Similarity=0.312  Sum_probs=29.3

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcC---CCCceeEEeCCCCCCHHHH
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGK---AWKRGYLLYGPPGTGKSSL  269 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~---~~~rg~LL~GPpGtGKT~l  269 (473)
                      +..+|+++...+.+.+.+.+.  .| ..+..++....   .-.+.+++.+|.|+|||..
T Consensus        22 ~~~~f~~l~l~~~l~~~l~~~--g~-~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~   77 (230)
T 2oxc_A           22 EPADFESLLLSRPVLEGLRAA--GF-ERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCV   77 (230)
T ss_dssp             --CCGGGGTCCHHHHHHHHHT--TC-CSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             CCCCHhhcCCCHHHHHHHHHC--CC-CCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHH
Confidence            346788887777666655331  01 11111111111   1135799999999999976

>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=95.50  E-value=0.025  Score=48.92  Aligned_cols=21  Identities=33%  Similarity=0.586  Sum_probs=19.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      .+++.|++|+|||+|+.++.+
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

>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=95.48  E-value=0.017  Score=51.66  Aligned_cols=23  Identities=26%  Similarity=0.395  Sum_probs=20.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++|.|++|+|||+|+..+.+.-
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            58999999999999999998754

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=95.48  E-value=0.017  Score=49.86  Aligned_cols=22  Identities=32%  Similarity=0.508  Sum_probs=20.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+.++.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.47  E-value=0.011  Score=59.34  Aligned_cols=52  Identities=17%  Similarity=0.252  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHHHhchhHHhhhc--CCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          226 EQKTKIMQDLERFVKRKDYYRRVG--KAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       226 ~~k~~l~~~l~~fl~~~~~y~~~g--~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+++.+.+.+...+........+.  ...+.-+.|.||.|+||||+++.||..+
T Consensus       128 ~~~~~l~~~l~~~l~~~~~~~~l~l~~~~g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          128 EIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             HHHHHHHHHHHHHHCCC---CSCCCCSSSSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCcccCCCcceecCCCeEEEEEcCCCChHHHHHHHHHhhc
Confidence            345555555555553221001121  2334568999999999999999999987

>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=95.47  E-value=0.013  Score=57.49  Aligned_cols=59  Identities=14%  Similarity=0.072  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          227 QKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       227 ~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +++.+.+.+...+...... ......+.-+++.||+|+||||++..||..+   +..+..+++
T Consensus        79 ~~~~~~~~l~~~l~~~~~~-~~~~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~  140 (306)
T 1vma_A           79 ALESLKEIILEILNFDTKL-NVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA  140 (306)
T ss_dssp             HHHHHHHHHHHHTCSCCCC-CCCSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHHHHHhCCCCCC-cccCCCCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEcc
Confidence            4455555555555322100 1112234568999999999999999999877   445554443

>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=95.47  E-value=0.0071  Score=58.57  Aligned_cols=29  Identities=21%  Similarity=0.216  Sum_probs=25.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.+...-++|.||||+|||+|+..+|..+
T Consensus        31 ~l~~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           31 GARGGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             SBCTTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            45556679999999999999999999875

>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=95.40  E-value=0.01  Score=55.51  Aligned_cols=30  Identities=30%  Similarity=0.464  Sum_probs=25.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC--CceEE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN--FDVYD  283 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~--~~~~~  283 (473)
                      .-+.|.||||+||||+++.|++.++  .+++.
T Consensus        27 ~~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~   58 (229)
T 4eaq_A           27 AFITFEGPEGSGKTTVINEVYHRLVKDYDVIM   58 (229)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHTTTSCEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhcCCCcee
Confidence            3588999999999999999999986  45543

>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=95.38  E-value=0.032  Score=48.64  Aligned_cols=23  Identities=26%  Similarity=0.394  Sum_probs=20.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        10 ~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           10 HKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999999875

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.35  E-value=0.011  Score=56.67  Aligned_cols=25  Identities=44%  Similarity=0.731  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-++|.||+|+||||++++|+..+
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHHhC
Confidence            4468999999999999999999876

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.35  E-value=0.013  Score=57.52  Aligned_cols=38  Identities=21%  Similarity=0.190  Sum_probs=29.8

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      |.++..-++|.|+||+|||+++..+|...   +.++..+++
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            56667779999999999999999888654   456665553

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=95.32  E-value=0.037  Score=49.15  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=21.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         8 ~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            8 YKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999999976

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=95.30  E-value=0.05  Score=48.71  Aligned_cols=23  Identities=17%  Similarity=0.345  Sum_probs=20.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ...+++.|++|+|||+|+..+..
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            34699999999999999999964

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.30  E-value=0.017  Score=56.94  Aligned_cols=36  Identities=33%  Similarity=0.491  Sum_probs=28.3

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      .++-+++.||+|+|||+++..||..+   +..+..+++.
T Consensus       104 ~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D  142 (320)
T 1zu4_A          104 RLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAAD  142 (320)
T ss_dssp             SCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            35568999999999999999999877   5556555543

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=95.28  E-value=0.035  Score=49.38  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=20.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+.++.+.
T Consensus        24 ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999864

>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=95.21  E-value=0.052  Score=63.56  Aligned_cols=27  Identities=30%  Similarity=0.487  Sum_probs=23.7

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++..-+.|.||+|+|||||+++|.+++
T Consensus       442 ~~G~~vaivG~sGsGKSTll~ll~~~~  468 (1321)
T 4f4c_A          442 NAGQTVALVGSSGCGKSTIISLLLRYY  468 (1321)
T ss_dssp             CTTCEEEEEECSSSCHHHHHHHHTTSS
T ss_pred             cCCcEEEEEecCCCcHHHHHHHhcccc
Confidence            445568999999999999999999987

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=95.20  E-value=0.028  Score=50.49  Aligned_cols=24  Identities=25%  Similarity=0.314  Sum_probs=21.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~~   32 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADDS   32 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTCC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcCC
Confidence            468999999999999999998643

>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=95.20  E-value=0.016  Score=56.47  Aligned_cols=27  Identities=30%  Similarity=0.253  Sum_probs=23.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      +.-+.|.||+|+||||+++.|+..++.
T Consensus        31 ~~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           31 PLFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            446889999999999999999998853

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=95.17  E-value=0.035  Score=49.28  Aligned_cols=23  Identities=17%  Similarity=0.225  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        21 ~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           21 FKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            36999999999999999999853

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=95.16  E-value=0.022  Score=50.99  Aligned_cols=24  Identities=29%  Similarity=0.396  Sum_probs=21.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus        24 ~ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           24 LKVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            368999999999999999998643

>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=95.15  E-value=0.059  Score=59.59  Aligned_cols=59  Identities=15%  Similarity=0.235  Sum_probs=32.4

Q ss_pred             CCccccccchHHHHHHHHHHHHHHh--chhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVK--RKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~--~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+|+++...+...+.+...-..+..  .......+  .....+++.||+|+|||+++..++..
T Consensus        72 ~~f~~~~l~~~~~~~l~~r~~lP~~~q~~~i~~~l--~~~~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A           72 NPFTGREFTPKYVDILKIRRELPVHAQRDEFLKLY--QNNQIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             CTTTCSBCCHHHHHHHHHHTTSGGGGGHHHHHHHH--HHCSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCccccCCCHHHHHHHHHhhcCChHHHHHHHHHHH--hCCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4688887776655544322111110  11111111  11346999999999999977766543

>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=95.14  E-value=0.012  Score=50.85  Aligned_cols=23  Identities=26%  Similarity=0.301  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            46899999999999999999875

>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=95.13  E-value=0.025  Score=57.87  Aligned_cols=50  Identities=28%  Similarity=0.383  Sum_probs=34.0

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.+++++....+.+.. +..+   +.          ....-+++.||+|+||||++++|++.+.
T Consensus       143 ~~~l~~Lg~~~~~~~~-L~~l---~~----------~~ggii~I~GpnGSGKTTlL~allg~l~  192 (418)
T 1p9r_A          143 RLDLHSLGMTAHNHDN-FRRL---IK----------RPHGIILVTGPTGSGKSTTLYAGLQELN  192 (418)
T ss_dssp             CCCGGGSCCCHHHHHH-HHHH---HT----------SSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             CCCHHHcCCCHHHHHH-HHHH---HH----------hcCCeEEEECCCCCCHHHHHHHHHhhcC
Confidence            3567888776654332 2222   11          1123479999999999999999999884

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=95.13  E-value=0.005  Score=59.95  Aligned_cols=36  Identities=14%  Similarity=0.223  Sum_probs=24.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELTEL  289 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~~~  289 (473)
                      .-+.|.||+|+||||+++.++..++   ..+..+++..+
T Consensus         6 ~iIgItG~sGSGKSTva~~L~~~lg~~~~~~~vI~~D~~   44 (290)
T 1a7j_A            6 PIISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAF   44 (290)
T ss_dssp             CEEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCCeeEeecchh
Confidence            3588999999999999999999876   33444444444

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.13  E-value=0.0093  Score=56.19  Aligned_cols=26  Identities=19%  Similarity=0.233  Sum_probs=23.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      -+-|.||+|+||||+++.|+..+|..
T Consensus        27 iigI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           27 LIGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhchh
Confidence            47899999999999999999988755

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.11  E-value=0.011  Score=53.82  Aligned_cols=23  Identities=43%  Similarity=0.780  Sum_probs=21.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+.|.||+|+|||||++.|+..+
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhc
Confidence            47899999999999999999976

>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=95.11  E-value=0.017  Score=50.46  Aligned_cols=23  Identities=26%  Similarity=0.349  Sum_probs=20.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
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            36899999999999999999864

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=95.11  E-value=0.01  Score=53.25  Aligned_cols=29  Identities=31%  Similarity=0.438  Sum_probs=24.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .+|+||.||+|+|||+++.++... |..++
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r-G~~lv   44 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR-GHQLV   44 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT-TCEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCeEe
Confidence            569999999999999999999884 44443

>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=95.11  E-value=0.0042  Score=56.77  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=21.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -+.|.||+|+||||+++.|+..++
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999999884

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=95.10  E-value=0.036  Score=50.05  Aligned_cols=23  Identities=17%  Similarity=0.294  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+..+.+.
T Consensus        30 ~ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           30 FKLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhhC
Confidence            35899999999999999999864

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=95.10  E-value=0.0085  Score=63.08  Aligned_cols=26  Identities=19%  Similarity=0.423  Sum_probs=23.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.++++.||+|+||||++++|++.+.
T Consensus       260 g~~i~I~GptGSGKTTlL~aL~~~i~  285 (511)
T 2oap_1          260 KFSAIVVGETASGKTTTLNAIMMFIP  285 (511)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            34799999999999999999999884

>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=95.09  E-value=0.017  Score=62.29  Aligned_cols=24  Identities=42%  Similarity=0.584  Sum_probs=20.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...++.||||||||+++..++..+
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            357999999999999888777654

>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=95.06  E-value=0.014  Score=52.40  Aligned_cols=26  Identities=23%  Similarity=0.218  Sum_probs=22.7

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...-+.|.||+|+|||+++..++..+
T Consensus         5 ~~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            5 MIPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            34578999999999999999999875

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.05  E-value=0.029  Score=55.42  Aligned_cols=25  Identities=20%  Similarity=0.159  Sum_probs=22.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .-+-|.||+|+||||+++.|+..++
T Consensus        93 ~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           93 YIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhc
Confidence            3588999999999999999999875

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=95.04  E-value=0.021  Score=51.42  Aligned_cols=24  Identities=25%  Similarity=0.268  Sum_probs=21.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..++|.|++|+|||+|+.++.+.-
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCcCHHHHHHHHHhCC
Confidence            468999999999999999999753

>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=95.03  E-value=0.026  Score=55.84  Aligned_cols=27  Identities=33%  Similarity=0.475  Sum_probs=23.6

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +.+.-+.|.||+|+||||+++.||..+
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            345568999999999999999999987

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=95.01  E-value=0.016  Score=53.62  Aligned_cols=31  Identities=26%  Similarity=0.337  Sum_probs=28.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      .+-|.|..|||||++++.++. +|+++++.|.
T Consensus        11 ~iglTGgigsGKStv~~~l~~-~g~~vidaD~   41 (210)
T 4i1u_A           11 AIGLTGGIGSGKTTVADLFAA-RGASLVDTDL   41 (210)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-TTCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcEEECcH
Confidence            578999999999999999998 9999999885

>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=95.01  E-value=0.086  Score=47.90  Aligned_cols=63  Identities=13%  Similarity=0.174  Sum_probs=38.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc--------cccC----------chHHHHHHHHhcc-CceEEEe
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT--------ELRS----------NSDLRTLLVATAN-RSILVVE  311 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~--------~~~~----------~~~l~~l~~~~~~-~sIL~iD  311 (473)
                      +-++++||+|+|||+.+..+++.+   +..++.+...        .+.+          -....+++..... ..+|+||
T Consensus         9 ~i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~~~~~dvViID   88 (191)
T 1xx6_A            9 WVEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAID   88 (191)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEEEC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHHhccCCEEEEE
Confidence            357899999999999888777765   5555544211        0000          0111244444433 5799999


Q ss_pred             ccccc
Q 012016          312 DIDCT  316 (473)
Q Consensus       312 diD~l  316 (473)
                      |+..+
T Consensus        89 Eaqfl   93 (191)
T 1xx6_A           89 EVQFF   93 (191)
T ss_dssp             SGGGS
T ss_pred             CCCCC
Confidence            99765

>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=95.01  E-value=0.015  Score=58.62  Aligned_cols=27  Identities=41%  Similarity=0.626  Sum_probs=23.4

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+...++|.||+|+||||++++|++.+
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~  160 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYI  160 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            334568999999999999999999876

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.94  E-value=0.027  Score=50.15  Aligned_cols=26  Identities=23%  Similarity=0.544  Sum_probs=22.6

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ....+++.|++|+|||+|+.++++.-
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            34579999999999999999998754

>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=94.94  E-value=0.014  Score=61.56  Aligned_cols=26  Identities=27%  Similarity=0.511  Sum_probs=23.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.-|+|.|+||+|||++++.||.+++
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~~L~   60 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTRYLN   60 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            44689999999999999999999984

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=94.93  E-value=0.026  Score=50.26  Aligned_cols=24  Identities=21%  Similarity=0.265  Sum_probs=21.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            359999999999999999998654

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=94.91  E-value=0.12  Score=45.65  Aligned_cols=24  Identities=29%  Similarity=0.452  Sum_probs=21.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ...+++.|++|+|||+|+.++.+.
T Consensus        16 ~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           16 EVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            346999999999999999999865

>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=94.91  E-value=0.062  Score=59.19  Aligned_cols=24  Identities=29%  Similarity=0.368  Sum_probs=21.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ...+.|.||.|+|||++++.+|..
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            356899999999999999999874

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=94.90  E-value=0.028  Score=49.02  Aligned_cols=23  Identities=26%  Similarity=0.377  Sum_probs=20.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         7 ~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            7 LKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEEEECcCCCCHHHHHHHHHhC
Confidence            36899999999999999999854

>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=94.88  E-value=0.09  Score=51.45  Aligned_cols=22  Identities=18%  Similarity=0.170  Sum_probs=17.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      +.+++.+|+|+|||..+...+-
T Consensus        45 ~~~l~~~~TGsGKT~~~~~~~~   66 (367)
T 1hv8_A           45 YNIVAQARTGSGKTASFAIPLI   66 (367)
T ss_dssp             SEEEEECCSSSSHHHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHHHHHH
Confidence            5899999999999987654443

>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=94.88  E-value=0.025  Score=48.82  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
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            35899999999999999999864

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=94.87  E-value=0.035  Score=49.85  Aligned_cols=24  Identities=25%  Similarity=0.372  Sum_probs=21.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ...+++.|++|+|||+|+.++.+.
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhC
Confidence            346999999999999999999864

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=94.87  E-value=0.02  Score=50.51  Aligned_cols=24  Identities=33%  Similarity=0.506  Sum_probs=21.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus        11 ~ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           11 FKFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999998643

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.84  E-value=0.0088  Score=55.68  Aligned_cols=25  Identities=20%  Similarity=0.301  Sum_probs=16.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHH-Hhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMA-NYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA-~~l  277 (473)
                      +.-+.|.||+|+||||+++.|+ ..+
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3458899999999999999999 775

>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=94.83  E-value=0.26  Score=47.68  Aligned_cols=52  Identities=15%  Similarity=0.184  Sum_probs=30.7

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhch-----hHHhhhcCCCCceeEEeCCCCCCHHHH
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRK-----DYYRRVGKAWKRGYLLYGPPGTGKSSL  269 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~-----~~y~~~g~~~~rg~LL~GPpGtGKT~l  269 (473)
                      ..+|+++...+.+.+.+...  . +..+     ..+..+-...++.+++++|.|||||..
T Consensus        91 ~~~f~~l~l~~~l~~~l~~~--g-~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a  147 (300)
T 3fmo_B           91 VKSFEELRLKPQLLQGVYAM--G-FNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAA  147 (300)
T ss_dssp             CCCSGGGTCCHHHHHHHHHT--T-CCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHH
T ss_pred             cCCHhhcCCCHHHHHHHHHc--C-CCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHH
Confidence            35789998887766655331  0 0111     111111111247899999999999975

>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=94.79  E-value=0.019  Score=50.10  Aligned_cols=23  Identities=35%  Similarity=0.452  Sum_probs=20.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
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            36899999999999999999864

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.73  E-value=0.077  Score=46.93  Aligned_cols=23  Identities=13%  Similarity=0.367  Sum_probs=20.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ...+++.|++|+|||+|+.++.+
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            45799999999999999999985

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=94.73  E-value=0.029  Score=50.04  Aligned_cols=22  Identities=32%  Similarity=0.667  Sum_probs=20.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+.++.+.
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999999864

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=94.71  E-value=0.036  Score=49.39  Aligned_cols=23  Identities=30%  Similarity=0.504  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCcHHHHHHHHHcC
Confidence            46899999999999999999873

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=94.69  E-value=0.036  Score=49.59  Aligned_cols=22  Identities=27%  Similarity=0.554  Sum_probs=19.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+.++.+.
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999753

>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=94.69  E-value=0.02  Score=56.06  Aligned_cols=25  Identities=36%  Similarity=0.578  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +.-+.|.||+|+||||+++.||..+
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            4568899999999999999999887

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=94.64  E-value=0.045  Score=50.66  Aligned_cols=22  Identities=27%  Similarity=0.413  Sum_probs=19.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|.+|+|||+|+..+...
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4899999999999999988753

>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=94.62  E-value=0.068  Score=48.53  Aligned_cols=23  Identities=22%  Similarity=0.410  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..++|.|++|+|||+|+.++.+.
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            36899999999999999999864

>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=94.61  E-value=0.07  Score=55.25  Aligned_cols=23  Identities=30%  Similarity=0.544  Sum_probs=20.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++|.||+|+|||+|+..++...
T Consensus       153 ~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          153 KIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             EEEEECCSSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCccHHHHHHHhhh
Confidence            58999999999999999888764

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.60  E-value=0.033  Score=48.68  Aligned_cols=24  Identities=25%  Similarity=0.405  Sum_probs=21.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+++.|++|+|||+|+.++.+.-
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            468999999999999999998643

>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=94.60  E-value=0.017  Score=51.27  Aligned_cols=25  Identities=28%  Similarity=0.230  Sum_probs=22.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      -.+|+||.|+|||+++.||+..++.
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~~   52 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLGG   52 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTC
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHcC
Confidence            4689999999999999999998753

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.59  E-value=0.024  Score=58.50  Aligned_cols=38  Identities=16%  Similarity=0.108  Sum_probs=29.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~  286 (473)
                      |.++..-++|.|+||+|||+++..+|...    +.++..+++
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            56666679999999999999999887653    556666554

>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=94.59  E-value=0.066  Score=60.88  Aligned_cols=22  Identities=32%  Similarity=0.400  Sum_probs=19.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMA  274 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA  274 (473)
                      ...++|.||.|+|||++++.++
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            4679999999999999999984

>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=94.58  E-value=0.015  Score=54.65  Aligned_cols=26  Identities=23%  Similarity=0.414  Sum_probs=23.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||.|+|||||+++|+..+.
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl~~   56 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCLDK   56 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            44689999999999999999998774

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=94.57  E-value=0.024  Score=51.17  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..++|.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999999864

>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=94.56  E-value=0.021  Score=55.92  Aligned_cols=25  Identities=20%  Similarity=0.206  Sum_probs=22.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .-+-|.||+|+|||||++.|+..++
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3578999999999999999999876

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=94.55  E-value=0.052  Score=57.94  Aligned_cols=26  Identities=27%  Similarity=0.406  Sum_probs=22.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +..-+.|.||+|+|||||+++|++.+
T Consensus       366 ~G~~~~ivG~sGsGKSTll~~l~g~~  391 (578)
T 4a82_A          366 KGETVAFVGMSGGGKSTLINLIPRFY  391 (578)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            34458999999999999999999877

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=94.54  E-value=0.024  Score=50.47  Aligned_cols=24  Identities=29%  Similarity=0.340  Sum_probs=21.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|+.++.+.-
T Consensus        23 ~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           23 FKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            368999999999999999998753

>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=94.53  E-value=0.016  Score=54.63  Aligned_cols=25  Identities=32%  Similarity=0.387  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           31 GALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4468999999999999999999976

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.53  E-value=0.03  Score=58.68  Aligned_cols=34  Identities=18%  Similarity=0.344  Sum_probs=27.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      ++.+++.|+||+||||++..||..+   |..+..+++
T Consensus       101 ~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W          101 QNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             -EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            4579999999999999999999876   666665554

>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=94.53  E-value=0.028  Score=62.30  Aligned_cols=24  Identities=42%  Similarity=0.584  Sum_probs=20.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-.++.||||||||+++..++..+
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            357999999999999888777654

>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=94.51  E-value=0.011  Score=56.31  Aligned_cols=29  Identities=17%  Similarity=0.381  Sum_probs=24.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-CCceE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-NFDVY  282 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-~~~~~  282 (473)
                      .-|.|.|++|+||||+++.|+..+ +..++
T Consensus        25 ~~I~ieG~~GsGKST~~~~L~~~l~~~~~i   54 (263)
T 1p5z_B           25 KKISIEGNIAAGKSTFVNILKQLCEDWEVV   54 (263)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTTEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCEEE
Confidence            458999999999999999999999 54444

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=94.50  E-value=0.14  Score=45.52  Aligned_cols=23  Identities=22%  Similarity=0.190  Sum_probs=20.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .++|.|++|+|||+|+..+.+..
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~~   44 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTGT   44 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            58999999999999998887643

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=94.47  E-value=0.18  Score=54.90  Aligned_cols=19  Identities=32%  Similarity=0.557  Sum_probs=16.8

Q ss_pred             CceeEEeCCCCCCHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIA  271 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~  271 (473)
                      .+.+++.||+|+|||+.+.
T Consensus        46 ~~~~lv~apTGsGKT~~~~   64 (715)
T 2va8_A           46 GNRLLLTSPTGSGKTLIAE   64 (715)
T ss_dssp             TCCEEEECCTTSCHHHHHH
T ss_pred             CCcEEEEcCCCCcHHHHHH
Confidence            5689999999999999873

>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=94.46  E-value=0.023  Score=55.88  Aligned_cols=26  Identities=19%  Similarity=0.115  Sum_probs=22.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +.-+-|.||+|+|||||++.|+..+.
T Consensus        90 g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           90 PFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCchHHHHHHHHHhhcc
Confidence            34578999999999999999999874

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=94.43  E-value=0.028  Score=49.40  Aligned_cols=23  Identities=30%  Similarity=0.330  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         7 ~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            7 RKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            46899999999999999999853

>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=94.42  E-value=0.019  Score=61.19  Aligned_cols=34  Identities=26%  Similarity=0.151  Sum_probs=29.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC----CceEEcccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN----FDVYDLELT  287 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~----~~~~~l~~~  287 (473)
                      .-|+|.|+||+||||++++|+..|+    .+++.++..
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD~D  434 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLGD  434 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEEHH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEECcH
Confidence            4589999999999999999999986    777777643

>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=94.41  E-value=0.029  Score=58.87  Aligned_cols=26  Identities=12%  Similarity=0.002  Sum_probs=24.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      ..+.|.|++||||||++++||..|+.
T Consensus       396 ~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          396 FSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             eEEEecccCCCCHHHHHHHHHHHHHH
Confidence            46899999999999999999999985

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.40  E-value=0.038  Score=56.80  Aligned_cols=36  Identities=19%  Similarity=0.295  Sum_probs=29.0

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELT  287 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~  287 (473)
                      .++.+++.|++|+||||++..||..+    |..+..+++.
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D  138 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSAD  138 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            35678999999999999999999776    6666666554

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=94.40  E-value=0.075  Score=47.77  Aligned_cols=22  Identities=32%  Similarity=0.511  Sum_probs=19.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      .-++|.|++|+|||+|+..+++
T Consensus        24 ~ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           24 FKVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHTCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHh
Confidence            3589999999999999999964

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=94.38  E-value=0.056  Score=48.77  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        21 ~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           21 MKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999999864

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.37  E-value=0.025  Score=52.96  Aligned_cols=28  Identities=21%  Similarity=0.393  Sum_probs=24.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-CCce
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-NFDV  281 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-~~~~  281 (473)
                      .-+.|.|++|+||||+++.|+..+ +..+
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l~~~~~   31 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTYPEWHV   31 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCTTSEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHcCCCee
Confidence            458999999999999999999999 4433

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=94.36  E-value=0.06  Score=48.11  Aligned_cols=22  Identities=27%  Similarity=0.498  Sum_probs=20.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ..+++.|++|+|||+|+.++.+
T Consensus        24 ~ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           24 GKLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3689999999999999999997

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.36  E-value=0.029  Score=55.74  Aligned_cols=38  Identities=24%  Similarity=0.197  Sum_probs=30.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      |..+..-++|.|+||+|||+++..+|..+   +.++..+++
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            56666679999999999999999988764   666665544

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=94.32  E-value=0.097  Score=55.94  Aligned_cols=27  Identities=22%  Similarity=0.336  Sum_probs=23.4

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++..-+-|.||+|+|||||+++|++.+
T Consensus       367 ~~Ge~~~ivG~sGsGKSTll~~l~g~~  393 (587)
T 3qf4_A          367 KPGSLVAVLGETGSGKSTLMNLIPRLI  393 (587)
T ss_dssp             CTTCEEEEECSSSSSHHHHHHTTTTSS
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHhCCc
Confidence            334568999999999999999999977

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=94.29  E-value=0.033  Score=43.79  Aligned_cols=48  Identities=10%  Similarity=-0.135  Sum_probs=33.7

Q ss_pred             EeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          387 HMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       387 ~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      +-+.|+.++|.+|++.++.........++..+++.+ +||+|||.++|.
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~   55 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCT   55 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHH
Confidence            347899999999999999754322222334444433 799999998874

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=94.28  E-value=0.03  Score=50.88  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..++|.|++|+|||+|+..+.+.
T Consensus        27 ~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           27 FKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            46899999999999999999864

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=94.28  E-value=0.08  Score=47.39  Aligned_cols=24  Identities=29%  Similarity=0.350  Sum_probs=21.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|++.+.+..
T Consensus        21 ~ki~~vG~~~vGKTsLi~~l~~~~   44 (196)
T 3llu_A           21 PRILLMGLRRSGKSSIQKVVFHKM   44 (196)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHSCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhcC
Confidence            469999999999999999888754

>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=94.27  E-value=0.18  Score=49.79  Aligned_cols=56  Identities=16%  Similarity=0.150  Sum_probs=30.1

Q ss_pred             CCccccccchHHHHHHHHHHHHHHh--chhHHhhhcCCCCceeEEeCCCCCCHHHHHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVK--RKDYYRRVGKAWKRGYLLYGPPGTGKSSLIA  271 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~--~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~  271 (473)
                      .+|+++...+.+.+.+.+.-...+.  ..+.+..+-...++.+++.+|.|+|||..+.
T Consensus         5 ~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~   62 (395)
T 3pey_A            5 KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS   62 (395)
T ss_dssp             CSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHH
T ss_pred             cCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHH
Confidence            4677777777666655431000000  0011111111123789999999999998544

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=94.27  E-value=0.018  Score=50.82  Aligned_cols=23  Identities=26%  Similarity=0.433  Sum_probs=9.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEECCCCC------------
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46999999999999999998754

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.26  E-value=0.023  Score=53.61  Aligned_cols=24  Identities=33%  Similarity=0.605  Sum_probs=22.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||.|+|||||+++|+..+
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            468899999999999999999876

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.25  E-value=0.015  Score=54.25  Aligned_cols=26  Identities=23%  Similarity=0.280  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||.|+|||||+++|+..+.
T Consensus        30 Ge~~~iiG~nGsGKSTLl~~l~Gl~~   55 (224)
T 2pcj_A           30 GEFVSIIGASGSGKSTLLYILGLLDA   55 (224)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34588999999999999999998774

>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=94.24  E-value=0.025  Score=50.50  Aligned_cols=32  Identities=16%  Similarity=0.248  Sum_probs=25.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      +-+.|.|++|+|||+++..++..+   ++.+..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik   39 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   39 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEEE
Confidence            468899999999999999999886   45554443

>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=94.23  E-value=0.028  Score=52.07  Aligned_cols=31  Identities=32%  Similarity=0.290  Sum_probs=25.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l  284 (473)
                      .-+.|.||+|+||||+++.++..+   +++++..
T Consensus         7 ~~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~   40 (213)
T 4edh_A            7 LFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLT   40 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHHHcCCCcccc
Confidence            357889999999999999999988   4555543

>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=94.21  E-value=0.027  Score=55.81  Aligned_cols=26  Identities=19%  Similarity=0.583  Sum_probs=23.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ...+++.||+|+|||||+++|+..+.
T Consensus       171 g~~v~i~G~~GsGKTTll~~l~g~~~  196 (330)
T 2pt7_A          171 GKNVIVCGGTGSGKTTYIKSIMEFIP  196 (330)
T ss_dssp             TCCEEEEESTTSCHHHHHHHGGGGSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            34799999999999999999999873

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.18  E-value=0.02  Score=52.81  Aligned_cols=23  Identities=35%  Similarity=0.375  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      .-+.|.||.|+|||||+++|+..
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            45889999999999999999975

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=94.16  E-value=0.021  Score=54.58  Aligned_cols=26  Identities=19%  Similarity=0.327  Sum_probs=22.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||.|+|||||+++|+..+.
T Consensus        32 Ge~~~liG~nGsGKSTLlk~l~Gl~~   57 (262)
T 1b0u_A           32 GDVISIIGSSGSGKSTFLRCINFLEK   57 (262)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34588999999999999999999874

>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=94.15  E-value=0.02  Score=54.03  Aligned_cols=25  Identities=24%  Similarity=0.527  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4458999999999999999999876

>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=94.15  E-value=0.019  Score=53.67  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=22.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl~   58 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGEL   58 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4468899999999999999999987

>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=94.11  E-value=0.02  Score=53.19  Aligned_cols=26  Identities=31%  Similarity=0.608  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||.|+|||||+++|+..+.
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~Gl~~   60 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTISTYLK   60 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34588999999999999999998763

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=94.10  E-value=0.052  Score=49.21  Aligned_cols=25  Identities=24%  Similarity=0.315  Sum_probs=21.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...+++.|++|+|||+|+.++.+.-
T Consensus         7 ~~ki~vvG~~~~GKTsli~~l~~~~   31 (214)
T 2fh5_B            7 QRAVLFVGLCDSGKTLLFVRLLTGQ   31 (214)
T ss_dssp             -CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3469999999999999999998743

>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=94.08  E-value=0.027  Score=50.70  Aligned_cols=24  Identities=29%  Similarity=0.433  Sum_probs=21.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+.|.||+|+|||+|++.+++..
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            358999999999999999999863

>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=94.08  E-value=0.014  Score=60.57  Aligned_cols=26  Identities=27%  Similarity=0.497  Sum_probs=23.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +..++|.|.||+|||++++.+|..++
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            34699999999999999999999874

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.08  E-value=0.029  Score=52.56  Aligned_cols=24  Identities=21%  Similarity=0.303  Sum_probs=18.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-|.|.||+|+||||+++.+++.+
T Consensus        26 ~~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           26 KFITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             CEEEEECCC---CHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            347889999999999999999988

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=94.05  E-value=0.037  Score=57.13  Aligned_cols=39  Identities=21%  Similarity=0.185  Sum_probs=30.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      |.++..-++|.|+||+|||+++..+|...   |.++..+++.
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlE  234 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  234 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECC
Confidence            56666679999999999999998888765   6677766543

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=94.04  E-value=0.034  Score=55.75  Aligned_cols=26  Identities=27%  Similarity=0.525  Sum_probs=23.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ...++|.||+|+|||||+++|+..+.
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            45799999999999999999999874

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=94.03  E-value=0.023  Score=54.27  Aligned_cols=25  Identities=24%  Similarity=0.433  Sum_probs=22.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccC
Confidence            4468999999999999999999876

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=94.03  E-value=0.031  Score=47.83  Aligned_cols=23  Identities=30%  Similarity=0.456  Sum_probs=20.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+++.|++|+|||+|+.++++.-
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58999999999999999998753

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=94.01  E-value=0.063  Score=47.29  Aligned_cols=23  Identities=13%  Similarity=0.329  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        22 ~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           22 HKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35899999999999999999864

>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=94.00  E-value=0.021  Score=54.42  Aligned_cols=24  Identities=42%  Similarity=0.776  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||.|+|||||+++|+..+
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl~   57 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGFL   57 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            458899999999999999999876

>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=93.99  E-value=0.024  Score=54.29  Aligned_cols=26  Identities=23%  Similarity=0.483  Sum_probs=22.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||.|+|||||+++|+..+.
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl~~   75 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLLED   75 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcCCC
Confidence            34588999999999999999999873

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.98  E-value=0.024  Score=54.53  Aligned_cols=25  Identities=36%  Similarity=0.555  Sum_probs=22.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl~   69 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNLY   69 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4458899999999999999999977

>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=93.96  E-value=0.21  Score=54.55  Aligned_cols=18  Identities=22%  Similarity=0.392  Sum_probs=16.2

Q ss_pred             CceeEEeCCCCCCHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLI  270 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la  270 (473)
                      .+.+++.||.|+|||..+
T Consensus        39 ~~~~lv~apTGsGKT~~~   56 (720)
T 2zj8_A           39 GKNALISIPTASGKTLIA   56 (720)
T ss_dssp             TCEEEEECCGGGCHHHHH
T ss_pred             CCcEEEEcCCccHHHHHH
Confidence            568999999999999876

>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=93.94  E-value=0.027  Score=56.45  Aligned_cols=28  Identities=25%  Similarity=0.393  Sum_probs=24.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      ..-+.|.||+|+|||||++.|++.+..+
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            4468999999999999999999988654

>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=93.92  E-value=0.069  Score=54.73  Aligned_cols=35  Identities=23%  Similarity=0.278  Sum_probs=27.2

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      .+..+++.||+|+||||++..+|..+   +..+..+++
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            34568889999999999999999887   445554443

>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=93.91  E-value=0.027  Score=50.54  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=21.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+.|.||+|+|||+|++.+++..
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            58999999999999999999864

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=93.90  E-value=0.039  Score=61.24  Aligned_cols=23  Identities=43%  Similarity=0.622  Sum_probs=19.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+|+.||||||||+++..++..+
T Consensus       377 ~~lI~GppGTGKT~~i~~~i~~l  399 (802)
T 2xzl_A          377 LSLIQGPPGTGKTVTSATIVYHL  399 (802)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            57999999999999887766544

>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=93.89  E-value=0.023  Score=53.89  Aligned_cols=25  Identities=24%  Similarity=0.398  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~Gl~   59 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQRFY   59 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3458899999999999999999976

>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=93.87  E-value=0.023  Score=53.91  Aligned_cols=26  Identities=42%  Similarity=0.576  Sum_probs=22.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||.|+|||||+++|+..+.
T Consensus        26 Ge~~~liG~NGsGKSTLlk~l~Gl~~   51 (249)
T 2qi9_C           26 GEILHLVGPNGAGKSTLLARMAGMTS   51 (249)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34588999999999999999998764

>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=93.85  E-value=0.03  Score=60.19  Aligned_cols=25  Identities=36%  Similarity=0.602  Sum_probs=20.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .+-+++.||||||||+++.++...+
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            3579999999999999988777654

>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=93.83  E-value=0.38  Score=49.45  Aligned_cols=59  Identities=19%  Similarity=0.269  Sum_probs=33.2

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhc-----hhHHhhhcCCCCceeEEeCCCCCCHHHH-HHHHHHhc
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKR-----KDYYRRVGKAWKRGYLLYGPPGTGKSSL-IAAMANYL  277 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~-----~~~y~~~g~~~~rg~LL~GPpGtGKT~l-a~alA~~l  277 (473)
                      .+|+++...+...+.+...  .| ..     ...+..+-...++.+|+.||.|+|||.. +.++...+
T Consensus        92 ~~f~~~~l~~~l~~~l~~~--g~-~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l  156 (479)
T 3fmp_B           92 KSFEELRLKPQLLQGVYAM--GF-NRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (479)
T ss_dssp             CCSGGGTCCHHHHHHHHHT--TC-CSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTC
T ss_pred             CCHHHcCCCHHHHHHHHHc--CC-CCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHH
Confidence            4788888887766655331  00 00     0111111111247899999999999976 33444443

>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=93.82  E-value=0.024  Score=54.68  Aligned_cols=24  Identities=29%  Similarity=0.425  Sum_probs=21.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||.|+|||||+++|+..+
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl~   58 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGIL   58 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC
Confidence            458999999999999999999876

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.82  E-value=0.064  Score=48.95  Aligned_cols=26  Identities=23%  Similarity=0.347  Sum_probs=22.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .+.+++.|++|+|||+|+..++..+.
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            34789999999999999999998863

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.81  E-value=0.027  Score=54.17  Aligned_cols=24  Identities=25%  Similarity=0.443  Sum_probs=21.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .+.|.||+|+|||||+++|++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~~   27 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQV   27 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCC
Confidence            578999999999999999999763

>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=93.81  E-value=0.032  Score=53.46  Aligned_cols=25  Identities=36%  Similarity=0.485  Sum_probs=22.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl~   70 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGRE   70 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3458899999999999999999973

>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=93.80  E-value=0.024  Score=53.40  Aligned_cols=26  Identities=27%  Similarity=0.452  Sum_probs=22.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+.|.||.|+|||||+++|+..+.
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~Gl~~   57 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            34588999999999999999999774

>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=93.78  E-value=0.047  Score=53.20  Aligned_cols=35  Identities=26%  Similarity=0.342  Sum_probs=27.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      +.-+.+.||+|+|||+++..+|..+   +..+..+++.
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            4568889999999999999999877   5666655544

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=93.78  E-value=0.054  Score=48.80  Aligned_cols=22  Identities=18%  Similarity=0.440  Sum_probs=19.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ..+++.|++|+|||+|+.++.+
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3589999999999999999975

>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=93.77  E-value=0.028  Score=53.57  Aligned_cols=25  Identities=24%  Similarity=0.522  Sum_probs=22.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        41 Gei~~l~G~NGsGKSTLlk~l~Gl~   65 (256)
T 1vpl_A           41 GEIFGLIGPNGAGKTTTLRIISTLI   65 (256)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCC
Confidence            3458899999999999999999876

>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=93.70  E-value=0.028  Score=56.31  Aligned_cols=24  Identities=25%  Similarity=0.567  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||+|||||||+++||..+
T Consensus        31 e~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           31 EILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCchHHHHHHHHhcCC
Confidence            358899999999999999999976

>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=93.70  E-value=0.031  Score=48.67  Aligned_cols=22  Identities=32%  Similarity=0.528  Sum_probs=20.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+.|.|++|+|||+|+.++++.
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999864

>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=93.69  E-value=0.031  Score=53.03  Aligned_cols=24  Identities=38%  Similarity=0.439  Sum_probs=21.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..-+.|.||.|+|||||+++|+..
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            345889999999999999999996

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.69  E-value=0.029  Score=53.73  Aligned_cols=25  Identities=32%  Similarity=0.551  Sum_probs=22.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl~   57 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGLI   57 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCC
Confidence            3458899999999999999999876

>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=93.67  E-value=0.26  Score=47.51  Aligned_cols=28  Identities=18%  Similarity=0.247  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      +.+++.+|+|+|||..+...+-..+..+
T Consensus        32 ~~~lv~~~TGsGKT~~~~~~~~~~~~~~   59 (337)
T 2z0m_A           32 KNVVVRAKTGSGKTAAYAIPILELGMKS   59 (337)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTCCE
T ss_pred             CCEEEEcCCCCcHHHHHHHHHHhhcCCE
Confidence            5799999999999987665554444333

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.67  E-value=0.034  Score=55.79  Aligned_cols=24  Identities=38%  Similarity=0.609  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||+|||||||+++||..+
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~   53 (362)
T 2it1_A           30 EFMALLGPSGSGKSTLLYTIAGIY   53 (362)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCchHHHHHHHHhcCC
Confidence            357899999999999999999976

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.63  E-value=0.027  Score=53.58  Aligned_cols=25  Identities=24%  Similarity=0.328  Sum_probs=22.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~Gl~   55 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLGIH   55 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3458899999999999999999876

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.62  E-value=0.027  Score=54.40  Aligned_cols=24  Identities=33%  Similarity=0.744  Sum_probs=21.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||.|+|||||+++|+..+
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl~   71 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAYE   71 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            358899999999999999999877

>3def_A T7I23.11 protein; chloroplast, TOC33, GTPase, hydrolase; HET: GDP; 1.96A {Arabidopsis thaliana} PDB: 3bb3_A* 3bb4_A* 2j3e_A*

Probab=93.61  E-value=0.24  Score=46.88  Aligned_cols=25  Identities=28%  Similarity=0.373  Sum_probs=21.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...+++.|++|+|||+|+.++.+.-
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            3469999999999999999998754

>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=93.59  E-value=0.035  Score=55.61  Aligned_cols=24  Identities=29%  Similarity=0.486  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||+|||||||+++||..+
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           30 EFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEEcCCCchHHHHHHHHHCCC
Confidence            457899999999999999999876

>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=93.58  E-value=0.027  Score=54.06  Aligned_cols=26  Identities=35%  Similarity=0.655  Sum_probs=22.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+-|.||.|+|||||+++|+..+.
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~Gl~~   62 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTGYLS   62 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTSSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            34588999999999999999999773

>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=93.57  E-value=0.036  Score=55.83  Aligned_cols=25  Identities=28%  Similarity=0.482  Sum_probs=22.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||+|||||||+++||..+
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC
Confidence            3458899999999999999999876

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=93.55  E-value=0.043  Score=50.94  Aligned_cols=28  Identities=21%  Similarity=0.218  Sum_probs=24.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      .-+.|.||+|+||||+++.++..++.++
T Consensus         6 ~~i~~eG~~g~GKst~~~~l~~~l~~~~   33 (216)
T 3tmk_A            6 KLILIEGLDRTGKTTQCNILYKKLQPNC   33 (216)
T ss_dssp             CEEEEEECSSSSHHHHHHHHHHHHCSSE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcccc
Confidence            4588999999999999999999998643

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=93.53  E-value=0.029  Score=50.60  Aligned_cols=23  Identities=35%  Similarity=0.587  Sum_probs=20.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           26 FKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHC-
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            46999999999999999999753

>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=93.52  E-value=0.037  Score=55.86  Aligned_cols=24  Identities=33%  Similarity=0.542  Sum_probs=21.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+-|.||+|||||||+++||..+
T Consensus        30 e~~~llGpsGsGKSTLLr~iaGl~   53 (381)
T 3rlf_A           30 EFVVFVGPSGCGKSTLLRMIAGLE   53 (381)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEEcCCCchHHHHHHHHHcCC
Confidence            358899999999999999999977

>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=93.51  E-value=0.038  Score=47.99  Aligned_cols=23  Identities=43%  Similarity=0.522  Sum_probs=20.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -.+|+||.|+|||+++.||+-.+
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999998765

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.51  E-value=0.033  Score=55.74  Aligned_cols=24  Identities=29%  Similarity=0.517  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||+|||||||+++||..+
T Consensus        42 e~~~llGpnGsGKSTLLr~iaGl~   65 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAGLE   65 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            458899999999999999999876

>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=93.48  E-value=0.029  Score=49.80  Aligned_cols=22  Identities=23%  Similarity=0.569  Sum_probs=20.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|++|+|||+|++.+++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999999873

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.46  E-value=0.13  Score=51.13  Aligned_cols=25  Identities=40%  Similarity=0.600  Sum_probs=21.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||||+|||||+.+++..+
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            3458899999999999999999864

>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=93.43  E-value=0.044  Score=47.26  Aligned_cols=23  Identities=26%  Similarity=0.313  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         7 ~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            7 FKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46899999999999999999865

>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=93.38  E-value=0.046  Score=47.70  Aligned_cols=24  Identities=29%  Similarity=0.439  Sum_probs=21.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+++.|++|+|||+|+..+.+.-
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCc
Confidence            469999999999999999998753

>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=93.38  E-value=0.053  Score=54.10  Aligned_cols=32  Identities=34%  Similarity=0.396  Sum_probs=25.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      .-+.|.|+||+|||+++.+++..+   |..+..++
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~  114 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLA  114 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEe
Confidence            468999999999999999999876   55544443

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.37  E-value=0.022  Score=60.45  Aligned_cols=26  Identities=35%  Similarity=0.397  Sum_probs=23.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +..+.|.||+|+||||++++||..++
T Consensus       369 G~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          369 GFTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             CEEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCChHHHHHHHHHHhhc
Confidence            34589999999999999999999985

>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=93.36  E-value=0.038  Score=57.79  Aligned_cols=39  Identities=15%  Similarity=-0.016  Sum_probs=29.8

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELT  287 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~  287 (473)
                      |.++..-++|.|+||+|||+++..+|..+    |.++..+++.
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            45556669999999999999999888754    4566665543

>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=93.35  E-value=0.036  Score=55.83  Aligned_cols=24  Identities=29%  Similarity=0.528  Sum_probs=21.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||+|||||||+++||..+
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCcHHHHHHHHHHcCC
Confidence            458899999999999999999876

>3cpj_B GTP-binding protein YPT31/YPT8; RAB GTPase, prenylation, vesicular transport, acetylation, golgi apparatus, lipoprotein, membrane; HET: GDP; 2.35A {Saccharomyces cerevisiae}

Probab=93.32  E-value=0.051  Score=49.85  Aligned_cols=23  Identities=30%  Similarity=0.505  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.++|.|++|+|||+|+.++.+.
T Consensus        14 ~ki~v~G~~~vGKSsli~~l~~~   36 (223)
T 3cpj_B           14 FKIVLIGDSGVGKSNLLSRFTKN   36 (223)
T ss_dssp             EEEEEESCTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            36899999999999999999874

>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=93.27  E-value=0.096  Score=49.89  Aligned_cols=24  Identities=25%  Similarity=0.504  Sum_probs=21.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..+.|.|+||+|||+|+.++.+..
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~g~~   27 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALTGLR   27 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHTTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhCCC
Confidence            468999999999999999998753

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=93.23  E-value=0.041  Score=50.20  Aligned_cols=22  Identities=36%  Similarity=0.558  Sum_probs=20.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      -.+++.|++|+|||+|+.++.+
T Consensus        35 ~ki~vvG~~~vGKSsli~~l~~   56 (214)
T 2j1l_A           35 VKVVLVGDGGCGKTSLLMVFAD   56 (214)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHc
Confidence            3699999999999999999985

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.22  E-value=0.044  Score=48.42  Aligned_cols=23  Identities=30%  Similarity=0.479  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+.|.|++|+|||+|+.++++.
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            36899999999999999999974

>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=93.18  E-value=0.25  Score=49.98  Aligned_cols=25  Identities=28%  Similarity=0.521  Sum_probs=22.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-++|.||+|+|||+|++.||+..
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHH
Confidence            3459999999999999999999865

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.17  E-value=0.039  Score=52.79  Aligned_cols=25  Identities=32%  Similarity=0.713  Sum_probs=22.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            3458899999999999999999875

>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=93.15  E-value=0.085  Score=50.06  Aligned_cols=22  Identities=41%  Similarity=0.634  Sum_probs=20.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+.|.|+||+|||+|+.++.+.
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            5889999999999999999875

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=93.12  E-value=0.36  Score=47.95  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=20.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -+.+.|++|+|||||+.++.+
T Consensus        36 ~I~vvG~~~sGKSSLln~l~g   56 (360)
T 3t34_A           36 AIAVVGGQSSGKSSVLESIVG   56 (360)
T ss_dssp             EEEEECBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHhC
Confidence            689999999999999999998

>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=93.10  E-value=0.032  Score=55.67  Aligned_cols=25  Identities=24%  Similarity=0.638  Sum_probs=22.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||+|||||||+++||..+
T Consensus        26 Ge~~~llGpnGsGKSTLLr~iaGl~   50 (348)
T 3d31_A           26 GEYFVILGPTGAGKTLFLELIAGFH   50 (348)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCccHHHHHHHHHcCC
Confidence            3458899999999999999999876

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=93.09  E-value=0.06  Score=46.86  Aligned_cols=24  Identities=21%  Similarity=0.304  Sum_probs=21.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ...+++.|++|+|||+|+.++.+.
T Consensus         8 ~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            8 PPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            456999999999999999999863

>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=93.00  E-value=0.026  Score=50.27  Aligned_cols=24  Identities=33%  Similarity=0.385  Sum_probs=21.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ...+++.|++|+|||+|+.++.+.
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           23 LPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            457999999999999999999864

>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=92.99  E-value=0.078  Score=54.13  Aligned_cols=23  Identities=30%  Similarity=0.440  Sum_probs=20.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+-|.||+|+|||||+++|++..
T Consensus        71 ~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            57899999999999999999854

>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=92.98  E-value=0.13  Score=49.92  Aligned_cols=34  Identities=24%  Similarity=0.337  Sum_probs=26.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +..+.+.||+|+|||+++..+|..+   +..+..+++
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~  134 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAA  134 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecC
Confidence            4567888999999999999999876   455554443

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=92.98  E-value=0.025  Score=50.54  Aligned_cols=24  Identities=29%  Similarity=0.430  Sum_probs=22.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .+.|.||+|+|||||++.|+..+.
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            578999999999999999999874

>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=92.98  E-value=0.068  Score=46.09  Aligned_cols=23  Identities=22%  Similarity=0.381  Sum_probs=20.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         8 ~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            8 MRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            46999999999999999999763

>3gj0_A GTP-binding nuclear protein RAN; G protein, GDP, acetylation, cytoplasm, HOST- virus interaction, nucleotide-binding, nucleus, phosphoprotein; HET: GDP; 1.48A {Homo sapiens} SCOP: c.37.1.8 PDB: 3gj3_A* 3gj5_A* 3gj4_A* 3gj6_A* 3gj7_A* 3gj8_A* 1i2m_A 1a2k_C 1ibr_A* 1k5d_A* 1k5g_A* 1qbk_C* 3a6p_C* 3ch5_A* 4gmx_A* 4gpt_A* 4hat_A* 4hau_A* 4hav_A* 4haw_A* ...

Probab=92.97  E-value=0.076  Score=48.48  Aligned_cols=23  Identities=26%  Similarity=0.462  Sum_probs=19.4

Q ss_pred             ceeEEeCCCCCCHHHHHHH-HHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAA-MANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~a-lA~~  276 (473)
                      -.+++.|++|+|||+|+.. +.+.
T Consensus        16 ~ki~v~G~~~~GKSsli~~~~~~~   39 (221)
T 3gj0_A           16 FKLVLVGDGGTGKTTFVKRHLTGE   39 (221)
T ss_dssp             EEEEEEECTTSSHHHHHTTBHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            3589999999999999998 4443

>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=92.96  E-value=0.037  Score=53.75  Aligned_cols=25  Identities=28%  Similarity=0.416  Sum_probs=22.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||.|+|||||+++|+..+
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCC
Confidence            4458999999999999999999876

>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=92.91  E-value=0.61  Score=46.37  Aligned_cols=52  Identities=12%  Similarity=0.150  Sum_probs=29.2

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhc---CCCCceeEEeCCCCCCHHHHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVG---KAWKRGYLLYGPPGTGKSSLI  270 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g---~~~~rg~LL~GPpGtGKT~la  270 (473)
                      .+|+++...+.+.+.+.+.-   +..+..++...   ....+.+++.+|.|+|||..+
T Consensus        40 ~~f~~~~l~~~~~~~l~~~~---~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~   94 (414)
T 3eiq_A           40 DSFDDMNLSESLLRGIYAYG---FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF   94 (414)
T ss_dssp             CCGGGGCCCHHHHHHHHHTT---CCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHH
T ss_pred             cCHhhCCCCHHHHHHHHHcC---CCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHH
Confidence            46888877777666553310   00111111110   001356999999999999864

>4djt_A GTP-binding nuclear protein GSP1; structural genomics, seattle structural genomics center for infectious disease, ssgcid, RAN family; HET: GDP; 1.80A {Encephalitozoon cuniculi}

Probab=92.90  E-value=0.022  Score=51.94  Aligned_cols=22  Identities=27%  Similarity=0.419  Sum_probs=19.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ..+++.|++|+|||+|+.++.+
T Consensus        12 ~ki~vvG~~~~GKSsli~~l~~   33 (218)
T 4djt_A           12 YKICLIGDGGVGKTTYINRVLD   33 (218)
T ss_dssp             EEEEEECCTTSSHHHHHCBCTT
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            4689999999999999999884

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=92.85  E-value=0.15  Score=48.91  Aligned_cols=23  Identities=30%  Similarity=0.492  Sum_probs=20.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+.|.|+||+|||+|+.++.+.
T Consensus         4 ~kI~lvG~~nvGKSTL~n~L~g~   26 (272)
T 3b1v_A            4 TEIALIGNPNSGKTSLFNLITGH   26 (272)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHCC
Confidence            35899999999999999999874

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=92.84  E-value=0.32  Score=50.57  Aligned_cols=61  Identities=20%  Similarity=0.227  Sum_probs=38.9

Q ss_pred             eeEEeCCCCCCHHHH-HHHHHHhcCCceEEcccccccCchHHHHHHHHhc-----cCceEEEecccc
Q 012016          255 GYLLYGPPGTGKSSL-IAAMANYLNFDVYDLELTELRSNSDLRTLLVATA-----NRSILVVEDIDC  315 (473)
Q Consensus       255 g~LL~GPpGtGKT~l-a~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~-----~~sIL~iDdiD~  315 (473)
                      -.+|.|++|||||+| +..|++..+.+++.+=+.-=...+++.+++....     .++++|.--.|.
T Consensus       164 R~~Ifg~~g~GKT~Lal~~I~~~~~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~  230 (502)
T 2qe7_A          164 RELIIGDRQTGKTTIAIDTIINQKGQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASE  230 (502)
T ss_dssp             BCEEEECSSSCHHHHHHHHHHGGGSCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTS
T ss_pred             EEEEECCCCCCchHHHHHHHHHhhcCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCC
Confidence            389999999999999 6799999887754332211122344444443332     467777766553

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=92.84  E-value=0.056  Score=50.43  Aligned_cols=26  Identities=27%  Similarity=0.310  Sum_probs=22.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      .-+.|.|++|+|||++++.+++.++.
T Consensus        22 ~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           22 MFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            45788899999999999999998754

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=92.81  E-value=0.076  Score=49.86  Aligned_cols=32  Identities=28%  Similarity=0.541  Sum_probs=25.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc--CCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL--NFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l--~~~~~~l~  285 (473)
                      ..+++.|++|+||||++..+|..+  |..+..++
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd   48 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   48 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEe
Confidence            357889999999999999999776  55555444

>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=92.80  E-value=0.046  Score=55.42  Aligned_cols=25  Identities=36%  Similarity=0.538  Sum_probs=22.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||+|||||||+++||..+
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCC
Confidence            4468999999999999999999865

>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=92.80  E-value=0.23  Score=58.13  Aligned_cols=27  Identities=30%  Similarity=0.550  Sum_probs=23.3

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++...+-|.||+|+|||||+++|.+.+
T Consensus      1103 ~~Ge~vaIVG~SGsGKSTL~~lL~rl~ 1129 (1321)
T 4f4c_A         1103 EPGQTLALVGPSGCGKSTVVALLERFY 1129 (1321)
T ss_dssp             CTTCEEEEECSTTSSTTSHHHHHTTSS
T ss_pred             CCCCEEEEECCCCChHHHHHHHHhcCc
Confidence            344558899999999999999999877

>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=92.78  E-value=0.045  Score=57.66  Aligned_cols=28  Identities=25%  Similarity=0.347  Sum_probs=22.4

Q ss_pred             CCCCceeEEeCCCCCCHHHHHHH--HHHhc
Q 012016          250 KAWKRGYLLYGPPGTGKSSLIAA--MANYL  277 (473)
Q Consensus       250 ~~~~rg~LL~GPpGtGKT~la~a--lA~~l  277 (473)
                      ++....++|.||+|+|||+|++.  ++..+
T Consensus        36 i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~   65 (525)
T 1tf7_A           36 LPIGRSTLVSGTSGTGKTLFSIQFLYNGII   65 (525)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            44566799999999999999999  44443

>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=92.74  E-value=0.057  Score=50.82  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=22.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||+|+||||+++.++..+
T Consensus        28 ~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           28 KFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            458899999999999999999987

>3r7w_A Gtpase1, GTP-binding protein GTR1; RAG gtpases, GTR1P, GTR2P, MTOR, protein transport; HET: GNP; 2.77A {Saccharomyces cerevisiae} PDB: 4arz_A*

Probab=92.67  E-value=0.15  Score=49.67  Aligned_cols=24  Identities=33%  Similarity=0.476  Sum_probs=20.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      +.-++|.|+||+|||+|+..+.+.
T Consensus         3 ~~KI~lvG~~~vGKSSLi~~l~~~   26 (307)
T 3r7w_A            3 GSKLLLMGRSGSGKSSMRSIIFSN   26 (307)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            346899999999999999997754

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=92.66  E-value=0.068  Score=53.00  Aligned_cols=25  Identities=36%  Similarity=0.495  Sum_probs=21.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||||+|||||+++++..+
T Consensus        55 g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           55 AIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhh
Confidence            3458899999999999999999865

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.65  E-value=0.052  Score=50.20  Aligned_cols=24  Identities=21%  Similarity=0.343  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-|.|.|++|+||||.++.++..+
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            357889999999999999999988

>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=92.65  E-value=0.032  Score=55.81  Aligned_cols=24  Identities=25%  Similarity=0.582  Sum_probs=21.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+.|.||+|||||||+++||..+
T Consensus        32 e~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            458899999999999999999876

>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=92.65  E-value=0.071  Score=52.33  Aligned_cols=29  Identities=24%  Similarity=0.348  Sum_probs=24.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .+|++|.|++|+|||+++.++... |..++
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~-g~~lv  172 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR-GHRLV  172 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc-CCcee
Confidence            468999999999999999999885 54444

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=92.61  E-value=0.061  Score=55.72  Aligned_cols=27  Identities=26%  Similarity=0.325  Sum_probs=23.4

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ....-+.|.||.|+|||||++.|++.+
T Consensus       136 ~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          136 FEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            334559999999999999999999976

>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=92.61  E-value=0.051  Score=47.80  Aligned_cols=23  Identities=39%  Similarity=0.576  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      .-+.|.|+||+|||+|+.++++.
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35899999999999999999975

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=92.57  E-value=0.12  Score=47.18  Aligned_cols=25  Identities=28%  Similarity=0.477  Sum_probs=22.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+++.|++|+|||+|+..++..+
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            3568888999999999999999876

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=92.54  E-value=0.058  Score=47.67  Aligned_cols=23  Identities=22%  Similarity=0.346  Sum_probs=20.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+..+.+.
T Consensus         8 ~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            8 CKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999999875

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=92.53  E-value=0.064  Score=46.70  Aligned_cols=23  Identities=39%  Similarity=0.561  Sum_probs=20.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        10 ~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B           10 FKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHCSC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            46899999999999999998753

>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=92.45  E-value=0.055  Score=53.06  Aligned_cols=29  Identities=34%  Similarity=0.362  Sum_probs=23.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .+|+||.||+|+|||+++.++.. -|..++
T Consensus       147 g~gvli~G~sG~GKStlal~l~~-~G~~lv  175 (312)
T 1knx_A          147 GVGVLLTGRSGIGKSECALDLIN-KNHLFV  175 (312)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHT-TTCEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH-cCCEEE
Confidence            57899999999999999998765 354444

>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=92.42  E-value=0.037  Score=54.20  Aligned_cols=27  Identities=26%  Similarity=0.498  Sum_probs=23.6

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++..-+.|.||+|+|||||+++|+..+
T Consensus        78 ~~Ge~vaivG~sGsGKSTLl~ll~gl~  104 (306)
T 3nh6_A           78 MPGQTLALVGPSGAGKSTILRLLFRFY  104 (306)
T ss_dssp             CTTCEEEEESSSCHHHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCchHHHHHHHHHcCC
Confidence            334568999999999999999999977

>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=92.41  E-value=0.068  Score=53.63  Aligned_cols=25  Identities=32%  Similarity=0.425  Sum_probs=22.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+-|.||+|+|||||+++|+..+
T Consensus        54 Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           54 GQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEEcCCCchHHHHHHHHhcCC
Confidence            3458899999999999999999876

>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=92.39  E-value=0.52  Score=44.05  Aligned_cols=31  Identities=16%  Similarity=0.338  Sum_probs=20.2

Q ss_pred             ceeEEeCCCCCCHHHHH-HHHHHhc--CCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLI-AAMANYL--NFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la-~alA~~l--~~~~~~l  284 (473)
                      .-++++||.|+|||+.+ +.+-++.  |..++.+
T Consensus        20 ~l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~   53 (234)
T 2orv_A           20 QIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVI   53 (234)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEE
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEE
Confidence            34788999999999644 4444443  4455443

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=92.37  E-value=0.083  Score=52.63  Aligned_cols=28  Identities=25%  Similarity=0.445  Sum_probs=24.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      .-+.|.||+|+|||+|++.|++.+..+.
T Consensus        72 q~~gIiG~nGaGKTTLl~~I~g~~~~~~   99 (347)
T 2obl_A           72 QRIGIFAGSGVGKSTLLGMICNGASADI   99 (347)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHSCCSE
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCCE
Confidence            3589999999999999999999986543

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.34  E-value=0.092  Score=55.60  Aligned_cols=33  Identities=30%  Similarity=0.280  Sum_probs=26.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC---CceEEccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLEL  286 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~  286 (473)
                      .-++|.|+||+|||++++.++..++   .+++.++.
T Consensus       373 ~~I~l~G~~GsGKSTia~~La~~L~~~G~~~~~ld~  408 (546)
T 2gks_A          373 FCVWLTGLPCAGKSTIAEILATMLQARGRKVTLLDG  408 (546)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECH
T ss_pred             eEEEccCCCCCCHHHHHHHHHHHhhhcCCeEEEECc
Confidence            4589999999999999999999874   45555553

>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=92.33  E-value=0.03  Score=50.63  Aligned_cols=25  Identities=24%  Similarity=0.266  Sum_probs=20.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+.|.||+|+|||||++++++..
T Consensus        26 ~~~v~lvG~~g~GKSTLl~~l~g~~   50 (210)
T 1pui_A           26 GIEVAFAGRSNAGKSSALNTLTNQK   50 (210)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCCC-
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3458999999999999999987643

>2r9v_A ATP synthase subunit alpha; TM1612, structural genomics, JOI for structural genomics, JCSG, protein structure initiative ATP synthesis; HET: ATP PG4; 2.10A {Thermotoga maritima MSB8}

Probab=92.30  E-value=0.28  Score=51.04  Aligned_cols=61  Identities=20%  Similarity=0.240  Sum_probs=39.2

Q ss_pred             eeEEeCCCCCCHHHH-HHHHHHhcCCceEEcccccccCchHHHHHHHHhc-----cCceEEEecccc
Q 012016          255 GYLLYGPPGTGKSSL-IAAMANYLNFDVYDLELTELRSNSDLRTLLVATA-----NRSILVVEDIDC  315 (473)
Q Consensus       255 g~LL~GPpGtGKT~l-a~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~-----~~sIL~iDdiD~  315 (473)
                      -.+|.|++|||||+| +..|++..+.+++.+=+.-=...+++.+++....     .++++|.--.|.
T Consensus       177 R~~I~g~~g~GKT~Lal~~I~~~~~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~  243 (515)
T 2r9v_A          177 RELIIGDRQTGKTAIAIDTIINQKGQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASD  243 (515)
T ss_dssp             BEEEEEETTSSHHHHHHHHHHTTTTTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTS
T ss_pred             EEEEEcCCCCCccHHHHHHHHHhhcCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCC
Confidence            389999999999999 6799999887754332211123344444444332     457777766553

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=92.29  E-value=0.079  Score=46.29  Aligned_cols=23  Identities=17%  Similarity=0.271  Sum_probs=20.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            46999999999999999999864

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=92.27  E-value=0.076  Score=46.47  Aligned_cols=23  Identities=17%  Similarity=0.310  Sum_probs=20.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         6 ~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            6 IKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999999864

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=92.27  E-value=0.08  Score=47.07  Aligned_cols=22  Identities=27%  Similarity=0.440  Sum_probs=20.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+..+.+.
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHhC
Confidence            5899999999999999998864

>1fx0_A ATP synthase alpha chain; latent ATPase, thermal stability, potential tentoxin binding hydrolase; 3.20A {Spinacia oleracea} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1kmh_A*

Probab=92.25  E-value=0.3  Score=50.82  Aligned_cols=60  Identities=20%  Similarity=0.241  Sum_probs=39.2

Q ss_pred             eEEeCCCCCCHHHH-HHHHHHhcCCceEEcccccccCchHHHHHHHHhc-----cCceEEEecccc
Q 012016          256 YLLYGPPGTGKSSL-IAAMANYLNFDVYDLELTELRSNSDLRTLLVATA-----NRSILVVEDIDC  315 (473)
Q Consensus       256 ~LL~GPpGtGKT~l-a~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~-----~~sIL~iDdiD~  315 (473)
                      .+|.|++|||||+| +..|++..+.+++.+=+.-=...+++.+++....     .++++|.--.|.
T Consensus       166 ~~Ifg~~g~GKT~Lal~~I~~~~~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~  231 (507)
T 1fx0_A          166 ELIIGDRQTGKTAVATDTILNQQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADS  231 (507)
T ss_dssp             CBEEESSSSSHHHHHHHHHHTCCTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTS
T ss_pred             EEEecCCCCCccHHHHHHHHHhhcCCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCC
Confidence            89999999999999 6799999877644322211123345555555443     456777766654

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=92.23  E-value=0.053  Score=47.79  Aligned_cols=22  Identities=27%  Similarity=0.421  Sum_probs=19.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .+++.|++|+|||+|+.++.+.
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            4789999999999999999874

>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=92.23  E-value=0.079  Score=49.19  Aligned_cols=29  Identities=24%  Similarity=0.410  Sum_probs=23.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      .-+.|.||.|+||||+++.|+.. +..+..
T Consensus        21 ~~i~i~G~~GsGKSTl~~~L~~~-~g~v~~   49 (230)
T 2vp4_A           21 FTVLIEGNIGSGKTTYLNHFEKY-KNDICL   49 (230)
T ss_dssp             EEEEEECSTTSCHHHHHHTTGGG-TTTEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHhc-cCCeEE
Confidence            34789999999999999999998 444443

>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=92.22  E-value=0.062  Score=53.77  Aligned_cols=25  Identities=40%  Similarity=0.555  Sum_probs=22.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..+.|.||+|+|||||+++|+..+.
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CEEEEECCCCccHHHHHHHHhcccc
Confidence            4689999999999999999998765

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=92.16  E-value=0.082  Score=47.36  Aligned_cols=25  Identities=28%  Similarity=0.414  Sum_probs=21.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...+++.|++|+|||+|+.++.+.-
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~~   32 (207)
T 1vg8_A            8 LLKVIILGDSGVGKTSLMNQYVNKK   32 (207)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3468999999999999999998754

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=92.14  E-value=0.11  Score=47.70  Aligned_cols=30  Identities=30%  Similarity=0.505  Sum_probs=24.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc--CCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL--NFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l--~~~~~~l  284 (473)
                      =|.|-|+.|+||||.++.|+..|  +.+++..
T Consensus         4 FI~~EG~dGsGKsTq~~~L~~~L~~~~~v~~~   35 (205)
T 4hlc_A            4 FITFEGPEGSGKTTVINEVYHRLVKDYDVIMT   35 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHCCCCEEEe
Confidence            36788999999999999999988  5555543

---

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	473
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	1e-28
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	3e-27
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	1e-26
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	3e-18
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	1e-17
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	1e-14
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	6e-12
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	2e-09
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	5e-08
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	4e-07
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	5e-07
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	6e-06
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	2e-04
d1g8pa_	333	c.37.1.20 (A:) ATPase subunit of magnesium chelata	3e-04
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	4e-04
d1tuea_	205	c.37.1.20 (A:) Replication protein E1 helicase dom	9e-04
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	0.002

>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 =  111 bits (278), Expect = 1e-28
 Identities = 52/223 (23%), Positives = 90/223 (40%), Gaps = 19/223 (8%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF+ +A  +E K ++ + +E F+K    +  +G    +G LL GPPG GK+ L  A+A  
Sbjct: 7   TFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 65

Query: 277 LNFDVYDLELTELRSN------SDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIA 328
                     ++          + +R L          I+ +++ID     + R      
Sbjct: 66  ARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAV--GRKRGSGVGG 123

Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
           G  E      + TL+  L  +DG         +++  TN  + LDPALLRPGR D  + +
Sbjct: 124 GNDER-----EQTLNQLLVEMDGFEKDTA--IVVMAATNRPDILDPALLRPGRFDRQIAI 176

Query: 389 SYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQ-VTPAEVA 430
                 G + +   +   K      ++  L   T     A++ 
Sbjct: 177 DAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLE 219

>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 =  107 bits (269), Expect = 3e-27
 Identities = 50/264 (18%), Positives = 109/264 (41%), Gaps = 23/264 (8%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           T+E +   ++ K ++ + ++  V+  D + + G    +G L YGPPG GK+ L  A+AN 
Sbjct: 5   TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 64

Query: 277 LNFDVYDLELTELRS------NSDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIA 328
              +   ++  EL +       +++R +      A   +L  +++D     +     D  
Sbjct: 65  CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGG 124

Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
           G  +         ++  L  +DG+ +       I+  TN  + +DPA+LRPGR+D  +++
Sbjct: 125 GAAD-------RVINQILTEMDGMSTKKN--VFIIGATNRPDIIDPAILRPGRLDQLIYI 175

Query: 389 SYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQ-VTPAEVAEQLMRNDDPELVLNGLI 447
                     +    L         ++E L   T   + A++  ++ +          + 
Sbjct: 176 PLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADL-TEICQ----RACKLAIR 230

Query: 448 EFLKVKRKEDEDAKPRKIHEESTE 471
           E ++ + + + + +      E  E
Sbjct: 231 ESIESEIRRERERQTNPSAMEVEE 254

>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 =  105 bits (264), Expect = 1e-26
 Identities = 55/225 (24%), Positives = 98/225 (43%), Gaps = 23/225 (10%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
           TF  +A   E K ++ + +E +++    ++++G    +G L+ GPPGTGK+ L  A+A  
Sbjct: 10  TFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68

Query: 277 LNFDVYDLELTELR------SNSDLRTL--LVATANRSILVVEDIDCTIDLQDRLPADIA 328
                + +  ++          S +R +      A   I+ +++ID     + R      
Sbjct: 69  AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAV--GRQRGAGLGG 126

Query: 329 GEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHM 388
           G  E      + TL+  L  +DG   +  +  I++  TN  + LDPALLRPGR D  V +
Sbjct: 127 GHDE-----REQTLNQMLVEMDGFEGN--EGIIVIAATNRPDVLDPALLRPGRFDRQVVV 179

Query: 389 SYCTPSG-FKLLAANYLGIK--EHILFEEIEELISTTQVTPAEVA 430
                 G  ++L  +   +     I    I     T   + A++A
Sbjct: 180 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARG--TPGFSGADLA 222

>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 = 82.0 bits (201), Expect = 3e-18
 Identities = 53/247 (21%), Positives = 97/247 (39%), Gaps = 10/247 (4%)

Query: 217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANY 276
            ++ +   ++Q  +I + +E  ++    ++ +G    RG LLYGPPGTGK+ +  A+AN 
Sbjct: 2   GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 61

Query: 277 LNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQ 336
                + +   E+ S     +   +   ++    E     I   D L A      +   +
Sbjct: 62  TGAFFFLINGPEIMSKLAGESE--SNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGE 119

Query: 337 QNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGF 396
             +  +S  L  +D          I++  TN    +DPAL R GR D  V +     +G 
Sbjct: 120 VERRIVSQLLTLMD--GLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGR 177

Query: 397 K-LLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLKVKRK 455
             +L  +   +K     +  +    T     A++A  L      E  L  + + + +   
Sbjct: 178 LEILQIHTKNMKLADDVDLEQVANETHGHVGADLA-ALCS----EAALQAIRKKMDLIDL 232

Query: 456 EDEDAKP 462
           EDE    
Sbjct: 233 EDETIDA 239

>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 = 81.6 bits (201), Expect = 1e-17
 Identities = 39/255 (15%), Positives = 71/255 (27%), Gaps = 51/255 (20%)

Query: 225 QEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL 284
            +  + +   L+  V             KR +L  GP  +GK++L AA+         ++
Sbjct: 134 PKMDSVVYDFLKCMVY--------NIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNV 185

Query: 285 ELTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSG 344
            L   R N +L        ++ ++V ED+  T      LP+   G            L  
Sbjct: 186 NLPLDRLNFELGVA----IDQFLVVFEDVKGTGGESRDLPS-GQGINN---------LDN 231

Query: 345 FLNFIDGLWSSCGDE----------RIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPS 394
             +++DG      ++             + T N             R    +        
Sbjct: 232 LRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNE---YSVPKTLQARFVKQIDFRPKDYL 288

Query: 395 GFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFLK--- 451
              L  + +L  K  I+   I  L+      P           +    +   I   K   
Sbjct: 289 KHCLERSEFLLEKR-IIQSGIALLLMLIWYRP---------VAEFAQSIQSRIVEWKERL 338

Query: 452 ---VKRKEDEDAKPR 463
                    +  K  
Sbjct: 339 DKEFSLSVYQKMKFN 353

>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 = 71.5 bits (174), Expect = 1e-14
 Identities = 38/261 (14%), Positives = 78/261 (29%), Gaps = 22/261 (8%)

Query: 224 EQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYD 283
           +++ + ++  +LE  ++ K             +LL G PG+GK+SL +A+      +V  
Sbjct: 8   DKQFENRLNDNLEELIQGKK-----AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIV 62

Query: 284 LELTELRSNSDLRTLLV----------ATANRSILVVEDIDCTIDLQDRLPADIAGEGEG 333
           ++    +        LV           T   + +    I    D    L  +  G    
Sbjct: 63  IDNDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTD 122

Query: 334 PIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYC-- 391
              Q    L            +       + T    E +        R            
Sbjct: 123 VPIQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVK 182

Query: 392 -TPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMRNDDPELVLNGLIEFL 450
             P+  + L    L     +   E  +L S+ +       E L +  + ++    +   L
Sbjct: 183 NLPTNLETLHKTGLFSDIRLYNREGVKLYSSLETPSISPKETLEKELNRKVSGKEIQPTL 242

Query: 451 KVKRKEDEDAKPRKIHEESTE 471
           +   ++         H+E+ E
Sbjct: 243 ERIEQKMV----LNKHQETPE 259

>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 = 63.4 bits (153), Expect = 6e-12
 Identities = 37/238 (15%), Positives = 76/238 (31%), Gaps = 11/238 (4%)

Query: 226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE 285
           +  T+++ D E  V      +   +      LL GPP +GK++L A +A   NF    + 
Sbjct: 16  DPVTRVLDDGELLV---QQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKIC 72

Query: 286 LTELRSNSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGF 345
             +            A         +     + + D     +        + + + L   
Sbjct: 73  SPDKMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDI--ERLLDYVPIGPRFSNLVLQAL 130

Query: 346 LNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG 405
           L  +         + +I+ TT+ K+ L    +        +H+         L A   LG
Sbjct: 131 LVLLKKAPPQG-RKLLIIGTTSRKDVLQEMEML-NAFSTTIHVPNIATGEQLLEALELLG 188

Query: 406 IKEHILFEEIEELISTTQVTP----AEVAEQLMRNDDPELVLNGLIEFLKVKRKEDED 459
             +      I + +   +V        +  ++    DPE  +   +  L+ +     D
Sbjct: 189 NFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLREEGASPLD 246

>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 = 56.6 bits (136), Expect = 2e-09
 Identities = 25/176 (14%), Positives = 57/176 (32%), Gaps = 23/176 (13%)

Query: 246 RRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV--YDLELTELRS------NSDLRT 297
               +      ++ G   +GK+ L+ A+   L        +   E  S      N  +  
Sbjct: 116 FGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDD 175

Query: 298 LLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG 357
           +  A     ++V++ +   I       A       G I +        L+ I  + +S G
Sbjct: 176 IARAMLQHRVIVIDSLKNVI------GAAGGNTTSGGISR---GAFDLLSDIGAMAASRG 226

Query: 358 DERIIVFTTNHKE---KLDPALLRPGRMDVHVHMSYCTPSG-FKLLAANYLGIKEH 409
              +++ + N      K+   +    R +    +      G +++L     G++  
Sbjct: 227 --CVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRL 280

>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 = 51.7 bits (122), Expect = 5e-08
 Identities = 34/227 (14%), Positives = 72/227 (31%), Gaps = 19/227 (8%)

Query: 203 WTDAWIPVNLDHPATFETLAMEQEQKTKIMQDLERFVKRKDY----YRRVGKAWKRGYLL 258
           WT  +       P   + +   +    K+   L  +   K        + G    R  +L
Sbjct: 4   WTVKY------APTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAML 57

Query: 259 YGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDCTID 318
           YGPPG GK++    +A  L +D+ +   +++RS + L   +          ++++     
Sbjct: 58  YGPPGIGKTTAAHLVAQELGYDILEQNASDVRSKTLLNAGVKN-------ALDNMSVVGY 110

Query: 319 LQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR 378
            +    A         I  ++V      +       +    +          + +   +R
Sbjct: 111 FKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMR 170

Query: 379 PGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEE--IEELISTTQ 423
           P              +         + I+E    +   I+ LI TT+
Sbjct: 171 PFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTR 217

>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 = 49.0 bits (115), Expect = 4e-07
 Identities = 31/211 (14%), Positives = 59/211 (27%), Gaps = 8/211 (3%)

Query: 233 QDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN 292
            + + F  R+    ++        L+ G   TGKSS+I    N LN     L+L +    
Sbjct: 9   DNRKDFFDREKEIEKLKGLRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEER 68

Query: 293 -----SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN 347
                 D    L    N+ +  +  +   +     +            ++++++ +  L 
Sbjct: 69  NYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLE 128

Query: 348 FID---GLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL 404
             +           +            L PAL         +           L     +
Sbjct: 129 SFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRV 188

Query: 405 GIKEHILFEEIEELISTTQVTPAEVAEQLMR 435
              E  LF      +     +  E  E L R
Sbjct: 189 EDPESPLFGRAFSTVELKPFSREEAIEFLRR 219

>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 = 49.1 bits (116), Expect = 5e-07
 Identities = 34/197 (17%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATA--------- 303
            +  L+ GP G GK+ +   +A   N     +E T+      +   + +           
Sbjct: 49  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGG 108

Query: 304 ------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG 357
                    I+ +++ID      +   AD++ EG              L  ++G   S  
Sbjct: 109 AIDAVEQNGIVFIDEIDKICKKGEYSGADVSREG---------VQRDLLPLVEGSTVSTK 159

Query: 358 D-----ERIIVFTTNHKEKLDPALLRP---GRMDVHVHMSYCTPSGFKLLAANYLGIKEH 409
                 + I+   +   +   P+ L P   GR+ + V ++  + + F+      L     
Sbjct: 160 HGMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFE----RILTEPHA 215

Query: 410 ILFEEIEELISTTQVTP 426
            L E+ + L++T  V  
Sbjct: 216 SLTEQYKALMATEGVNI 232

>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 = 45.3 bits (106), Expect = 6e-06
 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 8/100 (8%)

Query: 215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMA 274
           P + +    ++  K K+   LE    R +             LL GPPG GK++L   +A
Sbjct: 5   PKSLDEFIGQENVKKKLSLALEAAKMRGEVLD--------HVLLAGPPGLGKTTLAHIIA 56

Query: 275 NYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDID 314
           + L  +++      L    D+  +L +     +L +++I 
Sbjct: 57  SELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIH 96

>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 = 40.7 bits (94), Expect = 2e-04
 Identities = 36/222 (16%), Positives = 67/222 (30%), Gaps = 17/222 (7%)

Query: 215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMA 274
           P T +    ++  K K+   LE    RK+             LL+GPPG GK++L   +A
Sbjct: 5   PKTLDEYIGQERLKQKLRVYLEAAKARKEP--------LEHLLLFGPPGLGKTTLAHVIA 56

Query: 275 NYLNFDVYDLELTELRSNSDLRTLLVA-TANRSILVVEDIDCTIDLQDRLPADIAGEGEG 333
           + L  ++       +    DL  +L        IL +++I       +        +   
Sbjct: 57  HELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVM 116

Query: 334 PIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTP 393
            I      +                   ++  T     +   LL    +  H+       
Sbjct: 117 DI-----VIGQGPAARTIRLELPR--FTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEE 169

Query: 394 SGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLMR 435
               ++    L +   I  E   E+   ++ T         R
Sbjct: 170 LAQGVMRDARL-LGVRITEEAALEIGRRSRGTMRVAKRLFRR 210

>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 = 40.3 bits (93), Expect = 3e-04
 Identities = 25/153 (16%), Positives = 52/153 (33%), Gaps = 10/153 (6%)

Query: 255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDID 314
           G L++G  GTGKS+ + A+A  L  ++  +E   + S +       AT   + ++ +   
Sbjct: 30  GVLVFGDRGTGKSTAVRALAALLP-EIEAVEGCPVSSPNVEMIPDWATVLSTNVIRKPTP 88

Query: 315 CTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIV-----FTTNHK 369
                       +     G +   +    G   F  GL +      + +        +  
Sbjct: 89  VVDLPLGVSEDRVV----GALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLEDHIV 144

Query: 370 EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAAN 402
           + L         +     +S   P+ F L+ + 
Sbjct: 145 DLLLDVAQSGENVVERDGLSIRHPARFVLVGSG 177

>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 = 39.7 bits (91), Expect = 4e-04
 Identities = 9/67 (13%), Positives = 19/67 (28%), Gaps = 4/67 (5%)

Query: 212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIA 271
            D       L + + +   + +     +        V       Y   G  G GK++L  
Sbjct: 9   FDENYIPPELRVRRGEAEALARIYLNRLLSGAGLSDVN----MIYGSIGRVGIGKTTLAK 64

Query: 272 AMANYLN 278
                ++
Sbjct: 65  FTVKRVS 71

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]} Length = 205

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]

 Score = 38.3 bits (89), Expect = 9e-04
 Identities = 16/87 (18%), Positives = 31/87 (35%), Gaps = 11/87 (12%)

Query: 227 QKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL 286
           Q+ + +  L      K + +   K  K   +  GP  TGKS    +  +++   V     
Sbjct: 32  QQIEFITFLGAL---KSFLKGTPK--KNCLVFCGPANTGKSYFGMSFIHFIQGAVIS--- 83

Query: 287 TELRSNSDLRTLLVATANRSILVVEDI 313
                NS     L    +  + +++D 
Sbjct: 84  ---FVNSTSHFWLEPLTDTKVAMLDDA 107

>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 = 37.9 bits (86), Expect = 0.002
 Identities = 10/69 (14%), Positives = 21/69 (30%), Gaps = 7/69 (10%)

Query: 212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIA 271
                  + L   ++Q  ++   L  +++                 L G PGTGK+  + 
Sbjct: 9   FSPSYVPKRLPHREQQLQQLDILLGNWLRNP-------GHHYPRATLLGRPGTGKTVTLR 61

Query: 272 AMANYLNFD 280
            +       
Sbjct: 62  KLWELYKDK 70

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	473
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	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
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.88
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.88
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.87
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.84
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.82
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.79
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.75
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.72
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.71
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.69
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.66
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.64
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.64
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.56
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.55
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.48
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.47
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.45
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.44
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.37
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.37
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.33
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.31
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.29
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.22
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.99
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	98.95
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.9
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.87
d1tuea_	205	Replication protein E1 helicase domain {Human papi	98.25
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.22
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.15
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.14
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.05
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	98.01
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.99
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.93
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.9
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.88
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.84
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.8
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.74
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.69
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.68
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.67
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.57
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.56
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.54
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.48
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.47
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.47
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.45
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.43
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.39
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.39
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.38
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.38
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.35
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.33
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.3
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.29
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.26
d1okkd2	207	GTPase domain of the signal recognition particle r	97.25
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.23
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.23
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.19
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.18
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.15
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	97.14
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	97.12
d1vmaa2	213	GTPase domain of the signal recognition particle r	97.11
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.11
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	97.08
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	97.08
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.06
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	97.05
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	97.0
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.99
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.98
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.95
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.94
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.92
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	96.88
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.86
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.84
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.81
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.78
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	96.69
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	96.66
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.65
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	96.64
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.61
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	96.61
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.59
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.59
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	96.58
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.57
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.57
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.54
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.52
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.51
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	96.49
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.39
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.32
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.29
d2fh5b1	207	Signal recognition particle receptor beta-subunit	96.27
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	96.25
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.24
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	96.21
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	96.2
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.19
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	96.15
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	96.07
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.04
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	95.99
d1nrjb_	209	Signal recognition particle receptor beta-subunit	95.95
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	95.93
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	95.9
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.85
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	95.84
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.79
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	95.78
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	95.76
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.73
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	95.72
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.71
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	95.67
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.64
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.62
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	95.62
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	95.61
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	95.56
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	95.55
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.48
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	95.45
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.45
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	95.44
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.4
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.39
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	95.38
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.36
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	95.27
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	95.26
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	95.25
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	95.24
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.23
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	95.23
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	95.14
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	95.05
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.0
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.99
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.97
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	94.97
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	94.96
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	94.94
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.85
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.85
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	94.81
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	94.78
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.7
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	94.68
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	94.59
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	94.57
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	94.53
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	94.52
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.52
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	94.51
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	94.49
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.42
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	94.32
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.17
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.04
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.01
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	94.0
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	93.93
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	93.92
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	93.89
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	93.87
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	93.84
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	93.83
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	93.82
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	93.62
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.6
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	93.57
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	93.57
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.49
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	93.47
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.4
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.3
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.16
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.14
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.13
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.13
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.1
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	93.02
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	92.93
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	92.93
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	92.63
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.54
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	92.51
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	92.48
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	92.32
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.26
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	92.19
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	92.17
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.06
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.03
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	91.93
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	91.86
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	91.72
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	91.71
d1xpua3	289	Transcription termination factor Rho, ATPase domai	91.66
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	91.6
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	91.55
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.43
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	91.41
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	91.29
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	91.16
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.11
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	91.11
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	91.1
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.97
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	90.89
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	90.88
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	90.7
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	90.66
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	90.54
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	90.34
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	90.11
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	89.89
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	89.42
d2axpa1	164	Hypothetical protein YorR {Bacillus subtilis [TaxI	89.37
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	89.2
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	88.99
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.74
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	88.59
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	88.15
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	87.83
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	87.57
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	87.31
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	87.16
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.01
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	85.5
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	84.95
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	84.77
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	84.32
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	84.28
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	83.71
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	83.49
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	83.16
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	82.46
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	82.34
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	82.33
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	82.26
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	82.05
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	81.89
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	81.82
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	81.25
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	80.51
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	80.19
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	80.13

>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=7.1e-37  Score=294.88  Aligned_cols=210  Identities=23%  Similarity=0.354  Sum_probs=170.5

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc---
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR---  290 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~---  290 (473)
                      .+.||+|++|.+++|++|.+.+ .|+..++.|++.|..+++|+|||||||||||++|+++|++++.+++.++++++.   
T Consensus         7 ~~~t~~Di~Gl~~~k~~l~e~v-~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~l~~~~   85 (256)
T d1lv7a_           7 IKTTFADVAGCDEAKEEVAELV-EYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMF   85 (256)
T ss_dssp             SCCCGGGSCSCHHHHHHTHHHH-HHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTSC
T ss_pred             CCCCHHHHhchHHHHHHHHHHH-HHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHHhhhcc
Confidence            4579999999999999998755 578899999999999999999999999999999999999999999999998873   


Q ss_pred             ---CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          291 ---SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       291 ---~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                         ++..++++|..+.  +||||||||+|.++..++.  ..     .+.+.....+++.||+.||++...  .+++||+|
T Consensus        86 ~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~--~~-----~~~~~~~~~~~~~ll~~~d~~~~~--~~v~vIat  156 (256)
T d1lv7a_          86 VGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGA--GL-----GGGHDEREQTLNQMLVEMDGFEGN--EGIIVIAA  156 (256)
T ss_dssp             CCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCST--TS-----CCTTCHHHHHHHHHHHHHHTCCSS--SCEEEEEE
T ss_pred             hhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCC--CC-----CCCcHHHHHHHHHHHHHhhCCCCC--CCEEEEEe
Confidence               3567889998764  6899999999999763221  11     122334567889999999998654  45999999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQL  433 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l  433 (473)
                      ||+|+.|||+++||||||.+|+|+.|+.++|..|++.++.........++..+.+.+ ++|++||..++
T Consensus       157 Tn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~  225 (256)
T d1lv7a_         157 TNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLV  225 (256)
T ss_dssp             ESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999999999765433334455555543 69999998776

>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=1.2e-36  Score=291.96  Aligned_cols=210  Identities=24%  Similarity=0.344  Sum_probs=171.7

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc---
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR---  290 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~---  290 (473)
                      |+.+|++|+|.+++|+.|.+ +..|+.+++.|.+.|.++++|+|||||||||||++|+++|++++.+++.++++.+.   
T Consensus         4 p~~~~~di~G~~~~k~~l~~-~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~~   82 (247)
T d1ixza_           4 PKVTFKDVAGAEEAKEELKE-IVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF   82 (247)
T ss_dssp             CSCCGGGCCSCHHHHHHHHH-HHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHSC
T ss_pred             CCCcHHHHccHHHHHHHHHH-HHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhhcc
Confidence            45799999999999999866 55688999999999999999999999999999999999999999999999998873   


Q ss_pred             ---CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEe
Q 012016          291 ---SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFT  365 (473)
Q Consensus       291 ---~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~t  365 (473)
                         +...++++|..+.  +||||||||+|.++..+..  ..     .+.+......++.||+.||++...  ..++||+|
T Consensus        83 ~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~--~~-----~~~~~~~~~~~~~ll~~~d~~~~~--~~vivi~t  153 (247)
T d1ixza_          83 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGS--GV-----GGGNDEREQTLNQLLVEMDGFEKD--TAIVVMAA  153 (247)
T ss_dssp             TTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC----------------CHHHHHHHHHHHHHHHTCCTT--CCEEEEEE
T ss_pred             ccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCC--CC-----CCCcHHHHHHHHHHHHHhhCCCCC--CCEEEEEe
Confidence               2456888888764  7899999999999753221  11     122334567899999999998654  45899999


Q ss_pred             cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHH
Q 012016          366 TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQL  433 (473)
Q Consensus       366 TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l  433 (473)
                      ||+|+.|||+++||||||.+|+|+.|+.++|..|++.++.........++..+.+.+ ++|++||..++
T Consensus       154 Tn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv  222 (247)
T d1ixza_         154 TNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLL  222 (247)
T ss_dssp             ESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHH
T ss_pred             CCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHH
Confidence            999999999999999999999999999999999999999765333333445555543 69999998776

>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=3.1e-36  Score=291.18  Aligned_cols=207  Identities=23%  Similarity=0.327  Sum_probs=174.1

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC----
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS----  291 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~----  291 (473)
                      .+|++|+|.++.|++|.+.+..++.+++.|.+.|.+|++|+|||||||||||++++++|++++.+++.++++.+.+    
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            4799999999999999999999999999999999999999999999999999999999999999999999987632    


Q ss_pred             --chHHHHHHHHh--ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecC
Q 012016          292 --NSDLRTLLVAT--ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTN  367 (473)
Q Consensus       292 --~~~l~~l~~~~--~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  367 (473)
                        ...++.+|..+  .+||||+|||+|.++..+..          +.+......++.+++.+++....  .+++||+|||
T Consensus        81 ~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~----------~~~~~~~~~~~~~~~~~~~~~~~--~~vlvi~tTn  148 (258)
T d1e32a2          81 ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREK----------THGEVERRIVSQLLTLMDGLKQR--AHVIVMAATN  148 (258)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHH----------CCCTTHHHHHHHHHHHHHTCCCS--SCEEEEEEES
T ss_pred             cHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCC----------CCCchHHHHHHHhcccccccccc--CCccEEEeCC
Confidence              46677777765  47899999999999863321          12234567888899999987554  4599999999


Q ss_pred             CCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcC-CCCHHHHHHHHh
Q 012016          368 HKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTT-QVTPAEVAEQLM  434 (473)
Q Consensus       368 ~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~-~~t~a~i~~~l~  434 (473)
                      +++.+||+++||||||.+|+|++|+.++|..|++.++.........++..++..+ ++|++||..++.
T Consensus       149 ~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv~  216 (258)
T d1e32a2         149 RPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCS  216 (258)
T ss_dssp             CGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHH
T ss_pred             CccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHHH
Confidence            9999999999999999999999999999999999999754332222345555433 699999987763

>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=7.6e-35  Score=282.43  Aligned_cols=208  Identities=21%  Similarity=0.335  Sum_probs=169.8

Q ss_pred             CCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc----
Q 012016          215 PATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR----  290 (473)
Q Consensus       215 p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~----  290 (473)
                      ..+|++|+|.+++|++|.+.+..|+.+++.|.+.|.++++|+|||||||||||++++++|++++.+++.++++++.    
T Consensus         3 ~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l~~~~~   82 (265)
T d1r7ra3           3 QVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWF   82 (265)
T ss_dssp             CCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHHHTSCT
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHhhhccc
Confidence            3699999999999999999999999999999999999999999999999999999999999999999999988762    


Q ss_pred             --CchHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEec
Q 012016          291 --SNSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTT  366 (473)
Q Consensus       291 --~~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tT  366 (473)
                        ....++.+|..+.  .||||+|||+|.++..++...       ........++++.|++.||++...  .+++||+||
T Consensus        83 ~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~-------~~~~~~~~~~~~~ll~~l~~~~~~--~~v~vi~tt  153 (265)
T d1r7ra3          83 GESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNI-------GDGGGAADRVINQILTEMDGMSTK--KNVFIIGAT  153 (265)
T ss_dssp             TTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCC-------CTTHHHHHHHHHHHHHTCC--------CCEEEECC
T ss_pred             cchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcC-------CCCcHHHHHHHHHHHHHhhCcCCC--CCEEEEEeC
Confidence              2466778887654  789999999999986322111       111233566889999999998765  359999999


Q ss_pred             CCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc---ccCCHHHHHHHHhcCCCCHHHHHHHH
Q 012016          367 NHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK---EHILFEEIEELISTTQVTPAEVAEQL  433 (473)
Q Consensus       367 N~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~---~~~l~~~i~~l~~~~~~t~a~i~~~l  433 (473)
                      |+++.|||+++||||||.+|+|++|+.++|..||+.++...   .....+++....+  ++|++||..++
T Consensus       154 n~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~--g~s~~di~~lv  221 (265)
T d1r7ra3         154 NRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTN--GFSGADLTEIC  221 (265)
T ss_dssp             BSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHC--SSCCHHHHHHH
T ss_pred             CCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCC--CCCHHHHHHHH
Confidence            99999999999999999999999999999999999998753   2223445555544  59999998776

>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=99.88  E-value=1.4e-22  Score=193.39  Aligned_cols=168  Identities=18%  Similarity=0.224  Sum_probs=123.0

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccC-------c
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRS-------N  292 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~-------~  292 (473)
                      .+++..+..+.+++.+..|+....   .....+++|+|||||||||||++|+++|++++.+++.+++++...       .
T Consensus        10 ~~i~~~~~i~~i~~~~~~~~~~~~---~~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~~~~~   86 (246)
T d1d2na_          10 GIIKWGDPVTRVLDDGELLVQQTK---NSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKC   86 (246)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHH---HCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHH
T ss_pred             CCcCcCHHHHHHHHHHHHHHHHHh---ccCCCCCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccccchh
Confidence            355555667788888887876432   223345789999999999999999999999999999998876421       2


Q ss_pred             hHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCC
Q 012016          293 SDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKE  370 (473)
Q Consensus       293 ~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~  370 (473)
                      ..++.+|..+.  +||||||||||.+++.+.           .+....+..+..|+..+++.... +.+++||+|||+++
T Consensus        87 ~~i~~if~~A~~~~p~il~iDEid~l~~~~~-----------~~~~~~~~~~~~ll~~l~~~~~~-~~~v~vi~tTn~~~  154 (246)
T d1d2na_          87 QAMKKIFDDAYKSQLSCVVVDDIERLLDYVP-----------IGPRFSNLVLQALLVLLKKAPPQ-GRKLLIIGTTSRKD  154 (246)
T ss_dssp             HHHHHHHHHHHTSSEEEEEECCHHHHTTCBT-----------TTTBCCHHHHHHHHHHTTCCCST-TCEEEEEEEESCHH
T ss_pred             hhhhhhhhhhhhcccceeehhhhhhHhhhcc-----------cccchhHHHHHHHHHHhcCCCcc-ccceeeeeccCChh
Confidence            45777887764  679999999999875221           11233467888999999987543 45688999999999


Q ss_pred             CCCccccCCCceeeEEEeCCCC-HHHHHHHHHHH
Q 012016          371 KLDPALLRPGRMDVHVHMSYCT-PSGFKLLAANY  403 (473)
Q Consensus       371 ~ld~aLlrpgRfd~~I~~~~p~-~~~r~~l~~~~  403 (473)
                      .+|++.++ +||+.+|++|.+. .+++..++...
T Consensus       155 ~ld~~~~~-~rF~~~i~~P~~~~r~~il~~l~~~  187 (246)
T d1d2na_         155 VLQEMEML-NAFSTTIHVPNIATGEQLLEALELL  187 (246)
T ss_dssp             HHHHTTCT-TTSSEEEECCCEEEHHHHHHHHHHH
T ss_pred             hccchhhc-CccceEEecCCchhHHHHHHHHHhc
Confidence            99876443 5999999986543 44444444443

>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=99.88  E-value=1.2e-21  Score=184.94  Aligned_cols=185  Identities=18%  Similarity=0.218  Sum_probs=139.1

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS  293 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~  293 (473)
                      .|.+|++++|++++++.+...+.....+        ..+.+++|||||||||||++|+++|++++.+++.++........
T Consensus         4 RP~~~~divGqe~~~~~l~~~i~~~~~~--------~~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~~~   75 (238)
T d1in4a2           4 RPKSLDEFIGQENVKKKLSLALEAAKMR--------GEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQG   75 (238)
T ss_dssp             SCSSGGGCCSCHHHHHHHHHHHHHHHHH--------TCCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSHH
T ss_pred             CCCcHHHcCChHHHHHHHHHHHHHHHhc--------CCCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCcccccHH
Confidence            5789999999999999988777654332        22346899999999999999999999999999999988887777


Q ss_pred             HHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--------------cCCCCc
Q 012016          294 DLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--------------SSCGDE  359 (473)
Q Consensus       294 ~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--------------~~~~~~  359 (473)
                      .+...+.....+++++|||+|.+..                     .....++..++...              ......
T Consensus        76 ~~~~~~~~~~~~~~~~ide~~~~~~---------------------~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (238)
T d1in4a2          76 DMAAILTSLERGDVLFIDEIHRLNK---------------------AVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQP  134 (238)
T ss_dssp             HHHHHHHHCCTTCEEEEETGGGCCH---------------------HHHHHHHHHHHTSCCCC---------------CC
T ss_pred             HHHHHHHhhccCCchHHHHHHHhhh---------------------HHHhhcccceeeeeeeeeecCcccccccccCCCC
Confidence            8888888888899999999998742                     11122222222110              001235


Q ss_pred             eEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHH-HHHHHhcCCCCHHHH
Q 012016          360 RIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEE-IEELISTTQVTPAEV  429 (473)
Q Consensus       360 ~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~-i~~l~~~~~~t~a~i  429 (473)
                      +++|++||++..+++++++  ||+..+.++.|+.+++..++..+.........++ +..++..+..+.+.+
T Consensus       135 ~~~I~at~~~~~~~~~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~gd~R~a  203 (238)
T d1in4a2         135 FTLVGATTRSGLLSSPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIA  203 (238)
T ss_dssp             CEEEEEESCGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTTCHHHH
T ss_pred             eEEEEecCCCcccccccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCCCHHHH
Confidence            7999999999999999999  9999999999999999999998887665554444 444444334444433

>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=99.87  E-value=2.8e-25  Score=218.26  Aligned_cols=152  Identities=13%  Similarity=0.105  Sum_probs=117.2

Q ss_pred             hHHhhhcCCCCceeE-EeCCCCCCHHHHHHHHHHhcC--CceEEccccccc------CchHHHHHHHHhccCceEEEecc
Q 012016          243 DYYRRVGKAWKRGYL-LYGPPGTGKSSLIAAMANYLN--FDVYDLELTELR------SNSDLRTLLVATANRSILVVEDI  313 (473)
Q Consensus       243 ~~y~~~g~~~~rg~L-L~GPpGtGKT~la~alA~~l~--~~~~~l~~~~~~------~~~~l~~l~~~~~~~sIL~iDdi  313 (473)
                      ..++.+|...++|++ ||||||||||.+|+++|.+++  .+++.++.+++.      .+..++.+|..+.++||||||||
T Consensus       112 ~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~~~ilf~DEi  191 (321)
T d1w44a_         112 VVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSL  191 (321)
T ss_dssp             EEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEECC
T ss_pred             HHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhhccEEEeehh
Confidence            344555555567765 489999999999999999986  788999988873      45789999999999999999999


Q ss_pred             ccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC---CCCCccccCCCceeeEEEeCC
Q 012016          314 DCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRMDVHVHMSY  390 (473)
Q Consensus       314 D~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRfd~~I~~~~  390 (473)
                      |.+...+..  .       +......+++++||..|||+.+.  .+++||+|||+.   +.+|++++||||||++|++++
T Consensus       192 d~~~~~r~~--~-------~~~~~~~r~v~~lL~e~dg~~~~--~~v~viaatN~~~~~~~i~~~~~r~~Rf~~~v~v~~  260 (321)
T d1w44a_         192 KNVIGAAGG--N-------TTSGGISRGAFDLLSDIGAMAAS--RGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVIS  260 (321)
T ss_dssp             TTTC--------------------CCHHHHHHHHHHHHHHHH--HTCEEEEECCCCCCCHHHHHHHHHHHHHSCSEEEEE
T ss_pred             hhhcccccc--C-------CCCCcchhhhhhhhhhccccccC--CCeEEEEeCCCcccccchhhhhhccCcccceeecCC
Confidence            999763321  1       11233457999999999999765  359999999952   335566689999999999999


Q ss_pred             CCHHHHHHHHHHHhC
Q 012016          391 CTPSGFKLLAANYLG  405 (473)
Q Consensus       391 p~~~~r~~l~~~~l~  405 (473)
                      |+.+.|.+|+..+..
T Consensus       261 pd~~~r~~il~~~~~  275 (321)
T d1w44a_         261 TDVDGEWQVLTRTGE  275 (321)
T ss_dssp             CSSTTEEEEEEECBT
T ss_pred             CChHHHHHHHHHhcc
Confidence            999999888876543

>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=99.84  E-value=6.7e-20  Score=173.05  Aligned_cols=167  Identities=19%  Similarity=0.247  Sum_probs=123.1

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCch
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNS  293 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~  293 (473)
                      .|.+|++++|++++++.+...+..+..        +...+.++|||||||||||++|+++|+++++++..++.+......
T Consensus         4 RP~~~ddivGq~~~~~~L~~~i~~~~~--------~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~~   75 (239)
T d1ixsb2           4 RPKTLDEYIGQERLKQKLRVYLEAAKA--------RKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPG   75 (239)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHHTT--------SSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHh--------cCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccch
Confidence            578999999999999988776553322        233457899999999999999999999999999999988776544


Q ss_pred             HHHHHHHHh-ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--------------cCCCC
Q 012016          294 DLRTLLVAT-ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--------------SSCGD  358 (473)
Q Consensus       294 ~l~~l~~~~-~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--------------~~~~~  358 (473)
                      .....+... .+++|++|||+|.+..                     .....++..|+...              .....
T Consensus        76 ~~~~~~~~~~~~~~i~~iDe~~~~~~---------------------~~~~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~  134 (239)
T d1ixsb2          76 DLAAILANSLEEGDILFIDEIHRLSR---------------------QAEEHLYPAMEDFVMDIVIGQGPAARTIRLELP  134 (239)
T ss_dssp             HHHHHHHTTCCTTCEEEEETGGGCCH---------------------HHHHHHHHHHHHSEEEEECSCTTCCCEEEEECC
T ss_pred             hhHHHHHhhccCCCeeeeecccccch---------------------hHHHhhhhhhhhhhhhhhhccchhhhhcccCCC
Confidence            444444333 3568999999998732                     22233333332110              01123


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCC
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHIL  411 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l  411 (473)
                      .+++|++||++...+++.++  |+...+.+..|+.+++..++.+.+.......
T Consensus       135 ~~~~i~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~  185 (239)
T d1ixsb2         135 RFTLIGATTRPGLITAPLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRI  185 (239)
T ss_dssp             CCEEEEEESCCSSCSCGGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCB
T ss_pred             CEEEEeeccCcccccchhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCcc
Confidence            47788999999988888888  7888999999999999999998876654433

>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=99.82  E-value=2.2e-20  Score=183.85  Aligned_cols=173  Identities=17%  Similarity=0.275  Sum_probs=124.4

Q ss_pred             cccchHHHHHHHHHHHHHHhchhHHhhh-cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccccc--------C
Q 012016          221 LAMEQEQKTKIMQDLERFVKRKDYYRRV-GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELR--------S  291 (473)
Q Consensus       221 l~~~~~~k~~l~~~l~~fl~~~~~y~~~-g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~--------~  291 (473)
                      |+|+++.|+.|...+...+++....... +..+++|+||+||||||||+||++||+.++.+++.++++.+.        .
T Consensus        16 ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~~   95 (309)
T d1ofha_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEV   95 (309)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGST
T ss_pred             ccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEeeec
Confidence            6899999999988775554432211111 112468999999999999999999999999999999998873        2


Q ss_pred             chHHHHHHHHhc-------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC------C
Q 012016          292 NSDLRTLLVATA-------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG------D  358 (473)
Q Consensus       292 ~~~l~~l~~~~~-------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~------~  358 (473)
                      ...++.++..+.       ++|||||||||.+.+.+.  .       ...+......++.||..+||.....+      .
T Consensus        96 ~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~--~-------~~~~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s  166 (309)
T d1ofha_          96 DSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGE--Y-------SGADVSREGVQRDLLPLVEGSTVSTKHGMVKTD  166 (309)
T ss_dssp             THHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSS--C-------CSSHHHHHHHHHHHHHHHHCCEEEETTEEEECT
T ss_pred             cccccccchhhhcccccccCCceEEehhhhhhhhhcc--C-------cccchhhhHHHHHhhHHhcCCEEecCCeEEEcc
Confidence            345677776653       479999999999965111  0       01112234467889999998532211      2


Q ss_pred             ceEEEEe----cCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          359 ERIIVFT----TNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       359 ~~iiI~t----TN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      ++++|++    +|.+..++|++++  ||+..+.++.|+..++.+|+..+.
T Consensus       167 ~ilfi~~ga~~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~~~Il~~~~  214 (309)
T d1ofha_         167 HILFIASGAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPH  214 (309)
T ss_dssp             TCEEEEEECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSST
T ss_pred             ceeEEeccchhhcCcccchhhhhh--hhheeeeccCCCHHHHHHHHHHHH
Confidence            3455655    5677788888875  999999999999999999987543

>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=99.79  E-value=1.2e-18  Score=165.36  Aligned_cols=170  Identities=16%  Similarity=0.278  Sum_probs=120.6

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchh----HHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKD----YYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT  287 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~----~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~  287 (473)
                      ...|.+|++|+|+++.+++|.+.+..+.....    .+...|..+.+++|||||||||||++|+++|++++.+++.++.+
T Consensus         7 ky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~~~~~~~   86 (253)
T d1sxja2           7 KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNAS   86 (253)
T ss_dssp             HTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECTT
T ss_pred             CcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhhhccccc
Confidence            35689999999999999999988877654322    22344566678999999999999999999999999999999998


Q ss_pred             cccCchHHHHHHHHh--------------------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHH
Q 012016          288 ELRSNSDLRTLLVAT--------------------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN  347 (473)
Q Consensus       288 ~~~~~~~l~~l~~~~--------------------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~  347 (473)
                      ...+...+...+...                    ....++++||+|.+..                  ..+..+..++.
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~------------------~~~~~~~~~~~  148 (253)
T d1sxja2          87 DVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSG------------------GDRGGVGQLAQ  148 (253)
T ss_dssp             SCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCT------------------TSTTHHHHHHH
T ss_pred             cchhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeecccccc------------------chhhhhHHHhh
Confidence            876555454432211                    1357999999998743                  12233444554


Q ss_pred             HhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          348 FIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       348 ~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      .....    ...++++++++....+++ + +  |+...|+|+.|+.+++..++.+.+..+
T Consensus       149 ~~~~~----~~~ii~i~~~~~~~~~~~-l-~--~~~~~i~f~~~~~~~i~~~l~~i~~~e  200 (253)
T d1sxja2         149 FCRKT----STPLILICNERNLPKMRP-F-D--RVCLDIQFRRPDANSIKSRLMTIAIRE  200 (253)
T ss_dssp             HHHHC----SSCEEEEESCTTSSTTGG-G-T--TTSEEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             hhccc----cccccccccccccccccc-c-c--ceeeeeeccccchhHHHHHHHHHHHHh
Confidence            44322    123455555555555554 4 3  556899999999999999999877543

>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=99.75  E-value=1.9e-17  Score=156.43  Aligned_cols=155  Identities=18%  Similarity=0.300  Sum_probs=118.4

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-------------
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-------------  279 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-------------  279 (473)
                      ..|.+|++++|++++++.+...+    ..        ...++++|||||||||||++|+++++.++.             
T Consensus         6 yrP~~~~dlig~~~~~~~L~~~i----~~--------~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~   73 (239)
T d1njfa_           6 WRPQTFADVVGQEHVLTALANGL----SL--------GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCD   73 (239)
T ss_dssp             TCCSSGGGSCSCHHHHHHHHHHH----HT--------TCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSH
T ss_pred             hCCCCHHHccChHHHHHHHHHHH----Hc--------CCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccch
Confidence            46799999999988877765443    22        123568999999999999999999998843             


Q ss_pred             -----------ceEEcccccccCchHHHHHHHHhc------cCceEEEeccccccccccCCccccCCCCCCCccchhHHH
Q 012016          280 -----------DVYDLELTELRSNSDLRTLLVATA------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTL  342 (473)
Q Consensus       280 -----------~~~~l~~~~~~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~l  342 (473)
                                 +++.++.++......+++++....      ...|+||||+|.+.                     ....
T Consensus        74 ~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~---------------------~~~q  132 (239)
T d1njfa_          74 NCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS---------------------RHSF  132 (239)
T ss_dssp             HHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC---------------------HHHH
T ss_pred             HHHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCC---------------------HHHH
Confidence                       355555554444556777766553      33599999999872                     3455


Q ss_pred             HHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc
Q 012016          343 SGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK  407 (473)
Q Consensus       343 s~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~  407 (473)
                      +.|+..|+..    +...++|++||.++.+.+++++  |+ ..+.|+.|+.++...++.+....+
T Consensus       133 ~~Llk~lE~~----~~~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e  190 (239)
T d1njfa_         133 NALLKTLEEP----PEHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEE  190 (239)
T ss_dssp             HHHHHHHHSC----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcC----CCCeEEEEEcCCccccChhHhh--hh-cccccccCcHHHhhhHHHHHHhhh
Confidence            7788888753    3568899999999999999998  88 579999999999888888776544

>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=99.72  E-value=2e-17  Score=154.99  Aligned_cols=158  Identities=13%  Similarity=0.172  Sum_probs=117.6

Q ss_pred             cCCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----CceEEcc
Q 012016          211 NLDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----FDVYDLE  285 (473)
Q Consensus       211 ~~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~l~  285 (473)
                      ....|.+|++|+|++++++.+...+.    ...         ..++|||||||||||++|+++|++++     .+++.++
T Consensus        16 ~ky~P~~~~diig~~~~~~~l~~~i~----~~~---------~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n   82 (231)
T d1iqpa2          16 EKYRPQRLDDIVGQEHIVKRLKHYVK----TGS---------MPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELN   82 (231)
T ss_dssp             HHTCCCSTTTCCSCHHHHHHHHHHHH----HTC---------CCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEE
T ss_pred             HHhCCCCHHHccCcHHHHHHHHHHHH----cCC---------CCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEe
Confidence            45678999999999988887665443    211         24699999999999999999999874     5777777


Q ss_pred             cccccCchHHHHHHHHh--------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          286 LTELRSNSDLRTLLVAT--------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       286 ~~~~~~~~~l~~l~~~~--------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      +++..+...++..+...        ..+.|++|||+|.+..                     .....|+..++..    .
T Consensus        83 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~---------------------~~~~~ll~~l~~~----~  137 (231)
T d1iqpa2          83 ASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ---------------------DAQQALRRTMEMF----S  137 (231)
T ss_dssp             TTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH---------------------HHHHHHHHHHHHT----T
T ss_pred             cCcccchhHHHHHHHHHHhhhhccCCCceEEeehhhhhcch---------------------hHHHHHhhhcccC----C
Confidence            76653333333333222        2568999999998742                     2344566666643    2


Q ss_pred             CceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcccc
Q 012016          358 DERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEH  409 (473)
Q Consensus       358 ~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~  409 (473)
                      ...++|++||++..+++++.+  |+. .+.++.|+..+...++.+.+..+..
T Consensus       138 ~~~~~i~~~n~~~~i~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~e~i  186 (231)
T d1iqpa2         138 SNVRFILSCNYSSKIIEPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEGL  186 (231)
T ss_dssp             TTEEEEEEESCGGGSCHHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTTC
T ss_pred             cceEEEeccCChhhchHhHhC--ccc-cccccccchhhHHHHHHHHHHHhCC
Confidence            457899999999999999998  885 6999999999999999988765543

>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=99.71  E-value=1.2e-16  Score=149.02  Aligned_cols=187  Identities=14%  Similarity=0.190  Sum_probs=133.5

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----CceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----FDVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~l~~  286 (473)
                      ...|.+|++++|++++++.+...    +...       .  ..++|||||||||||++|+++|++++     .+++.++.
T Consensus         8 KyrP~~~~d~ig~~~~~~~L~~~----~~~~-------~--~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~   74 (224)
T d1sxjb2           8 KYRPQVLSDIVGNKETIDRLQQI----AKDG-------N--MPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNA   74 (224)
T ss_dssp             HTCCSSGGGCCSCTHHHHHHHHH----HHSC-------C--CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECT
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHH----HHcC-------C--CCeEEEECCCCCCchhhHHHHHHHHhccccccccccccc
Confidence            46789999999999887776554    3321       1  23699999999999999999999985     45778888


Q ss_pred             ccccCchHHHHHHHHhc---------cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCC
Q 012016          287 TELRSNSDLRTLLVATA---------NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCG  357 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~~---------~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~  357 (473)
                      ++..+...+...+....         ...+++|||+|.+..                     .....|+..++..    .
T Consensus        75 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~---------------------~~~~~ll~~~e~~----~  129 (224)
T d1sxjb2          75 SDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA---------------------GAQQALRRTMELY----S  129 (224)
T ss_dssp             TSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH---------------------HHHHTTHHHHHHT----T
T ss_pred             cccCCceehhhHHHHHHHhhccCCCcceEEEEEecccccch---------------------hHHHHHhhhcccc----c
Confidence            77765555544443221         346999999998742                     2345566666543    3


Q ss_pred             CceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHHHHHh-cC
Q 012016          358 DERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQLM-RN  436 (473)
Q Consensus       358 ~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~~~l~-~~  436 (473)
                      ...+++++||....+.++|++  |+ ..|+|+.|+.++...++...+..++.             .+++..+...+- ..
T Consensus       130 ~~~~~i~~~~~~~~i~~~l~s--r~-~~i~~~~~~~~~i~~~l~~i~~~e~~-------------~i~~~~l~~I~~~s~  193 (224)
T d1sxjb2         130 NSTRFAFACNQSNKIIEPLQS--QC-AILRYSKLSDEDVLKRLLQIIKLEDV-------------KYTNDGLEAIIFTAE  193 (224)
T ss_dssp             TTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTC-------------CBCHHHHHHHHHHHT
T ss_pred             cceeeeeccCchhhhhhHHHH--HH-HHhhhcccchhhhHHHHHHHHHhccc-------------CCCHHHHHHHHHHcC
Confidence            458889999999999999998  88 47999999999999888877754432             233333322222 25


Q ss_pred             CCHHHHHHHHHHHHHH
Q 012016          437 DDPELVLNGLIEFLKV  452 (473)
Q Consensus       437 ~~~~~al~~l~~~l~~  452 (473)
                      +|++.|+..|..+...
T Consensus       194 Gd~R~ai~~Lq~~~~~  209 (224)
T d1sxjb2         194 GDMRQAINNLQSTVAG  209 (224)
T ss_dssp             TCHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHc
Confidence            7888888888766543

>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=99.69  E-value=7.1e-17  Score=150.63  Aligned_cols=156  Identities=22%  Similarity=0.288  Sum_probs=113.5

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCC-----ceEEccc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNF-----DVYDLEL  286 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~-----~~~~l~~  286 (473)
                      ...|.+|++++|++++++.+...+    ...       .  ..++|||||||||||++++++|++++.     .++..+.
T Consensus         7 kyrP~~~~divg~~~~~~~L~~~i----~~~-------~--~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~   73 (227)
T d1sxjc2           7 KYRPETLDEVYGQNEVITTVRKFV----DEG-------K--LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNA   73 (227)
T ss_dssp             HTCCSSGGGCCSCHHHHHHHHHHH----HTT-------C--CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECT
T ss_pred             hhCCCCHHHccCcHHHHHHHHHHH----HcC-------C--CCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecc
Confidence            457899999999988877765543    321       1  225999999999999999999999742     3455665


Q ss_pred             ccccCchHHHHHHHHh--------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC
Q 012016          287 TELRSNSDLRTLLVAT--------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD  358 (473)
Q Consensus       287 ~~~~~~~~l~~l~~~~--------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~  358 (473)
                      ++..+...........        ....|++|||+|.+.                     ....+.|+..|+..    ..
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~---------------------~~~~~~Ll~~le~~----~~  128 (227)
T d1sxjc2          74 SDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMT---------------------NAAQNALRRVIERY----TK  128 (227)
T ss_dssp             TSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSC---------------------HHHHHHHHHHHHHT----TT
T ss_pred             cccCCeeeeecchhhccccccccCCCeEEEEEeccccch---------------------hhHHHHHHHHhhhc----cc
Confidence            5543333222222211        133599999999873                     33566788888754    24


Q ss_pred             ceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccc
Q 012016          359 ERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKE  408 (473)
Q Consensus       359 ~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~  408 (473)
                      ..+++++||.+..+++++++  |+ ..+.|+.|+.++...++.+.+..+.
T Consensus       129 ~~~~~~~~~~~~~i~~~i~s--r~-~~i~~~~~~~~~i~~~l~~I~~~e~  175 (227)
T d1sxjc2         129 NTRFCVLANYAHKLTPALLS--QC-TRFRFQPLPQEAIERRIANVLVHEK  175 (227)
T ss_dssp             TEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHTTT
T ss_pred             ceeeccccCcHHHhHHHHHH--HH-hhhcccccccccccccccccccccc
Confidence            58899999999999999998  87 5789999999999988887766543

>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=99.66  E-value=1.7e-16  Score=149.92  Aligned_cols=186  Identities=11%  Similarity=0.182  Sum_probs=117.4

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCc---e-------
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFD---V-------  281 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~---~-------  281 (473)
                      ...|.+|++++|++++++.|..    ++...       . ...++|||||||||||++|+++|+++..+   .       
T Consensus         4 ky~P~~~~diig~~~~~~~L~~----~~~~~-------~-~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~   71 (252)
T d1sxje2           4 KYRPKSLNALSHNEELTNFLKS----LSDQP-------R-DLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQ   71 (252)
T ss_dssp             TTCCCSGGGCCSCHHHHHHHHT----TTTCT-------T-CCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-------
T ss_pred             ccCCCCHHHccCcHHHHHHHHH----HHHcC-------C-CCCeEEEECCCCCCHHHHHHHHHHhhcCcccccccccccc
Confidence            5678999999999877776543    33221       1 12369999999999999999999986111   1       


Q ss_pred             -------------------EEcccccccCc--hHHHHHHHHh----------------ccCceEEEeccccccccccCCc
Q 012016          282 -------------------YDLELTELRSN--SDLRTLLVAT----------------ANRSILVVEDIDCTIDLQDRLP  324 (473)
Q Consensus       282 -------------------~~l~~~~~~~~--~~l~~l~~~~----------------~~~sIL~iDdiD~l~~~~~r~~  324 (473)
                                         ..+........  ..........                ....+++|||+|.+.       
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~-------  144 (252)
T d1sxje2          72 FVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLT-------  144 (252)
T ss_dssp             -----------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSC-------
T ss_pred             ccccccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEeccccccc-------
Confidence                               11111111111  1111111111                123599999999873       


Q ss_pred             cccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          325 ADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       325 ~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                                    ......|+..++..    +....+|+|||+++.+++++++  || ..|+|+.|+.++...++...+
T Consensus       145 --------------~~~~~~l~~~~e~~----~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~i~  203 (252)
T d1sxje2         145 --------------KDAQAALRRTMEKY----SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVV  203 (252)
T ss_dssp             --------------HHHHHHHHHHHHHS----TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHH
T ss_pred             --------------cccchhhhcccccc----cccccceeeeccccchhhhhhc--ch-heeeecccchhhHHHHHHHHH
Confidence                          23455666666643    3457889999999999999998  88 589999999999999888766


Q ss_pred             CccccCCHHHHHHHHhcCCCCHHHHHHHHh--cCCCHHHHHHHHHHHH
Q 012016          405 GIKEHILFEEIEELISTTQVTPAEVAEQLM--RNDDPELVLNGLIEFL  450 (473)
Q Consensus       405 ~~~~~~l~~~i~~l~~~~~~t~a~i~~~l~--~~~~~~~al~~l~~~l  450 (473)
                      ..+...             +.+.++.+.+.  ..||.+.|+..|..+.
T Consensus       204 ~~e~~~-------------~~~~~~l~~i~~~s~Gd~R~ai~~Lq~~~  238 (252)
T d1sxje2         204 TNERIQ-------------LETKDILKRIAQASNGNLRVSLLMLESMA  238 (252)
T ss_dssp             HHHTCE-------------ECCSHHHHHHHHHHTTCHHHHHHHHTHHH
T ss_pred             HHcCCC-------------CCcHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence            543221             11112222222  2578888887665444

>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=99.64  E-value=1.1e-16  Score=160.03  Aligned_cols=147  Identities=20%  Similarity=0.164  Sum_probs=101.0

Q ss_pred             HHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccC
Q 012016          226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANR  305 (473)
Q Consensus       226 ~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~  305 (473)
                      +++..+.+.+..++        .|.|.++++|||||||||||++++++|++++.+++.+++++..+.    ..+......
T Consensus       135 ~~~~~i~~~l~~~~--------~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~----~~l~~~~~~  202 (362)
T d1svma_         135 KMDSVVYDFLKCMV--------YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLN----FELGVAIDQ  202 (362)
T ss_dssp             THHHHHHHHHHHHH--------HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHH----HHHGGGTTC
T ss_pred             chHHHHHHHHHHHH--------hCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhH----HHHHhHHHH
Confidence            34555555454443        377888999999999999999999999999999999998876432    223344567


Q ss_pred             ceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCC----------ceEEEEecCCCCCCCcc
Q 012016          306 SILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGD----------ERIIVFTTNHKEKLDPA  375 (473)
Q Consensus       306 sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~----------~~iiI~tTN~~~~ld~a  375 (473)
                      .+.++||+++....+...          .....-..+..|.+.+||....+.+          ...+|+|||+   ++++
T Consensus       203 ~~~l~d~~~~~~~~~~~~----------~~~~~~DeiD~l~~~~dg~~~~~~~~~~~~~~~~~~~p~i~ttN~---~~~~  269 (362)
T d1svma_         203 FLVVFEDVKGTGGESRDL----------PSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNE---YSVP  269 (362)
T ss_dssp             SCEEETTCCCSTTTTTTC----------CCCSHHHHHHTTHHHHHCSSCEEECCSSSCCEEECCCCEEEEECS---CCCC
T ss_pred             HHHHHHHHHHhhhhccCC----------CCeEEEehHhhcccccCCcchhhhhhhhhchhhhccCCceeeccc---cccc
Confidence            788899998765321110          0111223345566777765322111          1247889995   5778


Q ss_pred             ccCCCceeeEEEeCCCCHHHHH
Q 012016          376 LLRPGRMDVHVHMSYCTPSGFK  397 (473)
Q Consensus       376 LlrpgRfd~~I~~~~p~~~~r~  397 (473)
                      ++|||||++.|.+..|....+.
T Consensus       270 ~~r~~Rf~~~i~~~~~~~~~~~  291 (362)
T d1svma_         270 KTLQARFVKQIDFRPKDYLKHC  291 (362)
T ss_dssp             HHHHTTEEEEEECCCCHHHHHH
T ss_pred             ccccccCceEEeecCCCcHHHH
Confidence            8899999999999999877764

>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=99.64  E-value=1.3e-15  Score=142.30  Aligned_cols=188  Identities=16%  Similarity=0.147  Sum_probs=125.7

Q ss_pred             CCCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc------CCceEEcc
Q 012016          212 LDHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL------NFDVYDLE  285 (473)
Q Consensus       212 ~~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l------~~~~~~l~  285 (473)
                      ...|.+|++++|++++++.+..    ++....         ..++||+||||||||++++++|+++      +...+.++
T Consensus         5 ky~P~~~~diig~~~~~~~l~~----~i~~~~---------~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~   71 (237)
T d1sxjd2           5 KYRPKNLDEVTAQDHAVTVLKK----TLKSAN---------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELN   71 (237)
T ss_dssp             HTCCSSTTTCCSCCTTHHHHHH----HTTCTT---------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEEC
T ss_pred             hhCCCCHHHccCcHHHHHHHHH----HHHcCC---------CCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhhee
Confidence            3578999999999988776644    443221         2359999999999999999999987      56666666


Q ss_pred             cccccCchHHHHHHHHh------------------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHH
Q 012016          286 LTELRSNSDLRTLLVAT------------------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN  347 (473)
Q Consensus       286 ~~~~~~~~~l~~l~~~~------------------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~  347 (473)
                      .+...........+...                  ....|+||||+|.+..                     ...+.++.
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~---------------------~~~~~l~~  130 (237)
T d1sxjd2          72 ASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA---------------------DAQSALRR  130 (237)
T ss_dssp             SSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH---------------------HHHHHHHH
T ss_pred             ccccccchHHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCH---------------------HHHHHHhh
Confidence            65554332222222111                  1234899999998742                     23334454


Q ss_pred             HhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHH
Q 012016          348 FIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELISTTQVTPA  427 (473)
Q Consensus       348 ~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a  427 (473)
                      .++..    ....++|.+++....+.+++.+  |+ .+|.|+.|+.++...++...+..+...             +++.
T Consensus       131 ~~~~~----~~~~~~i~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~~~~~L~~i~~~e~i~-------------i~~~  190 (237)
T d1sxjd2         131 TMETY----SGVTRFCLICNYVTRIIDPLAS--QC-SKFRFKALDASNAIDRLRFISEQENVK-------------CDDG  190 (237)
T ss_dssp             HHHHT----TTTEEEEEEESCGGGSCHHHHH--HS-EEEECCCCCHHHHHHHHHHHHHTTTCC-------------CCHH
T ss_pred             ccccc----cccccccccccccccccccccc--hh-hhhccccccccccchhhhhhhhhhcCc-------------CCHH
Confidence            44432    2457788899999999999998  88 689999999999999988776554332             3332


Q ss_pred             HHHHHHhc-CCCHHHHHHHHHHHHHHh
Q 012016          428 EVAEQLMR-NDDPELVLNGLIEFLKVK  453 (473)
Q Consensus       428 ~i~~~l~~-~~~~~~al~~l~~~l~~~  453 (473)
                      .+....-. .+|...|+..|..+....
T Consensus       191 ~l~~ia~~s~gd~R~ai~~L~~~~~~~  217 (237)
T d1sxjd2         191 VLERILDISAGDLRRGITLLQSASKGA  217 (237)
T ss_dssp             HHHHHHHHTSSCHHHHHHHHHHTHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHHHHHhc
Confidence            22222222 478888887776554433

>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=99.56  E-value=6.9e-14  Score=128.86  Aligned_cols=124  Identities=18%  Similarity=0.161  Sum_probs=94.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcC------------------------CceEEcccccc---cCchHHHHHHHHhc-
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLN------------------------FDVYDLELTEL---RSNSDLRTLLVATA-  303 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~------------------------~~~~~l~~~~~---~~~~~l~~l~~~~~-  303 (473)
                      .+.++||+||||+|||++|+++|+.+.                        .+++.+....-   .....++++..... 
T Consensus        23 l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~l~~~~~~  102 (207)
T d1a5ta2          23 GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNE  102 (207)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTS
T ss_pred             cCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccchhhHHhhhhhh
Confidence            466899999999999999999999772                        23344332221   22345666665543 


Q ss_pred             -----cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccC
Q 012016          304 -----NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLR  378 (473)
Q Consensus       304 -----~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlr  378 (473)
                           +..|++|||+|.+.                     ....+.||..|+..    +.++++|++||++..+.|++++
T Consensus       103 ~~~~~~~kviIide~d~l~---------------------~~a~n~Llk~lEep----~~~~~fIl~t~~~~~ll~tI~S  157 (207)
T d1a5ta2         103 HARLGGAKVVWVTDAALLT---------------------DAAANALLKTLEEP----PAETWFFLATREPERLLATLRS  157 (207)
T ss_dssp             CCTTSSCEEEEESCGGGBC---------------------HHHHHHHHHHHTSC----CTTEEEEEEESCGGGSCHHHHT
T ss_pred             ccccCccceEEechhhhhh---------------------hhhhHHHHHHHHhh----cccceeeeeecChhhhhhhhcc
Confidence                 35699999999873                     45678899999863    4568999999999999999998


Q ss_pred             CCceeeEEEeCCCCHHHHHHHHHHH
Q 012016          379 PGRMDVHVHMSYCTPSGFKLLAANY  403 (473)
Q Consensus       379 pgRfd~~I~~~~p~~~~r~~l~~~~  403 (473)
                        |+ ..|.|+.|+.++...++..-
T Consensus       158 --Rc-~~i~~~~~~~~~~~~~L~~~  179 (207)
T d1a5ta2         158 --RC-RLHYLAPPPEQYAVTWLSRE  179 (207)
T ss_dssp             --TS-EEEECCCCCHHHHHHHHHHH
T ss_pred             --ee-EEEecCCCCHHHHHHHHHHc
Confidence              88 78999999999887777643

>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=99.55  E-value=2.1e-14  Score=133.06  Aligned_cols=175  Identities=15%  Similarity=0.259  Sum_probs=109.5

Q ss_pred             CCCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc
Q 012016          213 DHPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL  289 (473)
Q Consensus       213 ~~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~  289 (473)
                      ++..||++++..+. -+.....+..+...+      | ...+.++||||||||||+|++|+|+++   +..++.++..+.
T Consensus         4 n~~~tFdnF~vg~~-N~~a~~~~~~~~~~~------~-~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~   75 (213)
T d1l8qa2           4 NPKYTLENFIVGEG-NRLAYEVVKEALENL------G-SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF   75 (213)
T ss_dssp             CTTCCSSSCCCCTT-THHHHHHHHHHHHTT------T-TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CCCCChhhccCCCc-HHHHHHHHHHHHhCc------C-CCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHH
Confidence            44579999764322 222333344443322      1 223459999999999999999999988   567777776654


Q ss_pred             cC-------chHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEE
Q 012016          290 RS-------NSDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERII  362 (473)
Q Consensus       290 ~~-------~~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~ii  362 (473)
                      ..       .....+.+.......+|+|||||.+..                ....+..+..++|.+   ...  +..+|
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~~----------------~~~~~~~lf~lin~~---~~~--~~~ii  134 (213)
T d1l8qa2          76 AQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSG----------------KERTQIEFFHIFNTL---YLL--EKQII  134 (213)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTT----------------CHHHHHHHHHHHHHH---HHT--TCEEE
T ss_pred             HHHHHHHHHccchhhHHHHHhhccchhhhhhhhhcC----------------chHHHHHHHHHHHHH---hhc--cceEE
Confidence            21       122334444556789999999999853                222344444455443   332  34666


Q ss_pred             EEecCCCCCC---CccccCCCcee--eEEEeCCCCHHHHHHHHHHHhCccccCCHHHHHHHH
Q 012016          363 VFTTNHKEKL---DPALLRPGRMD--VHVHMSYCTPSGFKLLAANYLGIKEHILFEEIEELI  419 (473)
Q Consensus       363 I~tTN~~~~l---d~aLlrpgRfd--~~I~~~~p~~~~r~~l~~~~l~~~~~~l~~~i~~l~  419 (473)
                      |.+...|..+   .|.|..  |+.  ..+.++ |+.+.+..+++.+....+..+.+++...+
T Consensus       135 its~~~p~~l~~~~~dL~S--RL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl  193 (213)
T d1l8qa2         135 LASDRHPQKLDGVSDRLVS--RFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYL  193 (213)
T ss_dssp             EEESSCGGGCTTSCHHHHH--HHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHH
T ss_pred             EecCCcchhccccchHHHH--HhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            6666777655   466766  653  667776 67788999999888766555555554443

>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=99.48  E-value=6.1e-13  Score=125.48  Aligned_cols=160  Identities=15%  Similarity=0.080  Sum_probs=104.1

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccccccCc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTELRSN  292 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~~~~~  292 (473)
                      ..+++++.++..+.|.+.+...++++.       ..++++||+||||||||++++++++.+    +..++.+++......
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~~~-------~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~   86 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNF   86 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHSTT-------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCSH
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhCCC-------CCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhhhhh
Confidence            446788988888888887776665432       346789999999999999999999987    355555554432110


Q ss_pred             ----------------------hHH----HHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHH
Q 012016          293 ----------------------SDL----RTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFL  346 (473)
Q Consensus       293 ----------------------~~l----~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL  346 (473)
                                            ..+    ...+.......++++|++|.+..                  .....+..++
T Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~------------------~~~~~~~~~~  148 (276)
T d1fnna2          87 TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAP------------------DILSTFIRLG  148 (276)
T ss_dssp             HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCH------------------HHHHHHHHHT
T ss_pred             hhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhh------------------hhhhhHHHHH
Confidence                                  111    11122223467788899887632                  1122222233


Q ss_pred             HHhcccccCCCCceEEEEecCCC---CCCCccccCCCce-eeEEEeCCCCHHHHHHHHHHHhCc
Q 012016          347 NFIDGLWSSCGDERIIVFTTNHK---EKLDPALLRPGRM-DVHVHMSYCTPSGFKLLAANYLGI  406 (473)
Q Consensus       347 ~~ldg~~~~~~~~~iiI~tTN~~---~~ld~aLlrpgRf-d~~I~~~~p~~~~r~~l~~~~l~~  406 (473)
                      ..+..   .....+++|+++|..   +.+++++.+  |+ ...|+|+.|+.+++..|+...+..
T Consensus       149 ~~~~~---~~~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i~~~~~~~~e~~~il~~r~~~  207 (276)
T d1fnna2         149 QEADK---LGAFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKA  207 (276)
T ss_dssp             TCHHH---HSSCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             hcccc---ccccceEEeecCCchhhhhhcchhhhh--hhcchhccccchhHHHHHHHHHHHHHH
Confidence            22222   222457788888874   567888876  54 356899999999999999877653

>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=99.47  E-value=2.6e-13  Score=128.86  Aligned_cols=219  Identities=9%  Similarity=0.045  Sum_probs=125.2

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---------CceEEcccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---------FDVYDLELT  287 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---------~~~~~l~~~  287 (473)
                      ..+.+.+.++..+.|.+.+..++.+..    .+......++||||||||||++++++++.+.         ..+..+++.
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~~----~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~   89 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSGA----GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAF   89 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTSS----CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGG
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcCC----CCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccc
Confidence            446788888888888887766654321    0111122478899999999999999999872         334444443


Q ss_pred             cccCc----------------------hHHH----HHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHH
Q 012016          288 ELRSN----------------------SDLR----TLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVT  341 (473)
Q Consensus       288 ~~~~~----------------------~~l~----~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~  341 (473)
                      ...+.                      ..+.    ........+.++++|++|.+.....            ........
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~------------~~~~~~~~  157 (287)
T d1w5sa2          90 NAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPR------------IAAEDLYT  157 (287)
T ss_dssp             GCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTT------------SCHHHHHH
T ss_pred             cccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccc------------cchhHHHH
Confidence            33111                      1112    2222334567889999998854111            01112233


Q ss_pred             HHHHHHHhcccccCCCCceEEEEecCCCC------CCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc--ccCCHH
Q 012016          342 LSGFLNFIDGLWSSCGDERIIVFTTNHKE------KLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK--EHILFE  413 (473)
Q Consensus       342 ls~LL~~ldg~~~~~~~~~iiI~tTN~~~------~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~--~~~l~~  413 (473)
                      +..+.+.+......  ....+|+.+|.++      ..++++.+  |++.+++|+.++.++..+|+...+...  .....+
T Consensus       158 l~~l~~~l~~~~~~--~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~  233 (287)
T d1w5sa2         158 LLRVHEEIPSRDGV--NRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEP  233 (287)
T ss_dssp             HHTHHHHSCCTTSC--CBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCH
T ss_pred             HHHHHHhcchhhcc--cceeEEeecccHHHHHHHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCH
Confidence            44444444433222  3456666665543      23467777  899999999999999999998765421  111212


Q ss_pred             HHHHHHhcCCCCHHHHHHHH----hcCCCHHHHHHHHHHHHHHhhhcccccCcccc
Q 012016          414 EIEELISTTQVTPAEVAEQL----MRNDDPELVLNGLIEFLKVKRKEDEDAKPRKI  465 (473)
Q Consensus       414 ~i~~l~~~~~~t~a~i~~~l----~~~~~~~~al~~l~~~l~~~~~~~~~~~~~~~  465 (473)
                      +...++          ++..    -..+++..|++-+..++..........-+...
T Consensus       234 ~al~~i----------a~~~~~~~~~~gd~R~ai~~l~~a~~~A~~~~~~~It~~~  279 (287)
T d1w5sa2         234 RHLELI----------SDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDL  279 (287)
T ss_dssp             HHHHHH----------HHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHH
T ss_pred             HHHHHH----------HHHHhccccCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHH
Confidence            221111          1111    12478888888877777665544443333333

>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=99.45  E-value=2.6e-12  Score=122.35  Aligned_cols=198  Identities=19%  Similarity=0.262  Sum_probs=125.9

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLEL  286 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~  286 (473)
                      .++.++|.++..+++++.|    .+         ..+.++||.||||+|||++++.+|..+          +..++.+++
T Consensus        16 ~ld~~igRd~Ei~~l~~iL----~r---------~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~   82 (268)
T d1r6bx2          16 GIDPLIGREKELERAIQVL----CR---------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI   82 (268)
T ss_dssp             CSCCCCSCHHHHHHHHHHH----TS---------SSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCC
T ss_pred             CCCcccChHHHHHHHHHHH----hc---------CccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeee
Confidence            4567788776666655433    22         225789999999999999999999864          678999998


Q ss_pred             ccccC--------chHHHHHHHHhc--cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCC
Q 012016          287 TELRS--------NSDLRTLLVATA--NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSC  356 (473)
Q Consensus       287 ~~~~~--------~~~l~~l~~~~~--~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~  356 (473)
                      +.+..        +..+..++..+.  .+.||||||++.++..             +....+...+..+|   ...-+. 
T Consensus        83 ~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~-------------g~~~g~~~d~a~~L---kp~L~r-  145 (268)
T d1r6bx2          83 GSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGA-------------GAASGGQVDAANLI---KPLLSS-  145 (268)
T ss_dssp             C---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTS-------------CCSSSCHHHHHHHH---SSCSSS-
T ss_pred             chHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcC-------------CCCCCccccHHHHh---hHHHhC-
Confidence            88742        245666676654  4589999999999751             11111223334444   322222 


Q ss_pred             CCceEEEEecCCC-----CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhCcc----cc-CCHHHHHHHHhcCCCCH
Q 012016          357 GDERIIVFTTNHK-----EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLGIK----EH-ILFEEIEELISTTQVTP  426 (473)
Q Consensus       357 ~~~~iiI~tTN~~-----~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~~~----~~-~l~~~i~~l~~~~~~t~  426 (473)
                       +++-+|++|..-     ..-||+|.|  ||. .|.+..|+.++-..|+..+....    .. ...+.+...+       
T Consensus       146 -g~i~vIgatT~eey~~~~e~d~al~r--rF~-~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v-------  214 (268)
T d1r6bx2         146 -GKIRVIGSTTYQEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAV-------  214 (268)
T ss_dssp             -CCCEEEEEECHHHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHH-------
T ss_pred             -CCCeEEEeCCHHHHHHHHhhcHHHHh--hhc-ccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHH-------
Confidence             457777766532     355899999  996 79999999999888887543211    11 1122222222       


Q ss_pred             HHHHHHHhc-CCCHHHHHHHHHHHHHHhhhc
Q 012016          427 AEVAEQLMR-NDDPELVLNGLIEFLKVKRKE  456 (473)
Q Consensus       427 a~i~~~l~~-~~~~~~al~~l~~~l~~~~~~  456 (473)
                       ++++..+. ..-|+.|++-+-++....+..
T Consensus       215 -~ls~ryi~~~~~PdKAIdllDea~a~~~~~  244 (268)
T d1r6bx2         215 -ELAVKYINDRHLPDKAIDVIDEAGARARLM  244 (268)
T ss_dssp             -HHHHHHCTTSCTTHHHHHHHHHHHHHHHHS
T ss_pred             -HHHHhhccCCCCCcHHHHHHHHHHHHHHhh
Confidence             23444444 357999999777776665544

>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=99.44  E-value=4e-13  Score=131.60  Aligned_cols=159  Identities=13%  Similarity=0.220  Sum_probs=113.1

Q ss_pred             cccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc------
Q 012016          219 ETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN------  292 (473)
Q Consensus       219 ~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~------  292 (473)
                      ..|+|+++.++.|...+.....+   .... ..+...+||+||||+|||.||++||..++.+++.++++.+...      
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~---l~~~-~~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~~l   97 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAG---LGHE-HKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRL   97 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTT---CSCT-TSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSSS
T ss_pred             CeecChHHHHHHHHHHHHHHHcc---CCCC-CCCceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhhhh
Confidence            35789999999998876543321   0010 1223369999999999999999999999999999999887321      


Q ss_pred             -------------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccc--cCC-
Q 012016          293 -------------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLW--SSC-  356 (473)
Q Consensus       293 -------------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~--~~~-  356 (473)
                                   ..+...+ .....+|+++||||...                     ....+.||..+|.-.  ... 
T Consensus        98 ~g~~~gy~g~~~~~~l~~~~-~~~~~~vvl~DeieKa~---------------------~~V~~~lLqild~G~ltd~~G  155 (315)
T d1r6bx3          98 IGAPPGYVGFDQGGLLTDAV-IKHPHAVLLLDEIEKAH---------------------PDVFNILLQVMDNGTLTDNNG  155 (315)
T ss_dssp             CCCCSCSHHHHHTTHHHHHH-HHCSSEEEEEETGGGSC---------------------HHHHHHHHHHHHHSEEEETTT
T ss_pred             cccCCCccccccCChhhHHH-HhCccchhhhccccccc---------------------chHhhhhHHhhccceecCCCC
Confidence                         1122322 33567999999999762                     345677777775311  111 


Q ss_pred             ----CCceEEEEecCCC-------------------------CCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHhC
Q 012016          357 ----GDERIIVFTTNHK-------------------------EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYLG  405 (473)
Q Consensus       357 ----~~~~iiI~tTN~~-------------------------~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l~  405 (473)
                          -.+.|+|+|||--                         ..+.|.|+.  |+|..|.|.+.+.+....|+..++.
T Consensus       156 r~vdf~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~~~~~I~~~~l~  231 (315)
T d1r6bx3         156 RKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  231 (315)
T ss_dssp             EEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             CccCccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhhHHHHHHHHHHH
Confidence                1357899999942                         135677777  9999999999999999999887764

>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=99.37  E-value=3.6e-12  Score=126.93  Aligned_cols=173  Identities=20%  Similarity=0.245  Sum_probs=112.9

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhH---H---------------hhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDY---Y---------------RRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~---y---------------~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      .|+|+++.|+.+-..+.+..++...   .               ... ..++.++||.||+|||||.||++||..++.++
T Consensus        18 ~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~-~~p~~niLfiGPTGvGKTElAk~LA~~~~~~~   96 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEV-ELSKSNILLIGPTGSGKTLMAQTLAKHLDIPI   96 (364)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHT-TCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             eecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccc-cCCCcceeeeCCCCccHHHHHHHHHhhcccce
Confidence            4789999999887777544332111   0               111 23577899999999999999999999999999


Q ss_pred             EEcccccccC--------chHHHHHHHHh------ccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHH
Q 012016          282 YDLELTELRS--------NSDLRTLLVAT------ANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLN  347 (473)
Q Consensus       282 ~~l~~~~~~~--------~~~l~~l~~~~------~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~  347 (473)
                      +.++++.+..        ...+.+++...      ...+|+++||+|...+......       ...+.......+.||+
T Consensus        97 ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~-------~~~d~a~~~V~~~lLq  169 (364)
T d1um8a_          97 AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRS-------ITRDVSGEGVQQALLK  169 (364)
T ss_dssp             EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC---------------------CHHHHHHHHH
T ss_pred             eehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhcccccccc-------ccccccchHHHHhhhh
Confidence            9999998743        45566666544      2579999999998754211100       0112234567788899


Q ss_pred             Hhcccc----cC-----CCCceEEEEecCCC-------------------------------------------------
Q 012016          348 FIDGLW----SS-----CGDERIIVFTTNHK-------------------------------------------------  369 (473)
Q Consensus       348 ~ldg~~----~~-----~~~~~iiI~tTN~~-------------------------------------------------  369 (473)
                      .+|+-.    ..     ...+.++|.|+|-.                                                 
T Consensus       170 ild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (364)
T d1um8a_         170 IVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVT  249 (364)
T ss_dssp             HHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHH
T ss_pred             hhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHHhh
Confidence            888521    11     12345677777751                                                 


Q ss_pred             CCCCccccCCCceeeEEEeCCCCHHHHHHHHHH
Q 012016          370 EKLDPALLRPGRMDVHVHMSYCTPSGFKLLAAN  402 (473)
Q Consensus       370 ~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~  402 (473)
                      ..+-|.|+.  |+|..|.|...+.+...+|+..
T Consensus       250 ~~f~PEf~g--Ri~~iv~f~~L~~~~l~~Il~~  280 (364)
T d1um8a_         250 YGLIPELIG--RLPVLSTLDSISLEAMVDILQK  280 (364)
T ss_dssp             TTCCHHHHT--TCCEEEECCCCCHHHHHHHHHS
T ss_pred             hhhHHHHHH--HhcchhhHhhhhHHHHHHHHHH
Confidence            124455555  9999999999999999998864

>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=99.37  E-value=1.6e-12  Score=127.10  Aligned_cols=158  Identities=18%  Similarity=0.266  Sum_probs=112.1

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCc----
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSN----  292 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~----  292 (473)
                      .|+|+++.++.|.+.+......-.   . ...|...+||+||+|+|||.+|+++|..+   +.+++.+++++....    
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l~---~-~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~~~   99 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGLK---D-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVS   99 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGCS---C-SSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGGG
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCCC---C-CCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchhhh
Confidence            467888888888877765432100   0 11223358899999999999999999998   778999988776432    


Q ss_pred             ---------------hHHHHHHHHhccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC--
Q 012016          293 ---------------SDLRTLLVATANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS--  355 (473)
Q Consensus       293 ---------------~~l~~l~~~~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~--  355 (473)
                                     ..|.+.+.. ...+||+|||||..-                     ......|+..+|.-.-.  
T Consensus       100 ~L~g~~~gyvG~~~~~~l~~~~~~-~p~~Vvl~DEieK~~---------------------~~v~~~ll~~l~~g~~~~~  157 (315)
T d1qvra3         100 RLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFDEIEKAH---------------------PDVFNILLQILDDGRLTDS  157 (315)
T ss_dssp             GC--------------CHHHHHHH-CSSEEEEESSGGGSC---------------------HHHHHHHHHHHTTTEECCS
T ss_pred             hhcCCCCCCcCcccCChHHHHHHh-CCCcEEEEehHhhcC---------------------HHHHHHHHHHhccCceeCC
Confidence                           224433332 346999999999762                     34566677777542111  


Q ss_pred             C-----CCceEEEEecCC--------------------------CCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          356 C-----GDERIIVFTTNH--------------------------KEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       356 ~-----~~~~iiI~tTN~--------------------------~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      .     -.+.++|+|||-                          ...+.|.++.  |||..+.|...+.+...+|+...+
T Consensus       158 ~gr~v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l  235 (315)
T d1qvra3         158 HGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQL  235 (315)
T ss_dssp             SSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHH
T ss_pred             CCcEecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeeccchhhhhhHHHHHHHH
Confidence            1     135799999995                          2458888888  999999999999999998888665


Q ss_pred             C
Q 012016          405 G  405 (473)
Q Consensus       405 ~  405 (473)
                      .
T Consensus       236 ~  236 (315)
T d1qvra3         236 S  236 (315)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.33  E-value=1.8e-12  Score=127.57  Aligned_cols=149  Identities=21%  Similarity=0.267  Sum_probs=96.7

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC-----------------
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN-----------------  278 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~-----------------  278 (473)
                      -.|.+|+|++.+|..+.-.+..    .      |   ..++||+||||||||++|++++.-|.                 
T Consensus         4 ~~f~~I~Gq~~~kral~laa~~----~------~---~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~~   70 (333)
T d1g8pa_           4 FPFSAIVGQEDMKLALLLTAVD----P------G---IGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEM   70 (333)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHC----G------G---GCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGG
T ss_pred             CChhhccCcHHHHHHHHHHHhc----c------C---CCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCcccc
Confidence            4799999999998876543321    0      0   24799999999999999999998762                 


Q ss_pred             ----------------CceEEccccc----ccCchHHHHHHHH-----------hccCceEEEeccccccccccCCcccc
Q 012016          279 ----------------FDVYDLELTE----LRSNSDLRTLLVA-----------TANRSILVVEDIDCTIDLQDRLPADI  327 (473)
Q Consensus       279 ----------------~~~~~l~~~~----~~~~~~l~~l~~~-----------~~~~sIL~iDdiD~l~~~~~r~~~~~  327 (473)
                                      .+++....+.    +.+.-.+...+..           ...+.|+||||++.+           
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~-----------  139 (333)
T d1g8pa_          71 IPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLL-----------  139 (333)
T ss_dssp             SCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGS-----------
T ss_pred             ccchhhccccCcccccCceeeccCCCCcccccCcchhhhccccCcceeeccccccccccEeecccHHHH-----------
Confidence                            1111111100    0011111222211           124689999999866           


Q ss_pred             CCCCCCCccchhHHHHHHHHHhccc---------ccCCCCceEEEEecCCC-CCCCccccCCCceeeEEEeCCCC-HHHH
Q 012016          328 AGEGEGPIQQNKVTLSGFLNFIDGL---------WSSCGDERIIVFTTNHK-EKLDPALLRPGRMDVHVHMSYCT-PSGF  396 (473)
Q Consensus       328 ~~~~~~~~~~~~~~ls~LL~~ldg~---------~~~~~~~~iiI~tTN~~-~~ld~aLlrpgRfd~~I~~~~p~-~~~r  396 (473)
                                ...+++.|+..|+.-         ....+...++|+|+|.. ..++++++.  ||+.+|.+++|. .+.+
T Consensus       140 ----------~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~  207 (333)
T d1g8pa_         140 ----------EDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETR  207 (333)
T ss_dssp             ----------CHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHH
T ss_pred             ----------HHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhh--hhcceeeccCcchhhHH
Confidence                      356889999999632         11112346788888865 579999999  999999999884 4444


Q ss_pred             HHHH
Q 012016          397 KLLA  400 (473)
Q Consensus       397 ~~l~  400 (473)
                      ..+.
T Consensus       208 ~~~~  211 (333)
T d1g8pa_         208 VEVI  211 (333)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4443

>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=99.31  E-value=1.9e-12  Score=117.04  Aligned_cols=148  Identities=21%  Similarity=0.306  Sum_probs=97.1

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLEL  286 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~  286 (473)
                      .++.++|.++..+++++    .+.++         -+.+++|.||||+|||++++.+|..+          +.+++.+|+
T Consensus        20 ~ld~~igRd~Ei~~l~~----iL~r~---------~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~   86 (195)
T d1jbka_          20 KLDPVIGRDEEIRRTIQ----VLQRR---------TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM   86 (195)
T ss_dssp             CSCCCCSCHHHHHHHHH----HHTSS---------SSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECH
T ss_pred             CCCCCcCcHHHHHHHHH----HHhcc---------CCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            35667787766666544    33322         25789999999999999999999865          688999999


Q ss_pred             ccccC--------chHHHHHHHHhc---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC
Q 012016          287 TELRS--------NSDLRTLLVATA---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS  355 (473)
Q Consensus       287 ~~~~~--------~~~l~~l~~~~~---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~  355 (473)
                      +.+..        +..+..++....   .+.||||||++.++.....         .+. ......+...|   .     
T Consensus        87 ~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~---------~g~-~d~~~~Lkp~L---~-----  148 (195)
T d1jbka_          87 GALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKA---------DGA-MDAGNMLKPAL---A-----  148 (195)
T ss_dssp             HHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT---------------C-CCCHHHHHHHH---H-----
T ss_pred             HHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCC---------CCc-ccHHHHHHHHH---h-----
Confidence            88742        245666776652   3569999999999752110         010 11122333332   2     


Q ss_pred             CCCceEEEEecCCC-----CCCCccccCCCceeeEEEeCCCCHHHHHHH
Q 012016          356 CGDERIIVFTTNHK-----EKLDPALLRPGRMDVHVHMSYCTPSGFKLL  399 (473)
Q Consensus       356 ~~~~~iiI~tTN~~-----~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l  399 (473)
                      . ++..+|++|...     -.-||+|.|  ||. .|.+..|+.++-..|
T Consensus       149 r-g~l~~IgatT~eey~~~~e~d~aL~r--rF~-~I~V~Ep~~e~t~~I  193 (195)
T d1jbka_         149 R-GELHCVGATTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAI  193 (195)
T ss_dssp             T-TSCCEEEEECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTT
T ss_pred             C-CCceEEecCCHHHHHHHHHcCHHHHh--cCC-EeecCCCCHHHHHHH
Confidence            1 345566655432     244999999  996 799999999886654

>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=99.29  E-value=7.3e-12  Score=114.25  Aligned_cols=113  Identities=18%  Similarity=0.228  Sum_probs=89.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc------CCceEEcccccc-cCchHHHHHHHHhc------cCceEEEecccccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL------NFDVYDLELTEL-RSNSDLRTLLVATA------NRSILVVEDIDCTIDL  319 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l------~~~~~~l~~~~~-~~~~~l~~l~~~~~------~~sIL~iDdiD~l~~~  319 (473)
                      +..+|||||||||||++|..+++++      +.+++.+....- .+-..+|++.....      ..-|++|||+|.+   
T Consensus        15 ~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l---   91 (198)
T d2gnoa2          15 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERM---   91 (198)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGB---
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCcccc---
Confidence            5689999999999999999999987      246777776432 24567777766553      3459999999988   


Q ss_pred             ccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCCCCCCccccCCCceeeEEEeCCCCH
Q 012016          320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHKEKLDPALLRPGRMDVHVHMSYCTP  393 (473)
Q Consensus       320 ~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~~~ld~aLlrpgRfd~~I~~~~p~~  393 (473)
                                        .....+.||..|+.    ++.+.++|++||.++.+.|+++.  |+ .++.|+.|..
T Consensus        92 ------------------~~~aqNaLLK~LEE----Pp~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2          92 ------------------TQQAANAFLKALEE----PPEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             ------------------CHHHHHHTHHHHHS----CCTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCHH
T ss_pred             ------------------chhhhhHHHHHHhC----CCCCceeeeccCChhhCHHHHhc--ce-EEEeCCCchH
Confidence                              35677889999985    34678999999999999999998  87 5788887753

>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=99.22  E-value=9e-11  Score=117.34  Aligned_cols=152  Identities=22%  Similarity=0.326  Sum_probs=91.1

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc----------CCceEEccc
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL----------NFDVYDLEL  286 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l----------~~~~~~l~~  286 (473)
                      .++-++|.++..+++++.|.    ++         -+.+.+|.||||+|||+++..+|..+          +..++.+++
T Consensus        20 ~ld~~~gr~~ei~~~~~~L~----r~---------~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~   86 (387)
T d1qvra2          20 KLDPVIGRDEEIRRVIQILL----RR---------TKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQM   86 (387)
T ss_dssp             CSCCCCSCHHHHHHHHHHHH----CS---------SCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC
T ss_pred             CCCCCcCcHHHHHHHHHHHh----cC---------CCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            35667887776666655443    22         25689999999999999999999865          577999999


Q ss_pred             ccccC--------chHHHHHHHHhc---cCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccC
Q 012016          287 TELRS--------NSDLRTLLVATA---NRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSS  355 (473)
Q Consensus       287 ~~~~~--------~~~l~~l~~~~~---~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~  355 (473)
                      +.+..        ...+..++....   .+.||||||++.+++....         .+ .......+...|   .     
T Consensus        87 ~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~---------~g-~~d~a~~Lkp~L---~-----  148 (387)
T d1qvra2          87 GSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKA---------EG-AVDAGNMLKPAL---A-----  148 (387)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCSSEEEEECCC-----------------------------HHHH---H-----
T ss_pred             hhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCC---------CC-cccHHHHHHHHH---h-----
Confidence            88843        235556665542   3578999999999752110         00 001112222222   1     


Q ss_pred             CCCceEEEEecCC-----CCCCCccccCCCceeeEEEeCCCCHHHHHHHHHHHh
Q 012016          356 CGDERIIVFTTNH-----KEKLDPALLRPGRMDVHVHMSYCTPSGFKLLAANYL  404 (473)
Q Consensus       356 ~~~~~iiI~tTN~-----~~~ld~aLlrpgRfd~~I~~~~p~~~~r~~l~~~~l  404 (473)
                      .| ++-+|++|..     .+. |+||.|  ||. .|.+..|+.++-..|++...
T Consensus       149 rg-~~~~I~~tT~~ey~~~e~-d~al~r--rF~-~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         149 RG-ELRLIGATTLDEYREIEK-DPALER--RFQ-PVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             TT-CCCEEEEECHHHHHHHTT-CTTTCS--CCC-CEEECCCCHHHHHHHHHHHH
T ss_pred             CC-CcceeeecCHHHHHHhcc-cHHHHH--hcc-cccCCCCcHHHHHHHHHHHH
Confidence            23 3445554432     244 899999  996 68999999999888877543

>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=98.99  E-value=2.3e-09  Score=108.85  Aligned_cols=70  Identities=19%  Similarity=0.303  Sum_probs=53.5

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhh-cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRV-GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~-g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      -|+|+++.|+.+--.+.+..++...-... .-..|.++||.||+|||||.||+.||+.++.||+.++++.+
T Consensus        15 yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~f   85 (443)
T d1g41a_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKF   85 (443)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGG
T ss_pred             cccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeeccee
Confidence            37899999998877776554322110000 11236699999999999999999999999999999999887

>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=98.95  E-value=4.5e-09  Score=98.65  Aligned_cols=86  Identities=14%  Similarity=0.204  Sum_probs=60.5

Q ss_pred             cccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccccCchHHHH
Q 012016          221 LAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELRSNSDLRT  297 (473)
Q Consensus       221 l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~~~~~l~~  297 (473)
                      ++|.....+.+++.+......           ...+||+||+||||+.+|++|....   ..+++.+++..+........
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~-----------~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~   70 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCA-----------ECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAE   70 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTC-----------CSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHH
T ss_pred             eEecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHH
Confidence            466667777777776655432           3369999999999999999999876   45788888877643332333


Q ss_pred             HHH-----------------HhccCceEEEecccccc
Q 012016          298 LLV-----------------ATANRSILVVEDIDCTI  317 (473)
Q Consensus       298 l~~-----------------~~~~~sIL~iDdiD~l~  317 (473)
                      +|.                 ...+++.|||||||.+.
T Consensus        71 lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i~~L~  107 (247)
T d1ny5a2          71 LFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELS  107 (247)
T ss_dssp             HHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCC
T ss_pred             hcCcccCCcCCcccccCCHHHccCCCEEEEeChHhCC
Confidence            321                 22356789999999883

>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=98.90  E-value=1e-08  Score=95.83  Aligned_cols=196  Identities=18%  Similarity=0.190  Sum_probs=114.9

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCc---
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSN---  292 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~---  292 (473)
                      ..-++++|.++..+.+.+                 ..++.++|+||+|+|||+|++.+++.++.++..+++......   
T Consensus         9 ~~~~~f~GR~~el~~l~~-----------------~~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~~~~~~~   71 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKG-----------------LRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNYI   71 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHH-----------------TCSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSCC
T ss_pred             CChhhCCChHHHHHHHHh-----------------ccCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccccccccc
Confidence            456889998766555422                 135689999999999999999999999888877665443111   


Q ss_pred             -------------------------------------------------hHHHHHHHH----hccCceEEEecccccccc
Q 012016          293 -------------------------------------------------SDLRTLLVA----TANRSILVVEDIDCTIDL  319 (473)
Q Consensus       293 -------------------------------------------------~~l~~l~~~----~~~~sIL~iDdiD~l~~~  319 (473)
                                                                       ..+..++..    ...+.++++||++.+...
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~  151 (283)
T d2fnaa2          72 SYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKL  151 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGC
T ss_pred             cHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhccc
Confidence                                                             011112211    235678999999987531


Q ss_pred             ccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCCC-------CCCCccccCCCceeeEEEeCCCC
Q 012016          320 QDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNHK-------EKLDPALLRPGRMDVHVHMSYCT  392 (473)
Q Consensus       320 ~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~~-------~~ld~aLlrpgRfd~~I~~~~p~  392 (473)
                                       .....+..+...++..     ..+..|++....       ...+..---.||+...++++..+
T Consensus       152 -----------------~~~~~~~~l~~~~~~~-----~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~  209 (283)
T d2fnaa2         152 -----------------RGVNLLPALAYAYDNL-----KRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFS  209 (283)
T ss_dssp             -----------------TTCCCHHHHHHHHHHC-----TTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCC
T ss_pred             -----------------chHHHHHHHHHHHHhh-----hhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCC
Confidence                             0112223232222221     223344433221       11111101124667789999999


Q ss_pred             HHHHHHHHHHHhCccccCCHHHHHHHHhcCCCCHHHHHHH---HhcCCCHHHHHHHHHHHHH
Q 012016          393 PSGFKLLAANYLGIKEHILFEEIEELISTTQVTPAEVAEQ---LMRNDDPELVLNGLIEFLK  451 (473)
Q Consensus       393 ~~~r~~l~~~~l~~~~~~l~~~i~~l~~~~~~t~a~i~~~---l~~~~~~~~al~~l~~~l~  451 (473)
                      .++..+++.+.+.... ...++++.+.+.++-.|.-+..+   +....+.+.+++.+++...
T Consensus       210 ~~e~~~~l~~~~~~~~-~~~~~~~~i~~~~~G~P~~L~~~~~~~~~~~~~~~~~~~~~~~~~  270 (283)
T d2fnaa2         210 REEAIEFLRRGFQEAD-IDFKDYEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAK  270 (283)
T ss_dssp             HHHHHHHHHHHHHHHT-CCCCCHHHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhhcC-CCHHHHHHHHHHhCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHH
Confidence            9999999887665322 22334556666666778755544   3345677777777766444

>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=98.87  E-value=7.8e-10  Score=104.07  Aligned_cols=59  Identities=24%  Similarity=0.388  Sum_probs=45.9

Q ss_pred             HHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          226 EQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       226 ~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +.+..+.+.+..+.....     +...|+|||||||||||||+||+++|++++.+++.++.+.+
T Consensus        10 ~~~~~~~~~~~~~~~~~~-----~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~   68 (273)
T d1gvnb_          10 QFENRLNDNLEELIQGKK-----AVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTF   68 (273)
T ss_dssp             HHHHHHHHHHHHHHTTCC-----CCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHH
T ss_pred             HHHHHHHHHHHHHHhccc-----CCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHH
Confidence            344455555554544322     55668899999999999999999999999999999998776

>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=98.25  E-value=8.9e-07  Score=79.16  Aligned_cols=61  Identities=18%  Similarity=0.283  Sum_probs=44.2

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEecccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDC  315 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~  315 (473)
                      |.|-++.++|||||+||||+++.+|++.++-.++...  .-.    .+-.|..+....++++||+-.
T Consensus        49 ~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vis~~--N~~----s~F~Lq~l~~~kv~l~dD~t~  109 (205)
T d1tuea_          49 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFV--NST----SHFWLEPLTDTKVAMLDDATT  109 (205)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCC--CSS----SCGGGGGGTTCSSEEEEEECH
T ss_pred             CCCCceEEEEECCCCccHHHHHHHHHHHhCCEEEecc--CCC----CCcccccccCCeEEEEecccc
Confidence            6677889999999999999999999999975443222  111    122344556778999999843

>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=98.22  E-value=3.2e-07  Score=78.14  Aligned_cols=34  Identities=41%  Similarity=0.690  Sum_probs=30.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ++.++|.|||||||||++++||..|++++++.+.
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L~~~~id~~~   35 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQ   35 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCEEEEHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCeEeech
Confidence            4679999999999999999999999999987654

>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=98.15  E-value=4.4e-06  Score=72.53  Aligned_cols=24  Identities=29%  Similarity=0.628  Sum_probs=22.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      ++|.||||||||||+++|+..++.
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCC
Confidence            899999999999999999998843

>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=98.14  E-value=0.0001  Score=69.16  Aligned_cols=48  Identities=17%  Similarity=0.221  Sum_probs=34.5

Q ss_pred             ccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          220 TLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       220 ~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++.|.+...++|++.+...-.          ...+-+.|||++|+|||+||+.+++..
T Consensus        21 ~~~gR~~~~~~i~~~L~~~~~----------~~~~~v~I~GmgGiGKTtLA~~v~~~~   68 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDEMCD----------LDSFFLFLHGRAGSGKSVIASQALSKS   68 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHHHTT----------SSSEEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             ceeCcHHHHHHHHHHHHhccC----------CCceEEEEECCCCCCHHHHHHHHHHhh
Confidence            355777777777776653211          123468899999999999999998874

>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=98.05  E-value=9.8e-07  Score=76.68  Aligned_cols=35  Identities=20%  Similarity=0.139  Sum_probs=31.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~  287 (473)
                      .+.|+|.|||||||||||++||+.++.+++..+..
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~~~   41 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVFNTTSAWEYGR   41 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCEEECCTTH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHhCCCeEeeehH
Confidence            46899999999999999999999999998866543

>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=98.01  E-value=1.3e-06  Score=75.29  Aligned_cols=31  Identities=29%  Similarity=0.483  Sum_probs=28.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      .++|.|||||||||++++||..+|+++++++
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~i~~~   36 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKYINVG   36 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEech
Confidence            5889999999999999999999999998643

>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=97.99  E-value=1.5e-06  Score=75.18  Aligned_cols=31  Identities=32%  Similarity=0.471  Sum_probs=29.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +++|.||||+|||+++++||..||+++++++
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            5889999999999999999999999999875

>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=97.93  E-value=2.5e-06  Score=74.33  Aligned_cols=32  Identities=19%  Similarity=0.412  Sum_probs=29.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      +.++|.||||+||||+++.+|+.||+++++.|
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~D   34 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEehh
Confidence            46889999999999999999999999999865

>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=97.90  E-value=2.3e-06  Score=74.03  Aligned_cols=35  Identities=31%  Similarity=0.459  Sum_probs=31.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE  288 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~  288 (473)
                      +-++|.|||||||||+++++|+.++.+++.++...
T Consensus         5 ~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~d~   39 (176)
T d1zp6a1           5 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHSDD   39 (176)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTTH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEecHHH
Confidence            45899999999999999999999999999887643

>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=97.88  E-value=3.3e-06  Score=73.11  Aligned_cols=30  Identities=33%  Similarity=0.550  Sum_probs=27.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++|.|+||+||||+++.+|..|+++++++|
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~fiD~D   33 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVGLLDTD   33 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            666699999999999999999999999876

>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=97.84  E-value=5.4e-06  Score=71.40  Aligned_cols=34  Identities=21%  Similarity=0.311  Sum_probs=30.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ++-|+|+||||+||||++++||+.++.+++.++.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~~   36 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCCeEEeec
Confidence            3579999999999999999999999998887664

>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=97.80  E-value=6.2e-06  Score=70.98  Aligned_cols=34  Identities=29%  Similarity=0.489  Sum_probs=29.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~  286 (473)
                      ++-++|.|||||||||++++||..++.+.+..+.
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d~   39 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGDF   39 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEEEEGGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeechhh
Confidence            4568899999999999999999999998877654

>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=97.74  E-value=8.2e-06  Score=69.81  Aligned_cols=29  Identities=34%  Similarity=0.641  Sum_probs=26.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      +-++|.|||||||||+|+.||..++..++
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~~~~~   31 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLDNSAY   31 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSSEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            46899999999999999999999987655

>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=97.69  E-value=7.9e-06  Score=70.57  Aligned_cols=24  Identities=46%  Similarity=0.812  Sum_probs=22.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |+++|+||||||||+|+++++..+
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            689999999999999999999988

>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=97.68  E-value=1.6e-05  Score=68.43  Aligned_cols=29  Identities=34%  Similarity=0.449  Sum_probs=25.5

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      |.+..++|.||||+||||+++.||..++.
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            44556999999999999999999999964

>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=97.67  E-value=2.3e-05  Score=68.50  Aligned_cols=62  Identities=18%  Similarity=0.148  Sum_probs=42.7

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHH-hccCceEEEeccc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVA-TANRSILVVEDID  314 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~-~~~~sIL~iDdiD  314 (473)
                      +.|.-++|.|+|||||||+++.++..+++..+..  ..+.+...+.+.+.. +.++..+++|...
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~~~~~~i~~--D~~~~~~~~~~~~~~~l~~g~~vIiD~t~   74 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNR--DTLGSWQRCVSSCQAALRQGKRVVIDNTN   74 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGGGTCEEEEH--HHHCSHHHHHHHHHHHHHTTCCEEEESCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhcCCEEEch--HHHHHHHHHHHHHHHHHHCCCCceeeCcC
Confidence            4466799999999999999999999888766544  444444444444333 3456667777543

>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=97.57  E-value=1.7e-05  Score=70.04  Aligned_cols=33  Identities=18%  Similarity=0.283  Sum_probs=28.8

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .|.-|+|.||||+||||+++.||.++|++.+..
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~~~g~~~i~~   37 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            355789999999999999999999999877653

>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=97.56  E-value=1.3e-05  Score=70.70  Aligned_cols=31  Identities=13%  Similarity=0.250  Sum_probs=27.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -.++|.|||||||||+++.||+.+|++.+..
T Consensus         4 m~I~i~GppGsGKsT~a~~La~~~~~~~is~   34 (189)
T d1zaka1           4 LKVMISGAPASGKGTQCELIKTKYQLAHISA   34 (189)
T ss_dssp             CCEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHCCcEEeh
Confidence            4589999999999999999999999987653

>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=97.54  E-value=2.1e-05  Score=68.42  Aligned_cols=29  Identities=21%  Similarity=0.356  Sum_probs=26.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ++|.||||+||||+++.||..+|++.+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~~~~i~~   31 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYGIPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceech
Confidence            78999999999999999999999988764

>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=97.48  E-value=3.5e-05  Score=67.78  Aligned_cols=30  Identities=27%  Similarity=0.433  Sum_probs=26.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -++|.||||+||||+++.||..+|+..+..
T Consensus         5 riil~G~pGSGKsT~a~~La~~~g~~~i~~   34 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   34 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            467889999999999999999999887664

>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=97.47  E-value=2.9e-05  Score=67.78  Aligned_cols=30  Identities=33%  Similarity=0.552  Sum_probs=27.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .++|.|||||||||+++.||+.+|+..+.+
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            478999999999999999999999988765

>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=97.47  E-value=1.3e-05  Score=69.03  Aligned_cols=26  Identities=27%  Similarity=0.323  Sum_probs=23.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      .|+|.|+||+||||++++||..|+..
T Consensus         8 ~I~l~G~~GsGKTTia~~La~~L~~~   33 (183)
T d1m8pa3           8 TIFLTGYMNSGKDAIARALQVTLNQQ   33 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhc
Confidence            48899999999999999999998543

>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=97.45  E-value=0.0002  Score=66.77  Aligned_cols=59  Identities=20%  Similarity=0.271  Sum_probs=41.7

Q ss_pred             CCCCceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccccCchHHHHHHHHhccCceEEEecccc
Q 012016          250 KAWKRGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTELRSNSDLRTLLVATANRSILVVEDIDC  315 (473)
Q Consensus       250 ~~~~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~~~~~~l~~l~~~~~~~sIL~iDdiD~  315 (473)
                      .+....+.|+|||+||||+++.+|++.+|.-. .++-+.  +.-    -+.......++++||.+.
T Consensus       101 ~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~~~-~~~~~~--~~f----~l~~l~~k~~~~~~e~~~  159 (267)
T d1u0ja_         101 FGKRNTIWLFGPATTGKTNIAEAIAHTVPFYG-CVNWTN--ENF----PFNDCVDKMVIWWEEGKM  159 (267)
T ss_dssp             STTCCEEEEECSTTSSHHHHHHHHHHHSSCEE-ECCTTC--SSC----TTGGGSSCSEEEECSCCE
T ss_pred             CCccEEEEEEcCCCCCHHHHHHHHHHHhcchh-hccccC--CCc----cccccCCCEEEEEeCCCc
Confidence            45677899999999999999999999996533 222111  111    134456788999999863

>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=97.43  E-value=0.00013  Score=66.24  Aligned_cols=37  Identities=22%  Similarity=0.186  Sum_probs=29.1

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      |.+...-++|+||||+|||+++..+|...   +.++..++
T Consensus        22 Gi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is   61 (242)
T d1tf7a2          22 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA   61 (242)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceee
Confidence            56777789999999999999999888875   44444443

>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=97.39  E-value=4.6e-05  Score=67.39  Aligned_cols=30  Identities=17%  Similarity=0.407  Sum_probs=26.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -++|.||||+||||+++.||..+|++.+.+
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~g~~~is~   37 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHFELKHLSS   37 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHBCCEEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHCCeEEcH
Confidence            478889999999999999999999887654

>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=97.39  E-value=4.5e-05  Score=66.62  Aligned_cols=29  Identities=21%  Similarity=0.321  Sum_probs=26.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ++|.||||+||||+++.||..+|++.+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~g~~~is~   31 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKYGTPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceeeH
Confidence            78999999999999999999999988764

>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=97.38  E-value=5.4e-05  Score=66.87  Aligned_cols=31  Identities=19%  Similarity=0.337  Sum_probs=27.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      .-++|.||||+||||+|+.||..+|+..+..
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~g~~~is~   39 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   39 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEEeh
Confidence            4588899999999999999999999987664

>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=97.38  E-value=4.4e-05  Score=67.47  Aligned_cols=32  Identities=16%  Similarity=0.350  Sum_probs=28.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ++-++|.||||+||||+++.||..+|++.+..
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~is~   39 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTHLST   39 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeeEec
Confidence            45689999999999999999999999877654

>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=97.35  E-value=4.9e-05  Score=66.35  Aligned_cols=30  Identities=23%  Similarity=0.458  Sum_probs=26.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ++|.||||+||||+++.||..+|++.+..+
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g~~~i~~~   34 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFHAAHLATG   34 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceEecc
Confidence            678899999999999999999998877653

>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=97.33  E-value=1.2e-05  Score=70.60  Aligned_cols=28  Identities=29%  Similarity=0.394  Sum_probs=23.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      ..|+|.|+||+||||+|++||..++..+
T Consensus        20 ~vI~L~G~pGSGKTTiAk~La~~l~~~~   47 (195)
T d1x6va3          20 CTVWLTGLSGAGKTTVSMALEEYLVCHG   47 (195)
T ss_dssp             EEEEEESSCHHHHHHHHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhcC
Confidence            3477999999999999999999985433

>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=97.30  E-value=8e-05  Score=66.50  Aligned_cols=29  Identities=38%  Similarity=0.618  Sum_probs=26.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      -|.+.||||+||+|+++.||+.+|++.+.
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~gl~~iS   33 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEALQWHLLD   33 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            67888999999999999999999998854

>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=97.29  E-value=7.1e-05  Score=65.85  Aligned_cols=30  Identities=20%  Similarity=0.381  Sum_probs=26.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -++|.||||+||||.|+.||+.+|+..+..
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~g~~~i~~   32 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKYGYTHLSA   32 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceEcH
Confidence            589999999999999999999999877643

>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=97.26  E-value=0.0007  Score=60.69  Aligned_cols=36  Identities=22%  Similarity=0.195  Sum_probs=27.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTE  288 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~  288 (473)
                      |.-++|.||+|+||||.+.-||..+   |..+..+.+..
T Consensus         9 p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt   47 (211)
T d2qy9a2           9 PFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDT   47 (211)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeccc
Confidence            4568899999999999999999776   45555544443

>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=97.25  E-value=0.00073  Score=60.39  Aligned_cols=35  Identities=29%  Similarity=0.322  Sum_probs=26.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      ++-++|.||+|+||||.+.-||.++   |..+..+.+.
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~D   43 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGD   43 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEec
Confidence            4568999999999999999888876   4445444443

>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=97.23  E-value=8.1e-05  Score=62.42  Aligned_cols=25  Identities=32%  Similarity=0.384  Sum_probs=21.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++-|+|+||||+||||+|+.++...
T Consensus         2 kklIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           2 KKIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhC
Confidence            3468899999999999999987654

>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=97.23  E-value=6.8e-05  Score=65.18  Aligned_cols=29  Identities=17%  Similarity=0.266  Sum_probs=26.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      ++|.||||+||||+++.||..+++..+..
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~~~~~i~~   31 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceech
Confidence            68899999999999999999999887754

>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=97.19  E-value=0.0001  Score=66.13  Aligned_cols=28  Identities=29%  Similarity=0.521  Sum_probs=25.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      +-+.||||+||||+|+.||.++|++++.
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            4577999999999999999999998765

>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=97.18  E-value=0.00021  Score=66.61  Aligned_cols=70  Identities=14%  Similarity=0.206  Sum_probs=45.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHH---H
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLV---A  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~---~  301 (473)
                      |++..+-..|+||||+|||+++-.+|...   +..++++|...-.                     +.++..+.+.   .
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            56667789999999999999988777655   4555555433220                     1122222222   2


Q ss_pred             hccCceEEEeccccccc
Q 012016          302 TANRSILVVEDIDCTID  318 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~  318 (473)
                      .....+|+||-+.++.+
T Consensus       130 ~~~~~liViDSi~al~~  146 (263)
T d1u94a1         130 SGAVDVIVVDSVAALTP  146 (263)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEECcccccc
Confidence            34578999999988763

>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=97.15  E-value=0.00024  Score=66.36  Aligned_cols=113  Identities=12%  Similarity=0.168  Sum_probs=62.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHH---H
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLV---A  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~---~  301 (473)
                      |++..+-..|+||||||||+++..+|...   |..++.+|...-.                     ..+...+++.   .
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            67778889999999999999986555433   5555555544321                     1122222222   2


Q ss_pred             hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecC
Q 012016          302 TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTN  367 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN  367 (473)
                      .....+||||-+..+.+..+-.+..    .+.......+.++.++..+..+...  .++.+|+|..
T Consensus       136 ~~~~~liIiDSi~al~~~~E~e~~~----~~~~~~~~a~~l~~~l~~l~~~~~~--~~~~vi~~NQ  195 (269)
T d1mo6a1         136 SGALDIVVIDSVAALVPRAELEGEM----GDSHVGLQARLMSQALRKMTGALNN--SGTTAIFINQ  195 (269)
T ss_dssp             TTCEEEEEEECSTTCCCHHHHC-----------CCHHHHHHHHHHHHHHHHHHH--HTCEEEEEEC
T ss_pred             cCCCCEEEEecccccccHHHhcccc----ccchHHHHHHHHHHHHHHHHHHHhh--cCchhhhhhe
Confidence            3456899999999887411111000    0011122345566666665554332  2356666643

>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=97.14  E-value=0.00077  Score=61.46  Aligned_cols=63  Identities=19%  Similarity=0.294  Sum_probs=42.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc-----CCce------------E--Eccccc-cc--------CchHHHHHHHHhcc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL-----NFDV------------Y--DLELTE-LR--------SNSDLRTLLVATAN  304 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l-----~~~~------------~--~l~~~~-~~--------~~~~l~~l~~~~~~  304 (473)
                      .+.++|+||.++|||++++++|-..     |..+            +  .+...+ +.        .-.++..++..+..
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~  120 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE  120 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCT
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHhccc
Confidence            4679999999999999999988643     2111            1  111111 11        12456677778888


Q ss_pred             CceEEEecccc
Q 012016          305 RSILVVEDIDC  315 (473)
Q Consensus       305 ~sIL~iDdiD~  315 (473)
                      +++++|||+-.
T Consensus       121 ~sLvliDE~~~  131 (234)
T d1wb9a2         121 YSLVLMDEIGR  131 (234)
T ss_dssp             TEEEEEESCCC
T ss_pred             ccEEeeccccc
Confidence            99999999964

>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=97.12  E-value=0.00053  Score=63.40  Aligned_cols=26  Identities=27%  Similarity=0.406  Sum_probs=22.9

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +..-+.|.||+|+|||||++.|+..+
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~gl~   68 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPRFY   68 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhcC
Confidence            34569999999999999999999876

>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=97.11  E-value=0.00089  Score=60.08  Aligned_cols=34  Identities=21%  Similarity=0.195  Sum_probs=25.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      |.-++|.||+|+||||.+.-||.++   +..+..+.+
T Consensus        11 p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~   47 (213)
T d1vmaa2          11 PFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA   47 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEee
Confidence            4568999999999999999888776   444444333

>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=97.11  E-value=0.00039  Score=64.78  Aligned_cols=114  Identities=13%  Similarity=0.116  Sum_probs=64.0

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEccccccc---------------------CchHHHHHHHH---
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTELR---------------------SNSDLRTLLVA---  301 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~~---------------------~~~~l~~l~~~---  301 (473)
                      |+|..+-+.++||||||||+++..+|...   |..++++|...-.                     +.++..+++..   
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            55667789999999999999998777655   5555655544321                     11222222322   


Q ss_pred             hccCceEEEeccccccccccCCccccCCCCCCCccchhHHHHHHHHHhcccccCCCCceEEEEecCC
Q 012016          302 TANRSILVVEDIDCTIDLQDRLPADIAGEGEGPIQQNKVTLSGFLNFIDGLWSSCGDERIIVFTTNH  368 (473)
Q Consensus       302 ~~~~sIL~iDdiD~l~~~~~r~~~~~~~~~~~~~~~~~~~ls~LL~~ldg~~~~~~~~~iiI~tTN~  368 (473)
                      .....+|+||-+..+.+..+-.+...    +.......+.++.+++.+-.+...  .++.+|+|.+-
T Consensus       133 ~~~~~liIiDSi~al~~r~e~~~~~~----~~~~~~~a~~l~~~lr~l~~~~~~--~~~~vi~tNQv  193 (268)
T d1xp8a1         133 SGAIDVVVVDSVAALTPRAEIEGDMG----DSLPGLQARLMSQALRKLTAILSK--TGTAAIFINQV  193 (268)
T ss_dssp             TTCCSEEEEECTTTCCCSTTC------------CCHHHHHHHHHHHHHHHHHTT--TCCEEEEEEEC
T ss_pred             cCCCcEEEEecccccccHHHHccccc----chhHHHHHHHHHHHHHHHHhhhhh--cCCeEEEEeEE
Confidence            23578999999988864211111000    011123455666666666555433  34666666443

>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=97.08  E-value=0.0007  Score=60.34  Aligned_cols=27  Identities=30%  Similarity=0.404  Sum_probs=22.6

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHH
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      |.++..-++|+||||+|||+++..+|.
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~   48 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLY   48 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHH
Confidence            567778899999999999999876543

>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=97.08  E-value=0.00072  Score=59.38  Aligned_cols=27  Identities=30%  Similarity=0.415  Sum_probs=23.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      -++|.||+|+|||++++.|+...+-.+
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~~~~~   28 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEHSSIF   28 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHHTTTE
T ss_pred             eEEEECCCCCCHHHHHHHHHHhCCCce
Confidence            488999999999999999999875443

>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=97.06  E-value=0.00084  Score=61.93  Aligned_cols=25  Identities=24%  Similarity=0.523  Sum_probs=22.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+-|.||+|+|||||+++|+..+
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhccc
Confidence            4569999999999999999999877

>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=97.05  E-value=0.0013  Score=55.96  Aligned_cols=63  Identities=22%  Similarity=0.293  Sum_probs=42.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC--------------------ceEEcccccccCchHHHHH-HHH-hccCceEEEe
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF--------------------DVYDLELTELRSNSDLRTL-LVA-TANRSILVVE  311 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~--------------------~~~~l~~~~~~~~~~l~~l-~~~-~~~~sIL~iD  311 (473)
                      .-++|+|+=|+|||++++++++.+|.                    +++.+|+=.+.+..++..+ +.. ....+|++||
T Consensus        34 ~ii~L~G~LGaGKTtfvr~~~~~lg~~~~V~SPTF~l~~~Y~~~~~~i~H~DlYRl~~~~El~~lg~~e~~~~~~i~~IE  113 (158)
T d1htwa_          34 IMVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIE  113 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTCCSCCCCCTTTCEEEEEETTEEEEEEECTTCSCTTHHHHSTHHHHHSSSCEEEEE
T ss_pred             eEEEEecCCCccHHHHHHHHHhhcccccccCCCceEEEEeeccCCceEEEEEEeccCChhhhhhCCchhHhccCCEEEEE
Confidence            34889999999999999999999953                    3444444444444555443 222 2456888888


Q ss_pred             ccccc
Q 012016          312 DIDCT  316 (473)
Q Consensus       312 diD~l  316 (473)
                      =.+.+
T Consensus       114 Wpe~~  118 (158)
T d1htwa_         114 WSEKG  118 (158)
T ss_dssp             SGGGG
T ss_pred             Cchhh
Confidence            66544

>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=97.00  E-value=0.00097  Score=61.02  Aligned_cols=25  Identities=24%  Similarity=0.398  Sum_probs=22.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+-|.||+|+|||||+++|+..+
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcC
Confidence            4569999999999999999999987

>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=96.99  E-value=0.0013  Score=58.65  Aligned_cols=34  Identities=24%  Similarity=0.310  Sum_probs=25.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      +-++|.||+|+||||.+.-||.++   +..+..+.+.
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~D   47 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAAD   47 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecc
Confidence            347889999999999999999877   4555444443

>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=96.98  E-value=0.0014  Score=63.43  Aligned_cols=22  Identities=36%  Similarity=0.616  Sum_probs=17.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      +-.+|.||||||||+++..+..
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~  185 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLA  185 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCceehHHHHHH
Confidence            4689999999999998765433

>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=96.95  E-value=0.00092  Score=61.57  Aligned_cols=26  Identities=35%  Similarity=0.441  Sum_probs=23.0

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +..-+-|.||+|+|||||++.|+..+
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhccc
Confidence            34568999999999999999999877

>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=96.94  E-value=0.0012  Score=60.76  Aligned_cols=29  Identities=28%  Similarity=0.239  Sum_probs=22.7

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |..+..-.+|+|+||+|||+|+..+|..+
T Consensus        25 G~~pg~~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          25 NMVAGTVGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CccCCcEEEEEeCCCCCHHHHHHHHHHHH
Confidence            33345568999999999999998887653

>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=96.92  E-value=0.00019  Score=61.63  Aligned_cols=26  Identities=19%  Similarity=0.307  Sum_probs=23.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      +-|+|.||||+||||+++.|+..|+.
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            45899999999999999999998843

>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=96.88  E-value=0.0013  Score=53.99  Aligned_cols=34  Identities=26%  Similarity=0.325  Sum_probs=26.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELT  287 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~  287 (473)
                      +..+|.+|.|+|||.++-.++...+..++.+-..
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcCh
Confidence            4679999999999999887777777776665544

>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=96.86  E-value=0.00023  Score=62.75  Aligned_cols=25  Identities=28%  Similarity=0.525  Sum_probs=22.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      --+++.|+||+||||++++||++++
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~   27 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLN   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3489999999999999999999874

>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=96.84  E-value=0.00025  Score=60.13  Aligned_cols=31  Identities=19%  Similarity=0.176  Sum_probs=25.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      -+.+.|+||||||||+..|++++   |+.+..+.
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~~   37 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIK   37 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEec
Confidence            57899999999999999999987   55554433

>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=96.81  E-value=0.0044  Score=51.32  Aligned_cols=21  Identities=19%  Similarity=0.333  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++|.|+||+|||+|+..++..
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999998754

>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=96.78  E-value=0.00044  Score=62.11  Aligned_cols=28  Identities=32%  Similarity=0.238  Sum_probs=24.4

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      |.+..+-++|+||||||||+++..+|..
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            6788888999999999999999877654

>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=96.69  E-value=0.0022  Score=58.53  Aligned_cols=26  Identities=23%  Similarity=0.443  Sum_probs=22.9

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +..-+-|.||+|+|||||++.|+..+
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            34468999999999999999999877

>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=96.66  E-value=0.0026  Score=58.60  Aligned_cols=38  Identities=21%  Similarity=0.141  Sum_probs=28.5

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh----cCCceEEccc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY----LNFDVYDLEL  286 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~----l~~~~~~l~~  286 (473)
                      |..+..-++|.|+||+|||+++..+|..    .|.++..+++
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            5555667999999999999988877743    2667766553

>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=96.65  E-value=0.00045  Score=60.33  Aligned_cols=29  Identities=21%  Similarity=0.172  Sum_probs=25.3

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.++..-++|+||||+|||+++..+|...
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            66777889999999999999999888654

>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=96.64  E-value=0.0032  Score=53.49  Aligned_cols=23  Identities=13%  Similarity=0.329  Sum_probs=20.6

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      .-++|.|.||+|||+|+..+.+.
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35999999999999999999875

>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=96.61  E-value=0.0037  Score=55.80  Aligned_cols=25  Identities=28%  Similarity=0.432  Sum_probs=17.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.-++|.||+|+||||.+.-||..+
T Consensus        12 p~vi~lvGptGvGKTTTiAKLA~~~   36 (211)
T d1j8yf2          12 PYVIMLVGVQGTGKATTAGKLAYFY   36 (211)
T ss_dssp             SEEEEEECSCCC----HHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Confidence            4568899999999999999888776

>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=96.61  E-value=0.0009  Score=59.67  Aligned_cols=24  Identities=42%  Similarity=0.614  Sum_probs=21.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -++|.||+|+|||+|++.+.....
T Consensus         4 livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCC
Confidence            488999999999999999998764

>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=96.59  E-value=0.0014  Score=58.98  Aligned_cols=28  Identities=21%  Similarity=0.126  Sum_probs=24.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHh
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      |+|..+-++|+||||||||+++..+|..
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            6777788999999999999999988864

>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=96.59  E-value=0.0083  Score=58.72  Aligned_cols=85  Identities=25%  Similarity=0.358  Sum_probs=54.6

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHHHHHHhcC---CceEEcccc-cc--
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIAAMANYLN---FDVYDLELT-EL--  289 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~alA~~l~---~~~~~l~~~-~~--  289 (473)
                      .+|+++...++..+.+.+    .+..          +...+|+.||.|+||||++.++.++++   .+++.++-. +.  
T Consensus       135 ~~l~~LG~~~~~~~~l~~----l~~~----------~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~~  200 (401)
T d1p9ra_         135 LDLHSLGMTAHNHDNFRR----LIKR----------PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFDI  200 (401)
T ss_dssp             CCGGGSCCCHHHHHHHHH----HHTS----------SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSCC
T ss_pred             hhhhhhcccHHHHHHHHH----HHhh----------hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCccccc
Confidence            578999888876665433    2221          123489999999999999999999873   344443311 00  


Q ss_pred             ----------cCchHHHHHHHHh--ccCceEEEeccc
Q 012016          290 ----------RSNSDLRTLLVAT--ANRSILVVEDID  314 (473)
Q Consensus       290 ----------~~~~~l~~l~~~~--~~~sIL~iDdiD  314 (473)
                                .........+..+  ..|.||+|.||-
T Consensus       201 ~~~~q~~v~~~~~~~~~~~l~~~lR~dPDvi~igEiR  237 (401)
T d1p9ra_         201 DGIGQTQVNPRVDMTFARGLRAILRQDPDVVMVGEIR  237 (401)
T ss_dssp             SSSEEEECBGGGTBCHHHHHHHHGGGCCSEEEESCCC
T ss_pred             CCCCeeeecCCcCCCHHHHHHHHHhhcCCEEEecCcC
Confidence                      1122344444433  479999999995

>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=96.58  E-value=0.0041  Score=55.00  Aligned_cols=25  Identities=32%  Similarity=0.622  Sum_probs=22.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+-|.||.|+|||||+++|++.+
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHhccc
Confidence            3457899999999999999999977

>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=96.57  E-value=0.0036  Score=58.44  Aligned_cols=26  Identities=27%  Similarity=0.368  Sum_probs=23.0

Q ss_pred             CCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          252 WKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       252 ~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ...-+-|.||.|+|||||+++|+..+
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCC
Confidence            34458899999999999999999987

>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=96.57  E-value=0.00083  Score=60.03  Aligned_cols=37  Identities=24%  Similarity=0.366  Sum_probs=30.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc----CCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL----NFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l----~~~~~~l~~~~~  289 (473)
                      +.-|+|.|.||+|||+++++|+..+    +.+++.++...+
T Consensus        24 g~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~i   64 (208)
T d1m7ga_          24 GLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDNI   64 (208)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchHH
Confidence            3469999999999999999999766    667777776654

>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=96.54  E-value=0.00031  Score=60.54  Aligned_cols=26  Identities=31%  Similarity=0.487  Sum_probs=22.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      -++|.|+||+||||+++.||..|+..
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            46889999999999999999998543

>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=96.52  E-value=0.0035  Score=56.50  Aligned_cols=62  Identities=18%  Similarity=0.284  Sum_probs=41.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc-----CCce--------------EEccccc-ccC--------chHHHHHHHHhccC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL-----NFDV--------------YDLELTE-LRS--------NSDLRTLLVATANR  305 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l-----~~~~--------------~~l~~~~-~~~--------~~~l~~l~~~~~~~  305 (473)
                      +.++|+||...|||++++++|-..     |..+              ..+...+ +..        -.++..++..+..+
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~~~~  115 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATEN  115 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHCCTT
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhccCCCC
Confidence            368999999999999999887643     2111              1121111 111        14566777777889


Q ss_pred             ceEEEecccc
Q 012016          306 SILVVEDIDC  315 (473)
Q Consensus       306 sIL~iDdiD~  315 (473)
                      ++++|||+-.
T Consensus       116 sLvliDE~~~  125 (224)
T d1ewqa2         116 SLVLLDEVGR  125 (224)
T ss_dssp             EEEEEESTTT
T ss_pred             cEEeeccccc
Confidence            9999999964

>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=96.51  E-value=0.0011  Score=59.97  Aligned_cols=29  Identities=24%  Similarity=0.336  Sum_probs=24.7

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.|..+-++|+||||||||+++..+|...
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            56777789999999999999999887654

>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=96.49  E-value=0.0011  Score=56.09  Aligned_cols=22  Identities=18%  Similarity=0.410  Sum_probs=19.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+++.|+||+|||+|+..+.+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            4899999999999999998764

>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=96.39  E-value=0.0031  Score=57.16  Aligned_cols=25  Identities=32%  Similarity=0.506  Sum_probs=22.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+-|.||+|||||||++.|+..+
T Consensus        26 Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          26 GEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcCC
Confidence            3458899999999999999999877

>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=96.32  E-value=0.0014  Score=57.11  Aligned_cols=27  Identities=33%  Similarity=0.506  Sum_probs=23.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      |-|+|.||+|+|||+|++.|++...-.
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~   28 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDS   28 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCcc
Confidence            348999999999999999999987543

>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=96.29  E-value=0.0046  Score=56.25  Aligned_cols=24  Identities=29%  Similarity=0.528  Sum_probs=21.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+-|.||+|+|||||+++|+..+
T Consensus        30 e~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          30 EFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhcCC
Confidence            358899999999999999999876

>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=96.27  E-value=0.0044  Score=54.41  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=20.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      |.|+|.|+||+|||+|+.++.+.
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            57999999999999999999874

>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=96.25  E-value=0.0068  Score=51.41  Aligned_cols=21  Identities=29%  Similarity=0.460  Sum_probs=19.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -++|.|++|+|||+|+..+.+
T Consensus         6 KivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999999875

>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=96.24  E-value=0.003  Score=60.14  Aligned_cols=62  Identities=15%  Similarity=0.348  Sum_probs=40.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC--CceEEcc-cccc-------------cCchHHHHHHHHh--ccCceEEEeccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN--FDVYDLE-LTEL-------------RSNSDLRTLLVAT--ANRSILVVEDID  314 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~--~~~~~l~-~~~~-------------~~~~~l~~l~~~~--~~~sIL~iDdiD  314 (473)
                      ++++|+.||+|+|||++++||+++..  ..++.++ ..++             ..+-.+.+++..+  .+|..|++.|+-
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            45899999999999999999999883  2233221 1111             1122344455433  378899999983

>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=96.21  E-value=0.009  Score=50.34  Aligned_cols=22  Identities=27%  Similarity=0.425  Sum_probs=19.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|++|+|||+|+..+.+.
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3899999999999999999874

>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=96.20  E-value=0.0043  Score=52.43  Aligned_cols=21  Identities=33%  Similarity=0.662  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++|.|+||+|||+|+..+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998863

>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=96.19  E-value=0.0034  Score=50.76  Aligned_cols=25  Identities=20%  Similarity=0.169  Sum_probs=18.1

Q ss_pred             CceeEEeCCCCCCHHHHH-HHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLI-AAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la-~alA~~l  277 (473)
                      .+.++|++|+|+|||..+ .++...+
T Consensus         7 ~~~~il~~~tGsGKT~~~~~~~~~~~   32 (140)
T d1yksa1           7 GMTTVLDFHPGAGKTRRFLPQILAEC   32 (140)
T ss_dssp             TCEEEECCCTTSSTTTTHHHHHHHHH
T ss_pred             CCcEEEEcCCCCChhHHHHHHHHHHh
Confidence            467899999999999655 3444433

>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=96.15  E-value=0.0023  Score=54.75  Aligned_cols=21  Identities=33%  Similarity=0.716  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|+||+|||+|+..+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            789999999999999998764

>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=96.07  E-value=0.0045  Score=52.53  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=19.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+++.|++|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3799999999999999999853

>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=96.04  E-value=0.0024  Score=55.01  Aligned_cols=24  Identities=21%  Similarity=0.279  Sum_probs=21.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -|-+.||+|+||||+|+.|+..++
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~l~   47 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQTLR   47 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            366999999999999999998774

>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=95.99  E-value=0.0063  Score=51.83  Aligned_cols=22  Identities=27%  Similarity=0.403  Sum_probs=19.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|.+|+|||+|+..+.+.
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999988763

>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=95.95  E-value=0.012  Score=51.06  Aligned_cols=23  Identities=26%  Similarity=0.564  Sum_probs=21.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      ..++|.|+||+|||||+.+|.+.
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            47999999999999999999876

>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=95.93  E-value=0.0095  Score=49.05  Aligned_cols=21  Identities=29%  Similarity=0.510  Sum_probs=19.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++|.|+||+|||+|+..+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999874

>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=95.90  E-value=0.0092  Score=50.26  Aligned_cols=21  Identities=29%  Similarity=0.496  Sum_probs=19.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|++|+|||+|+..+.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            799999999999999998874

>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=95.85  E-value=0.0031  Score=53.41  Aligned_cols=30  Identities=17%  Similarity=0.247  Sum_probs=24.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l  284 (473)
                      -+-+.|++|+|||||+..++.+|   |+.+..+
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~g~~v~vi   35 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTV   35 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEE
Confidence            45699999999999999999987   4555444

>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=95.84  E-value=0.0045  Score=52.56  Aligned_cols=21  Identities=29%  Similarity=0.460  Sum_probs=19.3

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|++|+|||+|+..+.+.
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            899999999999999998864

>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=95.79  E-value=0.0034  Score=54.15  Aligned_cols=25  Identities=28%  Similarity=0.545  Sum_probs=22.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      +-++|.||+|+|||++++.|+....
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4589999999999999999998864

>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=95.78  E-value=0.011  Score=50.12  Aligned_cols=21  Identities=29%  Similarity=0.453  Sum_probs=19.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -++|.|.||+|||+|+..+.+
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999998876

>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=95.76  E-value=0.0033  Score=54.44  Aligned_cols=30  Identities=23%  Similarity=0.351  Sum_probs=25.3

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      .+|+||.||+|+|||+++.++... |..++.
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~-g~~lv~   43 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQR-GHRLIA   43 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHT-TCEEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEEe
Confidence            469999999999999999988875 666553

>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=95.73  E-value=0.014  Score=49.25  Aligned_cols=22  Identities=32%  Similarity=0.505  Sum_probs=19.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+++.|+||+|||+|+..+.+.
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4899999999999999998653

>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=95.72  E-value=0.014  Score=49.06  Aligned_cols=21  Identities=29%  Similarity=0.483  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|.+|+|||+|+..+...
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            899999999999999998764

>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=95.71  E-value=0.0089  Score=49.65  Aligned_cols=22  Identities=23%  Similarity=0.424  Sum_probs=20.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|+||+|||||++++.+.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999875

>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=0.0071  Score=50.90  Aligned_cols=20  Identities=30%  Similarity=0.471  Sum_probs=18.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|+||+|||+|+..+.+
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998886

>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=95.64  E-value=0.0025  Score=56.36  Aligned_cols=26  Identities=27%  Similarity=0.280  Sum_probs=22.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      -|-+.||+|+||||+++.|+..++..
T Consensus         4 iIgI~G~~gSGKSTla~~L~~~l~~~   29 (213)
T d1uj2a_           4 LIGVSGGTASGKSSVCAKIVQLLGQN   29 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhchh
Confidence            35689999999999999999998754

>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=95.62  E-value=0.0023  Score=57.10  Aligned_cols=29  Identities=21%  Similarity=0.217  Sum_probs=24.9

Q ss_pred             cCCCCceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          249 GKAWKRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       249 g~~~~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      |.+...-++|+||||+|||+++..+|..+
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            46667779999999999999999998655

>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=95.62  E-value=0.01  Score=50.19  Aligned_cols=21  Identities=43%  Similarity=0.703  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++|.|++|+|||+|+..+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            789999999999999998764

>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=95.61  E-value=0.0038  Score=53.12  Aligned_cols=20  Identities=30%  Similarity=0.620  Sum_probs=19.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|++|+|||+|++.+.+
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999986

>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=95.56  E-value=0.028  Score=49.97  Aligned_cols=51  Identities=12%  Similarity=0.143  Sum_probs=31.6

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCC---CCceeEEeCCCCCCHHHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA---WKRGYLLYGPPGTGKSSL  269 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~---~~rg~LL~GPpGtGKT~l  269 (473)
                      .+|+++..++.+.+.|.+.   -+..+...+...+|   ..+.+++..|+|||||..
T Consensus        12 ~sF~~l~L~~~l~~~L~~~---g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTla   65 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYAY---GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTAT   65 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHHH---TCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHH
T ss_pred             CCHHHCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhh
Confidence            4899999888877776432   11111111111111   146899999999999984

>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=95.55  E-value=0.014  Score=49.63  Aligned_cols=21  Identities=38%  Similarity=0.651  Sum_probs=19.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -+++.|++|+|||+|+..+.+
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999999886

>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=95.48  E-value=0.021  Score=47.87  Aligned_cols=22  Identities=23%  Similarity=0.333  Sum_probs=19.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|++|+|||+|+..+...
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            4789999999999999998764

>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=95.45  E-value=0.0062  Score=51.36  Aligned_cols=21  Identities=38%  Similarity=0.599  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|+||+|||+|+..+++.
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>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=95.45  E-value=0.019  Score=51.96  Aligned_cols=25  Identities=24%  Similarity=0.522  Sum_probs=22.2

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+-|.||.|+|||||+++|+..+
T Consensus        28 Gei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          28 GEIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3457799999999999999999987

>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=95.44  E-value=0.028  Score=51.24  Aligned_cols=24  Identities=29%  Similarity=0.403  Sum_probs=21.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      +-.++|.|.||+|||+|+.+|.+.
T Consensus        32 ~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          32 SLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCcHHHHHHHHhCC
Confidence            457999999999999999999865

>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=95.40  E-value=0.0041  Score=55.24  Aligned_cols=30  Identities=23%  Similarity=0.209  Sum_probs=24.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      |.|.||.|+||||+++.|++.|   |++++.+.
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            4555999999999999999987   67776553

>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=95.39  E-value=0.098  Score=45.55  Aligned_cols=50  Identities=24%  Similarity=0.322  Sum_probs=28.5

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCC---CCceeEEeCCCCCCHHHH
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA---WKRGYLLYGPPGTGKSSL  269 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~---~~rg~LL~GPpGtGKT~l  269 (473)
                      +|+++...+++.+.|.+.  .| ..+.--+...+|   -.+.+++.+|+|+|||..
T Consensus         2 sF~~l~L~~~l~~~L~~~--g~-~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTla   54 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEA--GF-EKPSPIQEEAIPVAITGRDILARAKNGTGKTAA   54 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHT--TC-CSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHH
T ss_pred             ChHHcCCCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHcCCCEEEecCCcchhhhh
Confidence            688888777777666442  00 011000110000   135799999999999963

>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=95.38  E-value=0.012  Score=49.55  Aligned_cols=20  Identities=35%  Similarity=0.532  Sum_probs=18.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|.+|+|||+|+..+.+
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999886

>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=95.36  E-value=0.012  Score=54.69  Aligned_cols=37  Identities=22%  Similarity=0.248  Sum_probs=26.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc------CCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL------NFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l------~~~~~~l~~~~~  289 (473)
                      |--+-|.|++|+|||||+..|...|      +..+..++..++
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~Ddf   69 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDF   69 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGG
T ss_pred             CEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCC
Confidence            3345578999999999999988775      335555555554

>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=95.27  E-value=0.028  Score=48.87  Aligned_cols=18  Identities=33%  Similarity=0.473  Sum_probs=15.6

Q ss_pred             CceeEEeCCCCCCHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLI  270 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la  270 (473)
                      .+.+++.+|+|+|||..+
T Consensus        40 ~~~~il~apTGsGKT~~a   57 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLA   57 (202)
T ss_dssp             CSCEEEECSSHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHH
Confidence            457899999999999875

>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=95.26  E-value=0.0091  Score=50.07  Aligned_cols=20  Identities=30%  Similarity=0.519  Sum_probs=18.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      +++.|.+|+|||+|+..+.+
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999885

>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=95.25  E-value=0.0046  Score=53.51  Aligned_cols=30  Identities=33%  Similarity=0.351  Sum_probs=24.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      .+|+||.||+|+|||+++.++... |..++.
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~-G~~lva   44 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK-NHLFVG   44 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT-TCEEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCceec
Confidence            569999999999999999988764 665543

>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=95.24  E-value=0.018  Score=48.61  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=19.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|++|+|||+|+..+++.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3788999999999999998863

>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=95.23  E-value=0.0047  Score=53.48  Aligned_cols=30  Identities=30%  Similarity=0.427  Sum_probs=24.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      -+-++|++|+|||+++..+ ..+|++++..|
T Consensus         5 IIgitG~~gSGKstva~~l-~~~g~~~~~~D   34 (191)
T d1uf9a_           5 IIGITGNIGSGKSTVAALL-RSWGYPVLDLD   34 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHH-HHTTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCeEEEcc
Confidence            3558899999999999998 56899887654

>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=95.23  E-value=0.0054  Score=52.69  Aligned_cols=29  Identities=24%  Similarity=0.348  Sum_probs=24.4

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      .+|+||.||+|+|||+++.++... |..++
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~-g~~li   43 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR-GHRLV   43 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            469999999999999999888776 65554

>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=95.14  E-value=0.014  Score=51.72  Aligned_cols=51  Identities=12%  Similarity=0.152  Sum_probs=30.5

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCC---CCceeEEeCCCCCCHHHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA---WKRGYLLYGPPGTGKSSL  269 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~---~~rg~LL~GPpGtGKT~l  269 (473)
                      .+|+++..++++.+.+.+.-   +.++..-++..++   -++.+++.+|+|||||..
T Consensus        10 ~sF~~l~l~~~l~~~L~~~g---~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a   63 (212)
T d1qdea_          10 YKFDDMELDENLLRGVFGYG---FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT   63 (212)
T ss_dssp             CCGGGGTCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             cChhhCCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCEEeecccccchhhh
Confidence            47999988887777664310   1111111111111   146799999999999983

>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=95.05  E-value=0.13  Score=44.95  Aligned_cols=50  Identities=22%  Similarity=0.276  Sum_probs=28.9

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcCC---CCceeEEeCCCCCCHHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA---WKRGYLLYGPPGTGKSS  268 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~---~~rg~LL~GPpGtGKT~  268 (473)
                      .+|+++...+++.+.|.+.  .| ..+..-+...+|   -++.+++..|.|||||.
T Consensus         3 ~~F~~l~L~~~l~~~l~~~--g~-~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTl   55 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFEM--GW-EKPSPIQEESIPIALSGRDILARAKNGTGKSG   55 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHTT--TC-CSCCHHHHHHHHHHHTTCCEEEECCSSSTTHH
T ss_pred             CChhccCcCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHcCCCEEeeccCcccccc
Confidence            5788888777766665332  00 111111111111   14679999999999997

>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=95.00  E-value=0.013  Score=49.55  Aligned_cols=23  Identities=17%  Similarity=0.283  Sum_probs=20.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+++.|+||+|||+|+..+.+.-
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            59999999999999999987543

>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=94.99  E-value=0.0095  Score=51.39  Aligned_cols=25  Identities=16%  Similarity=0.413  Sum_probs=22.1

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ++-++|.||+|+|||+|++.|....
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhC
Confidence            4569999999999999999998765

>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=94.97  E-value=0.015  Score=54.69  Aligned_cols=37  Identities=16%  Similarity=0.097  Sum_probs=28.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC-----CceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN-----FDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~-----~~~~~l~~~~~  289 (473)
                      |--|-+.||+|+||||+++.|+..|.     ..+..++..+.
T Consensus        80 P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F  121 (308)
T d1sq5a_          80 PYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGF  121 (308)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGG
T ss_pred             CEEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeee
Confidence            44578999999999999999999873     45655665554

>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=94.97  E-value=0.021  Score=48.03  Aligned_cols=21  Identities=29%  Similarity=0.512  Sum_probs=18.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|++|+|||+|+..+.+.
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999987763

>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=94.96  E-value=0.014  Score=49.12  Aligned_cols=20  Identities=35%  Similarity=0.642  Sum_probs=18.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      +++.|.+|+|||+|+..+.+
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999998876

>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=94.94  E-value=0.0083  Score=51.33  Aligned_cols=23  Identities=22%  Similarity=0.440  Sum_probs=19.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      .--+++.|+||+|||+|+..+..
T Consensus        17 ~~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          17 ELRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             CEEEEEEEETTSSHHHHHHHTCC
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            44699999999999999998754

>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=94.85  E-value=0.0082  Score=52.98  Aligned_cols=30  Identities=37%  Similarity=0.447  Sum_probs=25.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      -+-|+|++|+|||++++.+. .+|+++++.|
T Consensus         5 iIgitG~igSGKStv~~~l~-~~G~~vidaD   34 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA-DLGINVIDAD   34 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH-HTTCEEEEHH
T ss_pred             EEEEECCCcCCHHHHHHHHH-HCCCcEEEch
Confidence            35589999999999999886 7899988765

>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=94.85  E-value=0.0081  Score=52.87  Aligned_cols=55  Identities=22%  Similarity=0.304  Sum_probs=34.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEccccc---ccCchHHHHHHHHhccCceEEEe
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE---LRSNSDLRTLLVATANRSILVVE  311 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~---~~~~~~l~~l~~~~~~~sIL~iD  311 (473)
                      +-|+|++|||||++++.+. .+|+++++.|.-.   +..+......+...-.+.++.-|
T Consensus         5 IgITG~igSGKStv~~~l~-~~G~~vidaD~i~~~l~~~~~~~~~~i~~~~~~~~~~~d   62 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT-DLGVPLVDADVVAREVVAKDSPLLSKIVEHFGAQILTEQ   62 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH-TTTCCEEEHHHHHHHTTCSSCHHHHHHHHHHCTTCC---
T ss_pred             EEEECCCCCCHHHHHHHHH-HCCCeEEEchHHHHHHHhccchhHHHHHHhcccceecCC
Confidence            4479999999999999886 6899999876321   12334444444444344444333

>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=94.81  E-value=0.025  Score=48.32  Aligned_cols=20  Identities=25%  Similarity=0.552  Sum_probs=18.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|+||+|||+|+..+.+
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            78999999999999999885

>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=94.78  E-value=0.013  Score=49.78  Aligned_cols=21  Identities=33%  Similarity=0.607  Sum_probs=19.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|+||+|||+|+..+.+.
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999998763

>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=94.70  E-value=0.0077  Score=53.65  Aligned_cols=22  Identities=32%  Similarity=0.721  Sum_probs=20.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +++.||+|+|||||+.+|..++
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~   24 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYL   24 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Confidence            6899999999999999998766

>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=94.68  E-value=0.24  Score=43.02  Aligned_cols=49  Identities=16%  Similarity=0.198  Sum_probs=28.7

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCC---CCceeEEeCCCCCCHHH
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA---WKRGYLLYGPPGTGKSS  268 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~---~~rg~LL~GPpGtGKT~  268 (473)
                      +|+++..++++.+.|.+.  .| ..+.-.+...+|   -++.+++..|.|||||.
T Consensus         2 ~F~dl~L~~~l~~~l~~~--g~-~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTl   53 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVDC--GF-EHPSEVQHECIPQAILGMDVLCQAKSGMGKTA   53 (207)
T ss_dssp             CSTTSCCCHHHHHHHHHT--TC-CCCCHHHHHHHHHHHTTCCEEEECCTTSCHHH
T ss_pred             CccccCcCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHcCCCeEEEecccccccc
Confidence            588888887777665431  01 111111111111   14689999999999997

>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=94.59  E-value=0.011  Score=51.22  Aligned_cols=21  Identities=38%  Similarity=0.623  Sum_probs=18.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +++.|++|+|||+|+..+.+.
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            789999999999999988753

>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=94.57  E-value=0.031  Score=47.11  Aligned_cols=20  Identities=40%  Similarity=0.748  Sum_probs=18.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|.||+|||+|+..+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999998875

>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=94.53  E-value=0.021  Score=51.06  Aligned_cols=23  Identities=35%  Similarity=0.496  Sum_probs=17.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      .+.+++.+|.|+|||..+...+-
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~   80 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSL   80 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHH
T ss_pred             CCCEEEEecCCChHHHHHHHHHH
Confidence            45799999999999976554443

>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=94.52  E-value=0.097  Score=44.82  Aligned_cols=22  Identities=27%  Similarity=0.449  Sum_probs=17.3

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ++.|+.+|.|+|||.++..++.
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEeCCCCcHHHHHHHHHH
Confidence            4688999999999986665554

>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=94.52  E-value=0.009  Score=55.17  Aligned_cols=18  Identities=28%  Similarity=0.510  Sum_probs=14.9

Q ss_pred             ceeEEeCCCCCCHHHHHH
Q 012016          254 RGYLLYGPPGTGKSSLIA  271 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~  271 (473)
                      ..+|+.||||||||+++.
T Consensus        15 ~~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             SEEEECCCTTSCHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHH
Confidence            358999999999998643

>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=94.51  E-value=0.03  Score=47.37  Aligned_cols=20  Identities=40%  Similarity=0.609  Sum_probs=18.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|++|+|||+|+..+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            79999999999999998875

>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=94.49  E-value=0.12  Score=45.00  Aligned_cols=56  Identities=14%  Similarity=0.144  Sum_probs=31.7

Q ss_pred             CCccccccchHHHHHHHHHHHHHHhchhHHhhhcC----CCCceeEEeCCCCCCHHHHHHHHH
Q 012016          216 ATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGK----AWKRGYLLYGPPGTGKSSLIAAMA  274 (473)
Q Consensus       216 ~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~----~~~rg~LL~GPpGtGKT~la~alA  274 (473)
                      .+|+++..++++.+.+.+.  .| .++.-.+...+    .-+..+++..|.|+|||...-..+
T Consensus         4 msf~~l~l~~~l~~~l~~~--g~-~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNK--GF-EKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHH--TC-CSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHH
T ss_pred             cCHHHcCCCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccc
Confidence            4788887777776665431  01 11110111111    113479999999999999665444

>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=94.42  E-value=0.07  Score=47.38  Aligned_cols=52  Identities=19%  Similarity=0.302  Sum_probs=32.0

Q ss_pred             CCCCccccccchHHHHHHHHHHHHHHhchhHHhhhcCC---CCceeEEeCCCCCCHHH
Q 012016          214 HPATFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKA---WKRGYLLYGPPGTGKSS  268 (473)
Q Consensus       214 ~p~~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~---~~rg~LL~GPpGtGKT~  268 (473)
                      .-.+|+++..++.+.+.|.+.  .| ..+..-+...+|   ..+.++...|.|||||.
T Consensus        15 ~~~sF~~l~L~~~l~~~L~~~--g~-~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          15 VTPTFDTMGLREDLLRGIYAY--GF-EKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHH--TC-CSCCHHHHHHHHHHHTTCCEEEECCTTSSHHH
T ss_pred             CCCCHHHCCCCHHHHHHHHHC--CC-CCCCHHHHHHHHHHHCCCCeEEEcCcchhhhh
Confidence            335899999888777776442  11 111111111111   14689999999999997

>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=94.32  E-value=0.02  Score=48.31  Aligned_cols=21  Identities=29%  Similarity=0.596  Sum_probs=19.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -+++.|++|+|||+|+..+.+
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999998876

>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=94.17  E-value=0.011  Score=51.12  Aligned_cols=30  Identities=23%  Similarity=0.289  Sum_probs=25.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDL  284 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l  284 (473)
                      -|.+.|+.|+||||+++.|+++++...+..
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~~~~~~~   40 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKNDICLLT   40 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTTTEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEEE
Confidence            578899999999999999999997655543

>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=94.04  E-value=0.014  Score=55.43  Aligned_cols=35  Identities=29%  Similarity=0.441  Sum_probs=26.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc-----CCceEEcccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL-----NFDVYDLELTEL  289 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l-----~~~~~~l~~~~~  289 (473)
                      -+=+.||||+|||||+.+++.++     +.-++.+|.++-
T Consensus        53 ~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss~   92 (323)
T d2qm8a1          53 RVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSST   92 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGGG
T ss_pred             EEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccccH
Confidence            37789999999999999999865     344566665543

>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=94.01  E-value=0.018  Score=50.04  Aligned_cols=30  Identities=23%  Similarity=0.382  Sum_probs=25.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc---CCceEEcc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL---NFDVYDLE  285 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l---~~~~~~l~  285 (473)
                      |.+.|+.|+||||+++.|++.|   |+++..+.
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            5688999999999999999987   66776553

>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=94.00  E-value=0.012  Score=49.71  Aligned_cols=22  Identities=32%  Similarity=0.555  Sum_probs=19.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .|.|.|+||+|||||+.+|.+.
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999753

>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=93.93  E-value=0.012  Score=55.94  Aligned_cols=35  Identities=26%  Similarity=0.428  Sum_probs=26.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---C--CceEEcccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---N--FDVYDLELTEL  289 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~--~~~~~l~~~~~  289 (473)
                      -+=+.||||+|||||+.+++.++   |  .-++.+|.++-
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss~   95 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSSP   95 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC--
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCcee
Confidence            47789999999999999999876   2  34566665543

>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=93.92  E-value=0.013  Score=53.05  Aligned_cols=22  Identities=36%  Similarity=0.724  Sum_probs=20.1

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l  277 (473)
                      +-|.||.|+|||||++.|+..+
T Consensus        27 ~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEECCCCChHHHHHHHHHcCC
Confidence            4578999999999999999987

>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=93.89  E-value=0.014  Score=52.63  Aligned_cols=26  Identities=23%  Similarity=0.414  Sum_probs=22.6

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .--+-|.||+|||||||+++|+....
T Consensus        31 Ge~~~iiG~sGsGKSTLl~~i~gl~~   56 (230)
T d1l2ta_          31 GEFVSIMGPSGSGKSTMLNIIGCLDK   56 (230)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCcchhhHhccCCCC
Confidence            34589999999999999999998763

>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=93.87  E-value=0.0098  Score=50.22  Aligned_cols=22  Identities=18%  Similarity=0.413  Sum_probs=19.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|+||+|||+|+.++...
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4999999999999999998653

>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=93.84  E-value=0.021  Score=51.12  Aligned_cols=28  Identities=36%  Similarity=0.444  Sum_probs=22.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCce
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDV  281 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~  281 (473)
                      +...|.|++|+|||||+.+|........
T Consensus        96 kt~~~~G~SGVGKSTLiN~L~~~~~~~T  123 (225)
T d1u0la2          96 KISTMAGLSGVGKSSLLNAINPGLKLRV  123 (225)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCCCC-
T ss_pred             CeEEEECCCCCCHHHHHHhhcchhhhhc
Confidence            4678999999999999999987665544

>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=93.83  E-value=0.017  Score=52.25  Aligned_cols=25  Identities=28%  Similarity=0.482  Sum_probs=22.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      ..-+-|.||+|+|||||++.|+..+
T Consensus        32 Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          32 GEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCC
Confidence            3458999999999999999999987

>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=93.82  E-value=0.01  Score=50.53  Aligned_cols=22  Identities=27%  Similarity=0.421  Sum_probs=20.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .|+|.|+||+|||||+.+|.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999864

>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=93.62  E-value=0.017  Score=51.72  Aligned_cols=28  Identities=18%  Similarity=0.230  Sum_probs=24.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEE
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYD  283 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~  283 (473)
                      +-|+|+.||||||+|+.+++.+|+.+++
T Consensus         4 IgiTG~igSGKsTva~~l~e~~g~~~i~   31 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNYSAVKYQ   31 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEECC
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCeEEc
Confidence            6789999999999999999998876654

>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=93.60  E-value=0.019  Score=48.43  Aligned_cols=21  Identities=29%  Similarity=0.600  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++|.|++|+|||+|+..+.+.
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999998864

>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=93.57  E-value=0.017  Score=49.52  Aligned_cols=21  Identities=29%  Similarity=0.455  Sum_probs=19.2

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++|.|.+|+|||+|+..+.+.
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhhC
Confidence            899999999999999998863

>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=93.57  E-value=0.014  Score=49.57  Aligned_cols=20  Identities=30%  Similarity=0.615  Sum_probs=8.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      +++.|.+|+|||+|+..+.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998875

>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=93.49  E-value=0.016  Score=50.90  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      =|.|.|+.|+||||+++.|++.|
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37788999999999999999987

>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=93.47  E-value=0.03  Score=51.27  Aligned_cols=37  Identities=24%  Similarity=0.191  Sum_probs=31.3

Q ss_pred             CCCceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          251 AWKRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       251 ~~~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      ..++-+++.|.-|+||||++.++|..+   |..+..+|+.
T Consensus         6 ~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1           6 NIPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             SCCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            347889999999999999999999887   7787777655

>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=93.30  E-value=0.019  Score=53.44  Aligned_cols=24  Identities=21%  Similarity=0.444  Sum_probs=17.5

Q ss_pred             ceeEEeCCCCCCHHHHH-HHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLI-AAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la-~alA~~l  277 (473)
                      ..+|+.||||||||+.+ ..+|..+
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~ll   49 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYLM   49 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEecCCccHHHHHHHHHHHHH
Confidence            35899999999999754 4454443

>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=93.16  E-value=0.016  Score=52.47  Aligned_cols=25  Identities=32%  Similarity=0.444  Sum_probs=22.2

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .-+-|.||+|||||||+++|+..+.
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~Gl~~   56 (240)
T d3dhwc1          32 QIYGVIGASGAGKSTLIRCVNLLER   56 (240)
T ss_dssp             CEEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHcCCcc
Confidence            3588999999999999999998774

>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=93.14  E-value=0.025  Score=47.74  Aligned_cols=20  Identities=35%  Similarity=0.662  Sum_probs=18.5

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      +++.|+||+|||+|+..+.+
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999999875

>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=93.13  E-value=0.018  Score=47.79  Aligned_cols=22  Identities=41%  Similarity=0.628  Sum_probs=19.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|+||+|||||+.+|.+.
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999753

>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=93.13  E-value=0.025  Score=47.50  Aligned_cols=20  Identities=30%  Similarity=0.454  Sum_probs=18.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|.+|+|||+|+..+.+
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            79999999999999998875

>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=93.10  E-value=0.025  Score=48.30  Aligned_cols=20  Identities=35%  Similarity=0.677  Sum_probs=18.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      +++.|.+|+|||+|+..+.+
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999886

>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=93.02  E-value=0.015  Score=52.32  Aligned_cols=24  Identities=25%  Similarity=0.679  Sum_probs=22.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      --+-|.||+|+|||||+++|+..+
T Consensus        27 e~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          27 EYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCc
Confidence            358999999999999999999987

>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=92.93  E-value=0.019  Score=49.60  Aligned_cols=21  Identities=38%  Similarity=0.515  Sum_probs=19.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -+.|.|+||+|||||+.+|.+
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            489999999999999999985

>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=92.93  E-value=0.028  Score=46.88  Aligned_cols=20  Identities=20%  Similarity=0.396  Sum_probs=18.8

Q ss_pred             eEEeCCCCCCHHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~  275 (473)
                      ++|.|++|+|||+|+..+.+
T Consensus         5 v~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            79999999999999999886

>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=92.63  E-value=0.026  Score=47.25  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=19.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|++|+|||+|+..+.+.
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999998763

>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=92.54  E-value=0.036  Score=49.24  Aligned_cols=30  Identities=17%  Similarity=0.123  Sum_probs=25.5

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcCCceE
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLNFDVY  282 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~~~~~  282 (473)
                      |+=+.+-|+-|+||||+++.|+++++-..+
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            456889999999999999999999965444

>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=92.51  E-value=0.14  Score=46.60  Aligned_cols=16  Identities=38%  Similarity=0.524  Sum_probs=14.4

Q ss_pred             CceeEEeCCCCCCHHH
Q 012016          253 KRGYLLYGPPGTGKSS  268 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~  268 (473)
                      ++..|+.+|+|+|||+
T Consensus         9 ~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           9 KRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TCEEEECCCTTSSTTT
T ss_pred             CCcEEEEECCCCCHHH
Confidence            5689999999999995

>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=92.48  E-value=0.029  Score=47.54  Aligned_cols=22  Identities=27%  Similarity=0.437  Sum_probs=20.2

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -|.|.|.||+|||+|+.++.+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999864

>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=92.32  E-value=0.018  Score=52.17  Aligned_cols=24  Identities=25%  Similarity=0.582  Sum_probs=21.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+-|.||+|||||||+++|+...
T Consensus        32 e~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCc
Confidence            458999999999999999999976

>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=92.26  E-value=0.031  Score=47.32  Aligned_cols=23  Identities=17%  Similarity=0.346  Sum_probs=20.0

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHh
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~  276 (473)
                      +-+++.|++|+|||+|+..+.+.
T Consensus         3 ~KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           3 KKLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            34789999999999999998864

>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=92.19  E-value=0.028  Score=51.40  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=21.7

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+-|.||+|+|||+|+++|+..+
T Consensus        29 Ei~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          29 DVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCc
Confidence            358899999999999999999866

>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=92.17  E-value=0.045  Score=48.28  Aligned_cols=31  Identities=23%  Similarity=0.159  Sum_probs=25.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      =|.|.|+-|+||||+++.|++.|....+.+.
T Consensus         5 ~I~iEG~DGsGKST~~~~L~~~L~~~~~~~~   35 (214)
T d1tmka_           5 LILIEGLDRTGKTTQCNILYKKLQPNCKLLK   35 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTTSEEEEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhCCEEEE
Confidence            3778899999999999999999976655443

>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=92.06  E-value=0.035  Score=46.81  Aligned_cols=22  Identities=36%  Similarity=0.520  Sum_probs=19.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+++.|+||+|||+|+..+.+.
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999888763

>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=92.03  E-value=0.03  Score=49.59  Aligned_cols=25  Identities=16%  Similarity=0.214  Sum_probs=22.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      =|.+-||-|+||||+++.|++.|..
T Consensus         4 ~I~ieG~dGsGKST~~~~L~~~l~~   28 (241)
T d1p5zb_           4 KISIEGNIAAGKSTFVNILKQLCED   28 (241)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhc
Confidence            4789999999999999999999854

>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=91.93  E-value=0.041  Score=46.83  Aligned_cols=22  Identities=18%  Similarity=0.360  Sum_probs=19.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+++.|.+|+|||+|+..+...
T Consensus         7 KivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999988764

>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=91.86  E-value=0.038  Score=46.51  Aligned_cols=22  Identities=27%  Similarity=0.428  Sum_probs=19.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .|.|.|.||+|||||+.+|.+.
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999999863

>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=91.72  E-value=0.088  Score=50.97  Aligned_cols=35  Identities=29%  Similarity=0.315  Sum_probs=27.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      .+++++.|++|+|||+++..+...+   +.+++.+|..
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~k   87 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN   87 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEET
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            3689999999999999887666543   7788877754

>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=91.71  E-value=0.037  Score=49.99  Aligned_cols=26  Identities=27%  Similarity=0.452  Sum_probs=22.8

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      ..-+-|.||.|+|||||+++|+..+.
T Consensus        32 Gei~~liGpnGaGKSTl~~~i~Gl~~   57 (240)
T d1ji0a_          32 GQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            34588999999999999999999873

>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=91.66  E-value=0.17  Score=46.63  Aligned_cols=24  Identities=29%  Similarity=0.533  Sum_probs=21.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -.+|.||+|||||+|+..+++...
T Consensus        45 r~~I~g~~g~GKT~l~~~i~~~~~   68 (289)
T d1xpua3          45 RGLIVAPPKAGKTMLLQNIAQSIA   68 (289)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             eeeEeCCCCCCHHHHHHHHHHHHh
Confidence            489999999999999999998663

>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=91.60  E-value=0.043  Score=46.58  Aligned_cols=22  Identities=36%  Similarity=0.540  Sum_probs=19.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+.+.|.+|+|||||+.+|.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4789999999999999999864

>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=91.55  E-value=0.14  Score=44.49  Aligned_cols=31  Identities=23%  Similarity=0.196  Sum_probs=24.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcCCceEEcc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLNFDVYDLE  285 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~~~~~~l~  285 (473)
                      ..++.+|+|+|||.++-+++.+++.+++.+-
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~  117 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAINELSTPTLIVV  117 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEE
T ss_pred             CcEEEeCCCCCceehHHhHHHHhcCceeEEE
Confidence            3467889999999999999998877665543

>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=91.43  E-value=0.023  Score=48.05  Aligned_cols=21  Identities=29%  Similarity=0.507  Sum_probs=17.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -+++.|++|+|||+|+..+.+
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC-
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999998765

>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=91.41  E-value=0.11  Score=47.14  Aligned_cols=35  Identities=34%  Similarity=0.405  Sum_probs=28.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      .+-++++|.-|+||||++..+|..+   |..+..+|+.
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            4568888999999999988888776   7788777766

>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=91.29  E-value=0.032  Score=46.94  Aligned_cols=23  Identities=26%  Similarity=0.343  Sum_probs=20.0

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      ..-|.|.|+|++|||+|+.+|.+
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            34599999999999999999854

>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=91.16  E-value=0.041  Score=51.04  Aligned_cols=35  Identities=14%  Similarity=0.239  Sum_probs=24.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELTEL  289 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~~~  289 (473)
                      -+-+.|++|+|||++++++++.+   +.+...++..+.
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            57899999999999999999877   455445544443

>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=91.11  E-value=0.049  Score=46.34  Aligned_cols=22  Identities=23%  Similarity=0.395  Sum_probs=19.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -++|.|.+|+|||+|+..+.+-
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4799999999999999988773

>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=91.11  E-value=0.017  Score=47.86  Aligned_cols=21  Identities=33%  Similarity=0.626  Sum_probs=19.4

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      +.|.|+||+|||||+.+|.+.
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999865

>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=90.89  E-value=0.053  Score=46.52  Aligned_cols=21  Identities=19%  Similarity=0.395  Sum_probs=18.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHh
Q 012016          256 YLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++|.|++|+|||+|+..+...
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999888753

>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=90.88  E-value=0.018  Score=48.93  Aligned_cols=23  Identities=39%  Similarity=0.449  Sum_probs=20.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcC
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      .+|+||.|+|||+++.||.-.|+
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            47899999999999999998774

>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=90.70  E-value=0.054  Score=49.27  Aligned_cols=24  Identities=42%  Similarity=0.776  Sum_probs=21.9

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      .-+-|.||.|+|||+|+++|+..+
T Consensus        31 ei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          31 DVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHHCCC
Confidence            358899999999999999999987

>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=90.66  E-value=0.047  Score=46.38  Aligned_cols=21  Identities=33%  Similarity=0.531  Sum_probs=18.6

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -|-|.|+||+|||||+.+|.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            377999999999999999865

>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=90.54  E-value=0.081  Score=45.67  Aligned_cols=33  Identities=15%  Similarity=0.289  Sum_probs=27.6

Q ss_pred             ceeEEeCC-CCCCHHHHHHHHHHhc---CCceEEccc
Q 012016          254 RGYLLYGP-PGTGKSSLIAAMANYL---NFDVYDLEL  286 (473)
Q Consensus       254 rg~LL~GP-pGtGKT~la~alA~~l---~~~~~~l~~  286 (473)
                      +.|++.|- +|+|||+++..||..|   |+.+..++.
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            35899999 5999999999999887   777777764

>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=90.34  E-value=0.054  Score=48.52  Aligned_cols=24  Identities=46%  Similarity=0.627  Sum_probs=21.1

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l  277 (473)
                      --+-|.||.|+|||||+++|+...
T Consensus        26 ei~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          26 EILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             CEEECBCCTTSSHHHHHHHHHTSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            358899999999999999999844

>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=90.11  E-value=0.36  Score=44.02  Aligned_cols=23  Identities=35%  Similarity=0.560  Sum_probs=20.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+++.|++|+|||+|+.-+++..
T Consensus        70 r~~If~~~g~GKt~l~~~i~~~~   92 (276)
T d2jdid3          70 KIGLFGGAGVGKTVLIMELINNV   92 (276)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHH
Confidence            38999999999999999998763

>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=89.89  E-value=0.057  Score=45.64  Aligned_cols=22  Identities=50%  Similarity=0.582  Sum_probs=19.4

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      .|.|.|+||+|||||+.+|.+.
T Consensus         3 ~VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999753

>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=89.42  E-value=0.51  Score=41.83  Aligned_cols=23  Identities=26%  Similarity=0.546  Sum_probs=17.7

Q ss_pred             CceeEEeCCCCCCHHH--HHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSS--LIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~--la~alA~  275 (473)
                      .+.+++..|+|||||.  ++-.+-+
T Consensus        58 g~dvvi~a~TGsGKTlayllp~l~~   82 (238)
T d1wrba1          58 HRDIMACAQTGSGKTAAFLIPIINH   82 (238)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCcceeeHHHHHHH
Confidence            3579999999999998  4444443

>d2axpa1 c.37.1.1 (A:2-165) Hypothetical protein YorR {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: Nucleotide and nucleoside kinases
domain: Hypothetical protein YorR
species: Bacillus subtilis [TaxId: 1423]

Probab=89.37  E-value=0.38  Score=37.16  Aligned_cols=59  Identities=20%  Similarity=0.256  Sum_probs=48.7

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc--cCchHHHHHHHHhccCceEEEeccc
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL--RSNSDLRTLLVATANRSILVVEDID  314 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~--~~~~~l~~l~~~~~~~sIL~iDdiD  314 (473)
                      ++|.||--|=||+.+..+..++++|++.-+.-++  .+++.+-+.|.+.....-++||-+-
T Consensus         3 iilegpdccfkstvaaklskelkypiikgssfelaksgneklfehfnkladednviidrfv   63 (164)
T d2axpa1           3 IILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFV   63 (164)
T ss_dssp             EEEECCSSSCHHHHHHHHHHHHTCCEEECCCHHHHHHCHHHHHHHHHHHTTCCSEEEESCH
T ss_pred             EEEeCCchhhHHHHHHHHHhhhcCceecCchhhhhhccCHHHHHHHHhhccccceeeehhh
Confidence            6889999999999999999999999987665554  3567888888888877777777653

>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=89.20  E-value=0.075  Score=48.77  Aligned_cols=23  Identities=35%  Similarity=0.603  Sum_probs=20.6

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcC
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -+|+||.|+|||+++.||+-.++
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~lg   49 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWVFG   49 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHTSC
T ss_pred             EEEECCCCCcHHHHHHHHHHHhC
Confidence            48999999999999999987664

>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=88.99  E-value=0.027  Score=50.60  Aligned_cols=27  Identities=33%  Similarity=0.543  Sum_probs=19.4

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFD  280 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~  280 (473)
                      +..+|.|++|+|||||+.+|.......
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~~~~~  124 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPELGLR  124 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-----
T ss_pred             ceEEEECCCCccHHHHHHhhccHhHhh
Confidence            456788999999999999997655443

>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=88.74  E-value=0.1  Score=44.36  Aligned_cols=19  Identities=37%  Similarity=0.609  Sum_probs=17.6

Q ss_pred             eEEeCCCCCCHHHHHHHHH
Q 012016          256 YLLYGPPGTGKSSLIAAMA  274 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA  274 (473)
                      ++|.|.+|+|||+|+..+.
T Consensus         5 ivllG~~~vGKTsll~r~~   23 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQMR   23 (200)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            7999999999999999983

>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=88.59  E-value=0.13  Score=43.58  Aligned_cols=22  Identities=32%  Similarity=0.317  Sum_probs=19.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+++.|++|+|||+|+..+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999988774

>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=88.15  E-value=0.12  Score=48.90  Aligned_cols=24  Identities=33%  Similarity=0.272  Sum_probs=22.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhcC
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYLN  278 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l~  278 (473)
                      -|.|-|+-|+||||+++.|+++++
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l~   31 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAAS   31 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGGG
T ss_pred             EEEEECCccCCHHHHHHHHHHHhc
Confidence            478899999999999999999984

>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=87.83  E-value=0.13  Score=48.99  Aligned_cols=24  Identities=33%  Similarity=0.607  Sum_probs=20.9

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      -+|+||.|+|||+++.||+-.||.
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~lg~   51 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVLGV   51 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            489999999999999999876654

>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=87.57  E-value=0.16  Score=45.65  Aligned_cols=33  Identities=21%  Similarity=0.301  Sum_probs=26.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      .|-++|.=|+||||++..+|..|   |.++..+|+.
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            46678999999999998888776   7777777764

>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=87.31  E-value=0.11  Score=45.91  Aligned_cols=23  Identities=35%  Similarity=0.401  Sum_probs=20.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+++.|..|+|||||++.+.+..
T Consensus         5 v~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHSC
T ss_pred             EEEEeeCCCCCHHHHHHHHHhcC
Confidence            57999999999999999888754

>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=87.16  E-value=0.15  Score=44.87  Aligned_cols=21  Identities=33%  Similarity=0.520  Sum_probs=18.8

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -+||.|++|+|||+|++.+..
T Consensus         8 KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999998764

>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=86.01  E-value=0.18  Score=42.63  Aligned_cols=23  Identities=35%  Similarity=0.434  Sum_probs=20.0

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -++|.|..|+|||+|+..+...-
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            48999999999999999987643

>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=85.50  E-value=0.99  Score=43.47  Aligned_cols=36  Identities=22%  Similarity=0.272  Sum_probs=31.8

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEcccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTEL  289 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~~  289 (473)
                      +..+|.|-.|+|||.++++++...+.|++.+..+..
T Consensus        32 ~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~~   67 (413)
T d1t5la1          32 KHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNKT   67 (413)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSHH
T ss_pred             CcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCHH
Confidence            467899999999999999999999999988876654

>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=84.95  E-value=0.48  Score=42.05  Aligned_cols=37  Identities=27%  Similarity=0.206  Sum_probs=26.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH-hc--CCceEEcccccc
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN-YL--NFDVYDLELTEL  289 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~-~l--~~~~~~l~~~~~  289 (473)
                      +...||+|..|+|||.++-..+. .+  |..+..+-....
T Consensus        76 ~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~  115 (233)
T d2eyqa3          76 AMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTL  115 (233)
T ss_dssp             CCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHH
T ss_pred             ccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHH
Confidence            56789999999999997654443 33  777776665554

>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=84.77  E-value=0.18  Score=47.51  Aligned_cols=24  Identities=21%  Similarity=0.324  Sum_probs=22.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      |.|-|+-|+||||+++.|+++++.
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            678899999999999999999864

>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=84.32  E-value=0.66  Score=42.42  Aligned_cols=22  Identities=27%  Similarity=0.270  Sum_probs=18.9

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      -+++.|++|+|||+++..++..
T Consensus        70 r~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          70 RELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             BCEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEeecCCCCChHHHHHHHHHh
Confidence            4899999999999998877754

>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=84.28  E-value=0.66  Score=37.62  Aligned_cols=61  Identities=11%  Similarity=0.252  Sum_probs=36.9

Q ss_pred             eEEeCCCCCCHHH-HHHHHHHh--cCCceEEcccccc--------------------cCchHHHHHHHHh---ccCceEE
Q 012016          256 YLLYGPPGTGKSS-LIAAMANY--LNFDVYDLELTEL--------------------RSNSDLRTLLVAT---ANRSILV  309 (473)
Q Consensus       256 ~LL~GPpGtGKT~-la~alA~~--l~~~~~~l~~~~~--------------------~~~~~l~~l~~~~---~~~sIL~  309 (473)
                      -+++||-.+|||+ |++.+-++  .|.+++.+....-                    ....++...+...   ....+|+
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dvI~   84 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIG   84 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEE
T ss_pred             EEEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccceEEcccCceeeeEEeccchhhHHHHHhhccccCcCEEE
Confidence            3789999999999 77776443  3666554433210                    1123333333322   2457999


Q ss_pred             Eeccccc
Q 012016          310 VEDIDCT  316 (473)
Q Consensus       310 iDdiD~l  316 (473)
                      |||+.-+
T Consensus        85 IDE~QFf   91 (139)
T d2b8ta1          85 IDEVQFF   91 (139)
T ss_dssp             ECSGGGS
T ss_pred             echhhhc
Confidence            9999765

>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=83.71  E-value=2.5  Score=40.38  Aligned_cols=35  Identities=29%  Similarity=0.300  Sum_probs=30.5

Q ss_pred             ceeEEeCCCCCCHHHHHHHHHHhcCCceEEccccc
Q 012016          254 RGYLLYGPPGTGKSSLIAAMANYLNFDVYDLELTE  288 (473)
Q Consensus       254 rg~LL~GPpGtGKT~la~alA~~l~~~~~~l~~~~  288 (473)
                      +..+|.|.+|+||+.++++++..++.|++.+-.+.
T Consensus        29 ~~~~L~GlsgS~ka~~~A~l~~~~~rp~LvVt~~~   63 (408)
T d1c4oa1          29 RFVTLLGATGTGKTVTMAKVIEALGRPALVLAPNK   63 (408)
T ss_dssp             SEEEEEECTTSCHHHHHHHHHHHHTCCEEEEESSH
T ss_pred             CcEEEecCCCCHHHHHHHHHHHHhCCCEEEEeCCH
Confidence            45799999999999999999999999998775443

>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=83.49  E-value=0.37  Score=44.88  Aligned_cols=50  Identities=14%  Similarity=0.402  Sum_probs=29.0

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHH
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIA  271 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~  271 (473)
                      +||.+.+.+...+++.+.+..++-.. .+.  |  ....++-||+.|+|||+.+-
T Consensus        45 ~FD~vf~~~~~q~~vf~~~~~~lv~~-~l~--G--~n~~i~aYGqtgSGKTyT~~   94 (323)
T d1bg2a_          45 AFDRVFQSSTSQEQVYNDCAKKIVKD-VLE--G--YNGTIFAYGQTSSGKTHTME   94 (323)
T ss_dssp             ECSEEECTTCCHHHHHHHHTHHHHHH-HHT--T--CCEEEEEECSTTSSHHHHHT
T ss_pred             ECCEEECCCCCHHHHHHHHHHHHHHH-HHc--C--CCcceeeecccCCCCceecc
Confidence            46666655544555544433322110 010  1  24579999999999999873

>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=83.16  E-value=0.35  Score=43.88  Aligned_cols=33  Identities=24%  Similarity=0.308  Sum_probs=25.1

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      -+-++|.=|+|||+++.-+|..|   |..+..+|+.
T Consensus         4 ~IaisgKGGVGKTT~a~NLA~~LA~~G~rVLlID~D   39 (289)
T d2afhe1           4 QCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCD   39 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEecC
Confidence            35569999999999777666655   8888777764

>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=82.46  E-value=1.2  Score=40.06  Aligned_cols=42  Identities=19%  Similarity=0.150  Sum_probs=29.9

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHHh---cCCceEEcccccccCchH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMANY---LNFDVYDLELTELRSNSD  294 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~~---l~~~~~~l~~~~~~~~~~  294 (473)
                      +..-||+|..|+|||-++-..+..   -|+.+..+-.+.+.....
T Consensus       104 ~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m~Pt~~La~Qh  148 (264)
T d1gm5a3         104 PMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFMVPTSILAIQH  148 (264)
T ss_dssp             CCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEECSCHHHHHHH
T ss_pred             cceeeeeccccccccHHHHHHHHHHHhcccceeEEeehHhhhHHH
Confidence            557899999999999977655443   377777777666544333

>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=82.34  E-value=1.3  Score=40.06  Aligned_cols=23  Identities=22%  Similarity=0.222  Sum_probs=18.5

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHhc
Q 012016          255 GYLLYGPPGTGKSSLIAAMANYL  277 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~l  277 (473)
                      -+++.|++|+|||+|+..++...
T Consensus        69 r~~Ifg~~g~GKt~l~~~~~~~~   91 (276)
T d1fx0a3          69 RELIIGDRQTGKTAVATDTILNQ   91 (276)
T ss_dssp             BCBEEESSSSSHHHHHHHHHHTC
T ss_pred             eEeeccCCCCChHHHHHHHHhhh
Confidence            38899999999999987655444

>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=82.33  E-value=0.48  Score=44.66  Aligned_cols=49  Identities=20%  Similarity=0.306  Sum_probs=28.1

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHH
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLI  270 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la  270 (473)
                      +||.+.+.+...++|.+.+..++-.. .+.  |  +...++-||+.|+|||+.+
T Consensus        49 ~FD~vf~~~~~q~~vy~~~~~plv~~-~l~--G--~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          49 TFDRVFDMSCKQSDIFDFSIKPTVDD-ILN--G--YNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             ECSEEECTTCCHHHHHHHHTHHHHHH-HTT--T--CCEEEEEECSTTSSHHHHH
T ss_pred             ECCeEcCCCCCHHHHHHHHHHHHHHH-hhc--c--CceeEEecccCCCCcceee
Confidence            46666655544555544433332211 000  1  2346999999999999876

>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=82.26  E-value=0.23  Score=46.62  Aligned_cols=24  Identities=21%  Similarity=0.326  Sum_probs=19.0

Q ss_pred             eEEeCCCCCCHHHHHHHHHHhcCC
Q 012016          256 YLLYGPPGTGKSSLIAAMANYLNF  279 (473)
Q Consensus       256 ~LL~GPpGtGKT~la~alA~~l~~  279 (473)
                      |.|-|+-|+||||+++.+++.++.
T Consensus         7 I~IEG~iGsGKTTl~~~La~~l~~   30 (329)
T d1e2ka_           7 VYIDGPHGMGKTTTTQLLVALGSR   30 (329)
T ss_dssp             EEECSCTTSSHHHHHHHHTC----
T ss_pred             EEEECCcCCCHHHHHHHHHHHhCC
Confidence            678899999999999999998854

>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=82.05  E-value=0.35  Score=40.42  Aligned_cols=21  Identities=33%  Similarity=0.521  Sum_probs=18.3

Q ss_pred             eeEEeCCCCCCHHHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~  275 (473)
                      -++|.|..|+|||+|++.+..
T Consensus         4 KivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            379999999999999997754

>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=81.89  E-value=0.51  Score=45.33  Aligned_cols=23  Identities=30%  Similarity=0.457  Sum_probs=20.7

Q ss_pred             CceeEEeCCCCCCHHHHHHHHHH
Q 012016          253 KRGYLLYGPPGTGKSSLIAAMAN  275 (473)
Q Consensus       253 ~rg~LL~GPpGtGKT~la~alA~  275 (473)
                      +-.|.+.|.||+|||||+.+|.+
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            45799999999999999999975

>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=81.82  E-value=0.49  Score=40.96  Aligned_cols=31  Identities=29%  Similarity=0.412  Sum_probs=24.7

Q ss_pred             EEeCCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          257 LLYGPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       257 LL~GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      +..|..|+|||+++..+|..+   |.++..+|+.
T Consensus         6 v~s~KGGvGKTtia~nlA~~la~~g~~VlliD~D   39 (232)
T d1hyqa_           6 VASGKGGTGKTTITANLGVALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEESSSCSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EECCCCCChHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            445889999999999988877   6777776654

>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=81.25  E-value=0.61  Score=40.31  Aligned_cols=33  Identities=24%  Similarity=0.288  Sum_probs=26.0

Q ss_pred             eeEEe-CCCCCCHHHHHHHHHHhc---CCceEEcccc
Q 012016          255 GYLLY-GPPGTGKSSLIAAMANYL---NFDVYDLELT  287 (473)
Q Consensus       255 g~LL~-GPpGtGKT~la~alA~~l---~~~~~~l~~~  287 (473)
                      -|-++ +-.|+|||+++..+|..+   |.++..+|+.
T Consensus         4 vIav~~~kGGvGKTtia~nLA~~la~~g~~VlliD~D   40 (237)
T d1g3qa_           4 IISIVSGKGGTGKTTVTANLSVALGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEEECSSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEEECCCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            35455 778999999999998877   7788777754

>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=80.51  E-value=0.26  Score=45.87  Aligned_cols=19  Identities=32%  Similarity=0.529  Sum_probs=16.2

Q ss_pred             eeEEeCCCCCCHHHHHHHH
Q 012016          255 GYLLYGPPGTGKSSLIAAM  273 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~al  273 (473)
                      .-||+|.+|||||+|...-
T Consensus        16 valffGLSGTGKTTLs~~~   34 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTDP   34 (318)
T ss_dssp             EEEEEECTTSCHHHHTCBT
T ss_pred             EEEEEccCCCCccccccCC
Confidence            4799999999999987643

>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=80.19  E-value=0.67  Score=43.37  Aligned_cols=49  Identities=18%  Similarity=0.478  Sum_probs=28.8

Q ss_pred             CccccccchHHHHHHHHHHHHHHhchhHHhhhcCCCCceeEEeCCCCCCHHHHHH
Q 012016          217 TFETLAMEQEQKTKIMQDLERFVKRKDYYRRVGKAWKRGYLLYGPPGTGKSSLIA  271 (473)
Q Consensus       217 ~f~~l~~~~~~k~~l~~~l~~fl~~~~~y~~~g~~~~rg~LL~GPpGtGKT~la~  271 (473)
                      +||.+.+.+...+++.+.+...+..  .+.  |  ....++-||+.|+|||+.+-
T Consensus        53 ~FD~vf~~~~~q~~vy~~v~~~v~~--~l~--G--~n~~i~aYGqtgSGKT~T~~  101 (342)
T d1f9va_          53 KFDKIFDQQDTNVDVFKEVGQLVQS--SLD--G--YNVCIFAYGQTGSGKTFTML  101 (342)
T ss_dssp             EESEEECTTCCHHHHHHHHHHHHGG--GGG--T--CCEEEEEECCTTSSHHHHHH
T ss_pred             ecCeEeCCCCCHHHHHHHhhhhhcc--hhc--c--cccceeeeeccCCccccccc
Confidence            3555555554555555554432221  111  2  24568899999999999773

>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=80.13  E-value=0.4  Score=40.21  Aligned_cols=22  Identities=18%  Similarity=0.379  Sum_probs=19.7

Q ss_pred             eeEEeCCCCCCHHHHHHHHHHh
Q 012016          255 GYLLYGPPGTGKSSLIAAMANY  276 (473)
Q Consensus       255 g~LL~GPpGtGKT~la~alA~~  276 (473)
                      ++=+.|.|++|||||+.+|.+.
T Consensus         7 nIaiiG~~naGKSTL~n~L~~~   28 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTEI   28 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTT
T ss_pred             EEEEEeCCCCcHHHHHHHHHHh
Confidence            5789999999999999999853