Citrus Sinensis ID: 043781

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------
Protein Sequence
SRSFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNTSTRPGMVSRYLMAEFCEPVCSVKAWCAGE
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHccccEEEEcccccHHHHHHHcccccccEEcccccHHHHHHHHHHccHHHHHccccccEEEEcccccHHHHHHHHHHHHHccccEEEEEEccccccccccHHHHHHHHHHHHHHHHccccccccccEEEEEcccHHHHHHHccccccccccccHHHHHHHHHHHHccccccccccccccccHHHHccHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHcccccccccEEEcccHHHHHHHHHHHccEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEcccccHHHHHHHHHHHHcccccEEEEEEEccccccHHHHHHHHHHHHHccccccEEEEEEccHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccccccccccHHHcHHHHHHHHHccHHHHHHHHccc
Coil and Loop (DISEMBL)
SRSFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEgvdenalvrkkpkiIEINENLDDIAKQKEVFNfnvirgstekseRIHSTALInvsdvrgmggigktTLAQFAYNDKDVIENFDKRIWvcvsdpfdeFRIAKAIIEGLEGSEKKFFLILDdvwtddyskwepfHNCLMRVLQEFAAievdgdenplsltsTCQEKLRHLTLTlglrakfpvsifdakkiwgwevfgrntstrpgmvsRYLMAefcepvcsvkawcage
Flexible Loop (DISEMBL)
SRSFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQiegvdenalvrkkpkiieinenlddiakqkeVFNFNVirgstekserihstalinvsdvrgmGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIeglegsekKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTltlglrakfpvsifdakkiwgwevfgrntSTRPGMVSRYLMAEFCEPVCSVKAWCAGE
Low Complexity Region (SEG)
SRSFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNTSTRPGMVSRYLMAEFCEPVCSVKAWCAGE
Disordered region (IsUnstruct)
*************KLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNTSTRPGMVSRYLMAEFCEPVCSVKAWCA**
Disordered Region (DISOPRED)
*RSFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLK********************INENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNT*********YLMAEFCEPVCSVKAWCAGE
Disordered Region (DISEMBL)
********GKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNTSTRPGMVSRYLMAEFCEPVCSVKAWCAGE
Disordered Region (DISPRO)
*RSFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNTSTRPGMVSRYLMAEFCEPVCSVKAWCAG*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
SRSFFQDFGKQxxxxxxxxxxxxxxxxxxxxxQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNTSTRPGMVSRYLMAEFCEPVCSVKAWCAGE
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	297	2.2.26 [Sep-21-2011]
Q7XA40	992	Putative disease resistan	N/A	no	0.841	0.252	0.307	3e-31
Q7XBQ9	970	Disease resistance protei	N/A	no	0.851	0.260	0.280	5e-28
Q7XA39	988	Putative disease resistan	N/A	no	0.868	0.261	0.287	5e-28
Q7XA42	979	Putative disease resistan	N/A	no	0.851	0.258	0.272	1e-26
Q9LRR4	1054	Putative disease resistan	yes	no	0.673	0.189	0.259	3e-19
Q38834	852	Disease resistance RPP13-	no	no	0.649	0.226	0.277	1e-16
Q9LRR5	1424	Putative disease resistan	no	no	0.646	0.134	0.267	7e-15
Q9LQ54	870	Probable disease resistan	no	no	0.659	0.225	0.289	7e-12
Q8W474	907	Probable disease resistan	no	no	0.592	0.194	0.236	1e-11
Q8W3K3	910	Putative disease resistan	no	no	0.585	0.191	0.242	8e-11

>sp|Q7XA40|RGA3_SOLBU Putative disease resistance protein RGA3 OS=Solanum bulbocastanum GN=RGA3 PE=2 SV=2

 Score =  135 bits (340), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 101/328 (30%), Positives = 155/328 (47%), Gaps = 78/328 (23%)

Query: 8   FGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWIT--ARL 65
           F K+ KKL+S    IQAVL DA+++Q+K  +++ WL +L  A+Y+++D+LD+  T  AR 
Sbjct: 27  FEKEFKKLSSMFSMIQAVLEDAQEKQLKYKAIKNWLQKLNVAAYEVDDILDDCKTEAARF 86

Query: 66  KLQIEGVDENALVRKKPKII-----------EINENLDDIAKQKEVFNFN---------- 104
           K  + G       R  P+ I           E+ E LD IA+++  F+ +          
Sbjct: 87  KQAVLG-------RYHPRTITFCYKVGKRMKEMMEKLDAIAEERRNFHLDERIIERQAAR 139

Query: 105 ----------VIRGSTEKSERIHSTALINVS--------DVRGMGGIGKTTLAQFAYNDK 146
                      + G  ++ + I    + NVS         + GMGG+GKTTLAQ  +ND+
Sbjct: 140 RQTGFVLTEPKVYGREKEEDEIVKILINNVSYSEEVPVLPILGMGGLGKTTLAQMVFNDQ 199

Query: 147 DVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE-------------------KKFFLI 187
            + E+F+ +IWVCVSD FDE R+ KAI+E +EG                     K++FL+
Sbjct: 200 RITEHFNLKIWVCVSDDFDEKRLIKAIVESIEGKSLGDMDLAPLQKKLQELLNGKRYFLV 259

Query: 188 LDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAK 247
           LDDVW +D  KW+              A+   G      L +T  EK+  +  TL L   
Sbjct: 260 LDDVWNEDQEKWD-----------NLRAVLKIGASGASILITTRLEKIGSIMGTLQLYQL 308

Query: 248 FPVSIFDAKKIWGWEVFGRNTSTRPGMV 275
             +S  D   ++    F   T T P ++
Sbjct: 309 SNLSQEDCWLLFKQRAFCHQTETSPKLM 336

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.
Solanum bulbocastanum (taxid: 147425)

>sp|Q7XBQ9|RGA2_SOLBU Disease resistance protein RGA2 OS=Solanum bulbocastanum GN=RGA2 PE=1 SV=1

 Score =  125 bits (313), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 93/331 (28%), Positives = 152/331 (45%), Gaps = 78/331 (23%)

Query: 5   FQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITAR 64
           FQD   + ++L+S    IQAVL DA+++Q+    +  WL +L  A+Y+++D+LDE+ T  
Sbjct: 27  FQD---EFQRLSSMFSTIQAVLEDAQEKQLNNKPLENWLQKLNAATYEVDDILDEYKTKA 83

Query: 65  LKLQIEGVDENALVRKKPKII-----------EINENLDDIAKQKEVFNFN--------- 104
            +       ++   R  PK+I           ++ + L  IA++++ F+ +         
Sbjct: 84  TRF-----SQSEYGRYHPKVIPFRHKVGKRMDQVMKKLKAIAEERKNFHLHEKIVERQAV 138

Query: 105 -----------VIRGSTEKSERIHSTALINVSD--------VRGMGGIGKTTLAQFAYND 145
                       + G  ++ + I    + NVSD        + GMGG+GKTTLAQ  +ND
Sbjct: 139 RRETGSVLTEPQVYGRDKEKDEIVKILINNVSDAQHLSVLPILGMGGLGKTTLAQMVFND 198

Query: 146 KDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG--------------------SEKKFF 185
           + V E+F  +IW+CVS+ FDE R+ KAI+E +EG                    + K++ 
Sbjct: 199 QRVTEHFHSKIWICVSEDFDEKRLIKAIVESIEGRPLLGEMDLAPLQKKLQELLNGKRYL 258

Query: 186 LILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLR 245
           L+LDDVW +D  KW               A+   G      LT+T  EK+  +  TL   
Sbjct: 259 LVLDDVWNEDQQKW-----------ANLRAVLKVGASGASVLTTTRLEKVGSIMGTLQPY 307

Query: 246 AKFPVSIFDAKKIWGWEVFGRNTSTRPGMVS 276
               +S  D   ++    FG      P +V+
Sbjct: 308 ELSNLSQEDCWLLFMQRAFGHQEEINPNLVA 338

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth. Confers a broad resistance to all known races of P.infestans.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA39|RGA4_SOLBU Putative disease resistance protein RGA4 OS=Solanum bulbocastanum GN=RGA4 PE=2 SV=1

 Score =  125 bits (313), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 93/324 (28%), Positives = 151/324 (46%), Gaps = 66/324 (20%)

Query: 8   FGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKL 67
           F K+ +KL+S    IQAVL DA+++Q+K+ ++  WL +L  A+Y+++D+L E     ++ 
Sbjct: 27  FEKECEKLSSVFSTIQAVLQDAQEKQLKDKAIENWLQKLNSAAYEVDDILGECKNEAIRF 86

Query: 68  QIE--GVDENALVRKKPKI----IEINENLDDIAKQKEVFNF------------------ 103
           +    G     ++  + KI     EI E LD I++++  F+F                  
Sbjct: 87  EQSRLGFYHPGIINFRHKIGRRMKEIMEKLDAISEERRKFHFLEKITERQAAAATRETGF 146

Query: 104 ----NVIRGSTEKSERIHSTALINVS--------DVRGMGGIGKTTLAQFAYNDKDVIEN 151
                 + G  ++ + I    + NV+         + GMGG+GKTTLAQ  +ND+ V ++
Sbjct: 147 VLTEPKVYGRDKEEDEIVKILINNVNVAEELPVFPIIGMGGLGKTTLAQMIFNDERVTKH 206

Query: 152 FDKRIWVCVSDPFDEFRIAKAIIEGLEGSE-------------------KKFFLILDDVW 192
           F+ +IWVCVSD FDE R+ K II  +E S                    K++ L+LDDVW
Sbjct: 207 FNPKIWVCVSDDFDEKRLIKTIIGNIERSSPHVEDLASFQKKLQELLNGKRYLLVLDDVW 266

Query: 193 TDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSI 252
            DD  KW            +  A+   G      L +T  EK+  +  TL       +S 
Sbjct: 267 NDDLEKW-----------AKLRAVLTVGARGASILATTRLEKVGSIMGTLQPYHLSNLSP 315

Query: 253 FDAKKIWGWEVFGRNTSTRPGMVS 276
            D+  ++    FG+     P +V+
Sbjct: 316 HDSLLLFMQRAFGQQKEANPNLVA 339

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q7XA42|RGA1_SOLBU Putative disease resistance protein RGA1 OS=Solanum bulbocastanum GN=RGA1 PE=2 SV=2

 Score =  120 bits (301), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 90/330 (27%), Positives = 152/330 (46%), Gaps = 77/330 (23%)

Query: 5   FQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITAR 64
           FQD   + ++L+S    IQAVL DA+++Q+ +  +  WL +L  A+Y+++D+LDE+ T  
Sbjct: 27  FQD---EFQRLSSMFSTIQAVLEDAQEKQLNDKPLENWLQKLNAATYEVDDILDEYKTKA 83

Query: 65  LKLQIEGVDENALVRKKPKII-----------EINENLDDIAKQKEVFNFN--------- 104
            +       ++   R  PK+I           ++ + L+ IA++++ F+           
Sbjct: 84  TRFL-----QSEYGRYHPKVIPFRHKVGKRMDQVMKKLNAIAEERKKFHLQEKIIERQAA 138

Query: 105 -----------VIRGSTEKSERIHSTALINVSD--------VRGMGGIGKTTLAQFAYND 145
                       + G  ++ + I    +   SD        + GMGG+GKTTL+Q  +ND
Sbjct: 139 TRETGSVLTEPQVYGRDKEKDEIVKILINTASDAQKLSVLPILGMGGLGKTTLSQMVFND 198

Query: 146 KDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE-------------------KKFFL 186
           + V E F  +IW+C+SD F+E R+ KAI+E +EG                     K++FL
Sbjct: 199 QRVTERFYPKIWICISDDFNEKRLIKAIVESIEGKSLSDMDLAPLQKKLQELLNGKRYFL 258

Query: 187 ILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRA 246
           +LDDVW +D  KW              A ++V G      LT+T  EK+  +  TL    
Sbjct: 259 VLDDVWNEDQHKWANLR----------AVLKV-GASGAFVLTTTRLEKVGSIMGTLQPYE 307

Query: 247 KFPVSIFDAKKIWGWEVFGRNTSTRPGMVS 276
              +S  D   ++    FG      P +++
Sbjct: 308 LSNLSPEDCWFLFMQRAFGHQEEINPNLMA 337

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via a direct or indirect interaction with this avirulence protein. That triggers a defense system which restricts the pathogen growth.

Solanum bulbocastanum (taxid: 147425)

>sp|Q9LRR4|R13L1_ARATH Putative disease resistance RPP13-like protein 1 OS=Arabidopsis thaliana GN=RPPL1 PE=3 SV=1

 Score = 95.9 bits (237), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/277 (25%), Positives = 125/277 (45%), Gaps = 77/277 (27%)

Query: 2   RSFFQ--DFGKQV-KKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLD 58
           RSFF+  +  + + ++L++ L  I AVL DAE++Q+    V  W+++L++  Y  ED LD
Sbjct: 26  RSFFKRRELNENLLERLSTALLTITAVLIDAEEKQITNPVVEKWVNELRDVVYHAEDALD 85

Query: 59  EWITARLKLQI--EGVDENALVRKK-----------------PKIIEINENLDDIAKQKE 99
           +  T  L+L I  E    N L + +                  ++ ++   L+ +A Q+ 
Sbjct: 86  DIATEALRLNIGAESSSSNRLRQLRGRMSLGDFLDGNSEHLETRLEKVTIRLERLASQRN 145

Query: 100 VFNFNVIRGSTEKSERIHSTALINVSDV-----------------------------RGM 130
           +     +     K +R+ +T+L++ S+V                              G+
Sbjct: 146 ILGLKELTAMIPK-QRLPTTSLVDESEVFGRDDDKDEIMRFLIPENGKDNGITVVAIVGI 204

Query: 131 GGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEG-------------- 176
           GG+GKTTL+Q  YND+ V   F  ++W  VS+ FD F+I K + E               
Sbjct: 205 GGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTSRPCEFTDLDVL 264

Query: 177 -------LEGSEKKFFLILDDVWTDDYSKW----EPF 202
                  L G+   F L+LDD+W ++++ W    +PF
Sbjct: 265 QVKLKERLTGTGLPFLLVLDDLWNENFADWDLLRQPF 301

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q38834|R13L4_ARATH Disease resistance RPP13-like protein 4 OS=Arabidopsis thaliana GN=RPP13L4 PE=2 SV=2

 Score = 87.0 bits (214), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/270 (27%), Positives = 122/270 (45%), Gaps = 77/270 (28%)

Query: 7   DFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVL--------- 57
           D+ KQ++ L S L+ +Q+ L DAE+++    ++R  +  L+E  Y+ ED+L         
Sbjct: 26  DYRKQLEDLQSELKYMQSFLKDAERQKRTNETLRTLVADLRELVYEAEDILVDCQLADGD 85

Query: 58  --------DEWIT----ARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQKE-VFNF- 103
                   + W++    AR+ LQ          +K  ++ EINE +  I  Q E  F F 
Sbjct: 86  DGNEQRSSNAWLSRLHPARVPLQ---------YKKSKRLQEINERITKIKSQVEPYFEFI 136

Query: 104 ---NVIR--GSTEKSERI--HSTALINVSDVR--------------------GMGGIGKT 136
              NV R  G+   S  +  H+  +    D R                    GMGG+GKT
Sbjct: 137 TPSNVGRDNGTDRWSSPVYDHTQVVGLEGDKRKIKEWLFRSNDSQLLIMAFVGMGGLGKT 196

Query: 137 TLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE--------------- 181
           T+AQ  +NDK++   F++RIWV VS  F E +I ++I+  L  +                
Sbjct: 197 TIAQEVFNDKEIEHRFERRIWVSVSQTFTEEQIMRSILRNLGDASVGDDIGTLLRKIQQY 256

Query: 182 ---KKFFLILDDVWTDDYSKWEPFHNCLMR 208
              K++ +++DDVW  + S W+  +  L R
Sbjct: 257 LLGKRYLIVMDDVWDKNLSWWDKIYQGLPR 286

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LRR5|DRL21_ARATH Putative disease resistance protein At3g14460 OS=Arabidopsis thaliana GN=At3g14460 PE=3 SV=1

 Score = 81.6 bits (200), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 69/258 (26%), Positives = 110/258 (42%), Gaps = 66/258 (25%)

Query: 12  VKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQI-- 69
           +K+L   L     VL DA+QR      V+ WL  +K+A +  ED+LDE  T  L+ ++  
Sbjct: 36  LKRLKVALVTANPVLADADQRAEHVREVKHWLTGIKDAFFQAEDILDELQTEALRRRVVA 95

Query: 70  -----EGVDENAL-----VRKK--PKIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIH 117
                 G+ +N +     ++KK  PK+ ++   L+   K  EV        + E   R  
Sbjct: 96  EAGGLGGLFQNLMAGREAIQKKIEPKMEKVVRLLEHHVKHIEVIGLKEYSETREPQWRQA 155

Query: 118 S-------------------TALIN--------------VSDVRGMGGIGKTTLAQFAYN 144
           S                    AL+N              V  V GM G+GKTTL +  +N
Sbjct: 156 SRSRPDDLPQGRLVGRVEDKLALVNLLLSDDEISIGKPAVISVVGMPGVGKTTLTEIVFN 215

Query: 145 DKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE-------------------KKFF 185
           D  V E+F+ ++W+     F+ F + KA+++ +  S                    K+F 
Sbjct: 216 DYRVTEHFEVKMWISAGINFNVFTVTKAVLQDITSSAVNTEDLPSLQIQLKKTLSGKRFL 275

Query: 186 LILDDVWTDDYSKWEPFH 203
           L+LDD W++  S+WE F 
Sbjct: 276 LVLDDFWSESDSEWESFQ 293

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LQ54|DRL12_ARATH Probable disease resistance protein At1g59620 OS=Arabidopsis thaliana GN=At1g59620 PE=2 SV=3

 Score = 71.6 bits (174), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 115/238 (48%), Gaps = 42/238 (17%)

Query: 5   FQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITAR 64
           FQ   KQ  +L S+L  ++  L DA+ ++ + A V   + ++KE  YD ED+++ ++  +
Sbjct: 24  FQGVKKQFNELRSDLNKLRCFLEDADAKKHQSAMVSNTVKEVKEIVYDTEDIIETFLRKK 83

Query: 65  LKLQIEG----VDENALVRKKPKIIEIN-ENLDD-IAKQ-----KEVFNFN---VIRGST 110
              +  G    + E A V    + I I+ E L   IAK+     ++ F+ N   V+ G  
Sbjct: 84  QLGRTRGMKKRIKEFACVLPDRRKIAIDMEGLSKRIAKKDKRNMRQTFSNNNESVLVGLE 143

Query: 111 EKSERIHSTALINVSD------VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF 164
           E  +++    L+ V D      + GMGGIGKTTLA+  +N + V  +F +  WVCVS  F
Sbjct: 144 ENVKKL-VGHLVEVEDSSQVVSITGMGGIGKTTLARQVFNHETVKSHFAQLAWVCVSQQF 202

Query: 165 DEFRIAKAIIE-------GLEGSE-------------KKFFLILDDVWT-DDYSKWEP 201
               + + I+         LE +E             +K  ++LDD+W  +D+   EP
Sbjct: 203 TRKYVWQTILRKVGPEYIKLEMTEDELQEKLFRLLGTRKALIVLDDIWREEDWDMIEP 260

Probable disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W474|DRL7_ARATH Probable disease resistance protein At1g58390 OS=Arabidopsis thaliana GN=At1g58390 PE=2 SV=4

 Score = 70.9 bits (172), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 97/224 (43%), Gaps = 48/224 (21%)

Query: 5   FQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDE----- 59
           FQ    QV  L  +L  + + L DA+ ++   A VR  ++++KE  YD ED+++      
Sbjct: 24  FQGVEDQVTGLKRDLNLLSSFLKDADAKKHTTAVVRNVVEEIKEIVYDAEDIIETYLLKE 83

Query: 60  --WITARLKLQIE------------GVDENALVRKKPKIIEINENLDDIAKQKEVFNFNV 105
             W T+ +K++I              +D   +   + +I ++  ++     Q+ + +   
Sbjct: 84  KLWKTSGIKMRIRRHACIISDRRRNALDVGGI---RTRISDVIRDMQSFGVQQAIVDGGY 140

Query: 106 IRGSTEKSERIHSTAL--------------------------INVSDVRGMGGIGKTTLA 139
           ++   ++   +  T                            + V  + GMGG+GKTTLA
Sbjct: 141 MQPQGDRQREMRQTFSKDYESDFVGLEVNVKKLVGYLVDEENVQVVSITGMGGLGKTTLA 200

Query: 140 QFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKK 183
           +  +N +DV   FD+  WVCVS  F    + + I++ L   EKK
Sbjct: 201 RQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQNLTSREKK 244

Possible disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q8W3K3|DRL8_ARATH Putative disease resistance protein At1g58400 OS=Arabidopsis thaliana GN=At1g58400 PE=3 SV=1

 Score = 68.2 bits (165), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 100/227 (44%), Gaps = 53/227 (23%)

Query: 5   FQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITAR 64
           FQ    ++ +L SNL  +++ L DAE ++     VR  ++++KE  YD E++++ +I   
Sbjct: 24  FQGVEDRIAELKSNLNLLKSFLKDAEAKKNTSQMVRHCVEEIKEIVYDTENMIETFI--- 80

Query: 65  LKLQIEGVDENALVRKKPKII-------EINENLDDIAKQ-----KEVFNFNVIRGSTEK 112
             L+      + ++R+  K+        E   ++  I+K+     +++ +F V +  ++ 
Sbjct: 81  --LKEAARKRSGIIRRITKLTCIKVHRWEFASDIGGISKRISKVIQDMHSFGVQQMISDG 138

Query: 113 SERIHSTAL------------------------------------INVSDVRGMGGIGKT 136
           S+  H                                        I +  V GMGG+GKT
Sbjct: 139 SQSSHLLQEREREMRQTFSRGYESDFVGLEVNVKKLVGYLVEEDDIQIVSVTGMGGLGKT 198

Query: 137 TLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKK 183
           TLA+  +N +DV   FD+  WVCVS  F    + + I++ L   E K
Sbjct: 199 TLARQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQNLTSRETK 245

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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	297
147775713	886	hypothetical protein VITISV_014504 [Viti	0.861	0.288	0.400	4e-46
224122696	906	cc-nbs-lrr resistance protein [Populus t	0.646	0.211	0.438	2e-45
224114824	941	cc-nbs-lrr resistance protein [Populus t	0.659	0.208	0.405	9e-43
224122712	945	cc-nbs-lrr resistance protein [Populus t	0.659	0.207	0.394	4e-42
224114794	742	cc-nbs-lrr resistance protein [Populus t	0.639	0.256	0.42	6e-42
224115608	922	cc-nbs-lrr resistance protein [Populus t	0.656	0.211	0.417	1e-41
224114848	571	cc-nbs resistance protein [Populus trich	0.659	0.343	0.397	1e-41
224110232	486	cc-nbs resistance protein [Populus trich	0.680	0.415	0.394	2e-41
224115686	938	cc-nbs-lrr resistance protein [Populus t	0.656	0.207	0.402	9e-41
224122720	746	cc-nbs-lrr resistance protein [Populus t	0.659	0.262	0.382	6e-40

>gi|147775713|emb|CAN69300.1| hypothetical protein VITISV_014504 [Vitis vinifera]

 Score =  191 bits (485), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 133/332 (40%), Positives = 180/332 (54%), Gaps = 76/332 (22%)

Query: 12  VKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEG 71
           V+KLT+ LR I+AVL DAE+RQVK+ +V++WL+ LK  +YDM++VLDEW ++ LK+QI+G
Sbjct: 35  VQKLTNTLRNIRAVLLDAEKRQVKDEAVKIWLEDLKGLAYDMDNVLDEWSSSILKVQIQG 94

Query: 72  VDENALVRKKP-----------------------KIIEINENLDDIAKQKEVFNFNVIRG 108
           VD NAL  KK                        KI EIN  LD IA++K+ +NFN I G
Sbjct: 95  VD-NALTHKKKVCSCIPFPCFPIRGIHLCHDIALKIGEINRRLDVIAQEKDRYNFNFISG 153

Query: 109 STEKSERIHSTALINVSDVRG-----------------MGGIGKTTLAQFAYNDKDVIEN 151
             E+ ER  +T+ I+V +V+G                 +GGIGKTTLAQ AYND  V  +
Sbjct: 154 -MEEPERPXTTSFIDVPEVQGXGEDKDIIISKLLCGSSLGGIGKTTLAQLAYNDVKVCSH 212

Query: 152 FDKRIWVCVSDPFDEFRIAKAIIEGLEG--------------------SEKKFFLILDDV 191
           FDKRIWVCVSDPFD  RI++AI+E LE                     + KKF L+ DDV
Sbjct: 213 FDKRIWVCVSDPFDAMRISRAILEALERKTSSHLHELEIVQQEIQNSIARKKFLLVSDDV 272

Query: 192 WTDDYSKWEPFHNCL-----MRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRA 246
           W ++Y  WE   NCL     +  L+E      D  +  L L +     L HL      R 
Sbjct: 273 WNENYQIWE-LVNCLKTKKGIEELEEIGQKIADKCKG-LPLAAKTLGSLLHLK----ERK 326

Query: 247 KFPVSIFDAKKIWGWEVFGRNTSTRPGMVSRY 278
           +  V++ +   +W  EVF R+ S  P ++  Y
Sbjct: 327 EDWVNVLN-NDVWQLEVFERDLS--PALLLSY 355

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122696|ref|XP_002318903.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222859576|gb|EEE97123.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  188 bits (478), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 107/244 (43%), Positives = 150/244 (61%), Gaps = 52/244 (21%)

Query: 10  KQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQI 69
           KQ  KL SNL  IQ+VL DA+++QVK+ +VR WLD+LK+A YDM+DVLDEW TA L+ ++
Sbjct: 33  KQCDKLKSNLLDIQSVLEDADRKQVKDKAVRDWLDKLKDACYDMDDVLDEWSTAILRWKM 92

Query: 70  EGVDENALVRKKP-----------------------KIIEINENLDDIAKQKEVFNFNVI 106
           E  +EN   R+K                        KI E+ E +DDIAK++  + F+  
Sbjct: 93  EEAEENTRSRQKMRCSFLRSPCFCFNQVVRRRDIALKIKEVCEKVDDIAKERAKYGFDPY 152

Query: 107 RGSTEKSERIHSTALIN---------VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIW 157
           R +T++ +R+ ST+ ++         V  + G+GG+GKTTLAQ A+ND +V  +F+K+IW
Sbjct: 153 R-ATDELQRLTSTSFVDESSEARDVDVISLVGLGGMGKTTLAQLAFNDAEVTAHFEKKIW 211

Query: 158 VCVSDPFDEFRIAKAIIEGLEGSE-------------------KKFFLILDDVWTDDYSK 198
           VCVS+PFDE RIAKAIIE LEGS                    K+F L+LDDVWT+++ +
Sbjct: 212 VCVSEPFDEVRIAKAIIEQLEGSPTNLVELQSLLQRVSESIKGKRFLLVLDDVWTENHGQ 271

Query: 199 WEPF 202
           WEP 
Sbjct: 272 WEPL 275

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114824|ref|XP_002332291.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222832453|gb|EEE70930.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  179 bits (455), Expect = 9e-43,   Method: Compositional matrix adjust.
 Identities = 109/269 (40%), Positives = 152/269 (56%), Gaps = 73/269 (27%)

Query: 10  KQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQI 69
           KQV KL +NL AIQ+VL DA+++QVK+ ++R W+D+LK+  YDM+DVLDEW TA L+ ++
Sbjct: 29  KQVDKLKNNLLAIQSVLEDADRKQVKDKALRDWVDKLKDVCYDMDDVLDEWSTAILRWKM 88

Query: 70  EGVDENALVRKK--------P---------------KIIEINENLDDIAKQKEVFNFNVI 106
           E  +EN   RKK        P               KI E+ E +DDIAK++ ++ F + 
Sbjct: 89  EEAEENTPSRKKIRCSFLGSPFFCLNQVVQRRDIALKIKEVCEKVDDIAKERAMYGFELY 148

Query: 107 RGSTEKSERIHSTALINVSDV------------------------------RGMGGIGKT 136
           R +T++ +RI ST+L++ S V                               GMGGIGKT
Sbjct: 149 R-ATDELQRITSTSLVDESSVIGRDDKREAVVSKLLGESIQEAGDVEVISLVGMGGIGKT 207

Query: 137 TLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE--------------- 181
           TLAQ A+ND +V  +F+K+IWVCVSDPFDE RI KAI+E LEG                 
Sbjct: 208 TLAQLAFNDDEVTAHFEKKIWVCVSDPFDEVRIGKAILEQLEGRAPDLVELQSLLQRVSE 267

Query: 182 ----KKFFLILDDVWTDDYSKWEPFHNCL 206
               ++F L+LDDVWT+++ +WE     L
Sbjct: 268 SIKGERFLLVLDDVWTENHRQWEQLKPSL 296

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122712|ref|XP_002318907.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222859580|gb|EEE97127.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  177 bits (450), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 106/269 (39%), Positives = 153/269 (56%), Gaps = 73/269 (27%)

Query: 10  KQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQI 69
           KQV KL SNL  IQ+VL DA+++QVK+ +VR W+D+LK+A YDM+DVLDEW TA L+ ++
Sbjct: 33  KQVDKLKSNLLDIQSVLEDADRKQVKDKAVRDWVDKLKDACYDMDDVLDEWSTAILRWKM 92

Query: 70  EGVDENALVRKK--------P---------------KIIEINENLDDIAKQKEVFNFNVI 106
           E  +EN   R+K        P               KI E++E +DDIAK++  + F++ 
Sbjct: 93  EEAEENTHSRQKIRCSFLGSPCFCFNQVVRRRDIALKIKEVSEKVDDIAKERAKYGFDLY 152

Query: 107 RGSTEKSERIHSTALINVSDV------------------------------RGMGGIGKT 136
           +G T++ +R+ +T+ ++ S V                               G+GGIGKT
Sbjct: 153 KG-TDELQRLTTTSFVDESSVIGRDGEKRNVVSKLLAESSHEARDVDVISLVGLGGIGKT 211

Query: 137 TLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG----------------- 179
           TLAQ A+ND +V  +F+K+IWVCVS+PFDE RIAKAI+E LEG                 
Sbjct: 212 TLAQLAFNDSEVTAHFEKKIWVCVSEPFDEIRIAKAILEQLEGRPTNLVELQSLLQGVSE 271

Query: 180 --SEKKFFLILDDVWTDDYSKWEPFHNCL 206
             + K+  L+LDDVWT+++ +WE     L
Sbjct: 272 SITGKRLLLVLDDVWTENHGQWEQLKPSL 300

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114794|ref|XP_002332284.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222832446|gb|EEE70923.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  177 bits (448), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 105/250 (42%), Positives = 148/250 (59%), Gaps = 60/250 (24%)

Query: 10  KQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQI 69
           KQ  KL SNL  IQ+VL DA+++QVK+ +VR W+D+LK+A YDM+DVLDEW TA L+ ++
Sbjct: 20  KQCDKLKSNLLDIQSVLEDADRKQVKDKAVRDWVDKLKDACYDMDDVLDEWSTAILRWKM 79

Query: 70  EGVDENALVRKKPK---II-------EINENLDDIAKQKEVFNFNVIRGSTEKSERIHST 119
           E  +EN   R+K +   +I       +++E +DDIAK++ V+ F++ R + E  +R  ST
Sbjct: 80  EEAEENTPSRQKIRRSFLISLLLSQSKVSEKVDDIAKERVVYGFDLYRATYE-LQRPTST 138

Query: 120 ALINVSDV------------------------------RGMGGIGKTTLAQFAYNDKDVI 149
           + ++ S V                               G+GGIGKTTLAQ AY D +V 
Sbjct: 139 SFVDESSVIGRDVEKKTIVSKLVGESSQEARDVDVITLVGLGGIGKTTLAQLAYKDAEVT 198

Query: 150 ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE-------------------KKFFLILDD 190
            +F+K+IWVCVS+PFDE RIAKAI+E LEGS                    K+  L+LDD
Sbjct: 199 AHFEKKIWVCVSEPFDEVRIAKAILEQLEGSAPNLIELQSLLQMVSESIKGKRLLLVLDD 258

Query: 191 VWTDDYSKWE 200
           VWTD++ +WE
Sbjct: 259 VWTDNHRQWE 268

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115608|ref|XP_002332098.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222874918|gb|EEF12049.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 111/266 (41%), Positives = 144/266 (54%), Gaps = 71/266 (26%)

Query: 11  QVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIE 70
           +VKKLTSN +AIQ VL DAE+RQ+K+ S++ W+DQLK  SYDM+DVLDEW T+  K Q++
Sbjct: 34  EVKKLTSNFQAIQDVLADAEERQLKDGSIKRWIDQLKGVSYDMDDVLDEWGTSIAKSQMK 93

Query: 71  GVDENA--LVRK--------------------KPKIIEINENLDDIAKQKEVFNFNVIRG 108
            V+E+     RK                      KI E+NE +D I  +K+ F+F     
Sbjct: 94  -VNEHPRKTARKVCSMIFSYLCFREVGLRRDIAHKIKELNERIDGIVIEKDKFHFKSSEV 152

Query: 109 STEKSERIHSTALINVSDVRG-----------------------------MGGIGKTTLA 139
             ++ E   +T++I+ ++ +G                             MGGIGKTTLA
Sbjct: 153 GIKQLEYQKTTSVIDATETKGREKDKDRVINMLLSESSQGLALRTISLVGMGGIGKTTLA 212

Query: 140 QFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE------------------ 181
           Q  YND+ V   F+KRIWVCVSDPFDE RIAKAI+EGL GS                   
Sbjct: 213 QLVYNDRVVESYFEKRIWVCVSDPFDEIRIAKAILEGLMGSTQNLNELQNLVQHVQQSIR 272

Query: 182 -KKFFLILDDVWTDDYSKWEPFHNCL 206
            KKF L+LDDVW +D SKWE   N L
Sbjct: 273 GKKFLLVLDDVWNEDSSKWEQLKNSL 298

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224114848|ref|XP_002332297.1| cc-nbs resistance protein [Populus trichocarpa] gi|222832459|gb|EEE70936.1| cc-nbs resistance protein [Populus trichocarpa]

 Score =  176 bits (446), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 107/269 (39%), Positives = 152/269 (56%), Gaps = 73/269 (27%)

Query: 10  KQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQI 69
           KQV KL SNL A+ +VL DA+++QVK+ +VR W+D+LK+  YDM+DVLDEW +A L+ ++
Sbjct: 33  KQVDKLKSNLLAMHSVLEDADRKQVKDEAVRDWVDKLKDVCYDMDDVLDEWSSAILRWKM 92

Query: 70  EGVDENA--------------------LVRKKP---KIIEINENLDDIAKQKEVFNFNVI 106
              +EN                     +VR++    KI E+ E LD+IAK+K ++ F + 
Sbjct: 93  GDAEENTHSQQKIRCSFLGFPCFCFNQVVRRRDIALKIKEVCEKLDEIAKEKAMYGFELY 152

Query: 107 RGSTEKSERIHSTALINVSDVRG------------------------------MGGIGKT 136
           R +T++ +RI ST+L++ S V G                              +GGIGKT
Sbjct: 153 R-ATDELQRITSTSLVDESIVSGRDDEREAVVSKLLGESRQEAWDVYAISLVGLGGIGKT 211

Query: 137 TLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE--------------- 181
           TLAQ A+ND +V  +F+K+IWVCVSDPFDE RIAKAI+E LEG                 
Sbjct: 212 TLAQLAFNDAEVTAHFEKKIWVCVSDPFDEVRIAKAILEQLEGRAPDLVELQSLLQRVSE 271

Query: 182 ----KKFFLILDDVWTDDYSKWEPFHNCL 206
               K+F L+LDDVWT+++ +WE     L
Sbjct: 272 SIKGKRFLLVLDDVWTENHRQWEQLKPSL 300

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224110232|ref|XP_002333124.1| cc-nbs resistance protein [Populus trichocarpa] gi|222834935|gb|EEE73384.1| cc-nbs resistance protein [Populus trichocarpa]

 Score =  175 bits (444), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 109/276 (39%), Positives = 149/276 (53%), Gaps = 74/276 (26%)

Query: 3   SFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWIT 62
           S      KQV KL SNL AIQ+VL DA+++QVK+ +VR W+D+LK+  YDM+DVLDEW +
Sbjct: 26  SLVGGVKKQVDKLKSNLIAIQSVLEDADRKQVKDKAVRDWVDKLKDVCYDMDDVLDEWSS 85

Query: 63  ARLKLQIEGVDENALVRKKP-----------------------KIIEINENLDDIAKQKE 99
           A L  ++E  +EN    +K                        KI E+ E +DDIAK + 
Sbjct: 86  AILTWKMEEAEENTRSLQKMRCSFLGSPCFCLNQVGRRRDIALKIKEVCEKVDDIAKARA 145

Query: 100 VFNFNVIRGSTEKSERIHSTALIN------------------------------VSDVRG 129
           ++ F + R +T++ +RI ST+L++                              V  + G
Sbjct: 146 MYGFELYR-ATDELQRITSTSLVDESIVTGRDDEREAVVSKLLGESIQEAGDVEVISIVG 204

Query: 130 MGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE-------- 181
           MGGIGKTTLAQ A+ND +V  +F+K IWVCVSDPFDE RI KAI+E LEG          
Sbjct: 205 MGGIGKTTLAQLAFNDAEVTAHFEK-IWVCVSDPFDEVRIGKAILEQLEGRAPDLVELQS 263

Query: 182 -----------KKFFLILDDVWTDDYSKWEPFHNCL 206
                      K+F L+LDDVWT+++ +WEP    L
Sbjct: 264 LLQRVSESIKGKRFLLVLDDVWTENHGQWEPLKLSL 299

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115686|ref|XP_002332117.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222874937|gb|EEF12068.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  173 bits (438), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 107/266 (40%), Positives = 145/266 (54%), Gaps = 71/266 (26%)

Query: 11  QVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIE 70
           +V+KLT+N + IQAVL DAE+R++K+ S++ W+DQLK  SYDM+DVLDEW TA  K Q++
Sbjct: 34  EVQKLTNNFQTIQAVLADAEERELKDGSIKRWIDQLKGVSYDMDDVLDEWGTAIAKSQMK 93

Query: 71  GVDENA--LVRK--------------------KPKIIEINENLDDIAKQKEVFNFNVIRG 108
            V+E+     RK                      KI E+NE +D I  +K+ F+F     
Sbjct: 94  -VNEHPRKTARKVCSMIFSCLCFREVGLRRDIAHKIKELNERIDGIVIEKDRFHFKSSEV 152

Query: 109 STEKSERIHSTALINVSDVRG-----------------------------MGGIGKTTLA 139
             ++ E   +T++I+ ++V+G                             MGGIGKTTLA
Sbjct: 153 GIKQLEHQKTTSVIDAAEVKGRENDKDRVKNMLLSESSQGPALRTISLVGMGGIGKTTLA 212

Query: 140 QFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS------------------- 180
           +  YND DV  +FDKRIWVCVSDPF+E  IAKAI+E L GS                   
Sbjct: 213 KLVYNDHDVTTHFDKRIWVCVSDPFNEITIAKAILEDLTGSAPNLNELQTLVKHVQESIR 272

Query: 181 EKKFFLILDDVWTDDYSKWEPFHNCL 206
           EKKF L+LDDVW +D +KWE   + L
Sbjct: 273 EKKFLLVLDDVWNEDSTKWEQLKDSL 298

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224122720|ref|XP_002318909.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222859582|gb|EEE97129.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  170 bits (431), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 103/269 (38%), Positives = 148/269 (55%), Gaps = 73/269 (27%)

Query: 10  KQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQI 69
           KQV KL SN  +IQ+VL DA+++QVK+ +V+ WLD+LK+  Y M+DVLDEW TA L+ ++
Sbjct: 33  KQVDKLKSNRVSIQSVLEDADRKQVKDEAVKGWLDKLKDVCYHMDDVLDEWSTAILRWKM 92

Query: 70  EGVDENALVRKKP-----------------------KIIEINENLDDIAKQKEVFNFNVI 106
           E  +EN   R+K                        KI E+ E +DDIAK++  + F+  
Sbjct: 93  EEAEENTRSRQKMRCSFLKSPCSCLNQVVRRRDIALKIKEVCEKVDDIAKERATYAFDPY 152

Query: 107 RGSTEKSERIHSTALINVSDV------------------------------RGMGGIGKT 136
           R +T++ +R+ ST+ ++ S V                               G+GGIGKT
Sbjct: 153 R-ATDELQRLTSTSFVDESSVIGRDVEKTTVISKLVGESSQEARDVDVISLVGLGGIGKT 211

Query: 137 TLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE--------------- 181
           TLAQ A+ND +V  +F+K+IWVCVS+PFD+ RIAKAI+E LEG                 
Sbjct: 212 TLAQLAFNDAEVTTHFEKKIWVCVSEPFDQVRIAKAILEQLEGRAPDLVELQSLLQRVSE 271

Query: 182 ----KKFFLILDDVWTDDYSKWEPFHNCL 206
               K+F L+LDDVWT+++ +WE     L
Sbjct: 272 SIKGKRFLLVLDDVWTENHRQWEQLKPSL 300

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	297
TAIR|locus:2091672	1054	AT3G14470 [Arabidopsis thalian	0.212	0.059	0.412	3e-13
TAIR|locus:2091662	1424	AT3G14460 [Arabidopsis thalian	0.191	0.040	0.368	1.5e-11
TAIR|locus:2037639	907	AT1G58390 "AT1G58390" [Arabido	0.208	0.068	0.435	3e-11
TAIR|locus:504956182	1049	AT1G58848 [Arabidopsis thalian	0.215	0.061	0.406	1.6e-09
TAIR|locus:2826978	1049	AT1G59218 [Arabidopsis thalian	0.215	0.061	0.406	1.6e-09
TAIR|locus:2025916	906	AT1G59780 "AT1G59780" [Arabido	0.468	0.153	0.28	1.7e-09
TAIR|locus:504956184	1017	AT1G58807 "AT1G58807" [Arabido	0.215	0.062	0.406	2.4e-09
TAIR|locus:2827038	1017	AT1G59124 "AT1G59124" [Arabido	0.215	0.062	0.406	2.4e-09
TAIR|locus:2176486	908	RPP8 "RECOGNITION OF PERONOSPO	0.185	0.060	0.418	7.1e-09
TAIR|locus:2169523	901	AT5G35450 [Arabidopsis thalian	0.188	0.062	0.428	1.3e-08

TAIR|locus:2091672 AT3G14470 [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 3.0e-13, Sum P(2) = 3.0e-13
 Identities = 26/63 (41%), Positives = 38/63 (60%)

Query:   122 INVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE 181
             I V  + G+GG+GKTTL+Q  YND+ V   F  ++W  VS+ FD F+I K + E +    
Sbjct:   196 ITVVAIVGIGGVGKTTLSQLLYNDQHVRSYFGTKVWAHVSEEFDVFKITKKVYESVTSRP 255

Query:   182 KKF 184
              +F
Sbjct:   256 CEF 258

GO:0005576 "extracellular region" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009627 "systemic acquired resistance" evidence=RCA

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

TAIR|locus:2091662 AT3G14460 [Arabidopsis thaliana (taxid:3702)]

 Score = 118 (46.6 bits), Expect = 1.5e-11, Sum P(3) = 1.5e-11
 Identities = 21/57 (36%), Positives = 35/57 (61%)

Query:   124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS 180
             V  V GM G+GKTTL +  +ND  V E+F+ ++W+     F+ F + KA+++ +  S
Sbjct:   195 VISVVGMPGVGKTTLTEIVFNDYRVTEHFEVKMWISAGINFNVFTVTKAVLQDITSS 251

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2037639 AT1G58390 "AT1G58390" [Arabidopsis thaliana (taxid:3702)]

 Score = 144 (55.7 bits), Expect = 3.0e-11, Sum P(2) = 3.0e-11
 Identities = 27/62 (43%), Positives = 38/62 (61%)

Query:   122 INVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSE 181
             + V  + GMGG+GKTTLA+  +N +DV   FD+  WVCVS  F    + + I++ L   E
Sbjct:   183 VQVVSITGMGGLGKTTLARQVFNHEDVKHQFDRLAWVCVSQEFTRKNVWQMILQNLTSRE 242

Query:   182 KK 183
             KK
Sbjct:   243 KK 244

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:504956182 AT1G58848 [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 1.6e-09, Sum P(2) = 1.6e-09
 Identities = 26/64 (40%), Positives = 38/64 (59%)

Query:   120 ALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG 179
             A + V  + GMGG+GKTTLA+  +N +DV   FD   WVCVS  F    + + I+  L+ 
Sbjct:   181 ANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDLKP 240

Query:   180 SEKK 183
              E++
Sbjct:   241 KEEE 244

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2826978 AT1G59218 [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 1.6e-09, Sum P(2) = 1.6e-09
 Identities = 26/64 (40%), Positives = 38/64 (59%)

Query:   120 ALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG 179
             A + V  + GMGG+GKTTLA+  +N +DV   FD   WVCVS  F    + + I+  L+ 
Sbjct:   181 ANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDLKP 240

Query:   180 SEKK 183
              E++
Sbjct:   241 KEEE 244

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2025916 AT1G59780 "AT1G59780" [Arabidopsis thaliana (taxid:3702)]

 Score = 118 (46.6 bits), Expect = 1.7e-09, Sum P(2) = 1.7e-09
 Identities = 42/150 (28%), Positives = 68/150 (45%)

Query:    45 QLKEASYDMEDVLDEWITARLKLQI-EGVDENALVRKKPKIIEINENLDDIAKQKEVFNF 103
             Q+   S  +  V+       +K  I +GVD +A + +K    E+       ++     N 
Sbjct:   108 QITSISKRISKVIQVMQNLGIKSDIMDGVDSHAQLERKR---ELRHTFSSESES----NL 160

Query:   104 NVIRGSTEK--SERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS 161
               +  + EK   E + + +   VS + G+GG+GKTTLA+  ++   V  +FD   WVCVS
Sbjct:   161 VGLEKNVEKLVEELVGNDSSHGVS-ITGLGGLGKTTLARQIFDHDKVKSHFDGLAWVCVS 219

Query:   162 DPFDEFRIAKAIIEGLEGSEKKFFLILDDV 191
               F    + K I+  L    K   L  DD+
Sbjct:   220 QEFTRKDVWKTILGNLSPKYKDSDLPEDDI 249

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:504956184 AT1G58807 "AT1G58807" [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 2.4e-09, Sum P(2) = 2.4e-09
 Identities = 26/64 (40%), Positives = 38/64 (59%)

Query:   120 ALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG 179
             A + V  + GMGG+GKTTLA+  +N +DV   FD   WVCVS  F    + + I+  L+ 
Sbjct:   181 ANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDLKP 240

Query:   180 SEKK 183
              E++
Sbjct:   241 KEEE 244

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2827038 AT1G59124 "AT1G59124" [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 2.4e-09, Sum P(2) = 2.4e-09
 Identities = 26/64 (40%), Positives = 38/64 (59%)

Query:   120 ALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG 179
             A + V  + GMGG+GKTTLA+  +N +DV   FD   WVCVS  F    + + I+  L+ 
Sbjct:   181 ANVQVVSITGMGGLGKTTLAKQVFNHEDVKHQFDGLSWVCVSQDFTRMNVWQKILRDLKP 240

Query:   180 SEKK 183
              E++
Sbjct:   241 KEEE 244

GO:0005575 "cellular_component" evidence=ND

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2176486 RPP8 "RECOGNITION OF PERONOSPORA PARASITICA 8" [Arabidopsis thaliana (taxid:3702)]

 Score = 111 (44.1 bits), Expect = 7.1e-09, Sum P(3) = 7.1e-09
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query:   124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE 178
             V  + GMGGIGKTTLA+  ++   V  +FD   WVCVS  F +  + + I++ L+
Sbjct:   187 VVSIAGMGGIGKTTLARQVFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQELQ 241

GO:0006952 "defense response" evidence=IEA;ISS;TAS

GO:0043531 "ADP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=ISS

GO:0009416 "response to light stimulus" evidence=IMP

GO:0051607 "defense response to virus" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

GO:0009626 "plant-type hypersensitive response" evidence=IMP

GO:0051707 "response to other organism" evidence=IMP

TAIR|locus:2169523 AT5G35450 [Arabidopsis thaliana (taxid:3702)]

 Score = 112 (44.5 bits), Expect = 1.3e-08, Sum P(2) = 1.3e-08
 Identities = 24/56 (42%), Positives = 34/56 (60%)

Query:   122 INVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGL 177
             I V  + GMGGIGKTTLA+  ++   V  +FD   WVCVS  F +  + + I++ L
Sbjct:   183 IQVVSISGMGGIGKTTLARQIFHHDLVRRHFDGFAWVCVSQQFTQKHVWQRILQEL 238

GO:0006952 "defense response" evidence=IEA;ISS

GO:0043531 "ADP binding" evidence=IEA

GO:0005886 "plasma membrane" 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

Your Input: eugene3.00121282 cc-nbs-lrr resistance protein (906 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	297
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	5e-16

>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain

 Score = 75.8 bits (187), Expect = 5e-16
 Identities = 37/102 (36%), Positives = 51/102 (50%), Gaps = 23/102 (22%)

Query: 129 GMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIE--GLEGSE----- 181
           GMGG+GKTTLA+  YND  V  +FD   WV VS  + EFR+ K I++  GL+ S+     
Sbjct: 26  GMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRLQKDILQELGLDDSDWVEKN 85

Query: 182 --------------KKFFLILDDVWTDDYSKWEPFHNCLMRV 209
                         K+F L+LDDVW  + + W+         
Sbjct: 86  ESELAVKIKEALLRKRFLLVLDDVW--EKNDWDKIGVPFPDG 125

Length = 285

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	297
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	99.85
PLN03210	1153	Resistant to P. syringae 6; Provisional	99.74
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.81
PF05729	166	NACHT: NACHT domain	98.71
cd01128	249	rho_factor Transcription termination factor rho is	98.66
PRK06893	229	DNA replication initiation factor; Validated	98.61
PRK09376	416	rho transcription termination factor Rho; Provisio	98.54
PF13173	128	AAA_14: AAA domain	98.41
KOG2028	554	consensus ATPase related to the helicase subunit o	98.37
PRK13342	413	recombination factor protein RarA; Reviewed	98.36
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.34
PRK13341	725	recombination factor protein RarA/unknown domain f	98.31
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.29
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.28
TIGR00767	415	rho transcription termination factor Rho. Members	98.23
PRK00411	394	cdc6 cell division control protein 6; Reviewed	98.21
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.17
PRK08727	233	hypothetical protein; Validated	98.14
PRK08084	235	DNA replication initiation factor; Provisional	98.06
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.03
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.01
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	97.96
PRK08116	268	hypothetical protein; Validated	97.94
PRK05642	234	DNA replication initiation factor; Validated	97.93
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.93
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	97.92
PLN03025	319	replication factor C subunit; Provisional	97.91
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	97.9
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	97.9
PF00004	132	AAA: ATPase family associated with various cellula	97.89
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	97.87
PRK06620	214	hypothetical protein; Validated	97.87
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	97.86
PRK09087	226	hypothetical protein; Validated	97.82
PRK12402	337	replication factor C small subunit 2; Reviewed	97.82
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	97.81
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.79
PRK12377	248	putative replication protein; Provisional	97.79
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	97.77
PRK04841	903	transcriptional regulator MalT; Provisional	97.75
PRK12422	445	chromosomal replication initiation protein; Provis	97.75
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.71
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	97.71
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	97.71
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	97.7
PRK08181	269	transposase; Validated	97.69
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.69
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	97.65
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	97.63
PRK07940	394	DNA polymerase III subunit delta'; Validated	97.62
PRK04195	482	replication factor C large subunit; Provisional	97.59
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.58
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.58
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.57
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.56
PRK00149	450	dnaA chromosomal replication initiation protein; R	97.55
PRK06921	266	hypothetical protein; Provisional	97.55
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.53
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.53
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.53
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.53
PRK06526	254	transposase; Provisional	97.53
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.51
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.51
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.49
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.48
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.48
PRK08118	167	topology modulation protein; Reviewed	97.48
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.48
PHA02544	316	44 clamp loader, small subunit; Provisional	97.46
PRK08939	306	primosomal protein DnaI; Reviewed	97.46
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.46
PRK09183	259	transposase/IS protein; Provisional	97.42
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.42
PRK07952	244	DNA replication protein DnaC; Validated	97.41
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.39
PHA00729	226	NTP-binding motif containing protein	97.39
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	97.39
smart00382	148	AAA ATPases associated with a variety of cellular	97.39
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.39
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.38
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.37
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.36
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	97.35
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.33
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.32
PRK06835	329	DNA replication protein DnaC; Validated	97.31
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.29
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.26
PTZ00112	1164	origin recognition complex 1 protein; Provisional	97.24
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.2
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.2
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.18
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.18
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.18
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.17
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.14
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.11
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	97.11
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.1
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.08
PRK12608	380	transcription termination factor Rho; Provisional	97.07
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.05
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.05
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.05
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.04
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.01
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	96.99
PRK07261	171	topology modulation protein; Provisional	96.98
PRK08058	329	DNA polymerase III subunit delta'; Validated	96.98
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	96.97
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	96.92
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	96.88
PRK10865	857	protein disaggregation chaperone; Provisional	96.87
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	96.84
CHL00181	287	cbbX CbbX; Provisional	96.83
PRK10536	262	hypothetical protein; Provisional	96.82
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	96.82
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	96.81
COG0593	408	DnaA ATPase involved in DNA replication initiation	96.8
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	96.79
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	96.79
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.78
PRK09112	351	DNA polymerase III subunit delta'; Validated	96.77
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.76
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	96.75
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	96.74
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	96.72
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	96.7
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	96.66
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	96.66
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.63
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.6
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	96.6
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	96.53
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.52
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.52
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.5
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.48
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	96.46
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	96.41
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.37
CHL00095	821	clpC Clp protease ATP binding subunit	96.35
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	96.32
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	96.31
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	96.3
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.29
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	96.27
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.25
CHL00176	638	ftsH cell division protein; Validated	96.24
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	96.24
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.23
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.22
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.21
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.2
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.18
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	96.17
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.15
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	96.12
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	96.11
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.09
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	96.08
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.08
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	96.03
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	96.03
PRK04132	846	replication factor C small subunit; Provisional	96.02
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	96.02
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	96.0
PRK13695	174	putative NTPase; Provisional	96.0
CHL00195	489	ycf46 Ycf46; Provisional	95.95
PRK10865	857	protein disaggregation chaperone; Provisional	95.94
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	95.94
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.92
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.9
PRK06964	342	DNA polymerase III subunit delta'; Validated	95.85
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	95.85
PRK07399	314	DNA polymerase III subunit delta'; Validated	95.83
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	95.82
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	95.81
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.81
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	95.78
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	95.78
PRK06090	319	DNA polymerase III subunit delta'; Validated	95.75
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	95.75
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.75
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	95.74
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	95.73
cd03269	210	ABC_putative_ATPase This subfamily is involved in	95.73
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	95.7
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	95.7
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	95.69
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	95.68
PTZ00202	550	tuzin; Provisional	95.68
PHA02774	613	E1; Provisional	95.66
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.65
PHA02244	383	ATPase-like protein	95.64
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	95.6
PRK06871	325	DNA polymerase III subunit delta'; Validated	95.58
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	95.56
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	95.56
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	95.56
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	95.53
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.53
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	95.52
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	95.51
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	95.5
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	95.48
PRK08769	319	DNA polymerase III subunit delta'; Validated	95.44
PRK10867	433	signal recognition particle protein; Provisional	95.44
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	95.44
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	95.41
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	95.41
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	95.4
TIGR01188	302	drrA daunorubicin resistance ABC transporter ATP-b	95.4
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	95.39
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	95.39
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	95.36
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	95.35
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	95.34
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	95.33
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	95.31
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	95.3
PTZ00185	574	ATPase alpha subunit; Provisional	95.29
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	95.28
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	95.27
PRK08149	428	ATP synthase SpaL; Validated	95.26
cd03215	182	ABC_Carb_Monos_II This family represents domain II	95.24
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	95.24
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.23
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	95.23
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	95.22
PRK05922	434	type III secretion system ATPase; Validated	95.2
PRK03839	180	putative kinase; Provisional	95.19
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	95.13
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.12
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.11
PRK09099	441	type III secretion system ATPase; Provisional	95.11
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.1
CHL00095	821	clpC Clp protease ATP binding subunit	95.09
TIGR02237	209	recomb_radB DNA repair and recombination protein R	95.07
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	95.07
PRK05541	176	adenylylsulfate kinase; Provisional	95.05
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	95.05
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	95.02
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	95.02
PRK13537	306	nodulation ABC transporter NodI; Provisional	95.0
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	95.0
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	95.0
PRK05973	237	replicative DNA helicase; Provisional	94.99
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	94.98
cd03236	255	ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 o	94.98
PRK00625	173	shikimate kinase; Provisional	94.98
PRK15177	213	Vi polysaccharide export ATP-binding protein VexC;	94.98
cd04159	159	Arl10_like Arl10-like subfamily. Arl9/Arl10 was id	94.97
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	94.97
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	94.95
cd03246	173	ABCC_Protease_Secretion This family represents the	94.95
PRK06936	439	type III secretion system ATPase; Provisional	94.94
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	94.94
TIGR01040	466	V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. Th	94.91
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	94.89
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.86
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	94.86
PRK13647	274	cbiO cobalt transporter ATP-binding subunit; Provi	94.83
PRK04296	190	thymidine kinase; Provisional	94.83
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	94.83
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	94.81
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	94.8
COG2884	223	FtsE Predicted ATPase involved in cell division [C	94.8
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	94.8
PRK14974	336	cell division protein FtsY; Provisional	94.79
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	94.78
TIGR01041	458	ATP_syn_B_arch ATP synthase archaeal, B subunit. A	94.77
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	94.77
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	94.76
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	94.76
PRK08233	182	hypothetical protein; Provisional	94.74
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	94.74
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	94.71
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	94.7
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	94.67
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	94.66
PRK12678	672	transcription termination factor Rho; Provisional	94.66
cd00983	325	recA RecA is a bacterial enzyme which has roles in	94.65
PRK07993	334	DNA polymerase III subunit delta'; Validated	94.64
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	94.64
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	94.63
PRK07594	433	type III secretion system ATPase SsaN; Validated	94.62
COG4133	209	CcmA ABC-type transport system involved in cytochr	94.61
PRK05480	209	uridine/cytidine kinase; Provisional	94.61
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	94.58
PRK09354	349	recA recombinase A; Provisional	94.57
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	94.55
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	94.54
TIGR00235	207	udk uridine kinase. Model contains a number of lon	94.51
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	94.51
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	94.51
PRK05917	290	DNA polymerase III subunit delta'; Validated	94.5
TIGR00959	428	ffh signal recognition particle protein. This mode	94.48
COG0714	329	MoxR-like ATPases [General function prediction onl	94.48
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	94.47
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	94.47
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	94.44
PTZ00301	210	uridine kinase; Provisional	94.44
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	94.42
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	94.42
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	94.4
TIGR02314	343	ABC_MetN D-methionine ABC transporter, ATP-binding	94.38
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	94.37
PRK06762	166	hypothetical protein; Provisional	94.37
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	94.33
PF07726	131	AAA_3: ATPase family associated with various cellu	94.33
PRK13536	340	nodulation factor exporter subunit NodI; Provision	94.3
PRK15064	530	ABC transporter ATP-binding protein; Provisional	94.28
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	94.25
COG1135	339	AbcC ABC-type metal ion transport system, ATPase c	94.25
PRK13947	171	shikimate kinase; Provisional	94.24
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	94.22
PTZ00035	337	Rad51 protein; Provisional	94.22
PRK06820	440	type III secretion system ATPase; Validated	94.21
CHL00059	485	atpA ATP synthase CF1 alpha subunit	94.2
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	94.19
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	94.19
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	94.18
PRK00131	175	aroK shikimate kinase; Reviewed	94.17
KOG0927	614	consensus Predicted transporter (ABC superfamily)	94.15
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	94.15
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	94.14
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	94.12
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	94.11
PRK07196	434	fliI flagellum-specific ATP synthase; Validated	94.11
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	94.1
PRK04040	188	adenylate kinase; Provisional	94.1
PRK04196	460	V-type ATP synthase subunit B; Provisional	94.09
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	94.09
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	94.09
PRK13949	169	shikimate kinase; Provisional	94.08
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	94.06
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	94.04
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	94.04
PRK13546	264	teichoic acids export protein ATP-binding subunit;	94.04
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	94.02
PRK06217	183	hypothetical protein; Validated	93.98
cd01878	204	HflX HflX subfamily. A distinct conserved domain w	93.96
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	93.96
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	93.93
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	93.91
TIGR01288	303	nodI ATP-binding ABC transporter family nodulation	93.91
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	93.9
PRK13531	498	regulatory ATPase RavA; Provisional	93.86
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	93.86
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	93.84
PF03029	238	ATP_bind_1: Conserved hypothetical ATP binding pro	93.83
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	93.83
PRK10938	490	putative molybdenum transport ATP-binding protein	93.82
smart00487	201	DEXDc DEAD-like helicases superfamily.	93.82
PRK10416	318	signal recognition particle-docking protein FtsY;	93.74
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	93.73
cd01394	218	radB RadB. The archaeal protein radB shares simila	93.73
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	93.72
COG4152	300	ABC-type uncharacterized transport system, ATPase	93.71
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	93.64
PRK06547	172	hypothetical protein; Provisional	93.64
PF12061	402	DUF3542: Protein of unknown function (DUF3542); In	93.63
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	93.61
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	93.6
TIGR00962	501	atpA proton translocating ATP synthase, F1 alpha s	93.6
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	93.59
PRK07960	455	fliI flagellum-specific ATP synthase; Validated	93.58
PRK05636	505	replicative DNA helicase; Provisional	93.57
PF00154	322	RecA: recA bacterial DNA recombination protein; In	93.56
COG4555	245	NatA ABC-type Na+ transport system, ATPase compone	93.56
PRK07132	299	DNA polymerase III subunit delta'; Validated	93.54
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	93.54
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	93.52
PRK13636	283	cbiO cobalt transporter ATP-binding subunit; Provi	93.5
PRK14530	215	adenylate kinase; Provisional	93.5
PRK13343	502	F0F1 ATP synthase subunit alpha; Provisional	93.47
TIGR02236	310	recomb_radA DNA repair and recombination protein R	93.44
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.41
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	93.41
PRK04301	317	radA DNA repair and recombination protein RadA; Va	93.4
PRK06696	223	uridine kinase; Validated	93.34
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	93.28
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	93.24
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	93.23
PF08477	119	Miro: Miro-like protein; InterPro: IPR013684 Mitoc	93.23
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	93.21
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	93.2
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	93.14
PRK14532	188	adenylate kinase; Provisional	93.14
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	93.13
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	93.13
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	93.12
KOG1514	767	consensus Origin recognition complex, subunit 1, a	93.08
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	93.07
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	93.04
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	92.99
PRK13975	196	thymidylate kinase; Provisional	92.95
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	92.91
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	92.9
cd01672	200	TMPK Thymidine monophosphate kinase (TMPK), also k	92.9
TIGR00450	442	mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE	92.89
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	92.88
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	92.88
PRK02118	436	V-type ATP synthase subunit B; Provisional	92.86
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	92.83
TIGR00665	434	DnaB replicative DNA helicase. This model describe	92.82
COG4586	325	ABC-type uncharacterized transport system, ATPase	92.82
PRK13409	590	putative ATPase RIL; Provisional	92.82
PRK00889	175	adenylylsulfate kinase; Provisional	92.8
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	92.78
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	92.77
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	92.74
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	92.74
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	92.73
PRK00300	205	gmk guanylate kinase; Provisional	92.71
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	92.69
PRK13409	590	putative ATPase RIL; Provisional	92.68
KOG0056	790	consensus Heavy metal exporter HMT1, ABC superfami	92.66
PRK07667	193	uridine kinase; Provisional	92.65
COG3899	849	Predicted ATPase [General function prediction only	92.64
TIGR02528	142	EutP ethanolamine utilization protein, EutP. This	92.64
cd00880	163	Era_like Era (E. coli Ras-like protein)-like. This	92.64
PRK13948	182	shikimate kinase; Provisional	92.6
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	92.6
PRK05057	172	aroK shikimate kinase I; Reviewed	92.6
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	92.57
PRK03731	171	aroL shikimate kinase II; Reviewed	92.56
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	92.56
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	92.55
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	92.52
PTZ00088	229	adenylate kinase 1; Provisional	92.51
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	92.5
COG0055	468	AtpD F0F1-type ATP synthase, beta subunit [Energy	92.49
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	92.49
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	92.49
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	92.48
PRK11823	446	DNA repair protein RadA; Provisional	92.47
cd04115	170	Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is u	92.46
PF08303	168	tRNA_lig_kinase: tRNA ligase kinase domain; InterP	92.46
COG1100	219	GTPase SAR1 and related small G proteins [General	92.45
COG0488	530	Uup ATPase components of ABC transporters with dup	92.44
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	92.44
PF01926	116	MMR_HSR1: 50S ribosome-binding GTPase; InterPro: I	92.41
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	92.4
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	92.39
PRK13946	184	shikimate kinase; Provisional	92.38
PRK06851	367	hypothetical protein; Provisional	92.38
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	92.35
PRK11608	326	pspF phage shock protein operon transcriptional ac	92.33
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	92.31
PRK11650	356	ugpC glycerol-3-phosphate transporter ATP-binding	92.24
cd04139	164	RalA_RalB RalA/RalB subfamily. The Ral (Ras-like)	92.2
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	92.19
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	92.17
COG0194	191	Gmk Guanylate kinase [Nucleotide transport and met	92.16
PRK04328	249	hypothetical protein; Provisional	92.14
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	92.14
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	92.11
PRK05022	509	anaerobic nitric oxide reductase transcription reg	92.11
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	92.07
PRK02496	184	adk adenylate kinase; Provisional	92.04
PRK03846	198	adenylylsulfate kinase; Provisional	92.03
KOG0059	885	consensus Lipid exporter ABCA1 and related protein	92.03
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	92.02
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	92.01
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	92.0
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	92.0
CHL00060	494	atpB ATP synthase CF1 beta subunit	91.98
PF00005	137	ABC_tran: ABC transporter This structure is on hol	91.98
PRK14531	183	adenylate kinase; Provisional	91.97
PRK06904	472	replicative DNA helicase; Validated	91.97
PRK11607	377	potG putrescine transporter ATP-binding subunit; P	91.93
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	91.91
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	91.83
COG0488	530	Uup ATPase components of ABC transporters with dup	91.83
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	91.81
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	91.81
cd00882	157	Ras_like_GTPase Ras-like GTPase superfamily. The R	91.81
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	91.81
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	91.81
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	91.79
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	91.78
COG0125	208	Tmk Thymidylate kinase [Nucleotide transport and m	91.76
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	91.76
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	91.74
PF13245	76	AAA_19: Part of AAA domain	91.7
PF10662	143	PduV-EutP: Ethanolamine utilisation - propanediol	91.7
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	91.68
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	91.65
PRK09452	375	potA putrescine/spermidine ABC transporter ATPase	91.65
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	91.63
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	91.6
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	91.6
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	91.59
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	91.59
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	91.58
COG1123	539	ATPase components of various ABC-type transport sy	91.56

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=7.2e-33  Score=278.17  Aligned_cols=253  Identities=21%  Similarity=0.356  Sum_probs=192.5

Q ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhhcCCccc------
Q 043781            3 SFFQDFGKQVKKLTSNLRAIQAVLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENA------   76 (297)
Q Consensus         3 ~ll~~~~~~~~~L~~eL~~i~a~l~~ae~~~~~~~~v~~Wl~~lr~~ayd~eD~ld~~~~~~~~~~~~~~~~~~------   76 (297)
                      ..+.+.+..+..|+..|..++.++++++.++.....+..|...+++++|++||.++.|..+....+..+.-...      
T Consensus        21 ~~~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~~~~~~~~~~e~~~~~~~~~e~~~~~~~v~~~~~~~~~~l~~~~~~~~~  100 (889)
T KOG4658|consen   21 ECLDGKDNYILELKENLKALQSALEDLDAKRDDLERRVNWEEDVGDLVYLAEDIIWLFLVEEIERKANDLLSTRSVERQR  100 (889)
T ss_pred             HHHhchHHHHHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhHHHHHH
Confidence            45678888999999999999999999999999889999999999999999999999999887654322211100      


Q ss_pred             ----hhccch--hHHHHHHHHHHHHHhhhhcccccc--cCCc--c---cccccccccc--------------------cc
Q 043781           77 ----LVRKKP--KIIEINENLDDIAKQKEVFNFNVI--RGST--E---KSERIHSTAL--------------------IN  123 (297)
Q Consensus        77 ----~~~~~~--~i~~i~~~l~~i~~~~~~~~~~~~--~~~~--~---~~~~~~~~~~--------------------~~  123 (297)
                          ...++.  .+..+.+++..+.+..+.++....  .++.  .   .....+..+.                    ..
T Consensus       101 ~c~~~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e~~~~~~~~~VG~e~~~~kl~~~L~~d~~~  180 (889)
T KOG4658|consen  101 LCLCGFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVETRPIQSESDVGLETMLEKLWNRLMEDDVG  180 (889)
T ss_pred             HhhhhhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcccCCCCccccccHHHHHHHHHHHhccCCCC
Confidence                111221  556667777777777666653321  0110  0   0000000000                    12


Q ss_pred             cccccccCCcchHHHHHHHhcccc-cccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------------------C
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKD-VIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------------------E  181 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~-~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------------------~  181 (297)
                      .++|+||||+||||||+.++|+.. ++++||.++||+||+.|+...++++|+..++..                     +
T Consensus       181 iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VSk~f~~~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~  260 (889)
T KOG4658|consen  181 IVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVSKEFTTRKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEG  260 (889)
T ss_pred             EEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEcccccHHhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhcc
Confidence            457999999999999999999988 999999999999999999999999999988763                     9


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCcc---chhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIF---DAKK  257 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l---~~~~  257 (297)
                      |||||||||||+.  .+|+.|..++|..          .+||+|++|||+    ..||.. |++...+++..|   ++|+
T Consensus       261 krfllvLDDIW~~--~dw~~I~~~~p~~----------~~g~KvvlTTRs----~~V~~~~m~~~~~~~v~~L~~~eaW~  324 (889)
T KOG4658|consen  261 KRFLLVLDDIWEE--VDWDKIGVPFPSR----------ENGSKVVLTTRS----EEVCGRAMGVDYPIEVECLTPEEAWD  324 (889)
T ss_pred             CceEEEEeccccc--ccHHhcCCCCCCc----------cCCeEEEEEecc----HhhhhccccCCccccccccCccccHH
Confidence            9999999999999  5799999999984          789999999994    556655 676655555555   6777


Q ss_pred             hhhhhhccCCCCCC
Q 043781          258 IWGWEVFGRNTSTR  271 (297)
Q Consensus       258 lf~~~~f~~~~~~~  271 (297)
                      ||.+.+|....+..
T Consensus       325 LF~~~v~~~~~~~~  338 (889)
T KOG4658|consen  325 LFQKKVGPNTLGSH  338 (889)
T ss_pred             HHHHhhcccccccc
Confidence            77777777655443

>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=99.85  E-value=4.5e-22  Score=178.26  Aligned_cols=130  Identities=26%  Similarity=0.408  Sum_probs=95.5

Q ss_pred             cccccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------------------
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------------------  180 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------------------  180 (297)
                      ...+.|+||||+||||||..++++..++++|+.++|+.++...+..+++..|+.+++..                     
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            45567999999999999999999877999999999999999999999999999988554                     


Q ss_pred             -CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccc---h
Q 043781          181 -EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFD---A  255 (297)
Q Consensus       181 -~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~---~  255 (297)
                       ++++||||||||+.  ..|+.+...++..          +.||+||||||...+    +..++. ...+.|+.|+   +
T Consensus        99 ~~~~~LlVlDdv~~~--~~~~~l~~~~~~~----------~~~~kilvTTR~~~v----~~~~~~~~~~~~l~~L~~~ea  162 (287)
T PF00931_consen   99 KDKRCLLVLDDVWDE--EDLEELREPLPSF----------SSGSKILVTTRDRSV----AGSLGGTDKVIELEPLSEEEA  162 (287)
T ss_dssp             CCTSEEEEEEEE-SH--HHH-------HCH----------HSS-EEEEEESCGGG----GTTHHSCEEEEECSS--HHHH
T ss_pred             ccccceeeeeeeccc--ccccccccccccc----------ccccccccccccccc----ccccccccccccccccccccc
Confidence             77999999999998  6898888888764          678999999996544    333332 3566666665   6


Q ss_pred             hhhhhhhhccCC
Q 043781          256 KKIWGWEVFGRN  267 (297)
Q Consensus       256 ~~lf~~~~f~~~  267 (297)
                      .+||...++...
T Consensus       163 ~~L~~~~~~~~~  174 (287)
T PF00931_consen  163 LELFKKRAGRKE  174 (287)
T ss_dssp             HHHHHHHHTSHS
T ss_pred             cccccccccccc
Confidence            677777776655

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>PLN03210 Resistant to P

Probab=99.74  E-value=8.8e-18  Score=176.04  Aligned_cols=130  Identities=16%  Similarity=0.369  Sum_probs=94.1

Q ss_pred             cccccccccCCcchHHHHHHHhcccccccCCCceEEEEe---CCC-----------CC-HHHHHHHHHHhhcC----C--
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV---SDP-----------FD-EFRIAKAIIEGLEG----S--  180 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v---s~~-----------~~-~~~~~~~i~~~~~~----~--  180 (297)
                      ...++||||||+||||||+.+|+  ++..+|+..+|+..   +..           ++ ...++++++.++..    .  
T Consensus       207 ~~vvgI~G~gGiGKTTLA~~l~~--~l~~~F~g~vfv~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~  284 (1153)
T PLN03210        207 VRMVGIWGSSGIGKTTIARALFS--RLSRQFQSSVFIDRAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIY  284 (1153)
T ss_pred             eEEEEEEcCCCCchHHHHHHHHH--HHhhcCCeEEEeeccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccC
Confidence            45678999999999999999999  68889999888742   111           11 12233333333211    1  


Q ss_pred             ----------CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCCCccccC
Q 043781          181 ----------EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPV  250 (297)
Q Consensus       181 ----------~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~~~~~~l  250 (297)
                                ++|+||||||||+.  .+|+.+......          .++||+||||||+    .+++..+++.++|.+
T Consensus       285 ~~~~~~~~L~~krvLLVLDdv~~~--~~l~~L~~~~~~----------~~~GsrIIiTTrd----~~vl~~~~~~~~~~v  348 (1153)
T PLN03210        285 HLGAMEERLKHRKVLIFIDDLDDQ--DVLDALAGQTQW----------FGSGSRIIVITKD----KHFLRAHGIDHIYEV  348 (1153)
T ss_pred             CHHHHHHHHhCCeEEEEEeCCCCH--HHHHHHHhhCcc----------CCCCcEEEEEeCc----HHHHHhcCCCeEEEe
Confidence                      79999999999987  688888765433          2789999999994    556666677777887


Q ss_pred             Cccc---hhhhhhhhhccCCCC
Q 043781          251 SIFD---AKKIWGWEVFGRNTS  269 (297)
Q Consensus       251 ~~l~---~~~lf~~~~f~~~~~  269 (297)
                      ..++   +++||+++||++..+
T Consensus       349 ~~l~~~ea~~LF~~~Af~~~~~  370 (1153)
T PLN03210        349 CLPSNELALEMFCRSAFKKNSP  370 (1153)
T ss_pred             cCCCHHHHHHHHHHHhcCCCCC
Confidence            7774   778899999986543

syringae 6; Provisional

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

Probab=98.81  E-value=4.8e-09  Score=95.56  Aligned_cols=118  Identities=17%  Similarity=0.144  Sum_probs=75.6

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFH  203 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~  203 (297)
                      -.=+||++|+||||||+.+..  ....+|...- -..+..-++..++.+--..... +++.+|++|.|..-+..+-+.+.
T Consensus        50 SmIl~GPPG~GKTTlA~liA~--~~~~~f~~~s-Av~~gvkdlr~i~e~a~~~~~~-gr~tiLflDEIHRfnK~QQD~lL  125 (436)
T COG2256          50 SMILWGPPGTGKTTLARLIAG--TTNAAFEALS-AVTSGVKDLREIIEEARKNRLL-GRRTILFLDEIHRFNKAQQDALL  125 (436)
T ss_pred             eeEEECCCCCCHHHHHHHHHH--hhCCceEEec-cccccHHHHHHHHHHHHHHHhc-CCceEEEEehhhhcChhhhhhhh
Confidence            344799999999999999999  4555552211 1112222333333332222222 89999999999988766777765


Q ss_pred             HHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhh
Q 043781          204 NCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKI  258 (297)
Q Consensus       204 ~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~l  258 (297)
                      +.+             .+|.-|+|-+.+++....+...+-. ..++.|++|+++++
T Consensus       126 p~v-------------E~G~iilIGATTENPsF~ln~ALlSR~~vf~lk~L~~~di  168 (436)
T COG2256         126 PHV-------------ENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDI  168 (436)
T ss_pred             hhh-------------cCCeEEEEeccCCCCCeeecHHHhhhhheeeeecCCHHHH
Confidence            555             7888888866555555454433222 37889999987764

>PF05729 NACHT: NACHT domain

Probab=98.71  E-value=7e-08  Score=78.65  Aligned_cols=122  Identities=20%  Similarity=0.172  Sum_probs=71.6

Q ss_pred             cccccCCcchHHHHHHHhcccccccC----CCceEEEEeCCCCCHH---HHHHHHHHhhcCC--------------CceE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIEN----FDKRIWVCVSDPFDEF---RIAKAIIEGLEGS--------------EKKF  184 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~---~~~~~i~~~~~~~--------------~kr~  184 (297)
                      -|.|.+|+||||+++.++..-.....    +...+|++........   .+...|..+....              .+++
T Consensus         4 ~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   83 (166)
T PF05729_consen    4 WISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKNKRV   83 (166)
T ss_pred             EEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcCCce
Confidence            47899999999999999885333222    3456677654433221   2333333332221              8899


Q ss_pred             EEEEeCCCCCCcc--C-----HHH-HHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCCCccccCCccchh
Q 043781          185 FLILDDVWTDDYS--K-----WEP-FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAK  256 (297)
Q Consensus       185 LiVlDdv~~~~~~--~-----w~~-l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~~~~~~l~~l~~~  256 (297)
                      |||||++.+....  .     +.. +...++..         ..++.++|||+|.... ..+.........+.+.+++..
T Consensus        84 llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~---------~~~~~~liit~r~~~~-~~~~~~~~~~~~~~l~~~~~~  153 (166)
T PF05729_consen   84 LLILDGLDELEEQDQSQERQRLLDLLSQLLPQA---------LPPGVKLIITSRPRAF-PDLRRRLKQAQILELEPFSEE  153 (166)
T ss_pred             EEEEechHhcccchhhhHHHHHHHHHHHHhhhc---------cCCCCeEEEEEcCChH-HHHHHhcCCCcEEEECCCCHH
Confidence            9999999875321  1     111 22222221         1568999999996543 224444444456778787755


Q ss_pred             h
Q 043781          257 K  257 (297)
Q Consensus       257 ~  257 (297)
                      +
T Consensus       154 ~  154 (166)
T PF05729_consen  154 D  154 (166)
T ss_pred             H
Confidence            5

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=98.66  E-value=4e-08  Score=86.24  Aligned_cols=69  Identities=17%  Similarity=0.131  Sum_probs=57.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC--CCHHHHHHHH-----HHhhcCC-----------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP--FDEFRIAKAI-----IEGLEGS-----------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i-----~~~~~~~-----------------  180 (297)
                      ..|+|.+|+|||||++.+|++.... +|+.++|+++++.  +++.++++.|     +.+++.+                 
T Consensus        19 ~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~~~~~a~~   97 (249)
T cd01128          19 GLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEMVLEKAKR   97 (249)
T ss_pred             EEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999975444 8999999998777  7899999998     4444444                 


Q ss_pred             ----CceEEEEEeCCCCC
Q 043781          181 ----EKKFFLILDDVWTD  194 (297)
Q Consensus       181 ----~kr~LiVlDdv~~~  194 (297)
                          +++.++++|++...
T Consensus        98 ~~~~G~~vll~iDei~r~  115 (249)
T cd01128          98 LVEHGKDVVILLDSITRL  115 (249)
T ss_pred             HHHCCCCEEEEEECHHHh
Confidence                89999999999743

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=98.61  E-value=1e-07  Score=82.86  Aligned_cols=124  Identities=20%  Similarity=0.275  Sum_probs=71.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCC-ccCHHH-HH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDD-YSKWEP-FH  203 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~-~~~w~~-l~  203 (297)
                      -+||.+|+|||+|++.+++.  .........|++++..   ......+++.+   .+.-+|+|||+|... ...|+. +.
T Consensus        43 ~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~~~~---~~~~~~~~~~~---~~~dlLilDDi~~~~~~~~~~~~l~  114 (229)
T PRK06893         43 YIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPLSKS---QYFSPAVLENL---EQQDLVCLDDLQAVIGNEEWELAIF  114 (229)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeHHHh---hhhhHHHHhhc---ccCCEEEEeChhhhcCChHHHHHHH
Confidence            48899999999999999984  3323334567766421   12222344443   234599999999742 245663 44


Q ss_pred             HHHhhhhhhhceeeecCCCCeEEEEeccHHH------HHHHHHhhCCCccccCCccchhh---hhhhhhccC
Q 043781          204 NCLMRVLQEFAAIEVDGDENPLSLTSTCQEK------LRHLTLTLGLRAKFPVSIFDAKK---IWGWEVFGR  266 (297)
Q Consensus       204 ~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~------~~~v~~~~~~~~~~~l~~l~~~~---lf~~~~f~~  266 (297)
                      ..+...         ...|+.+||+|.+...      ...+...++...++.+..++.++   ++.+.++..
T Consensus       115 ~l~n~~---------~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~  177 (229)
T PRK06893        115 DLFNRI---------KEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQR  177 (229)
T ss_pred             HHHHHH---------HHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHHc
Confidence            444432         1456666554432211      13556666655667777777554   344444443

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.54  E-value=7.5e-08  Score=88.66  Aligned_cols=67  Identities=18%  Similarity=0.148  Sum_probs=54.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC--CHHHHHHHHHHhhcCC-----------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF--DEFRIAKAIIEGLEGS-----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~~~~~-----------------------  180 (297)
                      .|+|++|+||||||+.||++...+ +|+.++||.+++..  .+.++++.|...+-.+                       
T Consensus       173 lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~ie~Ae~~  251 (416)
T PRK09376        173 LIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMVIEKAKRL  251 (416)
T ss_pred             EEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999975444 89999999999887  7788888875222111                       


Q ss_pred             ---CceEEEEEeCCCC
Q 043781          181 ---EKKFFLILDDVWT  193 (297)
Q Consensus       181 ---~kr~LiVlDdv~~  193 (297)
                         ++..||++|++..
T Consensus       252 ~e~G~dVlL~iDsItR  267 (416)
T PRK09376        252 VEHGKDVVILLDSITR  267 (416)
T ss_pred             HHcCCCEEEEEEChHH
Confidence               8999999999964

>PF13173 AAA_14: AAA domain

Probab=98.41  E-value=6.7e-07  Score=70.46  Aligned_cols=116  Identities=19%  Similarity=0.261  Sum_probs=69.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHH----HHHHHHHhhcCCCceEEEEEeCCCCCCccCHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFR----IAKAIIEGLEGSEKKFFLILDDVWTDDYSKWE  200 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~----~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~  200 (297)
                      .-|.|+.|+|||||+++++.+..   .....++++..+......    +...+.+...  .++.+|+||++...  ..|.
T Consensus         5 ~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~i~iDEiq~~--~~~~   77 (128)
T PF13173_consen    5 IILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDRRLADPDLLEYFLELIK--PGKKYIFIDEIQYL--PDWE   77 (128)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHHHHhhhhhHHHHHHhhc--cCCcEEEEehhhhh--ccHH
Confidence            35789999999999999997532   334567776655433221    2233333321  37788999999988  4677


Q ss_pred             HHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHH-HHH-hhCCCccccCCccchhh
Q 043781          201 PFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRH-LTL-TLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       201 ~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~-v~~-~~~~~~~~~l~~l~~~~  257 (297)
                      ..-..+.+.          .+..+|++|+........ ... ..|-...+.|.+++-.|
T Consensus        78 ~~lk~l~d~----------~~~~~ii~tgS~~~~l~~~~~~~l~gr~~~~~l~Plsf~E  126 (128)
T PF13173_consen   78 DALKFLVDN----------GPNIKIILTGSSSSLLSKDIAESLAGRVIEIELYPLSFRE  126 (128)
T ss_pred             HHHHHHHHh----------ccCceEEEEccchHHHhhcccccCCCeEEEEEECCCCHHH
Confidence            655555542          556899999875443322 111 12222445555555443

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=98.37  E-value=3.8e-07  Score=82.33  Aligned_cols=116  Identities=20%  Similarity=0.212  Sum_probs=75.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC----CceEEEEEeCCCCCCccCHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS----EKKFFLILDDVWTDDYSKWE  200 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~----~kr~LiVlDdv~~~~~~~w~  200 (297)
                      .-+||++|+||||||+.+.+..+...    ..||..|-...-..-.+.|+++....    ++|.+|.+|.|..-+..+-+
T Consensus       165 mIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFNksQQD  240 (554)
T KOG2028|consen  165 MILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAKTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFNKSQQD  240 (554)
T ss_pred             eEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccchHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhhhhhhh
Confidence            34799999999999999999533322    56777665544344444454444332    79999999999887655555


Q ss_pred             HHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccchhh
Q 043781          201 PFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFDAKK  257 (297)
Q Consensus       201 ~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~~~~  257 (297)
                      .+   ||..          .+|+.++|-..+++...++... +.-..++.|+.|....
T Consensus       241 ~f---LP~V----------E~G~I~lIGATTENPSFqln~aLlSRC~VfvLekL~~n~  285 (554)
T KOG2028|consen  241 TF---LPHV----------ENGDITLIGATTENPSFQLNAALLSRCRVFVLEKLPVNA  285 (554)
T ss_pred             cc---ccee----------ccCceEEEecccCCCccchhHHHHhccceeEeccCCHHH
Confidence            44   4443          7888888854444444454333 3334677888886443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.36  E-value=1.1e-06  Score=82.91  Aligned_cols=74  Identities=19%  Similarity=0.248  Sum_probs=45.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcC---CCceEEEEEeCCCCCCccCHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG---SEKKFFLILDDVWTDDYSKWEPF  202 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~---~~kr~LiVlDdv~~~~~~~w~~l  202 (297)
                      -++|++|+||||||+.+++.  ....|     +.++....-..-++.+++....   .+++.+|+||+++.....+.+.|
T Consensus        40 lL~GppGtGKTtLA~~ia~~--~~~~~-----~~l~a~~~~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~~~q~~L  112 (413)
T PRK13342         40 ILWGPPGTGKTTLARIIAGA--TDAPF-----EALSAVTSGVKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDAL  112 (413)
T ss_pred             EEECCCCCCHHHHHHHHHHH--hCCCE-----EEEecccccHHHHHHHHHHHHHhhhcCCceEEEEechhhhCHHHHHHH
Confidence            47899999999999999984  33333     2222222112222333333321   25889999999998754555555


Q ss_pred             HHHH
Q 043781          203 HNCL  206 (297)
Q Consensus       203 ~~~l  206 (297)
                      ...+
T Consensus       113 L~~l  116 (413)
T PRK13342        113 LPHV  116 (413)
T ss_pred             HHHh
Confidence            5544

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.34  E-value=4.8e-06  Score=73.77  Aligned_cols=77  Identities=18%  Similarity=0.161  Sum_probs=52.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-----------------------C
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-----------------------E  181 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----------------------~  181 (297)
                      .-|+|++|+|||||++.+++.... ..+ ..+|+. ....+..+++..|+..++.+                       +
T Consensus        46 ~~l~G~~G~GKTtl~~~l~~~l~~-~~~-~~~~~~-~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~  122 (269)
T TIGR03015        46 ILITGEVGAGKTTLIRNLLKRLDQ-ERV-VAAKLV-NTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAG  122 (269)
T ss_pred             EEEEcCCCCCHHHHHHHHHHhcCC-CCe-EEeeee-CCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCC
Confidence            357899999999999999985321 111 223332 33446667777777666542                       6


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHH
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      ++.+||+||+|......++.++.
T Consensus       123 ~~~vliiDe~~~l~~~~~~~l~~  145 (269)
T TIGR03015       123 KRALLVVDEAQNLTPELLEELRM  145 (269)
T ss_pred             CCeEEEEECcccCCHHHHHHHHH
Confidence            78999999999976556666654

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.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=98.31  E-value=1.4e-06  Score=87.16  Aligned_cols=115  Identities=18%  Similarity=0.177  Sum_probs=63.1

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeC--CCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS--DPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFH  203 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs--~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~  203 (297)
                      -++|++|+||||||+.+++  ....+|.   .++.+  ...++.+++..+...+...+++.+|||||++..+...++.|.
T Consensus        56 LL~GPpGtGKTTLA~aIA~--~~~~~f~---~lna~~~~i~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQdaLL  130 (725)
T PRK13341         56 ILYGPPGVGKTTLARIIAN--HTRAHFS---SLNAVLAGVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQDALL  130 (725)
T ss_pred             EEECCCCCCHHHHHHHHHH--HhcCcce---eehhhhhhhHHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHHHHHH
Confidence            4789999999999999998  3445552   12111  111222333333222222256789999999876545566565


Q ss_pred             HHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCccccCCccchhhh
Q 043781          204 NCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFPVSIFDAKKI  258 (297)
Q Consensus       204 ~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~l~~l~~~~l  258 (297)
                      ..+             .+|+.++|++++++....+....- -..++.+.+++.+++
T Consensus       131 ~~l-------------E~g~IiLI~aTTenp~~~l~~aL~SR~~v~~l~pLs~edi  173 (725)
T PRK13341        131 PWV-------------ENGTITLIGATTENPYFEVNKALVSRSRLFRLKSLSDEDL  173 (725)
T ss_pred             HHh-------------cCceEEEEEecCCChHhhhhhHhhccccceecCCCCHHHH
Confidence            444             455666664433322222222111 124677777776554

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.29  E-value=7.3e-07  Score=69.98  Aligned_cols=91  Identities=21%  Similarity=0.207  Sum_probs=62.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccC-----CCceEEEEeCCCCCHHHHHHHHHHhhcCC--------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIEN-----FDKRIWVCVSDPFDEFRIAKAIIEGLEGS--------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~-----F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--------------------  180 (297)
                      -|+|.+|+|||++++.+.+.  ....     -...+|+..+...+...+...|+.+++..                    
T Consensus         8 ~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~   85 (131)
T PF13401_consen    8 VISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDALDR   85 (131)
T ss_dssp             EEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHHHh
Confidence            47899999999999999984  2211     23556898888778999999999998765                    


Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEec
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      .+..+||||++..- ....++.|+..+            +..+.++|+..+
T Consensus        86 ~~~~~lviDe~~~l~~~~~l~~l~~l~------------~~~~~~vvl~G~  124 (131)
T PF13401_consen   86 RRVVLLVIDEADHLFSDEFLEFLRSLL------------NESNIKVVLVGT  124 (131)
T ss_dssp             CTEEEEEEETTHHHHTHHHHHHHHHHT------------CSCBEEEEEEES
T ss_pred             cCCeEEEEeChHhcCCHHHHHHHHHHH------------hCCCCeEEEEEC
Confidence            55689999999765 333333343322            145556776654

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.28  E-value=3.7e-06  Score=72.53  Aligned_cols=115  Identities=22%  Similarity=0.274  Sum_probs=63.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCcc-CH-HHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYS-KW-EPFH  203 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~-~w-~~l~  203 (297)
                      -++|.+|+|||+||+.+++.  ........+++.++.-..   -...++..+.   +.-+|||||+...... .| +.+.
T Consensus        42 ll~G~~G~GKT~la~~~~~~--~~~~~~~~~~i~~~~~~~---~~~~~~~~~~---~~~lLvIDdi~~l~~~~~~~~~L~  113 (226)
T TIGR03420        42 YLWGESGSGKSHLLQAACAA--AEERGKSAIYLPLAELAQ---ADPEVLEGLE---QADLVCLDDVEAIAGQPEWQEALF  113 (226)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhcCCcEEEEeHHHHHH---hHHHHHhhcc---cCCEEEEeChhhhcCChHHHHHHH
Confidence            48899999999999999984  333333445665432211   1123333332   2348999999876422 33 3455


Q ss_pred             HHHhhhhhhhceeeecCCCCeEEEEeccHHHH-----HHHHHhhCCCccccCCccchhh
Q 043781          204 NCLMRVLQEFAAIEVDGDENPLSLTSTCQEKL-----RHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       204 ~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~-----~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ..+...         ...+.++|+||+.....     ..+...+.....+.+.+++..+
T Consensus       114 ~~l~~~---------~~~~~~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e  163 (226)
T TIGR03420       114 HLYNRV---------REAGGRLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEE  163 (226)
T ss_pred             HHHHHH---------HHcCCeEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHH
Confidence            555432         13445788888743211     3334344322445666665444

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.

>TIGR00767 rho transcription termination factor Rho

Probab=98.23  E-value=1.9e-06  Score=79.75  Aligned_cols=69  Identities=14%  Similarity=0.136  Sum_probs=55.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC--CCHHHHHHHH-----HHhhcCC-----------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP--FDEFRIAKAI-----IEGLEGS-----------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i-----~~~~~~~-----------------  180 (297)
                      ..|+|.+|+|||||++.+++... .++|+..+|+.+++.  .++.++++.|     +..+..+                 
T Consensus       171 ~~IvG~~g~GKTtL~~~i~~~I~-~nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~e~Ae~  249 (415)
T TIGR00767       171 GLIVAPPKAGKTVLLQKIAQAIT-RNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVIEKAKR  249 (415)
T ss_pred             EEEECCCCCChhHHHHHHHHhhc-ccCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHHHHHHH
Confidence            36899999999999999999633 347999999999866  7888999888     3333332                 


Q ss_pred             ----CceEEEEEeCCCCC
Q 043781          181 ----EKKFFLILDDVWTD  194 (297)
Q Consensus       181 ----~kr~LiVlDdv~~~  194 (297)
                          +++.+|++|.+...
T Consensus       250 ~~~~GkdVVLlIDEitR~  267 (415)
T TIGR00767       250 LVEHKKDVVILLDSITRL  267 (415)
T ss_pred             HHHcCCCeEEEEEChhHH
Confidence                99999999999753

Members of this family differ in the specificity of RNA binding.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=98.21  E-value=6.2e-06  Score=77.27  Aligned_cols=69  Identities=20%  Similarity=0.237  Sum_probs=48.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcC-----------------------CCc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG-----------------------SEK  182 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~-----------------------~~k  182 (297)
                      -|+|++|+|||++++.++++.......-..++++.....+...++..|+.++..                       .++
T Consensus        59 lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~  138 (394)
T PRK00411         59 LIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDR  138 (394)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCC
Confidence            489999999999999999853222212345566655555666777777776643                       156


Q ss_pred             eEEEEEeCCCCC
Q 043781          183 KFFLILDDVWTD  194 (297)
Q Consensus       183 r~LiVlDdv~~~  194 (297)
                      ..+||||+++.-
T Consensus       139 ~~viviDE~d~l  150 (394)
T PRK00411        139 VLIVALDDINYL  150 (394)
T ss_pred             EEEEEECCHhHh
Confidence            689999999874

>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=98.17  E-value=7.6e-06  Score=64.46  Aligned_cols=102  Identities=18%  Similarity=0.159  Sum_probs=56.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHH-------HHhhcCCCceEEEEEeCCCCCCcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAI-------IEGLEGSEKKFFLILDDVWTDDYS  197 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i-------~~~~~~~~kr~LiVlDdv~~~~~~  197 (297)
                      .-|+|.+|+|||+|++.+++.  ....-...+++..+...........+       ........+..+||+||++.....
T Consensus        22 v~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~~~~   99 (151)
T cd00009          22 LLLYGPPGTGKTTLARAIANE--LFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRG   99 (151)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhhhHH
Confidence            458899999999999999984  32222345566655443332222111       111222267899999999865212


Q ss_pred             CHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          198 KWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       198 ~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      ....+...+......   . ....+..||+||...
T Consensus       100 ~~~~~~~~i~~~~~~---~-~~~~~~~ii~~~~~~  130 (151)
T cd00009         100 AQNALLRVLETLNDL---R-IDRENVRVIGATNRP  130 (151)
T ss_pred             HHHHHHHHHHhcCce---e-ccCCCeEEEEecCcc
Confidence            233344444432100   0 013567788888743

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.

>PRK08727 hypothetical protein; Validated

Probab=98.14  E-value=1e-05  Score=70.43  Aligned_cols=117  Identities=17%  Similarity=0.121  Sum_probs=69.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCc-cCHHH-H
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDY-SKWEP-F  202 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~-~~w~~-l  202 (297)
                      .-++|..|+|||+|++.+++.  ..++.-...|+++.+.   ...+.++++.+   .+--+|||||+..... ..|.. +
T Consensus        44 l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~~~~~---~~~~~~~~~~l---~~~dlLiIDDi~~l~~~~~~~~~l  115 (233)
T PRK08727         44 LYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLPLQAA---AGRLRDALEAL---EGRSLVALDGLESIAGQREDEVAL  115 (233)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEeHHHh---hhhHHHHHHHH---hcCCEEEEeCcccccCChHHHHHH
Confidence            568999999999999999884  3333335567764431   12223344444   3456999999975421 23443 2


Q ss_pred             HHHHhhhhhhhceeeecCCCCeEEEEeccHHH-----HHHHHHhhCCCccccCCccchhhh
Q 043781          203 HNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-----LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-----~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      -..+...         ..+|..||+|++..-.     ...+...+....+++|.+++.+++
T Consensus       116 f~l~n~~---------~~~~~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~  167 (233)
T PRK08727        116 FDFHNRA---------RAAGITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVAR  167 (233)
T ss_pred             HHHHHHH---------HHcCCeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHH
Confidence            2222221         1456779999874321     234445554446778888876664

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.06  E-value=1.9e-05  Score=68.94  Aligned_cols=117  Identities=15%  Similarity=0.199  Sum_probs=67.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCc-cCHHH-H
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDY-SKWEP-F  202 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~-~~w~~-l  202 (297)
                      .-|+|++|+|||+|++.+++.  ....-..+.++++.....   ...++.+.+.   +--+|+|||+..... ..|+. +
T Consensus        48 l~l~Gp~G~GKThLl~a~~~~--~~~~~~~v~y~~~~~~~~---~~~~~~~~~~---~~dlliiDdi~~~~~~~~~~~~l  119 (235)
T PRK08084         48 IYLWSREGAGRSHLLHAACAE--LSQRGRAVGYVPLDKRAW---FVPEVLEGME---QLSLVCIDNIECIAGDELWEMAI  119 (235)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEEHHHHhh---hhHHHHHHhh---hCCEEEEeChhhhcCCHHHHHHH
Confidence            358999999999999999883  332223445665543211   1112222221   224899999976421 35654 3


Q ss_pred             HHHHhhhhhhhceeeecCCC-CeEEEEeccHHH-----HHHHHHhhCCCccccCCccchhhh
Q 043781          203 HNCLMRVLQEFAAIEVDGDE-NPLSLTSTCQEK-----LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~g-s~iiiTTr~~~~-----~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      ...+....         .+| .++|+||+..-.     ...+...+....++.+.+++.+++
T Consensus       120 f~l~n~~~---------e~g~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~  172 (235)
T PRK08084        120 FDLYNRIL---------ESGRTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEK  172 (235)
T ss_pred             HHHHHHHH---------HcCCCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHH
Confidence            33443321         334 478999875421     245666676667788888865553

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.03  E-value=2.3e-05  Score=71.27  Aligned_cols=121  Identities=17%  Similarity=0.099  Sum_probs=78.9

Q ss_pred             ccccCCcchHHHHHHHhccc----ccccCCCceEEEE-eCCCCCHHHHHHHHHHhhcCC---CceEEEEEeCCCCCCccC
Q 043781          127 VRGMGGIGKTTLAQFAYNDK----DVIENFDKRIWVC-VSDPFDEFRIAKAIIEGLEGS---EKKFFLILDDVWTDDYSK  198 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~----~~~~~F~~~~wv~-vs~~~~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~~~~~~  198 (297)
                      ++|+.|+||||+|+.+++.-    ....|+|...|.. -+....+.++ +++.+.+...   +++=++|+|++.....+.
T Consensus        31 f~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~v~~i-r~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a  109 (313)
T PRK05564         31 IVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGVDDI-RNIIEEVNKKPYEGDKKVIIIYNSEKMTEQA  109 (313)
T ss_pred             eECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCCHHHH-HHHHHHHhcCcccCCceEEEEechhhcCHHH
Confidence            67999999999998888731    1245677777765 3445566663 3455544322   666777788887766578


Q ss_pred             HHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCccccCCccchhhhhhh
Q 043781          199 WEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       199 w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~l~~l~~~~lf~~  261 (297)
                      |+.|...+..-          .+++.+|++|.+.+   .+..+.. -..++.+..++..++..|
T Consensus       110 ~naLLK~LEep----------p~~t~~il~~~~~~---~ll~TI~SRc~~~~~~~~~~~~~~~~  160 (313)
T PRK05564        110 QNAFLKTIEEP----------PKGVFIILLCENLE---QILDTIKSRCQIYKLNRLSKEEIEKF  160 (313)
T ss_pred             HHHHHHHhcCC----------CCCeEEEEEeCChH---hCcHHHHhhceeeeCCCcCHHHHHHH
Confidence            99898888752          66788888886543   3322211 125778888877765443

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.01  E-value=5.2e-05  Score=63.67  Aligned_cols=123  Identities=15%  Similarity=0.147  Sum_probs=72.4

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      ++|+.|+||||+|+.+.+.-.-.                    .+.|...............+ +++.+.+...   +.+
T Consensus        19 ~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i-~~i~~~~~~~~~~~~~   97 (188)
T TIGR00678        19 FAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQV-RELVEFLSRTPQESGR   97 (188)
T ss_pred             EECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHH-HHHHHHHccCcccCCe
Confidence            68999999999998887631111                    22233322222223444443 3444444332   677


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCccccCCccchhhhhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFPVSIFDAKKIWGWE  262 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~l~~l~~~~lf~~~  262 (297)
                      -++|+|++.....+.++.|...+...          ...+.+|++|+...   .+..... -..++.+.+++..++..|-
T Consensus        98 kviiide~~~l~~~~~~~Ll~~le~~----------~~~~~~il~~~~~~---~l~~~i~sr~~~~~~~~~~~~~~~~~l  164 (188)
T TIGR00678        98 RVVIIEDAERMNEAAANALLKTLEEP----------PPNTLFILITPSPE---KLLPTIRSRCQVLPFPPLSEEALLQWL  164 (188)
T ss_pred             EEEEEechhhhCHHHHHHHHHHhcCC----------CCCeEEEEEECChH---hChHHHHhhcEEeeCCCCCHHHHHHHH
Confidence            79999999887655677777777542          44566777765432   2222111 1257888888888865554


Q ss_pred             h
Q 043781          263 V  263 (297)
Q Consensus       263 ~  263 (297)
                      .
T Consensus       165 ~  165 (188)
T TIGR00678       165 I  165 (188)
T ss_pred             H
Confidence            3

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.

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.96  E-value=4.1e-05  Score=74.35  Aligned_cols=120  Identities=16%  Similarity=0.173  Sum_probs=71.6

Q ss_pred             ccccCCcchHHHHHHHhccccc-------------------ccCCCceEEEEeCCCCCHHHHHHHHHHhhcC---CCceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV-------------------IENFDKRIWVCVSDPFDEFRIAKAIIEGLEG---SEKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~-------------------~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~---~~kr~  184 (297)
                      ++|+.|+||||+|+.+.+.-.-                   ...|.-.+++.......+.++ ++|++.+..   .+++-
T Consensus        43 f~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~~~dlieidaas~~gvd~i-r~ii~~~~~~p~~g~~k  121 (546)
T PRK14957         43 FTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASRTGVEET-KEILDNIQYMPSQGRYK  121 (546)
T ss_pred             EECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCCCCceEEeecccccCHHHH-HHHHHHHHhhhhcCCcE
Confidence            6899999999999998873110                   012333444544444444443 444444432   26777


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccchhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~~~~lf~  260 (297)
                      ++|+|++.....+.++.|...+...          .....+|++|.+.   ..+... ..-...+.+..++.+++..
T Consensus       122 ViIIDEa~~ls~~a~naLLK~LEep----------p~~v~fIL~Ttd~---~kil~tI~SRc~~~~f~~Ls~~eI~~  185 (546)
T PRK14957        122 VYLIDEVHMLSKQSFNALLKTLEEP----------PEYVKFILATTDY---HKIPVTILSRCIQLHLKHISQADIKD  185 (546)
T ss_pred             EEEEechhhccHHHHHHHHHHHhcC----------CCCceEEEEECCh---hhhhhhHHHheeeEEeCCCCHHHHHH
Confidence            9999999887656777888777652          3455566555432   222222 1112677888887776643

>PRK08116 hypothetical protein; Validated

Probab=97.94  E-value=3.2e-05  Score=68.82  Aligned_cols=91  Identities=25%  Similarity=0.245  Sum_probs=53.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC------------CceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS------------EKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~------------~kr~LiVlDdv~  192 (297)
                      .-++|.+|+|||+||..+++.  +..+--..+++++      .+++..|.......            ..-=||||||+-
T Consensus       117 l~l~G~~GtGKThLa~aia~~--l~~~~~~v~~~~~------~~ll~~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg  188 (268)
T PRK08116        117 LLLWGSVGTGKTYLAACIANE--LIEKGVPVIFVNF------PQLLNRIKSTYKSSGKEDENEIIRSLVNADLLILDDLG  188 (268)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEH------HHHHHHHHHHHhccccccHHHHHHHhcCCCEEEEeccc
Confidence            347899999999999999994  4333334556643      33444433222110            222389999996


Q ss_pred             CCCccCHHH--HHHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          193 TDDYSKWEP--FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       193 ~~~~~~w~~--l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      ......|..  |-..+...         -.+|..+||||...
T Consensus       189 ~e~~t~~~~~~l~~iin~r---------~~~~~~~IiTsN~~  221 (268)
T PRK08116        189 AERDTEWAREKVYNIIDSR---------YRKGLPTIVTTNLS  221 (268)
T ss_pred             CCCCCHHHHHHHHHHHHHH---------HHCCCCEEEECCCC
Confidence            544356654  33333221         15677899999743

>PRK05642 DNA replication initiation factor; Validated

Probab=97.93  E-value=3.8e-05  Score=66.96  Aligned_cols=117  Identities=19%  Similarity=0.276  Sum_probs=66.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCC-ccCHHH-H
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDD-YSKWEP-F  202 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~-~~~w~~-l  202 (297)
                      .-|+|..|+|||+|++.+.+.  ....-..++|++...-..   ....+.+.+..   -=++|+||+.... ...|+. +
T Consensus        48 l~l~G~~G~GKTHLl~a~~~~--~~~~~~~v~y~~~~~~~~---~~~~~~~~~~~---~d~LiiDDi~~~~~~~~~~~~L  119 (234)
T PRK05642         48 IYLWGKDGVGRSHLLQAACLR--FEQRGEPAVYLPLAELLD---RGPELLDNLEQ---YELVCLDDLDVIAGKADWEEAL  119 (234)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHhCCCcEEEeeHHHHHh---hhHHHHHhhhh---CCEEEEechhhhcCChHHHHHH
Confidence            358899999999999999873  322223456775432111   11223333321   1278899997542 135654 4


Q ss_pred             HHHHhhhhhhhceeeecCCCCeEEEEeccHHH-----HHHHHHhhCCCccccCCccchhhh
Q 043781          203 HNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-----LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-----~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      -..+...         ..+|..+|+|++....     ...+..+++...++.+++++.+++
T Consensus       120 f~l~n~~---------~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~  171 (234)
T PRK05642        120 FHLFNRL---------RDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDK  171 (234)
T ss_pred             HHHHHHH---------HhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHH
Confidence            4444332         1567789999874322     133344554446677788776654

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.93  E-value=7.2e-05  Score=72.12  Aligned_cols=121  Identities=17%  Similarity=0.182  Sum_probs=71.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccC-----------------------CCceEEEEeCCCCCHHHHHHHHHHhhcCC---
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIEN-----------------------FDKRIWVCVSDPFDEFRIAKAIIEGLEGS---  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~-----------------------F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---  180 (297)
                      ++|++|+||||+|+.+++.-.....                       ..-...+.......+.++ +++++.....   
T Consensus        48 f~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~I-r~iie~a~~~P~~  126 (507)
T PRK06645         48 LTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDI-RRIIESAEYKPLQ  126 (507)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHH-HHHHHHHHhcccc
Confidence            6799999999999999874211110                       011223334444455544 3444444322   


Q ss_pred             CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhhh
Q 043781          181 EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKIW  259 (297)
Q Consensus       181 ~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~lf  259 (297)
                      +++-++|+|+++......|+.|...+..-          ...+.+|++|...   ..+...... ...+.+..++..+++
T Consensus       127 ~~~KVvIIDEa~~Ls~~a~naLLk~LEep----------p~~~vfI~aTte~---~kI~~tI~SRc~~~ef~~ls~~el~  193 (507)
T PRK06645        127 GKHKIFIIDEVHMLSKGAFNALLKTLEEP----------PPHIIFIFATTEV---QKIPATIISRCQRYDLRRLSFEEIF  193 (507)
T ss_pred             CCcEEEEEEChhhcCHHHHHHHHHHHhhc----------CCCEEEEEEeCCh---HHhhHHHHhcceEEEccCCCHHHHH
Confidence            67889999999987656788887777642          4445555544322   223322211 246778888877765


Q ss_pred             hh
Q 043781          260 GW  261 (297)
Q Consensus       260 ~~  261 (297)
                      .|
T Consensus       194 ~~  195 (507)
T PRK06645        194 KL  195 (507)
T ss_pred             HH
Confidence            43

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=7.9e-05  Score=69.25  Aligned_cols=122  Identities=18%  Similarity=0.211  Sum_probs=71.1

Q ss_pred             cccccCCcchHHHHHHHhccccccc-------------------CCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE-------------------NFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~-------------------~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      =++|++|+||||+|+.+.+.-....                   .+.-..++..+....+.+ .+++++.+...   +++
T Consensus        42 L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~~~~~~d~~~~~~~~~~~v~~-ir~i~~~~~~~p~~~~~  120 (363)
T PRK14961         42 LLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIEKGLCLDLIEIDAASRTKVEE-MREILDNIYYSPSKSRF  120 (363)
T ss_pred             EEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceEEecccccCCHHH-HHHHHHHHhcCcccCCc
Confidence            3789999999999999887421111                   111123333333334433 45555554322   566


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccchhhhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~~~~lf~~  261 (297)
                      -++|+|++.......++.+...+...          ....++|++|...+   .+..+ .+-...+++.+++.+++..|
T Consensus       121 kviIIDEa~~l~~~a~naLLk~lEe~----------~~~~~fIl~t~~~~---~l~~tI~SRc~~~~~~~l~~~el~~~  186 (363)
T PRK14961        121 KVYLIDEVHMLSRHSFNALLKTLEEP----------PQHIKFILATTDVE---KIPKTILSRCLQFKLKIISEEKIFNF  186 (363)
T ss_pred             eEEEEEChhhcCHHHHHHHHHHHhcC----------CCCeEEEEEcCChH---hhhHHHHhhceEEeCCCCCHHHHHHH
Confidence            79999999887655677776666542          44566777765432   22222 11125678888887776443

>PLN03025 replication factor C subunit; Provisional

Probab=97.91  E-value=6.5e-05  Score=68.53  Aligned_cols=120  Identities=16%  Similarity=0.159  Sum_probs=67.3

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCC-ceEEEEeCCCCCHHHHHHHHHHhhcC------CCceEEEEEeCCCCCCccCH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFD-KRIWVCVSDPFDEFRIAKAIIEGLEG------SEKKFFLILDDVWTDDYSKW  199 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~~~~------~~kr~LiVlDdv~~~~~~~w  199 (297)
                      ++|++|+||||+|+.+.+.- ....|. ..+-++.+...+.. ..++++..+..      .++.-+++||++.....+..
T Consensus        39 l~Gp~G~GKTtla~~la~~l-~~~~~~~~~~eln~sd~~~~~-~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~aq  116 (319)
T PLN03025         39 LSGPPGTGKTTSILALAHEL-LGPNYKEAVLELNASDDRGID-VVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQ  116 (319)
T ss_pred             EECCCCCCHHHHHHHHHHHH-hcccCccceeeecccccccHH-HHHHHHHHHHhccccCCCCCeEEEEEechhhcCHHHH
Confidence            78999999999999988731 122232 12223334433333 23333322111      14677999999988754455


Q ss_pred             HHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhhhh
Q 043781          200 EPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       200 ~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf~~  261 (297)
                      +.|...+...          .+.+++|+++..... ...+-...   .++++..++..++..|
T Consensus       117 ~aL~~~lE~~----------~~~t~~il~~n~~~~i~~~L~SRc---~~i~f~~l~~~~l~~~  166 (319)
T PLN03025        117 QALRRTMEIY----------SNTTRFALACNTSSKIIEPIQSRC---AIVRFSRLSDQEILGR  166 (319)
T ss_pred             HHHHHHHhcc----------cCCceEEEEeCCccccchhHHHhh---hcccCCCCCHHHHHHH
Confidence            5566555432          455677777653321 12222221   4678888877776443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.90  E-value=4.9e-05  Score=73.44  Aligned_cols=122  Identities=16%  Similarity=0.109  Sum_probs=71.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCC------------------ceEEEEeCCCCCHHHHHHHHHHhhcC---CCceE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFD------------------KRIWVCVSDPFDEFRIAKAIIEGLEG---SEKKF  184 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~------------------~~~wv~vs~~~~~~~~~~~i~~~~~~---~~kr~  184 (297)
                      -++|++|+||||+|+.+.+.-...+.+.                  -..++..+....+.. .+++.+.+..   .+++-
T Consensus        40 Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~h~dv~el~~~~~~~vd~-iR~l~~~~~~~p~~~~~k  118 (504)
T PRK14963         40 LFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVED-VRDLREKVLLAPLRGGRK  118 (504)
T ss_pred             EEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCCCCceEEecccccCCHHH-HHHHHHHHhhccccCCCe
Confidence            4789999999999999987432222221                  133444443444433 3444443332   15677


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhh-CCCccccCCccchhhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTL-GLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~-~~~~~~~l~~l~~~~lf~~  261 (297)
                      ++|||+++......++.|...+...          .....+|++|...   ..+.... .-...+.+..++..++..|
T Consensus       119 VVIIDEad~ls~~a~naLLk~LEep----------~~~t~~Il~t~~~---~kl~~~I~SRc~~~~f~~ls~~el~~~  183 (504)
T PRK14963        119 VYILDEAHMMSKSAFNALLKTLEEP----------PEHVIFILATTEP---EKMPPTILSRTQHFRFRRLTEEEIAGK  183 (504)
T ss_pred             EEEEECccccCHHHHHHHHHHHHhC----------CCCEEEEEEcCCh---hhCChHHhcceEEEEecCCCHHHHHHH
Confidence            9999999877655677777777542          3445556665432   2222111 1125678888888776554

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=97.90  E-value=3.5e-05  Score=71.41  Aligned_cols=70  Identities=14%  Similarity=0.224  Sum_probs=48.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccc-cCC---CceEEEEeCCCCCHHHHHHHHHHhhc---C------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI-ENF---DKRIWVCVSDPFDEFRIAKAIIEGLE---G------------------  179 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~-~~F---~~~~wv~vs~~~~~~~~~~~i~~~~~---~------------------  179 (297)
                      .-|+|++|+|||++++.+++.-.-. ...   -..+|++.....+...++..|++++.   .                  
T Consensus        43 i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~  122 (365)
T TIGR02928        43 VFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYK  122 (365)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHH
Confidence            3488999999999999999842110 111   13457776665666677777777662   1                  


Q ss_pred             ----CCceEEEEEeCCCCC
Q 043781          180 ----SEKKFFLILDDVWTD  194 (297)
Q Consensus       180 ----~~kr~LiVlDdv~~~  194 (297)
                          .+++++||||+++.-
T Consensus       123 ~l~~~~~~~vlvIDE~d~L  141 (365)
T TIGR02928       123 ELNERGDSLIIVLDEIDYL  141 (365)
T ss_pred             HHHhcCCeEEEEECchhhh
Confidence                156789999999876

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.

>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=97.89  E-value=3.2e-05  Score=60.38  Aligned_cols=64  Identities=23%  Similarity=0.110  Sum_probs=43.0

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC-----CCHHHHHHHHHHhhcCCCceEEEEEeCCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP-----FDEFRIAKAIIEGLEGSEKKFFLILDDVWTDD  195 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~  195 (297)
                      |+|++|+|||++|+.+.+.  ...+   .+.+..+.-     .+..+.+..++.+.....++.+|+|||+....
T Consensus         3 l~G~~G~GKT~l~~~la~~--l~~~---~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~   71 (132)
T PF00004_consen    3 LHGPPGTGKTTLARALAQY--LGFP---FIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLF   71 (132)
T ss_dssp             EESSTTSSHHHHHHHHHHH--TTSE---EEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTS
T ss_pred             EECcCCCCeeHHHHHHHhh--cccc---cccccccccccccccccccccccccccccccccceeeeeccchhcc
Confidence            6899999999999999995  3322   244443221     23455666666665442347999999998753

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 ....

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.87  E-value=7.2e-05  Score=71.70  Aligned_cols=120  Identities=17%  Similarity=0.097  Sum_probs=67.2

Q ss_pred             ccccCCcchHHHHHHHhccccccc-------------------CCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIE-------------------NFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~-------------------~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|++|+||||+|+.+.+.-....                   .+.....+..+...++.++ ++|.+.....   +++-
T Consensus        41 f~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~g~~~dv~el~aa~~~gid~i-R~i~~~~~~~p~~~~~k  119 (472)
T PRK14962         41 FAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVIELDAASNRGIDEI-RKIRDAVGYRPMEGKYK  119 (472)
T ss_pred             EECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhcCCCCccEEEeCcccCCHHHH-HHHHHHHhhChhcCCeE
Confidence            789999999999999977421110                   0112334444444445443 3455444322   6777


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      ++|+|++.....+..+.|...+...          .....+|++|.... +...+..+   ..++.+.+++..++..
T Consensus       120 VvIIDE~h~Lt~~a~~~LLk~LE~p----------~~~vv~Ilattn~~kl~~~L~SR---~~vv~f~~l~~~el~~  183 (472)
T PRK14962        120 VYIIDEVHMLTKEAFNALLKTLEEP----------PSHVVFVLATTNLEKVPPTIISR---CQVIEFRNISDELIIK  183 (472)
T ss_pred             EEEEEChHHhHHHHHHHHHHHHHhC----------CCcEEEEEEeCChHhhhHHHhcC---cEEEEECCccHHHHHH
Confidence            9999999765444556666666541          23344444554332 22222222   2577788887776644

>PRK06620 hypothetical protein; Validated

Probab=97.87  E-value=3.8e-05  Score=66.03  Aligned_cols=102  Identities=19%  Similarity=0.151  Sum_probs=58.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-|||++|+|||+|++.+.+...  .     .++.  ..+...    +.+      ...-++++||+....  . ..+-.
T Consensus        47 l~l~Gp~G~GKThLl~a~~~~~~--~-----~~~~--~~~~~~----~~~------~~~d~lliDdi~~~~--~-~~lf~  104 (214)
T PRK06620         47 LLIKGPSSSGKTYLTKIWQNLSN--A-----YIIK--DIFFNE----EIL------EKYNAFIIEDIENWQ--E-PALLH  104 (214)
T ss_pred             EEEECCCCCCHHHHHHHHHhccC--C-----EEcc--hhhhch----hHH------hcCCEEEEeccccch--H-HHHHH
Confidence            45899999999999999887432  1     1221  111111    111      134578999996321  0 12322


Q ss_pred             HHhhhhhhhceeeecCCCCeEEEEeccHHHH---HHHHHhhCCCccccCCccchhh
Q 043781          205 CLMRVLQEFAAIEVDGDENPLSLTSTCQEKL---RHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       205 ~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~---~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      .+...         ..+|..||+|++.+...   ..+..++...-++.+++++.++
T Consensus       105 l~N~~---------~e~g~~ilits~~~p~~l~l~~L~SRl~~gl~~~l~~pd~~~  151 (214)
T PRK06620        105 IFNII---------NEKQKYLLLTSSDKSRNFTLPDLSSRIKSVLSILLNSPDDEL  151 (214)
T ss_pred             HHHHH---------HhcCCEEEEEcCCCccccchHHHHHHHhCCceEeeCCCCHHH
Confidence            22221         15677899998755332   3455555544577888887655

>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=97.86  E-value=3.2e-05  Score=66.26  Aligned_cols=75  Identities=23%  Similarity=0.201  Sum_probs=44.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNC  205 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~~  205 (297)
                      =+||++|+||||||..+.+  +....|.   +++.+.--...+ +..++.++   +++-+|.+|.++.-+..+-+.|-+.
T Consensus        54 lf~GPPG~GKTTLA~IIA~--e~~~~~~---~~sg~~i~k~~d-l~~il~~l---~~~~ILFIDEIHRlnk~~qe~Llpa  124 (233)
T PF05496_consen   54 LFYGPPGLGKTTLARIIAN--ELGVNFK---ITSGPAIEKAGD-LAAILTNL---KEGDILFIDEIHRLNKAQQEILLPA  124 (233)
T ss_dssp             EEESSTTSSHHHHHHHHHH--HCT--EE---EEECCC--SCHH-HHHHHHT-----TT-EEEECTCCC--HHHHHHHHHH
T ss_pred             EEECCCccchhHHHHHHHh--ccCCCeE---eccchhhhhHHH-HHHHHHhc---CCCcEEEEechhhccHHHHHHHHHH
Confidence            4789999999999999999  4555552   333221112222 33445555   3567899999998876556666666


Q ss_pred             Hhhh
Q 043781          206 LMRV  209 (297)
Q Consensus       206 l~~~  209 (297)
                      +.++
T Consensus       125 mEd~  128 (233)
T PF05496_consen  125 MEDG  128 (233)
T ss_dssp             HHCS
T ss_pred             hccC
Confidence            6553

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.

>PRK09087 hypothetical protein; Validated

Probab=97.82  E-value=6.6e-05  Score=65.10  Aligned_cols=106  Identities=17%  Similarity=0.112  Sum_probs=62.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-|||..|+|||+|++.+++...       ..+++.      ..+..+++..+.    .-+|+|||+.... ..-+.+-.
T Consensus        47 l~l~G~~GsGKThLl~~~~~~~~-------~~~i~~------~~~~~~~~~~~~----~~~l~iDDi~~~~-~~~~~lf~  108 (226)
T PRK09087         47 VVLAGPVGSGKTHLASIWREKSD-------ALLIHP------NEIGSDAANAAA----EGPVLIEDIDAGG-FDETGLFH  108 (226)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcC-------CEEecH------HHcchHHHHhhh----cCeEEEECCCCCC-CCHHHHHH
Confidence            46999999999999999887421       124432      233333333332    2378889996542 11223333


Q ss_pred             HHhhhhhhhceeeecCCCCeEEEEeccHHH-----HHHHHHhhCCCccccCCccchhh
Q 043781          205 CLMRVLQEFAAIEVDGDENPLSLTSTCQEK-----LRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       205 ~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-----~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      .+...         ...|..||+|++.+..     ...+...+....++.+++++.++
T Consensus       109 l~n~~---------~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~  157 (226)
T PRK09087        109 LINSV---------RQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDAL  157 (226)
T ss_pred             HHHHH---------HhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHH
Confidence            33322         2567889999874322     23344555555677888887655

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=97.82  E-value=9e-05  Score=67.78  Aligned_cols=94  Identities=13%  Similarity=0.110  Sum_probs=52.6

Q ss_pred             cccccCCcchHHHHHHHhcccccc-cCCC-ceEEEEeCCC-----------C--------------CHHHHHHHHHHhhc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVI-ENFD-KRIWVCVSDP-----------F--------------DEFRIAKAIIEGLE  178 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~-~~F~-~~~wv~vs~~-----------~--------------~~~~~~~~i~~~~~  178 (297)
                      -++|++|+||||+|+.+.+.  +. ..+. ..+.++++..           +              ...+.++.++....
T Consensus        40 ll~Gp~GtGKT~la~~~~~~--l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  117 (337)
T PRK12402         40 LVQGPPGSGKTAAVRALARE--LYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYA  117 (337)
T ss_pred             EEECCCCCCHHHHHHHHHHH--hcCcccccceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHH
Confidence            47899999999999998873  32 1222 1234443321           0              01233444433321


Q ss_pred             C----CCceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          179 G----SEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       179 ~----~~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      .    .+.+-+|||||+..........|...+...          .+.+++|+||..
T Consensus       118 ~~~~~~~~~~vlilDe~~~l~~~~~~~L~~~le~~----------~~~~~~Il~~~~  164 (337)
T PRK12402        118 SYRPLSADYKTILLDNAEALREDAQQALRRIMEQY----------SRTCRFIIATRQ  164 (337)
T ss_pred             hcCCCCCCCcEEEEeCcccCCHHHHHHHHHHHHhc----------cCCCeEEEEeCC
Confidence            1    134558999999766433445565555432          445778888754

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.81  E-value=7.3e-05  Score=75.62  Aligned_cols=119  Identities=16%  Similarity=0.180  Sum_probs=71.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccC-------------------CCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIEN-------------------FDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~-------------------F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|..|+||||+|+.+.+.-.....                   |.-.+++..+....+.. +++|.+.+...   +++-
T Consensus        43 FtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~DviEidAas~~kVDd-IReLie~v~~~P~~gk~K  121 (944)
T PRK14949         43 FTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIAQGRFVDLIEVDAASRTKVDD-TRELLDNVQYRPSRGRFK  121 (944)
T ss_pred             EECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHhcCCCceEEEeccccccCHHH-HHHHHHHHHhhhhcCCcE
Confidence            7899999999999999974211111                   11123443332333333 35555544322   6788


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIW  259 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf  259 (297)
                      ++|||++.....+.++.|...+..-          ....++|++|..... ...+..+   ...+++..++..++.
T Consensus       122 ViIIDEAh~LT~eAqNALLKtLEEP----------P~~vrFILaTTe~~kLl~TIlSR---Cq~f~fkpLs~eEI~  184 (944)
T PRK14949        122 VYLIDEVHMLSRSSFNALLKTLEEP----------PEHVKFLLATTDPQKLPVTVLSR---CLQFNLKSLTQDEIG  184 (944)
T ss_pred             EEEEechHhcCHHHHHHHHHHHhcc----------CCCeEEEEECCCchhchHHHHHh---heEEeCCCCCHHHHH
Confidence            9999999988767888887777542          345566666554322 2122111   256788888766653

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.79  E-value=0.00012  Score=72.96  Aligned_cols=119  Identities=17%  Similarity=0.159  Sum_probs=72.5

Q ss_pred             ccccCCcchHHHHHHHhcccccc-------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI-------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~-------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|..|+||||+|+.+.+.-...                   ..|.-.+++..+.+..+.+ ++++++.....   ++.-
T Consensus        43 FtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~G~h~DviEIDAas~rgVDd-IReLIe~a~~~P~~gr~K  121 (830)
T PRK07003         43 FTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDEGRFVDYVEMDAASNRGVDE-MAALLERAVYAPVDARFK  121 (830)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhcCCCceEEEecccccccHHH-HHHHHHHHHhccccCCce
Confidence            77999999999998777632111                   1232345555554444444 33444443322   4556


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccchhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFDAKKIW  259 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~~~~lf  259 (297)
                      ++|||++.......|+.|...|..-          ....++|+||+...   .+..+ ..-...+++..++..++.
T Consensus       122 VIIIDEah~LT~~A~NALLKtLEEP----------P~~v~FILaTtd~~---KIp~TIrSRCq~f~Fk~Ls~eeIv  184 (830)
T PRK07003        122 VYMIDEVHMLTNHAFNAMLKTLEEP----------PPHVKFILATTDPQ---KIPVTVLSRCLQFNLKQMPAGHIV  184 (830)
T ss_pred             EEEEeChhhCCHHHHHHHHHHHHhc----------CCCeEEEEEECChh---hccchhhhheEEEecCCcCHHHHH
Confidence            8889999988666788887777552          45677777776543   22211 111256788888776654

>PRK12377 putative replication protein; Provisional

Probab=97.79  E-value=9.2e-05  Score=65.01  Aligned_cols=89  Identities=20%  Similarity=0.220  Sum_probs=53.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC----------CceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS----------EKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~----------~kr~LiVlDdv~~~  194 (297)
                      .-++|.+|+|||+||..+.+.  +....-.+++++++      +++..|-......          .+-=||||||+-..
T Consensus       104 l~l~G~~GtGKThLa~AIa~~--l~~~g~~v~~i~~~------~l~~~l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~  175 (248)
T PRK12377        104 FVFSGKPGTGKNHLAAAIGNR--LLAKGRSVIVVTVP------DVMSRLHESYDNGQSGEKFLQELCKVDLLVLDEIGIQ  175 (248)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEHH------HHHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            347899999999999999994  43333345666543      3333332221100          45679999999665


Q ss_pred             CccCHHH--HHHHHhhhhhhhceeeecCCCCeEEEEec
Q 043781          195 DYSKWEP--FHNCLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       195 ~~~~w~~--l~~~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      ....|..  |-..+..-         -++.-.+||||.
T Consensus       176 ~~s~~~~~~l~~ii~~R---------~~~~~ptiitSN  204 (248)
T PRK12377        176 RETKNEQVVLNQIIDRR---------TASMRSVGMLTN  204 (248)
T ss_pred             CCCHHHHHHHHHHHHHH---------HhcCCCEEEEcC
Confidence            4456653  33333221         144456788875

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.77  E-value=0.00015  Score=71.29  Aligned_cols=120  Identities=13%  Similarity=0.142  Sum_probs=71.9

Q ss_pred             ccccCCcchHHHHHHHhcccccc-------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI-------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~-------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|+.|+||||+|+.+.+.-...                   ..|.-.+.+..+.+..+.++ ++++..+...   +++-
T Consensus        42 F~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~g~hpDviEIDAAs~~~VddI-Reli~~~~y~P~~gk~K  120 (702)
T PRK14960         42 FTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDT-RELLDNVPYAPTQGRFK  120 (702)
T ss_pred             EECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhcCCCCceEEecccccCCHHHH-HHHHHHHhhhhhcCCcE
Confidence            67999999999999887632110                   12222344444444455443 4455544322   5677


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      ++|+|++.......++.|...+..-          .++..+|++|..... ...+.   .-...+.+..++..++..
T Consensus       121 V~IIDEVh~LS~~A~NALLKtLEEP----------P~~v~FILaTtd~~kIp~TIl---SRCq~feFkpLs~eEI~k  184 (702)
T PRK14960        121 VYLIDEVHMLSTHSFNALLKTLEEP----------PEHVKFLFATTDPQKLPITVI---SRCLQFTLRPLAVDEITK  184 (702)
T ss_pred             EEEEechHhcCHHHHHHHHHHHhcC----------CCCcEEEEEECChHhhhHHHH---HhhheeeccCCCHHHHHH
Confidence            8999999987656777777777542          455677777764322 11221   112567788887666543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.75  E-value=0.00013  Score=75.55  Aligned_cols=91  Identities=20%  Similarity=0.199  Sum_probs=60.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHhhc-------------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEGLE-------------------------  178 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~-------------------------  178 (297)
                      .-|.|++|.|||||+......      ++..+|+++.... +...++..++..+.                         
T Consensus        35 ~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  108 (903)
T PRK04841         35 VLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSL  108 (903)
T ss_pred             EEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHH
Confidence            457899999999999988752      2368899886443 44444444444442                         


Q ss_pred             ---------CCCceEEEEEeCCCCCCccCHH-HHHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          179 ---------GSEKKFFLILDDVWTDDYSKWE-PFHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       179 ---------~~~kr~LiVlDdv~~~~~~~w~-~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                               ..+.+++|||||+...+..... .+...++..          ..+..+|||||.
T Consensus       109 ~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~~~~l~~l~~~~----------~~~~~lv~~sR~  161 (903)
T PRK04841        109 FAQLFIELADWHQPLYLVIDDYHLITNPEIHEAMRFFLRHQ----------PENLTLVVLSRN  161 (903)
T ss_pred             HHHHHHHHhcCCCCEEEEEeCcCcCCChHHHHHHHHHHHhC----------CCCeEEEEEeCC
Confidence                     1157899999999876433333 444444432          556788899996

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.75  E-value=0.00016  Score=68.95  Aligned_cols=116  Identities=17%  Similarity=0.208  Sum_probs=64.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      .-|+|..|+|||+|++.+.+.  +...--..++++      ...+...+...+...         .+.-+|++||+....
T Consensus       144 l~L~G~~G~GKTHLl~Ai~~~--l~~~~~~v~yi~------~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~  215 (445)
T PRK12422        144 IYLFGPEGSGKTHLMQAAVHA--LRESGGKILYVR------SELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFS  215 (445)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH--HHHcCCCEEEee------HHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhc
Confidence            458999999999999999984  332222344553      233333333333221         234589999997653


Q ss_pred             ccCH--HHHHHHHhhhhhhhceeeecCCCCeEEEEecc-HHH----HHHHHHhhCCCccccCCccchhh
Q 043781          196 YSKW--EPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC-QEK----LRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       196 ~~~w--~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~-~~~----~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ...|  +.+...+...         ...|..||+||.. +..    ...+...+...-++++.+++.++
T Consensus       216 ~k~~~qeelf~l~N~l---------~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~  275 (445)
T PRK12422        216 GKGATQEEFFHTFNSL---------HTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEG  275 (445)
T ss_pred             CChhhHHHHHHHHHHH---------HHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHH
Confidence            2222  2233333221         1345678888854 222    23444455434566777776555

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.71  E-value=4.3e-05  Score=71.02  Aligned_cols=67  Identities=18%  Similarity=0.196  Sum_probs=38.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEe-CCCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV-SDPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v-s~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+++  ....+|-....... .... .....++.++..... ....+|+||+++..
T Consensus       159 vLL~GppGtGKT~lakaia~--~l~~~~~~v~~~~l~~~~~g~~~~~i~~~f~~a~~-~~p~il~iDEiD~l  227 (364)
T TIGR01242       159 VLLYGPPGTGKTLLAKAVAH--ETNATFIRVVGSELVRKYIGEGARLVREIFELAKE-KAPSIIFIDEIDAI  227 (364)
T ss_pred             EEEECCCCCCHHHHHHHHHH--hCCCCEEecchHHHHHHhhhHHHHHHHHHHHHHHh-cCCcEEEhhhhhhh
Confidence            45789999999999999998  34444411110000 0000 112233444433322 46789999999753

Many proteins may score above the trusted cutoff because an internal

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=97.71  E-value=8.9e-05  Score=67.01  Aligned_cols=73  Identities=23%  Similarity=0.165  Sum_probs=41.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-++|++|+|||+||+.+.+.  ....|   ..+..+....... +...+..+   +...+|++|++........+.+..
T Consensus        33 ~ll~Gp~G~GKT~la~~ia~~--~~~~~---~~~~~~~~~~~~~-l~~~l~~~---~~~~vl~iDEi~~l~~~~~e~l~~  103 (305)
T TIGR00635        33 LLLYGPPGLGKTTLAHIIANE--MGVNL---KITSGPALEKPGD-LAAILTNL---EEGDVLFIDEIHRLSPAVEELLYP  103 (305)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCCCE---EEeccchhcCchh-HHHHHHhc---ccCCEEEEehHhhhCHHHHHHhhH
Confidence            348899999999999999984  33222   1222221112222 23333444   356799999998764333344444


Q ss_pred             HH
Q 043781          205 CL  206 (297)
Q Consensus       205 ~l  206 (297)
                      .+
T Consensus       104 ~~  105 (305)
T TIGR00635       104 AM  105 (305)
T ss_pred             HH
Confidence            44

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.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.71  E-value=0.00028  Score=67.70  Aligned_cols=121  Identities=18%  Similarity=0.118  Sum_probs=73.0

Q ss_pred             ccccCCcchHHHHHHHhccc------------------ccc-cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDK------------------DVI-ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~------------------~~~-~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|+.|+||||+|+.+.+.-                  .+. ..+.-.+.+..+...++.+ .++|++.....   +++=
T Consensus        40 f~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~~~~~Dv~eidaas~~~vdd-IR~Iie~~~~~P~~~~~K  118 (491)
T PRK14964         40 LVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVDD-IKVILENSCYLPISSKFK  118 (491)
T ss_pred             EECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhccCCCCEEEEecccCCCHHH-HHHHHHHHHhccccCCce
Confidence            67999999999998887620                  011 1222344566665556655 34455544322   6777


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf~~  261 (297)
                      ++|+|++.....+.++.|...+..-          .+...+|++|.... +...+-..   ...+.+..++..++..|
T Consensus       119 VvIIDEah~Ls~~A~NaLLK~LEeP----------p~~v~fIlatte~~Kl~~tI~SR---c~~~~f~~l~~~el~~~  183 (491)
T PRK14964        119 VYIIDEVHMLSNSAFNALLKTLEEP----------APHVKFILATTEVKKIPVTIISR---CQRFDLQKIPTDKLVEH  183 (491)
T ss_pred             EEEEeChHhCCHHHHHHHHHHHhCC----------CCCeEEEEEeCChHHHHHHHHHh---heeeecccccHHHHHHH
Confidence            8999999877555677777777542          45566776664322 22222222   25678888887776544

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.70  E-value=0.00022  Score=67.06  Aligned_cols=119  Identities=14%  Similarity=0.142  Sum_probs=67.7

Q ss_pred             ccccCCcchHHHHHHHhccccccc----------------------------CCCceEEEEeCCCCCHHHHHHHHHHhhc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIE----------------------------NFDKRIWVCVSDPFDEFRIAKAIIEGLE  178 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~----------------------------~F~~~~wv~vs~~~~~~~~~~~i~~~~~  178 (297)
                      ++|++|+||||+|+.+.+.-.-..                            +++.. .+..+....+.++ +++.+.+.
T Consensus        43 f~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c~~c~~~~~~~~~n~~-~~~~~~~~~id~I-r~l~~~~~  120 (397)
T PRK14955         43 FSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGECESCRDFDAGTSLNIS-EFDAASNNSVDDI-RLLRENVR  120 (397)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCCHHHHHHhcCCCCCeE-eecccccCCHHHH-HHHHHHHh
Confidence            689999999999988876321111                            22221 1222222334443 34555553


Q ss_pred             CC---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEecc-HHHHHHHHHhhCCCccccCCccc
Q 043781          179 GS---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC-QEKLRHLTLTLGLRAKFPVSIFD  254 (297)
Q Consensus       179 ~~---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~-~~~~~~v~~~~~~~~~~~l~~l~  254 (297)
                      ..   +++-++|+|++.......++.|...+..-          .+.+.+|++|.. ......+....   .++++.+++
T Consensus       121 ~~p~~~~~kvvIIdea~~l~~~~~~~LLk~LEep----------~~~t~~Il~t~~~~kl~~tl~sR~---~~v~f~~l~  187 (397)
T PRK14955        121 YGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEP----------PPHAIFIFATTELHKIPATIASRC---QRFNFKRIP  187 (397)
T ss_pred             hchhcCCeEEEEEeChhhCCHHHHHHHHHHHhcC----------CCCeEEEEEeCChHHhHHHHHHHH---HHhhcCCCC
Confidence            22   66778999999887555788887777642          445666655532 22222222221   456777777


Q ss_pred             hhhhhh
Q 043781          255 AKKIWG  260 (297)
Q Consensus       255 ~~~lf~  260 (297)
                      ..++..
T Consensus       188 ~~ei~~  193 (397)
T PRK14955        188 LEEIQQ  193 (397)
T ss_pred             HHHHHH
Confidence            766644

>PRK08181 transposase; Validated

Probab=97.69  E-value=0.00012  Score=64.98  Aligned_cols=90  Identities=19%  Similarity=0.087  Sum_probs=51.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      .-++|.+|+|||.||..+.+.  .....-.++|+.+      .+++..+.......         .+-=||||||+-...
T Consensus       109 lll~Gp~GtGKTHLa~Aia~~--a~~~g~~v~f~~~------~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~~  180 (269)
T PRK08181        109 LLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTRT------TDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYVT  180 (269)
T ss_pred             EEEEecCCCcHHHHHHHHHHH--HHHcCCceeeeeH------HHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEecccccc
Confidence            458899999999999999873  3333333455543      34444332221111         345699999997654


Q ss_pred             ccCHH--HHHHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          196 YSKWE--PFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       196 ~~~w~--~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      .+.|.  .|-..+...         -++ ..+||||...
T Consensus       181 ~~~~~~~~Lf~lin~R---------~~~-~s~IiTSN~~  209 (269)
T PRK08181        181 KDQAETSVLFELISAR---------YER-RSILITANQP  209 (269)
T ss_pred             CCHHHHHHHHHHHHHH---------HhC-CCEEEEcCCC
Confidence            33443  233333221         133 4688888643

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.69  E-value=0.00016  Score=71.06  Aligned_cols=121  Identities=13%  Similarity=0.117  Sum_probs=71.5

Q ss_pred             ccccCCcchHHHHHHHhcccccc------------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC--
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI------------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS--  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~------------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--  180 (297)
                      ++|..|+||||+|+.+.+.-.-.                        ..|.-.+++..+.+.++.++ ++|++.+...  
T Consensus        43 FtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas~~gVDdI-ReLie~~~~~P~  121 (700)
T PRK12323         43 FTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGRFVDYIEMDAASNRGVDEM-AQLLDKAVYAPT  121 (700)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHHHHHHcCCCCcceEecccccCCHHHH-HHHHHHHHhchh
Confidence            67999999999998887632110                        11222345555544455443 3444444322  


Q ss_pred             -CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH-HHHHHHHHhhCCCccccCCccchhhh
Q 043781          181 -EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-EKLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       181 -~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-~~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                       ++.-++|||++.......++.|...|..-          .....+|++|... .+...+...   ...+.+..++..++
T Consensus       122 ~gr~KViIIDEah~Ls~~AaNALLKTLEEP----------P~~v~FILaTtep~kLlpTIrSR---Cq~f~f~~ls~eei  188 (700)
T PRK12323        122 AGRFKVYMIDEVHMLTNHAFNAMLKTLEEP----------PEHVKFILATTDPQKIPVTVLSR---CLQFNLKQMPPGHI  188 (700)
T ss_pred             cCCceEEEEEChHhcCHHHHHHHHHhhccC----------CCCceEEEEeCChHhhhhHHHHH---HHhcccCCCChHHH
Confidence             67779999999988766777776666431          3455655555433 222222222   25678888877766


Q ss_pred             hhh
Q 043781          259 WGW  261 (297)
Q Consensus       259 f~~  261 (297)
                      ..|
T Consensus       189 ~~~  191 (700)
T PRK12323        189 VSH  191 (700)
T ss_pred             HHH
Confidence            544

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.65  E-value=0.00026  Score=68.52  Aligned_cols=120  Identities=13%  Similarity=0.120  Sum_probs=73.1

Q ss_pred             ccccCCcchHHHHHHHhcccccc-------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI-------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~-------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|+.|+||||+|+.+.+.-.-.                   ..|.-.+.+..+....+.++ +++++.+...   ++.-
T Consensus        43 f~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~g~~~d~~eidaas~~~v~~i-R~l~~~~~~~p~~~~~k  121 (509)
T PRK14958         43 FTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDT-RELLDNIPYAPTKGRFK  121 (509)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhcCCCceEEEEcccccCCHHHH-HHHHHHHhhccccCCcE
Confidence            67999999999998888732111                   12222445555555566664 4566655432   6777


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      ++|+|++.....+.++.|...+..-          ...+++|++|.... ....+...   ...+.+..++..++..
T Consensus       122 V~iIDE~~~ls~~a~naLLk~LEep----------p~~~~fIlattd~~kl~~tI~SR---c~~~~f~~l~~~~i~~  185 (509)
T PRK14958        122 VYLIDEVHMLSGHSFNALLKTLEEP----------PSHVKFILATTDHHKLPVTVLSR---CLQFHLAQLPPLQIAA  185 (509)
T ss_pred             EEEEEChHhcCHHHHHHHHHHHhcc----------CCCeEEEEEECChHhchHHHHHH---hhhhhcCCCCHHHHHH
Confidence            8999999987666777777777542          34566666654332 12122221   2456777777666544

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=97.63  E-value=0.00019  Score=65.74  Aligned_cols=73  Identities=23%  Similarity=0.194  Sum_probs=42.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-++|++|+|||+||+.+.+.  ....+   .++..+ .......+..++..+   ++.-+|++|++........+.+..
T Consensus        54 ~ll~GppG~GKT~la~~ia~~--l~~~~---~~~~~~-~~~~~~~l~~~l~~l---~~~~vl~IDEi~~l~~~~~e~l~~  124 (328)
T PRK00080         54 VLLYGPPGLGKTTLANIIANE--MGVNI---RITSGP-ALEKPGDLAAILTNL---EEGDVLFIDEIHRLSPVVEEILYP  124 (328)
T ss_pred             EEEECCCCccHHHHHHHHHHH--hCCCe---EEEecc-cccChHHHHHHHHhc---ccCCEEEEecHhhcchHHHHHHHH
Confidence            348999999999999999984  33222   122221 122223344455544   356699999998754333334444


Q ss_pred             HH
Q 043781          205 CL  206 (297)
Q Consensus       205 ~l  206 (297)
                      .+
T Consensus       125 ~~  126 (328)
T PRK00080        125 AM  126 (328)
T ss_pred             HH
Confidence            33

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=97.62  E-value=0.00028  Score=66.10  Aligned_cols=121  Identities=9%  Similarity=-0.015  Sum_probs=69.3

Q ss_pred             cccccCCcchHHHHHHHhccccc-------------------ccCCCceEEEE-eCCCCCHHHHHHHHHHhhcCC---Cc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDV-------------------IENFDKRIWVC-VSDPFDEFRIAKAIIEGLEGS---EK  182 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~-------------------~~~F~~~~wv~-vs~~~~~~~~~~~i~~~~~~~---~k  182 (297)
                      =++|++|+|||++|+.+.+.-.-                   ..|.|.. ++. -.....+.+ .+++.+.+...   ++
T Consensus        40 Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~~hpD~~-~i~~~~~~i~i~~-iR~l~~~~~~~p~~~~  117 (394)
T PRK07940         40 LFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAGTHPDVR-VVAPEGLSIGVDE-VRELVTIAARRPSTGR  117 (394)
T ss_pred             EEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEE-EeccccccCCHHH-HHHHHHHHHhCcccCC
Confidence            37899999999999888652111                   1122222 232 223344444 33555544322   56


Q ss_pred             eEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCccccCCccchhhhhhh
Q 043781          183 KFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       183 r~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~l~~l~~~~lf~~  261 (297)
                      +-++|+|++........+.|...+..-          .++..+|++|.+.+   .+..+.- -...+++..++.+++..|
T Consensus       118 ~kViiIDead~m~~~aanaLLk~LEep----------~~~~~fIL~a~~~~---~llpTIrSRc~~i~f~~~~~~~i~~~  184 (394)
T PRK07940        118 WRIVVIEDADRLTERAANALLKAVEEP----------PPRTVWLLCAPSPE---DVLPTIRSRCRHVALRTPSVEAVAEV  184 (394)
T ss_pred             cEEEEEechhhcCHHHHHHHHHHhhcC----------CCCCeEEEEECChH---HChHHHHhhCeEEECCCCCHHHHHHH
Confidence            668888999888656666666666432          45666777666532   2222211 125778888887775444

>PRK04195 replication factor C large subunit; Provisional

Probab=97.59  E-value=0.00041  Score=66.92  Aligned_cols=113  Identities=19%  Similarity=0.140  Sum_probs=61.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC----C-ceEEEEEeCCCCCCc---
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS----E-KKFFLILDDVWTDDY---  196 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~----~-kr~LiVlDdv~~~~~---  196 (297)
                      .-|+|++|+||||+|+.+++.  ..  |+ .+-++.+...+... +..++......    + ++-+||||++.....   
T Consensus        42 lLL~GppG~GKTtla~ala~e--l~--~~-~ielnasd~r~~~~-i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~~d  115 (482)
T PRK04195         42 LLLYGPPGVGKTSLAHALAND--YG--WE-VIELNASDQRTADV-IERVAGEAATSGSLFGARRKLILLDEVDGIHGNED  115 (482)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--cC--CC-EEEEcccccccHHH-HHHHHHHhhccCcccCCCCeEEEEecCcccccccc
Confidence            347899999999999999984  31  22 23334454433333 33333222211    3 688999999987532   


Q ss_pred             -cCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HH-HHHHhhCCCccccCCccchhhh
Q 043781          197 -SKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LR-HLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       197 -~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~-~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                       ..+..|...+.            ..+..||+|+..... .. .+.   .....+.+..++..++
T Consensus       116 ~~~~~aL~~~l~------------~~~~~iIli~n~~~~~~~k~Lr---sr~~~I~f~~~~~~~i  165 (482)
T PRK04195        116 RGGARAILELIK------------KAKQPIILTANDPYDPSLRELR---NACLMIEFKRLSTRSI  165 (482)
T ss_pred             hhHHHHHHHHHH------------cCCCCEEEeccCccccchhhHh---ccceEEEecCCCHHHH
Confidence             23445554443            344566776643211 11 111   1124556666665554

>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=97.58  E-value=0.00019  Score=61.99  Aligned_cols=116  Identities=19%  Similarity=0.198  Sum_probs=65.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCC-C-ceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENF-D-KRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F-~-~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~  193 (297)
                      .-|+|..|+|||.|.+.+++.  ..+.. . .+++++      ..++...+...+...         ..-=+|+|||+..
T Consensus        37 l~l~G~~G~GKTHLL~Ai~~~--~~~~~~~~~v~y~~------~~~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~  108 (219)
T PF00308_consen   37 LFLYGPSGLGKTHLLQAIANE--AQKQHPGKRVVYLS------AEEFIREFADALRDGEIEEFKDRLRSADLLIIDDIQF  108 (219)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH--HHHHCTTS-EEEEE------HHHHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGG
T ss_pred             eEEECCCCCCHHHHHHHHHHH--HHhccccccceeec------HHHHHHHHHHHHHcccchhhhhhhhcCCEEEEecchh
Confidence            458999999999999999994  43322 2 344553      445444444443221         4456899999987


Q ss_pred             CCcc-CHHH-HHHHHhhhhhhhceeeecCCCCeEEEEeccH-H----HHHHHHHhhCCCccccCCccchhh
Q 043781          194 DDYS-KWEP-FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-E----KLRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       194 ~~~~-~w~~-l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-~----~~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      .... .|+. +-..+...         ...|.+||+|+... .    ....+...+...-++++.+++.+.
T Consensus       109 l~~~~~~q~~lf~l~n~~---------~~~~k~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~  170 (219)
T PF00308_consen  109 LAGKQRTQEELFHLFNRL---------IESGKQLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDED  170 (219)
T ss_dssp             GTTHHHHHHHHHHHHHHH---------HHTTSEEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHH
T ss_pred             hcCchHHHHHHHHHHHHH---------HhhCCeEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHH
Confidence            5322 2333 33333222         15677999999532 1    234555665555667777776554

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.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.58  E-value=0.00031  Score=69.22  Aligned_cols=121  Identities=12%  Similarity=0.108  Sum_probs=70.5

Q ss_pred             ccccCCcchHHHHHHHhccccc------------------------ccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC--
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV------------------------IENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS--  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~------------------------~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--  180 (297)
                      ++|..|+||||+|+.+.+.-.-                        .+.+.-.+++..+....+.++ +++++.+...  
T Consensus        43 f~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~i-Reli~~~~~~p~  121 (618)
T PRK14951         43 FTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQACRDIDSGRFVDYTELDAASNRGVDEV-QQLLEQAVYKPV  121 (618)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHHHHHHcCCCCceeecCcccccCHHHH-HHHHHHHHhCcc
Confidence            6799999999999988542110                        011222344444444455443 4555554332  


Q ss_pred             -CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH-HHHHHHHHhhCCCccccCCccchhhh
Q 043781          181 -EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-EKLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       181 -~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-~~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                       ++.=++|||++.....+.++.|...+..-          .....+|++|... .+...+...   ...+.+..++.+++
T Consensus       122 ~g~~KV~IIDEvh~Ls~~a~NaLLKtLEEP----------P~~~~fIL~Ttd~~kil~TIlSR---c~~~~f~~Ls~eei  188 (618)
T PRK14951        122 QGRFKVFMIDEVHMLTNTAFNAMLKTLEEP----------PEYLKFVLATTDPQKVPVTVLSR---CLQFNLRPMAPETV  188 (618)
T ss_pred             cCCceEEEEEChhhCCHHHHHHHHHhcccC----------CCCeEEEEEECCchhhhHHHHHh---ceeeecCCCCHHHH
Confidence             56668999999988766777777666542          3445666665432 222222221   25678888877766


Q ss_pred             hhh
Q 043781          259 WGW  261 (297)
Q Consensus       259 f~~  261 (297)
                      ..|
T Consensus       189 ~~~  191 (618)
T PRK14951        189 LEH  191 (618)
T ss_pred             HHH
Confidence            443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.57  E-value=0.00051  Score=66.87  Aligned_cols=120  Identities=18%  Similarity=0.159  Sum_probs=69.2

Q ss_pred             ccccCCcchHHHHHHHhcccccc-------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI-------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~-------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|+.|+||||+|+.+.+.-...                   ..|.-.+++..+.+..+.+ ++++++.+...   +++-
T Consensus        43 f~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~~~d~~ei~~~~~~~vd~-ir~l~~~~~~~p~~~~~k  121 (527)
T PRK14969         43 FTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLIEVDAASNTQVDA-MRELLDNAQYAPTRGRFK  121 (527)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCceeEeeccccCCHHH-HHHHHHHHhhCcccCCce
Confidence            67999999999999887632111                   1122234454444444444 34555544332   6778


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      ++|+|++.....+..+.|...+..-          .....+|++|.+... ...+...   ...+++..++..++..
T Consensus       122 VvIIDEad~ls~~a~naLLK~LEep----------p~~~~fIL~t~d~~kil~tI~SR---c~~~~f~~l~~~~i~~  185 (527)
T PRK14969        122 VYIIDEVHMLSKSAFNAMLKTLEEP----------PEHVKFILATTDPQKIPVTVLSR---CLQFNLKQMPPPLIVS  185 (527)
T ss_pred             EEEEcCcccCCHHHHHHHHHHHhCC----------CCCEEEEEEeCChhhCchhHHHH---HHHHhcCCCCHHHHHH
Confidence            9999999877555666676666542          344556665543321 1111111   1566777777666543

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.56  E-value=0.00029  Score=67.26  Aligned_cols=116  Identities=23%  Similarity=0.249  Sum_probs=65.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCC--CceEEEEeCCCCCHHHHHHHHHHhhcCC-----------CceEEEEEeCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENF--DKRIWVCVSDPFDEFRIAKAIIEGLEGS-----------EKKFFLILDDV  191 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----------~kr~LiVlDdv  191 (297)
                      .-|+|..|+|||+|++.+.+.  +....  -.+++++      ..+++..+..++...           .+.-+|||||+
T Consensus       144 l~i~G~~G~GKTHLl~Ai~~~--l~~~~~~~~v~yv~------~~~f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDi  215 (450)
T PRK14087        144 LFIYGESGMGKTHLLKAAKNY--IESNFSDLKVSYMS------GDEFARKAVDILQKTHKEIEQFKNEICQNDVLIIDDV  215 (450)
T ss_pred             eEEECCCCCcHHHHHHHHHHH--HHHhCCCCeEEEEE------HHHHHHHHHHHHHHhhhHHHHHHHHhccCCEEEEecc
Confidence            347899999999999999983  33221  1233443      334444444433320           33448999999


Q ss_pred             CCCCc-cCH-HHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-H----HHHHHHhhCCCccccCCccchhh
Q 043781          192 WTDDY-SKW-EPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-K----LRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       192 ~~~~~-~~w-~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~----~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ..... ..| +.+...|...         ...|..||+|+..+. .    ..++...+...-+..+++++.++
T Consensus       216 q~l~~k~~~~e~lf~l~N~~---------~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~  279 (450)
T PRK14087        216 QFLSYKEKTNEIFFTIFNNF---------IENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKT  279 (450)
T ss_pred             ccccCCHHHHHHHHHHHHHH---------HHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHH
Confidence            76531 122 3344444332         145667888875431 1    23445555544566777776554

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=97.55  E-value=0.00031  Score=67.15  Aligned_cols=116  Identities=18%  Similarity=0.172  Sum_probs=63.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC--ceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD--KRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~  193 (297)
                      .-|+|.+|+|||+|++.+.+.  +...+.  ..++++.      .++...+...+...         .+--+|||||+..
T Consensus       151 l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~v~yi~~------~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~  222 (450)
T PRK00149        151 LFIYGGVGLGKTHLLHAIGNY--ILEKNPNAKVVYVTS------EKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQF  222 (450)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEEEH------HHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhh
Confidence            347899999999999999994  444432  2345543      22233332222211         2344899999976


Q ss_pred             CCccC-H-HHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-----HHHHHHHhhCCCccccCCccchhh
Q 043781          194 DDYSK-W-EPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-----KLRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       194 ~~~~~-w-~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-----~~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ..... + +.+-..|...         ...|..||+||....     ....+...+....++.+++.+.+.
T Consensus       223 l~~~~~~~~~l~~~~n~l---------~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~  284 (450)
T PRK00149        223 LAGKERTQEEFFHTFNAL---------HEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLET  284 (450)
T ss_pred             hcCCHHHHHHHHHHHHHH---------HHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHH
Confidence            42111 2 2333333221         145566888876431     123344555444567777777655

>PRK06921 hypothetical protein; Provisional

Probab=97.55  E-value=0.00022  Score=63.40  Aligned_cols=92  Identities=20%  Similarity=0.278  Sum_probs=51.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC-CCceEEEEeCCCCCH-HHH---HHHHHHhhcCCCceEEEEEeCCCC-----C
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN-FDKRIWVCVSDPFDE-FRI---AKAIIEGLEGSEKKFFLILDDVWT-----D  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~-F~~~~wv~vs~~~~~-~~~---~~~i~~~~~~~~kr~LiVlDdv~~-----~  194 (297)
                      .-++|.+|+|||+||..+.+.  +... --.+++++...-+.. ...   ..+.+..+   .+-=||||||+..     .
T Consensus       120 l~l~G~~G~GKThLa~aia~~--l~~~~g~~v~y~~~~~l~~~l~~~~~~~~~~~~~~---~~~dlLiIDDl~~~~~g~e  194 (266)
T PRK06921        120 IALLGQPGSGKTHLLTAAANE--LMRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRM---KKVEVLFIDDLFKPVNGKP  194 (266)
T ss_pred             EEEECCCCCcHHHHHHHHHHH--HhhhcCceEEEEEHHHHHHHHHHHHHHHHHHHHHh---cCCCEEEEeccccccCCCc
Confidence            347899999999999999984  4333 234556654321110 000   11122222   3566999999933     2


Q ss_pred             CccCHHH--HHHHHhhhhhhhceeeecCCCCeEEEEec
Q 043781          195 DYSKWEP--FHNCLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       195 ~~~~w~~--l~~~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      ....|..  |-..+...         ..++..+||||.
T Consensus       195 ~~t~~~~~~lf~iin~R---------~~~~k~tIitsn  223 (266)
T PRK06921        195 RATEWQIEQMYSVLNYR---------YLNHKPILISSE  223 (266)
T ss_pred             cCCHHHHHHHHHHHHHH---------HHCCCCEEEECC
Confidence            2235653  43333321         134567888886

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.53  E-value=0.0012  Score=65.45  Aligned_cols=24  Identities=33%  Similarity=0.422  Sum_probs=20.3

Q ss_pred             cccccccCCcchHHHHHHHhcccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKD  147 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~  147 (297)
                      ..-|+|++|+||||||+.+++...
T Consensus       177 ~vlL~Gp~GtGKTTLAr~i~~~~~  200 (615)
T TIGR02903       177 HIILYGPPGVGKTTAARLALEEAK  200 (615)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhh
Confidence            456889999999999999988543

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.53  E-value=0.00029  Score=69.73  Aligned_cols=119  Identities=15%  Similarity=0.203  Sum_probs=71.0

Q ss_pred             ccccCCcchHHHHHHHhccccccc-------------------CCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIE-------------------NFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~-------------------~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|..|+||||+|+.+.+.-....                   .|.-.+.+..+....+.+ .++|++.+...   +++-
T Consensus        43 f~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~g~~~D~ieidaas~~~Vdd-iR~li~~~~~~p~~g~~K  121 (647)
T PRK07994         43 FSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQGRFVDLIEIDAASRTKVED-TRELLDNVQYAPARGRFK  121 (647)
T ss_pred             EECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHcCCCCCceeecccccCCHHH-HHHHHHHHHhhhhcCCCE
Confidence            679999999999998877421110                   111123344433344444 34555554432   6777


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIW  259 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf  259 (297)
                      ++|||++.....+.++.|...+..-          ....++|++|..... ...+-.+   ...+.+..++..++.
T Consensus       122 V~IIDEah~Ls~~a~NALLKtLEEP----------p~~v~FIL~Tt~~~kLl~TI~SR---C~~~~f~~Ls~~ei~  184 (647)
T PRK07994        122 VYLIDEVHMLSRHSFNALLKTLEEP----------PEHVKFLLATTDPQKLPVTILSR---CLQFHLKALDVEQIR  184 (647)
T ss_pred             EEEEechHhCCHHHHHHHHHHHHcC----------CCCeEEEEecCCccccchHHHhh---heEeeCCCCCHHHHH
Confidence            9999999988766788887777642          344555665554322 1222222   256788888776654

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.53  E-value=0.00035  Score=71.19  Aligned_cols=119  Identities=12%  Similarity=0.128  Sum_probs=70.2

Q ss_pred             ccccCCcchHHHHHHHhcccccc----------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---C
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI----------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---E  181 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~----------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~  181 (297)
                      ++|..|+||||+|+.+.+.-.-.                      .+++ .+++.......+.++ ++|.+.+...   +
T Consensus        42 f~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~g~~~~~d-v~eidaas~~~Vd~i-R~l~~~~~~~p~~~  119 (824)
T PRK07764         42 FSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLD-VTEIDAASHGGVDDA-RELRERAFFAPAES  119 (824)
T ss_pred             EECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHcCCCCCCc-EEEecccccCCHHHH-HHHHHHHHhchhcC
Confidence            67999999999999887642211                      1222 234444333344444 3343333221   5


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCccccCCccchhhhhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~l~~l~~~~lf~  260 (297)
                      +.-++|||++.....+.++.|...+..-          ...+.+|++|...+   .+...+. -..+|++..++..++..
T Consensus       120 ~~KV~IIDEad~lt~~a~NaLLK~LEEp----------P~~~~fIl~tt~~~---kLl~TIrSRc~~v~F~~l~~~~l~~  186 (824)
T PRK07764        120 RYKIFIIDEAHMVTPQGFNALLKIVEEP----------PEHLKFIFATTEPD---KVIGTIRSRTHHYPFRLVPPEVMRG  186 (824)
T ss_pred             CceEEEEechhhcCHHHHHHHHHHHhCC----------CCCeEEEEEeCChh---hhhHHHHhheeEEEeeCCCHHHHHH
Confidence            6667889999988767788888888652          45556666554332   2332211 12677888887666643

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.53  E-value=0.00043  Score=68.59  Aligned_cols=120  Identities=15%  Similarity=0.143  Sum_probs=67.1

Q ss_pred             ccccCCcchHHHHHHHhcccccc-------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI-------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~-------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~  184 (297)
                      ++|..|+||||+|+.+.+.-...                   ..|--.+.+..+....+. .++++++.....   +++-
T Consensus        43 f~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~g~~~DvlEidaAs~~gVd-~IRelle~a~~~P~~gk~K  121 (709)
T PRK08691         43 LTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGID-NIREVLENAQYAPTAGKYK  121 (709)
T ss_pred             EECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhccCccceEEEeccccCCHH-HHHHHHHHHHhhhhhCCcE
Confidence            78999999999999887631111                   112122344444444443 345555543221   5677


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      ++|||++........+.|...+..-          ....++|++|.... +...+...   ...+.+..++..++..
T Consensus       122 VIIIDEad~Ls~~A~NALLKtLEEP----------p~~v~fILaTtd~~kL~~TIrSR---C~~f~f~~Ls~eeI~~  185 (709)
T PRK08691        122 VYIIDEVHMLSKSAFNAMLKTLEEP----------PEHVKFILATTDPHKVPVTVLSR---CLQFVLRNMTAQQVAD  185 (709)
T ss_pred             EEEEECccccCHHHHHHHHHHHHhC----------CCCcEEEEEeCCccccchHHHHH---HhhhhcCCCCHHHHHH
Confidence            9999999876544566666666542          34556666664332 11122111   1456667777666544

>PRK06526 transposase; Provisional

Probab=97.53  E-value=0.00021  Score=63.06  Aligned_cols=89  Identities=17%  Similarity=0.083  Sum_probs=48.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      .-++|++|+|||+||..+.+.. .+..+. +.|+      +..+++..+.......         .+.-||||||+....
T Consensus       101 lll~Gp~GtGKThLa~al~~~a-~~~g~~-v~f~------t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~  172 (254)
T PRK06526        101 VVFLGPPGTGKTHLAIGLGIRA-CQAGHR-VLFA------TAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIP  172 (254)
T ss_pred             EEEEeCCCCchHHHHHHHHHHH-HHCCCc-hhhh------hHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCC
Confidence            3588999999999999988742 222232 2333      2333443332221110         345689999997653


Q ss_pred             ccCHH-H-HHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          196 YSKWE-P-FHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       196 ~~~w~-~-l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      .+.|. . +-..+...         .++++ +|+||..
T Consensus       173 ~~~~~~~~L~~li~~r---------~~~~s-~IitSn~  200 (254)
T PRK06526        173 FEPEAANLFFQLVSSR---------YERAS-LIVTSNK  200 (254)
T ss_pred             CCHHHHHHHHHHHHHH---------HhcCC-EEEEcCC
Confidence            23333 2 33333221         13444 8888864

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.51  E-value=0.00091  Score=60.58  Aligned_cols=119  Identities=14%  Similarity=0.065  Sum_probs=61.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCc-eEEEEeCCCCCHH---HHHHHHHHhhcCC-CceEEEEEeCCCCCCccCHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDK-RIWVCVSDPFDEF---RIAKAIIEGLEGS-EKKFFLILDDVWTDDYSKWE  200 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~---~~~~~i~~~~~~~-~kr~LiVlDdv~~~~~~~w~  200 (297)
                      -++|.+|+||||+++.+.+.- ....+.. .+-+..+......   +.+.++....... ..+-+|++|++.......++
T Consensus        42 ll~G~~G~GKt~~~~~l~~~l-~~~~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~~~~~  120 (319)
T PRK00440         42 LFAGPPGTGKTTAALALAREL-YGEDWRENFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTSDAQQ  120 (319)
T ss_pred             EEECCCCCCHHHHHHHHHHHH-cCCccccceEEeccccccchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCHHHHH
Confidence            588999999999999998842 1112211 1112223332222   2223333222111 34668999999765433455


Q ss_pred             HHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhh
Q 043781          201 PFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       201 ~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      .|...+...          ...+.+|+++.... ....+....   ..+.+.+++..++
T Consensus       121 ~L~~~le~~----------~~~~~lIl~~~~~~~l~~~l~sr~---~~~~~~~l~~~ei  166 (319)
T PRK00440        121 ALRRTMEMY----------SQNTRFILSCNYSSKIIDPIQSRC---AVFRFSPLKKEAV  166 (319)
T ss_pred             HHHHHHhcC----------CCCCeEEEEeCCccccchhHHHHh---heeeeCCCCHHHH
Confidence            566555432          34567777764321 122222222   3456666665554

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.51  E-value=0.00074  Score=66.11  Aligned_cols=119  Identities=16%  Similarity=0.189  Sum_probs=68.0

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      ++|+.|+||||+|+.+.+.-.-.                    .|.+ ..++..+....+.++ +.+.+.+...   +++
T Consensus        43 f~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~~~h~D-iieIdaas~igVd~I-ReIi~~~~~~P~~~~~  120 (605)
T PRK05896         43 FSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVD-IVELDAASNNGVDEI-RNIIDNINYLPTTFKY  120 (605)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHcCCCCc-eEEeccccccCHHHH-HHHHHHHHhchhhCCc
Confidence            68999999999999887632111                    1122 344544434444443 4444433322   444


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      =++|+|++.....+.++.|...+..-          .....+|++|..... ...+..+   ...+++..++..++..
T Consensus       121 KVIIIDEad~Lt~~A~NaLLKtLEEP----------p~~tvfIL~Tt~~~KLl~TI~SR---cq~ieF~~Ls~~eL~~  185 (605)
T PRK05896        121 KVYIIDEAHMLSTSAWNALLKTLEEP----------PKHVVFIFATTEFQKIPLTIISR---CQRYNFKKLNNSELQE  185 (605)
T ss_pred             EEEEEechHhCCHHHHHHHHHHHHhC----------CCcEEEEEECCChHhhhHHHHhh---hhhcccCCCCHHHHHH
Confidence            57999999887656777777777642          344555555543221 1122222   2567888887776543

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.49  E-value=0.00015  Score=62.64  Aligned_cols=112  Identities=17%  Similarity=0.147  Sum_probs=56.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-++|..|+|||+||+.+++.. ..... ...+++....      ...+ ...   ...-+||+||+.......-..|..
T Consensus        45 ~~l~G~~G~GKT~La~ai~~~~-~~~~~-~~~~i~~~~~------~~~~-~~~---~~~~~liiDdi~~l~~~~~~~L~~  112 (227)
T PRK08903         45 FYLWGEAGSGRSHLLQALVADA-SYGGR-NARYLDAASP------LLAF-DFD---PEAELYAVDDVERLDDAQQIALFN  112 (227)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-HhCCC-cEEEEehHHh------HHHH-hhc---ccCCEEEEeChhhcCchHHHHHHH
Confidence            3588999999999999999842 12222 2334443221      1111 111   233479999997653222233444


Q ss_pred             HHhhhhhhhceeeecCCCCe-EEEEeccHHHH----HHHHHhhCCCccccCCccchhh
Q 043781          205 CLMRVLQEFAAIEVDGDENP-LSLTSTCQEKL----RHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       205 ~l~~~~~~~~~~~~~~~gs~-iiiTTr~~~~~----~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      .+...         ...+.. +|+|++.....    ..+...+.....+.+.+++..+
T Consensus       113 ~~~~~---------~~~~~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~  161 (227)
T PRK08903        113 LFNRV---------RAHGQGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDAD  161 (227)
T ss_pred             HHHHH---------HHcCCcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHH
Confidence            44332         134443 55555532211    2222233222455666666443

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.48  E-value=0.00057  Score=65.15  Aligned_cols=116  Identities=18%  Similarity=0.201  Sum_probs=64.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC-CC-ceEEEEeCCCCCHHHHHHHHHHhhcCC----------CceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN-FD-KRIWVCVSDPFDEFRIAKAIIEGLEGS----------EKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~-F~-~~~wv~vs~~~~~~~~~~~i~~~~~~~----------~kr~LiVlDdv~  192 (297)
                      .-|+|.+|+|||+|++.+.+.  +... .. .++|++.      .+++.++...+...          .+.-+|+|||+.
T Consensus       133 l~lyG~~G~GKTHLl~ai~~~--l~~~~~~~~v~yi~~------~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~  204 (440)
T PRK14088        133 LFIYGGVGLGKTHLLQSIGNY--VVQNEPDLRVMYITS------EKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQ  204 (440)
T ss_pred             EEEEcCCCCcHHHHHHHHHHH--HHHhCCCCeEEEEEH------HHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechh
Confidence            458899999999999999994  4333 33 3445543      44555555444321          134589999997


Q ss_pred             CCC-ccCH-HHHHHHHhhhhhhhceeeecCCCCeEEEEec-cHHHHHH----HHHhhCCCccccCCccchhh
Q 043781          193 TDD-YSKW-EPFHNCLMRVLQEFAAIEVDGDENPLSLTST-CQEKLRH----LTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       193 ~~~-~~~w-~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr-~~~~~~~----v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ... ...+ +.+...+...         ...|..||+||. .+.....    +...+...-+..+++.+.+.
T Consensus       205 ~l~~~~~~q~elf~~~n~l---------~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~  267 (440)
T PRK14088        205 FLIGKTGVQTELFHTFNEL---------HDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEET  267 (440)
T ss_pred             hhcCcHHHHHHHHHHHHHH---------HHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHH
Confidence            541 1112 2233333322         134567888874 3332222    33334333456677666543

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.48  E-value=0.00041  Score=65.42  Aligned_cols=115  Identities=19%  Similarity=0.248  Sum_probs=61.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCC--CceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENF--DKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTD  194 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~  194 (297)
                      -|+|..|+|||+|++.+++.  +....  -..++++.      .++...+..++...         .+.-+|||||+...
T Consensus       140 ~l~G~~G~GKThL~~ai~~~--l~~~~~~~~v~yi~~------~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l  211 (405)
T TIGR00362       140 FIYGGVGLGKTHLLHAIGNE--ILENNPNAKVVYVSS------EKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFL  211 (405)
T ss_pred             EEECCCCCcHHHHHHHHHHH--HHHhCCCCcEEEEEH------HHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhh
Confidence            47899999999999999984  43332  23445543      33333333333211         22348999999864


Q ss_pred             Ccc-CHH-HHHHHHhhhhhhhceeeecCCCCeEEEEeccH-HHH----HHHHHhhCCCccccCCccchhh
Q 043781          195 DYS-KWE-PFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-EKL----RHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       195 ~~~-~w~-~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-~~~----~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ... .+. .+-..+...         ..+|..+|+|+... ...    ..+...+....++.+.+.+.+.
T Consensus       212 ~~~~~~~~~l~~~~n~~---------~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~  272 (405)
T TIGR00362       212 AGKERTQEEFFHTFNAL---------HENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLET  272 (405)
T ss_pred             cCCHHHHHHHHHHHHHH---------HHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHH
Confidence            211 122 233333221         14556788887532 211    2233344333456666666554

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).

>PRK08118 topology modulation protein; Reviewed

Probab=97.48  E-value=4.3e-05  Score=63.10  Aligned_cols=62  Identities=23%  Similarity=0.432  Sum_probs=39.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccc-cCCCceEE----EEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI-ENFDKRIW----VCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~-~~F~~~~w----v~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      +-|+|++|+||||||+.+++...+. -+||..+|    ..+++. ....++++++.     +..  .|+|+.+..
T Consensus         4 I~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~~~w~~~~~~-~~~~~~~~~~~-----~~~--wVidG~~~~   70 (167)
T PRK08118          4 IILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWKPNWEGVPKE-EQITVQNELVK-----EDE--WIIDGNYGG   70 (167)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCceecchhhcccCCcCCCHH-HHHHHHHHHhc-----CCC--EEEeCCcch
Confidence            5689999999999999999965443 45787774    444322 23334444433     233  578887553

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.48  E-value=0.00011  Score=69.43  Aligned_cols=81  Identities=17%  Similarity=0.183  Sum_probs=55.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHH-----------------HHHhhcC-CCceEEEE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKA-----------------IIEGLEG-SEKKFFLI  187 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~-----------------i~~~~~~-~~kr~LiV  187 (297)
                      -++|++|+|||++|+.+++.......|+.+.||++++.++..+++..                 ++..... +.+++++|
T Consensus       198 il~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vli  277 (459)
T PRK11331        198 ILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFI  277 (459)
T ss_pred             EEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccCCcEEE
Confidence            46799999999999999986444557788889999887766665422                 2222221 26789999


Q ss_pred             EeCCCCCCccC-HHHHHHHH
Q 043781          188 LDDVWTDDYSK-WEPFHNCL  206 (297)
Q Consensus       188 lDdv~~~~~~~-w~~l~~~l  206 (297)
                      +|++...+.+. +-.+...+
T Consensus       278 IDEINRani~kiFGel~~lL  297 (459)
T PRK11331        278 IDEINRANLSKVFGEVMMLM  297 (459)
T ss_pred             EehhhccCHHHhhhhhhhhc
Confidence            99998775332 33444433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.46  E-value=0.00028  Score=64.06  Aligned_cols=90  Identities=16%  Similarity=0.080  Sum_probs=50.7

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHH---HHHHHHhhcCCCceEEEEEeCCCCC-CccCHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRI---AKAIIEGLEGSEKKFFLILDDVWTD-DYSKWEPF  202 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~---~~~i~~~~~~~~kr~LiVlDdv~~~-~~~~w~~l  202 (297)
                      ++|.+|+||||+|+.+++.  ....   ...++.+. .....+   +..........+.+-+||+|++... ..+....|
T Consensus        48 l~G~~G~GKT~la~~l~~~--~~~~---~~~i~~~~-~~~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~~~~~~~L  121 (316)
T PHA02544         48 HSPSPGTGKTTVAKALCNE--VGAE---VLFVNGSD-CRIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGLADAQRHL  121 (316)
T ss_pred             eeCcCCCCHHHHHHHHHHH--hCcc---ceEeccCc-ccHHHHHHHHHHHHHhhcccCCCeEEEEECcccccCHHHHHHH
Confidence            4799999999999999883  3222   23344443 222222   2222222221135568999999765 22223345


Q ss_pred             HHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          203 HNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      +..+...          ..++++|+||...
T Consensus       122 ~~~le~~----------~~~~~~Ilt~n~~  141 (316)
T PHA02544        122 RSFMEAY----------SKNCSFIITANNK  141 (316)
T ss_pred             HHHHHhc----------CCCceEEEEcCCh
Confidence            4444432          4667888888643

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.46  E-value=0.00046  Score=62.59  Aligned_cols=88  Identities=19%  Similarity=0.252  Sum_probs=54.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCCc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDDY  196 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~~  196 (297)
                      -++|..|+|||.||..+++.. .+..+ .+.+++++      +++.++.......         .+-=||||||+-....
T Consensus       160 ~L~G~~G~GKThLa~Aia~~l-~~~g~-~v~~~~~~------~l~~~lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e~~  231 (306)
T PRK08939        160 YLYGDFGVGKSYLLAAIANEL-AKKGV-SSTLLHFP------EFIRELKNSISDGSVKEKIDAVKEAPVLMLDDIGAEQM  231 (306)
T ss_pred             EEECCCCCCHHHHHHHHHHHH-HHcCC-CEEEEEHH------HHHHHHHHHHhcCcHHHHHHHhcCCCEEEEecCCCccc
Confidence            478999999999999999952 23333 34556443      3334333332211         5677999999987765


Q ss_pred             cCHHH--HHH-HHhhhhhhhceeeecCCCCeEEEEec
Q 043781          197 SKWEP--FHN-CLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       197 ~~w~~--l~~-~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      +.|..  +-. .+..-         -.++-.+|+||.
T Consensus       232 s~~~~~~ll~~Il~~R---------~~~~~~ti~TSN  259 (306)
T PRK08939        232 SSWVRDEVLGVILQYR---------MQEELPTFFTSN  259 (306)
T ss_pred             cHHHHHHHHHHHHHHH---------HHCCCeEEEECC
Confidence            67864  333 33211         035667888886

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.46  E-value=0.00063  Score=67.02  Aligned_cols=121  Identities=15%  Similarity=0.132  Sum_probs=70.9

Q ss_pred             ccccCCcchHHHHHHHhcccccccC------------------------CCceEEEEeCCCCCHHHHHHHHHHhhcCC--
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIEN------------------------FDKRIWVCVSDPFDEFRIAKAIIEGLEGS--  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~------------------------F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--  180 (297)
                      ++|+.|+||||+|+.+.+.-.....                        ..-.+++..+....+.++ ++|++.+...  
T Consensus        51 ~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~I-ReIie~~~~~P~  129 (598)
T PRK09111         51 LTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDI-REIIESVRYRPV  129 (598)
T ss_pred             EECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHHHHHHhcCCCCceEEecccccCCHHHH-HHHHHHHHhchh
Confidence            7899999999999998773211110                        011234443444445443 4565555432  


Q ss_pred             -CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEecc-HHHHHHHHHhhCCCccccCCccchhhh
Q 043781          181 -EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC-QEKLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       181 -~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~-~~~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                       +++=++|+|++........+.|...+..-          ...+.+|++|.. ..+...+...   ...+.+..++..++
T Consensus       130 ~a~~KVvIIDEad~Ls~~a~naLLKtLEeP----------p~~~~fIl~tte~~kll~tI~SR---cq~~~f~~l~~~el  196 (598)
T PRK09111        130 SARYKVYIIDEVHMLSTAAFNALLKTLEEP----------PPHVKFIFATTEIRKVPVTVLSR---CQRFDLRRIEADVL  196 (598)
T ss_pred             cCCcEEEEEEChHhCCHHHHHHHHHHHHhC----------CCCeEEEEEeCChhhhhHHHHhh---eeEEEecCCCHHHH
Confidence             56668999999877655677777777652          455666665532 2222222111   25677888877776


Q ss_pred             hhh
Q 043781          259 WGW  261 (297)
Q Consensus       259 f~~  261 (297)
                      ..|
T Consensus       197 ~~~  199 (598)
T PRK09111        197 AAH  199 (598)
T ss_pred             HHH
Confidence            554

>PRK09183 transposase/IS protein; Provisional

Probab=97.42  E-value=0.00053  Score=60.72  Aligned_cols=21  Identities=33%  Similarity=0.311  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|.+|+|||+||..+.+.
T Consensus       105 v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        105 IVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            458899999999999999763

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.42  E-value=0.00061  Score=66.77  Aligned_cols=115  Identities=14%  Similarity=0.141  Sum_probs=65.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCC--CceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENF--DKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTD  194 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~  194 (297)
                      -|||..|+|||.|++.+.+.  ....+  -.+++++      ..+++.++...+...         .+-=||||||+...
T Consensus       318 ~LyG~sGsGKTHLL~AIa~~--a~~~~~g~~V~Yit------aeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l  389 (617)
T PRK14086        318 FIYGESGLGKTHLLHAIGHY--ARRLYPGTRVRYVS------SEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFL  389 (617)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHHhCCCCeEEEee------HHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccc
Confidence            47899999999999999994  43322  1334553      334444443333221         12238999999875


Q ss_pred             Cc-cCHHH-HHHHHhhhhhhhceeeecCCCCeEEEEeccH-----HHHHHHHHhhCCCccccCCccchhh
Q 043781          195 DY-SKWEP-FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-----EKLRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       195 ~~-~~w~~-l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-----~~~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      .. ..|+. |-..|...         ..+|..|||||...     .....+...+...-++.|...+.+.
T Consensus       390 ~gke~tqeeLF~l~N~l---------~e~gk~IIITSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~Et  450 (617)
T PRK14086        390 EDKESTQEEFFHTFNTL---------HNANKQIVLSSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELET  450 (617)
T ss_pred             cCCHHHHHHHHHHHHHH---------HhcCCCEEEecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHH
Confidence            32 23332 33333221         15567799988753     1234455566555667777776543

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.41  E-value=0.00062  Score=59.64  Aligned_cols=86  Identities=19%  Similarity=0.305  Sum_probs=51.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHH--------------HHHHhhcCCCceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAK--------------AIIEGLEGSEKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~--------------~i~~~~~~~~kr~LiVlDdv  191 (297)
                      -++|.+|+|||+||..+.+.  ....-..++++++      .+++.              .+++.+   .+-=||||||+
T Consensus       103 ~l~G~~GtGKThLa~aia~~--l~~~g~~v~~it~------~~l~~~l~~~~~~~~~~~~~~l~~l---~~~dlLvIDDi  171 (244)
T PRK07952        103 IFSGKPGTGKNHLAAAICNE--LLLRGKSVLIITV------ADIMSAMKDTFSNSETSEEQLLNDL---SNVDLLVIDEI  171 (244)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEH------HHHHHHHHHHHhhccccHHHHHHHh---ccCCEEEEeCC
Confidence            47899999999999999984  3222234455543      23322              223332   34558999999


Q ss_pred             CCCCccCHHH--HHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          192 WTDDYSKWEP--FHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       192 ~~~~~~~w~~--l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      -......|..  +-..+..-         .++.-.+||||..
T Consensus       172 g~~~~s~~~~~~l~~Ii~~R---------y~~~~~tiitSNl  204 (244)
T PRK07952        172 GVQTESRYEKVIINQIVDRR---------SSSKRPTGMLTNS  204 (244)
T ss_pred             CCCCCCHHHHHHHHHHHHHH---------HhCCCCEEEeCCC
Confidence            8876566764  32333211         1345667888763

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.0012  Score=65.40  Aligned_cols=120  Identities=15%  Similarity=0.144  Sum_probs=68.1

Q ss_pred             ccccCCcchHHHHHHHhcccccc----------------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI----------------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLE  178 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~----------------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~  178 (297)
                      ++|+.|+||||+|+.+.+.-...                            .||+...+ .......+.++. ++.+.+.
T Consensus        43 f~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C~sC~~~~~g~~~n~~~~-d~~s~~~vd~Ir-~l~e~~~  120 (620)
T PRK14954         43 FSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGECESCRDFDAGTSLNISEF-DAASNNSVDDIR-QLRENVR  120 (620)
T ss_pred             EECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccCHHHHHHhccCCCCeEEe-cccccCCHHHHH-HHHHHHH
Confidence            67999999999998877632111                            12332222 222233344443 4455553


Q ss_pred             CC---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccc
Q 043781          179 GS---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFD  254 (297)
Q Consensus       179 ~~---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~  254 (297)
                      ..   +++-++|+|++.......++.|...+..-          ...+.+|++|...   ..+... ..-..++++..++
T Consensus       121 ~~P~~~~~KVvIIdEad~Lt~~a~naLLK~LEeP----------p~~tv~IL~t~~~---~kLl~TI~SRc~~vef~~l~  187 (620)
T PRK14954        121 YGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEP----------PPHAIFIFATTEL---HKIPATIASRCQRFNFKRIP  187 (620)
T ss_pred             hhhhcCCCEEEEEeChhhcCHHHHHHHHHHHhCC----------CCCeEEEEEeCCh---hhhhHHHHhhceEEecCCCC
Confidence            22   56668999999877545677777777542          3345555555322   233322 1122677888888


Q ss_pred             hhhhhhh
Q 043781          255 AKKIWGW  261 (297)
Q Consensus       255 ~~~lf~~  261 (297)
                      ..++..|
T Consensus       188 ~~ei~~~  194 (620)
T PRK14954        188 LDEIQSQ  194 (620)
T ss_pred             HHHHHHH
Confidence            7776443

>PHA00729 NTP-binding motif containing protein

Probab=97.39  E-value=0.0013  Score=56.67  Aligned_cols=65  Identities=26%  Similarity=0.338  Sum_probs=36.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC-----ceEEEEe--CCCCCHHHHHHHHHHhhcCCCceEEEEEeCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD-----KRIWVCV--SDPFDEFRIAKAIIEGLEGSEKKFFLILDDV  191 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-----~~~wv~v--s~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv  191 (297)
                      +-|+|.+|+||||||..+.+.  +..++.     ...|-..  ..-++..+++..|........+-=|||+||+
T Consensus        20 IlItG~pGvGKT~LA~aLa~~--l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~   91 (226)
T PHA00729         20 AVIFGKQGSGKTTYALKVARD--VFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAIDNDYRIPLIIFDDA   91 (226)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCC
Confidence            468899999999999999884  210000     0111100  0112566666666554433211138999993

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.39  E-value=0.00077  Score=64.29  Aligned_cols=119  Identities=13%  Similarity=0.057  Sum_probs=64.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccC--C-----------------CceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIEN--F-----------------DKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~--F-----------------~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      =++|+.|+||||+|+.+.+.-.-...  +                 .-.+-+..+.+.++.+ .+++.+.+...   ++.
T Consensus        44 Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~~g~~~dviEIdaas~~gVd~-IReL~e~l~~~p~~g~~  122 (484)
T PRK14956         44 IFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAASNRGIEN-IRELRDNVKFAPMGGKY  122 (484)
T ss_pred             EEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHHccCCccceeechhhcccHHH-HHHHHHHHHhhhhcCCC
Confidence            37899999999999999873211100  0                 0011222222333332 34444443321   567


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH-HHHHHHHHhhCCCccccCCccchhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-EKLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-~~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      -++|+|++.....+.++.|...+..-          .....+|++|... .+...+..+.   ..|.+..++..++
T Consensus       123 KV~IIDEah~Ls~~A~NALLKtLEEP----------p~~viFILaTte~~kI~~TI~SRC---q~~~f~~ls~~~i  185 (484)
T PRK14956        123 KVYIIDEVHMLTDQSFNALLKTLEEP----------PAHIVFILATTEFHKIPETILSRC---QDFIFKKVPLSVL  185 (484)
T ss_pred             EEEEEechhhcCHHHHHHHHHHhhcC----------CCceEEEeecCChhhccHHHHhhh---heeeecCCCHHHH
Confidence            79999999988767788887777531          2344445455432 2222222221   4567777765544

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.39  E-value=0.0013  Score=50.99  Aligned_cols=68  Identities=22%  Similarity=0.073  Sum_probs=41.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------------------CHHHHHHHHHHhhcCCCceEE
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------------------DEFRIAKAIIEGLEGSEKKFF  185 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------------------~~~~~~~~i~~~~~~~~kr~L  185 (297)
                      .-|+|++|+||||+++.+...  ........+++..+...                   ........++..... .+..+
T Consensus         5 ~~l~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~v   81 (148)
T smart00382        5 ILIVGPPGSGKTTLARALARE--LGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARK-LKPDV   81 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHhc--cCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHh-cCCCE
Confidence            357899999999999999984  33322234445433221                   122233333333332 22499


Q ss_pred             EEEeCCCCCC
Q 043781          186 LILDDVWTDD  195 (297)
Q Consensus       186 iVlDdv~~~~  195 (297)
                      |++|++....
T Consensus        82 iiiDei~~~~   91 (148)
T smart00382       82 LILDEITSLL   91 (148)
T ss_pred             EEEECCcccC
Confidence            9999998874

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.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.39  E-value=0.00018  Score=60.07  Aligned_cols=68  Identities=24%  Similarity=0.371  Sum_probs=39.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      .-++|.+|+|||.||..+.+. -+...+ .+.|+.      ..+++..+-..-...         .+-=||||||+-...
T Consensus        50 l~l~G~~G~GKThLa~ai~~~-~~~~g~-~v~f~~------~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~~  121 (178)
T PF01695_consen   50 LILYGPPGTGKTHLAVAIANE-AIRKGY-SVLFIT------ASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYEP  121 (178)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH-HHHTT---EEEEE------HHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS-
T ss_pred             EEEEhhHhHHHHHHHHHHHHH-hccCCc-ceeEee------cCceeccccccccccchhhhcCccccccEecccccceee
Confidence            347899999999999999874 223333 345564      334444433222111         345688999998765


Q ss_pred             ccCHH
Q 043781          196 YSKWE  200 (297)
Q Consensus       196 ~~~w~  200 (297)
                      .+.|.
T Consensus       122 ~~~~~  126 (178)
T PF01695_consen  122 LSEWE  126 (178)
T ss_dssp             --HHH
T ss_pred             ecccc
Confidence            44554

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.

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

Probab=97.38  E-value=0.00063  Score=63.15  Aligned_cols=123  Identities=17%  Similarity=0.218  Sum_probs=77.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC-c-eEEEEeCCCCCHHHHHHHHHHhhcCC---------------------C
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD-K-RIWVCVSDPFDEFRIAKAIIEGLEGS---------------------E  181 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-~-~~wv~vs~~~~~~~~~~~i~~~~~~~---------------------~  181 (297)
                      .-|+|.+|+|||+.++.+.+  ++.+... . .++|+.-......+++..|+++++..                     +
T Consensus        45 ~~iyG~~GTGKT~~~~~v~~--~l~~~~~~~~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~  122 (366)
T COG1474          45 IIIYGPTGTGKTATVKFVME--ELEESSANVEVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKG  122 (366)
T ss_pred             EEEECCCCCCHhHHHHHHHH--HHHhhhccCceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcC
Confidence            45889999999999999999  4544432 2 68888888888999999999988532                     8


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEE--eccHHH----HHHHHHhhCCCccccCCccch
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLT--STCQEK----LRHLTLTLGLRAKFPVSIFDA  255 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiT--Tr~~~~----~~~v~~~~~~~~~~~l~~l~~  255 (297)
                      +.++||||++..-....- .+...|.+..        +.+.++|++-  +-....    ...+...++..+ +...+-++
T Consensus       123 ~~~IvvLDEid~L~~~~~-~~LY~L~r~~--------~~~~~~v~vi~i~n~~~~~~~ld~rv~s~l~~~~-I~F~pY~a  192 (366)
T COG1474         123 KTVIVILDEVDALVDKDG-EVLYSLLRAP--------GENKVKVSIIAVSNDDKFLDYLDPRVKSSLGPSE-IVFPPYTA  192 (366)
T ss_pred             CeEEEEEcchhhhccccc-hHHHHHHhhc--------cccceeEEEEEEeccHHHHHHhhhhhhhccCcce-eeeCCCCH
Confidence            899999999987522111 3333343321        1234544332  322211    223334455444 56667777


Q ss_pred             hhhh
Q 043781          256 KKIW  259 (297)
Q Consensus       256 ~~lf  259 (297)
                      .||.
T Consensus       193 ~el~  196 (366)
T COG1474         193 EELY  196 (366)
T ss_pred             HHHH
Confidence            7764

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.37  E-value=0.0018  Score=63.73  Aligned_cols=118  Identities=14%  Similarity=0.105  Sum_probs=66.4

Q ss_pred             ccccCCcchHHHHHHHhccccccc--------------------CCCceEEEEeCCCCCHHHHHHHHHHhhcC---CCce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIE--------------------NFDKRIWVCVSDPFDEFRIAKAIIEGLEG---SEKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~--------------------~F~~~~wv~vs~~~~~~~~~~~i~~~~~~---~~kr  183 (297)
                      ++|+.|+||||+|+.+.+.-.-..                    |.| .+++..+....+.++ +.|.+.+..   .+++
T Consensus        43 f~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~g~hpD-v~eId~a~~~~Id~i-R~L~~~~~~~p~~g~~  120 (624)
T PRK14959         43 FSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVD-VVEIDGASNRGIDDA-KRLKEAIGYAPMEGRY  120 (624)
T ss_pred             EECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhcCCCCc-eEEEecccccCHHHH-HHHHHHHHhhhhcCCc
Confidence            579999999999998887422111                    111 334443333344432 334333332   2667


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIW  259 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf  259 (297)
                      -+||||++.......++.|...+..-          .....+|++|.... ....+....   ..+++..++..++.
T Consensus       121 kVIIIDEad~Lt~~a~naLLk~LEEP----------~~~~ifILaTt~~~kll~TI~SRc---q~i~F~pLs~~eL~  184 (624)
T PRK14959        121 KVFIIDEAHMLTREAFNALLKTLEEP----------PARVTFVLATTEPHKFPVTIVSRC---QHFTFTRLSEAGLE  184 (624)
T ss_pred             eEEEEEChHhCCHHHHHHHHHHhhcc----------CCCEEEEEecCChhhhhHHHHhhh---hccccCCCCHHHHH
Confidence            79999999887655667776666431          33455666555332 222222221   45678888766653

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.36  E-value=0.00042  Score=64.99  Aligned_cols=62  Identities=23%  Similarity=0.303  Sum_probs=38.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC----C-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP----F-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~----~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|++|+|||+||+.+++.  ....|   +.+..+.-    . ......+.++..... ....+|+||++..
T Consensus       169 LL~GppGtGKT~lAkaia~~--~~~~~---i~v~~~~l~~~~~g~~~~~i~~~f~~a~~-~~p~IlfiDEiD~  235 (389)
T PRK03992        169 LLYGPPGTGKTLLAKAVAHE--TNATF---IRVVGSELVQKFIGEGARLVRELFELARE-KAPSIIFIDEIDA  235 (389)
T ss_pred             EEECCCCCChHHHHHHHHHH--hCCCE---EEeehHHHhHhhccchHHHHHHHHHHHHh-cCCeEEEEechhh
Confidence            46899999999999999983  33332   11111110    0 123445555554433 4578999999975

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.35  E-value=0.0016  Score=64.04  Aligned_cols=120  Identities=10%  Similarity=0.116  Sum_probs=69.2

Q ss_pred             ccccCCcchHHHHHHHhcccccc----------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---C
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI----------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---E  181 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~----------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~  181 (297)
                      ++|+.|+||||+|+.+.+.-.-.                      .+.+ ++.+..+....+.++ ++|.+.+...   +
T Consensus        40 f~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~~~~~~d-vieidaas~~gvd~i-Rel~~~~~~~P~~~  117 (584)
T PRK14952         40 FSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSID-VVELDAASHGGVDDT-RELRDRAFYAPAQS  117 (584)
T ss_pred             EECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcccCCCce-EEEeccccccCHHHH-HHHHHHHHhhhhcC
Confidence            67999999999999888732110                      1122 234444433344443 4444443221   5


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH-HHHHHHHHhhCCCccccCCccchhhhhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-EKLRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-~~~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      ++=++|+|++.....+..+.|...+..-          .....+|++|... .+...+...   ...+.+..++..++..
T Consensus       118 ~~KVvIIDEah~Lt~~A~NALLK~LEEp----------p~~~~fIL~tte~~kll~TI~SR---c~~~~F~~l~~~~i~~  184 (584)
T PRK14952        118 RYRIFIVDEAHMVTTAGFNALLKIVEEP----------PEHLIFIFATTEPEKVLPTIRSR---THHYPFRLLPPRTMRA  184 (584)
T ss_pred             CceEEEEECCCcCCHHHHHHHHHHHhcC----------CCCeEEEEEeCChHhhHHHHHHh---ceEEEeeCCCHHHHHH
Confidence            6668999999887666777787777652          3455555555432 222222222   2567777777666544


Q ss_pred             h
Q 043781          261 W  261 (297)
Q Consensus       261 ~  261 (297)
                      |
T Consensus       185 ~  185 (584)
T PRK14952        185 L  185 (584)
T ss_pred             H
Confidence            3

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.33  E-value=0.0022  Score=59.11  Aligned_cols=118  Identities=17%  Similarity=0.166  Sum_probs=63.6

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      ++|++|+||||+|+.+...-.-.                    .+++. +++..+....... .+++++.+...   +++
T Consensus        41 l~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~~~-~~~~~~~~~~~~~-~~~l~~~~~~~p~~~~~  118 (355)
T TIGR02397        41 FSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDV-IEIDAASNNGVDD-IREILDNVKYAPSSGKY  118 (355)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EEeeccccCCHHH-HHHHHHHHhcCcccCCc
Confidence            68999999999998887631100                    13333 3443332233222 33344433221   566


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIW  259 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf  259 (297)
                      -++|+|++.......++.+...+...          ...+.+|++|..... ...+...   ...+.+.+++..++.
T Consensus       119 ~vviidea~~l~~~~~~~Ll~~le~~----------~~~~~lIl~~~~~~~l~~~l~sr---~~~~~~~~~~~~~l~  182 (355)
T TIGR02397       119 KVYIIDEVHMLSKSAFNALLKTLEEP----------PEHVVFILATTEPHKIPATILSR---CQRFDFKRIPLEDIV  182 (355)
T ss_pred             eEEEEeChhhcCHHHHHHHHHHHhCC----------ccceeEEEEeCCHHHHHHHHHhh---eeEEEcCCCCHHHHH
Confidence            68999999765434556666555431          345566667654332 2222222   145566677666653

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.32  E-value=0.00059  Score=65.78  Aligned_cols=65  Identities=20%  Similarity=0.311  Sum_probs=39.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccC-----CCceEEEEeCCCC-------CHHHHHHHHHHhhcC---CCceEEEEEeCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIEN-----FDKRIWVCVSDPF-------DEFRIAKAIIEGLEG---SEKKFFLILDDV  191 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~-----F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~---~~kr~LiVlDdv  191 (297)
                      ++|++|+|||++|+.+++.  +..+     +....++.+....       .....++.++.....   .+++.+|+||++
T Consensus       221 LyGPPGTGKT~LAKAlA~e--L~~~i~~~~~~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEi  298 (512)
T TIGR03689       221 LYGPPGCGKTLIAKAVANS--LAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEM  298 (512)
T ss_pred             EECCCCCcHHHHHHHHHHh--hccccccccCCceeEEeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehh
Confidence            6899999999999999994  3332     2233444433211       112233344333322   257899999999


Q ss_pred             CC
Q 043781          192 WT  193 (297)
Q Consensus       192 ~~  193 (297)
                      ..
T Consensus       299 D~  300 (512)
T TIGR03689       299 DS  300 (512)
T ss_pred             hh
Confidence            75

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.31  E-value=0.00082  Score=61.50  Aligned_cols=87  Identities=16%  Similarity=0.223  Sum_probs=51.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHH--------------HHhhcCCCceEEEEEeC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAI--------------IEGLEGSEKKFFLILDD  190 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i--------------~~~~~~~~kr~LiVlDd  190 (297)
                      .-++|.+|+|||+||..+.+.  +...--.+++++++      +++..+              +..+   .+-=||||||
T Consensus       186 Lll~G~~GtGKThLa~aIa~~--l~~~g~~V~y~t~~------~l~~~l~~~~~~~~~~~~~~~~~l---~~~DLLIIDD  254 (329)
T PRK06835        186 LLFYGNTGTGKTFLSNCIAKE--LLDRGKSVIYRTAD------ELIEILREIRFNNDKELEEVYDLL---INCDLLIIDD  254 (329)
T ss_pred             EEEECCCCCcHHHHHHHHHHH--HHHCCCeEEEEEHH------HHHHHHHHHHhccchhHHHHHHHh---ccCCEEEEec
Confidence            347899999999999999984  32222245566543      222222              1221   2345899999


Q ss_pred             CCCCCccCHHH--HHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          191 VWTDDYSKWEP--FHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       191 v~~~~~~~w~~--l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      +-......|..  |-..+...         -.++..+||||..
T Consensus       255 lG~e~~t~~~~~~Lf~iin~R---------~~~~k~tIiTSNl  288 (329)
T PRK06835        255 LGTEKITEFSKSELFNLINKR---------LLRQKKMIISTNL  288 (329)
T ss_pred             cCCCCCCHHHHHHHHHHHHHH---------HHCCCCEEEECCC
Confidence            97764445543  33333221         1445678888863

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.29  E-value=0.0012  Score=61.38  Aligned_cols=120  Identities=18%  Similarity=0.158  Sum_probs=62.4

Q ss_pred             ccccCCcchHHHHHHHhccccc------ccCCCceE-EEEeCCCCCHHHHHHHHHHhhcC-C--CceEEEEEeCCCCCCc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV------IENFDKRI-WVCVSDPFDEFRIAKAIIEGLEG-S--EKKFFLILDDVWTDDY  196 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~------~~~F~~~~-wv~vs~~~~~~~~~~~i~~~~~~-~--~kr~LiVlDdv~~~~~  196 (297)
                      ++|++|+||||+|+.+.+.-.-      ...|...+ -+......+..+ ..++++.+.. +  +++-++++|++.....
T Consensus        44 ~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~-i~~l~~~~~~~p~~~~~kiviIDE~~~l~~  122 (367)
T PRK14970         44 FCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD-IRNLIDQVRIPPQTGKYKIYIIDEVHMLSS  122 (367)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccccCCCHHH-HHHHHHHHhhccccCCcEEEEEeChhhcCH
Confidence            7899999999999998773211      11222222 122222222333 3344443321 1  5666899999976543


Q ss_pred             cCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhhh
Q 043781          197 SKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       197 ~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      ..++.+...+...          ...+.+|++|.... ....+...   ...+++..++..++..
T Consensus       123 ~~~~~ll~~le~~----------~~~~~~Il~~~~~~kl~~~l~sr---~~~v~~~~~~~~~l~~  174 (367)
T PRK14970        123 AAFNAFLKTLEEP----------PAHAIFILATTEKHKIIPTILSR---CQIFDFKRITIKDIKE  174 (367)
T ss_pred             HHHHHHHHHHhCC----------CCceEEEEEeCCcccCCHHHHhc---ceeEecCCccHHHHHH
Confidence            4566665555431          33455665553221 11222211   2456777777666543

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.26  E-value=0.0032  Score=60.76  Aligned_cols=121  Identities=17%  Similarity=0.114  Sum_probs=66.1

Q ss_pred             ccccCCcchHHHHHHHhccccc-------------------ccCCCceEEEEeCCCCCHHHHHHHHHHhhc---CCCceE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV-------------------IENFDKRIWVCVSDPFDEFRIAKAIIEGLE---GSEKKF  184 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~-------------------~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~---~~~kr~  184 (297)
                      ++|+.|+||||+|+.+...-.-                   ...|.-...+..+.+..+.++ +.|.+.+.   ..+++-
T Consensus        43 f~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~~~d~~eidaas~~gvd~i-r~I~~~~~~~P~~~~~K  121 (486)
T PRK14953         43 FAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLIEIDAASNRGIDDI-RALRDAVSYTPIKGKYK  121 (486)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCCCCcEEEEeCccCCCHHHH-HHHHHHHHhCcccCCee
Confidence            6899999999999987763110                   011222334444443444332 33433332   226778


Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf~~  261 (297)
                      ++|+|++.......++.|...+..-          .+...+|++|.... ....+...   ...+.+.+++..++..|
T Consensus       122 VvIIDEad~Lt~~a~naLLk~LEep----------p~~~v~Il~tt~~~kl~~tI~SR---c~~i~f~~ls~~el~~~  186 (486)
T PRK14953        122 VYIIDEAHMLTKEAFNALLKTLEEP----------PPRTIFILCTTEYDKIPPTILSR---CQRFIFSKPTKEQIKEY  186 (486)
T ss_pred             EEEEEChhhcCHHHHHHHHHHHhcC----------CCCeEEEEEECCHHHHHHHHHHh---ceEEEcCCCCHHHHHHH
Confidence            9999999876544566666666431          33455555553322 11222211   24567778877766443

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=97.24  E-value=0.0018  Score=65.54  Aligned_cols=68  Identities=15%  Similarity=0.072  Sum_probs=44.1

Q ss_pred             ccccCCcchHHHHHHHhccccc---ccCCC--ceEEEEeCCCCCHHHHHHHHHHhhcCC---------------------
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV---IENFD--KRIWVCVSDPFDEFRIAKAIIEGLEGS---------------------  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~---~~~F~--~~~wv~vs~~~~~~~~~~~i~~~~~~~---------------------  180 (297)
                      |+|++|.|||++++.|.+.-.-   +....  ..++|....-.+...++..|+.++...                     
T Consensus       786 IyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k  865 (1164)
T PTZ00112        786 ISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKK  865 (1164)
T ss_pred             EECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhc
Confidence            6899999999999999874211   11111  245666555455666666666666221                     


Q ss_pred             --CceEEEEEeCCCCC
Q 043781          181 --EKKFFLILDDVWTD  194 (297)
Q Consensus       181 --~kr~LiVlDdv~~~  194 (297)
                        ....+||||+|..-
T Consensus       866 ~~r~v~IIILDEID~L  881 (1164)
T PTZ00112        866 DNRNVSILIIDEIDYL  881 (1164)
T ss_pred             ccccceEEEeehHhhh
Confidence              23469999999765

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=97.20  E-value=0.00045  Score=58.78  Aligned_cols=94  Identities=29%  Similarity=0.294  Sum_probs=51.6

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEE--eC--CC--C---CHH-------HHHHHHHHhhcCC-------
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC--VS--DP--F---DEF-------RIAKAIIEGLEGS-------  180 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~--vs--~~--~---~~~-------~~~~~i~~~~~~~-------  180 (297)
                      .+.+.|++|.|||.||....-+.-...+|+..+++.  ++  +.  |   +..       .-+.+.+..+...       
T Consensus        21 ~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~~~eK~~p~~~p~~d~l~~~~~~~~~~~~~  100 (205)
T PF02562_consen   21 LVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGDLEEKMEPYLRPIYDALEELFGKEKLEELI  100 (205)
T ss_dssp             EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---------TTTHHHHHHHTTTS-TTCHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCCHHHHHHHHHHHHHHHHHHHhChHhHHHHh
Confidence            345679999999999987776544457788777773  11  11  0   111       1122233332211       


Q ss_pred             -----------------CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEec
Q 043781          181 -----------------EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       181 -----------------~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                                       =..-+||+|++.+.   .-++++..+.+.          +.||++|++=-
T Consensus       101 ~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~---t~~~~k~ilTR~----------g~~skii~~GD  154 (205)
T PF02562_consen  101 QNGKIEIEPLAFIRGRTFDNAFIIVDEAQNL---TPEELKMILTRI----------GEGSKIIITGD  154 (205)
T ss_dssp             HTTSEEEEEGGGGTT--B-SEEEEE-SGGG-----HHHHHHHHTTB-----------TT-EEEEEE-
T ss_pred             hcCeEEEEehhhhcCccccceEEEEecccCC---CHHHHHHHHccc----------CCCcEEEEecC
Confidence                             23468999999887   455677778886          89999999864

; GO: 0005524 ATP binding; PDB: 3B85_A.

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.20  E-value=0.0022  Score=63.55  Aligned_cols=120  Identities=17%  Similarity=0.136  Sum_probs=70.8

Q ss_pred             ccccCCcchHHHHHHHhcccc---------------------cccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKD---------------------VIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EK  182 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~---------------------~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~k  182 (297)
                      ++|..|+||||+|+.+...-.                     ...+|+.. .+..+...++.++. +++.++...   ++
T Consensus        44 f~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~~~~n~~-~ld~~~~~~vd~Ir-~li~~~~~~P~~~~  121 (614)
T PRK14971         44 FCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQRSYNIH-ELDAASNNSVDDIR-NLIEQVRIPPQIGK  121 (614)
T ss_pred             EECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcCCCCceE-EecccccCCHHHHH-HHHHHHhhCcccCC
Confidence            679999999999988766311                     11245532 33444444444444 344443322   56


Q ss_pred             eEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEe-ccHHHHHHHHHhhCCCccccCCccchhhhhhh
Q 043781          183 KFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTS-TCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       183 r~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTT-r~~~~~~~v~~~~~~~~~~~l~~l~~~~lf~~  261 (297)
                      +=++|+|++.....+.++.|...+..-          ...+.+|++| ....+...+-..   ..++++..++.+++..|
T Consensus       122 ~KVvIIdea~~Ls~~a~naLLK~LEep----------p~~tifIL~tt~~~kIl~tI~SR---c~iv~f~~ls~~ei~~~  188 (614)
T PRK14971        122 YKIYIIDEVHMLSQAAFNAFLKTLEEP----------PSYAIFILATTEKHKILPTILSR---CQIFDFNRIQVADIVNH  188 (614)
T ss_pred             cEEEEEECcccCCHHHHHHHHHHHhCC----------CCCeEEEEEeCCchhchHHHHhh---hheeecCCCCHHHHHHH
Confidence            668899999887656777788877652          3456665555 322222222222   25678888877776443

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

Probab=97.18  E-value=0.00065  Score=63.81  Aligned_cols=62  Identities=23%  Similarity=0.285  Sum_probs=37.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|++|+|||+||+.+.+.  ....|   +.+..+.    .. .....+++++..... ..+.+|+||++..
T Consensus       183 LL~GppGTGKT~LAkalA~~--l~~~f---i~i~~s~l~~k~~ge~~~~lr~lf~~A~~-~~P~ILfIDEID~  249 (398)
T PTZ00454        183 LLYGPPGTGKTMLAKAVAHH--TTATF---IRVVGSEFVQKYLGEGPRMVRDVFRLARE-NAPSIIFIDEVDS  249 (398)
T ss_pred             EEECCCCCCHHHHHHHHHHh--cCCCE---EEEehHHHHHHhcchhHHHHHHHHHHHHh-cCCeEEEEECHhh
Confidence            47899999999999999984  33333   1221111    00 112344455544333 5778999999864

>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=97.18  E-value=0.00076  Score=58.73  Aligned_cols=34  Identities=26%  Similarity=0.293  Sum_probs=27.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEe
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV  160 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v  160 (297)
                      ..|+|..|+|||||...+..  ...+.|..+++++-
T Consensus        16 ~viIG~sGSGKT~li~~lL~--~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   16 MVIIGKSGSGKTTLIKSLLY--YLRHKFDHIFLITP   49 (241)
T ss_pred             EEEECCCCCCHHHHHHHHHH--hhcccCCEEEEEec
Confidence            45899999999999999887  47778877777643

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.18  E-value=0.0034  Score=60.95  Aligned_cols=120  Identities=17%  Similarity=0.106  Sum_probs=69.8

Q ss_pred             ccccCCcchHHHHHHHhccccc---c-----------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcC-C--Cce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV---I-----------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEG-S--EKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~---~-----------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~-~--~kr  183 (297)
                      ++|..|+||||+|+.+.+.---   .                 .|++ .+.+..+....+.++. +++..... +  +++
T Consensus        41 f~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~~~h~d-v~eldaas~~gId~IR-elie~~~~~P~~~~~  118 (535)
T PRK08451         41 FSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHID-IIEMDAASNRGIDDIR-ELIEQTKYKPSMARF  118 (535)
T ss_pred             EECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhhcCCCe-EEEeccccccCHHHHH-HHHHHHhhCcccCCe
Confidence            6899999999999977663100   0                 1122 2333333333454444 34343321 1  667


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf~~  261 (297)
                      =++|+|++.....+..+.|...+..-          ...+.+|++|..... ...+..+   ...+.+.+++..++..|
T Consensus       119 KVvIIDEad~Lt~~A~NALLK~LEEp----------p~~t~FIL~ttd~~kL~~tI~SR---c~~~~F~~Ls~~ei~~~  184 (535)
T PRK08451        119 KIFIIDEVHMLTKEAFNALLKTLEEP----------PSYVKFILATTDPLKLPATILSR---TQHFRFKQIPQNSIISH  184 (535)
T ss_pred             EEEEEECcccCCHHHHHHHHHHHhhc----------CCceEEEEEECChhhCchHHHhh---ceeEEcCCCCHHHHHHH
Confidence            79999999887666777777777542          455666766654321 1222222   25678888877776544

>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=97.17  E-value=0.00018  Score=57.09  Aligned_cols=76  Identities=22%  Similarity=0.101  Sum_probs=49.8

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-----------CceEEEEEeCCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-----------EKKFFLILDDVWTDD  195 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----------~kr~LiVlDdv~~~~  195 (297)
                      ++|.+|+|||+||+.+++.  ...   ...-+.++...+..+++...--.-+..           .+..++|||++...+
T Consensus         4 L~G~~G~GKt~l~~~la~~--~~~---~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~a~   78 (139)
T PF07728_consen    4 LVGPPGTGKTTLARELAAL--LGR---PVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINRAP   78 (139)
T ss_dssp             EEESSSSSHHHHHHHHHHH--HTC---EEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG--
T ss_pred             EECCCCCCHHHHHHHHHHH--hhc---ceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcccCC
Confidence            7899999999999999983  321   223456777777777765432111111           589999999998765


Q ss_pred             ccCHHHHHHHHh
Q 043781          196 YSKWEPFHNCLM  207 (297)
Q Consensus       196 ~~~w~~l~~~l~  207 (297)
                      .+.+..|...+.
T Consensus        79 ~~v~~~L~~ll~   90 (139)
T PF07728_consen   79 PEVLESLLSLLE   90 (139)
T ss_dssp             HHHHHTTHHHHS
T ss_pred             HHHHHHHHHHHh
Confidence            556666766664

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.

>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=97.14  E-value=0.00042  Score=59.36  Aligned_cols=21  Identities=33%  Similarity=0.317  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|+|+.|+|||+|++.+.+.
T Consensus        23 ~~l~G~rg~GKTsLl~~~~~~   43 (234)
T PF01637_consen   23 ILLYGPRGSGKTSLLKEFINE   43 (234)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCcCCHHHHHHHHHHH
Confidence            458899999999999999984

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.11  E-value=0.005  Score=60.88  Aligned_cols=117  Identities=15%  Similarity=0.135  Sum_probs=65.0

Q ss_pred             ccccCCcchHHHHHHHhccccccc---------------------CCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIE---------------------NFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EK  182 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~---------------------~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~k  182 (297)
                      ++|..|+||||+|+.+.+.-....                     |.+ .+.+..+....+.++ ++|.+.+...   ++
T Consensus        43 f~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~~~~~~d-~~~i~~~~~~~vd~i-r~ii~~~~~~p~~~~  120 (585)
T PRK14950         43 FTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVD-VIEMDAASHTSVDDA-REIIERVQFRPALAR  120 (585)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHhcCCCCe-EEEEeccccCCHHHH-HHHHHHHhhCcccCC
Confidence            689999999999998886321111                     111 223333333444443 4555544332   67


Q ss_pred             eEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhh
Q 043781          183 KFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       183 r~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      +-++|+|++.....+..+.|...+..-          ...+.+|++|...+ ....+-..   ...+.+..++..++
T Consensus       121 ~kVvIIDEa~~L~~~a~naLLk~LEep----------p~~tv~Il~t~~~~kll~tI~SR---~~~i~f~~l~~~el  184 (585)
T PRK14950        121 YKVYIIDEVHMLSTAAFNALLKTLEEP----------PPHAIFILATTEVHKVPATILSR---CQRFDFHRHSVADM  184 (585)
T ss_pred             eEEEEEeChHhCCHHHHHHHHHHHhcC----------CCCeEEEEEeCChhhhhHHHHhc---cceeeCCCCCHHHH
Confidence            789999999876545666676666542          34556666654322 11222111   13456666665554

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=97.11  E-value=0.0015  Score=57.76  Aligned_cols=19  Identities=37%  Similarity=0.438  Sum_probs=17.3

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -++|++|+||||+|+.+++
T Consensus        46 ll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881        46 IFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             EEEcCCCCCHHHHHHHHHH
Confidence            4789999999999999976

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.10  E-value=0.003  Score=57.87  Aligned_cols=121  Identities=12%  Similarity=0.103  Sum_probs=71.1

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEe---CCCCCHHHHHHHHHHhhcCC---
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCV---SDPFDEFRIAKAIIEGLEGS---  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~v---s~~~~~~~~~~~i~~~~~~~---  180 (297)
                      +.|+.|+|||++|..+...---.                    .|-| ..|+.-   ++...+.++- ++.+.+...   
T Consensus        27 f~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD-~~~i~~~~~~~~i~id~iR-~l~~~~~~~~~~  104 (328)
T PRK05707         27 LHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPD-NFVLEPEEADKTIKVDQVR-ELVSFVVQTAQL  104 (328)
T ss_pred             eECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccCCCCCCCHHHHH-HHHHHHhhcccc
Confidence            67999999999998777642111                    1222 234422   2334554443 344444332   


Q ss_pred             CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhhh
Q 043781          181 EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKIW  259 (297)
Q Consensus       181 ~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~lf  259 (297)
                      +++=++|+|++...+.+..+.|...+..-          ..++.+|+||.+.+   .+..+.-. ...+++.+++.++..
T Consensus       105 ~~~kv~iI~~a~~m~~~aaNaLLK~LEEP----------p~~~~fiL~t~~~~---~ll~TI~SRc~~~~~~~~~~~~~~  171 (328)
T PRK05707        105 GGRKVVLIEPAEAMNRNAANALLKSLEEP----------SGDTVLLLISHQPS---RLLPTIKSRCQQQACPLPSNEESL  171 (328)
T ss_pred             CCCeEEEECChhhCCHHHHHHHHHHHhCC----------CCCeEEEEEECChh---hCcHHHHhhceeeeCCCcCHHHHH
Confidence            44445567999998777888888888652          45677777776543   23222111 255778888777655


Q ss_pred             hhh
Q 043781          260 GWE  262 (297)
Q Consensus       260 ~~~  262 (297)
                      .|-
T Consensus       172 ~~L  174 (328)
T PRK05707        172 QWL  174 (328)
T ss_pred             HHH
Confidence            443

>cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain

Probab=97.08  E-value=0.00094  Score=59.27  Aligned_cols=49  Identities=18%  Similarity=0.258  Sum_probs=33.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC-ceEEEEeCCCC-CHHHHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD-KRIWVCVSDPF-DEFRIAKAIIE  175 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~-~~~~~~~~i~~  175 (297)
                      ..|+|..|+|||||++.++++  ++.+|+ ..+++-+.... .+.++.+++..
T Consensus        72 ~~If~~~G~GKTtLa~~i~~~--i~~~~~~~~V~~~iGer~~Ev~e~~~~~~~  122 (274)
T cd01133          72 IGLFGGAGVGKTVLIMELINN--IAKAHGGYSVFAGVGERTREGNDLYHEMKE  122 (274)
T ss_pred             EEEecCCCCChhHHHHHHHHH--HHhcCCCEEEEEEeccCcHHHHHHHHHHHh
Confidence            368999999999999999994  554554 44455555543 34566666554

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic.

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.07  E-value=0.0013  Score=60.72  Aligned_cols=65  Identities=15%  Similarity=0.146  Sum_probs=45.0

Q ss_pred             cccccCCcchHHHHHHHhccccccc-CCCce-EEEEeCCC-CCHHHHHHHHHHhhcCC----------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE-NFDKR-IWVCVSDP-FDEFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~-~F~~~-~wv~vs~~-~~~~~~~~~i~~~~~~~----------------------  180 (297)
                      .|+|.+|+|||||++.+.+.  +.. +-+.. +|+.+.+. ..+.++++.+...+..+                      
T Consensus       137 LIvG~pGtGKTTLl~~la~~--i~~~~~dv~~vv~lIgER~~EV~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~Ae~  214 (380)
T PRK12608        137 LIVAPPRAGKTVLLQQIAAA--VAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERAKR  214 (380)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEEecCCCCCHHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHHHH
Confidence            58899999999999998884  322 33443 56555443 35566666665544331                      


Q ss_pred             ----CceEEEEEeCCC
Q 043781          181 ----EKKFFLILDDVW  192 (297)
Q Consensus       181 ----~kr~LiVlDdv~  192 (297)
                          +++.+||+|++-
T Consensus       215 f~~~GkdVVLvlDslt  230 (380)
T PRK12608        215 LVEQGKDVVILLDSLT  230 (380)
T ss_pred             HHHcCCCEEEEEeCcH
Confidence                999999999996

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.05  E-value=0.0047  Score=57.43  Aligned_cols=79  Identities=11%  Similarity=0.023  Sum_probs=50.8

Q ss_pred             HHHHHHhhcCC---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCC
Q 043781          170 AKAIIEGLEGS---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLR  245 (297)
Q Consensus       170 ~~~i~~~~~~~---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~  245 (297)
                      .+++.+.+...   +++-++|+|++...+....+.|...+..-          .+++.+|++|...+.   +..+ ..-.
T Consensus       126 iR~l~~~~~~~~~~~~~kVviIDead~m~~~aanaLLK~LEep----------p~~~~~IL~t~~~~~---llpti~SRc  192 (365)
T PRK07471        126 VRELISFFGLTAAEGGWRVVIVDTADEMNANAANALLKVLEEP----------PARSLFLLVSHAPAR---LLPTIRSRC  192 (365)
T ss_pred             HHHHHHHhCcCcccCCCEEEEEechHhcCHHHHHHHHHHHhcC----------CCCeEEEEEECCchh---chHHhhccc
Confidence            44555555433   67779999999988777777787777652          456667777765432   2222 1123


Q ss_pred             ccccCCccchhhhhhh
Q 043781          246 AKFPVSIFDAKKIWGW  261 (297)
Q Consensus       246 ~~~~l~~l~~~~lf~~  261 (297)
                      ..+++.+++..++..|
T Consensus       193 ~~i~l~~l~~~~i~~~  208 (365)
T PRK07471        193 RKLRLRPLAPEDVIDA  208 (365)
T ss_pred             eEEECCCCCHHHHHHH
Confidence            6778888887775444

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.05  E-value=0.0004  Score=57.52  Aligned_cols=21  Identities=29%  Similarity=0.347  Sum_probs=16.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|+|.+|+|||+|.+.++..
T Consensus        27 ~ll~G~~G~GKT~ll~~~~~~   47 (185)
T PF13191_consen   27 LLLTGESGSGKTSLLRALLDR   47 (185)
T ss_dssp             EEE-B-TTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999998884

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.05  E-value=0.0018  Score=57.14  Aligned_cols=67  Identities=22%  Similarity=0.278  Sum_probs=44.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC----------CceEEEEEeCCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS----------EKKFFLILDDVWTDD  195 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~----------~kr~LiVlDdv~~~~  195 (297)
                      -++|.+|+|||.||..+.+.-- +..+ .+.+++      ..+++.++.......          .+-=||||||+-...
T Consensus       109 ~l~G~~G~GKThLa~Ai~~~l~-~~g~-sv~f~~------~~el~~~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~  180 (254)
T COG1484         109 VLLGPPGVGKTHLAIAIGNELL-KAGI-SVLFIT------APDLLSKLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEP  180 (254)
T ss_pred             EEECCCCCcHHHHHHHHHHHHH-HcCC-eEEEEE------HHHHHHHHHHHHhcCchHHHHHHHhhcCCEEEEecccCcc
Confidence            4789999999999999999532 3223 334453      345555554444321          456699999998875


Q ss_pred             ccCHH
Q 043781          196 YSKWE  200 (297)
Q Consensus       196 ~~~w~  200 (297)
                      .+.|.
T Consensus       181 ~~~~~  185 (254)
T COG1484         181 FSQEE  185 (254)
T ss_pred             CCHHH
Confidence            56665

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.04  E-value=0.004  Score=61.40  Aligned_cols=120  Identities=14%  Similarity=0.117  Sum_probs=67.3

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      ++|..|+||||+|+.+.+.-.-.                    .+++. +.+.......+.++ ++|.+.+...   +++
T Consensus        43 f~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~g~~~d~-~eid~~s~~~v~~i-r~l~~~~~~~p~~~~~  120 (576)
T PRK14965         43 FTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDV-FEIDGASNTGVDDI-RELRENVKYLPSRSRY  120 (576)
T ss_pred             EECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhcCCCCCe-eeeeccCccCHHHH-HHHHHHHHhccccCCc
Confidence            67999999999998887631111                    12222 22232333344443 4455544322   566


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf~~  261 (297)
                      -++|+|++........+.|...+..-          .....+|++|...+ +...+-..   ...+.+..++..++..|
T Consensus       121 KVvIIdev~~Lt~~a~naLLk~LEep----------p~~~~fIl~t~~~~kl~~tI~SR---c~~~~f~~l~~~~i~~~  186 (576)
T PRK14965        121 KIFIIDEVHMLSTNAFNALLKTLEEP----------PPHVKFIFATTEPHKVPITILSR---CQRFDFRRIPLQKIVDR  186 (576)
T ss_pred             eEEEEEChhhCCHHHHHHHHHHHHcC----------CCCeEEEEEeCChhhhhHHHHHh---hhhhhcCCCCHHHHHHH
Confidence            68899999877655677777777642          34556665554322 22222211   24567777776665443

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.01  E-value=0.002  Score=57.13  Aligned_cols=77  Identities=16%  Similarity=0.192  Sum_probs=46.7

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHH--------HHhh----------------cCC--
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAI--------IEGL----------------EGS--  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i--------~~~~----------------~~~--  180 (297)
                      +.|.+|+|||+||+.+.+  .....   .+.++.+...+..+++...        ..++                .++  
T Consensus        26 L~G~~GtGKT~lA~~la~--~lg~~---~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~  100 (262)
T TIGR02640        26 LRGPAGTGKTTLAMHVAR--KRDRP---VMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLT  100 (262)
T ss_pred             EEcCCCCCHHHHHHHHHH--HhCCC---EEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCchHH
Confidence            679999999999999987  33222   2344444444444443221        0000                000  


Q ss_pred             ---CceEEEEEeCCCCCCccCHHHHHHHHhh
Q 043781          181 ---EKKFFLILDDVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       181 ---~kr~LiVlDdv~~~~~~~w~~l~~~l~~  208 (297)
                         .+...++||++...+.+.+..|...+..
T Consensus       101 ~A~~~g~~lllDEi~r~~~~~q~~Ll~~Le~  131 (262)
T TIGR02640       101 LAVREGFTLVYDEFTRSKPETNNVLLSVFEE  131 (262)
T ss_pred             HHHHcCCEEEEcchhhCCHHHHHHHHHHhcC
Confidence               3446899999998776667677776643

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).

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

Probab=96.99  E-value=0.0025  Score=55.38  Aligned_cols=75  Identities=21%  Similarity=0.257  Sum_probs=48.8

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCC--CCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCC-ccCHHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD--PFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDD-YSKWEPFH  203 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~--~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~-~~~w~~l~  203 (297)
                      +||..|.|||+|++.+.+...-+.   .+ -|.|++  -.++.+++..|    .....||+|.+||+.-.. ......|+
T Consensus        57 L~G~rGtGKSSlVkall~~y~~~G---LR-lIev~k~~L~~l~~l~~~l----~~~~~kFIlf~DDLsFe~~d~~yk~LK  128 (249)
T PF05673_consen   57 LWGARGTGKSSLVKALLNEYADQG---LR-LIEVSKEDLGDLPELLDLL----RDRPYKFILFCDDLSFEEGDTEYKALK  128 (249)
T ss_pred             EecCCCCCHHHHHHHHHHHHhhcC---ce-EEEECHHHhccHHHHHHHH----hcCCCCEEEEecCCCCCCCcHHHHHHH
Confidence            799999999999999988322221   22 233333  23445544444    333689999999997542 24577788


Q ss_pred             HHHhhh
Q 043781          204 NCLMRV  209 (297)
Q Consensus       204 ~~l~~~  209 (297)
                      ..|..+
T Consensus       129 s~LeGg  134 (249)
T PF05673_consen  129 SVLEGG  134 (249)
T ss_pred             HHhcCc
Confidence            888654

>PRK07261 topology modulation protein; Provisional

Probab=96.98  E-value=0.0015  Score=54.11  Aligned_cols=65  Identities=20%  Similarity=0.169  Sum_probs=40.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccc-cCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI-ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~-~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      +.|+|++|+||||||+.+.....+. -+.|...|-+.....+..+....+...+..  .+  .|+|+...
T Consensus         3 i~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~~~~~~~~~~~~~~~~~~~~--~~--wIidg~~~   68 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPNWQERDDDDMIADISNFLLK--HD--WIIDGNYS   68 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccccccCCHHHHHHHHHHHHhC--CC--EEEcCcch
Confidence            4689999999999999988743221 245666675443344445555544444432  33  67888744

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=96.98  E-value=0.0037  Score=57.29  Aligned_cols=118  Identities=12%  Similarity=0.066  Sum_probs=69.3

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcC---CCce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEG---SEKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~---~~kr  183 (297)
                      ++|+.|+||||+|+.+.+.---.                    .|.|.......+....+.++. ++.+.+..   .+++
T Consensus        33 f~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i~~~~~~i~id~ir-~l~~~~~~~~~~~~~  111 (329)
T PRK08058         33 FEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLVAPDGQSIKKDQIR-YLKEEFSKSGVESNK  111 (329)
T ss_pred             EECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEeccccccCCHHHHH-HHHHHHhhCCcccCc
Confidence            78999999999998876531111                    133433332233334444443 33444331   2566


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKI  258 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~l  258 (297)
                      =++|+|++.....+..+.|...+..-          ..++.+|++|...+   .+..+... ...+++.+++..++
T Consensus       112 kvviI~~a~~~~~~a~NaLLK~LEEP----------p~~~~~Il~t~~~~---~ll~TIrSRc~~i~~~~~~~~~~  174 (329)
T PRK08058        112 KVYIIEHADKMTASAANSLLKFLEEP----------SGGTTAILLTENKH---QILPTILSRCQVVEFRPLPPESL  174 (329)
T ss_pred             eEEEeehHhhhCHHHHHHHHHHhcCC----------CCCceEEEEeCChH---hCcHHHHhhceeeeCCCCCHHHH
Confidence            67999999887656677777777542          56677777776432   33322222 25677888877664

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=96.97  E-value=0.0021  Score=48.81  Aligned_cols=19  Identities=47%  Similarity=0.604  Sum_probs=17.2

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      |+|.+|+|||+||+.+..+
T Consensus         3 i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    3 IYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             EECCCCCCHHHHHHHHHHH
Confidence            7899999999999998874

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

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=96.92  E-value=0.0064  Score=60.91  Aligned_cols=120  Identities=20%  Similarity=0.205  Sum_probs=67.2

Q ss_pred             ccccCCcchHHHHHHHhcccccc-----------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---CceEEE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI-----------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKKFFL  186 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~-----------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr~Li  186 (297)
                      ++|+.|+||||+|+.+.+.---.                 .+++ .+++..+....+.+ .+++.+.+...   +++-++
T Consensus        45 F~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~~~D-vieidaasn~~vd~-IReLie~~~~~P~~g~~KV~  122 (725)
T PRK07133         45 FSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLD-IIEMDAASNNGVDE-IRELIENVKNLPTQSKYKIY  122 (725)
T ss_pred             EECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcCCCc-EEEEeccccCCHHH-HHHHHHHHHhchhcCCCEEE
Confidence            67999999999998887631110                 1111 12333322233433 34444444322   677799


Q ss_pred             EEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccchhhhhhh
Q 043781          187 ILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       187 VlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~~~~lf~~  261 (297)
                      |+|++.....+.++.|...+..-          .....+|++|...+   .+..+ ..-...+.+.+++..++..|
T Consensus       123 IIDEa~~LT~~A~NALLKtLEEP----------P~~tifILaTte~~---KLl~TI~SRcq~ieF~~L~~eeI~~~  185 (725)
T PRK07133        123 IIDEVHMLSKSAFNALLKTLEEP----------PKHVIFILATTEVH---KIPLTILSRVQRFNFRRISEDEIVSR  185 (725)
T ss_pred             EEEChhhCCHHHHHHHHHHhhcC----------CCceEEEEEcCChh---hhhHHHHhhceeEEccCCCHHHHHHH
Confidence            99999877656777777777541          33445555543322   22222 11124678888877766433

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=96.88  E-value=0.0066  Score=58.08  Aligned_cols=120  Identities=18%  Similarity=0.130  Sum_probs=65.2

Q ss_pred             ccccCCcchHHHHHHHhccccc---------------------ccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV---------------------IENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EK  182 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~---------------------~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~k  182 (297)
                      ++|.+|+||||+|+.+.+.-.-                     ..+++. +++.......+.++ +++.+.+...   ++
T Consensus        44 f~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~~~~d~-~~i~g~~~~gid~i-r~i~~~l~~~~~~~~  121 (451)
T PRK06305         44 FSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLDV-LEIDGASHRGIEDI-RQINETVLFTPSKSR  121 (451)
T ss_pred             EEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcCCCCce-EEeeccccCCHHHH-HHHHHHHHhhhhcCC
Confidence            6899999999999888763111                     112332 22332223333333 2333333321   56


Q ss_pred             eEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccchhhhhhh
Q 043781          183 KFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       183 r~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~~~~lf~~  261 (297)
                      +-++|+|++........+.|...+..-          .....+|++|...   ..+... ..-..++.+..++..++..|
T Consensus       122 ~kvvIIdead~lt~~~~n~LLk~lEep----------~~~~~~Il~t~~~---~kl~~tI~sRc~~v~f~~l~~~el~~~  188 (451)
T PRK06305        122 YKIYIIDEVHMLTKEAFNSLLKTLEEP----------PQHVKFFLATTEI---HKIPGTILSRCQKMHLKRIPEETIIDK  188 (451)
T ss_pred             CEEEEEecHHhhCHHHHHHHHHHhhcC----------CCCceEEEEeCCh---HhcchHHHHhceEEeCCCCCHHHHHHH
Confidence            778999999766444555666666541          3455666666422   222222 11124678888877776443

>PRK10865 protein disaggregation chaperone; Provisional

Probab=96.87  E-value=0.012  Score=60.62  Aligned_cols=82  Identities=18%  Similarity=0.175  Sum_probs=46.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC---HHHHH------------HHHHHhhcCCCceEEEEEe
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD---EFRIA------------KAIIEGLEGSEKKFFLILD  189 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~---~~~~~------------~~i~~~~~~~~kr~LiVlD  189 (297)
                      .-++|+.|+|||+||+.+.+.  ....-...+.+.++.-..   ..+++            ..+.+.+.. ...-+|+||
T Consensus       601 ~Lf~Gp~G~GKT~lA~aLa~~--l~~~~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~~g~l~~~v~~-~p~~vLllD  677 (857)
T PRK10865        601 FLFLGPTGVGKTELCKALANF--MFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRR-RPYSVILLD  677 (857)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hhcCCCcEEEEEhHHhhhhhhHHHHhCCCCcccccchhHHHHHHHHh-CCCCeEEEe
Confidence            347899999999999999873  221112233443332111   11111            001111110 223599999


Q ss_pred             CCCCCCccCHHHHHHHHhhh
Q 043781          190 DVWTDDYSKWEPFHNCLMRV  209 (297)
Q Consensus       190 dv~~~~~~~w~~l~~~l~~~  209 (297)
                      ++...+.+.++.|...+..+
T Consensus       678 Eieka~~~v~~~Ll~ile~g  697 (857)
T PRK10865        678 EVEKAHPDVFNILLQVLDDG  697 (857)
T ss_pred             ehhhCCHHHHHHHHHHHhhC
Confidence            99887777787787777553

>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=96.84  E-value=0.0064  Score=49.84  Aligned_cols=95  Identities=21%  Similarity=0.092  Sum_probs=64.5

Q ss_pred             ccccCCcchHHHHHHHhccccc---c---------------cCCCceEEEEeCC---CCCHHHHHHHHHHhhcCC---Cc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV---I---------------ENFDKRIWVCVSD---PFDEFRIAKAIIEGLEGS---EK  182 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~---~---------------~~F~~~~wv~vs~---~~~~~~~~~~i~~~~~~~---~k  182 (297)
                      ++|..|+||+++|..+.+.---   .               ....-..|+....   ...+.++. ++.+.+...   ++
T Consensus        24 ~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir-~i~~~~~~~~~~~~  102 (162)
T PF13177_consen   24 FHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIR-EIIEFLSLSPSEGK  102 (162)
T ss_dssp             EECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHH-HHHHHCTSS-TTSS
T ss_pred             EECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHH-HHHHHHHHHHhcCC
Confidence            6799999999999877663111   1               1223344555443   35666655 777766554   67


Q ss_pred             eEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          183 KFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       183 r~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      +=++|+|++.....+.+..|...+..-          ..++.+|++|++.
T Consensus       103 ~KviiI~~ad~l~~~a~NaLLK~LEep----------p~~~~fiL~t~~~  142 (162)
T PF13177_consen  103 YKVIIIDEADKLTEEAQNALLKTLEEP----------PENTYFILITNNP  142 (162)
T ss_dssp             SEEEEEETGGGS-HHHHHHHHHHHHST----------TTTEEEEEEES-G
T ss_pred             ceEEEeehHhhhhHHHHHHHHHHhcCC----------CCCEEEEEEECCh
Confidence            888999999998777888888888763          6678888888754

...

>CHL00181 cbbX CbbX; Provisional

Probab=96.83  E-value=0.0043  Score=55.76  Aligned_cols=19  Identities=37%  Similarity=0.412  Sum_probs=17.2

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -++|.+|+||||+|+.+++
T Consensus        63 ll~G~pGtGKT~lAr~la~   81 (287)
T CHL00181         63 SFTGSPGTGKTTVALKMAD   81 (287)
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3689999999999999977

>PRK10536 hypothetical protein; Provisional

Probab=96.82  E-value=0.0053  Score=53.93  Aligned_cols=34  Identities=18%  Similarity=0.258  Sum_probs=27.2

Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEec
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      -+||+|.+.+.+   -.+++..+.+.          +.+|++|+|=-
T Consensus       178 ~~vIvDEaqn~~---~~~~k~~ltR~----------g~~sk~v~~GD  211 (262)
T PRK10536        178 AVVILDEAQNVT---AAQMKMFLTRL----------GENVTVIVNGD  211 (262)
T ss_pred             CEEEEechhcCC---HHHHHHHHhhc----------CCCCEEEEeCC
Confidence            489999999884   46677777775          89999999865

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=96.82  E-value=0.0068  Score=48.58  Aligned_cols=34  Identities=32%  Similarity=0.263  Sum_probs=22.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS  161 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs  161 (297)
                      .|+|.+|+||||++..+...  ....-..++|+...
T Consensus         3 ~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~e   36 (165)
T cd01120           3 LVFGPTGSGKTTLALQLALN--IATKGGKVVYVDIE   36 (165)
T ss_pred             eEeCCCCCCHHHHHHHHHHH--HHhcCCEEEEEECC
Confidence            47899999999999988774  22222344455443

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.

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

Probab=96.81  E-value=0.0013  Score=62.35  Aligned_cols=62  Identities=23%  Similarity=0.329  Sum_probs=38.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC---C--CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP---F--DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~---~--~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|++|+|||+||+.+++  .....|   +.+..+.-   +  .....++.++..... +.+.+|+||++..
T Consensus       221 LL~GPPGTGKT~LAraIA~--el~~~f---i~V~~seL~~k~~Ge~~~~vr~lF~~A~~-~~P~ILfIDEID~  287 (438)
T PTZ00361        221 ILYGPPGTGKTLLAKAVAN--ETSATF---LRVVGSELIQKYLGDGPKLVRELFRVAEE-NAPSIVFIDEIDA  287 (438)
T ss_pred             EEECCCCCCHHHHHHHHHH--hhCCCE---EEEecchhhhhhcchHHHHHHHHHHHHHh-CCCcEEeHHHHHH
Confidence            4789999999999999999  444444   22221111   1  123344555544333 5778999999853

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=96.80  E-value=0.0028  Score=59.21  Aligned_cols=118  Identities=18%  Similarity=0.131  Sum_probs=67.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC--------CceEEEEEeCCCCCCc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS--------EKKFFLILDDVWTDDY  196 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--------~kr~LiVlDdv~~~~~  196 (297)
                      .-|||..|+|||.|++.+.+  ....+......++++    .......++..+...        -.-=++++||++.-..
T Consensus       116 lfi~G~~GlGKTHLl~Aign--~~~~~~~~a~v~y~~----se~f~~~~v~a~~~~~~~~Fk~~y~~dlllIDDiq~l~g  189 (408)
T COG0593         116 LFIYGGVGLGKTHLLQAIGN--EALANGPNARVVYLT----SEDFTNDFVKALRDNEMEKFKEKYSLDLLLIDDIQFLAG  189 (408)
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHhhCCCceEEecc----HHHHHHHHHHHHHhhhHHHHHHhhccCeeeechHhHhcC
Confidence            45899999999999999999  455555433333332    233333333333221        1122899999987411


Q ss_pred             -cCHHH-HHHHHhhhhhhhceeeecCCCCeEEEEeccHH-----HHHHHHHhhCCCccccCCccchhh
Q 043781          197 -SKWEP-FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-----KLRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       197 -~~w~~-l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-----~~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                       +.|+. +-..|...         ..+|..||+|++..-     ...++..++...-++.+.+++.+.
T Consensus       190 k~~~qeefFh~FN~l---------~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~  248 (408)
T COG0593         190 KERTQEEFFHTFNAL---------LENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDET  248 (408)
T ss_pred             ChhHHHHHHHHHHHH---------HhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHH
Confidence             23332 33333332         145558999985321     123555666655677777777554

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

Probab=96.79  E-value=0.0037  Score=55.28  Aligned_cols=111  Identities=20%  Similarity=0.169  Sum_probs=59.8

Q ss_pred             ccccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHH
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPF  202 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l  202 (297)
                      |-+=++|++|+||||||..+.+  ++.-.+    -++-.....-..-+-.|+..+   ...=++.+|.++......-+-|
T Consensus        53 DHvLl~GPPGlGKTTLA~IIA~--Emgvn~----k~tsGp~leK~gDlaaiLt~L---e~~DVLFIDEIHrl~~~vEE~L  123 (332)
T COG2255          53 DHVLLFGPPGLGKTTLAHIIAN--ELGVNL----KITSGPALEKPGDLAAILTNL---EEGDVLFIDEIHRLSPAVEEVL  123 (332)
T ss_pred             CeEEeeCCCCCcHHHHHHHHHH--HhcCCe----EecccccccChhhHHHHHhcC---CcCCeEEEehhhhcChhHHHHh
Confidence            3445899999999999999999  443332    111111112222233445555   4566788999988764333334


Q ss_pred             HHHHhhhhhhhceeeecCCCCeEE-----------EEeccHHHHHHHHHhhCC
Q 043781          203 HNCLMRVLQEFAAIEVDGDENPLS-----------LTSTCQEKLRHLTLTLGL  244 (297)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~gs~ii-----------iTTr~~~~~~~v~~~~~~  244 (297)
                      =+.+.+.  ..+++.-.++++|.|           -|||--.....+-..+|+
T Consensus       124 YpaMEDf--~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~lt~PLrdRFGi  174 (332)
T COG2255         124 YPAMEDF--RLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTNPLRDRFGI  174 (332)
T ss_pred             hhhhhhe--eEEEEEccCCccceEeccCCCeeEeeeccccccccchhHHhcCC
Confidence            4444332  122333345555543           388833333334445564

>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=96.79  E-value=0.0013  Score=54.51  Aligned_cols=103  Identities=17%  Similarity=0.098  Sum_probs=58.8

Q ss_pred             cccccCCcchHHHHHHHhcccccc-cCCCceEEEEeCCCCCH---HHHHHHHHHhhcCC---CceEEEEEeCCCCCCc--
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVI-ENFDKRIWVCVSDPFDE---FRIAKAIIEGLEGS---EKKFFLILDDVWTDDY--  196 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~-~~F~~~~wv~vs~~~~~---~~~~~~i~~~~~~~---~kr~LiVlDdv~~~~~--  196 (297)
                      -++|+.|+|||.||+.+.+  .+. ......+-+..+.-...   ...+..........   ...-+|+||++...+.  
T Consensus         7 ll~GpsGvGKT~la~~la~--~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~~~~   84 (171)
T PF07724_consen    7 LLAGPSGVGKTELAKALAE--LLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAHPSN   84 (171)
T ss_dssp             EEESSTTSSHHHHHHHHHH--HHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCSHTT
T ss_pred             EEECCCCCCHHHHHHHHHH--HhccCCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhHHHhhccccc
Confidence            3679999999999999988  343 34445555555443331   11111111111111   2223999999999887  


Q ss_pred             ---------cCHHHHHHHHhhhhhh-hceeeecCCCCeEEEEec
Q 043781          197 ---------SKWEPFHNCLMRVLQE-FAAIEVDGDENPLSLTST  230 (297)
Q Consensus       197 ---------~~w~~l~~~l~~~~~~-~~~~~~~~~gs~iiiTTr  230 (297)
                               ..|+.|...|..+... ..-..++-.++-+|.||.
T Consensus        85 ~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn  128 (171)
T PF07724_consen   85 SGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSN  128 (171)
T ss_dssp             TTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEES
T ss_pred             cccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecc
Confidence                     7788888888665211 111223334455666665

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 ....

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.78  E-value=0.014  Score=53.43  Aligned_cols=121  Identities=16%  Similarity=0.096  Sum_probs=67.5

Q ss_pred             ccccCCcchHHHHHHHhccccc---------------------ccCCCceEEEEe-C---------CCCCHHHHHHHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV---------------------IENFDKRIWVCV-S---------DPFDEFRIAKAIIE  175 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~---------------------~~~F~~~~wv~v-s---------~~~~~~~~~~~i~~  175 (297)
                      ++|+.|+||||+|..+..--.-                     ..|-|. .++.. +         ....+.++ +++.+
T Consensus        26 f~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~-~~~~p~~~~~~~g~~~~~I~id~i-R~l~~  103 (325)
T PRK08699         26 FAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDF-YEITPLSDEPENGRKLLQIKIDAV-REIID  103 (325)
T ss_pred             eECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCE-EEEecccccccccccCCCcCHHHH-HHHHH
Confidence            7899999999999887763110                     112232 22321 1         11344443 33545


Q ss_pred             hhcCC---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCccccCC
Q 043781          176 GLEGS---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFPVS  251 (297)
Q Consensus       176 ~~~~~---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~l~  251 (297)
                      .+...   +++=++|+|++...+...-+.+...+...          ..+..+|++|++.+.   +..... -...+++.
T Consensus       104 ~~~~~p~~~~~kV~iiEp~~~Ld~~a~naLLk~LEep----------~~~~~~Ilvth~~~~---ll~ti~SRc~~~~~~  170 (325)
T PRK08699        104 NVYLTSVRGGLRVILIHPAESMNLQAANSLLKVLEEP----------PPQVVFLLVSHAADK---VLPTIKSRCRKMVLP  170 (325)
T ss_pred             HHhhCcccCCceEEEEechhhCCHHHHHHHHHHHHhC----------cCCCEEEEEeCChHh---ChHHHHHHhhhhcCC
Confidence            44432   44455567999887655666676666542          345667778876432   221111 12567788


Q ss_pred             ccchhhhhhhh
Q 043781          252 IFDAKKIWGWE  262 (297)
Q Consensus       252 ~l~~~~lf~~~  262 (297)
                      +++.++...|-
T Consensus       171 ~~~~~~~~~~L  181 (325)
T PRK08699        171 APSHEEALAYL  181 (325)
T ss_pred             CCCHHHHHHHH
Confidence            88777655553

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=96.77  E-value=0.0085  Score=55.40  Aligned_cols=78  Identities=12%  Similarity=0.012  Sum_probs=47.0

Q ss_pred             HHHHHhhcCC---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCc
Q 043781          171 KAIIEGLEGS---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRA  246 (297)
Q Consensus       171 ~~i~~~~~~~---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~  246 (297)
                      +.+.+.+...   +++-++|+|++...+.+..+.|...+..-          .....+|++|...+   .+..+.. -..
T Consensus       127 R~l~~~l~~~~~~g~~rVviIDeAd~l~~~aanaLLk~LEEp----------p~~~~fiLit~~~~---~llptIrSRc~  193 (351)
T PRK09112        127 RRVGHFLSQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEP----------PARALFILISHSSG---RLLPTIRSRCQ  193 (351)
T ss_pred             HHHHHHhhhccccCCceEEEEEchhhcCHHHHHHHHHHHhcC----------CCCceEEEEECChh---hccHHHHhhcc
Confidence            3455444432   67779999999998777777787777542          33455555554332   2222111 125


Q ss_pred             cccCCccchhhhhhh
Q 043781          247 KFPVSIFDAKKIWGW  261 (297)
Q Consensus       247 ~~~l~~l~~~~lf~~  261 (297)
                      .+++.+++..++..|
T Consensus       194 ~i~l~pl~~~~~~~~  208 (351)
T PRK09112        194 PISLKPLDDDELKKA  208 (351)
T ss_pred             EEEecCCCHHHHHHH
Confidence            778888887776444

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.76  E-value=0.0073  Score=53.12  Aligned_cols=110  Identities=15%  Similarity=0.107  Sum_probs=71.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC-----CCCHHHHHHHHHHhhcCC-------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD-----PFDEFRIAKAIIEGLEGS-------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~-----~~~~~~~~~~i~~~~~~~-------------------  180 (297)
                      .++||-.|+|||||++.+..   ....-...++....+     .....+-..++++.++..                   
T Consensus        42 ~glVGESG~GKSTlgr~i~~---L~~pt~G~i~f~g~~i~~~~~~~~~~~v~elL~~Vgl~~~~~~ryPhelSGGQrQRi  118 (268)
T COG4608          42 LGLVGESGCGKSTLGRLILG---LEEPTSGEILFEGKDITKLSKEERRERVLELLEKVGLPEEFLYRYPHELSGGQRQRI  118 (268)
T ss_pred             EEEEecCCCCHHHHHHHHHc---CcCCCCceEEEcCcchhhcchhHHHHHHHHHHHHhCCCHHHhhcCCcccCchhhhhH
Confidence            57999999999999999998   434444455443221     112334455666666654                   


Q ss_pred             -------CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCCC
Q 043781          181 -------EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLR  245 (297)
Q Consensus       181 -------~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~~  245 (297)
                             -+.-|||.|..-+. +.+.-.++...|.+.-        ...|-..+..|++-+++++++....+.
T Consensus       119 ~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq--------~~~~lt~lFIsHDL~vv~~isdri~VM  183 (268)
T COG4608         119 GIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQ--------EELGLTYLFISHDLSVVRYISDRIAVM  183 (268)
T ss_pred             HHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHH--------HHhCCeEEEEEEEHHhhhhhcccEEEE
Confidence                   67889999987664 2222334444554321        145677888899888899988765443

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

Probab=96.75  E-value=0.0019  Score=57.29  Aligned_cols=160  Identities=16%  Similarity=0.160  Sum_probs=82.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC--CCHHHHHHHHHHhhcCCCceEEEEEeCCCCC-------Ccc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP--FDEFRIAKAIIEGLEGSEKKFFLILDDVWTD-------DYS  197 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~--~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~-------~~~  197 (297)
                      +||.+|.|||-||+.|.|  .....|-.++--..-+.  -+-.++.++++.-... .-..++.+|.+...       +..
T Consensus       224 lyG~PGTGKTLLAKAVAN--qTSATFlRvvGseLiQkylGdGpklvRqlF~vA~e-~apSIvFiDEIdAiGtKRyds~Sg  300 (440)
T KOG0726|consen  224 LYGEPGTGKTLLAKAVAN--QTSATFLRVVGSELIQKYLGDGPKLVRELFRVAEE-HAPSIVFIDEIDAIGTKRYDSNSG  300 (440)
T ss_pred             EeCCCCCchhHHHHHHhc--ccchhhhhhhhHHHHHHHhccchHHHHHHHHHHHh-cCCceEEeehhhhhccccccCCCc
Confidence            689999999999999999  45555532221000000  1233455555544433 56677888887532       101


Q ss_pred             CHHHHHH-HH--hhhhhhhceeeecCCCCeEEEEec-cHHHHHHHHHhhCCCccccCCccchhhhhhhhhccCCCCCC--
Q 043781          198 KWEPFHN-CL--MRVLQEFAAIEVDGDENPLSLTST-CQEKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRNTSTR--  271 (297)
Q Consensus       198 ~w~~l~~-~l--~~~~~~~~~~~~~~~gs~iiiTTr-~~~~~~~v~~~~~~~~~~~l~~l~~~~lf~~~~f~~~~~~~--  271 (297)
                      --..+.. .|  -+.+.+|.    +...-+||.+|. .+...-.+.....+.+-+.+..-|..-  .+++|.-+.+.-  
T Consensus       301 gerEiQrtmLELLNQldGFd----srgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~T--kkkIf~IHTs~Mtl  374 (440)
T KOG0726|consen  301 GEREIQRTMLELLNQLDGFD----SRGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKT--KKKIFQIHTSRMTL  374 (440)
T ss_pred             cHHHHHHHHHHHHHhccCcc----ccCCeEEEEecccccccCHhhcCCCccccccccCCCchhh--hceeEEEeecccch
Confidence            1111221 11  11122221    123346776664 222233333444444445555445444  567776443321  


Q ss_pred             --chhhHhhhhhhccccccccchhhc
Q 043781          272 --PGMVSRYLMAEFCEPVCSVKAWCA  295 (297)
Q Consensus       272 --~~~~~~~~~~~~c~~~c~~~~~~~  295 (297)
                        .-.+..++..+.-+|+.-|+|.|.
T Consensus       375 ~~dVnle~li~~kddlSGAdIkAict  400 (440)
T KOG0726|consen  375 AEDVNLEELIMTKDDLSGADIKAICT  400 (440)
T ss_pred             hccccHHHHhhcccccccccHHHHHH
Confidence              224455555667899999999994

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=96.74  E-value=0.0026  Score=61.64  Aligned_cols=60  Identities=18%  Similarity=0.197  Sum_probs=36.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|++|+|||+||+.+.+.  ..-+|     +.++...       .....++.++..... ..+.+|+||++..
T Consensus        92 LL~GppGtGKT~la~alA~~--~~~~~-----~~i~~~~~~~~~~g~~~~~l~~~f~~a~~-~~p~Il~iDEid~  158 (495)
T TIGR01241        92 LLVGPPGTGKTLLAKAVAGE--AGVPF-----FSISGSDFVEMFVGVGASRVRDLFEQAKK-NAPCIIFIDEIDA  158 (495)
T ss_pred             EEECCCCCCHHHHHHHHHHH--cCCCe-----eeccHHHHHHHHhcccHHHHHHHHHHHHh-cCCCEEEEechhh
Confidence            47899999999999999984  32222     2222110       011233444444332 4568999999965

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.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=96.72  E-value=0.0051  Score=55.72  Aligned_cols=96  Identities=18%  Similarity=0.048  Sum_probs=63.8

Q ss_pred             cccccCCcchHHHHHHHhccccccc-------------------CCCceEEEEeCCCCC---HHHHHHHHHHhhcCC---
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE-------------------NFDKRIWVCVSDPFD---EFRIAKAIIEGLEGS---  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~-------------------~F~~~~wv~vs~~~~---~~~~~~~i~~~~~~~---  180 (297)
                      =++|++|+||||+|..+.+.-.-..                   ...-...+..+....   ..+..+++.+.....   
T Consensus        28 L~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~~~~~  107 (325)
T COG0470          28 LFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLSESPLE  107 (325)
T ss_pred             eeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecccccCCCcchHHHHHHHHHHhccCCCC
Confidence            3779999999999998887422111                   123445555555554   466677777766554   


Q ss_pred             CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          181 EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       181 ~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      ++.-+++||++.....+.-..+...+..          ....+++|++|..
T Consensus       108 ~~~kviiidead~mt~~A~nallk~lEe----------p~~~~~~il~~n~  148 (325)
T COG0470         108 GGYKVVIIDEADKLTEDAANALLKTLEE----------PPKNTRFILITND  148 (325)
T ss_pred             CCceEEEeCcHHHHhHHHHHHHHHHhcc----------CCCCeEEEEEcCC
Confidence            7889999999988754445555555543          2667788888763

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

Probab=96.70  E-value=0.017  Score=57.09  Aligned_cols=66  Identities=24%  Similarity=0.345  Sum_probs=41.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHH-----------HHHHHHhhcCC-CceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRI-----------AKAIIEGLEGS-EKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~-----------~~~i~~~~~~~-~kr~LiVlDdv~  192 (297)
                      .-+||++|+|||.|++.|++  .+.+.|   +-+++..--|..+|           -..|+..+... .+.=|++||.+.
T Consensus       353 LcLVGPPGVGKTSLgkSIA~--al~Rkf---vR~sLGGvrDEAEIRGHRRTYIGamPGrIiQ~mkka~~~NPv~LLDEID  427 (782)
T COG0466         353 LCLVGPPGVGKTSLGKSIAK--ALGRKF---VRISLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKAGVKNPVFLLDEID  427 (782)
T ss_pred             EEEECCCCCCchhHHHHHHH--HhCCCE---EEEecCccccHHHhccccccccccCChHHHHHHHHhCCcCCeEEeechh
Confidence            45899999999999999999  566666   22333333333322           12233333222 467789999998


Q ss_pred             CCC
Q 043781          193 TDD  195 (297)
Q Consensus       193 ~~~  195 (297)
                      ...
T Consensus       428 Km~  430 (782)
T COG0466         428 KMG  430 (782)
T ss_pred             hcc
Confidence            653

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=96.66  E-value=0.0031  Score=57.88  Aligned_cols=65  Identities=23%  Similarity=0.356  Sum_probs=54.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc-CC-----------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE-GS-----------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~-~~-----------------------  180 (297)
                      .-|+|-.|.|||.+.+.+++..  ..   ..+|+++-.-++...++..|+.+++ .+                       
T Consensus        33 ~~iyG~sgTGKT~~~r~~l~~~--n~---~~vw~n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~  107 (438)
T KOG2543|consen   33 VHIYGHSGTGKTYLVRQLLRKL--NL---ENVWLNCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQW  107 (438)
T ss_pred             EEEeccCCCchhHHHHHHHhhc--CC---cceeeehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhh
Confidence            3589999999999999999953  22   3589999999999999999999985 21                       


Q ss_pred             ------CceEEEEEeCCCCC
Q 043781          181 ------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 ------~kr~LiVlDdv~~~  194 (297)
                            ++.++||||++..-
T Consensus       108 ~~~t~~d~~~~liLDnad~l  127 (438)
T KOG2543|consen  108 PAATNRDQKVFLILDNADAL  127 (438)
T ss_pred             HHhhccCceEEEEEcCHHhh
Confidence                  57999999999764

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=96.66  E-value=0.015  Score=57.22  Aligned_cols=118  Identities=18%  Similarity=0.169  Sum_probs=65.9

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEeCCCCCHHHHHHHHHHhhcC---CCce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCVSDPFDEFRIAKAIIEGLEG---SEKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~---~~kr  183 (297)
                      ++|+.|+||||+|+.+.+.---.                    .+++. +++.......+.++. ++.+.+..   .+++
T Consensus        43 f~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~~~~~dv-~~idgas~~~vddIr-~l~e~~~~~p~~~~~  120 (563)
T PRK06647         43 FSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDV-IEIDGASNTSVQDVR-QIKEEIMFPPASSRY  120 (563)
T ss_pred             EECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHcCCCCCe-EEecCcccCCHHHHH-HHHHHHHhchhcCCC
Confidence            78999999999999988742111                    12332 333333334454443 34333221   1566


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCccccCCccchhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFPVSIFDAKKIW  259 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~l~~l~~~~lf  259 (297)
                      =++|+|++.......++.|...+..-          .+...+|++|...   ..+....- -...+.+..++..++.
T Consensus       121 KVvIIDEa~~Ls~~a~naLLK~LEep----------p~~~vfI~~tte~---~kL~~tI~SRc~~~~f~~l~~~el~  184 (563)
T PRK06647        121 RVYIIDEVHMLSNSAFNALLKTIEEP----------PPYIVFIFATTEV---HKLPATIKSRCQHFNFRLLSLEKIY  184 (563)
T ss_pred             EEEEEEChhhcCHHHHHHHHHhhccC----------CCCEEEEEecCCh---HHhHHHHHHhceEEEecCCCHHHHH
Confidence            68999999877655677776666541          3455565555432   22322211 1145677777666653

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=96.63  E-value=0.011  Score=59.40  Aligned_cols=75  Identities=20%  Similarity=0.265  Sum_probs=47.8

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHH-HHHhhcCC------------------CceE-EE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKA-IIEGLEGS------------------EKKF-FL  186 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~-i~~~~~~~------------------~kr~-Li  186 (297)
                      ..|+.|||||.||+.+...  +-+.-+..+-+      |+.+.+.. -.+.+-++                  .+.| +|
T Consensus       526 F~GPTGVGKTELAkaLA~~--Lfg~e~aliR~------DMSEy~EkHsVSrLIGaPPGYVGyeeGG~LTEaVRr~PySVi  597 (786)
T COG0542         526 FLGPTGVGKTELAKALAEA--LFGDEQALIRI------DMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVI  597 (786)
T ss_pred             eeCCCcccHHHHHHHHHHH--hcCCCccceee------chHHHHHHHHHHHHhCCCCCCceeccccchhHhhhcCCCeEE
Confidence            5799999999999988872  21111233333      44443322 22333222                  5656 88


Q ss_pred             EEeCCCCCCccCHHHHHHHHhhh
Q 043781          187 ILDDVWTDDYSKWEPFHNCLMRV  209 (297)
Q Consensus       187 VlDdv~~~~~~~w~~l~~~l~~~  209 (297)
                      .||.|-..+++.++-+...|.++
T Consensus       598 LlDEIEKAHpdV~nilLQVlDdG  620 (786)
T COG0542         598 LLDEIEKAHPDVFNLLLQVLDDG  620 (786)
T ss_pred             EechhhhcCHHHHHHHHHHhcCC
Confidence            89999988888888888888765

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=96.60  E-value=0.0083  Score=53.02  Aligned_cols=69  Identities=20%  Similarity=0.297  Sum_probs=48.7

Q ss_pred             cccccccCCcchHHHHHHHhcccccccC----CCceEEEEeCCCCCHHHHHHHHHHhhcCC-------------------
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIEN----FDKRIWVCVSDPFDEFRIAKAIIEGLEGS-------------------  180 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-------------------  180 (297)
                      ..+|+|.+|+|||.|+.+++-+..+...    =...+|++....|+..++. +|++..+..                   
T Consensus        40 itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~Rl~-~i~~~~~~~~~~~l~~I~v~~~~~~~~l  118 (256)
T PF08423_consen   40 ITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPERLQ-QIAERFGLDPEEILDNIFVIRVFDLEEL  118 (256)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHHHH-HHHHHTTS-HHHHHHTEEEEE-SSHHHH
T ss_pred             EEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHHHH-HHhhccccccchhhhceeeeecCCHHHH
Confidence            4579999999999999877654333221    2358899999999887764 566654432                   


Q ss_pred             -------------CceEEEEEeCCCC
Q 043781          181 -------------EKKFFLILDDVWT  193 (297)
Q Consensus       181 -------------~kr~LiVlDdv~~  193 (297)
                                   .+-=|||+|.+-.
T Consensus       119 ~~~L~~l~~~l~~~~ikLIVIDSIaa  144 (256)
T PF08423_consen  119 LELLEQLPKLLSESKIKLIVIDSIAA  144 (256)
T ss_dssp             HHHHHHHHHHHHHSCEEEEEEETSSH
T ss_pred             HHHHHHHHhhccccceEEEEecchHH
Confidence                         6677999999854

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=96.60  E-value=0.0086  Score=56.35  Aligned_cols=114  Identities=20%  Similarity=0.341  Sum_probs=65.6

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC----CCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP----FDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKW  199 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~----~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w  199 (297)
                      ..-|+|+-++|||||++.+...  ..+.   .+++...+.    ....+.+.........  ++.+|+||.|...  ..|
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~--~~~~---~iy~~~~d~~~~~~~l~d~~~~~~~~~~~--~~~yifLDEIq~v--~~W  109 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKG--LLEE---IIYINFDDLRLDRIELLDLLRAYIELKER--EKSYIFLDEIQNV--PDW  109 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhh--CCcc---eEEEEecchhcchhhHHHHHHHHHHhhcc--CCceEEEecccCc--hhH
Confidence            4568899999999999777663  2222   455543322    2233333333333222  7799999999998  578


Q ss_pred             HHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHH-HHHHHh-hCCCccccCCccchhh
Q 043781          200 EPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKL-RHLTLT-LGLRAKFPVSIFDAKK  257 (297)
Q Consensus       200 ~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~-~~v~~~-~~~~~~~~l~~l~~~~  257 (297)
                      +..-..+.+.          ++. +|++|+-+.... ...+.. .|-...+.+-+++=.|
T Consensus       110 ~~~lk~l~d~----------~~~-~v~itgsss~ll~~~~~~~L~GR~~~~~l~PlSF~E  158 (398)
T COG1373         110 ERALKYLYDR----------GNL-DVLITGSSSSLLSKEISESLAGRGKDLELYPLSFRE  158 (398)
T ss_pred             HHHHHHHHcc----------ccc-eEEEECCchhhhccchhhhcCCCceeEEECCCCHHH
Confidence            8766666553          344 777876543221 222222 2223455566665444

>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=96.53  E-value=0.0021  Score=57.34  Aligned_cols=73  Identities=27%  Similarity=0.302  Sum_probs=40.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCCc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDDY  196 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~~  196 (297)
                      =++|..|+|||++++.....-. ...| ...-++.|.......+++-|-..+...         +|+.++.+||+--...
T Consensus        37 Ll~G~~GtGKT~li~~~l~~l~-~~~~-~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDDlN~p~~  114 (272)
T PF12775_consen   37 LLVGPSGTGKTSLIQNFLSSLD-SDKY-LVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDDLNMPQP  114 (272)
T ss_dssp             EEESSTTSSHHHHHHHHHHCST-TCCE-EEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEETTT-S--
T ss_pred             EEECCCCCchhHHHHhhhccCC-cccc-ceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecccCCCCC
Confidence            3789999999999998876311 1111 123344554444444433222222111         8999999999987654


Q ss_pred             cCHH
Q 043781          197 SKWE  200 (297)
Q Consensus       197 ~~w~  200 (297)
                      +.|.
T Consensus       115 d~yg  118 (272)
T PF12775_consen  115 DKYG  118 (272)
T ss_dssp             -TTS
T ss_pred             CCCC
Confidence            5543

>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=96.52  E-value=0.015  Score=48.36  Aligned_cols=104  Identities=15%  Similarity=0.163  Sum_probs=59.2

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEE---eCCCCCHHHHHH------HHHHhhcCC--------------
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC---VSDPFDEFRIAK------AIIEGLEGS--------------  180 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~---vs~~~~~~~~~~------~i~~~~~~~--------------  180 (297)
                      ...|+|..|.|||||.+.+...   .......+++.   +.. .+......      ++++.++..              
T Consensus        27 ~~~l~G~nGsGKStLl~~i~G~---~~~~~G~v~~~g~~~~~-~~~~~~~~~i~~~~q~l~~~gl~~~~~~~~~~LS~G~  102 (180)
T cd03214          27 IVGILGPNGAGKSTLLKTLAGL---LKPSSGEILLDGKDLAS-LSPKELARKIAYVPQALELLGLAHLADRPFNELSGGE  102 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC---CCCCCcEEEECCEECCc-CCHHHHHHHHhHHHHHHHHcCCHhHhcCCcccCCHHH
Confidence            3468899999999999999983   23344445442   221 12211111      133333221              


Q ss_pred             -----------CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHH
Q 043781          181 -----------EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLT  239 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~  239 (297)
                                 ...-+++||+--.. +....+.+...+....        ...|..||++|+..+....++
T Consensus       103 ~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~--------~~~~~tiii~sh~~~~~~~~~  165 (180)
T cd03214         103 RQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLA--------RERGKTVVMVLHDLNLAARYA  165 (180)
T ss_pred             HHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHH--------HhcCCEEEEEeCCHHHHHHhC
Confidence                       77889999988754 2233444555554431        022678899998655444443

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.52  E-value=0.16  Score=49.22  Aligned_cols=22  Identities=32%  Similarity=0.258  Sum_probs=18.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ....++|.+|+||||++.++..
T Consensus       351 ~vIaLVGPtGvGKTTtaakLAa  372 (559)
T PRK12727        351 GVIALVGPTGAGKTTTIAKLAQ  372 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4557889999999999988776

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.50  E-value=0.086  Score=49.08  Aligned_cols=22  Identities=32%  Similarity=0.302  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...++|+.|+||||++.++...
T Consensus       139 ii~lvGptGvGKTTtiakLA~~  160 (374)
T PRK14722        139 VFALMGPTGVGKTTTTAKLAAR  160 (374)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4458999999999999988874

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.48  E-value=0.0078  Score=53.95  Aligned_cols=93  Identities=19%  Similarity=0.156  Sum_probs=65.3

Q ss_pred             hHHHHHHHHHHHHHhhhhcccccccCCcccccccccccccccccccccCCcchHHHHHHHhccccccc----CCCceEEE
Q 043781           83 KIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWV  158 (297)
Q Consensus        83 ~i~~i~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv  158 (297)
                      +.+++.++|+++...-               ....    +.-.-|||..|.|||++++.+.+.--...    .--.++.|
T Consensus        41 ~A~~~L~~L~~Ll~~P---------------~~~R----mp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~v  101 (302)
T PF05621_consen   41 RAKEALDRLEELLEYP---------------KRHR----MPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYV  101 (302)
T ss_pred             HHHHHHHHHHHHHhCC---------------cccC----CCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEE
Confidence            6677778888775211               1111    11234899999999999999886421111    01146677


Q ss_pred             EeCCCCCHHHHHHHHHHhhcCC--------------------CceEEEEEeCCCCC
Q 043781          159 CVSDPFDEFRIAKAIIEGLEGS--------------------EKKFFLILDDVWTD  194 (297)
Q Consensus       159 ~vs~~~~~~~~~~~i~~~~~~~--------------------~kr~LiVlDdv~~~  194 (297)
                      .+...++...+...|+.+++.+                    -+-=+||+|.+.+.
T Consensus       102 q~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~l  157 (302)
T PF05621_consen  102 QMPPEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNL  157 (302)
T ss_pred             ecCCCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHH
Confidence            8889999999999999999887                    44557889999873

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=96.46  E-value=0.0085  Score=61.87  Aligned_cols=103  Identities=17%  Similarity=0.164  Sum_probs=55.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC---HHHHH------------HHHHHhhcCCCceEEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD---EFRIA------------KAIIEGLEGSEKKFFLILDD  190 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~---~~~~~------------~~i~~~~~~~~kr~LiVlDd  190 (297)
                      -++|++|+|||+||+.+...  ....-...+.+..+....   ...+.            ..+...+.. ....+|+||+
T Consensus       599 Lf~Gp~GvGKt~lA~~La~~--l~~~~~~~i~~d~s~~~~~~~~~~l~g~~~g~~g~~~~g~l~~~v~~-~p~~vlllDe  675 (852)
T TIGR03346       599 LFLGPTGVGKTELAKALAEF--LFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRR-KPYSVVLFDE  675 (852)
T ss_pred             EEEcCCCCCHHHHHHHHHHH--hcCCCCcEEEEechhhcccchHHHhcCCCCCccCcccccHHHHHHHc-CCCcEEEEec
Confidence            47899999999999999873  221112223333332211   11110            011111111 2335999999


Q ss_pred             CCCCCccCHHHHHHHHhhhh-hhhceeeecCCCCeEEEEecc
Q 043781          191 VWTDDYSKWEPFHNCLMRVL-QEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       191 v~~~~~~~w~~l~~~l~~~~-~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      +...+.+.++.|...|..+. .......++-.++-||+||..
T Consensus       676 ieka~~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~  717 (852)
T TIGR03346       676 VEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNL  717 (852)
T ss_pred             cccCCHHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeCCc
Confidence            99888788888888886541 101111112234557777763

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=96.41  E-value=0.0067  Score=54.46  Aligned_cols=19  Identities=37%  Similarity=0.373  Sum_probs=16.3

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -++|.+|+||||+|+.+.+
T Consensus        62 ll~G~pGTGKT~lA~~ia~   80 (284)
T TIGR02880        62 SFTGNPGTGKTTVALRMAQ   80 (284)
T ss_pred             EEEcCCCCCHHHHHHHHHH
Confidence            4789999999999977665

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.

>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=96.37  E-value=0.0018  Score=49.91  Aligned_cols=21  Identities=33%  Similarity=0.314  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+|+.+.+.
T Consensus         2 I~I~G~~gsGKST~a~~La~~   22 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAER   22 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999999884

...

>CHL00095 clpC Clp protease ATP binding subunit

Probab=96.35  E-value=0.0076  Score=62.00  Aligned_cols=101  Identities=15%  Similarity=0.154  Sum_probs=54.0

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC---CHHHHH------------HHHHHhhcCCCceEEEEEeCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF---DEFRIA------------KAIIEGLEGSEKKFFLILDDV  191 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~---~~~~~~------------~~i~~~~~~~~kr~LiVlDdv  191 (297)
                      ++|+.|+|||+||+.+.+.  +-..-...+-+..+.-.   .+..+.            ..+.+.+.. ...-+++||++
T Consensus       544 f~Gp~GvGKt~lA~~LA~~--l~~~~~~~~~~d~s~~~~~~~~~~l~g~~~gyvg~~~~~~l~~~~~~-~p~~VvllDei  620 (821)
T CHL00095        544 FSGPTGVGKTELTKALASY--FFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAVRK-KPYTVVLFDEI  620 (821)
T ss_pred             EECCCCCcHHHHHHHHHHH--hcCCccceEEEEchhccccccHHHhcCCCCcccCcCccchHHHHHHh-CCCeEEEECCh
Confidence            6799999999999988872  21111122222222211   111111            011122211 23468999999


Q ss_pred             CCCCccCHHHHHHHHhhhh-hhhceeeecCCCCeEEEEec
Q 043781          192 WTDDYSKWEPFHNCLMRVL-QEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       192 ~~~~~~~w~~l~~~l~~~~-~~~~~~~~~~~gs~iiiTTr  230 (297)
                      ...+.+.++.|...|..+- ....-..++-..+-+|+||.
T Consensus       621 eka~~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn  660 (821)
T CHL00095        621 EKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSN  660 (821)
T ss_pred             hhCCHHHHHHHHHHhccCceecCCCcEEecCceEEEEeCC
Confidence            9888778888888876541 11111222234566777765

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=96.32  E-value=0.013  Score=60.36  Aligned_cols=67  Identities=18%  Similarity=0.194  Sum_probs=44.1

Q ss_pred             cccccCCcchHHHHHHHhccccccc------CCCceEE-EEeC-------CCCCHHHHHHHHHHhhcCCCceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE------NFDKRIW-VCVS-------DPFDEFRIAKAIIEGLEGSEKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~------~F~~~~w-v~vs-------~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv  191 (297)
                      -++|.+|+||||||+.+.+.  +..      -.+..+| +.++       ..-...+-++.++..+...+++.+|++|++
T Consensus       212 lLvG~pGvGKTal~~~La~~--i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEi  289 (852)
T TIGR03345       212 ILTGEAGVGKTAVVEGLALR--IAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEA  289 (852)
T ss_pred             eEECCCCCCHHHHHHHHHHH--HhhCCCCccccCCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeCh
Confidence            37899999999999999884  321      1234444 2222       112344566677776654467899999999


Q ss_pred             CCC
Q 043781          192 WTD  194 (297)
Q Consensus       192 ~~~  194 (297)
                      ...
T Consensus       290 h~l  292 (852)
T TIGR03345       290 HTL  292 (852)
T ss_pred             HHh
Confidence            864

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.

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

Probab=96.31  E-value=0.011  Score=57.86  Aligned_cols=60  Identities=22%  Similarity=0.230  Sum_probs=43.1

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCce-------EEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKR-------IWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~-------~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =+||+||+|||++|+.+.+  +..-.|-.+       -||.     .-++.+++++++... .-..+|.||.+..
T Consensus       472 LlyGPPGC~KT~lAkalAn--e~~~nFlsvkgpEL~sk~vG-----eSEr~ir~iF~kAR~-~aP~IiFfDEiDs  538 (693)
T KOG0730|consen  472 LLYGPPGCGKTLLAKALAN--EAGMNFLSVKGPELFSKYVG-----ESERAIREVFRKARQ-VAPCIIFFDEIDA  538 (693)
T ss_pred             EEECCCCcchHHHHHHHhh--hhcCCeeeccCHHHHHHhcC-----chHHHHHHHHHHHhh-cCCeEEehhhHHh
Confidence            3689999999999999999  455556222       1332     346677778777766 3459999999975

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=96.30  E-value=0.034  Score=55.31  Aligned_cols=81  Identities=14%  Similarity=0.109  Sum_probs=49.1

Q ss_pred             ccccCCcchHHHHHHHhcccccccCC---------------------CceEEEEeCCCCCHHHHHHHHHHhhcCC---Cc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENF---------------------DKRIWVCVSDPFDEFRIAKAIIEGLEGS---EK  182 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F---------------------~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~k  182 (297)
                      ++|..|+||||+|+.+.+.-......                     .-.+.+.......+. -.+++++.+...   ++
T Consensus        43 f~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~i~~g~h~D~~ei~~~~~~~vd-~IReii~~a~~~p~~~~  121 (620)
T PRK14948         43 FTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEIDAASNTGVD-NIRELIERAQFAPVQAR  121 (620)
T ss_pred             EECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHHHhcCCCccEEEEeccccCCHH-HHHHHHHHHhhChhcCC
Confidence            68999999999999988742111100                     012223322233343 345555554332   56


Q ss_pred             eEEEEEeCCCCCCccCHHHHHHHHhh
Q 043781          183 KFFLILDDVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       183 r~LiVlDdv~~~~~~~w~~l~~~l~~  208 (297)
                      +-++|+|++.......++.|...+..
T Consensus       122 ~KViIIDEad~Lt~~a~naLLK~LEe  147 (620)
T PRK14948        122 WKVYVIDECHMLSTAAFNALLKTLEE  147 (620)
T ss_pred             ceEEEEECccccCHHHHHHHHHHHhc
Confidence            67899999988765677778777754

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.29  E-value=0.12  Score=46.32  Aligned_cols=23  Identities=30%  Similarity=0.278  Sum_probs=19.3

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|+.|+||||++..+...
T Consensus       195 ~vi~~vGptGvGKTTt~~kLa~~  217 (282)
T TIGR03499       195 GVIALVGPTGVGKTTTLAKLAAR  217 (282)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35678899999999999888774

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=96.27  E-value=0.011  Score=60.15  Aligned_cols=62  Identities=21%  Similarity=0.191  Sum_probs=38.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|++|+|||+||+.+.+.  ....|   +.+..+    ... .....++.++..... ....+|+||++..
T Consensus       491 LL~GppGtGKT~lakalA~e--~~~~f---i~v~~~~l~~~~vGese~~i~~~f~~A~~-~~p~iifiDEid~  557 (733)
T TIGR01243       491 LLFGPPGTGKTLLAKAVATE--SGANF---IAVRGPEILSKWVGESEKAIREIFRKARQ-AAPAIIFFDEIDA  557 (733)
T ss_pred             EEECCCCCCHHHHHHHHHHh--cCCCE---EEEehHHHhhcccCcHHHHHHHHHHHHHh-cCCEEEEEEChhh
Confidence            36899999999999999983  43333   222211    111 123345555554433 5678999999964

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.

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=96.25  E-value=0.032  Score=47.94  Aligned_cols=44  Identities=20%  Similarity=0.219  Sum_probs=30.0

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCC------CceEEEEeCCCCCHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENF------DKRIWVCVSDPFDEFRI  169 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F------~~~~wv~vs~~~~~~~~  169 (297)
                      ...|+|.+|+|||+|+..+....  ...-      ...+|+.....++..++
T Consensus        21 v~~I~G~~GsGKT~l~~~ia~~~--~~~~~~~g~~~~v~yi~~e~~~~~~rl   70 (226)
T cd01393          21 ITEIFGEFGSGKTQLCLQLAVEA--QLPGELGGLEGKVVYIDTEGAFRPERL   70 (226)
T ss_pred             EEEEeCCCCCChhHHHHHHHHHh--hcccccCCCcceEEEEecCCCCCHHHH
Confidence            34689999999999998887632  1122      45678877666655443

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.

>CHL00176 ftsH cell division protein; Validated

Probab=96.24  E-value=0.0045  Score=61.56  Aligned_cols=61  Identities=18%  Similarity=0.255  Sum_probs=37.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC-C-----C-HHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP-F-----D-EFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~-----~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .-++|++|+|||+||+.+.+.  ..-+|     +.++.. +     . ...-++.++.+... ....+|+||++..
T Consensus       219 VLL~GPpGTGKT~LAralA~e--~~~p~-----i~is~s~f~~~~~g~~~~~vr~lF~~A~~-~~P~ILfIDEID~  286 (638)
T CHL00176        219 VLLVGPPGTGKTLLAKAIAGE--AEVPF-----FSISGSEFVEMFVGVGAARVRDLFKKAKE-NSPCIVFIDEIDA  286 (638)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCCCe-----eeccHHHHHHHhhhhhHHHHHHHHHHHhc-CCCcEEEEecchh
Confidence            458899999999999999884  22222     222211 0     0 11223344444433 5789999999964

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.24  E-value=0.43  Score=46.00  Aligned_cols=23  Identities=30%  Similarity=0.294  Sum_probs=19.9

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|+.|+||||++.++...
T Consensus       257 ~Vi~LvGpnGvGKTTTiaKLA~~  279 (484)
T PRK06995        257 GVFALMGPTGVGKTTTTAKLAAR  279 (484)
T ss_pred             cEEEEECCCCccHHHHHHHHHHH
Confidence            45779999999999999988874

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.23  E-value=0.46  Score=45.13  Aligned_cols=21  Identities=33%  Similarity=0.316  Sum_probs=17.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...++|++|+||||++..+..
T Consensus       223 ~i~~vGptGvGKTTt~~kLA~  243 (424)
T PRK05703        223 VVALVGPTGVGKTTTLAKLAA  243 (424)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            567899999999998877765

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.22  E-value=0.018  Score=47.14  Aligned_cols=100  Identities=17%  Similarity=0.143  Sum_probs=55.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC--CCCHHH----------------HHH-HHHHhhcCCCceEE
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD--PFDEFR----------------IAK-AIIEGLEGSEKKFF  185 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~--~~~~~~----------------~~~-~i~~~~~~~~kr~L  185 (297)
                      ..|+|..|+|||||.+.+...   .......+++.-..  ..+..+                .++ .++..+.  .+.-+
T Consensus        29 ~~l~G~nGsGKSTLl~~i~G~---~~~~~G~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~~qrl~laral~--~~p~i  103 (163)
T cd03216          29 HALLGENGAGKSTLMKILSGL---YKPDSGEILVDGKEVSFASPRDARRAGIAMVYQLSVGERQMVEIARALA--RNARL  103 (163)
T ss_pred             EEEECCCCCCHHHHHHHHhCC---CCCCCeEEEECCEECCcCCHHHHHhcCeEEEEecCHHHHHHHHHHHHHh--cCCCE
Confidence            468899999999999999873   22334444442110  011111                111 1122222  57788


Q ss_pred             EEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHH
Q 043781          186 LILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHL  238 (297)
Q Consensus       186 iVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v  238 (297)
                      ++||+--.. |....+.+...+...         ...|..||++|++.+.....
T Consensus       104 lllDEP~~~LD~~~~~~l~~~l~~~---------~~~~~tiii~sh~~~~~~~~  148 (163)
T cd03216         104 LILDEPTAALTPAEVERLFKVIRRL---------RAQGVAVIFISHRLDEVFEI  148 (163)
T ss_pred             EEEECCCcCCCHHHHHHHHHHHHHH---------HHCCCEEEEEeCCHHHHHHh
Confidence            999998654 323344455555442         13467788999865544443

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=96.21  E-value=0.072  Score=44.32  Aligned_cols=102  Identities=16%  Similarity=0.090  Sum_probs=55.2

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEE------EeCCCC--CHHHHHH-HHHHhhcCCCceEEEEEeCCCCC
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWV------CVSDPF--DEFRIAK-AIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv------~vs~~~--~~~~~~~-~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      ...|+|..|+|||||.+.+..-..   .....+++      .+.+..  +.-+-++ .++..+.  .+.=+++||.--..
T Consensus        27 ~~~l~G~nGsGKSTLl~~l~Gl~~---p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~--~~p~lllLDEPts~  101 (177)
T cd03222          27 VIGIVGPNGTGKTTAVKILAGQLI---PNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALL--RNATFYLFDEPSAY  101 (177)
T ss_pred             EEEEECCCCChHHHHHHHHHcCCC---CCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHh--cCCCEEEEECCccc
Confidence            356899999999999999988422   22222222      123332  2211111 2333333  46778999988654


Q ss_pred             -CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHH
Q 043781          195 -DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHL  238 (297)
Q Consensus       195 -~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v  238 (297)
                       +....+.+...+.....        ..+..||++|++.+....+
T Consensus       102 LD~~~~~~l~~~l~~~~~--------~~~~tiiivsH~~~~~~~~  138 (177)
T cd03222         102 LDIEQRLNAARAIRRLSE--------EGKKTALVVEHDLAVLDYL  138 (177)
T ss_pred             CCHHHHHHHHHHHHHHHH--------cCCCEEEEEECCHHHHHHh
Confidence             22233334444443211        2236788888865544444

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.

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.20  E-value=0.017  Score=49.92  Aligned_cols=45  Identities=20%  Similarity=0.230  Sum_probs=31.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC----CCceEEEEeCCCCCHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN----FDKRIWVCVSDPFDEFRI  169 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~~  169 (297)
                      ..|+|.+|+|||+|+.++.-.......    -...+|+.....++..++
T Consensus        22 ~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl   70 (235)
T cd01123          22 TEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERL   70 (235)
T ss_pred             EEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHH
Confidence            468999999999999988753222221    357889987776665443

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 .

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.18  E-value=0.021  Score=58.03  Aligned_cols=67  Identities=27%  Similarity=0.308  Sum_probs=42.4

Q ss_pred             cccccCCcchHHHHHHHhcccc---cccCC-CceEEE-EeC------C-CCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD---VIENF-DKRIWV-CVS------D-PFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~---~~~~F-~~~~wv-~vs------~-~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|.+|+|||+||+.+.+.-.   +...+ +..+|. ..+      . .-...+-++.+++.+.. .++.+|++|++..
T Consensus       207 lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~-~~~~ILfiDEih~  285 (731)
T TIGR02639       207 LLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEK-EPNAILFIDEIHT  285 (731)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHHHHHHHHhc-cCCeEEEEecHHH
Confidence            4789999999999999988421   11111 344553 211      1 11344566777776644 3578999999974

>COG4618 ArpD ABC-type protease/lipase transport system, ATPase and permease components [General function prediction only]

Probab=96.17  E-value=0.013  Score=55.70  Aligned_cols=20  Identities=35%  Similarity=0.499  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+|+|+.|+||||||+.+..
T Consensus       365 lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         365 LGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             EEEECCCCccHHHHHHHHHc
Confidence            47999999999999999986

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.15  E-value=0.033  Score=56.09  Aligned_cols=93  Identities=22%  Similarity=0.245  Sum_probs=63.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHhhcCC------------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEGLEGS------------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~------------------------  180 (297)
                      -|-.+.|-|||||+-....  +.. .=..+.|.+....- +...++..++.+++..                        
T Consensus        41 li~APAGfGKttl~aq~~~--~~~-~~~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~  117 (894)
T COG2909          41 LISAPAGFGKTTLLAQWRE--LAA-DGAAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLL  117 (894)
T ss_pred             EEeCCCCCcHHHHHHHHHH--hcC-cccceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHH
Confidence            3568999999999988865  111 22357899876643 5566666666666532                        


Q ss_pred             ----------CceEEEEEeCCCCCCccCHHH-HHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          181 ----------EKKFFLILDDVWTDDYSKWEP-FHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       181 ----------~kr~LiVlDdv~~~~~~~w~~-l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                                .++.++||||.........+. ++..+...          ..+=.+|+|||.
T Consensus       118 ~~L~~Ela~~~~pl~LVlDDyHli~~~~l~~~l~fLl~~~----------P~~l~lvv~SR~  169 (894)
T COG2909         118 SSLLNELASYEGPLYLVLDDYHLISDPALHEALRFLLKHA----------PENLTLVVTSRS  169 (894)
T ss_pred             HHHHHHHHhhcCceEEEeccccccCcccHHHHHHHHHHhC----------CCCeEEEEEecc
Confidence                      778999999998764344443 54444442          566789999984

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=96.12  E-value=0.0081  Score=61.01  Aligned_cols=78  Identities=17%  Similarity=0.149  Sum_probs=46.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC---CHHHHHH------------HHHHhhcCCCceEEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF---DEFRIAK------------AIIEGLEGSEKKFFLILDD  190 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~---~~~~~~~------------~i~~~~~~~~kr~LiVlDd  190 (297)
                      -++|++|+|||+||+.+...  ..   ...+.+..+...   .+..+..            .+.+.+.. ...-+|+||+
T Consensus       488 lf~Gp~GvGKT~lA~~la~~--l~---~~~~~~d~se~~~~~~~~~lig~~~gyvg~~~~~~l~~~~~~-~p~~VvllDE  561 (731)
T TIGR02639       488 LFTGPTGVGKTELAKQLAEA--LG---VHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQGGLLTEAVRK-HPHCVLLLDE  561 (731)
T ss_pred             EEECCCCccHHHHHHHHHHH--hc---CCeEEEeCchhhhcccHHHHhcCCCCCcccchhhHHHHHHHh-CCCeEEEEec
Confidence            47799999999999999883  32   223344433311   1111110            11111111 3456999999


Q ss_pred             CCCCCccCHHHHHHHHhhh
Q 043781          191 VWTDDYSKWEPFHNCLMRV  209 (297)
Q Consensus       191 v~~~~~~~w~~l~~~l~~~  209 (297)
                      +...+.+.++.|...+..+
T Consensus       562 ieka~~~~~~~Ll~~ld~g  580 (731)
T TIGR02639       562 IEKAHPDIYNILLQVMDYA  580 (731)
T ss_pred             hhhcCHHHHHHHHHhhccC
Confidence            9988877787777777554

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

Probab=96.11  E-value=0.0083  Score=55.37  Aligned_cols=65  Identities=12%  Similarity=0.155  Sum_probs=43.3

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CC-CHHHHHHHHHHhhc----CCCceEEEEEeCCCC
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PF-DEFRIAKAIIEGLE----GSEKKFFLILDDVWT  193 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~-~~~~~~~~i~~~~~----~~~kr~LiVlDdv~~  193 (297)
                      ...|||++|+|||.+|+.+++.  ..-.|   +-+..+.    .. ..++.+++++....    ..++.++|++|++..
T Consensus       150 gllL~GPPGcGKTllAraiA~e--lg~~~---i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA  223 (413)
T PLN00020        150 ILGIWGGKGQGKSFQCELVFKK--MGIEP---IVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDA  223 (413)
T ss_pred             EEEeeCCCCCCHHHHHHHHHHH--cCCCe---EEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhh
Confidence            3578999999999999999994  44333   2222221    11 34556666655443    236899999999974

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.09  E-value=0.66  Score=43.95  Aligned_cols=22  Identities=32%  Similarity=0.315  Sum_probs=18.9

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ....++|..|+||||++..+..
T Consensus       192 ~vi~lvGpnG~GKTTtlakLA~  213 (420)
T PRK14721        192 GVYALIGPTGVGKTTTTAKLAA  213 (420)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999987765

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=96.08  E-value=0.013  Score=52.29  Aligned_cols=83  Identities=16%  Similarity=0.075  Sum_probs=51.1

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEE-EEeCCCCCHH----------HHHHHHHHhhcCCCce-EEEEEeCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIW-VCVSDPFDEF----------RIAKAIIEGLEGSEKK-FFLILDDVWTD  194 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~w-v~vs~~~~~~----------~~~~~i~~~~~~~~kr-~LiVlDdv~~~  194 (297)
                      .+|++|.|||+-|..+...---.+.|.+++- .++|..-...          .+....-...+.+.++ =.+|||+....
T Consensus        62 FyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsm  141 (346)
T KOG0989|consen   62 FYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSM  141 (346)
T ss_pred             eeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhh
Confidence            6799999999999887773222445655542 3455432221          1111111111112344 47889999998


Q ss_pred             CccCHHHHHHHHhhh
Q 043781          195 DYSKWEPFHNCLMRV  209 (297)
Q Consensus       195 ~~~~w~~l~~~l~~~  209 (297)
                      -.+.|..|+..+.+.
T Consensus       142 tsdaq~aLrr~mE~~  156 (346)
T KOG0989|consen  142 TSDAQAALRRTMEDF  156 (346)
T ss_pred             hHHHHHHHHHHHhcc
Confidence            778999999998764

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.08  E-value=0.015  Score=57.44  Aligned_cols=76  Identities=17%  Similarity=0.241  Sum_probs=55.3

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC------CceEEEEEeCCCCCCccCHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS------EKKFFLILDDVWTDDYSKWE  200 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~------~kr~LiVlDdv~~~~~~~w~  200 (297)
                      +.|++|+||||||..|+++.    .| .++=|++|+.-....+-..|...+...      ++..-||+|.+.-.....-+
T Consensus       331 L~GppGlGKTTLAHViAkqa----GY-sVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~~~~Vd  405 (877)
T KOG1969|consen  331 LCGPPGLGKTTLAHVIAKQA----GY-SVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAPRAAVD  405 (877)
T ss_pred             eecCCCCChhHHHHHHHHhc----Cc-eEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCcHHHHH
Confidence            67999999999999999852    23 245578888888887777777766543      67888999999876433344


Q ss_pred             HHHHHHh
Q 043781          201 PFHNCLM  207 (297)
Q Consensus       201 ~l~~~l~  207 (297)
                      .|...+.
T Consensus       406 vilslv~  412 (877)
T KOG1969|consen  406 VILSLVK  412 (877)
T ss_pred             HHHHHHH
Confidence            5555553

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

Probab=96.03  E-value=0.021  Score=49.45  Aligned_cols=78  Identities=22%  Similarity=0.276  Sum_probs=53.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCC-CccCHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTD-DYSKWEPFHN  204 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~-~~~~w~~l~~  204 (297)
                      =+||.-|.||+.|++.+.+  .+....-.  -|.|++. ++ .-+-.|++.+....+||+|..||+.-+ +.+.+..|+.
T Consensus        89 LLwGaRGtGKSSLVKA~~~--e~~~~glr--LVEV~k~-dl-~~Lp~l~~~Lr~~~~kFIlFcDDLSFe~gd~~yK~LKs  162 (287)
T COG2607          89 LLWGARGTGKSSLVKALLN--EYADEGLR--LVEVDKE-DL-ATLPDLVELLRARPEKFILFCDDLSFEEGDDAYKALKS  162 (287)
T ss_pred             EEecCCCCChHHHHHHHHH--HHHhcCCe--EEEEcHH-HH-hhHHHHHHHHhcCCceEEEEecCCCCCCCchHHHHHHH
Confidence            3899999999999999998  45544433  3444322 11 123355666666689999999999754 3357778888


Q ss_pred             HHhhh
Q 043781          205 CLMRV  209 (297)
Q Consensus       205 ~l~~~  209 (297)
                      .|..+
T Consensus       163 ~LeG~  167 (287)
T COG2607         163 ALEGG  167 (287)
T ss_pred             HhcCC
Confidence            88654

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

Probab=96.03  E-value=0.0029  Score=57.61  Aligned_cols=154  Identities=17%  Similarity=0.144  Sum_probs=78.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCCCceEEEEEeCCCCC-----
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGSEKKFFLILDDVWTD-----  194 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~-----  194 (297)
                      +||++|.|||-||+.|++  +....|     +.|..+-       .-.++.++++.-... .....|.+|.+...     
T Consensus       190 LYGPPGTGKTLLAkAVA~--~T~AtF-----IrvvgSElVqKYiGEGaRlVRelF~lAre-kaPsIIFiDEIDAIg~kR~  261 (406)
T COG1222         190 LYGPPGTGKTLLAKAVAN--QTDATF-----IRVVGSELVQKYIGEGARLVRELFELARE-KAPSIIFIDEIDAIGAKRF  261 (406)
T ss_pred             eeCCCCCcHHHHHHHHHh--ccCceE-----EEeccHHHHHHHhccchHHHHHHHHHHhh-cCCeEEEEechhhhhcccc
Confidence            689999999999999999  455555     3322211       224566666655444 78999999999742     


Q ss_pred             ------CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHH-HHHHHhhCCCccccCCccchh---hhhhhhhc
Q 043781          195 ------DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKL-RHLTLTLGLRAKFPVSIFDAK---KIWGWEVF  264 (297)
Q Consensus       195 ------~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~-~~v~~~~~~~~~~~l~~l~~~---~lf~~~~f  264 (297)
                            +.+.-..+...|.. +.+|.    ....-|||.+|...+.. -.+.........+.+..-+..   ++|.-+.-
T Consensus       262 d~~t~gDrEVQRTmleLL~q-lDGFD----~~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtr  336 (406)
T COG1222         262 DSGTSGDREVQRTMLELLNQ-LDGFD----PRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTR  336 (406)
T ss_pred             cCCCCchHHHHHHHHHHHHh-ccCCC----CCCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhh
Confidence                  11111223333322 22231    13445788877644442 223333334444444433322   33333332


Q ss_pred             cCCCCCCchhhHhhhhhhccccccccchhh
Q 043781          265 GRNTSTRPGMVSRYLMAEFCEPVCSVKAWC  294 (297)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~c~~~c~~~~~~  294 (297)
                      +-+...+- -...+.-....++|.-++|.|
T Consensus       337 kM~l~~dv-d~e~la~~~~g~sGAdlkaic  365 (406)
T COG1222         337 KMNLADDV-DLELLARLTEGFSGADLKAIC  365 (406)
T ss_pred             hccCccCc-CHHHHHHhcCCCchHHHHHHH
Confidence            22222221 111111122357777788887

>PRK04132 replication factor C small subunit; Provisional

Probab=96.02  E-value=0.044  Score=56.06  Aligned_cols=115  Identities=12%  Similarity=0.019  Sum_probs=70.5

Q ss_pred             cCCcchHHHHHHHhcccccccCCC-ceEEEEeCCCCCHHHHHHHHHHhh----cCC-CceEEEEEeCCCCCCccCHHHHH
Q 043781          130 MGGIGKTTLAQFAYNDKDVIENFD-KRIWVCVSDPFDEFRIAKAIIEGL----EGS-EKKFFLILDDVWTDDYSKWEPFH  203 (297)
Q Consensus       130 ~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~~----~~~-~kr~LiVlDdv~~~~~~~w~~l~  203 (297)
                      +.++||||+|..+.+.- ..+.++ ..+-++.|+..++..+. +++..+    ... .+.-++|||++.....+..+.|+
T Consensus       574 Ph~lGKTT~A~ala~~l-~g~~~~~~~lElNASd~rgid~IR-~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt~~AQnALL  651 (846)
T PRK04132        574 PTVLHNTTAALALAREL-FGENWRHNFLELNASDERGINVIR-EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALR  651 (846)
T ss_pred             CCcccHHHHHHHHHHhh-hcccccCeEEEEeCCCcccHHHHH-HHHHHHHhcCCcCCCCCEEEEEECcccCCHHHHHHHH
Confidence            78899999999999841 112221 34566777765555443 333222    111 25689999999998766777888


Q ss_pred             HHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhhh
Q 043781          204 NCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKIW  259 (297)
Q Consensus       204 ~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~lf  259 (297)
                      ..+...          ...+++|++|...+   .+..+... ..++++.+++..++.
T Consensus       652 k~lEep----------~~~~~FILi~N~~~---kIi~tIrSRC~~i~F~~ls~~~i~  695 (846)
T PRK04132        652 RTMEMF----------SSNVRFILSCNYSS---KIIEPIQSRCAIFRFRPLRDEDIA  695 (846)
T ss_pred             HHhhCC----------CCCeEEEEEeCChh---hCchHHhhhceEEeCCCCCHHHHH
Confidence            777642          45667777665432   23222221 257788888766654

>cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B

Probab=96.02  E-value=0.017  Score=51.24  Aligned_cols=70  Identities=16%  Similarity=0.070  Sum_probs=48.3

Q ss_pred             ccccccCCcchHHHHHHHhccccc--ccCCCceEEEEeCCCC-CHHHHHHHHHHhhcCC---------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDV--IENFDKRIWVCVSDPF-DEFRIAKAIIEGLEGS---------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~--~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~---------------------  180 (297)
                      .+|+|-.|+|||+|+..+.++..+  +.+-+.++++-+.+.. .+.++..++...-...                     
T Consensus        72 ~gIfgg~GvGKt~L~~~i~~~~~~~~~~~~~v~V~~~IGeR~rev~e~~~~~~~~~~l~~tv~v~~t~~~~~~~r~~a~~  151 (276)
T cd01135          72 IPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMEDARFFKDDFEETGALERVVLFLNLANDPTIERIITPR  151 (276)
T ss_pred             EEeecCCCCChhHHHHHHHHhhhccccCCCCEEEEEEeccccHHHHHHHHHhhhcCCcceEEEEEecCCCCHHHHHHHHH
Confidence            478999999999999988875331  1234677788776654 4566666665543221                     


Q ss_pred             -------------CceEEEEEeCCCCC
Q 043781          181 -------------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 -------------~kr~LiVlDdv~~~  194 (297)
                                   +++.|+++||+-..
T Consensus       152 ~a~aiAEyfrd~~g~~VLl~~D~ltr~  178 (276)
T cd01135         152 MALTTAEYLAYEKGKHVLVILTDMTNY  178 (276)
T ss_pred             HHHHHHHHHHhccCCeEEEEEcChhHH
Confidence                         68999999998543

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit.

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=96.00  E-value=0.067  Score=46.43  Aligned_cols=56  Identities=18%  Similarity=0.157  Sum_probs=34.0

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL  244 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~  244 (297)
                      -+.=+||+|..-+. |...-.++...|.+.-.        ..+-.+|+.|++-....++|....+
T Consensus       158 ~~PklLIlDEptSaLD~siQa~IlnlL~~l~~--------~~~lt~l~IsHdl~~v~~~cdRi~V  214 (252)
T COG1124         158 PEPKLLILDEPTSALDVSVQAQILNLLLELKK--------ERGLTYLFISHDLALVEHMCDRIAV  214 (252)
T ss_pred             cCCCEEEecCchhhhcHHHHHHHHHHHHHHHH--------hcCceEEEEeCcHHHHHHHhhheee
Confidence            66778899987653 11111223333332211        4566788899988888888876443

>PRK13695 putative NTPase; Provisional

Probab=96.00  E-value=0.0064  Score=50.23  Aligned_cols=21  Identities=33%  Similarity=0.341  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|.|.+|+|||||++.+++.
T Consensus         3 i~ltG~~G~GKTTll~~i~~~   23 (174)
T PRK13695          3 IGITGPPGVGKTTLVLKIAEL   23 (174)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999998764

>CHL00195 ycf46 Ycf46; Provisional

Probab=95.95  E-value=0.031  Score=53.93  Aligned_cols=62  Identities=19%  Similarity=0.174  Sum_probs=37.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|++|+|||.+|+.+.+.  ..-.|   +-+..+.    .. .....+++++..... ..+++|++|++..
T Consensus       263 LL~GPpGTGKTllAkaiA~e--~~~~~---~~l~~~~l~~~~vGese~~l~~~f~~A~~-~~P~IL~IDEID~  329 (489)
T CHL00195        263 LLVGIQGTGKSLTAKAIAND--WQLPL---LRLDVGKLFGGIVGESESRMRQMIRIAEA-LSPCILWIDEIDK  329 (489)
T ss_pred             EEECCCCCcHHHHHHHHHHH--hCCCE---EEEEhHHhcccccChHHHHHHHHHHHHHh-cCCcEEEehhhhh
Confidence            47899999999999999984  33222   1111111    11 123344555543332 5789999999964

>PRK10865 protein disaggregation chaperone; Provisional

Probab=95.94  E-value=0.025  Score=58.41  Aligned_cols=67  Identities=19%  Similarity=0.258  Sum_probs=43.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccC------CCceEEE-EeCC-------CCCHHHHHHHHHHhhcCCCceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIEN------FDKRIWV-CVSD-------PFDEFRIAKAIIEGLEGSEKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~------F~~~~wv-~vs~-------~~~~~~~~~~i~~~~~~~~kr~LiVlDdv  191 (297)
                      -++|.+|+|||+||+.+...  +...      ....+|. .++.       .-...+-++.++..+...+++.+|++|++
T Consensus       203 lL~G~pGvGKT~l~~~la~~--i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEi  280 (857)
T PRK10865        203 VLIGEPGVGKTAIVEGLAQR--IINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDEL  280 (857)
T ss_pred             EEECCCCCCHHHHHHHHHHH--hhcCCCchhhCCCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecH
Confidence            37899999999999998884  3211      1333333 2222       11334556667766544467899999999


Q ss_pred             CCC
Q 043781          192 WTD  194 (297)
Q Consensus       192 ~~~  194 (297)
                      ..-
T Consensus       281 h~l  283 (857)
T PRK10865        281 HTM  283 (857)
T ss_pred             HHh
Confidence            754

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=95.94  E-value=0.066  Score=52.67  Aligned_cols=80  Identities=18%  Similarity=0.140  Sum_probs=47.8

Q ss_pred             ccccCCcchHHHHHHHhccccc--------------------ccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV--------------------IENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~--------------------~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      ++|+.|+||||+|+.+.+.-..                    ..+++. +.+..+.+..+.+ .++|.+.+...   +++
T Consensus        43 f~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~g~~~dv-~eidaas~~~vd~-ir~i~~~v~~~p~~~~~  120 (559)
T PRK05563         43 FSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITNGSLMDV-IEIDAASNNGVDE-IRDIRDKVKYAPSEAKY  120 (559)
T ss_pred             EECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhcCCCCCe-EEeeccccCCHHH-HHHHHHHHhhCcccCCe
Confidence            5899999999999888763111                    113332 3344433334333 33444443322   677


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~  208 (297)
                      -++|+|++.......+..|...+..
T Consensus       121 kViIIDE~~~Lt~~a~naLLKtLEe  145 (559)
T PRK05563        121 KVYIIDEVHMLSTGAFNALLKTLEE  145 (559)
T ss_pred             EEEEEECcccCCHHHHHHHHHHhcC
Confidence            7889999987654567777666643

>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=95.92  E-value=0.077  Score=42.42  Aligned_cols=97  Identities=19%  Similarity=0.177  Sum_probs=55.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEE------EeCCCCCHHHHHH-HHHHhhcCCCceEEEEEeCCCCC-Cc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWV------CVSDPFDEFRIAK-AIIEGLEGSEKKFFLILDDVWTD-DY  196 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv------~vs~~~~~~~~~~-~i~~~~~~~~kr~LiVlDdv~~~-~~  196 (297)
                      ..|+|..|.|||||++.+.....   .....+|+      ......+.-+..+ .|+..+-  .+.=+++||+--.. |.
T Consensus        29 ~~i~G~nGsGKStLl~~l~G~~~---~~~G~i~~~~~~~i~~~~~lS~G~~~rv~laral~--~~p~illlDEP~~~LD~  103 (144)
T cd03221          29 IGLVGRNGAGKSTLLKLIAGELE---PDEGIVTWGSTVKIGYFEQLSGGEKMRLALAKLLL--ENPNLLLLDEPTNHLDL  103 (144)
T ss_pred             EEEECCCCCCHHHHHHHHcCCCC---CCceEEEECCeEEEEEEccCCHHHHHHHHHHHHHh--cCCCEEEEeCCccCCCH
Confidence            46889999999999999988422   22233332      1111133333322 2344443  36678899988654 32


Q ss_pred             cCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHH
Q 043781          197 SKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHL  238 (297)
Q Consensus       197 ~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v  238 (297)
                      ...+.+...+...            +..||++|+..+.....
T Consensus       104 ~~~~~l~~~l~~~------------~~til~~th~~~~~~~~  133 (144)
T cd03221         104 ESIEALEEALKEY------------PGTVILVSHDRYFLDQV  133 (144)
T ss_pred             HHHHHHHHHHHHc------------CCEEEEEECCHHHHHHh
Confidence            3444555555431            24688888865544333

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.

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.90  E-value=0.017  Score=54.84  Aligned_cols=21  Identities=24%  Similarity=0.317  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||++.+...
T Consensus       168 i~I~G~SGsGKTTLL~~Ia~l  188 (450)
T PRK06002        168 IGIFAGSGVGKSTLLAMLARA  188 (450)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            368899999999999998874

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=95.85  E-value=0.057  Score=49.73  Aligned_cols=77  Identities=13%  Similarity=0.096  Sum_probs=48.1

Q ss_pred             HHHHhhcCC---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-Ccc
Q 043781          172 AIIEGLEGS---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAK  247 (297)
Q Consensus       172 ~i~~~~~~~---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~  247 (297)
                      ++.+.+...   +++=++|+|++...+.+.++.|...+..          ..+++.+|++|...+   .+..+.-. ...
T Consensus       119 ~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEE----------Pp~~t~fiL~t~~~~---~LLpTI~SRcq~  185 (342)
T PRK06964        119 ALLDFCGVGTHRGGARVVVLYPAEALNVAAANALLKTLEE----------PPPGTVFLLVSARID---RLLPTILSRCRQ  185 (342)
T ss_pred             HHHHHhccCCccCCceEEEEechhhcCHHHHHHHHHHhcC----------CCcCcEEEEEECChh---hCcHHHHhcCEE
Confidence            455555433   6666888999999887888888888865          256666666665432   22222111 256


Q ss_pred             ccCCccchhhhhhh
Q 043781          248 FPVSIFDAKKIWGW  261 (297)
Q Consensus       248 ~~l~~l~~~~lf~~  261 (297)
                      +++.+++.+++..|
T Consensus       186 i~~~~~~~~~~~~~  199 (342)
T PRK06964        186 FPMTVPAPEAAAAW  199 (342)
T ss_pred             EEecCCCHHHHHHH
Confidence            67777776665444

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=95.85  E-value=0.0091  Score=61.51  Aligned_cols=99  Identities=18%  Similarity=0.115  Sum_probs=53.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC---CH---------------HHHHHHHHHhhcCCCceEEEE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF---DE---------------FRIAKAIIEGLEGSEKKFFLI  187 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~---~~---------------~~~~~~i~~~~~~~~kr~LiV  187 (297)
                      -++|++|+|||.||+.+...  +-......+-+.++...   ++               ...+...+.+    ...-+|+
T Consensus       600 lf~Gp~GvGKT~lA~~La~~--l~~~~~~~~~~dmse~~~~~~~~~l~g~~~gyvg~~~~g~L~~~v~~----~p~svvl  673 (852)
T TIGR03345       600 LLVGPSGVGKTETALALAEL--LYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVRR----KPYSVVL  673 (852)
T ss_pred             EEECCCCCCHHHHHHHHHHH--HhCCCcceEEEeHHHhhhhhhhccccCCCCCcccccccchHHHHHHh----CCCcEEE
Confidence            47799999999999877763  21111111112222110   00               0111111111    4567999


Q ss_pred             EeCCCCCCccCHHHHHHHHhhhh-hhhceeeecCCCCeEEEEec
Q 043781          188 LDDVWTDDYSKWEPFHNCLMRVL-QEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       188 lDdv~~~~~~~w~~l~~~l~~~~-~~~~~~~~~~~gs~iiiTTr  230 (297)
                      ||++...+.+.++.|...+.++. ....-..++-..+-||+||.
T Consensus       674 lDEieka~~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSN  717 (852)
T TIGR03345       674 LDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSN  717 (852)
T ss_pred             EechhhcCHHHHHHHHHHhhcceeecCCCcEEeccccEEEEeCC
Confidence            99998877777887877776541 11111122224566777775

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=95.83  E-value=0.074  Score=48.44  Aligned_cols=78  Identities=14%  Similarity=0.112  Sum_probs=49.0

Q ss_pred             HHHHHHhhcCC---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-C
Q 043781          170 AKAIIEGLEGS---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-R  245 (297)
Q Consensus       170 ~~~i~~~~~~~---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~  245 (297)
                      .++|.+.+...   +++=++|+|++...+....+.|...+..-          . .+.+|++|...   ..+..+... .
T Consensus       109 ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~aaNaLLK~LEEP----------p-~~~fILi~~~~---~~Ll~TI~SRc  174 (314)
T PRK07399        109 IREIKRFLSRPPLEAPRKVVVIEDAETMNEAAANALLKTLEEP----------G-NGTLILIAPSP---ESLLPTIVSRC  174 (314)
T ss_pred             HHHHHHHHccCcccCCceEEEEEchhhcCHHHHHHHHHHHhCC----------C-CCeEEEEECCh---HhCcHHHHhhc
Confidence            34565555433   77889999999888767788888888651          3 44566666543   233332222 2


Q ss_pred             ccccCCccchhhhhhh
Q 043781          246 AKFPVSIFDAKKIWGW  261 (297)
Q Consensus       246 ~~~~l~~l~~~~lf~~  261 (297)
                      ..+++.+++..++..|
T Consensus       175 q~i~f~~l~~~~~~~~  190 (314)
T PRK07399        175 QIIPFYRLSDEQLEQV  190 (314)
T ss_pred             eEEecCCCCHHHHHHH
Confidence            6778888887776444

>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=95.82  E-value=0.074  Score=42.98  Aligned_cols=101  Identities=17%  Similarity=0.129  Sum_probs=57.0

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC-----------------CCHHHHHH-HHHHhhcCCCceEE
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP-----------------FDEFRIAK-AIIEGLEGSEKKFF  185 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----------------~~~~~~~~-~i~~~~~~~~kr~L  185 (297)
                      ...|+|..|.|||||.+.+....   ......+++.....                 .+.-+..+ .|+..+.  ...=+
T Consensus        27 ~~~i~G~nGsGKStll~~l~g~~---~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~r~~l~~~l~--~~~~i  101 (157)
T cd00267          27 IVALVGPNGSGKSTLLRAIAGLL---KPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARALL--LNPDL  101 (157)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC---CCCccEEEECCEEcccCCHHHHHhceEEEeeCCHHHHHHHHHHHHHh--cCCCE
Confidence            34689999999999999999842   22334444321100                 11111111 1333333  46788


Q ss_pred             EEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHH
Q 043781          186 LILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHL  238 (297)
Q Consensus       186 iVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v  238 (297)
                      ++||+.-.. |......+...+....         .++..+|++|+..+.....
T Consensus       102 ~ilDEp~~~lD~~~~~~l~~~l~~~~---------~~~~tii~~sh~~~~~~~~  146 (157)
T cd00267         102 LLLDEPTSGLDPASRERLLELLRELA---------EEGRTVIIVTHDPELAELA  146 (157)
T ss_pred             EEEeCCCcCCCHHHHHHHHHHHHHHH---------HCCCEEEEEeCCHHHHHHh
Confidence            999998764 2233444555554421         3357789999876554444

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.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=95.81  E-value=0.01  Score=60.13  Aligned_cols=78  Identities=13%  Similarity=0.134  Sum_probs=46.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC---CHHHHHH------------HHHHhhcCCCceEEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF---DEFRIAK------------AIIEGLEGSEKKFFLILDD  190 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~---~~~~~~~------------~i~~~~~~~~kr~LiVlDd  190 (297)
                      -++|++|+|||+||+.+...  ....|   +.+..+...   .+.+++.            .+-+.+.. ....+|+||+
T Consensus       492 Lf~GP~GvGKT~lAk~LA~~--l~~~~---i~id~se~~~~~~~~~LiG~~~gyvg~~~~g~L~~~v~~-~p~sVlllDE  565 (758)
T PRK11034        492 LFAGPTGVGKTEVTVQLSKA--LGIEL---LRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIK-HPHAVLLLDE  565 (758)
T ss_pred             EEECCCCCCHHHHHHHHHHH--hCCCc---EEeechhhcccccHHHHcCCCCCcccccccchHHHHHHh-CCCcEEEecc
Confidence            46799999999999999884  32222   233333211   1222211            01111111 3456999999


Q ss_pred             CCCCCccCHHHHHHHHhhh
Q 043781          191 VWTDDYSKWEPFHNCLMRV  209 (297)
Q Consensus       191 v~~~~~~~w~~l~~~l~~~  209 (297)
                      +...+.+.++.|...|..+
T Consensus       566 ieka~~~v~~~LLq~ld~G  584 (758)
T PRK11034        566 IEKAHPDVFNLLLQVMDNG  584 (758)
T ss_pred             HhhhhHHHHHHHHHHHhcC
Confidence            9998777788887777654

>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=95.81  E-value=0.0048  Score=47.66  Aligned_cols=20  Identities=35%  Similarity=0.503  Sum_probs=18.1

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|.|.+|+||||||+.+...
T Consensus         2 ~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    2 GISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEESTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            57899999999999999885

...

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=95.78  E-value=0.017  Score=55.19  Aligned_cols=67  Identities=15%  Similarity=0.246  Sum_probs=45.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHhhcC------------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEGLEG------------------------  179 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~------------------------  179 (297)
                      .+|+|..|+|||||+.++.++.. +.+-+.++++-+.... .+.++..++...-..                        
T Consensus       146 ~gIfa~~G~GKt~Ll~~~~~~~~-~~~~dv~V~~liGER~rEv~ef~~~~~~~~~l~rsvvv~atsd~~~~~R~~a~~~a  224 (461)
T PRK12597        146 TGLFGGAGVGKTVLMMELIFNIS-KQHSGSSVFAGVGERSREGHELYHEMKESGVLDKTVMVYGQMNEPPGARMRVVLTG  224 (461)
T ss_pred             EEeecCCCCChhHHHHHHHHHHH-hhCCCEEEEEcCCcchHHHHHHHHHHHhcCCcceeEEEecCCCCCHHHHHHHHHHH
Confidence            47899999999999988887533 2355777777655443 345555555443211                        


Q ss_pred             ---------C-CceEEEEEeCCC
Q 043781          180 ---------S-EKKFFLILDDVW  192 (297)
Q Consensus       180 ---------~-~kr~LiVlDdv~  192 (297)
                               . ++..|+++|++-
T Consensus       225 ~tiAEyfrd~~G~~VLl~~DslT  247 (461)
T PRK12597        225 LTIAEYLRDEEKEDVLLFIDNIF  247 (461)
T ss_pred             HHHHHHHHHhcCCceEEEeccch
Confidence                     1 799999999994

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=95.78  E-value=0.046  Score=49.78  Aligned_cols=47  Identities=21%  Similarity=0.210  Sum_probs=31.8

Q ss_pred             cccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCCHHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFDEFRIA  170 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~  170 (297)
                      ...|+|.+|+|||+|+.++.-......    .=...+|+.....|+..++.
T Consensus        98 iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~  148 (313)
T TIGR02238        98 ITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIR  148 (313)
T ss_pred             EEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHH
Confidence            346899999999999977654222211    11367788887777766654

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=95.75  E-value=0.067  Score=48.76  Aligned_cols=121  Identities=12%  Similarity=0.058  Sum_probs=73.0

Q ss_pred             ccccCCcchHHHHHHHhcccc-------------------cccCCCceEEEEe---CCCCCHHHHHHHHHHhhcCC---C
Q 043781          127 VRGMGGIGKTTLAQFAYNDKD-------------------VIENFDKRIWVCV---SDPFDEFRIAKAIIEGLEGS---E  181 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~-------------------~~~~F~~~~wv~v---s~~~~~~~~~~~i~~~~~~~---~  181 (297)
                      +.|+.|+||+++|..+..---                   ...|-|.. |+.-   ++...+.++ +++.+.+...   +
T Consensus        30 ~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~-~i~p~~~~~~I~vdqi-R~l~~~~~~~~~~~  107 (319)
T PRK06090         30 LQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLH-VIKPEKEGKSITVEQI-RQCNRLAQESSQLN  107 (319)
T ss_pred             eECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEE-EEecCcCCCcCCHHHH-HHHHHHHhhCcccC
Confidence            679999999999987765210                   01233332 3332   234556665 4554444332   5


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhhhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKIWG  260 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~lf~  260 (297)
                      ++=++|+|++.....+..+.|...+..          ...++.+|++|.+.   ..+..+.-. ...+++..++.++...
T Consensus       108 ~~kV~iI~~ae~m~~~AaNaLLKtLEE----------Pp~~t~fiL~t~~~---~~lLpTI~SRCq~~~~~~~~~~~~~~  174 (319)
T PRK06090        108 GYRLFVIEPADAMNESASNALLKTLEE----------PAPNCLFLLVTHNQ---KRLLPTIVSRCQQWVVTPPSTAQAMQ  174 (319)
T ss_pred             CceEEEecchhhhCHHHHHHHHHHhcC----------CCCCeEEEEEECCh---hhChHHHHhcceeEeCCCCCHHHHHH
Confidence            666889999998877788888888865          24556666666543   233322222 2566788877776555


Q ss_pred             hh
Q 043781          261 WE  262 (297)
Q Consensus       261 ~~  262 (297)
                      |-
T Consensus       175 ~L  176 (319)
T PRK06090        175 WL  176 (319)
T ss_pred             HH
Confidence            53

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=95.75  E-value=0.039  Score=45.68  Aligned_cols=21  Identities=38%  Similarity=0.491  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+..-
T Consensus        31 ~~i~G~nGsGKStLl~~l~G~   51 (178)
T cd03247          31 IALLGRSGSGKSTLLQLLTGD   51 (178)
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            468899999999999999885

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.

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

Probab=95.75  E-value=0.014  Score=57.68  Aligned_cols=66  Identities=20%  Similarity=0.167  Sum_probs=43.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCC--CCCHHHHHHHHHHhhcCC--CceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD--PFDEFRIAKAIIEGLEGS--EKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~--~~~~~~~~~~i~~~~~~~--~kr~LiVlDdv~~  193 (297)
                      |.|..|+|||+||+.+++... +++.-...+|+.+.  .-....+++.+.+-+...  ...-+|||||+.-
T Consensus       436 l~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~PSiIvLDdld~  505 (952)
T KOG0735|consen  436 LNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYAPSIIVLDDLDC  505 (952)
T ss_pred             EeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechhccchhHHHHHHHHHHHHHHHHhhCCcEEEEcchhh
Confidence            569999999999999999533 44443444554433  234555555444433322  7899999999963

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=95.74  E-value=0.017  Score=52.92  Aligned_cols=36  Identities=22%  Similarity=0.350  Sum_probs=29.4

Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEec
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      ..-+||+|...+-   .-.+++..+.+.          |.||||++|--
T Consensus       351 ~~~FiIIDEaQNL---TpheikTiltR~----------G~GsKIVl~gd  386 (436)
T COG1875         351 PDSFIIIDEAQNL---TPHELKTILTRA----------GEGSKIVLTGD  386 (436)
T ss_pred             ccceEEEehhhcc---CHHHHHHHHHhc----------cCCCEEEEcCC
Confidence            3567899999886   455788888886          99999999975

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=95.73  E-value=0.055  Score=55.30  Aligned_cols=21  Identities=33%  Similarity=0.412  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..-++|++|+||||+++.+..
T Consensus       351 ~i~l~GppG~GKTtl~~~ia~  371 (784)
T PRK10787        351 ILCLVGPPGVGKTSLGQSIAK  371 (784)
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999997

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=95.73  E-value=0.12  Score=43.84  Aligned_cols=21  Identities=29%  Similarity=0.302  Sum_probs=19.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+...
T Consensus        29 ~~i~G~nGsGKSTLl~~l~G~   49 (210)
T cd03269          29 FGLLGPNGAGKTTTIRMILGI   49 (210)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            578999999999999999974

In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs. Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=95.70  E-value=0.093  Score=44.66  Aligned_cols=22  Identities=27%  Similarity=0.314  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+...
T Consensus        27 ~~~l~G~nGsGKSTLl~~l~G~   48 (213)
T cd03235          27 FLAIVGPNGAGKSTLLKAILGL   48 (213)
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            3578999999999999999874

This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=95.70  E-value=0.02  Score=48.46  Aligned_cols=20  Identities=30%  Similarity=0.263  Sum_probs=16.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|+.|+||||++..+..
T Consensus         4 ilI~GptGSGKTTll~~ll~   23 (198)
T cd01131           4 VLVTGPTGSGKSTTLAAMID   23 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34789999999999987665

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=95.69  E-value=0.024  Score=47.98  Aligned_cols=85  Identities=20%  Similarity=0.132  Sum_probs=45.6

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC----------------------Cce
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS----------------------EKK  183 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~----------------------~kr  183 (297)
                      -|.|.+|+||||+++.+...  .... ...+.+......-...+.+.    .+..                      .+.
T Consensus        22 ~l~G~aGtGKT~~l~~~~~~--~~~~-g~~v~~~apT~~Aa~~L~~~----~~~~a~Ti~~~l~~~~~~~~~~~~~~~~~   94 (196)
T PF13604_consen   22 VLQGPAGTGKTTLLKALAEA--LEAA-GKRVIGLAPTNKAAKELREK----TGIEAQTIHSFLYRIPNGDDEGRPELPKK   94 (196)
T ss_dssp             EEEESTTSTHHHHHHHHHHH--HHHT-T--EEEEESSHHHHHHHHHH----HTS-EEEHHHHTTEECCEECCSSCC-TST
T ss_pred             EEEECCCCCHHHHHHHHHHH--HHhC-CCeEEEECCcHHHHHHHHHh----hCcchhhHHHHHhcCCcccccccccCCcc
Confidence            46799999999999988773  3222 23444443333223333322    2221                      234


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEe
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTS  229 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTT  229 (297)
                      -+||+|++.-.+...+..|....+            ..|+++|+.=
T Consensus        95 ~vliVDEasmv~~~~~~~ll~~~~------------~~~~klilvG  128 (196)
T PF13604_consen   95 DVLIVDEASMVDSRQLARLLRLAK------------KSGAKLILVG  128 (196)
T ss_dssp             SEEEESSGGG-BHHHHHHHHHHS-------------T-T-EEEEEE
T ss_pred             cEEEEecccccCHHHHHHHHHHHH------------hcCCEEEEEC
Confidence            699999998765444444444332            4467777754

>PF00006 ATP-synt_ab: ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f; InterPro: IPR000194 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane

Probab=95.68  E-value=0.02  Score=49.20  Aligned_cols=64  Identities=22%  Similarity=0.259  Sum_probs=44.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHhhcCC-----------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEGLEGS-----------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~-----------------------  180 (297)
                      ..|+|.+|+|||+|+..+.++..    -+..+++.+.+.. .+.++.+++...-...                       
T Consensus        18 ~~I~g~~g~GKt~Ll~~i~~~~~----~d~~V~~~iGer~~Ev~~~~~~~~~~~~~~~t~vv~~t~~~~~~~r~~~~~~a   93 (215)
T PF00006_consen   18 IGIFGGAGVGKTVLLQEIANNQD----ADVVVYALIGERGREVTEFIEELKGEGALERTVVVAATSDEPPAARYRAPYTA   93 (215)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHCT----TTEEEEEEESECHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHHHHHH
T ss_pred             EEEEcCcccccchhhHHHHhccc----ccceeeeeccccchhHHHHHHHHhhcccccccccccccchhhHHHHhhhhccc
Confidence            46899999999999999988532    2344777776553 4556666554431111                       


Q ss_pred             ----------CceEEEEEeCCC
Q 043781          181 ----------EKKFFLILDDVW  192 (297)
Q Consensus       181 ----------~kr~LiVlDdv~  192 (297)
                                ++..|+++||+-
T Consensus        94 ~t~AEyfrd~G~dVlli~Dslt  115 (215)
T PF00006_consen   94 LTIAEYFRDQGKDVLLIIDSLT  115 (215)
T ss_dssp             HHHHHHHHHTTSEEEEEEETHH
T ss_pred             hhhhHHHhhcCCceeehhhhhH
Confidence                      999999999994

ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, ]. In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself driven by the movement of protons through the F0 complex C subunit []. In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory. The structure of the alpha and beta subunits is almost identical. Each subunit consists of a N-terminal beta-barrel, a central domain containing the nucleotide-binding site and a C-terminal alpha bundle domain []. This entry represents the central domain. It is found in the alpha and beta subunits from F1, V1, and A1 complexes, as well as in flagellar ATPase and the termination factor Rho. ; GO: 0005524 ATP binding; PDB: 3OEE_N 2HLD_W 3FKS_N 3OE7_O 3OFN_M 2XOK_D 3OEH_V 2WPD_F 3ZRY_D 2OBL_A ....

>PTZ00202 tuzin; Provisional

Probab=95.68  E-value=0.031  Score=52.83  Aligned_cols=48  Identities=15%  Similarity=0.157  Sum_probs=35.3

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcC
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG  179 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~  179 (297)
                      ...|.|++|+|||||++.+...  ..  +  ..++.-+.  +..+++..|+.+++.
T Consensus       288 ivvLtG~~G~GKTTLlR~~~~~--l~--~--~qL~vNpr--g~eElLr~LL~ALGV  335 (550)
T PTZ00202        288 IVVFTGFRGCGKSSLCRSAVRK--EG--M--PAVFVDVR--GTEDTLRSVVKALGV  335 (550)
T ss_pred             EEEEECCCCCCHHHHHHHHHhc--CC--c--eEEEECCC--CHHHHHHHHHHHcCC
Confidence            3458899999999999999973  22  2  13332222  779999999999985

>PHA02774 E1; Provisional

Probab=95.66  E-value=0.032  Score=54.34  Aligned_cols=88  Identities=19%  Similarity=0.130  Sum_probs=52.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-|+|++|.|||.+|..+.+-  ..  -....||+....|-+..+.           ..-++||||+-.   ..|+.+..
T Consensus       437 iv~~GPP~TGKS~fa~sL~~~--L~--G~vi~fvN~~s~FwLqpl~-----------d~ki~vlDD~t~---~~w~y~d~  498 (613)
T PHA02774        437 LVIYGPPDTGKSMFCMSLIKF--LK--GKVISFVNSKSHFWLQPLA-----------DAKIALLDDATH---PCWDYIDT  498 (613)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hC--CCEEEEEECccccccchhc-----------cCCEEEEecCcc---hHHHHHHH
Confidence            358899999999999988872  22  1234566654444422222           344799999933   36776666


Q ss_pred             HHhhhhhhhc-------eeeecCCCCeEEEEec
Q 043781          205 CLMRVLQEFA-------AIEVDGDENPLSLTST  230 (297)
Q Consensus       205 ~l~~~~~~~~-------~~~~~~~gs~iiiTTr  230 (297)
                      .|...+.+..       .-+..-..-++||||.
T Consensus       499 ~Lrn~LdG~~v~lD~Khk~~~q~k~pPlIITSN  531 (613)
T PHA02774        499 YLRNALDGNPVSIDCKHKAPVQIKCPPLLITSN  531 (613)
T ss_pred             HHHHHcCCCcceeeecccCcccccCCCEEEecC
Confidence            6766543210       0001112467999995

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.65  E-value=0.81  Score=43.63  Aligned_cols=23  Identities=30%  Similarity=0.225  Sum_probs=19.2

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+-++|.+|+||||++..+...
T Consensus        96 ~vI~lvG~~GsGKTTtaakLA~~  118 (437)
T PRK00771         96 QTIMLVGLQGSGKTTTAAKLARY  118 (437)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH
Confidence            34568899999999999888764

>PHA02244 ATPase-like protein

Probab=95.64  E-value=0.026  Score=52.27  Aligned_cols=95  Identities=13%  Similarity=0.162  Sum_probs=49.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHH-----------HHHHhhcCCCceEEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAK-----------AIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~-----------~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      -|+|.+|+|||+||+.+.+.  ....|     +.++...+...+..           .++.++   .+--+++||++...
T Consensus       123 LL~GppGtGKTtLA~aLA~~--lg~pf-----v~In~l~d~~~L~G~i~~~g~~~dgpLl~A~---~~GgvLiLDEId~a  192 (383)
T PHA02244        123 FLKGGAGSGKNHIAEQIAEA--LDLDF-----YFMNAIMDEFELKGFIDANGKFHETPFYEAF---KKGGLFFIDEIDAS  192 (383)
T ss_pred             EEECCCCCCHHHHHHHHHHH--hCCCE-----EEEecChHHHhhcccccccccccchHHHHHh---hcCCEEEEeCcCcC
Confidence            46799999999999999984  33222     22221111111100           111111   23459999999876


Q ss_pred             CccCHHHHHHHHhhhhhh-hceeeecCCCCeEEEEec
Q 043781          195 DYSKWEPFHNCLMRVLQE-FAAIEVDGDENPLSLTST  230 (297)
Q Consensus       195 ~~~~w~~l~~~l~~~~~~-~~~~~~~~~gs~iiiTTr  230 (297)
                      ..+....|...+....-. ..-.....++.++|+|+.
T Consensus       193 ~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN  229 (383)
T PHA02244        193 IPEALIIINSAIANKFFDFADERVTAHEDFRVISAGN  229 (383)
T ss_pred             CHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeC
Confidence            544455555555322100 000111235678888876

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=95.60  E-value=0.016  Score=46.01  Aligned_cols=83  Identities=19%  Similarity=0.101  Sum_probs=51.1

Q ss_pred             cccccCCcchHHHHHHHhccccc-ccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDV-IENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      -|+|-.|+||+++|+.++....- ...|...         +...+..+++++.    +.--|+|+|+..-..+....|..
T Consensus        25 li~GE~GtGK~~~A~~lh~~~~~~~~~~~~~---------~~~~~~~~~l~~a----~~gtL~l~~i~~L~~~~Q~~L~~   91 (138)
T PF14532_consen   25 LITGEPGTGKSLLARALHRYSGRANGPFIVI---------DCASLPAELLEQA----KGGTLYLKNIDRLSPEAQRRLLD   91 (138)
T ss_dssp             EEECCTTSSHHHHHHCCHHTTTTCCS-CCCC---------CHHCTCHHHHHHC----TTSEEEEECGCCS-HHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHhhcCccCCCeEEe---------chhhCcHHHHHHc----CCCEEEECChHHCCHHHHHHHHH
Confidence            47899999999999999985332 2233221         1111113444443    34457799998876555566666


Q ss_pred             HHhhhhhhhceeeecCCCCeEEEEec
Q 043781          205 CLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       205 ~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      .+...         .....|+|.||.
T Consensus        92 ~l~~~---------~~~~~RlI~ss~  108 (138)
T PF14532_consen   92 LLKRQ---------ERSNVRLIASSS  108 (138)
T ss_dssp             HHHHC---------TTTTSEEEEEEC
T ss_pred             HHHhc---------CCCCeEEEEEeC
Confidence            66542         146679999987

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=95.58  E-value=0.064  Score=49.02  Aligned_cols=120  Identities=9%  Similarity=0.019  Sum_probs=70.0

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEE--eCCCCCHHHHHHHHHHhhcCC---C
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVC--VSDPFDEFRIAKAIIEGLEGS---E  181 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~--vs~~~~~~~~~~~i~~~~~~~---~  181 (297)
                      +.|+.|+||+++|..+..----.                    .|-|. .++.  .+....+.++ +++.+.+...   +
T Consensus        29 f~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~-~~i~p~~~~~I~id~i-R~l~~~~~~~~~~g  106 (325)
T PRK06871         29 FKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDF-HILEPIDNKDIGVDQV-REINEKVSQHAQQG  106 (325)
T ss_pred             eECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCE-EEEccccCCCCCHHHH-HHHHHHHhhccccC
Confidence            67999999999998777631111                    12222 2232  1223445444 3444444322   6


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhhhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKIWG  260 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~lf~  260 (297)
                      ++=++|+|++........+.|...+..          ...++.+|++|...+   .+..+.-. ...+.+.+++.+++-.
T Consensus       107 ~~KV~iI~~a~~m~~~AaNaLLKtLEE----------Pp~~~~fiL~t~~~~---~llpTI~SRC~~~~~~~~~~~~~~~  173 (325)
T PRK06871        107 GNKVVYIQGAERLTEAAANALLKTLEE----------PRPNTYFLLQADLSA---ALLPTIYSRCQTWLIHPPEEQQALD  173 (325)
T ss_pred             CceEEEEechhhhCHHHHHHHHHHhcC----------CCCCeEEEEEECChH---hCchHHHhhceEEeCCCCCHHHHHH
Confidence            777888999998876778888877765          255566777766432   33322221 2566777777666433


Q ss_pred             h
Q 043781          261 W  261 (297)
Q Consensus       261 ~  261 (297)
                      |
T Consensus       174 ~  174 (325)
T PRK06871        174 W  174 (325)
T ss_pred             H
Confidence            3

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=95.56  E-value=0.024  Score=53.84  Aligned_cols=68  Identities=15%  Similarity=0.249  Sum_probs=47.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHhhcCC-----------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEGLEGS-----------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~-----------------------  180 (297)
                      .+|+|..|+|||+|+..+..+.. +.+-+.++++-+.... .+.++.+++...-...                       
T Consensus       141 ~~Ifg~~G~GKt~l~~~~~~~~~-~~~~~v~V~~~iGeR~rEv~e~~~~~~~~~~l~rtvvv~~ts~~~~~~r~~~~~~a  219 (449)
T TIGR03305       141 AGLFGGAGVGKTVLLTEMIHNMV-GQHQGVSIFCGIGERCREGEELYREMKEAGVLDNTVMVFGQMNEPPGARFRVGHTA  219 (449)
T ss_pred             EEeecCCCCChhHHHHHHHHHHH-hcCCCEEEEEEeccCcHHHHHHHHHHhhccccceEEEEEeCCCCCHHHHHHHHHHH
Confidence            36889999999999988877632 2344678888776554 3456666655432211                       


Q ss_pred             -----------CceEEEEEeCCCC
Q 043781          181 -----------EKKFFLILDDVWT  193 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~  193 (297)
                                 ++..|+++||+-.
T Consensus       220 ~tiAEyfrd~~G~~VLl~~DslTR  243 (449)
T TIGR03305       220 LTMAEYFRDDEKQDVLLLIDNIFR  243 (449)
T ss_pred             HHHHHHHHHhcCCceEEEecChHH
Confidence                       8999999999954

A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase.

>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=95.56  E-value=0.041  Score=45.34  Aligned_cols=21  Identities=33%  Similarity=0.387  Sum_probs=19.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|.|||||.+.+...
T Consensus        29 ~~i~G~nGsGKStLl~~l~G~   49 (173)
T cd03230          29 YGLLGPNGAGKTTLIKIILGL   49 (173)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999999884

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.

>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=95.56  E-value=0.071  Score=44.31  Aligned_cols=21  Identities=33%  Similarity=0.450  Sum_probs=18.1

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|+|||||.+.+..
T Consensus        23 ~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          23 LVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            346899999999999999863

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.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=95.53  E-value=0.049  Score=46.63  Aligned_cols=49  Identities=16%  Similarity=0.237  Sum_probs=30.9

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLT  239 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~  239 (297)
                      .+.-+++||.--.. |....+.+...+...          ..+..||++|++.+....++
T Consensus       150 ~~p~llllDEP~~~LD~~~~~~l~~~l~~~----------~~~~tii~~sH~~~~~~~~~  199 (220)
T cd03263         150 GGPSVLLLDEPTSGLDPASRRAIWDLILEV----------RKGRSIILTTHSMDEAEALC  199 (220)
T ss_pred             cCCCEEEECCCCCCCCHHHHHHHHHHHHHH----------hcCCEEEEEcCCHHHHHHhc
Confidence            78889999998765 323344455555543          23467889998765544443

Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.53  E-value=1.1  Score=45.64  Aligned_cols=23  Identities=30%  Similarity=0.300  Sum_probs=19.2

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|+.|+||||++.++...
T Consensus       186 ~Vi~lVGpnGvGKTTTiaKLA~~  208 (767)
T PRK14723        186 GVLALVGPTGVGKTTTTAKLAAR  208 (767)
T ss_pred             eEEEEECCCCCcHHHHHHHHHhh
Confidence            35679999999999999888763

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=95.52  E-value=0.044  Score=51.76  Aligned_cols=69  Identities=17%  Similarity=0.074  Sum_probs=39.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CCCHHHHHHHHHHhhcCC---CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PFDEFRIAKAIIEGLEGS---EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~~~  195 (297)
                      .-++|++|+|||+||+.+..  .....|-..-......    ..++..++..++......   ..+-+|+||++....
T Consensus       111 iLl~Gp~GtGKT~lAr~lA~--~l~~pf~~id~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~  186 (412)
T PRK05342        111 ILLIGPTGSGKTLLAQTLAR--ILDVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIA  186 (412)
T ss_pred             EEEEcCCCCCHHHHHHHHHH--HhCCCceecchhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhc
Confidence            34789999999999999987  3433441110000111    113445554444332111   456799999998763

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=95.51  E-value=0.041  Score=45.61  Aligned_cols=22  Identities=27%  Similarity=0.327  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||++.+...
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~G~   49 (178)
T cd03229          28 IVALLGPSGSGKSTLLRCIAGL   49 (178)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999863

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=95.50  E-value=0.039  Score=50.38  Aligned_cols=21  Identities=24%  Similarity=0.313  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+.+.
T Consensus        72 i~I~G~sG~GKTtLl~~Ia~~   92 (326)
T cd01136          72 LGIFAGSGVGKSTLLGMIARG   92 (326)
T ss_pred             EEEECCCCCChHHHHHHHhCC
Confidence            468899999999999999874

This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway.

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=95.48  E-value=0.032  Score=51.33  Aligned_cols=53  Identities=23%  Similarity=0.195  Sum_probs=35.3

Q ss_pred             ccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCCHHHHHHHHHHhhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFDEFRIAKAIIEGLE  178 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~~~  178 (297)
                      ..|+|.+|+|||+|+..++-......    .-...+|+.....|+..++.+ ++++++
T Consensus       129 tEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~-ia~~~g  185 (344)
T PLN03187        129 TEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVP-IAERFG  185 (344)
T ss_pred             EEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHH-HHHHcC
Confidence            46899999999999987754322211    123678998888888776543 444443

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=95.44  E-value=0.093  Score=47.86  Aligned_cols=122  Identities=16%  Similarity=0.113  Sum_probs=70.2

Q ss_pred             ccccCCcchHHHHHHHhcccccc-----------------cCCCceEEEE-eCC--------CCCHHHHHHHHHHhhcCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI-----------------ENFDKRIWVC-VSD--------PFDEFRIAKAIIEGLEGS  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~-----------------~~F~~~~wv~-vs~--------~~~~~~~~~~i~~~~~~~  180 (297)
                      +.|+.|+||+++|..+.+.---.                 .|-| ..|+. ...        ...+. -.+++.+.+...
T Consensus        31 f~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD-~~~i~~~p~~~~~k~~~~I~id-qIR~l~~~~~~~  108 (319)
T PRK08769         31 ICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPD-LQLVSFIPNRTGDKLRTEIVIE-QVREISQKLALT  108 (319)
T ss_pred             eECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCC-EEEEecCCCcccccccccccHH-HHHHHHHHHhhC
Confidence            67999999999997776531111                 1222 23332 111        11222 344555544433


Q ss_pred             ---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchh
Q 043781          181 ---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAK  256 (297)
Q Consensus       181 ---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~  256 (297)
                         +++=++|+|++...+.+.-+.|...+..          ...++.+|++|...+   .+..+.-. ...+++..++.+
T Consensus       109 p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEE----------Pp~~~~fiL~~~~~~---~lLpTIrSRCq~i~~~~~~~~  175 (319)
T PRK08769        109 PQYGIAQVVIVDPADAINRAACNALLKTLEE----------PSPGRYLWLISAQPA---RLPATIRSRCQRLEFKLPPAH  175 (319)
T ss_pred             cccCCcEEEEeccHhhhCHHHHHHHHHHhhC----------CCCCCeEEEEECChh---hCchHHHhhheEeeCCCcCHH
Confidence               6778999999988765666667777754          245677777776432   23222221 256677777777


Q ss_pred             hhhhhhh
Q 043781          257 KIWGWEV  263 (297)
Q Consensus       257 ~lf~~~~  263 (297)
                      +...|-.
T Consensus       176 ~~~~~L~  182 (319)
T PRK08769        176 EALAWLL  182 (319)
T ss_pred             HHHHHHH
Confidence            7655543

>PRK10867 signal recognition particle protein; Provisional

Probab=95.44  E-value=0.5  Score=44.97  Aligned_cols=22  Identities=36%  Similarity=0.333  Sum_probs=17.0

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+-++|.+|+||||++..+..
T Consensus       101 ~vI~~vG~~GsGKTTtaakLA~  122 (433)
T PRK10867        101 TVIMMVGLQGAGKTTTAGKLAK  122 (433)
T ss_pred             EEEEEECCCCCcHHHHHHHHHH
Confidence            4556889999999997755554

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=95.44  E-value=0.047  Score=49.34  Aligned_cols=50  Identities=18%  Similarity=0.294  Sum_probs=32.4

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      ++.=+++||.--+. |...-+.+...+...          ..+..||+||+..+....+|.
T Consensus       150 ~~p~lliLDEPt~gLD~~~~~~l~~~l~~~----------~~~~tiii~sH~l~~~~~~~d  200 (301)
T TIGR03522       150 HDPKVLILDEPTTGLDPNQLVEIRNVIKNI----------GKDKTIILSTHIMQEVEAICD  200 (301)
T ss_pred             cCCCEEEEcCCcccCCHHHHHHHHHHHHHh----------cCCCEEEEEcCCHHHHHHhCC
Confidence            88889999988764 222333454555442          235779999997766666654

Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=95.41  E-value=0.034  Score=52.74  Aligned_cols=20  Identities=20%  Similarity=0.370  Sum_probs=18.3

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +|+|..|+|||||++.+.+.
T Consensus       162 ~I~G~sG~GKTtLL~~I~~~  181 (442)
T PRK08927        162 GIFAGSGVGKSVLLSMLARN  181 (442)
T ss_pred             EEECCCCCCHHHHHHHHHhc
Confidence            68899999999999999974

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=95.41  E-value=0.027  Score=53.36  Aligned_cols=64  Identities=14%  Similarity=0.176  Sum_probs=41.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHh----------------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEG----------------------------  176 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~----------------------------  176 (297)
                      +|+|..|+|||||++.+.+..    ..+..+.+-+.... .+.++..+++..                            
T Consensus       166 gI~G~sG~GKSTLL~~I~~~~----~~dv~Vi~lIGER~rEv~efi~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~A~  241 (444)
T PRK08972        166 GLFAGSGVGKSVLLGMMTRGT----TADVIVVGLVGERGREVKEFIEEILGEEGRARSVVVAAPADTSPLMRLKGCETAT  241 (444)
T ss_pred             EEECCCCCChhHHHHHhccCC----CCCEEEEEEEcCChHHHHHHHHHhhccCCcccEEEEEECCCCCHHHHHHHHHHHH
Confidence            688999999999999998732    12344444444433 234444444333                            


Q ss_pred             -----hcCCCceEEEEEeCCCC
Q 043781          177 -----LEGSEKKFFLILDDVWT  193 (297)
Q Consensus       177 -----~~~~~kr~LiVlDdv~~  193 (297)
                           +...++..|+++||+-.
T Consensus       242 tiAEyfrd~G~~VLl~~DslTR  263 (444)
T PRK08972        242 TIAEYFRDQGLNVLLLMDSLTR  263 (444)
T ss_pred             HHHHHHHHcCCCEEEEEcChHH
Confidence                 22229999999999954

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=95.40  E-value=0.057  Score=45.79  Aligned_cols=21  Identities=29%  Similarity=0.278  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+..-
T Consensus        29 ~~i~G~nGsGKSTLl~~l~Gl   49 (208)
T cd03268          29 YGFLGPNGAGKTTTMKIILGL   49 (208)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            468899999999999999874

Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.

>TIGR01188 drrA daunorubicin resistance ABC transporter ATP-binding subunit

Probab=95.40  E-value=0.053  Score=49.04  Aligned_cols=51  Identities=18%  Similarity=0.167  Sum_probs=31.9

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.=+|+||.--+. |...-..+...+...         ...|..||++|++.+....+|.
T Consensus       141 ~~p~lllLDEPt~gLD~~~~~~l~~~l~~~---------~~~g~tvi~~sH~~~~~~~~~d  192 (302)
T TIGR01188       141 HQPDVLFLDEPTTGLDPRTRRAIWDYIRAL---------KEEGVTILLTTHYMEEADKLCD  192 (302)
T ss_pred             cCCCEEEEeCCCcCCCHHHHHHHHHHHHHH---------HhCCCEEEEECCCHHHHHHhCC
Confidence            88889999988664 222222344444332         1347789999998766666554

This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc.

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=95.39  E-value=0.16  Score=44.54  Aligned_cols=22  Identities=36%  Similarity=0.471  Sum_probs=19.6

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+...
T Consensus        27 ~~~i~G~NGsGKSTLlk~L~G~   48 (246)
T cd03237          27 VIGILGPNGIGKTTFIKMLAGV   48 (246)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3579999999999999999884

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=95.39  E-value=0.042  Score=56.85  Aligned_cols=67  Identities=21%  Similarity=0.271  Sum_probs=43.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccC------CCceEEE-EeCC-------CCCHHHHHHHHHHhhcCCCceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIEN------FDKRIWV-CVSD-------PFDEFRIAKAIIEGLEGSEKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~------F~~~~wv-~vs~-------~~~~~~~~~~i~~~~~~~~kr~LiVlDdv  191 (297)
                      -++|.+|+|||+||+.+...  +...      ....+|. .++.       .-...+-++.++..+...+++.+|++|++
T Consensus       198 lL~G~pGvGKT~l~~~la~~--i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEi  275 (852)
T TIGR03346       198 VLIGEPGVGKTAIVEGLAQR--IVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDEL  275 (852)
T ss_pred             EEEcCCCCCHHHHHHHHHHH--HhccCCchhhcCCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccH
Confidence            37899999999999998874  3221      1344443 2111       11344456677776654457899999999


Q ss_pred             CCC
Q 043781          192 WTD  194 (297)
Q Consensus       192 ~~~  194 (297)
                      ..-
T Consensus       276 h~l  278 (852)
T TIGR03346       276 HTL  278 (852)
T ss_pred             HHh
Confidence            753

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.

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=95.36  E-value=2.5  Score=39.88  Aligned_cols=143  Identities=18%  Similarity=0.188  Sum_probs=66.2

Q ss_pred             HHHHHHHHHhcc-cccHHHHHHHHHHHHHHhhHH---HHHHHHHHHHHHHhhhcCCccchhccchhHHHHHHHHHHHHHh
Q 043781           22 IQAVLNDAEQRQ-VKEASVRLWLDQLKEASYDME---DVLDEWITARLKLQIEGVDENALVRKKPKIIEINENLDDIAKQ   97 (297)
Q Consensus        22 i~a~l~~ae~~~-~~~~~v~~Wl~~lr~~ayd~e---D~ld~~~~~~~~~~~~~~~~~~~~~~~~~i~~i~~~l~~i~~~   97 (297)
                      ++..+....... .....++.-++++|-+.-+++   .++-+|.....+................-|+-+.++|-++...
T Consensus         9 l~~~l~kl~g~~~i~E~~i~e~~reir~ALLeADVnl~vVk~fi~~ikera~g~ev~~~l~p~q~~iKiV~eELv~llG~   88 (451)
T COG0541           9 LSNALKKLRGKGRITEKDVKEALREIRRALLEADVNLKVVKDFIKRIKERALGEEVPKGLTPGQQFIKIVYEELVKLLGG   88 (451)
T ss_pred             HHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHhccccCCCCCCHHHHHHHHHHHHHHHHhCC
Confidence            334444444433 344668888888888776654   2333333333222221111111111111234444444444311


Q ss_pred             hhhcccccccCCcccccccccccccccccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHH--HHHHHHHH
Q 043781           98 KEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEF--RIAKAIIE  175 (297)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~~~~~i~~  175 (297)
                                   +............++-.+|.-|.||||-+-++.+.  .++ ....+-+...+.+.+.  +=++.+.+
T Consensus        89 -------------~~~~~~l~~~~P~vImmvGLQGsGKTTt~~KLA~~--lkk-~~~kvllVaaD~~RpAA~eQL~~La~  152 (451)
T COG0541          89 -------------ENSELNLAKKPPTVILMVGLQGSGKTTTAGKLAKY--LKK-KGKKVLLVAADTYRPAAIEQLKQLAE  152 (451)
T ss_pred             -------------CCcccccCCCCCeEEEEEeccCCChHhHHHHHHHH--HHH-cCCceEEEecccCChHHHHHHHHHHH
Confidence                         00001111112334557899999999999777763  333 4444444444444332  23445555


Q ss_pred             hhcCC
Q 043781          176 GLEGS  180 (297)
Q Consensus       176 ~~~~~  180 (297)
                      +.+.+
T Consensus       153 q~~v~  157 (451)
T COG0541         153 QVGVP  157 (451)
T ss_pred             HcCCc
Confidence            55443

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=95.35  E-value=0.029  Score=49.82  Aligned_cols=75  Identities=19%  Similarity=0.208  Sum_probs=43.7

Q ss_pred             ccccccCCcchHHHH-HHHhcccccccCCCce-EEEEeCCCC-CHHHHHHHHHHhhc-----------------------
Q 043781          125 SDVRGMGGIGKTTLA-QFAYNDKDVIENFDKR-IWVCVSDPF-DEFRIAKAIIEGLE-----------------------  178 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~~~-----------------------  178 (297)
                      ..|+|..|+|||+|| ..+.+.  .  .-+.+ +++-+.... .+.++.+++.+.-.                       
T Consensus        72 ~~Ifg~~g~GKt~L~l~~i~~~--~--~~~v~~V~~~iGer~~ev~e~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~a~~  147 (274)
T cd01132          72 ELIIGDRQTGKTAIAIDTIINQ--K--GKKVYCIYVAIGQKASTVAQVVKTLEEHGAMEYTIVVAATASDPAPLQYLAPY  147 (274)
T ss_pred             EEeeCCCCCCccHHHHHHHHHh--c--CCCeEEEEEecccchHHHHHHHHHHHhcCccceeEEEEeCCCCchhHHHHHHH
Confidence            468999999999995 666552  1  22333 444444433 34555555543321                       


Q ss_pred             ----------CCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          179 ----------GSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       179 ----------~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                                ..++..||++||+-... ..|..+..
T Consensus       148 ~a~aiAE~fr~~G~~Vlvl~DslTr~A-~A~rEisl  182 (274)
T cd01132         148 TGCAMGEYFMDNGKHALIIYDDLSKQA-VAYRQMSL  182 (274)
T ss_pred             HHHHHHHHHHHCCCCEEEEEcChHHHH-HHHHHHHH
Confidence                      11889999999985432 24444433

The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=95.34  E-value=0.078  Score=47.19  Aligned_cols=21  Identities=24%  Similarity=0.006  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+...
T Consensus       114 ~~i~g~~g~GKttl~~~l~~~  134 (270)
T TIGR02858       114 TLIISPPQCGKTTLLRDLARI  134 (270)
T ss_pred             EEEEcCCCCCHHHHHHHHhCc
Confidence            468899999999999999984

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.

>PRK09280 F0F1 ATP synthase subunit beta; Validated

Probab=95.33  E-value=0.033  Score=53.06  Aligned_cols=68  Identities=18%  Similarity=0.246  Sum_probs=41.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHH-----------------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAII-----------------------------  174 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~-----------------------------  174 (297)
                      .+|+|..|+|||||+.++..+..... =+.++++-+.... .+.+++.+++                             
T Consensus       147 ~gIfa~~GvGKt~Ll~~i~~~~~~~~-~~v~V~~liGER~rEv~efi~~~~~~~~l~rsvvV~atsd~p~~~r~~a~~~a  225 (463)
T PRK09280        147 IGLFGGAGVGKTVLIQELINNIAKEH-GGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARLRVALTG  225 (463)
T ss_pred             EEeecCCCCChhHHHHHHHHHHHhcC-CCEEEEEEeccCcHHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHH
Confidence            36899999999999988765432211 1344444443332 2344444443                             


Q ss_pred             ----HhhcC-CCceEEEEEeCCCC
Q 043781          175 ----EGLEG-SEKKFFLILDDVWT  193 (297)
Q Consensus       175 ----~~~~~-~~kr~LiVlDdv~~  193 (297)
                          +.+.. .++..||++|++-.
T Consensus       226 ~tiAEyfrd~~G~~VLll~DslTR  249 (463)
T PRK09280        226 LTMAEYFRDVEGQDVLLFIDNIFR  249 (463)
T ss_pred             HHHHHHHHHhcCCceEEEecchHH
Confidence                33332 28999999999953

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=95.31  E-value=0.18  Score=42.70  Aligned_cols=105  Identities=16%  Similarity=0.134  Sum_probs=56.0

Q ss_pred             cccccccCCcchHHHHHHHhccccc--cc--------CCC-ceE--EEEeCCCCC------HH--HHHHHHHHhhcCCCc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDV--IE--------NFD-KRI--WVCVSDPFD------EF--RIAKAIIEGLEGSEK  182 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~--~~--------~F~-~~~--wv~vs~~~~------~~--~~~~~i~~~~~~~~k  182 (297)
                      ...|.|+.|.|||||.+.+.....+  ..        .|. ..+  +.++.++..      ..  .-+..+++.++. .+
T Consensus        27 ~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~l~~~~s~~~~e~~~~~~iL~~~~~-~~  105 (199)
T cd03283          27 GILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKK-GE  105 (199)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcccceEEEeccchhccccccChHHHHHHHHHHHHHhccC-CC
Confidence            4568899999999999888753211  00        011 112  222222210      01  224555665542 37


Q ss_pred             eEEEEEeCCCCCC-ccCHHHHH-HHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHH
Q 043781          183 KFFLILDDVWTDD-YSKWEPFH-NCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHL  238 (297)
Q Consensus       183 r~LiVlDdv~~~~-~~~w~~l~-~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v  238 (297)
                      +-|+++|..-..- ......+. ..+...         ...|..+|++|++.+.+..+
T Consensus       106 p~llllDEp~~glD~~~~~~l~~~ll~~l---------~~~~~tiiivTH~~~~~~~~  154 (199)
T cd03283         106 PVLFLLDEIFKGTNSRERQAASAAVLKFL---------KNKNTIGIISTHDLELADLL  154 (199)
T ss_pred             CeEEEEecccCCCCHHHHHHHHHHHHHHH---------HHCCCEEEEEcCcHHHHHhh
Confidence            8999999975431 11222232 223221         13477899999977655443

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

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=95.30  E-value=0.23  Score=43.74  Aligned_cols=22  Identities=36%  Similarity=0.324  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+..-
T Consensus        29 ~~~i~G~nGsGKSTLl~~l~Gl   50 (255)
T PRK11248         29 LLVVLGPSGCGKTTLLNLIAGF   50 (255)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999874

>PTZ00185 ATPase alpha subunit; Provisional

Probab=95.29  E-value=0.049  Score=52.43  Aligned_cols=69  Identities=16%  Similarity=0.201  Sum_probs=45.6

Q ss_pred             cccccCCcchHHHH-HHHhcccccc-----cCCCceEEEEeCCCCCHHHHHHHHHHhhc-CC------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVI-----ENFDKRIWVCVSDPFDEFRIAKAIIEGLE-GS------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~-----~~F~~~~wv~vs~~~~~~~~~~~i~~~~~-~~------------------  180 (297)
                      .|+|-.|+|||+|| ..+.+...+.     ++-+.++++.+.+..+-..-+.+.++.-+ ..                  
T Consensus       193 lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGeR~rEV~ei~~~L~e~GaL~~TvVV~AtAdep~~~r~~  272 (574)
T PTZ00185        193 LIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQRCSNVARIHRLLRSYGALRYTTVMAATAAEPAGLQYL  272 (574)
T ss_pred             EeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEeccchHHHHHHHHHHHhcCCccceEEEEECCCCCHHHHHH
Confidence            68899999999997 6666643221     23456778888776543322333333333 11                  


Q ss_pred             ---------------CceEEEEEeCCCCC
Q 043781          181 ---------------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 ---------------~kr~LiVlDdv~~~  194 (297)
                                     ++..|||+||+-..
T Consensus       273 Apy~a~tiAEYFrd~GkdVLiv~DDLTr~  301 (574)
T PTZ00185        273 APYSGVTMGEYFMNRGRHCLCVYDDLSKQ  301 (574)
T ss_pred             HHHHHHHHHHHHHHcCCCEEEEEcCchHH
Confidence                           99999999999654

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.28  E-value=0.012  Score=47.92  Aligned_cols=21  Identities=33%  Similarity=0.351  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.||+|+|||||++.+.+.
T Consensus         8 i~ITG~PGvGKtTl~~ki~e~   28 (179)
T COG1618           8 IFITGRPGVGKTTLVLKIAEK   28 (179)
T ss_pred             EEEeCCCCccHHHHHHHHHHH
Confidence            468899999999999999873

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=95.27  E-value=0.11  Score=43.96  Aligned_cols=22  Identities=36%  Similarity=0.466  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+..-
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~Gl   49 (205)
T cd03226          28 IIALTGKNGAGKTTLAKILAGL   49 (205)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3478999999999999999884

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>PRK08149 ATP synthase SpaL; Validated

Probab=95.26  E-value=0.044  Score=51.87  Aligned_cols=21  Identities=24%  Similarity=0.359  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||+..+.+.
T Consensus       154 i~I~G~sG~GKTTLl~~i~~~  174 (428)
T PRK08149        154 MGIFASAGCGKTSLMNMLIEH  174 (428)
T ss_pred             EEEECCCCCChhHHHHHHhcC
Confidence            368899999999999999874

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=95.24  E-value=0.15  Score=42.40  Aligned_cols=50  Identities=18%  Similarity=0.145  Sum_probs=31.3

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLT  239 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~  239 (297)
                      .+.-+++||+--.. |....+.+...+...         ...|..||++|++.+....++
T Consensus       121 ~~p~llllDEP~~~LD~~~~~~l~~~l~~~---------~~~~~tiii~sh~~~~~~~~~  171 (182)
T cd03215         121 RDPRVLILDEPTRGVDVGAKAEIYRLIREL---------ADAGKAVLLISSELDELLGLC  171 (182)
T ss_pred             cCCCEEEECCCCcCCCHHHHHHHHHHHHHH---------HHCCCEEEEEeCCHHHHHHhC
Confidence            67789999988664 323444555555443         134678999998755444443

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=95.24  E-value=0.031  Score=52.80  Aligned_cols=21  Identities=24%  Similarity=0.358  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+...
T Consensus       143 i~I~G~sG~GKTtLl~~I~~~  163 (418)
T TIGR03498       143 LGIFAGSGVGKSTLLSMLARN  163 (418)
T ss_pred             EEEECCCCCChHHHHHHHhCC
Confidence            468899999999999999874

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.23  E-value=0.037  Score=56.35  Aligned_cols=62  Identities=21%  Similarity=0.241  Sum_probs=37.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|++|+|||+||+.+.+.  ....|   +.+..+    ... .....++.++..... ....+|+||++..
T Consensus       216 LL~GppGtGKT~laraia~~--~~~~~---i~i~~~~i~~~~~g~~~~~l~~lf~~a~~-~~p~il~iDEid~  282 (733)
T TIGR01243       216 LLYGPPGTGKTLLAKAVANE--AGAYF---ISINGPEIMSKYYGESEERLREIFKEAEE-NAPSIIFIDEIDA  282 (733)
T ss_pred             EEECCCCCChHHHHHHHHHH--hCCeE---EEEecHHHhcccccHHHHHHHHHHHHHHh-cCCcEEEeehhhh
Confidence            47899999999999999983  33332   222211    111 123344555554433 4567999999864

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=95.23  E-value=0.37  Score=45.68  Aligned_cols=22  Identities=36%  Similarity=0.299  Sum_probs=19.0

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.++|.+|+||||++..+..
T Consensus       101 ~vi~lvG~~GvGKTTtaaKLA~  122 (429)
T TIGR01425       101 NVIMFVGLQGSGKTTTCTKLAY  122 (429)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999988876

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>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=95.22  E-value=0.032  Score=49.63  Aligned_cols=76  Identities=20%  Similarity=0.182  Sum_probs=50.9

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceE-EEEeCCCCCHHH---HHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRI-WVCVSDPFDEFR---IAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPF  202 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~-wv~vs~~~~~~~---~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l  202 (297)
                      ++|+||+||++|++.+..-   .   +..+ -+.+++.++..+   -++.++...+..+++..+++.|-+-.+...++.+
T Consensus        36 LvG~~GsGr~sl~rLaa~i---~---~~~~~~i~~~~~y~~~~f~~dLk~~~~~ag~~~~~~vfll~d~qi~~~~fLe~i  109 (268)
T PF12780_consen   36 LVGVGGSGRQSLARLAAFI---C---GYEVFQIEITKGYSIKDFKEDLKKALQKAGIKGKPTVFLLTDSQIVDESFLEDI  109 (268)
T ss_dssp             EECTTTSCHHHHHHHHHHH---T---TEEEE-TTTSTTTHHHHHHHHHHHHHHHHHCS-S-EEEEEECCCSSSCHHHHHH
T ss_pred             EecCCCccHHHHHHHHHHH---h---ccceEEEEeeCCcCHHHHHHHHHHHHHHHhccCCCeEEEecCcccchHhHHHHH
Confidence            7899999999999987762   1   1111 123566666655   4666677777778999999999876654566777


Q ss_pred             HHHHhh
Q 043781          203 HNCLMR  208 (297)
Q Consensus       203 ~~~l~~  208 (297)
                      ...+..
T Consensus       110 n~LL~s  115 (268)
T PF12780_consen  110 NSLLSS  115 (268)
T ss_dssp             HHHHHC
T ss_pred             HHHHhC
Confidence            666643

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.

>PRK05922 type III secretion system ATPase; Validated

Probab=95.20  E-value=0.052  Score=51.41  Aligned_cols=21  Identities=24%  Similarity=0.186  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+.+.
T Consensus       160 igI~G~nG~GKSTLL~~Ia~~  180 (434)
T PRK05922        160 IGVFSEPGSGKSSLLSTIAKG  180 (434)
T ss_pred             EEEECCCCCChHHHHHHHhcc
Confidence            368899999999999999864

>PRK03839 putative kinase; Provisional

Probab=95.19  E-value=0.01  Score=49.20  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|++|+||||+++.+++.
T Consensus         3 I~l~G~pGsGKsT~~~~La~~   23 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAEK   23 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999984

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=95.13  E-value=0.043  Score=50.56  Aligned_cols=54  Identities=19%  Similarity=0.224  Sum_probs=35.7

Q ss_pred             cccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCCHHHHHHHHHHhhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFDEFRIAKAIIEGLE  178 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~~~i~~~~~  178 (297)
                      ...|+|.+|+|||+|+..++-......    .-...+|+.....|+..++. +|+++++
T Consensus       125 i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~-qia~~~~  182 (342)
T PLN03186        125 ITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLI-QIAERFG  182 (342)
T ss_pred             EEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHH-HHHHHcC
Confidence            346889999999999987775322211    11268899888887776653 4444443

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.12  E-value=0.18  Score=41.46  Aligned_cols=21  Identities=29%  Similarity=0.388  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|.|||||.+.+..-
T Consensus        31 ~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          31 VAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            468899999999999999884

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.

>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=95.11  E-value=0.012  Score=46.47  Aligned_cols=19  Identities=37%  Similarity=0.336  Sum_probs=17.0

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -++|++|+||||+|+.+..
T Consensus         3 i~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    3 ILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEESTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3679999999999999885

...

>PRK09099 type III secretion system ATPase; Provisional

Probab=95.11  E-value=0.042  Score=52.21  Aligned_cols=20  Identities=25%  Similarity=0.366  Sum_probs=18.1

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|+|..|+|||||++.+...
T Consensus       167 ~I~G~sG~GKTtLl~~ia~~  186 (441)
T PRK09099        167 GIFAPAGVGKSTLMGMFARG  186 (441)
T ss_pred             EEECCCCCCHHHHHHHHhCC
Confidence            68899999999999999874

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=95.10  E-value=0.046  Score=47.24  Aligned_cols=81  Identities=15%  Similarity=0.054  Sum_probs=49.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHH--HHh--hcCC-CceEEEEEeCCCCCCccCHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAI--IEG--LEGS-EKKFFLILDDVWTDDYSKWEP  201 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i--~~~--~~~~-~kr~LiVlDdv~~~~~~~w~~  201 (297)
                      |-||+|+||||-+..+.+.---...=+...=++.|+...+.-+-..|  +.|  +..+ ++--+||||...+.....-+.
T Consensus        53 isGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~gAQQA  132 (333)
T KOG0991|consen   53 ISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTAGAQQA  132 (333)
T ss_pred             eeCCCCCchhhHHHHHHHHHhChhhhhHhhhccCccccccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhhHHHHH
Confidence            56999999999887777731111122455556667665544433333  222  2222 777889999998875445556


Q ss_pred             HHHHHh
Q 043781          202 FHNCLM  207 (297)
Q Consensus       202 l~~~l~  207 (297)
                      ++..+.
T Consensus       133 lRRtME  138 (333)
T KOG0991|consen  133 LRRTME  138 (333)
T ss_pred             HHHHHH
Confidence            666654

>CHL00095 clpC Clp protease ATP binding subunit

Probab=95.09  E-value=0.054  Score=55.81  Aligned_cols=67  Identities=22%  Similarity=0.227  Sum_probs=41.7

Q ss_pred             cccccCCcchHHHHHHHhcccc---cccC-CCceEEE-EeC------C-CCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD---VIEN-FDKRIWV-CVS------D-PFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~---~~~~-F~~~~wv-~vs------~-~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|.+|+|||+||+.+...-.   +... -+..+|. .++      . .-...+-++.+++.+.. .++.+|++|++..
T Consensus       204 lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~-~~~~ILfiDEih~  282 (821)
T CHL00095        204 ILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQE-NNNIILVIDEVHT  282 (821)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHh-cCCeEEEEecHHH
Confidence            4889999999999999888421   1111 1344554 211      1 11244556677766643 4689999999963

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=95.07  E-value=0.029  Score=47.66  Aligned_cols=42  Identities=17%  Similarity=0.271  Sum_probs=29.7

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFR  168 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~  168 (297)
                      ...|+|.+|+|||+|+.++..+  ....-...+|+.... ++..+
T Consensus        14 i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~-~~~~r   55 (209)
T TIGR02237        14 ITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEG-LSPER   55 (209)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCC-CCHHH
Confidence            3468999999999999887763  323345778887764 44443

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=95.07  E-value=0.15  Score=45.05  Aligned_cols=22  Identities=32%  Similarity=0.367  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+..-
T Consensus        40 ~~~I~G~NGsGKSTLlk~l~Gl   61 (257)
T PRK11247         40 FVAVVGRSGCGKSTLLRLLAGL   61 (257)
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3578999999999999999874

>PRK05541 adenylylsulfate kinase; Provisional

Probab=95.05  E-value=0.016  Score=47.92  Aligned_cols=33  Identities=30%  Similarity=0.530  Sum_probs=24.8

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEE
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWV  158 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv  158 (297)
                      .+.+.|++|+||||+|+.+++  +...++...+++
T Consensus         9 ~I~i~G~~GsGKst~a~~l~~--~l~~~~~~~~~~   41 (176)
T PRK05541          9 VIWITGLAGSGKTTIAKALYE--RLKLKYSNVIYL   41 (176)
T ss_pred             EEEEEcCCCCCHHHHHHHHHH--HHHHcCCcEEEE
Confidence            345789999999999999998  454455555555

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=95.05  E-value=0.11  Score=44.16  Aligned_cols=22  Identities=32%  Similarity=0.357  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||++.+..-
T Consensus        27 ~~~i~G~nGsGKSTLl~~l~Gl   48 (211)
T cd03264          27 MYGLLGPNGAGKTTLMRILATL   48 (211)
T ss_pred             cEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999974

The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.02  E-value=0.16  Score=43.37  Aligned_cols=21  Identities=38%  Similarity=0.332  Sum_probs=19.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|.|||||.+.+...
T Consensus        40 ~~i~G~nGsGKSTLl~~i~G~   60 (214)
T PRK13543         40 LLVQGDNGAGKTTLLRVLAGL   60 (214)
T ss_pred             EEEEcCCCCCHHHHHHHHhCC
Confidence            468899999999999999975

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

Probab=95.02  E-value=0.1  Score=48.34  Aligned_cols=157  Identities=12%  Similarity=0.091  Sum_probs=74.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCCCceEEEEEeCCCCC-----
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGSEKKFFLILDDVWTD-----  194 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~-----  194 (297)
                      ++|++|.|||.||+.|+.  +...     -|++||...       .-+++++-+++-... .-...|.+|.+...     
T Consensus       250 m~GPPGTGKTlLAKAvAT--Ec~t-----TFFNVSsstltSKwRGeSEKlvRlLFemARf-yAPStIFiDEIDslcs~RG  321 (491)
T KOG0738|consen  250 MVGPPGTGKTLLAKAVAT--ECGT-----TFFNVSSSTLTSKWRGESEKLVRLLFEMARF-YAPSTIFIDEIDSLCSQRG  321 (491)
T ss_pred             eeCCCCCcHHHHHHHHHH--hhcC-----eEEEechhhhhhhhccchHHHHHHHHHHHHH-hCCceeehhhHHHHHhcCC
Confidence            459999999999999998  3332     234444321       223444433332221 34667888888641     


Q ss_pred             ---CccCHHHHHHHHhhhhhhhceeeecCCCCeEEE---EeccH-HHHHHHHHhhCCCccccCCccchhhhhhhhhccCC
Q 043781          195 ---DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSL---TSTCQ-EKLRHLTLTLGLRAKFPVSIFDAKKIWGWEVFGRN  267 (297)
Q Consensus       195 ---~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iii---TTr~~-~~~~~v~~~~~~~~~~~l~~l~~~~lf~~~~f~~~  267 (297)
                         +.+.-..++.-|-   .+-+-+..+..++++|.   .|..+ +..+.+-..+--.-.+||-..+..+-+-....+..
T Consensus       322 ~s~EHEaSRRvKsELL---vQmDG~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~~l~~~  398 (491)
T KOG0738|consen  322 GSSEHEASRRVKSELL---VQMDGVQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDAEARSALIKILLRSV  398 (491)
T ss_pred             CccchhHHHHHHHHHH---HHhhccccccccceeEEEEeccCCCcchHHHHHHHHhhheeeeCCCHHHHHHHHHHhhccc
Confidence               1112222333331   11111122244555433   34322 44444444444333456666655543333333433


Q ss_pred             CCCCchhhHhhhhhhccccccccchhh
Q 043781          268 TSTRPGMVSRYLMAEFCEPVCSVKAWC  294 (297)
Q Consensus       268 ~~~~~~~~~~~~~~~~c~~~c~~~~~~  294 (297)
                      ...+|-.+..+......+++--|-..|
T Consensus       399 ~~~~~~~~~~lae~~eGySGaDI~nvC  425 (491)
T KOG0738|consen  399 ELDDPVNLEDLAERSEGYSGADITNVC  425 (491)
T ss_pred             cCCCCccHHHHHHHhcCCChHHHHHHH
Confidence            333343444444333456665555555

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=95.00  E-value=0.072  Score=48.32  Aligned_cols=51  Identities=20%  Similarity=0.136  Sum_probs=32.0

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.=+++||.--+. |...-..+...+...         ...|..||+||+..+.+..+|.
T Consensus       155 ~~P~lllLDEPt~gLD~~~~~~l~~~l~~l---------~~~g~till~sH~l~e~~~~~d  206 (306)
T PRK13537        155 NDPDVLVLDEPTTGLDPQARHLMWERLRSL---------LARGKTILLTTHFMEEAERLCD  206 (306)
T ss_pred             CCCCEEEEeCCCcCCCHHHHHHHHHHHHHH---------HhCCCEEEEECCCHHHHHHhCC
Confidence            88889999988664 222222333334332         1457889999998776666654

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=95.00  E-value=0.099  Score=44.52  Aligned_cols=21  Identities=19%  Similarity=0.063  Sum_probs=17.6

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|.|+.|.||||+.+.+..
T Consensus        31 ~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          31 FHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999988863

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

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=95.00  E-value=0.26  Score=42.46  Aligned_cols=22  Identities=27%  Similarity=0.306  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|.|..|+|||||++.+...
T Consensus        50 ~~~i~G~nGsGKSTLl~~l~G~   71 (224)
T cd03220          50 RIGLIGRNGAGKSTLLRLLAGI   71 (224)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3568899999999999999984

Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.

>PRK05973 replicative DNA helicase; Provisional

Probab=94.99  E-value=0.2  Score=43.63  Aligned_cols=20  Identities=25%  Similarity=0.094  Sum_probs=16.4

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|.+|+|||+++.++...
T Consensus        68 LIaG~PG~GKT~lalqfa~~   87 (237)
T PRK05973         68 LLGARPGHGKTLLGLELAVE   87 (237)
T ss_pred             EEEeCCCCCHHHHHHHHHHH
Confidence            46799999999999876553

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=94.98  E-value=0.079  Score=45.24  Aligned_cols=21  Identities=29%  Similarity=0.319  Sum_probs=19.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|.|||||.+.+..-
T Consensus        34 ~~i~G~nGsGKSTLl~~l~Gl   54 (218)
T cd03266          34 TGLLGPNGAGKTTTLRMLAGL   54 (218)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            578999999999999999974

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.

>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor

Probab=94.98  E-value=0.23  Score=43.79  Aligned_cols=22  Identities=32%  Similarity=0.422  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|.|||||.+.+..-
T Consensus        28 ~~~IvG~nGsGKSTLlk~l~Gl   49 (255)
T cd03236          28 VLGLVGPNGIGKSTALKILAGK   49 (255)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3579999999999999999884

The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI s are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLIs 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.

>PRK00625 shikimate kinase; Provisional

Probab=94.98  E-value=0.013  Score=48.57  Aligned_cols=21  Identities=19%  Similarity=0.184  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++||+|+||||+++.+.+.
T Consensus         3 I~LiG~pGsGKTT~~k~La~~   23 (173)
T PRK00625          3 IFLCGLPTVGKTSFGKALAKF   23 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999874

>PRK15177 Vi polysaccharide export ATP-binding protein VexC; Provisional

Probab=94.98  E-value=0.24  Score=42.37  Aligned_cols=22  Identities=27%  Similarity=0.271  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||.+.+..-
T Consensus        15 ~~~l~G~NGsGKSTLlk~i~Gl   36 (213)
T PRK15177         15 HIGILAAPGSGKTTLTRLLCGL   36 (213)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999974

>cd04159 Arl10_like Arl10-like subfamily

Probab=94.97  E-value=0.065  Score=42.32  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=19.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|.+|+|||||.+.+...
T Consensus         2 i~i~G~~~~GKssl~~~l~~~   22 (159)
T cd04159           2 ITLVGLQNSGKTTLVNVIAGG   22 (159)
T ss_pred             EEEEcCCCCCHHHHHHHHccC
Confidence            568999999999999999886

Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved.

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=94.97  E-value=0.099  Score=47.14  Aligned_cols=22  Identities=32%  Similarity=0.357  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..++.|+.|.|||||.+.+..-
T Consensus        33 i~gllG~NGAGKTTllk~l~gl   54 (293)
T COG1131          33 IFGLLGPNGAGKTTLLKILAGL   54 (293)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3478899999999999999984

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

Probab=94.95  E-value=0.021  Score=49.86  Aligned_cols=59  Identities=22%  Similarity=0.355  Sum_probs=35.7

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC-C------CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP-F------DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~------~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      +||++|+|||.||+.|.++  ....|     +.|... |      .-.++.+++++-... +-.-+|.+|.+..
T Consensus       194 lygppg~gktml~kava~~--t~a~f-----irvvgsefvqkylgegprmvrdvfrlake-napsiifideida  259 (408)
T KOG0727|consen  194 LYGPPGTGKTMLAKAVANH--TTAAF-----IRVVGSEFVQKYLGEGPRMVRDVFRLAKE-NAPSIIFIDEIDA  259 (408)
T ss_pred             EeCCCCCcHHHHHHHHhhc--cchhe-----eeeccHHHHHHHhccCcHHHHHHHHHHhc-cCCcEEEeehhhh
Confidence            6799999999999999995  33344     222111 0      012233333332222 6678889998864

>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=94.95  E-value=0.14  Score=42.13  Aligned_cols=21  Identities=33%  Similarity=0.430  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|.|||||.+.+..-
T Consensus        31 ~~i~G~nGsGKStLl~~l~G~   51 (173)
T cd03246          31 LAIIGPSGSGKSTLARLILGL   51 (173)
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            478999999999999999974

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

>PRK06936 type III secretion system ATPase; Provisional

Probab=94.94  E-value=0.057  Score=51.22  Aligned_cols=64  Identities=16%  Similarity=0.228  Sum_probs=41.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHh----------------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEG----------------------------  176 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~----------------------------  176 (297)
                      +|+|..|+|||||.+.+++...    -+..+++-+.... .+.++....+..                            
T Consensus       166 ~I~G~sG~GKStLl~~Ia~~~~----~dv~V~~liGERgrEv~ef~~~~l~~~~l~rtvvv~atsd~p~~~R~~a~~~a~  241 (439)
T PRK06936        166 GIFAAAGGGKSTLLASLIRSAE----VDVTVLALIGERGREVREFIESDLGEEGLRKAVLVVATSDRPSMERAKAGFVAT  241 (439)
T ss_pred             EEECCCCCChHHHHHHHhcCCC----CCEEEEEEEccCcHHHHHHHHHHhcccccceeEEEEECCCCCHHHHHHHHHHHH
Confidence            6889999999999999998532    2455555554433 334444333322                            


Q ss_pred             -----hcCCCceEEEEEeCCCC
Q 043781          177 -----LEGSEKKFFLILDDVWT  193 (297)
Q Consensus       177 -----~~~~~kr~LiVlDdv~~  193 (297)
                           +...++..|+++|++-.
T Consensus       242 tiAEyfrd~G~~Vll~~DslTR  263 (439)
T PRK06936        242 SIAEYFRDQGKRVLLLMDSVTR  263 (439)
T ss_pred             HHHHHHHHcCCCEEEeccchhH
Confidence                 21119999999999953

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=94.94  E-value=0.35  Score=41.44  Aligned_cols=50  Identities=16%  Similarity=0.179  Sum_probs=31.7

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLT  239 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~  239 (297)
                      ...-+++||+--.. |....+.+...+...         ...|..||++|++.+....+|
T Consensus       141 ~~p~llllDEP~~~LD~~~~~~l~~~L~~~---------~~~~~tiii~sH~~~~~~~~~  191 (223)
T TIGR03740       141 NHPKLLILDEPTNGLDPIGIQELRELIRSF---------PEQGITVILSSHILSEVQQLA  191 (223)
T ss_pred             cCCCEEEECCCccCCCHHHHHHHHHHHHHH---------HHCCCEEEEEcCCHHHHHHhc
Confidence            77889999988665 323344455555442         134667999999766554444

Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes.

>TIGR01040 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit

Probab=94.91  E-value=0.055  Score=51.41  Aligned_cols=69  Identities=16%  Similarity=0.215  Sum_probs=46.5

Q ss_pred             ccccccCCcchHHHHHHHhccccccc--CCC---------ceEEEEeCCCCCHHHHHHHHHHhhc-CC------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE--NFD---------KRIWVCVSDPFDEFRIAKAIIEGLE-GS------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~--~F~---------~~~wv~vs~~~~~~~~~~~i~~~~~-~~------------  180 (297)
                      .+|+|-.|+|||||+.++.++....+  ..|         .++++-+.......+.+.+.+..-+ ..            
T Consensus       144 igIfagsGvGKs~L~~~i~~~~~~~~~~~aD~~~~~~~~~v~V~a~IGerre~~efi~~~l~~~g~l~rtvvv~atsd~p  223 (466)
T TIGR01040       144 IPIFSAAGLPHNEIAAQICRQAGLVKLPTKDVHDGHEDNFAIVFAAMGVNMETARFFKQDFEENGSMERVCLFLNLANDP  223 (466)
T ss_pred             eeeecCCCCCHHHHHHHHHHhhccccccccccccccCCceEEEEEEeeeehHHHHHHHHHHHhcCCcceEEEEEECCCCC
Confidence            47889999999999999887643100  011         4556666666555555555555443 11            


Q ss_pred             ----------------------CceEEEEEeCCCC
Q 043781          181 ----------------------EKKFFLILDDVWT  193 (297)
Q Consensus       181 ----------------------~kr~LiVlDdv~~  193 (297)
                                            ++..|+++||+-.
T Consensus       224 ~~~R~~a~~~a~tiAEyfr~~~G~~VLl~~DslTr  258 (466)
T TIGR01040       224 TIERIITPRLALTTAEYLAYQCEKHVLVILTDMSS  258 (466)
T ss_pred             HHHHHHHHhhhHHHHHHHHHhcCCcEEEeccChHH
Confidence                                  8999999999954

This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase.

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=94.89  E-value=0.058  Score=51.35  Aligned_cols=21  Identities=19%  Similarity=0.162  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||++.+...
T Consensus       171 igI~G~sG~GKSTLl~~I~g~  191 (451)
T PRK05688        171 LGLFAGTGVGKSVLLGMMTRF  191 (451)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            368899999999999999873

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.86  E-value=0.076  Score=54.01  Aligned_cols=67  Identities=24%  Similarity=0.229  Sum_probs=40.6

Q ss_pred             cccccCCcchHHHHHHHhccccccc-C---CCceEEEE-eC-----C--CCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE-N---FDKRIWVC-VS-----D--PFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~-~---F~~~~wv~-vs-----~--~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|.+|+|||+||+.+...-.-.. .   .++.+|.. .+     .  .-....-++.++..+.. .+..+|+||++..
T Consensus       211 LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~-~~~~ILfIDEIh~  289 (758)
T PRK11034        211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQ-DTNSILFIDEIHT  289 (758)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhHHHHHHHHHHHHHh-cCCCEEEeccHHH
Confidence            3789999999999999987311111 1   24555542 11     0  11234445566655543 3567999999974

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=94.86  E-value=0.063  Score=48.94  Aligned_cols=46  Identities=17%  Similarity=0.177  Sum_probs=29.9

Q ss_pred             ccccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCCHHH
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFDEFR  168 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~  168 (297)
                      ....|+|.+|+|||||+..+........    .-...+|+.....++..+
T Consensus        97 ~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~R  146 (316)
T TIGR02239        97 SITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPER  146 (316)
T ss_pred             eEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHH
Confidence            3456899999999999988765322211    112457887766666554

This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).

>PRK13647 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=94.83  E-value=0.23  Score=44.25  Aligned_cols=51  Identities=12%  Similarity=0.074  Sum_probs=32.7

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.=+++||+--.. |......+...+...         ...|..||++|++.+....+|.
T Consensus       155 ~~p~llllDEPt~~LD~~~~~~l~~~l~~~---------~~~g~tili~tH~~~~~~~~~d  206 (274)
T PRK13647        155 MDPDVIVLDEPMAYLDPRGQETLMEILDRL---------HNQGKTVIVATHDVDLAAEWAD  206 (274)
T ss_pred             cCCCEEEEECCCcCCCHHHHHHHHHHHHHH---------HHCCCEEEEEeCCHHHHHHhCC
Confidence            88889999998765 223344455555443         1336788999987665555543

>PRK04296 thymidine kinase; Provisional

Probab=94.83  E-value=0.029  Score=47.17  Aligned_cols=19  Identities=21%  Similarity=0.106  Sum_probs=16.1

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      ++|..|.||||++..+...
T Consensus         7 itG~~GsGKTT~~l~~~~~   25 (190)
T PRK04296          7 IYGAMNSGKSTELLQRAYN   25 (190)
T ss_pred             EECCCCCHHHHHHHHHHHH
Confidence            6799999999999777664

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

Probab=94.83  E-value=0.061  Score=50.57  Aligned_cols=58  Identities=17%  Similarity=0.230  Sum_probs=40.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|+||.|||++..++++.  .  .|+. .=+..+...+-.+ ++.++...   ..+-+|||.|+.-
T Consensus       240 LYGPPGTGKSS~IaAmAn~--L--~ydI-ydLeLt~v~~n~d-Lr~LL~~t---~~kSIivIEDIDc  297 (457)
T KOG0743|consen  240 LYGPPGTGKSSFIAAMANY--L--NYDI-YDLELTEVKLDSD-LRHLLLAT---PNKSILLIEDIDC  297 (457)
T ss_pred             eeCCCCCCHHHHHHHHHhh--c--CCce-EEeeeccccCcHH-HHHHHHhC---CCCcEEEEeeccc
Confidence            6799999999999999983  2  1332 1234444444444 77777776   4688999999974

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=94.81  E-value=0.12  Score=44.24  Aligned_cols=21  Identities=14%  Similarity=0.142  Sum_probs=17.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..-|.|+.|.|||||.+.+..
T Consensus        31 ~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          31 IMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             EEEEECCCCCChHHHHHHHHH
Confidence            346889999999999998874

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

>TIGR02012 tigrfam_recA protein RecA

Probab=94.80  E-value=0.036  Score=50.48  Aligned_cols=66  Identities=24%  Similarity=0.209  Sum_probs=38.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEe---------------------CCCCCHHHHHHHHHHhhcCCCce
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV---------------------SDPFDEFRIAKAIIEGLEGSEKK  183 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v---------------------s~~~~~~~~~~~i~~~~~~~~kr  183 (297)
                      ..|+|.+|+||||||.++...  ....=...+|+..                     +++....+.+ .++.++-..+.-
T Consensus        58 teI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l-~~~~~li~~~~~  134 (321)
T TIGR02012        58 IEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQAL-EIAETLVRSGAV  134 (321)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHH-HHHHHHhhccCC
Confidence            458999999999999876653  2222233444432                     3333444433 333333333566


Q ss_pred             EEEEEeCCCC
Q 043781          184 FFLILDDVWT  193 (297)
Q Consensus       184 ~LiVlDdv~~  193 (297)
                      -+||+|-|-.
T Consensus       135 ~lIVIDSv~a  144 (321)
T TIGR02012       135 DIIVVDSVAA  144 (321)
T ss_pred             cEEEEcchhh
Confidence            7999999864

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.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=94.80  E-value=0.1  Score=43.80  Aligned_cols=22  Identities=32%  Similarity=0.585  Sum_probs=19.4

Q ss_pred             cccccCCcchHHHHHHHhcccc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD  147 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~  147 (297)
                      -++|+.|.|||||.+.+|..++
T Consensus        32 fl~GpSGAGKSTllkLi~~~e~   53 (223)
T COG2884          32 FLTGPSGAGKSTLLKLIYGEER   53 (223)
T ss_pred             EEECCCCCCHHHHHHHHHhhhc
Confidence            4789999999999999999644

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=94.80  E-value=0.25  Score=43.36  Aligned_cols=22  Identities=27%  Similarity=0.410  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||++.++.-
T Consensus        32 ~~~I~G~NGsGKSTLl~~i~Gl   53 (251)
T PRK09544         32 ILTLLGPNGAGKSTLVRVVLGL   53 (251)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999974

>PRK14974 cell division protein FtsY; Provisional

Probab=94.79  E-value=2.7  Score=38.63  Aligned_cols=22  Identities=32%  Similarity=0.208  Sum_probs=18.1

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.++|++|+||||++..+..
T Consensus       141 ~vi~~~G~~GvGKTTtiakLA~  162 (336)
T PRK14974        141 VVIVFVGVNGTGKTTTIAKLAY  162 (336)
T ss_pred             eEEEEEcCCCCCHHHHHHHHHH
Confidence            4567899999999997777765

>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=94.78  E-value=0.23  Score=40.89  Aligned_cols=98  Identities=15%  Similarity=0.076  Sum_probs=51.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC--------------CceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS--------------EKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--------------~kr~LiVlDdv  191 (297)
                      -|+|-.|+||+.+|+.+++.  ....-..-+-|+.+ ..+...+-.+++-...+.              ...=-|+||+|
T Consensus        26 lI~GE~GtGK~~lA~~IH~~--s~r~~~pfi~vnc~-~~~~~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I  102 (168)
T PF00158_consen   26 LITGETGTGKELLARAIHNN--SPRKNGPFISVNCA-ALPEELLESELFGHEKGAFTGARSDKKGLLEQANGGTLFLDEI  102 (168)
T ss_dssp             EEECSTTSSHHHHHHHHHHC--STTTTS-EEEEETT-TS-HHHHHHHHHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETG
T ss_pred             EEEcCCCCcHHHHHHHHHHh--hhcccCCeEEEehh-hhhcchhhhhhhccccccccccccccCCceeeccceEEeecch
Confidence            48899999999999999994  22111222334333 233343444444322110              23346889999


Q ss_pred             CCCCccCHHHHHHHHhhhhhhhceeeec-----CCCCeEEEEec
Q 043781          192 WTDDYSKWEPFHNCLMRVLQEFAAIEVD-----GDENPLSLTST  230 (297)
Q Consensus       192 ~~~~~~~w~~l~~~l~~~~~~~~~~~~~-----~~gs~iiiTTr  230 (297)
                      .+.....-..|...+...    ...+.+     .-..|||.||.
T Consensus       103 ~~L~~~~Q~~Ll~~l~~~----~~~~~g~~~~~~~~~RiI~st~  142 (168)
T PF00158_consen  103 EDLPPELQAKLLRVLEEG----KFTRLGSDKPVPVDVRIIASTS  142 (168)
T ss_dssp             GGS-HHHHHHHHHHHHHS----EEECCTSSSEEE--EEEEEEES
T ss_pred             hhhHHHHHHHHHHHHhhc----hhccccccccccccceEEeecC
Confidence            887544444455555432    111111     12457888886

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 ....

>TIGR01041 ATP_syn_B_arch ATP synthase archaeal, B subunit

Probab=94.77  E-value=0.051  Score=51.90  Aligned_cols=69  Identities=14%  Similarity=0.154  Sum_probs=43.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC--ceEEEEeCCCC-CHHHHHHHHHHh-------------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD--KRIWVCVSDPF-DEFRIAKAIIEG-------------------------  176 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~-~~~~~~~~i~~~-------------------------  176 (297)
                      .+|+|-.|+|||||+.++.+.......+.  .++++-+.+.- .+.+++.+++..                         
T Consensus       144 ~gIfgg~G~GKs~L~~~ia~~~~ad~~~~~~v~V~~~iGERgrEv~efi~~~~~~~~l~rtvvv~atsd~p~~~R~~a~~  223 (458)
T TIGR01041       144 LPIFSGSGLPHNELAAQIARQATVRGEESEFAVVFAAMGITYEEANFFMKDFEETGALERAVVFLNLADDPAVERIVTPR  223 (458)
T ss_pred             EEeeCCCCCCHHHHHHHHHHhhcccCCCCceEEEEEEccccchHHHHHHHHHHhcCCcceEEEEEECCCCCHHHHHHHHH
Confidence            36889999999999999988644321111  44455444432 344555544433                         


Q ss_pred             --------hc-CCCceEEEEEeCCCC
Q 043781          177 --------LE-GSEKKFFLILDDVWT  193 (297)
Q Consensus       177 --------~~-~~~kr~LiVlDdv~~  193 (297)
                              +. ..+++.|+++||+-.
T Consensus       224 ~a~tiAEyfr~d~G~~VLli~DslTR  249 (458)
T TIGR01041       224 MALTAAEYLAFEKDMHVLVILTDMTN  249 (458)
T ss_pred             HHHHHHHHHHHccCCcEEEEEcChhH
Confidence                    22 128999999999954

Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases.

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=94.77  E-value=0.016  Score=48.89  Aligned_cols=20  Identities=40%  Similarity=0.451  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ++|.|.+|+||||||+.+..
T Consensus         2 IgI~G~sgSGKTTla~~L~~   21 (194)
T PF00485_consen    2 IGIAGPSGSGKTTLAKRLAQ   21 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            57889999999999999988

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

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

Probab=94.76  E-value=0.05  Score=52.17  Aligned_cols=74  Identities=20%  Similarity=0.161  Sum_probs=41.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHH-----HHHHHHHhhcCCCceEEEEEeCCCCCCccCHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFR-----IAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEP  201 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~-----~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~  201 (297)
                      +.|++|+|||+||-.+...    +.|..+--++...-..+.+     ..+.+++.... ..--.||+||+-.-  -+|-.
T Consensus       543 l~Gp~~sGKTaLAA~iA~~----S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYk-S~lsiivvDdiErL--iD~vp  615 (744)
T KOG0741|consen  543 LEGPPGSGKTALAAKIALS----SDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYK-SPLSIIVVDDIERL--LDYVP  615 (744)
T ss_pred             EecCCCCChHHHHHHHHhh----cCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhc-CcceEEEEcchhhh--hcccc
Confidence            4499999999999998873    4565443332211111111     12222222222 46678999999665  35555


Q ss_pred             HHHHHh
Q 043781          202 FHNCLM  207 (297)
Q Consensus       202 l~~~l~  207 (297)
                      |.+.|+
T Consensus       616 IGPRfS  621 (744)
T KOG0741|consen  616 IGPRFS  621 (744)
T ss_pred             cCchhh
Confidence            554444

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

Probab=94.76  E-value=0.38  Score=47.94  Aligned_cols=65  Identities=23%  Similarity=0.258  Sum_probs=41.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHH-----------HHHHhhcCC-CceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAK-----------AIIEGLEGS-EKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~-----------~i~~~~~~~-~kr~LiVlDdv~  192 (297)
                      .-.+|++|+|||.+|+.|+.  ...+.|   +-++|..-.|+.+|-.           .|...+..- -..=|+.||.|.
T Consensus       441 lCf~GPPGVGKTSI~kSIA~--ALnRkF---fRfSvGG~tDvAeIkGHRRTYVGAMPGkiIq~LK~v~t~NPliLiDEvD  515 (906)
T KOG2004|consen  441 LCFVGPPGVGKTSIAKSIAR--ALNRKF---FRFSVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKVKTENPLILIDEVD  515 (906)
T ss_pred             EEEeCCCCCCcccHHHHHHH--HhCCce---EEEeccccccHHhhcccceeeeccCChHHHHHHHhhCCCCceEEeehhh
Confidence            45789999999999999998  566666   2334455445544322           333333221 355688899997


Q ss_pred             CC
Q 043781          193 TD  194 (297)
Q Consensus       193 ~~  194 (297)
                      ..
T Consensus       516 Kl  517 (906)
T KOG2004|consen  516 KL  517 (906)
T ss_pred             hh
Confidence            53

>PRK08233 hypothetical protein; Provisional

Probab=94.74  E-value=0.016  Score=47.76  Aligned_cols=22  Identities=27%  Similarity=0.379  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|.|.+|+||||||+.+...
T Consensus         5 iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHhh
Confidence            3567899999999999999874

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=94.74  E-value=0.084  Score=50.06  Aligned_cols=21  Identities=24%  Similarity=0.319  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+...
T Consensus       148 ~~I~G~sG~GKStLl~~I~~~  168 (422)
T TIGR02546       148 IGIFAGAGVGKSTLLGMIARG  168 (422)
T ss_pred             EEEECCCCCChHHHHHHHhCC
Confidence            468899999999999999874

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=94.71  E-value=0.17  Score=42.53  Aligned_cols=21  Identities=29%  Similarity=0.393  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|.|..|.|||||.+.+..-
T Consensus        38 ~~l~G~nGsGKStLl~~i~Gl   58 (194)
T cd03213          38 TAIMGPSGAGKSTLLNALAGR   58 (194)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            468899999999999999884

DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=94.70  E-value=0.11  Score=45.23  Aligned_cols=22  Identities=32%  Similarity=0.327  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||++.+...
T Consensus        29 ~~~l~G~nGsGKSTLl~~l~G~   50 (240)
T PRK09493         29 VVVIIGPSGSGKSTLLRCINKL   50 (240)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999874

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=94.67  E-value=0.068  Score=50.87  Aligned_cols=68  Identities=19%  Similarity=0.239  Sum_probs=43.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHhhcCC-----------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEGLEGS-----------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~-----------------------  180 (297)
                      .+|+|..|+|||||+.++..+... ++=+.++++-+.... .+.+++.++...-...                       
T Consensus       146 ~~If~~~G~GKt~L~~~~~~~~~~-~~~~v~V~alIGER~rEv~ef~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~~~a  224 (461)
T TIGR01039       146 IGLFGGAGVGKTVLIQELINNIAK-EHGGYSVFAGVGERTREGNDLYHEMKESGVIDKTALVYGQMNEPPGARMRVALTG  224 (461)
T ss_pred             EEeecCCCCChHHHHHHHHHHHHh-cCCCeEEEEEecCCchHHHHHHHHHHhcCCcceeEEEEECCCCCHHHHHHHHHHH
Confidence            368899999999999887764222 222355566554433 3455555554332111                       


Q ss_pred             -----------CceEEEEEeCCCC
Q 043781          181 -----------EKKFFLILDDVWT  193 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~  193 (297)
                                 ++..|+++||+-.
T Consensus       225 ~tiAEyfrd~~G~~VLll~DslTR  248 (461)
T TIGR01039       225 LTMAEYFRDEQGQDVLLFIDNIFR  248 (461)
T ss_pred             HHHHHHHHHhcCCeeEEEecchhH
Confidence                       7899999999954

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit.

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=94.66  E-value=0.27  Score=47.82  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||.+.+..-
T Consensus        52 ivgIiGpNGSGKSTLLkiLaGL   73 (549)
T PRK13545         52 IVGIIGLNGSGKSTLSNLIAGV   73 (549)
T ss_pred             EEEEEcCCCCCHHHHHHHHhCC
Confidence            3578999999999999999984

>PRK12678 transcription termination factor Rho; Provisional

Probab=94.66  E-value=0.067  Score=52.17  Aligned_cols=67  Identities=19%  Similarity=0.126  Sum_probs=39.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEE-eCCCC-CHHHHH--------------------------HHHHHhh
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC-VSDPF-DEFRIA--------------------------KAIIEGL  177 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~-vs~~~-~~~~~~--------------------------~~i~~~~  177 (297)
                      .|+|.+|+|||||++.|.+.. ..++-++.++|. |.... .+.++.                          -.+++.+
T Consensus       420 LIvgpp~aGKTtLL~~IAn~i-~~n~~~~~~ivvLIgERpeEVtdm~rsVkgeVVasT~D~p~~~~~~~a~~ai~~Ae~f  498 (672)
T PRK12678        420 LIVSPPKAGKTTILQNIANAI-TTNNPECHLMVVLVDERPEEVTDMQRSVKGEVIASTFDRPPSDHTTVAELAIERAKRL  498 (672)
T ss_pred             EEeCCCCCCHHHHHHHHHHHH-hhcCCCeEEEEEEEeCchhhHHHHHHhccceEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999831 122334444432 22211 222222                          2233333


Q ss_pred             cCCCceEEEEEeCCCC
Q 043781          178 EGSEKKFFLILDDVWT  193 (297)
Q Consensus       178 ~~~~kr~LiVlDdv~~  193 (297)
                      -..++.+||+||++-.
T Consensus       499 re~G~dVlillDSlTR  514 (672)
T PRK12678        499 VELGKDVVVLLDSITR  514 (672)
T ss_pred             HHcCCCEEEEEeCchH
Confidence            3339999999999953

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=94.65  E-value=0.038  Score=50.43  Aligned_cols=66  Identities=21%  Similarity=0.184  Sum_probs=39.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC---------------------CCCHHHHHHHHHHhhcCCCce
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD---------------------PFDEFRIAKAIIEGLEGSEKK  183 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~---------------------~~~~~~~~~~i~~~~~~~~kr  183 (297)
                      ..|+|++|+||||||.++...  ....-...+|+....                     +.+..+.+ .++.++-..+.-
T Consensus        58 teI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l-~i~~~li~s~~~  134 (325)
T cd00983          58 IEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQAL-EIADSLVRSGAV  134 (325)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHH-HHHHHHHhccCC
Confidence            458999999999999887653  222233455554433                     33333332 233333333567


Q ss_pred             EEEEEeCCCC
Q 043781          184 FFLILDDVWT  193 (297)
Q Consensus       184 ~LiVlDdv~~  193 (297)
                      -|||+|-|-.
T Consensus       135 ~lIVIDSvaa  144 (325)
T cd00983         135 DLIVVDSVAA  144 (325)
T ss_pred             CEEEEcchHh
Confidence            7999999864

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=94.64  E-value=0.24  Score=45.49  Aligned_cols=121  Identities=12%  Similarity=-0.016  Sum_probs=70.3

Q ss_pred             ccccCCcchHHHHHHHhccccc--------------------ccCCCceEEEE-eC--CCCCHHHHHHHHHHhhcCC---
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV--------------------IENFDKRIWVC-VS--DPFDEFRIAKAIIEGLEGS---  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~--------------------~~~F~~~~wv~-vs--~~~~~~~~~~~i~~~~~~~---  180 (297)
                      +.|+.|+||+++|..+..----                    ..|-|.. ++. ..  ....+.++- ++.+.+...   
T Consensus        29 f~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~-~i~p~~~~~~I~idqiR-~l~~~~~~~~~~  106 (334)
T PRK07993         29 IQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYY-TLTPEKGKSSLGVDAVR-EVTEKLYEHARL  106 (334)
T ss_pred             eECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEE-EEecccccccCCHHHHH-HHHHHHhhcccc
Confidence            6799999999999776552110                    1233332 332 21  224455443 344444322   


Q ss_pred             CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC-CccccCCccchhhhh
Q 043781          181 EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL-RAKFPVSIFDAKKIW  259 (297)
Q Consensus       181 ~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~-~~~~~l~~l~~~~lf  259 (297)
                      +++=++|+|++.....+.-+.|...|..          ...++-+|++|...+   .+..+.-. ...+++.+++.++..
T Consensus       107 g~~kV~iI~~ae~m~~~AaNaLLKtLEE----------Pp~~t~fiL~t~~~~---~lLpTIrSRCq~~~~~~~~~~~~~  173 (334)
T PRK07993        107 GGAKVVWLPDAALLTDAAANALLKTLEE----------PPENTWFFLACREPA---RLLATLRSRCRLHYLAPPPEQYAL  173 (334)
T ss_pred             CCceEEEEcchHhhCHHHHHHHHHHhcC----------CCCCeEEEEEECChh---hChHHHHhccccccCCCCCHHHHH
Confidence            7788999999998876777788887854          255666666666432   23222111 145677777766644


Q ss_pred             hhh
Q 043781          260 GWE  262 (297)
Q Consensus       260 ~~~  262 (297)
                      .|-
T Consensus       174 ~~L  176 (334)
T PRK07993        174 TWL  176 (334)
T ss_pred             HHH
Confidence            443

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=94.64  E-value=0.3  Score=39.75  Aligned_cols=104  Identities=13%  Similarity=0.042  Sum_probs=53.8

Q ss_pred             cccccccCCcchHHHHHHHhcccccc-----------cCCCceEEE----EeCCCCC-HHHHHHHHHHhhcCC--CceEE
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVI-----------ENFDKRIWV----CVSDPFD-EFRIAKAIIEGLEGS--EKKFF  185 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~-----------~~F~~~~wv----~vs~~~~-~~~~~~~i~~~~~~~--~kr~L  185 (297)
                      ...|+|+.|.|||++.+.+.--.-..           ..+..-.|-    ......+ -..-...+...+...  +++-|
T Consensus        23 ~~~i~G~NgsGKS~~l~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~lS~G~~~~~~la~~L~~~~~~~~~l  102 (162)
T cd03227          23 LTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAELIFTRLQLSGGEKELSALALILALASLKPRPL  102 (162)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcchhhhccCcccCCCcceeeEEEEehheeeccccHHHHHHHHHHHHhcCCCCCCE
Confidence            45689999999999998863321111           112111111    1111111 122222333333321  36789


Q ss_pred             EEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHH
Q 043781          186 LILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLR  236 (297)
Q Consensus       186 iVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~  236 (297)
                      ++||+.-.. +...-..+...+.+..         ..|+.+|++|+..+...
T Consensus       103 lllDEp~~gld~~~~~~l~~~l~~~~---------~~~~~vii~TH~~~~~~  145 (162)
T cd03227         103 YILDEIDRGLDPRDGQALAEAILEHL---------VKGAQVIVITHLPELAE  145 (162)
T ss_pred             EEEeCCCCCCCHHHHHHHHHHHHHHH---------hcCCEEEEEcCCHHHHH
Confidence            999999775 2122233444444432         23788999999765443

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.

>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=94.63  E-value=0.2  Score=45.34  Aligned_cols=22  Identities=23%  Similarity=0.354  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|.|.=|+|||++.+.+.+.
T Consensus        22 ~IgL~G~WGsGKSs~l~~l~~~   43 (325)
T PF07693_consen   22 VIGLYGEWGSGKSSFLNMLKEE   43 (325)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4578999999999999998774

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 [].

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=94.62  E-value=0.062  Score=50.95  Aligned_cols=21  Identities=29%  Similarity=0.423  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||++.+.+.
T Consensus       158 igI~G~sG~GKSTLL~~I~~~  178 (433)
T PRK07594        158 VGIFSAPGVGKSTLLAMLCNA  178 (433)
T ss_pred             EEEECCCCCCccHHHHHhcCC
Confidence            468899999999999999874

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=94.61  E-value=0.27  Score=41.15  Aligned_cols=20  Identities=35%  Similarity=0.488  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .-|.|+.|+|||||.+.+.-
T Consensus        31 ~~i~G~NG~GKTtLLRilaG   50 (209)
T COG4133          31 LQITGPNGAGKTTLLRILAG   50 (209)
T ss_pred             EEEECCCCCcHHHHHHHHHc
Confidence            34789999999999999987

>PRK05480 uridine/cytidine kinase; Provisional

Probab=94.61  E-value=0.018  Score=49.05  Aligned_cols=23  Identities=35%  Similarity=0.537  Sum_probs=20.1

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..++|.|.+|+|||||++.++..
T Consensus         7 ~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          7 IIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999884

>TIGR00763 lon ATP-dependent protease La

Probab=94.58  E-value=1  Score=46.23  Aligned_cols=21  Identities=29%  Similarity=0.339  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|+|||+||+.+.+.
T Consensus       350 lll~GppG~GKT~lAk~iA~~  370 (775)
T TIGR00763       350 LCLVGPPGVGKTSLGKSIAKA  370 (775)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999983

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.

>PRK09354 recA recombinase A; Provisional

Probab=94.57  E-value=0.048  Score=50.22  Aligned_cols=66  Identities=21%  Similarity=0.203  Sum_probs=39.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeC---------------------CCCCHHHHHHHHHHhhcCCCce
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS---------------------DPFDEFRIAKAIIEGLEGSEKK  183 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs---------------------~~~~~~~~~~~i~~~~~~~~kr  183 (297)
                      ..|+|++|+|||||+.++...  ....=...+|+...                     ++.+.++.+ .++.++-..++-
T Consensus        63 teI~G~~GsGKTtLal~~~~~--~~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~l-~i~~~li~s~~~  139 (349)
T PRK09354         63 VEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQAL-EIADTLVRSGAV  139 (349)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHHH-HHHHHHhhcCCC
Confidence            458999999999999877653  22222344555433                     333333332 333343333567


Q ss_pred             EEEEEeCCCC
Q 043781          184 FFLILDDVWT  193 (297)
Q Consensus       184 ~LiVlDdv~~  193 (297)
                      -|||+|-|-.
T Consensus       140 ~lIVIDSvaa  149 (349)
T PRK09354        140 DLIVVDSVAA  149 (349)
T ss_pred             CEEEEeChhh
Confidence            7999999864

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=94.55  E-value=0.15  Score=49.84  Aligned_cols=21  Identities=29%  Similarity=0.317  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+..-
T Consensus       364 vaIvG~SGsGKSTLl~lL~g~  384 (529)
T TIGR02868       364 VAILGPSGSGKSTLLMLLTGL  384 (529)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            368999999999999999763

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=94.54  E-value=0.052  Score=49.48  Aligned_cols=77  Identities=16%  Similarity=0.083  Sum_probs=44.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhh--c--------CC-----CceEEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGL--E--------GS-----EKKFFLILDD  190 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~--~--------~~-----~kr~LiVlDd  190 (297)
                      -+.|.+|+||||||+.+..  +....|   +.|..+...+..+++..-.-.+  +        ++     .+.+.++||.
T Consensus        68 lL~G~pGtGKTtla~~lA~--~l~~~~---~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~~g~illlDE  142 (327)
T TIGR01650        68 MVQGYHGTGKSTHIEQIAA--RLNWPC---VRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQHNVALCFDE  142 (327)
T ss_pred             EEEeCCCChHHHHHHHHHH--HHCCCe---EEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHhCCeEEEech
Confidence            4679999999999999988  343332   2333333333333333210000  0        00     3557799999


Q ss_pred             CCCCCccCHHHHHHHHh
Q 043781          191 VWTDDYSKWEPFHNCLM  207 (297)
Q Consensus       191 v~~~~~~~w~~l~~~l~  207 (297)
                      +.....+....|...|.
T Consensus       143 in~a~p~~~~~L~~lLE  159 (327)
T TIGR01650       143 YDAGRPDVMFVIQRVLE  159 (327)
T ss_pred             hhccCHHHHHHHHHHhc
Confidence            98765555555555554

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.

>TIGR00235 udk uridine kinase

Probab=94.51  E-value=0.019  Score=48.84  Aligned_cols=22  Identities=36%  Similarity=0.573  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|+|++|+|||||++.+...
T Consensus         8 vi~I~G~sGsGKSTl~~~l~~~   29 (207)
T TIGR00235         8 IIGIGGGSGSGKTTVARKIYEQ   29 (207)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999874

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=94.51  E-value=0.095  Score=44.29  Aligned_cols=22  Identities=36%  Similarity=0.374  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||.+.+..-
T Consensus        28 ~~~i~G~nGsGKSTLl~~l~G~   49 (201)
T cd03231          28 ALQVTGPNGSGKTTLLRILAGL   49 (201)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999874

The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=94.51  E-value=0.079  Score=50.02  Aligned_cols=21  Identities=24%  Similarity=0.279  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+.+.
T Consensus       140 ~~I~G~sG~GKTtLl~~I~~~  160 (411)
T TIGR03496       140 MGIFAGSGVGKSTLLGMMARY  160 (411)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468899999999999988874

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=94.50  E-value=0.23  Score=44.57  Aligned_cols=94  Identities=12%  Similarity=-0.097  Sum_probs=59.4

Q ss_pred             ccccCCcchHHHHHHHhcccc------------cccCCCceEEEEeCC--CCCHHHHHHHHHHhhcCC---CceEEEEEe
Q 043781          127 VRGMGGIGKTTLAQFAYNDKD------------VIENFDKRIWVCVSD--PFDEFRIAKAIIEGLEGS---EKKFFLILD  189 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~------------~~~~F~~~~wv~vs~--~~~~~~~~~~i~~~~~~~---~kr~LiVlD  189 (297)
                      ++|+.|+||+++|..+...--            -..|-|.....+...  ...+.++ +++.+.+...   +++=++|+|
T Consensus        24 f~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqi-R~l~~~~~~~p~e~~~kv~ii~  102 (290)
T PRK05917         24 LHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETP-RAIKKQIWIHPYESPYKIYIIH  102 (290)
T ss_pred             eECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHH-HHHHHHHhhCccCCCceEEEEe
Confidence            679999999999976655311            112444443333322  2455554 4555555433   677788999


Q ss_pred             CCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          190 DVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       190 dv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      ++.....+.+..|...+..-          .+++.+|++|..
T Consensus       103 ~ad~mt~~AaNaLLK~LEEP----------p~~~~fiL~~~~  134 (290)
T PRK05917        103 EADRMTLDAISAFLKVLEDP----------PQHGVIILTSAK  134 (290)
T ss_pred             chhhcCHHHHHHHHHHhhcC----------CCCeEEEEEeCC
Confidence            99998777888888888652          455666666554

>TIGR00959 ffh signal recognition particle protein

Probab=94.48  E-value=1.2  Score=42.29  Aligned_cols=22  Identities=32%  Similarity=0.241  Sum_probs=17.4

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...-++|.+|+||||++..+..
T Consensus       100 ~vi~~vG~~GsGKTTtaakLA~  121 (428)
T TIGR00959       100 TVILMVGLQGSGKTTTCGKLAY  121 (428)
T ss_pred             EEEEEECCCCCcHHHHHHHHHH
Confidence            3456889999999999766655

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.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=94.48  E-value=0.1  Score=47.84  Aligned_cols=78  Identities=15%  Similarity=0.119  Sum_probs=50.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc----CC----------CceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE----GS----------EKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~----~~----------~kr~LiVlDdv  191 (297)
                      -+.|.+|+|||+||+.+..  .....   .+++.........++.....-...    ..          .-+.++.+|.+
T Consensus        47 ll~G~PG~gKT~la~~lA~--~l~~~---~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEI  121 (329)
T COG0714          47 LLEGPPGVGKTLLARALAR--ALGLP---FVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEI  121 (329)
T ss_pred             EEECCCCccHHHHHHHHHH--HhCCC---eEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEecc
Confidence            3679999999999999998  34333   355666666666666554332221    11          22259999999


Q ss_pred             CCCCccCHHHHHHHHhh
Q 043781          192 WTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       192 ~~~~~~~w~~l~~~l~~  208 (297)
                      +......-..|...+..
T Consensus       122 nra~p~~q~aLl~~l~e  138 (329)
T COG0714         122 NRAPPEVQNALLEALEE  138 (329)
T ss_pred             ccCCHHHHHHHHHHHhC
Confidence            99865445555555543

>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=94.47  E-value=0.032  Score=49.69  Aligned_cols=20  Identities=30%  Similarity=0.121  Sum_probs=15.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|.||+||||+|+.+...
T Consensus         5 il~G~P~SGKTt~a~~L~~~   24 (270)
T PF08433_consen    5 ILCGLPCSGKTTRAKELKKY   24 (270)
T ss_dssp             EEE--TTSSHHHHHHHHHHH
T ss_pred             EEEcCCCCcHHHHHHHHHHH
Confidence            36799999999999999884

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=94.47  E-value=0.34  Score=47.17  Aligned_cols=21  Identities=29%  Similarity=0.344  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+..-
T Consensus        40 ~~liG~NGsGKSTLl~~l~Gl   60 (510)
T PRK15439         40 HALLGGNGAGKSTLMKIIAGI   60 (510)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            478999999999999999874

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=94.44  E-value=0.089  Score=50.10  Aligned_cols=68  Identities=25%  Similarity=0.285  Sum_probs=40.3

Q ss_pred             cccccCCcchHHHHHHHhccccccc--------------CC-----------CceEEEEeCCCCCHHH-----HHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE--------------NF-----------DKRIWVCVSDPFDEFR-----IAKAIIE  175 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~--------------~F-----------~~~~wv~vs~~~~~~~-----~~~~i~~  175 (297)
                      .|+|..|+|||||++.+........              .|           ..++++.-++.+-..+     ..-.|++
T Consensus       162 ~I~G~sG~GKStLl~~I~~~~~~~~gvI~~~Gerg~ev~e~~~~~l~~~~l~r~v~vv~~~~~~~~~r~~~~~~a~~iAE  241 (438)
T PRK07721        162 GIFAGSGVGKSTLMGMIARNTSADLNVIALIGERGREVREFIERDLGPEGLKRSIVVVATSDQPALMRIKGAYTATAIAE  241 (438)
T ss_pred             EEECCCCCCHHHHHHHHhcccCCCeEEEEEEecCCccHHHHHHhhcChhhhcCeEEEEECCCCCHHHHHHHHHHHHHHHH
Confidence            6889999999999998886421100              01           1223333333322222     2223555


Q ss_pred             hhcCCCceEEEEEeCCCC
Q 043781          176 GLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       176 ~~~~~~kr~LiVlDdv~~  193 (297)
                      .+...++..||++||+-.
T Consensus       242 yfr~~g~~Vll~~Dsltr  259 (438)
T PRK07721        242 YFRDQGLNVMLMMDSVTR  259 (438)
T ss_pred             HHHHCCCcEEEEEeChHH
Confidence            554449999999999954

>PTZ00301 uridine kinase; Provisional

Probab=94.44  E-value=0.029  Score=48.06  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=18.3

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|-|.+|+||||||+.+.+
T Consensus         5 iIgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          5 VIGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             EEEEECCCcCCHHHHHHHHHH
Confidence            457889999999999988865

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=94.42  E-value=0.15  Score=48.39  Aligned_cols=21  Identities=24%  Similarity=0.359  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+...
T Consensus       159 i~I~G~sG~GKTtLl~~Ia~~  179 (432)
T PRK06793        159 IGIFAGSGVGKSTLLGMIAKN  179 (432)
T ss_pred             EEEECCCCCChHHHHHHHhcc
Confidence            368899999999999999875

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=94.42  E-value=0.085  Score=50.25  Aligned_cols=21  Identities=24%  Similarity=0.351  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+...
T Consensus       166 ~~I~G~sG~GKStLl~~I~~~  186 (440)
T TIGR01026       166 IGIFAGSGVGKSTLLGMIARN  186 (440)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            368899999999999998874

This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins.

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=94.40  E-value=0.056  Score=48.23  Aligned_cols=45  Identities=22%  Similarity=0.243  Sum_probs=35.5

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIA  170 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~  170 (297)
                      ...|+|+.|+||||||.+++-.  .+..-...+|+.....+++.++.
T Consensus        62 ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~~  106 (279)
T COG0468          62 ITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERAK  106 (279)
T ss_pred             EEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHHH
Confidence            3579999999999999887763  44455588999988888877643

>TIGR02314 ABC_MetN D-methionine ABC transporter, ATP-binding protein

Probab=94.38  E-value=0.16  Score=46.87  Aligned_cols=52  Identities=10%  Similarity=0.061  Sum_probs=32.9

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.=++++|.--.. |...-..+...+.+...        ..|..||++|+..+....+|.
T Consensus       157 ~~P~iLLlDEPts~LD~~t~~~i~~lL~~l~~--------~~g~tiiliTH~~~~v~~~~d  209 (343)
T TIGR02314       157 SNPKVLLCDEATSALDPATTQSILELLKEINR--------RLGLTILLITHEMDVVKRICD  209 (343)
T ss_pred             hCCCEEEEeCCcccCCHHHHHHHHHHHHHHHH--------hcCCEEEEEeCCHHHHHHhCC
Confidence            77789999988664 22222334445544311        336789999998777777664

Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.

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

Probab=94.37  E-value=0.024  Score=49.83  Aligned_cols=64  Identities=20%  Similarity=0.257  Sum_probs=39.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC--CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF--DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      +||++|.|||.+|+.|.|  +...-|-.++--...+.+  .-.++.+++++-... .|-++|.+|.+..
T Consensus       216 lygppgtgktl~aravan--rtdacfirvigselvqkyvgegarmvrelf~mart-kkaciiffdeida  281 (435)
T KOG0729|consen  216 LYGPPGTGKTLCARAVAN--RTDACFIRVIGSELVQKYVGEGARMVRELFEMART-KKACIIFFDEIDA  281 (435)
T ss_pred             EeCCCCCchhHHHHHHhc--ccCceEEeehhHHHHHHHhhhhHHHHHHHHHHhcc-cceEEEEeecccc
Confidence            679999999999999999  454444222100000111  123455555554433 7899999999864

>PRK06762 hypothetical protein; Provisional

Probab=94.37  E-value=0.023  Score=46.40  Aligned_cols=21  Identities=38%  Similarity=0.452  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+|+.+.+.
T Consensus         5 i~i~G~~GsGKST~A~~L~~~   25 (166)
T PRK06762          5 IIIRGNSGSGKTTIAKQLQER   25 (166)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999998874

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

Probab=94.33  E-value=0.056  Score=52.67  Aligned_cols=65  Identities=17%  Similarity=0.164  Sum_probs=40.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCc-eEEEEeCCCCC-HHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDK-RIWVCVSDPFD-EFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      ++|++|+|||.||+.+.+.  ..=.|-. .+---||+... -++-+++++++... .-.+++++|++.-.
T Consensus       228 lHGPPGCGKT~lA~AiAge--l~vPf~~isApeivSGvSGESEkkiRelF~~A~~-~aPcivFiDeIDAI  294 (802)
T KOG0733|consen  228 LHGPPGCGKTSLANAIAGE--LGVPFLSISAPEIVSGVSGESEKKIRELFDQAKS-NAPCIVFIDEIDAI  294 (802)
T ss_pred             eeCCCCccHHHHHHHHhhh--cCCceEeecchhhhcccCcccHHHHHHHHHHHhc-cCCeEEEeeccccc
Confidence            6699999999999999994  4334411 11001222221 23445555555544 67999999999753

>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=94.33  E-value=0.014  Score=45.69  Aligned_cols=64  Identities=20%  Similarity=0.206  Sum_probs=30.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC--------CceEEEEEeCCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS--------EKKFFLILDDVWTDD  195 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--------~kr~LiVlDdv~~~~  195 (297)
                      ++|.+|+||||||+.+..  .+...|..   |..+......++...-+-.....        --.-++.+|.+-...
T Consensus         4 leg~PG~GKT~la~~lA~--~~~~~f~R---Iq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNrap   75 (131)
T PF07726_consen    4 LEGVPGVGKTTLAKALAR--SLGLSFKR---IQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRAP   75 (131)
T ss_dssp             EES---HHHHHHHHHHHH--HTT--EEE---EE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS-
T ss_pred             eECCCccHHHHHHHHHHH--HcCCceeE---EEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccCC
Confidence            679999999999999998  46666632   22233334444443211110000        112378888886654

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.

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=94.30  E-value=0.11  Score=47.83  Aligned_cols=51  Identities=22%  Similarity=0.160  Sum_probs=32.3

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.=+++||.--+. |...-..+...+...         ...|..||++|++.+....+|.
T Consensus       189 ~~P~lLiLDEPt~gLD~~~r~~l~~~l~~l---------~~~g~tilisSH~l~e~~~~~d  240 (340)
T PRK13536        189 NDPQLLILDEPTTGLDPHARHLIWERLRSL---------LARGKTILLTTHFMEEAERLCD  240 (340)
T ss_pred             cCCCEEEEECCCCCCCHHHHHHHHHHHHHH---------HhCCCEEEEECCCHHHHHHhCC
Confidence            78889999988765 222222344444332         1357789999998776666664

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=94.28  E-value=0.36  Score=47.21  Aligned_cols=22  Identities=27%  Similarity=0.379  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||.+.+...
T Consensus        29 ~~~liG~NGsGKSTLl~~l~Gl   50 (530)
T PRK15064         29 RYGLIGANGCGKSTFMKILGGD   50 (530)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999974

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=94.25  E-value=4.8  Score=37.78  Aligned_cols=22  Identities=32%  Similarity=0.170  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|..|+||||.+..+...
T Consensus       176 vi~lvGptGvGKTTT~aKLA~~  197 (388)
T PRK12723        176 VFILVGPTGVGKTTTIAKLAAI  197 (388)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5568999999999999888763

>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.25  E-value=0.2  Score=45.05  Aligned_cols=56  Identities=11%  Similarity=0.093  Sum_probs=40.1

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL  244 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~  244 (297)
                      ...=++..|..-+. |+..=..|...|.+...        .-|-.|++.|+-.++.+.+|...-+
T Consensus       158 ~~P~iLL~DEaTSALDP~TT~sIL~LL~~In~--------~lglTIvlITHEm~Vvk~ic~rVav  214 (339)
T COG1135         158 NNPKILLCDEATSALDPETTQSILELLKDINR--------ELGLTIVLITHEMEVVKRICDRVAV  214 (339)
T ss_pred             cCCCEEEecCccccCChHHHHHHHHHHHHHHH--------HcCCEEEEEechHHHHHHHhhhheE
Confidence            66677888888664 44455567777766432        6778899999989999999976443

>PRK13947 shikimate kinase; Provisional

Probab=94.24  E-value=0.025  Score=46.35  Aligned_cols=21  Identities=29%  Similarity=0.306  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|++|+||||+|+.+.+.
T Consensus         4 I~l~G~~GsGKst~a~~La~~   24 (171)
T PRK13947          4 IVLIGFMGTGKTTVGKRVATT   24 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            457899999999999999883

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=94.22  E-value=0.15  Score=46.98  Aligned_cols=44  Identities=23%  Similarity=0.209  Sum_probs=31.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAI  173 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i  173 (297)
                      .|+|..|+|||+|++.+.+..    +-+.++++-+.... .+.+++.++
T Consensus       161 ~I~G~~G~GKT~L~~~Iak~~----~~dvvVyv~iGERg~Ev~e~l~ef  205 (369)
T cd01134         161 AIPGPFGCGKTVIQQSLSKYS----NSDIVIYVGCGERGNEMTEVLEEF  205 (369)
T ss_pred             EEECCCCCChHHHHHHHHhCC----CCCEEEEEEeCCChHHHHHHHHHH
Confidence            588999999999999999852    23567777665543 445555554

These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria.

>PTZ00035 Rad51 protein; Provisional

Probab=94.22  E-value=0.14  Score=47.17  Aligned_cols=44  Identities=18%  Similarity=0.161  Sum_probs=28.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccc---c-CCCceEEEEeCCCCCHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI---E-NFDKRIWVCVSDPFDEFR  168 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~---~-~F~~~~wv~vs~~~~~~~  168 (297)
                      ..|+|.+|+|||||+..+.-.....   . .=...+|+.....|+..+
T Consensus       121 teI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~er  168 (337)
T PTZ00035        121 TELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER  168 (337)
T ss_pred             EEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHH
Confidence            4689999999999998886532221   0 112455777666655554

>PRK06820 type III secretion system ATPase; Validated

Probab=94.21  E-value=0.1  Score=49.65  Aligned_cols=21  Identities=29%  Similarity=0.447  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+...
T Consensus       166 i~I~G~sG~GKStLl~~I~~~  186 (440)
T PRK06820        166 IGIFAAAGVGKSTLLGMLCAD  186 (440)
T ss_pred             EEEECCCCCChHHHHHHHhcc
Confidence            368899999999999999874

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=94.20  E-value=0.083  Score=50.58  Aligned_cols=65  Identities=18%  Similarity=0.230  Sum_probs=42.4

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCce-EEEEeCCCC-CHHHHHHHHHHhhcCC----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDKR-IWVCVSDPF-DEFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~~~~~----------------------  180 (297)
                      +|+|-.|+|||+|| ..+.+..    .-+.. +++.+.+.. .+.++.+.+...-...                      
T Consensus       145 ~I~g~~g~GKt~Lal~~I~~q~----~~dv~cV~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atad~~~~~r~~ap~~  220 (485)
T CHL00059        145 LIIGDRQTGKTAVATDTILNQK----GQNVICVYVAIGQKASSVAQVVTTLQERGAMEYTIVVAETADSPATLQYLAPYT  220 (485)
T ss_pred             EeecCCCCCHHHHHHHHHHhcc----cCCeEEEEEEecCCchHHHHHHHHhhcccchhceEEEEeCCCCCHHHHHHHHHH
Confidence            68899999999995 5666531    23434 566665443 3455555554432211                      


Q ss_pred             -----------CceEEEEEeCCCCC
Q 043781          181 -----------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~~  194 (297)
                                 ++..|+|+||+-..
T Consensus       221 a~aiAEyfr~~G~~VLlv~DdlTr~  245 (485)
T CHL00059        221 GAALAEYFMYRGRHTLIIYDDLSKQ  245 (485)
T ss_pred             HhhHHHHHHHcCCCEEEEEcChhHH
Confidence                       89999999999654

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

Probab=94.19  E-value=0.039  Score=53.47  Aligned_cols=65  Identities=15%  Similarity=0.081  Sum_probs=40.8

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCC-CC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD-PF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~-~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|++|.|||.||+.+.+  ....+|-.+.+-.... .. ......++++..... .....|.+|.+..
T Consensus       280 Ll~GpPGtGKT~lAkava~--~~~~~fi~v~~~~l~sk~vGesek~ir~~F~~A~~-~~p~iiFiDEiDs  346 (494)
T COG0464         280 LLYGPPGTGKTLLAKAVAL--ESRSRFISVKGSELLSKWVGESEKNIRELFEKARK-LAPSIIFIDEIDS  346 (494)
T ss_pred             EEECCCCCCHHHHHHHHHh--hCCCeEEEeeCHHHhccccchHHHHHHHHHHHHHc-CCCcEEEEEchhh
Confidence            3789999999999999999  4555553222111111 11 223444444444432 5789999999975

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=94.19  E-value=0.026  Score=47.59  Aligned_cols=21  Identities=33%  Similarity=0.417  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ++|.|..|+|||||++.+..-
T Consensus         2 igi~G~~GsGKSTl~~~l~~~   22 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQ   22 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999773

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=94.18  E-value=0.097  Score=49.46  Aligned_cols=69  Identities=25%  Similarity=0.282  Sum_probs=41.9

Q ss_pred             ccccccCCcchHHHHHHHhccccccc-------------------CC------CceEEEEeCCCCCHHH-----HHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE-------------------NF------DKRIWVCVSDPFDEFR-----IAKAII  174 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~-------------------~F------~~~~wv~vs~~~~~~~-----~~~~i~  174 (297)
                      ..|+|..|+|||||++.+.+......                   .+      ..++++.-++.+...+     ..-.++
T Consensus       140 i~I~G~sG~GKTtLl~~i~~~~~~~~gvi~~~Ger~~ev~e~~~~~l~~~~~~~~v~v~~tsd~~~~~r~~~~~~a~tiA  219 (413)
T TIGR03497       140 VGIFAGSGVGKSTLLGMIARNAKADINVIALIGERGREVRDFIEKDLGEEGLKRSVVVVATSDQPALMRLKAAFTATAIA  219 (413)
T ss_pred             EEEECCCCCCHHHHHHHHhCCCCCCeEEEEEEccchHHHHHHHHHHhcccccceEEEEEECCCCCHHHHHHHHHHHHHHH
Confidence            46889999999999998887421100                   01      1233444444433222     223445


Q ss_pred             HhhcCCCceEEEEEeCCCC
Q 043781          175 EGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       175 ~~~~~~~kr~LiVlDdv~~  193 (297)
                      +.+...++..|+++||+-.
T Consensus       220 Eyfr~~G~~Vll~~Dsltr  238 (413)
T TIGR03497       220 EYFRDQGKDVLLMMDSVTR  238 (413)
T ss_pred             HHHHHCCCCEEEEEcCcHH
Confidence            5554449999999999954

Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively.

>PRK00131 aroK shikimate kinase; Reviewed

Probab=94.17  E-value=0.026  Score=46.04  Aligned_cols=21  Identities=24%  Similarity=0.365  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|++|+||||+|+.+...
T Consensus         7 i~l~G~~GsGKstla~~La~~   27 (175)
T PRK00131          7 IVLIGFMGAGKSTIGRLLAKR   27 (175)
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            457899999999999999884

>KOG0927 consensus Predicted transporter (ABC superfamily) [General function prediction only]

Probab=94.15  E-value=0.25  Score=47.68  Aligned_cols=48  Identities=21%  Similarity=0.229  Sum_probs=33.8

Q ss_pred             CceEEEEEeCCCCCCccCHHH---HHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTDDYSKWEP---FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~~~~~w~~---l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      -+..|+.||+=-+.  -+.+.   |...|...          ..+ .++|++|.++....+|..
T Consensus       238 ~kP~LLLLDEPtnh--LDleA~~wLee~L~k~----------d~~-~lVi~sh~QDfln~vCT~  288 (614)
T KOG0927|consen  238 QKPDLLLLDEPTNH--LDLEAIVWLEEYLAKY----------DRI-ILVIVSHSQDFLNGVCTN  288 (614)
T ss_pred             cCCCEEEecCCccC--CCHHHHHHHHHHHHhc----------cCc-eEEEEecchhhhhhHhhh
Confidence            88999999998775  23333   55555443          222 799999999888888764

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=94.15  E-value=0.34  Score=41.48  Aligned_cols=33  Identities=27%  Similarity=0.227  Sum_probs=24.5

Q ss_pred             ccccccccCCcchHHHHHHHhcccccccCCCceEEE
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWV  158 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv  158 (297)
                      .+..|+|+.|+|||||.+.+..-+..   =...+|+
T Consensus        29 evv~iiGpSGSGKSTlLRclN~LE~~---~~G~I~i   61 (240)
T COG1126          29 EVVVIIGPSGSGKSTLLRCLNGLEEP---DSGSITV   61 (240)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCcCC---CCceEEE
Confidence            34578999999999999999884433   2345555

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

Probab=94.14  E-value=0.11  Score=47.06  Aligned_cols=66  Identities=20%  Similarity=0.259  Sum_probs=45.0

Q ss_pred             ccccCCcchHHHHHHHhccccc--ccCCCceEEEEeCC-----------CCCHHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV--IENFDKRIWVCVSD-----------PFDEFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~--~~~F~~~~wv~vs~-----------~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      +.|+||.|||+|.+.+++.-.+  .+.+.....+.++.           .-.+..++++|-+-+...+.-..+.+|.|-
T Consensus       182 lhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVE  260 (423)
T KOG0744|consen  182 LHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVE  260 (423)
T ss_pred             EeCCCCCChhHHHHHHHHhheeeecCccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHH
Confidence            5699999999999999996544  33443333333221           124667788887777766777778889884

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=94.12  E-value=0.029  Score=44.95  Aligned_cols=20  Identities=30%  Similarity=0.413  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -+.|++|+||||+|+.+...
T Consensus         3 ~l~G~~GsGKST~a~~l~~~   22 (150)
T cd02021           3 VVMGVSGSGKSTVGKALAER   22 (150)
T ss_pred             EEEcCCCCCHHHHHHHHHhh
Confidence            36799999999999999884

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.11  E-value=0.35  Score=41.78  Aligned_cols=22  Identities=32%  Similarity=0.403  Sum_probs=19.7

Q ss_pred             cccccCCcchHHHHHHHhcccc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD  147 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~  147 (297)
                      .|.|+.|.||||||..+.-++.
T Consensus        34 aiMGPNGsGKSTLa~~i~G~p~   55 (251)
T COG0396          34 AIMGPNGSGKSTLAYTIMGHPK   55 (251)
T ss_pred             EEECCCCCCHHHHHHHHhCCCC
Confidence            4779999999999999999864

>PRK07196 fliI flagellum-specific ATP synthase; Validated

Probab=94.11  E-value=0.09  Score=49.87  Aligned_cols=21  Identities=19%  Similarity=0.253  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||++.+...
T Consensus       158 igI~G~sGaGKSTLl~~I~g~  178 (434)
T PRK07196        158 VGLMAGSGVGKSVLLGMITRY  178 (434)
T ss_pred             EEEECCCCCCccHHHHHHhcc
Confidence            368899999999999998874

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=94.10  E-value=0.094  Score=46.26  Aligned_cols=64  Identities=19%  Similarity=0.173  Sum_probs=41.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-----CceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-----EKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----~kr~LiVlDdv~~  193 (297)
                      .-|+|.+|+|||+++.++..  +..++....+||+....  ..++.+.+.+ ++-.     .+-.|.++|-.-.
T Consensus        26 ~lI~G~pGsGKT~f~~qfl~--~~~~~ge~vlyvs~~e~--~~~l~~~~~~-~g~d~~~~~~~g~l~i~d~~~~   94 (260)
T COG0467          26 VLITGPPGTGKTIFALQFLY--EGAREGEPVLYVSTEES--PEELLENARS-FGWDLEVYIEKGKLAILDAFLS   94 (260)
T ss_pred             EEEEcCCCCcHHHHHHHHHH--HHHhcCCcEEEEEecCC--HHHHHHHHHH-cCCCHHHHhhcCCEEEEEcccc
Confidence            35889999999999988777  45555888999987654  3444444333 4333     4444555555443

>PRK04040 adenylate kinase; Provisional

Probab=94.10  E-value=0.027  Score=47.38  Aligned_cols=21  Identities=43%  Similarity=0.558  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+|++|+||||+++.+.+
T Consensus         4 ~i~v~G~pG~GKtt~~~~l~~   24 (188)
T PRK04040          4 VVVVTGVPGVGKTTVLNKALE   24 (188)
T ss_pred             EEEEEeCCCCCHHHHHHHHHH
Confidence            356889999999999999988

>PRK04196 V-type ATP synthase subunit B; Provisional

Probab=94.09  E-value=0.081  Score=50.64  Aligned_cols=68  Identities=18%  Similarity=0.195  Sum_probs=45.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccc---cCCCceEEEEeCCCC-CHHHHHHHHHHhhcCC--------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI---ENFDKRIWVCVSDPF-DEFRIAKAIIEGLEGS--------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~---~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~--------------------  180 (297)
                      .+|+|-.|+|||||+..+.++....   ..| .++++-+.+.- .+.+++.++...-...                    
T Consensus       146 ~gIfgg~G~GKs~L~~~ia~~~~~d~~~~~~-v~V~~~iGeRgrEv~e~~~~~~~~~~l~rtvvV~atsd~p~~~R~~a~  224 (460)
T PRK04196        146 LPIFSGSGLPHNELAAQIARQAKVLGEEENF-AVVFAAMGITFEEANFFMEDFEETGALERSVVFLNLADDPAIERILTP  224 (460)
T ss_pred             EEeeCCCCCCccHHHHHHHHhhhhccCCCce-EEEEEEeccccHHHHHHHHHHHhcCCcceEEEEEEcCCCCHHHHHHHH
Confidence            3688999999999999998864432   122 45566554443 4556666555543221                    


Q ss_pred             --------------CceEEEEEeCCCC
Q 043781          181 --------------EKKFFLILDDVWT  193 (297)
Q Consensus       181 --------------~kr~LiVlDdv~~  193 (297)
                                    +++.|+++||+-.
T Consensus       225 ~~a~tiAEyfr~d~G~~VLli~DslTR  251 (460)
T PRK04196        225 RMALTAAEYLAFEKGMHVLVILTDMTN  251 (460)
T ss_pred             HHHHHHHHHHHHhcCCcEEEEEcChHH
Confidence                          7999999999954

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

Probab=94.09  E-value=0.17  Score=46.51  Aligned_cols=118  Identities=21%  Similarity=0.171  Sum_probs=65.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCCC-HHHHHHHHHHhhcCCCceEEEEEeCCCCC-----
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPFD-EFRIAKAIIEGLEGSEKKFFLILDDVWTD-----  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~~-----  194 (297)
                      +-++|++|.|||.||+.+..  +....|   +-|.+|    .-|. ...+.+.++..... =+...|.+|.|...     
T Consensus       130 iLL~GPpG~GKTmlAKA~Ak--eaga~f---Inv~~s~lt~KWfgE~eKlv~AvFslAsK-l~P~iIFIDEvds~L~~R~  203 (386)
T KOG0737|consen  130 ILLYGPPGTGKTMLAKAIAK--EAGANF---INVSVSNLTSKWFGEAQKLVKAVFSLASK-LQPSIIFIDEVDSFLGQRR  203 (386)
T ss_pred             ceecCCCCchHHHHHHHHHH--HcCCCc---ceeeccccchhhHHHHHHHHHHHHhhhhh-cCcceeehhhHHHHHhhcc
Confidence            34789999999999999999  555566   223333    2232 23344444333322 57889999998642     


Q ss_pred             --CccCHHHHHHHHhhhhhhhceeeecCCCCeEEE---EeccHHHHHHHHHhhCCCccccCCc
Q 043781          195 --DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSL---TSTCQEKLRHLTLTLGLRAKFPVSI  252 (297)
Q Consensus       195 --~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iii---TTr~~~~~~~v~~~~~~~~~~~l~~  252 (297)
                        +.+.-..++.-|.-.=.++.    ++.+.+|||   |-|-.+....+.+.|...-.+.|..
T Consensus       204 s~dHEa~a~mK~eFM~~WDGl~----s~~~~rVlVlgATNRP~DlDeAiiRR~p~rf~V~lP~  262 (386)
T KOG0737|consen  204 STDHEATAMMKNEFMALWDGLS----SKDSERVLVLGATNRPFDLDEAIIRRLPRRFHVGLPD  262 (386)
T ss_pred             cchHHHHHHHHHHHHHHhcccc----CCCCceEEEEeCCCCCccHHHHHHHhCcceeeeCCCc
Confidence              11222223333321101110    244457777   5565666777777777543334433

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=94.09  E-value=0.24  Score=43.12  Aligned_cols=21  Identities=29%  Similarity=0.314  Sum_probs=18.4

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|..|+|||||++.+.-
T Consensus        32 ~~~i~G~nGsGKSTL~~~l~G   52 (235)
T COG1122          32 RVLLIGPNGSGKSTLLKLLNG   52 (235)
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            346899999999999999876

>PRK13949 shikimate kinase; Provisional

Probab=94.08  E-value=0.029  Score=46.27  Aligned_cols=21  Identities=33%  Similarity=0.324  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|++|+|||||++.+.+.
T Consensus         4 I~liG~~GsGKstl~~~La~~   24 (169)
T PRK13949          4 IFLVGYMGAGKTTLGKALARE   24 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            568899999999999999884

>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=94.06  E-value=0.032  Score=38.65  Aligned_cols=20  Identities=30%  Similarity=0.426  Sum_probs=17.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|.|.+|+||||+++.+.+.
T Consensus         3 ~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           3 AITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47799999999999998884

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.

>TIGR00602 rad24 checkpoint protein rad24

Probab=94.04  E-value=0.12  Score=51.56  Aligned_cols=21  Identities=24%  Similarity=0.343  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..++|++|+||||+++.+...
T Consensus       113 llL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602       113 LLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999974

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=94.04  E-value=0.029  Score=46.49  Aligned_cols=20  Identities=30%  Similarity=0.182  Sum_probs=17.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|+|++|+||||+|+.+...
T Consensus         3 ~i~G~pGsGKst~a~~la~~   22 (183)
T TIGR01359         3 FVLGGPGSGKGTQCAKIVEN   22 (183)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999873

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.

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=94.04  E-value=0.53  Score=41.72  Aligned_cols=22  Identities=32%  Similarity=0.493  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||.+.+...
T Consensus        52 ~~~liG~NGsGKSTLlk~L~Gl   73 (264)
T PRK13546         52 VIGLVGINGSGKSTLSNIIGGS   73 (264)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999984

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=94.02  E-value=0.11  Score=50.09  Aligned_cols=65  Identities=17%  Similarity=0.215  Sum_probs=44.7

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCc-eEEEEeCCCC-CHHHHHHHHHHhhcCC----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDK-RIWVCVSDPF-DEFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~~~~~i~~~~~~~----------------------  180 (297)
                      +|+|-.|+|||||| ..+.+..    .-+. .+++-+.+.. .+.++.+.+...-...                      
T Consensus       166 ~Ifg~~g~GKT~Lal~~I~~q~----~~dv~~V~~~IGeR~rev~e~i~~l~~~~~l~~tvvV~atsd~p~~~r~~ap~~  241 (497)
T TIGR03324       166 LILGDRQTGKTAIAIDTILNQK----GRNVLCIYCAIGQRASAVAKVVANLREHGAMDYTIVVVTEGNDPPGLQYIAPYA  241 (497)
T ss_pred             EeecCCCCCHHHHHHHHHHHhc----CCCcEEEEEEeccCcHHHHHHHHHhhhcCCcceeEEEEeCCCCCHHHHHHHHHH
Confidence            68899999999996 5777742    2344 5677776654 3556666555443222                      


Q ss_pred             -----------CceEEEEEeCCCCC
Q 043781          181 -----------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~~  194 (297)
                                 ++..|||+||+-..
T Consensus       242 a~aiAEyfrd~G~~VLlv~DdlTr~  266 (497)
T TIGR03324       242 ATSIGEHFMEQGRDVLIVYDDLTQH  266 (497)
T ss_pred             HHHHHHHHHhCCCCEEEEEcChhHH
Confidence                       99999999999653

A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase.

>PRK06217 hypothetical protein; Validated

Probab=93.98  E-value=0.03  Score=46.63  Aligned_cols=34  Identities=26%  Similarity=0.483  Sum_probs=24.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCC--CceEEEE
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENF--DKRIWVC  159 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F--~~~~wv~  159 (297)
                      +.|.|.+|+||||||+.+...... .+|  |...|..
T Consensus         4 I~i~G~~GsGKSTla~~L~~~l~~-~~~~~D~~~~~~   39 (183)
T PRK06217          4 IHITGASGSGTTTLGAALAERLDI-PHLDTDDYFWLP   39 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCC-cEEEcCceeecc
Confidence            568899999999999999985332 233  4556654

>cd01878 HflX HflX subfamily

Probab=93.96  E-value=0.065  Score=45.14  Aligned_cols=52  Identities=21%  Similarity=0.292  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHHHHHhhhhcccccccCCcccccccccccccccccccccCCcchHHHHHHHhccc
Q 043781           83 KIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus        83 ~i~~i~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      ++..+++.++.+.+.+..-...            ...+....+.|+|.+|+|||||.+.+.+..
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~~~I~iiG~~g~GKStLl~~l~~~~   65 (204)
T cd01878          14 RIAKLRRELEKVKKQRELQRRR------------RKRSGIPTVALVGYTNAGKSTLFNALTGAD   65 (204)
T ss_pred             HHHHHHHHHHHHHHhHHHHHHh------------hhhcCCCeEEEECCCCCCHHHHHHHHhcch
Confidence            5666777777766554333211            111223456789999999999999988763

A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms.

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=93.96  E-value=0.085  Score=51.00  Aligned_cols=65  Identities=20%  Similarity=0.217  Sum_probs=42.2

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCce-EEEEeCCCC-CHHHHHHHHHHhhcCC----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDKR-IWVCVSDPF-DEFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~~~~~----------------------  180 (297)
                      +|+|-.|+|||+|| ..+.+.  .  .-+.. +++.+.+.. .+.++...+...-...                      
T Consensus       166 ~Ifg~~g~GKt~lal~~i~~~--~--~~dv~~V~~~IGer~~ev~e~~~~~~~~~~l~~tvvv~atsd~p~~~r~~a~~~  241 (502)
T PRK09281        166 LIIGDRQTGKTAIAIDTIINQ--K--GKDVICIYVAIGQKASTVAQVVRKLEEHGAMEYTIVVAATASDPAPLQYLAPYA  241 (502)
T ss_pred             EeecCCCCCchHHHHHHHHHh--c--CCCeEEEEEEecCChHHHHHHHHHHhhcCCccceEEEEeCCCCCHHHHHHHHHH
Confidence            68899999999995 555552  1  23443 666665554 3455555554432221                      


Q ss_pred             -----------CceEEEEEeCCCCC
Q 043781          181 -----------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~~  194 (297)
                                 ++..|+|+||+-..
T Consensus       242 a~tiAEyfrd~G~~VLli~DdlTr~  266 (502)
T PRK09281        242 GCAMGEYFMDNGKDALIVYDDLSKQ  266 (502)
T ss_pred             HHHHHHHHHHcCCCEEEEecCchHH
Confidence                       89999999999654

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=93.93  E-value=0.22  Score=42.04  Aligned_cols=22  Identities=36%  Similarity=0.481  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|.|||||.+.+...
T Consensus        28 ~~~i~G~nGsGKStLl~~l~G~   49 (200)
T cd03217          28 VHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999999885

Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=93.91  E-value=0.032  Score=46.29  Aligned_cols=21  Identities=24%  Similarity=0.188  Sum_probs=18.3

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+|++|+||||+++.+..
T Consensus         5 ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999999885

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.

>TIGR01288 nodI ATP-binding ABC transporter family nodulation protein NodI

Probab=93.91  E-value=0.16  Score=45.85  Aligned_cols=22  Identities=27%  Similarity=0.389  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||.+.+...
T Consensus        32 ~~~l~G~NGaGKSTLl~~l~Gl   53 (303)
T TIGR01288        32 CFGLLGPNGAGKSTIARMLLGM   53 (303)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999874

This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=93.90  E-value=0.11  Score=48.94  Aligned_cols=68  Identities=19%  Similarity=0.089  Sum_probs=37.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CCCHHHHHHHHHHhhcCC---CceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PFDEFRIAKAIIEGLEGS---EKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+..  ...-.|...-....+.    ..+...++...+......   ..+-+|+||++...
T Consensus       119 iLL~GP~GsGKT~lAraLA~--~l~~pf~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl  193 (413)
T TIGR00382       119 ILLIGPTGSGKTLLAQTLAR--ILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKI  193 (413)
T ss_pred             EEEECCCCcCHHHHHHHHHH--hcCCCeEEechhhccccccccccHHHHHHHHHHhCcccHHhcccceEEecccchh
Confidence            34779999999999999987  3433441110001111    113444454444432211   23447899999754

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=93.86  E-value=0.07  Score=51.16  Aligned_cols=76  Identities=17%  Similarity=0.239  Sum_probs=42.2

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCce-EEEEeCCCCCHHHHHHHH-HHhh---------c-CC-CceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKR-IWVCVSDPFDEFRIAKAI-IEGL---------E-GS-EKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~-~wv~vs~~~~~~~~~~~i-~~~~---------~-~~-~kr~LiVlDdv~~  193 (297)
                      +.|++|+|||+||+.+.....-...|... +-.  +   ...+++..+ +...         . +. ..--++++|+++.
T Consensus        44 L~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~f--t---tp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~r  118 (498)
T PRK13531         44 LLGPPGIAKSLIARRLKFAFQNARAFEYLMTRF--S---TPEEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWK  118 (498)
T ss_pred             EECCCChhHHHHHHHHHHHhcccCcceeeeeee--c---CcHHhcCcHHHhhhhhcCchhhhcCCccccccEEeeccccc
Confidence            77999999999999999832222234311 111  1   123443322 1111         0 00 1222899999998


Q ss_pred             CCccCHHHHHHHHh
Q 043781          194 DDYSKWEPFHNCLM  207 (297)
Q Consensus       194 ~~~~~w~~l~~~l~  207 (297)
                      ........|...+.
T Consensus       119 asp~~QsaLLeam~  132 (498)
T PRK13531        119 AGPAILNTLLTAIN  132 (498)
T ss_pred             CCHHHHHHHHHHHH
Confidence            76656666666663

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=93.86  E-value=0.033  Score=46.42  Aligned_cols=20  Identities=35%  Similarity=0.361  Sum_probs=18.3

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|+|.+|+||||+|+.+.+.
T Consensus         4 iilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           4 LILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999995

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=93.84  E-value=0.032  Score=48.08  Aligned_cols=21  Identities=24%  Similarity=0.249  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ++|.|..|+||||||+.+...
T Consensus         2 igI~G~sGSGKTTla~~L~~~   22 (220)
T cd02025           2 IGIAGSVAVGKSTTARVLQAL   22 (220)
T ss_pred             EEeeCCCCCCHHHHHHHHHHH
Confidence            478899999999999999873

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PF03029 ATP_bind_1: Conserved hypothetical ATP binding protein; InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity

Probab=93.83  E-value=0.033  Score=48.67  Aligned_cols=21  Identities=33%  Similarity=0.276  Sum_probs=17.6

Q ss_pred             ccccCCcchHHHHHHHhcccc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKD  147 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~  147 (297)
                      |+|++|+||||+++.+.+.-.
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~   21 (238)
T PF03029_consen    1 VIGPAGSGKTTFCKGLSEWLE   21 (238)
T ss_dssp             -EESTTSSHHHHHHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHH
Confidence            689999999999999988543

; GO: 0000166 nucleotide binding; PDB: 1YR7_A 1YRA_B 1YR8_A 1YR6_A 1YR9_A 1YRB_A 2OXR_A.

>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=93.83  E-value=0.034  Score=44.49  Aligned_cols=20  Identities=35%  Similarity=0.458  Sum_probs=17.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|++|+||||||+.+...
T Consensus         3 ~l~G~~GsGKstla~~la~~   22 (154)
T cd00464           3 VLIGMMGAGKTTVGRLLAKA   22 (154)
T ss_pred             EEEcCCCCCHHHHHHHHHHH
Confidence            47899999999999999873

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.

>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional

Probab=93.82  E-value=0.4  Score=46.34  Aligned_cols=22  Identities=27%  Similarity=0.332  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||.+.+...
T Consensus        31 ~~~liG~nGsGKSTLl~~l~G~   52 (490)
T PRK10938         31 SWAFVGANGSGKSALARALAGE   52 (490)
T ss_pred             EEEEECCCCCCHHHHHHHHhcc
Confidence            3579999999999999999874

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=93.82  E-value=0.28  Score=40.02  Aligned_cols=21  Identities=24%  Similarity=0.031  Sum_probs=15.6

Q ss_pred             cccccccCCcchHH-HHHHHhc
Q 043781          124 VSDVRGMGGIGKTT-LAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTt-La~~v~~  144 (297)
                      ..-|.|..|+|||+ ++..+++
T Consensus        26 ~~~i~~~~GsGKT~~~~~~~~~   47 (201)
T smart00487       26 DVILAAPTGSGKTLAALLPALE   47 (201)
T ss_pred             cEEEECCCCCchhHHHHHHHHH
Confidence            34577999999999 5555555

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=93.74  E-value=0.92  Score=41.41  Aligned_cols=23  Identities=35%  Similarity=0.304  Sum_probs=19.7

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|++|+||||++..+...
T Consensus       115 ~vi~lvGpnGsGKTTt~~kLA~~  137 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIGKLAHK  137 (318)
T ss_pred             eEEEEECCCCCcHHHHHHHHHHH
Confidence            45678999999999999888774

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=93.73  E-value=0.19  Score=50.77  Aligned_cols=20  Identities=30%  Similarity=0.488  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ++|+|..|+|||||+|.+..
T Consensus       502 vaIvG~SGsGKSTL~KLL~g  521 (709)
T COG2274         502 VAIVGRSGSGKSTLLKLLLG  521 (709)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            57999999999999999987

>cd01394 radB RadB

Probab=93.73  E-value=0.089  Score=44.94  Aligned_cols=21  Identities=33%  Similarity=0.370  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|.+|+|||||+.++...
T Consensus        22 ~~i~G~~GsGKT~l~~~~a~~   42 (218)
T cd01394          22 TQVYGPPGTGKTNIAIQLAVE   42 (218)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            458899999999999888763

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>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=93.72  E-value=0.037  Score=44.48  Aligned_cols=19  Identities=32%  Similarity=0.277  Sum_probs=17.5

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      |+|++|+||||+|+.+...
T Consensus         1 i~G~PgsGK~t~~~~la~~   19 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKR   19 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHh
Confidence            6899999999999999984

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 ....

>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=93.71  E-value=0.29  Score=42.77  Aligned_cols=52  Identities=17%  Similarity=0.287  Sum_probs=38.2

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      ++.=|+|||.=.+. |+..-+.|+....+.         ...|..||..|+..+.+..+|..
T Consensus       147 HePeLlILDEPFSGLDPVN~elLk~~I~~l---------k~~GatIifSsH~Me~vEeLCD~  199 (300)
T COG4152         147 HEPELLILDEPFSGLDPVNVELLKDAIFEL---------KEEGATIIFSSHRMEHVEELCDR  199 (300)
T ss_pred             cCCCEEEecCCccCCChhhHHHHHHHHHHH---------HhcCCEEEEecchHHHHHHHhhh
Confidence            88999999987664 333445566665543         37889999999988888888754

>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=93.64  E-value=0.26  Score=41.69  Aligned_cols=22  Identities=18%  Similarity=-0.013  Sum_probs=19.1

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +...|.|..|.|||||.+.+..
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHH
Confidence            4567889999999999999984

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

>PRK06547 hypothetical protein; Provisional

Probab=93.64  E-value=0.037  Score=45.80  Aligned_cols=23  Identities=35%  Similarity=0.277  Sum_probs=19.6

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+.|.|.+|+||||||+.+.+.
T Consensus        16 ~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         16 ITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            34568899999999999999874

>PF12061 DUF3542: Protein of unknown function (DUF3542); InterPro: IPR021929 R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide

Probab=93.63  E-value=0.074  Score=47.68  Aligned_cols=58  Identities=21%  Similarity=0.313  Sum_probs=47.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHH-HhcccccHHHHHHHHHHHHHHhhHHHHHHHHH
Q 043781            4 FFQDFGKQVKKLTSNLRAIQAVLNDA-EQRQVKEASVRLWLDQLKEASYDMEDVLDEWI   61 (297)
Q Consensus         4 ll~~~~~~~~~L~~eL~~i~a~l~~a-e~~~~~~~~v~~Wl~~lr~~ayd~eD~ld~~~   61 (297)
                      .+.-++.+++.++.+|+.++.|++.. +.....-.....+..++-+.||++|.++|.+.
T Consensus       315 SlaflKnQiqvIQ~elesLqpFLk~V~ee~~nkh~~~ed~a~~ii~kAyevEYVVDaCi  373 (402)
T PF12061_consen  315 SLAFLKNQIQVIQTELESLQPFLKHVVEEPHNKHDTNEDCATQIIRKAYEVEYVVDACI  373 (402)
T ss_pred             hHHHHHHHHHHHHHHHHHhhHHHHHHHhccchhhhhhhhHHHHHHHHHhheeeeeehhh
Confidence            45567899999999999999999987 44233334489999999999999999999884

The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain []. Most proteins matching this entry are found associated with PF00931 from PFAM.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=93.61  E-value=0.092  Score=45.15  Aligned_cols=40  Identities=20%  Similarity=0.273  Sum_probs=28.3

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDE  166 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  166 (297)
                      ...|+|.+|+|||+|+.++...  ....-...+|+... .++.
T Consensus        25 i~~i~G~~GsGKT~l~~~la~~--~~~~~~~v~yi~~e-~~~~   64 (225)
T PRK09361         25 ITQIYGPPGSGKTNICLQLAVE--AAKNGKKVIYIDTE-GLSP   64 (225)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEECC-CCCH
Confidence            3468899999999999888874  22233567788766 4443

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=93.60  E-value=0.04  Score=44.81  Aligned_cols=20  Identities=30%  Similarity=0.419  Sum_probs=17.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|++|+||||+|+.+.+.
T Consensus         2 ~l~G~~GsGKSTla~~l~~~   21 (163)
T TIGR01313         2 VLMGVAGSGKSTIASALAHR   21 (163)
T ss_pred             EEECCCCCCHHHHHHHHHHh
Confidence            47899999999999998874

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.

>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit

Probab=93.60  E-value=0.1  Score=50.39  Aligned_cols=65  Identities=22%  Similarity=0.251  Sum_probs=44.5

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCce-EEEEeCCCC-CHHHHHHHHHHhhcCC----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDKR-IWVCVSDPF-DEFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~~~~~----------------------  180 (297)
                      +|+|-.|+|||+|| ..+.+..    ..+.. +++-+.+.. .+.++.+.+...-...                      
T Consensus       165 ~I~g~~g~GKt~Lal~~i~~~~----~~dv~~V~~~IGer~rev~e~~~~~~~~~~l~~tvvV~atsd~p~~~r~~a~~~  240 (501)
T TIGR00962       165 LIIGDRQTGKTAVAIDTIINQK----DSDVYCVYVAIGQKASTVAQVVRKLEEHGAMDYTIVVAATASDSASLQYLAPYT  240 (501)
T ss_pred             EeecCCCCCccHHHHHHHHhhc----CCCeEEEEEEccCChHHHHHHHHHHHhcCccceeEEEEecCCCCHHHHHHHHHH
Confidence            68899999999996 6676631    34554 677666644 4456666655543222                      


Q ss_pred             -----------CceEEEEEeCCCCC
Q 043781          181 -----------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~~  194 (297)
                                 ++..|||+||+-..
T Consensus       241 a~aiAEyfrd~G~~VLlv~Ddltr~  265 (501)
T TIGR00962       241 GCTMAEYFRDNGKHALIIYDDLSKH  265 (501)
T ss_pred             HHHHHHHHHHcCCCEEEEecchHHH
Confidence                       89999999999654

The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.

>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=93.59  E-value=0.34  Score=40.99  Aligned_cols=22  Identities=32%  Similarity=0.291  Sum_probs=17.7

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...++|+.|+||||.+-++...
T Consensus         3 vi~lvGptGvGKTTt~aKLAa~   24 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAAR   24 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCchHhHHHHHHHH
Confidence            3458999999999988777664

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 ....

>PRK07960 fliI flagellum-specific ATP synthase; Validated

Probab=93.58  E-value=0.11  Score=49.37  Aligned_cols=20  Identities=20%  Similarity=0.253  Sum_probs=17.9

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +|+|..|+|||||.+.+.+.
T Consensus       179 ~I~G~sG~GKTTLL~~Ia~~  198 (455)
T PRK07960        179 GLFAGSGVGKSVLLGMMARY  198 (455)
T ss_pred             EEECCCCCCccHHHHHHhCC
Confidence            68899999999999988874

>PRK05636 replicative DNA helicase; Provisional

Probab=93.57  E-value=2.8  Score=40.85  Aligned_cols=49  Identities=20%  Similarity=0.175  Sum_probs=30.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhh
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGL  177 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~  177 (297)
                      -|-|.+|+|||+||..+..+...+.... ++++  |-..+..++...++...
T Consensus       269 iiaarpg~GKT~~al~~a~~~a~~~g~~-v~~f--SlEMs~~ql~~R~ls~~  317 (505)
T PRK05636        269 IVAARPGVGKSTLALDFMRSASIKHNKA-SVIF--SLEMSKSEIVMRLLSAE  317 (505)
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHHhCCCe-EEEE--EeeCCHHHHHHHHHHHh
Confidence            3569999999999988876533333332 2222  44455666666665554

>PF00154 RecA: recA bacterial DNA recombination protein; InterPro: IPR013765 The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response []

Probab=93.56  E-value=0.12  Score=47.04  Aligned_cols=41  Identities=22%  Similarity=0.264  Sum_probs=28.2

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDE  166 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  166 (297)
                      .+.|+|..|+||||||..+...  ....-...+|+.....++.
T Consensus        55 ivEi~G~~ssGKttLaL~~ia~--~q~~g~~~a~ID~e~~ld~   95 (322)
T PF00154_consen   55 IVEIYGPESSGKTTLALHAIAE--AQKQGGICAFIDAEHALDP   95 (322)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH--HHHTT-EEEEEESSS---H
T ss_pred             eEEEeCCCCCchhhhHHHHHHh--hhcccceeEEecCcccchh
Confidence            4579999999999999888773  4444456788877665544

In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs []. RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage []. RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved [, , ] among eubacterial species. It is also found in the chloroplast of plants []. RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, beta-strand 3, the loop C-terminal to beta-strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and beta-strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation []. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between beta-strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at beta-strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at beta-strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; GO: 0003697 single-stranded DNA binding, 0005524 ATP binding, 0006281 DNA repair; PDB: 2IN0_A 1MO3_A 3IFJ_A 2IN8_A 2IMZ_B 1G18_A 1MO4_A 3IGD_A 2L8L_A 2IN9_A ....

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]

Probab=93.56  E-value=0.54  Score=39.96  Aligned_cols=21  Identities=33%  Similarity=0.529  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+|.|..|.||||+.+.++.
T Consensus        30 i~GlLG~NGAGKTT~LRmiat   50 (245)
T COG4555          30 ITGLLGENGAGKTTLLRMIAT   50 (245)
T ss_pred             EEEEEcCCCCCchhHHHHHHH
Confidence            357889999999999999997

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=93.54  E-value=0.62  Score=42.13  Aligned_cols=121  Identities=15%  Similarity=0.067  Sum_probs=73.4

Q ss_pred             ccccCCcchHHHHHHHhccc---c---cc--cCCCceEEEEe-CCCCCHHHHHHHHHHhhcCC----CceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDK---D---VI--ENFDKRIWVCV-SDPFDEFRIAKAIIEGLEGS----EKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~---~---~~--~~F~~~~wv~v-s~~~~~~~~~~~i~~~~~~~----~kr~LiVlDdv~~  193 (297)
                      ++|..|.||+++|+.+.+.-   .   +.  .|-+-..++.. .....+.++. ++.+.+...    +++=++|+|++..
T Consensus        23 f~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir-~l~~~~~~~~~~~~~~KvvII~~~e~  101 (299)
T PRK07132         23 LKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFL-SAINKLYFSSFVQSQKKILIIKNIEK  101 (299)
T ss_pred             EeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHH-HHHHHhccCCcccCCceEEEEecccc
Confidence            67999999999998887631   0   11  12112333332 2345555554 555555432    5888899999977


Q ss_pred             CCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCccchhhhhhh
Q 043781          194 DDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       194 ~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~l~~~~lf~~  261 (297)
                      ......+.|...+..-          ...+.+|++|...   ..+..+ ..-..++++.+++..++..|
T Consensus       102 m~~~a~NaLLK~LEEP----------p~~t~~il~~~~~---~kll~TI~SRc~~~~f~~l~~~~l~~~  157 (299)
T PRK07132        102 TSNSLLNALLKTIEEP----------PKDTYFLLTTKNI---NKVLPTIVSRCQVFNVKEPDQQKILAK  157 (299)
T ss_pred             cCHHHHHHHHHHhhCC----------CCCeEEEEEeCCh---HhChHHHHhCeEEEECCCCCHHHHHHH
Confidence            6555667777777652          5566666666533   344333 22236788888887776555

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=93.54  E-value=0.041  Score=45.48  Aligned_cols=21  Identities=38%  Similarity=0.450  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+...
T Consensus         4 ~~i~G~sGsGKttl~~~l~~~   24 (179)
T TIGR02322         4 IYVVGPSGAGKDTLLDYARAR   24 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            358899999999999998774

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.

>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=93.52  E-value=0.16  Score=47.21  Aligned_cols=90  Identities=18%  Similarity=0.159  Sum_probs=48.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccc----cCCCce-EEEE-----e-CCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI----ENFDKR-IWVC-----V-SDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~----~~F~~~-~wv~-----v-s~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .=|||..|.|||.|+-.+|+.-.++    -||-.- ..|+     . .....+..+.+.|.      ++..||.||...=
T Consensus        65 lYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~------~~~~lLcfDEF~V  138 (362)
T PF03969_consen   65 LYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELA------KESRLLCFDEFQV  138 (362)
T ss_pred             EEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHH------hcCCEEEEeeeec
Confidence            3478999999999999999964442    233100 0000     0 11112222222222      4666999999876


Q ss_pred             CCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEe
Q 043781          194 DDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTS  229 (297)
Q Consensus       194 ~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTT  229 (297)
                      .|..+=--|...|....         ..|..+|.||
T Consensus       139 ~DiaDAmil~rLf~~l~---------~~gvvlVaTS  165 (362)
T PF03969_consen  139 TDIADAMILKRLFEALF---------KRGVVLVATS  165 (362)
T ss_pred             cchhHHHHHHHHHHHHH---------HCCCEEEecC
Confidence            64333223444444331         5566566665

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

>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=93.50  E-value=0.29  Score=43.74  Aligned_cols=51  Identities=10%  Similarity=0.023  Sum_probs=31.2

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLT  239 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~  239 (297)
                      .+.=+++||..-.. |......+...+.....        ..|..||++|++.+.....|
T Consensus       158 ~~p~lLilDEPt~gLD~~~~~~l~~~l~~l~~--------~~g~tillvsH~~~~~~~~~  209 (283)
T PRK13636        158 MEPKVLVLDEPTAGLDPMGVSEIMKLLVEMQK--------ELGLTIIIATHDIDIVPLYC  209 (283)
T ss_pred             cCCCEEEEeCCccCCCHHHHHHHHHHHHHHHH--------hCCCEEEEEecCHHHHHHhC
Confidence            77889999998765 22333345455543211        33678899998765544444

>PRK14530 adenylate kinase; Provisional

Probab=93.50  E-value=0.041  Score=47.11  Aligned_cols=21  Identities=24%  Similarity=0.191  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|++|+||||+++.+...
T Consensus         6 I~i~G~pGsGKsT~~~~La~~   26 (215)
T PRK14530          6 ILLLGAPGAGKGTQSSNLAEE   26 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999999763

>PRK13343 F0F1 ATP synthase subunit alpha; Provisional

Probab=93.47  E-value=0.1  Score=50.34  Aligned_cols=65  Identities=18%  Similarity=0.257  Sum_probs=41.3

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCce-EEEEeCCCC-CHHHHHHHHHHhh-------------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDKR-IWVCVSDPF-DEFRIAKAIIEGL-------------------------  177 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~~-~wv~vs~~~-~~~~~~~~i~~~~-------------------------  177 (297)
                      .|+|-.|+|||+|| ..+.+.    ..-+.. +++-+.+.. .+.++.+.+...-                         
T Consensus       166 ~I~g~~g~GKt~Lal~~i~~~----~~~dv~~V~~~IGer~rev~e~~~~l~~~~~l~~tvvV~atsd~~~~~r~~ap~~  241 (502)
T PRK13343        166 LIIGDRQTGKTAIAIDAIINQ----KDSDVICVYVAIGQKASAVARVIETLREHGALEYTTVVVAEASDPPGLQYLAPFA  241 (502)
T ss_pred             EeeCCCCCCccHHHHHHHHhh----cCCCEEEEEEEeccChHHHHHHHHHHHhcCccceeEEEEecccccHHHHHHHHHH
Confidence            58899999999995 666653    123443 555555543 2344444444332                         


Q ss_pred             --------cCCCceEEEEEeCCCCC
Q 043781          178 --------EGSEKKFFLILDDVWTD  194 (297)
Q Consensus       178 --------~~~~kr~LiVlDdv~~~  194 (297)
                              ...++..|||+||+-..
T Consensus       242 a~aiAEyfrd~G~~VLlv~DdlTr~  266 (502)
T PRK13343        242 GCAIAEYFRDQGQDALIVYDDLSKH  266 (502)
T ss_pred             HHHHHHHHHhCCCCEEEEecchHHH
Confidence                    21299999999999654

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=93.44  E-value=0.13  Score=46.73  Aligned_cols=47  Identities=23%  Similarity=0.277  Sum_probs=33.0

Q ss_pred             cccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCCHHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFDEFRIA  170 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~~  170 (297)
                      ...|+|.+|+|||||+.+++.+.....    .=...+||.....|+..++.
T Consensus        97 i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~  147 (310)
T TIGR02236        97 ITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIM  147 (310)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHH
Confidence            446899999999999988876432211    11268899988877766543

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.

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.41  E-value=0.34  Score=42.16  Aligned_cols=43  Identities=16%  Similarity=0.251  Sum_probs=25.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKA  172 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~  172 (297)
                      -|.|.+|+|||+||.++... ..+ .=+..+|++...  +..++.+.
T Consensus        25 lI~G~pGsGKT~la~~~l~~-~~~-~ge~~lyvs~ee--~~~~i~~~   67 (237)
T TIGR03877        25 LLSGGPGTGKSIFSQQFLWN-GLQ-MGEPGIYVALEE--HPVQVRRN   67 (237)
T ss_pred             EEEcCCCCCHHHHHHHHHHH-HHH-cCCcEEEEEeeC--CHHHHHHH
Confidence            47799999999999765442 122 233455665433  33344443

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.

>KOG0924 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]

Probab=93.41  E-value=0.47  Score=47.00  Aligned_cols=115  Identities=24%  Similarity=0.320  Sum_probs=68.6

Q ss_pred             ccccccCCcchHH-HHHHHhcccccccCCCceEEEEeCCCCCHHH--HHHHHHHhhcCC---------------------
Q 043781          125 SDVRGMGGIGKTT-LAQFAYNDKDVIENFDKRIWVCVSDPFDEFR--IAKAIIEGLEGS---------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTt-La~~v~~~~~~~~~F~~~~wv~vs~~~~~~~--~~~~i~~~~~~~---------------------  180 (297)
                      +-|+|-.|+|||| |++++|.+.-..+     -.|.+.++-.+..  +.+.+.+.++..                     
T Consensus       374 vvivgETGSGKTTQl~QyL~edGY~~~-----GmIGcTQPRRvAAiSVAkrVa~EM~~~lG~~VGYsIRFEdvT~~~T~I  448 (1042)
T KOG0924|consen  374 VVIVGETGSGKTTQLAQYLYEDGYADN-----GMIGCTQPRRVAAISVAKRVAEEMGVTLGDTVGYSIRFEDVTSEDTKI  448 (1042)
T ss_pred             EEEEecCCCCchhhhHHHHHhcccccC-----CeeeecCchHHHHHHHHHHHHHHhCCccccccceEEEeeecCCCceeE
Confidence            3578999999987 7799998643332     2455566655443  344555555332                     


Q ss_pred             ------------------CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhh
Q 043781          181 ------------------EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTL  242 (297)
Q Consensus       181 ------------------~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~  242 (297)
                                        .|=-.||+|.+.+.. -.-+-|-..|+....       -...-++|||+-+.+ +.+.+.-+
T Consensus       449 kymTDGiLLrEsL~d~~L~kYSviImDEAHERs-lNtDilfGllk~~la-------rRrdlKliVtSATm~-a~kf~nfF  519 (1042)
T KOG0924|consen  449 KYMTDGILLRESLKDRDLDKYSVIIMDEAHERS-LNTDILFGLLKKVLA-------RRRDLKLIVTSATMD-AQKFSNFF  519 (1042)
T ss_pred             EEeccchHHHHHhhhhhhhheeEEEechhhhcc-cchHHHHHHHHHHHH-------hhccceEEEeecccc-HHHHHHHh
Confidence                              666788899987652 233333333433322       155679999986555 45565555


Q ss_pred             CC-------CccccCCcc
Q 043781          243 GL-------RAKFPVSIF  253 (297)
Q Consensus       243 ~~-------~~~~~l~~l  253 (297)
                      |-       ...||++.+
T Consensus       520 gn~p~f~IpGRTyPV~~~  537 (1042)
T KOG0924|consen  520 GNCPQFTIPGRTYPVEIM  537 (1042)
T ss_pred             CCCceeeecCCccceEEE
Confidence            51       245666655

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=93.40  E-value=0.12  Score=47.04  Aligned_cols=47  Identities=21%  Similarity=0.295  Sum_probs=32.6

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCC----CceEEEEeCCCCCHHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENF----DKRIWVCVSDPFDEFRIA  170 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F----~~~~wv~vs~~~~~~~~~  170 (297)
                      ...|+|.+|+|||+|+.++.-+......+    ...+||.....|+..++.
T Consensus       104 vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~  154 (317)
T PRK04301        104 ITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIE  154 (317)
T ss_pred             EEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHH
Confidence            34689999999999998887542221111    367899888777766544

>PRK06696 uridine kinase; Validated

Probab=93.34  E-value=0.043  Score=47.28  Aligned_cols=23  Identities=26%  Similarity=0.286  Sum_probs=19.8

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -.++|-|.+|+||||||+.+...
T Consensus        23 ~iI~I~G~sgsGKSTlA~~L~~~   45 (223)
T PRK06696         23 LRVAIDGITASGKTTFADELAEE   45 (223)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35678899999999999999883

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.28  E-value=1  Score=42.19  Aligned_cols=23  Identities=26%  Similarity=0.224  Sum_probs=19.1

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|+.|+||||++..+...
T Consensus       207 ~ii~lvGptGvGKTTt~akLA~~  229 (407)
T PRK12726        207 RIISLIGQTGVGKTTTLVKLGWQ  229 (407)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            34578999999999999888763

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=93.24  E-value=0.05  Score=45.44  Aligned_cols=21  Identities=24%  Similarity=0.185  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+...
T Consensus         5 i~l~G~sGsGKsTl~~~l~~~   25 (186)
T PRK10078          5 IWLMGPSGSGKDSLLAALRQR   25 (186)
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            458899999999999999874

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=93.23  E-value=0.46  Score=40.09  Aligned_cols=20  Identities=25%  Similarity=0.099  Sum_probs=17.9

Q ss_pred             cccccccCCcchHHHHHHHh
Q 043781          124 VSDVRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~  143 (297)
                      ...|.|+.|.|||||.+.+.
T Consensus        30 ~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          30 VLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             EEEEECCCCCChHHHHHHHH
Confidence            36788999999999999988

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

>PF08477 Miro: Miro-like protein; InterPro: IPR013684 Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT and Miro-2, Q8IXI1 from SWISSPROT) are atypical Rho GTPases

Probab=93.23  E-value=0.055  Score=41.16  Aligned_cols=22  Identities=32%  Similarity=0.347  Sum_probs=18.6

Q ss_pred             cccccCCcchHHHHHHHhcccc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD  147 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~  147 (297)
                      -|+|..|+|||||.+.+.+.+.
T Consensus         3 ~V~G~~g~GKTsLi~~l~~~~~   24 (119)
T PF08477_consen    3 VVLGDSGVGKTSLIRRLCGGEF   24 (119)
T ss_dssp             EEECSTTSSHHHHHHHHHHSS-
T ss_pred             EEECcCCCCHHHHHHHHhcCCC
Confidence            4789999999999999987643

They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis []. ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IWR_A 2BMJ_A 3IHW_A 2ZEJ_A 3D6T_B 3DPU_A.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=93.21  E-value=0.24  Score=42.58  Aligned_cols=62  Identities=21%  Similarity=0.246  Sum_probs=37.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-----CceEEEEEeCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-----EKKFFLILDDV  191 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----~kr~LiVlDdv  191 (297)
                      ..|.|.+|+|||||+..+.... .+ .-...+|++...  +..++... +++++..     .+..|.++|++
T Consensus        23 ~~i~G~~G~GKT~l~~~~~~~~-~~-~g~~~~~is~e~--~~~~i~~~-~~~~g~~~~~~~~~~~l~i~d~~   89 (229)
T TIGR03881        23 VAVTGEPGTGKTIFCLHFAYKG-LR-DGDPVIYVTTEE--SRESIIRQ-AAQFGMDFEKAIEEGKLVIIDAL   89 (229)
T ss_pred             EEEECCCCCChHHHHHHHHHHH-Hh-cCCeEEEEEccC--CHHHHHHH-HHHhCCCHHHHhhcCCEEEEEcc
Confidence            3578999999999998765531 22 234567776543  34444433 4444433     23346778876

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

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

Probab=93.20  E-value=0.3  Score=49.18  Aligned_cols=60  Identities=20%  Similarity=0.202  Sum_probs=36.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC------CH-HHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF------DE-FRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~------~~-~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|++|+|||-||+.++....+  .|     +++|..-      .+ ..-.++++..... ...++|.+|++..
T Consensus       348 LL~GPPGTGKTLLAKAiAGEAgV--PF-----~svSGSEFvE~~~g~~asrvr~lf~~ar~-~aP~iifideida  414 (774)
T KOG0731|consen  348 LLVGPPGTGKTLLAKAIAGEAGV--PF-----FSVSGSEFVEMFVGVGASRVRDLFPLARK-NAPSIIFIDEIDA  414 (774)
T ss_pred             EEECCCCCcHHHHHHHHhcccCC--ce-----eeechHHHHHHhcccchHHHHHHHHHhhc-cCCeEEEeccccc
Confidence            37899999999999999994333  33     2222210      00 1222333333322 6788999998875

>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=93.14  E-value=0.052  Score=42.94  Aligned_cols=21  Identities=29%  Similarity=0.471  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|.+|+||||+|+.+...
T Consensus         2 I~i~G~~GsGKst~a~~la~~   22 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKK   22 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            357899999999999999873

>PRK14532 adenylate kinase; Provisional

Probab=93.14  E-value=0.051  Score=45.31  Aligned_cols=20  Identities=25%  Similarity=0.147  Sum_probs=17.6

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|++|+||||+|+.+...
T Consensus         4 ~~~G~pGsGKsT~a~~la~~   23 (188)
T PRK14532          4 ILFGPPAAGKGTQAKRLVEE   23 (188)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999873

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=93.13  E-value=0.052  Score=45.62  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ++|.|.+|+||||||+.+...
T Consensus         2 i~i~G~sgsGKTtla~~l~~~   22 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRI   22 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999999884

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=93.13  E-value=0.069  Score=45.44  Aligned_cols=51  Identities=20%  Similarity=0.110  Sum_probs=30.8

Q ss_pred             ccccccCCcchHHHHHHHhcccc-----cccCCCceEEEEeCCCCCHHHHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKD-----VIENFDKRIWVCVSDPFDEFRIAKAIIE  175 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~-----~~~~F~~~~wv~vs~~~~~~~~~~~i~~  175 (297)
                      .-|.|++|.||||++..+...-.     ....-...+-++...+..+..++..+.+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             EEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            45789999999976655555310     1134455566666666666777777666

>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=93.12  E-value=0.073  Score=43.31  Aligned_cols=19  Identities=42%  Similarity=0.574  Sum_probs=17.2

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.+|+||||||+.+...
T Consensus         7 ltGlsGsGKtTlA~~L~~~   25 (156)
T PF01583_consen    7 LTGLSGSGKTTLARALERR   25 (156)
T ss_dssp             EESSTTSSHHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHH
Confidence            5699999999999999983

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 ....

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=93.08  E-value=0.32  Score=48.22  Aligned_cols=93  Identities=14%  Similarity=0.143  Sum_probs=59.7

Q ss_pred             ccccCCcchHHHHHHHhcccc------cccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC--------------------
Q 043781          127 VRGMGGIGKTTLAQFAYNDKD------VIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS--------------------  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~------~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--------------------  180 (297)
                      |-|.+|+|||..+..|.+.-+      --..| ..+.|+.-.-..+.++...|+.++.+.                    
T Consensus       427 IsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f-~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~  505 (767)
T KOG1514|consen  427 ISGVPGTGKTATVLEVMKELQTSSAQKELPKF-DYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKP  505 (767)
T ss_pred             EecCCCCCceehHHHHHHHHHHHHhhcCCCCc-cEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCC
Confidence            569999999999999988422      12234 334455555557889999999999876                    


Q ss_pred             -CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEe
Q 043781          181 -EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTS  229 (297)
Q Consensus       181 -~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTT  229 (297)
                       .+..+|++|++...- .-=+++...|-+.        ++.++|+++|-+
T Consensus       506 ~~~~~VvLiDElD~Lv-tr~QdVlYn~fdW--------pt~~~sKLvvi~  546 (767)
T KOG1514|consen  506 KRSTTVVLIDELDILV-TRSQDVLYNIFDW--------PTLKNSKLVVIA  546 (767)
T ss_pred             CCCCEEEEeccHHHHh-cccHHHHHHHhcC--------CcCCCCceEEEE
Confidence             677888988885431 0011232223221        147888877754

>TIGR03263 guanyl_kin guanylate kinase

Probab=93.07  E-value=0.056  Score=44.64  Aligned_cols=21  Identities=29%  Similarity=0.509  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+...
T Consensus         4 i~l~G~~GsGKsTl~~~L~~~   24 (180)
T TIGR03263         4 IVISGPSGVGKSTLVKALLEE   24 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHcc
Confidence            457899999999999999983

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.

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

Probab=93.04  E-value=0.42  Score=46.16  Aligned_cols=94  Identities=19%  Similarity=0.228  Sum_probs=53.4

Q ss_pred             hHHHHHHHHHHHHHhhhhcccccccCCcccccccccccccccccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC
Q 043781           83 KIIEINENLDDIAKQKEVFNFNVIRGSTEKSERIHSTALINVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD  162 (297)
Q Consensus        83 ~i~~i~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~  162 (297)
                      .+.+.+..|+++.+-.+.-.-..          +.--.+...+=++|++|.|||.||+.|.....|  .|    |.....
T Consensus       308 G~DEAK~ELeEiVefLkdP~kft----------rLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~V--PF----F~~sGS  371 (752)
T KOG0734|consen  308 GVDEAKQELEEIVEFLKDPTKFT----------RLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGV--PF----FYASGS  371 (752)
T ss_pred             ChHHHHHHHHHHHHHhcCcHHhh----------hccCcCCCceEEeCCCCCchhHHHHHhhcccCC--Ce----Eecccc
Confidence            46777788888875542221110          111112233458899999999999999985433  22    222222


Q ss_pred             CCCH------HHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          163 PFDE------FRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       163 ~~~~------~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .|+-      .+-.++++.+... .-.++|.+|.+..
T Consensus       372 EFdEm~VGvGArRVRdLF~aAk~-~APcIIFIDEiDa  407 (752)
T KOG0734|consen  372 EFDEMFVGVGARRVRDLFAAAKA-RAPCIIFIDEIDA  407 (752)
T ss_pred             chhhhhhcccHHHHHHHHHHHHh-cCCeEEEEechhh
Confidence            2221      1223444444433 5689999999975

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=92.99  E-value=0.37  Score=48.75  Aligned_cols=20  Identities=30%  Similarity=0.400  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|..|+|||||++.+..
T Consensus       494 iaIvG~sGsGKSTLlklL~g  513 (694)
T TIGR03375       494 VAIIGRIGSGKSTLLKLLLG  513 (694)
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            46899999999999999976

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>PRK13975 thymidylate kinase; Provisional

Probab=92.95  E-value=0.055  Score=45.35  Aligned_cols=21  Identities=33%  Similarity=0.428  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|+.|+||||+++.+.+.
T Consensus         5 I~ieG~~GsGKtT~~~~L~~~   25 (196)
T PRK13975          5 IVFEGIDGSGKTTQAKLLAEK   25 (196)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            357799999999999999984

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=92.91  E-value=0.058  Score=44.55  Aligned_cols=21  Identities=19%  Similarity=0.191  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-+.|++|+||||+|+.+...
T Consensus         5 i~l~G~~gsGKst~a~~l~~~   25 (175)
T cd00227           5 IILNGGSSAGKSSIARALQSV   25 (175)
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            346799999999999999874

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=92.90  E-value=1.5  Score=36.47  Aligned_cols=19  Identities=21%  Similarity=0.008  Sum_probs=16.7

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -|.|..|.||||+.+.+.-
T Consensus         3 ~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        3 IITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            3789999999999999883

>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor

Probab=92.90  E-value=0.16  Score=42.28  Aligned_cols=21  Identities=33%  Similarity=0.472  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|+.|+||||+++.+.+.
T Consensus         3 I~ieG~~GsGKtT~~~~L~~~   23 (200)
T cd01672           3 IVFEGIDGAGKTTLIELLAER   23 (200)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            346799999999999999884

TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).

>TIGR00450 mnmE_trmE_thdF tRNA modification GTPase TrmE

Probab=92.89  E-value=0.32  Score=46.46  Aligned_cols=22  Identities=18%  Similarity=0.317  Sum_probs=19.2

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +.|+|.+|+|||||...+.+..
T Consensus       206 VvIvG~~nvGKSSLiN~L~~~~  227 (442)
T TIGR00450       206 LAIVGSPNVGKSSLLNALLKQD  227 (442)
T ss_pred             EEEECCCCCcHHHHHHHHhCCC
Confidence            4689999999999999998753

TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer.

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=92.88  E-value=0.057  Score=44.95  Aligned_cols=21  Identities=38%  Similarity=0.477  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ++|.|.+|+||||||+.+...
T Consensus         2 i~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            468899999999999999874

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=92.88  E-value=0.063  Score=44.28  Aligned_cols=26  Identities=23%  Similarity=0.270  Sum_probs=21.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENF  152 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F  152 (297)
                      +-++||.|+||||+.+.+.+  ...-+|
T Consensus         5 IvLiG~mGaGKSTIGr~LAk--~L~~~F   30 (172)
T COG0703           5 IVLIGFMGAGKSTIGRALAK--ALNLPF   30 (172)
T ss_pred             EEEEcCCCCCHhHHHHHHHH--HcCCCc
Confidence            35789999999999999988  454455

>PRK02118 V-type ATP synthase subunit B; Provisional

Probab=92.86  E-value=0.23  Score=47.05  Aligned_cols=66  Identities=15%  Similarity=0.041  Sum_probs=44.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC-HHHHHHHHHHhhcCC-----------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD-EFRIAKAIIEGLEGS-----------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~~~~~-----------------------  180 (297)
                      .+|+|-.|+|||+|+.++.+...    -+..+++-+..... +.++..++.+.-..+                       
T Consensus       143 igIF~gaGvgk~~L~~~ia~~~~----~~v~Vfa~iGeR~rE~~ef~~~~~~~~~l~rtvlv~~~adep~~~R~~~~~~A  218 (436)
T PRK02118        143 IPIFSVSGEPYNALLARIALQAE----ADIIILGGMGLTFDDYLFFKDTFENAGALDRTVMFIHTASDPPVECLLVPDMA  218 (436)
T ss_pred             EEEEeCCCCCHHHHHHHHHHhhC----CCeEEEEEeccchhHHHHHHHHHhhCCCcceEEEEEECCCCCHHHHHHHHHHH
Confidence            47889999999999999877422    24566776655543 344555444433222                       


Q ss_pred             ----------C-ceEEEEEeCCCCC
Q 043781          181 ----------E-KKFFLILDDVWTD  194 (297)
Q Consensus       181 ----------~-kr~LiVlDdv~~~  194 (297)
                                + +..|+++||+-..
T Consensus       219 ltiAEyfrd~g~~~VLli~DdlTr~  243 (436)
T PRK02118        219 LAVAEKFALEGKKKVLVLLTDMTNF  243 (436)
T ss_pred             HHHHHHHHhcCCCCEEEeccCchHH
Confidence                      4 9999999999654

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=92.83  E-value=0.39  Score=36.62  Aligned_cols=34  Identities=15%  Similarity=-0.046  Sum_probs=22.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC  159 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~  159 (297)
                      -|.|..|+|||+.+................+|++
T Consensus         4 ~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~   37 (144)
T cd00046           4 LLAAPTGSGKTLAALLPILELLDSLKGGQVLVLA   37 (144)
T ss_pred             EEECCCCCchhHHHHHHHHHHHhcccCCCEEEEc
Confidence            3679999999999977766433222334555554

A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

>TIGR00665 DnaB replicative DNA helicase

Probab=92.82  E-value=5.2  Score=37.99  Aligned_cols=47  Identities=13%  Similarity=0.153  Sum_probs=28.1

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIE  175 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  175 (297)
                      -|-|.+|+|||+++..+..+....... .++|++.  ..+..++...++.
T Consensus       199 vi~g~pg~GKT~~~l~~a~~~a~~~g~-~vl~~Sl--Em~~~~i~~R~~~  245 (434)
T TIGR00665       199 ILAARPSMGKTAFALNIAENAAIKEGK-PVAFFSL--EMSAEQLAMRMLS  245 (434)
T ss_pred             EEEeCCCCChHHHHHHHHHHHHHhCCC-eEEEEeC--cCCHHHHHHHHHH
Confidence            355999999999998877643222222 3455543  3344555554444

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=92.82  E-value=0.94  Score=40.28  Aligned_cols=53  Identities=15%  Similarity=0.119  Sum_probs=37.2

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      ++.-++.||..--. |...-..++..+.....        ..++.|++||+.-+.....|..
T Consensus       173 h~p~VLfLDEpTvgLDV~aq~~ir~Flke~n~--------~~~aTVllTTH~~~di~~lc~r  226 (325)
T COG4586         173 HPPKVLFLDEPTVGLDVNAQANIREFLKEYNE--------ERQATVLLTTHIFDDIATLCDR  226 (325)
T ss_pred             CCCcEEEecCCccCcchhHHHHHHHHHHHHHH--------hhCceEEEEecchhhHHHhhhh
Confidence            77888999987432 22345567777776533        7789999999987666666653

>PRK13409 putative ATPase RIL; Provisional

Probab=92.82  E-value=0.82  Score=45.39  Aligned_cols=21  Identities=38%  Similarity=0.499  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||++.+...
T Consensus       368 v~l~G~NGsGKSTLlk~L~Gl  388 (590)
T PRK13409        368 IGIVGPNGIGKTTFAKLLAGV  388 (590)
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            368899999999999999974

>PRK00889 adenylylsulfate kinase; Provisional

Probab=92.80  E-value=0.061  Score=44.31  Aligned_cols=22  Identities=32%  Similarity=0.403  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.+.|++|+||||+|+.+...
T Consensus         6 ~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          6 TVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4567899999999999999884

>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=92.78  E-value=0.062  Score=44.30  Aligned_cols=20  Identities=35%  Similarity=0.492  Sum_probs=16.5

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|.+|+|||||++.+.+.
T Consensus         3 ~iTG~pG~GKTTll~k~i~~   22 (168)
T PF03266_consen    3 FITGPPGVGKTTLLKKVIEE   22 (168)
T ss_dssp             EEES-TTSSHHHHHHHHHHH
T ss_pred             EEECcCCCCHHHHHHHHHHH
Confidence            36799999999999998874

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.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=92.77  E-value=0.32  Score=49.20  Aligned_cols=80  Identities=18%  Similarity=0.089  Sum_probs=42.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc----C----------CCceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE----G----------SEKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~----~----------~~kr~LiVlDdv  191 (297)
                      -|+|..|+|||++|+.+++...- .. ...+.+....-. ...+-..++....    +          ....=.|+||+|
T Consensus       403 LI~GE~GTGK~~lA~~ih~~s~r-~~-~~~v~i~c~~~~-~~~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei  479 (686)
T PRK15429        403 LILGETGTGKELIARAIHNLSGR-NN-RRMVKMNCAAMP-AGLLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEV  479 (686)
T ss_pred             EEECCCCcCHHHHHHHHHHhcCC-CC-CCeEEEecccCC-hhHhhhhhcCcccccccccccchhhHHHhcCCCeEEEech
Confidence            47799999999999999884211 11 122333322211 1111111111000    0          012336999999


Q ss_pred             CCCCccCHHHHHHHHhh
Q 043781          192 WTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       192 ~~~~~~~w~~l~~~l~~  208 (297)
                      ..-..+....|...+..
T Consensus       480 ~~L~~~~Q~~L~~~l~~  496 (686)
T PRK15429        480 GDMPLELQPKLLRVLQE  496 (686)
T ss_pred             hhCCHHHHHHHHHHHHh
Confidence            88765555566666643

>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=92.74  E-value=0.062  Score=44.79  Aligned_cols=20  Identities=30%  Similarity=0.192  Sum_probs=17.9

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|+|++|+||||+|+.+...
T Consensus         3 ~i~G~pGsGKst~a~~La~~   22 (194)
T cd01428           3 LLLGPPGSGKGTQAERLAKK   22 (194)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999874

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=92.74  E-value=0.44  Score=43.53  Aligned_cols=71  Identities=20%  Similarity=0.174  Sum_probs=42.6

Q ss_pred             cccccCCcchHHHHHHHhcc-------ccc---ccC----CCceEEEE--eCCCCCHHHHHHHHHHhhcCCCceEEEEEe
Q 043781          126 DVRGMGGIGKTTLAQFAYND-------KDV---IEN----FDKRIWVC--VSDPFDEFRIAKAIIEGLEGSEKKFFLILD  189 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~-------~~~---~~~----F~~~~wv~--vs~~~~~~~~~~~i~~~~~~~~kr~LiVlD  189 (297)
                      -|.|..|+|||||++.+...       +++   .+.    +...-|+.  .+...+..++++..++.     ..=.||+.
T Consensus       152 lI~G~tGSGKTTll~aL~~~~~~~~~~~rivtIEd~~El~~~~~~~v~~~~~~~~~~~~ll~~aLR~-----~PD~IivG  226 (319)
T PRK13894        152 LVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGEIQCAAENYVQYHTSIDVNMTALLKTTLRM-----RPDRILVG  226 (319)
T ss_pred             EEECCCCCCHHHHHHHHHHhhhhcCCCceEEEEcCCCccccCCCCEEEEecCCCCCHHHHHHHHhcC-----CCCEEEEe
Confidence            46799999999999988753       110   011    11112332  34456677777666643     34458889


Q ss_pred             CCCCCCccCHHHHH
Q 043781          190 DVWTDDYSKWEPFH  203 (297)
Q Consensus       190 dv~~~~~~~w~~l~  203 (297)
                      .+...  +.|+.|+
T Consensus       227 EiR~~--Ea~~~l~  238 (319)
T PRK13894        227 EVRGP--EALDLLM  238 (319)
T ss_pred             ccCCH--HHHHHHH
Confidence            99877  4665543

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.73  E-value=0.49  Score=44.43  Aligned_cols=22  Identities=27%  Similarity=0.200  Sum_probs=19.2

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.++|.+|+||||++..+..
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA~  263 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMAW  263 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHHH
Confidence            3567999999999999988876

>PRK00300 gmk guanylate kinase; Provisional

Probab=92.71  E-value=0.063  Score=45.37  Aligned_cols=21  Identities=29%  Similarity=0.379  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+...
T Consensus         8 i~i~G~sGsGKstl~~~l~~~   28 (205)
T PRK00300          8 IVLSGPSGAGKSTLVKALLER   28 (205)
T ss_pred             EEEECCCCCCHHHHHHHHHhh
Confidence            468999999999999999884

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=92.69  E-value=0.46  Score=40.78  Aligned_cols=21  Identities=19%  Similarity=0.165  Sum_probs=18.0

Q ss_pred             ccccccccCCcchHHHHHHHh
Q 043781          123 NVSDVRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~  143 (297)
                      ....|.|+.|.||||+.+.+.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~   51 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVA   51 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            345788999999999999985

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

>PRK13409 putative ATPase RIL; Provisional

Probab=92.68  E-value=0.72  Score=45.81  Aligned_cols=23  Identities=35%  Similarity=0.553  Sum_probs=19.9

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...+|+|..|+|||||.+.+..-
T Consensus       100 ev~gLvG~NGaGKSTLlkiL~G~  122 (590)
T PRK13409        100 KVTGILGPNGIGKTTAVKILSGE  122 (590)
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            34579999999999999999884

>KOG0056 consensus Heavy metal exporter HMT1, ABC superfamily [Inorganic ion transport and metabolism]

Probab=92.66  E-value=1  Score=43.22  Aligned_cols=41  Identities=12%  Similarity=0.259  Sum_probs=28.5

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEec
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      ...-+|.||..-+. |...=.+|...+.+..         .+.+.|+|.-|
T Consensus       691 K~P~iIlLDEATSALDT~tER~IQaaL~rlc---------a~RTtIVvAHR  732 (790)
T KOG0056|consen  691 KAPSIILLDEATSALDTNTERAIQAALARLC---------ANRTTIVVAHR  732 (790)
T ss_pred             cCCcEEEEcchhhhcCCccHHHHHHHHHHHh---------cCCceEEEeee
Confidence            67889999988654 2234456888887753         56667777766

>PRK07667 uridine kinase; Provisional

Probab=92.65  E-value=0.064  Score=45.17  Aligned_cols=22  Identities=23%  Similarity=0.370  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|-|.+|+||||||+.+...
T Consensus        19 iIgI~G~~gsGKStla~~L~~~   40 (193)
T PRK07667         19 ILGIDGLSRSGKTTFVANLKEN   40 (193)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4678899999999999999873

>COG3899 Predicted ATPase [General function prediction only]

Probab=92.64  E-value=0.7  Score=47.86  Aligned_cols=22  Identities=36%  Similarity=0.419  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.+.|..|+|||.|++.|...
T Consensus        26 ~~lv~G~sGIGKsalv~ev~~~   47 (849)
T COG3899          26 VVLVAGESGIGKSALVNEVHKP   47 (849)
T ss_pred             EEEEeecCCCcHHHHHHHHHHH
Confidence            4568899999999999999983

>TIGR02528 EutP ethanolamine utilization protein, EutP

Probab=92.64  E-value=0.21  Score=39.17  Aligned_cols=22  Identities=36%  Similarity=0.327  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +.++|.+|+|||+|...+.+..
T Consensus         3 v~liG~~~vGKSsL~~~l~~~~   24 (142)
T TIGR02528         3 IMFIGSVGCGKTTLTQALQGEE   24 (142)
T ss_pred             EEEECCCCCCHHHHHHHHcCCc
Confidence            4589999999999999987753

This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site.

>cd00880 Era_like Era (E

Probab=92.64  E-value=0.071  Score=41.79  Aligned_cols=19  Identities=21%  Similarity=0.284  Sum_probs=17.3

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      |+|.+|+|||||++.+++.
T Consensus         1 i~G~~gsGKstl~~~l~~~   19 (163)
T cd00880           1 LFGRTNAGKSSLLNALLGQ   19 (163)
T ss_pred             CcCCCCCCHHHHHHHHhCc
Confidence            5799999999999999875

coli Ras-like protein)-like. This family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngG), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the se

>PRK13948 shikimate kinase; Provisional

Probab=92.60  E-value=0.067  Score=44.72  Aligned_cols=22  Identities=18%  Similarity=0.194  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-++||.|+||||+++.+.+.
T Consensus        12 ~I~LiG~~GsGKSTvg~~La~~   33 (182)
T PRK13948         12 WVALAGFMGTGKSRIGWELSRA   33 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3458899999999999999883

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=92.60  E-value=0.51  Score=46.69  Aligned_cols=21  Identities=29%  Similarity=0.284  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+..-
T Consensus       379 vaIvG~SGsGKSTL~~lL~g~  399 (588)
T PRK11174        379 IALVGPSGAGKTSLLNALLGF  399 (588)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            368999999999999999873

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=92.60  E-value=0.067  Score=44.18  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|+.|+|||||++.+.+.
T Consensus         7 I~liG~~GaGKStl~~~La~~   27 (172)
T PRK05057          7 IFLVGPMGAGKSTIGRQLAQQ   27 (172)
T ss_pred             EEEECCCCcCHHHHHHHHHHH
Confidence            568899999999999999874

>TIGR01069 mutS2 MutS2 family protein

Probab=92.57  E-value=8.2  Score=39.71  Aligned_cols=22  Identities=23%  Similarity=-0.001  Sum_probs=18.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|.|+.|.|||||.+.+...
T Consensus       324 ~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       324 VLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             EEEEECCCCCCchHHHHHHHHH
Confidence            4568899999999999988653

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.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=92.56  E-value=0.069  Score=43.74  Aligned_cols=21  Identities=29%  Similarity=0.230  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|+|++|+||||+++.+.+.
T Consensus         5 i~~~G~~GsGKst~~~~la~~   25 (171)
T PRK03731          5 LFLVGARGCGKTTVGMALAQA   25 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999983

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=92.56  E-value=0.43  Score=46.58  Aligned_cols=21  Identities=29%  Similarity=0.365  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+..-
T Consensus       351 ~~ivG~sGsGKSTL~~ll~g~  371 (529)
T TIGR02857       351 VALVGPSGAGKSTLLNLLLGF  371 (529)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            368999999999999999773

Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=92.55  E-value=0.066  Score=46.90  Aligned_cols=20  Identities=25%  Similarity=0.463  Sum_probs=17.5

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|++|+||||+|+.+...
T Consensus         3 vl~G~pGSGKST~a~~La~~   22 (249)
T TIGR03574         3 ILTGLPGVGKSTFSKELAKK   22 (249)
T ss_pred             EEEcCCCCCHHHHHHHHHHH
Confidence            36799999999999998873

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=92.52  E-value=0.21  Score=46.00  Aligned_cols=19  Identities=32%  Similarity=0.286  Sum_probs=16.9

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -|.|+.|+||||+.+.+.+
T Consensus       126 li~G~tGSGKTT~l~al~~  144 (343)
T TIGR01420       126 LVTGPTGSGKSTTLASMID  144 (343)
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4679999999999998876

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PTZ00088 adenylate kinase 1; Provisional

Probab=92.51  E-value=0.069  Score=46.36  Aligned_cols=21  Identities=29%  Similarity=0.389  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|++|+||||+|+.+.+.
T Consensus         9 Ivl~G~PGsGK~T~a~~La~~   29 (229)
T PTZ00088          9 IVLFGAPGVGKGTFAEILSKK   29 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            557899999999999999874

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

Probab=92.50  E-value=0.17  Score=47.67  Aligned_cols=64  Identities=19%  Similarity=0.212  Sum_probs=37.8

Q ss_pred             ccccCCcchHHHHHHHhcccccccCC-CceEEEEeCCCCCH-HHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENF-DKRIWVCVSDPFDE-FRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~-~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|++|.|||.|++.|+-  +....| +..+.--.+...+. +.+.+.++.-... .+..+|++|++..
T Consensus       191 LfGPpgtGKtmL~~aiAs--E~~atff~iSassLtsK~~Ge~eK~vralf~vAr~-~qPsvifidEids  256 (428)
T KOG0740|consen  191 LFGPPGTGKTMLAKAIAT--ESGATFFNISASSLTSKYVGESEKLVRALFKVARS-LQPSVIFIDEIDS  256 (428)
T ss_pred             eecCCCCchHHHHHHHHh--hhcceEeeccHHHhhhhccChHHHHHHHHHHHHHh-cCCeEEEechhHH
Confidence            779999999999999998  454443 22221111222222 2333333322222 5889999999975

>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]

Probab=92.49  E-value=0.16  Score=46.77  Aligned_cols=69  Identities=19%  Similarity=0.206  Sum_probs=50.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHhhcCC-----------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEGLEGS-----------------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~-----------------------  180 (297)
                      ++++|=+|+|||.|.+.+-++ -.+.|=...+|.-+.... .-.++..++.++--.+                       
T Consensus       150 iGLFGGAGVGKTVl~~ELI~N-ia~~h~g~SVFaGvGERtREGndLy~Em~es~vl~ktalv~gQMNEpPGaR~RValtG  228 (468)
T COG0055         150 IGLFGGAGVGKTVLIQELINN-IAKEHGGYSVFAGVGERTREGNDLYHEMKESGVLDKTALVFGQMNEPPGARMRVALTG  228 (468)
T ss_pred             eeeeccCCccceeeHHHHHHH-HHHHcCCeEEEEeccccccchHHHHHHHHhcCCCCceeEEEeecCCCCcceeeehhhh
Confidence            478899999999999888885 223455567777766554 3466777776664332                       


Q ss_pred             -----------CceEEEEEeCCCCC
Q 043781          181 -----------EKKFFLILDDVWTD  194 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~~  194 (297)
                                 ++..|+.+||+..-
T Consensus       229 lT~AEyfRD~~gqdVLlFIDNIfRf  253 (468)
T COG0055         229 LTMAEYFRDEEGQDVLLFIDNIFRF  253 (468)
T ss_pred             hhHHHHhhcccCCeEEEEehhhhHH
Confidence                       89999999999763

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=92.49  E-value=0.14  Score=51.38  Aligned_cols=63  Identities=19%  Similarity=0.195  Sum_probs=37.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC------CCCHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD------PFDEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~------~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||++|+.+.+.  ..-+|   +.+..+.      ... ...++.++..... ....+|+||+++..
T Consensus       188 ill~G~~G~GKt~~~~~~a~~--~~~~f---~~is~~~~~~~~~g~~-~~~~~~~f~~a~~-~~P~IifIDEiD~l  256 (644)
T PRK10733        188 VLMVGPPGTGKTLLAKAIAGE--AKVPF---FTISGSDFVEMFVGVG-ASRVRDMFEQAKK-AAPCIIFIDEIDAV  256 (644)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--cCCCE---EEEehHHhHHhhhccc-HHHHHHHHHHHHh-cCCcEEEehhHhhh
Confidence            558999999999999999883  33333   2222211      111 1223334444322 46789999999653

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=92.49  E-value=0.076  Score=42.14  Aligned_cols=20  Identities=30%  Similarity=0.506  Sum_probs=18.1

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|+|+.|+|||||++.+...
T Consensus         3 ~i~GpsGsGKstl~~~L~~~   22 (137)
T cd00071           3 VLSGPSGVGKSTLLKRLLEE   22 (137)
T ss_pred             EEECCCCCCHHHHHHHHHhc
Confidence            57899999999999999983

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=92.48  E-value=0.47  Score=46.98  Aligned_cols=21  Identities=29%  Similarity=0.365  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|.|||||++.+..-
T Consensus       364 v~IvG~sGsGKSTLl~lL~gl  384 (588)
T PRK13657        364 VAIVGPTGAGKSTLINLLQRV  384 (588)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999863

>PRK11823 DNA repair protein RadA; Provisional

Probab=92.47  E-value=0.42  Score=45.77  Aligned_cols=34  Identities=26%  Similarity=0.209  Sum_probs=22.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS  161 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs  161 (297)
                      -|.|.+|+|||||+.++..+..  .+-...+|++..
T Consensus        84 lI~G~pG~GKTtL~lq~a~~~a--~~g~~vlYvs~E  117 (446)
T PRK11823         84 LIGGDPGIGKSTLLLQVAARLA--AAGGKVLYVSGE  117 (446)
T ss_pred             EEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEEcc
Confidence            4779999999999988877422  112245566543

>cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily

Probab=92.46  E-value=0.52  Score=38.28  Aligned_cols=21  Identities=29%  Similarity=0.183  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||+|...+...
T Consensus         5 i~vvG~~~vGKTsli~~~~~~   25 (170)
T cd04115           5 IIVIGDSNVGKTCLTYRFCAG   25 (170)
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            468899999999999988664

Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine

>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []

Probab=92.46  E-value=0.25  Score=40.42  Aligned_cols=53  Identities=28%  Similarity=0.351  Sum_probs=37.2

Q ss_pred             cccCCcchHHHHHHHhcccccccCCCceEEEE-----eCCCCCHHHHHHHHHHhhcCCCceEEEEEeC
Q 043781          128 RGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC-----VSDPFDEFRIAKAIIEGLEGSEKKFFLILDD  190 (297)
Q Consensus       128 ~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~-----vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDd  190 (297)
                      ++..|+||||++..+.+      -|..  |-+     ++.. ....+.+.+++.+.. ...-.++.|-
T Consensus         5 IAtiGCGKTTva~aL~~------LFg~--wgHvQnDnI~~k-~~~~f~~~~l~~L~~-~~~~vViaDR   62 (168)
T PF08303_consen    5 IATIGCGKTTVALALSN------LFGE--WGHVQNDNITGK-RKPKFIKAVLELLAK-DTHPVVIADR   62 (168)
T ss_pred             ecCCCcCHHHHHHHHHH------HcCC--CCccccCCCCCC-CHHHHHHHHHHHHhh-CCCCEEEEeC
Confidence            57789999999999888      3543  443     4444 678888888988843 2345555663

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]

Probab=92.45  E-value=0.073  Score=45.22  Aligned_cols=23  Identities=43%  Similarity=0.491  Sum_probs=19.9

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|++|+|||||+..+.++.
T Consensus         7 kivv~G~~g~GKTtl~~~l~~~~   29 (219)
T COG1100           7 KIVVLGDGGVGKTTLLNRLVGDE   29 (219)
T ss_pred             EEEEEcCCCccHHHHHHHHhcCc
Confidence            35688999999999999998863

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=92.44  E-value=0.99  Score=44.11  Aligned_cols=49  Identities=20%  Similarity=0.172  Sum_probs=32.2

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      .+.=+++||.=-|. |.+.-.-|...|..           -+| .+||.|++..-...||..
T Consensus       170 ~~pDlLLLDEPTNHLD~~~i~WLe~~L~~-----------~~g-tviiVSHDR~FLd~V~t~  219 (530)
T COG0488         170 EEPDLLLLDEPTNHLDLESIEWLEDYLKR-----------YPG-TVIVVSHDRYFLDNVATH  219 (530)
T ss_pred             cCCCEEEEcCCCcccCHHHHHHHHHHHHh-----------CCC-cEEEEeCCHHHHHHHhhh
Confidence            77779999976654 11222225555554           355 799999988888888753

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=92.44  E-value=0.17  Score=47.79  Aligned_cols=50  Identities=18%  Similarity=0.166  Sum_probs=30.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCC---CceEEEEeCC-CCCHHHHHHHHHHh
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENF---DKRIWVCVSD-PFDEFRIAKAIIEG  176 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F---~~~~wv~vs~-~~~~~~~~~~i~~~  176 (297)
                      +-++|++|+|||+||+.+...  +...|   +..-+..... ..+...+++.++..
T Consensus        50 ILLiGppG~GKT~lAraLA~~--l~~~fi~vdat~~~e~g~vG~dvE~i~r~l~e~  103 (441)
T TIGR00390        50 ILMIGPTGVGKTEIARRLAKL--ANAPFIKVEATKFTEVGYVGRDVESMVRDLTDA  103 (441)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCCeEEEeecceeecCCcccCCHHHHHHHHHHH
Confidence            458899999999999999983  44444   2222222111 22555665555444

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.

>PF01926 MMR_HSR1: 50S ribosome-binding GTPase; InterPro: IPR002917 Human HSR1, has been localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse

Probab=92.41  E-value=0.08  Score=40.28  Aligned_cols=21  Identities=24%  Similarity=0.309  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|++|+|||||...+.+.
T Consensus         2 V~iiG~~~~GKSTlin~l~~~   22 (116)
T PF01926_consen    2 VAIIGRPNVGKSTLINALTGK   22 (116)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            468999999999999999974

These proteins represent a new subfamily of GTP-binding proteins that has both prokaryote and eukaryote members [].; GO: 0005525 GTP binding, 0005622 intracellular; PDB: 2DWQ_B 2DBY_A 3CNN_A 3CNO_A 3CNL_A 3IBY_A 1PUI_B 1WXQ_A 1LNZ_A 3GEE_A ....

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=92.40  E-value=0.54  Score=46.61  Aligned_cols=21  Identities=33%  Similarity=0.381  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|.|||||++.+..-
T Consensus       364 ~~ivG~sGsGKSTL~~ll~g~  384 (585)
T TIGR01192       364 VAIVGPTGAGKTTLINLLQRV  384 (585)
T ss_pred             EEEECCCCCCHHHHHHHHccC
Confidence            368999999999999999763

This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=92.39  E-value=0.41  Score=46.87  Aligned_cols=78  Identities=18%  Similarity=0.128  Sum_probs=43.2

Q ss_pred             cccccCCcchHHHHHHHhcccc-cccCCCceEEEEeCCCCCHHHHHHHHH-Hhhc----C----------CCceEEEEEe
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD-VIENFDKRIWVCVSDPFDEFRIAKAII-EGLE----G----------SEKKFFLILD  189 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~-~~~~F~~~~wv~vs~~~~~~~~~~~i~-~~~~----~----------~~kr~LiVlD  189 (297)
                      -|+|..|+|||++|+.+++... -...|   +.|+.+.- .. ..+...+ -...    +          ....=.|+||
T Consensus       223 li~Ge~GtGK~~lA~~ih~~s~r~~~pf---v~i~c~~~-~~-~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ld  297 (534)
T TIGR01817       223 LLRGESGTGKELIAKAIHYLSPRAKRPF---VKVNCAAL-SE-TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLD  297 (534)
T ss_pred             EEECCCCccHHHHHHHHHHhCCCCCCCe---EEeecCCC-CH-HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEe
Confidence            4789999999999999998422 12223   33333322 11 2222221 1000    0          0223458899


Q ss_pred             CCCCCCccCHHHHHHHHhh
Q 043781          190 DVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       190 dv~~~~~~~w~~l~~~l~~  208 (297)
                      +|..-.......|...+..
T Consensus       298 ei~~L~~~~Q~~Ll~~l~~  316 (534)
T TIGR01817       298 EIGEISPAFQAKLLRVLQE  316 (534)
T ss_pred             chhhCCHHHHHHHHHHHhc
Confidence            9988765556666666643

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.

>PRK13946 shikimate kinase; Provisional

Probab=92.38  E-value=0.078  Score=44.22  Aligned_cols=22  Identities=23%  Similarity=0.246  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|++|+||||+++.+.+.
T Consensus        12 ~I~l~G~~GsGKsti~~~LA~~   33 (184)
T PRK13946         12 TVVLVGLMGAGKSTVGRRLATM   33 (184)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3568899999999999999983

>PRK06851 hypothetical protein; Provisional

Probab=92.38  E-value=2  Score=39.92  Aligned_cols=41  Identities=24%  Similarity=0.333  Sum_probs=30.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDE  166 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  166 (297)
                      .-|-|.+|+|||||++.++... .++.++.-++-|.+.+-++
T Consensus       217 ~~i~G~pG~GKstl~~~i~~~a-~~~G~~v~~~hC~~dPdsl  257 (367)
T PRK06851        217 YFLKGRPGTGKSTMLKKIAKAA-EERGFDVEVYHCGFDPDSL  257 (367)
T ss_pred             EEEeCCCCCcHHHHHHHHHHHH-HhCCCeEEEEeCCCCCCCc
Confidence            4567999999999999999852 3556777777776666443

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=92.35  E-value=0.29  Score=46.26  Aligned_cols=22  Identities=32%  Similarity=0.140  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...++|++|+||||++.++...
T Consensus       225 vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4568899999999999888763

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=92.33  E-value=0.45  Score=43.56  Aligned_cols=79  Identities=18%  Similarity=0.090  Sum_probs=42.5

Q ss_pred             cccccCCcchHHHHHHHhcccc-cccCCCceEEEEeCCCCCHHHHHHHHHHhhc----C----------CCceEEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD-VIENFDKRIWVCVSDPFDEFRIAKAIIEGLE----G----------SEKKFFLILDD  190 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~-~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~----~----------~~kr~LiVlDd  190 (297)
                      -|+|-.|+||+++|+.++.... -...|   +.|+.+.. +...+...++..-.    +          ....=.|+||+
T Consensus        33 lI~GE~GtGK~~lA~~iH~~s~r~~~pf---v~v~c~~~-~~~~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~~  108 (326)
T PRK11608         33 LIIGERGTGKELIASRLHYLSSRWQGPF---ISLNCAAL-NENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDE  108 (326)
T ss_pred             EEECCCCCcHHHHHHHHHHhCCccCCCe---EEEeCCCC-CHHHHHHHHccccccccCCcccccCCchhccCCCeEEeCC
Confidence            4789999999999999986311 11222   33433332 22222222211000    0          01223478999


Q ss_pred             CCCCCccCHHHHHHHHhh
Q 043781          191 VWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       191 v~~~~~~~w~~l~~~l~~  208 (297)
                      |..-.......|...+..
T Consensus       109 i~~L~~~~Q~~L~~~l~~  126 (326)
T PRK11608        109 LATAPMLVQEKLLRVIEY  126 (326)
T ss_pred             hhhCCHHHHHHHHHHHhc
Confidence            988765556666666644

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

Probab=92.31  E-value=0.21  Score=45.06  Aligned_cols=63  Identities=21%  Similarity=0.233  Sum_probs=43.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEE----eCCCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC----VSDPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~----vs~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ..|||++|.|||-||+.|+.  .+.-.|   +.+.    ++... ...++.++++..... ...+.|.+|++..
T Consensus       169 ~ll~GppGtGKTlla~~Vaa--~mg~nf---l~v~ss~lv~kyiGEsaRlIRemf~yA~~-~~pciifmdeiDA  236 (388)
T KOG0651|consen  169 LLLYGPPGTGKTLLARAVAA--TMGVNF---LKVVSSALVDKYIGESARLIRDMFRYARE-VIPCIIFMDEIDA  236 (388)
T ss_pred             eEEeCCCCCchhHHHHHHHH--hcCCce---EEeeHhhhhhhhcccHHHHHHHHHHHHhh-hCceEEeehhhhh
Confidence            36899999999999999998  455455   1222    12222 345677777766655 5679999999974

>PRK11650 ugpC glycerol-3-phosphate transporter ATP-binding subunit; Provisional

Probab=92.24  E-value=0.21  Score=46.28  Aligned_cols=21  Identities=29%  Similarity=0.306  Sum_probs=19.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+..-
T Consensus        33 ~~llG~sGsGKSTLLr~iaGl   53 (356)
T PRK11650         33 IVLVGPSGCGKSTLLRMVAGL   53 (356)
T ss_pred             EEEECCCCCcHHHHHHHHHCC
Confidence            468999999999999999984

>cd04139 RalA_RalB RalA/RalB subfamily

Probab=92.20  E-value=0.095  Score=41.91  Aligned_cols=22  Identities=36%  Similarity=0.502  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +.++|.+|+|||||+..+.+++
T Consensus         3 i~~~G~~~~GKTsl~~~l~~~~   24 (164)
T cd04139           3 VIVVGAGGVGKSALTLQFMYDE   24 (164)
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            4588999999999999988753

The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=92.19  E-value=0.58  Score=42.29  Aligned_cols=19  Identities=47%  Similarity=0.392  Sum_probs=16.8

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -|.|..|+||||+++.+.+
T Consensus       136 lI~G~tGSGKTTll~al~~  154 (299)
T TIGR02782       136 LVVGGTGSGKTTLANALLA  154 (299)
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            3779999999999998876

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.

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=92.17  E-value=0.084  Score=42.50  Aligned_cols=20  Identities=30%  Similarity=0.446  Sum_probs=17.6

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|+|.+|+||||||+.+...
T Consensus         3 ~i~G~~GsGKSTla~~L~~~   22 (149)
T cd02027           3 WLTGLSGSGKSTIARALEEK   22 (149)
T ss_pred             EEEcCCCCCHHHHHHHHHHH
Confidence            46799999999999998874

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]

Probab=92.16  E-value=2.8  Score=35.08  Aligned_cols=20  Identities=35%  Similarity=0.632  Sum_probs=18.0

Q ss_pred             ccccCCcchHHHHHHHhccc
Q 043781          127 VRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~  146 (297)
                      |.|+.|+||+||++.++.+.
T Consensus         9 lsgPSG~GKsTl~k~L~~~~   28 (191)
T COG0194           9 LSGPSGVGKSTLVKALLEDD   28 (191)
T ss_pred             EECCCCCCHHHHHHHHHhhc
Confidence            66999999999999999953

>PRK04328 hypothetical protein; Provisional

Probab=92.14  E-value=0.23  Score=43.61  Aligned_cols=60  Identities=17%  Similarity=0.233  Sum_probs=36.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-----CceEEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-----EKKFFLILDD  190 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----~kr~LiVlDd  190 (297)
                      -|.|.+|+|||+|+.++... ..++ -...+|++...  +..++. ..+++++-.     .+..|.++|-
T Consensus        27 li~G~pGsGKT~l~~~fl~~-~~~~-ge~~lyis~ee--~~~~i~-~~~~~~g~d~~~~~~~~~l~iid~   91 (249)
T PRK04328         27 LLSGGPGTGKSIFSQQFLWN-GLQM-GEPGVYVALEE--HPVQVR-RNMRQFGWDVRKYEEEGKFAIVDA   91 (249)
T ss_pred             EEEcCCCCCHHHHHHHHHHH-HHhc-CCcEEEEEeeC--CHHHHH-HHHHHcCCCHHHHhhcCCEEEEec
Confidence            37799999999999776553 2222 34567887655  333433 344555543     3334666663

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=92.14  E-value=0.46  Score=48.82  Aligned_cols=80  Identities=16%  Similarity=0.141  Sum_probs=47.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC------------CCHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP------------FDEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~------------~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      +.|+.|+|||-||+.+..  .+-+..+.-+-+..|.-            +--..-...+.+.+.. .--.+|.||||...
T Consensus       596 flGpdgvGKt~lAkaLA~--~~Fgse~~~IriDmse~~evskligsp~gyvG~e~gg~Lteavrr-rP~sVVLfdeIEkA  672 (898)
T KOG1051|consen  596 FLGPDGVGKTELAKALAE--YVFGSEENFIRLDMSEFQEVSKLIGSPPGYVGKEEGGQLTEAVKR-RPYSVVLFEEIEKA  672 (898)
T ss_pred             EECCCchhHHHHHHHHHH--HHcCCccceEEechhhhhhhhhccCCCcccccchhHHHHHHHHhc-CCceEEEEechhhc
Confidence            449999999999988887  34333333333433320            1111222233333332 44567788999888


Q ss_pred             CccCHHHHHHHHhhh
Q 043781          195 DYSKWEPFHNCLMRV  209 (297)
Q Consensus       195 ~~~~w~~l~~~l~~~  209 (297)
                      +......+...+.++
T Consensus       673 h~~v~n~llq~lD~G  687 (898)
T KOG1051|consen  673 HPDVLNILLQLLDRG  687 (898)
T ss_pred             CHHHHHHHHHHHhcC
Confidence            766666677777665

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

Probab=92.11  E-value=0.083  Score=51.55  Aligned_cols=59  Identities=24%  Similarity=0.373  Sum_probs=39.0

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      +||++|+|||-||+.|.|  +..-+|     ++|-.+-       .-++..++++..... .-.++|.+|.+..
T Consensus       550 L~GPPGCGKTLlAKAVAN--Eag~NF-----isVKGPELlNkYVGESErAVR~vFqRAR~-saPCVIFFDEiDa  615 (802)
T KOG0733|consen  550 LCGPPGCGKTLLAKAVAN--EAGANF-----ISVKGPELLNKYVGESERAVRQVFQRARA-SAPCVIFFDEIDA  615 (802)
T ss_pred             EeCCCCccHHHHHHHHhh--hccCce-----EeecCHHHHHHHhhhHHHHHHHHHHHhhc-CCCeEEEecchhh
Confidence            789999999999999999  455556     3322210       112333444443333 6899999999975

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=92.11  E-value=0.48  Score=46.14  Aligned_cols=99  Identities=11%  Similarity=0.053  Sum_probs=51.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcC----C----------CceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG----S----------EKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~----~----------~kr~LiVlDdv  191 (297)
                      -|+|-.|+||+++|+.+++...  ..-...+.|+.+.-.. ..+-..++-...+    .          ...=.|+||+|
T Consensus       214 lI~Ge~GtGK~~~A~~ih~~s~--r~~~p~v~v~c~~~~~-~~~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI  290 (509)
T PRK05022        214 LILGETGVGKELVARAIHAASP--RADKPLVYLNCAALPE-SLAESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEI  290 (509)
T ss_pred             EEECCCCccHHHHHHHHHHhCC--cCCCCeEEEEcccCCh-HHHHHHhcCccccccCCCcccCCcchhhcCCCEEEecCh
Confidence            4789999999999999998422  1111234444333221 1111122211100    0          11223789999


Q ss_pred             CCCCccCHHHHHHHHhhhhhhhceeeec-----CCCCeEEEEecc
Q 043781          192 WTDDYSKWEPFHNCLMRVLQEFAAIEVD-----GDENPLSLTSTC  231 (297)
Q Consensus       192 ~~~~~~~w~~l~~~l~~~~~~~~~~~~~-----~~gs~iiiTTr~  231 (297)
                      ..-..+....|...+...    .....+     ....|||.||..
T Consensus       291 ~~L~~~~Q~~Ll~~l~~~----~~~~~g~~~~~~~~~RiI~~t~~  331 (509)
T PRK05022        291 GELPLALQAKLLRVLQYG----EIQRVGSDRSLRVDVRVIAATNR  331 (509)
T ss_pred             hhCCHHHHHHHHHHHhcC----CEeeCCCCcceecceEEEEecCC
Confidence            887655555666655432    001111     124588888853

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

Probab=92.07  E-value=0.24  Score=44.44  Aligned_cols=59  Identities=22%  Similarity=0.322  Sum_probs=40.2

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|++|.||+.||+.|.-.  ....|     ++||..-       .-+.+.+++++-... +|..+|.+|.|..
T Consensus       171 LyGPPGTGKSYLAKAVATE--AnSTF-----FSvSSSDLvSKWmGESEkLVknLFemARe-~kPSIIFiDEiDs  236 (439)
T KOG0739|consen  171 LYGPPGTGKSYLAKAVATE--ANSTF-----FSVSSSDLVSKWMGESEKLVKNLFEMARE-NKPSIIFIDEIDS  236 (439)
T ss_pred             EeCCCCCcHHHHHHHHHhh--cCCce-----EEeehHHHHHHHhccHHHHHHHHHHHHHh-cCCcEEEeehhhh
Confidence            6799999999999999983  33333     3343321       123455555544443 8999999999974

>PRK02496 adk adenylate kinase; Provisional

Probab=92.04  E-value=0.087  Score=43.78  Aligned_cols=20  Identities=30%  Similarity=0.144  Sum_probs=17.5

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .-|+|++|+||||+|+.+..
T Consensus         4 i~i~G~pGsGKst~a~~la~   23 (184)
T PRK02496          4 LIFLGPPGAGKGTQAVVLAE   23 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34789999999999999876

>PRK03846 adenylylsulfate kinase; Provisional

Probab=92.03  E-value=0.084  Score=44.56  Aligned_cols=22  Identities=32%  Similarity=0.335  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|++|+||||||+.+...
T Consensus        26 ~i~i~G~~GsGKSTla~~l~~~   47 (198)
T PRK03846         26 VLWFTGLSGSGKSTVAGALEEA   47 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4578899999999999999873

>KOG0059 consensus Lipid exporter ABCA1 and related proteins, ABC superfamily [Lipid transport and metabolism; General function prediction only]

Probab=92.03  E-value=0.44  Score=49.60  Aligned_cols=61  Identities=16%  Similarity=0.176  Sum_probs=43.7

Q ss_pred             CceEEEEEeCCCCC-C----ccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCCCccccCCccc
Q 043781          181 EKKFFLILDDVWTD-D----YSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFD  254 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~----~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~~~~~~l~~l~  254 (297)
                      +..-+|.||.--.. |    ...|+-+.....             +|..||+||+..+-++.+|.++++...-.|..+.
T Consensus       715 g~p~vi~LDEPstGmDP~arr~lW~ii~~~~k-------------~g~aiiLTSHsMeE~EaLCtR~aImv~G~l~ciG  780 (885)
T KOG0059|consen  715 GDPSVILLDEPSTGLDPKARRHLWDIIARLRK-------------NGKAIILTSHSMEEAEALCTRTAIMVIGQLRCIG  780 (885)
T ss_pred             cCCCEEEecCCCCCCCHHHHHHHHHHHHHHHh-------------cCCEEEEEcCCHHHHHHHhhhhheeecCeeEEec
Confidence            88899999995442 2    246777766553             3338999999999999999988776444555543

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=92.02  E-value=1.3  Score=38.94  Aligned_cols=47  Identities=17%  Similarity=0.148  Sum_probs=29.1

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIE  175 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  175 (297)
                      -|.|.+|+||||++.++..+. ...+=..++|++...  +..++...+..
T Consensus        34 ~i~g~~G~GKT~l~~~~~~~~-~~~~g~~vl~iS~E~--~~~~~~~r~~~   80 (271)
T cd01122          34 ILTAGTGVGKTTFLREYALDL-ITQHGVRVGTISLEE--PVVRTARRLLG   80 (271)
T ss_pred             EEEcCCCCCHHHHHHHHHHHH-HHhcCceEEEEEccc--CHHHHHHHHHH
Confidence            467999999999998877642 222123566776544  33444444433

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=92.01  E-value=0.084  Score=45.68  Aligned_cols=23  Identities=35%  Similarity=0.498  Sum_probs=19.7

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..++|.|..|+|||||++.+..-
T Consensus        34 ~iigi~G~~GsGKTTl~~~L~~~   56 (229)
T PRK09270         34 TIVGIAGPPGAGKSTLAEFLEAL   56 (229)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            45678999999999999988873

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=92.00  E-value=0.33  Score=46.12  Aligned_cols=21  Identities=24%  Similarity=0.346  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+...
T Consensus       160 ~~i~G~sG~GKStLl~~i~~~  180 (434)
T PRK08472        160 LGIFAGSGVGKSTLMGMIVKG  180 (434)
T ss_pred             EEEECCCCCCHHHHHHHHhhc
Confidence            368899999999999999864

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=92.00  E-value=0.39  Score=49.02  Aligned_cols=21  Identities=33%  Similarity=0.480  Sum_probs=18.2

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|.|.+|.||||+++.+..
T Consensus       370 ~~il~G~aGTGKTtll~~i~~  390 (744)
T TIGR02768       370 IAVVVGRAGTGKSTMLKAARE  390 (744)
T ss_pred             EEEEEecCCCCHHHHHHHHHH
Confidence            346889999999999999876

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.

>CHL00060 atpB ATP synthase CF1 beta subunit

Probab=91.98  E-value=0.31  Score=46.87  Aligned_cols=50  Identities=18%  Similarity=0.145  Sum_probs=32.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIE  175 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~  175 (297)
                      .+|+|-.|+|||+|+..+..+. .+.+=+..+++-+...- .+.++...++.
T Consensus       164 ~gIfgg~GvGKs~L~~~~~~~~-~~~~~dv~V~~lIGERgrEv~efi~~~~~  214 (494)
T CHL00060        164 IGLFGGAGVGKTVLIMELINNI-AKAHGGVSVFGGVGERTREGNDLYMEMKE  214 (494)
T ss_pred             EeeecCCCCChhHHHHHHHHHH-HHhcCCeEEEEEeccCchHHHHHHHHHHh
Confidence            3689999999999998777641 11112566676665543 34556665555

>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems

Probab=91.98  E-value=0.09  Score=41.17  Aligned_cols=22  Identities=27%  Similarity=0.321  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+...
T Consensus        13 ~~~i~G~nGsGKStLl~~l~g~   34 (137)
T PF00005_consen   13 IVAIVGPNGSGKSTLLKALAGL   34 (137)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTS
T ss_pred             EEEEEccCCCccccceeeeccc
Confidence            3478999999999999999983

ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....

>PRK14531 adenylate kinase; Provisional

Probab=91.97  E-value=0.09  Score=43.80  Aligned_cols=21  Identities=29%  Similarity=0.105  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|++|+||||+++.+...
T Consensus         5 i~i~G~pGsGKsT~~~~la~~   25 (183)
T PRK14531          5 LLFLGPPGAGKGTQAARLCAA   25 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999874

>PRK06904 replicative DNA helicase; Validated

Probab=91.97  E-value=2.2  Score=41.23  Aligned_cols=49  Identities=18%  Similarity=0.154  Sum_probs=31.8

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE  178 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~  178 (297)
                      |-|.+|+|||++|..+..+...+... .++++  |-..+..++...++.+..
T Consensus       226 IaarPg~GKTafalnia~~~a~~~g~-~Vl~f--SlEMs~~ql~~Rlla~~s  274 (472)
T PRK06904        226 VAARPSMGKTTFAMNLCENAAMASEK-PVLVF--SLEMPAEQIMMRMLASLS  274 (472)
T ss_pred             EEeCCCCChHHHHHHHHHHHHHhcCC-eEEEE--eccCCHHHHHHHHHHhhC
Confidence            44899999999998777653222222 34444  445677777777776654

>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional

Probab=91.93  E-value=0.23  Score=46.45  Aligned_cols=21  Identities=29%  Similarity=0.327  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+..-
T Consensus        48 ~~llGpsGsGKSTLLr~IaGl   68 (377)
T PRK11607         48 FALLGASGCGKSTLLRMLAGF   68 (377)
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            468899999999999999974

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=91.91  E-value=1.4  Score=38.41  Aligned_cols=22  Identities=27%  Similarity=0.421  Sum_probs=19.9

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +..+|+|..|.|||||.+.+..
T Consensus        54 e~vGiiG~NGaGKSTLlkliaG   75 (249)
T COG1134          54 ERVGIIGHNGAGKSTLLKLIAG   75 (249)
T ss_pred             CEEEEECCCCCcHHHHHHHHhC
Confidence            3468999999999999999998

>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=91.83  E-value=0.15  Score=42.09  Aligned_cols=19  Identities=37%  Similarity=0.354  Sum_probs=16.2

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      |.|.+|+|||+|+..+...
T Consensus         4 i~G~~G~GKT~l~~~~~~~   22 (187)
T cd01124           4 LSGGPGTGKTTFALQFLYA   22 (187)
T ss_pred             EEcCCCCCHHHHHHHHHHH
Confidence            6799999999999877653

A related protein is found in archaea.

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=91.83  E-value=0.3  Score=47.64  Aligned_cols=47  Identities=21%  Similarity=0.251  Sum_probs=31.5

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLT  239 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~  239 (297)
                      .+.-|+|||.=-|. |.+..+.|...|..            -.+.||+.|++......++
T Consensus       456 ~~pNvLiLDEPTNhLDi~s~~aLe~aL~~------------f~Gtvl~VSHDr~Fl~~va  503 (530)
T COG0488         456 QPPNLLLLDEPTNHLDIESLEALEEALLD------------FEGTVLLVSHDRYFLDRVA  503 (530)
T ss_pred             cCCCEEEEcCCCccCCHHHHHHHHHHHHh------------CCCeEEEEeCCHHHHHhhc
Confidence            88899999987665 33445556666654            3355888888666555554

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=91.81  E-value=0.61  Score=42.76  Aligned_cols=78  Identities=14%  Similarity=0.056  Sum_probs=42.3

Q ss_pred             cccccCCcchHHHHHHHhcccc-cccCCCceEEEEeCCCCCHHHHHHH-HHHhh----cC----------CCceEEEEEe
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD-VIENFDKRIWVCVSDPFDEFRIAKA-IIEGL----EG----------SEKKFFLILD  189 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~-~~~~F~~~~wv~vs~~~~~~~~~~~-i~~~~----~~----------~~kr~LiVlD  189 (297)
                      -|+|-.|+||+++|+.+++... -...|   +-|+.+.. . ...+.. ++-..    .+          ....=.|+||
T Consensus        26 LI~GE~GtGK~~lAr~iH~~s~r~~~pf---v~vnc~~~-~-~~~l~~~lfG~~~g~~~ga~~~~~G~~~~a~gGtL~Ld  100 (329)
T TIGR02974        26 LIIGERGTGKELIAARLHYLSKRWQGPL---VKLNCAAL-S-ENLLDSELFGHEAGAFTGAQKRHQGRFERADGGTLFLD  100 (329)
T ss_pred             EEECCCCChHHHHHHHHHHhcCccCCCe---EEEeCCCC-C-hHHHHHHHhccccccccCcccccCCchhhCCCCEEEeC
Confidence            4789999999999999987422 12233   33333321 1 122222 21100    00          0234458999


Q ss_pred             CCCCCCccCHHHHHHHHhh
Q 043781          190 DVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       190 dv~~~~~~~w~~l~~~l~~  208 (297)
                      +|.....+....|...+..
T Consensus       101 ei~~L~~~~Q~~Ll~~l~~  119 (329)
T TIGR02974       101 ELATASLLVQEKLLRVIEY  119 (329)
T ss_pred             ChHhCCHHHHHHHHHHHHc
Confidence            9987754455556555543

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

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=91.81  E-value=0.094  Score=43.17  Aligned_cols=19  Identities=32%  Similarity=0.571  Sum_probs=16.9

Q ss_pred             ccccccCCcchHHHHHHHh
Q 043781          125 SDVRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~  143 (297)
                      +.|.|.||+||||+++.+.
T Consensus         3 I~ITGTPGvGKTT~~~~L~   21 (180)
T COG1936           3 IAITGTPGVGKTTVCKLLR   21 (180)
T ss_pred             EEEeCCCCCchHHHHHHHH
Confidence            4578999999999999887

>cd00882 Ras_like_GTPase Ras-like GTPase superfamily

Probab=91.81  E-value=0.11  Score=40.18  Aligned_cols=21  Identities=33%  Similarity=0.401  Sum_probs=18.1

Q ss_pred             ccccCCcchHHHHHHHhcccc
Q 043781          127 VRGMGGIGKTTLAQFAYNDKD  147 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~  147 (297)
                      |+|.+|+|||||++.+.....
T Consensus         1 iiG~~~~GKStl~~~l~~~~~   21 (157)
T cd00882           1 VVGDSGVGKTSLLNRLLGGEF   21 (157)
T ss_pred             CCCcCCCcHHHHHHHHHhCCc
Confidence            589999999999999987543

The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulate initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Memb

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=91.81  E-value=0.16  Score=43.30  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+..-
T Consensus        31 ~~~i~G~nGsGKSTLl~~l~Gl   52 (216)
T TIGR00960        31 MVFLVGHSGAGKSTFLKLILGI   52 (216)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999884

>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE)

Probab=91.81  E-value=0.16  Score=43.34  Aligned_cols=22  Identities=27%  Similarity=0.286  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+..-
T Consensus        32 ~~~l~G~nGsGKSTLl~~i~Gl   53 (218)
T cd03255          32 FVAIVGPSGSGKSTLLNILGGL   53 (218)
T ss_pred             EEEEEcCCCCCHHHHHHHHhCC
Confidence            3578999999999999999874

They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport. The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=91.79  E-value=0.16  Score=43.13  Aligned_cols=22  Identities=36%  Similarity=0.505  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+..-
T Consensus        30 ~~~l~G~nGsGKSTLl~~i~Gl   51 (214)
T TIGR02673        30 FLFLTGPSGAGKTTLLKLLYGA   51 (214)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999874

This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein.

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=91.78  E-value=0.27  Score=45.89  Aligned_cols=33  Identities=27%  Similarity=0.265  Sum_probs=22.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEe
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV  160 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v  160 (297)
                      -|.|.+|+|||||+.++...  ....-...+|++.
T Consensus        86 LI~G~pG~GKStLllq~a~~--~a~~g~~VlYvs~  118 (372)
T cd01121          86 LIGGDPGIGKSTLLLQVAAR--LAKRGGKVLYVSG  118 (372)
T ss_pred             EEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEEC
Confidence            46799999999999888763  2222234556654

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.

>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]

Probab=91.76  E-value=0.26  Score=42.15  Aligned_cols=46  Identities=20%  Similarity=0.165  Sum_probs=30.1

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAII  174 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  174 (297)
                      |=|+.|+||||+++.++.  ..+.+.-.++|..-+....+.+..++++
T Consensus         8 iEGiDGaGKTT~~~~L~~--~l~~~g~~v~~trEP~~~~ige~iR~~l   53 (208)
T COG0125           8 IEGIDGAGKTTQAELLKE--RLEERGIKVVLTREPGGTPIGEKIRELL   53 (208)
T ss_pred             EECCCCCCHHHHHHHHHH--HHHHcCCeEEEEeCCCCChHHHHHHHHH
Confidence            349999999999999999  4555443555554444444455555544

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=91.76  E-value=0.45  Score=44.96  Aligned_cols=72  Identities=17%  Similarity=0.077  Sum_probs=44.3

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-CceEEEEEeCCCCCCccCHHHHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-EKKFFLILDDVWTDDYSKWEPFHNC  205 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-~kr~LiVlDdv~~~~~~~w~~l~~~  205 (297)
                      ++|+.|+|||+||..+.....+...          ...++..++.++....-+. .+-=|||||++-....+.-+++...
T Consensus       214 ~lGp~GTGKThla~~l~~~~a~~sG----------~f~T~a~Lf~~L~~~~lg~v~~~DlLI~DEvgylp~~~~~~~v~i  283 (449)
T TIGR02688       214 ELGPKGTGKSYIYNNLSPYVILISG----------GTITVAKLFYNISTRQIGLVGRWDVVAFDEVATLKFAKPKELIGI  283 (449)
T ss_pred             EECCCCCCHHHHHHHHhHHHHHHcC----------CcCcHHHHHHHHHHHHHhhhccCCEEEEEcCCCCcCCchHHHHHH
Confidence            4599999999999987764112111          2346666666665533222 6778999999988422333344444


Q ss_pred             Hhh
Q 043781          206 LMR  208 (297)
Q Consensus       206 l~~  208 (297)
                      +++
T Consensus       284 mK~  286 (449)
T TIGR02688       284 LKN  286 (449)
T ss_pred             HHH
Confidence            443

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.

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=91.74  E-value=0.095  Score=44.89  Aligned_cols=23  Identities=30%  Similarity=0.359  Sum_probs=19.9

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -.++|-|.+|+||||+|+.++..
T Consensus         9 iiIgIaG~SgSGKTTva~~l~~~   31 (218)
T COG0572           9 IIIGIAGGSGSGKTTVAKELSEQ   31 (218)
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHH
Confidence            34678899999999999999983

>PF13245 AAA_19: Part of AAA domain

Probab=91.70  E-value=0.21  Score=35.32  Aligned_cols=18  Identities=50%  Similarity=0.541  Sum_probs=13.3

Q ss_pred             ccccCCcchH-HHHHHHhc
Q 043781          127 VRGMGGIGKT-TLAQFAYN  144 (297)
Q Consensus       127 i~G~~G~GKT-tLa~~v~~  144 (297)
                      |.|.+|.||| |++..+.+
T Consensus        15 v~g~pGtGKT~~~~~~i~~   33 (76)
T PF13245_consen   15 VQGPPGTGKTTTLAARIAE   33 (76)
T ss_pred             EECCCCCCHHHHHHHHHHH
Confidence            4799999999 45555554

>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways

Probab=91.70  E-value=0.11  Score=41.67  Aligned_cols=22  Identities=41%  Similarity=0.415  Sum_probs=19.2

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +-++|..|+|||||++.+...+
T Consensus         4 imliG~~g~GKTTL~q~L~~~~   25 (143)
T PF10662_consen    4 IMLIGPSGSGKTTLAQALNGEE   25 (143)
T ss_pred             EEEECCCCCCHHHHHHHHcCCC
Confidence            4578999999999999998864

Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=91.68  E-value=0.75  Score=37.91  Aligned_cols=21  Identities=24%  Similarity=0.151  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|.|.+|+||||+|..+...
T Consensus         4 ili~G~~~sGKS~~a~~l~~~   24 (170)
T PRK05800          4 ILVTGGARSGKSRFAERLAAQ   24 (170)
T ss_pred             EEEECCCCccHHHHHHHHHHH
Confidence            357899999999999988763

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=91.65  E-value=0.095  Score=47.12  Aligned_cols=22  Identities=23%  Similarity=0.344  Sum_probs=18.5

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      -.++|.|..|+||||||+.+..
T Consensus        63 ~IIGIaG~~GSGKSTlar~L~~   84 (290)
T TIGR00554        63 YIISIAGSVAVGKSTTARILQA   84 (290)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999987644

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>PRK09452 potA putrescine/spermidine ABC transporter ATPase protein; Reviewed

Probab=91.65  E-value=0.28  Score=45.81  Aligned_cols=52  Identities=19%  Similarity=0.205  Sum_probs=31.8

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.=+++||+--.. |...-+.+...+.....        ..|..+|++|++.+.+..++.
T Consensus       161 ~~P~llLLDEP~s~LD~~~r~~l~~~L~~l~~--------~~g~tiI~vTHd~~ea~~laD  213 (375)
T PRK09452        161 NKPKVLLLDESLSALDYKLRKQMQNELKALQR--------KLGITFVFVTHDQEEALTMSD  213 (375)
T ss_pred             cCCCEEEEeCCCCcCCHHHHHHHHHHHHHHHH--------hcCCEEEEEeCCHHHHHHhCC
Confidence            66779999987654 32233445555554321        346788888887765555543

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=91.63  E-value=1.4  Score=39.94  Aligned_cols=71  Identities=17%  Similarity=0.194  Sum_probs=40.6

Q ss_pred             ccccccCCcchHHHHHHHhccc----c---cc---c-CCCceEEEEe--C------CCCCHHHHHHHHHHhhcCCCceEE
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK----D---VI---E-NFDKRIWVCV--S------DPFDEFRIAKAIIEGLEGSEKKFF  185 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~----~---~~---~-~F~~~~wv~v--s------~~~~~~~~~~~i~~~~~~~~kr~L  185 (297)
                      ..|.|..|+|||||++.+....    +   +.   + .+...-|+.+  .      ...+..+++...+.+     ..=.
T Consensus       147 ili~G~tGsGKTTll~al~~~~~~~~~iv~ied~~El~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~Lr~-----~pd~  221 (308)
T TIGR02788       147 IIISGGTGSGKTTFLKSLVDEIPKDERIITIEDTREIFLPHPNYVHLFYSKGGQGLAKVTPKDLLQSCLRM-----RPDR  221 (308)
T ss_pred             EEEECCCCCCHHHHHHHHHccCCccccEEEEcCccccCCCCCCEEEEEecCCCCCcCccCHHHHHHHHhcC-----CCCe
Confidence            4578999999999999887631    1   00   1 1111122211  1      124556666555543     4556


Q ss_pred             EEEeCCCCCCccCHHHH
Q 043781          186 LILDDVWTDDYSKWEPF  202 (297)
Q Consensus       186 iVlDdv~~~~~~~w~~l  202 (297)
                      |++|.+...  +.|+.+
T Consensus       222 ii~gE~r~~--e~~~~l  236 (308)
T TIGR02788       222 IILGELRGD--EAFDFI  236 (308)
T ss_pred             EEEeccCCH--HHHHHH
Confidence            899999875  445433

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=91.60  E-value=0.82  Score=44.26  Aligned_cols=19  Identities=32%  Similarity=0.309  Sum_probs=15.9

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -|.|.+|+||||||.++..
T Consensus        25 Li~G~pGsGKT~la~qfl~   43 (484)
T TIGR02655        25 LVSGTSGTGKTLFSIQFLY   43 (484)
T ss_pred             EEEcCCCCCHHHHHHHHHH
Confidence            3779999999999987643

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.

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=91.60  E-value=0.18  Score=42.12  Aligned_cols=22  Identities=32%  Similarity=0.326  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|.|||||.+.+...
T Consensus        20 ~~~i~G~nGsGKSTLl~~i~G~   41 (190)
T TIGR01166        20 VLALLGANGAGKSTLLLHLNGL   41 (190)
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999983

This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=91.59  E-value=0.45  Score=40.84  Aligned_cols=93  Identities=17%  Similarity=0.187  Sum_probs=47.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-----CceEEEEEeCCCCCC---cc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-----EKKFFLILDDVWTDD---YS  197 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----~kr~LiVlDdv~~~~---~~  197 (297)
                      -|.|.+|+|||+|+.++... ..++.=+..+|++...+  ..++.+.+ ++++-.     ..-.|.++|-.....   ..
T Consensus        23 li~G~~GsGKT~l~~q~l~~-~~~~~ge~vlyvs~ee~--~~~l~~~~-~s~g~d~~~~~~~g~l~~~d~~~~~~~~~~~   98 (226)
T PF06745_consen   23 LISGPPGSGKTTLALQFLYN-GLKNFGEKVLYVSFEEP--PEELIENM-KSFGWDLEEYEDSGKLKIIDAFPERIGWSPN   98 (226)
T ss_dssp             EEEESTTSSHHHHHHHHHHH-HHHHHT--EEEEESSS---HHHHHHHH-HTTTS-HHHHHHTTSEEEEESSGGGST-TSC
T ss_pred             EEEeCCCCCcHHHHHHHHHH-hhhhcCCcEEEEEecCC--HHHHHHHH-HHcCCcHHHHhhcCCEEEEeccccccccccc
Confidence            47799999999999765542 22221134567765443  34444443 345443     222366777665531   13


Q ss_pred             CHHHHHHHHhhhhhhhceeeecCCCCeEEEEe
Q 043781          198 KWEPFHNCLMRVLQEFAAIEVDGDENPLSLTS  229 (297)
Q Consensus       198 ~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTT  229 (297)
                      .++.+...+......       .+..+++|-+
T Consensus        99 ~~~~l~~~i~~~i~~-------~~~~~vVIDs  123 (226)
T PF06745_consen   99 DLEELLSKIREAIEE-------LKPDRVVIDS  123 (226)
T ss_dssp             CHHHHHHHHHHHHHH-------HTSSEEEEET
T ss_pred             CHHHHHHHHHHHHHh-------cCCCEEEEEC
Confidence            455554444433221       2236777755

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 ....

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=91.59  E-value=0.086  Score=42.87  Aligned_cols=21  Identities=29%  Similarity=0.207  Sum_probs=16.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|.+|+|||||++.+...
T Consensus         2 I~i~G~~stGKTTL~~~L~~~   22 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR   22 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHc
Confidence            458899999999999999974

>TIGR01351 adk adenylate kinases

Probab=91.58  E-value=0.1  Score=44.42  Aligned_cols=20  Identities=30%  Similarity=0.215  Sum_probs=17.6

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|+|++|+||||+|+.+...
T Consensus         3 ~i~G~pGsGKsT~a~~La~~   22 (210)
T TIGR01351         3 VLLGPPGSGKGTQAKRIAEK   22 (210)
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47899999999999998863

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.

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=91.56  E-value=0.79  Score=44.56  Aligned_cols=54  Identities=15%  Similarity=0.035  Sum_probs=37.1

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTL  242 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~  242 (297)
                      .+.-|||+|.=-.. |...-.+|...+.+..        ...|..+|++|++.++...+|...
T Consensus       171 ~~P~LLIaDEPTTaLDvt~q~qIL~llk~l~--------~e~g~a~l~ITHDl~Vva~~aDrv  225 (539)
T COG1123         171 LKPKLLIADEPTTALDVTTQAQILDLLKDLQ--------RELGMAVLFITHDLGVVAELADRV  225 (539)
T ss_pred             CCCCEEEECCCccccCHHHHHHHHHHHHHHH--------HHcCcEEEEEcCCHHHHHHhcCeE
Confidence            77889999976543 2223334555555432        167888999999999988888653

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	297
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-26
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	1e-23
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	4e-23
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	6e-09
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	8e-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 =  106 bits (266), Expect = 6e-26
 Identities = 55/343 (16%), Positives = 112/343 (32%), Gaps = 105/343 (30%)

Query: 3   SFFQDFGKQVKKLTSNLRAIQAVLNDAE------QRQVKEASVRL-W--LDQLKEASYD- 52
           +F  +F    K +    ++   +L+  E       +     ++RL W  L + +E     
Sbjct: 28  AFVDNF--DCKDVQDMPKS---ILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF 82

Query: 53  MEDVLD---EWITARLKLQIEGVDENALVRKKPKIIEI--NENLDDIAKQKEVFN-FNVI 106
           +E+VL    +++ + +K +          +++P ++     E  D +    +VF  +NV 
Sbjct: 83  VEEVLRINYKFLMSPIKTE----------QRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132

Query: 107 RGSTEKSERIHSTALINVSD-----VRGMGGIGKTTLAQFAYNDKDVIENFDKRI-WVCV 160
           R   +   ++   AL+ +       + G+ G GKT +A        V    D +I W+ +
Sbjct: 133 RL--QPYLKLR-QALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNL 189

Query: 161 SDPFDE-----------FRIAKAIIEGLEGSE-------------KKFF---------LI 187
            +               ++I        + S              ++           L+
Sbjct: 190 KNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLV 249

Query: 188 LDDVWTDDYSKWEPF-HNC----------LMRVLQEFAAIEVDGDENPLSLTSTCQEKLR 236
           L +V   +   W  F  +C          +   L       +  D + ++LT    E   
Sbjct: 250 LLNVQ--NAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPD--EVKS 305

Query: 237 HLTLTLGLRAK-----------FPVSIF-----DAKKIW-GWE 262
            L   L  R +             +SI      D    W  W+
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK 348

>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 = 42.9 bits (100), Expect = 9e-05
 Identities = 51/251 (20%), Positives = 94/251 (37%), Gaps = 73/251 (29%)

Query: 7   DFGKQV--KKLTSNLRAIQAVLNDAEQRQV-KEASV-------------RLWLDQLKEAS 50
           D  K V   KLT+ + +   VL  AE R++    SV              +W D +K   
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS-- 402

Query: 51  YDMEDVLDEWITARL-----------------KLQIEGVDENALVRKKPKIIE---INEN 90
            D+  V+++     L                 +L+++  +E AL R    I++   I + 
Sbjct: 403 -DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR---SIVDHYNIPKT 458

Query: 91  LD--DIAKQKE---VFNFNVIRG----STEKSERIHSTALINVSDVRGMGG-IGKTTLAQ 140
            D  D+         ++   I G    + E  ER+    ++ + D R +   I   + A 
Sbjct: 459 FDSDDLIPPYLDQYFYSH--I-GHHLKNIEHPERMTLFRMVFL-DFRFLEQKIRHDSTAW 514

Query: 141 FAYND-KDVIENFDK-RIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSK 198
            A     + ++     + ++C +DP  E R+  AI++ L   E+   LI           
Sbjct: 515 NASGSILNTLQQLKFYKPYICDNDPKYE-RLVNAILDFLPKIEEN--LICSK-------- 563

Query: 199 WEPFHNCLMRV 209
               +  L+R+
Sbjct: 564 ----YTDLLRI 570

>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* Length = 549

 Score = 99.3 bits (247), Expect = 1e-23
 Identities = 35/263 (13%), Positives = 68/263 (25%), Gaps = 79/263 (30%)

Query: 25  VLNDAEQRQVKEASVRLWLDQLKEASYDMEDVLDEWITARLKLQIEGVDENALVRKK--- 81
            L+ A  R + +   R  L  L+  +   ED  +       +L+          R+    
Sbjct: 9   ALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLRIYRRQASEL 68

Query: 82  ------------PKIIEINENLDDIAK-QKEVFNFNVIRGSTEKSERIHSTALINVSD-- 126
                         + +  E+  D A  + ++    VI     +        L NV    
Sbjct: 69  GPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKLLLGNVPKQM 128

Query: 127 ----------------------------VRGMGGIGKTTLAQFAYNDKDVIEN--FDKRI 156
                                       + G  G GK+ +A  A +  D +    +D  +
Sbjct: 129 TCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIV 188

Query: 157 WVCVSDPFDE-----FRIAKAIIEGLEG------------------------SEKKFFLI 187
           W+  S    +     F     +++  +                                +
Sbjct: 189 WLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFV 248

Query: 188 LDDVWTDDYSKWEPFHNCLMRVL 210
            DDV  ++  +W        R L
Sbjct: 249 FDDVVQEETIRWAQELRL--RCL 269

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score = 98.0 bits (244), Expect = 4e-23
 Identities = 35/253 (13%), Positives = 63/253 (24%), Gaps = 73/253 (28%)

Query: 23  QAVLNDAEQRQVKEASVRLWLDQLKE---ASYDMEDVLDEWITARLKLQ-----IEGVDE 74
           +  L    +   K+      +D +      +   E+ +    T + +       I   D 
Sbjct: 6   RNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDN 65

Query: 75  NALVR-----KKPKIIEINENLDDIAKQKEVFNF--NVIRGSTEKSERIHSTALINVSDV 127
           ++ V            ++   L D        +   +V   ++     +    +     V
Sbjct: 66  DSYVSFYNALLHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEGGVPQRPVV 125

Query: 128 ---R------------------------GMGGIGKTTLAQFAYNDKDVIENF--DKRIWV 158
              R                        GM G GK+ LA  A  D  ++E        WV
Sbjct: 126 FVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWV 185

Query: 159 CVSDPFDEFRIAKAII---------------------------EGLEGSEKKFFLILDDV 191
            V        + K                                +     +  LILDDV
Sbjct: 186 SVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDV 245

Query: 192 WTDDYSKWEPFHN 204
           W       + F +
Sbjct: 246 WDSWV--LKAFDS 256

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare} Length = 115

 Score = 52.1 bits (125), Expect = 6e-09
 Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 10 KQVKKLTSNLRAIQAVLNDAEQRQVKEAS--VRLWLDQLKEASYDMEDVLDEWI 61
          K ++ L   L ++ A L    +   ++     +LW D+++E SY +EDV+D+++
Sbjct: 26 KNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDKFL 79

>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* Length = 1249

 Score = 40.2 bits (94), Expect = 8e-04
 Identities = 26/153 (16%), Positives = 46/153 (30%), Gaps = 32/153 (20%)

Query: 127 VRGMGGIGKTTLAQFAYNDKDVIENF--DKRIWV-------------------------- 158
           + GM G GK+ LA  A  D  ++E        WV                          
Sbjct: 152 IYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEES 211

Query: 159 -CVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCLM---RVLQEFA 214
                P +       +   +     +  LILDDVW     K       ++   R      
Sbjct: 212 FSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPWVLKAFDNQCQILLTTRDKSVTD 271

Query: 215 AIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAK 247
           ++       P+      ++ L  L+L + ++ +
Sbjct: 272 SVMGPKHVVPVESGLGREKGLEILSLFVNMKKE 304

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	297
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	99.87
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	99.7
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	99.63
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.5
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	99.48
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	98.73
2chg_A	226	Replication factor C small subunit; DNA-binding pr	98.63
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	98.6
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	98.33
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	98.32
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	98.23
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	98.21
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.18
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.17
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	98.15
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	98.1
2fna_A	357	Conserved hypothetical protein; structural genomic	98.08
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.08
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.07
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.04
3bos_A	242	Putative DNA replication factor; P-loop containing	97.94
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.92
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.8
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.68
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	97.67
3pvs_A	447	Replication-associated recombination protein A; ma	97.67
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.67
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.67
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.62
3co5_A	143	Putative two-component system transcriptional RES	97.56
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.54
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.52
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.51
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.5
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	97.48
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.47
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.42
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.41
2qgz_A	308	Helicase loader, putative primosome component; str	97.39
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.38
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.34
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.33
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.26
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.22
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.22
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.21
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.2
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	97.2
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.19
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.19
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.16
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.16
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.04
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.03
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.89
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	96.89
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	96.87
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	96.85
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	96.82
1tue_A	212	Replication protein E1; helicase, replication, E1E	96.81
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.7
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.69
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.63
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	96.6
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	96.42
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.39
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	96.32
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	96.31
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	96.22
2r44_A	331	Uncharacterized protein; putative ATPase, structur	96.21
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	96.18
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	96.11
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.04
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	95.98
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	95.94
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	95.94
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	95.93
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.89
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.82
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.66
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	95.58
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.57
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.51
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	95.46
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.45
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	95.42
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.4
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	95.37
1xp8_A	366	RECA protein, recombinase A; recombination, radior	95.24
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	95.16
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	95.13
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	95.12
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.1
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	94.99
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.86
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	94.79
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	94.79
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	94.74
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	94.73
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	94.68
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	94.67
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.64
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	94.62
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	94.61
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	94.57
3ice_A	422	Transcription termination factor RHO; transcriptio	94.56
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	94.54
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.51
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	94.37
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	94.33
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	94.33
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.31
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	94.3
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	94.29
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	94.24
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	94.23
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	94.22
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.14
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	94.13
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	94.12
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.07
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.07
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.01
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.01
3l0o_A	427	Transcription termination factor RHO; helicase, RH	94.0
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	94.0
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.0
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	93.99
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	93.96
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	93.95
3io5_A	333	Recombination and repair protein; storage dimer, i	93.91
1via_A	175	Shikimate kinase; structural genomics, transferase	93.9
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	93.87
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	93.87
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	93.86
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	93.82
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	93.81
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	93.78
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	93.74
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	93.74
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	93.72
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	93.69
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	93.68
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	93.66
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	93.65
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	93.63
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	93.62
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	93.61
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	93.56
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	93.56
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	93.52
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	93.51
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	93.51
2xxa_A	433	Signal recognition particle protein; protein trans	93.49
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	93.44
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	93.43
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	93.43
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	93.41
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	93.4
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	93.37
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	93.33
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	93.31
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	93.29
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	93.28
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	93.26
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	93.25
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	93.24
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	93.23
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	93.2
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	93.1
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	93.09
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	93.06
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	92.97
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	92.94
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	92.92
2vli_A	183	Antibiotic resistance protein; transferase, tunica	92.89
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	92.89
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	92.89
4a74_A	231	DNA repair and recombination protein RADA; hydrola	92.88
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	92.88
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	92.86
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	92.85
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	92.76
2z43_A	324	DNA repair and recombination protein RADA; archaea	92.73
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	92.71
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	92.7
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.7
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	92.65
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	92.63
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	92.63
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	92.6
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	92.57
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	92.53
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	92.53
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	92.49
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	92.47
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	92.47
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	92.46
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	92.44
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	92.42
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	92.41
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	92.41
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	92.4
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	92.39
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	92.34
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	92.32
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.31
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	92.3
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.21
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	92.21
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	92.18
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	92.05
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	92.05
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.01
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	91.99
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	91.99
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	91.97
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	91.94
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	91.91
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	91.9
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	91.87
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	91.87
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	91.84
1sgw_A	214	Putative ABC transporter; structural genomics, P p	91.81
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	91.78
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	91.74
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	91.71
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	91.67
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	91.63
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	91.58
1g6h_A	257	High-affinity branched-chain amino acid transport	91.45
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.45
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.44
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	91.44
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	91.42
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.41
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	91.38
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	91.38
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	91.3
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	91.3
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	91.27
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.24
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	91.24
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	91.2
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	91.19
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	91.13
2wji_A	165	Ferrous iron transport protein B homolog; membrane	91.09
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	91.09
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	91.06
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.03
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	91.02
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	91.01
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	91.01
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	91.0
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	90.99
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	90.97
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	90.88
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	90.85
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	90.83
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	90.79
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	90.72
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	90.7
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	90.69
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	90.67
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	90.64
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	90.55
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	90.49
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	90.49
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	90.48
2ghi_A	260	Transport protein; multidrug resistance protein, M	90.45
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	90.45
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	90.43
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	90.34
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	90.24
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	90.22
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	90.22
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	90.21
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	90.18
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	90.14
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	90.14
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	90.04
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	90.03
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	89.99
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	89.96
2hf9_A	226	Probable hydrogenase nickel incorporation protein	89.92
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	89.9
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	89.87
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	89.87
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	89.83
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	89.79
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	89.73
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	89.67
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	89.66
3gqb_A	578	V-type ATP synthase alpha chain; A3B3, V-ATPase, A	89.59
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	89.55
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	89.52
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	89.5
2e87_A	357	Hypothetical protein PH1320; GTP-binding, GTPase,	89.4
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	89.4
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	89.4
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	89.3
2og2_A	359	Putative signal recognition particle receptor; nuc	89.25
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	89.24
2eyu_A	261	Twitching motility protein PILT; pilus retraction	89.24
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	89.22
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	89.15
2r6a_A	454	DNAB helicase, replicative helicase; replication,	89.15
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	89.11
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	89.07
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	89.06
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	89.05
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	89.05
3kta_A	182	Chromosome segregation protein SMC; structural mai	89.04
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	89.0
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	88.94
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	88.93
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	88.92
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	88.9
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	88.9
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	88.89
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	88.87
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	88.86
2ged_A	193	SR-beta, signal recognition particle receptor beta	88.78
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	88.7
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	88.7
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	88.69
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	88.68
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	88.67
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	88.66
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	88.66
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	88.57
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	88.56
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	88.55
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	88.45
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	88.37
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	88.33
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	88.3
3llu_A	196	RAS-related GTP-binding protein C; structural geno	88.29
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	88.26
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	88.22
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	88.2
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	88.17
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	88.17
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	88.15
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	88.13
1nrj_B	218	SR-beta, signal recognition particle receptor beta	88.1
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	88.09
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	88.06
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	88.06
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	88.05
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	88.05
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	88.04
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	88.02
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	88.0
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	87.99
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	87.99
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	87.97
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	87.97
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	87.94
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	87.93
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	87.91
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	87.89
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	87.89
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	87.88
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	87.86
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	87.85
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	87.78
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	87.74
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	87.69
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	87.67
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	87.62
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	87.62
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	87.59
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	87.58
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	87.51
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	87.51
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	87.51
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	87.48
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	87.47
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	87.39
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	87.34
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	87.33
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	87.32
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	87.27
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	87.26
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	87.24
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	87.21
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	87.21
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	87.19
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	87.15
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	87.03
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	87.0
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	86.99
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	86.96
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	86.93
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	86.9
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	86.87
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	86.82
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	86.82
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	86.81
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	86.71
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	86.67
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	86.66
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	86.65
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	86.62
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	86.6
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	86.59
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	86.55
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	86.53
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	86.47
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	86.44
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	86.41
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	86.38
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	86.36
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	86.35
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	86.35
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	86.25
2fh5_B	214	SR-beta, signal recognition particle receptor beta	86.22
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	86.21
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	86.21
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	86.2
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	86.2
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	86.16
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	86.16
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	86.12
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	86.06
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	86.05
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	86.05
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	86.04
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	86.03
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	85.86
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	85.86
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	85.85
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	85.8
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	85.78
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	85.71
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	85.7
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	85.67
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	85.66
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	85.64
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	85.64
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	85.61
3fwy_A	314	Light-independent protochlorophyllide reductase I	85.6
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	85.55
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	85.48
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	85.42
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	85.32
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	85.32
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	85.27
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	85.17
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	85.16
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	85.16
2qag_C	418	Septin-7; cell cycle, cell division, GTP-binding,	85.05
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	85.05
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	84.96
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	84.92
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	84.9
2ewv_A	372	Twitching motility protein PILT; pilus retraction	84.86
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	84.83
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	84.8
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	84.79
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	84.74
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	84.73
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	84.63
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	84.62
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	84.6
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	84.57
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	84.54
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	84.53
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	84.44
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	84.31
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	84.07
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	84.02
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	83.97
2x77_A	189	ADP-ribosylation factor; GTP-binding protein, smal	83.93
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	83.87
1qhl_A	227	Protein (cell division protein MUKB); SMC, chromos	83.83
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	83.81
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	83.72
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	83.56
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	83.55
1wf3_A	301	GTP-binding protein; GTPase, riken structural geno	83.55
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	83.48
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	83.46
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	83.33
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	83.19
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	83.15
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	83.15
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	83.04
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	82.98
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	82.98
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	82.83
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	82.77
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	82.72
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	82.69
3ez2_A	398	Plasmid partition protein A; type IA, DNA binding,	82.62
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	82.59
3end_A	307	Light-independent protochlorophyllide reductase ir	82.58
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	82.56
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	82.47

>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=99.87  E-value=1.3e-22  Score=196.42  Aligned_cols=123  Identities=15%  Similarity=0.162  Sum_probs=95.2

Q ss_pred             cccccccccCCcchHHHHHHHhc--ccccccCCCceEEEEeCCCC--CHHHHHHHHHHhhcCC-----------------
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYN--DKDVIENFDKRIWVCVSDPF--DEFRIAKAIIEGLEGS-----------------  180 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~--~~~~~~~F~~~~wv~vs~~~--~~~~~~~~i~~~~~~~-----------------  180 (297)
                      ...++|+||||+||||||+.+|+  +.+++.+|+.++||++++.+  ++..++..|+.+++..                 
T Consensus       152 ~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l  231 (549)
T 2a5y_B          152 SFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVL  231 (549)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCHHHHHHHHHHHHhcCcccccccccccccHHHH
Confidence            35578999999999999999998  67899999999999999985  7899999999887631                 


Q ss_pred             ---------Cc-eEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-CCcccc
Q 043781          181 ---------EK-KFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-LRAKFP  249 (297)
Q Consensus       181 ---------~k-r~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~~~~~~  249 (297)
                               ++ ||||||||||+.+  ++     .++.           .+||+||||||..    .++..++ ...+|+
T Consensus       232 ~~~l~~~L~~~kr~LlVLDdv~~~~--~~-----~~~~-----------~~gs~ilvTTR~~----~v~~~~~~~~~~~~  289 (549)
T 2a5y_B          232 KRMICNALIDRPNTLFVFDDVVQEE--TI-----RWAQ-----------ELRLRCLVTTRDV----EISNAASQTCEFIE  289 (549)
T ss_dssp             HHHHHHHHTTSTTEEEEEEEECCHH--HH-----HHHH-----------HTTCEEEEEESBG----GGGGGCCSCEEEEE
T ss_pred             HHHHHHHHcCCCcEEEEEECCCCch--hh-----cccc-----------cCCCEEEEEcCCH----HHHHHcCCCCeEEE
Confidence                     54 9999999999862  33     3332           4789999999954    4455554 335677


Q ss_pred             CCccc---hhhhhhhhhccC
Q 043781          250 VSIFD---AKKIWGWEVFGR  266 (297)
Q Consensus       250 l~~l~---~~~lf~~~~f~~  266 (297)
                      |++|+   +++||.+.+|..
T Consensus       290 l~~L~~~ea~~Lf~~~a~~~  309 (549)
T 2a5y_B          290 VTSLEIDECYDFLEAYGMPM  309 (549)
T ss_dssp             CCCCCHHHHHHHHHHTSCCC
T ss_pred             CCCCCHHHHHHHHHHHhcCC
Confidence            77776   555666665544

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=99.70  E-value=2.7e-18  Score=172.90  Aligned_cols=97  Identities=18%  Similarity=0.175  Sum_probs=77.5

Q ss_pred             ccccccccCCcchHHHHHHHhcccccccCCCc-eEEEEeCCCCCHHHHHHHHHHhhc-----------------------
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDKDVIENFDK-RIWVCVSDPFDEFRIAKAIIEGLE-----------------------  178 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~-~~wv~vs~~~~~~~~~~~i~~~~~-----------------------  178 (297)
                      ..+.|+||||+||||||+.+|++.+++.+|+. ++|+++++.++...++..|+..++                       
T Consensus       151 RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~~~IL~~Ll~lL~~i~~~~~~~~d~~~~ip~~leeL  230 (1221)
T 1vt4_I          151 KNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI  230 (1221)
T ss_dssp             CEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSHHHHHHHHHHHHHHHCSSSTTTSCCCSSHHHHHHHH
T ss_pred             eEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCHHHHHHHHHHHHhhcCcccccccccccCCCCCHHHH
Confidence            45789999999999999999998888999986 899999999988777776655321                       


Q ss_pred             ----------CCCceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHH
Q 043781          179 ----------GSEKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHL  238 (297)
Q Consensus       179 ----------~~~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v  238 (297)
                                ..++|+||||||||+.  +.|+.    |             .+||+||||||...++..+
T Consensus       231 ~e~Lr~lL~~l~~KRvLLVLDDVwd~--eqLe~----f-------------~pGSRILVTTRd~~Va~~l  281 (1221)
T 1vt4_I          231 QAELRRLLKSKPYENCLLVLLNVQNA--KAWNA----F-------------NLSCKILLTTRFKQVTDFL  281 (1221)
T ss_dssp             HHHHHHHHHHSTTSSCEEEEESCCCH--HHHHH----H-------------HSSCCEEEECSCSHHHHHH
T ss_pred             HHHHHHHHHhhcCCCEEEEEeCcChH--HHHHh----h-------------CCCeEEEEeccChHHHHhc
Confidence                      0159999999999995  45543    2             3679999999987665433

>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=99.63  E-value=1e-16  Score=167.19  Aligned_cols=119  Identities=24%  Similarity=0.347  Sum_probs=81.5

Q ss_pred             ccccccccCCcchHHHHHHHhccccc-ccCC-CceEEEEeCCCCC--HHHHHHHHHHhhcCC------------------
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDKDV-IENF-DKRIWVCVSDPFD--EFRIAKAIIEGLEGS------------------  180 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~~~-~~~F-~~~~wv~vs~~~~--~~~~~~~i~~~~~~~------------------  180 (297)
                      ..+.|+||||+||||||+.+|++.+. ..+| +.++||++++..+  ....+..++..+...                  
T Consensus       148 ~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l  227 (1249)
T 3sfz_A          148 GWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRL  227 (1249)
T ss_dssp             EEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHH
Confidence            34679999999999999999997544 4555 5777999998643  333455555555432                  


Q ss_pred             -------CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh-hCCCccccCCc
Q 043781          181 -------EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT-LGLRAKFPVSI  252 (297)
Q Consensus       181 -------~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~-~~~~~~~~l~~  252 (297)
                             ++||||||||||+.  .+|+.+                 ++||+||||||.+.    ++.. ++..+.+++..
T Consensus       228 ~~~l~~~~~~~LlvlDd~~~~--~~~~~~-----------------~~~~~ilvTtR~~~----~~~~~~~~~~~~~~~~  284 (1249)
T 3sfz_A          228 RVLMLRKHPRSLLILDDVWDP--WVLKAF-----------------DNQCQILLTTRDKS----VTDSVMGPKHVVPVES  284 (1249)
T ss_dssp             HHHTSSSSCSCEEEEESCCCH--HHHTTT-----------------CSSCEEEEEESSTT----TTTTCCSCBCCEECCS
T ss_pred             HHHHhccCCCEEEEEecCCCH--HHHHhh-----------------cCCCEEEEEcCCHH----HHHhhcCCceEEEecC
Confidence                   34999999999986  333332                 68899999999554    4422 34456666664


Q ss_pred             -cc---hhhhhhhhhc
Q 043781          253 -FD---AKKIWGWEVF  264 (297)
Q Consensus       253 -l~---~~~lf~~~~f  264 (297)
                       |+   +++||...++
T Consensus       285 ~l~~~~a~~l~~~~~~  300 (1249)
T 3sfz_A          285 GLGREKGLEILSLFVN  300 (1249)
T ss_dssp             SCCHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhhC
Confidence             54   5566665554

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.50  E-value=5.5e-14  Score=107.82  Aligned_cols=65  Identities=23%  Similarity=0.428  Sum_probs=60.3

Q ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHHHHHhc--ccccHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 043781            2 RSFFQDFGKQVKKLTSNLRAIQAVLNDAEQR--QVKEASVRLWLDQLKEASYDMEDVLDEWITARLK   66 (297)
Q Consensus         2 ~~ll~~~~~~~~~L~~eL~~i~a~l~~ae~~--~~~~~~v~~Wl~~lr~~ayd~eD~ld~~~~~~~~   66 (297)
                      ++++.+++++++.|+++|..|+++|.+|+.+  +..++.++.|+++||+++||+||+||+|.++...
T Consensus        18 ~~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~~d~~vk~W~~~vrdlaYD~ED~iD~f~~~~~~   84 (115)
T 3qfl_A           18 FKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQLDSQDKLWADEVRELSYVIEDVVDKFLVQVDG   84 (115)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4678999999999999999999999999988  5688999999999999999999999999988753

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=99.48  E-value=7.5e-15  Score=142.73  Aligned_cols=119  Identities=24%  Similarity=0.273  Sum_probs=77.3

Q ss_pred             ccccccccCCcchHHHHHHHhccccc-ccCC-CceEEEEeCCCCCHHHHHHHH---HHhhcC------C-----------
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDKDV-IENF-DKRIWVCVSDPFDEFRIAKAI---IEGLEG------S-----------  180 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~~~-~~~F-~~~~wv~vs~~~~~~~~~~~i---~~~~~~------~-----------  180 (297)
                      ..+.|+||||+||||||..++++.++ ..+| +.++|++++.. +...++..+   +..++.      .           
T Consensus       148 ~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~-~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~  226 (591)
T 1z6t_A          148 GWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQ-DKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDR  226 (591)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESC-CHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHH
T ss_pred             ceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCC-chHHHHHHHHHHHHHhccccccccCCCCCHHHHHHH
Confidence            45679999999999999999997655 7889 58999998765 333333333   333331      0           


Q ss_pred             --------CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhC-C-CccccC
Q 043781          181 --------EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLG-L-RAKFPV  250 (297)
Q Consensus       181 --------~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~-~-~~~~~l  250 (297)
                              .+++||||||+|+.  .   .+. .+             ++|++||||||...+    +..++ . ..+..+
T Consensus       227 l~~~l~~~~~~~LLVLDdv~~~--~---~l~-~l-------------~~~~~ilvTsR~~~~----~~~~~~~~~~v~~l  283 (591)
T 1z6t_A          227 LRILMLRKHPRSLLILDDVWDS--W---VLK-AF-------------DSQCQILLTTRDKSV----TDSVMGPKYVVPVE  283 (591)
T ss_dssp             HHHHHHHTCTTCEEEEEEECCH--H---HHH-TT-------------CSSCEEEEEESCGGG----GTTCCSCEEEEECC
T ss_pred             HHHHHccCCCCeEEEEeCCCCH--H---HHH-Hh-------------cCCCeEEEECCCcHH----HHhcCCCceEeecC
Confidence                    37899999999874  2   221 11             678999999996543    32222 1 123322


Q ss_pred             Ccc---chhhhhhhhhcc
Q 043781          251 SIF---DAKKIWGWEVFG  265 (297)
Q Consensus       251 ~~l---~~~~lf~~~~f~  265 (297)
                      ++|   ++.+||...++.
T Consensus       284 ~~L~~~ea~~L~~~~~~~  301 (591)
T 1z6t_A          284 SSLGKEKGLEILSLFVNM  301 (591)
T ss_dssp             SSCCHHHHHHHHHHHHTS
T ss_pred             CCCCHHHHHHHHHHHhCC
Confidence            345   456666666554

>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=98.73  E-value=1.3e-08  Score=93.92  Aligned_cols=68  Identities=26%  Similarity=0.342  Sum_probs=48.7

Q ss_pred             ccccCCcchHHHHHHHhcccccc---cCCC-ceEEEEeCCCCCHHHHHHHHHHhhcCC----------------------
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI---ENFD-KRIWVCVSDPFDEFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~---~~F~-~~~wv~vs~~~~~~~~~~~i~~~~~~~----------------------  180 (297)
                      |+|++|+|||||++.+++.....   ..|. ..+|+......+...++..|+.+++..                      
T Consensus        57 i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~  136 (412)
T 1w5s_A           57 SIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVE  136 (412)
T ss_dssp             CTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHH
T ss_pred             CcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhc
Confidence            39999999999999999842211   1123 356777666667777777777665421                      


Q ss_pred             CceEEEEEeCCCCC
Q 043781          181 EKKFFLILDDVWTD  194 (297)
Q Consensus       181 ~kr~LiVlDdv~~~  194 (297)
                      +++++|||||+|..
T Consensus       137 ~~~~llvlDe~~~l  150 (412)
T 1w5s_A          137 NHYLLVILDEFQSM  150 (412)
T ss_dssp             TCEEEEEEESTHHH
T ss_pred             CCeEEEEEeCHHHH
Confidence            57999999999874

>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=98.63  E-value=1.1e-07  Score=79.38  Aligned_cols=119  Identities=16%  Similarity=0.040  Sum_probs=70.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC-ceEEEEeCCCCCHHHHHHHHHHhhcC----CCceEEEEEeCCCCCCccCH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD-KRIWVCVSDPFDEFRIAKAIIEGLEG----SEKKFFLILDDVWTDDYSKW  199 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~~~~----~~kr~LiVlDdv~~~~~~~w  199 (297)
                      .-|+|.+|+|||+||+.+++... ...+. ..+.+..+.......+...+......    .+++.+|||||++......+
T Consensus        41 ~ll~G~~G~GKT~l~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~  119 (226)
T 2chg_A           41 LLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQ  119 (226)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH-GGGGGGGEEEEETTCTTCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh-ccccccceEEeccccccChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCHHHH
Confidence            45889999999999999987311 11222 23444555555544443333222221    16789999999988754556


Q ss_pred             HHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhh
Q 043781          200 EPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       200 ~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      +.|...+...          ..+.++|+||+.... ...+....   ..+.+.+++..+
T Consensus       120 ~~l~~~l~~~----------~~~~~~i~~~~~~~~~~~~l~~r~---~~i~~~~~~~~~  165 (226)
T 2chg_A          120 AALRRTMEMY----------SKSCRFILSCNYVSRIIEPIQSRC---AVFRFKPVPKEA  165 (226)
T ss_dssp             HHHHHHHHHT----------TTTEEEEEEESCGGGSCHHHHTTS---EEEECCCCCHHH
T ss_pred             HHHHHHHHhc----------CCCCeEEEEeCChhhcCHHHHHhC---ceeecCCCCHHH
Confidence            6666666542          556788888875432 12222222   255666666554

>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=98.60  E-value=9.3e-08  Score=80.75  Aligned_cols=119  Identities=13%  Similarity=0.186  Sum_probs=70.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC-------------------CCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN-------------------FDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EK  182 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~-------------------F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~k  182 (297)
                      .-|+|++|+||||||+.+++.......                   +.....+.... ......+..++..+...   ++
T Consensus        48 ~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~  126 (250)
T 1njg_A           48 YLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAAS-RTKVEDTRDLLDNVQYAPARGR  126 (250)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHTTCCSSEEEEETTC-GGGHHHHHHHHHSCCCSCSSSS
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhccCCcceEEecCcc-cccHHHHHHHHHHhhhchhcCC
Confidence            358899999999999999874221111                   11122333222 22334455666665432   67


Q ss_pred             eEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhh
Q 043781          183 KFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       183 r~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      +.+|||||++..+...++.|...+...          ..+..+|+||+.... ...+...   ...+.+.+++..+
T Consensus       127 ~~vlviDe~~~l~~~~~~~l~~~l~~~----------~~~~~~i~~t~~~~~~~~~l~~r---~~~i~l~~l~~~e  189 (250)
T 1njg_A          127 FKVYLIDEVHMLSRHSFNALLKTLEEP----------PEHVKFLLATTDPQKLPVTILSR---CLQFHLKALDVEQ  189 (250)
T ss_dssp             SEEEEEETGGGSCHHHHHHHHHHHHSC----------CTTEEEEEEESCGGGSCHHHHTT---SEEEECCCCCHHH
T ss_pred             ceEEEEECcccccHHHHHHHHHHHhcC----------CCceEEEEEeCChHhCCHHHHHH---hhhccCCCCCHHH
Confidence            899999999886555666776666442          456778888865432 1222222   2456677776554

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=98.33  E-value=9.2e-07  Score=80.42  Aligned_cols=125  Identities=18%  Similarity=0.181  Sum_probs=68.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC------CCceEEEEeCCCCCHHHHHHHHHHhhcC-------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN------FDKRIWVCVSDPFDEFRIAKAIIEGLEG-------------------  179 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~------F~~~~wv~vs~~~~~~~~~~~i~~~~~~-------------------  179 (297)
                      .-|+|++|+||||||+.+++.  ....      --..+|++.....+...++..++.+++.                   
T Consensus        47 vll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~  124 (387)
T 2v1u_A           47 ALLYGLTGTGKTAVARLVLRR--LEARASSLGVLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKR  124 (387)
T ss_dssp             EEECBCTTSSHHHHHHHHHHH--HHHHHHHHTCCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHHHhccCCCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHH
Confidence            458899999999999999984  3221      1235677766655655555555544432                   


Q ss_pred             ---CCceEEEEEeCCCCCCcc--CHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH----HHHHHHHhhCCCccccC
Q 043781          180 ---SEKKFFLILDDVWTDDYS--KWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE----KLRHLTLTLGLRAKFPV  250 (297)
Q Consensus       180 ---~~kr~LiVlDdv~~~~~~--~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~----~~~~v~~~~~~~~~~~l  250 (297)
                         .+++.+||||+++.....  ..+.+...+... ...   . ...+..+|.||+...    ....+...++. ..+.+
T Consensus       125 l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~-~~~---~-~~~~~~~I~~t~~~~~~~~l~~~l~~r~~~-~~i~l  198 (387)
T 2v1u_A          125 LSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRIN-QEL---G-DRVWVSLVGITNSLGFVENLEPRVKSSLGE-VELVF  198 (387)
T ss_dssp             HTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGG-GCC---------CEEEEECSCSTTSSSSCHHHHTTTTS-EECCB
T ss_pred             HhccCCeEEEEEccHhhhcccCCCChHHHhHhhch-hhc---C-CCceEEEEEEECCCchHhhhCHHHHhcCCC-eEEee
Confidence               267999999999775321  122233333211 000   0 033456777776431    12233333332 35677


Q ss_pred             Cccchhh
Q 043781          251 SIFDAKK  257 (297)
Q Consensus       251 ~~l~~~~  257 (297)
                      .+++..+
T Consensus       199 ~~l~~~~  205 (387)
T 2v1u_A          199 PPYTAPQ  205 (387)
T ss_dssp             CCCCHHH
T ss_pred             CCCCHHH
Confidence            7776554

>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=98.32  E-value=3.2e-07  Score=83.71  Aligned_cols=119  Identities=18%  Similarity=0.197  Sum_probs=69.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC--------CCceEEEEeCCCC-CHHHHHHHHHHhhcCC---------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN--------FDKRIWVCVSDPF-DEFRIAKAIIEGLEGS---------------  180 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~--------F~~~~wv~vs~~~-~~~~~~~~i~~~~~~~---------------  180 (297)
                      .-|+|++|+|||+||+.+++.  ....        ....+|++.+... +...++..++.++.+.               
T Consensus        48 vll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~  125 (384)
T 2qby_B           48 NLFLGLTGTGKTFVSKYIFNE--IEEVKKEDEEYKDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDK  125 (384)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH--HHHHHHHSSSSTTCEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHHhhhhcCCCCceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHH
Confidence            458899999999999999984  3111        2345677765555 5666666666555100               


Q ss_pred             ------CceEEEEEeCCCCCCccCHHHH-HHHHhhhhhhhceeeecCCCCeEEEEeccHH----HHHHHHHhhCCCcccc
Q 043781          181 ------EKKFFLILDDVWTDDYSKWEPF-HNCLMRVLQEFAAIEVDGDENPLSLTSTCQE----KLRHLTLTLGLRAKFP  249 (297)
Q Consensus       181 ------~kr~LiVlDdv~~~~~~~w~~l-~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~----~~~~v~~~~~~~~~~~  249 (297)
                            .++.+|||||++......+..+ ...+.+.          ..+..+|+||+...    ....+...++  ..+.
T Consensus       126 l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~----------~~~~~iI~~t~~~~~~~~l~~~l~sr~~--~~i~  193 (384)
T 2qby_B          126 IKNGTRNIRAIIYLDEVDTLVKRRGGDIVLYQLLRS----------DANISVIMISNDINVRDYMEPRVLSSLG--PSVI  193 (384)
T ss_dssp             HHHHHSSSCEEEEEETTHHHHHSTTSHHHHHHHHTS----------SSCEEEEEECSSTTTTTTSCHHHHHTCC--CEEE
T ss_pred             HHHHhccCCCEEEEECHHHhccCCCCceeHHHHhcC----------CcceEEEEEECCCchHhhhCHHHHhcCC--CeEE
Confidence                  2334999999977532222233 3344332          25677888887542    1223333333  2667


Q ss_pred             CCccchhh
Q 043781          250 VSIFDAKK  257 (297)
Q Consensus       250 l~~l~~~~  257 (297)
                      +.+++..+
T Consensus       194 l~~l~~~~  201 (384)
T 2qby_B          194 FKPYDAEQ  201 (384)
T ss_dssp             ECCCCHHH
T ss_pred             ECCCCHHH
Confidence            77776554

>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=98.23  E-value=9.4e-07  Score=78.45  Aligned_cols=118  Identities=16%  Similarity=0.182  Sum_probs=70.5

Q ss_pred             ccccccCCcchHHHHHHHhccccccc-CCC-ceEEEEeCCCCCHHHHHHHHHHhhc-----C-CCceEEEEEeCCCCCCc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE-NFD-KRIWVCVSDPFDEFRIAKAIIEGLE-----G-SEKKFFLILDDVWTDDY  196 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~-~F~-~~~wv~vs~~~~~~~~~~~i~~~~~-----~-~~kr~LiVlDdv~~~~~  196 (297)
                      .-++|++|+|||++|+.+++.  +.. .+. ..+++..+.......+ ++++..+.     . .+++.+|||||++....
T Consensus        45 ~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~i-~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~  121 (323)
T 1sxj_B           45 MIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDVV-RNQIKHFAQKKLHLPPGKHKIVILDEADSMTA  121 (323)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHHH-HTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH
T ss_pred             EEEECcCCCCHHHHHHHHHHH--hcCCcccCCEEEecCccccChHHH-HHHHHHHHhccccCCCCCceEEEEECcccCCH
Confidence            458899999999999999884  211 111 2344444444444333 33444332     1 25689999999988754


Q ss_pred             cCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhh
Q 043781          197 SKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       197 ~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      ..++.|...+...          ..++.+|+||+.... ...+...   ...+.+.+++..++
T Consensus       122 ~~~~~L~~~le~~----------~~~~~~il~~~~~~~l~~~l~sr---~~~i~~~~~~~~~~  171 (323)
T 1sxj_B          122 GAQQALRRTMELY----------SNSTRFAFACNQSNKIIEPLQSQ---CAILRYSKLSDEDV  171 (323)
T ss_dssp             HHHHTTHHHHHHT----------TTTEEEEEEESCGGGSCHHHHTT---SEEEECCCCCHHHH
T ss_pred             HHHHHHHHHHhcc----------CCCceEEEEeCChhhchhHHHhh---ceEEeecCCCHHHH
Confidence            5666676666542          456778888764321 1222222   23667777766554

>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=98.21  E-value=3e-06  Score=77.18  Aligned_cols=124  Identities=15%  Similarity=0.112  Sum_probs=76.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCC-CceEEEEeCCCCCHHHHHHHHHHhhcCC----------------------C
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENF-DKRIWVCVSDPFDEFRIAKAIIEGLEGS----------------------E  181 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F-~~~~wv~vs~~~~~~~~~~~i~~~~~~~----------------------~  181 (297)
                      .-|+|++|+|||||++.+.+.  ..... -..+|+..+...+...++..++..++..                      +
T Consensus        47 ~li~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~  124 (389)
T 1fnn_A           47 ATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERD  124 (389)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HhhhcCeeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcC
Confidence            458999999999999999984  33321 2456777777777777777777766431                      4


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHH----HHHhhCCCccccCCccchhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRH----LTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~----v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ++.+||||+++..+......|...+... ..     ....+..+|++|+..+....    +...++. ..+.+.+++..+
T Consensus       125 ~~~vlilDE~~~l~~~~~~~L~~~~~~~-~~-----~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~-~~i~~~pl~~~~  197 (389)
T 1fnn_A          125 LYMFLVLDDAFNLAPDILSTFIRLGQEA-DK-----LGAFRIALVIVGHNDAVLNNLDPSTRGIMGK-YVIRFSPYTKDQ  197 (389)
T ss_dssp             CCEEEEEETGGGSCHHHHHHHHHHTTCH-HH-----HSSCCEEEEEEESSTHHHHTSCHHHHHHHTT-CEEECCCCBHHH
T ss_pred             CeEEEEEECccccchHHHHHHHHHHHhC-CC-----CCcCCEEEEEEECCchHHHHhCHHhhhcCCC-ceEEeCCCCHHH
Confidence            6889999999887544444454444221 00     00145677778775532222    2223332 346777776554

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.18  E-value=2.8e-06  Score=76.05  Aligned_cols=31  Identities=19%  Similarity=0.296  Sum_probs=23.7

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeC
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS  161 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs  161 (297)
                      ..-|+|++|+|||||++.+.+.  .    . .+|+...
T Consensus        33 ~v~i~G~~G~GKT~Ll~~~~~~--~----~-~~~~~~~   63 (350)
T 2qen_A           33 LTLLLGIRRVGKSSLLRAFLNE--R----P-GILIDCR   63 (350)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH--S----S-EEEEEHH
T ss_pred             eEEEECCCcCCHHHHHHHHHHH--c----C-cEEEEee
Confidence            3458899999999999999884  2    1 5677654

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.17  E-value=5.4e-06  Score=67.18  Aligned_cols=70  Identities=17%  Similarity=0.135  Sum_probs=41.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccc---c--CCCceEEEEeCC----CC---CHHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI---E--NFDKRIWVCVSD----PF---DEFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~---~--~F~~~~wv~vs~----~~---~~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      .-|+|.+|+|||+||+.+++.-.-.   .  .....+++..+.    ..   .....+..++..+...++..+|||||+.
T Consensus        46 ~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~  125 (195)
T 1jbk_A           46 PVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELH  125 (195)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGG
T ss_pred             eEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHH
Confidence            3488999999999999998842110   0  112233443211    11   1223344555544434678899999997


Q ss_pred             CC
Q 043781          193 TD  194 (297)
Q Consensus       193 ~~  194 (297)
                      ..
T Consensus       126 ~l  127 (195)
T 1jbk_A          126 TM  127 (195)
T ss_dssp             GG
T ss_pred             HH
Confidence            65

>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=98.15  E-value=4.6e-07  Score=82.29  Aligned_cols=122  Identities=11%  Similarity=0.134  Sum_probs=65.6

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCC---CceEEEEeCCCCC----------------------HHHHHHHHHHhhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENF---DKRIWVCVSDPFD----------------------EFRIAKAIIEGLE  178 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F---~~~~wv~vs~~~~----------------------~~~~~~~i~~~~~  178 (297)
                      ..-|+|++|+|||||++.+++.  ....+   -..+|+..+...+                      ..++...+...+.
T Consensus        47 ~vli~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~  124 (386)
T 2qby_A           47 NIFIYGLTGTGKTAVVKFVLSK--LHKKFLGKFKHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVR  124 (386)
T ss_dssp             CEEEEECTTSSHHHHHHHHHHH--HHHHTCSSCEEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH--HHHHhcCCceEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHh
Confidence            3458899999999999999983  43332   2456666443323                      3333444444443


Q ss_pred             CCCceEEEEEeCCCCCC----ccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH----HHHHHHhhCCCccccC
Q 043781          179 GSEKKFFLILDDVWTDD----YSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK----LRHLTLTLGLRAKFPV  250 (297)
Q Consensus       179 ~~~kr~LiVlDdv~~~~----~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~----~~~v~~~~~~~~~~~l  250 (297)
                      ..+++.+||||+++...    .+.+..+...+...         ...+..+|+||+....    ...+...+.. ..+.+
T Consensus       125 ~~~~~~vlilDE~~~l~~~~~~~~l~~l~~~~~~~---------~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~-~~i~l  194 (386)
T 2qby_A          125 DYGSQVVIVLDEIDAFVKKYNDDILYKLSRINSEV---------NKSKISFIGITNDVKFVDLLDPRVKSSLSE-EEIIF  194 (386)
T ss_dssp             TCCSCEEEEEETHHHHHHSSCSTHHHHHHHHHHSC---------CC--EEEEEEESCGGGGGGCTTHHHHTTTT-EEEEE
T ss_pred             ccCCeEEEEEcChhhhhccCcCHHHHHHhhchhhc---------CCCeEEEEEEECCCChHhhhCHHHhccCCC-eeEEe
Confidence            33569999999997642    11222232222110         1334566777775432    1222233321 35677


Q ss_pred             Cccchhh
Q 043781          251 SIFDAKK  257 (297)
Q Consensus       251 ~~l~~~~  257 (297)
                      .+++..+
T Consensus       195 ~~l~~~~  201 (386)
T 2qby_A          195 PPYNAEE  201 (386)
T ss_dssp             CCCCHHH
T ss_pred             CCCCHHH
Confidence            7776554

>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=98.10  E-value=2e-06  Score=76.42  Aligned_cols=119  Identities=14%  Similarity=0.088  Sum_probs=66.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC-C-CceEEEEeCCCCCHHH---HHHHHHHhhcCC-CceEEEEEeCCCCCCccC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN-F-DKRIWVCVSDPFDEFR---IAKAIIEGLEGS-EKKFFLILDDVWTDDYSK  198 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~-F-~~~~wv~vs~~~~~~~---~~~~i~~~~~~~-~kr~LiVlDdv~~~~~~~  198 (297)
                      .-++|++|+||||+|+.+++.  +... + ...+.+..+.......   .+.......... +++.+||+|+++......
T Consensus        49 ~ll~G~~G~GKT~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~  126 (327)
T 1iqp_A           49 LLFAGPPGVGKTTAALALARE--LFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDA  126 (327)
T ss_dssp             EEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH--hcCCcccCceEEeeccccCchHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHH
Confidence            347899999999999999984  2211 1 1223344333212221   222222211111 578899999998875556


Q ss_pred             HHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhh
Q 043781          199 WEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       199 w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      ++.|...+...          ..++++|+||..... ...+....   ..+.+.+++..++
T Consensus       127 ~~~L~~~le~~----------~~~~~~i~~~~~~~~l~~~l~sr~---~~~~~~~l~~~~~  174 (327)
T 1iqp_A          127 QQALRRTMEMF----------SSNVRFILSCNYSSKIIEPIQSRC---AIFRFRPLRDEDI  174 (327)
T ss_dssp             HHHHHHHHHHT----------TTTEEEEEEESCGGGSCHHHHHTE---EEEECCCCCHHHH
T ss_pred             HHHHHHHHHhc----------CCCCeEEEEeCCccccCHHHHhhC---cEEEecCCCHHHH
Confidence            66677666542          456788888865432 12222222   2456666665553

>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=98.08  E-value=1.8e-05  Score=70.91  Aligned_cols=33  Identities=18%  Similarity=0.348  Sum_probs=24.9

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeC
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS  161 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs  161 (297)
                      ..-|+|++|+|||+|++.+.+.  ...   ..+|+...
T Consensus        32 ~v~i~G~~G~GKT~L~~~~~~~--~~~---~~~~~~~~   64 (357)
T 2fna_A           32 ITLVLGLRRTGKSSIIKIGINE--LNL---PYIYLDLR   64 (357)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH--HTC---CEEEEEGG
T ss_pred             cEEEECCCCCCHHHHHHHHHHh--cCC---CEEEEEch
Confidence            4568899999999999999884  222   24677655

>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=98.08  E-value=6.2e-06  Score=77.25  Aligned_cols=116  Identities=16%  Similarity=0.142  Sum_probs=66.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC--ceEEEEeCCCCCHHHHHHHHHHhhcCC---------C-ceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD--KRIWVCVSDPFDEFRIAKAIIEGLEGS---------E-KKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~--~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~-kr~LiVlDdv~  192 (297)
                      .-|+|.+|+||||||+.+++  .....+.  ..++++.      ..+..++...+...         . +.-+|+|||+.
T Consensus       133 lll~Gp~G~GKTtLa~aia~--~l~~~~~~~~v~~v~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~  204 (440)
T 2z4s_A          133 LFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYITS------EKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQ  204 (440)
T ss_dssp             EEEECSSSSSHHHHHHHHHH--HHHHHCCSSCEEEEEH------HHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGG
T ss_pred             EEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeH------HHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcc
Confidence            45889999999999999998  3433332  2344433      23333333333221         3 67799999998


Q ss_pred             CCCc--cCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-----HHHHHHHhhCCCccccCCccchhh
Q 043781          193 TDDY--SKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-----KLRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       193 ~~~~--~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-----~~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ....  ...+.+...+...         ...|..||+||....     ....+...+....++.+.+++.++
T Consensus       205 ~l~~~~~~q~~l~~~l~~l---------~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~  267 (440)
T 2z4s_A          205 FLIGKTGVQTELFHTFNEL---------HDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEET  267 (440)
T ss_dssp             GGSSCHHHHHHHHHHHHHH---------HTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHH
T ss_pred             cccCChHHHHHHHHHHHHH---------HHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHH
Confidence            7532  1223344444332         156788999987531     124444444323455666665444

>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=98.07  E-value=3.6e-06  Score=68.67  Aligned_cols=91  Identities=16%  Similarity=0.211  Sum_probs=52.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      ..++|++|+|||||++.+++.......+ ..+++      +..++...+.......         .+.-+|||||++...
T Consensus        41 ~~l~G~~G~GKTtL~~~i~~~~~~~~g~-~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~~~  113 (180)
T 3ec2_A           41 LTFVGSPGVGKTHLAVATLKAIYEKKGI-RGYFF------DTKDLIFRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGSER  113 (180)
T ss_dssp             EEECCSSSSSHHHHHHHHHHHHHHHSCC-CCCEE------EHHHHHHHHHHHHHHTCCSHHHHHHHTCSEEEEETCSSSC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHcCC-eEEEE------EHHHHHHHHHHHhcCchHHHHHHHhcCCCEEEEeCCCCCc
Confidence            4689999999999999999842212222 22334      3344444333222211         356799999998532


Q ss_pred             ccCHHH--HHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          196 YSKWEP--FHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       196 ~~~w~~--l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      .+.|..  +...+...         ...|..+|+||..
T Consensus       114 ~~~~~~~~l~~ll~~~---------~~~~~~ii~tsn~  142 (180)
T 3ec2_A          114 LSDWQRELISYIITYR---------YNNLKSTIITTNY  142 (180)
T ss_dssp             CCHHHHHHHHHHHHHH---------HHTTCEEEEECCC
T ss_pred             CCHHHHHHHHHHHHHH---------HHcCCCEEEEcCC
Confidence            244542  33334322         1467788998863

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.04  E-value=4.3e-06  Score=69.41  Aligned_cols=90  Identities=23%  Similarity=0.258  Sum_probs=50.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      .-|+|.+|+|||+||+.+++.  ........++++.+      .+...+.......         .+.-+|||||++...
T Consensus        57 ~~l~G~~GtGKT~la~~i~~~--~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDei~~~~  128 (202)
T 2w58_A           57 LYLHGSFGVGKTYLLAAIANE--LAKRNVSSLIVYVP------ELFRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAEA  128 (202)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEEEHH------HHHHHHHHC---CCCHHHHHHHHHSSEEEEEEECCC-
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEhH------HHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCc
Confidence            458899999999999999984  43333445666532      3333332221110         122399999997753


Q ss_pred             ccCHHH--HH-HHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          196 YSKWEP--FH-NCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       196 ~~~w~~--l~-~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      ...|.+  +- ..+...         ...+.++|+||..
T Consensus       129 ~~~~~~~~ll~~~l~~~---------~~~~~~~i~tsn~  158 (202)
T 2w58_A          129 MSSWVRDDVFGPILQYR---------MFENLPTFFTSNF  158 (202)
T ss_dssp             --CCGGGTTHHHHHHHH---------HHTTCCEEEEESS
T ss_pred             CCHHHHHHHHHHHHHHH---------HhCCCCEEEEcCC
Confidence            344432  22 233221         0345678888873

>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=97.94  E-value=5.3e-06  Score=70.14  Aligned_cols=89  Identities=21%  Similarity=0.199  Sum_probs=50.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccC--HHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSK--WEPF  202 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~--w~~l  202 (297)
                      .-|+|++|+||||||+.+++.  .........|+..+....   .+..++..+   .+.-+|||||+.......  .+.+
T Consensus        55 ~ll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~~~~~---~~~~~~~~~---~~~~vliiDe~~~~~~~~~~~~~l  126 (242)
T 3bos_A           55 IYLWGPVKSGRTHLIHAACAR--ANELERRSFYIPLGIHAS---ISTALLEGL---EQFDLICIDDVDAVAGHPLWEEAI  126 (242)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEGGGGGG---SCGGGGTTG---GGSSEEEEETGGGGTTCHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHHHHHH---HHHHHHHhc---cCCCEEEEeccccccCCHHHHHHH
Confidence            348899999999999999884  333333456666543211   011111222   456799999998764322  3334


Q ss_pred             HHHHhhhhhhhceeeecCCCC-eEEEEec
Q 043781          203 HNCLMRVLQEFAAIEVDGDEN-PLSLTST  230 (297)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~gs-~iiiTTr  230 (297)
                      ...+....         ..+. ++|+||+
T Consensus       127 ~~~l~~~~---------~~~~~~ii~~~~  146 (242)
T 3bos_A          127 FDLYNRVA---------EQKRGSLIVSAS  146 (242)
T ss_dssp             HHHHHHHH---------HHCSCEEEEEES
T ss_pred             HHHHHHHH---------HcCCCeEEEEcC
Confidence            44443321         2223 4788776

>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=97.92  E-value=8.6e-06  Score=72.80  Aligned_cols=115  Identities=23%  Similarity=0.152  Sum_probs=61.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      .-|+|++|+||||||+.+++.  ....-...++++.      .++...+...+...         .+.-+|+|||+....
T Consensus        40 lll~G~~GtGKT~la~~i~~~--~~~~~~~~~~i~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~iDEi~~l~  111 (324)
T 1l8q_A           40 IFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSSA------DDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLS  111 (324)
T ss_dssp             EEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEEH------HHHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGT
T ss_pred             EEEECCCCCcHHHHHHHHHHH--HHHCCCEEEEEEH------HHHHHHHHHHHHcCcHHHHHHHhcCCCEEEEcCccccc
Confidence            348899999999999999984  3221112344532      23333333222111         236799999998753


Q ss_pred             cc--CHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH-----HHHHHHHHhhCCCccccCCccchhh
Q 043781          196 YS--KWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-----EKLRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       196 ~~--~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-----~~~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ..  ..+.+...+...         ...|..||+||...     .....+...+....++.+.+ +.++
T Consensus       112 ~~~~~~~~l~~~l~~~---------~~~~~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e  170 (324)
T 1l8q_A          112 GKERTQIEFFHIFNTL---------YLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKT  170 (324)
T ss_dssp             TCHHHHHHHHHHHHHH---------HHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHH
T ss_pred             CChHHHHHHHHHHHHH---------HHCCCeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHH
Confidence            21  223344444322         14566788887533     12344444443333455655 5443

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.80  E-value=3.5e-05  Score=62.20  Aligned_cols=67  Identities=19%  Similarity=0.280  Sum_probs=39.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccC------CC-ceEEEEeCCC-----C--CHHHHHHHHHHhhcCCCceEEEEEeCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIEN------FD-KRIWVCVSDP-----F--DEFRIAKAIIEGLEGSEKKFFLILDDV  191 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~------F~-~~~wv~vs~~-----~--~~~~~~~~i~~~~~~~~kr~LiVlDdv  191 (297)
                      -|+|.+|+|||+||+.+.+.  ....      .. ..+++..+..     .  .....+..++..+...++..+|||||+
T Consensus        47 ll~G~~G~GKT~la~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~  124 (187)
T 2p65_A           47 ILLGDPGVGKTAIVEGLAIK--IVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEI  124 (187)
T ss_dssp             EEESCGGGCHHHHHHHHHHH--HHTTCSCTTTTTCEEEEECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTG
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHhcCCcchhcCCeEEEEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCH
Confidence            48899999999999999874  2110      11 2223322110     0  112234444444444356789999999


Q ss_pred             CCC
Q 043781          192 WTD  194 (297)
Q Consensus       192 ~~~  194 (297)
                      ...
T Consensus       125 ~~l  127 (187)
T 2p65_A          125 HTV  127 (187)
T ss_dssp             GGG
T ss_pred             HHh
Confidence            764

>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=97.68  E-value=6.9e-05  Score=67.75  Aligned_cols=119  Identities=13%  Similarity=0.175  Sum_probs=65.1

Q ss_pred             cccccCCcchHHHHHHHhcccccccCC-------------------CceEEEEeCCCCCHHHHHHHHHHhhcC---CCce
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENF-------------------DKRIWVCVSDPFDEFRIAKAIIEGLEG---SEKK  183 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F-------------------~~~~wv~vs~~~~~~~~~~~i~~~~~~---~~kr  183 (297)
                      -++|++|+||||+|+.+.+.......+                   ...+.+..+..... +-.+.++..+..   .+++
T Consensus        42 ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~l~~~~~~~~~~~~~  120 (373)
T 1jr3_A           42 LFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKV-EDTRDLLDNVQYAPARGRF  120 (373)
T ss_dssp             EEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHTSCCSSCEEEETTCSCCS-SCHHHHHHHTTSCCSSSSS
T ss_pred             EEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhccCCCceEEecccccCCH-HHHHHHHHHHhhccccCCe
Confidence            478999999999999998742211110                   01233333321111 112334444332   2678


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      .+||+||+.......++.|...+...          ..+..+|++|..... ...+...   ...+.+.+++..++
T Consensus       121 ~vliiDe~~~l~~~~~~~Ll~~le~~----------~~~~~~Il~~~~~~~l~~~l~sr---~~~i~~~~l~~~~~  183 (373)
T 1jr3_A          121 KVYLIDEVHMLSRHSFNALLKTLEEP----------PEHVKFLLATTDPQKLPVTILSR---CLQFHLKALDVEQI  183 (373)
T ss_dssp             EEEEEECGGGSCHHHHHHHHHHHHSC----------CSSEEEEEEESCGGGSCHHHHTT---SEEEECCCCCHHHH
T ss_pred             EEEEEECcchhcHHHHHHHHHHHhcC----------CCceEEEEEeCChHhCcHHHHhh---eeEeeCCCCCHHHH
Confidence            89999999876545566666666431          345567777754321 1222211   24566777765554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=97.67  E-value=8.2e-05  Score=58.45  Aligned_cols=86  Identities=13%  Similarity=-0.044  Sum_probs=49.9

Q ss_pred             cccccCCcchHHHHHHHhccccc-ccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDV-IENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      -|+|.+|+|||+||+.+++...- ...|   + +..+...+... ....+...    ..-.|+||++.....+....|..
T Consensus        28 ll~G~~GtGKt~lA~~i~~~~~~~~~~~---v-~~~~~~~~~~~-~~~~~~~a----~~g~l~ldei~~l~~~~q~~Ll~   98 (145)
T 3n70_A           28 WLYGAPGTGRMTGARYLHQFGRNAQGEF---V-YRELTPDNAPQ-LNDFIALA----QGGTLVLSHPEHLTREQQYHLVQ   98 (145)
T ss_dssp             EEESSTTSSHHHHHHHHHHSSTTTTSCC---E-EEECCTTTSSC-HHHHHHHH----TTSCEEEECGGGSCHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHhCCccCCCE---E-EECCCCCcchh-hhcHHHHc----CCcEEEEcChHHCCHHHHHHHHH
Confidence            48899999999999999984211 2222   2 54443322111 11222222    22478999998875444555555


Q ss_pred             HHhhhhhhhceeeecCCCCeEEEEec
Q 043781          205 CLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       205 ~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      .+...          ....++|.||.
T Consensus        99 ~l~~~----------~~~~~~I~~t~  114 (145)
T 3n70_A           99 LQSQE----------HRPFRLIGIGD  114 (145)
T ss_dssp             HHHSS----------SCSSCEEEEES
T ss_pred             HHhhc----------CCCEEEEEECC
Confidence            55321          34467777775

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.67  E-value=4.3e-05  Score=71.65  Aligned_cols=76  Identities=21%  Similarity=0.203  Sum_probs=42.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc---CCCceEEEEEeCCCCCCccCHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE---GSEKKFFLILDDVWTDDYSKWEP  201 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~---~~~kr~LiVlDdv~~~~~~~w~~  201 (297)
                      .-++|.+|+||||||+.+.+.  ....|   .-+.. ......++ +.++....   ..+++.+|+||++........+.
T Consensus        53 vLL~GppGtGKTtlAr~ia~~--~~~~f---~~l~a-~~~~~~~i-r~~~~~a~~~~~~~~~~iLfIDEI~~l~~~~q~~  125 (447)
T 3pvs_A           53 MILWGPPGTGKTTLAEVIARY--ANADV---ERISA-VTSGVKEI-REAIERARQNRNAGRRTILFVDEVHRFNKSQQDA  125 (447)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--TTCEE---EEEET-TTCCHHHH-HHHHHHHHHHHHTTCCEEEEEETTTCC------C
T ss_pred             EEEECCCCCcHHHHHHHHHHH--hCCCe---EEEEe-ccCCHHHH-HHHHHHHHHhhhcCCCcEEEEeChhhhCHHHHHH
Confidence            358899999999999999983  43333   12222 12233332 22222211   12678999999998876556666


Q ss_pred             HHHHHh
Q 043781          202 FHNCLM  207 (297)
Q Consensus       202 l~~~l~  207 (297)
                      |...+.
T Consensus       126 LL~~le  131 (447)
T 3pvs_A          126 FLPHIE  131 (447)
T ss_dssp             CHHHHH
T ss_pred             HHHHHh
Confidence            666664

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.67  E-value=0.00017  Score=64.49  Aligned_cols=121  Identities=8%  Similarity=-0.003  Sum_probs=67.5

Q ss_pred             cccccCCcchHHHHHHHhccccccc------CCCceEEEEeCCCCCHHHHHHHHHHhhcCC-------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE------NFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~------~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-------------------  180 (297)
                      -|+|++|+|||++++.+.+.-....      .| ..+.++.....+...++..|++++.+.                   
T Consensus        49 li~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~-~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~  127 (318)
T 3te6_A           49 YITNADDSTKFQLVNDVMDELITSSARKELPIF-DYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVP  127 (318)
T ss_dssp             EEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCE-EEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSC
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHhhhccCCce-EEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhh
Confidence            3789999999999999998532111      12 345566555556666666666666321                   


Q ss_pred             ---CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEE--EEeccHH-----HHHHHHHhhCCCccccC
Q 043781          181 ---EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLS--LTSTCQE-----KLRHLTLTLGLRAKFPV  250 (297)
Q Consensus       181 ---~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~ii--iTTr~~~-----~~~~v~~~~~~~~~~~l  250 (297)
                         +++++|+||++..-.  .-+.|...+...         ....++++  .++...+     ....+...++. ..+.+
T Consensus       128 ~~~~~~~ii~lDE~d~l~--~q~~L~~l~~~~---------~~~~s~~~vI~i~n~~d~~~~~L~~~v~SR~~~-~~i~F  195 (318)
T 3te6_A          128 KAKKRKTLILIQNPENLL--SEKILQYFEKWI---------SSKNSKLSIICVGGHNVTIREQINIMPSLKAHF-TEIKL  195 (318)
T ss_dssp             GGGSCEEEEEEECCSSSC--CTHHHHHHHHHH---------HCSSCCEEEEEECCSSCCCHHHHHTCHHHHTTE-EEEEC
T ss_pred             hccCCceEEEEecHHHhh--cchHHHHHHhcc---------cccCCcEEEEEEecCcccchhhcchhhhccCCc-eEEEe
Confidence               568999999998763  223343333211         12334332  2332211     12223344542 45678


Q ss_pred             Cccchhhhh
Q 043781          251 SIFDAKKIW  259 (297)
Q Consensus       251 ~~l~~~~lf  259 (297)
                      .+++..++.
T Consensus       196 ~pYt~~el~  204 (318)
T 3te6_A          196 NKVDKNELQ  204 (318)
T ss_dssp             CCCCHHHHH
T ss_pred             CCCCHHHHH
Confidence            888877764

>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=97.67  E-value=4.7e-05  Score=67.77  Aligned_cols=119  Identities=14%  Similarity=0.020  Sum_probs=76.3

Q ss_pred             ccccCCcchHHHHHHHhccc-ccc-cCCCceEEEEeCC-CCCHHHHHHHHHHhhcCC---CceEEEEEeCCCCCCccCHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDK-DVI-ENFDKRIWVCVSD-PFDEFRIAKAIIEGLEGS---EKKFFLILDDVWTDDYSKWE  200 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~-~~~-~~F~~~~wv~vs~-~~~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~~~~~~w~  200 (297)
                      ++|++|+||||+|+.+.+.. ... .+.+ ...+..+. ...+.++ +++.+.+...   +++-++|+|++.....+..+
T Consensus        23 f~Gp~G~GKtt~a~~la~~~~~~~~~~~d-~~~l~~~~~~~~id~i-r~li~~~~~~p~~~~~kvviIdead~lt~~a~n  100 (305)
T 2gno_A           23 INGEDLSYPREVSLELPEYVEKFPPKASD-VLEIDPEGENIGIDDI-RTIKDFLNYSPELYTRKYVIVHDCERMTQQAAN  100 (305)
T ss_dssp             EECSSSSHHHHHHHHHHHHHHTSCCCTTT-EEEECCSSSCBCHHHH-HHHHHHHTSCCSSSSSEEEEETTGGGBCHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHhCchhhccCCC-EEEEcCCcCCCCHHHH-HHHHHHHhhccccCCceEEEeccHHHhCHHHHH
Confidence            78999999999999998731 111 2333 34555443 4555443 3455555332   67889999999987666777


Q ss_pred             HHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCCCccccCCccchhhhhhh
Q 043781          201 PFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLRAKFPVSIFDAKKIWGW  261 (297)
Q Consensus       201 ~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~~~~~~l~~l~~~~lf~~  261 (297)
                      .|...+...          .+.+.+|++|...+   .+..+.... ++++.+++..++..|
T Consensus       101 aLLk~LEep----------~~~t~fIl~t~~~~---kl~~tI~SR-~~~f~~l~~~~i~~~  147 (305)
T 2gno_A          101 AFLKALEEP----------PEYAVIVLNTRRWH---YLLPTIKSR-VFRVVVNVPKEFRDL  147 (305)
T ss_dssp             HTHHHHHSC----------CTTEEEEEEESCGG---GSCHHHHTT-SEEEECCCCHHHHHH
T ss_pred             HHHHHHhCC----------CCCeEEEEEECChH---hChHHHHce-eEeCCCCCHHHHHHH
Confidence            787777642          45677777775432   344444444 788888887776444

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.62  E-value=0.00022  Score=63.79  Aligned_cols=64  Identities=19%  Similarity=0.237  Sum_probs=40.3

Q ss_pred             ccccccCCcchHHHHHHHhccccc-ccCCCceEEEEeCCCC-----CHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDV-IENFDKRIWVCVSDPF-----DEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~-~~~F~~~~wv~vs~~~-----~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+++.  . ...|   +.+..+.-.     .....++.++..... .+..+|+||++...
T Consensus        48 iLL~GppGtGKT~la~ala~~--~~~~~~---~~i~~~~l~~~~~g~~~~~~~~lf~~a~~-~~~~vl~iDEid~l  117 (322)
T 1xwi_A           48 ILLFGPPGTGKSYLAKAVATE--ANNSTF---FSISSSDLVSKWLGESEKLVKNLFQLARE-NKPSIIFIDEIDSL  117 (322)
T ss_dssp             EEEESSSSSCHHHHHHHHHHH--TTSCEE---EEEECCSSCCSSCCSCHHHHHHHHHHHHH-TSSEEEEEETTTGG
T ss_pred             EEEECCCCccHHHHHHHHHHH--cCCCcE---EEEEhHHHHhhhhhHHHHHHHHHHHHHHh-cCCcEEEeecHHHh
Confidence            447899999999999999983  3 2122   223322211     224455555554433 46789999999754

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=97.56  E-value=7.1e-05  Score=58.70  Aligned_cols=85  Identities=9%  Similarity=0.049  Sum_probs=50.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      +-|+|.+|+|||++|+.+.+..  .      -++.+.-..-.......++...    +.-.|+||++.....+....|..
T Consensus        30 vll~G~~GtGKt~lA~~i~~~~--~------~~~~~~~~~~~~~~~~~~~~~a----~~~~l~lDei~~l~~~~q~~Ll~   97 (143)
T 3co5_A           30 VFLTGEAGSPFETVARYFHKNG--T------PWVSPARVEYLIDMPMELLQKA----EGGVLYVGDIAQYSRNIQTGITF   97 (143)
T ss_dssp             EEEEEETTCCHHHHHGGGCCTT--S------CEECCSSTTHHHHCHHHHHHHT----TTSEEEEEECTTCCHHHHHHHHH
T ss_pred             EEEECCCCccHHHHHHHHHHhC--C------CeEEechhhCChHhhhhHHHhC----CCCeEEEeChHHCCHHHHHHHHH
Confidence            3488999999999999999842  2      2232222211122234444443    23478999998875444555555


Q ss_pred             HHhhhhhhhceeeecCCCCeEEEEec
Q 043781          205 CLMRVLQEFAAIEVDGDENPLSLTST  230 (297)
Q Consensus       205 ~l~~~~~~~~~~~~~~~gs~iiiTTr  230 (297)
                      .+...         ...+.++|.||.
T Consensus        98 ~l~~~---------~~~~~~iI~~tn  114 (143)
T 3co5_A           98 IIGKA---------ERCRVRVIASCS  114 (143)
T ss_dssp             HHHHH---------TTTTCEEEEEEE
T ss_pred             HHHhC---------CCCCEEEEEecC
Confidence            55442         134567888775

>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=97.54  E-value=2.7e-05  Score=68.81  Aligned_cols=120  Identities=15%  Similarity=0.032  Sum_probs=64.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC-ceEEEEeCCCCC---HHHHHHHHHHhhcCC-CceEEEEEeCCCCCCccCH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD-KRIWVCVSDPFD---EFRIAKAIIEGLEGS-EKKFFLILDDVWTDDYSKW  199 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~---~~~~~~~i~~~~~~~-~kr~LiVlDdv~~~~~~~w  199 (297)
                      .-++|++|+|||++|+.+.+.-. ...+. ..+.++.+....   +.+.+.......... +++-++|+|++........
T Consensus        41 ~ll~G~~G~GKt~la~~l~~~l~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~~  119 (319)
T 2chq_A           41 LLFSGPPGTGKTATAIALARDLF-GENWRDNFIEMNASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADAQ  119 (319)
T ss_dssp             EEEESSSSSSHHHHHHHHHHHHH-TTCHHHHCEEEETTSTTCTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHHHH
T ss_pred             EEEECcCCcCHHHHHHHHHHHhc-CCcccCCeEEEeCccccChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHHHH
Confidence            45889999999999999988411 11111 123344443322   233334443222222 5688999999977643333


Q ss_pred             HHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhh
Q 043781          200 EPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       200 ~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      +.|...+..          ...+..+|+||..... ...+...   ...+.+.+++..++
T Consensus       120 ~~L~~~le~----------~~~~~~~i~~~~~~~~l~~~l~sr---~~~i~~~~~~~~~~  166 (319)
T 2chq_A          120 AALRRTMEM----------YSKSCRFILSCNYVSRIIEPIQSR---CAVFRFKPVPKEAM  166 (319)
T ss_dssp             HTTGGGTSS----------SSSSEEEEEEESCGGGSCHHHHTT---CEEEECCCCCHHHH
T ss_pred             HHHHHHHHh----------cCCCCeEEEEeCChhhcchHHHhh---CeEEEecCCCHHHH
Confidence            444333322          1355677777764331 2222222   13566777765554

>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=97.52  E-value=0.00021  Score=64.18  Aligned_cols=120  Identities=12%  Similarity=0.025  Sum_probs=71.6

Q ss_pred             ccccCCcchHHHHHHHhcccccc--------------------cCCCceEEEEeC---CCCCHHHHHHHHHHhhcCC---
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVI--------------------ENFDKRIWVCVS---DPFDEFRIAKAIIEGLEGS---  180 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~--------------------~~F~~~~wv~vs---~~~~~~~~~~~i~~~~~~~---  180 (297)
                      ++|++|+|||++|+.+.+.-.-.                    .|++ ..++...   ....+.++ +++.+.+...   
T Consensus        29 ~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d-~~~~~~~~~~~~~~i~~i-r~l~~~~~~~~~~  106 (334)
T 1a5t_A           29 IQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPD-YYTLAPEKGKNTLGVDAV-REVTEKLNEHARL  106 (334)
T ss_dssp             EECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTT-EEEECCCTTCSSBCHHHH-HHHHHHTTSCCTT
T ss_pred             EECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCC-EEEEeccccCCCCCHHHH-HHHHHHHhhcccc
Confidence            78999999999999887731111                    1233 2344432   33455443 4566655432   


Q ss_pred             CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhhh
Q 043781          181 EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKIW  259 (297)
Q Consensus       181 ~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~lf  259 (297)
                      +++-++|+|++.....+..+.|...+..-          ..+..+|++|...+ ....+-..   ...+.+.+++..++.
T Consensus       107 ~~~kvviIdead~l~~~a~naLLk~lEep----------~~~~~~Il~t~~~~~l~~ti~SR---c~~~~~~~~~~~~~~  173 (334)
T 1a5t_A          107 GGAKVVWVTDAALLTDAAANALLKTLEEP----------PAETWFFLATREPERLLATLRSR---CRLHYLAPPPEQYAV  173 (334)
T ss_dssp             SSCEEEEESCGGGBCHHHHHHHHHHHTSC----------CTTEEEEEEESCGGGSCHHHHTT---SEEEECCCCCHHHHH
T ss_pred             CCcEEEEECchhhcCHHHHHHHHHHhcCC----------CCCeEEEEEeCChHhCcHHHhhc---ceeeeCCCCCHHHHH
Confidence            67889999999887545556666666431          44566777776543 22222222   246778888777654


Q ss_pred             hh
Q 043781          260 GW  261 (297)
Q Consensus       260 ~~  261 (297)
                      .|
T Consensus       174 ~~  175 (334)
T 1a5t_A          174 TW  175 (334)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=97.51  E-value=0.00011  Score=65.57  Aligned_cols=64  Identities=20%  Similarity=0.202  Sum_probs=39.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+++.  ....|   +.+..+    ... .....++.++..... .+..+|+||++...
T Consensus        54 vLl~GppGtGKT~la~aia~~--~~~~~---~~v~~~~l~~~~~g~~~~~~~~~f~~a~~-~~~~vl~iDEid~l  122 (322)
T 3eie_A           54 ILLYGPPGTGKSYLAKAVATE--ANSTF---FSVSSSDLVSKWMGESEKLVKQLFAMARE-NKPSIIFIDQVDAL  122 (322)
T ss_dssp             EEEECSSSSCHHHHHHHHHHH--HTCEE---EEEEHHHHHTTTGGGHHHHHHHHHHHHHH-TSSEEEEEECGGGG
T ss_pred             EEEECCCCCcHHHHHHHHHHH--HCCCE---EEEchHHHhhcccchHHHHHHHHHHHHHh-cCCeEEEechhhhh
Confidence            358899999999999999983  33332   223321    111 233444555444433 46689999999754

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.50  E-value=9.9e-05  Score=58.48  Aligned_cols=85  Identities=16%  Similarity=0.036  Sum_probs=49.2

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFH  203 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~  203 (297)
                      ...|+|..|+|||||++.+++.... ..+ ..+++....-...         .+.  .+.-+|||||+.......-+.+.
T Consensus        38 ~~~l~G~~G~GKTtL~~~i~~~~~~-~g~-~~~~~~~~~~~~~---------~~~--~~~~lLilDE~~~~~~~~~~~l~  104 (149)
T 2kjq_A           38 FIYVWGEEGAGKSHLLQAWVAQALE-AGK-NAAYIDAASMPLT---------DAA--FEAEYLAVDQVEKLGNEEQALLF  104 (149)
T ss_dssp             EEEEESSSTTTTCHHHHHHHHHHHT-TTC-CEEEEETTTSCCC---------GGG--GGCSEEEEESTTCCCSHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh-cCC-cEEEEcHHHhhHH---------HHH--hCCCEEEEeCccccChHHHHHHH
Confidence            3568999999999999999984321 111 2556655433221         111  24568899999775322222343


Q ss_pred             HHHhhhhhhhceeeecCCCC-eEEEEec
Q 043781          204 NCLMRVLQEFAAIEVDGDEN-PLSLTST  230 (297)
Q Consensus       204 ~~l~~~~~~~~~~~~~~~gs-~iiiTTr  230 (297)
                      ..+....         ..|. .||+||+
T Consensus       105 ~li~~~~---------~~g~~~iiits~  123 (149)
T 2kjq_A          105 SIFNRFR---------NSGKGFLLLGSE  123 (149)
T ss_dssp             HHHHHHH---------HHTCCEEEEEES
T ss_pred             HHHHHHH---------HcCCcEEEEECC
Confidence            4333221         2344 4888887

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=97.48  E-value=7.1e-05  Score=65.32  Aligned_cols=63  Identities=22%  Similarity=0.250  Sum_probs=38.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .-|+|++|+|||+||+.+++.  ....|   +.+..+.    .. .....+..++..... .+..+|+||++..
T Consensus        54 ~ll~G~~GtGKT~la~~la~~--~~~~~---~~v~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~vl~iDEid~  121 (285)
T 3h4m_A           54 ILLYGPPGTGKTLLAKAVATE--TNATF---IRVVGSELVKKFIGEGASLVKDIFKLAKE-KAPSIIFIDEIDA  121 (285)
T ss_dssp             EEEESSSSSSHHHHHHHHHHH--TTCEE---EEEEGGGGCCCSTTHHHHHHHHHHHHHHH-TCSEEEEEETTHH
T ss_pred             EEEECCCCCcHHHHHHHHHHH--hCCCE---EEEehHHHHHhccchHHHHHHHHHHHHHH-cCCeEEEEECHHH
Confidence            458899999999999999984  32222   2232221    11 123444455444433 4568999999965

>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=97.47  E-value=0.00013  Score=65.50  Aligned_cols=121  Identities=13%  Similarity=0.043  Sum_probs=64.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC-ceEEEEeCCCCCHHHHHHHH---HHh-----------hcCCCceEEEEEe
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD-KRIWVCVSDPFDEFRIAKAI---IEG-----------LEGSEKKFFLILD  189 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i---~~~-----------~~~~~kr~LiVlD  189 (297)
                      .-++|++|+||||||+.+.+.-.....+. ....+..+.......+...+   ...           ....++.-+|++|
T Consensus        61 ~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiD  140 (353)
T 1sxj_D           61 MLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILD  140 (353)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEET
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccchHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEE
Confidence            45889999999999999988421111121 12333444333333322211   111           0011456799999


Q ss_pred             CCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH-HHHHHHHhhCCCccccCCccchhhh
Q 043781          190 DVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-KLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       190 dv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      ++........+.|...+...          ....++|++|.... ....+....   ..+.+.+++..++
T Consensus       141 E~~~l~~~~~~~Ll~~le~~----------~~~~~~il~~~~~~~l~~~l~sR~---~~i~~~~~~~~~~  197 (353)
T 1sxj_D          141 EADSMTADAQSALRRTMETY----------SGVTRFCLICNYVTRIIDPLASQC---SKFRFKALDASNA  197 (353)
T ss_dssp             TGGGSCHHHHHHHHHHHHHT----------TTTEEEEEEESCGGGSCHHHHHHS---EEEECCCCCHHHH
T ss_pred             CCCccCHHHHHHHHHHHHhc----------CCCceEEEEeCchhhCcchhhccC---ceEEeCCCCHHHH
Confidence            99876544555666666542          34566777765332 223333332   2456666665554

>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=97.42  E-value=0.00018  Score=63.72  Aligned_cols=76  Identities=20%  Similarity=0.117  Sum_probs=46.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-|+|++|+|||+||+.+++.  ....   ..++..+......++...+...+   .+..+|+||++..........|..
T Consensus        41 vll~G~~GtGKT~la~~i~~~--~~~~---~~~~~~~~~~~~~~l~~~l~~~~---~~~~~l~lDEi~~l~~~~~~~L~~  112 (324)
T 1hqc_A           41 LLLFGPPGLGKTTLAHVIAHE--LGVN---LRVTSGPAIEKPGDLAAILANSL---EEGDILFIDEIHRLSRQAEEHLYP  112 (324)
T ss_dssp             CEEECCTTCCCHHHHHHHHHH--HTCC---EEEECTTTCCSHHHHHHHHTTTC---CTTCEEEETTTTSCCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCCC---EEEEeccccCChHHHHHHHHHhc---cCCCEEEEECCcccccchHHHHHH
Confidence            458899999999999999883  3222   23454444444444443222212   456699999998775434445555


Q ss_pred             HHhh
Q 043781          205 CLMR  208 (297)
Q Consensus       205 ~l~~  208 (297)
                      .+..
T Consensus       113 ~l~~  116 (324)
T 1hqc_A          113 AMED  116 (324)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            5543

>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=97.41  E-value=0.00045  Score=61.35  Aligned_cols=112  Identities=13%  Similarity=0.099  Sum_probs=63.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHH---HHHhhcCCCceEEEEEeCCCCCC-ccCHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKA---IIEGLEGSEKKFFLILDDVWTDD-YSKWEPF  202 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~---i~~~~~~~~kr~LiVlDdv~~~~-~~~w~~l  202 (297)
                      +.|++|+|||++|+.+.+.  ...   ..+.++.+. .....+...   ........+++-+|+||++.... .+..+.|
T Consensus        53 ~~G~~G~GKT~la~~la~~--l~~---~~~~i~~~~-~~~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L  126 (324)
T 3u61_B           53 HSPSPGTGKTTVAKALCHD--VNA---DMMFVNGSD-CKIDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAESQRHL  126 (324)
T ss_dssp             ECSSTTSSHHHHHHHHHHH--TTE---EEEEEETTT-CCHHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGGHHHHHHH
T ss_pred             eeCcCCCCHHHHHHHHHHH--hCC---CEEEEcccc-cCHHHHHHHHHHHHhhcccCCCCeEEEEECCcccCcHHHHHHH
Confidence            5588999999999999883  321   234455443 333333222   22222222588999999998764 3455556


Q ss_pred             HHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhh
Q 043781          203 HNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKK  257 (297)
Q Consensus       203 ~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~  257 (297)
                      ...+...          ..+.++|+||..... ...+....   .++.+..++..+
T Consensus       127 ~~~le~~----------~~~~~iI~~~n~~~~l~~~l~sR~---~~i~~~~~~~~e  169 (324)
T 3u61_B          127 RSFMEAY----------SSNCSIIITANNIDGIIKPLQSRC---RVITFGQPTDED  169 (324)
T ss_dssp             HHHHHHH----------GGGCEEEEEESSGGGSCTTHHHHS---EEEECCCCCHHH
T ss_pred             HHHHHhC----------CCCcEEEEEeCCccccCHHHHhhC---cEEEeCCCCHHH
Confidence            6555442          345778888764331 12222222   346666666443

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.39  E-value=0.00012  Score=65.22  Aligned_cols=67  Identities=19%  Similarity=0.239  Sum_probs=36.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccc-cCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI-ENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~-~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~  194 (297)
                      .-++|.+|+|||+||..+++.  .. ..--..+++++      .+++..+.......         .+.-||||||+...
T Consensus       155 lll~G~~GtGKT~La~aia~~--~~~~~g~~v~~~~~------~~l~~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~  226 (308)
T 2qgz_A          155 LYLYGDMGIGKSYLLAAMAHE--LSEKKGVSTTLLHF------PSFAIDVKNAISNGSVKEEIDAVKNVPVLILDDIGAE  226 (308)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HHHHSCCCEEEEEH------HHHHHHHHCCCC----CCTTHHHHTSSEEEEETCCC-
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHhcCCcEEEEEH------HHHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCC
Confidence            347899999999999999984  32 22223445543      33444443322110         22348999999654


Q ss_pred             CccCH
Q 043781          195 DYSKW  199 (297)
Q Consensus       195 ~~~~w  199 (297)
                      ..+.|
T Consensus       227 ~~~~~  231 (308)
T 2qgz_A          227 QATSW  231 (308)
T ss_dssp             -----
T ss_pred             CCCHH
Confidence            32344

>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=97.38  E-value=0.00026  Score=63.58  Aligned_cols=64  Identities=5%  Similarity=0.027  Sum_probs=39.3

Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      +.-++|||++...+....+.|...+...          ..+..+|++|...+. ...+....   ..+.+.+++..++
T Consensus       134 ~~~vlilDE~~~L~~~~~~~L~~~le~~----------~~~~~~Il~t~~~~~l~~~l~sR~---~~~~~~~~~~~~~  198 (354)
T 1sxj_E          134 RYKCVIINEANSLTKDAQAALRRTMEKY----------SKNIRLIMVCDSMSPIIAPIKSQC---LLIRCPAPSDSEI  198 (354)
T ss_dssp             CCEEEEEECTTSSCHHHHHHHHHHHHHS----------TTTEEEEEEESCSCSSCHHHHTTS---EEEECCCCCHHHH
T ss_pred             CCeEEEEeCccccCHHHHHHHHHHHHhh----------cCCCEEEEEeCCHHHHHHHHHhhc---eEEecCCcCHHHH
Confidence            6679999999887655566676666542          456778888764321 22222221   4567777766654

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.34  E-value=0.00075  Score=62.06  Aligned_cols=62  Identities=19%  Similarity=0.220  Sum_probs=41.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CCC-HHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PFD-EFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      ++|++|+|||.||+.+++  +...+|   +.+..+.    ... ....++.++..... ...++|++|++...
T Consensus       187 L~GPPGTGKTllAkAiA~--e~~~~f---~~v~~s~l~sk~vGese~~vr~lF~~Ar~-~aP~IIFiDEiDai  253 (405)
T 4b4t_J          187 LYGPPGTGKTLLARAVAH--HTDCKF---IRVSGAELVQKYIGEGSRMVRELFVMARE-HAPSIIFMDEIDSI  253 (405)
T ss_dssp             EESCSSSSHHHHHHHHHH--HHTCEE---EEEEGGGGSCSSTTHHHHHHHHHHHHHHH-TCSEEEEEESSSCC
T ss_pred             EeCCCCCCHHHHHHHHHH--hhCCCc---eEEEhHHhhccccchHHHHHHHHHHHHHH-hCCceEeeecchhh
Confidence            579999999999999999  344443   3344332    222 34556666655543 57899999999853

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.33  E-value=0.00014  Score=65.77  Aligned_cols=21  Identities=29%  Similarity=0.270  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|+|||+||+.+.+.
T Consensus        73 vLl~GppGtGKT~la~~la~~   93 (368)
T 3uk6_A           73 VLIAGQPGTGKTAIAMGMAQA   93 (368)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999984

>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=97.26  E-value=0.00096  Score=62.32  Aligned_cols=21  Identities=29%  Similarity=0.279  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|+|||+||+.+++.
T Consensus       170 vLL~GppGtGKT~lA~aia~~  190 (444)
T 2zan_A          170 ILLFGPPGTGKSYLAKAVATE  190 (444)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999984

>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=97.22  E-value=0.00099  Score=56.96  Aligned_cols=64  Identities=14%  Similarity=0.178  Sum_probs=37.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC-----HHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD-----EFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-----~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+++.  ...+|   +.+..+.-.+     ....+..++..... ....+|+||++...
T Consensus        42 vll~G~~GtGKT~la~~la~~--~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~a~~-~~~~vl~iDeid~l  110 (262)
T 2qz4_A           42 ALLLGPPGCGKTLLAKAVATE--AQVPF---LAMAGAEFVEVIGGLGAARVRSLFKEARA-RAPCIVYIDEIDAV  110 (262)
T ss_dssp             EEEESCTTSSHHHHHHHHHHH--HTCCE---EEEETTTTSSSSTTHHHHHHHHHHHHHHH-TCSEEEEEECC---
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCCCE---EEechHHHHhhccChhHHHHHHHHHHHHh-cCCeEEEEeCcchh
Confidence            348899999999999999983  33222   3344332211     12334444444332 35789999999764

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.22  E-value=0.00057  Score=60.11  Aligned_cols=93  Identities=16%  Similarity=0.096  Sum_probs=49.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC--ceEEEEeCC----CC-CHHHHHHHHHHhhcCCCceEEEEEeCCCCC---
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD--KRIWVCVSD----PF-DEFRIAKAIIEGLEGSEKKFFLILDDVWTD---  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~--~~~wv~vs~----~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~---  194 (297)
                      .-++|.+|+|||+||+.+.+.-.......  ..+.+..+.    .+ ....-...++...    +.-+|+||++...   
T Consensus        70 vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~----~~~vl~iDEid~l~~~  145 (309)
T 3syl_A           70 MSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRA----MGGVLFIDEAYYLYRP  145 (309)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGTCCSSTTCHHHHHHHHHHHH----TTSEEEEETGGGSCCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHhhhhcccccHHHHHHHHHhc----CCCEEEEEChhhhccC
Confidence            34889999999999998877321111111  122222111    11 1223334444444    2349999999843   


Q ss_pred             ------CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          195 ------DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       195 ------~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                            .......|...+...          ..+..+|+||..
T Consensus       146 ~~~~~~~~~~~~~Ll~~l~~~----------~~~~~~i~~~~~  178 (309)
T 3syl_A          146 DNERDYGQEAIEILLQVMENN----------RDDLVVILAGYA  178 (309)
T ss_dssp             C---CCTHHHHHHHHHHHHHC----------TTTCEEEEEECH
T ss_pred             CCcccccHHHHHHHHHHHhcC----------CCCEEEEEeCCh
Confidence                  222334454444432          445667777753

>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=97.21  E-value=0.00026  Score=64.25  Aligned_cols=64  Identities=20%  Similarity=0.202  Sum_probs=38.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+++.  ....|   +.+..+    ... .....++.++..... .+..+|+||++...
T Consensus        87 iLL~GppGtGKT~la~ala~~--~~~~~---~~v~~~~l~~~~~g~~~~~~~~~f~~a~~-~~~~vl~iDEid~l  155 (355)
T 2qp9_X           87 ILLYGPPGTGKSYLAKAVATE--ANSTF---FSVSSSDLVSKWMGESEKLVKQLFAMARE-NKPSIIFIDQVDAL  155 (355)
T ss_dssp             EEEECSTTSCHHHHHHHHHHH--HTCEE---EEEEHHHHHSCC---CHHHHHHHHHHHHH-TSSEEEEEECGGGG
T ss_pred             EEEECCCCCcHHHHHHHHHHH--hCCCE---EEeeHHHHhhhhcchHHHHHHHHHHHHHH-cCCeEEEEechHhh
Confidence            347899999999999999984  33222   222211    111 112334444443322 46789999999864

>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=97.20  E-value=0.00044  Score=59.92  Aligned_cols=63  Identities=24%  Similarity=0.269  Sum_probs=37.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC-C--CH---HHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP-F--DE---FRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-~--~~---~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .-++|++|+|||+||+.+.+.  ....|   +.+..+.. +  ..   ...+..++..... .+..+|+||++..
T Consensus        67 vLl~G~~GtGKT~la~~ia~~--~~~~~---~~i~~~~~~~g~~~~~~~~~~~~~~~~~~~-~~~~vl~iDEid~  135 (272)
T 1d2n_A           67 VLLEGPPHSGKTALAAKIAEE--SNFPF---IKICSPDKMIGFSETAKCQAMKKIFDDAYK-SQLSCVVVDDIER  135 (272)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HTCSE---EEEECGGGCTTCCHHHHHHHHHHHHHHHHT-SSEEEEEECCHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHH--hCCCE---EEEeCHHHhcCCchHHHHHHHHHHHHHHHh-cCCcEEEEEChhh
Confidence            347899999999999999984  32222   22222211 1  11   1233344444322 4688999999865

>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=97.20  E-value=0.00044  Score=62.06  Aligned_cols=94  Identities=15%  Similarity=0.105  Sum_probs=54.6

Q ss_pred             ccccccCCcchHHHHHHHhccccccc-CCC-ceEEEEeCCCCCHHHHHHHHHHhhc-----CCCceEEEEEeCCCCCCcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE-NFD-KRIWVCVSDPFDEFRIAKAIIEGLE-----GSEKKFFLILDDVWTDDYS  197 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~-~F~-~~~wv~vs~~~~~~~~~~~i~~~~~-----~~~kr~LiVlDdv~~~~~~  197 (297)
                      .-++|++|+||||+|+.+.+.  +.. .+. ...-++.+.......+.. ++..+.     ..+.+-++|+|++.....+
T Consensus        49 ~ll~Gp~G~GKTtla~~la~~--l~~~~~~~~~~~~~~~~~~~~~~ir~-~i~~~~~~~~~~~~~~~viiiDe~~~l~~~  125 (340)
T 1sxj_C           49 LLFYGPPGTGKTSTIVALARE--IYGKNYSNMVLELNASDDRGIDVVRN-QIKDFASTRQIFSKGFKLIILDEADAMTNA  125 (340)
T ss_dssp             EEEECSSSSSHHHHHHHHHHH--HHTTSHHHHEEEECTTSCCSHHHHHT-HHHHHHHBCCSSSCSCEEEEETTGGGSCHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HcCCCccceEEEEcCcccccHHHHHH-HHHHHHhhcccCCCCceEEEEeCCCCCCHH
Confidence            358899999999999999884  211 111 122333444334444332 222221     1145788999999876545


Q ss_pred             CHHHHHHHHhhhhhhhceeeecCCCCeEEEEecc
Q 043781          198 KWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTC  231 (297)
Q Consensus       198 ~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~  231 (297)
                      ..+.|...+...          .....+|++|..
T Consensus       126 ~~~~L~~~le~~----------~~~~~~il~~n~  149 (340)
T 1sxj_C          126 AQNALRRVIERY----------TKNTRFCVLANY  149 (340)
T ss_dssp             HHHHHHHHHHHT----------TTTEEEEEEESC
T ss_pred             HHHHHHHHHhcC----------CCCeEEEEEecC
Confidence            566676666542          345566666653

>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=97.19  E-value=0.00047  Score=62.50  Aligned_cols=63  Identities=13%  Similarity=0.140  Sum_probs=39.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-----CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-----DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-----~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .-|+|++|+|||+||+.+++.  ....   .+.+..+.-.     ......+.++..... .+..+|+||++..
T Consensus       120 vLl~GppGtGKT~la~aia~~--~~~~---~~~i~~~~l~~~~~g~~~~~~~~~~~~a~~-~~~~vl~iDEid~  187 (357)
T 3d8b_A          120 ILLFGPPGTGKTLIGKCIASQ--SGAT---FFSISASSLTSKWVGEGEKMVRALFAVARC-QQPAVIFIDEIDS  187 (357)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH--TTCE---EEEEEGGGGCCSSTTHHHHHHHHHHHHHHH-TCSEEEEEETHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--cCCe---EEEEehHHhhccccchHHHHHHHHHHHHHh-cCCeEEEEeCchh
Confidence            458899999999999999883  3222   2344433221     123444555544432 4678999999954

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.19  E-value=0.0014  Score=57.24  Aligned_cols=64  Identities=19%  Similarity=0.183  Sum_probs=40.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC-----CCHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP-----FDEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-----~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+||||||+.+.+.  ....|   +.+..+.-     .......+.++..... .+..+|+||++...
T Consensus        57 vll~Gp~GtGKT~la~~la~~--~~~~~---~~i~~~~l~~~~~~~~~~~~~~~~~~~~~-~~~~vl~iDEid~l  125 (297)
T 3b9p_A           57 LLLFGPPGNGKTLLARAVATE--CSATF---LNISAASLTSKYVGDGEKLVRALFAVARH-MQPSIIFIDEVDSL  125 (297)
T ss_dssp             EEEESSSSSCHHHHHHHHHHH--TTCEE---EEEESTTTSSSSCSCHHHHHHHHHHHHHH-TCSEEEEEETGGGT
T ss_pred             EEEECcCCCCHHHHHHHHHHH--hCCCe---EEeeHHHHhhcccchHHHHHHHHHHHHHH-cCCcEEEeccHHHh
Confidence            358899999999999999983  32222   23443322     1234555555544433 46789999999764

>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=97.16  E-value=0.00055  Score=60.00  Aligned_cols=67  Identities=18%  Similarity=0.120  Sum_probs=40.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCC----CceEEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGS----EKKFFLILDDVWTD  194 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~----~kr~LiVlDdv~~~  194 (297)
                      -++|.+|+|||+||+.+.+.  ....   .+.+..+.-.       +....+..+.....+.    +...+|+||++...
T Consensus        54 ll~G~~GtGKT~la~~la~~--l~~~---~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l  128 (310)
T 1ofh_A           54 LMIGPTGVGKTEIARRLAKL--ANAP---FIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKI  128 (310)
T ss_dssp             EEECCTTSSHHHHHHHHHHH--HTCC---EEEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGG
T ss_pred             EEECCCCCCHHHHHHHHHHH--hCCC---EEEEcchhcccCCccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhc
Confidence            47899999999999999883  3222   2333332211       1234455554433211    24679999999876


Q ss_pred             Ccc
Q 043781          195 DYS  197 (297)
Q Consensus       195 ~~~  197 (297)
                      ...
T Consensus       129 ~~~  131 (310)
T 1ofh_A          129 CKK  131 (310)
T ss_dssp             SCC
T ss_pred             Ccc
Confidence            433

>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=97.16  E-value=0.00056  Score=61.03  Aligned_cols=61  Identities=21%  Similarity=0.232  Sum_probs=42.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEe--CCC-----CCHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV--SDP-----FDEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v--s~~-----~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      -|+|++|+||||||.++...     .-...+|+++  +..     .+...++..+.+.+..  .+ |||+|++...
T Consensus       127 LI~GpPGsGKTtLAlqlA~~-----~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~--~~-LLVIDsI~aL  194 (331)
T 2vhj_A          127 IVTGKGNSGKTPLVHALGEA-----LGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQ--HR-VIVIDSLKNV  194 (331)
T ss_dssp             EEECSCSSSHHHHHHHHHHH-----HHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHH--CS-EEEEECCTTT
T ss_pred             EEEcCCCCCHHHHHHHHHHh-----CCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhh--CC-EEEEeccccc
Confidence            47899999999999998874     1113345555  111     3567777777776654  23 9999999865

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.04  E-value=0.00083  Score=61.51  Aligned_cols=64  Identities=17%  Similarity=0.157  Sum_probs=37.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-----CHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-----DEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-----~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-|+|.+|+|||+||+.+.+.  ....|   +.+..+.-.     .....+..++..... .+..+|+||++...
T Consensus       151 vLL~GppGtGKT~la~aia~~--~~~~~---~~v~~~~l~~~~~g~~~~~~~~~~~~a~~-~~~~il~iDEid~l  219 (389)
T 3vfd_A          151 LLLFGPPGNGKTMLAKAVAAE--SNATF---FNISAASLTSKYVGEGEKLVRALFAVARE-LQPSIIFIDQVDSL  219 (389)
T ss_dssp             EEEESSTTSCHHHHHHHHHHH--TTCEE---EEECSCCC-------CHHHHHHHHHHHHH-SSSEEEEEETGGGG
T ss_pred             EEEECCCCCCHHHHHHHHHHh--hcCcE---EEeeHHHhhccccchHHHHHHHHHHHHHh-cCCeEEEEECchhh
Confidence            348899999999999999873  32222   223222211     112334444444332 35579999999643

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.03  E-value=0.00087  Score=58.94  Aligned_cols=81  Identities=15%  Similarity=0.177  Sum_probs=45.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC---HHHHH------------HHHHHhhcCCCceEEEEEe
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD---EFRIA------------KAIIEGLEGSEKKFFLILD  189 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~---~~~~~------------~~i~~~~~~~~kr~LiVlD  189 (297)
                      .-++|.+|+|||+||+.+.+.  ....-...+.+..+....   ...++            ..+...+.. ...-+|+||
T Consensus        50 ~ll~G~~GtGKt~la~~la~~--~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~~~-~~~~vl~lD  126 (311)
T 4fcw_A           50 FLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILFD  126 (311)
T ss_dssp             EEEESCSSSSHHHHHHHHHHH--HHSCGGGEEEEEGGGCCSTTHHHHHHCCCTTSTTTTTCCHHHHHHHH-CSSEEEEEE
T ss_pred             EEEECCCCcCHHHHHHHHHHH--HcCCCcceEEeecccccccccHHHhcCCCCccccccccchHHHHHHh-CCCeEEEEe
Confidence            458899999999999999983  322112234444332211   11111            011111111 234699999


Q ss_pred             CCCCCCccCHHHHHHHHhh
Q 043781          190 DVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       190 dv~~~~~~~w~~l~~~l~~  208 (297)
                      ++..........|...+..
T Consensus       127 Ei~~l~~~~~~~Ll~~le~  145 (311)
T 4fcw_A          127 AIEKAHPDVFNILLQMLDD  145 (311)
T ss_dssp             TGGGSCHHHHHHHHHHHHH
T ss_pred             ChhhcCHHHHHHHHHHHhc
Confidence            9988765566666666654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.89  E-value=0.0018  Score=57.77  Aligned_cols=75  Identities=20%  Similarity=0.141  Sum_probs=45.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHN  204 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~  204 (297)
                      .-|+|++|+|||+||+.+.+.  ....|   +.+..+....... +..++...   .+.-+|+||++..........|..
T Consensus        58 vll~G~~GtGKT~la~~ia~~--~~~~~---~~~~~~~~~~~~~-~~~~~~~~---~~~~vl~lDEi~~l~~~~~~~Ll~  128 (338)
T 3pfi_A           58 ILFSGPAGLGKTTLANIISYE--MSANI---KTTAAPMIEKSGD-LAAILTNL---SEGDILFIDEIHRLSPAIEEVLYP  128 (338)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--TTCCE---EEEEGGGCCSHHH-HHHHHHTC---CTTCEEEEETGGGCCHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH--hCCCe---EEecchhccchhH-HHHHHHhc---cCCCEEEEechhhcCHHHHHHHHH
Confidence            348899999999999999873  33332   2333332223333 33333332   456799999998875444555555


Q ss_pred             HHhh
Q 043781          205 CLMR  208 (297)
Q Consensus       205 ~l~~  208 (297)
                      .+..
T Consensus       129 ~l~~  132 (338)
T 3pfi_A          129 AMED  132 (338)
T ss_dssp             HHHT
T ss_pred             HHHh
Confidence            5543

>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=96.89  E-value=0.0016  Score=61.92  Aligned_cols=65  Identities=25%  Similarity=0.247  Sum_probs=39.6

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc-----------------CCCceEEE
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE-----------------GSEKKFFL  186 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~-----------------~~~kr~Li  186 (297)
                      ..-|+|++|+||||||+.+.+.  ..  + ..+.+..+...... +....+....                 ..+++.+|
T Consensus        79 ~lLL~GppGtGKTtla~~la~~--l~--~-~~i~in~s~~~~~~-~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vl  152 (516)
T 1sxj_A           79 AAMLYGPPGIGKTTAAHLVAQE--LG--Y-DILEQNASDVRSKT-LLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVI  152 (516)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH--TT--C-EEEEECTTSCCCHH-HHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--cC--C-CEEEEeCCCcchHH-HHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEE
Confidence            3457899999999999999984  31  1 22344444443332 2222222110                 11578899


Q ss_pred             EEeCCCCC
Q 043781          187 ILDDVWTD  194 (297)
Q Consensus       187 VlDdv~~~  194 (297)
                      +||++...
T Consensus       153 iIDEid~l  160 (516)
T 1sxj_A          153 IMDEVDGM  160 (516)
T ss_dssp             EECSGGGC
T ss_pred             EEECCCcc
Confidence            99999875

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.87  E-value=0.0017  Score=60.43  Aligned_cols=61  Identities=25%  Similarity=0.317  Sum_probs=40.5

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC----CC-HHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP----FD-EFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~----~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|++|+|||+||+.+++.  ...+|   +.+..+.-    .. ....++.++..... ...++|++|++..
T Consensus       220 L~GPPGtGKTllAkAiA~e--~~~~~---~~v~~s~l~sk~~Gese~~ir~~F~~A~~-~~P~IifiDEiDa  285 (437)
T 4b4t_L          220 LYGPPGTGKTLLAKAVAAT--IGANF---IFSPASGIVDKYIGESARIIREMFAYAKE-HEPCIIFMDEVDA  285 (437)
T ss_dssp             EESCTTSSHHHHHHHHHHH--HTCEE---EEEEGGGTCCSSSSHHHHHHHHHHHHHHH-SCSEEEEEECCCS
T ss_pred             EECCCCCcHHHHHHHHHHH--hCCCE---EEEehhhhccccchHHHHHHHHHHHHHHh-cCCceeeeecccc
Confidence            5799999999999999993  43333   33443322    22 24455555554433 5789999999975

>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=96.85  E-value=0.0028  Score=54.52  Aligned_cols=80  Identities=16%  Similarity=0.041  Sum_probs=42.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc----C-----C-----CceEEEEEeC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE----G-----S-----EKKFFLILDD  190 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~----~-----~-----~kr~LiVlDd  190 (297)
                      .-|+|.+|+|||+||+.+++.  ....-...+.++.+.. ....+...++....    +     .     ...-+|+||+
T Consensus        32 vll~G~~GtGKt~la~~i~~~--~~~~~~~~~~v~~~~~-~~~~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lDE  108 (265)
T 2bjv_A           32 VLIIGERGTGKELIASRLHYL--SSRWQGPFISLNCAAL-NENLLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDE  108 (265)
T ss_dssp             EEEECCTTSCHHHHHHHHHHT--STTTTSCEEEEEGGGS-CHHHHHHHHHCCC---------CCCCHHHHTTTSEEEEES
T ss_pred             EEEECCCCCcHHHHHHHHHHh--cCccCCCeEEEecCCC-ChhHHHHHhcCCcccccccccccccchhhhcCCcEEEEec
Confidence            347899999999999999984  2211112334444432 22211111211000    0     0     1234899999


Q ss_pred             CCCCCccCHHHHHHHHh
Q 043781          191 VWTDDYSKWEPFHNCLM  207 (297)
Q Consensus       191 v~~~~~~~w~~l~~~l~  207 (297)
                      +.....+....|...+.
T Consensus       109 i~~l~~~~q~~Ll~~l~  125 (265)
T 2bjv_A          109 LATAPMMVQEKLLRVIE  125 (265)
T ss_dssp             GGGSCHHHHHHHHHHHH
T ss_pred             hHhcCHHHHHHHHHHHH
Confidence            98875444445555554

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.82  E-value=0.0032  Score=58.75  Aligned_cols=61  Identities=25%  Similarity=0.279  Sum_probs=40.8

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCCC-HHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPFD-EFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|++|+|||+||+.+++  +...+|   +.+..+    .... ....++.++..... ...++|++|++..
T Consensus       248 LyGPPGTGKTlLAkAiA~--e~~~~f---i~vs~s~L~sk~vGesek~ir~lF~~Ar~-~aP~IIfiDEiDa  313 (467)
T 4b4t_H          248 LYGPPGTGKTLCARAVAN--RTDATF---IRVIGSELVQKYVGEGARMVRELFEMART-KKACIIFFDEIDA  313 (467)
T ss_dssp             ECSCTTSSHHHHHHHHHH--HHTCEE---EEEEGGGGCCCSSSHHHHHHHHHHHHHHH-TCSEEEEEECCTT
T ss_pred             eeCCCCCcHHHHHHHHHh--ccCCCe---EEEEhHHhhcccCCHHHHHHHHHHHHHHh-cCCceEeeccccc
Confidence            569999999999999999  344333   333322    2222 24455666555443 5789999999975

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=96.81  E-value=0.00021  Score=59.72  Aligned_cols=87  Identities=20%  Similarity=0.185  Sum_probs=46.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNC  205 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~~  205 (297)
                      -++|++|+||||+|..+.+.  +...  ...+++  .....      .+..+.  +.+ |++|||+...   .|+.+...
T Consensus        62 li~GPPGtGKTt~a~ala~~--l~g~--i~~fan--s~s~f------~l~~l~--~~k-IiiLDEad~~---~~~~~d~~  123 (212)
T 1tue_A           62 VFCGPANTGKSYFGMSFIHF--IQGA--VISFVN--STSHF------WLEPLT--DTK-VAMLDDATTT---CWTYFDTY  123 (212)
T ss_dssp             EEESCGGGCHHHHHHHHHHH--HTCE--ECCCCC--SSSCG------GGGGGT--TCS-SEEEEEECHH---HHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH--hCCC--eeeEEe--ccchh------hhcccC--CCC-EEEEECCCch---hHHHHHHH
Confidence            47899999999999888873  3221  011111  11000      011111  223 8999999643   57666656


Q ss_pred             Hhhhhhhhceee-------ecCCCCeEEEEec
Q 043781          206 LMRVLQEFAAIE-------VDGDENPLSLTST  230 (297)
Q Consensus       206 l~~~~~~~~~~~-------~~~~gs~iiiTTr  230 (297)
                      +...+.+.....       ..-+.-.+||||.
T Consensus       124 lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN  155 (212)
T 1tue_A          124 MRNALDGNPISIDRKHKPLIQLKCPPILLTTN  155 (212)
T ss_dssp             CHHHHHTCCEEEC----CCEEECCCCEEEEES
T ss_pred             HHHHhCCCcccHHHhhcCccccCCCCEEEecC
Confidence            555443321000       0113458999996

>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=96.70  E-value=0.0035  Score=63.34  Aligned_cols=69  Identities=22%  Similarity=0.198  Sum_probs=40.2

Q ss_pred             cccccCCcchHHHHHHHhcccc---cccCC-Cc-eEEEEeCCC-------CCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD---VIENF-DK-RIWVCVSDP-------FDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~---~~~~F-~~-~~wv~vs~~-------~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|.+|+|||+||+.+.+.-.   +.... .. .+++..+.-       -.....++.++..+...+++.+|+||++..
T Consensus       195 lL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~  274 (854)
T 1qvr_A          195 VLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHT  274 (854)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC--
T ss_pred             EEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHH
Confidence            4789999999999999988421   00011 22 223322221       134445666777666545789999999976


Q ss_pred             C
Q 043781          194 D  194 (297)
Q Consensus       194 ~  194 (297)
                      .
T Consensus       275 l  275 (854)
T 1qvr_A          275 V  275 (854)
T ss_dssp             -
T ss_pred             H
Confidence            4

>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=96.69  E-value=0.0097  Score=49.98  Aligned_cols=41  Identities=15%  Similarity=0.139  Sum_probs=27.5

Q ss_pred             ccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFD  165 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~  165 (297)
                      ..|+|.+|+|||||+..+........    .-...+|+.....++
T Consensus        27 ~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~   71 (243)
T 1n0w_A           27 TEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFR   71 (243)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCC
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcC
Confidence            46889999999999998887321211    124567777655433

>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=96.63  E-value=0.00075  Score=63.88  Aligned_cols=62  Identities=19%  Similarity=0.144  Sum_probs=37.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEe----CCCCC-HHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV----SDPFD-EFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v----s~~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      .-|+|.+|+|||+||+.+.+.  ....|   +.++.    +..+. ....+..++..... ++..+|+||++.
T Consensus       241 vLL~GppGtGKT~lAraia~~--~~~~f---v~vn~~~l~~~~~g~~~~~~~~~f~~A~~-~~p~iLfLDEId  307 (489)
T 3hu3_A          241 ILLYGPPGTGKTLIARAVANE--TGAFF---FLINGPEIMSKLAGESESNLRKAFEEAEK-NAPAIIFIDELD  307 (489)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--CSSEE---EEEEHHHHHTSCTTHHHHHHHHHHHHHHH-TCSEEEEEESHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH--hCCCE---EEEEchHhhhhhcchhHHHHHHHHHHHHh-cCCcEEEecchh
Confidence            347899999999999999883  33222   23331    11221 22233444444332 567899999994

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=96.60  E-value=0.001  Score=58.48  Aligned_cols=63  Identities=13%  Similarity=0.162  Sum_probs=37.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCCC-HHHHHHHHHHhhc---CCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPFD-EFRIAKAIIEGLE---GSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~~-~~~~~~~i~~~~~---~~~kr~LiVlDdv~~  193 (297)
                      -++|++|+|||+||+.+++.  ...+|   +.+..+    .... ....+.+++....   ...+..+|+||++..
T Consensus        40 Ll~GppGtGKT~la~aiA~~--l~~~~---i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~  110 (293)
T 3t15_A           40 GIWGGKGQGKSFQCELVFRK--MGINP---IMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLDA  110 (293)
T ss_dssp             EEEECTTSCHHHHHHHHHHH--HTCCC---EEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC-
T ss_pred             EEECCCCCCHHHHHHHHHHH--hCCCE---EEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechhh
Confidence            47899999999999999983  43333   233321    1111 2233344443331   125789999999964

>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=96.42  E-value=0.0056  Score=57.62  Aligned_cols=64  Identities=17%  Similarity=0.174  Sum_probs=39.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC----C-HHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF----D-EFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~----~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+.+.  ....|   +.++.+.-.    . ...-++.++.+... +...+|+||++...
T Consensus        52 vLL~GppGtGKT~Laraia~~--~~~~f---~~is~~~~~~~~~g~~~~~~r~lf~~A~~-~~p~ILfIDEid~l  120 (476)
T 2ce7_A           52 ILLVGPPGTGKTLLARAVAGE--ANVPF---FHISGSDFVELFVGVGAARVRDLFAQAKA-HAPCIVFIDEIDAV  120 (476)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--HTCCE---EEEEGGGTTTCCTTHHHHHHHHHHHHHHH-TCSEEEEEETGGGT
T ss_pred             EEEECCCCCCHHHHHHHHHHH--cCCCe---eeCCHHHHHHHHhcccHHHHHHHHHHHHh-cCCCEEEEechhhh
Confidence            458999999999999999983  33222   233333211    1 12223444444432 46789999999653

>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=96.39  E-value=0.014  Score=48.08  Aligned_cols=38  Identities=29%  Similarity=0.126  Sum_probs=26.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEF  167 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~  167 (297)
                      ..|+|.+|+|||||+..+.. .    .-..++|+.....++..
T Consensus        23 ~~i~G~~GsGKTtl~~~l~~-~----~~~~v~~i~~~~~~~~~   60 (220)
T 2cvh_A           23 TQVYGPYASGKTTLALQTGL-L----SGKKVAYVDTEGGFSPE   60 (220)
T ss_dssp             EEEECSTTSSHHHHHHHHHH-H----HCSEEEEEESSCCCCHH
T ss_pred             EEEECCCCCCHHHHHHHHHH-H----cCCcEEEEECCCCCCHH
Confidence            46889999999999999876 1    11345666655544443

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=96.32  E-value=0.003  Score=54.00  Aligned_cols=63  Identities=19%  Similarity=0.178  Sum_probs=37.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-----CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-----DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-----~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .-|+|++|+||||||+.+.+.  ....|   +.+..+.-.     ....-+..++..... ....++++|++..
T Consensus        48 vll~G~~GtGKT~la~~la~~--~~~~~---~~i~~~~~~~~~~~~~~~~~~~~~~~a~~-~~~~il~iDeid~  115 (257)
T 1lv7_A           48 VLMVGPPGTGKTLLAKAIAGE--AKVPF---FTISGSDFVEMFVGVGASRVRDMFEQAKK-AAPCIIFIDEIDA  115 (257)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH--HTCCE---EEECSCSSTTSCCCCCHHHHHHHHHHHHT-TCSEEEEETTHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHH--cCCCE---EEEeHHHHHHHhhhhhHHHHHHHHHHHHH-cCCeeehhhhhhh
Confidence            458999999999999999984  32222   333322111     112233444444332 3567999999943

>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=96.31  E-value=0.0027  Score=55.96  Aligned_cols=21  Identities=38%  Similarity=0.343  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|+|||+||+.+++.
T Consensus        52 vLL~Gp~GtGKT~la~ala~~   72 (301)
T 3cf0_A           52 VLFYGPPGCGKTLLAKAIANE   72 (301)
T ss_dssp             EEEECSSSSSHHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHHH
Confidence            458899999999999999983

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.22  E-value=0.0044  Score=57.53  Aligned_cols=60  Identities=23%  Similarity=0.273  Sum_probs=40.0

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CCC-HHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PFD-EFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      ++|++|+|||+||+.+++.  ...+|   +.+..+.    ... ....++.++..... ...++|++|++.
T Consensus       211 L~GPPGtGKT~lakAiA~~--~~~~~---~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~-~aP~IifiDEiD  275 (428)
T 4b4t_K          211 LYGPPGTGKTMLVKAVANS--TKAAF---IRVNGSEFVHKYLGEGPRMVRDVFRLARE-NAPSIIFIDEVD  275 (428)
T ss_dssp             EESCTTTTHHHHHHHHHHH--HTCEE---EEEEGGGTCCSSCSHHHHHHHHHHHHHHH-TCSEEEEEECTH
T ss_pred             EECCCCCCHHHHHHHHHHH--hCCCe---EEEecchhhccccchhHHHHHHHHHHHHH-cCCCeeechhhh
Confidence            6799999999999999993  44333   3344332    222 34455666555433 568999999996

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=96.21  E-value=0.0029  Score=56.24  Aligned_cols=79  Identities=13%  Similarity=0.131  Sum_probs=43.9

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC------C--ceEEEEEeCCCCCCc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS------E--KKFFLILDDVWTDDY  196 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~------~--kr~LiVlDdv~~~~~  196 (297)
                      .-++|.+|+|||+||+.+.+  .....|   ..+..+......++.....-.....      +  ...+++||++.....
T Consensus        49 vll~G~pGtGKT~la~~la~--~~~~~~---~~i~~~~~~~~~~l~g~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~~  123 (331)
T 2r44_A           49 ILLEGVPGLAKTLSVNTLAK--TMDLDF---HRIQFTPDLLPSDLIGTMIYNQHKGNFEVKKGPVFSNFILADEVNRSPA  123 (331)
T ss_dssp             EEEESCCCHHHHHHHHHHHH--HTTCCE---EEEECCTTCCHHHHHEEEEEETTTTEEEEEECTTCSSEEEEETGGGSCH
T ss_pred             EEEECCCCCcHHHHHHHHHH--HhCCCe---EEEecCCCCChhhcCCceeecCCCCceEeccCcccccEEEEEccccCCH
Confidence            34789999999999999988  333222   2233333333343332111000000      0  124899999988765


Q ss_pred             cCHHHHHHHHhh
Q 043781          197 SKWEPFHNCLMR  208 (297)
Q Consensus       197 ~~w~~l~~~l~~  208 (297)
                      .....|...+..
T Consensus       124 ~~~~~Ll~~l~~  135 (331)
T 2r44_A          124 KVQSALLECMQE  135 (331)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhc
Confidence            555556555543

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=96.18  E-value=0.0033  Score=58.46  Aligned_cols=61  Identities=15%  Similarity=0.219  Sum_probs=39.5

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CCC-HHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PFD-EFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      +||++|+|||.||+.+++.  ...+|   +.+..+.    ... ....++.++..... ...++|++|++..
T Consensus       220 LyGPPGTGKTllAkAiA~e--~~~~f---~~v~~s~l~~~~vGese~~ir~lF~~A~~-~aP~IifiDEiDa  285 (434)
T 4b4t_M          220 MYGPPGTGKTLLARACAAQ--TNATF---LKLAAPQLVQMYIGEGAKLVRDAFALAKE-KAPTIIFIDELDA  285 (434)
T ss_dssp             EESCTTSSHHHHHHHHHHH--HTCEE---EEEEGGGGCSSCSSHHHHHHHHHHHHHHH-HCSEEEEEECTHH
T ss_pred             EECcCCCCHHHHHHHHHHH--hCCCE---EEEehhhhhhcccchHHHHHHHHHHHHHh-cCCeEEeecchhh
Confidence            5799999999999999993  43333   3333222    222 24455555554433 4689999999963

>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=96.11  E-value=0.008  Score=53.51  Aligned_cols=21  Identities=29%  Similarity=0.129  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|.+|+|||+||+.+.+.
T Consensus        48 vLl~G~~GtGKT~la~~la~~   68 (350)
T 1g8p_A           48 VLVFGDRGTGKSTAVRALAAL   68 (350)
T ss_dssp             EEEECCGGGCTTHHHHHHHHH
T ss_pred             EEEECCCCccHHHHHHHHHHh
Confidence            447899999999999999883

>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=96.04  E-value=0.03  Score=51.45  Aligned_cols=43  Identities=14%  Similarity=0.132  Sum_probs=26.9

Q ss_pred             ccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCCHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFDEF  167 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~  167 (297)
                      ..|+|.+|+|||||+..+.-......    .-...+|+.....++..
T Consensus       181 ~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~  227 (400)
T 3lda_A          181 TELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPV  227 (400)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHH
T ss_pred             EEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHH
Confidence            46889999999999997653211111    12346777766555443

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=95.98  E-value=0.012  Score=51.21  Aligned_cols=63  Identities=21%  Similarity=0.193  Sum_probs=39.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC-----HHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD-----EFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-----~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ..++|++|+|||||++.+...  ...   ..+.+..+.-.+     ....+..++..... ....++++|++..
T Consensus        47 vlL~Gp~GtGKTtLakala~~--~~~---~~i~i~g~~l~~~~~~~~~~~i~~vf~~a~~-~~p~i~~~Deid~  114 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVANE--SGL---NFISVKGPELLNMYVGESERAVRQVFQRAKN-SAPCVIFFDEVDA  114 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHHH--TTC---EEEEEETTTTCSSTTHHHHHHHHHHHHHHHH-TCSEEEEEETCTT
T ss_pred             EEEECCCCCcHHHHHHHHHHH--cCC---CEEEEEcHHHHhhhhhHHHHHHHHHHHHHHh-cCCCeEeeehhhh
Confidence            568999999999999999983  222   234454333211     12233344443211 3578999999975

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=95.94  E-value=0.002  Score=64.27  Aligned_cols=100  Identities=17%  Similarity=0.109  Sum_probs=53.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCH----HHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDE----FRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWE  200 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~----~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~  200 (297)
                      .-++|++|+|||+||+.+.+.  ....-...+.+..+.....    ...+...+..    ...-+|+||++.....+...
T Consensus       524 ~Ll~Gp~GtGKT~lA~ala~~--l~~~~~~~i~i~~s~~~~~~~~~~~~l~~~~~~----~~~~vl~lDEi~~~~~~~~~  597 (758)
T 3pxi_A          524 FIFLGPTGVGKTELARALAES--IFGDEESMIRIDMSEYMEKHSTSGGQLTEKVRR----KPYSVVLLDAIEKAHPDVFN  597 (758)
T ss_dssp             EEEESCTTSSHHHHHHHHHHH--HHSCTTCEEEEEGGGGCSSCCCC---CHHHHHH----CSSSEEEEECGGGSCHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hcCCCcceEEEechhcccccccccchhhHHHHh----CCCeEEEEeCccccCHHHHH
Confidence            347899999999999999884  2221122344443322110    1111111221    23348999999887666666


Q ss_pred             HHHHHHhhhhhh-hceeeecCCCCeEEEEec
Q 043781          201 PFHNCLMRVLQE-FAAIEVDGDENPLSLTST  230 (297)
Q Consensus       201 ~l~~~l~~~~~~-~~~~~~~~~gs~iiiTTr  230 (297)
                      .|...+..+... ..-........+||.||.
T Consensus       598 ~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn  628 (758)
T 3pxi_A          598 ILLQVLEDGRLTDSKGRTVDFRNTILIMTSN  628 (758)
T ss_dssp             HHHHHHHHSBCC-----CCBCTTCEEEEEES
T ss_pred             HHHHHhccCeEEcCCCCEeccCCeEEEEeCC
Confidence            676666543100 000011234567888886

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=95.94  E-value=0.011  Score=52.16  Aligned_cols=20  Identities=25%  Similarity=0.245  Sum_probs=18.0

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|+|.+|+|||++|+.+.+.
T Consensus        29 Li~Ge~GtGKt~lAr~i~~~   48 (304)
T 1ojl_A           29 LIHGDSGTGKELVARALHAC   48 (304)
T ss_dssp             EEESCTTSCHHHHHHHHHHH
T ss_pred             EEECCCCchHHHHHHHHHHh
Confidence            47899999999999999884

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=95.93  E-value=0.0056  Score=56.62  Aligned_cols=61  Identities=21%  Similarity=0.294  Sum_probs=40.6

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCCC-HHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPFD-EFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|++|+|||.||+.+++.  ...+|   +.+..+    .... ....++.++..... ...++|++|++..
T Consensus       221 LyGPPGTGKTlLAkAiA~e--~~~~f---i~v~~s~l~sk~vGesek~ir~lF~~Ar~-~aP~IIfiDEiDa  286 (437)
T 4b4t_I          221 LYGAPGTGKTLLAKAVANQ--TSATF---LRIVGSELIQKYLGDGPRLCRQIFKVAGE-NAPSIVFIDEIDA  286 (437)
T ss_dssp             EESSTTTTHHHHHHHHHHH--HTCEE---EEEESGGGCCSSSSHHHHHHHHHHHHHHH-TCSEEEEEEEESS
T ss_pred             eECCCCchHHHHHHHHHHH--hCCCE---EEEEHHHhhhccCchHHHHHHHHHHHHHh-cCCcEEEEehhhh
Confidence            6799999999999999993  44333   233322    2222 34556666655543 5689999999974

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.89  E-value=0.017  Score=47.92  Aligned_cols=20  Identities=25%  Similarity=0.307  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|.+|+|||||++.+..
T Consensus        26 ~~i~G~~GsGKTtl~~~l~~   45 (235)
T 2w0m_A           26 IALTGEPGTGKTIFSLHFIA   45 (235)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            46889999999999998885

>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=95.82  E-value=0.037  Score=49.43  Aligned_cols=23  Identities=35%  Similarity=0.192  Sum_probs=19.8

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|+.|+|||||++.+...
T Consensus       130 ~vi~lvG~nGaGKTTll~~Lag~  152 (328)
T 3e70_C          130 YVIMFVGFNGSGKTTTIAKLANW  152 (328)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999998873

>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=95.66  E-value=0.0077  Score=54.60  Aligned_cols=66  Identities=17%  Similarity=0.081  Sum_probs=37.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC-------CCHHHHHHHHHHhhcCC---CceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP-------FDEFRIAKAIIEGLEGS---EKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~-------~~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||+||+.+.+.  ....|   +.+..+.-       .+....+..++......   ...-+|+||++...
T Consensus        75 ill~Gp~GtGKT~la~~la~~--l~~~~---~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l  149 (376)
T 1um8_A           75 ILLIGPTGSGKTLMAQTLAKH--LDIPI---AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKI  149 (376)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--TTCCE---EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCCCE---EEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHH
Confidence            347899999999999999983  33222   22222211       11223344444333221   24568899999876


Q ss_pred             C
Q 043781          195 D  195 (297)
Q Consensus       195 ~  195 (297)
                      .
T Consensus       150 ~  150 (376)
T 1um8_A          150 S  150 (376)
T ss_dssp             -
T ss_pred             h
Confidence            4

>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=95.58  E-value=0.058  Score=46.61  Aligned_cols=20  Identities=30%  Similarity=0.454  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+|+|..|+|||||.+.+..
T Consensus        40 ~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           40 VAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             EEEECCTTSCHHHHHHHHTS
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            47899999999999999987

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.57  E-value=0.013  Score=55.43  Aligned_cols=78  Identities=14%  Similarity=0.138  Sum_probs=41.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHH--HHHh-----hcCCC-----ceEEEEEeCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKA--IIEG-----LEGSE-----KKFFLILDDV  191 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~--i~~~-----~~~~~-----kr~LiVlDdv  191 (297)
                      +-++|.+|+|||+||+.+.+.-.....     +....-.+ ...+++..  +...     +....     ..-++++|++
T Consensus        44 VLL~GpPGtGKT~LAraLa~~l~~~~~-----f~~~~~~~~t~~dL~G~~~~~~~~~~g~~~~~~~g~l~~~~IL~IDEI  118 (500)
T 3nbx_X           44 VFLLGPPGIAKSLIARRLKFAFQNARA-----FEYLMTRFSTPEEVFGPLSIQALKDEGRYERLTSGYLPEAEIVFLDEI  118 (500)
T ss_dssp             EEEECCSSSSHHHHHHHGGGGBSSCCE-----EEEECCTTCCHHHHHCCBC----------CBCCTTSGGGCSEEEEESG
T ss_pred             eEeecCchHHHHHHHHHHHHHHhhhhH-----HHHHHHhcCCHHHhcCcccHHHHhhchhHHhhhccCCCcceeeeHHhH
Confidence            347899999999999999984211111     22222222 33333321  1000     00002     2337999999


Q ss_pred             CCCCccCHHHHHHHHh
Q 043781          192 WTDDYSKWEPFHNCLM  207 (297)
Q Consensus       192 ~~~~~~~w~~l~~~l~  207 (297)
                      ..........|...+.
T Consensus       119 ~r~~~~~q~~LL~~le  134 (500)
T 3nbx_X          119 WKAGPAILNTLLTAIN  134 (500)
T ss_dssp             GGCCHHHHHHHHHHHH
T ss_pred             hhhcHHHHHHHHHHHH
Confidence            8765445555666664

>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=95.51  E-value=0.045  Score=54.31  Aligned_cols=68  Identities=25%  Similarity=0.188  Sum_probs=43.0

Q ss_pred             cccccCCcchHHHHHHHhcccc---cc-cCCCceEEE-Ee-------CCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD---VI-ENFDKRIWV-CV-------SDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~---~~-~~F~~~~wv-~v-------s~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -++|.+|+|||+||+.+.+.-.   +. ..+.+.+|. ..       ...-.....++.++..+.. .+..+|+||++..
T Consensus       211 lL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~-~~~~iL~IDEi~~  289 (758)
T 1r6b_X          211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQ-DTNSILFIDEIHT  289 (758)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSS-SSCEEEEETTTTT
T ss_pred             EEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccccchHHHHHHHHHHHHHh-cCCeEEEEechHH
Confidence            3789999999999999987321   00 012333332 11       1122456677777777755 3568999999975


Q ss_pred             C
Q 043781          194 D  194 (297)
Q Consensus       194 ~  194 (297)
                      .
T Consensus       290 l  290 (758)
T 1r6b_X          290 I  290 (758)
T ss_dssp             T
T ss_pred             H
Confidence            4

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=95.46  E-value=0.014  Score=58.87  Aligned_cols=82  Identities=15%  Similarity=0.182  Sum_probs=43.5

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC---HHHHH------------HHHHHhhcCCCceEEEEE
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD---EFRIA------------KAIIEGLEGSEKKFFLIL  188 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~---~~~~~------------~~i~~~~~~~~kr~LiVl  188 (297)
                      ..-++|.+|+|||+||+.+.+.  ....-...+.+..+....   ...++            ..+...+.. ...-+|+|
T Consensus       590 ~vLl~Gp~GtGKT~lA~~la~~--~~~~~~~~i~i~~~~~~~~~~~s~l~g~~~~~~G~~~~g~l~~~~~~-~~~~vl~l  666 (854)
T 1qvr_A          590 SFLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRR-RPYSVILF  666 (854)
T ss_dssp             EEEEBSCSSSSHHHHHHHHHHH--HHSSGGGEEEECTTTCCSSGGGGGC--------------CHHHHHHH-CSSEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--hcCCCCcEEEEechhccchhHHHHHcCCCCCCcCccccchHHHHHHh-CCCeEEEE
Confidence            3458899999999999999873  211101122333222111   00000            011111111 23458999


Q ss_pred             eCCCCCCccCHHHHHHHHhh
Q 043781          189 DDVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       189 Ddv~~~~~~~w~~l~~~l~~  208 (297)
                      |++.....+..+.|...+..
T Consensus       667 DEi~~l~~~~~~~Ll~~l~~  686 (854)
T 1qvr_A          667 DEIEKAHPDVFNILLQILDD  686 (854)
T ss_dssp             SSGGGSCHHHHHHHHHHHTT
T ss_pred             ecccccCHHHHHHHHHHhcc
Confidence            99987765566666666654

>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=95.45  E-value=0.021  Score=57.08  Aligned_cols=61  Identities=20%  Similarity=0.208  Sum_probs=42.2

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEE----eCCCCC-HHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC----VSDPFD-EFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~----vs~~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|++|+|||+||+.+++.  ...+|   +.|.    ++.... ....++.++..... ....+|+||++..
T Consensus       243 L~GPPGTGKT~LAraiA~e--lg~~~---~~v~~~~l~sk~~gese~~lr~lF~~A~~-~~PsIIfIDEiDa  308 (806)
T 3cf2_A          243 LYGPPGTGKTLIARAVANE--TGAFF---FLINGPEIMSKLAGESESNLRKAFEEAEK-NAPAIIFIDELDA  308 (806)
T ss_dssp             EECCTTSCHHHHHHHHHTT--TTCEE---EEEEHHHHHSSCTTHHHHHHHHHHHHHTT-SCSEEEEEESGGG
T ss_pred             EECCCCCCHHHHHHHHHHH--hCCeE---EEEEhHHhhcccchHHHHHHHHHHHHHHH-cCCeEEEEehhcc
Confidence            6799999999999999983  44333   3343    233333 34556666666544 5789999999975

>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=95.42  E-value=0.0079  Score=60.10  Aligned_cols=59  Identities=24%  Similarity=0.311  Sum_probs=39.0

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeC------CCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS------DPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs------~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      ++|++|+|||.||+.+.+.  ....|     +.++      ... ..+..+++++..... ....+|++|++..
T Consensus       516 l~GPPGtGKT~lAkaiA~e--~~~~f-----~~v~~~~l~s~~vGese~~vr~lF~~Ar~-~~P~IifiDEiDs  581 (806)
T 3cf2_A          516 FYGPPGCGKTLLAKAIANE--CQANF-----ISIKGPELLTMWFGESEANVREIFDKARQ-AAPCVLFFDELDS  581 (806)
T ss_dssp             EESSTTSSHHHHHHHHHHT--TTCEE-----EECCHHHHHTTTCSSCHHHHHHHHHHHHT-TCSEEEECSCGGG
T ss_pred             EecCCCCCchHHHHHHHHH--hCCce-----EEeccchhhccccchHHHHHHHHHHHHHH-cCCceeechhhhH
Confidence            6899999999999999993  33322     2221      111 123455566655543 5689999999975

>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=95.40  E-value=0.013  Score=54.78  Aligned_cols=67  Identities=16%  Similarity=0.231  Sum_probs=43.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHH--------------------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKA--------------------------------  172 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~--------------------------------  172 (297)
                      .|+|..|+|||||++.+..+.... +-+..+++.+.+.. .+.+++.+                                
T Consensus       155 ~i~G~sGvGKTtL~~~l~~~~~~~-~~~i~V~~~iGerttev~el~~~l~~~~~l~~tvvv~~~~~d~pg~r~~~~~~~l  233 (473)
T 1sky_E          155 GLFGGAGVGKTVLIQELIHNIAQE-HGGISVFAGVGERTREGNDLYHEMKDSGVISKTAMVFGQMNEPPGARMRVALTGL  233 (473)
T ss_dssp             EEECCSSSCHHHHHHHHHHHHHHH-TCCCEEEEEESSCHHHHHHHHHHHHHTSGGGGEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEECCCCCCccHHHHHHHhhhhhc-cCcEEEEeeeccCchHHHHHHHHhhhcCCcceeEEEEEcCCCCHHHHHHHHHHHH
Confidence            688999999999999888753222 22445666665543 23343332                                


Q ss_pred             -HHHhhcC-CCceEEEEEeCCCC
Q 043781          173 -IIEGLEG-SEKKFFLILDDVWT  193 (297)
Q Consensus       173 -i~~~~~~-~~kr~LiVlDdv~~  193 (297)
                       +.+.+.. .+++.||++||+..
T Consensus       234 tiAEyFrd~~G~~VLl~~D~itR  256 (473)
T 1sky_E          234 TMAEYFRDEQGQDGLLFIDNIFR  256 (473)
T ss_dssp             HHHHHHHHHSCCEEEEEEECTHH
T ss_pred             HHHHHHHHhcCCcEEEEeccHHH
Confidence             3333333 38999999999954

>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=95.37  E-value=0.054  Score=48.91  Aligned_cols=36  Identities=22%  Similarity=0.225  Sum_probs=23.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD  162 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~  162 (297)
                      ..|+|.+|+|||||+..+.....  ..=..++|+....
T Consensus        64 ~~I~GppGsGKSTLal~la~~~~--~~gg~VlyId~E~   99 (356)
T 3hr8_A           64 VEIFGQESSGKTTLALHAIAEAQ--KMGGVAAFIDAEH   99 (356)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH--hcCCeEEEEeccc
Confidence            45789999999999998887421  1112345665444

>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=95.24  E-value=0.082  Score=47.93  Aligned_cols=67  Identities=21%  Similarity=0.152  Sum_probs=40.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCH---------------------HHHHHHHHHhhcCCCce
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDE---------------------FRIAKAIIEGLEGSEKK  183 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~---------------------~~~~~~i~~~~~~~~kr  183 (297)
                      +.|+|.+|+||||||..+.....  ..=..++|+.....++.                     .+++ .+++.+...++-
T Consensus        77 i~I~G~pGsGKTtlal~la~~~~--~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l-~~l~~l~~~~~~  153 (366)
T 1xp8_A           77 TEIYGPESGGKTTLALAIVAQAQ--KAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQAL-EIMELLVRSGAI  153 (366)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHH-HHHHHHHTTTCC
T ss_pred             EEEEcCCCCChHHHHHHHHHHHH--HCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHH-HHHHHHHhcCCC
Confidence            45789999999999988776421  11235667765554432                     2322 233333222445


Q ss_pred             EEEEEeCCCCC
Q 043781          184 FFLILDDVWTD  194 (297)
Q Consensus       184 ~LiVlDdv~~~  194 (297)
                      -+||+|.+-..
T Consensus       154 ~lVVIDsl~~l  164 (366)
T 1xp8_A          154 DVVVVDSVAAL  164 (366)
T ss_dssp             SEEEEECTTTC
T ss_pred             CEEEEeChHHh
Confidence            68999998654

>2ck3_D ATP synthase subunit beta\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1cow_D* 1bmf_D* 1e1q_D* 1e1r_D* 1efr_D* 1e79_D* 1h8h_D* 1ohh_D* 1qo1_D 1w0j_D* 1w0k_D* 1h8e_D* 2jdi_D* 2jiz_D* 2jj1_D* 2jj2_D* 2v7q_D* 2wss_D* 2w6j_D 2w6e_D ...

Probab=95.16  E-value=0.037  Score=51.80  Aligned_cols=50  Identities=20%  Similarity=0.236  Sum_probs=34.8

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHh
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEG  176 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~  176 (297)
                      +|+|..|+|||+|+..+.++. .+.+-+.++++-+.... .+.++.+++...
T Consensus       157 ~Ifgg~G~GKT~L~~~i~~~~-~~~~~~v~V~~~iGER~rEv~e~~~~~~~~  207 (482)
T 2ck3_D          157 GLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIES  207 (482)
T ss_dssp             EEEECTTSSHHHHHHHHHHHT-TTTCSSEEEEEEESCCHHHHHHHHHHHHHH
T ss_pred             eeecCCCCChHHHHHHHHHhh-HhhCCCEEEEEECCCcchHHHHHHHHhhhc
Confidence            689999999999998888742 23344666777666654 346666666554

>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=95.13  E-value=0.049  Score=48.54  Aligned_cols=122  Identities=9%  Similarity=-0.083  Sum_probs=71.1

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC-CCccCHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT-DDYSKWEPFHN  204 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~-~~~~~w~~l~~  204 (297)
                      =++|..|.||++.+..+.+.- ....|+....+.+....++.++...+.. ...-+++=++|+|++.. ...+.++.|..
T Consensus        22 l~~G~e~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~-~plf~~~kvvii~~~~~kl~~~~~~aLl~   99 (343)
T 1jr3_D           22 LLLGNDPLLLQESQDAVRQVA-AAQGFEEHHTFSIDPNTDWNAIFSLCQA-MSLFASRQTLLLLLPENGPNAAINEQLLT   99 (343)
T ss_dssp             EEEESCHHHHHHHHHHHHHHH-HHHTCCEEEEEECCTTCCHHHHHHHHHH-HHHCCSCEEEEEECCSSCCCTTHHHHHHH
T ss_pred             EEECCcHHHHHHHHHHHHHHH-HhCCCCeeEEEEecCCCCHHHHHHHhcC-cCCccCCeEEEEECCCCCCChHHHHHHHH
Confidence            377999999999998887731 1223543223344455677777666432 22225677889999977 44457788887


Q ss_pred             HHhhhhhhhceeeecCCCCeEEEEeccHHH---HHHHHHhhC-CCccccCCccchhhhh
Q 043781          205 CLMRVLQEFAAIEVDGDENPLSLTSTCQEK---LRHLTLTLG-LRAKFPVSIFDAKKIW  259 (297)
Q Consensus       205 ~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~---~~~v~~~~~-~~~~~~l~~l~~~~lf  259 (297)
                      .+..-          .+++.+|++|...+.   ...+..... ...++.+.+++..++.
T Consensus       100 ~le~p----------~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l~~~~l~  148 (343)
T 1jr3_D          100 LTGLL----------HDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLP  148 (343)
T ss_dssp             HHTTC----------BTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCCCTTHHH
T ss_pred             HHhcC----------CCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCCCHHHHH
Confidence            77642          456777776643111   112332222 1245666666655543

>1fx0_B ATP synthase beta 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_B*

Probab=95.12  E-value=0.049  Score=51.14  Aligned_cols=50  Identities=18%  Similarity=0.160  Sum_probs=36.2

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHHh
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIEG  176 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~~  176 (297)
                      +|+|..|+|||+|+..+.++. .+.+-+.++++-+.... .+.++..++...
T Consensus       169 gIfgg~GvGKT~L~~~l~~~~-a~~~~~v~V~~~iGER~rEv~e~~~~~~~~  219 (498)
T 1fx0_B          169 GLFGGAGVGKTVLIMELINNI-AKAHGGVSVFGGVGERTREGNDLYMEMKES  219 (498)
T ss_dssp             EEEECSSSSHHHHHHHHHHHT-TTTCSSCEEEEEESCCSHHHHHHHHHHHHT
T ss_pred             EeecCCCCCchHHHHHHHHHH-HhhCCCEEEEEEcccCcHHHHHHHHhhhcc
Confidence            688999999999998888741 23345777888777665 356677666653

>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=95.10  E-value=0.021  Score=53.31  Aligned_cols=65  Identities=15%  Similarity=0.034  Sum_probs=40.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeC----CCCCHHHHHHHHHHhhcC--CCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS----DPFDEFRIAKAIIEGLEG--SEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs----~~~~~~~~~~~i~~~~~~--~~kr~LiVlDdv~~  193 (297)
                      =++|++|+|||+||+.+.+.  ....+ ..+.+..+    ......+.+.+++....+  ..+..+|++|++..
T Consensus        67 Ll~GppGtGKT~la~ala~~--l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~il~iDEid~  137 (456)
T 2c9o_A           67 LLAGPPGTGKTALALAIAQE--LGSKV-PFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTE  137 (456)
T ss_dssp             EEECCTTSSHHHHHHHHHHH--HCTTS-CEEEEEGGGGCCSSSCHHHHHHHHHHHTEEEEEEEEEEEEEEEEEE
T ss_pred             EEECCCcCCHHHHHHHHHHH--hCCCc-eEEEEeHHHHHHHhhhhhHHHHHHHHHHHhhhhcCCcEEEEechhh
Confidence            47899999999999999984  33221 11223322    233444445566655411  15678999999965

>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=94.99  E-value=0.0081  Score=47.42  Aligned_cols=18  Identities=33%  Similarity=0.540  Sum_probs=16.5

Q ss_pred             ccccccCCcchHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFA  142 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v  142 (297)
                      +.|.|++|+||||+|+.+
T Consensus         4 I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            4 ILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEEECCTTSCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            457899999999999999

>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=94.86  E-value=0.074  Score=47.46  Aligned_cols=20  Identities=35%  Similarity=0.207  Sum_probs=17.9

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|+|..|+|||||++.+..-
T Consensus       175 ~i~G~~GsGKTTll~~l~g~  194 (330)
T 2pt7_A          175 IVCGGTGSGKTTYIKSIMEF  194 (330)
T ss_dssp             EEEESTTSCHHHHHHHGGGG
T ss_pred             EEECCCCCCHHHHHHHHhCC
Confidence            57899999999999999873

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=94.79  E-value=0.02  Score=46.59  Aligned_cols=19  Identities=26%  Similarity=-0.019  Sum_probs=15.4

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -++|..|+||||++..+..
T Consensus         7 vi~G~~gsGKTT~ll~~~~   25 (184)
T 2orw_A            7 VITGPMYSGKTTELLSFVE   25 (184)
T ss_dssp             EEEESTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4789999999999955554

>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=94.79  E-value=0.01  Score=47.41  Aligned_cols=20  Identities=15%  Similarity=0.192  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|++|+||||+|+.+.+
T Consensus         6 i~l~G~~GsGKST~a~~La~   25 (178)
T 1qhx_A            6 IILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34779999999999999987

>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=94.74  E-value=0.056  Score=53.67  Aligned_cols=75  Identities=12%  Similarity=0.104  Sum_probs=44.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC-------------HH-----HHHHHHHHhhcCCCceEEE
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD-------------EF-----RIAKAIIEGLEGSEKKFFL  186 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-------------~~-----~~~~~i~~~~~~~~kr~Li  186 (297)
                      .-++|.+|+|||+||+.+.+.  ...   ..+.+..+....             ..     ..+...+..    ...-+|
T Consensus       491 ~ll~G~~GtGKT~la~~la~~--l~~---~~~~i~~s~~~~~~~~~~l~g~~~g~~g~~~~~~l~~~~~~----~~~~vl  561 (758)
T 1r6b_X          491 FLFAGPTGVGKTEVTVQLSKA--LGI---ELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIK----HPHAVL  561 (758)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH--HTC---EEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHHHH----CSSEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHH--hcC---CEEEEechhhcchhhHhhhcCCCCCCcCccccchHHHHHHh----CCCcEE
Confidence            457899999999999999883  321   122333222111             00     111222222    346799


Q ss_pred             EEeCCCCCCccCHHHHHHHHhh
Q 043781          187 ILDDVWTDDYSKWEPFHNCLMR  208 (297)
Q Consensus       187 VlDdv~~~~~~~w~~l~~~l~~  208 (297)
                      +||++.....+.++.|...+..
T Consensus       562 ~lDEi~~~~~~~~~~Ll~~le~  583 (758)
T 1r6b_X          562 LLDEIEKAHPDVFNILLQVMDN  583 (758)
T ss_dssp             EEETGGGSCHHHHHHHHHHHHH
T ss_pred             EEeCccccCHHHHHHHHHHhcC
Confidence            9999988766666667766654

>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=94.73  E-value=0.011  Score=47.87  Aligned_cols=21  Identities=33%  Similarity=0.300  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|++|+|||||++.+...
T Consensus        12 i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A           12 LLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             EEEEECTTSCHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhc
Confidence            568999999999999999874

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=94.68  E-value=0.011  Score=47.00  Aligned_cols=22  Identities=23%  Similarity=0.184  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|+.|+|||||++.+...
T Consensus         6 ~i~l~G~~GsGKSTl~~~La~~   27 (173)
T 1kag_A            6 NIFLVGPMGAGKSTIGRQLAQQ   27 (173)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3578999999999999999873

>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=94.67  E-value=0.012  Score=46.62  Aligned_cols=21  Identities=19%  Similarity=0.017  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+...
T Consensus         4 i~l~G~~GsGKsT~~~~L~~~   24 (173)
T 3kb2_A            4 IILEGPDCCFKSTVAAKLSKE   24 (173)
T ss_dssp             EEEECSSSSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999999873

>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=94.64  E-value=0.11  Score=48.15  Aligned_cols=22  Identities=32%  Similarity=0.211  Sum_probs=18.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.++|.+|+||||++..+..
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~  119 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAY  119 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4567889999999999988775

>3vr4_D V-type sodium ATPase subunit D; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_D* 3vr2_D* 3vr5_D 3vr6_D*

Probab=94.62  E-value=0.037  Score=51.51  Aligned_cols=69  Identities=14%  Similarity=0.158  Sum_probs=42.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccc-cCCC-ceEEEEeCCCC-CHHHHHHHHHHh-------------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI-ENFD-KRIWVCVSDPF-DEFRIAKAIIEG-------------------------  176 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~-~~F~-~~~wv~vs~~~-~~~~~~~~i~~~-------------------------  176 (297)
                      .+|+|..|+|||+|+.++.+..... ++=+ ..+++-+.+.. .+.++.+++...                         
T Consensus       154 ~~Ifgg~G~GKt~L~~~Ia~~~~~~~d~~~~~~V~~~iGeR~~Ev~e~~~~~~~~g~~~rtvvV~atsd~p~~~r~~a~~  233 (465)
T 3vr4_D          154 LPVFSGSGLPHKELAAQIARQATVLDSSDDFAVVFAAIGITFEEAEFFMEDFRQTGAIDRSVMFMNLANDPAIERIATPR  233 (465)
T ss_dssp             CCEEECTTSCHHHHHHHHHHHCBCSSCSSCEEEEEEEEEECHHHHHHHHHHHHHHTGGGGEEEEEEETTSCHHHHHHHHH
T ss_pred             EEEeCCCCcChHHHHHHHHHHHHhccCCCceEEEEEEecCCcHHHHHHHHHHhhcCCccceEEEEECCCCCHHHHHHHHH
Confidence            3688999999999999998854331 1111 44455444432 334444444332                         


Q ss_pred             --------hcC-CCceEEEEEeCCCC
Q 043781          177 --------LEG-SEKKFFLILDDVWT  193 (297)
Q Consensus       177 --------~~~-~~kr~LiVlDdv~~  193 (297)
                              +.. .++..||++||+-.
T Consensus       234 ~a~tiAEyfrd~~G~~VLl~~DslTr  259 (465)
T 3vr4_D          234 MALTAAEYLAYEKGMHVLVIMTDMTN  259 (465)
T ss_dssp             HHHHHHHHHHHTTCCEEEEEEECHHH
T ss_pred             HHHHHHHHHHHhcCCeEEEEEcChHH
Confidence                    221 18999999999953

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=94.61  E-value=0.029  Score=53.05  Aligned_cols=63  Identities=19%  Similarity=0.160  Sum_probs=37.2

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC----CCH-HHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP----FDE-FRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~----~~~-~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      .-|+|++|+||||||+.+.+.  ....   .+.+..+.-    ... ..-+..+++.... ....++++|++..
T Consensus        67 vLL~GppGtGKTtLaraIa~~--~~~~---~i~i~g~~~~~~~~g~~~~~v~~lfq~a~~-~~p~il~IDEId~  134 (499)
T 2dhr_A           67 VLLVGPPGVGKTHLARAVAGE--ARVP---FITASGSDFVEMFVGVGAARVRDLFETAKR-HAPCIVFIDEIDA  134 (499)
T ss_dssp             EEEECSSSSSHHHHHHHHHHH--TTCC---EEEEEGGGGTSSCTTHHHHHHHHHTTTSSS-SSSCEEEEECGGG
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCCC---EEEEehhHHHHhhhhhHHHHHHHHHHHHHh-cCCCEEEEehHHH
Confidence            568999999999999999984  3322   234443221    111 1223333333221 2457999999964

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=94.57  E-value=0.037  Score=52.05  Aligned_cols=64  Identities=22%  Similarity=0.223  Sum_probs=42.2

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCc-eEEEEeCCCC-CHHHHHHHHHHhhcC-----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDK-RIWVCVSDPF-DEFRIAKAIIEGLEG-----------------------  179 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~~~~~i~~~~~~-----------------------  179 (297)
                      .|+|..|+|||+|| ..+.+..    +-+. .+++-+.+.. .+.++.+.+...-..                       
T Consensus       166 ~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~a~~~  241 (502)
T 2qe7_A          166 LIIGDRQTGKTTIAIDTIINQK----GQDVICIYVAIGQKQSTVAGVVETLRQHDALDYTIVVTASASEPAPLLYLAPYA  241 (502)
T ss_dssp             EEEECSSSCHHHHHHHHHHGGG----SCSEEEEEEEESCCHHHHHHHHHHHHHTTCSTTEEEEEECTTSCHHHHHHHHHH
T ss_pred             EEECCCCCCchHHHHHHHHHhh----cCCcEEEEEECCCcchHHHHHHHHHhhCCCcceeEEEEECCCCCHHHHHHHHHH
Confidence            68899999999995 6777742    2443 3556565544 345555555443221                       


Q ss_pred             ----------CCceEEEEEeCCCC
Q 043781          180 ----------SEKKFFLILDDVWT  193 (297)
Q Consensus       180 ----------~~kr~LiVlDdv~~  193 (297)
                                .++..||++||+-.
T Consensus       242 a~tiAEyfrd~G~dVLl~~Dsltr  265 (502)
T 2qe7_A          242 GCAMGEYFMYKGKHALVVYDDLSK  265 (502)
T ss_dssp             HHHHHHHHHTTTCEEEEEEECHHH
T ss_pred             HHHHHHHHHHcCCcEEEEEecHHH
Confidence                      19999999999853

>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=94.56  E-value=0.035  Score=50.74  Aligned_cols=20  Identities=25%  Similarity=0.067  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|..|+|||||++.+.+
T Consensus       177 ~~IvG~sG~GKTtLl~~Iar  196 (422)
T 3ice_A          177 GLIVAPPKAGKTMLLQNIAQ  196 (422)
T ss_dssp             EEEECCSSSSHHHHHHHHHH
T ss_pred             EEEecCCCCChhHHHHHHHH
Confidence            36899999999999998876

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=94.54  E-value=0.013  Score=46.74  Aligned_cols=20  Identities=30%  Similarity=0.177  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|++|+||||+|+.+..
T Consensus         5 I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            5 ILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEecCCCCCHHHHHHHHHh
Confidence            45789999999999999987

>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=94.51  E-value=0.034  Score=50.29  Aligned_cols=39  Identities=18%  Similarity=0.210  Sum_probs=26.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD  165 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  165 (297)
                      ..|+|.+|+||||||..+.....  ..=..++|+.....++
T Consensus        66 i~I~G~pGsGKTtLal~la~~~~--~~g~~vlyid~E~s~~  104 (356)
T 1u94_A           66 VEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALD  104 (356)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH--HCCCeEEEEeCCCCcc
Confidence            45789999999999988876421  1112466776655443

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=94.37  E-value=0.015  Score=47.74  Aligned_cols=21  Identities=33%  Similarity=0.260  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+|++|+||||+++.+..
T Consensus        27 ~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           27 RIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            456889999999999999987

>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase, A1AO, ATP synthesis, hydrogen ION transport, ION transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A* 3b2q_A* 2rkw_A* 3eiu_A*

Probab=94.33  E-value=0.031  Score=52.17  Aligned_cols=50  Identities=6%  Similarity=-0.011  Sum_probs=31.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCC--CceEEEEeCCCC-CHHHHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENF--DKRIWVCVSDPF-DEFRIAKAIIE  175 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F--~~~~wv~vs~~~-~~~~~~~~i~~  175 (297)
                      +|+|..|+|||+|+.++.++......-  +..+++-+.... .+.++.+++..
T Consensus       156 ~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~Ev~e~~~~~~~  208 (469)
T 2c61_A          156 PIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEEAQYFMSDFEK  208 (469)
T ss_dssp             CEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHHHHHHHHHHHh
Confidence            688999999999999998864432211  245555554433 34555555544

>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=94.33  E-value=0.033  Score=52.45  Aligned_cols=64  Identities=22%  Similarity=0.197  Sum_probs=42.4

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCc-eEEEEeCCCC-CHHHHHHHHHHhhcC-----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDK-RIWVCVSDPF-DEFRIAKAIIEGLEG-----------------------  179 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~~~~~i~~~~~~-----------------------  179 (297)
                      .|+|..|+|||+|| ..+.+..    .-+. .+++-+.+.. .+.++.+.+...-..                       
T Consensus       179 ~I~g~~g~GKT~Lal~~I~~~~----~~dv~~V~~~IGeR~~Ev~e~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~~~  254 (515)
T 2r9v_A          179 LIIGDRQTGKTAIAIDTIINQK----GQGVYCIYVAIGQKKSAIARIIDKLRQYGAMEYTTVVVASASDPASLQYIAPYA  254 (515)
T ss_dssp             EEEEETTSSHHHHHHHHHHTTT----TTTEEEEEEEESCCHHHHHHHHHHHHHTTGGGGEEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEcCCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCcHHHHHHHHHHHhCCCcceeEEEEECCCCCHHHHHHHHHH
Confidence            58899999999995 6777742    2443 3566665544 345555555442211                       


Q ss_pred             ----------CCceEEEEEeCCCC
Q 043781          180 ----------SEKKFFLILDDVWT  193 (297)
Q Consensus       180 ----------~~kr~LiVlDdv~~  193 (297)
                                .++..||++||+-.
T Consensus       255 a~tiAEyfrd~G~dVLli~DslTr  278 (515)
T 2r9v_A          255 GCAMGEYFAYSGRDALVVYDDLSK  278 (515)
T ss_dssp             HHHHHHHHHTTTCEEEEEEETHHH
T ss_pred             HHHHHHHHHHcCCcEEEEeccHHH
Confidence                      19999999999953

>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=94.31  E-value=0.061  Score=48.41  Aligned_cols=67  Identities=19%  Similarity=0.159  Sum_probs=40.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC---------------------HHHHHHHHHHhhcCCCce
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD---------------------EFRIAKAIIEGLEGSEKK  183 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~---------------------~~~~~~~i~~~~~~~~kr  183 (297)
                      ..|+|.+|+||||||.++.....  ..=...+|+.....++                     ..+++ .++..+-...+.
T Consensus        64 v~I~G~pGsGKTtLal~la~~~~--~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l-~~~~~l~~~~~~  140 (349)
T 2zr9_A           64 IEIYGPESSGKTTVALHAVANAQ--AAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQAL-EIADMLVRSGAL  140 (349)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHH-HHHHHHHTTTCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH--hCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHH-HHHHHHHhcCCC
Confidence            46889999999999988876321  1112455666554433                     22222 233333222456


Q ss_pred             EEEEEeCCCCC
Q 043781          184 FFLILDDVWTD  194 (297)
Q Consensus       184 ~LiVlDdv~~~  194 (297)
                      -+||+|.+-..
T Consensus       141 ~lIVIDsl~~l  151 (349)
T 2zr9_A          141 DIIVIDSVAAL  151 (349)
T ss_dssp             SEEEEECGGGC
T ss_pred             CEEEEcChHhh
Confidence            69999998764

>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D 3j0j_D*

Probab=94.30  E-value=0.03  Score=52.09  Aligned_cols=24  Identities=13%  Similarity=0.083  Sum_probs=19.9

Q ss_pred             ccccccCCcchHHHHHHHhccccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDV  148 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~  148 (297)
                      .+|+|..|+|||+|+.++.+....
T Consensus       150 ~~Ifgg~G~GKt~L~~~Ia~~~~a  173 (464)
T 3gqb_B          150 LPIFSGSGLPANEIAAQIARQATV  173 (464)
T ss_dssp             CCEEEETTSCHHHHHHHHHHHCBC
T ss_pred             EEEecCCCCCchHHHHHHHHHHHh
Confidence            368899999999999998886443

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=94.29  E-value=0.016  Score=46.68  Aligned_cols=20  Identities=25%  Similarity=0.295  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.++|++|+||||+++.+..
T Consensus         8 i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            8 IYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45889999999999999987

>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=94.24  E-value=0.035  Score=48.06  Aligned_cols=21  Identities=24%  Similarity=0.164  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|.|||.+|..+.+.
T Consensus       107 ~~l~GppgtGKt~~a~ala~~  127 (267)
T 1u0j_A          107 IWLFGPATTGKTNIAEAIAHT  127 (267)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHhh
Confidence            458899999999999999873

>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=94.23  E-value=0.033  Score=52.42  Aligned_cols=64  Identities=19%  Similarity=0.205  Sum_probs=42.1

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCc-eEEEEeCCCC-CHHHHHHHHHHhhcCC----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDK-RIWVCVSDPF-DEFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~-~~~~~~~~i~~~~~~~----------------------  180 (297)
                      .|+|..|+|||+|| ..+.+..  .  -+. .+++-+.+.. .+.++.+.+...-...                      
T Consensus       167 ~Ifg~~g~GKT~Lal~~I~~~~--~--~dv~~V~~~iGeR~~Ev~~~~~~~~~~g~m~rtvvV~atad~p~~~r~~a~~~  242 (507)
T 1fx0_A          167 LIIGDRQTGKTAVATDTILNQQ--G--QNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYT  242 (507)
T ss_dssp             BEEESSSSSHHHHHHHHHHTCC--T--TTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHH
T ss_pred             EEecCCCCCccHHHHHHHHHhh--c--CCcEEEEEEcCCCchHHHHHHHHHHhcCccccceEEEECCCCCHHHHHHHHHH
Confidence            68899999999995 6888742  2  343 4566666554 3445555544321111                      


Q ss_pred             -----------CceEEEEEeCCCC
Q 043781          181 -----------EKKFFLILDDVWT  193 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~  193 (297)
                                 ++..||++||+-.
T Consensus       243 a~tiAEyfrd~G~dVLli~Dsltr  266 (507)
T 1fx0_A          243 GAALAEYFMYRERHTLIIYDDLSK  266 (507)
T ss_dssp             HHHHHHHHHHTTCEEEEEEECHHH
T ss_pred             HHHHHHHHHHcCCcEEEEEecHHH
Confidence                       9999999999854

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=94.22  E-value=0.14  Score=49.43  Aligned_cols=25  Identities=12%  Similarity=0.182  Sum_probs=20.6

Q ss_pred             EEEEeCCCCCCccCHHHHHHHHhhh
Q 043781          185 FLILDDVWTDDYSKWEPFHNCLMRV  209 (297)
Q Consensus       185 LiVlDdv~~~~~~~w~~l~~~l~~~  209 (297)
                      .++||++.......|+.|...+...
T Consensus       204 vL~LDEi~~l~~~~q~~Ll~~Le~~  228 (604)
T 3k1j_A          204 VLFIDEIATLSLKMQQSLLTAMQEK  228 (604)
T ss_dssp             EEEETTGGGSCHHHHHHHHHHHHHS
T ss_pred             EEEEechhhCCHHHHHHHHHHHHcC
Confidence            7899999988777898888888653

>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=94.14  E-value=0.046  Score=49.40  Aligned_cols=91  Identities=13%  Similarity=0.055  Sum_probs=50.0

Q ss_pred             ccccccCCcchHHHHHHHhcccc------c---cc--CCCc---eEEE---EeCC-CCCHHHHHHHHHHhhcCCCceEEE
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKD------V---IE--NFDK---RIWV---CVSD-PFDEFRIAKAIIEGLEGSEKKFFL  186 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~------~---~~--~F~~---~~wv---~vs~-~~~~~~~~~~i~~~~~~~~kr~Li  186 (297)
                      ..|+|+.|+|||||.+.+..-..      +   .+  .|..   ..++   .+.. ..+..+   .|...+..  ..=+|
T Consensus       126 i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~~~~~~~---~La~aL~~--~Pdvi  200 (356)
T 3jvv_A          126 VLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSE---ALRSALRE--DPDII  200 (356)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHH---HHHHHTTS--CCSEE
T ss_pred             EEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeeeeccccCCHHH---HHHHHhhh--CcCEE
Confidence            46889999999999998865211      0   00  0110   0111   1111 123333   33444433  56688


Q ss_pred             EEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHH
Q 043781          187 ILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKL  235 (297)
Q Consensus       187 VlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~  235 (297)
                      ++|...+.  +.++.+....             ..|..||+||+..+..
T Consensus       201 llDEp~d~--e~~~~~~~~~-------------~~G~~vl~t~H~~~~~  234 (356)
T 3jvv_A          201 LVGEMRDL--ETIRLALTAA-------------ETGHLVFGTLHTTSAA  234 (356)
T ss_dssp             EESCCCSH--HHHHHHHHHH-------------HTTCEEEEEESCSSHH
T ss_pred             ecCCCCCH--HHHHHHHHHH-------------hcCCEEEEEEccChHH
Confidence            99999754  3444433322             3466789999876654

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=94.13  E-value=0.017  Score=47.02  Aligned_cols=21  Identities=24%  Similarity=0.295  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+.+.
T Consensus         3 I~i~G~~GsGKsT~~~~L~~~   23 (205)
T 2jaq_A            3 IAIFGTVGAGKSTISAEISKK   23 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCccCHHHHHHHHHHh
Confidence            457899999999999999873

>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=94.12  E-value=0.26  Score=44.54  Aligned_cols=52  Identities=10%  Similarity=0.026  Sum_probs=32.5

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.=+|+||.--.. |...-..+...+.+..        ...|..||++|++.+.+..+|.
T Consensus       180 ~~P~lLLlDEPTs~LD~~~~~~i~~lL~~l~--------~~~g~Tii~vTHdl~~~~~~aD  232 (366)
T 3tui_C          180 SNPKVLLCDQATSALDPATTRSILELLKDIN--------RRLGLTILLITHEMDVVKRICD  232 (366)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHH--------HHSCCEEEEEESCHHHHHHHCS
T ss_pred             cCCCEEEEECCCccCCHHHHHHHHHHHHHHH--------HhCCCEEEEEecCHHHHHHhCC
Confidence            77779999988654 2222233444444321        1347889999998777766654

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.07  E-value=0.018  Score=46.35  Aligned_cols=21  Identities=29%  Similarity=0.366  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+.+.
T Consensus         4 I~i~G~~GsGKsT~~~~L~~~   24 (194)
T 1nks_A            4 GIVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999873

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.07  E-value=0.018  Score=45.56  Aligned_cols=23  Identities=30%  Similarity=0.218  Sum_probs=19.7

Q ss_pred             cccccccccCCcchHHHHHHHhc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +..+.|.|++|+||||+++.+..
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHH
Confidence            45567899999999999999987

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.01  E-value=0.018  Score=46.97  Aligned_cols=22  Identities=23%  Similarity=0.270  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|+.|+|||||++.+...
T Consensus         9 ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            9 LFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECcCCCCHHHHHHHHHhh
Confidence            3578999999999999999873

>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=94.01  E-value=0.019  Score=46.50  Aligned_cols=21  Identities=33%  Similarity=0.411  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||++.+...
T Consensus         3 i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            3 IIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999988864

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=94.00  E-value=0.072  Score=48.68  Aligned_cols=20  Identities=25%  Similarity=0.129  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|+|.+|+|||+|+..+.+.
T Consensus       179 lIfg~~g~GKT~Ll~~Ia~~  198 (427)
T 3l0o_A          179 MIVAPPKAGKTTILKEIANG  198 (427)
T ss_dssp             EEEECTTCCHHHHHHHHHHH
T ss_pred             EEecCCCCChhHHHHHHHHH
Confidence            68899999999999888773

>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=94.00  E-value=0.019  Score=46.13  Aligned_cols=20  Identities=40%  Similarity=0.591  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+++.+..
T Consensus         6 I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            6 VVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999987

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.00  E-value=0.019  Score=46.31  Aligned_cols=22  Identities=14%  Similarity=0.268  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||++.+...
T Consensus         7 ~i~i~GpsGsGKSTL~~~L~~~   28 (180)
T 1kgd_A            7 TLVLLGAHGVGRRHIKNTLITK   28 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhh
Confidence            3568999999999999999873

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=93.99  E-value=0.019  Score=47.37  Aligned_cols=23  Identities=26%  Similarity=0.345  Sum_probs=19.7

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..++|+|..|+|||||++.+..-
T Consensus        23 ~~v~I~G~sGsGKSTl~~~l~~~   45 (208)
T 3c8u_A           23 QLVALSGAPGSGKSTLSNPLAAA   45 (208)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            34679999999999999998873

>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=93.96  E-value=0.019  Score=45.71  Aligned_cols=21  Identities=24%  Similarity=0.371  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|+|||||++.+..
T Consensus        10 ~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A           10 IYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            457899999999999999876

>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=93.95  E-value=0.019  Score=51.26  Aligned_cols=72  Identities=22%  Similarity=0.225  Sum_probs=40.4

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFH  203 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~  203 (297)
                      ...++|++|+||||||+.+.+.  ....|.   ....+-.....++ ..++..+   .++-++++|++........+.+.
T Consensus        53 ~~ll~Gp~G~GKTTLa~~ia~~--l~~~~~---~~sg~~~~~~~~l-~~~~~~~---~~~~v~~iDE~~~l~~~~~e~L~  123 (334)
T 1in4_A           53 HVLLAGPPGLGKTTLAHIIASE--LQTNIH---VTSGPVLVKQGDM-AAILTSL---ERGDVLFIDEIHRLNKAVEELLY  123 (334)
T ss_dssp             CEEEESSTTSSHHHHHHHHHHH--HTCCEE---EEETTTCCSHHHH-HHHHHHC---CTTCEEEEETGGGCCHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHH--hCCCEE---EEechHhcCHHHH-HHHHHHc---cCCCEEEEcchhhcCHHHHHHHH
Confidence            3568999999999999999983  322221   1121112233333 2333333   24457889998765433344443


Q ss_pred             H
Q 043781          204 N  204 (297)
Q Consensus       204 ~  204 (297)
                      .
T Consensus       124 ~  124 (334)
T 1in4_A          124 S  124 (334)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=93.91  E-value=0.13  Score=45.77  Aligned_cols=68  Identities=7%  Similarity=-0.021  Sum_probs=42.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC--CCceEEEEeCCCC---------------------CHHHHHHHHHHhh--cC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN--FDKRIWVCVSDPF---------------------DEFRIAKAIIEGL--EG  179 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~--F~~~~wv~vs~~~---------------------~~~~~~~~i~~~~--~~  179 (297)
                      ..|+|.+|+|||||+.++...  ....  =...+|+.....+                     +.+++.-++++++  -.
T Consensus        31 teI~G~pGsGKTtL~Lq~~~~--~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~i~  108 (333)
T 3io5_A           31 LILAGPSKSFKSNFGLTMVSS--YMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDAIE  108 (333)
T ss_dssp             EEEEESSSSSHHHHHHHHHHH--HHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHHhh
Confidence            468999999999999777653  2222  1346677655443                     3334312344444  22


Q ss_pred             CCceEEEEEeCCCCC
Q 043781          180 SEKKFFLILDDVWTD  194 (297)
Q Consensus       180 ~~kr~LiVlDdv~~~  194 (297)
                      .++.-|||+|-|...
T Consensus       109 ~~~~~lvVIDSI~aL  123 (333)
T 3io5_A          109 RGEKVVVFIDSLGNL  123 (333)
T ss_dssp             TTCCEEEEEECSTTC
T ss_pred             ccCceEEEEeccccc
Confidence            367889999999765

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=93.90  E-value=0.021  Score=45.61  Aligned_cols=22  Identities=36%  Similarity=0.332  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|.|++|+||||+|+.+...
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~   27 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKD   27 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            3568899999999999999873

>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=93.87  E-value=0.021  Score=46.10  Aligned_cols=20  Identities=40%  Similarity=0.311  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|++|+||||+++.+..
T Consensus         8 I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            8 IIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999877

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=93.86  E-value=0.02  Score=46.70  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||++.+...
T Consensus         8 ~i~l~G~~GsGKSTl~~~L~~~   29 (207)
T 2j41_A            8 LIVLSGPSGVGKGTVRKRIFED   29 (207)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            3578999999999999999873

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=93.82  E-value=0.021  Score=46.80  Aligned_cols=21  Identities=38%  Similarity=0.403  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|+|||||++.+..
T Consensus        31 ~i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           31 HVVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            457889999999999999987

>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=93.81  E-value=0.021  Score=46.75  Aligned_cols=21  Identities=33%  Similarity=0.357  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|+.|+||||+++.+..
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH
Confidence            357899999999999999876

>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=93.78  E-value=0.021  Score=47.43  Aligned_cols=21  Identities=33%  Similarity=0.441  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+|+.|+||||+++.+..
T Consensus         7 ~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            7 VITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999876

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=93.74  E-value=0.022  Score=45.72  Aligned_cols=20  Identities=30%  Similarity=0.132  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.+.|++|+||||+++.+.+
T Consensus         7 I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            7 VIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46789999999999999986

>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=93.74  E-value=0.023  Score=45.51  Aligned_cols=21  Identities=33%  Similarity=0.395  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+...
T Consensus        14 i~i~G~~GsGKst~~~~l~~~   34 (180)
T 3iij_A           14 ILLTGTPGVGKTTLGKELASK   34 (180)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            568899999999999999863

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=93.72  E-value=0.023  Score=46.49  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=19.7

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+.|.|+.|+||||||+.+...
T Consensus        19 ~~I~l~G~~GsGKSTla~~L~~~   41 (202)
T 3t61_A           19 GSIVVMGVSGSGKSSVGEAIAEA   41 (202)
T ss_dssp             SCEEEECSTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35678899999999999998773

>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=93.69  E-value=0.024  Score=48.48  Aligned_cols=21  Identities=33%  Similarity=0.335  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|+|||+||+.+++.
T Consensus        47 vll~G~~GtGKT~la~~la~~   67 (268)
T 2r62_A           47 VLLVGPPGTGKTLLAKAVAGE   67 (268)
T ss_dssp             CCCBCSSCSSHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHH
Confidence            348899999999999999984

>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=93.68  E-value=0.023  Score=48.27  Aligned_cols=62  Identities=19%  Similarity=0.167  Sum_probs=36.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CCC-HHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PFD-EFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      ..|+|++|+|||||++.+.+.  ...   ..+.+....    ... ...-+..+++.... ....++++|++.
T Consensus        52 ~ll~G~~G~GKTtl~~~i~~~--~~~---~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~~~i~~~Deid  118 (254)
T 1ixz_A           52 VLLVGPPGVGKTHLARAVAGE--ARV---PFITASGSDFVEMFVGVGAARVRDLFETAKR-HAPCIVFIDEID  118 (254)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--TTC---CEEEEEHHHHHHSCTTHHHHHHHHHHHHHTT-SSSEEEEEETHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--hCC---CEEEeeHHHHHHHHhhHHHHHHHHHHHHHHh-cCCeEEEehhhh
Confidence            568999999999999999984  322   223333211    111 11223344444321 346899999994

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=93.66  E-value=0.03  Score=45.74  Aligned_cols=22  Identities=32%  Similarity=0.206  Sum_probs=19.2

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.|.|++|+||||+++.+.+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~   37 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVK   37 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3467889999999999999886

>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=93.65  E-value=0.025  Score=45.72  Aligned_cols=20  Identities=25%  Similarity=0.321  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|+.|+|||||++.+..
T Consensus         5 i~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            5 YIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            46889999999999999975

>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=93.63  E-value=0.025  Score=46.38  Aligned_cols=21  Identities=33%  Similarity=0.444  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|+.|+||||+++.+..
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            367899999999999999976

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=93.62  E-value=0.023  Score=45.45  Aligned_cols=20  Identities=30%  Similarity=0.474  Sum_probs=16.7

Q ss_pred             cccccccCCcchHHHHHHHh
Q 043781          124 VSDVRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~  143 (297)
                      ...|+|+.|+|||||++.++
T Consensus        11 i~~l~G~nGsGKSTl~~~~~   30 (171)
T 4gp7_A           11 LVVLIGSSGSGKSTFAKKHF   30 (171)
T ss_dssp             EEEEECCTTSCHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHc
Confidence            35689999999999999644

>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=93.61  E-value=0.024  Score=45.50  Aligned_cols=20  Identities=25%  Similarity=0.391  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+|+.+..
T Consensus         5 I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            5 AVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56889999999999999987

>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=93.56  E-value=0.026  Score=46.27  Aligned_cols=22  Identities=41%  Similarity=0.377  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|+.|+|||||++.+...
T Consensus        27 ~i~l~G~sGsGKSTl~~~La~~   48 (200)
T 3uie_A           27 VIWVTGLSGSGKSTLACALNQM   48 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4568899999999999999874

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=93.56  E-value=0.025  Score=45.55  Aligned_cols=20  Identities=30%  Similarity=0.147  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+|+.+..
T Consensus         6 I~l~G~~GsGKsT~a~~L~~   25 (196)
T 1tev_A            6 VFVLGGPGAGKGTQCARIVE   25 (196)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            46889999999999998876

>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=93.52  E-value=0.026  Score=45.64  Aligned_cols=22  Identities=27%  Similarity=0.410  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|++|+||||+++.+.+.
T Consensus        12 ~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A           12 NILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            3678999999999999998773

>2ck3_A ATP synthase subunit alpha\, mitochondrial; hydrolase; HET: ANP ADP; 1.9A {Bos taurus} SCOP: a.69.1.1 b.49.1.1 c.37.1.11 PDB: 1bmf_A* 1e1q_A* 1e1r_A* 1e79_A* 1h8h_A* 1nbm_A* 1ohh_A* 1qo1_A 1w0j_A* 1w0k_A* 1h8e_A* 2jdi_A* 2wss_A* 2w6j_A 2w6e_A 2w6g_A 2w6f_A 2w6h_A 2w6i_A 1cow_A* ...

Probab=93.51  E-value=0.056  Score=50.92  Aligned_cols=68  Identities=22%  Similarity=0.231  Sum_probs=43.9

Q ss_pred             cccccCCcchHHHH-HHHhccccc----ccCCC-ceEEEEeCCCC-CHHHHHHHHHHhhcC-------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDV----IENFD-KRIWVCVSDPF-DEFRIAKAIIEGLEG-------------------  179 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~----~~~F~-~~~wv~vs~~~-~~~~~~~~i~~~~~~-------------------  179 (297)
                      .|+|..|+|||+|| ..+.+....    .++-+ ..+++-+.+.. .+.++.+.+...-..                   
T Consensus       166 ~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~Ev~~~~~~~~~~g~m~~tvvV~atad~p~~~r~~  245 (510)
T 2ck3_A          166 LIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATASDAAPLQYL  245 (510)
T ss_dssp             EEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHHHHHHHHHHHHTTCGGGEEEEEECTTSCHHHHHH
T ss_pred             EEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHHHHHHHHHHHhcCCcccceEEEECCCCCHHHHHH
Confidence            68899999999994 577774321    12344 35666666554 345555555542211                   


Q ss_pred             --------------CCceEEEEEeCCCC
Q 043781          180 --------------SEKKFFLILDDVWT  193 (297)
Q Consensus       180 --------------~~kr~LiVlDdv~~  193 (297)
                                    .++..||++||+-.
T Consensus       246 a~~~a~tiAEyfrd~G~dVLli~Dsltr  273 (510)
T 2ck3_A          246 APYSGCSMGEYFRDNGKHALIIYDDLSK  273 (510)
T ss_dssp             HHHHHHHHHHHHHTTTCEEEEEEETHHH
T ss_pred             HHHHHHHHHHHHHHcCCcEEEEEcCHHH
Confidence                          19999999999954

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=93.51  E-value=0.025  Score=46.51  Aligned_cols=22  Identities=41%  Similarity=0.356  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|+|..|+|||||++.+..-
T Consensus         8 ~i~i~G~~GsGKSTl~~~l~~~   29 (211)
T 3asz_A            8 VIGIAGGTASGKTTLAQALART   29 (211)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999999873

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.49  E-value=0.53  Score=43.51  Aligned_cols=22  Identities=32%  Similarity=0.265  Sum_probs=18.2

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.++|.+|+||||++..+..
T Consensus       101 ~vI~ivG~~GvGKTT~a~~LA~  122 (433)
T 2xxa_A          101 AVVLMAGLQGAGKTTSVGKLGK  122 (433)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4556789999999999987774

>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=93.44  E-value=0.027  Score=47.70  Aligned_cols=22  Identities=27%  Similarity=0.187  Sum_probs=19.4

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.|+|++|+|||||++.+.+
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999994

>3oaa_A ATP synthase subunit alpha; rossmann fold, hydrolase, hydrolase-transport PROT complex; HET: ANP ADP; 3.26A {Escherichia coli DH1} PDB: 2a7u_A

Probab=93.43  E-value=0.09  Score=49.42  Aligned_cols=64  Identities=20%  Similarity=0.203  Sum_probs=43.3

Q ss_pred             cccccCCcchHHHH-HHHhcccccccCCCc-eEEEEeCCCCC-HHHHHHHHHHhhcCC----------------------
Q 043781          126 DVRGMGGIGKTTLA-QFAYNDKDVIENFDK-RIWVCVSDPFD-EFRIAKAIIEGLEGS----------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa-~~v~~~~~~~~~F~~-~~wv~vs~~~~-~~~~~~~i~~~~~~~----------------------  180 (297)
                      .|+|..|+|||+|+ ..+.+.    .+-+. ++++-+.+..+ +.++.+++.+.-...                      
T Consensus       166 ~Ifg~~g~GKT~l~l~~I~n~----~~~dv~~V~~~IGeR~~ev~e~~~~l~~~g~m~~tvvV~atad~p~~~r~~a~~~  241 (513)
T 3oaa_A          166 LIIGDRQTGKTALAIDAIINQ----RDSGIKCIYVAIGQKASTISNVVRKLEEHGALANTIVVVATASESAALQYLAPYA  241 (513)
T ss_dssp             EEEESSSSSHHHHHHHHHHTT----SSSSCEEEEEEESCCHHHHHHHHHHHHHHSCSTTEEEEEECTTSCHHHHHHHHHH
T ss_pred             EeecCCCCCcchHHHHHHHhh----ccCCceEEEEEecCChHHHHHHHHHHhhcCcccceEEEEECCCCChHHHHHHHHH
Confidence            58899999999996 677763    22333 46777766543 456666654432111                      


Q ss_pred             -----------CceEEEEEeCCCC
Q 043781          181 -----------EKKFFLILDDVWT  193 (297)
Q Consensus       181 -----------~kr~LiVlDdv~~  193 (297)
                                 ++..||++||+-.
T Consensus       242 a~tiAEyfrd~G~dVLli~Dsltr  265 (513)
T 3oaa_A          242 GCAMGEYFRDRGEDALIIYDDLSK  265 (513)
T ss_dssp             HHHHHHHHHHTTCEEEEEEETHHH
T ss_pred             HHHHHHHHHhcCCCEEEEecChHH
Confidence                       9999999999954

>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=93.43  E-value=0.097  Score=44.00  Aligned_cols=20  Identities=20%  Similarity=-0.044  Sum_probs=16.2

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|..|+||||++..+.++
T Consensus        16 litG~mGsGKTT~ll~~~~r   35 (223)
T 2b8t_A           16 FITGPMFAGKTAELIRRLHR   35 (223)
T ss_dssp             EEECSTTSCHHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHHH
Confidence            36799999999999776664

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=93.41  E-value=0.028  Score=44.34  Aligned_cols=20  Identities=20%  Similarity=0.189  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+|+.+.+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            3 IYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEESCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999987

>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=93.40  E-value=0.028  Score=44.51  Aligned_cols=20  Identities=25%  Similarity=0.180  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+|+.+..
T Consensus         5 I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            5 IFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             EEEESCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56889999999999999987

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=93.37  E-value=0.029  Score=46.11  Aligned_cols=21  Identities=33%  Similarity=0.426  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|++|+|||||++.+...
T Consensus        15 i~l~G~sGsGKsTl~~~L~~~   35 (204)
T 2qor_A           15 LVVCGPSGVGKGTLIKKVLSE   35 (204)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            457899999999999999873

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=93.33  E-value=0.028  Score=45.41  Aligned_cols=21  Identities=29%  Similarity=0.189  Sum_probs=18.5

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|++|+||||+++.+.+
T Consensus        11 ~I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A           11 IIFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999999986

>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=93.31  E-value=0.035  Score=45.38  Aligned_cols=21  Identities=29%  Similarity=0.093  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|++|+||||+|+.+..
T Consensus        22 ~I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           22 RVLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999999987

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=93.29  E-value=0.029  Score=45.47  Aligned_cols=22  Identities=23%  Similarity=0.175  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|.|++|+||||+|+.+...
T Consensus        14 ~I~l~G~~GsGKsT~a~~L~~~   35 (199)
T 2bwj_A           14 IIFIIGGPGSGKGTQCEKLVEK   35 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3568899999999999999873

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=93.28  E-value=0.03  Score=45.13  Aligned_cols=20  Identities=40%  Similarity=0.562  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+++.+.+
T Consensus         3 I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999987

>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=93.25  E-value=0.031  Score=45.90  Aligned_cols=23  Identities=30%  Similarity=0.361  Sum_probs=19.9

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..++|+|++|+|||||++.+...
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~   44 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKH   44 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            34679999999999999999873

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=93.24  E-value=0.03  Score=45.94  Aligned_cols=21  Identities=29%  Similarity=0.409  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|+|||||++.+..
T Consensus         6 ~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            6 PVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            356899999999999999976

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=93.23  E-value=0.032  Score=45.02  Aligned_cols=21  Identities=33%  Similarity=0.313  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.+.|++|+||||+++.+...
T Consensus        16 i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           16 VWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            568899999999999999874

>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=93.20  E-value=0.052  Score=51.85  Aligned_cols=21  Identities=33%  Similarity=0.404  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|+||||||+.+...
T Consensus       111 vll~Gp~GtGKTtlar~ia~~  131 (543)
T 3m6a_A          111 LCLAGPPGVGKTSLAKSIAKS  131 (543)
T ss_dssp             EEEESSSSSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            458899999999999999883

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=93.10  E-value=0.034  Score=45.49  Aligned_cols=21  Identities=24%  Similarity=0.346  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+...
T Consensus         7 I~i~G~~GsGKsT~~~~L~~~   27 (213)
T 2plr_A            7 IAFEGIDGSGKSSQATLLKDW   27 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            457899999999999999873

>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=93.09  E-value=0.033  Score=47.79  Aligned_cols=20  Identities=25%  Similarity=0.438  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-+.|++|+||||+|+.+..
T Consensus         7 Ivl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            7 IILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHH
Confidence            45789999999999999887

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=93.06  E-value=0.034  Score=47.61  Aligned_cols=21  Identities=24%  Similarity=0.158  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|.|++|+||||||+.+...
T Consensus         4 i~I~G~~GSGKSTla~~La~~   24 (253)
T 2ze6_A            4 HLIYGPTCSGKTDMAIQIAQE   24 (253)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHhc
Confidence            457899999999999998763

>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=92.97  E-value=0.035  Score=44.62  Aligned_cols=21  Identities=33%  Similarity=0.170  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|++|+||||+++.+..
T Consensus         8 ~I~l~G~~GsGKsT~~~~L~~   28 (194)
T 1qf9_A            8 VVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            457889999999999999976

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=92.94  E-value=0.036  Score=47.92  Aligned_cols=62  Identities=19%  Similarity=0.167  Sum_probs=36.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CCC-HHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PFD-EFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      ..|+|++|+|||||++.+...  ...   ..+.+..+.    ... ...-+..+++.... ....++++|++.
T Consensus        76 vll~Gp~GtGKTtl~~~i~~~--~~~---~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~~~i~~iDeid  142 (278)
T 1iy2_A           76 VLLVGPPGVGKTHLARAVAGE--ARV---PFITASGSDFVEMFVGVGAARVRDLFETAKR-HAPCIVFIDEID  142 (278)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--TTC---CEEEEEHHHHHHSTTTHHHHHHHHHHHHHHT-SCSEEEEEETHH
T ss_pred             EEEECCCcChHHHHHHHHHHH--cCC---CEEEecHHHHHHHHhhHHHHHHHHHHHHHHh-cCCcEEehhhhH
Confidence            569999999999999999984  322   233333211    111 11223334444321 246899999995

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=92.92  E-value=0.034  Score=55.29  Aligned_cols=20  Identities=30%  Similarity=0.368  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      =++|.+|+|||++|+.+.+.
T Consensus       205 LL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          205 VLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             EEESCTTTTTHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            37799999999999999874

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=92.89  E-value=0.027  Score=45.08  Aligned_cols=21  Identities=29%  Similarity=0.284  Sum_probs=14.3

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|++|+||||+|+.+..
T Consensus         7 ~I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            7 IIWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             EEEEECCC----CHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356789999999999999876

>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=92.89  E-value=0.037  Score=45.91  Aligned_cols=21  Identities=29%  Similarity=0.159  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.+.|++|+||||+++.+...
T Consensus         7 I~l~G~~GsGKsT~a~~La~~   27 (220)
T 1aky_A            7 MVLIGPPGAGKGTQAPNLQER   27 (220)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999873

>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=92.88  E-value=0.12  Score=42.68  Aligned_cols=21  Identities=38%  Similarity=0.379  Sum_probs=18.5

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|..|+|||||++.+..
T Consensus        27 ~~~l~G~nGsGKSTll~~l~g   47 (231)
T 4a74_A           27 ITEVFGEFGSGKTQLAHTLAV   47 (231)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999976

>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=92.88  E-value=0.041  Score=44.97  Aligned_cols=19  Identities=32%  Similarity=0.509  Sum_probs=17.2

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -|.|+.|+|||||++.+..
T Consensus         5 Vi~GPSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            5 VISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             EEECCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4789999999999999876

>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=92.86  E-value=0.037  Score=45.71  Aligned_cols=22  Identities=27%  Similarity=0.539  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||++.+...
T Consensus        10 ~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A           10 LIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhh
Confidence            3568899999999999999873

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=92.85  E-value=0.037  Score=45.66  Aligned_cols=20  Identities=30%  Similarity=0.327  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+|+.+..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999976

>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=92.76  E-value=0.039  Score=45.58  Aligned_cols=20  Identities=25%  Similarity=0.273  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+|+.+..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999876

>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=92.73  E-value=0.12  Score=45.83  Aligned_cols=44  Identities=20%  Similarity=0.206  Sum_probs=29.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC----CCceEEEEeCCCCCHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN----FDKRIWVCVSDPFDEFR  168 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~~  168 (297)
                      ..|+|.+|+|||||+..+.........    -...+|++....++..+
T Consensus       110 ~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~  157 (324)
T 2z43_A          110 TEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWER  157 (324)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHH
T ss_pred             EEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHH
Confidence            468899999999999888764211110    23567887776655443

>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=92.71  E-value=0.043  Score=45.22  Aligned_cols=22  Identities=23%  Similarity=0.354  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|+.|+|||||++.+..-
T Consensus        22 i~~l~GpnGsGKSTLl~~l~gl   43 (207)
T 1znw_A           22 VVVLSGPSAVGKSTVVRCLRER   43 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhh
Confidence            3578999999999999998763

>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=92.70  E-value=0.19  Score=56.44  Aligned_cols=77  Identities=16%  Similarity=0.117  Sum_probs=50.4

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcC-------------CCceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEG-------------SEKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~-------------~~kr~LiVlDdv~~  193 (297)
                      ++|++|+|||+||+.+....   ..+ ..+.++.+...+...+++.+-..+..             .+++.++.+||+.-
T Consensus      1272 L~GPpGtGKT~la~~~l~~~---~~~-~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEinm 1347 (2695)
T 4akg_A         1272 LCGPPGSGKTMIMNNALRNS---SLY-DVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEINL 1347 (2695)
T ss_dssp             EECSTTSSHHHHHHHHHHSC---SSC-EEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETTTC
T ss_pred             EECCCCCCHHHHHHHHHhcC---CCC-ceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEeccccc
Confidence            56999999999997766531   122 33456777777777777666554321             26889999999755


Q ss_pred             CCcc------CHHHHHHHHh
Q 043781          194 DDYS------KWEPFHNCLM  207 (297)
Q Consensus       194 ~~~~------~w~~l~~~l~  207 (297)
                      ...+      ..+.|+..+.
T Consensus      1348 p~~d~yg~q~~lelLRq~le 1367 (2695)
T 4akg_A         1348 PKLDKYGSQNVVLFLRQLME 1367 (2695)
T ss_dssp             SCCCSSSCCHHHHHHHHHHH
T ss_pred             ccccccCchhHHHHHHHHHh
Confidence            4333      3455666664

>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=92.70  E-value=0.044  Score=46.02  Aligned_cols=22  Identities=27%  Similarity=0.188  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -+.+.|++|+||||+|+.+.+.
T Consensus        18 ~I~l~G~~GsGKsT~a~~La~~   39 (233)
T 1ak2_A           18 RAVLLGPPGAGKGTQAPKLAKN   39 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3567899999999999999873

>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=92.65  E-value=0.04  Score=44.74  Aligned_cols=21  Identities=29%  Similarity=0.425  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|+.|+||||+++.+..
T Consensus        10 ~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A           10 IIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             EEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999999987

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=92.63  E-value=0.041  Score=45.91  Aligned_cols=20  Identities=25%  Similarity=0.295  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+++.+..
T Consensus        10 I~l~G~~GsGKsT~a~~La~   29 (227)
T 1zd8_A           10 AVIMGAPGSGKGTVSSRITT   29 (227)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56889999999999999986

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=92.63  E-value=0.041  Score=45.11  Aligned_cols=21  Identities=19%  Similarity=0.241  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+.+.
T Consensus        13 I~l~G~~GsGKST~~~~L~~~   33 (212)
T 2wwf_A           13 IVFEGLDRSGKSTQSKLLVEY   33 (212)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            568899999999999999873

>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=92.60  E-value=0.12  Score=48.01  Aligned_cols=21  Identities=33%  Similarity=0.580  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|.|.+|+||||++..+...
T Consensus        48 ~li~G~aGTGKT~ll~~~~~~   68 (459)
T 3upu_A           48 VTINGPAGTGATTLTKFIIEA   68 (459)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            347799999999999888874

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=92.57  E-value=0.043  Score=45.62  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|.|++|+||||+++.+...
T Consensus         8 I~l~G~~GsGKsT~~~~La~~   28 (222)
T 1zak_A            8 VMISGAPASGKGTQCELIKTK   28 (222)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999873

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=92.53  E-value=0.048  Score=44.60  Aligned_cols=21  Identities=38%  Similarity=0.363  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+...
T Consensus         4 i~i~G~nG~GKTTll~~l~g~   24 (189)
T 2i3b_A            4 VFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             EEEESCCSSCHHHHHHHHHHH
T ss_pred             EEEECCCCChHHHHHHHHHhh
Confidence            568999999999999988874

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=92.53  E-value=0.046  Score=45.57  Aligned_cols=22  Identities=32%  Similarity=0.400  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||++.+...
T Consensus        25 ~~~lvGpsGsGKSTLl~~L~g~   46 (218)
T 1z6g_A           25 PLVICGPSGVGKGTLIKKLLNE   46 (218)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHhh
Confidence            3578999999999999999873

>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=92.49  E-value=0.044  Score=44.57  Aligned_cols=21  Identities=24%  Similarity=0.199  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+.+.
T Consensus         7 I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            7 IVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             EEEECCTTSSHHHHHHHHHHT
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            468899999999999999883

>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=92.47  E-value=0.044  Score=44.97  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+.+.
T Consensus        12 I~l~G~~GsGKsT~~~~L~~~   32 (215)
T 1nn5_A           12 IVLEGVDRAGKSTQSRKLVEA   32 (215)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            568899999999999999873

>3mfy_A V-type ATP synthase alpha chain; A-type ATP synthase, P loop, phenylalanine mutant, hydrolase; 2.35A {Pyrococcus horikoshii} PDB: 3i4l_A* 3i72_A 3i73_A* 3p20_A 3ikj_A 3qg1_A 3nd8_A 3nd9_A 1vdz_A 3qia_A 3qjy_A 3m4y_A 3se0_A 3sdz_A

Probab=92.46  E-value=0.17  Score=48.18  Aligned_cols=44  Identities=14%  Similarity=0.140  Sum_probs=30.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC-HHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD-EFRIAKAI  173 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i  173 (297)
                      .|+|..|+|||+|+..+.+..    +-+..+++-+.+..+ +.++++++
T Consensus       231 ~I~g~~g~GKT~L~~~ia~~~----~~~~~V~~~iGER~~Ev~e~~~~~  275 (588)
T 3mfy_A          231 AIPGPAGSGKTVTQHQLAKWS----DAQVVIYIGCGERGNEMTDVLEEF  275 (588)
T ss_dssp             EECSCCSHHHHHHHHHHHHHS----SCSEEEEEECCSSSSHHHHHHHHT
T ss_pred             EeecCCCCCHHHHHHHHHhcc----CCCEEEEEEecccHHHHHHHHHHH
Confidence            588999999999999987732    234566666666554 44555553

>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=92.44  E-value=0.046  Score=48.45  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=19.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..++|+|..|+|||||++.+..
T Consensus        91 ~ivgI~G~sGsGKSTL~~~L~g  112 (312)
T 3aez_A           91 FIIGVAGSVAVGKSTTARVLQA  112 (312)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEEECCCCchHHHHHHHHHh
Confidence            4568999999999999999887

>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=92.42  E-value=0.046  Score=44.82  Aligned_cols=22  Identities=36%  Similarity=0.436  Sum_probs=19.3

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      -.++|.|+.|+||||+++.+..
T Consensus        13 ~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           13 MVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999887

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=92.41  E-value=0.18  Score=41.34  Aligned_cols=45  Identities=20%  Similarity=0.152  Sum_probs=26.4

Q ss_pred             cccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHH
Q 043781          128 RGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAII  174 (297)
Q Consensus       128 ~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  174 (297)
                      =|..|+||||.++.+++.  .+..--.++...-+......+.++.++
T Consensus         6 EG~DGsGKsTq~~~L~~~--L~~~g~~v~~treP~~t~~~~~ir~~l   50 (197)
T 3hjn_A            6 EGIDGSGKSTQIQLLAQY--LEKRGKKVILKREPGGTETGEKIRKIL   50 (197)
T ss_dssp             ECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCSSHHHHHHHHHH
T ss_pred             ECCCCCCHHHHHHHHHHH--HHHCCCcEEEEECCCCCcHHHHHHHHh
Confidence            399999999999999883  433322333343333333444444444

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=92.41  E-value=0.045  Score=46.37  Aligned_cols=21  Identities=24%  Similarity=0.294  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+|||||++.+..
T Consensus        27 iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           27 LIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999876

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=92.40  E-value=0.15  Score=44.98  Aligned_cols=48  Identities=15%  Similarity=0.052  Sum_probs=31.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHh
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEG  176 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~  176 (297)
                      .-|.|.+|+||||||..+..+...+.  ..++|++..  .+..++...++..
T Consensus        71 ~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE--~s~~~l~~R~~~~  118 (315)
T 3bh0_A           71 VLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLE--MGKKENIKRLIVT  118 (315)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESS--SCHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECC--CCHHHHHHHHHHH
Confidence            34679999999999988876532222  567777654  4555555555443

>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=92.39  E-value=1.1  Score=41.59  Aligned_cols=22  Identities=27%  Similarity=0.259  Sum_probs=18.5

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.++|.+|+||||++..+..
T Consensus       101 ~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A          101 TILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECcCCCCHHHHHHHHHH
Confidence            4567889999999999987775

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=92.34  E-value=0.049  Score=46.51  Aligned_cols=22  Identities=36%  Similarity=0.404  Sum_probs=19.5

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.|+|+.|+|||||++.+..
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3568999999999999999985

>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=92.32  E-value=0.049  Score=43.57  Aligned_cols=20  Identities=30%  Similarity=0.375  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.+.|+.|+||||+++.+..
T Consensus         8 i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            8 VWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45889999999999999977

>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=92.31  E-value=0.07  Score=45.13  Aligned_cols=21  Identities=24%  Similarity=0.333  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+|+|+.|+|||||.+.+..
T Consensus        33 ~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           33 FVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHhc
Confidence            357999999999999999987

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=92.30  E-value=0.048  Score=44.73  Aligned_cols=21  Identities=38%  Similarity=0.447  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+|||||++.+..
T Consensus        24 ~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A           24 VLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999876

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.21  E-value=0.072  Score=44.68  Aligned_cols=21  Identities=29%  Similarity=0.240  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|+.|+|||||.+.+..-
T Consensus        33 ~~iiG~nGsGKSTLl~~l~Gl   53 (224)
T 2pcj_A           33 VSIIGASGSGKSTLLYILGLL   53 (224)
T ss_dssp             EEEEECTTSCHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            578999999999999999873

>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=92.21  E-value=0.03  Score=46.01  Aligned_cols=21  Identities=29%  Similarity=0.431  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|..|+||||+++.+...
T Consensus         3 I~i~G~~GsGKsTl~~~L~~~   23 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSGA   23 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            457899999999999998763

>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=92.18  E-value=0.055  Score=42.90  Aligned_cols=22  Identities=32%  Similarity=0.315  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...++|..|.|||||++.+..-
T Consensus        35 ~v~L~G~nGaGKTTLlr~l~g~   56 (158)
T 1htw_A           35 MVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            3568999999999999999883

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=92.05  E-value=0.053  Score=47.34  Aligned_cols=20  Identities=30%  Similarity=0.386  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|++|+||||||+.+..
T Consensus        36 ivl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           36 FLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             EEEECCTTSCTHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999976

>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=92.05  E-value=0.054  Score=44.73  Aligned_cols=20  Identities=35%  Similarity=0.265  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|++|+||||+|+.+.+
T Consensus         3 I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999987

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.01  E-value=0.079  Score=45.61  Aligned_cols=21  Identities=24%  Similarity=0.253  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|+.|+|||||.+.+..-
T Consensus        35 ~~liG~nGsGKSTLlk~l~Gl   55 (262)
T 1b0u_A           35 ISIIGSSGSGKSTFLRCINFL   55 (262)
T ss_dssp             EEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            478999999999999999873

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=91.99  E-value=0.086  Score=44.80  Aligned_cols=23  Identities=17%  Similarity=0.236  Sum_probs=20.2

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...+|+|+.|+|||||.+.+..-
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl   47 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCC
Confidence            55679999999999999999873

>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=91.99  E-value=0.21  Score=44.62  Aligned_cols=45  Identities=20%  Similarity=0.182  Sum_probs=30.5

Q ss_pred             ccccccCCcchHHHHHHHhccccccc----CCCceEEEEeCCCCCHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE----NFDKRIWVCVSDPFDEFRI  169 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~----~F~~~~wv~vs~~~~~~~~  169 (297)
                      ..|+|.+|+||||||..+........    .-...+|+.....++..++
T Consensus       125 ~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l  173 (343)
T 1v5w_A          125 TEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRL  173 (343)
T ss_dssp             EEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHH
Confidence            46889999999999988877422211    1235678887776665443

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=91.97  E-value=0.056  Score=44.83  Aligned_cols=21  Identities=29%  Similarity=0.351  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.+.|++|+||||+|+.+...
T Consensus         8 I~l~G~~GsGKsT~a~~La~~   28 (217)
T 3be4_A            8 LILIGAPGSGKGTQCEFIKKE   28 (217)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999773

>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=91.94  E-value=0.055  Score=47.39  Aligned_cols=22  Identities=27%  Similarity=0.264  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|+|..|+|||||++.+...
T Consensus        33 ii~I~G~sGsGKSTla~~L~~~   54 (290)
T 1odf_A           33 FIFFSGPQGSGKSFTSIQIYNH   54 (290)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5689999999999999988763

>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=91.91  E-value=0.059  Score=44.45  Aligned_cols=21  Identities=29%  Similarity=0.257  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+...
T Consensus        28 i~~~G~~GsGKsT~~~~l~~~   48 (211)
T 1m7g_A           28 IWLTGLSASGKSTLAVELEHQ   48 (211)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999998773

>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=91.90  E-value=0.082  Score=45.91  Aligned_cols=20  Identities=35%  Similarity=0.453  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+|+|+.|+|||||.+.+..
T Consensus        37 ~~iiGpnGsGKSTLl~~l~G   56 (275)
T 3gfo_A           37 TAILGGNGVGKSTLFQNFNG   56 (275)
T ss_dssp             EEEECCTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            47899999999999999986

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=91.87  E-value=0.059  Score=44.95  Aligned_cols=19  Identities=26%  Similarity=0.323  Sum_probs=17.2

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      .|.|++|+||||+++.+..
T Consensus         4 ~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            4 LIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEECCTTSCHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4789999999999999977

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=91.87  E-value=0.057  Score=46.24  Aligned_cols=21  Identities=33%  Similarity=0.379  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+|+.|+||||+++.+..
T Consensus        50 ~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           50 SMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             CEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999987

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=91.84  E-value=0.05  Score=46.42  Aligned_cols=21  Identities=29%  Similarity=0.396  Sum_probs=18.5

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+-++|++|+||||+|+.+..
T Consensus        34 ~i~l~G~~GsGKSTla~~L~~   54 (253)
T 2p5t_B           34 AILLGGQSGAGKTTIHRIKQK   54 (253)
T ss_dssp             EEEEESCGGGTTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999999877

>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=91.81  E-value=0.09  Score=43.86  Aligned_cols=22  Identities=41%  Similarity=0.492  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||.+.+..-
T Consensus        37 ~~~iiG~NGsGKSTLlk~l~Gl   58 (214)
T 1sgw_A           37 VVNFHGPNGIGKTTLLKTISTY   58 (214)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3468999999999999999873

>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=91.78  E-value=0.17  Score=44.59  Aligned_cols=46  Identities=22%  Similarity=0.291  Sum_probs=30.8

Q ss_pred             ccccccCCcchHHHHHHHhccccccc---------CC-----CceEEEEeCCCCCHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIE---------NF-----DKRIWVCVSDPFDEFRIA  170 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~---------~F-----~~~~wv~vs~~~~~~~~~  170 (297)
                      ..|+|.+|+|||+||..+..+.....         ..     ..++|++....++..++.
T Consensus       101 ~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~  160 (322)
T 2i1q_A          101 TEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIM  160 (322)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHHHH
Confidence            46889999999999988876422211         11     356788877776555443

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=91.74  E-value=0.058  Score=44.83  Aligned_cols=21  Identities=33%  Similarity=0.131  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|+.|+|||||.+.+..-
T Consensus        25 ~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           25 VFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             EEEECCTTSSTTHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999863

>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=91.71  E-value=0.062  Score=44.44  Aligned_cols=21  Identities=29%  Similarity=0.333  Sum_probs=18.4

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|+.|+||||+++.+..
T Consensus         6 ~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            6 IVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            357889999999999999865

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=91.67  E-value=0.11  Score=49.74  Aligned_cols=34  Identities=24%  Similarity=0.256  Sum_probs=24.1

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP  163 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~  163 (297)
                      +|+|..|+|||+|+..+.+..    +-+..+++-+...
T Consensus       236 ~Ifgg~g~GKT~L~~~ia~~~----~~~v~V~~~iGER  269 (600)
T 3vr4_A          236 AVPGPFGAGKTVVQHQIAKWS----DVDLVVYVGCGER  269 (600)
T ss_dssp             EEECCTTSCHHHHHHHHHHHS----SCSEEEEEEEEEC
T ss_pred             eeecCCCccHHHHHHHHHhcc----CCCEEEEEEeccc
Confidence            688999999999999998742    2244555544443

>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=91.63  E-value=0.063  Score=45.67  Aligned_cols=21  Identities=19%  Similarity=0.230  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|+.|+||||+|+.+..
T Consensus        24 iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999877

>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=91.58  E-value=0.062  Score=48.31  Aligned_cols=65  Identities=17%  Similarity=0.089  Sum_probs=37.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCC---CceEEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGS---EKKFFLILDDVWTD  194 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~~  194 (297)
                      .-++|++|+|||++|+.+.+.  ....|   +-+..+.-.       +....+..++......   ....+|+||++...
T Consensus        54 vll~GppGtGKT~la~~ia~~--~~~~~---~~~~~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l  128 (363)
T 3hws_A           54 ILLIGPTGSGKTLLAETLARL--LDVPF---TMADATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKI  128 (363)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--TTCCE---EEEEHHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH--cCCCE---EEechHHhcccccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhh
Confidence            347899999999999999983  33222   222221111       1123334444433221   34568999999754

>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=91.45  E-value=0.099  Score=44.81  Aligned_cols=21  Identities=29%  Similarity=0.297  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|+.|+|||||.+.+..-
T Consensus        36 ~~liG~nGsGKSTLlk~l~Gl   56 (257)
T 1g6h_A           36 TLIIGPNGSGKSTLINVITGF   56 (257)
T ss_dssp             EEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            478999999999999999863

>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=91.45  E-value=0.1  Score=44.29  Aligned_cols=21  Identities=29%  Similarity=0.226  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+..-
T Consensus        35 ~~l~G~nGsGKSTLl~~l~Gl   55 (240)
T 1ji0_A           35 VTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             EEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            578999999999999999874

>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=91.44  E-value=0.099  Score=45.06  Aligned_cols=21  Identities=29%  Similarity=0.195  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|+.|+|||||.+.+..-
T Consensus        53 ~~liG~NGsGKSTLlk~l~Gl   73 (263)
T 2olj_A           53 VVVIGPSGSGKSTFLRCLNLL   73 (263)
T ss_dssp             EEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEcCCCCcHHHHHHHHHcC
Confidence            468999999999999999873

>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=91.44  E-value=0.2  Score=43.44  Aligned_cols=35  Identities=20%  Similarity=0.126  Sum_probs=24.1

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCC-ceEEEEe
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFD-KRIWVCV  160 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~v  160 (297)
                      ...|+|.+|+|||||++.+.......  -. .++|+..
T Consensus        37 ~~~i~G~~G~GKTTl~~~ia~~~~~~--~G~~v~~~~~   72 (296)
T 1cr0_A           37 VIMVTSGSGMGKSTFVRQQALQWGTA--MGKKVGLAML   72 (296)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT--SCCCEEEEES
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHHH--cCCeEEEEeC
Confidence            34688999999999999988743222  22 3556654

>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=91.42  E-value=0.4  Score=44.00  Aligned_cols=21  Identities=29%  Similarity=0.286  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|++|+||||+|+.+...
T Consensus       261 Iil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          261 VVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             EEEESCTTSSHHHHHHHHTGG
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            347799999999999998874

>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=91.41  E-value=0.1  Score=44.51  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||.+.+..-
T Consensus        37 ~~~i~G~nGsGKSTLl~~l~Gl   58 (247)
T 2ff7_A           37 VIGIVGRSGSGKSTLTKLIQRF   58 (247)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3578999999999999999874

>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=91.38  E-value=0.07  Score=43.11  Aligned_cols=22  Identities=23%  Similarity=0.265  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+...
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4679999999999999998875

>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=91.38  E-value=0.1  Score=44.78  Aligned_cols=22  Identities=27%  Similarity=0.286  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|+.|+|||||.+.+..-
T Consensus        43 i~~l~G~NGsGKSTLlk~l~Gl   64 (256)
T 1vpl_A           43 IFGLIGPNGAGKTTTLRIISTL   64 (256)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3578999999999999999873

>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=91.30  E-value=0.1  Score=44.26  Aligned_cols=22  Identities=23%  Similarity=0.238  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+..-
T Consensus        30 ~~~i~G~nGsGKSTLl~~l~Gl   51 (243)
T 1mv5_A           30 IIAFAGPSGGGKSTIFSLLERF   51 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3579999999999999999873

>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=91.30  E-value=0.072  Score=45.12  Aligned_cols=22  Identities=27%  Similarity=0.371  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+..-
T Consensus        33 ~~~i~G~nGsGKSTLl~~l~Gl   54 (237)
T 2cbz_A           33 LVAVVGQVGCGKSSLLSALLAE   54 (237)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3578999999999999999874

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=91.27  E-value=0.049  Score=45.62  Aligned_cols=20  Identities=30%  Similarity=0.315  Sum_probs=14.2

Q ss_pred             cccccccCCcchHHHHHHHh
Q 043781          124 VSDVRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~  143 (297)
                      ..+|+|+.|+|||||++.+.
T Consensus        29 ii~l~Gp~GsGKSTl~~~L~   48 (231)
T 3lnc_A           29 ILVLSSPSGCGKTTVANKLL   48 (231)
T ss_dssp             EEEEECSCC----CHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            45789999999999999998

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.24  E-value=0.11  Score=45.04  Aligned_cols=21  Identities=33%  Similarity=0.431  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+..-
T Consensus        48 ~~i~G~nGsGKSTLlk~l~Gl   68 (271)
T 2ixe_A           48 TALVGPNGSGKSTVAALLQNL   68 (271)
T ss_dssp             EEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999873

>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=91.24  E-value=0.073  Score=45.11  Aligned_cols=21  Identities=24%  Similarity=0.047  Sum_probs=18.4

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|++|+||||+|+.+.+
T Consensus        31 ~I~l~G~~GsGKsT~a~~L~~   51 (243)
T 3tlx_A           31 RYIFLGAPGSGKGTQSLNLKK   51 (243)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999999976

>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=91.20  E-value=0.08  Score=44.31  Aligned_cols=22  Identities=27%  Similarity=0.298  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||.+.+...
T Consensus        18 ii~l~GpsGsGKSTLlk~L~g~   39 (219)
T 1s96_A           18 LYIVSAPSGAGKSSLIQALLKT   39 (219)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcc
Confidence            3468899999999999998874

>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=91.19  E-value=0.078  Score=46.76  Aligned_cols=22  Identities=36%  Similarity=0.345  Sum_probs=19.4

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ....|+|+.|+|||||++.+..
T Consensus       103 ~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          103 RVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHH
Confidence            4567999999999999999886

>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=91.13  E-value=0.078  Score=43.00  Aligned_cols=22  Identities=23%  Similarity=0.265  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+...
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            3578999999999999998875

>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=91.09  E-value=0.085  Score=41.34  Aligned_cols=21  Identities=19%  Similarity=0.260  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||.+.+...
T Consensus         6 v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            6 IALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999998874

>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=91.09  E-value=0.18  Score=45.27  Aligned_cols=21  Identities=38%  Similarity=0.283  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|.+|+|||||+..+...
T Consensus       134 ~~I~G~~GsGKTTL~~~l~~~  154 (349)
T 1pzn_A          134 TEVFGEFGSGKTQLAHTLAVM  154 (349)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999998874

>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=91.06  E-value=0.079  Score=43.11  Aligned_cols=21  Identities=19%  Similarity=0.336  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|+.|+||||+++.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            457889999999999999987

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.03  E-value=0.11  Score=44.66  Aligned_cols=22  Identities=36%  Similarity=0.296  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||.+.+..-
T Consensus        35 ~~~liG~nGsGKSTLl~~i~Gl   56 (266)
T 2yz2_A           35 CLLVAGNTGSGKSTLLQIVAGL   56 (266)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCcHHHHHHHHhCC
Confidence            3578999999999999999873

>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=91.02  E-value=0.23  Score=55.77  Aligned_cols=76  Identities=21%  Similarity=0.137  Sum_probs=55.2

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHH---HHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFR---IAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFH  203 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~---~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~  203 (297)
                      +||.||+||++|++.+..-   .+ + ..+-+.+++.++..+   -++.++...+..+++..++++|..-.+....+.|-
T Consensus      1614 LvGvgGsGkqSltrLaa~i---~~-~-~~fqi~~~~~Y~~~~f~eDLk~l~~~aG~~~~~~vFL~tD~qi~~e~FLE~IN 1688 (2695)
T 4akg_A         1614 LIGASRTGKTILTRFVAWL---NG-L-KIVQPKIHRHSNLSDFDMILKKAISDCSLKESRTCLIIDESNILETAFLERMN 1688 (2695)
T ss_dssp             EECTTTSCHHHHHHHHHHH---TT-C-EEECCCCCTTCCHHHHHHHHHHHHHHHHHSCCCEEEEEETTTCCSHHHHHHHH
T ss_pred             EECCCCCcHHHHHHHHHHH---hC-C-eeEEEEeeCCCCHHHHHHHHHHHHHHcCCCCCceEEEEeccccccHHHHHHHH
Confidence            7899999999999998872   11 1 122345788887654   56677777777799999999999766555666666


Q ss_pred             HHHh
Q 043781          204 NCLM  207 (297)
Q Consensus       204 ~~l~  207 (297)
                      ..|.
T Consensus      1689 ~lL~ 1692 (2695)
T 4akg_A         1689 TLLA 1692 (2695)
T ss_dssp             HHHH
T ss_pred             HHHc
Confidence            6664

>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=91.01  E-value=0.084  Score=45.06  Aligned_cols=21  Identities=33%  Similarity=0.496  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+|+|..|+|||||.+.+..
T Consensus        31 ~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           31 VHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            357899999999999999998

>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=91.01  E-value=0.076  Score=46.75  Aligned_cols=22  Identities=23%  Similarity=0.330  Sum_probs=19.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..++|+|..|+|||||++.+..
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999887

>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=91.00  E-value=0.084  Score=43.77  Aligned_cols=20  Identities=30%  Similarity=0.232  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -+.|++|+||+|+|+.+.+.
T Consensus         4 il~GpPGsGKgTqa~~La~~   23 (206)
T 3sr0_A            4 VFLGPPGAGKGTQAKRLAKE   23 (206)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            46799999999999999874

>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=90.99  E-value=0.085  Score=43.49  Aligned_cols=21  Identities=14%  Similarity=0.355  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+...
T Consensus        22 ivl~GPSGaGKsTL~~~L~~~   42 (197)
T 3ney_A           22 LVLIGASGVGRSHIKNALLSQ   42 (197)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHhh
Confidence            468899999999999998863

>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=90.97  E-value=0.088  Score=42.28  Aligned_cols=23  Identities=39%  Similarity=0.284  Sum_probs=19.6

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....|.|..|+|||||+..+...
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~   27 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAA   27 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            35678899999999999998873

>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=90.88  E-value=0.084  Score=45.86  Aligned_cols=22  Identities=36%  Similarity=0.499  Sum_probs=19.1

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      -.+.|.|+.|+||||+|+.+..
T Consensus        76 ~iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999873

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=90.85  E-value=0.052  Score=43.68  Aligned_cols=22  Identities=27%  Similarity=0.252  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||++.+..-
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~   25 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPI   25 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4679999999999999998873

>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=90.83  E-value=0.089  Score=45.41  Aligned_cols=21  Identities=29%  Similarity=0.374  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+..-
T Consensus        49 ~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           49 HAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999883

>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=90.79  E-value=0.087  Score=44.34  Aligned_cols=22  Identities=32%  Similarity=0.477  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||.+.+..-
T Consensus        36 ~~~i~G~nGsGKSTLl~~l~Gl   57 (229)
T 2pze_A           36 LLAVAGSTGAGKTSLLMMIMGE   57 (229)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999873

>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=90.72  E-value=0.093  Score=41.93  Aligned_cols=21  Identities=38%  Similarity=0.338  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|.+|+|||||.+.+...
T Consensus         5 v~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            5 LMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999998873

>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=90.70  E-value=0.089  Score=45.74  Aligned_cols=20  Identities=30%  Similarity=0.177  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|++|+||||+|+.+..
T Consensus         5 I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            5 ILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999987

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=90.69  E-value=0.091  Score=46.27  Aligned_cols=23  Identities=30%  Similarity=0.216  Sum_probs=19.7

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|+.|+|||||++.+...
T Consensus       101 ~vi~lvG~nGsGKTTll~~Lag~  123 (302)
T 3b9q_A          101 AVIMIVGVNGGGKTTSLGKLAHR  123 (302)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHH
Confidence            35679999999999999998873

>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=90.67  E-value=0.38  Score=40.42  Aligned_cols=21  Identities=33%  Similarity=0.260  Sum_probs=17.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|..|.|||.+|..+...
T Consensus       111 ~ll~~~tG~GKT~~a~~~~~~  131 (237)
T 2fz4_A          111 GCIVLPTGSGKTHVAMAAINE  131 (237)
T ss_dssp             EEEEESSSTTHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            346799999999999877763

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=90.64  E-value=0.089  Score=45.51  Aligned_cols=21  Identities=33%  Similarity=0.534  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.++.-
T Consensus         5 v~lvG~nGaGKSTLln~L~g~   25 (270)
T 3sop_A            5 IMVVGQSGLGKSTLVNTLFKS   25 (270)
T ss_dssp             EEEEESSSSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999998863

>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=90.55  E-value=1.9  Score=37.60  Aligned_cols=22  Identities=36%  Similarity=0.259  Sum_probs=18.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ....++|.+|+||||++..+..
T Consensus        99 ~vi~i~G~~G~GKTT~~~~la~  120 (297)
T 1j8m_F           99 YVIMLVGVQGTGKTTTAGKLAY  120 (297)
T ss_dssp             EEEEEECSSCSSTTHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4456789999999999988876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=90.49  E-value=0.097  Score=46.55  Aligned_cols=21  Identities=19%  Similarity=0.335  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+|||||++.+..
T Consensus        94 iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           94 IIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            568999999999999998876

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=90.49  E-value=0.098  Score=43.77  Aligned_cols=22  Identities=32%  Similarity=0.184  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|.|++|+||+|+|+.+.+.
T Consensus        31 iI~llGpPGsGKgTqa~~L~~~   52 (217)
T 3umf_A           31 VIFVLGGPGSGKGTQCEKLVQK   52 (217)
T ss_dssp             EEEEECCTTCCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3457799999999999999874

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=90.48  E-value=0.095  Score=45.60  Aligned_cols=21  Identities=33%  Similarity=0.352  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+..-
T Consensus        50 ~~liG~NGsGKSTLlk~l~Gl   70 (279)
T 2ihy_A           50 WILYGLNGAGKTTLLNILNAY   70 (279)
T ss_dssp             EEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            478999999999999999874

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=90.45  E-value=0.096  Score=45.03  Aligned_cols=21  Identities=33%  Similarity=0.532  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||||.+.+..-
T Consensus        49 ~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           49 CALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             EEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            578999999999999999873

>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=90.45  E-value=0.096  Score=44.75  Aligned_cols=21  Identities=29%  Similarity=0.259  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        29 ~~liG~NGsGKSTLlk~l~Gl   49 (249)
T 2qi9_C           29 LHLVGPNGAGKSTLLARMAGM   49 (249)
T ss_dssp             EEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            468999999999999998873

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=90.43  E-value=0.098  Score=44.77  Aligned_cols=21  Identities=33%  Similarity=0.401  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+..-
T Consensus        34 ~~l~G~nGsGKSTLl~~l~Gl   54 (253)
T 2nq2_C           34 LAVLGQNGCGKSTLLDLLLGI   54 (253)
T ss_dssp             EEEECCSSSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            578999999999999999874

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=90.34  E-value=0.11  Score=41.36  Aligned_cols=22  Identities=18%  Similarity=0.220  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus         9 ~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            9 EIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999874

>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=90.24  E-value=0.081  Score=44.33  Aligned_cols=22  Identities=27%  Similarity=0.160  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|.|..|+|||||++.+...
T Consensus        22 ~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           22 TVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            4578899999999999999873

>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=90.22  E-value=0.11  Score=44.91  Aligned_cols=21  Identities=33%  Similarity=0.365  Sum_probs=18.2

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|.+|+|||||+..+..
T Consensus        32 i~~i~G~~GsGKTtl~~~l~~   52 (279)
T 1nlf_A           32 VGALVSPGGAGKSMLALQLAA   52 (279)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            346889999999999998876

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=90.22  E-value=0.12  Score=39.85  Aligned_cols=21  Identities=19%  Similarity=0.257  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         4 i~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            4 VVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEECCTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            468899999999999988765

>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=90.21  E-value=0.16  Score=42.61  Aligned_cols=21  Identities=33%  Similarity=0.450  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+.+.
T Consensus        29 i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           29 ITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            457799999999999999984

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=90.18  E-value=0.099  Score=48.90  Aligned_cols=20  Identities=30%  Similarity=0.368  Sum_probs=17.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||+||+.+.+.
T Consensus       205 LL~G~pG~GKT~la~~la~~  224 (468)
T 3pxg_A          205 VLIGEPGVGKTAIAEGLAQQ  224 (468)
T ss_dssp             EEESCTTTTTHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            37799999999999999884

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=90.14  E-value=0.11  Score=43.92  Aligned_cols=21  Identities=33%  Similarity=0.351  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|.|++|+||||+|+.+.+.
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~~   31 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKEK   31 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             eeeECCCCCCHHHHHHHHHHH
Confidence            478999999999999998773

>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=90.14  E-value=0.11  Score=45.62  Aligned_cols=23  Identities=26%  Similarity=0.072  Sum_probs=19.4

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|.+|+||||++..+...
T Consensus       106 ~vi~lvG~~GsGKTTl~~~LA~~  128 (296)
T 2px0_A          106 KYIVLFGSTGAGKTTTLAKLAAI  128 (296)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH
Confidence            35678999999999999888763

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=90.04  E-value=0.11  Score=41.64  Aligned_cols=25  Identities=20%  Similarity=0.138  Sum_probs=20.7

Q ss_pred             cccccccccCCcchHHHHHHHhccc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      ...+.|+|.+|+|||||...+.+..
T Consensus        17 ~~ki~v~G~~~~GKSsl~~~l~~~~   41 (199)
T 4bas_A           17 KLQVVMCGLDNSGKTTIINQVKPAQ   41 (199)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHSCCC
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcCC
Confidence            3456789999999999999988753

>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=90.03  E-value=0.12  Score=39.75  Aligned_cols=21  Identities=33%  Similarity=0.502  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus         6 i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            468899999999999998765

>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=89.99  E-value=0.43  Score=45.79  Aligned_cols=21  Identities=24%  Similarity=0.218  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|.|.+|+||||++..+...
T Consensus       207 ~~I~G~pGTGKTt~i~~l~~~  227 (574)
T 3e1s_A          207 VVLTGGPGTGKSTTTKAVADL  227 (574)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            347799999999999888873

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=89.96  E-value=0.33  Score=55.26  Aligned_cols=76  Identities=18%  Similarity=0.230  Sum_probs=51.5

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHH---HHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFR---IAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFH  203 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~---~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~  203 (297)
                      +||.||+||++|++.+..   +.+ + ..+=+.+++.++..+   -++.++...+..+++..++++|-.-.+....+.|-
T Consensus      1651 LVGvgGSGkqSLtrLAa~---i~~-~-~vfqi~i~k~Y~~~~f~eDLk~l~~~aG~~~~~~vFL~tD~qi~~e~FLE~IN 1725 (3245)
T 3vkg_A         1651 LIGVSGGGKSVLSRFVAW---MNG-L-SIYTIKVNNNYKSSDFDDDLRMLLKRAGCKEEKICFIFDESNVLESSFLERMN 1725 (3245)
T ss_dssp             EEESTTSSHHHHHHHHHH---HTT-C-EEECCC----CCHHHHHHHHHHHHHHHHTSCCCEEEEEEGGGCSSTHHHHHHH
T ss_pred             EecCCCCcHHHHHHHHHH---HhC-C-eeEEEeeeCCCCHHHHHHHHHHHHHHHhcCCCCEEEEEeccccccHHHHHHHH
Confidence            789999999999999887   221 1 122345678777654   56677888888899999999998755545556665


Q ss_pred             HHHh
Q 043781          204 NCLM  207 (297)
Q Consensus       204 ~~l~  207 (297)
                      ..|.
T Consensus      1726 ~lL~ 1729 (3245)
T 3vkg_A         1726 TLLA 1729 (3245)
T ss_dssp             HHHH
T ss_pred             HHhc
Confidence            5554

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=89.92  E-value=0.11  Score=42.78  Aligned_cols=22  Identities=32%  Similarity=0.330  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||+..+...
T Consensus        40 ~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           40 AFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            4568899999999999888774

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=89.90  E-value=0.17  Score=42.15  Aligned_cols=20  Identities=30%  Similarity=0.220  Sum_probs=16.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|.+|+|||||+..+..
T Consensus        26 ~~i~G~~GsGKTtl~~~~~~   45 (247)
T 2dr3_A           26 VLLSGGPGTGKTIFSQQFLW   45 (247)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45889999999999877765

>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=89.87  E-value=0.12  Score=45.61  Aligned_cols=21  Identities=19%  Similarity=0.162  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|+|||||++.+..
T Consensus       128 ~vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          128 CLAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             EEEEECSSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHhh
Confidence            357999999999999999987

>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=89.87  E-value=0.12  Score=43.72  Aligned_cols=21  Identities=33%  Similarity=0.273  Sum_probs=17.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...+.|.||+|||||+..+..
T Consensus        16 i~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           16 IVVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEeCCCCCCHHHHHHHHHH
Confidence            345779999999999998874

>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=89.83  E-value=0.13  Score=41.51  Aligned_cols=24  Identities=29%  Similarity=0.288  Sum_probs=20.1

Q ss_pred             cccccccccCCcchHHHHHHHhcc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +....|.|..|+|||||+..+...
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHh
Confidence            345678999999999999998873

>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=89.79  E-value=0.12  Score=43.79  Aligned_cols=21  Identities=29%  Similarity=0.395  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|++|+||||+++.+..
T Consensus        11 ~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A           11 VVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            356889999999999999986

>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=89.73  E-value=5.8  Score=36.43  Aligned_cols=23  Identities=35%  Similarity=0.205  Sum_probs=19.0

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|.+|+||||++..+...
T Consensus        99 ~vi~i~G~~GsGKTT~~~~LA~~  121 (425)
T 2ffh_A           99 NLWFLVGLQGSGKTTTAAKLALY  121 (425)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            34568899999999999888763

>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=89.67  E-value=0.13  Score=39.73  Aligned_cols=21  Identities=29%  Similarity=0.385  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         8 i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            8 MVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            468899999999999998875

>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=89.66  E-value=0.14  Score=39.94  Aligned_cols=22  Identities=32%  Similarity=0.368  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCccHHHHHHHHhcC
Confidence            3568999999999999998775

>3gqb_A V-type ATP synthase alpha chain; A3B3, V-ATPase, ATP synthesis, ATP-binding, hydrogen ION TRA hydrolase, ION transport; 2.80A {Thermus thermophilus HB8} PDB: 3a5c_A* 3a5d_A 3j0j_A* 1um2_C

Probab=89.59  E-value=0.12  Score=49.14  Aligned_cols=20  Identities=25%  Similarity=0.129  Sum_probs=18.1

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +|+|..|+|||+|+..+.+.
T Consensus       225 ~Ifg~~g~GKT~l~~~ia~~  244 (578)
T 3gqb_A          225 AIPGPFGSGKSVTQQSLAKW  244 (578)
T ss_dssp             EECCCTTSCHHHHHHHHHHH
T ss_pred             eeeCCCCccHHHHHHHHHhc
Confidence            68899999999999998874

>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=89.55  E-value=0.15  Score=40.82  Aligned_cols=22  Identities=18%  Similarity=0.146  Sum_probs=18.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+.+.
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999777664

>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=89.52  E-value=0.14  Score=40.58  Aligned_cols=21  Identities=19%  Similarity=0.196  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|.+|+|||||...+...
T Consensus         7 i~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            7 VVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999999875

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=89.50  E-value=0.13  Score=44.38  Aligned_cols=21  Identities=33%  Similarity=0.292  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|..|+|||||.+.+..
T Consensus        32 ~~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           32 KVIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             EEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            457899999999999999986

>2e87_A Hypothetical protein PH1320; GTP-binding, GTPase, OBG, bundle, GDP, complex, structural G NPPSFA; HET: GDP; 2.35A {Pyrococcus horikoshii}

Probab=89.40  E-value=0.95  Score=40.43  Aligned_cols=24  Identities=25%  Similarity=0.293  Sum_probs=20.3

Q ss_pred             ccccccccCCcchHHHHHHHhccc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      ..+.++|.+|+|||||...+....
T Consensus       168 ~~v~lvG~~gvGKSTLin~L~~~~  191 (357)
T 2e87_A          168 PTVVIAGHPNVGKSTLLKALTTAK  191 (357)
T ss_dssp             CEEEEECSTTSSHHHHHHHHCSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            356799999999999999988753

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=89.40  E-value=0.52  Score=53.66  Aligned_cols=77  Identities=14%  Similarity=0.080  Sum_probs=50.5

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhc-------C----C---CceEEEEEeCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLE-------G----S---EKKFFLILDDVW  192 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~-------~----~---~kr~LiVlDdv~  192 (297)
                      ++|++|+|||+++..+...  ..+ + ..+.++.|...+...++..+-..+.       +    +   ||+.++.+||+.
T Consensus      1309 L~GptGtGKT~li~~~L~~--l~~-~-~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiDDiN 1384 (3245)
T 3vkg_A         1309 LCGPPGSGKTMTLTSTLRA--FPD-F-EVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEIN 1384 (3245)
T ss_dssp             EESSTTSSHHHHHHHHGGG--CTT-E-EEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEETTTT
T ss_pred             EECCCCCCHHHHHHHHHHh--CCC-C-ceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEecccC
Confidence            6699999999888776652  221 2 2356777888788887777654221       1    1   788999999997


Q ss_pred             CCCcc------CHHHHHHHHh
Q 043781          193 TDDYS------KWEPFHNCLM  207 (297)
Q Consensus       193 ~~~~~------~w~~l~~~l~  207 (297)
                      -...+      ..+-|+..+.
T Consensus      1385 mp~~D~yGtQ~~ielLrqlld 1405 (3245)
T 3vkg_A         1385 LPSTDKYGTQRVITFIRQMVE 1405 (3245)
T ss_dssp             CCCCCTTSCCHHHHHHHHHHH
T ss_pred             CCCccccccccHHHHHHHHHH
Confidence            65433      2344555553

>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=89.40  E-value=0.12  Score=41.86  Aligned_cols=22  Identities=32%  Similarity=0.256  Sum_probs=18.7

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      -.+.++|.+|+|||||...+..
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            4567999999999999999853

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=89.30  E-value=0.14  Score=43.05  Aligned_cols=21  Identities=24%  Similarity=0.332  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|+.|+||||+++.+..
T Consensus        18 ~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           18 QIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             EEEEECSSCSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999886

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=89.25  E-value=0.14  Score=46.29  Aligned_cols=23  Identities=30%  Similarity=0.216  Sum_probs=19.8

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|..|+|||||++.+...
T Consensus       158 ~vi~lvG~nGsGKTTll~~Lag~  180 (359)
T 2og2_A          158 AVIMIVGVNGGGKTTSLGKLAHR  180 (359)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHH
T ss_pred             eEEEEEcCCCChHHHHHHHHHhh
Confidence            45679999999999999998874

>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=89.24  E-value=0.15  Score=39.25  Aligned_cols=21  Identities=33%  Similarity=0.468  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         7 i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            7 VIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            468899999999999988765

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=89.24  E-value=0.14  Score=44.11  Aligned_cols=21  Identities=29%  Similarity=0.265  Sum_probs=18.3

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|+|||||.+.+..
T Consensus        27 ~v~i~Gp~GsGKSTll~~l~g   47 (261)
T 2eyu_A           27 LILVTGPTGSGKSTTIASMID   47 (261)
T ss_dssp             EEEEECSTTCSHHHHHHHHHH
T ss_pred             EEEEECCCCccHHHHHHHHHH
Confidence            356899999999999998876

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=89.22  E-value=0.29  Score=53.44  Aligned_cols=21  Identities=29%  Similarity=0.303  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|++|+|||+||.++...
T Consensus      1430 vll~GppGtGKT~LA~ala~e 1450 (2050)
T 3cmu_A         1430 VEIYGPESSGKTTLTLQVIAA 1450 (2050)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999888763

>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=89.15  E-value=0.44  Score=51.31  Aligned_cols=93  Identities=17%  Similarity=0.118  Sum_probs=0.0

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHH--------------------HHHHhhcCCCceEEE
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAK--------------------AIIEGLEGSEKKFFL  186 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~--------------------~i~~~~~~~~kr~Li  186 (297)
                      |+|.+|+|||+||..+..  .....=...+|++....++......                    .++..+....+.-||
T Consensus        39 I~G~pGsGKT~LAlqla~--~~~~~G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L~~~~~~~LV  116 (1706)
T 3cmw_A           39 IYGPESSGKTTLTLQVIA--AAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVI  116 (1706)
T ss_dssp             EECSTTSSHHHHHHHHHH--HHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSEE
T ss_pred             EECCCCCCHHHHHHHHHH--HHhhCCCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHHHhccCCCEE


Q ss_pred             EEeCCCCCCccC-----------------HHHHHHHHhhhhhhhceeeecCCCCeEEEEe
Q 043781          187 ILDDVWTDDYSK-----------------WEPFHNCLMRVLQEFAAIEVDGDENPLSLTS  229 (297)
Q Consensus       187 VlDdv~~~~~~~-----------------w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTT  229 (297)
                      |+|.+-......                 ...+...|.....        ..++.||+|.
T Consensus       117 VIDSLt~L~~~~e~e~~~~~~~~~~~~r~~~~ll~~L~~~ak--------e~~~tVIvTN  168 (1706)
T 3cmw_A          117 VVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLK--------QSNTLLIFIN  168 (1706)
T ss_dssp             EESCSTTCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHH--------HHTCEEEEEE
T ss_pred             EEcchhhhccccccccccccchhHHHHHHHHHHHHHHHHHHH--------HcCCEEEEEe

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=89.15  E-value=0.9  Score=42.08  Aligned_cols=35  Identities=14%  Similarity=0.041  Sum_probs=23.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEe
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV  160 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v  160 (297)
                      .-|.|.+|+|||||+..+..+..... =..++|++.
T Consensus       206 iiI~G~pG~GKTtl~l~ia~~~~~~~-g~~Vl~~s~  240 (454)
T 2r6a_A          206 IIVAARPSVGKTAFALNIAQNVATKT-NENVAIFSL  240 (454)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHHS-SCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHhC-CCcEEEEEC
Confidence            45779999999999988887532211 124556653

>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=89.11  E-value=0.21  Score=45.12  Aligned_cols=21  Identities=33%  Similarity=0.267  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        33 ~~llGpsGsGKSTLLr~iaGl   53 (359)
T 3fvq_A           33 LFIIGASGCGKTTLLRCLAGF   53 (359)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCchHHHHHHHHhcC
Confidence            468999999999999999873

>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=89.07  E-value=0.2  Score=38.80  Aligned_cols=21  Identities=29%  Similarity=0.343  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         9 i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            9 VVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHcC
Confidence            468899999999999888865

>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=89.06  E-value=0.14  Score=47.64  Aligned_cols=21  Identities=29%  Similarity=0.245  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|++|+||||+|+.+...
T Consensus        53 iLl~GppGtGKT~lar~lA~~   73 (444)
T 1g41_A           53 ILMIGPTGVGKTEIARRLAKL   73 (444)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            447899999999999999883

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=89.05  E-value=0.41  Score=39.84  Aligned_cols=20  Identities=15%  Similarity=-0.112  Sum_probs=16.3

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|..|.||||.+.....+
T Consensus        32 vitG~MgsGKTT~lL~~a~r   51 (214)
T 2j9r_A           32 VICGSMFSGKSEELIRRVRR   51 (214)
T ss_dssp             EEECSTTSCHHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHHH
Confidence            36899999999999766664

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=89.05  E-value=0.14  Score=46.05  Aligned_cols=20  Identities=30%  Similarity=0.322  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.++|++|+||||+++.+..
T Consensus        27 i~l~G~~G~GKTTl~~~la~   46 (359)
T 2ga8_A           27 VILVGSPGSGKSTIAEELCQ   46 (359)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            45899999999999998877

>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=89.04  E-value=0.16  Score=40.53  Aligned_cols=21  Identities=19%  Similarity=0.371  Sum_probs=18.3

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|..|+|||||+..++-
T Consensus        28 ~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             cEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999875

>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=89.00  E-value=0.16  Score=40.50  Aligned_cols=22  Identities=32%  Similarity=0.454  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||+..+...
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3568899999999999998865

>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=88.94  E-value=0.17  Score=39.30  Aligned_cols=20  Identities=35%  Similarity=0.361  Sum_probs=17.4

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.++|.+|+|||||...+..
T Consensus         5 i~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            5 VMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            45889999999999998864

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=88.93  E-value=0.15  Score=41.88  Aligned_cols=23  Identities=26%  Similarity=0.290  Sum_probs=19.3

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+.++|.+|+|||||+..+...
T Consensus        31 ~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           31 VAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH
Confidence            34678999999999999888764

>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=88.92  E-value=0.15  Score=39.47  Aligned_cols=21  Identities=29%  Similarity=0.328  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         5 i~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            5 VLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEECCCCCCHHHHHHHHcCc
Confidence            458899999999999988754

>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=88.90  E-value=0.17  Score=39.17  Aligned_cols=22  Identities=14%  Similarity=0.220  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +.++|.+|+|||||...+.+..
T Consensus         6 i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            6 LVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            4578999999999998887653

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=88.90  E-value=0.17  Score=39.22  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            6 VAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            458899999999999998864

>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=88.89  E-value=0.16  Score=40.25  Aligned_cols=22  Identities=23%  Similarity=0.178  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        23 ~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           23 KVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEETTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4578999999999999998864

>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=88.87  E-value=0.2  Score=40.01  Aligned_cols=24  Identities=21%  Similarity=0.116  Sum_probs=20.1

Q ss_pred             ccccccccCCcchHHHHHHHhccc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      -.+.++|.+|+|||||...+....
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            356789999999999999887653

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=88.86  E-value=0.15  Score=45.30  Aligned_cols=22  Identities=27%  Similarity=0.163  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|+|+.|+||||||+.+...
T Consensus         7 ~i~i~GptGsGKTtla~~La~~   28 (323)
T 3crm_A            7 AIFLMGPTAAGKTDLAMALADA   28 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3568899999999999999873

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=88.78  E-value=0.17  Score=40.44  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus        50 ~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           50 SIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999988875

>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=88.70  E-value=0.17  Score=40.37  Aligned_cols=21  Identities=33%  Similarity=0.301  Sum_probs=17.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.++|.+|+|||||.+.+.+
T Consensus        16 ki~vvG~~~~GKssL~~~l~~   36 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYS   36 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            356899999999999987765

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=88.70  E-value=0.15  Score=45.59  Aligned_cols=22  Identities=23%  Similarity=0.164  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|.|+.|+||||||+.+...
T Consensus         9 lI~I~GptgSGKTtla~~La~~   30 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKK   30 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCcCcHHHHHHHHHHH
Confidence            4678999999999999988873

>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=88.69  E-value=0.18  Score=39.10  Aligned_cols=22  Identities=23%  Similarity=0.288  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +.++|.+|+|||||...+.+..
T Consensus         9 i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            9 VCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECcCCCCHHHHHHHHHcCC
Confidence            4688999999999999887753

>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=88.68  E-value=0.14  Score=46.09  Aligned_cols=23  Identities=17%  Similarity=0.111  Sum_probs=19.5

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....|+|..|+|||||++.+..-
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L~gl  193 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKLAAV  193 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHH
Confidence            34579999999999999998763

>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=88.67  E-value=0.12  Score=45.66  Aligned_cols=20  Identities=25%  Similarity=0.516  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+|+|..|+|||||++.+..
T Consensus        83 vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           83 LALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             EEEESSSCHHHHHHHHHHTT
T ss_pred             EEEECCCCchHHHHHHHHHc
Confidence            47999999999999999976

>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=88.66  E-value=0.17  Score=38.99  Aligned_cols=21  Identities=33%  Similarity=0.438  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            468899999999999998764

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=88.66  E-value=0.16  Score=40.75  Aligned_cols=22  Identities=32%  Similarity=0.404  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
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            4678999999999999998865

>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=88.57  E-value=0.16  Score=46.24  Aligned_cols=21  Identities=33%  Similarity=0.173  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|++|+|||||++.+..
T Consensus       171 ~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          171 YWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            356899999999999999997

>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=88.56  E-value=0.18  Score=38.75  Aligned_cols=21  Identities=33%  Similarity=0.452  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         6 i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            468899999999999888764

>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=88.55  E-value=0.16  Score=44.45  Aligned_cols=22  Identities=32%  Similarity=0.477  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+..-
T Consensus        66 ~~~i~G~NGsGKSTLlk~l~Gl   87 (290)
T 2bbs_A           66 LLAVAGSTGAGKTSLLMMIMGE   87 (290)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCcHHHHHHHHhcC
Confidence            3578999999999999999874

>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=88.45  E-value=0.18  Score=40.12  Aligned_cols=21  Identities=33%  Similarity=0.265  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus        10 i~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A           10 IVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468899999999999988775

>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=88.37  E-value=0.19  Score=39.42  Aligned_cols=22  Identities=36%  Similarity=0.431  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
T Consensus        10 ~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A           10 KVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3568999999999999888765

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=88.33  E-value=0.21  Score=39.07  Aligned_cols=21  Identities=33%  Similarity=0.349  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         9 i~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            9 IVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHGG
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            468899999999999988765

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=88.30  E-value=0.17  Score=44.42  Aligned_cols=19  Identities=37%  Similarity=0.503  Sum_probs=17.6

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      .|+|..|+|||||.+.++.
T Consensus        22 ~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           22 MVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEETTSSHHHHHHHHHC
T ss_pred             EEECCCCCCHHHHHHHHhC
Confidence            7999999999999999775

>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=88.29  E-value=0.19  Score=40.47  Aligned_cols=22  Identities=14%  Similarity=0.332  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||+|.+.+.+.
T Consensus        22 ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           22 RILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             EEEEEESTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            4568999999999999987764

>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=88.26  E-value=0.17  Score=47.70  Aligned_cols=23  Identities=30%  Similarity=0.271  Sum_probs=19.7

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....|+|..|+|||||++.+...
T Consensus       294 eVI~LVGpNGSGKTTLl~~LAgl  316 (503)
T 2yhs_A          294 FVILMVGVNGVGKTTTIGKLARQ  316 (503)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCcccHHHHHHHHHHH
Confidence            35679999999999999998873

>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=88.22  E-value=0.21  Score=39.08  Aligned_cols=24  Identities=25%  Similarity=0.177  Sum_probs=20.1

Q ss_pred             ccccccccCCcchHHHHHHHhccc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      -.+.++|.+|+|||||...+.+..
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            346789999999999999988753

>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=88.20  E-value=0.49  Score=39.24  Aligned_cols=20  Identities=25%  Similarity=0.414  Sum_probs=17.5

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|+.|+||||+++.+.+.
T Consensus        10 ~~eG~~gsGKsT~~~~l~~~   29 (213)
T 4edh_A           10 TLEGPEGAGKSTNRDYLAER   29 (213)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEEcCCCCCHHHHHHHHHHH
Confidence            45699999999999999874

>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=88.17  E-value=0.26  Score=44.41  Aligned_cols=21  Identities=29%  Similarity=0.223  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        32 ~~llGpnGsGKSTLLr~iaGl   52 (359)
T 2yyz_A           32 VALLGPSGCGKTTTLLMLAGI   52 (359)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEcCCCchHHHHHHHHHCC
Confidence            468999999999999999874

>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=88.17  E-value=0.2  Score=39.99  Aligned_cols=23  Identities=17%  Similarity=0.271  Sum_probs=19.7

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -.+.++|.+|+|||||...+.+.
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           24 PEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            34578999999999999998875

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=88.15  E-value=0.26  Score=38.58  Aligned_cols=22  Identities=32%  Similarity=0.289  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        10 ~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A           10 VVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             EEEEESCTTTTHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999998764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=88.13  E-value=0.19  Score=39.42  Aligned_cols=22  Identities=23%  Similarity=0.264  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        11 ~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHCSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3568999999999999998875

>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=88.10  E-value=0.19  Score=41.05  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        14 ~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           14 SIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999988875

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=88.09  E-value=0.27  Score=44.41  Aligned_cols=21  Identities=29%  Similarity=0.218  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        32 ~~llGpnGsGKSTLLr~iaGl   52 (362)
T 2it1_A           32 MALLGPSGSGKSTLLYTIAGI   52 (362)
T ss_dssp             EEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCchHHHHHHHHhcC
Confidence            468999999999999999874

>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=88.06  E-value=0.27  Score=44.57  Aligned_cols=21  Identities=29%  Similarity=0.213  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        32 ~~llGpnGsGKSTLLr~iaGl   52 (372)
T 1g29_1           32 MILLGPSGCGKTTTLRMIAGL   52 (372)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCcHHHHHHHHHHcC
Confidence            468999999999999999874

>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=88.06  E-value=0.21  Score=39.60  Aligned_cols=21  Identities=24%  Similarity=0.202  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         4 i~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            4 IIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            458899999999999998875

>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=88.05  E-value=0.19  Score=44.34  Aligned_cols=23  Identities=35%  Similarity=0.216  Sum_probs=19.5

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....|+|.+|+||||++..+...
T Consensus       105 ~vi~ivG~~GsGKTTl~~~LA~~  127 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGKLAKM  127 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCChHHHHHHHHHHH
Confidence            45678999999999999988873

>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=88.05  E-value=0.1  Score=42.43  Aligned_cols=22  Identities=18%  Similarity=0.179  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|..|+|||||.+.+...
T Consensus        28 ~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           28 EVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             EEEEEECTTSSHHHHHTTTCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4679999999999999988764

>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=88.04  E-value=0.2  Score=39.13  Aligned_cols=22  Identities=27%  Similarity=0.395  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3568999999999999988764

>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=88.02  E-value=0.2  Score=39.25  Aligned_cols=22  Identities=32%  Similarity=0.369  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        11 ~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           11 KLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4578999999999999988775

>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=88.00  E-value=0.27  Score=44.67  Aligned_cols=21  Identities=29%  Similarity=0.278  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        32 ~~llGpsGsGKSTLLr~iaGl   52 (381)
T 3rlf_A           32 VVFVGPSGCGKSTLLRMIAGL   52 (381)
T ss_dssp             EEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEcCCCchHHHHHHHHHcC
Confidence            468999999999999999874

>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=87.99  E-value=0.27  Score=44.53  Aligned_cols=21  Identities=29%  Similarity=0.216  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        40 ~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           40 LVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             EEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCChHHHHHHHHHcC
Confidence            468999999999999999873

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=87.99  E-value=0.21  Score=39.65  Aligned_cols=24  Identities=25%  Similarity=0.400  Sum_probs=20.2

Q ss_pred             ccccccccCCcchHHHHHHHhccc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      ..+.++|.+|+|||||...+.+..
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~~   47 (195)
T 3pqc_A           24 GEVAFVGRSNVGKSSLLNALFNRK   47 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCc
Confidence            346789999999999999988763

>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=87.97  E-value=0.27  Score=40.53  Aligned_cols=25  Identities=32%  Similarity=0.643  Sum_probs=19.2

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFD  153 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~  153 (297)
                      +=|..|+||||+++.+.+.  ....++
T Consensus         7 ~EG~dGsGKsTq~~~L~~~--L~~~~~   31 (205)
T 4hlc_A            7 FEGPEGSGKTTVINEVYHR--LVKDYD   31 (205)
T ss_dssp             EECCTTSCHHHHHHHHHHH--HTTTSC
T ss_pred             EECCCCCcHHHHHHHHHHH--HHCCCC
Confidence            4499999999999999884  434444

>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=87.97  E-value=0.21  Score=38.59  Aligned_cols=21  Identities=19%  Similarity=0.205  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus         9 i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            468899999999999888764

>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=87.94  E-value=0.21  Score=44.83  Aligned_cols=21  Identities=24%  Similarity=0.200  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        29 ~~llGpnGsGKSTLLr~iaGl   49 (348)
T 3d31_A           29 FVILGPTGAGKTLFLELIAGF   49 (348)
T ss_dssp             EEEECCCTHHHHHHHHHHHTS
T ss_pred             EEEECCCCccHHHHHHHHHcC
Confidence            468999999999999999874

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=87.93  E-value=0.18  Score=42.30  Aligned_cols=21  Identities=19%  Similarity=0.358  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|..|+||||+++.+.+.
T Consensus         5 i~~~G~~g~GKtt~~~~l~~~   25 (241)
T 2ocp_A            5 LSIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHH
Confidence            356799999999999999874

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=87.91  E-value=0.19  Score=45.22  Aligned_cols=21  Identities=29%  Similarity=0.341  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        44 ~~llGpnGsGKSTLLr~iaGl   64 (355)
T 1z47_A           44 VGLLGPSGSGKTTILRLIAGL   64 (355)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            468999999999999999873

>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=87.89  E-value=0.21  Score=38.67  Aligned_cols=21  Identities=29%  Similarity=0.294  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus         6 i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            6 ILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            468899999999999888764

>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=87.89  E-value=1.5  Score=35.88  Aligned_cols=42  Identities=17%  Similarity=0.110  Sum_probs=26.6

Q ss_pred             CceEEEEEeCCCCC---CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          181 EKKFFLILDDVWTD---DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       181 ~kr~LiVlDdv~~~---~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      ++==|||||++-..   ..-..+.+...+..-          -...-||||+|..
T Consensus       119 ~~yDlvILDEi~~al~~g~l~~~ev~~~l~~R----------p~~~~vIlTGr~a  163 (196)
T 1g5t_A          119 PLLDMVVLDELTYMVAYDYLPLEEVISALNAR----------PGHQTVIITGRGC  163 (196)
T ss_dssp             TTCSEEEEETHHHHHHTTSSCHHHHHHHHHTS----------CTTCEEEEECSSC
T ss_pred             CCCCEEEEeCCCccccCCCCCHHHHHHHHHhC----------cCCCEEEEECCCC
Confidence            56679999999432   112445555555432          4556799999965

>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=87.88  E-value=0.19  Score=39.98  Aligned_cols=22  Identities=27%  Similarity=0.268  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        18 ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           18 RILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999998875

>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=87.86  E-value=0.18  Score=40.83  Aligned_cols=22  Identities=32%  Similarity=0.370  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
T Consensus        27 ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           27 KLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             EEEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3578999999999999998764

>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=87.85  E-value=0.21  Score=39.45  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +.++|.+|+|||||...+.+..
T Consensus         7 i~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            7 LVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            4588999999999999988753

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=87.78  E-value=0.18  Score=39.60  Aligned_cols=21  Identities=24%  Similarity=0.205  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||+|...+.+.
T Consensus        10 i~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A           10 LGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEECCGGGCHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            468899999999999988764

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=87.74  E-value=0.21  Score=44.67  Aligned_cols=22  Identities=23%  Similarity=0.217  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|+|+.|+|||||+..+...
T Consensus        42 lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           42 LLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4568899999999999999884

>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=87.69  E-value=0.18  Score=40.21  Aligned_cols=23  Identities=22%  Similarity=0.150  Sum_probs=19.9

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+....
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           23 HVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEECTTSSHHHHHHHTSCGG
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            45789999999999999988764

>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=87.67  E-value=0.21  Score=38.46  Aligned_cols=21  Identities=24%  Similarity=0.132  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+..+
T Consensus         3 i~~~G~~~~GKssl~~~l~~~   23 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLG   23 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            357899999999999988764

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=87.62  E-value=0.2  Score=41.15  Aligned_cols=20  Identities=25%  Similarity=0.333  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|+.|+||||+++.+..
T Consensus         6 i~i~G~~gsGkst~~~~l~~   25 (219)
T 2h92_A            6 IALDGPAAAGKSTIAKRVAS   25 (219)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            56889999999999999877

>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=87.62  E-value=0.22  Score=38.58  Aligned_cols=21  Identities=29%  Similarity=0.270  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus        10 i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A           10 ILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            568999999999999998764

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=87.59  E-value=0.29  Score=39.53  Aligned_cols=22  Identities=32%  Similarity=0.276  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+..+
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           27 KLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4678999999999999988875

>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=87.58  E-value=0.22  Score=39.36  Aligned_cols=22  Identities=27%  Similarity=0.214  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
T Consensus        12 ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           12 KFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4568899999999999988765

>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=87.51  E-value=0.73  Score=48.70  Aligned_cols=21  Identities=24%  Similarity=0.381  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|||..|+|||||++.+..-
T Consensus       447 vaivG~sGsGKSTll~ll~~~  467 (1321)
T 4f4c_A          447 VALVGSSGCGKSTIISLLLRY  467 (1321)
T ss_dssp             EEEEECSSSCHHHHHHHHTTS
T ss_pred             EEEEecCCCcHHHHHHHhccc
Confidence            368999999999999999873

>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=87.51  E-value=0.22  Score=39.95  Aligned_cols=22  Identities=36%  Similarity=0.377  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
T Consensus        25 ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           25 KLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3568999999999999988864

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=87.51  E-value=0.22  Score=43.73  Aligned_cols=26  Identities=19%  Similarity=0.257  Sum_probs=21.5

Q ss_pred             cccccccccccCCcchHHHHHHHhcc
Q 043781          120 ALINVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       120 ~~~~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +...-+.|+|.+|+|||||...+...
T Consensus         8 ~~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            8 MKVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             CEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            33455679999999999999988875

>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=87.48  E-value=0.23  Score=39.76  Aligned_cols=22  Identities=23%  Similarity=0.250  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
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            4578999999999999888765

>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=87.47  E-value=0.27  Score=38.78  Aligned_cols=22  Identities=32%  Similarity=0.465  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        20 ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           20 KLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3568999999999999998865

>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=87.39  E-value=0.23  Score=39.04  Aligned_cols=22  Identities=32%  Similarity=0.421  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        20 ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           20 KVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4578999999999999998865

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=87.34  E-value=0.21  Score=44.86  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+.+.
T Consensus        74 ~gIiG~nGaGKTTLl~~I~g~   94 (347)
T 2obl_A           74 IGIFAGSGVGKSTLLGMICNG   94 (347)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            368899999999999999885

>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=87.33  E-value=0.23  Score=38.74  Aligned_cols=22  Identities=27%  Similarity=0.197  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+..+
T Consensus        16 ~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3568899999999999988754

>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=87.32  E-value=0.24  Score=38.89  Aligned_cols=22  Identities=27%  Similarity=0.202  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4568999999999999888765

>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=87.27  E-value=0.31  Score=38.94  Aligned_cols=22  Identities=23%  Similarity=0.205  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
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            4568899999999999988765

>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=87.26  E-value=0.27  Score=38.65  Aligned_cols=22  Identities=18%  Similarity=0.252  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
T Consensus         8 ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            8 KIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3568999999999999988854

>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=87.24  E-value=0.24  Score=39.03  Aligned_cols=21  Identities=33%  Similarity=0.333  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.++
T Consensus         8 i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            8 CVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            468899999999999888764

>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=87.21  E-value=0.24  Score=39.19  Aligned_cols=22  Identities=23%  Similarity=0.175  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+.+.
T Consensus        13 ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           13 KFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999998864

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=87.21  E-value=0.99  Score=37.55  Aligned_cols=18  Identities=39%  Similarity=0.400  Sum_probs=14.1

Q ss_pred             ccccccCCcchHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFA  142 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v  142 (297)
                      .-+.|..|+||||+....
T Consensus        79 ~~i~g~TGsGKTt~~~~~   96 (235)
T 3llm_A           79 VIIRGATGCGKTTQVPQF   96 (235)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEEeCCCCCcHHhHHHH
Confidence            457899999999866444

>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=87.19  E-value=0.24  Score=39.84  Aligned_cols=22  Identities=32%  Similarity=0.421  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+..+
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4578999999999999888765

>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=87.15  E-value=0.24  Score=39.51  Aligned_cols=22  Identities=27%  Similarity=0.295  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+...
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           27 KVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4578999999999999988775

>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=87.03  E-value=0.15  Score=43.54  Aligned_cols=22  Identities=18%  Similarity=0.170  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -+.|.|..|+||||+++.+.+.
T Consensus        26 ~I~ieG~~GsGKST~~~~L~~~   47 (263)
T 1p5z_B           26 KISIEGNIAAGKSTFVNILKQL   47 (263)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            3467799999999999998873

>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=87.00  E-value=0.25  Score=38.80  Aligned_cols=21  Identities=29%  Similarity=0.286  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus        11 i~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D           11 CVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            568899999999999888765

>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=86.96  E-value=0.57  Score=39.56  Aligned_cols=49  Identities=16%  Similarity=0.133  Sum_probs=28.7

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAII  174 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  174 (297)
                      +.+-|++|+||||+++.+.+.-. ...+.....+.-+......+.+++++
T Consensus        30 i~~eG~~GsGKsT~~~~l~~~l~-~~~~~~~~~~rep~~t~~g~~ir~~l   78 (236)
T 3lv8_A           30 IVIEGLEGAGKSTAIQVVVETLQ-QNGIDHITRTREPGGTLLAEKLRALV   78 (236)
T ss_dssp             EEEEESTTSCHHHHHHHHHHHHH-HTTCCCEEEEESSCSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHH-hcCCCeeeeecCCCCCHHHHHHHHHH
Confidence            34679999999999999988422 23455344443332222334444444

>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=86.93  E-value=0.26  Score=38.64  Aligned_cols=23  Identities=26%  Similarity=0.222  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+.+..
T Consensus        12 ~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A           12 KVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHhCC
Confidence            35688999999999999887653

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=86.90  E-value=0.24  Score=44.23  Aligned_cols=22  Identities=23%  Similarity=0.297  Sum_probs=19.0

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...+|+|.+|+|||||.+.+..
T Consensus        56 ~~v~i~G~~GaGKSTLl~~l~g   77 (337)
T 2qm8_A           56 IRVGITGVPGVGKSTTIDALGS   77 (337)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3467999999999999999874

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=86.87  E-value=0.2  Score=39.49  Aligned_cols=22  Identities=27%  Similarity=0.218  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus        20 ~i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A           20 RILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             EEEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999998754

>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=86.82  E-value=0.22  Score=44.82  Aligned_cols=21  Identities=29%  Similarity=0.328  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||.+.+..-
T Consensus        34 ~~llGpnGsGKSTLLr~iaGl   54 (353)
T 1oxx_K           34 FGILGPSGAGKTTFMRIIAGL   54 (353)
T ss_dssp             EEEECSCHHHHHHHHHHHHTS
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            468999999999999999873

>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=86.82  E-value=0.25  Score=39.58  Aligned_cols=23  Identities=22%  Similarity=0.271  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+.+..
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~~   47 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQDH   47 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            35789999999999999887653

>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=86.81  E-value=0.26  Score=39.72  Aligned_cols=22  Identities=32%  Similarity=0.370  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+.+.
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A           10 KVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            3568999999999999988765

>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=86.71  E-value=0.26  Score=41.25  Aligned_cols=23  Identities=22%  Similarity=0.212  Sum_probs=20.0

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+....
T Consensus        31 ~i~lvG~~g~GKStlin~l~g~~   53 (239)
T 3lxx_A           31 RIVLVGKTGAGKSATGNSILGRK   53 (239)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCC
Confidence            45799999999999999988753

>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=86.67  E-value=0.28  Score=39.47  Aligned_cols=23  Identities=22%  Similarity=0.189  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+.+..
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~~   32 (203)
T 1zbd_A           10 KILIIGNSSVGKTSFLFRYADDS   32 (203)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            45689999999999999888753

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=86.66  E-value=0.24  Score=45.77  Aligned_cols=21  Identities=33%  Similarity=0.455  Sum_probs=19.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.++.-
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            579999999999999999874

>1nij_A Hypothetical protein YJIA; structural genomics, P-loop protein, GTP binding, structure function project, S2F, unknown function; 2.00A {Escherichia coli} SCOP: c.37.1.10 d.237.1.1

Probab=86.65  E-value=0.23  Score=43.81  Aligned_cols=24  Identities=42%  Similarity=0.563  Sum_probs=20.3

Q ss_pred             cccccccccCCcchHHHHHHHhcc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +....|.|+.|.|||||.+.+...
T Consensus         4 i~v~~i~G~~GaGKTTll~~l~~~   27 (318)
T 1nij_A            4 IAVTLLTGFLGAGKTTLLRHILNE   27 (318)
T ss_dssp             EEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             ccEEEEEecCCCCHHHHHHHHHhh
Confidence            445678899999999999999864

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=86.62  E-value=0.27  Score=38.91  Aligned_cols=23  Identities=22%  Similarity=0.218  Sum_probs=19.7

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+.+..
T Consensus        20 ~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           20 RLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            35688999999999999988754

>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=86.60  E-value=0.27  Score=39.47  Aligned_cols=22  Identities=23%  Similarity=0.318  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        30 ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           30 KLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3568899999999999888765

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=86.59  E-value=0.14  Score=44.69  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=15.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+||||+|+.+.+
T Consensus         7 iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            467889999999999998876

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=86.55  E-value=0.26  Score=41.45  Aligned_cols=20  Identities=25%  Similarity=0.162  Sum_probs=16.4

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -+.|.||+||||+|..+...
T Consensus        10 ~~~~kgGvGKTt~a~~la~~   29 (228)
T 2r8r_A           10 FLGAAPGVGKTYAMLQAAHA   29 (228)
T ss_dssp             EEESSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHHH
Confidence            35699999999998777764

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=86.53  E-value=0.65  Score=38.50  Aligned_cols=49  Identities=12%  Similarity=0.161  Sum_probs=29.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIE  175 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  175 (297)
                      .+-|..|+||||+++.+.+.-. ...+..+.+..-+....+.+.+++++.
T Consensus         7 ~~eG~~gsGKsT~~~~l~~~l~-~~~~~~v~~~rep~~t~~g~~ir~~l~   55 (213)
T 4tmk_A            7 VIEGLEGAGKTTARNVVVETLE-QLGIRDMVFTREPGGTQLAEKLRSLLL   55 (213)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHH-HTTCCCEEEEESSCSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHHH-HcCCCcceeeeCCCCCHHHHHHHHHHh
Confidence            3569999999999999988422 223423333333222234455555554

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=86.47  E-value=0.27  Score=43.06  Aligned_cols=22  Identities=23%  Similarity=0.305  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+...
T Consensus        10 ~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A           10 FIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4679999999999999998875

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=86.44  E-value=0.46  Score=39.89  Aligned_cols=20  Identities=35%  Similarity=0.544  Sum_probs=14.6

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|++|+||||+++.+.+.
T Consensus        29 ~~eG~~GsGKsT~~~~l~~~   48 (227)
T 3v9p_A           29 TFEGIDGAGKTTHLQWFCDR   48 (227)
T ss_dssp             EEECCC---CHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            45699999999999999884

>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=86.41  E-value=0.25  Score=46.86  Aligned_cols=20  Identities=20%  Similarity=0.177  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-++|++|+||||+|+.+..
T Consensus        38 IvlvGlpGSGKSTia~~La~   57 (520)
T 2axn_A           38 IVMVGLPARGKTYISKKLTR   57 (520)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999876

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=86.38  E-value=0.37  Score=38.38  Aligned_cols=23  Identities=26%  Similarity=0.242  Sum_probs=19.7

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+.++.
T Consensus        18 ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           18 KLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            45789999999999999988753

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=86.36  E-value=0.29  Score=39.34  Aligned_cols=22  Identities=27%  Similarity=0.324  Sum_probs=18.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        22 ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           22 KCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4568899999999999988865

>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=86.35  E-value=0.25  Score=46.06  Aligned_cols=21  Identities=19%  Similarity=0.124  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|++|+||||+++.+...
T Consensus        42 IvlvGlpGsGKSTia~~La~~   62 (469)
T 1bif_A           42 IVMVGLPARGKTYISKKLTRY   62 (469)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999998874

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=86.35  E-value=0.29  Score=39.18  Aligned_cols=23  Identities=30%  Similarity=0.254  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+.+..
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~~   47 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKGE   47 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            35689999999999999988753

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=86.25  E-value=0.28  Score=40.05  Aligned_cols=22  Identities=32%  Similarity=0.228  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+..+
T Consensus        30 ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           30 KIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3568999999999999988875

>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=86.22  E-value=0.29  Score=39.82  Aligned_cols=21  Identities=24%  Similarity=0.101  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus        10 i~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B           10 VLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            468899999999999988765

>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=86.21  E-value=0.5  Score=49.93  Aligned_cols=20  Identities=25%  Similarity=0.358  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ++|||..|+|||||++.+.+
T Consensus      1108 vaIVG~SGsGKSTL~~lL~r 1127 (1321)
T 4f4c_A         1108 LALVGPSGCGKSTVVALLER 1127 (1321)
T ss_dssp             EEEECSTTSSTTSHHHHHTT
T ss_pred             EEEECCCCChHHHHHHHHhc
Confidence            47999999999999999987

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=86.21  E-value=0.27  Score=44.27  Aligned_cols=20  Identities=40%  Similarity=0.459  Sum_probs=17.9

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|+|..|+|||||++.+..-
T Consensus       179 ~ivG~sGsGKSTll~~l~~~  198 (361)
T 2gza_A          179 VVAGETGSGKTTLMKALMQE  198 (361)
T ss_dssp             EEEESSSSCHHHHHHHHHTT
T ss_pred             EEECCCCCCHHHHHHHHHhc
Confidence            57899999999999999873

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=86.20  E-value=0.29  Score=38.96  Aligned_cols=21  Identities=19%  Similarity=0.319  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus        10 i~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A           10 TVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            568999999999999998875

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=86.20  E-value=0.29  Score=39.52  Aligned_cols=23  Identities=26%  Similarity=0.283  Sum_probs=19.6

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.++|.+|+|||||...+.+..
T Consensus        26 ki~vvG~~~~GKSsli~~l~~~~   48 (201)
T 3oes_A           26 KVVILGYRCVGKTSLAHQFVEGE   48 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            35689999999999999988753

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=86.16  E-value=0.28  Score=43.52  Aligned_cols=23  Identities=35%  Similarity=0.315  Sum_probs=19.2

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|.+|+||||++..+...
T Consensus       106 ~vI~ivG~~G~GKTT~~~~LA~~  128 (320)
T 1zu4_A          106 NIFMLVGVNGTGKTTSLAKMANY  128 (320)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            45678899999999999888763

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=86.16  E-value=0.27  Score=44.03  Aligned_cols=22  Identities=23%  Similarity=0.309  Sum_probs=19.3

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..++|+|.+|+|||||...+..
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~   96 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGK   96 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHH
Confidence            4567999999999999999875

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=86.12  E-value=0.3  Score=39.32  Aligned_cols=21  Identities=33%  Similarity=0.392  Sum_probs=17.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+|.+|+|||||...+..
T Consensus         8 kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            8 RVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999988764

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=86.06  E-value=0.3  Score=40.71  Aligned_cols=20  Identities=35%  Similarity=0.278  Sum_probs=16.6

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .-|.|.+|+|||+||.++..
T Consensus        33 ~~i~G~pG~GKT~l~l~~~~   52 (251)
T 2zts_A           33 VLLTGGTGTGKTTFAAQFIY   52 (251)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHH
Confidence            35789999999999977654

>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=86.05  E-value=1.1  Score=45.43  Aligned_cols=18  Identities=22%  Similarity=0.150  Sum_probs=16.2

Q ss_pred             ccccccCCcchHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFA  142 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v  142 (297)
                      ..|+|+.|.|||||.+.+
T Consensus       665 ~~ItGpNGsGKSTlLr~i  682 (934)
T 3thx_A          665 HIITGPNMGGKSTYIRQT  682 (934)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHH
Confidence            357899999999999998

>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=86.05  E-value=0.28  Score=44.79  Aligned_cols=20  Identities=30%  Similarity=0.331  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|+.|+|||||.+.+..
T Consensus        50 ~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           50 VGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCChHHHHHHHHhC
Confidence            46889999999999999986

>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=86.04  E-value=0.31  Score=38.90  Aligned_cols=22  Identities=23%  Similarity=0.215  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
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            3568999999999999988865

>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=86.03  E-value=0.28  Score=42.88  Aligned_cols=23  Identities=35%  Similarity=0.205  Sum_probs=19.3

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ....++|.+|+||||++..+...
T Consensus        99 ~~i~i~g~~G~GKTT~~~~la~~  121 (295)
T 1ls1_A           99 NLWFLVGLQGSGKTTTAAKLALY  121 (295)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            35668899999999999888874

>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=85.86  E-value=0.31  Score=38.68  Aligned_cols=22  Identities=27%  Similarity=0.326  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        17 ~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           17 KILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3568899999999999998765

>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=85.86  E-value=0.31  Score=39.36  Aligned_cols=22  Identities=27%  Similarity=0.252  Sum_probs=18.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+.+.
T Consensus        27 ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           27 KFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHC-
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            4578899999999999988765

>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=85.85  E-value=0.3  Score=39.03  Aligned_cols=23  Identities=22%  Similarity=0.138  Sum_probs=19.6

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -.+.|+|.+|+|||||...+.++
T Consensus        24 ~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           24 FKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHhcC
Confidence            34578999999999999988875

>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=85.80  E-value=0.29  Score=39.32  Aligned_cols=22  Identities=23%  Similarity=0.096  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus        31 ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           31 RILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             EEEEEESTTSSHHHHHHHHCSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3578999999999999998764

>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=85.78  E-value=0.3  Score=41.81  Aligned_cols=22  Identities=23%  Similarity=0.181  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus         5 ~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            5 TVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             EEEEEECSSSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999998875

>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=85.71  E-value=0.33  Score=38.51  Aligned_cols=21  Identities=24%  Similarity=0.213  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus        19 i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           19 VIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             EEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999998854

>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=85.70  E-value=0.32  Score=38.67  Aligned_cols=22  Identities=27%  Similarity=0.149  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus        22 ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4578999999999999988764

>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=85.67  E-value=0.31  Score=39.66  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            4578999999999999988764

>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=85.66  E-value=0.32  Score=39.13  Aligned_cols=22  Identities=14%  Similarity=0.202  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+...
T Consensus        30 ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           30 KIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            4578999999999999988765

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=85.64  E-value=0.29  Score=45.69  Aligned_cols=22  Identities=23%  Similarity=0.179  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||++.+..-
T Consensus       140 ~v~IvGpnGsGKSTLlr~L~Gl  161 (460)
T 2npi_A          140 RVVIVGGSQTGKTSLSRTLCSY  161 (460)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            3568999999999999998774

>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=85.64  E-value=0.3  Score=44.01  Aligned_cols=22  Identities=27%  Similarity=0.394  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|..|+|||||.+.+...
T Consensus       217 ~~~lvG~sG~GKSTLln~L~g~  238 (358)
T 2rcn_A          217 ISIFAGQSGVGKSSLLNALLGL  238 (358)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCccHHHHHHHHhcc
Confidence            4579999999999999999974

>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=85.61  E-value=0.31  Score=38.93  Aligned_cols=22  Identities=32%  Similarity=0.397  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus        10 ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A           10 RVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHcC
Confidence            3568999999999999988764

>3fwy_A Light-independent protochlorophyllide reductase I ATP-binding protein; BCHL, electron donor, DPOR, Fe protein, nitrogenase; HET: ADP; 1.63A {Rhodobacter sphaeroides 2}

Probab=85.60  E-value=0.31  Score=43.10  Aligned_cols=22  Identities=41%  Similarity=0.492  Sum_probs=18.0

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.|+|=|||||||.+-.+.-
T Consensus        49 KVIAIaGKGGVGKTTtavNLA~   70 (314)
T 3fwy_A           49 KVFAVYGKGGIGKSTTSSNLSA   70 (314)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCccCHHHHHHHHHH
Confidence            4567889999999999876655

>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=85.55  E-value=0.32  Score=39.27  Aligned_cols=22  Identities=27%  Similarity=0.268  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        10 ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y           10 KLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4568899999999999998765

>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=85.48  E-value=0.31  Score=43.15  Aligned_cols=21  Identities=19%  Similarity=0.254  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|+.|+||||||..+...
T Consensus         6 i~i~GptgsGKt~la~~La~~   26 (322)
T 3exa_A            6 VAIVGPTAVGKTKTSVMLAKR   26 (322)
T ss_dssp             EEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEECCCcCCHHHHHHHHHHh
Confidence            457899999999999998863

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=85.42  E-value=0.32  Score=42.60  Aligned_cols=21  Identities=19%  Similarity=0.371  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...++|+.|+|||||.+.+. .
T Consensus       167 i~~l~G~sG~GKSTLln~l~-~  187 (302)
T 2yv5_A          167 ICILAGPSGVGKSSILSRLT-G  187 (302)
T ss_dssp             EEEEECSTTSSHHHHHHHHH-S
T ss_pred             EEEEECCCCCCHHHHHHHHH-H
Confidence            35789999999999999998 5

>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=85.32  E-value=0.36  Score=37.56  Aligned_cols=21  Identities=24%  Similarity=0.362  Sum_probs=17.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|.|||||...++-
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~   45 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILV   45 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999988764

>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=85.32  E-value=0.32  Score=42.97  Aligned_cols=22  Identities=27%  Similarity=0.051  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|.|+.|+||||||..+...
T Consensus        12 ~i~i~GptgsGKt~la~~La~~   33 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELRKI   33 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHh
Confidence            3468899999999999998863

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=85.27  E-value=0.94  Score=41.83  Aligned_cols=48  Identities=10%  Similarity=0.017  Sum_probs=31.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIE  175 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  175 (297)
                      .-|.|.+|+||||||..+..+..... =..++|++..  .+..++...++.
T Consensus       203 ~ii~G~pg~GKT~lal~ia~~~a~~~-g~~vl~~slE--~~~~~l~~R~~~  250 (444)
T 2q6t_A          203 NIIAARPAMGKTAFALTIAQNAALKE-GVGVGIYSLE--MPAAQLTLRMMC  250 (444)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTT-CCCEEEEESS--SCHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhC-CCeEEEEECC--CCHHHHHHHHHH
Confidence            35779999999999988887532221 1246676554  445566665554

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=85.17  E-value=0.35  Score=40.04  Aligned_cols=22  Identities=14%  Similarity=0.271  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+...
T Consensus        31 kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           31 TIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTT
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999998875

>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=85.16  E-value=0.35  Score=39.56  Aligned_cols=22  Identities=32%  Similarity=0.356  Sum_probs=18.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        36 ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           36 KVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEECTTSSHHHHHHHHHC-
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            4568999999999999988764

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=85.16  E-value=0.63  Score=38.95  Aligned_cols=21  Identities=29%  Similarity=0.397  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.+-|+.|+||||+++.+.+.
T Consensus        24 i~~~G~~g~GKst~~~~l~~~   44 (223)
T 3ld9_A           24 ITFEGIDGSGKTTQSHLLAEY   44 (223)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            346699999999999999884

>2qag_C Septin-7; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=85.05  E-value=0.32  Score=44.79  Aligned_cols=21  Identities=33%  Similarity=0.422  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|..|+|||||.+.+...
T Consensus        34 I~lvG~sGaGKSTLln~L~g~   54 (418)
T 2qag_C           34 LMVVGESGLGKSTLINSLFLT   54 (418)
T ss_dssp             EEEECCTTSSHHHHHHHHTTC
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            389999999999999999874

>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=85.05  E-value=0.29  Score=45.35  Aligned_cols=23  Identities=39%  Similarity=0.300  Sum_probs=18.9

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+.++|.+|+||||++..+...
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~  122 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARY  122 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            34668999999999999887763

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=84.96  E-value=0.81  Score=40.82  Aligned_cols=49  Identities=12%  Similarity=0.005  Sum_probs=32.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhh
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGL  177 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~  177 (297)
                      .-|.|.+|+||||||..+..+...  +=..++|++.  ..+..++...++...
T Consensus        49 iiIaG~pG~GKTt~al~ia~~~a~--~g~~Vl~fSl--Ems~~ql~~Rlls~~   97 (338)
T 4a1f_A           49 VIIGARPSMGKTSLMMNMVLSALN--DDRGVAVFSL--EMSAEQLALRALSDL   97 (338)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHH--TTCEEEEEES--SSCHHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEeC--CCCHHHHHHHHHHHh
Confidence            346799999999999888875322  1124556654  456667766665543

>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=84.92  E-value=0.34  Score=43.43  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=18.7

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.|+|.+|+|||||+..+..
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            3567899999999999988764

>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=84.90  E-value=0.37  Score=39.77  Aligned_cols=21  Identities=24%  Similarity=0.264  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|.|..|+||||||..+...
T Consensus        37 ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           37 VLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             EEEECCCTTTTHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHh
Confidence            357899999999999998774

>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=84.86  E-value=0.34  Score=43.82  Aligned_cols=20  Identities=30%  Similarity=0.248  Sum_probs=17.6

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|+.|+|||||++.+..
T Consensus       139 i~ivG~~GsGKTTll~~l~~  158 (372)
T 2ewv_A          139 ILVTGPTGSGKSTTIASMID  158 (372)
T ss_dssp             EEEECSSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            45889999999999988876

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=84.83  E-value=0.7  Score=41.64  Aligned_cols=23  Identities=22%  Similarity=0.134  Sum_probs=19.7

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.|+|.+|+|||||.+.+....
T Consensus       181 ~V~lvG~~naGKSTLln~L~~~~  203 (364)
T 2qtf_A          181 SIGIVGYTNSGKTSLFNSLTGLT  203 (364)
T ss_dssp             EEEEECBTTSSHHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHHHCCC
Confidence            46799999999999999998753

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=84.80  E-value=0.37  Score=39.12  Aligned_cols=22  Identities=36%  Similarity=0.280  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+..+
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           27 KLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4578999999999999988875

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=84.79  E-value=0.33  Score=45.00  Aligned_cols=21  Identities=19%  Similarity=0.219  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+.+.
T Consensus       160 ~~IvG~sGsGKSTLl~~Iag~  180 (438)
T 2dpy_A          160 MGLFAGSGVGKSVLLGMMARY  180 (438)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcc
Confidence            368899999999999999884

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=84.74  E-value=0.37  Score=38.45  Aligned_cols=22  Identities=41%  Similarity=0.389  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        20 ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4578999999999999988865

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=84.73  E-value=0.37  Score=39.14  Aligned_cols=22  Identities=23%  Similarity=0.259  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        11 ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A           11 KCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            3568899999999999888765

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=84.63  E-value=0.36  Score=40.83  Aligned_cols=23  Identities=17%  Similarity=0.189  Sum_probs=19.6

Q ss_pred             cccccccCCcchHHHHHHHhccc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      .+.|+|.+|+|||||...+....
T Consensus        24 ~I~lvG~~g~GKStl~n~l~~~~   46 (260)
T 2xtp_A           24 RIILVGKTGTGKSAAGNSILRKQ   46 (260)
T ss_dssp             EEEEEECTTSCHHHHHHHHHTSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            46799999999999998887653

>4gzl_A RAS-related C3 botulinum toxin substrate 1; rossmann fold, GTP binding, membrane, hydrolase; HET: GNP; 2.00A {Homo sapiens} PDB: 3th5_A* 4gzm_A*

Probab=84.62  E-value=0.37  Score=39.07  Aligned_cols=21  Identities=33%  Similarity=0.333  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.++
T Consensus        33 i~vvG~~~~GKSsLi~~l~~~   53 (204)
T 4gzl_A           33 CVVVGDGAVGKTCLLISYTTN   53 (204)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCCCHHHHHHHHHhC
Confidence            468899999999999888765

>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=84.60  E-value=0.41  Score=39.00  Aligned_cols=22  Identities=27%  Similarity=0.226  Sum_probs=19.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+.+.
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4578999999999999988864

>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=84.57  E-value=0.39  Score=38.85  Aligned_cols=22  Identities=27%  Similarity=0.255  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+...
T Consensus        22 ~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           22 KILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4578999999999999988765

>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=84.54  E-value=0.38  Score=38.88  Aligned_cols=23  Identities=22%  Similarity=0.104  Sum_probs=19.4

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -.+.++|.+|+|||||...+.+.
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            34678999999999999888765

>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=84.53  E-value=0.36  Score=44.41  Aligned_cols=21  Identities=24%  Similarity=0.286  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+|+|..|+|||||.+.+..
T Consensus        71 ~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHhC
Confidence            457999999999999999988

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=84.44  E-value=0.27  Score=47.00  Aligned_cols=21  Identities=33%  Similarity=0.404  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+...
T Consensus       372 I~LiG~sGSGKSTLar~La~~  392 (552)
T 3cr8_A          372 VFFTGLSGAGKSTLARALAAR  392 (552)
T ss_dssp             EEEEESSCHHHHHHHHHHHHH
T ss_pred             EEEECCCCChHHHHHHHHHHh
Confidence            468899999999999999883

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=84.31  E-value=0.41  Score=39.50  Aligned_cols=21  Identities=33%  Similarity=0.392  Sum_probs=18.3

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+|.+|+|||||...+..
T Consensus        39 kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           39 RVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            467899999999999988874

>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=84.07  E-value=1.7  Score=44.69  Aligned_cols=18  Identities=39%  Similarity=0.246  Sum_probs=16.1

Q ss_pred             ccccccCCcchHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFA  142 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v  142 (297)
                      ..|+|+.|.|||||.+.+
T Consensus       792 ~~ItGpNgsGKSTlLr~i  809 (1022)
T 2o8b_B          792 VLVTGPNMGGKSTLMRQA  809 (1022)
T ss_dssp             EEEECCTTSSHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHH
Confidence            458899999999999988

>3q3j_B RHO-related GTP-binding protein RHO6; RAS-binding domain, plexin, small GTPase, structural genomic consortium, SGC; HET: GNP; 1.97A {Homo sapiens} PDB: 2rex_B* 2cls_A*

Probab=84.02  E-value=0.42  Score=39.18  Aligned_cols=22  Identities=27%  Similarity=0.164  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~   50 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKD   50 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            3568899999999999988765

>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=83.97  E-value=0.25  Score=38.98  Aligned_cols=22  Identities=27%  Similarity=0.203  Sum_probs=8.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.++
T Consensus        10 ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C           10 KLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEECCCCC------------
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4568999999999999888764

>2x77_A ADP-ribosylation factor; GTP-binding protein, small GTPase, nucleotide-binding; HET: GDP; 2.10A {Leishmania major}

Probab=83.93  E-value=0.34  Score=38.51  Aligned_cols=22  Identities=18%  Similarity=0.089  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+..+
T Consensus        24 ~i~v~G~~~~GKssli~~l~~~   45 (189)
T 2x77_A           24 RVLMLGLDNAGKTSILYRLHLG   45 (189)
T ss_dssp             EEEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3568999999999999998654

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=83.87  E-value=0.4  Score=45.66  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+..-
T Consensus        49 ~~~LvG~NGaGKSTLlk~l~Gl   70 (538)
T 1yqt_A           49 VVGIVGPNGTGKSTAVKILAGQ   70 (538)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3578999999999999999873

>1qhl_A Protein (cell division protein MUKB); SMC, chromosome partitioning; 2.20A {Escherichia coli} SCOP: c.37.1.12

Probab=83.83  E-value=0.29  Score=41.19  Aligned_cols=21  Identities=29%  Similarity=0.354  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...|+|+.|+|||||.+.+..
T Consensus        29 ~~~i~GpnGsGKSTll~~i~g   49 (227)
T 1qhl_A           29 VTTLSGGNGAGKSTTMAAFVT   49 (227)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            457899999999999998887

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=83.81  E-value=0.4  Score=45.63  Aligned_cols=21  Identities=33%  Similarity=0.457  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||++.++.-
T Consensus       315 ~~i~G~NGsGKSTLlk~l~Gl  335 (538)
T 1yqt_A          315 IGIVGPNGIGKTTFVKMLAGV  335 (538)
T ss_dssp             EEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            368899999999999999984

>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=83.72  E-value=2  Score=42.71  Aligned_cols=19  Identities=32%  Similarity=0.148  Sum_probs=14.7

Q ss_pred             ccccccCCcchHHHHHHHh
Q 043781          125 SDVRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~  143 (297)
                      .-|+|..|+||||++..+.
T Consensus       112 vii~gpTGSGKTtllp~ll  130 (773)
T 2xau_A          112 MVFVGETGSGKTTQIPQFV  130 (773)
T ss_dssp             EEEECCTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            4578999999999665443

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=83.56  E-value=0.4  Score=45.69  Aligned_cols=21  Identities=38%  Similarity=0.586  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||++.++.-
T Consensus       297 ~~i~G~nGsGKSTLl~~l~Gl  317 (538)
T 3ozx_A          297 IGILGPNGIGKTTFARILVGE  317 (538)
T ss_dssp             EEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            368899999999999999974

>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=83.55  E-value=0.56  Score=45.44  Aligned_cols=48  Identities=17%  Similarity=0.238  Sum_probs=31.3

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIE  175 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~  175 (297)
                      -|.|++|.|||+++..+...  ....-..++.++...+..+..+...+..
T Consensus       199 li~GppGTGKT~~~~~~i~~--l~~~~~~~ilv~a~tn~A~~~l~~~l~~  246 (624)
T 2gk6_A          199 LIQGPPGTGKTVTSATIVYH--LARQGNGPVLVCAPSNIAVDQLTEKIHQ  246 (624)
T ss_dssp             EEECCTTSCHHHHHHHHHHH--HHTSSSCCEEEEESSHHHHHHHHHHHHT
T ss_pred             EEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEeCcHHHHHHHHHHHHh
Confidence            47799999999987666542  2222345777777766556666655543

>1wf3_A GTP-binding protein; GTPase, riken structural genomics/prote initiative, RSGI, structural genomics, hydrolase; HET: GNP; 1.88A {Thermus thermophilus} SCOP: c.37.1.8 d.52.3.1

Probab=83.55  E-value=0.43  Score=41.76  Aligned_cols=22  Identities=23%  Similarity=0.267  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+...
T Consensus         9 ~V~ivG~~nvGKSTLln~l~g~   30 (301)
T 1wf3_A            9 FVAIVGKPNVGKSTLLNNLLGV   30 (301)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3679999999999999988875

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=83.48  E-value=0.65  Score=44.53  Aligned_cols=21  Identities=29%  Similarity=0.349  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+..-
T Consensus       372 ~~ivG~sGsGKSTll~~l~g~  392 (582)
T 3b5x_A          372 VALVGRSGSGKSTIANLFTRF  392 (582)
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            368999999999999999863

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=83.46  E-value=0.8  Score=50.12  Aligned_cols=67  Identities=21%  Similarity=0.168  Sum_probs=41.6

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHH--------------------HHHHHHHhhcCCCceEE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFR--------------------IAKAIIEGLEGSEKKFF  185 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~--------------------~~~~i~~~~~~~~kr~L  185 (297)
                      -++|.+|+||||||.++.... .+. =...+|+++....+...                    ....+...+....+.-+
T Consensus      1085 ll~G~~GtGKT~la~~~~~ea-~k~-Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~~~~~dl 1162 (2050)
T 3cmu_A         1085 EIYGPESSGKTTLTLQVIAAA-QRE-GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDV 1162 (2050)
T ss_dssp             EEECCTTSSHHHHHHHHHHHH-HTT-TCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHHHTCCSE
T ss_pred             EEECCCCCCHHHHHHHHHHHH-HHc-CCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHHhCCCCE
Confidence            477999999999998888742 222 23456676665443322                    22233333322256789


Q ss_pred             EEEeCCCCC
Q 043781          186 LILDDVWTD  194 (297)
Q Consensus       186 iVlDdv~~~  194 (297)
                      ||+|++-..
T Consensus      1163 vVIDsl~~L 1171 (2050)
T 3cmu_A         1163 IVVDSVAAL 1171 (2050)
T ss_dssp             EEESCGGGC
T ss_pred             EEECCcccc
Confidence            999998654

>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=83.33  E-value=1  Score=36.40  Aligned_cols=34  Identities=24%  Similarity=0.303  Sum_probs=23.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD  165 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~  165 (297)
                      -|+|.+|+|||++|..+...    .  ..++++..+..++
T Consensus         3 lV~Gg~~SGKS~~A~~la~~----~--~~~~yiaT~~~~d   36 (180)
T 1c9k_A            3 LVTGGARSGKSRHAEALIGD----A--PQVLYIATSQILD   36 (180)
T ss_dssp             EEEECTTSSHHHHHHHHHCS----C--SSEEEEECCCC--
T ss_pred             EEECCCCCcHHHHHHHHHhc----C--CCeEEEecCCCCC
Confidence            37899999999999998863    1  2356666555543

>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=83.19  E-value=0.48  Score=39.30  Aligned_cols=21  Identities=29%  Similarity=0.233  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|-+|+|||+|...+.++
T Consensus        16 ivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           16 LVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECcCCcCHHHHHHHHHhC
Confidence            458899999999999887654

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=83.15  E-value=0.44  Score=42.45  Aligned_cols=22  Identities=27%  Similarity=0.182  Sum_probs=18.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.|+|.+|+|||||+..+..
T Consensus        57 ~~i~i~G~~g~GKSTl~~~l~~   78 (341)
T 2p67_A           57 LRLGVTGTPGAGKSTFLEAFGM   78 (341)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH
Confidence            4457899999999999988864

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=83.15  E-value=0.44  Score=41.63  Aligned_cols=22  Identities=27%  Similarity=0.558  Sum_probs=19.3

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...++|+.|+|||||.+.+...
T Consensus       171 iv~l~G~sG~GKSTll~~l~g~  192 (301)
T 1u0l_A          171 ISTMAGLSGVGKSSLLNAINPG  192 (301)
T ss_dssp             EEEEECSTTSSHHHHHHHHSTT
T ss_pred             eEEEECCCCCcHHHHHHHhccc
Confidence            3468999999999999999874

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=82.98  E-value=0.28  Score=47.35  Aligned_cols=20  Identities=25%  Similarity=0.267  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      =++|.+|+|||+||+.+.+.
T Consensus       331 LL~GppGtGKT~LAr~la~~  350 (595)
T 3f9v_A          331 LIIGDPGTAKSQMLQFISRV  350 (595)
T ss_dssp             EEEESSCCTHHHHHHSSSTT
T ss_pred             EEECCCchHHHHHHHHHHHh
Confidence            36799999999999999873

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=82.98  E-value=0.53  Score=44.82  Aligned_cols=23  Identities=30%  Similarity=0.518  Sum_probs=20.1

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...+|+|+.|+|||||.+.+..-
T Consensus        26 ei~gLiGpNGaGKSTLlkiL~Gl   48 (538)
T 3ozx_A           26 TILGVLGKNGVGKTTVLKILAGE   48 (538)
T ss_dssp             EEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CEEEEECCCCCcHHHHHHHHhcC
Confidence            45689999999999999999873

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=82.83  E-value=0.6  Score=44.77  Aligned_cols=21  Identities=29%  Similarity=0.365  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|+.|+|||||++.+..-
T Consensus       372 ~~ivG~sGsGKSTLl~~l~g~  392 (582)
T 3b60_A          372 VALVGRSGSGKSTIASLITRF  392 (582)
T ss_dssp             EEEEECTTSSHHHHHHHHTTT
T ss_pred             EEEECCCCCCHHHHHHHHhhc
Confidence            468999999999999999863

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=82.77  E-value=0.49  Score=40.14  Aligned_cols=20  Identities=40%  Similarity=0.549  Sum_probs=16.4

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +.|.|-||+||||+|..+..
T Consensus         4 I~vs~KGGvGKTT~a~nLA~   23 (269)
T 1cp2_A            4 VAIYGKGGIGKSTTTQNLTS   23 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEecCCCCcHHHHHHHHHH
Confidence            34568999999999987776

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=82.72  E-value=1.3  Score=41.67  Aligned_cols=22  Identities=36%  Similarity=0.302  Sum_probs=18.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+.|+|.+|+||||++..+..
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~  123 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAY  123 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4567889999999999988873

>3euj_A Chromosome partition protein MUKB, linker; MUKB, MUKE, chromosome condensation, condensin, SMC, N subunit, ABC-type ATPase, WHD, ATP-binding; HET: AGS; 3.10A {Haemophilus ducreyi} PDB: 3euk_A*

Probab=82.69  E-value=0.48  Score=44.45  Aligned_cols=22  Identities=27%  Similarity=0.249  Sum_probs=19.6

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...+|+|+.|+|||||.+.+..
T Consensus        30 e~~~liG~nGsGKSTLl~~l~G   51 (483)
T 3euj_A           30 LVTTLSGGNGAGKSTTMAGFVT   51 (483)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCcHHHHHHHHhc
Confidence            4567999999999999999886

>3ez2_A Plasmid partition protein A; type IA, DNA binding, winged-HTH, DNA bindin; HET: ADP EPE; 2.05A {Escherichia coli} PDB: 3ez6_A* 3ez7_A

Probab=82.62  E-value=4  Score=36.77  Aligned_cols=21  Identities=24%  Similarity=0.139  Sum_probs=16.2

Q ss_pred             ccccc-ccCCcchHHHHHHHhc
Q 043781          124 VSDVR-GMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~-G~~G~GKTtLa~~v~~  144 (297)
                      .+.|+ |-||+||||+|-.+..
T Consensus       110 vIav~s~KGGvGKTT~a~nLA~  131 (398)
T 3ez2_A          110 VIFISNLKGGVSKTVSTVSLAH  131 (398)
T ss_dssp             EEEECCSSSSSSHHHHHHHHHH
T ss_pred             EEEEEeCCCCccHHHHHHHHHH
Confidence            34455 7899999999977765

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=82.59  E-value=0.49  Score=39.27  Aligned_cols=23  Identities=30%  Similarity=0.315  Sum_probs=19.9

Q ss_pred             cccccccccCCcchHHHHHHHhc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-.+++.|.-|+||||+++.+..
T Consensus         9 ~~~iglTGgigsGKStv~~~l~~   31 (210)
T 4i1u_A            9 MYAIGLTGGIGSGKTTVADLFAA   31 (210)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHH
Confidence            45678999999999999998865

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=82.56  E-value=0.48  Score=45.81  Aligned_cols=21  Identities=33%  Similarity=0.457  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+..-
T Consensus       385 ~~i~G~NGsGKSTLlk~l~Gl  405 (607)
T 3bk7_A          385 IGIVGPNGIGKTTFVKMLAGV  405 (607)
T ss_dssp             EEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            368899999999999999984

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=82.47  E-value=0.24  Score=43.72  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...|+|+.|+|||||.+.+...
T Consensus       175 ~~~lvG~sG~GKSTLln~L~g~  196 (307)
T 1t9h_A          175 TTVFAGQSGVGKSSLLNAISPE  196 (307)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC-
T ss_pred             EEEEECCCCCCHHHHHHHhccc
Confidence            4579999999999999999874

---

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	297
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	2e-13

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

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]

 Score = 66.4 bits (161), Expect = 2e-13
 Identities = 19/145 (13%), Positives = 37/145 (25%), Gaps = 33/145 (22%)

Query: 127 VRGMGGIGKTTLAQFAYNDKDVIE--NFDKRIWVCVSDPFDEFRIAKAIIEGLE------ 178
           + G  G GK+ +A  A +  D +   N+D  +W+  S    +          L       
Sbjct: 49  LHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDD 108

Query: 179 -----------------------GSEKKFFLILDDVWTDDYSKWEPFHNCLMRVL--QEF 213
                                          + DDV  ++  +W         V      
Sbjct: 109 LLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVE 168

Query: 214 AAIEVDGDENPLSLTSTCQEKLRHL 238
            +         + +TS   ++    
Sbjct: 169 ISNAASQTCEFIEVTSLEIDECYDF 193

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	297
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	99.89
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	97.98
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.98
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	97.96
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	97.9
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	97.9
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	97.87
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	97.71
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.7
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.67
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.54
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	97.49
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	97.47
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.34
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	97.33
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.24
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.23
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	97.22
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.17
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	97.01
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.92
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.88
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	96.78
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	96.75
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.43
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.41
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.3
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.24
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.19
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.18
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.16
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.14
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.07
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.01
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	95.99
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.89
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	95.84
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	95.83
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.8
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	95.79
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	95.79
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	95.78
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	95.73
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	95.72
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	95.71
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.68
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	95.65
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	95.57
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.47
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	95.33
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.32
d1g2912	240	Maltose transport protein MalK, N-terminal domain	95.32
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	95.31
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	95.29
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.25
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	95.17
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.15
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	95.08
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.07
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	94.98
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	94.97
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.95
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	94.95
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	94.93
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	94.9
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	94.89
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	94.87
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	94.85
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.79
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.71
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.69
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	94.66
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	94.46
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	94.41
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.38
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	94.38
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.35
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.32
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	94.31
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	94.27
d1xpua3	289	Transcription termination factor Rho, ATPase domai	94.22
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	94.12
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	94.12
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	94.12
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	94.07
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	94.05
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.03
d2qy9a2	211	GTPase domain of the signal recognition particle r	94.0
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	93.67
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	93.58
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	93.5
d1ls1a2	207	GTPase domain of the signal sequence recognition p	93.33
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.28
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	93.27
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	93.11
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	92.98
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	92.94
d1okkd2	207	GTPase domain of the signal recognition particle r	92.94
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	92.81
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	92.72
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.72
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.67
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	92.6
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	92.3
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	92.1
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	92.07
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	92.06
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.01
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.92
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	91.88
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	91.78
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	91.75
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	91.71
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	91.62
d1vmaa2	213	GTPase domain of the signal recognition particle r	91.61
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.23
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	91.21
d1j8yf2	211	GTPase domain of the signal sequence recognition p	91.12
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	91.06
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	91.04
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	91.04
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	90.85
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	90.75
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	90.73
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	90.54
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	90.5
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	90.49
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	90.25
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	90.1
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	90.09
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	90.07
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	90.02
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	89.98
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	89.96
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.95
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	89.94
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	89.89
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	89.88
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	89.88
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	89.8
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	89.77
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	89.73
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	89.68
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	89.56
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	89.56
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	89.55
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	89.54
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	89.54
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	89.54
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	89.51
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	89.49
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	89.48
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	89.43
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	89.29
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	89.28
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	89.24
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	89.18
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	89.13
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	89.12
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	89.11
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	89.07
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	88.94
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	88.93
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	88.82
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	88.82
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	88.81
d1nrjb_	209	Signal recognition particle receptor beta-subunit	88.75
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	88.74
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	88.74
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	88.73
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	88.71
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	88.64
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	88.49
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	88.18
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	88.14
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	88.13
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	88.11
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	88.06
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	88.04
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	87.96
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	87.96
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	87.91
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	87.84
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	87.77
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	87.75
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	87.57
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	87.55
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	87.43
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	87.42
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	87.34
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	87.3
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	87.29
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	87.26
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	87.21
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	87.08
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	87.01
d2fh5b1	207	Signal recognition particle receptor beta-subunit	86.91
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	86.91
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	86.84
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	86.78
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	86.72
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	86.69
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	86.41
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	86.4
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	86.36
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	86.05
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	85.89
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	85.67
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	85.58
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	85.17
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	85.07
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	84.99
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	84.88
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	84.57
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	84.51
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	84.5
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	83.91
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	83.7
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	83.69
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	83.55
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	83.43
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	83.23
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	82.79
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	81.44

>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=99.89  E-value=4.9e-24  Score=187.08  Aligned_cols=121  Identities=14%  Similarity=0.078  Sum_probs=89.1

Q ss_pred             cccccccCCcchHHHHHHHhcccc--cccCCCceEEEEeCCCCCHHHHHHHHHHhh---cCC------------------
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKD--VIENFDKRIWVCVSDPFDEFRIAKAIIEGL---EGS------------------  180 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~--~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~---~~~------------------  180 (297)
                      .+.|+||||+||||||+++|++..  ...+|++++||++++.++...+...+...+   +..                  
T Consensus        46 ~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (277)
T d2a5yb3          46 FLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKR  125 (277)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHH
Confidence            567999999999999999998643  677899999999999998777766553332   111                  


Q ss_pred             --------CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCCC-ccccCC
Q 043781          181 --------EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGLR-AKFPVS  251 (297)
Q Consensus       181 --------~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~~-~~~~l~  251 (297)
                              ++|+|+||||||+.  ++|+.+    .            ..||+||||||+.    .++..+... +.|+|+
T Consensus       126 ~~~~~~L~~kr~LlVLDDv~~~--~~~~~~----~------------~~~srilvTTR~~----~v~~~~~~~~~~~~l~  183 (277)
T d2a5yb3         126 MICNALIDRPNTLFVFDDVVQE--ETIRWA----Q------------ELRLRCLVTTRDV----EISNAASQTCEFIEVT  183 (277)
T ss_dssp             HHHHHHTTSTTEEEEEEEECCH--HHHHHH----H------------HTTCEEEEEESBG----GGGGGCCSCEEEEECC
T ss_pred             HHHHHHhccCCeeEecchhhHH--hhhhhh----c------------ccCceEEEEeehH----HHHHhcCCCCceEECC
Confidence                    78999999999987  455432    1            4679999999965    445544433 567777


Q ss_pred             ccc---hhhhhhhhhccC
Q 043781          252 IFD---AKKIWGWEVFGR  266 (297)
Q Consensus       252 ~l~---~~~lf~~~~f~~  266 (297)
                      .|+   +++||.+.+|..
T Consensus       184 ~L~~~ea~~Lf~~~~~~~  201 (277)
T d2a5yb3         184 SLEIDECYDFLEAYGMPM  201 (277)
T ss_dssp             CCCHHHHHHHHHHTSCCC
T ss_pred             CCCHHHHHHHHHHHhCCc
Confidence            775   555666655544

>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=97.98  E-value=5.2e-06  Score=68.20  Aligned_cols=122  Identities=13%  Similarity=0.031  Sum_probs=67.8

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC----CceEEEEEeCCCCCCccCHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS----EKKFFLILDDVWTDDYSKWEP  201 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~----~kr~LiVlDdv~~~~~~~w~~  201 (297)
                      =++|++|+||||+|+.+.+.-..........-.+.+...+.......+.......    +++-++|+|++.......-..
T Consensus        39 Ll~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~~~~~~  118 (227)
T d1sxjc2          39 LFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAAQNA  118 (227)
T ss_dssp             EEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHHHHH
T ss_pred             EEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCCeeeeecchhhccccccccCCCeEEEEEeccccchhhHHHH
Confidence            3789999999999999988421111111222233444444444333332222111    555688899998775444455


Q ss_pred             HHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhhh
Q 043781          202 FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       202 l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      |...+...          ...+.++++|..... ...+.   .-...+.+.+++..++..
T Consensus       119 Ll~~le~~----------~~~~~~~~~~~~~~~i~~~i~---sr~~~i~~~~~~~~~i~~  165 (227)
T d1sxjc2         119 LRRVIERY----------TKNTRFCVLANYAHKLTPALL---SQCTRFRFQPLPQEAIER  165 (227)
T ss_dssp             HHHHHHHT----------TTTEEEEEEESCGGGSCHHHH---TTSEEEECCCCCHHHHHH
T ss_pred             HHHHhhhc----------ccceeeccccCcHHHhHHHHH---HHHhhhcccccccccccc
Confidence            66666543          556777777764432 22221   222556777777666533

>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=97.98  E-value=3.8e-06  Score=68.94  Aligned_cols=110  Identities=22%  Similarity=0.147  Sum_probs=65.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------CceEEEEEeCCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------EKKFFLILDDVWTDD  195 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------~kr~LiVlDdv~~~~  195 (297)
                      .-|||.+|+|||.|++.+++.  ........++++.      .++...+...+...         ..--+|+|||+....
T Consensus        39 l~l~G~~G~GKTHLl~A~~~~--~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~  110 (213)
T d1l8qa2          39 IFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSSA------DDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLS  110 (213)
T ss_dssp             EEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEEH------HHHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGT
T ss_pred             EEEECCCCCcHHHHHHHHHHH--hccCccceEEech------HHHHHHHHHHHHccchhhHHHHHhhccchhhhhhhhhc
Confidence            458999999999999999994  4444445666643      33333333332211         345789999998642


Q ss_pred             -ccCHHH-HHHHHhhhhhhhceeeecCCCCeEEEEeccHH-----HHHHHHHhhCCCccccCC
Q 043781          196 -YSKWEP-FHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE-----KLRHLTLTLGLRAKFPVS  251 (297)
Q Consensus       196 -~~~w~~-l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~-----~~~~v~~~~~~~~~~~l~  251 (297)
                       ...|+. |-..+...         ...|.+||+|++..-     ...++..++...-++.++
T Consensus       111 ~~~~~~~~lf~lin~~---------~~~~~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~  164 (213)
T d1l8qa2         111 GKERTQIEFFHIFNTL---------YLLEKQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE  164 (213)
T ss_dssp             TCHHHHHHHHHHHHHH---------HHTTCEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC
T ss_pred             CchHHHHHHHHHHHHH---------hhccceEEEecCCcchhccccchHHHHHhhCceEEEEC
Confidence             135655 33333332         267889999997331     123344444444455554

>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=97.96  E-value=4.5e-06  Score=68.58  Aligned_cols=119  Identities=16%  Similarity=0.141  Sum_probs=69.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCC-C-ceEEEEeCCCCCHHHHHHHHHHhhcCC-----CceEEEEEeCCCCCCccC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENF-D-KRIWVCVSDPFDEFRIAKAIIEGLEGS-----EKKFFLILDDVWTDDYSK  198 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F-~-~~~wv~vs~~~~~~~~~~~i~~~~~~~-----~kr~LiVlDdv~~~~~~~  198 (297)
                      =++|++|+||||+|+.+.+.  +...+ . ...-+..+...+...+...+..-....     ++.-++|+|++.......
T Consensus        40 ll~Gp~G~GKTt~a~~la~~--l~~~~~~~~~~~~n~~~~~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~~~  117 (224)
T d1sxjb2          40 IISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGA  117 (224)
T ss_dssp             EEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHH
T ss_pred             EEECCCCCCchhhHHHHHHH--HhccccccccccccccccCCceehhhHHHHHHHhhccCCCcceEEEEEecccccchhH
Confidence            37899999999999988873  32221 1 233345555555555444433322211     567789999998876545


Q ss_pred             HHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhhh
Q 043781          199 WEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKIW  259 (297)
Q Consensus       199 w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~lf  259 (297)
                      ...|+..+...          ...++++++|...+. ...+   ......+.+.+++..++.
T Consensus       118 ~~~ll~~~e~~----------~~~~~~i~~~~~~~~i~~~l---~sr~~~i~~~~~~~~~i~  166 (224)
T d1sxjb2         118 QQALRRTMELY----------SNSTRFAFACNQSNKIIEPL---QSQCAILRYSKLSDEDVL  166 (224)
T ss_dssp             HHTTHHHHHHT----------TTTEEEEEEESCGGGSCHHH---HTTSEEEECCCCCHHHHH
T ss_pred             HHHHhhhcccc----------ccceeeeeccCchhhhhhHH---HHHHHHhhhcccchhhhH
Confidence            55566666542          555666666654332 1222   122356788888777653

>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=97.90  E-value=2e-05  Score=65.41  Aligned_cols=119  Identities=15%  Similarity=0.202  Sum_probs=71.1

Q ss_pred             ccccCCcchHHHHHHHhccccc--------------------ccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---Cce
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV--------------------IENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---EKK  183 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~--------------------~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---~kr  183 (297)
                      ++|++|+||||+|+.+.+.-..                    ..+|+ .+.+..+....... .+++++.+...   ++.
T Consensus        39 l~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~-~~~~~~~~~~~i~~-ir~~~~~~~~~~~~~~~  116 (239)
T d1njfa_          39 FSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVD-LIEIDAASRTKVED-TRDLLDNVQYAPARGRF  116 (239)
T ss_dssp             EECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHTCCTT-EEEEETTCSSSHHH-HHHHHHSCCCSCSSSSS
T ss_pred             EECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcCCCCe-EEEecchhcCCHHH-HHHHHHHHHhccccCCC
Confidence            6899999999999987653110                    01122 34555555555544 44566665433   666


Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHH-HHHHHhhCCCccccCCccchhhhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKL-RHLTLTLGLRAKFPVSIFDAKKIWG  260 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~-~~v~~~~~~~~~~~l~~l~~~~lf~  260 (297)
                      -++|||++.....+.-..|...+...          ...+.+|++|...... ..+-   .-...+++..++..++..
T Consensus       117 kviiIde~d~l~~~~q~~Llk~lE~~----------~~~~~~il~tn~~~~i~~~i~---SRc~~i~~~~~~~~~i~~  181 (239)
T d1njfa_         117 KVYLIDEVHMLSRHSFNALLKTLEEP----------PEHVKFLLATTDPQKLPVTIL---SRCLQFHLKALDVEQIRH  181 (239)
T ss_dssp             EEEEEETGGGSCHHHHHHHHHHHHSC----------CTTEEEEEEESCGGGSCHHHH---TTSEEEECCCCCHHHHHH
T ss_pred             EEEEEECcccCCHHHHHHHHHHHhcC----------CCCeEEEEEcCCccccChhHh---hhhcccccccCcHHHhhh
Confidence            79999999887544445566666442          4566777777654321 2221   112566777777666533

>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=97.90  E-value=2.9e-06  Score=69.98  Aligned_cols=81  Identities=17%  Similarity=0.110  Sum_probs=47.5

Q ss_pred             cccccCCcchHHHHHHHhccccccc-CCCce-EEEEeCCCCCHHHHHHHHHHhhcC----CCceEEEEEeCCCCCCccCH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE-NFDKR-IWVCVSDPFDEFRIAKAIIEGLEG----SEKKFFLILDDVWTDDYSKW  199 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~-~F~~~-~wv~vs~~~~~~~~~~~i~~~~~~----~~kr~LiVlDdv~~~~~~~w  199 (297)
                      =++|++|+||||+|+.+.+.  +.. .+... +-++.+...+...+...+......    ..+..++++|++.......+
T Consensus        49 ll~Gp~G~GKTtla~~iak~--l~~~~~~~~~~e~n~s~~~~~~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~~~~  126 (231)
T d1iqpa2          49 LFAGPPGVGKTTAALALARE--LFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQ  126 (231)
T ss_dssp             EEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETTCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHH
T ss_pred             EEECCCCCcHHHHHHHHHHH--HHhcccCCCeeEEecCcccchhHHHHHHHHHHhhhhccCCCceEEeehhhhhcchhHH
Confidence            47899999999999999873  221 22211 223334322222222222222111    16788999999988766667


Q ss_pred             HHHHHHHhh
Q 043781          200 EPFHNCLMR  208 (297)
Q Consensus       200 ~~l~~~l~~  208 (297)
                      ..|...+..
T Consensus       127 ~~ll~~l~~  135 (231)
T d1iqpa2         127 QALRRTMEM  135 (231)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHhhhccc
Confidence            777666654

>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=97.87  E-value=1.4e-05  Score=65.64  Aligned_cols=120  Identities=13%  Similarity=0.042  Sum_probs=64.7

Q ss_pred             cccccCCcchHHHHHHHhccccccc-CCCceEEEEeCCCCCHHHHHHHHHHhhcCC--------------CceEEEEEeC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE-NFDKRIWVCVSDPFDEFRIAKAIIEGLEGS--------------EKKFFLILDD  190 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~-~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~--------------~kr~LiVlDd  190 (297)
                      =++|++|+||||||+.+.+.-.-.. .......++.+.......+...+-......              .+.-++|+|+
T Consensus        37 ll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe  116 (237)
T d1sxjd2          37 LFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDE  116 (237)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETT
T ss_pred             EEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEec
Confidence            4889999999999999988421111 122333444555545444333322211110              3444789999


Q ss_pred             CCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH-HHHHHHHHhhCCCccccCCccchhhh
Q 043781          191 VWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ-EKLRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       191 v~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~-~~~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      +.......+..+...+...          ....++|+||... .....+....   ..+.+++++..++
T Consensus       117 ~d~l~~~~~~~l~~~~~~~----------~~~~~~i~~~~~~~~~~~~l~sr~---~~i~f~~~~~~~~  172 (237)
T d1sxjd2         117 ADSMTADAQSALRRTMETY----------SGVTRFCLICNYVTRIIDPLASQC---SKFRFKALDASNA  172 (237)
T ss_dssp             GGGSCHHHHHHHHHHHHHT----------TTTEEEEEEESCGGGSCHHHHHHS---EEEECCCCCHHHH
T ss_pred             ccccCHHHHHHHhhccccc----------cccccccccccccccccccccchh---hhhcccccccccc
Confidence            9877545555555555442          4445566665433 2233333332   4556777766554

>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=97.71  E-value=2.9e-05  Score=64.38  Aligned_cols=65  Identities=5%  Similarity=0.029  Sum_probs=37.5

Q ss_pred             CceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH-HHHHHHhhCCCccccCCccchhhh
Q 043781          181 EKKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK-LRHLTLTLGLRAKFPVSIFDAKKI  258 (297)
Q Consensus       181 ~kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~-~~~v~~~~~~~~~~~l~~l~~~~l  258 (297)
                      ++.-++|||++.....+.+..++..+...          ...+++|+||...+. ...+-..  + ..+++.+++..++
T Consensus       130 ~~~~iiiide~d~l~~~~~~~l~~~~e~~----------~~~~~~Il~tn~~~~i~~~l~sR--~-~~i~~~~~~~~~~  195 (252)
T d1sxje2         130 HRYKCVIINEANSLTKDAQAALRRTMEKY----------SKNIRLIMVCDSMSPIIAPIKSQ--C-LLIRCPAPSDSEI  195 (252)
T ss_dssp             -CCEEEEEECTTSSCHHHHHHHHHHHHHS----------TTTEEEEEEESCSCSSCHHHHTT--S-EEEECCCCCHHHH
T ss_pred             CCceEEEeccccccccccchhhhcccccc----------cccccceeeeccccchhhhhhcc--h-heeeecccchhhH
Confidence            45568999999887555666677777542          555677777754321 1111111  1 3456666665554

>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=97.70  E-value=2.3e-05  Score=63.72  Aligned_cols=118  Identities=11%  Similarity=-0.006  Sum_probs=70.8

Q ss_pred             ccccCCcchHHHHHHHhcccc------------------cccC-CCceEEEEeCC---CCCHHHHHHHHHHhhcCC---C
Q 043781          127 VRGMGGIGKTTLAQFAYNDKD------------------VIEN-FDKRIWVCVSD---PFDEFRIAKAIIEGLEGS---E  181 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~------------------~~~~-F~~~~wv~vs~---~~~~~~~~~~i~~~~~~~---~  181 (297)
                      ++|++|+||||+|+.+.+.-.                  +... .....++....   .....+ .+++.+.+...   +
T Consensus        29 l~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~-ir~l~~~~~~~~~~~  107 (207)
T d1a5ta2          29 IQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDA-VREVTEKLNEHARLG  107 (207)
T ss_dssp             EECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHH-HHHHHHHTTSCCTTS
T ss_pred             EECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccch-hhHHhhhhhhccccC
Confidence            689999999999998776210                  0111 12223333222   223333 45566655433   6


Q ss_pred             ceEEEEEeCCCCCCccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhh-CCCccccCCccchhhh
Q 043781          182 KKFFLILDDVWTDDYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTL-GLRAKFPVSIFDAKKI  258 (297)
Q Consensus       182 kr~LiVlDdv~~~~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~-~~~~~~~l~~l~~~~l  258 (297)
                      ++-++|+|++.....+....|...+..-          ..++.+|+||++..   .+..+. .-...+++.+++.+++
T Consensus       108 ~~kviIide~d~l~~~a~n~Llk~lEep----------~~~~~fIl~t~~~~---~ll~tI~SRc~~i~~~~~~~~~~  172 (207)
T d1a5ta2         108 GAKVVWVTDAALLTDAAANALLKTLEEP----------PAETWFFLATREPE---RLLATLRSRCRLHYLAPPPEQYA  172 (207)
T ss_dssp             SCEEEEESCGGGBCHHHHHHHHHHHTSC----------CTTEEEEEEESCGG---GSCHHHHTTSEEEECCCCCHHHH
T ss_pred             ccceEEechhhhhhhhhhHHHHHHHHhh----------cccceeeeeecChh---hhhhhhcceeEEEecCCCCHHHH
Confidence            7789999999988766777777777542          56677787777543   222221 1125677777776664

>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=97.67  E-value=5.6e-05  Score=63.06  Aligned_cols=62  Identities=24%  Similarity=0.294  Sum_probs=41.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCC---C---CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDP---F---DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~---~---~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|++|+|||+||+.+++  ....+|   +.+..+..   .   +....++++++.... ..+.+|+||++..
T Consensus        44 LL~GppGtGKT~la~alA~--~~~~~~---~~i~~~~~~~g~~~~~~~~~i~~if~~A~~-~~p~il~iDEid~  111 (246)
T d1d2na_          44 LLEGPPHSGKTALAAKIAE--ESNFPF---IKICSPDKMIGFSETAKCQAMKKIFDDAYK-SQLSCVVVDDIER  111 (246)
T ss_dssp             EEECSTTSSHHHHHHHHHH--HHTCSE---EEEECGGGCTTCCHHHHHHHHHHHHHHHHT-SSEEEEEECCHHH
T ss_pred             EEECcCCCCHHHHHHHHhh--cccccc---cccccccccccccccchhhhhhhhhhhhhh-cccceeehhhhhh
Confidence            3889999999999999998  344333   23332221   1   123456666666554 5789999999953

>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=97.54  E-value=6.7e-05  Score=62.12  Aligned_cols=64  Identities=23%  Similarity=0.230  Sum_probs=40.8

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC-----------------CceEEEEE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS-----------------EKKFFLIL  188 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~-----------------~kr~LiVl  188 (297)
                      -++|++|+||||+|+.+++.  ..   -...++..+...+...+-.. .......                 ++..++++
T Consensus        56 ll~GPpG~GKTt~a~~la~~--~~---~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~i  129 (253)
T d1sxja2          56 MLYGPPGIGKTTAAHLVAQE--LG---YDILEQNASDVRSKTLLNAG-VKNALDNMSVVGYFKHNEEAQNLNGKHFVIIM  129 (253)
T ss_dssp             EEECSTTSSHHHHHHHHHHH--TT---CEEEEECTTSCCCHHHHHHT-GGGGTTBCCSTTTTTC----CCSSTTSEEEEE
T ss_pred             EEECCCCCCHHHHHHHHHHH--HH---hhhhccccccchhhHHHHHH-HHHHhhcchhhhhhhhhhhcccccccceEEEe
Confidence            48899999999999999984  22   12345555555454443322 2221110                 67889999


Q ss_pred             eCCCCCC
Q 043781          189 DDVWTDD  195 (297)
Q Consensus       189 Ddv~~~~  195 (297)
                      |++....
T Consensus       130 de~~~~~  136 (253)
T d1sxja2         130 DEVDGMS  136 (253)
T ss_dssp             CSGGGCC
T ss_pred             eeccccc
Confidence            9988653

>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=97.49  E-value=5.1e-05  Score=63.10  Aligned_cols=21  Identities=24%  Similarity=0.463  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|++|+|||+|++.+.+.
T Consensus        32 i~i~G~~G~GKTsLl~~~~~~   52 (283)
T d2fnaa2          32 TLVLGLRRTGKSSIIKIGINE   52 (283)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHHH
Confidence            458899999999999998873

>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=97.47  E-value=0.00019  Score=59.35  Aligned_cols=69  Identities=19%  Similarity=0.184  Sum_probs=48.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCC-ceEEEEeCCCCCHHHHHHHHHHhhcCC----------------------C
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFD-KRIWVCVSDPFDEFRIAKAIIEGLEGS----------------------E  181 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~-~~~wv~vs~~~~~~~~~~~i~~~~~~~----------------------~  181 (297)
                      .-|+|++|+|||++|+.+++.  ..+.+. ..+|+..............+....+..                      .
T Consensus        46 lll~GppGtGKT~l~~~l~~~--l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (276)
T d1fnna2          46 ATLLGRPGTGKTVTLRKLWEL--YKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERD  123 (276)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH--HTTSCCCEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTT
T ss_pred             eEEECCCCCCHHHHHHHHHHH--HhcccCCcEEEecchhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcc
Confidence            348899999999999999984  444443 334666655566666666666655432                      6


Q ss_pred             ceEEEEEeCCCCCC
Q 043781          182 KKFFLILDDVWTDD  195 (297)
Q Consensus       182 kr~LiVlDdv~~~~  195 (297)
                      ...++++|++++..
T Consensus       124 ~~~~~~~~~~d~~~  137 (276)
T d1fnna2         124 LYMFLVLDDAFNLA  137 (276)
T ss_dssp             CCEEEEEETGGGSC
T ss_pred             cccccchhHHHHhh
Confidence            78888899888764

>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=97.34  E-value=0.00023  Score=57.18  Aligned_cols=94  Identities=12%  Similarity=-0.020  Sum_probs=63.2

Q ss_pred             ccccCCcchHHHHHHHhccccc--ccCCCceEEEE-eCCCCCHHHHHHHHHHhhcCC---CceEEEEEeCCCCCCccCHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDV--IENFDKRIWVC-VSDPFDEFRIAKAIIEGLEGS---EKKFFLILDDVWTDDYSKWE  200 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~--~~~F~~~~wv~-vs~~~~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~~~~~~w~  200 (297)
                      ++|.+|+|||++|..+.+.-..  ..|.|. .++. -+....+.++- ++.+.+...   +++=++|+|++.....+.++
T Consensus        20 ~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~-~~i~~~~~~I~Id~IR-~i~~~~~~~~~~~~~KviIId~ad~l~~~aqN   97 (198)
T d2gnoa2          20 INGEDLSYPREVSLELPEYVEKFPPKASDV-LEIDPEGENIGIDDIR-TIKDFLNYSPELYTRKYVIVHDCERMTQQAAN   97 (198)
T ss_dssp             EECSSSSHHHHHHHHHHHHHHTSCCCTTTE-EEECCSSSCBCHHHHH-HHHHHHTSCCSSSSSEEEEETTGGGBCHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHHHhccccCCCCE-EEEeCCcCCCCHHHHH-HHHHHHhhCcccCCCEEEEEeCccccchhhhh
Confidence            7899999999999988873211  223343 3333 23344566654 455555443   56669999999998878888


Q ss_pred             HHHHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          201 PFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       201 ~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      .|...+..-          .+++.+|++|...
T Consensus        98 aLLK~LEEP----------p~~t~fiLit~~~  119 (198)
T d2gnoa2          98 AFLKALEEP----------PEYAVIVLNTRRW  119 (198)
T ss_dssp             HTHHHHHSC----------CTTEEEEEEESCG
T ss_pred             HHHHHHhCC----------CCCceeeeccCCh
Confidence            898888652          5667777777654

>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=97.33  E-value=0.00021  Score=59.52  Aligned_cols=61  Identities=21%  Similarity=0.212  Sum_probs=39.4

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCC----CC-CHHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD----PF-DEFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~----~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      =++|++|+|||+||+.+.+.  ...+|   +.+..++    .. .....+++++..... ..+.+|+|||+.
T Consensus        46 Ll~GppGtGKT~la~aia~~--~~~~~---~~i~~~~l~~~~~g~~~~~l~~~f~~a~~-~~p~Ii~iDeid  111 (247)
T d1ixza_          46 LLVGPPGVGKTHLARAVAGE--ARVPF---ITASGSDFVEMFVGVGAARVRDLFETAKR-HAPCIVFIDEID  111 (247)
T ss_dssp             EEECCTTSSHHHHHHHHHHH--TTCCE---EEEEHHHHHHSCTTHHHHHHHHHHHHHTT-SSSEEEEEETHH
T ss_pred             EEecCCCCChhHHHHHHHHH--cCCCE---EEEEhHHhhhccccHHHHHHHHHHHHHHH-cCCEEEEEEChh
Confidence            48899999999999999983  33222   2333221    12 223345566655543 578899999986

>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=97.24  E-value=0.00018  Score=60.26  Aligned_cols=63  Identities=19%  Similarity=0.134  Sum_probs=38.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEe----CCCCC-HHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV----SDPFD-EFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v----s~~~~-~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      =++|++|+|||+||+.+.+.  ...+|   +.+..    +.... ....++.++..... .++.+|+|||+...
T Consensus        42 LL~GppGtGKT~l~~ala~~--~~~~~---~~i~~~~l~~~~~g~~~~~l~~~f~~A~~-~~p~il~iDeid~l  109 (258)
T d1e32a2          42 LLYGPPGTGKTLIARAVANE--TGAFF---FLINGPEIMSKLAGESESNLRKAFEEAEK-NAPAIIFIDELDAI  109 (258)
T ss_dssp             EEECCTTSSHHHHHHHHHHH--TTCEE---EEECHHHHTTSCTTHHHHHHHHHHHHHHH-TCSEEEEESSGGGT
T ss_pred             EEecCCCCCchHHHHHHHHH--hCCeE---EEEEchhhcccccccHHHHHHHHHHHHHh-cCCeEEEehhhhhh
Confidence            38899999999999999983  33222   22221    11111 23334444444332 57899999999764

>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=97.23  E-value=0.00048  Score=56.31  Aligned_cols=61  Identities=26%  Similarity=0.292  Sum_probs=40.5

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDD  195 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~  195 (297)
                      =++|++|+||||+|+.+.+.  ....   ...++.+......++. .++...   .++..+++|.+....
T Consensus        39 L~~GPpGtGKT~lA~~la~~--~~~~---~~~~~~~~~~~~~~~~-~~~~~~---~~~~~~~ide~~~~~   99 (238)
T d1in4a2          39 LLAGPPGLGKTTLAHIIASE--LQTN---IHVTSGPVLVKQGDMA-AILTSL---ERGDVLFIDEIHRLN   99 (238)
T ss_dssp             EEESSTTSSHHHHHHHHHHH--HTCC---EEEEETTTCCSHHHHH-HHHHHC---CTTCEEEEETGGGCC
T ss_pred             EEECCCCCcHHHHHHHHHhc--cCCC---cccccCcccccHHHHH-HHHHhh---ccCCchHHHHHHHhh
Confidence            37899999999999999983  3322   2345555555554433 334333   466788899987764

>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=97.22  E-value=0.00048  Score=56.39  Aligned_cols=72  Identities=21%  Similarity=0.162  Sum_probs=42.9

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCCCccCHHHHHHHH
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTDDYSKWEPFHNCL  206 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~~~~~w~~l~~~l  206 (297)
                      ++|++|+||||+|+.+.+.  ...+   ..+++.+...........+...+   +.+.++++|.+.......-+.+...+
T Consensus        40 l~GPpG~GKTtla~~la~~--~~~~---~~~~~~~~~~~~~~~~~~~~~~~---~~~~i~~iDe~~~~~~~~~~~l~~~~  111 (239)
T d1ixsb2          40 LFGPPGLGKTTLAHVIAHE--LGVN---LRVTSGPAIEKPGDLAAILANSL---EEGDILFIDEIHRLSRQAEEHLYPAM  111 (239)
T ss_dssp             EECCTTSCHHHHHHHHHHH--HTCC---EEEEETTTCCSHHHHHHHHHTTC---CTTCEEEEETGGGCCHHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHH--hCCC---eEeccCCccccchhhHHHHHhhc---cCCCeeeeecccccchhHHHhhhhhh
Confidence            7899999999999999984  2222   34555555444444333333322   23456778998776433333344444

>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=97.17  E-value=0.001  Score=52.98  Aligned_cols=95  Identities=18%  Similarity=0.146  Sum_probs=59.6

Q ss_pred             cccccCCcchHHHHHHHhccc---cc-ccCCCceEEEE-----eCCCC---CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDK---DV-IENFDKRIWVC-----VSDPF---DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~---~~-~~~F~~~~wv~-----vs~~~---~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -+||.+|+|||+|+..++..-   ++ ....+.++|.-     ++...   ..++-++.+++.+....++.++++|++..
T Consensus        47 lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~  126 (195)
T d1jbka_          47 VLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHT  126 (195)
T ss_dssp             EEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGG
T ss_pred             EEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHH
Confidence            489999999999998777631   12 12335566652     23222   45666777887775445689999999986


Q ss_pred             CC--------ccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccH
Q 043781          194 DD--------YSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQ  232 (297)
Q Consensus       194 ~~--------~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~  232 (297)
                      --        .+.-+-|+++|.            ...=++|.||.-+
T Consensus       127 l~~~g~~~g~~d~~~~Lkp~L~------------rg~l~~IgatT~e  161 (195)
T d1jbka_         127 MVGAGKADGAMDAGNMLKPALA------------RGELHCVGATTLD  161 (195)
T ss_dssp             GTT------CCCCHHHHHHHHH------------TTSCCEEEEECHH
T ss_pred             HhcCCCCCCcccHHHHHHHHHh------------CCCceEEecCCHH
Confidence            41        123345666664            3345677777633

>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=97.01  E-value=0.00032  Score=58.33  Aligned_cols=68  Identities=25%  Similarity=0.275  Sum_probs=43.0

Q ss_pred             cccccCCcchHHHHHHHhccccc----ccCCCceEEEEeCCCCCHHHHHHHHHHhhcCC---------------------
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDV----IENFDKRIWVCVSDPFDEFRIAKAIIEGLEGS---------------------  180 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~----~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~---------------------  180 (297)
                      -++|++|+|||++++.+.+.-.-    ........++..............+...++..                     
T Consensus        50 ~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  129 (287)
T d1w5sa2          50 GSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYV  129 (287)
T ss_dssp             ECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHH
T ss_pred             EeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHh
Confidence            46799999999999999984210    11112344565555555555555555444332                     


Q ss_pred             -CceEEEEEeCCCC
Q 043781          181 -EKKFFLILDDVWT  193 (297)
Q Consensus       181 -~kr~LiVlDdv~~  193 (297)
                       +...++++|.+..
T Consensus       130 ~~~~~~~iide~d~  143 (287)
T d1w5sa2         130 ENHYLLVILDEFQS  143 (287)
T ss_dssp             HTCEEEEEEESTHH
T ss_pred             ccCccccceeEEEE
Confidence             6788889998864

>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=96.92  E-value=0.0026  Score=53.26  Aligned_cols=68  Identities=28%  Similarity=0.254  Sum_probs=46.9

Q ss_pred             cccccCCcchHHHHHHHhccc---cccc-CCCceEEEE-----e---CCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDK---DVIE-NFDKRIWVC-----V---SDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~---~~~~-~F~~~~wv~-----v---s~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -+||.+|+|||+|+..++..-   .+.. .....+|.-     +   +..-...+.++.|++.+.. .+..++++|++..
T Consensus        43 lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~-~~~iIlfiDeih~  121 (268)
T d1r6bx2          43 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQ-DTNSILFIDEIHT  121 (268)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSS-SSCEEEEETTTTT
T ss_pred             EEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechHhccCccchhHHHHHHHHHHHhhc-cCCceEEecchHH
Confidence            389999999999998877631   1111 234556551     1   2234678888888888865 6778999999876


Q ss_pred             C
Q 043781          194 D  194 (297)
Q Consensus       194 ~  194 (297)
                      -
T Consensus       122 l  122 (268)
T d1r6bx2         122 I  122 (268)
T ss_dssp             T
T ss_pred             H
Confidence            4

>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=96.88  E-value=0.002  Score=56.87  Aligned_cols=119  Identities=21%  Similarity=0.119  Sum_probs=65.2

Q ss_pred             cccccCCcchHHHHHHHhcc---ccc-ccCCCceEEEE-eC-------CCCCHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYND---KDV-IENFDKRIWVC-VS-------DPFDEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~---~~~-~~~F~~~~wv~-vs-------~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      -+||.+|+|||+|+..++..   ..+ ....+.++|.- ++       ..-...+-+..|+..+.......+|++|++..
T Consensus        47 llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~  126 (387)
T d1qvra2          47 VLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHT  126 (387)
T ss_dssp             EEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC--
T ss_pred             eEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHH
Confidence            48899999999988655542   122 22345666652 21       12256777788888887656689999999986


Q ss_pred             CC--------ccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHhhCC---CccccCCccchhh
Q 043781          194 DD--------YSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLTLGL---RAKFPVSIFDAKK  257 (297)
Q Consensus       194 ~~--------~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~~~~---~~~~~l~~l~~~~  257 (297)
                      .-        .+.-+-|+++|.            ...=++|-||..++ .+.+-..-..   -..+++.+.+..+
T Consensus       127 l~~~g~~~g~~d~a~~Lkp~L~------------rg~~~~I~~tT~~e-y~~~e~d~al~rrF~~v~v~ep~~~~  188 (387)
T d1qvra2         127 VVGAGKAEGAVDAGNMLKPALA------------RGELRLIGATTLDE-YREIEKDPALERRFQPVYVDEPTVEE  188 (387)
T ss_dssp             -----------------HHHHH------------TTCCCEEEEECHHH-HHHHTTCTTTCSCCCCEEECCCCHHH
T ss_pred             HhcCCCCCCcccHHHHHHHHHh------------CCCcceeeecCHHH-HHHhcccHHHHHhcccccCCCCcHHH
Confidence            41        122344666664            34456777776444 3444322111   1455666666444

>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=96.78  E-value=0.00048  Score=57.52  Aligned_cols=62  Identities=19%  Similarity=0.186  Sum_probs=39.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-----CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-----DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-----~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|++|+|||+||+.+.+.  ..-+|   +-+..+.-.     ....-++.++..... ..+++|+|||+..
T Consensus        49 LL~GppGtGKT~la~~iA~~--~~~~~---~~i~~~~l~~~~~g~~~~~l~~~f~~A~~-~~P~il~iDeiD~  115 (256)
T d1lv7a_          49 LMVGPPGTGKTLLAKAIAGE--AKVPF---FTISGSDFVEMFVGVGASRVRDMFEQAKK-AAPCIIFIDEIDA  115 (256)
T ss_dssp             EEECCTTSCHHHHHHHHHHH--HTCCE---EEECSCSSTTSCCCCCHHHHHHHHHHHHT-TCSEEEEETTHHH
T ss_pred             EeeCCCCCCccHHHHHHHHH--cCCCE---EEEEhHHhhhcchhHHHHHHHHHHHHHHH-cCCEEEEEEChhh
Confidence            47899999999999999983  33222   223222211     123445566655543 5778999999963

>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=96.75  E-value=0.0012  Score=55.20  Aligned_cols=62  Identities=24%  Similarity=0.263  Sum_probs=39.6

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEE----eCCCC-CHHHHHHHHHHhhcCCCceEEEEEeCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVC----VSDPF-DEFRIAKAIIEGLEGSEKKFFLILDDVWT  193 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~----vs~~~-~~~~~~~~i~~~~~~~~kr~LiVlDdv~~  193 (297)
                      =++|++|+|||+||+.+++.  ..-+|   +.+.    .+... .....++.++..... ..+.+|+|||+..
T Consensus        45 LL~Gp~GtGKT~l~~ala~~--~~~~~---~~~~~~~l~~~~~~~~~~~l~~~f~~A~~-~~p~il~ideid~  111 (265)
T d1r7ra3          45 LFYGPPGCGKTLLAKAIANE--CQANF---ISIKGPELLTMWFGESEANVREIFDKARQ-AAPCVLFFDELDS  111 (265)
T ss_dssp             EEBCCTTSSHHHHHHHHHHH--TTCEE---EEECHHHHHTSCTTTHHHHHHHHHHHHHH-TCSEEEEESSGGG
T ss_pred             EEECCCCCcchhHHHHHHHH--hCCcE---EEEEHHHhhhccccchHHHHHHHHHHHHh-cCCcceeHHhhhh
Confidence            38899999999999999983  33332   1111    11111 234445555554433 5789999999974

>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=96.43  E-value=0.00048  Score=52.07  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-+.|++|+||||+|+.+.+.
T Consensus         5 I~l~G~~GsGKSTvak~La~~   25 (169)
T d1kaga_           5 IFLVGPMGAGKSTIGRQLAQQ   25 (169)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            346799999999999999983

>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=96.41  E-value=0.00082  Score=57.81  Aligned_cols=100  Identities=17%  Similarity=0.123  Sum_probs=53.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC------------------HHHHHHHHHHhhcCCCceEEE
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD------------------EFRIAKAIIEGLEGSEKKFFL  186 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~------------------~~~~~~~i~~~~~~~~kr~Li  186 (297)
                      .-++|+.|+|||.||+.+.+.  +-..-...+-+..+.-.+                  ....+.   +.+.. ....+|
T Consensus        56 ~lf~Gp~G~GKt~lak~la~~--l~~~~~~~~~~~~~~~~~~~~~~~L~g~~~gyvG~~~~~~l~---~~~~~-~p~~Vv  129 (315)
T d1qvra3          56 FLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTEYMEKHAVSRLIGAPPGYVGYEEGGQLT---EAVRR-RPYSVI  129 (315)
T ss_dssp             EEEBSCSSSSHHHHHHHHHHH--HHSSGGGEEEECTTTCCSSGGGGGC--------------CHH---HHHHH-CSSEEE
T ss_pred             EEEECCCcchHHHHHHHHHHH--hcCCCcceEEEeccccccchhhhhhcCCCCCCcCcccCChHH---HHHHh-CCCcEE
Confidence            347899999999999988873  211001111122211111                  111122   22221 457899


Q ss_pred             EEeCCCCCCccCHHHHHHHHhhhhhh-hceeeecCCCCeEEEEec
Q 043781          187 ILDDVWTDDYSKWEPFHNCLMRVLQE-FAAIEVDGDENPLSLTST  230 (297)
Q Consensus       187 VlDdv~~~~~~~w~~l~~~l~~~~~~-~~~~~~~~~gs~iiiTTr  230 (297)
                      +||++...+.+.++.|...+..+... ..-..++-.++-+|.||.
T Consensus       130 l~DEieK~~~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~tsn  174 (315)
T d1qvra3         130 LFDEIEKAHPDVFNILLQILDDGRLTDSHGRTVDFRNTVIILTSN  174 (315)
T ss_dssp             EESSGGGSCHHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEECC
T ss_pred             EEehHhhcCHHHHHHHHHHhccCceeCCCCcEecCcceEEEEecc
Confidence            99999988877888888777654211 111112234455666665

>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=96.30  E-value=0.0033  Score=48.81  Aligned_cols=63  Identities=19%  Similarity=0.115  Sum_probs=36.1

Q ss_pred             cccccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      ...+-++|++|+||||+|+.+....       ...+++...-.....+.+.+-..+.   ++..+|+|+....
T Consensus        14 p~liil~G~pGsGKST~a~~l~~~~-------~~~~i~~D~~~~~~~~~~~~~~~l~---~g~~vIiD~t~~~   76 (172)
T d1yj5a2          14 PEVVVAVGFPGAGKSTFIQEHLVSA-------GYVHVNRDTLGSWQRCVSSCQAALR---QGKRVVIDNTNPD   76 (172)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHTGGG-------TCEEEEHHHHCSHHHHHHHHHHHHH---TTCCEEEESCCCS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhc-------CCEEEchHHHHHHHHHHHHHHHHHH---CCCCceeeCcCCC
Confidence            3445678999999999999887621       1233432211223334443333333   3456888987544

>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=96.24  E-value=0.0056  Score=49.94  Aligned_cols=53  Identities=11%  Similarity=0.060  Sum_probs=32.8

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      .+.=+|+||.--.. |...-..+...+.+..        ...|..||++|++.+.+..+|..
T Consensus       147 ~~P~illlDEPts~LD~~~~~~i~~~l~~l~--------~~~g~tii~vTHd~~~a~~~~dr  200 (232)
T d2awna2         147 AEPSVFLLDEPLSNLDAALRVQMRIEISRLH--------KRLGRTMIYVTHDQVEAMTLADK  200 (232)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHH--------HHSCCEEEEEESCHHHHHHHCSE
T ss_pred             cCCCEEEEcCCCCCCCHHHHHHHHHHHHHHH--------HhcCCEEEEEeCCHHHHHHhCCE
Confidence            77789999987654 2222223444443321        14678899999987777777643

>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=96.19  E-value=0.00078  Score=51.45  Aligned_cols=22  Identities=27%  Similarity=0.258  Sum_probs=19.8

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ....|+|..|+|||||++.+.+
T Consensus         3 Pvi~itG~~GSGKTTL~~~L~~   24 (170)
T d1np6a_           3 PLLAFAAWSGTGKTTLLKKLIP   24 (170)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            4567899999999999999987

>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=96.18  E-value=0.00065  Score=52.46  Aligned_cols=24  Identities=17%  Similarity=0.095  Sum_probs=20.4

Q ss_pred             cccccccccCCcchHHHHHHHhcc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...+.|.|++|+||||||+.+.+.
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~   30 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAV   30 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHH
Confidence            345678999999999999999883

>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=96.16  E-value=0.00081  Score=51.67  Aligned_cols=31  Identities=13%  Similarity=0.016  Sum_probs=22.4

Q ss_pred             cccccCCcchHHHHHHHhccccccc-CCCceEEE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIE-NFDKRIWV  158 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~-~F~~~~wv  158 (297)
                      -++|++|+||||+|+.+..  ++.. .++...++
T Consensus        10 ~l~G~~GsGKTTia~~La~--~L~~~~~~~~~~~   41 (183)
T d1m8pa3          10 FLTGYMNSGKDAIARALQV--TLNQQGGRSVSLL   41 (183)
T ss_dssp             EEECSTTSSHHHHHHHHHH--HHHHHCSSCEEEE
T ss_pred             EEECCCCCCHHHHHHHHHH--HHhhcCCCchhhh
Confidence            4679999999999999998  4433 34444444

>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=96.14  E-value=0.00084  Score=51.35  Aligned_cols=21  Identities=33%  Similarity=0.352  Sum_probs=18.3

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+-|.|++|+||||+|+.+.+
T Consensus         6 ~I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            345789999999999999987

>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=96.07  E-value=0.00085  Score=51.66  Aligned_cols=20  Identities=25%  Similarity=0.368  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++||+|+||||+++.+++.
T Consensus         5 vliG~~G~GKSTig~~La~~   24 (165)
T d2iyva1           5 VLVGLPGSGKSTIGRRLAKA   24 (165)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            36799999999999999983

>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=96.01  E-value=0.0011  Score=49.87  Aligned_cols=19  Identities=32%  Similarity=0.218  Sum_probs=16.7

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -|.|++|+||||||+.+..
T Consensus         6 ii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           6 LTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEECCTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4789999999999998865

>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=95.99  E-value=0.0011  Score=50.54  Aligned_cols=20  Identities=25%  Similarity=0.321  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|++|+||||+|+.+..
T Consensus         5 I~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           5 YIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999886

>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=95.89  E-value=0.002  Score=55.22  Aligned_cols=96  Identities=14%  Similarity=0.072  Sum_probs=55.7

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCC-------------CCC-H----HHHHHHHHHhhcCCCceEEEE
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD-------------PFD-E----FRIAKAIIEGLEGSEKKFFLI  187 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~-------------~~~-~----~~~~~~i~~~~~~~~kr~LiV  187 (297)
                      -++|++|+|||.||+.+..-  +..   ..+-+..+.             .+. .    ..++...+..    ....+++
T Consensus        56 lf~Gp~GvGKT~lak~la~~--l~~---~~i~~d~s~~~~~~~~~~l~g~~~gy~g~~~~~~l~~~~~~----~~~~vvl  126 (315)
T d1r6bx3          56 LFAGPTGVGKTEVTVQLSKA--LGI---ELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIK----HPHAVLL  126 (315)
T ss_dssp             EEECSTTSSHHHHHHHHHHH--HTC---EEEEEEGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHHHH----CSSEEEE
T ss_pred             EEECCCcchhHHHHHHHHhh--ccC---CeeEeccccccchhhhhhhcccCCCccccccCChhhHHHHh----Cccchhh
Confidence            47799999999999999873  322   222233221             111 1    1122222222    4677999


Q ss_pred             EeCCCCCCccCHHHHHHHHhhhhhh-hceeeecCCCCeEEEEec
Q 043781          188 LDDVWTDDYSKWEPFHNCLMRVLQE-FAAIEVDGDENPLSLTST  230 (297)
Q Consensus       188 lDdv~~~~~~~w~~l~~~l~~~~~~-~~~~~~~~~gs~iiiTTr  230 (297)
                      ||++...+.+.|+.+...+..+.-. ..-...+-..+-||.||.
T Consensus       127 ~DeieKa~~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsn  170 (315)
T d1r6bx3         127 LDEIEKAHPDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTN  170 (315)
T ss_dssp             EETGGGSCHHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEEC
T ss_pred             hcccccccchHhhhhHHhhccceecCCCCCccCccceEEEeccc
Confidence            9999999888888888888654210 011122344455666665

>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=95.84  E-value=0.001  Score=52.11  Aligned_cols=20  Identities=30%  Similarity=0.375  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-++|++|+||||||+.+..
T Consensus        22 I~L~G~pGSGKTTiAk~La~   41 (195)
T d1x6va3          22 VWLTGLSGAGKTTVSMALEE   41 (195)
T ss_dssp             EEEESSCHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34679999999999999987

>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=95.83  E-value=0.0086  Score=49.02  Aligned_cols=22  Identities=18%  Similarity=0.214  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|+.|+|||||.+.+..-
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl   47 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGI   47 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCChHHHHHHHHHcC
Confidence            4568999999999999999983

>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=95.80  E-value=0.0015  Score=50.19  Aligned_cols=21  Identities=38%  Similarity=0.382  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++||+|+||||+++.+...
T Consensus         3 I~liG~~GsGKsTi~k~La~~   23 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKD   23 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999984

>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=95.79  E-value=0.0083  Score=50.12  Aligned_cols=50  Identities=20%  Similarity=0.222  Sum_probs=34.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-CHHHHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-DEFRIAKAIIE  175 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-~~~~~~~~i~~  175 (297)
                      .+|+|..|+|||+|+..+.++. .+.+=+..+++-+.+.. .+.++.+++.+
T Consensus        71 ~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~iGer~~ev~~~~~~~~~  121 (276)
T d2jdid3          71 IGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTREGNDLYHEMIE  121 (276)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEEESCCHHHHHHHHHHHHH
T ss_pred             EEeeCCCCCCHHHHHHHHHHHH-HhhCCCeEEEEEeccChHHHHHHHHHHHh
Confidence            3688999999999998887752 23344566777776654 35566666655

>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=95.79  E-value=0.0016  Score=53.77  Aligned_cols=20  Identities=30%  Similarity=0.386  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +=++|++|+||||||+.+++
T Consensus        35 ilL~GpPGtGKT~la~~la~   54 (273)
T d1gvnb_          35 FLLGGQPGSGKTSLRSAIFE   54 (273)
T ss_dssp             EEEECCTTSCTHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34789999999999999998

>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=95.78  E-value=0.014  Score=47.71  Aligned_cols=53  Identities=9%  Similarity=0.008  Sum_probs=32.2

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      .+.=+|+||.--.. |...=..+...+.+...        ..|..||++|++.+.+..+|..
T Consensus       153 ~~P~iLllDEPts~LD~~~~~~i~~ll~~l~~--------~~g~tii~vTHd~~~a~~~~dr  206 (239)
T d1v43a3         153 VEPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQ--------KLKVTTIYVTHDQVEAMTMGDR  206 (239)
T ss_dssp             TCCSEEEEESTTTTSCHHHHHHHHHHHHHHHH--------HHTCEEEEEESCHHHHHHHCSE
T ss_pred             cCCCceeecCCcccCCHHHHHHHHHHHHHHHH--------hcCCeEEEEeCCHHHHHHhCCE
Confidence            78889999987553 21122223333333211        3478899999988777777643

>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=95.73  E-value=0.0016  Score=49.97  Aligned_cols=21  Identities=38%  Similarity=0.363  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+|||||++.+...
T Consensus         4 v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           4 VFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             EEEESCCSSCHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHH
Confidence            458899999999999999874

>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=95.72  E-value=0.023  Score=46.05  Aligned_cols=21  Identities=24%  Similarity=0.268  Sum_probs=18.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|..|+|||||.+.+..-
T Consensus        34 ~~iiG~sGsGKSTLl~~i~gl   54 (230)
T d1l2ta_          34 VSIMGPSGSGKSTMLNIIGCL   54 (230)
T ss_dssp             EEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCCcchhhHhccCC
Confidence            478999999999999999873

>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=95.71  E-value=0.0017  Score=49.76  Aligned_cols=21  Identities=29%  Similarity=0.465  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|.|++|+||||+|+.+.+.
T Consensus         8 I~i~G~~GsGKTT~~~~La~~   28 (174)
T d1y63a_           8 ILITGTPGTGKTSMAEMIAAE   28 (174)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            457799999999999999873

>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=95.68  E-value=0.0017  Score=50.06  Aligned_cols=21  Identities=24%  Similarity=0.167  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|++|+||||+|+.+++.
T Consensus         5 Iil~G~~GsGKSTia~~LA~~   25 (170)
T d1e6ca_           5 IFMVGARGCGMTTVGRELARA   25 (170)
T ss_dssp             EEEESCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999883

>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=95.65  E-value=0.002  Score=52.99  Aligned_cols=52  Identities=13%  Similarity=0.080  Sum_probs=32.4

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      .+.=+|+||.--.. |......+...+...         ...|-.||+||++.+.+..+|..
T Consensus       150 ~~p~illLDEPt~gLD~~~~~~i~~~i~~~---------~~~g~tii~~tH~l~~~~~~~dr  202 (238)
T d1vpla_         150 VNPRLAILDEPTSGLDVLNAREVRKILKQA---------SQEGLTILVSSHNMLEVEFLCDR  202 (238)
T ss_dssp             TCCSEEEEESTTTTCCHHHHHHHHHHHHHH---------HHTTCEEEEEECCHHHHTTTCSE
T ss_pred             cCCCEEEecCCCCCCCHHHHHHHHHHHHHH---------HhcCCEEEEEeCCHHHHHHhCCE
Confidence            77778899987654 222333444444332         14577899999976666655543

>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=95.57  E-value=0.002  Score=51.00  Aligned_cols=20  Identities=20%  Similarity=0.177  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-++|.+|+||||||+.+.+
T Consensus         5 i~l~GlpgsGKSTla~~L~~   24 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTR   24 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34789999999999999987

>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=95.47  E-value=0.008  Score=51.41  Aligned_cols=62  Identities=19%  Similarity=0.191  Sum_probs=41.5

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-----CHHHHHHHHHHhhcCCCceEEEEEeCCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-----DEFRIAKAIIEGLEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-----~~~~~~~~i~~~~~~~~kr~LiVlDdv~~~  194 (297)
                      ++|++|+|||.||+.+..  ++...+.. +-+..+.-.     ..+.-++.++++..   +..+|++|.+...
T Consensus       128 ~~G~pG~GKT~la~ala~--~~~~~~~~-~~~~~~~~~~~~~G~~e~~~~~~f~~a~---~~~ilf~DEid~~  194 (321)
T d1w44a_         128 VTGKGNSGKTPLVHALGE--ALGGKDKY-ATVRFGEPLSGYNTDFNVFVDDIARAML---QHRVIVIDSLKNV  194 (321)
T ss_dssp             EECSSSSCHHHHHHHHHH--HHHTTSCC-EEEEBSCSSTTCBCCHHHHHHHHHHHHH---HCSEEEEECCTTT
T ss_pred             EECCCCccHHHHHHHHHH--HhcCCCCe-EEEEhhHhhhcccchHHHHHHHHHHHHh---hccEEEeehhhhh
Confidence            369999999999999998  44333211 224433322     45666677777664   3569999999863

>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=95.33  E-value=0.015  Score=48.47  Aligned_cols=67  Identities=19%  Similarity=0.134  Sum_probs=44.1

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHH---------------------HHHHHHHhhcCCCce
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFR---------------------IAKAIIEGLEGSEKK  183 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~---------------------~~~~i~~~~~~~~kr  183 (297)
                      ..++|.+|+||||||.+++.....  .=...+|+.....++...                     ++ ++++.+...++.
T Consensus        63 ~e~~G~~~~GKT~l~l~~~~~~q~--~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~-~~~~~l~~~~~~  139 (269)
T d1mo6a1          63 IEIYGPESSGKTTVALHAVANAQA--AGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQAL-EIADMLIRSGAL  139 (269)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHH--TTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHH-HHHHHHHHTTCE
T ss_pred             EEEecCCCcHHHHHHHHHHHHHhc--CCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHH-HHHHHHHhcCCC
Confidence            358899999999999777764332  233578887766665433                     22 233333333678


Q ss_pred             EEEEEeCCCCC
Q 043781          184 FFLILDDVWTD  194 (297)
Q Consensus       184 ~LiVlDdv~~~  194 (297)
                      -|||+|-+-..
T Consensus       140 ~liIiDSi~al  150 (269)
T d1mo6a1         140 DIVVIDSVAAL  150 (269)
T ss_dssp             EEEEEECSTTC
T ss_pred             CEEEEeccccc
Confidence            89999999654

>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=95.32  E-value=0.0028  Score=48.51  Aligned_cols=22  Identities=41%  Similarity=0.301  Sum_probs=19.5

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...+|+|..|+|||||+..+..
T Consensus         2 kii~I~G~~gSGKTTli~~l~~   23 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVA   23 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            3568999999999999998887

>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=95.32  E-value=0.034  Score=45.36  Aligned_cols=53  Identities=9%  Similarity=0.015  Sum_probs=33.2

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      .+.-+|++|.--.. |...-..+...+.+...        ..|..||++|++.+.+..+|..
T Consensus       156 ~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~~--------~~g~tvi~vTHd~~~~~~~~dr  209 (240)
T d1g2912         156 RKPQVFLMDEPLSNLDAKLRVRMRAELKKLQR--------QLGVTTIYVTHDQVEAMTMGDR  209 (240)
T ss_dssp             TCCSEEEEECTTTTSCHHHHHHHHHHHHHHHH--------HHTCEEEEEESCHHHHHHHCSE
T ss_pred             cCCCEEEecCCCcccCHHHHHHHHHHHHHHHh--------ccCCEEEEEcCCHHHHHHhCCE
Confidence            88889999987554 22222234444433211        3478899999987777777643

>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=95.31  E-value=0.0034  Score=49.36  Aligned_cols=24  Identities=33%  Similarity=0.297  Sum_probs=20.5

Q ss_pred             cccccccccCCcchHHHHHHHhcc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...+-|+|++|+||||+|+.+.+.
T Consensus         8 ~~iI~i~GppGSGKsT~a~~La~~   31 (196)
T d1ukza_           8 VSVIFVLGGPGAGKGTQCEKLVKD   31 (196)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            445678899999999999999884

>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=95.29  E-value=0.0029  Score=48.24  Aligned_cols=21  Identities=24%  Similarity=0.336  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|.|++|+||||+|+.+...
T Consensus         9 ivl~G~~GsGKsT~a~~La~~   29 (171)
T d1knqa_           9 YVLMGVSGSGKSAVASEVAHQ   29 (171)
T ss_dssp             EEEECSTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999873

>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=95.25  E-value=0.003  Score=48.53  Aligned_cols=21  Identities=33%  Similarity=0.411  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|++|+|||||++.+...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~   23 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhc
Confidence            458999999999999999873

>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=95.17  E-value=0.012  Score=48.31  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|..|+|||||++.+..-
T Consensus        31 ~vaIvG~sGsGKSTLl~ll~gl   52 (241)
T d2pmka1          31 VIGIVGRSGSGKSTLTKLIQRF   52 (241)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhc
Confidence            3579999999999999999873

>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=95.15  E-value=0.038  Score=45.51  Aligned_cols=21  Identities=29%  Similarity=0.370  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+|+|+.|+|||||++.+..
T Consensus        30 i~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          30 VISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCcHHHHHHHHHc
Confidence            357999999999999999987

>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=95.08  E-value=0.0037  Score=47.68  Aligned_cols=20  Identities=35%  Similarity=0.381  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|++|+||||+|+.+.+
T Consensus         7 I~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           7 LLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             EEEEECTTSCHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999977

>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=95.07  E-value=0.018  Score=45.94  Aligned_cols=41  Identities=15%  Similarity=0.195  Sum_probs=27.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCC----CceEEEEeCCCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENF----DKRIWVCVSDPFD  165 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F----~~~~wv~vs~~~~  165 (297)
                      .-|+|.+|+|||||+.++..+......+    ...+|+.....++
T Consensus        37 ~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~   81 (251)
T d1szpa2          37 TELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFR   81 (251)
T ss_dssp             EEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCC
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHH
Confidence            4588999999999998876643222222    3567777666554

>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=94.98  E-value=0.023  Score=46.44  Aligned_cols=52  Identities=13%  Similarity=0.122  Sum_probs=32.5

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHH
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTL  240 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~  240 (297)
                      .+.-+|++|.--.. |...-..+...+.+...        ..|..||++|++.+.+..+|.
T Consensus       157 ~~P~llllDEPt~~LD~~~~~~i~~~i~~l~~--------~~g~tvi~vTHd~~~~~~~~d  209 (242)
T d1oxxk2         157 KDPSLLLLDEPFSNLDARMRDSARALVKEVQS--------RLGVTLLVVSHDPADIFAIAD  209 (242)
T ss_dssp             TCCSEEEEESTTTTSCGGGHHHHHHHHHHHHH--------HHCCEEEEEESCHHHHHHHCS
T ss_pred             hcccceeecCCccCCCHHHHHHHHHHHHHHHh--------ccCCEEEEEECCHHHHHHhCC
Confidence            88889999987543 32233334444443211        347789999998766666654

>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=94.97  E-value=0.0039  Score=48.88  Aligned_cols=22  Identities=36%  Similarity=0.234  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|+|++|+||||+|+.+.+.
T Consensus         8 iI~i~G~pGSGKsT~a~~La~~   29 (194)
T d1qf9a_           8 VVFVLGGPGSGKGTQCANIVRD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4568899999999999999873

>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=94.95  E-value=0.0041  Score=48.02  Aligned_cols=20  Identities=30%  Similarity=0.313  Sum_probs=17.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|++|+||||+|+.+...
T Consensus         4 ~i~G~pGSGKsT~a~~La~~   23 (182)
T d1zina1           4 VLMGLPGAGKGTQAEKIVAA   23 (182)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999873

>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=94.95  E-value=0.014  Score=48.71  Aligned_cols=68  Identities=16%  Similarity=0.145  Sum_probs=41.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCC-HHHHHHHHHHh---------------------------
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFD-EFRIAKAIIEG---------------------------  176 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~-~~~~~~~i~~~---------------------------  176 (297)
                      ..|+|..|+|||+|+.....+  ...+-+..+++-+..... +.++..++...                           
T Consensus        70 ~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer~~Ev~e~~~~~~~~~~~~~tvvv~~tsd~p~~~r~~a~~~a  147 (276)
T d1fx0a3          70 ELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQKASSVAQVVTNFQERGAMEYTIVVAETADSPATLQYLAPYTG  147 (276)
T ss_dssp             CBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCCHHHHHHHHHHTGGGTGGGSEEEEEECTTSCGGGTTHHHHHH
T ss_pred             EeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecchhHHHHHHHHhhccCCcceeeeecccccCccHHHHHHHHHHH
Confidence            468999999999999765443  233344566665554432 23333333322                           


Q ss_pred             ------hcCCCceEEEEEeCCCCC
Q 043781          177 ------LEGSEKKFFLILDDVWTD  194 (297)
Q Consensus       177 ------~~~~~kr~LiVlDdv~~~  194 (297)
                            +...+++.|+++||+-..
T Consensus       148 ~tiAEyfrd~G~~Vlll~Dsltr~  171 (276)
T d1fx0a3         148 AALAEYFMYRERHTLIIYDDLSKQ  171 (276)
T ss_dssp             HHHHHHHHHTTCEEEEEEECHHHH
T ss_pred             HHHHHHHHHcCCceeEEeeccHHH
Confidence                  221189999999999543

>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=94.93  E-value=0.0036  Score=53.37  Aligned_cols=65  Identities=20%  Similarity=0.186  Sum_probs=39.6

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCC-------CHHHHHHHHHHhhcCC----CceEEEEEeCCCCC
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPF-------DEFRIAKAIIEGLEGS----EKKFFLILDDVWTD  194 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~-------~~~~~~~~i~~~~~~~----~kr~LiVlDdv~~~  194 (297)
                      -++|++|+|||.||+.+++.  ....|   +-+..+.-.       ......+.+.......    .++.+|.||.+...
T Consensus        53 Ll~GPpG~GKT~lAkalA~~--~~~~~---~~i~~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki  127 (309)
T d1ofha_          53 LMIGPTGVGKTEIARRLAKL--ANAPF---IKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKI  127 (309)
T ss_dssp             EEECCTTSSHHHHHHHHHHH--HTCCE---EEEEGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGG
T ss_pred             EEECCCCCCHHHHHHHHhhc--cccch---hcccccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhh
Confidence            47899999999999999983  33222   333332211       1123344444444332    24789999999875


Q ss_pred             C
Q 043781          195 D  195 (297)
Q Consensus       195 ~  195 (297)
                      .
T Consensus       128 ~  128 (309)
T d1ofha_         128 C  128 (309)
T ss_dssp             S
T ss_pred             h
Confidence            3

>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=94.90  E-value=0.0043  Score=47.19  Aligned_cols=20  Identities=15%  Similarity=0.192  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|.|.+|+||||+|+.+.+
T Consensus         6 I~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           6 IILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45779999999999999988

>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=94.89  E-value=0.0042  Score=47.68  Aligned_cols=21  Identities=38%  Similarity=0.597  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|++|+||||+++.+.+.
T Consensus         4 I~i~G~~GsGKsT~~~~L~~~   24 (190)
T d1khta_           4 VVVTGVPGVGSTTSSQLAMDN   24 (190)
T ss_dssp             EEEECCTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999999773

>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=94.87  E-value=0.0042  Score=48.30  Aligned_cols=22  Identities=36%  Similarity=0.427  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|.|..|+||||||+.+.+.
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~   45 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQT   45 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999873

>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=94.85  E-value=0.017  Score=46.48  Aligned_cols=36  Identities=22%  Similarity=0.249  Sum_probs=27.6

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD  162 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~  162 (297)
                      .-|+|.+|+|||+|+.++..+  ...+....+|++...
T Consensus        29 ~li~G~pGsGKT~l~~qia~~--~~~~~~~~~~is~e~   64 (242)
T d1tf7a2          29 ILATGATGTGKTLLVSRFVEN--ACANKERAILFAYEE   64 (242)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEESSS
T ss_pred             EEEEeCCCCCHHHHHHHHHHH--HHHhccccceeeccC
Confidence            358899999999999888884  445566677887543

>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=94.79  E-value=0.0048  Score=48.56  Aligned_cols=22  Identities=23%  Similarity=0.288  Sum_probs=18.9

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|+|++|+||||+|+.+...
T Consensus         8 rIiliG~PGSGKtT~a~~La~~   29 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKH   29 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3457899999999999999983

>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=94.71  E-value=0.0052  Score=47.62  Aligned_cols=20  Identities=30%  Similarity=0.155  Sum_probs=17.9

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|++|+||||+|+.+++.
T Consensus         4 ~i~G~pGsGKsT~a~~La~~   23 (181)
T d2cdna1           4 LLLGPPGAGKGTQAVKLAEK   23 (181)
T ss_dssp             EEECCTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            46799999999999999884

>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=94.69  E-value=0.0053  Score=47.66  Aligned_cols=20  Identities=30%  Similarity=0.335  Sum_probs=18.1

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|++|+||||+|+.+++.
T Consensus         4 ~i~G~pGSGKsT~a~~La~~   23 (182)
T d1s3ga1           4 VLMGLPGAGKGTQADRIVEK   23 (182)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            47899999999999999984

>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=94.66  E-value=0.0053  Score=47.97  Aligned_cols=21  Identities=19%  Similarity=0.221  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|.|++|+||||+|+.+.+.
T Consensus         6 I~i~GppGsGKsT~a~~La~~   26 (189)
T d1zaka1           6 VMISGAPASGKGTQCELIKTK   26 (189)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347799999999999999874

>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=94.46  E-value=0.023  Score=47.22  Aligned_cols=66  Identities=21%  Similarity=0.199  Sum_probs=43.0

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHH---------------------HHHHHHHHhhcCCCce
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEF---------------------RIAKAIIEGLEGSEKK  183 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~---------------------~~~~~i~~~~~~~~kr  183 (297)
                      ..|+|.+|+|||+||..+.....-..  ...+|+.....++..                     +.+ ++++.+...+..
T Consensus        60 tei~G~~~sGKT~l~l~~~~~aqk~g--~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~-~~~~~l~~~~~~  136 (268)
T d1xp8a1          60 TEIYGPESGGKTTLALAIVAQAQKAG--GTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQAL-EIMELLVRSGAI  136 (268)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT--CCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHH-HHHHHHHTTTCC
T ss_pred             EEEecCCccchHHHHHHHHHHHHhCC--CEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHH-HHHHHHHhcCCC
Confidence            46889999999999988777433222  356788766665543                     221 233444333566


Q ss_pred             EEEEEeCCCC
Q 043781          184 FFLILDDVWT  193 (297)
Q Consensus       184 ~LiVlDdv~~  193 (297)
                      -|||+|-+-.
T Consensus       137 ~liIiDSi~a  146 (268)
T d1xp8a1         137 DVVVVDSVAA  146 (268)
T ss_dssp             SEEEEECTTT
T ss_pred             cEEEEecccc
Confidence            7999999865

>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=94.41  E-value=0.022  Score=46.53  Aligned_cols=21  Identities=29%  Similarity=0.226  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|+.|.|||||.+.+..-
T Consensus        35 ~~liGpnGaGKSTl~~~i~Gl   55 (240)
T d1ji0a_          35 VTLIGANGAGKTTTLSAIAGL   55 (240)
T ss_dssp             EEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEECCCCCcHHHHHHHHhCC
Confidence            478999999999999999874

>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=94.38  E-value=0.0068  Score=46.96  Aligned_cols=19  Identities=32%  Similarity=0.251  Sum_probs=17.2

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      |.|++|+||||+|+.+.+.
T Consensus         7 l~G~pGSGKtT~a~~La~~   25 (180)
T d1akya1           7 LIGPPGAGKGTQAPNLQER   25 (180)
T ss_dssp             EECCTTSSHHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHHH
Confidence            6699999999999999873

>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=94.38  E-value=0.0068  Score=47.36  Aligned_cols=21  Identities=29%  Similarity=0.148  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|.|++|+||||+|+.+++.
T Consensus         4 I~i~GppGSGKsT~a~~La~~   24 (194)
T d1teva_           4 VFVLGGPGAGKGTQCARIVEK   24 (194)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999883

>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=94.35  E-value=0.025  Score=46.88  Aligned_cols=40  Identities=18%  Similarity=0.201  Sum_probs=28.3

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDE  166 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~  166 (297)
                      ..|+|.+|+|||||+-++.....  ..=...+|+.....++.
T Consensus        57 tei~G~~gsGKTtl~l~~~~~~q--~~g~~~vyidtE~~~~~   96 (263)
T d1u94a1          57 VEIYGPESSGKTTLTLQVIAAAQ--REGKTCAFIDAEHALDP   96 (263)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH--HTTCCEEEEESSCCCCH
T ss_pred             EEEecCCCcHHHHHHHHHHHHHH--cCCCEEEEEccccccCH
Confidence            46889999999999988877533  22235678776665544

>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=94.32  E-value=0.0072  Score=47.15  Aligned_cols=18  Identities=33%  Similarity=0.259  Sum_probs=16.9

Q ss_pred             ccccCCcchHHHHHHHhc
Q 043781          127 VRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~  144 (297)
                      |+|++|+||||+|+.+.+
T Consensus         8 l~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           8 LLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             EECCTTSSHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHH
Confidence            679999999999999987

>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=94.31  E-value=0.0071  Score=46.56  Aligned_cols=20  Identities=30%  Similarity=0.378  Sum_probs=17.4

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|++|+||||+++.+...
T Consensus         5 vi~G~~GsGKTT~~~~La~~   24 (194)
T d1nksa_           5 IVTGIPGVGKSTVLAKVKEI   24 (194)
T ss_dssp             EEEECTTSCHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            46799999999999999873

>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=94.27  E-value=0.06  Score=39.12  Aligned_cols=46  Identities=15%  Similarity=0.151  Sum_probs=28.6

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHHHhh
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAIIEGL  177 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~~~~  177 (297)
                      -|+++.|.|||+++-.++..      ...++.+.+....-..+..+.+.+.+
T Consensus        12 ll~apTGsGKT~~~~~~~~~------~~~~vli~~P~~~l~~q~~~~~~~~~   57 (136)
T d1a1va1          12 HLHAPTGSGKSTKVPAAYAA------QGYKVLVLNPSVAATLGFGAYMSKAH   57 (136)
T ss_dssp             EEECCTTSCTTTHHHHHHHT------TTCCEEEEESCHHHHHHHHHHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHHHHH------cCCcEEEEcChHHHHHHHHHHHHHHh
Confidence            36789999999998665542      23456666655444455555554444

>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=94.22  E-value=0.0079  Score=50.58  Aligned_cols=68  Identities=18%  Similarity=0.093  Sum_probs=40.8

Q ss_pred             ccccccCCcchHHHHHHHhcccccccCCCceEEE-----------------------EeCCCCCHH-----HHHHHHHHh
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWV-----------------------CVSDPFDEF-----RIAKAIIEG  176 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv-----------------------~vs~~~~~~-----~~~~~i~~~  176 (297)
                      ..|+|..|+|||+|+..+.++.. .++-++++.+                       ..+..+...     ...-.+++.
T Consensus        46 ~~I~g~~g~GKT~l~~~i~~~~~-~~~~~~v~~~~~iger~~ev~~~~~~~~~~vv~~t~d~~~~~r~~~~~~a~~iAEy  124 (289)
T d1xpua3          46 GLIVAPPKAGKTMLLQNIAQSIA-YNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKR  124 (289)
T ss_dssp             EEEEECSSSSHHHHHHHHHHHHH-HHCTTSEEEEEEEEECHHHHHHHHHHCSSEEEEEETTSCHHHHHHHHHHHHHHHHH
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEEEeeceeHHHHHhHHhhcceEEEeccCCCchhHHHHHHHHHHHHHHH
Confidence            46899999999999988887532 1222333322                       222222111     222334444


Q ss_pred             hcCCCceEEEEEeCCCC
Q 043781          177 LEGSEKKFFLILDDVWT  193 (297)
Q Consensus       177 ~~~~~kr~LiVlDdv~~  193 (297)
                      +...++..|+++||+-.
T Consensus       125 frd~G~dVLli~Dsltr  141 (289)
T d1xpua3         125 LVEHKKDVIILLDSITR  141 (289)
T ss_dssp             HHTTTCEEEEEESCHHH
T ss_pred             HHHhccCceeecCcHHH
Confidence            44449999999999943

>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=94.12  E-value=0.0082  Score=46.32  Aligned_cols=20  Identities=35%  Similarity=0.303  Sum_probs=17.8

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|++|+||||+|+.+.+.
T Consensus         4 ~i~G~pGSGKsT~~~~La~~   23 (179)
T d1e4va1           4 ILLGAPVAGKGTQAQFIMEK   23 (179)
T ss_dssp             EEEESTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999874

>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=94.12  E-value=0.01  Score=49.03  Aligned_cols=20  Identities=35%  Similarity=0.439  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..|+|..|+|||||++.+..
T Consensus        47 vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          47 VAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             EEEECSTTSSHHHHHTTTTT
T ss_pred             EEEECCCCCcHHHHHHHHHh
Confidence            47999999999999999875

>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=94.12  E-value=0.0077  Score=47.80  Aligned_cols=22  Identities=32%  Similarity=0.416  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|.|++|+||||+|+.+.++
T Consensus         5 iI~I~GppGSGKgT~ak~La~~   26 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEA   26 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4567799999999999999984

>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=94.07  E-value=0.08  Score=43.12  Aligned_cols=20  Identities=25%  Similarity=0.415  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|.|..|+|||++|+.+.+.
T Consensus        27 lI~Ge~GtGK~~~A~~ih~~   46 (247)
T d1ny5a2          27 LITGESGVGKEVVARLIHKL   46 (247)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCcCHHHHHHHHHHh
Confidence            47899999999999999873

>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=94.05  E-value=0.012  Score=47.70  Aligned_cols=53  Identities=15%  Similarity=0.099  Sum_probs=32.0

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      .+.=+|+||.=-.. |...-..+...+.+...        ..|..||++|++.+.+..+|..
T Consensus       144 ~~P~iLllDEPts~LD~~~~~~i~~~l~~l~~--------~~g~tii~vtHd~~~~~~~~dr  197 (229)
T d3d31a2         144 TNPKILLLDEPLSALDPRTQENAREMLSVLHK--------KNKLTVLHITHDQTEARIMADR  197 (229)
T ss_dssp             SCCSEEEEESSSTTSCHHHHHHHHHHHHHHHH--------HTTCEEEEEESCHHHHHHHCSE
T ss_pred             ccCCceeecCCCcCCCHHHHHHHHHHHHHHHh--------cCCcEEEEEcCCHHHHHHhCCE
Confidence            77788899986553 22122234444433211        4577899999987767776643

>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=94.03  E-value=0.058  Score=43.20  Aligned_cols=43  Identities=26%  Similarity=0.237  Sum_probs=28.5

Q ss_pred             ccccccCCcchHHHHHHHhcccccc----cCCCceEEEEeCCCCCHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVI----ENFDKRIWVCVSDPFDEF  167 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~----~~F~~~~wv~vs~~~~~~  167 (297)
                      .-|+|.+|+||||++.++..+....    ......+|+......+..
T Consensus        39 ~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (254)
T d1pzna2          39 TEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPE   85 (254)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHH
Confidence            4588999999999998776542211    123456777766665543

>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=94.00  E-value=0.15  Score=40.47  Aligned_cols=54  Identities=19%  Similarity=0.135  Sum_probs=34.0

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHH--HHHHHHHHhhcCC
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEF--RIAKAIIEGLEGS  180 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~--~~~~~i~~~~~~~  180 (297)
                      ++.++|+.|+||||.+-++...  .+ .....+.+-..+.+...  +=++...+.++.+
T Consensus        11 vi~lvGptGvGKTTTiAKLA~~--~~-~~g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~   66 (211)
T d2qy9a2          11 VILMVGVNGVGKTTTIGKLARQ--FE-QQGKSVMLAAGDTFRAAAVEQLQVWGQRNNIP   66 (211)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHH--HH-TTTCCEEEECCCTTCHHHHHHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHHHH--HH-HCCCcEEEEecccccccchhhhhhhhhhcCCc
Confidence            4567899999999988666663  32 23456777666777653  3344455555443

>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=93.67  E-value=0.011  Score=47.17  Aligned_cols=20  Identities=30%  Similarity=0.255  Sum_probs=17.2

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-+.|++|+||||||+.+..
T Consensus        27 IwltGlsGsGKTTia~~L~~   46 (208)
T d1m7ga_          27 IWLTGLSASGKSTLAVELEH   46 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34669999999999999886

>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=93.58  E-value=0.012  Score=46.79  Aligned_cols=21  Identities=19%  Similarity=0.139  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ++|.|..|+||||||+.+.+.
T Consensus         5 IgI~G~~gSGKSTla~~L~~~   25 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQL   25 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            578899999999999988763

>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=93.50  E-value=0.012  Score=45.96  Aligned_cols=21  Identities=29%  Similarity=0.148  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|.|++|+||||+|+.+.+.
T Consensus        11 I~l~G~pGSGKsT~a~~La~~   31 (194)
T d3adka_          11 IFVVGGPGSGKGTQCEKIVQK   31 (194)
T ss_dssp             EEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457899999999999999883

>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=93.33  E-value=0.12  Score=41.00  Aligned_cols=22  Identities=32%  Similarity=0.156  Sum_probs=17.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..-++|+.|+||||.+-++...
T Consensus        12 vi~lvGp~GvGKTTTiaKLA~~   33 (207)
T d1ls1a2          12 LWFLVGLQGSGKTTTAAKLALY   33 (207)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3457899999999887666653

>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=93.28  E-value=0.084  Score=41.77  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=18.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..-|.|.+|+|||+++..+..+
T Consensus        36 l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          36 VTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            3458899999999999888764

>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=93.27  E-value=0.014  Score=45.49  Aligned_cols=21  Identities=29%  Similarity=0.425  Sum_probs=17.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+||||+|+.+-+
T Consensus         5 IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           5 IIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            357889999999999998754

>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=93.11  E-value=0.051  Score=46.97  Aligned_cols=49  Identities=20%  Similarity=0.201  Sum_probs=28.2

Q ss_pred             ccccccCCcchHHHHHHHhccc-ccccCCCceEEEEeCCCCCHHHHHHHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK-DVIENFDKRIWVCVSDPFDEFRIAKAI  173 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~-~~~~~F~~~~wv~vs~~~~~~~~~~~i  173 (297)
                      .-|.|.+|.||||++..+...- +....-..++.++.+..--...+.+.+
T Consensus       166 ~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApTgkAA~~L~e~~  215 (359)
T d1w36d1         166 SVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPTGKAAARLTESL  215 (359)
T ss_dssp             EEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCcHHHHHHHHHHH
Confidence            3477999999999885544310 111222356777766554444444443

>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=92.98  E-value=0.12  Score=43.90  Aligned_cols=71  Identities=14%  Similarity=0.127  Sum_probs=44.6

Q ss_pred             ccccCCcchHHHHHHHhccc----c---cccCC-------CceEEEEeCCCCCHHHHHHHHHHhhcCCCceEEEEEeCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDK----D---VIENF-------DKRIWVCVSDPFDEFRIAKAIIEGLEGSEKKFFLILDDVW  192 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~----~---~~~~F-------~~~~wv~vs~~~~~~~~~~~i~~~~~~~~kr~LiVlDdv~  192 (297)
                      |.|..|+||||+.+.+...-    +   +.+.+       ...+-+......+..++++..+++     ..=.||+..+.
T Consensus       171 i~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~l~~~~~~~~~~~~~~~~~~~ll~~~lR~-----~pd~iivgEiR  245 (323)
T d1g6oa_         171 VCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRM-----RPDRIILGELR  245 (323)
T ss_dssp             EEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTS-----CCSEEEESCCC
T ss_pred             EEeeccccchHHHHHHhhhcccccceeeccchhhhhcccccccceeccccchhHHHHHHHHhcc-----CCCcccCCccC
Confidence            66999999999999988741    0   01111       112222334456777777776654     33458899998


Q ss_pred             CCCccCHHHHHH
Q 043781          193 TDDYSKWEPFHN  204 (297)
Q Consensus       193 ~~~~~~w~~l~~  204 (297)
                      ..  +.|+.++.
T Consensus       246 ~~--ea~~~l~a  255 (323)
T d1g6oa_         246 SS--EAYDFYNV  255 (323)
T ss_dssp             ST--HHHHHHHH
T ss_pred             ch--hHHHHHHH
Confidence            77  57776643

>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=92.94  E-value=0.017  Score=45.92  Aligned_cols=20  Identities=30%  Similarity=0.481  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|-|++|+||||+|+.+..+
T Consensus         7 aIdGp~GsGKgT~ak~La~~   26 (223)
T d1q3ta_           7 AIDGPASSGKSTVAKIIAKD   26 (223)
T ss_dssp             EEECSSCSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            45599999999999999984

>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=92.94  E-value=0.26  Score=38.82  Aligned_cols=54  Identities=19%  Similarity=-0.028  Sum_probs=29.2

Q ss_pred             cccccccCCcchHHHHHHHhcccccccCCCceEEEEeC-CCCCHHHHHHHHHHhhcC
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVS-DPFDEFRIAKAIIEGLEG  179 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs-~~~~~~~~~~~i~~~~~~  179 (297)
                      .+-++|+.|+||||.+-++..... +.. ..+..++.- ......+=++...+.++.
T Consensus         8 vi~lvGptGvGKTTTiaKLA~~~~-~~g-~kV~lit~Dt~R~gA~eQL~~~a~~l~i   62 (207)
T d1okkd2           8 VVLVVGVNGVGKTTTIAKLGRYYQ-NLG-KKVMFCAGDTFRAAGGTQLSEWGKRLSI   62 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH-TTT-CCEEEECCCCSSTTHHHHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH-HCC-CcEEEEEeccccccchhhHhhcccccCc
Confidence            345789999999998866666422 222 234444432 123334444444444443

>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=92.81  E-value=0.019  Score=44.97  Aligned_cols=20  Identities=30%  Similarity=0.459  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|+|+.|+|||||++.+..
T Consensus         3 Ivl~GPsGsGK~tl~~~L~~   22 (190)
T d1lvga_           3 VVLSGPSGAGKSTLLKKLFQ   22 (190)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            34789999999999999877

>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=92.72  E-value=0.057  Score=45.06  Aligned_cols=21  Identities=24%  Similarity=0.158  Sum_probs=17.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..|+|..|+|||+|+..+..+
T Consensus        71 ~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          71 ELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             CEEEESTTSSHHHHHHHHHHH
T ss_pred             EEeecCCCCChHHHHHHHHHh
Confidence            368899999999998766543

>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=92.72  E-value=0.019  Score=42.65  Aligned_cols=21  Identities=24%  Similarity=0.180  Sum_probs=18.1

Q ss_pred             cccccCCcchHHHHHHHhccc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      -++|.+|+|||||...+..++
T Consensus         4 vlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           4 LMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEECSTTSSHHHHHHHHHHHC
T ss_pred             EEECCCCCCHHHHHHHHhcCC
Confidence            478999999999999887653

>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=92.67  E-value=0.029  Score=44.38  Aligned_cols=22  Identities=41%  Similarity=0.492  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|+.|+|||||.+.+..-
T Consensus        29 i~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          29 VVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCChHHHHHHHHhcc
Confidence            3478999999999999999873

>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=92.60  E-value=0.021  Score=44.46  Aligned_cols=20  Identities=30%  Similarity=0.454  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|+|+.|+|||||++.+.+
T Consensus         4 Ivl~GpsG~GK~tl~~~L~~   23 (186)
T d1gkya_           4 IVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35789999999999999877

>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=92.30  E-value=0.019  Score=44.05  Aligned_cols=22  Identities=18%  Similarity=0.167  Sum_probs=19.4

Q ss_pred             ccccccccCCcchHHHHHHHhc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+++|+|.+|+|||||...+.+
T Consensus         2 ~~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           2 ADVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             CSEEEECCGGGCHHHHHHHHCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4578999999999999999875

>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=92.10  E-value=0.026  Score=43.54  Aligned_cols=20  Identities=20%  Similarity=0.350  Sum_probs=17.5

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -|+|+.|+|||||++.+.+.
T Consensus         6 vl~GpsG~GK~tl~~~L~~~   25 (182)
T d1znwa1           6 VLSGPSAVGKSTVVRCLRER   25 (182)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHhh
Confidence            47899999999999998763

>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=92.07  E-value=0.02  Score=44.51  Aligned_cols=21  Identities=29%  Similarity=0.167  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|-|..|+||||+++.+.+.
T Consensus        12 I~ieG~~GsGKTTl~~~L~~~   32 (197)
T d2vp4a1          12 VLIEGNIGSGKTTYLNHFEKY   32 (197)
T ss_dssp             EEEECSTTSCHHHHHHTTGGG
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457799999999999998873

>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=92.06  E-value=0.21  Score=39.55  Aligned_cols=43  Identities=19%  Similarity=0.122  Sum_probs=28.4

Q ss_pred             cccccccCCcchHHHHHHHhcccc----cccCCCceEEEEeCCCCCH
Q 043781          124 VSDVRGMGGIGKTTLAQFAYNDKD----VIENFDKRIWVCVSDPFDE  166 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~~~----~~~~F~~~~wv~vs~~~~~  166 (297)
                      ...|+|.+|+|||++|.++..+..    ....+....|+.....+..
T Consensus        39 ~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (258)
T d1v5wa_          39 ITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRP   85 (258)
T ss_dssp             EEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHH
Confidence            346889999999999988765321    1223455667766655543

>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=92.01  E-value=0.028  Score=41.90  Aligned_cols=22  Identities=27%  Similarity=0.276  Sum_probs=19.0

Q ss_pred             ccccccCCcchHHHHHHHhccc
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      +.|+|.+|+|||||.+.+.+++
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            4589999999999999887764

>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=91.92  E-value=0.34  Score=39.30  Aligned_cols=46  Identities=17%  Similarity=0.039  Sum_probs=26.9

Q ss_pred             cccccCCcchHHHHHHHhcccccccCCCceEEEEeCCCCCHHHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSDPFDEFRIAKAII  174 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~~~~~~~~~~~i~  174 (297)
                      -|.|.+|+|||+++..+..+......+ .+++++.  ..+..++...++
T Consensus        39 vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s~--E~~~~~~~~r~~   84 (277)
T d1cr2a_          39 MVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAML--EESVEETAEDLI   84 (277)
T ss_dssp             EEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEES--SSCHHHHHHHHH
T ss_pred             EEEeCCCCCHHHHHHHHHHhhhhhccc-ceeEeee--ccchhhHHhHHH
Confidence            466999999999998877642223333 2344443  334454444444

>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=91.88  E-value=0.022  Score=43.85  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=20.1

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+++|+|.+++|||||...+.+.
T Consensus         2 ~~VaiiG~~nvGKSSLin~L~~~   24 (185)
T d1lnza2           2 ADVGLVGFPSVGKSTLLSVVSSA   24 (185)
T ss_dssp             CCEEEESSTTSSHHHHHHHSEEE
T ss_pred             CeEEEECCCCCCHHHHHHHHhCC
Confidence            46789999999999999998653

>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=91.78  E-value=0.029  Score=46.04  Aligned_cols=22  Identities=36%  Similarity=0.478  Sum_probs=18.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|-||+||||+|-.+..-
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~   24 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSG   24 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHHHH
Confidence            4568899999999999777663

>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=91.75  E-value=0.041  Score=45.14  Aligned_cols=20  Identities=35%  Similarity=0.519  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+|+|..|+|||||++.+..
T Consensus        43 vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          43 TALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCcHHHHHHHHhc
Confidence            57999999999999999987

>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=91.71  E-value=0.028  Score=45.80  Aligned_cols=53  Identities=9%  Similarity=0.033  Sum_probs=32.1

Q ss_pred             CceEEEEEeCCCCC-CccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHHHHHHHHh
Q 043781          181 EKKFFLILDDVWTD-DYSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEKLRHLTLT  241 (297)
Q Consensus       181 ~kr~LiVlDdv~~~-~~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~~~~v~~~  241 (297)
                      .+.-+|++|.=-.. |...-..+...+.+..        ...|..||++|++.+.+..+|..
T Consensus       157 ~~P~lLllDEPt~~LD~~~~~~i~~~l~~l~--------~~~g~tvi~vTHdl~~~~~~~dr  210 (240)
T d3dhwc1         157 SNPKVLLCDEATSALDPATTRSILELLKDIN--------RRLGLTILLITHEMDVVKRICDC  210 (240)
T ss_dssp             TCCSEEEEESGGGSSCHHHHHHHHHHHHHHH--------HHHCCEEEEEBSCHHHHHHHCSE
T ss_pred             cCCCeEEeccccccCCHHHhhHHHHHHHHHH--------hccCCEEEEEcCCHHHHHHhCCE
Confidence            78889999976543 2222223444443321        13478899999987777776643

>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=91.62  E-value=0.03  Score=44.80  Aligned_cols=21  Identities=33%  Similarity=0.180  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|.|+.|+|||||...+.++
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~   23 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRY   23 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEcCCCCcHHHHHHHHHHH
Confidence            468899999999999888753

>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=91.61  E-value=0.23  Score=39.35  Aligned_cols=22  Identities=36%  Similarity=0.273  Sum_probs=17.1

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|+.|+||||.+-+++..
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~   34 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKM   34 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4567899999999977666653

>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=91.23  E-value=0.038  Score=41.49  Aligned_cols=21  Identities=29%  Similarity=0.183  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|+..+.++
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            347899999999999888765

>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=91.21  E-value=0.034  Score=45.73  Aligned_cols=20  Identities=30%  Similarity=0.458  Sum_probs=18.4

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+|+|..|+|||||++.+..
T Consensus        44 iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          44 VALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             EEEEECTTSSHHHHHHHHTT
T ss_pred             EEEECCCCChHHHHHHHHhc
Confidence            57999999999999999976

>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=91.12  E-value=0.36  Score=38.08  Aligned_cols=23  Identities=30%  Similarity=0.156  Sum_probs=13.3

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++.++|+.|+||||.+-++...
T Consensus        13 ~vi~lvGptGvGKTTTiAKLA~~   35 (211)
T d1j8yf2          13 YVIMLVGVQGTGKATTAGKLAYF   35 (211)
T ss_dssp             EEEEEECSCCC----HHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            34567899999999877555553

>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=91.06  E-value=0.036  Score=45.21  Aligned_cols=21  Identities=24%  Similarity=0.320  Sum_probs=18.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ..+|+|+.|+|||||++.+..
T Consensus        30 ~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          30 IIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999976

>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=91.04  E-value=0.048  Score=41.00  Aligned_cols=20  Identities=30%  Similarity=0.428  Sum_probs=17.2

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||||+..+.++
T Consensus         6 ~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           6 VVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEECSTTSSHHHHHHHHHHC
T ss_pred             EEECCCCcCHHHHHHHHHhC
Confidence            47899999999999877764

>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=91.04  E-value=0.036  Score=42.95  Aligned_cols=43  Identities=14%  Similarity=0.112  Sum_probs=26.4

Q ss_pred             ccccccCCcchHHHHHHHhcccccccC----CCceEEEEeCCCCCHH
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKDVIEN----FDKRIWVCVSDPFDEF  167 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~~~~~----F~~~~wv~vs~~~~~~  167 (297)
                      ..|.|.+|+|||+|+.++..+......    +....++.........
T Consensus        26 ~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~   72 (242)
T d1n0wa_          26 TEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPE   72 (242)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHH
Confidence            458899999999999887764322221    2334455544444433

>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=90.85  E-value=0.04  Score=45.98  Aligned_cols=21  Identities=29%  Similarity=0.466  Sum_probs=18.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+|+|+.|+|||||++.+..-
T Consensus        65 vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          65 LAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCChHHHHHHHHhCC
Confidence            579999999999999999874

>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=90.75  E-value=0.041  Score=42.98  Aligned_cols=19  Identities=32%  Similarity=0.513  Sum_probs=16.9

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      .|-|+.|+||||+++.+.+
T Consensus         4 ~ieG~dGsGKST~~~~L~~   22 (208)
T d1gsia_           4 AIEGVDGAGKRTLVEKLSG   22 (208)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4669999999999999887

>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=90.73  E-value=0.046  Score=41.59  Aligned_cols=22  Identities=23%  Similarity=0.205  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-++|.+|+|||+|+..+.++
T Consensus         5 KivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           5 KYIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3458899999999999987765

>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=90.54  E-value=0.043  Score=43.51  Aligned_cols=20  Identities=20%  Similarity=0.262  Sum_probs=17.1

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|-|+.|+||||+++.+.+.
T Consensus         7 ~ieG~dGsGKsT~~~~L~~~   26 (209)
T d1nn5a_           7 VLEGVDRAGKSTQSRKLVEA   26 (209)
T ss_dssp             EEEESTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHH
Confidence            35599999999999999883

>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=90.50  E-value=0.045  Score=42.24  Aligned_cols=20  Identities=15%  Similarity=0.286  Sum_probs=17.6

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      +-|+|+.|+|||||++.+..
T Consensus         6 ivl~Gpsg~GK~tl~~~L~~   25 (178)
T d1kgda_           6 LVLLGAHGVGRRHIKNTLIT   25 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45789999999999998886

>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=90.49  E-value=0.049  Score=40.84  Aligned_cols=20  Identities=25%  Similarity=0.310  Sum_probs=17.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||||...+.++
T Consensus         6 ~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           6 LMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEECSTTSSHHHHHHHHTTC
T ss_pred             EEECCCCCCHHHHHHHHcCC
Confidence            48899999999999998764

>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=90.25  E-value=0.053  Score=41.00  Aligned_cols=21  Identities=24%  Similarity=0.232  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||||...+.++
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            458899999999999987664

>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=90.10  E-value=0.05  Score=41.16  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus        16 I~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          16 LVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             EEEEEETTSSHHHHHHHHSCC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999888765

>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=90.09  E-value=0.059  Score=41.36  Aligned_cols=21  Identities=29%  Similarity=0.264  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||||+..+.++
T Consensus         8 i~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            458899999999999888764

>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=90.07  E-value=0.052  Score=46.32  Aligned_cols=23  Identities=26%  Similarity=0.166  Sum_probs=19.4

Q ss_pred             cccccccccCCcchHHHHHHHhc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...++|.|.+|+|||||...+..
T Consensus        54 ~~~IgitG~pGaGKSTLi~~l~~   76 (327)
T d2p67a1          54 TLRLGVTGTPGAGKSTFLEAFGM   76 (327)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHHH
T ss_pred             ceEEEeeCCCCCCHHHHHHHHHH
Confidence            44578999999999999987764

>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=90.02  E-value=0.056  Score=40.93  Aligned_cols=21  Identities=29%  Similarity=0.321  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|.+.+.++
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458899999999999988764

>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=89.98  E-value=0.077  Score=40.99  Aligned_cols=23  Identities=17%  Similarity=0.271  Sum_probs=20.1

Q ss_pred             ccccccccCCcchHHHHHHHhcc
Q 043781          123 NVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       123 ~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+.|+|.+|+|||||...+.+.
T Consensus        24 ~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          24 PEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHhcCC
Confidence            45789999999999999999863

>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=89.96  E-value=0.058  Score=40.80  Aligned_cols=21  Identities=24%  Similarity=0.237  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||.+.+...
T Consensus         3 V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           3 VLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999988764

>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=89.95  E-value=0.072  Score=40.17  Aligned_cols=21  Identities=33%  Similarity=0.488  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            357899999999999887765

>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=89.94  E-value=0.053  Score=46.94  Aligned_cols=21  Identities=33%  Similarity=0.127  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-++|++|+|||++|+.+.+.
T Consensus       157 ~~~~g~~~~gk~~~~~~~~~~  177 (362)
T d1svma_         157 WLFKGPIDSGKTTLAAALLEL  177 (362)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            347899999999999999983

>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=89.89  E-value=0.035  Score=44.37  Aligned_cols=21  Identities=19%  Similarity=0.205  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|-|+.|+||||+++.+.+.
T Consensus         5 I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           5 ISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             EEEECSTTSSHHHHHTTTGGG
T ss_pred             EEEECCCCCCHHHHHHHHHHH
Confidence            457799999999999998874

>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=89.88  E-value=0.054  Score=41.02  Aligned_cols=21  Identities=29%  Similarity=0.313  Sum_probs=18.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||||...+...
T Consensus        19 I~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          19 ILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            568999999999999988775

>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=89.88  E-value=0.06  Score=40.53  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|+..+.++
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458899999999999887764

>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=89.80  E-value=0.06  Score=40.34  Aligned_cols=20  Identities=30%  Similarity=0.280  Sum_probs=17.4

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||+|+..+.++
T Consensus         4 ~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           4 VFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEESTTSSHHHHHHHHHHS
T ss_pred             EEECCCCcCHHHHHHHHHhC
Confidence            47899999999999987764

>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=89.77  E-value=0.056  Score=42.66  Aligned_cols=21  Identities=29%  Similarity=0.333  Sum_probs=17.9

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|+.|+||||+++.+-.
T Consensus         5 iIgitG~igSGKStv~~~l~~   25 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFAD   25 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHHH
Confidence            468999999999999987643

>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=89.73  E-value=0.57  Score=37.47  Aligned_cols=98  Identities=12%  Similarity=0.002  Sum_probs=52.2

Q ss_pred             cccccCCcchHHHHHHHhcccc-------------cccCCCceEEEEeCCCCCHH----------HHHHHHHHhhcCCCc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKD-------------VIENFDKRIWVCVSDPFDEF----------RIAKAIIEGLEGSEK  182 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~-------------~~~~F~~~~wv~vs~~~~~~----------~~~~~i~~~~~~~~k  182 (297)
                      -|.|+...||||+.+.+.-..-             .-..||.+ +..+...-++.          .-+..|++..   .+
T Consensus        45 iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I-~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~---~~  120 (234)
T d1wb9a2          45 IITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRI-FTRVGAADDLASGRSTFMVEMTETANILHNA---TE  120 (234)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEE-EEEEC-----------CHHHHHHHHHHHHHC---CT
T ss_pred             EEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhh-eeEEccCcccccchhHHHHHHHHHHHHHHhc---cc
Confidence            3679999999999998876411             11234433 33332222211          1233455444   57


Q ss_pred             eEEEEEeCCCCCC-ccCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHHH
Q 043781          183 KFFLILDDVWTDD-YSKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQEK  234 (297)
Q Consensus       183 r~LiVlDdv~~~~-~~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~~  234 (297)
                      +.|+++|.+-..- ..+=..+-..+-..+.       ...++.+++||+..+.
T Consensus       121 ~sLvliDE~~~gT~~~eg~~l~~a~l~~l~-------~~~~~~~i~tTH~~~l  166 (234)
T d1wb9a2         121 YSLVLMDEIGRGTSTYDGLSLAWACAENLA-------NKIKALTLFATHYFEL  166 (234)
T ss_dssp             TEEEEEESCCCCSSSSHHHHHHHHHHHHHH-------HTTCCEEEEECSCGGG
T ss_pred             ccEEeecccccCCChhhhhHHHHHhhhhhh-------ccccceEEEecchHHH
Confidence            8999999998752 1111122222211111       1566789999986554

>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=89.68  E-value=0.065  Score=40.44  Aligned_cols=21  Identities=24%  Similarity=0.213  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||||...+..+
T Consensus        18 I~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          18 VIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            348899999999999887765

>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=89.56  E-value=0.063  Score=40.86  Aligned_cols=21  Identities=24%  Similarity=0.202  Sum_probs=18.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         3 I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           3 IIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999998864

>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=89.56  E-value=0.075  Score=40.18  Aligned_cols=21  Identities=38%  Similarity=0.479  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.++
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            358899999999999887654

>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=89.55  E-value=0.065  Score=40.34  Aligned_cols=21  Identities=29%  Similarity=0.343  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|+..+.++
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            357899999999999987764

>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=89.54  E-value=0.069  Score=40.35  Aligned_cols=21  Identities=29%  Similarity=0.328  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            347899999999999988764

>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=89.54  E-value=0.061  Score=44.56  Aligned_cols=21  Identities=38%  Similarity=0.510  Sum_probs=16.8

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+.|.|-||+||||+|-.+..
T Consensus         4 ~IaisgKGGVGKTT~a~NLA~   24 (289)
T d2afhe1           4 QCAIYGKGGIGKSTTTQNLVA   24 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            345789999999998877655

>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=89.54  E-value=0.076  Score=39.95  Aligned_cols=21  Identities=24%  Similarity=0.300  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            347899999999999888765

>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=89.51  E-value=0.06  Score=44.17  Aligned_cols=22  Identities=32%  Similarity=0.335  Sum_probs=19.5

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..+|+|+.|.|||||++.+..-
T Consensus        32 i~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          32 VTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTS
T ss_pred             EEEEECCCCCcHHHHHHHHHCC
Confidence            3478999999999999999984

>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=89.49  E-value=0.12  Score=40.89  Aligned_cols=19  Identities=32%  Similarity=0.531  Sum_probs=16.8

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      .|=|+.|+||||+++.+.+
T Consensus         7 ~iEG~DGsGKST~~~~L~~   25 (214)
T d1tmka_           7 LIEGLDRTGKTTQCNILYK   25 (214)
T ss_dssp             EEEESTTSSHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHH
Confidence            3559999999999999987

>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=89.48  E-value=0.42  Score=38.04  Aligned_cols=97  Identities=14%  Similarity=0.091  Sum_probs=53.2

Q ss_pred             ccccccCCcchHHHHHHHhcccc-------------cccCCCceEEEEeCCCCCHH----------HHHHHHHHhhcCCC
Q 043781          125 SDVRGMGGIGKTTLAQFAYNDKD-------------VIENFDKRIWVCVSDPFDEF----------RIAKAIIEGLEGSE  181 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~~~-------------~~~~F~~~~wv~vs~~~~~~----------~~~~~i~~~~~~~~  181 (297)
                      .-|.|+...||||+.+.+.-..-             .-..|+. ++..+...-++.          .-++.|++..   +
T Consensus        38 ~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~-I~~~~~~~d~~~~~~StF~~el~~~~~il~~~---~  113 (224)
T d1ewqa2          38 VLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDG-IYTRIGASDDLAGGKSTFMVEMEEVALILKEA---T  113 (224)
T ss_dssp             EEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSE-EEEECCC------CCSHHHHHHHHHHHHHHHC---C
T ss_pred             EEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecce-EEEEECCCccccCCccHHHHhHHHHHHHhccC---C
Confidence            34779999999999988765311             1124443 344333322211          2234455544   5


Q ss_pred             ceEEEEEeCCCCCCc-cCHHHHHHHHhhhhhhhceeeecCCCCeEEEEeccHH
Q 043781          182 KKFFLILDDVWTDDY-SKWEPFHNCLMRVLQEFAAIEVDGDENPLSLTSTCQE  233 (297)
Q Consensus       182 kr~LiVlDdv~~~~~-~~w~~l~~~l~~~~~~~~~~~~~~~gs~iiiTTr~~~  233 (297)
                      ++.|+++|.+-..-. .+=..+...+-..+.        ..++.+++||+..+
T Consensus       114 ~~sLvliDE~~~gT~~~eg~ala~aile~L~--------~~~~~~i~tTH~~e  158 (224)
T d1ewqa2         114 ENSLVLLDEVGRGTSSLDGVAIATAVAEALH--------ERRAYTLFATHYFE  158 (224)
T ss_dssp             TTEEEEEESTTTTSCHHHHHHHHHHHHHHHH--------HHTCEEEEECCCHH
T ss_pred             CCcEEeecccccCcchhhhcchHHHHHHHHh--------hcCcceEEeeechh
Confidence            789999999987521 111112222222221        45688999998544

>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=89.43  E-value=0.068  Score=40.20  Aligned_cols=21  Identities=33%  Similarity=0.452  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|-+|+|||+|...+.++
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            357899999999999888765

>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=89.29  E-value=0.066  Score=42.33  Aligned_cols=19  Identities=32%  Similarity=0.347  Sum_probs=17.0

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -|+|+.|+|||||.+.+..
T Consensus         6 vi~GPSG~GK~tl~~~L~~   24 (205)
T d1s96a_           6 IVSAPSGAGKSSLIQALLK   24 (205)
T ss_dssp             EEECCTTSCHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHh
Confidence            3789999999999998877

>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=89.28  E-value=0.069  Score=40.11  Aligned_cols=21  Identities=29%  Similarity=0.294  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            347899999999999988765

>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=89.24  E-value=0.061  Score=47.81  Aligned_cols=50  Identities=18%  Similarity=0.139  Sum_probs=30.0

Q ss_pred             cccccCCcchHHHHHHHhcccccccCC---CceEEEEe-CCCCCHHHHHHHHHHhh
Q 043781          126 DVRGMGGIGKTTLAQFAYNDKDVIENF---DKRIWVCV-SDPFDEFRIAKAIIEGL  177 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~~~~~~F---~~~~wv~v-s~~~~~~~~~~~i~~~~  177 (297)
                      =++|+.|+|||.||+.+..  .+.-.|   |+.-+..+ --.-++..+++.++...
T Consensus        53 LliGPTGvGKTlLAr~LAk--~l~VPFv~~daT~fTeaGYvG~DVesii~~L~~~a  106 (443)
T d1g41a_          53 LMIGPTGVGKTEIARRLAK--LANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSA  106 (443)
T ss_dssp             EEECCTTSSHHHHHHHHHH--HTTCCEEEEEGGGGC----CCCCTHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH--HhCCCEEEeecceeeecceeecchhHHHHHHHHHH
Confidence            3789999999999999998  344444   11111111 11236667776665443

>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=89.18  E-value=0.065  Score=42.86  Aligned_cols=20  Identities=20%  Similarity=0.411  Sum_probs=17.2

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .|=|+.|+||||+++.+.+.
T Consensus         6 viEG~~GsGKST~~~~L~~~   25 (241)
T d2ocpa1           6 SIEGNIAVGKSTFVKLLTKT   25 (241)
T ss_dssp             EEEECTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCcHHHHHHHHHHH
Confidence            35599999999999999874

>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=89.13  E-value=0.073  Score=40.17  Aligned_cols=21  Identities=19%  Similarity=0.205  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|+..+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            358899999999999887754

>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=89.12  E-value=0.072  Score=40.48  Aligned_cols=21  Identities=24%  Similarity=0.305  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||||+..+.++
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458899999999999887664

>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=89.11  E-value=0.074  Score=39.07  Aligned_cols=21  Identities=38%  Similarity=0.422  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            458999999999999887764

>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=89.07  E-value=0.073  Score=40.32  Aligned_cols=21  Identities=29%  Similarity=0.251  Sum_probs=17.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|+..+..+
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            568899999999999877654

>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=88.94  E-value=0.077  Score=40.14  Aligned_cols=22  Identities=23%  Similarity=0.305  Sum_probs=19.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3568999999999999999864

>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=88.93  E-value=0.18  Score=39.37  Aligned_cols=18  Identities=33%  Similarity=0.586  Sum_probs=16.2

Q ss_pred             ccccCCcchHHHHHHHhc
Q 043781          127 VRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~  144 (297)
                      |-|+.|+||||+++.+.+
T Consensus         7 iEG~dGsGKsT~~~~L~~   24 (210)
T d4tmka_           7 IEGLEGAGKTTARNVVVE   24 (210)
T ss_dssp             EEECTTSCHHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHHH
Confidence            459999999999999887

>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=88.82  E-value=0.092  Score=39.57  Aligned_cols=20  Identities=25%  Similarity=0.413  Sum_probs=17.6

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||+|...+.++
T Consensus         6 ~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           6 AIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEECCTTSSHHHHHHHHHHS
T ss_pred             EEECCCCCCHHHHHHHHHhC
Confidence            47899999999999888765

>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=88.82  E-value=0.069  Score=45.08  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|-|..|+||||+|+.+..
T Consensus        82 iIGIaG~sgSGKSTla~~L~~  102 (308)
T d1sq5a_          82 IISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEeCCCCCCCcHHHHHHHH
Confidence            467899999999999999876

>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=88.81  E-value=0.078  Score=40.23  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458999999999999887765

>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=88.75  E-value=0.085  Score=40.92  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=19.0

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.|+|.+|+|||||...+.+.
T Consensus         5 ~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           5 SIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999888765

>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=88.74  E-value=0.079  Score=40.01  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            458899999999999877664

>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=88.74  E-value=0.09  Score=40.72  Aligned_cols=21  Identities=29%  Similarity=0.308  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|.+|+|||||...+..+
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            458899999999999987765

>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=88.73  E-value=0.055  Score=45.89  Aligned_cols=26  Identities=8%  Similarity=-0.042  Sum_probs=20.2

Q ss_pred             EEEEEeCCCCCCccCHHHHHHHHhhh
Q 043781          184 FFLILDDVWTDDYSKWEPFHNCLMRV  209 (297)
Q Consensus       184 ~LiVlDdv~~~~~~~w~~l~~~l~~~  209 (297)
                      =++++|++........+.|..++.++
T Consensus       129 gvl~iDEi~~~~~~~~~aLl~~me~~  154 (333)
T d1g8pa_         129 GYLYIDECNLLEDHIVDLLLDVAQSG  154 (333)
T ss_dssp             EEEEETTGGGSCHHHHHHHHHHHHHS
T ss_pred             cEeecccHHHHHHHHHHHHhhhhcCC
Confidence            47788999987766777888888654

>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=88.71  E-value=0.083  Score=42.61  Aligned_cols=20  Identities=30%  Similarity=0.321  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .+|+|..|.|||||.+.+..
T Consensus        28 ~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          28 LHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             EECBCCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHhC
Confidence            47899999999999999887

>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=88.64  E-value=0.076  Score=41.72  Aligned_cols=21  Identities=33%  Similarity=0.444  Sum_probs=17.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+||||+|+.+-.
T Consensus         4 iIgITG~igSGKStv~~~l~~   24 (205)
T d1jjva_           4 IVGLTGGIGSGKTTIANLFTD   24 (205)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            368899999999999987743

>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=88.49  E-value=0.098  Score=39.24  Aligned_cols=21  Identities=19%  Similarity=0.291  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|.+|+|||+|...+.++
T Consensus         7 v~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           7 IAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458899999999999887664

>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=88.18  E-value=0.091  Score=39.95  Aligned_cols=22  Identities=23%  Similarity=0.267  Sum_probs=19.4

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+.++|.+|+|||||...+.+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4678999999999999998865

>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=88.14  E-value=0.11  Score=39.02  Aligned_cols=21  Identities=33%  Similarity=0.502  Sum_probs=18.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            457899999999999888765

>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=88.13  E-value=0.092  Score=39.88  Aligned_cols=21  Identities=33%  Similarity=0.347  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|.+|+|||+|...+.++
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            347899999999999887765

>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=88.11  E-value=0.077  Score=40.16  Aligned_cols=21  Identities=24%  Similarity=0.181  Sum_probs=18.2

Q ss_pred             cccccCCcchHHHHHHHhccc
Q 043781          126 DVRGMGGIGKTTLAQFAYNDK  146 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~~  146 (297)
                      -++|.+|+|||||...+.++.
T Consensus        16 vlvG~~~vGKTSli~rl~~~~   36 (173)
T d1e0sa_          16 LMLGLDAAGKTTILYKLKLGQ   36 (173)
T ss_dssp             EEEEETTSSHHHHHHHTTCCC
T ss_pred             EEECCCCCCHHHHHHHHhcCC
Confidence            478999999999999987653

>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=88.06  E-value=0.096  Score=39.44  Aligned_cols=20  Identities=15%  Similarity=0.268  Sum_probs=17.2

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||+|...+.++
T Consensus         7 ~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           7 VLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEECSTTSSHHHHHHHHHHS
T ss_pred             EEECCCCcCHHHHHHHHHhC
Confidence            47899999999999877664

>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=88.04  E-value=0.11  Score=38.95  Aligned_cols=21  Identities=33%  Similarity=0.438  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+..+
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            357899999999999887665

>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=87.96  E-value=0.086  Score=44.79  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=19.3

Q ss_pred             cccccccccCCcchHHHHHHHhc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      ...++|.|+||+|||||...+..
T Consensus        51 ~~~igitG~pGaGKSTli~~l~~   73 (323)
T d2qm8a1          51 AIRVGITGVPGVGKSTTIDALGS   73 (323)
T ss_dssp             SEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEeeeCCCCCCHHHHHHHHHH
Confidence            34578999999999999977765

>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=87.96  E-value=0.39  Score=37.40  Aligned_cols=18  Identities=39%  Similarity=0.305  Sum_probs=14.9

Q ss_pred             ccccCCcchHHHHHHHhc
Q 043781          127 VRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~  144 (297)
                      +++..|.|||.+|-.+..
T Consensus        90 l~~~tG~GKT~~a~~~~~  107 (206)
T d2fz4a1          90 IVLPTGSGKTHVAMAAIN  107 (206)
T ss_dssp             EEESSSTTHHHHHHHHHH
T ss_pred             EEeCCCCCceehHHhHHH
Confidence            567899999999877765

>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=87.91  E-value=0.098  Score=40.00  Aligned_cols=21  Identities=33%  Similarity=0.333  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|.+|+|||+|...+.++
T Consensus         8 ivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           8 CVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            458899999999999887765

>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=87.84  E-value=0.095  Score=39.98  Aligned_cols=20  Identities=25%  Similarity=0.197  Sum_probs=17.0

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|-+|+|||+|.+.+..+
T Consensus         6 vllG~~~vGKTsl~~r~~~~   25 (195)
T d1svsa1           6 LLLGAGESGKSTIVKQMKII   25 (195)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHhhC
Confidence            47899999999999887654

>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=87.77  E-value=0.096  Score=40.30  Aligned_cols=17  Identities=29%  Similarity=0.360  Sum_probs=15.3

Q ss_pred             cccccCCcchHHHHHHH
Q 043781          126 DVRGMGGIGKTTLAQFA  142 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v  142 (297)
                      -++|.+|+|||+|...+
T Consensus         6 vllG~~~vGKTsll~r~   22 (200)
T d1zcba2           6 LLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEECSTTSSHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHH
Confidence            47899999999999887

>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=87.75  E-value=0.091  Score=43.80  Aligned_cols=21  Identities=29%  Similarity=0.270  Sum_probs=17.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|-|..|+|||||+..+..
T Consensus        29 iIGi~G~qGSGKSTl~~~l~~   49 (286)
T d1odfa_          29 FIFFSGPQGSGKSFTSIQIYN   49 (286)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEeECCCCCCHHHHHHHHHH
Confidence            357889999999999988765

>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=87.57  E-value=0.11  Score=39.79  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            347899999999999887764

>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=87.55  E-value=0.081  Score=40.36  Aligned_cols=21  Identities=29%  Similarity=0.260  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||||...+...
T Consensus        20 I~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          20 ILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             EEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            348899999999999988665

>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=87.43  E-value=0.11  Score=38.86  Aligned_cols=20  Identities=25%  Similarity=0.303  Sum_probs=17.2

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .++|.+|+|||||...+..+
T Consensus         6 ~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           6 TLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEECSTTSSHHHHHHHHHHS
T ss_pred             EEECCCCCCHHHHHHHHHcC
Confidence            47899999999999877665

>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=87.42  E-value=1.7  Score=32.75  Aligned_cols=17  Identities=29%  Similarity=0.323  Sum_probs=12.6

Q ss_pred             ccccCCcchHHHHHHHh
Q 043781          127 VRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~  143 (297)
                      ++++.|.|||.++-.+.
T Consensus        28 v~~pTGsGKT~i~~~~~   44 (200)
T d1wp9a1          28 IVLPTGLGKTLIAMMIA   44 (200)
T ss_dssp             EECCTTSCHHHHHHHHH
T ss_pred             EEeCCCCcHHHHHHHHH
Confidence            66889999998654443

>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=87.34  E-value=0.11  Score=39.42  Aligned_cols=21  Identities=29%  Similarity=0.368  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458899999999999987664

>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=87.30  E-value=0.13  Score=38.70  Aligned_cols=22  Identities=32%  Similarity=0.421  Sum_probs=18.2

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-++|.+|+|||+|...+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3458899999999999887654

>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=87.29  E-value=0.11  Score=39.56  Aligned_cols=21  Identities=29%  Similarity=0.382  Sum_probs=18.6

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.|+|.+|+|||||...+.+.
T Consensus        11 V~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHHCC
Confidence            579999999999999888764

>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=87.26  E-value=0.15  Score=38.36  Aligned_cols=21  Identities=29%  Similarity=0.276  Sum_probs=17.9

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||+|+..+.+.
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            468899999999999877664

>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=87.21  E-value=0.13  Score=38.72  Aligned_cols=21  Identities=33%  Similarity=0.514  Sum_probs=18.0

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            347899999999999988765

>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=87.08  E-value=0.12  Score=39.09  Aligned_cols=19  Identities=37%  Similarity=0.485  Sum_probs=16.6

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -++|.+|+|||+|+..+..
T Consensus         7 ~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           7 VLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEECCTTSSHHHHHHHHHC
T ss_pred             EEECCCCcCHHHHHHHHHh
Confidence            4789999999999988765

>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=87.01  E-value=0.12  Score=39.70  Aligned_cols=22  Identities=41%  Similarity=0.389  Sum_probs=18.6

Q ss_pred             cccccccCCcchHHHHHHHhcc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .+-|+|.+|+|||+|...+.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            3568899999999999887765

>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=86.91  E-value=0.12  Score=40.24  Aligned_cols=21  Identities=24%  Similarity=0.101  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-|+|.+|+|||||...+...
T Consensus         3 V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           3 VLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            458899999999999888765

>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=86.91  E-value=0.11  Score=44.85  Aligned_cols=62  Identities=18%  Similarity=0.138  Sum_probs=34.1

Q ss_pred             ccccCCcchHHHHHHHhcccccccCCCceEEEEeCC-------CCCHHHHHHHHHHhhcCC---CceEEEEEeCCCC
Q 043781          127 VRGMGGIGKTTLAQFAYNDKDVIENFDKRIWVCVSD-------PFDEFRIAKAIIEGLEGS---EKKFFLILDDVWT  193 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~vs~-------~~~~~~~~~~i~~~~~~~---~kr~LiVlDdv~~  193 (297)
                      .+|+.|+|||.||+.+...  ....|   +-+.++.       ..++..++..++......   ...-++.||.+..
T Consensus        73 fiGPTGvGKTElAk~LA~~--~~~~~---ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK  144 (364)
T d1um8a_          73 LIGPTGSGKTLMAQTLAKH--LDIPI---AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDK  144 (364)
T ss_dssp             EECCTTSSHHHHHHHHHHH--TTCCE---EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGG
T ss_pred             eeCCCCccHHHHHHHHHhh--cccce---eehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhh
Confidence            6799999999999998763  22221   1222211       123334444444333222   3456778888866

>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=86.84  E-value=0.087  Score=39.81  Aligned_cols=24  Identities=17%  Similarity=0.064  Sum_probs=19.9

Q ss_pred             cccccccccCCcchHHHHHHHhcc
Q 043781          122 INVSDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       122 ~~~~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ...+.++|.+++|||||...+...
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            345789999999999999888653

>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=86.78  E-value=0.13  Score=38.77  Aligned_cols=21  Identities=29%  Similarity=0.441  Sum_probs=17.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|+..+.++
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            458899999999999777654

>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=86.72  E-value=0.08  Score=40.09  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=16.5

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            357899999999999887664

>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=86.69  E-value=0.12  Score=38.18  Aligned_cols=21  Identities=19%  Similarity=0.196  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
T Consensus         4 I~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            458899999999999888753

>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=86.41  E-value=0.15  Score=38.82  Aligned_cols=20  Identities=35%  Similarity=0.308  Sum_probs=17.3

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|..|+|||+|++.+.++
T Consensus         6 vliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           6 VVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEESTTSSHHHHHHHHHHS
T ss_pred             EEECCCCcCHHHHHHHHHhC
Confidence            47899999999999877765

>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=86.40  E-value=0.23  Score=40.52  Aligned_cols=19  Identities=32%  Similarity=0.448  Sum_probs=15.1

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -+.|-||+||||+|-.+..
T Consensus        12 ~~sGKGGVGKTTvaa~lA~   30 (296)
T d1ihua1          12 FFTGKGGVGKTSISCATAI   30 (296)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCcChHHHHHHHHHH
Confidence            4569999999997766655

>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=86.36  E-value=0.13  Score=40.35  Aligned_cols=19  Identities=32%  Similarity=0.359  Sum_probs=15.7

Q ss_pred             ccccccCCcchHHHHHHHh
Q 043781          125 SDVRGMGGIGKTTLAQFAY  143 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~  143 (297)
                      ..|+|.+|+|||+||..+.
T Consensus        29 ~~I~G~~G~GKT~la~~~~   47 (242)
T d1tf7a1          29 TLVSGTSGTGKTLFSIQFL   47 (242)
T ss_dssp             EEEEESTTSSHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHH
Confidence            3588999999999996644

>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=86.05  E-value=1.1  Score=34.20  Aligned_cols=15  Identities=33%  Similarity=0.202  Sum_probs=12.2

Q ss_pred             cccccCCcchHHHHH
Q 043781          126 DVRGMGGIGKTTLAQ  140 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~  140 (297)
                      -+.++.|.|||+.|.
T Consensus        44 il~apTGsGKT~~a~   58 (202)
T d2p6ra3          44 LLAMPTAAGKTLLAE   58 (202)
T ss_dssp             EEECSSHHHHHHHHH
T ss_pred             EEEcCCCCchhHHHH
Confidence            366899999999874

>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=85.89  E-value=0.14  Score=41.62  Aligned_cols=21  Identities=29%  Similarity=0.325  Sum_probs=17.1

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|+|.+|+|||||+..+.-.
T Consensus        32 ~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          32 GALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHH
Confidence            347899999999999777653

>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=85.67  E-value=0.11  Score=39.56  Aligned_cols=20  Identities=25%  Similarity=0.315  Sum_probs=17.1

Q ss_pred             ccccccCCcchHHHHHHHhc
Q 043781          125 SDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .-|+|..|+|||||...+.-
T Consensus        27 tvi~G~NGsGKStil~Ai~~   46 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVT   46 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            35789999999999988864

>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=85.58  E-value=0.14  Score=39.15  Aligned_cols=20  Identities=25%  Similarity=0.175  Sum_probs=16.9

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||+|...+..+
T Consensus         6 v~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           6 LLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEESTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHhCC
Confidence            46899999999999887654

>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=85.17  E-value=0.16  Score=40.57  Aligned_cols=21  Identities=29%  Similarity=0.360  Sum_probs=18.7

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+||||+|+.+.+
T Consensus         3 iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            468899999999999999866

>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=85.07  E-value=0.17  Score=38.54  Aligned_cols=21  Identities=24%  Similarity=0.205  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||+|...+.++
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            457899999999999877664

>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=84.99  E-value=0.16  Score=40.21  Aligned_cols=20  Identities=25%  Similarity=0.199  Sum_probs=16.7

Q ss_pred             cccccCCcchHHHHHHHhcc
Q 043781          126 DVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~~  145 (297)
                      -++|.+|+|||||.+.+...
T Consensus        10 lllG~~~vGKTsll~~~~~~   29 (221)
T d1azta2          10 LLLGAGESGKSTIVKQMRIL   29 (221)
T ss_dssp             EEECSTTSSHHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHhcC
Confidence            47899999999999887543

>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=84.88  E-value=0.17  Score=40.37  Aligned_cols=21  Identities=38%  Similarity=0.531  Sum_probs=17.8

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      .-|.|+-|.|||||.+.+.+.
T Consensus         6 ~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           6 TLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             EEEEESSSSSCHHHHHHHHHS
T ss_pred             EEEeeCCCCCHHHHHHHHHhc
Confidence            346799999999999998774

>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=84.57  E-value=0.18  Score=41.10  Aligned_cols=19  Identities=42%  Similarity=0.543  Sum_probs=14.7

Q ss_pred             cccccCCcchHHHHHHHhc
Q 043781          126 DVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       126 ~i~G~~G~GKTtLa~~v~~  144 (297)
                      -+.|-||+||||++-.+..
T Consensus        24 i~sGKGGVGKTT~a~nLA~   42 (279)
T d1ihua2          24 MLMGKGGVGKTTMAAAIAV   42 (279)
T ss_dssp             EEECSTTSSHHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHHH
Confidence            4559999999998765554

>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=84.51  E-value=0.18  Score=39.64  Aligned_cols=34  Identities=26%  Similarity=0.172  Sum_probs=22.1

Q ss_pred             cccc-ccCCcchHHHHHHHhcccccccCCCceEEEEe
Q 043781          125 SDVR-GMGGIGKTTLAQFAYNDKDVIENFDKRIWVCV  160 (297)
Q Consensus       125 ~~i~-G~~G~GKTtLa~~v~~~~~~~~~F~~~~wv~v  160 (297)
                      +.|+ |-||+||||+|..+...  ..+.=..++.|..
T Consensus         4 Iav~s~KGGvGKTtia~nlA~~--la~~g~~VlliD~   38 (232)
T d1hyqa_           4 ITVASGKGGTGKTTITANLGVA--LAQLGHDVTIVDA   38 (232)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHH--HHHTTCCEEEEEC
T ss_pred             EEEECCCCCChHHHHHHHHHHH--HHhCCCCEEEEeC
Confidence            4455 78999999999887763  3222234555543

>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=84.50  E-value=0.21  Score=38.28  Aligned_cols=21  Identities=33%  Similarity=0.333  Sum_probs=17.4

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|.+|+|||+|...+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            457899999999999777654

>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=83.70  E-value=0.34  Score=41.08  Aligned_cols=19  Identities=32%  Similarity=0.503  Sum_probs=16.9

Q ss_pred             ccccCCcchHHHHHHHhcc
Q 043781          127 VRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       127 i~G~~G~GKTtLa~~v~~~  145 (297)
                      |=|.-|+||||+++.+.+.
T Consensus        11 iEG~iGsGKSTl~~~L~~~   29 (333)
T d1p6xa_          11 LDGVYGIGKSTTGRVMASA   29 (333)
T ss_dssp             EECSTTSSHHHHHHHHHSG
T ss_pred             EECCccCCHHHHHHHHHHH
Confidence            4499999999999999984

>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=83.69  E-value=0.12  Score=39.02  Aligned_cols=21  Identities=29%  Similarity=0.240  Sum_probs=7.7

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +-++|-+|+|||||...+..+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            458899999999999766654

>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=83.55  E-value=1.2  Score=31.04  Aligned_cols=14  Identities=29%  Similarity=0.126  Sum_probs=11.3

Q ss_pred             ccccCCcchHHHHH
Q 043781          127 VRGMGGIGKTTLAQ  140 (297)
Q Consensus       127 i~G~~G~GKTtLa~  140 (297)
                      |++..|.|||..|-
T Consensus        12 l~~~tGsGKT~~~~   25 (140)
T d1yksa1          12 LDFHPGAGKTRRFL   25 (140)
T ss_dssp             ECCCTTSSTTTTHH
T ss_pred             EEcCCCCChhHHHH
Confidence            56789999997764

>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=83.43  E-value=0.22  Score=39.84  Aligned_cols=21  Identities=29%  Similarity=0.536  Sum_probs=18.3

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      ..++|..|+|||||...+..+
T Consensus        98 ~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          98 STMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             EEEECSTTSSHHHHHHHHSTT
T ss_pred             EEEECCCCCCHHHHHHhhcch
Confidence            357899999999999999765

>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=83.23  E-value=0.082  Score=39.22  Aligned_cols=21  Identities=29%  Similarity=0.371  Sum_probs=18.2

Q ss_pred             ccccccCCcchHHHHHHHhcc
Q 043781          125 SDVRGMGGIGKTTLAQFAYND  145 (297)
Q Consensus       125 ~~i~G~~G~GKTtLa~~v~~~  145 (297)
                      +.++|.+|+|||||...+...
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            468999999999999998764

>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=82.79  E-value=0.13  Score=42.95  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=15.4

Q ss_pred             cccccccCCcchHHHHHHHhc
Q 043781          124 VSDVRGMGGIGKTTLAQFAYN  144 (297)
Q Consensus       124 ~~~i~G~~G~GKTtLa~~v~~  144 (297)
                      .++|.|..|+||||+++.+.+
T Consensus         6 IIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHHH
Confidence            578999999999999987766

>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=81.44  E-value=0.27  Score=38.01  Aligned_cols=20  Identities=25%  Similarity=0.232  Sum_probs=16.1

Q ss_pred             cccccC-CcchHHHHHHHhcc
Q 043781          126 DVRGMG-GIGKTTLAQFAYND  145 (297)
Q Consensus       126 ~i~G~~-G~GKTtLa~~v~~~  145 (297)
                      -|.|-| |+||||++-.+..-
T Consensus         5 ~i~gt~~GVGKTtvs~~La~a   25 (224)
T d1byia_           5 FVTGTDTEVGKTVASCALLQA   25 (224)
T ss_dssp             EEEESSTTSCHHHHHHHHHHH
T ss_pred             EEEECCCCccHHHHHHHHHHH
Confidence            366887 99999999777763