Citrus Sinensis ID: 035774

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------
Protein Sequence
MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR
Secondary Structure (PSIPRED)
cHHHHHHHccccHHHHHHHHHcccccHHHHHcccHHHHHHHHcccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHccccccccccHHHHHHcccccccccEEEEEccccccHHHHHHHHHHHHHccccccccccEEEEEEccccccHHHHHHHHHHccccccccccHHHHHcccEEEEEcccHHHHHHHHHHHHHHHHcccEEEEEEcccccccccccccccccHHHHHHHHHHHHHHHHHcccEEEEEccccccccccccccccccccccccccccccccccccccHHHHHHHcccEEEEEEEEccEEEEEEEEccccccEEEEEEEEccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHccccHHHHHHHHHccccEHHEEEEccHHHHHHHccccHHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHccccccHHHHHHHHccccccccEHHEHccccccccEEEEEEEEEEEccccccccccEEEEEEccccccHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcccEEEEEEcHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHcccEEEEEcEEEEccccHHHHccccccEEEEcccccEEccccccccccEEEEEcccEEEEEEcccccEEEEEEcccccccccEEEEEccccccccccccccccccccccEccc
Coil and Loop (DISEMBL)
MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEhlgghlptrlkgldaalcggvpFGVVTElvgpagtgktqFCLKLSLLAALpahyggldggviYIDVESTFTSRRMIEMgassfpeifhsKGMAQEMAGRILvlqptslseFTESLEKIKVSLLQNQVKLLVIDSMEalvpgvheqrapgqhplsWHISLITSLaefsripivvtnqvrpqshdesclypfqVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAksgqrfmnveksptspplafsftinpsgislltddgtemvvpetcnlssr
Flexible Loop (DISEMBL)
MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTnqvrpqshdesclypfqVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISlltddgtemvvpetcnlssr
Low Complexity Region (SEG)
MANKLISEMRLPKSIANIFAARNITTAKDAlsltelelmkllDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR
Disordered region (IsUnstruct)
************KSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS****************AFSFTINPSGISLLT*****************
Disordered Region (DISOPRED)
****LISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQ*************SHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGT*************
Disordered Region (DISEMBL)
MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR
Disordered Region (DISPRO)
MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLT*****************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR
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	357	2.2.26 [Sep-21-2011]
Q9SK02	370	DNA repair protein RAD51	yes	no	0.997	0.962	0.653	1e-132
O15315	384	DNA repair protein RAD51	no	no	0.943	0.877	0.321	8e-44
O35719	350	DNA repair protein RAD51	yes	no	0.929	0.948	0.348	2e-42
O43502	376	DNA repair protein RAD51	no	no	0.700	0.664	0.276	3e-20
Q8R2J9	366	DNA repair protein RAD51	no	no	0.795	0.775	0.271	3e-20
Q74MX9	325	DNA repair and recombinat	yes	no	0.803	0.883	0.286	4e-20
Q924H5	366	DNA repair protein RAD51	no	no	0.683	0.666	0.284	4e-20
A3MXX9	332	DNA repair and recombinat	yes	no	0.666	0.716	0.306	1e-19
B1YC14	330	DNA repair and recombinat	yes	no	0.649	0.703	0.292	1e-19
Q8ZYR9	333	DNA repair and recombinat	yes	no	0.649	0.696	0.289	6e-19

>sp|Q9SK02|RA51B_ARATH DNA repair protein RAD51 homolog 2 OS=Arabidopsis thaliana GN=RAD51B PE=2 SV=2

 Score =  471 bits (1212), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 234/358 (65%), Positives = 279/358 (77%), Gaps = 2/358 (0%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLI EM L   I+NIFAARNI TAKDALS+TE ELM+LLDV + E+RSA++ +SE  
Sbjct: 1   MANKLIGEMGLHTKISNIFAARNIITAKDALSMTEFELMELLDVGMKEIRSAISFISEAT 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP Q+A  L+E++   EHL GHLPT LKGLD  LCGG+PFGV+TELVGP G GK+QFC+
Sbjct: 61  SPPCQSARSLLEKKVENEHLSGHLPTHLKGLDDTLCGGIPFGVLTELVGPPGIGKSQFCM 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KL+L A+ P  YGGLDG VIYIDVES F+SRR+IEMG  SFPE+FH KGMAQEMAGRILV
Sbjct: 121 KLALSASFPVAYGGLDGRVIYIDVESKFSSRRVIEMGLESFPEVFHLKGMAQEMAGRILV 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L+PTSL+ FTES++++K S+LQNQVKLLVIDSM AL+ G ++  A  Q  L WHIS + S
Sbjct: 181 LRPTSLANFTESIQELKNSILQNQVKLLVIDSMTALLSGENKPGAQRQPQLGWHISFLKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYY-SHIVAVLGFHWAHAV 299
           LAEFSRIPIVVTNQVR Q+ DE+  Y FQ +  D   KD T+ Y SH+VA LG +WAHAV
Sbjct: 241 LAEFSRIPIVVTNQVRSQNRDETSQYSFQAKVKDE-FKDNTKTYDSHLVAALGINWAHAV 299

Query: 300 TIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR 357
           TIRLVLEAKSGQR + V KSP SPPLAF F I  +GISLL+D+GTE+  P    + +R
Sbjct: 300 TIRLVLEAKSGQRIIKVAKSPMSPPLAFPFHITSAGISLLSDNGTELKGPGINTIHAR 357

May be involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents.
Arabidopsis thaliana (taxid: 3702)

>sp|O15315|RA51B_HUMAN DNA repair protein RAD51 homolog 2 OS=Homo sapiens GN=RAD51B PE=1 SV=2

 Score =  177 bits (450), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 111/345 (32%), Positives = 184/345 (53%), Gaps = 8/345 (2%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           M +K +  + L + + +  +   I T +D L L+ LELMK+  +    V   L +VS   
Sbjct: 1   MGSKKLKRVGLSQELCDRLSRHQILTCQDFLCLSPLELMKVTGLSYRGVHELLCMVSRAC 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            P  QTA  +  QR+A +     L T L  LD AL GGV  G +TE+ GP G GKTQFC+
Sbjct: 61  APKMQTAYGIKAQRSA-DFSPAFLSTTLSALDEALHGGVACGSLTEITGPPGCGKTQFCI 119

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
            +S+LA LP + GGL+G V+YID ES F++ R++E+  S FP  F+++      + ++ +
Sbjct: 120 MMSILATLPTNMGGLEGAVVYIDTESAFSAERLVEIAESRFPRYFNTEEKLLLTSSKVHL 179

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHP-----LSWHI 235
            +  +  E  + +E ++  ++   +KL+++DS+ ++V    + +  G        L+   
Sbjct: 180 YRELTCDEVLQRIESLEEEIISKGIKLVILDSVASVVRKEFDAQLQGNLKERNKFLAREA 239

Query: 236 SLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRI-LKDRTRYYSHIVAVLGFH 294
           S +  LAE   IP+++TNQ+              V   D + L + T   S ++A LG  
Sbjct: 240 SSLKYLAEEFSIPVILTNQITTHLSGALASQADLVSPADDLSLSEGTSGSSCVIAALGNT 299

Query: 295 WAHAVTIRLVLEA-KSGQRFMNVEKSPTSPPLAFSFTINPSGISL 338
           W+H+V  RL+L+   S +R + + KSP +P  +F +TI   G+ L
Sbjct: 300 WSHSVNTRLILQYLDSERRQILIAKSPLAPFTSFVYTIKEEGLVL 344

Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. May promote the assembly of presynaptic RAD51 nucleoprotein filaments. The RAD51B-RAD51C dimer exhibits single-stranded DNA-dependent ATPase activity. The BCDX2 complex binds single-stranded DNA, single-stranded gaps in duplex DNA and specifically to nicks in duplex DNA.

Homo sapiens (taxid: 9606)

>sp|O35719|RA51B_MOUSE DNA repair protein RAD51 homolog 2 OS=Mus musculus GN=Rad51b PE=2 SV=2

 Score =  173 bits (438), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 122/350 (34%), Positives = 187/350 (53%), Gaps = 18/350 (5%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           M++K +  + L   + +  +   I   +  LSL+ LELMK+  +    V   L  VS+  
Sbjct: 1   MSSKKLRRVGLSPELCDRLSRYQIVNCQHFLSLSPLELMKVTGLSYRGVHELLHTVSKAC 60

Query: 61  CPPFQTALLLMEQRAATEHLG-GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFC 119
            P  QTA  L  +R+A  HL    L T L  LD AL GGVP G +TE+ GP G GKTQFC
Sbjct: 61  APQMQTAYELKTRRSA--HLSPAFLSTTLCALDEALHGGVPCGSLTEITGPPGCGKTQFC 118

Query: 120 LKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL 179
           + +S+LA LP   GGL+G V+YID ES FT+ R++E+  S FP+ F+++      + R+ 
Sbjct: 119 IMMSVLATLPTSLGGLEGAVVYIDTESAFTAERLVEIAESRFPQYFNTEEKLLLTSSRVH 178

Query: 180 VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPG-----QHPLSWH 234
           + +  +     + LE ++  ++   VKL+++DS+ ++V    + +  G        L   
Sbjct: 179 LCRELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPKLQGNIKERNKFLGKG 238

Query: 235 ISLITSLA-EFSRIPIVVTNQVRPQSHDESCLYPFQVQKM----DRILKDRTRYYSHIVA 289
            SL+  LA EFS IP+++TNQ+   +H    L P Q   +    D  L + T   S +VA
Sbjct: 239 ASLLKYLAGEFS-IPVILTNQI--TTHLSGAL-PSQADLVSPADDLSLSEGTSGSSCLVA 294

Query: 290 VLGFHWAHAVTIRLVLEA-KSGQRFMNVEKSPTSPPLAFSFTINPSGISL 338
            LG  W H V  RL+L+   S +R + + KSP +   +F +TI   G+ L
Sbjct: 295 ALGNTWGHCVNTRLILQYLDSERRQILIAKSPLAAFTSFVYTIKGEGLVL 344

Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. May promote the assembly of presynaptic RAD51 nucleoprotein filaments. The RAD51B-RAD51C dimer exhibits single-stranded DNA-dependent ATPase activity. The BCDX2 complex binds single-stranded DNA, single-stranded gaps in duplex DNA and specifically to nicks in duplex DNA.

Mus musculus (taxid: 10090)

>sp|O43502|RA51C_HUMAN DNA repair protein RAD51 homolog 3 OS=Homo sapiens GN=RAD51C PE=1 SV=1

 Score = 99.8 bits (247), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 87/315 (27%), Positives = 134/315 (42%), Gaps = 65/315 (20%)

Query: 66  TALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL 125
           TAL L+EQ    EH  G + T    LD  L GGVP    TE+ G  G GKTQ C++L++ 
Sbjct: 86  TALELLEQ----EHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKTQLCMQLAVD 141

Query: 126 AALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF----------HSKGMAQEMA 175
             +P  +GG+ G  ++ID E +F   R++++  +    +           H K +     
Sbjct: 142 VQIPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHLQLIAEKHKGEEHRKALEDFTL 201

Query: 176 GRILV-LQPTSLSEFTESLEKIKVSLL------QNQVKLLVIDSMEALVPGVHEQRAPGQ 228
             IL  +      ++TE L   +V LL       ++V+L+++D +    P  H+      
Sbjct: 202 DNILSHIYYFRCRDYTELL--AQVYLLPDFLSEHSKVRLVIVDGIA--FPFRHD-----L 252

Query: 229 HPLSWHISLIT-------SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRT 281
             LS    L+        SLA   R+ +++TNQ+                K+D       
Sbjct: 253 DDLSLRTRLLNGLAQQMISLANNHRLAVILTNQM--------------TTKID------- 291

Query: 282 RYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTD 341
           R  + +V  LG  W HA TIRL+      QR   + KSP+       F I P G      
Sbjct: 292 RNQALLVPALGESWGHAATIRLIFHWDRKQRLATLYKSPSQKECTVLFQIKPQGFR---- 347

Query: 342 DGTEMVVPETCNLSS 356
              + VV   C+L +
Sbjct: 348 ---DTVVTSACSLQT 359

Essential for the homologous recombination (HR) pathway of DNA repair. Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. The RAD51B-RAD51C dimer exhibits single-stranded DNA-dependent ATPase activity. The BCDX2 complex binds single-stranded DNA, single-stranded gaps in duplex DNA and specifically to nicks in duplex DNA. Participates in branch migration and Holliday junction resolution and thus is important for processing HR intermediates late in the DNA repair process. Also has an early function in DNA repair in facilitating phosphorylation of the checkpoint kinase CHEK2 and thereby transduction of the damage signal, leading to cell cycle arrest and HR activation. Protects RAD51 from ubiquitin-mediated degradation that is enhanced following DNA damage. Plays a role in regulating mitochondrial DNA copy number under conditions of oxidative stress in the presence of RAD51 and XRCC3. Contributes to DNA cross-link resistance, sister chromatid cohesion and genomic stability. Involved in maintaining centrosome number in mitosis.

Homo sapiens (taxid: 9606)

>sp|Q8R2J9|RA51C_CRIGR DNA repair protein RAD51 homolog 3 OS=Cricetulus griseus GN=RAD51C PE=2 SV=1

 Score = 99.8 bits (247), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 95/350 (27%), Positives = 147/350 (42%), Gaps = 66/350 (18%)

Query: 21  ARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE------------IVCPPFQTAL 68
           A    TA+D L +   EL K + +   E    L +V               V     TAL
Sbjct: 20  AAGFQTAEDVLGVKPSELSKEVGISKEEALETLQIVRRESLTDKPRCAGASVAGKKYTAL 79

Query: 69  LLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL 128
            L+EQ    EH  G + T    LD  L GG+P    TE+ G  G GKTQ C++L++   +
Sbjct: 80  ELLEQ----EHTQGFIITFCSALDNILGGGIPLMKTTEVCGVPGVGKTQLCMQLAVDVQI 135

Query: 129 PAHYGGLDGGVIYIDVESTFTSRRMIEMG----------ASSFPEIFHSKGMAQEMAGRI 178
           P  +GG+ G  ++ID E +F   R++ +           A +  +  H K +       I
Sbjct: 136 PECFGGVAGEAVFIDTEGSFMVDRVVTLANACIQHLHLIAGTHKDEEHQKALEGFTLENI 195

Query: 179 LV-LQPTSLSEFTESLEKIKV--SLLQN--QVKLLVIDSMEALVPGVHEQRAPGQHPLSW 233
           L  +      ++TE L ++ +    L N  +V+L++ID +   +P  H+        LS 
Sbjct: 196 LSHIYYFRCHDYTELLAQVYLLPDFLSNHSKVQLVIIDGIA--LPFRHD-----LDDLSL 248

Query: 234 HISLIT-------SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSH 286
              L+        SLA   R+ +++TNQ+                K+D       +  + 
Sbjct: 249 RTRLLNGLAQQMISLANNHRLAVILTNQM--------------TTKID-------KNQAL 287

Query: 287 IVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
           +V  LG  W HA TIRL+   +  QRF  + KSP+       F I P G 
Sbjct: 288 LVPALGESWGHAATIRLIFHWEQKQRFATLYKSPSQKESTIPFQITPQGF 337

Essential for the homologous recombination (HR) pathway of DNA repair. Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. The RAD51B-RAD51C dimer exhibits single-stranded DNA-dependent ATPase activity. The BCDX2 complex binds single-stranded DNA, single-stranded gaps in duplex DNA and specifically to nicks in duplex DNA. Participates in branch migration and Holliday junction resolution and thus is important for processing HR intermediates late in the DNA repair process. Also has an early function in DNA repair in facilitating phosphorylation of the checkpoint kinase CHEK2 and thereby transduction of the damage signal, leading to cell cycle arrest and HR activation. Protects RAD51 from ubiquitin-mediated degradation that is enhanced following DNA damage. Plays a role in regulating mitochondrial DNA copy number under conditions of oxidative stress in the presence of RAD51 and XRCC3 (By similarity). Essential for embryonic development and haploinsufficiency causes increased DNA damage sensitivity and genomic instability. Contributes to DNA cross-link resistance, sister chromatid cohesion and genomic stability. Involved in maintaining centrosome number in mitosis.

Cricetulus griseus (taxid: 10029)

>sp|Q74MX9|RADA_NANEQ DNA repair and recombination protein RadA OS=Nanoarchaeum equitans (strain Kin4-M) GN=radA PE=3 SV=1

 Score = 99.4 bits (246), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 97/339 (28%), Positives = 146/339 (43%), Gaps = 52/339 (15%)

Query: 12  PKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSAL-ALVSEIVCPPFQTALLL 70
           PK+   + +A   +  K A +  E ELM+  D+  +  R  + A +  +    F+TA  +
Sbjct: 21  PKTAEKLISAGYDSLIKIASASVE-ELMEAADIGEATARKIIEAAMERLGLLEFKTAEEV 79

Query: 71  MEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPA 130
           +E+R  T      + T  K LD+ L GG+    +TE  G  G+GKTQ   +L++   LP 
Sbjct: 80  LEERQKT----ARITTMSKNLDSLLGGGIETAALTEFYGEYGSGKTQVGHQLAVDVQLPP 135

Query: 131 HYGGLDGGVIYIDVESTFTSRRMIEMGAS-------SFPEIFHSKGMAQEMAGRILVLQP 183
             GGL+G  +YID E TF   R+ +M  +       +   ++H K    +      +L  
Sbjct: 136 EQGGLEGKAVYIDTEGTFRPERIKQMAEALDLDPKKALKNVYHMKVFNTDHQ----MLAA 191

Query: 184 TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITS 240
               E     E I         KL+V+DS+ AL    +  R   A  QH L  H+  +  
Sbjct: 192 RKAEELIRKGEPI---------KLIVVDSLTALFRAEYTGRGQLAERQHKLGRHVHDLLR 242

Query: 241 LAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHA 298
           +AE   + I VTNQV  +P S          +  +D            + AV G   AHA
Sbjct: 243 IAELYNVAIYVTNQVMAKPDSF---------IPGLD-----------SVQAVGGHVLAHA 282

Query: 299 VTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
            T R+ L + K G R   +  SP  P    +F I   GI
Sbjct: 283 STYRVFLRKGKKGIRIARLVDSPHLPERETTFVITEEGI 321

Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.

Nanoarchaeum equitans (strain Kin4-M) (taxid: 228908)

>sp|Q924H5|RA51C_MOUSE DNA repair protein RAD51 homolog 3 OS=Mus musculus GN=Rad51c PE=2 SV=1

 Score = 99.0 bits (245), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 82/288 (28%), Positives = 129/288 (44%), Gaps = 44/288 (15%)

Query: 66  TALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL 125
           TAL L+EQ    EH  G + T    LD  L GG+P    TE+ G  G GKTQ C++L++ 
Sbjct: 77  TALELLEQ----EHTQGFIITFCSALDNILGGGIPLMKTTEVCGVPGVGKTQLCMQLAVD 132

Query: 126 AALPAHYGGLDGGVIYIDVESTFTSRRMIEMG----------ASSFPEIFHSKGMAQEMA 175
             +P  +GG+ G  ++ID E +F   R++ +           A +  E  H K +     
Sbjct: 133 VQIPECFGGVAGEAVFIDTEGSFMVDRVVSLATACIQHLHLIAGTHTEEEHQKALKDFTL 192

Query: 176 GRILV-LQPTSLSEFTESLEKIKV--SLLQN--QVKLLVIDSMEALVPGVH--EQRAPGQ 228
             IL  +      ++TE L ++ +    L +  +V+L++ID +    P  H  E  +   
Sbjct: 193 ENILSHIYYFRCHDYTELLAQVYLLPDFLSDHPKVQLVIIDGIA--FPFRHDLEDLSLRT 250

Query: 229 HPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIV 288
             L+     + SLA   R+ +++TNQ+                K+D       +  + +V
Sbjct: 251 RLLNGLAQQMISLANNHRLAVILTNQM--------------TTKID-------KNQALLV 289

Query: 289 AVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
             LG  W HA TIRL+   +  QRF  + KSP+       F I P G 
Sbjct: 290 PALGESWGHAATIRLIFHWEQKQRFATLYKSPSQKESTIPFQITPQGF 337

Essential for the homologous recombination (HR) pathway of DNA repair. Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. The RAD51B-RAD51C dimer exhibits single-stranded DNA-dependent ATPase activity. The BCDX2 complex binds single-stranded DNA, single-stranded gaps in duplex DNA and specifically to nicks in duplex DNA. Participates in branch migration and Holliday junction resolution and thus is important for processing HR intermediates late in the DNA repair process. Also has an early function in DNA repair in facilitating phosphorylation of the checkpoint kinase CHEK2 and thereby transduction of the damage signal, leading to cell cycle arrest and HR activation. Protects RAD51 from ubiquitin-mediated degradation that is enhanced following DNA damage. Plays a role in regulating mitochondrial DNA copy number under conditions of oxidative stress in the presence of RAD51 and XRCC3. Contributes to DNA cross-link resistance, sister chromatid cohesion and genomic stability. Involved in maintaining centrosome number in mitosis (By similarity). Essential for embryonic development and haploinsufficiency causes increased DNA damage sensitivity and genomic instability.

Mus musculus (taxid: 10090)

>sp|A3MXX9|RADA_PYRCJ DNA repair and recombination protein RadA OS=Pyrobaculum calidifontis (strain JCM 11548 / VA1) GN=radA PE=3 SV=1

 Score = 97.8 bits (242), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 86/281 (30%), Positives = 126/281 (44%), Gaps = 43/281 (15%)

Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS 123
           F +AL + E+R     +     T ++ LD  L GG+    VTE+VG  G+GKTQ C +L+
Sbjct: 85  FISALEVYERRKKIRRI----STGVRALDELLGGGIETRAVTEVVGEFGSGKTQLCHQLA 140

Query: 124 LLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMA-GRILVLQ 182
           ++  LP   GGL    IYID E+TF   R++        +I  ++G+  + A   I   +
Sbjct: 141 VMVQLPEDRGGLGAKAIYIDTENTFRPERIM--------QIAKARGLDPDQALNNIFYAR 192

Query: 183 PTSLSEFTESLEKIKVSLLQNQVKLLVIDSM----EALVPGVHEQRAPGQHPLSWHISLI 238
             S       +E+ K  + Q+ V LLV+DS+     A  PG  E  A  Q  L+ HI+ +
Sbjct: 193 AYSADHQMVLVEQAKSLIRQHNVALLVVDSVIAHFRAEFPG-RENLAERQQKLNKHIADL 251

Query: 239 TSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWA 296
             LA+   + +VVTNQV  +P     + L P                        G   A
Sbjct: 252 LRLADAYDVAVVVTNQVMAQPDVFFGNPLRP----------------------AGGNILA 289

Query: 297 HAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
           H  T RL L ++K   R   +  SP  P    SF I   G+
Sbjct: 290 HGATYRLWLRKSKENIRIAKIFDSPYHPEGEVSFRITEEGL 330

Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.

Pyrobaculum calidifontis (strain JCM 11548 / VA1) (taxid: 410359)

>sp|B1YC14|RADA_PYRNV DNA repair and recombination protein RadA OS=Pyrobaculum neutrophilum (strain DSM 2338 / JCM 9278 / V24Sta) GN=radA PE=3 SV=1

 Score = 97.4 bits (241), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/287 (29%), Positives = 127/287 (44%), Gaps = 55/287 (19%)

Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS 123
           F +AL + E+R     +     T +K LD  L GG+    VTE+ G  G+GKTQ C +L+
Sbjct: 83  FVSALEVYERRKTIRRI----STGVKALDELLGGGIETRAVTEVAGEFGSGKTQLCHQLA 138

Query: 124 LLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS-------SFPEIFHSKGMAQEMAG 176
           ++  LP   GGL    IYID E+TF   R++++  +       +   IF+++  + +   
Sbjct: 139 VMVQLPEERGGLGAKAIYIDTENTFRPERIMQIAKARGLDPDQALNNIFYARAYSSDHQ- 197

Query: 177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSM----EALVPGVHEQRAPGQHPLS 232
            ILV Q  S+             + QN V LLV+DS+     +  PG  E  A  Q  L+
Sbjct: 198 MILVDQAKSI-------------IKQNNVALLVVDSVIAHFRSEFPG-RENLAERQQKLN 243

Query: 233 WHISLITSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAV 290
            H++ +  LA+   + +V+TNQV  +P     + L P                       
Sbjct: 244 KHVADLLRLADAYDVAVVITNQVMAQPDVFFGNPLRP----------------------A 281

Query: 291 LGFHWAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
            G   AH  T RL L ++K   R   +  SP  P    SF I   G+
Sbjct: 282 GGNILAHGATYRLWLRKSKENIRIAKIFDSPYHPEGEVSFRITEEGL 328

Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.

Thermoproteus neutrophilus (strain DSM 2338 / JCM 9278 / V24Sta) (taxid: 444157)

>sp|Q8ZYR9|RADA_PYRAE DNA repair and recombination protein RadA OS=Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827) GN=radA PE=3 SV=1

 Score = 95.5 bits (236), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 83/287 (28%), Positives = 128/287 (44%), Gaps = 55/287 (19%)

Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS 123
           F +AL + E+R     +     T ++ LD  L GG+    VTE+VG  G+GKTQ C +L+
Sbjct: 86  FISALEVYERRKKIRRI----STGVRSLDELLGGGIETRAVTEIVGEFGSGKTQLCHQLA 141

Query: 124 LLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS-------SFPEIFHSKGMAQEMAG 176
           ++  LP   GGL    IYID E+TF   R++++  +       +   IF+++  + +   
Sbjct: 142 VMVQLPEERGGLGAKAIYIDTENTFRPERIMQIAKARGLDSDQALHNIFYARAYSSDHQ- 200

Query: 177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSM----EALVPGVHEQRAPGQHPLS 232
            ILV Q  S+             + Q+ V LLV+DS+     +  PG  E  A  Q  L+
Sbjct: 201 MILVEQAKSI-------------IKQHNVALLVVDSVIAHFRSEFPG-RENLAERQQKLN 246

Query: 233 WHISLITSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAV 290
            H++ +  LA+   + +V+TNQV  +P     + L P                       
Sbjct: 247 KHVADLLRLADAYDVAVVITNQVMAQPDVFFGNPLRP----------------------A 284

Query: 291 LGFHWAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
            G   AH  T RL L ++K   R   +  SP  P    SF I   G+
Sbjct: 285 GGNILAHGATYRLWLRKSKENIRIAKIFDSPYHPEGEVSFRITEEGL 331

Involved in DNA repair and in homologous recombination. Binds and assemble on single-stranded DNA to form a nucleoprotein filament. Hydrolyzes ATP in a ssDNA-dependent manner and promotes DNA strand exchange between homologous DNA molecules.

Pyrobaculum aerophilum (strain ATCC 51768 / IM2 / DSM 7523 / JCM 9630 / NBRC 100827) (taxid: 178306)

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	357
225435171	439	PREDICTED: DNA repair protein RAD51 homo	0.991	0.806	0.723	1e-144
297746183	371	unnamed protein product [Vitis vinifera]	0.991	0.954	0.711	1e-141
356558427	378	PREDICTED: DNA repair protein RAD51 homo	0.980	0.925	0.697	1e-135
449463635	371	PREDICTED: DNA repair protein RAD51 homo	0.969	0.932	0.693	1e-133
449527239	379	PREDICTED: DNA repair protein RAD51 homo	0.969	0.912	0.669	1e-130
79323389	370	DNA repair protein RAD51-like 2 [Arabido	0.997	0.962	0.653	1e-130
79565337	371	DNA repair protein RAD51-like 2 [Arabido	0.997	0.959	0.653	1e-130
57283105	371	putative DNA recombination protein [Arab	0.997	0.959	0.639	1e-127
357453711	484	DNA repair protein RAD51-like protein [M	0.960	0.708	0.602	1e-126
186503833	338	DNA repair protein RAD51-like 2 [Arabido	0.907	0.958	0.641	1e-116

>gi|225435171|ref|XP_002281874.1| PREDICTED: DNA repair protein RAD51 homolog 2-like [Vitis vinifera]

 Score =  518 bits (1334), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 256/354 (72%), Positives = 289/354 (81%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLISEM LP SIANIFAARNITTAK+ALSLTE ELM+LLDV ++ V SA+A +SEIV
Sbjct: 1   MANKLISEMGLPTSIANIFAARNITTAKEALSLTEFELMELLDVGMARVTSAVAHISEIV 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP QTAL LMEQR   E++ GHLPTRLKGLD AL GG+PFGV+TELVGP G GKTQFCL
Sbjct: 61  SPPTQTALSLMEQRVQNEYMAGHLPTRLKGLDEALGGGIPFGVLTELVGPPGIGKTQFCL 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KLSLLA+LPA YGGLDG VIYID ES F+SRRMIE+G+ SFPEIFH +GMA+EMAGRILV
Sbjct: 121 KLSLLASLPASYGGLDGRVIYIDAESKFSSRRMIEIGSKSFPEIFHVEGMAKEMAGRILV 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L+PTSLSEFTESL+ IK+SLLQN VKLLVIDSM ALV G ++Q    QH L WHIS + S
Sbjct: 181 LRPTSLSEFTESLQHIKISLLQNHVKLLVIDSMAALVTGEYDQGPTRQHSLGWHISFVKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVT 300
           +AEFSRIPIVVTNQVR QSHD +  Y FQV+     + D TR+ SH+VA LG HWAHAVT
Sbjct: 241 VAEFSRIPIVVTNQVRSQSHDGTSQYSFQVESRGETVDDHTRFDSHLVAALGIHWAHAVT 300

Query: 301 IRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNL 354
           IRLVLEAK+GQRF+ V KSP SPPLAF F I PSGISLL D+G EM  P+   +
Sbjct: 301 IRLVLEAKAGQRFLKVAKSPISPPLAFPFNITPSGISLLNDEGIEMKGPQISTI 354

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297746183|emb|CBI16239.3| unnamed protein product [Vitis vinifera]

 Score =  507 bits (1305), Expect = e-141,   Method: Compositional matrix adjust.
 Identities = 252/354 (71%), Positives = 285/354 (80%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLISEM LP SIANIFAARNITTAK+ALSLTE ELM+LLDV ++ V SA+A +SEIV
Sbjct: 1   MANKLISEMGLPTSIANIFAARNITTAKEALSLTEFELMELLDVGMARVTSAVAHISEIV 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP QTAL LMEQR   E++ GHLPTRLKGLD AL GG+PFGV+TELVGP G GKTQFCL
Sbjct: 61  SPPTQTALSLMEQRVQNEYMAGHLPTRLKGLDEALGGGIPFGVLTELVGPPGIGKTQFCL 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KLSLLA+LPA YGGLDG VIYID ES F+SRRMIE+G+ SFPEIFH +GMA+E    ILV
Sbjct: 121 KLSLLASLPASYGGLDGRVIYIDAESKFSSRRMIEIGSKSFPEIFHVEGMAKEACPLILV 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L+PTSLSEFTESL+ IK+SLLQN VKLLVIDSM ALV G ++Q    QH L WHIS + S
Sbjct: 181 LRPTSLSEFTESLQHIKISLLQNHVKLLVIDSMAALVTGEYDQGPTRQHSLGWHISFVKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVT 300
           +AEFSRIPIVVTNQVR QSHD +  Y FQV+     + D TR+ SH+VA LG HWAHAVT
Sbjct: 241 VAEFSRIPIVVTNQVRSQSHDGTSQYSFQVESRGETVDDHTRFDSHLVAALGIHWAHAVT 300

Query: 301 IRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNL 354
           IRLVLEAK+GQRF+ V KSP SPPLAF F I PSGISLL D+G EM  P+   +
Sbjct: 301 IRLVLEAKAGQRFLKVAKSPISPPLAFPFNITPSGISLLNDEGIEMKGPQISTI 354

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558427|ref|XP_003547508.1| PREDICTED: DNA repair protein RAD51 homolog 2-like [Glycine max]

 Score =  487 bits (1253), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 244/350 (69%), Positives = 275/350 (78%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLI++M LPKSI NIF ARNI TAKDALS TE ELM+LLDV   EV SA+A VSE+V
Sbjct: 1   MANKLINQMGLPKSIVNIFTARNIITAKDALSHTEFELMELLDVGKEEVTSAMAHVSEVV 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
           CPP QTALLL+EQR   E L GHL TRLKGLD ALCGG+PFGV+TELVGPAG GKTQFCL
Sbjct: 61  CPPCQTALLLLEQRVLNESLAGHLSTRLKGLDEALCGGIPFGVLTELVGPAGIGKTQFCL 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KLSLLA+LP + GGLDG VIYIDVES F S+R+IE+G +SFPEIF  KGMAQEMAGRIL+
Sbjct: 121 KLSLLASLPTNCGGLDGRVIYIDVESKFRSKRLIEIGINSFPEIFLKKGMAQEMAGRILI 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L PTSLSEF ESL +I+VSLLQ QVKLL+IDSM ALV G H+  A  Q  L WH+S I S
Sbjct: 181 LHPTSLSEFAESLHQIRVSLLQQQVKLLIIDSMAALVLGEHDSEASRQQALGWHVSFIKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVT 300
           LAEFSRIP+V+TNQVR Q  DES +Y FQ Q    I  +   Y SH+VA LG +WAHAVT
Sbjct: 241 LAEFSRIPVVLTNQVRSQIGDESRMYSFQAQSHSIIKDNPATYDSHLVAALGINWAHAVT 300

Query: 301 IRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPE 350
           IRLVLEA+SGQRF+ + KSP S PLAF F I  SG+ LL D+G EM  PE
Sbjct: 301 IRLVLEARSGQRFIKLAKSPISAPLAFPFKITSSGLVLLDDEGIEMKGPE 350

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463635|ref|XP_004149537.1| PREDICTED: DNA repair protein RAD51 homolog 2-like [Cucumis sativus]

 Score =  482 bits (1241), Expect = e-133,   Method: Compositional matrix adjust.
 Identities = 240/346 (69%), Positives = 278/346 (80%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MAN+LI++M LP+SIANIFAARNI TAK+ALSLTE ELM+LLDV LSEV SA+A +SEI 
Sbjct: 1   MANRLINQMGLPRSIANIFAARNINTAKEALSLTEFELMELLDVGLSEVASAVAHISEIA 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP+QTAL LMEQR   EHL GHL T LKGLD AL GG+PFGV+TELVGPAG GKTQFCL
Sbjct: 61  SPPYQTALSLMEQRLQNEHLAGHLSTCLKGLDEALFGGIPFGVLTELVGPAGIGKTQFCL 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KLS LAALP  YGGLDG VIYIDVES F+S+RMIE+G  SFP++F+ K MAQEMAGRILV
Sbjct: 121 KLSFLAALPPSYGGLDGRVIYIDVESKFSSKRMIEIGMRSFPDVFNKKDMAQEMAGRILV 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L+P SLSEFTESL KIKVSLL+ +VKL++IDSM AL+ G +E  AP QH L WHIS I S
Sbjct: 181 LRPASLSEFTESLHKIKVSLLEQEVKLVIIDSMAALITGEYELGAPKQHSLGWHISFIKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVT 300
           +AEF+RIP+VVTNQVR ++  E   Y FQ        +  + Y SHIVA LG HWAH+VT
Sbjct: 241 IAEFARIPVVVTNQVRSRNRKEVSHYSFQGWSRSECQEYSSGYGSHIVAALGVHWAHSVT 300

Query: 301 IRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEM 346
           IRLVLEAKSGQRF+ + KSP SPPLAF FTI  SGISLL+++G E+
Sbjct: 301 IRLVLEAKSGQRFIKLAKSPMSPPLAFPFTITASGISLLSNNGEEL 346

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449527239|ref|XP_004170620.1| PREDICTED: DNA repair protein RAD51 homolog 2-like [Cucumis sativus]

 Score =  471 bits (1213), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 237/354 (66%), Positives = 277/354 (78%), Gaps = 8/354 (2%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MAN+LI++M LP+SIANIFAARNI TAK+ALSLTE ELM+LLDV LSEV SA+A +SEI 
Sbjct: 1   MANRLINQMGLPRSIANIFAARNINTAKEALSLTEFELMELLDVGLSEVASAVAHISEIA 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP+QTAL LMEQR   EHL GHL T LKGLD AL GG+PFGV+TELVGPAG GKTQFCL
Sbjct: 61  SPPYQTALSLMEQRLQNEHLAGHLSTCLKGLDEALFGGIPFGVLTELVGPAGIGKTQFCL 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRR--------MIEMGASSFPEIFHSKGMAQ 172
           KLS LAALP  YGGLDG VIYIDVES F+S+R        +++ G  SFP++F+ K MAQ
Sbjct: 121 KLSFLAALPPSYGGLDGRVIYIDVESKFSSKRYFKYSIDVLVKFGMRSFPDVFNKKDMAQ 180

Query: 173 EMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLS 232
           EMAGRILVL+P SLSEFTESL KIKVSLL+ +VKL++IDSM AL+ G +E  AP QH L 
Sbjct: 181 EMAGRILVLRPASLSEFTESLHKIKVSLLEQEVKLVIIDSMAALITGEYELGAPKQHSLG 240

Query: 233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLG 292
           WHIS I S+AEF+RIP+VVTNQVR ++  E   Y FQ        +  + Y SHIVA LG
Sbjct: 241 WHISFIKSIAEFARIPVVVTNQVRSRNRKEVSHYSFQGWSRSECQEYSSGYGSHIVAALG 300

Query: 293 FHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEM 346
            HWAH+VTIRLVLEAKSGQRF+ + KSP SPPLAF FTI  SGISLL+++G E+
Sbjct: 301 VHWAHSVTIRLVLEAKSGQRFIKLAKSPMSPPLAFPFTITASGISLLSNNGEEL 354

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79323389|ref|NP_001031438.1| DNA repair protein RAD51-like 2 [Arabidopsis thaliana] gi|83305358|sp|Q9SK02.2|RA51B_ARATH RecName: Full=DNA repair protein RAD51 homolog 2; Short=AtRAD51B gi|58430738|dbj|BAD89163.1| AtRAD51Balpha [Arabidopsis thaliana] gi|330253047|gb|AEC08141.1| DNA repair protein RAD51-like 2 [Arabidopsis thaliana]

 Score =  471 bits (1212), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 234/358 (65%), Positives = 279/358 (77%), Gaps = 2/358 (0%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLI EM L   I+NIFAARNI TAKDALS+TE ELM+LLDV + E+RSA++ +SE  
Sbjct: 1   MANKLIGEMGLHTKISNIFAARNIITAKDALSMTEFELMELLDVGMKEIRSAISFISEAT 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP Q+A  L+E++   EHL GHLPT LKGLD  LCGG+PFGV+TELVGP G GK+QFC+
Sbjct: 61  SPPCQSARSLLEKKVENEHLSGHLPTHLKGLDDTLCGGIPFGVLTELVGPPGIGKSQFCM 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KL+L A+ P  YGGLDG VIYIDVES F+SRR+IEMG  SFPE+FH KGMAQEMAGRILV
Sbjct: 121 KLALSASFPVAYGGLDGRVIYIDVESKFSSRRVIEMGLESFPEVFHLKGMAQEMAGRILV 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L+PTSL+ FTES++++K S+LQNQVKLLVIDSM AL+ G ++  A  Q  L WHIS + S
Sbjct: 181 LRPTSLANFTESIQELKNSILQNQVKLLVIDSMTALLSGENKPGAQRQPQLGWHISFLKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYY-SHIVAVLGFHWAHAV 299
           LAEFSRIPIVVTNQVR Q+ DE+  Y FQ +  D   KD T+ Y SH+VA LG +WAHAV
Sbjct: 241 LAEFSRIPIVVTNQVRSQNRDETSQYSFQAKVKDE-FKDNTKTYDSHLVAALGINWAHAV 299

Query: 300 TIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR 357
           TIRLVLEAKSGQR + V KSP SPPLAF F I  +GISLL+D+GTE+  P    + +R
Sbjct: 300 TIRLVLEAKSGQRIIKVAKSPMSPPLAFPFHITSAGISLLSDNGTELKGPGINTIHAR 357

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|79565337|ref|NP_180423.3| DNA repair protein RAD51-like 2 [Arabidopsis thaliana] gi|330253046|gb|AEC08140.1| DNA repair protein RAD51-like 2 [Arabidopsis thaliana]

 Score =  471 bits (1212), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 234/358 (65%), Positives = 279/358 (77%), Gaps = 2/358 (0%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLI EM L   I+NIFAARNI TAKDALS+TE ELM+LLDV + E+RSA++ +SE  
Sbjct: 1   MANKLIGEMGLHTKISNIFAARNIITAKDALSMTEFELMELLDVGMKEIRSAISFISEAT 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP Q+A  L+E++   EHL GHLPT LKGLD  LCGG+PFGV+TELVGP G GK+QFC+
Sbjct: 61  SPPCQSARSLLEKKVENEHLSGHLPTHLKGLDDTLCGGIPFGVLTELVGPPGIGKSQFCM 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KL+L A+ P  YGGLDG VIYIDVES F+SRR+IEMG  SFPE+FH KGMAQEMAGRILV
Sbjct: 121 KLALSASFPVAYGGLDGRVIYIDVESKFSSRRVIEMGLESFPEVFHLKGMAQEMAGRILV 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L+PTSL+ FTES++++K S+LQNQVKLLVIDSM AL+ G ++  A  Q  L WHIS + S
Sbjct: 181 LRPTSLANFTESIQELKNSILQNQVKLLVIDSMTALLSGENKPGAQRQPQLGWHISFLKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYY-SHIVAVLGFHWAHAV 299
           LAEFSRIPIVVTNQVR Q+ DE+  Y FQ +  D   KD T+ Y SH+VA LG +WAHAV
Sbjct: 241 LAEFSRIPIVVTNQVRSQNRDETSQYSFQAKVKDE-FKDNTKTYDSHLVAALGINWAHAV 299

Query: 300 TIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR 357
           TIRLVLEAKSGQR + V KSP SPPLAF F I  +GISLL+D+GTE+  P    + +R
Sbjct: 300 TIRLVLEAKSGQRIIKVAKSPMSPPLAFPFHITSAGISLLSDNGTELKGPGINTIHAR 357

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|57283105|emb|CAD70704.1| putative DNA recombination protein [Arabidopsis thaliana]

 Score =  460 bits (1183), Expect = e-127,   Method: Compositional matrix adjust.
 Identities = 229/358 (63%), Positives = 274/358 (76%), Gaps = 2/358 (0%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLI E         +FAARNI TAKDALS+TE ELM+LLDV + E+RSA++ +SE  
Sbjct: 1   MANKLIGEWVFTPKSQTLFAARNIITAKDALSMTEFELMELLDVGMKEIRSAISFISEAT 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
            PP Q+A  L+E++   EHL GHLPT LKGLD  LCGG+PFGV+TELVGP G GK+QFC+
Sbjct: 61  SPPCQSARSLLEKKVENEHLSGHLPTHLKGLDDTLCGGIPFGVLTELVGPPGIGKSQFCM 120

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KL+L A+ P  YGGLDG VIYIDVES F+SRR+IEMG  SFPE+FH KGMAQEMAGRILV
Sbjct: 121 KLALSASFPVAYGGLDGRVIYIDVESKFSSRRVIEMGLESFPEVFHLKGMAQEMAGRILV 180

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS 240
           L+PTSL+ FTES++++K S+LQNQVKLLVIDSM AL+ G ++  A  Q  L WHIS + S
Sbjct: 181 LRPTSLANFTESIQELKNSILQNQVKLLVIDSMTALLSGENKPGAQRQPQLGWHISFLKS 240

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYY-SHIVAVLGFHWAHAV 299
           LAEFSRIPIVVTNQVR Q+ DE+  Y FQ +  D   KD T+ Y SH+VA LG +WAHAV
Sbjct: 241 LAEFSRIPIVVTNQVRSQNRDETSQYSFQAKVKDE-FKDNTKTYDSHLVAALGINWAHAV 299

Query: 300 TIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPETCNLSSR 357
           TIRLVLEAKSGQR + V KSP SPPLAF F I  +GISLL+D+GTE+  P    + +R
Sbjct: 300 TIRLVLEAKSGQRIIKVAKSPMSPPLAFPFQITSAGISLLSDNGTELKGPGINPIHAR 357

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357453711|ref|XP_003597136.1| DNA repair protein RAD51-like protein [Medicago truncatula] gi|355486184|gb|AES67387.1| DNA repair protein RAD51-like protein [Medicago truncatula]

 Score =  456 bits (1174), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 244/405 (60%), Positives = 282/405 (69%), Gaps = 62/405 (15%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           MANKLI+++ LPKSIANIF ARNI TAKDALSLTE ELM+LLDV +SEV SA+A +SE+V
Sbjct: 1   MANKLINQLGLPKSIANIFTARNIITAKDALSLTEFELMELLDVGMSEVTSAMAHISELV 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
           CPP QT      QR   E L GHLPT+LKGLD ALCGG+PFGVVTELVGP G GKTQFCL
Sbjct: 61  CPPCQT------QRVRNESLAGHLPTQLKGLDEALCGGIPFGVVTELVGPPGIGKTQFCL 114

Query: 121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
           KLSLLA+LP +YGGLDG VIYIDVES F+S+R+IE+G  SFPEIFH KGMAQEMAGRIL+
Sbjct: 115 KLSLLASLPVNYGGLDGRVIYIDVESKFSSKRLIEIGTKSFPEIFHKKGMAQEMAGRILI 174

Query: 181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---------------- 224
           L+PTSLSEF ESL++IKVSLLQ QVKLL+IDSM ALV G   Q+                
Sbjct: 175 LRPTSLSEFAESLQRIKVSLLQQQVKLLIIDSMAALVLGTTNQKCWPQVLNQSPNPVSEH 234

Query: 225 -----------------------------APGQHPLSWHISLITSLAEFSRIPIVVTNQV 255
                                        A  Q  L WH+S I SLAEFSRIPIV+TNQV
Sbjct: 235 WGQTAEVGPSDLDPRLSSTRRVENEHDCGASRQQALGWHVSFIKSLAEFSRIPIVLTNQV 294

Query: 256 RPQSHDESCLYPFQVQKMDRILKD-RTR---------YYSHIVAVLGFHWAHAVTIRLVL 305
           R    DES +Y FQ   M+++  D ++R         + SH+VA LG +WAHAVTIRLVL
Sbjct: 295 RSHVGDESLMYSFQ-GMMNKLFSDTQSRSTKGDIPVTFDSHLVAALGINWAHAVTIRLVL 353

Query: 306 EAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTDDGTEMVVPE 350
           E+KSG+RF+ + KSP SPPLAF F I  SGI LL +DG EM  PE
Sbjct: 354 ESKSGKRFIKLAKSPMSPPLAFPFHITSSGIVLLDNDGIEMKGPE 398

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|186503833|ref|NP_001118403.1| DNA repair protein RAD51-like 2 [Arabidopsis thaliana] gi|330253048|gb|AEC08142.1| DNA repair protein RAD51-like 2 [Arabidopsis thaliana]

 Score =  424 bits (1090), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 209/326 (64%), Positives = 253/326 (77%), Gaps = 2/326 (0%)

Query: 33  LTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLD 92
           +TE ELM+LLDV + E+RSA++ +SE   PP Q+A  L+E++   EHL GHLPT LKGLD
Sbjct: 1   MTEFELMELLDVGMKEIRSAISFISEATSPPCQSARSLLEKKVENEHLSGHLPTHLKGLD 60

Query: 93  AALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRR 152
             LCGG+PFGV+TELVGP G GK+QFC+KL+L A+ P  YGGLDG VIYIDVES F+SRR
Sbjct: 61  DTLCGGIPFGVLTELVGPPGIGKSQFCMKLALSASFPVAYGGLDGRVIYIDVESKFSSRR 120

Query: 153 MIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDS 212
           +IEMG  SFPE+FH KGMAQEMAGRILVL+PTSL+ FTES++++K S+LQNQVKLLVIDS
Sbjct: 121 VIEMGLESFPEVFHLKGMAQEMAGRILVLRPTSLANFTESIQELKNSILQNQVKLLVIDS 180

Query: 213 MEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQK 272
           M AL+ G ++  A  Q  L WHIS + SLAEFSRIPIVVTNQVR Q+ DE+  Y FQ + 
Sbjct: 181 MTALLSGENKPGAQRQPQLGWHISFLKSLAEFSRIPIVVTNQVRSQNRDETSQYSFQAKV 240

Query: 273 MDRILKDRTRYY-SHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTI 331
            D   KD T+ Y SH+VA LG +WAHAVTIRLVLEAKSGQR + V KSP SPPLAF F I
Sbjct: 241 KDE-FKDNTKTYDSHLVAALGINWAHAVTIRLVLEAKSGQRIIKVAKSPMSPPLAFPFHI 299

Query: 332 NPSGISLLTDDGTEMVVPETCNLSSR 357
             +GISLL+D+GTE+  P    + +R
Sbjct: 300 TSAGISLLSDNGTELKGPGINTIHAR 325

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	357
UNIPROTKB|E1BE93	364	RAD51B "Uncharacterized protei	0.943	0.925	0.315	7.5e-41
UNIPROTKB|C9JYJ0	425	RAD51B "DNA repair protein RAD	0.943	0.792	0.301	4.2e-40
UNIPROTKB|O15315	384	RAD51B "DNA repair protein RAD	0.943	0.877	0.301	4.2e-40
MGI|MGI:1099436	350	Rad51b "RAD51 homolog B" [Mus	0.795	0.811	0.364	3.7e-39
ZFIN|ZDB-GENE-040426-2750	373	rad51b "RAD51 homolog B (S. ce	0.767	0.734	0.351	7e-38
UNIPROTKB|F1SA21	252	RAD51B "Uncharacterized protei	0.605	0.857	0.341	2.3e-30
RGD|1560681	258	Rad51b "RAD51 homolog B (S. ce	0.602	0.833	0.339	1.6e-29
UNIPROTKB|E1BVI8	275	RAD51B "Uncharacterized protei	0.694	0.901	0.318	9.1e-29
UNIPROTKB|E2R3P3	272	RAD51B "Uncharacterized protei	0.605	0.794	0.313	8.2e-28
ZFIN|ZDB-GENE-041010-204	362	rad51c "rad51 homolog C (S. ce	0.677	0.668	0.294	2.8e-17

UNIPROTKB|E1BE93 RAD51B "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 434 (157.8 bits), Expect = 7.5e-41, P = 7.5e-41
 Identities = 109/345 (31%), Positives = 171/345 (49%)

Query:     1 MANKLISEMRLPKSIANIFAARNITTAKDAXXXXXXXXXXXXDVELSEVRSALALVSEIV 60
             M +K +  + L + + +      I T +D              +    V   L LVS   
Sbjct:    15 MGSKKLRRVGLSQELCDRLNRHQIVTCQDFLCLSPLELMKMTGLSYQGVHELLCLVSRAC 74

Query:    61 CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
              P  QTA  +  QR A  H    L T L  LD AL GGV  G +TE+ GP G GKTQFC+
Sbjct:    75 APQMQTAYEIKTQRCAA-HSSAFLSTTLSALDEALHGGVACGSLTEITGPPGCGKTQFCI 133

Query:   121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
              +S+LA LP + GGL+G V+YID ES F++ R++E+  S FP  F ++      + ++ +
Sbjct:   134 MMSILATLPTNMGGLEGAVVYIDTESAFSAERLVEIAESRFPRYFDTEEKLLLTSSKVHL 193

Query:   181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHP-----LSWHI 235
              +  S  E  + +E ++  ++   VKL++IDS+ ++V    + +  G        L+   
Sbjct:   194 YRELSCDEVLQRIESLEEEIISKGVKLVIIDSVASVVRKEFDTQLQGNVRERNKFLAREA 253

Query:   236 SLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRI-LKDRTRYYSHIVAVLGFH 294
             + +  LAE   IP+++TNQ+              V   D + L + T   S + A LG  
Sbjct:   254 ASLKYLAEEFSIPVILTNQITTHLSGALASQADLVSPADDLSLSEGTSGSSCLTAALGNT 313

Query:   295 WAHAVTIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGISL 338
             W+H+V  RL+L+   S +R + + KSP +P  AF +TI   G+ L
Sbjct:   314 WSHSVNTRLILQYLGSERRQILIAKSPLAPFTAFVYTIEKEGLVL 358

GO:0005524 "ATP binding" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|C9JYJ0 RAD51B "DNA repair protein RAD51 homolog 2" [Homo sapiens (taxid:9606)]

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 104/345 (30%), Positives = 175/345 (50%)

Query:     1 MANKLISEMRLPKSIANIFAARNITTAKDAXXXXXXXXXXXXDVELSEVRSALALVSEIV 60
             M +K +  + L + + +  +   I T +D              +    V   L +VS   
Sbjct:     1 MGSKKLKRVGLSQELCDRLSRHQILTCQDFLCLSPLELMKVTGLSYRGVHELLCMVSRAC 60

Query:    61 CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
              P  QTA  +  QR+A +     L T L  LD AL GGV  G +TE+ GP G GKTQFC+
Sbjct:    61 APKMQTAYGIKAQRSA-DFSPAFLSTTLSALDEALHGGVACGSLTEITGPPGCGKTQFCI 119

Query:   121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
              +S+LA LP + GGL+G V+YID ES F++ R++E+  S FP  F+++      + ++ +
Sbjct:   120 MMSILATLPTNMGGLEGAVVYIDTESAFSAERLVEIAESRFPRYFNTEEKLLLTSSKVHL 179

Query:   181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHP-----LSWHI 235
              +  +  E  + +E ++  ++   +KL+++DS+ ++V    + +  G        L+   
Sbjct:   180 YRELTCDEVLQRIESLEEEIISKGIKLVILDSVASVVRKEFDAQLQGNLKERNKFLAREA 239

Query:   236 SLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRI-LKDRTRYYSHIVAVLGFH 294
             S +  LAE   IP+++TNQ+              V   D + L + T   S ++A LG  
Sbjct:   240 SSLKYLAEEFSIPVILTNQITTHLSGALASQADLVSPADDLSLSEGTSGSSCVIAALGNT 299

Query:   295 WAHAVTIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGISL 338
             W+H+V  RL+L+   S +R + + KSP +P  +F +TI   G+ L
Sbjct:   300 WSHSVNTRLILQYLDSERRQILIAKSPLAPFTSFVYTIKEEGLVL 344

GO:0003677 "DNA binding" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|O15315 RAD51B "DNA repair protein RAD51 homolog 2" [Homo sapiens (taxid:9606)]

 Score = 427 (155.4 bits), Expect = 4.2e-40, P = 4.2e-40
 Identities = 104/345 (30%), Positives = 175/345 (50%)

Query:     1 MANKLISEMRLPKSIANIFAARNITTAKDAXXXXXXXXXXXXDVELSEVRSALALVSEIV 60
             M +K +  + L + + +  +   I T +D              +    V   L +VS   
Sbjct:     1 MGSKKLKRVGLSQELCDRLSRHQILTCQDFLCLSPLELMKVTGLSYRGVHELLCMVSRAC 60

Query:    61 CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
              P  QTA  +  QR+A +     L T L  LD AL GGV  G +TE+ GP G GKTQFC+
Sbjct:    61 APKMQTAYGIKAQRSA-DFSPAFLSTTLSALDEALHGGVACGSLTEITGPPGCGKTQFCI 119

Query:   121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
              +S+LA LP + GGL+G V+YID ES F++ R++E+  S FP  F+++      + ++ +
Sbjct:   120 MMSILATLPTNMGGLEGAVVYIDTESAFSAERLVEIAESRFPRYFNTEEKLLLTSSKVHL 179

Query:   181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHP-----LSWHI 235
              +  +  E  + +E ++  ++   +KL+++DS+ ++V    + +  G        L+   
Sbjct:   180 YRELTCDEVLQRIESLEEEIISKGIKLVILDSVASVVRKEFDAQLQGNLKERNKFLAREA 239

Query:   236 SLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRI-LKDRTRYYSHIVAVLGFH 294
             S +  LAE   IP+++TNQ+              V   D + L + T   S ++A LG  
Sbjct:   240 SSLKYLAEEFSIPVILTNQITTHLSGALASQADLVSPADDLSLSEGTSGSSCVIAALGNT 299

Query:   295 WAHAVTIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGISL 338
             W+H+V  RL+L+   S +R + + KSP +P  +F +TI   G+ L
Sbjct:   300 WSHSVNTRLILQYLDSERRQILIAKSPLAPFTSFVYTIKEEGLVL 344

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0005634 "nucleus" evidence=TAS

GO:0006310 "DNA recombination" evidence=TAS

GO:0007131 "reciprocal meiotic recombination" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0007596 "blood coagulation" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

MGI|MGI:1099436 Rad51b "RAD51 homolog B" [Mus musculus (taxid:10090)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 110/302 (36%), Positives = 164/302 (54%)

Query:    49 VRSALALVSEIVCPPFQTALLLMEQRAATEHLG-GHLPTRLKGLDAALCGGVPFGVVTEL 107
             V   L  VS+   P  QTA  L  +R+A  HL    L T L  LD AL GGVP G +TE+
Sbjct:    49 VHELLHTVSKACAPQMQTAYELKTRRSA--HLSPAFLSTTLCALDEALHGGVPCGSLTEI 106

Query:   108 VGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHS 167
              GP G GKTQFC+ +S+LA LP   GGL+G V+YID ES FT+ R++E+  S FP+ F++
Sbjct:   107 TGPPGCGKTQFCIMMSVLATLPTSLGGLEGAVVYIDTESAFTAERLVEIAESRFPQYFNT 166

Query:   168 KGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPG 227
             +      + R+ + +  +     + LE ++  ++   VKL+++DS+ ++V    + +  G
Sbjct:   167 EEKLLLTSSRVHLCRELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVVRKEFDPKLQG 226

Query:   228 QHP-----LSWHISLITSLA-EFSRIPIVVTNQVRPQSHDESCLYPFQVQKM----DRIL 277
                     L    SL+  LA EFS IP+++TNQ+   +H    L P Q   +    D  L
Sbjct:   227 NIKERNKFLGKGASLLKYLAGEFS-IPVILTNQIT--THLSGAL-PSQADLVSPADDLSL 282

Query:   278 KDRTRYYSHIVAVLGFHWAHAVTIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
              + T   S +VA LG  W H V  RL+L+   S +R + + KSP +   +F +TI   G+
Sbjct:   283 SEGTSGSSCLVAALGNTWGHCVNTRLILQYLDSERRQILIAKSPLAAFTSFVYTIKGEGL 342

Query:   337 SL 338
              L
Sbjct:   343 VL 344

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

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

ZFIN|ZDB-GENE-040426-2750 rad51b "RAD51 homolog B (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 406 (148.0 bits), Expect = 7.0e-38, P = 7.0e-38
 Identities = 102/290 (35%), Positives = 162/290 (55%)

Query:    55 LVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTG 114
             LVS+   P   TAL L +++   E L     T L  LD  L GG+P G +TE+ GP+G G
Sbjct:    55 LVSKACAPAVITALDLWKRK---EELC--FSTSLPALDRLLHGGLPRGALTEVTGPSGCG 109

Query:   115 KTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEM 174
             KTQ C+ LS+LA LP   GGLD GVIYID ES F++ R++EM  S FPE F  K    EM
Sbjct:   110 KTQLCMMLSVLATLPKSLGGLDSGVIYIDTESAFSAERLVEMAQSRFPEFFSVKERLLEM 169

Query:   175 AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQ--HP-- 230
             A R+ + +  +  +  + LE+++  ++  +  L+++DS+ ++V    +   PG   H   
Sbjct:   170 AARVHLFRELTCQDVLKRLERLEEDIIACRAGLVILDSVASVVRKEFDTSLPGNLTHRSN 229

Query:   231 -LSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVA 289
              L    +++  L++   IP+V+TNQ+   +H    L+  Q  + D   ++ + +   + A
Sbjct:   230 FLGQEAAVLKYLSQEFCIPVVLTNQIT--THVGEKLHCPQWNQTDASFEEDSGF---VTA 284

Query:   290 VLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSPTSPPLAFSFTINPSGISL 338
              LG  W+H+V  RL+++ + S +R + + KSP +P    S+TI   GI L
Sbjct:   285 ALGNTWSHSVNTRLIVQYEDSERRQIVIAKSPVAPFAVLSYTIQKEGIRL 334

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1SA21 RAD51B "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 335 (123.0 bits), Expect = 2.3e-30, P = 2.3e-30
 Identities = 74/217 (34%), Positives = 113/217 (52%)

Query:     1 MANKLISEMRLPKSIANIFAARNITTAKDAXXXXXXXXXXXXDVELSEVRSALALVSEIV 60
             M +K +  + L + + +     +I T +D              +    V   L LVS   
Sbjct:     1 MGSKKLRRVGLSQELCDRLNRHHIITCQDFLCLSPLELMKMTGLSYQGVHDLLCLVSRAC 60

Query:    61 CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
              PP QTA  +  QR+A       L T L  LD AL GGV  G +TE+ GP G GKTQFC+
Sbjct:    61 APPMQTAYEIKTQRSAVPS-PAFLSTTLSALDEALHGGVACGSLTEITGPPGCGKTQFCI 119

Query:   121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
              +S+LA LP   GGL+G V+YID ES F++ R++EM  S FP  F ++        ++ +
Sbjct:   120 MMSILATLPIDMGGLEGAVVYIDTESAFSAERLVEMAESRFPRYFSTEEKLLLTVSKVHL 179

Query:   181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALV 217
              +  S  E  + +E ++  ++   VKL++IDS+ ++V
Sbjct:   180 YRELSCDEVLQRIESLEEEIISKGVKLVIIDSVASVV 216

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

RGD|1560681 Rad51b "RAD51 homolog B (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 327 (120.2 bits), Expect = 1.6e-29, P = 1.6e-29
 Identities = 74/218 (33%), Positives = 115/218 (52%)

Query:     1 MANKLISEMRLPKSIANIFAARNITTAKDAXXXXXXXXXXXXDVELSEVRSALALVSEIV 60
             M++K +    L + + +      I   +D              +    V   L  VS+  
Sbjct:     1 MSSKKLRRAGLSQELCDRLCRYQIVNCQDFLNLSPLELMKVTGLSYRGVHELLHTVSKAC 60

Query:    61 CPPFQTALLLMEQRAATEHLG-GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFC 119
              P  QTA  L  +R+A  HL    L T L  LD AL GGVP G +TE+ GP G GKTQFC
Sbjct:    61 APQMQTAYELKTRRSA--HLSPAFLSTTLGALDEALHGGVPCGSLTEVTGPPGCGKTQFC 118

Query:   120 LKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL 179
             + +S+LA LP   GGL+G V+YID ES FT+ R++E+  S FP+ F+++      + R+ 
Sbjct:   119 IMMSVLATLPTRLGGLEGAVLYIDTESAFTAERLVEIAESRFPQYFNTEEKLLLTSSRVH 178

Query:   180 VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALV 217
             + Q  +     + LE ++  ++   VKL+++DS+ ++V
Sbjct:   179 LCQELTCEGLLQRLESLEEEIISKGVKLVIVDSIASVV 216

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

UNIPROTKB|E1BVI8 RAD51B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 320 (117.7 bits), Expect = 9.1e-29, P = 9.1e-29
 Identities = 81/254 (31%), Positives = 124/254 (48%)

Query:     1 MANKLISEMRLPKSIANIFAARNITTAKDAXXXXXXXXXXXXDVELSEVRSALALVSEIV 60
             MA K +   +L + +    +   ITT +D                   V+  L  VS   
Sbjct:     1 MATKKLRRAKLSQELCERLSRYQITTCQDFLCLSLLELMKVTGESYRNVQKLLRKVSLAC 60

Query:    61 CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
              P  QTA   M+ R +       LPT L  LD  L GG+P G +TEL  P G GKTQFC+
Sbjct:    61 APKMQTAYE-MKVRRSINPSAAFLPTSLHSLDKVLHGGIPCGSLTELTSPPGCGKTQFCI 119

Query:   121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
              +S+LA LP   GGLDG VIYID ES F++ R+IE+  + FP  F S      M   I +
Sbjct:   120 TMSVLATLPVSMGGLDGAVIYIDTESAFSAERLIEIAGNRFPTYFDSDEKLFCMTRSIHL 179

Query:   181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQ-----HPLSWHI 235
              +  +     + ++ ++  ++  ++KL++IDS+ ++V    + +  G      + L+   
Sbjct:   180 YRELTCDSVLKRIKSLEEEIISKKIKLIIIDSVASVVRKEFDTKLQGNLAERSNFLARGA 239

Query:   236 SLITSLAEFSRIPI 249
             SL+  +AE   IP+
Sbjct:   240 SLLKYVAEEFSIPV 253

GO:0003677 "DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

UNIPROTKB|E2R3P3 RAD51B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 311 (114.5 bits), Expect = 8.2e-28, P = 8.2e-28
 Identities = 68/217 (31%), Positives = 115/217 (52%)

Query:     1 MANKLISEMRLPKSIANIFAARNITTAKDAXXXXXXXXXXXXDVELSEVRSALALVSEIV 60
             M+++ +  + L + + +      I T +D              +    V   L +VS   
Sbjct:     1 MSSRKLRRVGLSQELCDRLNRYQIVTCQDFLCLSPLELMKMTGLSYKGVHELLCMVSRAC 60

Query:    61 CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
              P  QTA  +  + +A+  L   L T L  LD AL GGV  G +TE+ GP G GKTQFC+
Sbjct:    61 APKMQTAYRIKMETSASL-LPAFLATTLSALDEALHGGVACGSLTEITGPPGCGKTQFCI 119

Query:   121 KLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV 180
              +S+LA LP + GGL+G V+YID ES F++ R++E+  S FP  F+++      + ++ +
Sbjct:   120 MMSILATLPTNMGGLEGDVVYIDTESAFSAERLVEIAESRFPRYFNTEEKLLLTSSKVHL 179

Query:   181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALV 217
              +  S     + +E ++  ++   VKL++IDS+ ++V
Sbjct:   180 YRELSCDAVLQRIESLEEEIISKGVKLVIIDSVASVV 216

GO:0005524 "ATP binding" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

ZFIN|ZDB-GENE-041010-204 rad51c "rad51 homolog C (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 228 (85.3 bits), Expect = 2.8e-17, P = 2.8e-17
 Identities = 84/285 (29%), Positives = 131/285 (45%)

Query:    66 TALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL 125
             TAL L+ Q    E   G + T   GLD A+ GGVP G  TE+ G  G GKTQ C++L++ 
Sbjct:    72 TALDLLHQ----EQTLGSIVTFCSGLDDAIGGGVPVGKTTEICGAPGVGKTQLCMQLAVD 127

Query:   126 AALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS------FPEIFHSKGMAQEM-AGRI 178
               +P  +GGL G  +YID E +F  +R+ +M  ++        E    KG  +E+   +I
Sbjct:   128 VQIPVFFGGLGGKALYIDTEGSFLVQRVADMAEAAVQHCTLLAEDTEQKGALEELNVEKI 187

Query:   179 LV-LQPTSLSEFTESLEKIKV--SLLQN--QVKLLVIDSMEALVPGVHEQRAPGQHP--L 231
             L  L      ++ + L ++ +    L    +V+L+VIDS+    P  H+     Q    L
Sbjct:   188 LSNLFLVRCHDYVKLLAEVYLLPDFLSEHPEVRLVVIDSIA--FPFRHDFEDLSQRTRLL 245

Query:   232 SWHISLITSLAEFSRIPIVVTNQVRPQ-SHDESCLYPFQVQKMDRILKDRTRYYSHIVAV 290
             +     +  LA   R+ +V+TNQ+  + S+ +S L P                       
Sbjct:   246 NGLAQQLIQLATQHRVAVVLTNQMTTRVSNGQSKLVP----------------------A 283

Query:   291 LGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSG 335
             LG  W HA T RL+L  +  +R  ++ KSP+       + I   G
Sbjct:   284 LGESWGHAATQRLILHWEGQRRLASLYKSPSQMEATVQYQITVQG 328

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

GO:0005524 "ATP binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006259 "DNA metabolic process" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0008094 "DNA-dependent ATPase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O35719	RA51B_MOUSE	No assigned EC number	0.3485	0.9299	0.9485	yes	no
Q9SK02	RA51B_ARATH	No assigned EC number	0.6536	0.9971	0.9621	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

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	357
cd01123	235	cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B	9e-45
cd01393	226	cd01393, recA_like, RecA is a bacterial enzyme whi	2e-41
PRK04301	317	PRK04301, radA, DNA repair and recombination prote	2e-26
TIGR02236	310	TIGR02236, recomb_radA, DNA repair and recombinati	1e-25
COG0468	279	COG0468, RecA, RecA/RadA recombinase [DNA replicat	5e-24
TIGR02238	313	TIGR02238, recomb_DMC1, meiotic recombinase Dmc1	3e-22
pfam08423	261	pfam08423, Rad51, Rad51	2e-21
PLN03186	342	PLN03186, PLN03186, DNA repair protein RAD51 homol	9e-21
PTZ00035	337	PTZ00035, PTZ00035, Rad51 protein; Provisional	3e-20
PRK09361	225	PRK09361, radB, DNA repair and recombination prote	6e-20
cd01394	218	cd01394, radB, RadB	2e-18
PLN03187	344	PLN03187, PLN03187, meiotic recombination protein	1e-17
TIGR02237	209	TIGR02237, recomb_radB, DNA repair and recombinati	2e-17
TIGR02239	316	TIGR02239, recomb_RAD51, DNA repair protein RAD51	3e-15
TIGR03881	229	TIGR03881, KaiC_arch_4, KaiC domain protein, PAE11	9e-09
pfam06745	231	pfam06745, KaiC, KaiC	1e-07
COG0467	260	COG0467, RAD55, RecA-superfamily ATPases implicate	3e-07
cd00983	325	cd00983, recA, RecA is a bacterial enzyme which ha	5e-06
cd01120	165	cd01120, RecA-like_NTPases, RecA-like NTPases	1e-05
COG2874	235	COG2874, FlaH, Predicted ATPases involved in bioge	2e-04
cd01125	239	cd01125, repA, Hexameric Replicative Helicase RepA	2e-04
smart00382	148	smart00382, AAA, ATPases associated with a variety	6e-04
PRK09519	790	PRK09519, recA, DNA recombination protein RecA; Re	8e-04
TIGR02012	321	TIGR02012, tigrfam_recA, protein RecA	0.001
TIGR03880	224	TIGR03880, KaiC_arch_3, KaiC domain protein, AF_03	0.002
pfam00154	322	pfam00154, RecA, recA bacterial DNA recombination	0.004
PRK06067	234	PRK06067, PRK06067, flagellar accessory protein Fl	0.004

>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B

 Score =  153 bits (389), Expect = 9e-45
 Identities = 77/262 (29%), Positives = 112/262 (42%), Gaps = 35/262 (13%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           L T  K LD  L GG+  G +TE+ G  G+GKTQ C +L++   LP   GGL+G  +YID
Sbjct: 1   LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID 60

Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQP---TSLSEFTESLEKIKVSL 200
            E TF   R++++ A  F          +E+   I V +        +  E LE I +  
Sbjct: 61  TEGTFRPERLVQI-AERFGL------DPEEVLDNIYVARAYNSDHQLQLLEELEAILIE- 112

Query: 201 LQNQVKLLVIDSMEALV----PGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR 256
             +++KL+++DS+ AL      G  E     QH L+  +  +  LA+   + +V+TNQV 
Sbjct: 113 -SSRIKLVIVDSVTALFRAEFDGRGELAERQQH-LAKLLRTLKRLADEFNVAVVITNQV- 169

Query: 257 PQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE-AKSGQRFMN 315
                             R                G  WAHA T RL L   +  +R   
Sbjct: 170 ----------------TARPDGAAMFGGDPKKPAGGNIWAHASTTRLYLRKGRGEERIAK 213

Query: 316 VEKSPTSPPLAFSFTINPSGIS 337
           +  SP  P     F I   GI 
Sbjct: 214 IVDSPHLPEGEAVFAITEEGIR 235

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 . Length = 235

>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

 Score =  144 bits (366), Expect = 2e-41
 Identities = 77/253 (30%), Positives = 114/253 (45%), Gaps = 34/253 (13%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           + T  K LD  L GG+P G +TE+ G  G+GKTQ CL+L++ A LP   GGL+G V+YID
Sbjct: 1   ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID 60

Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN 203
            E  F   R++++      +        +E+   I V +P +  +  E +E+++  +   
Sbjct: 61  TEGAFRPERLVQLAVRFGLDP-------EEVLDNIYVARPYNGEQQLEIVEELERIMSSG 113

Query: 204 QVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSH 260
           +V L+V+DS+ AL       R   A     LS  +  +  LA+   + +V TNQVR    
Sbjct: 114 RVDLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVR---- 169

Query: 261 DESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVL----EAKSGQRFMNV 316
                      K+D +  D            G   AHA T RL L         +R   V
Sbjct: 170 ----------AKVDVMFGDPE------TPAGGNALAHASTTRLDLRKGRGIIGERRIAKV 213

Query: 317 EKSPTSPPLAFSF 329
            KSP  P     F
Sbjct: 214 VKSPALPEAEAEF 226

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. Length = 226

>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA; Validated

 Score =  106 bits (268), Expect = 2e-26
 Identities = 81/285 (28%), Positives = 122/285 (42%), Gaps = 50/285 (17%)

Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS 123
           F+TAL ++E+R       G + T  K LD  L GG+    +TE  G  G+GKTQ C +L+
Sbjct: 68  FETALEVLERRKNV----GKITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLA 123

Query: 124 LLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMA---QEMAGRILV 180
           +   LP   GGL+G  +YID E TF   R+ +M          ++ +     E+   I V
Sbjct: 124 VNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQM----------AEALGLDPDEVLDNIHV 173

Query: 181 LQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALV----PGVHEQRAPGQHPLSWH 234
            +  +        EK +  L++    +KL+++DS+ A       G     A  Q  L+ H
Sbjct: 174 ARAYNSDHQMLLAEKAE-ELIKEGENIKLVIVDSLTAHFRAEYVG-RGNLAERQQKLNKH 231

Query: 235 ISLITSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLG 292
           +  +  LA+     +VVTNQV  RP                D    D T+       + G
Sbjct: 232 LHDLLRLADLYNAAVVVTNQVMARP----------------DAFFGDPTQ------PIGG 269

Query: 293 FHWAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
               H  T R+ L ++K  +R   +  SP  P     F I   GI
Sbjct: 270 HILGHTATFRIYLRKSKGNKRIARLVDSPHLPEGEAVFRITEEGI 314

Length = 317

>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA

 Score =  104 bits (261), Expect = 1e-25
 Identities = 86/283 (30%), Positives = 126/283 (44%), Gaps = 45/283 (15%)

Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS 123
           F+TA  ++E+R       G + T  K LD  L GG+    +TE+ G  G+GKTQ C +L+
Sbjct: 61  FETADDVLERRKTI----GKITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLA 116

Query: 124 LLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGM-AQEMAGRILVLQ 182
           +   LP   GGL G  +YID E+TF   R+++M          ++G+   E+   I V +
Sbjct: 117 VNVQLPEEKGGLGGKAVYIDTENTFRPERIMQMA--------EARGLDPDEVLKNIYVAR 168

Query: 183 PTSLSEFTESLEKIK--VSLLQNQVKLLVIDSM----EALVPGVHEQRAPGQHPLSWHIS 236
             + +     +EK +  +  L N VKLL++DS+     A   G     A  Q  L+ H+ 
Sbjct: 169 AYNSNHQMLLVEKAEDLIKELNNPVKLLIVDSLTSHFRAEYVG-RGALAERQQKLNKHLH 227

Query: 237 LITSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFH 294
            +  LA+     +VVTNQV  RP                D    D TR       + G  
Sbjct: 228 DLLRLADLYNAAVVVTNQVMARP----------------DAFFGDPTR------PIGGHI 265

Query: 295 WAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
             HA T R+ L + K  +R   +  SP  P     F I   GI
Sbjct: 266 LGHAATFRVYLRKGKGDKRIARLVDSPHLPEGEAVFRITEKGI 308

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 310

>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication, recombination, and repair]

 Score = 99.3 bits (248), Expect = 5e-24
 Identities = 66/268 (24%), Positives = 97/268 (36%), Gaps = 58/268 (21%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           + T    LD AL GG+P G +TE+ GP  +GKT   L+L   A  P       G   +ID
Sbjct: 42  ISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQKP------GGKAAFID 95

Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN 203
            E      R               K +  ++   +LV QP +  +  E  EK+       
Sbjct: 96  TEHALDPERA--------------KQLGVDLLDNLLVSQPDTGEQQLEIAEKL-ARSGAE 140

Query: 204 QVKLLVIDSMEALVP----GVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQS 259
           ++ LLV+DS+ ALV              +  LS  +  +T LA      ++ TNQVR   
Sbjct: 141 KIDLLVVDSVAALVRAEEIEDGHLGLRARL-LSKALRKLTRLANKYNTAVIFTNQVR--- 196

Query: 260 HDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE-------AKSGQR 312
                       K+  +  D            G       ++RL L            +R
Sbjct: 197 -----------AKIGVMFGDPET------TTGGNALKFYASVRLDLRRIESLKEDVGNKR 239

Query: 313 FMNVEKSPTSPPLAFS---FTINPSGIS 337
            + V K+  +PP  F    F I   G  
Sbjct: 240 RVKVVKNKVAPP--FKEAEFDITYGGGI 265

Length = 279

>gnl|CDD|131292 TIGR02238, recomb_DMC1, meiotic recombinase Dmc1

 Score = 95.2 bits (237), Expect = 3e-22
 Identities = 84/318 (26%), Positives = 131/318 (41%), Gaps = 34/318 (10%)

Query: 24  ITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGH 83
           I T    +  T   L K+  +  ++V       S+I+ P F TA  + ++R     +   
Sbjct: 22  ICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKIINPGFITAFEISQKRKKVLKIT-- 79

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
             T  + LD  L GG+    +TE+ G    GKTQ    L + A LP   GG +G V YID
Sbjct: 80  --TGSQALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYID 137

Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMA-GRILVLQPTSLSEFTESLEKIKVSLLQ 202
            E TF   R+  + A  F       G+  +     IL  +  +     E L+ +     +
Sbjct: 138 TEGTFRPDRIRAI-AERF-------GVDPDAVLDNILYARAYTSEHQMELLDYLAAKFSE 189

Query: 203 NQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQS 259
              +LL++DS+ AL       R   +  Q  L+  +S +  ++E   + + VTNQV  Q+
Sbjct: 190 EPFRLLIVDSIMALFRVDFSGRGELSERQQKLAQMLSRLNKISEEFNVAVFVTNQV--QA 247

Query: 260 HDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVL-EAKSGQRFMNVEK 318
            D      F       I         H++       AHA T R++L + +  +R   +  
Sbjct: 248 -DPGATMTFIADPKKPI-------GGHVL-------AHASTTRILLRKGRGEERVAKLYD 292

Query: 319 SPTSPPLAFSFTINPSGI 336
           SP  P    SF I   GI
Sbjct: 293 SPDMPEAEASFQITEGGI 310

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. Length = 313

>gnl|CDD|117002 pfam08423, Rad51, Rad51

 Score = 92.0 bits (229), Expect = 2e-21
 Identities = 82/286 (28%), Positives = 123/286 (43%), Gaps = 36/286 (12%)

Query: 57  SEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKT 116
           S++V   F TA  L ++R+    +     T  K LD  L GG+  G +TE+ G   TGKT
Sbjct: 2   SKLVPMGFTTATELHQRRSEVIRI----TTGSKELDKLLGGGIETGSITEVFGEFRTGKT 57

Query: 117 QFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGM-AQEMA 175
           Q C  L +   LP   GG +G  +YID E TF   R++ + A  F       G+  +E+ 
Sbjct: 58  QLCHTLCVTCQLPLEMGGGEGKALYIDTEGTFRPERIVAI-AERF-------GLDPEEVL 109

Query: 176 GRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL----VPGVHEQRAPGQHPL 231
             I   +  +     + L +    + +++  LL++DS  AL      G  E     QH L
Sbjct: 110 DNIAYARAYNTEHQMQLLLQAAAMMSESRFALLIVDSATALYRTDFSGRGELAERQQH-L 168

Query: 232 SWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVL 291
           +  +  +  LA+   + +V+TNQV  Q    +    F       I         HI+   
Sbjct: 169 AKFLRSLQRLADEFGVAVVITNQVVAQVDGAA---MFAADPKKPI-------GGHIM--- 215

Query: 292 GFHWAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
               AHA T RL L + +  QR   +  SP  P     F I+  GI
Sbjct: 216 ----AHASTTRLYLRKGRGEQRVCKIYDSPCLPESEAVFAISEGGI 257

Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein. Length = 261

>gnl|CDD|178728 PLN03186, PLN03186, DNA repair protein RAD51 homolog; Provisional

 Score = 91.3 bits (227), Expect = 9e-21
 Identities = 86/317 (27%), Positives = 134/317 (42%), Gaps = 51/317 (16%)

Query: 40  KLLDVE-LSE--VRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALC 96
            LL ++ +SE  V   L   S++V   F TA  L  QR     +     T  + LD  L 
Sbjct: 62  DLLQIKGISEAKVEKILEAASKLVPLGFTTASQLHAQRQEIIQI----TTGSRELDKILE 117

Query: 97  GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEM 156
           GG+  G +TE+ G   TGKTQ C  L +   LP   GG +G  +YID E TF  +R+I++
Sbjct: 118 GGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQI 177

Query: 157 -------GASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLV 209
                  GA     + +++    +    +L+   + ++E               +  L++
Sbjct: 178 AERFGLNGADVLENVAYARAYNTDHQSELLLEAASMMAE--------------TRFALMI 223

Query: 210 IDSMEALV----PGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCL 265
           +DS  AL      G  E  A   H L   +  +  LA+   + +V+TNQV  Q    +  
Sbjct: 224 VDSATALYRTEFSGRGELSARQMH-LGKFLRSLQRLADEFGVAVVITNQVVAQVDGSA-- 280

Query: 266 YPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQ-RFMNVEKSPTSPP 324
             F   ++  I         +I+       AHA T RL L    G+ R   V  SP  P 
Sbjct: 281 -FFAGPQLKPI-------GGNIM-------AHASTTRLALRKGRGENRICKVISSPCLPE 325

Query: 325 LAFSFTINPSGISLLTD 341
               F+I+  G++ + D
Sbjct: 326 AEARFSISSEGVTDVKD 342

Length = 342

>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional

 Score = 90.1 bits (224), Expect = 3e-20
 Identities = 86/299 (28%), Positives = 119/299 (39%), Gaps = 38/299 (12%)

Query: 46  LSE--VRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGV 103
           +SE  V       S++V   F +A   +E R     +     T    LD  L GG+  G 
Sbjct: 64  ISEAKVEKIKEAASKLVPMGFISATEYLEARKNIIRI----TTGSTQLDKLLGGGIETGS 119

Query: 104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPE 163
           +TEL G   TGKTQ C  L +   LP   GG +G V+YID E TF   R I   A  F  
Sbjct: 120 ITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPER-IVQIAERF-- 176

Query: 164 IFHSKGM-AQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALV----P 218
                G+  +++   I   +  +     + L +    + + +  LL++DS  AL      
Sbjct: 177 -----GLDPEDVLDNIAYARAYNHEHQMQLLSQAAAKMAEERFALLIVDSATALFRVDYS 231

Query: 219 GVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILK 278
           G  E     QH L   +  +  LA+   + +V+TNQV       S    F       I  
Sbjct: 232 GRGELAERQQH-LGKFLRALQKLADEFNVAVVITNQVMADVDGASM---FVADPKKPI-- 285

Query: 279 DRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSG-QRFMNVEKSPTSPPLAFSFTINPSGI 336
                  HI+       AHA T RL L    G QR   +  SP  P     F I+  GI
Sbjct: 286 -----GGHII-------AHASTTRLSLRKGRGEQRICKIYDSPNLPESEAVFAISEGGI 332

Length = 337

>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB; Provisional

 Score = 86.8 bits (216), Expect = 6e-20
 Identities = 71/263 (26%), Positives = 111/263 (42%), Gaps = 52/263 (19%)

Query: 83  HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
            LPT  K LD  L GG   G +T++ GP G+GKT  CL+L++ AA           VIYI
Sbjct: 4   RLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAK------NGKKVIYI 57

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E   +  R  ++    F E+             I++ +P+S  E +E++ K +  L +
Sbjct: 58  DTEG-LSPERFKQIAGEDFEEL----------LSNIIIFEPSSFEEQSEAIRKAE-KLAK 105

Query: 203 NQVKLLVIDSMEA---LVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQS 259
             V L+V+DS  +   L     E  +     L   ++ +  LA    + +V+TNQV    
Sbjct: 106 ENVGLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVY--- 162

Query: 260 HDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGF---HWAHAVTIRLVLE-AKSGQRFMN 315
                           I  D  R       + G    HW+  + +R  LE  ++G+R   
Sbjct: 163 --------------SDIDSDGLR------PLGGHTLEHWSKTI-LR--LEKFRNGKRRAT 199

Query: 316 VEKSPTSPP-LAFSFTINPSGIS 337
           +EK  + P   +  F I   GI 
Sbjct: 200 LEKHRSRPEGESAEFRITDRGIE 222

Length = 225

>gnl|CDD|238688 cd01394, radB, RadB

 Score = 82.5 bits (204), Expect = 2e-18
 Identities = 53/175 (30%), Positives = 83/175 (47%), Gaps = 21/175 (12%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           LPT  KGLD  L GGV  G VT++ GP GTGKT   ++L++  A      G    V YID
Sbjct: 1   LPTGCKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETA------GQGKKVAYID 54

Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN 203
            E   + R         F +I   +   +  A  I+V +P   +E   ++++ + +    
Sbjct: 55  TEGLSSER---------FRQIAGDR--PERAASSIIVFEPMDFNEQGRAIQETE-TFADE 102

Query: 204 QVKLLVIDSMEALVP---GVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV 255
           +V L+V+DS  AL     G  +        L+  ++ +  LA    + +V+TNQV
Sbjct: 103 KVDLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLWLARKHDVAVVITNQV 157

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear. Length = 218

>gnl|CDD|215620 PLN03187, PLN03187, meiotic recombination protein DMC1 homolog; Provisional

 Score = 82.5 bits (204), Expect = 1e-17
 Identities = 76/289 (26%), Positives = 117/289 (40%), Gaps = 35/289 (12%)

Query: 58  EIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQ 117
           +++   F T    + +R +   +     T  + LD  L GG+    +TE  G   +GKTQ
Sbjct: 86  KLLNQGFITGSDALLKRKSVVRI----TTGSQALDELLGGGIETRCITEAFGEFRSGKTQ 141

Query: 118 FCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGM-AQEMAG 176
               L +   LP   GG +G V YID E TF   R++ + A  F       GM A  +  
Sbjct: 142 LAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPI-AERF-------GMDADAVLD 193

Query: 177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSW 233
            I+  +  +       L  +   + +   +LL++DS+ AL       R   A  Q  L+ 
Sbjct: 194 NIIYARAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVIALFRVDFTGRGELAERQQKLAQ 253

Query: 234 HISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGF 293
            +S +T +AE   + + +TNQV   +     ++    +K                   G 
Sbjct: 254 MLSRLTKIAEEFNVAVYMTNQV--IADPGGGMFISDPKK----------------PAGGH 295

Query: 294 HWAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGISLLTD 341
             AHA TIRL+L + K  QR   V  +P  P     F I   GI    D
Sbjct: 296 VLAHAATIRLMLRKGKGEQRVCKVFDAPNLPEAEAEFQITSGGIMDAKD 344

Length = 344

>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB

 Score = 79.4 bits (196), Expect = 2e-17
 Identities = 58/229 (25%), Positives = 98/229 (42%), Gaps = 41/229 (17%)

Query: 91  LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS 150
           +D  L GGV  G +T++ GP G+GKT  C+ L++ AA           V+YID E   + 
Sbjct: 1   IDELLGGGVERGTITQIYGPPGSGKTNICMILAVNAA------RQGKKVVYIDTEG-LSP 53

Query: 151 RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVI 210
            R  ++ A   PE   S           +V +     E   +++K    + ++   L+V+
Sbjct: 54  ERFKQI-AEDRPERALSN---------FIVFEVFDFDEQGVAIQKTSKFIDRDSASLVVV 103

Query: 211 DSMEALVPGVHEQRAPGQH-PLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQ 269
           DS  AL           ++  L+  ++L+ SLA    + +V+TNQV    ++ + L P  
Sbjct: 104 DSFTALYRLELSDDRISRNRELARQLTLLLSLARKKNLAVVITNQVYTDVNNGT-LRPLG 162

Query: 270 VQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEK 318
                           H++     HW+  +   L LE   G+R   +EK
Sbjct: 163 ---------------GHLLE----HWSKVI---LRLEKFRGRRLATLEK 189

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236). Length = 209

>gnl|CDD|233794 TIGR02239, recomb_RAD51, DNA repair protein RAD51

 Score = 75.5 bits (186), Expect = 3e-15
 Identities = 79/297 (26%), Positives = 119/297 (40%), Gaps = 47/297 (15%)

Query: 53  LALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAG 112
           LA  +++V   F TA    ++R     L     T  K LD  L GG+  G +TE+ G   
Sbjct: 51  LAEAAKLVPMGFTTATEFHQRRQEVIQL----TTGSKELDKLLGGGIETGSITEIFGEFR 106

Query: 113 TGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEM-------GASSFPEIF 165
           TGKTQ C  L++   LP   GG +G  +YID E TF   R++ +              + 
Sbjct: 107 TGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERLLAIAERYGLNPEDVLDNVA 166

Query: 166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL----VPGVH 221
           +++    +   ++L      +SE              ++  LL++DS  AL      G  
Sbjct: 167 YARAYNTDHQLQLLQQAAAMMSE--------------SRFALLIVDSATALYRTDFSGRG 212

Query: 222 EQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRT 281
           E  A   H L+  +  +  LA+   + +V+TNQV  Q      ++    +K         
Sbjct: 213 ELSARQMH-LARFLRSLQRLADEFGVAVVITNQVVAQVDGAGSMFAGDPKK--------- 262

Query: 282 RYYSHIVAVLGFHWAHAVTIRLVLEAKSG-QRFMNVEKSPTSPPLAFSFTINPSGIS 337
               +I+       AHA T RL L    G QR   +  SP  P     F I   GI 
Sbjct: 263 PIGGNIM-------AHASTTRLSLRKGRGEQRICKIYDSPCLPESEAMFAIYEDGIG 312

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). Length = 316

>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family

 Score = 54.7 bits (132), Expect = 9e-09
 Identities = 49/146 (33%), Positives = 63/146 (43%), Gaps = 27/146 (18%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VIY 141
           L T ++GLD  L GG+P G    + G  GTGKT FCL  +        Y GL  G  VIY
Sbjct: 2   LSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFA--------YKGLRDGDPVIY 53

Query: 142 IDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLL 201
           +  E    SR  I   A+ F   F     A E    +++       E   SL ++ +  L
Sbjct: 54  VTTE---ESRESIIRQAAQFGMDFEK---AIEEGKLVIIDALMKEKEDEWSLRELSIEEL 107

Query: 202 QNQV-----KL------LVIDSMEAL 216
            N+V      L      LVIDSM A 
Sbjct: 108 LNKVIEAKKYLGYGHARLVIDSMSAF 133

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. Length = 229

>gnl|CDD|219158 pfam06745, KaiC, KaiC

 Score = 51.5 bits (124), Expect = 1e-07
 Identities = 39/145 (26%), Positives = 55/145 (37%), Gaps = 26/145 (17%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           +PT + GLD  L GG+P G V  + G  GTGKT F L+     AL     G     +Y+ 
Sbjct: 1   VPTGIPGLDEILKGGIPRGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPG-----VYVT 55

Query: 144 VESTFTS------------RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTE 191
           +E                  ++ E G  +  +   S        G   V     L E  E
Sbjct: 56  LEEPPEDLRENAKSFGWDLEKLEEEGKLAIIDASTS------GIGIAEVKGRFDLEELIE 109

Query: 192 SLEKIKVSLLQNQVKLLVIDSMEAL 216
            L +    +     K +VIDS+  L
Sbjct: 110 RLREAIREI---GAKRVVIDSITTL 131

This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes 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. Length = 231

>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

 Score = 50.5 bits (121), Expect = 3e-07
 Identities = 42/148 (28%), Positives = 59/148 (39%), Gaps = 29/148 (19%)

Query: 83  HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VI 140
            +PT + GLD  L GG+P G V  + GP GTGKT F L+          Y G   G  V+
Sbjct: 4   RIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFL--------YEGAREGEPVL 55

Query: 141 YIDVESTFTS------------RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSE 188
           Y+  E +                  IE G  +  + F S+         I+V  P  L E
Sbjct: 56  YVSTEESPEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLV----SIVVGDPLDLEE 111

Query: 189 FTESLEKIKVSLLQNQVKLLVIDSMEAL 216
             + + +I           +VIDS+  L
Sbjct: 112 LLDRIREIVEKEGA---DRVVIDSITEL 136

Length = 260

>gnl|CDD|238483 cd00983, recA, RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

 Score = 47.2 bits (113), Expect = 5e-06
 Identities = 50/181 (27%), Positives = 73/181 (40%), Gaps = 32/181 (17%)

Query: 84  LPTRLKGLDAAL-CGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
           +PT    LD AL  GG P G + E+ GP  +GKT     L+L A   A   G  G V +I
Sbjct: 36  IPTGSLSLDIALGIGGYPKGRIIEIYGPESSGKT----TLALHAIAEAQKLG--GTVAFI 89

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E         ++G                    +L+ QP +  E  ++LE     +  
Sbjct: 90  DAEHALDPVYAKKLGVDL---------------DNLLISQPDT-GE--QALEIADSLVRS 131

Query: 203 NQVKLLVIDSMEALVP-----GVHEQRAPGQHP--LSWHISLITSLAEFSRIPIVVTNQV 255
             V L+V+DS+ ALVP     G       G     +S  +  +T     S   ++  NQ+
Sbjct: 132 GAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSINKSNTTVIFINQL 191

Query: 256 R 256
           R
Sbjct: 192 R 192

RecA couples ATP hydrolysis to DNA strand exchange. Length = 325

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

 Score = 44.8 bits (106), Expect = 1e-05
 Identities = 32/153 (20%), Positives = 57/153 (37%), Gaps = 18/153 (11%)

Query: 104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPE 163
           +  + GP G+GKT   L+L+L  A         G V+Y+D+E          +G      
Sbjct: 1   LILVFGPTGSGKTTLALQLALNIATK------GGKVVYVDIEEEIEELTERLIG------ 48

Query: 164 IFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQ-VKLLVIDSMEALVPGVHE 222
              S   A      ++++  T+       L      L +     L+++D +  LV  + E
Sbjct: 49  --ESLKGA---LDNLIIVFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALRE 103

Query: 223 QRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV 255
            R      L   +  +   A    + ++ T QV
Sbjct: 104 IREGYPGELDEELRELLERARKGGVTVIFTLQV 136

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

>gnl|CDD|225429 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

 Score = 42.3 bits (100), Expect = 2e-04
 Identities = 35/135 (25%), Positives = 55/135 (40%), Gaps = 25/135 (18%)

Query: 91  LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VIYIDVESTF 148
           LD  L GG+P G +  + G  GTGK+    + +        YG L  G  V Y+  E   
Sbjct: 17  LDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFA--------YGFLMNGYRVTYVSTEL-- 66

Query: 149 TSRRMI-EMGASSFPEI-FHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVK 206
           T R  I +M + S+    F   G           +    ++    S  K+ + LL   +K
Sbjct: 67  TVREFIKQMESLSYDVSDFLLSGRL-----LFFPVNLEPVNWGRRSARKL-LDLLLEFIK 120

Query: 207 -----LLVIDSMEAL 216
                +++IDS+ A 
Sbjct: 121 RWEKDVIIIDSLSAF 135

Length = 235

>gnl|CDD|238545 cd01125, repA, Hexameric Replicative Helicase RepA

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 53/264 (20%), Positives = 91/264 (34%), Gaps = 50/264 (18%)

Query: 102 GVVTELVGPAGTGKTQFCLKLSLLAAL-PAHYGGLD-----GGVIYIDVES--TFTSRRM 153
           G V+ LV P GTGK+   L L+L  AL    +GG       G V+Y+  E       RR+
Sbjct: 1   GYVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRL 60

Query: 154 IEMGASSFPEIFHSKGMAQEMAGRILV----LQPTSLSE-----FTESLEKIKVSLLQNQ 204
             +     P          +   R+ +    +QP S++           E+I   LL  +
Sbjct: 61  EAILQHLEP---------DDAGDRLFIDSGRIQPISIAREGRIIVVPEFERIIEQLLIRR 111

Query: 205 VKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESC 264
           + L+VID + +       +   G   +   I  +  +A  +   I++ + VR  S  +  
Sbjct: 112 IDLVVIDPLVSF--HGVSENDNG--AMDAVIKALRRIAAQTGAAILLVHHVRKGSAKD-- 165

Query: 265 LYPFQVQKMDRI-----LKDRTR---YYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNV 316
                    +       L D  R     + + +              +       RF   
Sbjct: 166 -----GDTQEAARGASALVDGARWVRALTRMTSEEAEKMGVGKAQPGLF-----FRFGVS 215

Query: 317 EKSPTSPPLAFSFTINPSGISLLT 340
           +K+  +   A  +    SG  LL 
Sbjct: 216 KKNNAAATEADRWYRRNSGGVLLP 239

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent. Length = 239

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

 Score = 39.7 bits (92), Expect = 6e-04
 Identities = 31/160 (19%), Positives = 51/160 (31%), Gaps = 30/160 (18%)

Query: 102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSF 161
           G V  +VGP G+GKT      +L  AL    G   GGVIYID E          +     
Sbjct: 2   GEVILIVGPPGSGKT------TLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVG 55

Query: 162 PEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVH 221
            +     G  +                    L        + +  +L++D + +L+    
Sbjct: 56  GKKASGSGELR--------------------LRLALALARKLKPDVLILDEITSLLDAEQ 95

Query: 222 EQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHD 261
           E        L   + L+  L     + +++T         
Sbjct: 96  EA----LLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGP 131

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

>gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed

 Score = 40.8 bits (95), Expect = 8e-04
 Identities = 40/136 (29%), Positives = 60/136 (44%), Gaps = 25/136 (18%)

Query: 84  LPTRLKGLDAAL-CGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
           +PT    LD AL  GG+P G V E+ GP  +GKT     ++L A   A   G  G   +I
Sbjct: 41  IPTGSIALDVALGIGGLPRGRVIEIYGPESSGKT----TVALHAVANAQAAG--GVAAFI 94

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E         ++G  +                 +LV QP +     ++LE   + +  
Sbjct: 95  DAEHALDPDYAKKLGVDT---------------DSLLVSQPDTGE---QALEIADMLIRS 136

Query: 203 NQVKLLVIDSMEALVP 218
             + ++VIDS+ ALVP
Sbjct: 137 GALDIVVIDSVAALVP 152

Length = 790

>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA

 Score = 40.0 bits (94), Expect = 0.001
 Identities = 40/136 (29%), Positives = 57/136 (41%), Gaps = 25/136 (18%)

Query: 84  LPTRLKGLDAAL-CGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
           + T    LD AL  GG+P G + E+ GP  +GKT     L+L A   A   G  G   +I
Sbjct: 36  ISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKT----TLALHAIAEAQKAG--GTAAFI 89

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E         ++G                    +LV QP +  +  E  E +  S   
Sbjct: 90  DAEHALDPVYARKLGVD---------------IDNLLVSQPDTGEQALEIAETLVRS--- 131

Query: 203 NQVKLLVIDSMEALVP 218
             V ++V+DS+ ALVP
Sbjct: 132 GAVDIIVVDSVAALVP 147

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 321

>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 24/60 (40%), Positives = 30/60 (50%), Gaps = 10/60 (16%)

Query: 88  LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VIYIDVE 145
           + GLD  L GG P G V  ++G  GTGKT F        +L   Y GL  G   +YI +E
Sbjct: 2   IPGLDEMLGGGFPEGHVIVVIGEYGTGKTTF--------SLQFLYQGLKNGEKAMYISLE 53

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself. Length = 224

>gnl|CDD|215755 pfam00154, RecA, recA bacterial DNA recombination protein

 Score = 38.4 bits (90), Expect = 0.004
 Identities = 41/136 (30%), Positives = 57/136 (41%), Gaps = 27/136 (19%)

Query: 85  PTRLKGLDAAL-CGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVI-YI 142
            T   GLD AL  GG+P G + E+ GP  +GKT   L L  +A          GG   +I
Sbjct: 34  STGSLGLDIALGIGGLPKGRIIEIYGPESSGKTT--LALHAIAEAQK-----AGGTAAFI 86

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E                P      G+  +    +LV QP +  +  E  + +  S   
Sbjct: 87  DAEHALD------------PVYAKKLGVDID---NLLVSQPDTGEQALEIADMLVRS--- 128

Query: 203 NQVKLLVIDSMEALVP 218
             V L+V+DS+ ALVP
Sbjct: 129 GAVDLIVVDSVAALVP 144

RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyzes an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination. Length = 322

>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated

 Score = 38.0 bits (89), Expect = 0.004
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 12/71 (16%)

Query: 91  LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VIYIDVESTF 148
           LD  L GG+PF  +  + G  GTGK+    +          YG L  G  V  I  E+T 
Sbjct: 14  LDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFV--------YGALKQGKKVYVITTENTS 65

Query: 149 TS--RRMIEMG 157
            S  ++M  + 
Sbjct: 66  KSYLKQMESVK 76

Length = 234

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	357
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	100.0
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	100.0
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	100.0
PTZ00035	337	Rad51 protein; Provisional	100.0
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	100.0
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	100.0
PRK04301	317	radA DNA repair and recombination protein RadA; Va	100.0
KOG1434	335	consensus Meiotic recombination protein Dmc1 [Cell	100.0
TIGR02236	310	recomb_radA DNA repair and recombination protein R	100.0
KOG1564	351	consensus DNA repair protein RHP57 [Replication, r	100.0
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	100.0
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	100.0
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	100.0
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	100.0
cd01394	218	radB RadB. The archaeal protein radB shares simila	100.0
TIGR02237	209	recomb_radB DNA repair and recombination protein R	100.0
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	100.0
PRK04328	249	hypothetical protein; Provisional	99.98
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	99.98
cd00983	325	recA RecA is a bacterial enzyme which has roles in	99.97
PRK09354	349	recA recombinase A; Provisional	99.97
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	99.97
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	99.97
PRK11823	446	DNA repair protein RadA; Provisional	99.97
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	99.97
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	99.97
PRK08760	476	replicative DNA helicase; Provisional	99.97
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	99.97
PRK08006	471	replicative DNA helicase; Provisional	99.97
PRK09165	497	replicative DNA helicase; Provisional	99.97
PRK07004	460	replicative DNA helicase; Provisional	99.97
PRK06321	472	replicative DNA helicase; Provisional	99.96
COG0305	435	DnaB Replicative DNA helicase [DNA replication, re	99.96
PRK06904	472	replicative DNA helicase; Validated	99.96
PHA02542	473	41 41 helicase; Provisional	99.96
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	99.96
PRK08840	464	replicative DNA helicase; Provisional	99.96
PRK05748	448	replicative DNA helicase; Provisional	99.96
PRK05636	505	replicative DNA helicase; Provisional	99.96
PRK05595	444	replicative DNA helicase; Provisional	99.96
PRK09519	790	recA DNA recombination protein RecA; Reviewed	99.96
PRK06749	428	replicative DNA helicase; Provisional	99.96
TIGR00665	434	DnaB replicative DNA helicase. This model describe	99.96
PRK08506	472	replicative DNA helicase; Provisional	99.96
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	99.95
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	99.95
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	99.95
KOG1433	326	consensus DNA repair protein RAD51/RHP55 [Replicat	99.95
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	99.94
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	99.94
PF00154	322	RecA: recA bacterial DNA recombination protein; In	99.94
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	99.94
PRK06067	234	flagellar accessory protein FlaH; Validated	99.94
PRK09302	509	circadian clock protein KaiC; Reviewed	99.94
PRK09302	509	circadian clock protein KaiC; Reviewed	99.93
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	99.92
PRK07773	886	replicative DNA helicase; Validated	99.91
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	99.89
PRK08533	230	flagellar accessory protein FlaH; Reviewed	99.88
PRK05973	237	replicative DNA helicase; Provisional	99.85
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	99.81
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	99.8
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	99.71
KOG2859	293	consensus DNA repair protein, member of the recA/R	99.7
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	99.66
KOG2373	514	consensus Predicted mitochondrial DNA helicase twi	99.51
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	99.46
COG3598	402	RepA RecA-family ATPase [DNA replication, recombin	99.35
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	99.18
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	98.83
PRK04296	190	thymidine kinase; Provisional	98.79
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	98.75
PF13479	213	AAA_24: AAA domain	98.69
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	98.68
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.66
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	98.6
COG1135	339	AbcC ABC-type metal ion transport system, ATPase c	98.59
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.55
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	98.54
smart00382	148	AAA ATPases associated with a variety of cellular	98.54
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	98.46
COG1127	263	Ttg2A ABC-type transport system involved in resist	98.46
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	98.43
COG0410	237	LivF ABC-type branched-chain amino acid transport	98.41
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	98.39
COG4604	252	CeuD ABC-type enterochelin transport system, ATPas	98.37
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	98.35
PF00004	132	AAA: ATPase family associated with various cellula	98.34
COG3845	501	ABC-type uncharacterized transport systems, ATPase	98.31
COG4619	223	ABC-type uncharacterized transport system, ATPase	98.31
cd03115	173	SRP The signal recognition particle (SRP) mediates	98.31
cd03216	163	ABC_Carb_Monos_I This family represents the domain	98.29
PF05625	363	PAXNEB: PAXNEB protein; InterPro: IPR008728 The RN	98.28
COG3638	258	ABC-type phosphate/phosphonate transport system, A	98.25
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	98.24
PRK10867	433	signal recognition particle protein; Provisional	98.24
PRK00771	437	signal recognition particle protein Srp54; Provisi	98.23
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	98.21
TIGR00064	272	ftsY signal recognition particle-docking protein F	98.2
PRK13650	279	cbiO cobalt transporter ATP-binding subunit; Provi	98.2
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	98.19
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	98.19
cd03246	173	ABCC_Protease_Secretion This family represents the	98.19
COG0444	316	DppD ABC-type dipeptide/oligopeptide/nickel transp	98.18
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	98.18
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	98.17
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	98.17
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	98.17
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	98.16
PRK13635	279	cbiO cobalt transporter ATP-binding subunit; Provi	98.16
PRK11701	258	phnK phosphonate C-P lyase system protein PhnK; Pr	98.16
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	98.16
PRK09473	330	oppD oligopeptide transporter ATP-binding componen	98.15
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	98.15
COG0411	250	LivG ABC-type branched-chain amino acid transport	98.14
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	98.14
TIGR02314	343	ABC_MetN D-methionine ABC transporter, ATP-binding	98.14
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.13
PRK13648	269	cbiO cobalt transporter ATP-binding subunit; Provi	98.13
PRK10416	318	signal recognition particle-docking protein FtsY;	98.13
TIGR00959	428	ffh signal recognition particle protein. This mode	98.12
PRK13633	280	cobalt transporter ATP-binding subunit; Provisiona	98.12
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	98.11
PRK13646	286	cbiO cobalt transporter ATP-binding subunit; Provi	98.11
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	98.11
PRK13636	283	cbiO cobalt transporter ATP-binding subunit; Provi	98.1
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	98.1
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	98.1
PRK13634	290	cbiO cobalt transporter ATP-binding subunit; Provi	98.09
cd03298	211	ABC_ThiQ_thiamine_transporter ABC-type thiamine tr	98.09
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	98.09
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	98.09
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	98.09
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	98.09
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	98.09
TIGR03415	382	ABC_choXWV_ATP choline ABC transporter, ATP-bindin	98.08
TIGR01186	363	proV glycine betaine/L-proline transport ATP bindi	98.08
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	98.08
TIGR01184	230	ntrCD nitrate transport ATP-binding subunits C and	98.07
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	98.07
PRK11022	326	dppD dipeptide transporter ATP-binding subunit; Pr	98.07
PRK13652	277	cbiO cobalt transporter ATP-binding subunit; Provi	98.07
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	98.06
PRK11308	327	dppF dipeptide transporter ATP-binding subunit; Pr	98.06
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	98.06
PRK13537	306	nodulation ABC transporter NodI; Provisional	98.05
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	98.05
COG1123	539	ATPase components of various ABC-type transport sy	98.05
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	98.05
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	98.04
PRK10070	400	glycine betaine transporter ATP-binding subunit; P	98.04
cd03294	269	ABC_Pro_Gly_Bertaine This family comprises the gly	98.03
TIGR01188	302	drrA daunorubicin resistance ABC transporter ATP-b	98.03
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	98.03
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	98.03
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	98.03
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	98.03
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	98.03
PRK11153	343	metN DL-methionine transporter ATP-binding subunit	98.02
PRK12377	248	putative replication protein; Provisional	98.02
TIGR02323	253	CP_lyasePhnK phosphonate C-P lyase system protein	98.02
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	98.02
COG2884	223	FtsE Predicted ATPase involved in cell division [C	98.02
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	98.02
PRK13640	282	cbiO cobalt transporter ATP-binding subunit; Provi	98.02
TIGR00968	237	3a0106s01 sulfate ABC transporter, ATP-binding pro	98.01
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	98.01
cd03300	232	ABC_PotA_N PotA is an ABC-type transporter and the	98.0
PRK13642	277	cbiO cobalt transporter ATP-binding subunit; Provi	98.0
PRK13647	274	cbiO cobalt transporter ATP-binding subunit; Provi	98.0
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	97.99
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	97.99
COG3842	352	PotA ABC-type spermidine/putrescine transport syst	97.98
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	97.98
PRK13632	271	cbiO cobalt transporter ATP-binding subunit; Provi	97.98
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.97
PRK13637	287	cbiO cobalt transporter ATP-binding subunit; Provi	97.97
PRK10771	232	thiQ thiamine transporter ATP-binding subunit; Pro	97.97
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	97.97
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	97.96
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	97.96
TIGR02982	220	heterocyst_DevA ABC exporter ATP-binding subunit,	97.95
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	97.95
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	97.94
PF13173	128	AAA_14: AAA domain	97.94
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	97.94
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	97.94
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	97.94
COG4107	258	PhnK ABC-type phosphonate transport system, ATPase	97.94
PRK10851	353	sulfate/thiosulfate transporter subunit; Provision	97.94
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	97.94
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	97.94
cd03215	182	ABC_Carb_Monos_II This family represents domain II	97.93
TIGR03005	252	ectoine_ehuA ectoine/hydroxyectoine ABC transporte	97.93
PRK11650	356	ugpC glycerol-3-phosphate transporter ATP-binding	97.93
PRK14974	336	cell division protein FtsY; Provisional	97.92
PRK13645	289	cbiO cobalt transporter ATP-binding subunit; Provi	97.92
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	97.92
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	97.92
PRK11432	351	fbpC ferric transporter ATP-binding subunit; Provi	97.92
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	97.92
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	97.91
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	97.91
PRK13536	340	nodulation factor exporter subunit NodI; Provision	97.91
PRK15079	331	oligopeptide ABC transporter ATP-binding protein O	97.91
cd03299	235	ABC_ModC_like Archeal protein closely related to M	97.91
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.91
PRK07952	244	DNA replication protein DnaC; Validated	97.91
cd03269	210	ABC_putative_ATPase This subfamily is involved in	97.9
PRK13651	305	cobalt transporter ATP-binding subunit; Provisiona	97.9
PRK13548	258	hmuV hemin importer ATP-binding subunit; Provision	97.9
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	97.9
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	97.9
TIGR01288	303	nodI ATP-binding ABC transporter family nodulation	97.9
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	97.89
PRK13638	271	cbiO cobalt transporter ATP-binding subunit; Provi	97.89
PRK13643	288	cbiO cobalt transporter ATP-binding subunit; Provi	97.89
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	97.89
PF05729	166	NACHT: NACHT domain	97.88
PRK11000	369	maltose/maltodextrin transporter ATP-binding prote	97.88
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	97.88
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	97.88
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	97.88
TIGR03265	353	PhnT2 putative 2-aminoethylphosphonate ABC transpo	97.88
PRK13639	275	cbiO cobalt transporter ATP-binding subunit; Provi	97.87
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	97.87
PRK08181	269	transposase; Validated	97.87
PRK06835	329	DNA replication protein DnaC; Validated	97.87
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	97.87
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	97.87
COG1118	345	CysA ABC-type sulfate/molybdate transport systems,	97.87
COG4586	325	ABC-type uncharacterized transport system, ATPase	97.86
PRK11831	269	putative ABC transporter ATP-binding protein YrbF;	97.86
COG4598	256	HisP ABC-type histidine transport system, ATPase c	97.86
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.86
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	97.86
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	97.86
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	97.86
PRK10908	222	cell division protein FtsE; Provisional	97.86
PRK11144	352	modC molybdate transporter ATP-binding protein; Pr	97.86
COG3839	338	MalK ABC-type sugar transport systems, ATPase comp	97.85
PRK09452	375	potA putrescine/spermidine ABC transporter ATPase	97.85
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	97.85
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	97.85
PRK13644	274	cbiO cobalt transporter ATP-binding subunit; Provi	97.84
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.84
PRK08727	233	hypothetical protein; Validated	97.84
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	97.84
PRK11607	377	potG putrescine transporter ATP-binding subunit; P	97.84
PRK15112	267	antimicrobial peptide ABC system ATP-binding prote	97.84
PRK13631	320	cbiO cobalt transporter ATP-binding subunit; Provi	97.84
PRK06526	254	transposase; Provisional	97.84
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	97.83
TIGR03258	362	PhnT 2-aminoethylphosphonate ABC transport system,	97.83
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.82
COG1129	500	MglA ABC-type sugar transport system, ATPase compo	97.82
PRK08116	268	hypothetical protein; Validated	97.82
TIGR02142	354	modC_ABC molybdenum ABC transporter, ATP-binding p	97.82
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.82
PRK15093	330	antimicrobial peptide ABC transporter ATP-binding	97.82
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	97.81
PRK13649	280	cbiO cobalt transporter ATP-binding subunit; Provi	97.81
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	97.81
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	97.81
PRK13641	287	cbiO cobalt transporter ATP-binding subunit; Provi	97.8
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	97.8
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.8
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	97.8
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.79
PRK10418	254	nikD nickel transporter ATP-binding protein NikD;	97.79
PRK07721	438	fliI flagellum-specific ATP synthase; Validated	97.79
COG1123	539	ATPase components of various ABC-type transport sy	97.78
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	97.78
KOG0061	613	consensus Transporter, ABC superfamily (Breast can	97.78
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	97.78
PRK09984	262	phosphonate/organophosphate ester transporter subu	97.77
cd03257	228	ABC_NikE_OppD_transporters The ABC transporter sub	97.77
PRK11614	237	livF leucine/isoleucine/valine transporter ATP-bin	97.77
TIGR03797	686	NHPM_micro_ABC2 NHPM bacteriocin system ABC transp	97.77
TIGR02770	230	nickel_nikD nickel import ATP-binding protein NikD	97.76
TIGR02769	265	nickel_nikE nickel import ATP-binding protein NikE	97.76
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	97.76
TIGR02324	224	CP_lyasePhnL phosphonate C-P lyase system protein	97.76
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	97.76
PRK03695	248	vitamin B12-transporter ATPase; Provisional	97.75
PRK10253	265	iron-enterobactin transporter ATP-binding protein;	97.75
cd03245	220	ABCC_bacteriocin_exporters ABC-type bacteriocin ex	97.75
PRK09536	402	btuD corrinoid ABC transporter ATPase; Reviewed	97.75
cd01132	274	F1_ATPase_alpha F1 ATP synthase alpha, central dom	97.75
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.75
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	97.74
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	97.74
PRK10419	268	nikE nickel transporter ATP-binding protein NikE;	97.74
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	97.74
PRK06921	266	hypothetical protein; Provisional	97.72
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	97.72
PRK10895	241	lipopolysaccharide ABC transporter ATP-binding pro	97.72
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	97.72
PRK11264	250	putative amino-acid ABC transporter ATP-binding pr	97.71
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	97.71
cd01128	249	rho_factor Transcription termination factor rho is	97.71
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.71
COG4175	386	ProV ABC-type proline/glycine betaine transport sy	97.7
TIGR03771	223	anch_rpt_ABC anchored repeat-type ABC transporter,	97.7
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	97.7
PRK10261	623	glutathione transporter ATP-binding protein; Provi	97.7
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	97.7
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	97.69
PRK13546	264	teichoic acids export protein ATP-binding subunit;	97.69
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	97.69
TIGR03411	242	urea_trans_UrtD urea ABC transporter, ATP-binding	97.69
PRK08939	306	primosomal protein DnaI; Reviewed	97.69
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	97.68
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	97.68
cd03248	226	ABCC_TAP TAP, the Transporter Associated with Anti	97.68
PRK13547	272	hmuV hemin importer ATP-binding subunit; Provision	97.67
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	97.67
PRK08084	235	DNA replication initiation factor; Provisional	97.67
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	97.66
COG2087	175	CobU Adenosyl cobinamide kinase/adenosyl cobinamid	97.66
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	97.66
TIGR02857	529	CydD thiol reductant ABC exporter, CydD subunit. U	97.66
TIGR03873	256	F420-0_ABC_ATP proposed F420-0 ABC transporter, AT	97.66
TIGR00750	300	lao LAO/AO transport system ATPase. Mutations have	97.66
cd03271	261	ABC_UvrA_II The excision repair protein UvrA domai	97.65
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	97.65
PRK09376	416	rho transcription termination factor Rho; Provisio	97.65
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	97.65
COG3840	231	ThiQ ABC-type thiamine transport system, ATPase co	97.65
TIGR02546	422	III_secr_ATP type III secretion apparatus H+-trans	97.65
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	97.64
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	97.64
PF02283	167	CobU: Cobinamide kinase / cobinamide phosphate gua	97.64
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	97.64
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.63
COG1245	591	Predicted ATPase, RNase L inhibitor (RLI) homolog	97.63
TIGR00767	415	rho transcription termination factor Rho. Members	97.63
PRK13409	590	putative ATPase RIL; Provisional	97.63
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	97.63
PRK06893	229	DNA replication initiation factor; Validated	97.62
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	97.62
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	97.62
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	97.62
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	97.62
COG4615	546	PvdE ABC-type siderophore export system, fused ATP	97.61
COG4674	249	Uncharacterized ABC-type transport system, ATPase	97.61
COG4555	245	NatA ABC-type Na+ transport system, ATPase compone	97.61
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	97.61
PF13245	76	AAA_19: Part of AAA domain	97.61
PRK10261	623	glutathione transporter ATP-binding protein; Provi	97.6
COG4172	534	ABC-type uncharacterized transport system, duplica	97.6
PRK14271	276	phosphate ABC transporter ATP-binding protein; Pro	97.59
PF09807	249	DUF2348: Uncharacterized conserved protein (DUF234	97.59
PRK05642	234	DNA replication initiation factor; Validated	97.59
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	97.59
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	97.58
TIGR01194	555	cyc_pep_trnsptr cyclic peptide transporter. This m	97.58
PRK09700	510	D-allose transporter ATP-binding protein; Provisio	97.58
PRK09099	441	type III secretion system ATPase; Provisional	97.58
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	97.58
cd03290	218	ABCC_SUR1_N The SUR domain 1. The sulfonylurea rec	97.57
PRK15056	272	manganese/iron transporter ATP-binding protein; Pr	97.57
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	97.57
PRK09580	248	sufC cysteine desulfurase ATPase component; Review	97.57
COG4181	228	Predicted ABC-type transport system involved in ly	97.57
PRK03992	389	proteasome-activating nucleotidase; Provisional	97.56
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	97.56
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.56
PF00006	215	ATP-synt_ab: ATP synthase alpha/beta family, nucle	97.55
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	97.55
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.55
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	97.55
KOG0736	953	consensus Peroxisome assembly factor 2 containing	97.55
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.55
TIGR01842	544	type_I_sec_PrtD type I secretion system ABC transp	97.55
cd03236	255	ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 o	97.55
PRK11231	255	fecE iron-dicitrate transporter ATP-binding subuni	97.54
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.54
TIGR03269	520	met_CoM_red_A2 methyl coenzyme M reductase system,	97.53
PRK07594	433	type III secretion system ATPase SsaN; Validated	97.52
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.51
CHL00059	485	atpA ATP synthase CF1 alpha subunit	97.51
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.51
PRK10762	501	D-ribose transporter ATP binding protein; Provisio	97.51
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.51
PLN03130	1622	ABC transporter C family member; Provisional	97.51
TIGR01846	694	type_I_sec_HlyB type I secretion system ABC transp	97.5
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	97.5
cd03234	226	ABCG_White The White subfamily represents ABC tran	97.5
PRK15134	529	microcin C ABC transporter ATP-binding protein Yej	97.5
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.49
PRK08233	182	hypothetical protein; Provisional	97.49
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	97.49
PRK11288	501	araG L-arabinose transporter ATP-binding protein;	97.49
PRK10789	569	putative multidrug transporter membrane\ATP-bindin	97.48
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	97.47
TIGR01192	585	chvA glucan exporter ATP-binding protein. This mod	97.47
PRK10522	547	multidrug transporter membrane component/ATP-bindi	97.47
PRK14258	261	phosphate ABC transporter ATP-binding protein; Pro	97.46
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.46
PRK14269	246	phosphate ABC transporter ATP-binding protein; Pro	97.46
PLN03232	1495	ABC transporter C family member; Provisional	97.46
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	97.46
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	97.46
cd01134	369	V_A-ATPase_A V/A-type ATP synthase catalytic subun	97.46
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.45
CHL00195	489	ycf46 Ycf46; Provisional	97.45
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	97.45
COG4161	242	ArtP ABC-type arginine transport system, ATPase co	97.44
PRK10938	490	putative molybdenum transport ATP-binding protein	97.44
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	97.44
PRK13549	506	xylose transporter ATP-binding subunit; Provisiona	97.43
TIGR00962	501	atpA proton translocating ATP synthase, F1 alpha s	97.43
PRK14086	617	dnaA chromosomal replication initiation protein; P	97.42
PRK10982	491	galactose/methyl galaxtoside transporter ATP-bindi	97.42
COG0541	451	Ffh Signal recognition particle GTPase [Intracellu	97.42
cd03291	282	ABCC_CFTR1 The CFTR subfamily domain 1. The cystic	97.42
PRK13343	502	F0F1 ATP synthase subunit alpha; Provisional	97.41
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	97.41
PRK06793	432	fliI flagellum-specific ATP synthase; Validated	97.41
PRK09700	510	D-allose transporter ATP-binding protein; Provisio	97.41
PRK06936	439	type III secretion system ATPase; Provisional	97.4
TIGR01039	461	atpD ATP synthase, F1 beta subunit. The sequences	97.4
PRK15134	529	microcin C ABC transporter ATP-binding protein Yej	97.4
PRK08472	434	fliI flagellum-specific ATP synthase; Validated	97.4
PTZ00243	1560	ABC transporter; Provisional	97.39
PRK00889	175	adenylylsulfate kinase; Provisional	97.39
COG4172	534	ABC-type uncharacterized transport system, duplica	97.39
cd03288	257	ABCC_SUR2 The SUR domain 2. The sulfonylurea recep	97.39
PRK06820	440	type III secretion system ATPase; Validated	97.39
PRK13768	253	GTPase; Provisional	97.39
COG4178	604	ABC-type uncharacterized transport system, permeas	97.38
PRK05922	434	type III secretion system ATPase; Validated	97.38
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.37
TIGR00957	1522	MRP_assoc_pro multi drug resistance-associated pro	97.36
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.36
PRK12608	380	transcription termination factor Rho; Provisional	97.35
TIGR01271	1490	CFTR_protein cystic fibrosis transmembrane conduct	97.35
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.35
TIGR03497	413	FliI_clade2 flagellar protein export ATPase FliI.	97.35
COG0488	530	Uup ATPase components of ABC transporters with dup	97.35
TIGR03269	520	met_CoM_red_A2 methyl coenzyme M reductase system,	97.34
cd03114	148	ArgK-like The function of this protein family is u	97.34
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	97.34
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	97.33
PRK07165	507	F0F1 ATP synthase subunit alpha; Validated	97.33
COG4148	352	ModC ABC-type molybdate transport system, ATPase c	97.33
PRK14087	450	dnaA chromosomal replication initiation protein; P	97.33
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	97.32
PRK08972	444	fliI flagellum-specific ATP synthase; Validated	97.32
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	97.32
PRK09435	332	membrane ATPase/protein kinase; Provisional	97.3
COG4988	559	CydD ABC-type transport system involved in cytochr	97.3
PRK12678	672	transcription termination factor Rho; Provisional	97.3
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	97.3
TIGR03324	497	alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit a	97.29
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	97.29
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	97.28
CHL00176	638	ftsH cell division protein; Validated	97.28
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.27
PRK09280	463	F0F1 ATP synthase subunit beta; Validated	97.27
PTZ00265	1466	multidrug resistance protein (mdr1); Provisional	97.27
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.27
PRK14088	440	dnaA chromosomal replication initiation protein; P	97.26
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.26
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	97.25
PTZ00265	1466	multidrug resistance protein (mdr1); Provisional	97.25
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	97.25
TIGR00955	617	3a01204 The Eye Pigment Precursor Transporter (EPP	97.24
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	97.24
TIGR01026	440	fliI_yscN ATPase FliI/YscN family. This family of	97.23
PRK12597	461	F0F1 ATP synthase subunit beta; Provisional	97.23
PRK05688	451	fliI flagellum-specific ATP synthase; Validated	97.22
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	97.22
PRK09183	259	transposase/IS protein; Provisional	97.21
cd01136	326	ATPase_flagellum-secretory_path_III Flagellum-spec	97.21
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	97.21
COG0552	340	FtsY Signal recognition particle GTPase [Intracell	97.2
TIGR02633	500	xylG D-xylose ABC transporter, ATP-binding protein	97.2
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	97.19
PRK08927	442	fliI flagellum-specific ATP synthase; Validated	97.19
PRK09281	502	F0F1 ATP synthase subunit alpha; Validated	97.19
COG4559	259	ABC-type hemin transport system, ATPase component	97.19
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	97.18
PRK10535	648	macrolide transporter ATP-binding /permease protei	97.18
PRK05541	176	adenylylsulfate kinase; Provisional	97.17
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.17
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	97.17
PRK11147	635	ABC transporter ATPase component; Reviewed	97.17
TIGR03498	418	FliI_clade3 flagellar protein export ATPase FliI.	97.17
PRK08699	325	DNA polymerase III subunit delta'; Validated	97.17
TIGR00954	659	3a01203 Peroxysomal Fatty Acyl CoA Transporter (FA	97.16
COG1101	263	PhnK ABC-type uncharacterized transport system, AT	97.15
cd01135	276	V_A-ATPase_B V/A-type ATP synthase (non-catalytic)	97.15
TIGR03305	449	alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit	97.15
PRK13695	174	putative NTPase; Provisional	97.14
TIGR03496	411	FliI_clade1 flagellar protein export ATPase FliI.	97.14
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	97.14
PRK13409	590	putative ATPase RIL; Provisional	97.14
PTZ00185	574	ATPase alpha subunit; Provisional	97.14

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=100.00  E-value=2.3e-52  Score=381.03  Aligned_cols=306  Identities=24%  Similarity=0.295  Sum_probs=265.8

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCC
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLP   85 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   85 (357)
                      +..+++++.+.++|+++|++|+++++..++.+|.++.+++++++.++++.+.+.++.++.++.++++++.+    ..+++
T Consensus        34 l~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~~~~~~~ta~~~~~~~~~----~~~is  109 (344)
T PLN03187         34 LISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKLLNQGFITGSDALLKRKS----VVRIT  109 (344)
T ss_pred             HhhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHhhcccCCcHHHHHhhhcc----Cceec
Confidence            45578999999999999999999999999999999999999999999999998888899999999987533    56899


Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhh
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF  165 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~  165 (357)
                      ||+++||++|+||+++|.+++|+|+||+|||+||+|++.+++++...||.+++|+|||+|++|+++|+.++++..     
T Consensus       110 TG~~~LD~lLgGGi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~peRl~~ia~~~-----  184 (344)
T PLN03187        110 TGSQALDELLGGGIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAERF-----  184 (344)
T ss_pred             CCcHhHHhhcCCCCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCHHHHHHHHHHc-----
Confidence            999999999999999999999999999999999999999999887777778999999999999999999988641     


Q ss_pred             cccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHHHH
Q 035774          166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLA  242 (357)
Q Consensus       166 ~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~la  242 (357)
                      ..+  .+..++++++.++.+.+++..++..+...+.+.++++|||||++++++.++.+.   ..|++.+.++++.|+++|
T Consensus       185 g~d--~~~~l~~I~~~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSital~r~~~~~rg~l~~rq~~L~~~~~~L~~lA  262 (344)
T PLN03187        185 GMD--ADAVLDNIIYARAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVIALFRVDFTGRGELAERQQKLAQMLSRLTKIA  262 (344)
T ss_pred             CCC--hhhhcCeEEEecCCCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHhhhccccCccchHHHHHHHHHHHHHHHHHH
Confidence            111  235678899999999999888888887778788999999999999998755432   235566889999999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEEEEeCCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSPT  321 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~v~K~r~  321 (357)
                      +++|++||+|||++.+.+.. ..                 +....+|++|.+|+|.+++|++|++. +..|.++|+|+|+
T Consensus       263 ~~~~vavvvTNqv~~~~~~~-~~-----------------~~~~~~pagG~~~~h~~~~Rl~l~k~~~~~R~~~v~ksp~  324 (344)
T PLN03187        263 EEFNVAVYMTNQVIADPGGG-MF-----------------ISDPKKPAGGHVLAHAATIRLMLRKGKGEQRVCKVFDAPN  324 (344)
T ss_pred             HHcCCEEEEEecEEEcCCcc-cc-----------------cCCCCCCCCchhhheeeeEEEEEEcCCCCeEEEEEEECCC
Confidence            99999999999998765411 11                 11224699999999999999999985 5689999999999


Q ss_pred             CCCceeEEEEcCCCceecc
Q 035774          322 SPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       322 ~~~~~~~f~I~~~Gi~~~~  340 (357)
                      .|...+.|.|+++||....
T Consensus       325 lp~~~~~f~It~~GI~d~~  343 (344)
T PLN03187        325 LPEAEAEFQITSGGIMDAK  343 (344)
T ss_pred             CCCceEEEEEeCCCccCCC
Confidence            9999999999999998754

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=100.00  E-value=5.5e-52  Score=376.59  Aligned_cols=305  Identities=25%  Similarity=0.330  Sum_probs=264.7

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCC
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLP   85 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   85 (357)
                      +..+++++..+++|+++|+.|+++++..++.+|.++.+++++++.++++++.+.....+.+|.++++++.+    ..+++
T Consensus         4 ~~~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~~~~~~~ta~~~~~~~~~----~~~is   79 (313)
T TIGR02238         4 LQAHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKIINPGFITAFEISQKRKK----VLKIT   79 (313)
T ss_pred             hhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhhhcccCccHHHHHHhhcc----CceeC
Confidence            34678999999999999999999999999999999999999999999999998888889999999887543    56899


Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhh
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF  165 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~  165 (357)
                      ||++.||.+|+||+++|.+++|+|+||+|||+||+|++.+++++...|+.+++|+|||+|++|+++|+.++++..     
T Consensus        80 TG~~~LD~lLgGGi~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~eRi~~~a~~~-----  154 (313)
T TIGR02238        80 TGSQALDGILGGGIESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERF-----  154 (313)
T ss_pred             CCCHHHHHHhCCCCcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCHHHHHHHHHHc-----
Confidence            999999999999999999999999999999999999999998876677778999999999999999999988652     


Q ss_pred             cccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHHHH
Q 035774          166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLA  242 (357)
Q Consensus       166 ~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~la  242 (357)
                      ..+  .+..++++++.++.+.++..+.+..+...+.+.++++|||||++++++.++.+.   ..|++.+.+++..|+++|
T Consensus       155 g~d--~~~~l~~i~~~~~~~~e~~~~~l~~l~~~i~~~~~~LvVIDSisal~r~~~~~~g~~~~r~~~l~~~~~~L~~la  232 (313)
T TIGR02238       155 GVD--PDAVLDNILYARAYTSEHQMELLDYLAAKFSEEPFRLLIVDSIMALFRVDFSGRGELSERQQKLAQMLSRLNKIS  232 (313)
T ss_pred             CCC--hHHhcCcEEEecCCCHHHHHHHHHHHHHHhhccCCCEEEEEcchHhhhhhccCccchHHHHHHHHHHHHHHHHHH
Confidence            111  245678899999999999988888888888778999999999999998755432   224556888999999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEEEEeCCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSPT  321 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~v~K~r~  321 (357)
                      +++|++||+|||++.+.+.. .+|.                ....+|++|..|+|.+++|++|++. +..|.++|+|+|+
T Consensus       233 ~~~~vavvitNqv~~~~~~~-~~~~----------------~~~~~p~gG~~~~h~~~~Rl~l~k~~~~~R~~~~~~sp~  295 (313)
T TIGR02238       233 EEFNVAVFVTNQVQADPGAT-MTFI----------------ADPKKPIGGHVLAHASTTRILLRKGRGEERVAKLYDSPD  295 (313)
T ss_pred             HHcCcEEEEECceEecCCcc-cccC----------------CCCccCcchhhhhhheeEEEEEEecCCCeEEEEEeeCCC
Confidence            99999999999998865421 1110                1245799999999999999999995 6789999999999


Q ss_pred             CCCceeEEEEcCCCcee
Q 035774          322 SPPLAFSFTINPSGISL  338 (357)
Q Consensus       322 ~~~~~~~f~I~~~Gi~~  338 (357)
                      .|...+.|.|+++||..
T Consensus       296 ~p~~~~~f~i~~~Gi~~  312 (313)
T TIGR02238       296 MPEAEASFQITEGGIAD  312 (313)
T ss_pred             CCCeEEEEEEeCCcccC
Confidence            99999999999999975

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.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=100.00  E-value=6.9e-50  Score=365.42  Aligned_cols=307  Identities=25%  Similarity=0.343  Sum_probs=262.6

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCC
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLP   85 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   85 (357)
                      +...++++..+++|+++|+.|+++++..++.+|.++.++++.++.+++..+.+.+...+.++.++++.+..    ..+++
T Consensus        31 l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~~~~~~~~~~ta~~~~~~~~~----~~~i~  106 (342)
T PLN03186         31 LQASGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAASKLVPLGFTTASQLHAQRQE----IIQIT  106 (342)
T ss_pred             HHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHhcccccchHHHHhhcccC----cceeC
Confidence            34578999999999999999999999999999999999999999999999988888899999888876432    67899


Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhh
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF  165 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~  165 (357)
                      ||+++||.+|+||+++|++++|+|+||+|||+||++++.+++++...||.+++|+|||+|++|+++|+.++++..     
T Consensus       107 tG~~~LD~lL~GG~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~eRl~qia~~~-----  181 (342)
T PLN03186        107 TGSRELDKILEGGIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAERF-----  181 (342)
T ss_pred             CCCHHHHHhhcCCCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccHHHHHHHHHHc-----
Confidence            999999999999999999999999999999999999999988876667677899999999999999999998652     


Q ss_pred             cccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC---CChHHHHHHHHHHHHHH
Q 035774          166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA---PGQHPLSWHISLITSLA  242 (357)
Q Consensus       166 ~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~---~r~~~~~~i~~~Lk~la  242 (357)
                      ...  .+..++++++.++.+.+++..++..+...+...++++|||||++++++.++.+..   .|+..+.++++.|+++|
T Consensus       182 ~~~--~~~~l~~i~~~~~~~~e~~~~ll~~~~~~~~~~~~~LIVIDSI~alfr~~~~~~g~l~~r~~~L~~~l~~L~~lA  259 (342)
T PLN03186        182 GLN--GADVLENVAYARAYNTDHQSELLLEAASMMAETRFALMIVDSATALYRTEFSGRGELSARQMHLGKFLRSLQRLA  259 (342)
T ss_pred             CCC--hhhhccceEEEecCCHHHHHHHHHHHHHHhhccCCCEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHH
Confidence            111  2346688999999999988888888777777789999999999999886543321   24456788999999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEEEEeCCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSPT  321 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~v~K~r~  321 (357)
                      +++|++||+|||+....+.. ..|.                .+.++|++|..|+|++++|++|++. +..|.++|+|+|+
T Consensus       260 ~~~~vaVviTNqv~~~~~~~-~~~~----------------~~~~~P~gG~~~~h~~~tRl~L~k~~~~~R~~~v~ksp~  322 (342)
T PLN03186        260 DEFGVAVVITNQVVAQVDGS-AFFA----------------GPQLKPIGGNIMAHASTTRLALRKGRGENRICKVISSPC  322 (342)
T ss_pred             HHcCCEEEEEcCEEEccCCc-cccC----------------CCccccchhHHHHhhccEEEEEEecCCCeEEEEEEECCC
Confidence            99999999999998765421 1111                1246899999999999999999974 5689999999999


Q ss_pred             CCCceeEEEEcCCCceecc
Q 035774          322 SPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       322 ~~~~~~~f~I~~~Gi~~~~  340 (357)
                      .|..++.|.|+++||....
T Consensus       323 ~p~~e~~F~I~~~Gi~~~~  341 (342)
T PLN03186        323 LPEAEARFSISSEGVTDVK  341 (342)
T ss_pred             CCCeEEEEEEECCceecCC
Confidence            9999899999999998653

>PTZ00035 Rad51 protein; Provisional

Probab=100.00  E-value=1.4e-49  Score=364.83  Aligned_cols=307  Identities=25%  Similarity=0.331  Sum_probs=264.3

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCC
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLP   85 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   85 (357)
                      +...++++..+++|+++|++|+++++..++.+|.++.+++++++.+++.++.+....++.+|.++++++.+    ..+++
T Consensus        26 l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~~~~~~~ta~~~~~~~~~----~~~is  101 (337)
T PTZ00035         26 LQSAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKLVPMGFISATEYLEARKN----IIRIT  101 (337)
T ss_pred             HhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHhcccCCCCHHHHHHhhcc----Ccccc
Confidence            44578999999999999999999999999999999999999999999999998888899999999988533    67899


Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhh
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF  165 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~  165 (357)
                      ||++.||.+|+||+++|++++|+|+||+|||+||++++.++.++...||.+++|+|||+|+.|+++|+.++.+..     
T Consensus       102 TG~~~LD~lLgGGi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~eri~~ia~~~-----  176 (337)
T PTZ00035        102 TGSTQLDKLLGGGIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERIVQIAERF-----  176 (337)
T ss_pred             CCcHHHHHHhCCCCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCHHHHHHHHHHh-----
Confidence            999999999999999999999999999999999999999988766677778999999999999999999887641     


Q ss_pred             cccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHHHH
Q 035774          166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLA  242 (357)
Q Consensus       166 ~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~la  242 (357)
                      ...  ....++++.+.++.+.+++.+.+..+...+.+.++++|||||++++++.++.+.   ..|++.+.+++..|+++|
T Consensus       177 g~~--~~~~l~nI~~~~~~~~e~~~~~l~~~~~~l~~~~~~lvVIDSital~r~~~~~~~~~~~r~~~l~~~~~~L~~la  254 (337)
T PTZ00035        177 GLD--PEDVLDNIAYARAYNHEHQMQLLSQAAAKMAEERFALLIVDSATALFRVDYSGRGELAERQQHLGKFLRALQKLA  254 (337)
T ss_pred             CCC--hHhHhhceEEEccCCHHHHHHHHHHHHHHhhccCccEEEEECcHHhhhhhccCcccHHHHHHHHHHHHHHHHHHH
Confidence            111  235678899999999998888888877777778999999999999988755432   125566888999999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEEEEeCCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSPT  321 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~v~K~r~  321 (357)
                      +++|++||+|||++...+.. .+|.                ....+|++|..|.|.+++|+++++. +..|.++|+|+|.
T Consensus       255 ~~~~vavvvtNqv~~~~~~~-~~~~----------------~~~~~p~gG~~~~h~~~~Rl~l~k~~~~~R~~~i~ksp~  317 (337)
T PTZ00035        255 DEFNVAVVITNQVMADVDGA-SMFV----------------ADPKKPIGGHIIAHASTTRLSLRKGRGEQRICKIYDSPN  317 (337)
T ss_pred             HHcCcEEEEecceEEecCCc-cccC----------------CCCccCCchHHHHhheeEEEEEEecCCCeeEEEEEECCC
Confidence            99999999999998875421 1110                1245799999999999999999986 5689999999999


Q ss_pred             CCCceeEEEEcCCCceecc
Q 035774          322 SPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       322 ~~~~~~~f~I~~~Gi~~~~  340 (357)
                      .|...+.|+|+++||....
T Consensus       318 ~p~~~~~f~It~~Gi~~~~  336 (337)
T PTZ00035        318 LPESEAVFAISEGGIIDAK  336 (337)
T ss_pred             CCCeeEEEEEeCCccccCC
Confidence            9998899999999998654

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=100.00  E-value=7.2e-49  Score=357.43  Aligned_cols=308  Identities=24%  Similarity=0.329  Sum_probs=262.0

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCC
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLP   85 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   85 (357)
                      +..+++++.+.++|+++|+.|+++++..++.+|.++.+++++++.++...+.+.+...+.++.++++.+.+    ..+++
T Consensus         4 ~~~~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~~~~~~~~~t~~~l~~~~~~----~~~~~   79 (316)
T TIGR02239         4 LEGNGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRQE----VIQLT   79 (316)
T ss_pred             hhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHhcccccccHHHHHhcccc----cceeC
Confidence            45688999999999999999999999999999999999999999999999888888899999988765432    67899


Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhh
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF  165 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~  165 (357)
                      ||++.||.+|+||+++|++++|+|+||+|||+||++++.+++.+...||.+++|+|||+|+.|++.|+.++.+..     
T Consensus        80 tg~~~lD~ll~gGi~~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~~Rl~~ia~~~-----  154 (316)
T TIGR02239        80 TGSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRPERLLAIAERY-----  154 (316)
T ss_pred             CCCHHHHHHhcCCCCCCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCHHHHHHHHHHc-----
Confidence            999999999999999999999999999999999999999888766666667899999999999999998887542     


Q ss_pred             cccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC---CChHHHHHHHHHHHHHH
Q 035774          166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA---PGQHPLSWHISLITSLA  242 (357)
Q Consensus       166 ~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~---~r~~~~~~i~~~Lk~la  242 (357)
                      ...  ...+.+++++.++.+.+++...+..+...+...++++|||||++++++..+.+..   .|+..+.+++..|+++|
T Consensus       155 ~~~--~~~~l~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~LvVIDSI~al~r~~~~~~~~~~~rq~~l~~~~~~L~~la  232 (316)
T TIGR02239       155 GLN--PEDVLDNVAYARAYNTDHQLQLLQQAAAMMSESRFALLIVDSATALYRTDFSGRGELSARQMHLARFLRSLQRLA  232 (316)
T ss_pred             CCC--hHHhhccEEEEecCChHHHHHHHHHHHHhhccCCccEEEEECcHHHhhhhcCCcchHHHHHHHHHHHHHHHHHHH
Confidence            111  2356778888888888888888888877777788999999999999876543321   24456788999999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEEEEeCCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSPT  321 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~v~K~r~  321 (357)
                      ++++++||+|||++...+..+..|.                ....+|++|..|+|++++|++|++. +..|.++|+|+|+
T Consensus       233 ~~~~vavv~tNqv~~~~~~~~~~~~----------------g~~~~p~gG~~~~h~~~~ri~l~k~~~~~R~~~v~ksp~  296 (316)
T TIGR02239       233 DEFGVAVVITNQVVAQVDGAGSMFA----------------GDPKKPIGGNIMAHASTTRLSLRKGRGEQRICKIYDSPC  296 (316)
T ss_pred             HHhCCEEEEECceEEecCCcccccc----------------CCCCcCCchHHHHhhccEEEEEEecCCCeEEEEEEECCC
Confidence            9999999999999876552111110                1246799999999999999999985 6789999999999


Q ss_pred             CCCceeEEEEcCCCceecc
Q 035774          322 SPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       322 ~~~~~~~f~I~~~Gi~~~~  340 (357)
                      .|...+.|+|+++||...+
T Consensus       297 ~p~~~~~f~i~~~Gi~~~~  315 (316)
T TIGR02239       297 LPESEAMFAIYEDGIGDPK  315 (316)
T ss_pred             CCCeEEEEEEeCCceecCC
Confidence            9998899999999998754

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).

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

Probab=100.00  E-value=2.6e-47  Score=338.16  Aligned_cols=250  Identities=38%  Similarity=0.572  Sum_probs=210.5

Q ss_pred             CCcccHHHHHHHHHhcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEE
Q 035774           62 PPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIY  141 (357)
Q Consensus        62 ~~~~~~~~~~~~~~~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~  141 (357)
                      .+|.+|.++++++.+    ...|+||++.||.+|+||++.|.+++|+|+||+|||+||+|++.+++++...||.+.+|+|
T Consensus         2 ~~f~ta~~~~~~~~~----~~~i~Tg~~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvy   77 (256)
T PF08423_consen    2 MGFQTAAELLEQRKR----WSRISTGCKSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVY   77 (256)
T ss_dssp             TSSEEHHHHHHHHHT----S-EE--SSHHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEE
T ss_pred             CCcccHHHHHHHhhc----CCeeCCCCHHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEE
Confidence            478899999988654    5689999999999999999999999999999999999999999999998888888999999


Q ss_pred             EeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCC
Q 035774          142 IDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVH  221 (357)
Q Consensus       142 i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~  221 (357)
                      ||+|..|+.+|+.++++..     ..+  .+..++++++.++.+..++.+++..+...+.+.+++||||||++++++.++
T Consensus        78 idTe~~f~~~Rl~~i~~~~-----~~~--~~~~l~~I~v~~~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSIaalfr~e~  150 (256)
T PF08423_consen   78 IDTEGTFSPERLQQIAERF-----GLD--PEEILDNIFVIRVFDLEELLELLEQLPKLLSESKIKLIVIDSIAALFRSEF  150 (256)
T ss_dssp             EESSSSS-HHHHHHHHHHT-----TS---HHHHHHTEEEEE-SSHHHHHHHHHHHHHHHHHSCEEEEEEETSSHHHHHHS
T ss_pred             EeCCCCCCHHHHHHHhhcc-----ccc--cchhhhceeeeecCCHHHHHHHHHHHHhhccccceEEEEecchHHHHHHHH
Confidence            9999999999999998642     222  245789999999999999999999998888888999999999999998765


Q ss_pred             CCC---CCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhh
Q 035774          222 EQR---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHA  298 (357)
Q Consensus       222 ~~~---~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~  298 (357)
                      .+.   ..|...+..++..|+++|++++++||+|||++...+..+ .+                .....+|+||.+|+|.
T Consensus       151 ~~~~~~~~R~~~L~~~~~~L~~lA~~~~iaVvvTNqv~~~~~~~~-~~----------------~~~~~~PalG~~w~h~  213 (256)
T PF08423_consen  151 SGRGDLAERQRMLARLARILKRLARKYNIAVVVTNQVTTKIDSNS-LF----------------DGDRLKPALGHSWSHA  213 (256)
T ss_dssp             GSTTTHHHHHHHHHHHHHHHHHHHHHTT-EEEEEEEECSSTT-----S----------------STTSEEETTHHHHHHH
T ss_pred             ccchhhHHHHHHHHHHHHHHHHHHHhCCceEEeeceeeecCCccc-cc----------------ccccceecCcchhhhh
Confidence            432   236678999999999999999999999999988655210 00                0135789999999999


Q ss_pred             ccEEEEEEEe-CCeEEEEEEeCCCCCCceeEEEEcCCCceec
Q 035774          299 VTIRLVLEAK-SGQRFMNVEKSPTSPPLAFSFTINPSGISLL  339 (357)
Q Consensus       299 ~~~rl~l~~~-~~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~  339 (357)
                      +++|+.|++. +..|.++|+|+|..|...+.|.|+++||+..
T Consensus       214 ~~~Rl~l~k~~~~~R~~~i~ksp~~p~~~~~f~It~~Gi~d~  255 (256)
T PF08423_consen  214 VTTRLFLSKGRGSERVATIVKSPSLPEGSASFQITEDGIRDV  255 (256)
T ss_dssp             SSEEEEEEECSTTEEEEEEEECSSSSSEEEEEEEETTEEEE-
T ss_pred             ccEEEEEEeCCCCeEEEEEeECCCCCCceEEEEEeCCCccCC
Confidence            9999999985 4689999999999999999999999999864

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 ....

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=100.00  E-value=3e-45  Score=336.66  Aligned_cols=307  Identities=26%  Similarity=0.358  Sum_probs=258.4

Q ss_pred             Ccccccccc-CCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCC-CcccHHHHHHHHHhcc
Q 035774            1 MANKLISEM-RLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCP-PFQTALLLMEQRAATE   78 (357)
Q Consensus         1 ~~~~~~~~~-~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~   78 (357)
                      |.+.++..+ ++.+.+.++|.++|+.|++++...++.+|.++++++.+.+..+.+.+...+.. ++.++.++++++.+  
T Consensus         3 ~~~~~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks--   80 (317)
T PRK04301          3 MKEKDLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN--   80 (317)
T ss_pred             cccccHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc--
Confidence            677888888 69999999999999999999999999999999999999999998887765555 67888887766422  


Q ss_pred             cCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh
Q 035774           79 HLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA  158 (357)
Q Consensus        79 ~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~  158 (357)
                        ...++||++.||++|+||+++|.+++|+|+||+|||+||+|++.+++.+...||.+.+|+|||+|++|++.|+.+++.
T Consensus        81 --~~~~~Tg~~~lD~~l~GGi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~~~  158 (317)
T PRK04301         81 --VGKITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQMAE  158 (317)
T ss_pred             --CCccCCCCHHHHHHhcCCccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHHHH
Confidence              568999999999999999999999999999999999999999999988766677788999999999999999998875


Q ss_pred             ccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhh-cCeeEEEEeccccccCCCCCCCC---CChHHHHHH
Q 035774          159 SSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPGVHEQRA---PGQHPLSWH  234 (357)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~~~~~~~---~r~~~~~~i  234 (357)
                      ..     ..  ..+..+++++++++.+..+...++..+...+.. .++++|||||++++++.+..+..   .|++.+.++
T Consensus       159 ~~-----g~--~~~~~l~~i~~~~~~~~~~~~~~~~~l~~~i~~~~~~~lvVIDSisa~~~~~~~~~~~~~~r~~~l~~~  231 (317)
T PRK04301        159 AL-----GL--DPDEVLDNIHVARAYNSDHQMLLAEKAEELIKEGENIKLVIVDSLTAHFRAEYVGRGNLAERQQKLNKH  231 (317)
T ss_pred             Hc-----CC--ChHhhhccEEEEeCCCHHHHHHHHHHHHHHHhccCceeEEEEECchHHhhhhccCCccHHHHHHHHHHH
Confidence            41     11  123456788888888877777777888777776 78999999999999876443321   244557788


Q ss_pred             HHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEE
Q 035774          235 ISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRF  313 (357)
Q Consensus       235 ~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~  313 (357)
                      +..|+++|++++++||+|||++...+.   .                 +.....|++|..|.|.+++||.+++. +..|.
T Consensus       232 ~~~L~~la~~~~vavl~tnqv~~~~~~---~-----------------~~~~~~~~~G~~~~~~~~~rl~l~k~~~~~R~  291 (317)
T PRK04301        232 LHDLLRLADLYNAAVVVTNQVMARPDA---F-----------------FGDPTQPIGGHILGHTATFRIYLRKSKGNKRI  291 (317)
T ss_pred             HHHHHHHHHHhCCEEEEeceEEecccc---c-----------------cCccccCCcchHhHhheeEEEEEEecCCCceE
Confidence            899999999999999999999875431   0                 11245799999999999999999985 67899


Q ss_pred             EEEEeCCCCCCceeEEEEcCCCcee
Q 035774          314 MNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       314 l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      ++|+|+|+.|.+.+.|+|+++||..
T Consensus       292 ~~v~k~~~~~~~~~~f~I~~~Gi~~  316 (317)
T PRK04301        292 ARLVDSPHLPEGEAVFRITEEGIRD  316 (317)
T ss_pred             EEEEeCCCCCCceEEEEEeCCcccC
Confidence            9999999999888999999999964

>KOG1434 consensus Meiotic recombination protein Dmc1 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=100.00  E-value=2e-47  Score=320.87  Aligned_cols=299  Identities=28%  Similarity=0.386  Sum_probs=265.5

Q ss_pred             HHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCCCCchhHH
Q 035774           13 KSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLD   92 (357)
Q Consensus        13 ~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~TG~~~LD   92 (357)
                      ..-..+|...|+.+++-++.+....|..+.++++..+.++.+++.+....++.+|.++++++..    ...|+||+..||
T Consensus        30 ~td~~kLk~~gi~tikgv~ist~r~l~~lkgise~kv~klkeaa~k~~~~~f~tA~e~le~r~~----v~~ItTgs~~lD  105 (335)
T KOG1434|consen   30 VTDIEKLKSKGICTIKGVLISTRRALCKLKGISEVKVDKLKEAANKSISHGFCTALELLEQRKT----VGSITTGSSALD  105 (335)
T ss_pred             hhhHHhhccCCeeeEeeeeehhHHHHHHHhhHHHHhhhhHHHhhCCccCcCcchHHHHHhhhhc----cceeecchHHHh
Confidence            4456778888888888888888888999999999999999998888888899999999998755    568999999999


Q ss_pred             hhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHH
Q 035774           93 AALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQ  172 (357)
Q Consensus        93 ~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~  172 (357)
                      .+||||++.=++++|+|.||+|||+++++++.++.+|...||.+++++|||+|++|.+.|+.++++.     +...  .+
T Consensus       106 ~ILGGGI~~m~iTEifGefr~GKTQlshtLcVt~QlPr~~Gg~~Gk~ifIDTEgtFrpdRi~~IAe~-----~~~d--~d  178 (335)
T KOG1434|consen  106 DILGGGIPSMSITEIFGEFRCGKTQLSHTLCVTVQLPREMGGVGGKAIFIDTEGTFRPDRIKDIAER-----FKVD--PD  178 (335)
T ss_pred             hhhcCCccchhhHHHcCCCCcCccceeeEEEEEeecchhhCCCCceEEEEecCCccchHHHHHHHHH-----hCCC--HH
Confidence            9999999999999999999999999999999999999999999999999999999999999999965     2222  35


Q ss_pred             HhhcCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHHHHHHcCCe
Q 035774          173 EMAGRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFSRIP  248 (357)
Q Consensus       173 ~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~la~~~~~~  248 (357)
                      ..++|++|.++.+.++..+++..+...+.++ ..++||||||.++|+.++++.   +.|++.+..++..|.++|+++|++
T Consensus       179 ~~LdNI~y~Ra~~se~qmelv~~L~~~~se~g~~rlvIVDsIma~FRvDy~grgeLseRqqkLn~ml~kl~~laeefnvA  258 (335)
T KOG1434|consen  179 FTLDNILYFRAYNSEEQMELVYLLGDFLSEHGKYRLVIVDSIMALFRVDYDGRGELSERQQKLNQMLQKLNKLAEEFNVA  258 (335)
T ss_pred             HHHHHHHHHHHcChHHHHHHHHHHHHHHhhcCcEEEEEEeceehheeecccccccHHHHHHHHHHHHHHHHHHHHhccEE
Confidence            6789999999999999999999999999886 789999999999999988743   348889999999999999999999


Q ss_pred             EEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-CeEEEEEEeCCCCCCcee
Q 035774          249 IVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-GQRFMNVEKSPTSPPLAF  327 (357)
Q Consensus       249 vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-~~R~l~v~K~r~~~~~~~  327 (357)
                      |+++||++.+.+. +.+|.                ....+|++|+.|+|...+|+.|+|+. ..|+.++.|||..|..++
T Consensus       259 VfltNQvttdpga-~~~f~----------------s~~~kp~gGh~~aHAsttRlilrkgrg~eR~Akl~dSP~mpe~e~  321 (335)
T KOG1434|consen  259 VFLTNQVTTDPGA-GMTFA----------------SQDLKPAGGHSWAHASTTRLILRKGRGDERVAKLYDSPSMPEAEA  321 (335)
T ss_pred             EEEecceecCCcc-ccccc----------------ccccCccccchhhhhhheeEEEEcCCcceeeeecccCCCCCcceE
Confidence            9999999988762 12221                12478999999999999999999987 799999999999999999


Q ss_pred             EEEEcCCCceec
Q 035774          328 SFTINPSGISLL  339 (357)
Q Consensus       328 ~f~I~~~Gi~~~  339 (357)
                      .|.|++.||...
T Consensus       322 ~y~It~~Gi~ds  333 (335)
T KOG1434|consen  322 SYVITPGGIRDS  333 (335)
T ss_pred             EEEEcCCccccC
Confidence            999999999764

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=100.00  E-value=2.3e-43  Score=323.98  Aligned_cols=299  Identities=26%  Similarity=0.353  Sum_probs=246.5

Q ss_pred             ccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCC-CcccHHHHHHHHHhcccCCCCCCC
Q 035774            8 EMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCP-PFQTALLLMEQRAATEHLGGHLPT   86 (357)
Q Consensus         8 ~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~i~T   86 (357)
                      .-++.+...++|.++|+.+++++...++.+|.++.+++.+.+..+...+.+.... .+.++.++++.+.+    ...++|
T Consensus         4 i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~~~~s----~~~~~T   79 (310)
T TIGR02236         4 LPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRKT----IGKITT   79 (310)
T ss_pred             cCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHHhhcc----CCeecC
Confidence            3578899999999999999999999999999999999988888888776654433 45788777776422    567999


Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhc
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFH  166 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~  166 (357)
                      |++.||.+|+||++.|.+++|+|+||+|||+||+|++.+++.+...|+.+++|+|||+|++|+++|+.+++...     .
T Consensus        80 g~~~lD~~l~GGi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~~~~~~~-----g  154 (310)
T TIGR02236        80 GSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQMAEAR-----G  154 (310)
T ss_pred             CCHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHHHHHHHc-----C
Confidence            99999999999999999999999999999999999999998876666667799999999999999999887541     1


Q ss_pred             ccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhc--CeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHHH
Q 035774          167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN--QVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSL  241 (357)
Q Consensus       167 ~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~--~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~l  241 (357)
                      ..  .....+++++..+.+..+...+++.+...+.+.  ++++|||||++++++.++.+.   ..|++.+.+++..|+.+
T Consensus       155 l~--~~~~~~~i~i~~~~~~~~~~~lld~l~~~i~~~~~~~~lVVIDSisa~~r~e~~~~~~~~~r~~~l~~~~~~L~~~  232 (310)
T TIGR02236       155 LD--PDEVLKNIYVARAYNSNHQMLLVEKAEDLIKELNNPVKLLIVDSLTSHFRAEYVGRGALAERQQKLNKHLHDLLRL  232 (310)
T ss_pred             CC--HHHHhhceEEEecCCHHHHHHHHHHHHHHHHhcCCCceEEEEecchHhhhHhhcCchhHHHHHHHHHHHHHHHHHH
Confidence            11  123567888888887777666777777777665  489999999999987754432   12445677888999999


Q ss_pred             HHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEEEEeCC
Q 035774          242 AEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSP  320 (357)
Q Consensus       242 a~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~v~K~r  320 (357)
                      |++++++||+|||++...+.   .                 +....+|++|..|+|++++|+.|++. +..|.++|.|+|
T Consensus       233 a~~~~~~v~~tnqv~~~~~~---~-----------------~~~~~~~~~G~~~~h~~~~rl~l~~~~~~~R~~~~~k~~  292 (310)
T TIGR02236       233 ADLYNAAVVVTNQVMARPDA---F-----------------FGDPTRPIGGHILGHAATFRVYLRKGKGDKRIARLVDSP  292 (310)
T ss_pred             HHHhCcEEEEeceeeecCcc---c-----------------cCccccCCcchhhhhheeEEEEEEecCCCeEEEEEEECC
Confidence            99999999999999876431   0                 11245799999999999999999984 568999999999


Q ss_pred             CCCCceeEEEEcCCCce
Q 035774          321 TSPPLAFSFTINPSGIS  337 (357)
Q Consensus       321 ~~~~~~~~f~I~~~Gi~  337 (357)
                      +.|.+.+.|+|+++||.
T Consensus       293 ~~~~~~~~f~i~~~Gi~  309 (310)
T TIGR02236       293 HLPEGEAVFRITEKGIE  309 (310)
T ss_pred             CCCCeeEEEEEeCCCcc
Confidence            99998889999999986

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.

>KOG1564 consensus DNA repair protein RHP57 [Replication, recombination and repair]

Probab=100.00  E-value=3.7e-39  Score=274.89  Aligned_cols=312  Identities=28%  Similarity=0.415  Sum_probs=229.0

Q ss_pred             cccCCCHHHHHHHHhCCCCCHH--------HHhcCCHHHHHHHhCCCHHHHHHHHH-HHHHhcCCCcccHHHHHHHHH--
Q 035774            7 SEMRLPKSIANIFAARNITTAK--------DALSLTELELMKLLDVELSEVRSALA-LVSEIVCPPFQTALLLMEQRA--   75 (357)
Q Consensus         7 ~~~~l~~~~~~~l~~~~~~~~~--------~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~--   75 (357)
                      ....++++++..-+.+...+.+        |++..+..++.+++..+..+.-++.. .+.+.        .+++.+..  
T Consensus         4 ~l~~ln~~i~~dee~a~llsa~evl~vs~vdfltlt~~sl~r~~h~s~~e~lr~~~~li~q~--------~~~~~e~~~~   75 (351)
T KOG1564|consen    4 FLDQLNKHIREDEEQANLLSAEEVLTVSKVDFLTLTQQSLHRIVHKSTPEDLRVLKDLIMQN--------LKLKPENLCS   75 (351)
T ss_pred             hhccccHHHHHHHHHhhhcCHHHhcCcCcccceecChhHHHHHHHhccHHHHHHHHHHHHHH--------HHhcchhhhc
Confidence            3456666666665555444443        55556667777777766655544332 23222        12222211  


Q ss_pred             hcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHH
Q 035774           76 ATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIE  155 (357)
Q Consensus        76 ~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~  155 (357)
                      ........++||...||++|+||++.+.+++|+|++|+|||+||+|++....+|...||.+++++||++|..|+.+|+.+
T Consensus        76 ~s~~~~~~lttgc~~LD~~L~GGi~~~giTEi~GeSg~GKtQL~lQL~L~VQLp~~~GGL~~~~vYI~TE~~fP~rRL~q  155 (351)
T KOG1564|consen   76 RSKTNRSKLTTGCVALDECLRGGIPTDGITEICGESGCGKTQLLLQLSLCVQLPRSHGGLGGGAVYICTESPFPTRRLHQ  155 (351)
T ss_pred             cccCCchhcccccHHHHHHhcCCcccccHHHHhhccCCcHHHHHHHHHHHhhCchhhCCCCCceEEEEcCCCCcHHHHHH
Confidence            11222346999999999999999999999999999999999999999999999999999999999999999999999888


Q ss_pred             HHhccCchhhcccc---hHHHhhcCeEEeCCCCHHHHHHHHHH-HHHHhhhcCeeEEEEeccccccCCCCCCCC----CC
Q 035774          156 MGASSFPEIFHSKG---MAQEMAGRILVLQPTSLSEFTESLEK-IKVSLLQNQVKLLVIDSMEALVPGVHEQRA----PG  227 (357)
Q Consensus       156 ~~~~~~~~~~~~~~---~~~~~~~~i~~~~~~~~~~~~~~l~~-l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~----~r  227 (357)
                      +... ++.....+.   ......+++++..+.+.+.+..++.. +.-.+.+.++++|||||+++.++.+++...    .|
T Consensus       156 L~~~-~~~rp~~~~~~~~~~Npgd~IFv~~~~d~d~l~~iv~~qlPiL~~r~~i~LVIiDSVAa~fR~E~d~~~Sdl~~r  234 (351)
T KOG1564|consen  156 LSHT-LPQRPNPEKELNYNDNPGDHIFVENVHDVDHLLHIVNRQLPILLNRKKIKLVIIDSVAALFRSEFDYNPSDLKKR  234 (351)
T ss_pred             HHHh-cccCCCcchhhhhccCCCceEEEEeccchhhHHHHHhhhccceeccCcceEEEEehhhHHHHHHhccChhhhhhH
Confidence            7643 211111111   01112345899999998888887754 566667778999999999999998765332    25


Q ss_pred             hHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcc-----cccccccccccccccCCCcceecccchhHhhhccEE
Q 035774          228 QHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLY-----PFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIR  302 (357)
Q Consensus       228 ~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~r  302 (357)
                      ...+..+...|+.+|.+++++||++||++.........+     .+...|..          +...|+||..|+|.+.+|
T Consensus       235 ~~~l~rla~~Lr~LA~~~~~aVV~~NQVtd~~~~~~~~~~l~~~d~r~~w~s----------gw~vPsLGL~WaN~v~tR  304 (351)
T KOG1564|consen  235 ARHLFRLAGKLRQLASKFDLAVVCANQVTDRVETSDDLSGLRIGDYRYLWSS----------GWVVPSLGLTWANCVSTR  304 (351)
T ss_pred             HHHHHHHHHHHHHHHHhcCccEEEeeccccccccccccCCccccchhhcccc----------ccccccccceecccccee
Confidence            677889999999999999999999999988744211111     11111111          236799999999999999


Q ss_pred             EEEEEe----------CCeEEEEEEeCCCCCCceeEEEEcCCCce
Q 035774          303 LVLEAK----------SGQRFMNVEKSPTSPPLAFSFTINPSGIS  337 (357)
Q Consensus       303 l~l~~~----------~~~R~l~v~K~r~~~~~~~~f~I~~~Gi~  337 (357)
                      +.+.+.          ...|.++|+.+++.|+..++|.|+.+||.
T Consensus       305 l~l~r~~k~~~sa~~~~~~R~l~VvySp~~p~~~~~~~It~eGI~  349 (351)
T KOG1564|consen  305 LLLSRSTKNCDSAVSRSAKRTLRVVYSPYLPPSSCEFMITAEGIC  349 (351)
T ss_pred             eeeeeccccccchhhcccceEEEEEecCCCCCcceEEEEecceEe
Confidence            999882          13799999999999999999999999996

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=100.00  E-value=5.5e-39  Score=284.10  Aligned_cols=230  Identities=31%  Similarity=0.475  Sum_probs=192.8

Q ss_pred             CCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCch
Q 035774           84 LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPE  163 (357)
Q Consensus        84 i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~  163 (357)
                      +|||++.||.+|+||+++|++++|+|+||+|||+||++++.+++.+..+||.+.+|+||++|+.++..|+.++.+...  
T Consensus         1 ~~tG~~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~~rl~~~~~~~~--   78 (235)
T cd01123           1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRPERLVQIAERFG--   78 (235)
T ss_pred             CCCCchhhHhhccCCCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCHHHHHHHHHHhc--
Confidence            689999999999999999999999999999999999999999877666666678999999999999999988875421  


Q ss_pred             hhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHH
Q 035774          164 IFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLIT  239 (357)
Q Consensus       164 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk  239 (357)
                         .  ......+++++.++.+..++...+..+...+.+. ++++|||||++++++......   ..+.+.+.+++..|+
T Consensus        79 ---~--~~~~~~~~i~~~~~~~~~~l~~~l~~l~~~l~~~~~~~liVIDSis~~~~~~~~~~~~~~~r~~~l~~~~~~L~  153 (235)
T cd01123          79 ---L--DPEEVLDNIYVARAYNSDHQLQLLEELEAILIESSRIKLVIVDSVTALFRAEFDGRGELAERQQHLAKLLRTLK  153 (235)
T ss_pred             ---c--ChHhHhcCEEEEecCCHHHHHHHHHHHHHHHhhcCCeeEEEEeCcHHHHHHHhcCCccHHHHHHHHHHHHHHHH
Confidence               1  1235678899999999889988888888888888 999999999999876533332   235567889999999


Q ss_pred             HHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-CeEEEEEEe
Q 035774          240 SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-GQRFMNVEK  318 (357)
Q Consensus       240 ~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-~~R~l~v~K  318 (357)
                      ++|++++|+||++||++...+...                 .......+|++|..|++.+++|+++++.. ..|+++|.|
T Consensus       154 ~la~~~~~avl~tn~~~~~~~~~~-----------------~~~~~~~~p~lG~~w~~~v~~Rl~l~~~~~~~r~~~i~k  216 (235)
T cd01123         154 RLADEFNVAVVITNQVTARPDGAA-----------------MFGGDPKKPAGGNIWAHASTTRLYLRKGRGEERIAKIVD  216 (235)
T ss_pred             HHHHHhCCEEEEeccEeecCCccc-----------------ccCCCCeeccCccHhhCCceEEEEEEECCCCceEEEEee
Confidence            999999999999999987544110                 00112457999999999999999998875 689999999


Q ss_pred             CCCCCCceeEEEEcCCCce
Q 035774          319 SPTSPPLAFSFTINPSGIS  337 (357)
Q Consensus       319 ~r~~~~~~~~f~I~~~Gi~  337 (357)
                      ++..+...+.|+|+++||+
T Consensus       217 ~~~~~~~~~~f~It~~Gi~  235 (235)
T cd01123         217 SPHLPEGEAVFAITEEGIR  235 (235)
T ss_pred             CCCCCCceEEEEEeCCccC
Confidence            9999988899999999985

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 .

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

Probab=100.00  E-value=1.5e-35  Score=260.61  Aligned_cols=219  Identities=34%  Similarity=0.482  Sum_probs=180.2

Q ss_pred             CCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCch
Q 035774           84 LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPE  163 (357)
Q Consensus        84 i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~  163 (357)
                      ++||++.||.+|+||+++|++++|+|+||+|||+||++++.+++.+...||.+.+|+||++|+.++..|+.++.....  
T Consensus         1 i~tG~~~lD~~l~GG~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~~~~~~rl~~~~~~~~--   78 (226)
T cd01393           1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEGAFRPERLVQLAVRFG--   78 (226)
T ss_pred             CCCCcHHHHHHhCCCCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCCCCCHHHHHHHHHHhc--
Confidence            689999999999999999999999999999999999999999887655556668999999999999999988775421  


Q ss_pred             hhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHH
Q 035774          164 IFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITS  240 (357)
Q Consensus       164 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~  240 (357)
                         ..  .....+++++.++.+.+++...+..+.......++++|||||++.+++......   ..|...+.++++.|+.
T Consensus        79 ---~~--~~~~~~~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~lvVIDsis~l~~~~~~~~~~~~~~~~~l~~~~~~L~~  153 (226)
T cd01393          79 ---LD--PEEVLDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVVVDSVAALFRKEFIGRGMLAERARLLSQALRKLLR  153 (226)
T ss_pred             ---cc--hhhhhccEEEEeCCCHHHHHHHHHHHHHHhhcCCeeEEEEcCcchhhhhhhcCCchHHHHHHHHHHHHHHHHH
Confidence               11  234568899999999888888888776666677899999999999987643322   2345678889999999


Q ss_pred             HHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC----CeEEEEE
Q 035774          241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS----GQRFMNV  316 (357)
Q Consensus       241 la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~----~~R~l~v  316 (357)
                      +|++++|+||++||++......                    +....+|++|..|++.+++|+.|++..    ..|.++|
T Consensus       154 ~a~~~~~~vi~tnq~~~~~~~~--------------------~~~~~~p~~G~~~~~~~~~ri~l~~~~~~~~~~r~~~~  213 (226)
T cd01393         154 LADKFNVAVVFTNQVRAKVDVM--------------------FGDPETPAGGNALAHASTTRLDLRKGRGIIGERRIAKV  213 (226)
T ss_pred             HHHHhCcEEEEEEEEeeecccc--------------------cCCCccccCchhhhCcccEEEEEEecCCccCcEEEEEE
Confidence            9999999999999998764410                    012356999999999999999999876    5899999


Q ss_pred             EeCCCCCCceeEE
Q 035774          317 EKSPTSPPLAFSF  329 (357)
Q Consensus       317 ~K~r~~~~~~~~f  329 (357)
                      +|++..|.+++.|
T Consensus       214 ~k~~~~~~~~~~~  226 (226)
T cd01393         214 VKSPALPEAEAEF  226 (226)
T ss_pred             EeCCCCCCccccC
Confidence            9999988876654

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.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=100.00  E-value=8.5e-35  Score=255.43  Aligned_cols=218  Identities=30%  Similarity=0.460  Sum_probs=177.0

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccC
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSF  161 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~  161 (357)
                      ++++||+++||++|+||+++|++++|+|+||+|||+||++++.+++..      +.+|+||++| .++.+|+.++.... 
T Consensus         3 ~~i~tGi~~lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~------~~~v~yi~~e-~~~~~r~~~~~~~~-   74 (225)
T PRK09361          3 ERLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKN------GKKVIYIDTE-GLSPERFKQIAGED-   74 (225)
T ss_pred             ccccCCcHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHHC------CCeEEEEECC-CCCHHHHHHHHhhC-
Confidence            479999999999999999999999999999999999999999998752      5899999999 78888888876541 


Q ss_pred             chhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC---CCCChHHHHHHHHHH
Q 035774          162 PEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ---RAPGQHPLSWHISLI  238 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~---~~~r~~~~~~i~~~L  238 (357)
                               .....++++++++.+..++.+.++.+...+. .++++|||||++++++.....   ...+.+.+..++..|
T Consensus        75 ---------~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~-~~~~lvVIDsi~al~~~~~~~~~~~~~~~~~l~~~l~~L  144 (225)
T PRK09361         75 ---------FEELLSNIIIFEPSSFEEQSEAIRKAEKLAK-ENVGLIVLDSATSLYRLELEDEEDNSKLNRELGRQLTHL  144 (225)
T ss_pred             ---------hHhHhhCeEEEeCCCHHHHHHHHHHHHHHHH-hcccEEEEeCcHHHhHHHhcCCccHHHHHHHHHHHHHHH
Confidence                     1234568888888888887777777766655 789999999999988653211   111345677778889


Q ss_pred             HHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEE-eCCeEEEEEE
Q 035774          239 TSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA-KSGQRFMNVE  317 (357)
Q Consensus       239 k~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~-~~~~R~l~v~  317 (357)
                      +++|+++|++|+++||+....+.                       ...+|++|..|++.++.++.|++ .+..|.+.+.
T Consensus       145 ~~~a~~~~v~vi~tnq~~~~~~~-----------------------~~~~~~gg~~~~~~~d~ii~l~~~~~~~r~~~i~  201 (225)
T PRK09361        145 LKLARKHDLAVVITNQVYSDIDS-----------------------DGLRPLGGHTLEHWSKTILRLEKFRNGKRRATLE  201 (225)
T ss_pred             HHHHHHhCCEEEEEccceecCCC-----------------------CcccCCCcchhhhhccEEEEEEEccCCeEEEEEE
Confidence            99999999999999999764331                       12356777889999999999998 4567888999


Q ss_pred             eCCCCCC-ceeEEEEcCCCceecc
Q 035774          318 KSPTSPP-LAFSFTINPSGISLLT  340 (357)
Q Consensus       318 K~r~~~~-~~~~f~I~~~Gi~~~~  340 (357)
                      |+|..++ ..++|+|+++||.+.+
T Consensus       202 k~~~~~~~~~~~f~It~~Gi~~~~  225 (225)
T PRK09361        202 KHRSRPEGESAEFRITDRGIEIID  225 (225)
T ss_pred             ECCCCCCCCeEEEEEeCCcEecCC
Confidence            9998875 6689999999998753

>COG0468 RecA RecA/RadA recombinase [DNA replication, recombination, and repair]

Probab=100.00  E-value=3.1e-34  Score=253.26  Aligned_cols=223  Identities=29%  Similarity=0.359  Sum_probs=191.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ...++||...||.+|+||+|+|.+++|+||+|||||++|+|++++++++      ++.|+|||+|+.++++|+.+++...
T Consensus        39 ~~~i~TGs~~LD~~LGGGl~~g~ItEiyG~~gsGKT~lal~~~~~aq~~------g~~a~fIDtE~~l~p~r~~~l~~~~  112 (279)
T COG0468          39 IEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQKP------GGKAAFIDTEHALDPERAKQLGVDL  112 (279)
T ss_pred             cccccccchhHHHHhcCCcccceEEEEecCCCcchhhHHHHHHHHhhcC------CCeEEEEeCCCCCCHHHHHHHHHhh
Confidence            6789999999999999999999999999999999999999999999874      4699999999999999999988541


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC---CChHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA---PGQHPLSWHISL  237 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~---~r~~~~~~i~~~  237 (357)
                                    .+++++.++.+.++...++..+.....+ ++++|||||++++++....+..   .+.+.+...++.
T Consensus       113 --------------~d~l~v~~~~~~e~q~~i~~~~~~~~~~-~i~LvVVDSvaa~~r~~~~~d~~~~~~~r~ls~~l~~  177 (279)
T COG0468         113 --------------LDNLLVSQPDTGEQQLEIAEKLARSGAE-KIDLLVVDSVAALVRAEEIEDGHLGLRARLLSKALRK  177 (279)
T ss_pred             --------------hcceeEecCCCHHHHHHHHHHHHHhccC-CCCEEEEecCcccchhhhcCcchHHHHHHHHHHHHHH
Confidence                          5789999999999998888887777655 7999999999999998654422   255778889999


Q ss_pred             HHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-------CC
Q 035774          238 ITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-------SG  310 (357)
Q Consensus       238 Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-------~~  310 (357)
                      |..+|+++|++|+++||+..+.+.   +|.                 +..+|.+|+...|...+|+.+++.       ++
T Consensus       178 L~~~a~~~~~~vi~~NQv~~k~~~---~f~-----------------~~~~~~GG~~L~~~as~rl~l~k~~~~~~~~g~  237 (279)
T COG0468         178 LTRLANKYNTAVIFTNQVRAKIGV---MFG-----------------DPETTTGGNALKFYASVRLDLRRIESLKEDVGN  237 (279)
T ss_pred             HHHHHHHcCcEEEEECceeeecCc---ccC-----------------CcccCCCchHHHhhhheEEEEeeccccccccCC
Confidence            999999999999999999887662   211                 123577788899999999999988       67


Q ss_pred             eEEEEEEeCCCCCCc-eeEEEEcCCCceeccCCCc
Q 035774          311 QRFMNVEKSPTSPPL-AFSFTINPSGISLLTDDGT  344 (357)
Q Consensus       311 ~R~l~v~K~r~~~~~-~~~f~I~~~Gi~~~~~~~~  344 (357)
                      .|.++++|++..|+. .+.|.|+.+|+......-+
T Consensus       238 ~r~~~vvk~~~~p~~~~a~f~I~~~~~~~~~~~~~  272 (279)
T COG0468         238 KRRVKVVKNKVAPPFKEAEFDITYGGGIDREGELI  272 (279)
T ss_pred             eEEEEEEeCCCCCCCceeEEEeecCcccccccchh
Confidence            999999999999986 8999999988877655433

>cd01394 radB RadB

Probab=100.00  E-value=1.1e-33  Score=247.27  Aligned_cols=213  Identities=30%  Similarity=0.410  Sum_probs=166.6

Q ss_pred             CCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCch
Q 035774           84 LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPE  163 (357)
Q Consensus        84 i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~  163 (357)
                      ++||+++||.+|+||+++|++++|+|+||+|||+||++++.+++..      +.+|+||++|..++ .++.++....   
T Consensus         1 i~TGi~~LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~------g~~v~yi~~e~~~~-~~~~~~~~~~---   70 (218)
T cd01394           1 LPTGCKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQ------GKKVAYIDTEGLSS-ERFRQIAGDR---   70 (218)
T ss_pred             CCcchhHHHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhc------CCeEEEEECCCCCH-HHHHHHHhHC---
Confidence            6899999999999999999999999999999999999999998742      58999999998776 6777665431   


Q ss_pred             hhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHH
Q 035774          164 IFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITS  240 (357)
Q Consensus       164 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~  240 (357)
                             ......+++++++.+..++...+..+...+. .++++|||||++++++......   ..+...+.+++..|+.
T Consensus        71 -------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~lvvIDsi~~l~~~~~~~~~~~~~~~~~l~~~~~~L~~  142 (218)
T cd01394          71 -------PERAASSIIVFEPMDFNEQGRAIQETETFAD-EKVDLVVVDSATALYRLELGDDDTTIKNYRELAKQLTFLLW  142 (218)
T ss_pred             -------hHhhhcCEEEEeCCCHHHHHHHHHHHHHHHh-cCCcEEEEechHHhhhHHhcCccchHHHHHHHHHHHHHHHH
Confidence                   1234567888888777676666666665543 4589999999999976533221   1133467778888999


Q ss_pred             HHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-CeEEEEEEeC
Q 035774          241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-GQRFMNVEKS  319 (357)
Q Consensus       241 la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-~~R~l~v~K~  319 (357)
                      +|++++|+||++||++...+.                       ...+|++|..|++++++++.|++.. ..|.+.+.|+
T Consensus       143 ~a~~~~~~vi~t~q~~~~~~~-----------------------~~~~p~~g~~~~~~~d~~i~l~~~~~~~r~~~~~~~  199 (218)
T cd01394         143 LARKHDVAVVITNQVYSDVGS-----------------------GSVRPLGGHTLEHWSKVILRLEKLRVGTRRAVLEKH  199 (218)
T ss_pred             HHHHhCCEEEEecCCEEcCCC-----------------------CcccccCCcchhcceeEEEEEEEcCCCeEEEEEeeC
Confidence            999999999999999764330                       1346888889999999999999865 5566667777


Q ss_pred             CCCCC-ceeEEEEcCCCce
Q 035774          320 PTSPP-LAFSFTINPSGIS  337 (357)
Q Consensus       320 r~~~~-~~~~f~I~~~Gi~  337 (357)
                      |..+. ..+.|+|++.||+
T Consensus       200 ~~~~~~~~~~f~It~~Gi~  218 (218)
T cd01394         200 RFRPEGSSVYFRITDKGIE  218 (218)
T ss_pred             CCCCCCceEEEEEeCCccC
Confidence            77774 4589999999984

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=100.00  E-value=9.4e-33  Score=239.81  Aligned_cols=207  Identities=27%  Similarity=0.436  Sum_probs=169.7

Q ss_pred             HHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccch
Q 035774           91 LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGM  170 (357)
Q Consensus        91 LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~  170 (357)
                      ||++|+||+++|++++|+|+||+|||+||++++.+.+..      +.+|+||++|+ +++.|+.++....          
T Consensus         1 lD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~------g~~v~yi~~e~-~~~~rl~~~~~~~----------   63 (209)
T TIGR02237         1 IDELLGGGVERGTITQIYGPPGSGKTNICMILAVNAARQ------GKKVVYIDTEG-LSPERFKQIAEDR----------   63 (209)
T ss_pred             ChhhhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhC------CCeEEEEECCC-CCHHHHHHHHHhC----------
Confidence            799999999999999999999999999999999998742      58999999997 8899998887542          


Q ss_pred             HHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC-CChHHHHHHHHHHHHHHHHcCCeE
Q 035774          171 AQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA-PGQHPLSWHISLITSLAEFSRIPI  249 (357)
Q Consensus       171 ~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~-~r~~~~~~i~~~Lk~la~~~~~~v  249 (357)
                      .+...++++++++.+..++...+..+...+..+++++|||||++++++....... .+...+.+++..|+++++++++++
T Consensus        64 ~~~~~~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~~lvVIDSis~l~~~~~~~~~~~~~~~l~~~~~~L~~~~~~~~v~v  143 (209)
T TIGR02237        64 PERALSNFIVFEVFDFDEQGVAIQKTSKFIDRDSASLVVVDSFTALYRLELSDDRISRNRELARQLTLLLSLARKKNLAV  143 (209)
T ss_pred             hHHHhcCEEEEECCCHHHHHHHHHHHHHHHhhcCccEEEEeCcHHHhHHHhCCccHHHHHHHHHHHHHHHHHHHHcCCEE
Confidence            1234578888888888888777888877777778999999999999765332221 134467777888999999999999


Q ss_pred             EEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeCCeEEEEEEeCCCCCC-ceeE
Q 035774          250 VVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPTSPP-LAFS  328 (357)
Q Consensus       250 v~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~~~R~l~v~K~r~~~~-~~~~  328 (357)
                      +++||++...+.                       ....|++|..|++.+++++.|++....|.+.|.|++..+. ..+.
T Consensus       144 l~t~~~~~~~~~-----------------------~~~~~~gg~~~~~~~d~vi~l~~~~~~r~~~i~k~~~~~~~~~~~  200 (209)
T TIGR02237       144 VITNQVYTDVNN-----------------------GTLRPLGGHLLEHWSKVILRLEKFRGRRLATLEKHRSRPEGESVY  200 (209)
T ss_pred             EEEcccEEecCC-----------------------CCCcCCCcchhheeeeEEEEEEecCCEEEEEEEECCCCCCCCeEE
Confidence            999998754331                       1235778888999999999999877788888999888885 5689


Q ss_pred             EEEcCCCce
Q 035774          329 FTINPSGIS  337 (357)
Q Consensus       329 f~I~~~Gi~  337 (357)
                      |+|+++||+
T Consensus       201 f~It~~Gi~  209 (209)
T TIGR02237       201 FRITDDGIE  209 (209)
T ss_pred             EEEeCCccC
Confidence            999999985

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=100.00  E-value=5.9e-31  Score=232.28  Aligned_cols=213  Identities=20%  Similarity=0.214  Sum_probs=154.8

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFP  162 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~  162 (357)
                      +++||+++||++|+||+++|++++|+|+||+|||+|++|++.+.+..      +++|+||++|++.. +.+.++....|+
T Consensus         2 ri~tGi~~LD~~l~GG~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~------ge~~lyvs~ee~~~-~i~~~~~~~g~~   74 (237)
T TIGR03877         2 RVKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQM------GEPGIYVALEEHPV-QVRRNMAQFGWD   74 (237)
T ss_pred             ccccCcHhHHHHhcCCCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHc------CCcEEEEEeeCCHH-HHHHHHHHhCCC
Confidence            68999999999999999999999999999999999999999988742      58999999998533 233333332221


Q ss_pred             hhhcccchHHHhhcCeEEeCCC----------------CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC
Q 035774          163 EIFHSKGMAQEMAGRILVLQPT----------------SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP  226 (357)
Q Consensus       163 ~~~~~~~~~~~~~~~i~~~~~~----------------~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~  226 (357)
                          ...+  ...+++.++++.                +..++.+++..+...+...+.++||||||+.++...      
T Consensus        75 ----~~~~--~~~g~l~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSls~l~~~~------  142 (237)
T TIGR03877        75 ----VRKY--EEEGKFAIVDAFTGGIGEAAEREKYVVKDPTDVRELIDVLRQAIRDINAKRVVIDSVTTLYITK------  142 (237)
T ss_pred             ----HHHH--hhcCCEEEEeccccccccccccccccccCcccHHHHHHHHHHHHHHhCCCEEEEcChhHhhcCC------
Confidence                0000  011234444322                234566777777777778899999999999986531      


Q ss_pred             ChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEE
Q 035774          227 GQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE  306 (357)
Q Consensus       227 r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~  306 (357)
                       ....++++..|+++++++|+|+++++|.+.....                            ..+..+++.+|.+|.|+
T Consensus       143 -~~~~r~~l~~l~~~lk~~~~t~llt~~~~~~~~~----------------------------~~~~~~~~~~D~vI~L~  193 (237)
T TIGR03877       143 -PAMARSIVMQLKRVLSGLGCTSIFVSQVSVGERG----------------------------FGGPGVEHAVDGIIRLD  193 (237)
T ss_pred             -hHHHHHHHHHHHHHHHhCCCEEEEEECccccccc----------------------------ccccceEEEEeEEEEEE
Confidence             1234467788999999999999999987642110                            00011356678888887


Q ss_pred             Ee----CCeEEEEEEeCCCCCC--ceeEEEEcCCCceeccCCC
Q 035774          307 AK----SGQRFMNVEKSPTSPP--LAFSFTINPSGISLLTDDG  343 (357)
Q Consensus       307 ~~----~~~R~l~v~K~r~~~~--~~~~f~I~~~Gi~~~~~~~  343 (357)
                      ..    ...|+++|.|+|++++  +.++|+|+++||+++|..+
T Consensus       194 ~~~~~~~~~R~l~i~K~Rg~~~~~~~~~~~It~~Gi~v~~~~~  236 (237)
T TIGR03877       194 LDEIDGELKRSLIVWKMRGTKHSMRRHPFEITDKGIIVYPDKV  236 (237)
T ss_pred             EEeeCCceEEEEEEEECCCCCCCCceEEEEEcCCCEEEEeCCC
Confidence            54    2379999999999984  6789999999999998643

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.

>PRK04328 hypothetical protein; Provisional

Probab=99.98  E-value=1e-30  Score=231.93  Aligned_cols=218  Identities=19%  Similarity=0.204  Sum_probs=158.4

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc-
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS-  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~-  159 (357)
                      .++++||+++||++|+||+|+|++++|+|+||+|||+||+||+.+.+..      +++++||++|++  +..+.+.+.. 
T Consensus         2 ~~rv~tGi~~LD~lL~GGip~gs~ili~G~pGsGKT~l~~~fl~~~~~~------ge~~lyis~ee~--~~~i~~~~~~~   73 (249)
T PRK04328          2 VKRVKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQFLWNGLQM------GEPGVYVALEEH--PVQVRRNMRQF   73 (249)
T ss_pred             CceecCCchhHHHHhcCCCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhc------CCcEEEEEeeCC--HHHHHHHHHHc
Confidence            3579999999999999999999999999999999999999999998742      589999999985  3344433322 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCC----------------CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPT----------------SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~----------------~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~  223 (357)
                      .|.    ....  ...+++.+++..                +..++..++..+...+.+.++++|||||++.++...   
T Consensus        74 g~d----~~~~--~~~~~l~iid~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDSlt~l~~~~---  144 (249)
T PRK04328         74 GWD----VRKY--EEEGKFAIVDAFTGGIGSAAKREKYVVKDPDDVRELIDVLRQAIKDIGAKRVVIDSVSTLYLTK---  144 (249)
T ss_pred             CCC----HHHH--hhcCCEEEEeccccccccccccccccccCcccHHHHHHHHHHHHHhhCCCEEEEeChhHhhcCC---
Confidence            221    0000  011234444332                234566777778888888899999999999986531   


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                          ....++++..|.++++++|+|+++|+|.......                            ..+...++.+|.++
T Consensus       145 ----~~~~r~~~~~l~~~lk~~g~t~llt~e~~~~~~~----------------------------~~~~~~~~~~D~vI  192 (249)
T PRK04328        145 ----PAMARSIVMQLKRVLSGLGCTAIFVSQVSVGERG----------------------------FGGPGVEHAVDGII  192 (249)
T ss_pred             ----hHHHHHHHHHHHHHHHhCCCEEEEEECccccccc----------------------------cCCCCcEEEEEEEE
Confidence                1234466778888899999999999988642110                            00011345678888


Q ss_pred             EEEEe----CCeEEEEEEeCCCCCC--ceeEEEEcCCCceeccCCCceec
Q 035774          304 VLEAK----SGQRFMNVEKSPTSPP--LAFSFTINPSGISLLTDDGTEMV  347 (357)
Q Consensus       304 ~l~~~----~~~R~l~v~K~r~~~~--~~~~f~I~~~Gi~~~~~~~~~~~  347 (357)
                      .|+..    ...|.++|.|+|++++  ..++|.|+++||+++|...+.+.
T Consensus       193 ~L~~~~~~~~~~R~l~I~K~Rg~~~~~~~~~~~It~~Gi~v~~~~~~~~~  242 (249)
T PRK04328        193 RLDLDEIDGELKRSLIVWKMRGTKHSMRRHPFEITDKGIVVYPDKVLKIT  242 (249)
T ss_pred             EEEEEecCCcEEEEEEEEEccCCCCCCceEEEEEcCCCEEEEecceEEee
Confidence            88764    2378999999999984  67899999999999998776643

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=99.98  E-value=1.4e-30  Score=232.20  Aligned_cols=214  Identities=19%  Similarity=0.263  Sum_probs=157.3

Q ss_pred             CCCCCchhHHhhh--------------cCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774           83 HLPTRLKGLDAAL--------------CGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus        83 ~i~TG~~~LD~~l--------------~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      +++||+++||++|              +||+|+|++++|+|+||+|||+||+|++.+.+..      +++|+||++|++.
T Consensus         3 ~~~tGi~glD~~l~~~~~~~~~~~~~~~GGip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~------Ge~vlyis~Ee~~   76 (259)
T TIGR03878         3 GVPTGVEGLDELFFKVEIEEGKIVRKPLGGIPAYSVINITGVSDTGKSLMVEQFAVTQASR------GNPVLFVTVESPA   76 (259)
T ss_pred             CccCCchhHHHhhccccccccccccccCCCeECCcEEEEEcCCCCCHHHHHHHHHHHHHhC------CCcEEEEEecCCc
Confidence            6899999999999              5999999999999999999999999999998752      5899999999743


Q ss_pred             ch--HHHHHHHhccCchhhcccchHHHhhcCeEEeCCCCH----HHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCC
Q 035774          149 TS--RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSL----SEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHE  222 (357)
Q Consensus       149 ~~--~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~----~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~  222 (357)
                      ..  .++.+.+.. +    ..+  .+...++++++++.+.    .++.+++..+...+.++++++|||||++.++..   
T Consensus        77 ~~~~~~l~~~a~~-~----g~d--~~~~~~~l~~id~~~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls~l~~~---  146 (259)
T TIGR03878        77 NFVYTSLKERAKA-M----GVD--FDKIEENIILIDAASSTELRENVPNLLATLAYAIKEYKVKNTVIDSITGLYEA---  146 (259)
T ss_pred             hHHHHHHHHHHHH-c----CCC--HHHHhCCEEEEECCCchhhhhhHHHHHHHHHHHHHhhCCCEEEEcCchHhccc---
Confidence            21  233322221 1    110  1234567888776653    245566777777777889999999999988653   


Q ss_pred             CCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEE
Q 035774          223 QRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIR  302 (357)
Q Consensus       223 ~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~r  302 (357)
                          .....++++..|..+++++++|+++++|........                       ...|+.+..+.+.+|.+
T Consensus       147 ----~~~~~r~~~~~L~~~lk~~~~t~ll~~e~~~~~~~~-----------------------~~~~~~~~~~~~l~D~v  199 (259)
T TIGR03878       147 ----KEMMAREIVRQLFNFMKKWYQTALFVSQKRSGHEEL-----------------------SAEAAGGYAVSHIVDGT  199 (259)
T ss_pred             ----chHHHHHHHHHHHHHHHHcCCeEEEEeccccCcccc-----------------------cccccCCcceeEeeccE
Confidence                124456778888999999999999999875532100                       00122233367888999


Q ss_pred             EEEEE----------------eCCeEEEEEEeCCCCC--CceeEEEEcCCCceec
Q 035774          303 LVLEA----------------KSGQRFMNVEKSPTSP--PLAFSFTINPSGISLL  339 (357)
Q Consensus       303 l~l~~----------------~~~~R~l~v~K~r~~~--~~~~~f~I~~~Gi~~~  339 (357)
                      |.|+.                ....|+++|.|+|+++  ..+++|+|+++||..+
T Consensus       200 I~L~~~~~~~~~~~~~~~~~~~~~~R~l~I~KmRg~~h~~~~~~~~It~~Gi~~i  254 (259)
T TIGR03878       200 IVLAKQLIMSRFDASLYKKPIGEIVRLFRIDGCRMCGHDTKTHVLEIDETGLVKI  254 (259)
T ss_pred             EEEeeeeccchhhhhhccccccceEEEEEEEEccCCCCCCceeEEEEcCCceEEe
Confidence            98873                1246999999999987  4778999999996655

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>cd00983 recA RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=99.97  E-value=1.2e-30  Score=235.73  Aligned_cols=216  Identities=26%  Similarity=0.324  Sum_probs=168.4

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ...+|||++.||.+|+ ||+|+|.+++|+||||+|||+||++++++++..      ++.|+|||+|+.+++.++..+.. 
T Consensus        33 ~~~isTGi~~LD~~Lg~GGlp~G~iteI~Gp~GsGKTtLal~~~~~~~~~------g~~~vyId~E~~~~~~~a~~lGv-  105 (325)
T cd00983          33 VEVIPTGSLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQKL------GGTVAFIDAEHALDPVYAKKLGV-  105 (325)
T ss_pred             CceecCCCHHHHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCCEEEECccccHHHHHHHHcCC-
Confidence            6789999999999999 999999999999999999999999999998742      58999999999988765544321 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC-CCCCCCC------ChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG-VHEQRAP------GQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~-~~~~~~~------r~~~~~  232 (357)
                                    ..+++++.++.+.++...++.   ..+.+..+++|||||++++++. +.++...      +...+.
T Consensus       106 --------------d~~~l~v~~p~~~eq~l~i~~---~li~s~~~~lIVIDSvaal~~~~E~~~~~~~~~~~~qaR~l~  168 (325)
T cd00983         106 --------------DLDNLLISQPDTGEQALEIAD---SLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS  168 (325)
T ss_pred             --------------CHHHheecCCCCHHHHHHHHH---HHHhccCCCEEEEcchHhhcccccccccccccchHHHHHHHH
Confidence                          124577888887777655554   4456678999999999999863 3332211      123456


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      ..++.|..++++++|++|+|||+....+   .+|.                 ....|.+|..|.+.+..|+.+++.+   
T Consensus       169 ~~Lr~L~~~~~k~~~~vI~tNQvr~~ig---~~~g-----------------~~e~~~GG~~L~~~ss~rl~lrk~~~~k  228 (325)
T cd00983         169 QALRKLTGSINKSNTTVIFINQLREKIG---VMFG-----------------NPETTTGGNALKFYSSVRLDIRRIETIK  228 (325)
T ss_pred             HHHHHHHHHHHhCCCEEEEEEccccccc---cccC-----------------CCccCCCchHHhhhcceEEEEEeecccc
Confidence            7888899999999999999999988654   1211                 1235778888999999999998753   


Q ss_pred             -------CeEEEEEEeCCCCCC-ceeEEEEc-CCCceecc
Q 035774          310 -------GQRFMNVEKSPTSPP-LAFSFTIN-PSGISLLT  340 (357)
Q Consensus       310 -------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi~~~~  340 (357)
                             ..+.++|+|++..|+ ..++|.|. ++||.-..
T Consensus       229 ~~~~~~G~~~~~~v~Knk~~~p~~~~~~~i~~~~Gi~~~~  268 (325)
T cd00983         229 DGDEVIGNRTKVKVVKNKVAPPFKTAEFDILFGEGISREG  268 (325)
T ss_pred             cCCcccccEEEEEEEecccCCCCCceEEEEEcCcccchhh
Confidence                   457899999999996 55789876 78887653

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK09354 recA recombinase A; Provisional

Probab=99.97  E-value=3e-30  Score=234.66  Aligned_cols=216  Identities=25%  Similarity=0.327  Sum_probs=167.4

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..++|||++.||.+|+ ||+|+|.+++|+|+||+|||+||++++++++..      ++.|+|||+|+++++.+...+...
T Consensus        38 ~~~isTGi~~LD~~LG~GGip~G~IteI~G~~GsGKTtLal~~~~~~~~~------G~~~~yId~E~s~~~~~a~~lGvd  111 (349)
T PRK09354         38 VEVISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKA------GGTAAFIDAEHALDPVYAKKLGVD  111 (349)
T ss_pred             CceecCCcHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCcEEEECCccchHHHHHHHcCCC
Confidence            6789999999999999 999999999999999999999999999998742      589999999999887654443211


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCCC------ChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRAP------GQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~~------r~~~~~  232 (357)
                                     .+++++..+.+.++...++   ...+++..+++|||||++++++ .+.++...      +...+.
T Consensus       112 ---------------ld~lli~qp~~~Eq~l~i~---~~li~s~~~~lIVIDSvaaL~~~~E~eg~~gd~~~~~qar~ms  173 (349)
T PRK09354        112 ---------------IDNLLVSQPDTGEQALEIA---DTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS  173 (349)
T ss_pred             ---------------HHHeEEecCCCHHHHHHHH---HHHhhcCCCCEEEEeChhhhcchhhhcCCccccchhHHHHHHH
Confidence                           2457777777776665444   4456677899999999999985 33332211      113455


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      ..++.|..+++++||++|+|||+....+   .+|.                 ....|.+|..|.+.+.+|+.+++..   
T Consensus       174 ~~Lr~L~~~l~k~~itvI~tNQvr~~ig---~~~g-----------------~pe~~~GG~aL~~~ss~rl~lrr~~~iK  233 (349)
T PRK09354        174 QALRKLTGNISKSNTTVIFINQIREKIG---VMFG-----------------NPETTTGGNALKFYASVRLDIRRIGTIK  233 (349)
T ss_pred             HHHHHHHHHHHHcCcEEEEEEeeeeccc---cccC-----------------CCCcCCCchhhHhhheeeeEEecccccc
Confidence            6678899999999999999999988654   1111                 1123667888999999999998742   


Q ss_pred             -------CeEEEEEEeCCCCCC-ceeEEEEc-CCCceecc
Q 035774          310 -------GQRFMNVEKSPTSPP-LAFSFTIN-PSGISLLT  340 (357)
Q Consensus       310 -------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi~~~~  340 (357)
                             ..+.++|+|++..|+ ..+.|.|. ++||.-..
T Consensus       234 ~~~~~~G~~~r~~vvKnk~~~p~~~a~~~i~~~~Gi~~~~  273 (349)
T PRK09354        234 DGDEVIGNRTKVKVVKNKVAPPFKQAEFDIMYGEGISREG  273 (349)
T ss_pred             cCCceecceEEEEEEecccCCCCCceEEEEEcCCccchhh
Confidence                   467899999999997 56789988 89987654

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=99.97  E-value=5.5e-30  Score=237.65  Aligned_cols=213  Identities=19%  Similarity=0.241  Sum_probs=161.0

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||+++||++|+||+++|++++|+|+||+|||+|+++++.+.+..      +++|+||++|++...  +...+.. 
T Consensus        61 ~~ri~TGi~eLD~vLgGGi~~GslvLI~G~pG~GKStLllq~a~~~a~~------g~~VlYvs~EEs~~q--i~~Ra~r-  131 (372)
T cd01121          61 EERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKR------GGKVLYVSGEESPEQ--IKLRADR-  131 (372)
T ss_pred             cCccccCCHHHHHhhcCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhc------CCeEEEEECCcCHHH--HHHHHHH-
Confidence            5689999999999999999999999999999999999999999988742      479999999986443  2221111 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS  240 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~  240 (357)
                      +    .      ...+++++....+.+++.       ..+...++++|||||++.++....+....+..++++++..|++
T Consensus       132 l----g------~~~~~l~l~~e~~le~I~-------~~i~~~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~  194 (372)
T cd01121         132 L----G------ISTENLYLLAETNLEDIL-------ASIEELKPDLVIIDSIQTVYSSELTSAPGSVSQVRECTAELMR  194 (372)
T ss_pred             c----C------CCcccEEEEccCcHHHHH-------HHHHhcCCcEEEEcchHHhhccccccCCCCHHHHHHHHHHHHH
Confidence            0    0      112455665554443333       2334568999999999999876544333455778899999999


Q ss_pred             HHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC--CeEEEEEEe
Q 035774          241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS--GQRFMNVEK  318 (357)
Q Consensus       241 la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~--~~R~l~v~K  318 (357)
                      +|+++++++++++|++++..                            .++...++|.+|++++++.+.  ..|.++++|
T Consensus       195 lak~~~itvilvghvtk~g~----------------------------~aG~~~leh~vD~Vi~le~~~~~~~R~Lri~K  246 (372)
T cd01121         195 FAKERNIPIFIVGHVTKEGS----------------------------IAGPKVLEHMVDTVLYFEGDRHSEYRILRSVK  246 (372)
T ss_pred             HHHHcCCeEEEEeeccCCCc----------------------------ccCcccchhhceEEEEEEcCCCCcEEEEEEEe
Confidence            99999999999999977422                            011123789999999998775  489999999


Q ss_pred             CCCCCC-ceeEEEEcCCCceec-cCCCceec
Q 035774          319 SPTSPP-LAFSFTINPSGISLL-TDDGTEMV  347 (357)
Q Consensus       319 ~r~~~~-~~~~f~I~~~Gi~~~-~~~~~~~~  347 (357)
                      +|+++. ....|+|+++||..+ ++..+++.
T Consensus       247 nR~g~~~ei~~F~i~~~Gl~~v~~ps~~fl~  277 (372)
T cd01121         247 NRFGSTNELGVFEMRENGLREVSNPSELFLS  277 (372)
T ss_pred             CCCCCCCCEEEEEECCCCeEEccChhhheec
Confidence            999885 447899999999964 45556554

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.

>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=8.8e-30  Score=229.55  Aligned_cols=211  Identities=21%  Similarity=0.278  Sum_probs=172.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||+.+||++||||+-+|++++|.|.||.|||||++|++...+.+       ++|+|++.|++..+-+++.-... 
T Consensus        72 ~~Ri~tg~~EldRVLGGG~V~Gs~iLIgGdPGIGKSTLLLQva~~lA~~-------~~vLYVsGEES~~QiklRA~RL~-  143 (456)
T COG1066          72 EPRISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKR-------GKVLYVSGEESLQQIKLRADRLG-  143 (456)
T ss_pred             cccccCChHHHHhhhcCCcccccEEEEccCCCCCHHHHHHHHHHHHHhc-------CcEEEEeCCcCHHHHHHHHHHhC-
Confidence            5799999999999999999999999999999999999999999999853       49999999998776666542211 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS  240 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~  240 (357)
                                  ...+++++....+.+++.+.++       +.+++++|||||+.++.+........-.++++....|.+
T Consensus       144 ------------~~~~~l~l~aEt~~e~I~~~l~-------~~~p~lvVIDSIQT~~s~~~~SapGsVsQVRe~t~~L~~  204 (456)
T COG1066         144 ------------LPTNNLYLLAETNLEDIIAELE-------QEKPDLVVIDSIQTLYSEEITSAPGSVSQVREVAAELMR  204 (456)
T ss_pred             ------------CCccceEEehhcCHHHHHHHHH-------hcCCCEEEEeccceeecccccCCCCcHHHHHHHHHHHHH
Confidence                        1125677777777666654443       468999999999999998776666667899999999999


Q ss_pred             HHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe--CCeEEEEEEe
Q 035774          241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK--SGQRFMNVEK  318 (357)
Q Consensus       241 la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~--~~~R~l~v~K  318 (357)
                      +||+.|++++++.|++++..                .++|            +..+|++|++++|+.+  ...|.+|-+|
T Consensus       205 ~AK~~~i~~fiVGHVTKeG~----------------IAGP------------rvLEHmVDtVlyFEGd~~~~~RiLR~vK  256 (456)
T COG1066         205 LAKTKNIAIFIVGHVTKEGA----------------IAGP------------RVLEHMVDTVLYFEGDRHSRYRILRSVK  256 (456)
T ss_pred             HHHHcCCeEEEEEEEccccc----------------ccCc------------hheeeeeeEEEEEeccCCCceeeeehhc
Confidence            99999999999999998633                2333            3368999999999986  5689999999


Q ss_pred             CCCCCCce-eEEEEcCCCceeccC-CCcee
Q 035774          319 SPTSPPLA-FSFTINPSGISLLTD-DGTEM  346 (357)
Q Consensus       319 ~r~~~~~~-~~f~I~~~Gi~~~~~-~~~~~  346 (357)
                      ||+++..+ --|+.++.|+..... ..+|.
T Consensus       257 NRFG~t~EiGvFeM~~~GL~eV~npS~lFL  286 (456)
T COG1066         257 NRFGATNELGVFEMTENGLREVSNPSALFL  286 (456)
T ss_pred             ccCCcccceeEEEEecCCeeEecCcHHhHh
Confidence            99999655 479999999987754 34444

>PRK11823 DNA repair protein RadA; Provisional

Probab=99.97  E-value=1.3e-29  Score=241.63  Aligned_cols=213  Identities=19%  Similarity=0.232  Sum_probs=160.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||+++||++|+||+++|++++|+|+||+|||+|++|++.+.+..      +++|+||++|+++..  +...+.. 
T Consensus        59 ~~ri~TGi~~LD~~LgGGi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~------g~~vlYvs~Ees~~q--i~~ra~r-  129 (446)
T PRK11823         59 EPRISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAA------GGKVLYVSGEESASQ--IKLRAER-  129 (446)
T ss_pred             CCcccCCcHHHHHHhcCCccCCEEEEEECCCCCCHHHHHHHHHHHHHhc------CCeEEEEEccccHHH--HHHHHHH-
Confidence            5689999999999999999999999999999999999999999988742      479999999986543  2221211 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS  240 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~  240 (357)
                      +    ..      ..+++++....+.+++       ...+.+.++++|||||++.++....++...+..++++++..|++
T Consensus       130 l----g~------~~~~l~~~~e~~l~~i-------~~~i~~~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~  192 (446)
T PRK11823        130 L----GL------PSDNLYLLAETNLEAI-------LATIEEEKPDLVVIDSIQTMYSPELESAPGSVSQVRECAAELMR  192 (446)
T ss_pred             c----CC------ChhcEEEeCCCCHHHH-------HHHHHhhCCCEEEEechhhhccccccCCCCCHHHHHHHHHHHHH
Confidence            1    00      1234555555444333       23334568999999999999876554434456778889999999


Q ss_pred             HHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEE--eCCeEEEEEEe
Q 035774          241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA--KSGQRFMNVEK  318 (357)
Q Consensus       241 la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~--~~~~R~l~v~K  318 (357)
                      +++++++++++++|+++...                            .++...|+|.+|++++++.  ....|.++++|
T Consensus       193 ~ak~~~itvilv~hvtk~~~----------------------------~ag~~~lehlvD~Vi~le~~~~~~~R~l~i~K  244 (446)
T PRK11823        193 LAKQRGIAVFLVGHVTKEGA----------------------------IAGPRVLEHMVDTVLYFEGDRHSRYRILRAVK  244 (446)
T ss_pred             HHHHcCCEEEEEeeccCCCC----------------------------cCCcchhhhhCeEEEEEEcCCCCceEEEEEcc
Confidence            99999999999999976422                            0111348999999999985  34689999999


Q ss_pred             CCCCCC-ceeEEEEcCCCceec-cCCCceec
Q 035774          319 SPTSPP-LAFSFTINPSGISLL-TDDGTEMV  347 (357)
Q Consensus       319 ~r~~~~-~~~~f~I~~~Gi~~~-~~~~~~~~  347 (357)
                      +|+++. ....|+|+++||... ++..+++.
T Consensus       245 ~R~g~~~e~~~f~it~~Gi~~v~~ps~~~~~  275 (446)
T PRK11823        245 NRFGATNEIGVFEMTEQGLREVSNPSELFLS  275 (446)
T ss_pred             CCCCCCCceEEEEEcCCCceECCCHHHHHhc
Confidence            998885 446899999999954 55556654

>TIGR02012 tigrfam_recA protein RecA

Probab=99.97  E-value=5.4e-30  Score=231.41  Aligned_cols=216  Identities=25%  Similarity=0.324  Sum_probs=165.5

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..++|||++.||.+|+ ||+|+|.+++|+||||+|||+||++++.+++..      +++|+|||+|+.+++.+...+.. 
T Consensus        33 ~~~i~TGi~~LD~~Lg~GGlp~G~iteI~G~~GsGKTtLaL~~~~~~~~~------g~~v~yId~E~~~~~~~a~~lGv-  105 (321)
T TIGR02012        33 VETISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQKA------GGTAAFIDAEHALDPVYARKLGV-  105 (321)
T ss_pred             CceecCCCHHHHHHhcCCCCcCCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCcEEEEcccchhHHHHHHHcCC-
Confidence            6789999999999999 999999999999999999999999999998753      58999999999888764433221 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC-CCCCCC------CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG-VHEQRA------PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~-~~~~~~------~r~~~~~  232 (357)
                                    ..+++++.++.+.++....   +...+++..+++|||||++++++. +.++..      .+...+.
T Consensus       106 --------------d~~~l~v~~p~~~eq~l~~---~~~li~~~~~~lIVIDSv~al~~~~E~e~~~g~~~~~~~aR~m~  168 (321)
T TIGR02012       106 --------------DIDNLLVSQPDTGEQALEI---AETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMS  168 (321)
T ss_pred             --------------CHHHeEEecCCCHHHHHHH---HHHHhhccCCcEEEEcchhhhccchhhcccccccchhHHHHHHH
Confidence                          1246777887776665444   444556678999999999999853 333221      1123345


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe----
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK----  308 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~----  308 (357)
                      .+++.|..+++++||++|+|||+....+   .+|.                 ....|.+|..|.+.+..|+.+++.    
T Consensus       169 ~~lr~L~~~l~~~~~tvi~tNQvr~~~g---~~~~-----------------~~e~~~GG~aL~~~ss~r~~lrr~~~iK  228 (321)
T TIGR02012       169 QALRKLTGALSKSNTTAIFINQIREKIG---VMFG-----------------NPETTTGGRALKFYASVRLDIRRIGQVK  228 (321)
T ss_pred             HHHHHHHHHHHhCCCEEEEEecceeccC---cccC-----------------CCccCcCccHHHHHHhHhHhhhhhhccc
Confidence            6788899999999999999999987654   1111                 112366777889999999888753    


Q ss_pred             ------CCeEEEEEEeCCCCCC-ceeEEEEc-CCCceecc
Q 035774          309 ------SGQRFMNVEKSPTSPP-LAFSFTIN-PSGISLLT  340 (357)
Q Consensus       309 ------~~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi~~~~  340 (357)
                            +..+.++|+||+..|+ ..++|.|. ++||.-..
T Consensus       229 ~~~~~~g~~~~~~v~Knk~~~p~~~~~~~i~~~~Gi~~~~  268 (321)
T TIGR02012       229 QGEEVVGNRTKVKVVKNKVAPPFKEAEFDILYGEGISKLG  268 (321)
T ss_pred             cCCceeccEEEEEEEECCCCCCCCceEEEEEcCCccchhh
Confidence                  3568899999999996 56889988 89987654

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.

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=99.97  E-value=1.2e-29  Score=222.82  Aligned_cols=212  Identities=25%  Similarity=0.377  Sum_probs=152.5

Q ss_pred             CCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCch
Q 035774           84 LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPE  163 (357)
Q Consensus        84 i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~  163 (357)
                      ++||+++||++|+||+|+|++++|.|+||+|||+|++|++.+.+..  .   +++|+||++|++  ++.+.+.+.. +. 
T Consensus         1 V~TGI~~LD~~l~GGip~gs~~li~G~~GsGKT~l~~q~l~~~~~~--~---ge~vlyvs~ee~--~~~l~~~~~s-~g-   71 (226)
T PF06745_consen    1 VPTGIPGLDELLGGGIPKGSVVLISGPPGSGKTTLALQFLYNGLKN--F---GEKVLYVSFEEP--PEELIENMKS-FG-   71 (226)
T ss_dssp             E--SSTTHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHHHHH--H---T--EEEEESSS---HHHHHHHHHT-TT-
T ss_pred             CCCCchhHHHhhcCCCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhh--c---CCcEEEEEecCC--HHHHHHHHHH-cC-
Confidence            5899999999999999999999999999999999999999998752  0   489999999884  4444443332 11 


Q ss_pred             hhcccchHHHhhcCeEEeCCCCH------HHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHH
Q 035774          164 IFHSKGMAQEMAGRILVLQPTSL------SEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISL  237 (357)
Q Consensus       164 ~~~~~~~~~~~~~~i~~~~~~~~------~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~  237 (357)
                       ++....  ...+++.+++..+.      .++..++..+...+...++++|||||++.+... .     ....++.++..
T Consensus        72 -~d~~~~--~~~g~l~~~d~~~~~~~~~~~~~~~l~~~i~~~i~~~~~~~vVIDsls~l~~~-~-----~~~~~r~~l~~  142 (226)
T PF06745_consen   72 -WDLEEY--EDSGKLKIIDAFPERIGWSPNDLEELLSKIREAIEELKPDRVVIDSLSALLLY-D-----DPEELRRFLRA  142 (226)
T ss_dssp             -S-HHHH--HHTTSEEEEESSGGGST-TSCCHHHHHHHHHHHHHHHTSSEEEEETHHHHTTS-S-----SGGGHHHHHHH
T ss_pred             -CcHHHH--hhcCCEEEEecccccccccccCHHHHHHHHHHHHHhcCCCEEEEECHHHHhhc-C-----CHHHHHHHHHH
Confidence             111111  11234666655533      356677777778787788899999999999322 1     23556778888


Q ss_pred             HHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhh-hccEEEEEEEe--C--CeE
Q 035774          238 ITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAH-AVTIRLVLEAK--S--GQR  312 (357)
Q Consensus       238 Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~-~~~~rl~l~~~--~--~~R  312 (357)
                      |...+++++++++++.|.......                            .....+.+ .+|..|.|+..  +  ..|
T Consensus       143 l~~~l~~~~~t~llt~~~~~~~~~----------------------------~~~~~i~~~l~D~vI~L~~~~~~~~~~R  194 (226)
T PF06745_consen  143 LIKFLKSRGVTTLLTSEMPSGSED----------------------------DGTFGIEHYLADGVIELRYEEEGGRIRR  194 (226)
T ss_dssp             HHHHHHHTTEEEEEEEEESSSSSS----------------------------SSSTSHHHHHSSEEEEEEEEEETTEEEE
T ss_pred             HHHHHHHCCCEEEEEEccccCccc----------------------------ccccchhhhcccEEEEEEEEeeCCEEEE
Confidence            999999999999999986442110                            01112566 89999999864  2  379


Q ss_pred             EEEEEeCCCCC--CceeEEEEcCCCceeccC
Q 035774          313 FMNVEKSPTSP--PLAFSFTINPSGISLLTD  341 (357)
Q Consensus       313 ~l~v~K~r~~~--~~~~~f~I~~~Gi~~~~~  341 (357)
                      .++|.|+|+++  ..+++|+|+++||+++++
T Consensus       195 ~l~I~K~Rg~~~~~~~~~f~I~~~Gi~i~~~  225 (226)
T PF06745_consen  195 RLRIVKMRGSRHSTGIHPFEITPGGIEIYPP  225 (226)
T ss_dssp             EEEEEEETTS----BEEEEEEETTEEEEETT
T ss_pred             EEEEEEcCCCCCCCcEEEEEEECCeEEEecC
Confidence            99999999988  478999999999999985

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 ....

>PRK08760 replicative DNA helicase; Provisional

Probab=99.97  E-value=1.2e-29  Score=243.37  Aligned_cols=236  Identities=14%  Similarity=0.127  Sum_probs=166.5

Q ss_pred             ccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHH
Q 035774           78 EHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMG  157 (357)
Q Consensus        78 ~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~  157 (357)
                      .....+++||++.||.+++ |+++|++++|+|+||+|||+|++++|.+++..  .   +.+|+||+.|++.... +.++.
T Consensus       206 ~~~~~Gi~TG~~~LD~~t~-G~~~G~LivIaarPg~GKTafal~iA~~~a~~--~---g~~V~~fSlEMs~~ql-~~Rl~  278 (476)
T PRK08760        206 GGNITGLPTGYNDFDAMTA-GLQPTDLIILAARPAMGKTTFALNIAEYAAIK--S---KKGVAVFSMEMSASQL-AMRLI  278 (476)
T ss_pred             CCCCCcccCCcHHHHHHhc-CCCCCceEEEEeCCCCChhHHHHHHHHHHHHh--c---CCceEEEeccCCHHHH-HHHHH
Confidence            3346789999999999985 59999999999999999999999999998752  1   4789999999964431 11211


Q ss_pred             hc--cCc--h----------hhcccchHHHhh-cCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCC
Q 035774          158 AS--SFP--E----------IFHSKGMAQEMA-GRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHE  222 (357)
Q Consensus       158 ~~--~~~--~----------~~~~~~~~~~~~-~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~  222 (357)
                      ..  .++  .          +.........+. .++++.+.. ...+.++...++....++++++||||||+.+....  
T Consensus       279 a~~s~i~~~~i~~g~l~~~e~~~~~~a~~~l~~~~l~I~d~~-~~t~~~I~~~~r~l~~~~~~~lVvIDyLql~~~~~--  355 (476)
T PRK08760        279 SSNGRINAQRLRTGALEDEDWARVTGAIKMLKETKIFIDDTP-GVSPEVLRSKCRRLKREHDLGLIVIDYLQLMSVPG--  355 (476)
T ss_pred             HhhCCCcHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEeCCC-CCCHHHHHHHHHHHHHhcCCCEEEEecHHhcCCCC--
Confidence            11  010  0          000000111111 244554433 23455555666666667889999999999885332  


Q ss_pred             CCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEE
Q 035774          223 QRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIR  302 (357)
Q Consensus       223 ~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~r  302 (357)
                      ...+|..++.++++.||.+|++++|+||+++|+++....               ..++.|..++++.|+.  |++.+|++
T Consensus       356 ~~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQLnR~~e~---------------r~~krP~lsDLreSg~--IeqdAD~v  418 (476)
T PRK08760        356 NSENRATEISEISRSLKGLAKELNVPVIALSQLNRSLET---------------RTDKRPVMADLRESGA--IEQDADMI  418 (476)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHhCCEEEEeeccCccccc---------------cCCCCCCHHHHhhccc--hhcCCCEE
Confidence            224577889999999999999999999999999986542               1223445567776655  89999999


Q ss_pred             EEEEEeC----------CeEEEEEEeCCCCCCceeEEEEcCCCceecc
Q 035774          303 LVLEAKS----------GQRFMNVEKSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       303 l~l~~~~----------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      ++|+++.          +...+.|.|+|.++.+.+.+.+...--.+.+
T Consensus       419 l~l~R~~~y~~~~~~~~~~~eliiaKnR~G~~g~~~l~f~~~~~~f~~  466 (476)
T PRK08760        419 VFIYRDDYYNKENSPDKGLAEIIIGKHRGGPTGSCKLKFFGEYTRFDN  466 (476)
T ss_pred             EEEechhhcccccccCCCceEEEEEccCCCCCceEEEEEecCCCceec
Confidence            9998742          2467999999999998888877665555544

>TIGR00416 sms DNA repair protein RadA

Probab=99.97  E-value=3.1e-29  Score=239.00  Aligned_cols=213  Identities=18%  Similarity=0.213  Sum_probs=160.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||+++||++|+||+++|++++|+|+||+|||+|++|++.+.+..      +++|+||++|++..+.+.+  +.. 
T Consensus        73 ~~ri~TGi~~LD~vLgGGi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~------g~kvlYvs~EEs~~qi~~r--a~r-  143 (454)
T TIGR00416        73 VPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKN------QMKVLYVSGEESLQQIKMR--AIR-  143 (454)
T ss_pred             cCccccCcHHHHHHhcCCccCCeEEEEEcCCCCCHHHHHHHHHHHHHhc------CCcEEEEECcCCHHHHHHH--HHH-
Confidence            5689999999999999999999999999999999999999999988742      4789999999865432221  111 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS  240 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~  240 (357)
                      +    .      ...+++++....+.+++       ...+.+.++++|||||++.++..+.........++++++..|.+
T Consensus       144 l----g------~~~~~l~~~~e~~~~~I-------~~~i~~~~~~~vVIDSIq~l~~~~~~~~~g~~~q~r~~~~~L~~  206 (454)
T TIGR00416       144 L----G------LPEPNLYVLSETNWEQI-------CANIEEENPQACVIDSIQTLYSPDISSAPGSVSQVRECTAELMR  206 (454)
T ss_pred             c----C------CChHHeEEcCCCCHHHH-------HHHHHhcCCcEEEEecchhhcccccccCCCCHHHHHHHHHHHHH
Confidence            1    0      01235566555544333       33344568999999999999876543333345678889999999


Q ss_pred             HHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC--CeEEEEEEe
Q 035774          241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS--GQRFMNVEK  318 (357)
Q Consensus       241 la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~--~~R~l~v~K  318 (357)
                      +|+++|+|+++++|+++...                ..+            ...+++.+|.+++|+.+.  ..|.++++|
T Consensus       207 ~ak~~giTvllt~hvtkeg~----------------~aG------------~~~le~lvD~VI~Le~~~~~~~R~L~v~K  258 (454)
T TIGR00416       207 LAKTRGIAIFIVGHVTKEGS----------------IAG------------PKVLEHMVDTVLYFEGDRDSRFRILRSVK  258 (454)
T ss_pred             HHHHhCCEEEEEeccccCCc----------------cCC------------cccEeeeceEEEEEeccCCCcEEEEEEec
Confidence            99999999999999876421                001            123688999999998654  479999999


Q ss_pred             CCCCCC-ceeEEEEcCCCce-eccCCCceec
Q 035774          319 SPTSPP-LAFSFTINPSGIS-LLTDDGTEMV  347 (357)
Q Consensus       319 ~r~~~~-~~~~f~I~~~Gi~-~~~~~~~~~~  347 (357)
                      +|+++. ....|+|++.|+. +.++..+++.
T Consensus       259 ~R~g~~~e~~~f~it~~Gl~~v~~ps~~f~~  289 (454)
T TIGR00416       259 NRFGATNEIGIFEMTEQGLREVLNPSAIFLS  289 (454)
T ss_pred             CCCCCCCcEEEEEEecCCceecCChhHhhhc
Confidence            998885 4578999999996 6666677664

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>PRK08006 replicative DNA helicase; Provisional

Probab=99.97  E-value=2.7e-29  Score=240.14  Aligned_cols=227  Identities=15%  Similarity=0.143  Sum_probs=161.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEMGA  158 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~~~  158 (357)
                      ..+++||++.||.++ ||+.+|++++|+|+||+|||+|++++|.+++..  .   +.+|+|||.||+...  .|+.....
T Consensus       204 ~~Gi~TG~~~LD~~~-~Gl~~G~LiiIaarPgmGKTafalnia~~~a~~--~---g~~V~~fSlEM~~~ql~~Rlla~~~  277 (471)
T PRK08006        204 VTGVNTGYDDLNKKT-AGLQPSDLIIVAARPSMGKTTFAMNLCENAAML--Q---DKPVLIFSLEMPGEQIMMRMLASLS  277 (471)
T ss_pred             CCcccCCCHHHHHhh-cCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--c---CCeEEEEeccCCHHHHHHHHHHHhc
Confidence            578999999999998 579999999999999999999999999998752  1   478999999986433  22221111


Q ss_pred             ccCc--hh----hcccch------HHHh-h-cCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCC
Q 035774          159 SSFP--EI----FHSKGM------AQEM-A-GRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       159 ~~~~--~~----~~~~~~------~~~~-~-~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~  223 (357)
                       .++  ..    .....+      .... . .++++.+ .....+.++...+++...++ ++++||||||+.+....  .
T Consensus       278 -~v~~~~i~~~~l~~~e~~~~~~a~~~~~~~~~l~I~d-~~~~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~--~  353 (471)
T PRK08006        278 -RVDQTRIRTGQLDDEDWARISGTMGILLEKRNMYIDD-SSGLTPTEVRSRARRIFREHGGLSLIMIDYLQLMRVPS--L  353 (471)
T ss_pred             -CCCHHHhhcCCCCHHHHHHHHHHHHHHHhcCCEEEEC-CCCCCHHHHHHHHHHHHHhcCCCCEEEEccHHHccCCC--C
Confidence             010  00    000111      1122 1 2444444 33334455555555555555 69999999999875432  1


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                      ..+|..++.++++.||.+|++++|+||+++|+++....               ..++.|..++++.|++  |++.+|+++
T Consensus       354 ~~~r~~ei~~isr~LK~lAkel~ipVi~LsQLnR~~e~---------------r~dkrP~lsDLreSG~--IEqdAD~v~  416 (471)
T PRK08006        354 SDNRTLEIAEISRSLKALAKELQVPVVALSQLNRSLEQ---------------RADKRPVNSDLRESGS--IEQDADLIM  416 (471)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccc---------------cCCCCCchhhhhhcCc--ccccCCEEE
Confidence            24577889999999999999999999999999997652               2234555677776666  899999999


Q ss_pred             EEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCC
Q 035774          304 VLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPS  334 (357)
Q Consensus       304 ~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~  334 (357)
                      +++++.         +.-.+.|.|+|.++.+.+.|.+...
T Consensus       417 ~l~R~~~y~~~~~~~g~~elivaKnR~G~~G~v~l~f~~~  456 (471)
T PRK08006        417 FIYRDEVYHENSDLKGIAEIIIGKQRNGPIGTVRLTFNGQ  456 (471)
T ss_pred             EEecccccccccCCCCceEEEEecccCCCCceEEEEEccC
Confidence            998753         3457899999999988877766543

>PRK09165 replicative DNA helicase; Provisional

Probab=99.97  E-value=3.2e-29  Score=242.00  Aligned_cols=243  Identities=15%  Similarity=0.160  Sum_probs=166.5

Q ss_pred             ccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCC---------CCCCeEEEEeCCCCC
Q 035774           78 EHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYG---------GLDGGVIYIDVESTF  148 (357)
Q Consensus        78 ~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~g---------g~~~~vl~i~~e~~~  148 (357)
                      .+...+++||++.||.++ ||+.+|++++|+|+||+|||+|+++++.+++....++         ..+.+|+||++|++.
T Consensus       194 ~~~~~gi~TG~~~LD~~~-gG~~~g~livIaarpg~GKT~~al~ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSlEMs~  272 (497)
T PRK09165        194 DGHLSGISTGLRDLDSKL-GGLHPSDLIILAGRPSMGKTALATNIAFNAAKAYRREAQPDGSKKAVNGGVVGFFSLEMSA  272 (497)
T ss_pred             CCCCCcccCChHHHhhhc-CCCCCCceEEEEeCCCCChHHHHHHHHHHHHHhhcccccccccccccCCCeEEEEeCcCCH
Confidence            334679999999999999 4799999999999999999999999999987532110         014789999999964


Q ss_pred             chHHHHHHHh-ccCch-hhc-----ccc---h---HHHhh-cCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccc
Q 035774          149 TSRRMIEMGA-SSFPE-IFH-----SKG---M---AQEMA-GRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSME  214 (357)
Q Consensus       149 ~~~rl~~~~~-~~~~~-~~~-----~~~---~---~~~~~-~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~  214 (357)
                      .....+-+.. ..++. ...     ...   +   ...+. .++++.+ .....+.++...+++...++++++||||||+
T Consensus       273 ~ql~~R~la~~s~v~~~~i~~~~l~~~e~~~l~~a~~~l~~~~l~I~d-~~~~ti~~i~~~ir~l~~~~~~~lvvIDyLq  351 (497)
T PRK09165        273 EQLATRILSEQSEISSSKIRRGKISEEDFEKLVDASQELQKLPLYIDD-TPALSISQLRARARRLKRQHGLDLLVVDYLQ  351 (497)
T ss_pred             HHHHHHHHHHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCeEEeC-CCCCCHHHHHHHHHHHHHhcCCCEEEEcchH
Confidence            4321111111 11110 000     000   0   11111 1344443 3333455566666666667889999999999


Q ss_pred             cccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchh
Q 035774          215 ALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFH  294 (357)
Q Consensus       215 ~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~  294 (357)
                      .+.........+|.+++..+++.||.+|++++|+||+++|+++....               ..++.|..++++.|+.  
T Consensus       352 li~~~~~~~~~~r~~ev~~is~~LK~lAkel~ipVi~lsQLnR~~e~---------------r~~krP~lsDLr~Sg~--  414 (497)
T PRK09165        352 LIRGSSKRSSDNRVQEISEITQGLKALAKELNIPVIALSQLSRQVEQ---------------RDDKRPQLSDLRESGS--  414 (497)
T ss_pred             hccCCCCCCCCchHHHHHHHHHHHHHHHHHhCCeEEEeecccchhhc---------------cCCCCCchhhhhhccc--
Confidence            88644221234577889999999999999999999999999987541               1233455567776655  


Q ss_pred             HhhhccEEEEEEEeC--------------------------CeEEEEEEeCCCCCCceeEEEEcCCCceec
Q 035774          295 WAHAVTIRLVLEAKS--------------------------GQRFMNVEKSPTSPPLAFSFTINPSGISLL  339 (357)
Q Consensus       295 w~~~~~~rl~l~~~~--------------------------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~  339 (357)
                      +++.+|++++++++.                          +.-.+.|.|+|.++.+.+.|.+...--.+.
T Consensus       415 IEqdAD~v~~l~R~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~e~ivaKnR~G~~g~~~~~f~~~~~~f~  485 (497)
T PRK09165        415 IEQDADVVMFVYREEYYLKRKEPREGTPKHEEWQEKMEKVHNKAEVIIAKQRHGPTGTVKLAFESEFTRFG  485 (497)
T ss_pred             hhccCCEEEEEeehhhhccccccccccchhhhhhhhhcccCCceEEEEeccCCCCCeeEEEEEecCCCccc
Confidence            899999999998741                          235688999999998887777665444443

>PRK07004 replicative DNA helicase; Provisional

Probab=99.97  E-value=3.3e-29  Score=239.64  Aligned_cols=232  Identities=17%  Similarity=0.151  Sum_probs=163.0

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ...+++||++.||++++ |+++|++++|+|+||+|||+|+++++.+++..  .   +.+|+||++||+.... ..++...
T Consensus       192 ~~~gi~TG~~~LD~~t~-G~~~g~liviaarpg~GKT~~al~ia~~~a~~--~---~~~v~~fSlEM~~~ql-~~R~la~  264 (460)
T PRK07004        192 DVTGTPTGFVDLDRMTS-GMHGGELIIVAGRPSMGKTAFSMNIGEYVAVE--Y---GLPVAVFSMEMPGTQL-AMRMLGS  264 (460)
T ss_pred             CCCCccCCcHHhccccc-CCCCCceEEEEeCCCCCccHHHHHHHHHHHHH--c---CCeEEEEeCCCCHHHH-HHHHHHh
Confidence            35689999999999986 79999999999999999999999999988752  2   4889999999964331 1222111


Q ss_pred             --cCc------------hhhcccchHHHhhc-CeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCC
Q 035774          160 --SFP------------EIFHSKGMAQEMAG-RILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       160 --~~~------------~~~~~~~~~~~~~~-~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~  223 (357)
                        ..+            ++.........+.+ ++++.+ ....++.++...+++...++ ++++||||||+.+....  .
T Consensus       265 ~~~v~~~~i~~g~l~~~e~~~~~~a~~~l~~~~l~I~d-~~~~~~~~i~~~~r~l~~~~~~~~lviIDYLql~~~~~--~  341 (460)
T PRK07004        265 VGRLDQHRMRTGRLTDEDWPKLTHAVQKMSEAQLFIDE-TGGLNPMELRSRARRLARQCGKLGLIIIDYLQLMSGSS--Q  341 (460)
T ss_pred             hcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEEC-CCCCCHHHHHHHHHHHHHhCCCCCEEEEChhhhccCCC--C
Confidence              110            00000111122222 344433 33334455555555555554 58999999999886432  2


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                      ..+|.+++.++++.||.||++++|+||+++|+++....               ..+..|..++++.|++  +++.+|+++
T Consensus       342 ~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQLnR~~e~---------------r~~krP~lsDLreSg~--IeqdAD~v~  404 (460)
T PRK07004        342 GENRATEISEISRSLKSLAKELDVPVIALSQLNRGLEQ---------------RPNKRPVMSDLRESGA--IEQDADVIL  404 (460)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCCeEEEEeccChhhhc---------------cCCCCCChHHHhcchh--hhhcCCEEE
Confidence            24577889999999999999999999999999986542               1233455567776665  999999999


Q ss_pred             EEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          304 VLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       304 ~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      +++++.         +.-.+.|.|+|.++.+.+.+.+...=-.+
T Consensus       405 ~l~R~~~y~~~~~~~g~~e~ivaKnR~G~~G~v~l~f~~~~~~F  448 (460)
T PRK07004        405 FIYRDEVYNPDSPDKGTAEIIIGKQRNGPIGPVRLTFLGQYTKF  448 (460)
T ss_pred             EeccccccCCCcCCCCceEEEEEccCCCCCceEEEEEecCCCcc
Confidence            998753         24578999999999888877765543333

>PRK06321 replicative DNA helicase; Provisional

Probab=99.96  E-value=6.8e-29  Score=237.20  Aligned_cols=235  Identities=15%  Similarity=0.153  Sum_probs=165.7

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh-
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA-  158 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~-  158 (357)
                      ...++|||+..||++++ |+++|++++|+|+||+|||+|+++++.+++..  .   +.+|+|||.|++..... .++.. 
T Consensus       205 ~~~Gi~tG~~~LD~~t~-Gl~~G~LiiiaarPgmGKTafal~ia~~~a~~--~---g~~v~~fSLEMs~~ql~-~Rlla~  277 (472)
T PRK06321        205 MISGIPTHFIDLDKMIN-GFSPSNLMILAARPAMGKTALALNIAENFCFQ--N---RLPVGIFSLEMTVDQLI-HRIICS  277 (472)
T ss_pred             CCCccccCcHHHHHHhc-CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHh--c---CCeEEEEeccCCHHHHH-HHHHHh
Confidence            35799999999999996 69999999999999999999999999998742  1   47899999999643311 12211 


Q ss_pred             -ccCc-hhhc-----ccch------HHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCC-CCCC
Q 035774          159 -SSFP-EIFH-----SKGM------AQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGV-HEQR  224 (357)
Q Consensus       159 -~~~~-~~~~-----~~~~------~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~-~~~~  224 (357)
                       ...+ ..+.     ...+      ...+.+..++++......+.++...++....++++++||||||+.+.... ....
T Consensus       278 ~s~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~~~idd~~~~ti~~i~~~~r~~~~~~~~~lvvIDyLql~~~~~~~~~~  357 (472)
T PRK06321        278 RSEVESKKISVGDLSGRDFQRIVSVVNEMQEHTLLIDDQPGLKITDLRARARRMKESYDIQFLIIDYLQLLSGSGNLRNS  357 (472)
T ss_pred             hcCCCHHHhhcCCCCHHHHHHHHHHHHHHHcCCEEEeCCCCCCHHHHHHHHHHHHHhcCCCEEEEcchHHcCCCCccCCc
Confidence             1110 0000     0011      12222333444444333555666666666667889999999999875321 1122


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEE
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLV  304 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~  304 (357)
                      .+|..++.++++.||.+|++++|+||+++|+++....               ..+..|..++++.|+.  +++.+|++++
T Consensus       358 ~~r~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~---------------r~~krP~lsDLReSG~--IEqdAD~v~~  420 (472)
T PRK06321        358 ESRQTEISEISRMLKNLARELNIPILCLSQLSRKVED---------------RANHRPMMSDLRESGS--IEQDSDLVMF  420 (472)
T ss_pred             chHHHHHHHHHHHHHHHHHHhCCcEEEEeecChhhhc---------------cCCCCCCHHHHhhccc--ccccCCEEEE
Confidence            3467889999999999999999999999999987652               1233455567776555  8999999999


Q ss_pred             EEEeC--------CeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          305 LEAKS--------GQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       305 l~~~~--------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      ++++.        +.-.+.|.|+|.++.+.+.|....+--.+
T Consensus       421 l~R~~~y~~~~~~~~~elivaKnR~G~~G~v~l~f~~~~~~f  462 (472)
T PRK06321        421 LLRREYYDPNDKPGTAELIVAKNRHGSIGSVPLVFEKEFARF  462 (472)
T ss_pred             EechhhcCCcCCCCceEEEEEecCCCCCceEEEEEecCCCcc
Confidence            98742        34689999999999888877776544333

>COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair]

Probab=99.96  E-value=9.2e-29  Score=229.40  Aligned_cols=301  Identities=16%  Similarity=0.145  Sum_probs=209.5

Q ss_pred             HHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH----hcCCCcccHHHHHHHHHhcccCCCCCCCCc
Q 035774           13 KSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE----IVCPPFQTALLLMEQRAATEHLGGHLPTRL   88 (357)
Q Consensus        13 ~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~i~TG~   88 (357)
                      ++++|.|.+.|....+.........-.++++..+..+.++......    .+......+.+.+++...... ..++|||+
T Consensus       105 ~s~~R~Li~~~~~i~~~~~~~~~~~~~~~l~~ae~~i~~i~~~~~~~~~~~~~~~l~~~~~~i~~~~~~~~-~~Gi~tgf  183 (435)
T COG0305         105 KALLRELIEAGNEIVNLGYESEKDLDEEVLDAAEKKIFDVAERKNSEDFVHIGDLLKETMDEIEARFENGG-LIGVPTGF  183 (435)
T ss_pred             HHHHHHHHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHhccCC-CcccccCc
Confidence            4567777777777665554433222234444445444444433111    011122344444555544444 78999999


Q ss_pred             hhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc-cCc-----
Q 035774           89 KGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS-SFP-----  162 (357)
Q Consensus        89 ~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~-~~~-----  162 (357)
                      ..||.+++| +.+|++++++|+||+|||+||+++|.+++..     .+.+|.+|+.||+......+-+... ...     
T Consensus       184 ~~LD~~t~G-~~~~dLii~AaRP~mGKTafalnia~n~a~~-----~~~~v~iFSLEM~~eql~~R~Ls~~s~v~~~kir  257 (435)
T COG0305         184 TDLDEITSG-FRPGDLIIVAARPGMGKTALALNIALNAAAD-----GRKPVAIFSLEMSEEQLVMRLLSSESGIESSKLR  257 (435)
T ss_pred             hhhHHHhcC-CccCCEEEEccCCCCChHHHHHHHHHHHHHh-----cCCCeEEEEccCCHHHHHHHhhccccccchhccc
Confidence            999999976 9999999999999999999999999999873     2578999999996443221111111 000     


Q ss_pred             --h-----hhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHH
Q 035774          163 --E-----IFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHI  235 (357)
Q Consensus       163 --~-----~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~  235 (357)
                        .     +.........+.+.-++++..+...+.++..++++...++++++++|||++.+......  .+|.+++.++.
T Consensus       258 tg~l~~~d~~~l~~a~~~l~~~~i~IdD~~~~si~eir~~aRrlk~~~~l~~i~iDYLqLm~~~~~~--~~r~qevs~iS  335 (435)
T COG0305         258 TGRLSDDEWERLIKAASELSEAPIFIDDTPGLTITEIRSKARRLKLKHNLGLIVIDYLQLMTGGKKS--ENRKQEVSEIS  335 (435)
T ss_pred             cccccHHHHHHHHHHHHHHhhCCeeecCCCcCCHHHHHHHHHHHHHhcCccEEEEEEEEeecccccc--hhHHHHHHHHH
Confidence              0     00000111222233355666666677777888888888899999999999998776322  56889999999


Q ss_pred             HHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC------
Q 035774          236 SLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS------  309 (357)
Q Consensus       236 ~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~------  309 (357)
                      +.||.+|++++|+|+.++|+++....               ..+.+|..++++.++.  +++..|.+++++++.      
T Consensus       336 r~LK~lAkEl~vpvialSQLsR~~E~---------------R~dkrP~lSDLRESGs--IEQDAD~VmflyRde~y~~~~  398 (435)
T COG0305         336 RSLKGLAKELGVPVIALSQLNRSVEQ---------------RTDKRPMLSDLRESGA--LEQDADIVIFLHRDEAYLKDT  398 (435)
T ss_pred             HHHHHHHHhcCCcEEehhhhcccchh---------------ccccCCccccCccCCc--hhhhCCEEEEEechhhccCCC
Confidence            99999999999999999999997662               3456677788888776  667889999998762      


Q ss_pred             ---CeEEEEEEeCCCCCCceeEEEEcCCCceec
Q 035774          310 ---GQRFMNVEKSPTSPPLAFSFTINPSGISLL  339 (357)
Q Consensus       310 ---~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~  339 (357)
                         +.-.+.|.|+|++|.+.+.+.+..+...+.
T Consensus       399 ~~~g~aeiIi~K~RnGp~GtV~l~f~~~~~~F~  431 (435)
T COG0305         399 PDRGEAEVIVAKNRNGPTGTVKLAFDPQFTKFK  431 (435)
T ss_pred             CCCceEEEEEEeccCCCCceEEEEEeccccccc
Confidence               456899999999999988888877765543

>PRK06904 replicative DNA helicase; Validated

Probab=99.96  E-value=5e-29  Score=238.69  Aligned_cols=234  Identities=13%  Similarity=0.125  Sum_probs=163.2

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHHH
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEMG  157 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~~  157 (357)
                      ...+++||++.||.++ ||+++|++++|+|+||+|||+|++++|.+++..  .   +.+|+|||.||+...  .|+....
T Consensus       200 ~~~Gi~TG~~~LD~~t-~Gl~~G~LiiIaarPg~GKTafalnia~~~a~~--~---g~~Vl~fSlEMs~~ql~~Rlla~~  273 (472)
T PRK06904        200 GVTGVTTGFTDLDKKT-AGLQPSDLIIVAARPSMGKTTFAMNLCENAAMA--S---EKPVLVFSLEMPAEQIMMRMLASL  273 (472)
T ss_pred             CCCCccCChHHHHHHH-hccCCCcEEEEEeCCCCChHHHHHHHHHHHHHh--c---CCeEEEEeccCCHHHHHHHHHHhh
Confidence            4679999999999998 579999999999999999999999999998752  1   478999999996433  2221111


Q ss_pred             hccCc--h-----hhcccch------HHHhh--cCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCC
Q 035774          158 ASSFP--E-----IFHSKGM------AQEMA--GRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVH  221 (357)
Q Consensus       158 ~~~~~--~-----~~~~~~~------~~~~~--~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~  221 (357)
                      . ..+  .     .+....+      ...+.  .++++.+..+ ..+.++...+++....+ ++++||||||+.+.....
T Consensus       274 s-~v~~~~i~~g~~l~~~e~~~~~~a~~~l~~~~~l~I~d~~~-~t~~~i~~~~r~~~~~~~~~~lvvIDYLqli~~~~~  351 (472)
T PRK06904        274 S-RVDQTKIRTGQNLDQQDWAKISSTVGMFKQKPNLYIDDSSG-LTPTELRSRARRVYRENGGLSLIMVDYLQLMRAPGF  351 (472)
T ss_pred             C-CCCHHHhccCCCCCHHHHHHHHHHHHHHhcCCCEEEECCCC-CCHHHHHHHHHHHHHhCCCCCEEEEecHHhcCCCCC
Confidence            0 000  0     0111111      11221  2355544332 23444455555554443 699999999998854421


Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccE
Q 035774          222 EQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTI  301 (357)
Q Consensus       222 ~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~  301 (357)
                        ..+|..+++++++.||.+|++++|+||+++|+++....               ..++.|..++++.|+.  +++.+|+
T Consensus       352 --~~~r~~ei~~isr~LK~lAkel~ipVi~lsQLnR~~e~---------------r~~krP~lsDLreSG~--IEqdAD~  412 (472)
T PRK06904        352 --EDNRTLEIAEISRSLKALAKELKVPVVALSQLNRTLEN---------------RGDKRPVNSDLRESGS--IEQDADL  412 (472)
T ss_pred             --CCcHHHHHHHHHHHHHHHHHHhCCeEEEEEecCchhhc---------------cCCCCCchHHHhhcCc--cccCCcE
Confidence              23477889999999999999999999999999986542               1233455567776655  8899999


Q ss_pred             EEEEEEeC----------CeEEEEEEeCCCCCCceeEEEEcCCCceecc
Q 035774          302 RLVLEAKS----------GQRFMNVEKSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       302 rl~l~~~~----------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      +++++++.          +.-.+.|.|+|.++.+.+.|.+...--.+.+
T Consensus       413 v~~l~R~~~y~~~~~~~~~~~elivaKnR~G~~G~v~l~f~~~~~~f~~  461 (472)
T PRK06904        413 IMFIYRDEVYNETTEDNKGVAEIIIGKQRNGPIGRVRLAFQGQYSRFDN  461 (472)
T ss_pred             EEEEeccccccCccccCCCceEEEEeccCCCCCceEEEEEccCCCCccc
Confidence            99998762          2357899999999998888777665544443

>PHA02542 41 41 helicase; Provisional

Probab=99.96  E-value=3.8e-28  Score=231.86  Aligned_cols=240  Identities=16%  Similarity=0.167  Sum_probs=162.7

Q ss_pred             cHHHHHHHHHhc-ccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           66 TALLLMEQRAAT-EHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        66 ~~~~~~~~~~~~-~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ...+.++++... .....++|||++.||.+++||+++|++++|+|+||+|||+|++++|.+++..      +.+|+|||+
T Consensus       153 ~~~~~ie~~~~~~~~~~~gi~TG~~~LD~~t~gGl~~G~LiiIaarPgmGKTtfalniA~~~a~~------g~~Vl~fSL  226 (473)
T PHA02542        153 DYFEDYEERYDSYQSKANKIPFKLEILNKITKGGAERKTLNVLLAGVNVGKSLGLCSLAADYLQQ------GYNVLYISM  226 (473)
T ss_pred             HHHHHHHHHHhhccCCCCccCCCcHHHHHhccCCCCCCcEEEEEcCCCccHHHHHHHHHHHHHhc------CCcEEEEec
Confidence            344445553211 2236799999999999998899999999999999999999999999998742      589999999


Q ss_pred             CCCCchH--HHHHHHhccCc--hhhc--ccchH------HH-hhcCeEEeC-CC---CHHHHHHHHHHHHHHhhhc--Ce
Q 035774          145 ESTFTSR--RMIEMGASSFP--EIFH--SKGMA------QE-MAGRILVLQ-PT---SLSEFTESLEKIKVSLLQN--QV  205 (357)
Q Consensus       145 e~~~~~~--rl~~~~~~~~~--~~~~--~~~~~------~~-~~~~i~~~~-~~---~~~~~~~~l~~l~~~~~~~--~~  205 (357)
                      |++....  |+.... ...+  ....  ...+.      .. ...++++.. +.   +..++...+.++   ..++  ++
T Consensus       227 EM~~~ql~~Rl~a~~-~~i~~~~l~~l~~~~~~~~~~~~~~~~~~~l~I~~~d~~~lt~~~ir~~~rrl---k~~~g~~~  302 (473)
T PHA02542        227 EMAEEVIAKRIDANL-LDVSLDDIDDLSKAEYKAKMEKLRSKTQGKLIIKQYPTGGAHAGHFRALLNEL---KLKKNFKP  302 (473)
T ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHhhcCHHHHHHHHHHHHHHhCCCceeecCCCCCCCHHHHHHHHHHH---HHhcCCCC
Confidence            9964432  221111 1111  1100  00110      11 123454432 22   334554444444   3334  48


Q ss_pred             eEEEEeccccccCCCCC-CCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCC
Q 035774          206 KLLVIDSMEALVPGVHE-QRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYY  284 (357)
Q Consensus       206 ~lvvIDsl~~l~~~~~~-~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  284 (357)
                      ++||||||+.+...... ...+|..++.++++.||.||++++|+||+++|+++.....               .+  |..
T Consensus       303 dlVvIDYLqL~~~~~~~~~~~nr~~ei~~Isr~LK~lAkel~vpVi~lsQLnR~~e~r---------------~d--P~l  365 (473)
T PHA02542        303 DVIIVDYLGICASSRLRVSSENSYTYVKAIAEELRGLAVEHDVVVWTAAQTTRSGWDS---------------SD--VDM  365 (473)
T ss_pred             CEEEEechhhccCCcccCCCCChHHHHHHHHHHHHHHHHHhCCeEEEEEeeCcccccc---------------CC--Ccc
Confidence            99999999988633211 2245788999999999999999999999999999975521               11  445


Q ss_pred             cceecccchhHhhhccEEEEEEEeC-----CeEEEEEEeCCCCCCc---eeEEEEcCC
Q 035774          285 SHIVAVLGFHWAHAVTIRLVLEAKS-----GQRFMNVEKSPTSPPL---AFSFTINPS  334 (357)
Q Consensus       285 ~~~~palg~~w~~~~~~rl~l~~~~-----~~R~l~v~K~r~~~~~---~~~f~I~~~  334 (357)
                      ++++.|+.  +++.+|++++|+++.     +...+.|.|+|+++.+   .+.+.+..+
T Consensus       366 sDLreSG~--IEqdAD~vl~l~r~~~~~~~~~~eliv~KnR~G~~g~~g~v~l~f~~~  421 (473)
T PHA02542        366 SDTAESAG--LPATADFMLAVIETEELAQMGQQLVKQLKSRYGDKNKFNKFLMGVDKG  421 (473)
T ss_pred             hhcccccc--hHhhcCEEEEEecCcccccCCeEEEEEecCCCCCCCCceEEEEEEECC
Confidence            67777666  889999999998854     4678999999999965   555555443

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=99.96  E-value=3.1e-28  Score=232.70  Aligned_cols=223  Identities=16%  Similarity=0.154  Sum_probs=154.8

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ...+++||++.||.+++ |+.+|++++|+|+||+|||+|+++++.+++..     .+.+|+|||+|++.... +.++...
T Consensus       173 ~~~gi~tG~~~LD~~~~-G~~~g~liviag~pg~GKT~~al~ia~~~a~~-----~g~~v~~fSlEm~~~~l-~~Rl~~~  245 (421)
T TIGR03600       173 ELTGLSTGLPKLDRLTN-GLVKGDLIVIGARPSMGKTTLALNIAENVALR-----EGKPVLFFSLEMSAEQL-GERLLAS  245 (421)
T ss_pred             CCcceeCCChhHHHHhc-CCCCCceEEEEeCCCCCHHHHHHHHHHHHHHh-----CCCcEEEEECCCCHHHH-HHHHHHH
Confidence            35789999999999997 79999999999999999999999999988742     14889999999853321 1121111


Q ss_pred             --cCc--hh----hc------ccchHHHhh-cCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCC
Q 035774          160 --SFP--EI----FH------SKGMAQEMA-GRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       160 --~~~--~~----~~------~~~~~~~~~-~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~  223 (357)
                        ..+  ..    ..      .......+. .++++.+. ...++.++...+++...++ ++++||||||+.+...   .
T Consensus       246 ~~~v~~~~~~~~~l~~~~~~~~~~~~~~l~~~~l~i~d~-~~~t~~~i~~~~r~~~~~~~~~~lvvIDyLql~~~~---~  321 (421)
T TIGR03600       246 KSGINTGNIRTGRFNDSDFNRLLNAVDRLSEKDLYIDDT-GGLTVAQIRSIARRIKRKKGGLDLIVVDYIQLMAPT---R  321 (421)
T ss_pred             HcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECC-CCCCHHHHHHHHHHHHHhcCCCCEEEEecccccCCC---C
Confidence              111  00    00      000111111 24554443 2234445555555555455 7999999999998653   2


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                      ..+|...+..+++.||.+|++++|+||+++|+++....               ..+..|..++++.|+.  +++.+|+++
T Consensus       322 ~~~~~~~~~~i~~~Lk~lAke~~i~Vi~lsQlnr~~~~---------------r~~krp~lsdlr~Sg~--Ieq~AD~v~  384 (421)
T TIGR03600       322 GRDRNEELGGISRGLKALAKELDVPVVLLAQLNRGSEK---------------RTDKRPIMSDLRDSGA--IEQDADVIG  384 (421)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHhCCcEEEecccCcchhh---------------cCCCCCChHHHhhcCC--ccccCcEEE
Confidence            23467889999999999999999999999999886542               1123344456665554  788899999


Q ss_pred             EEEEeC---------CeEEEEEEeCCCCCCceeEEE
Q 035774          304 VLEAKS---------GQRFMNVEKSPTSPPLAFSFT  330 (357)
Q Consensus       304 ~l~~~~---------~~R~l~v~K~r~~~~~~~~f~  330 (357)
                      +++++.         +.-.+.|.|+|.++.+.+.+.
T Consensus       385 ~l~R~~~~~~~~~~~~~~el~v~K~R~G~~g~~~l~  420 (421)
T TIGR03600       385 LIHREGYYDAREPPAGVAELILAKNRHGPTGTVELL  420 (421)
T ss_pred             EeccccccCCccCCCCceEEEEECCCCCCCceEEec
Confidence            998753         345799999999998877653

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK08840 replicative DNA helicase; Provisional

Probab=99.96  E-value=2.3e-28  Score=233.31  Aligned_cols=233  Identities=13%  Similarity=0.118  Sum_probs=163.6

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHHH
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEMG  157 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~~  157 (357)
                      ...+++||++.||.+++ |+.+|++++|+|+||+|||+|++++|.+++..  .   +.+|+|||.|++...  .|+....
T Consensus       196 ~~~gi~TG~~~LD~~~~-G~~~g~LiviaarPg~GKTafalnia~~~a~~--~---~~~v~~fSlEMs~~ql~~Rlla~~  269 (464)
T PRK08840        196 GVTGVDTGFTDLNKKTA-GLQGSDLIIVAARPSMGKTTFAMNLCENAAMD--Q---DKPVLIFSLEMPAEQLMMRMLASL  269 (464)
T ss_pred             CCCCcCCCcHHHHHhhc-CCCCCceEEEEeCCCCchHHHHHHHHHHHHHh--C---CCeEEEEeccCCHHHHHHHHHHhh
Confidence            36789999999999985 69999999999999999999999999998752  1   478999999996433  1221111


Q ss_pred             hccCc--hh----hcccch------HHHhh--cCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCC
Q 035774          158 ASSFP--EI----FHSKGM------AQEMA--GRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHE  222 (357)
Q Consensus       158 ~~~~~--~~----~~~~~~------~~~~~--~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~  222 (357)
                      . ..+  ..    .....+      ...+.  .++++.+. ....+.++...+++...++ ++++||||||+.+..... 
T Consensus       270 s-~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~~l~I~d~-~~~ti~~i~~~~r~~~~~~~~~~lvvIDYLql~~~~~~-  346 (464)
T PRK08840        270 S-RVDQTKIRTGQLDDEDWARISSTMGILMEKKNMYIDDS-SGLTPTEVRSRARRIAREHGGLSMIMVDYLQLMRVPAL-  346 (464)
T ss_pred             C-CCCHHHHhcCCCCHHHHHHHHHHHHHHHhcCCEEEECC-CCCCHHHHHHHHHHHHHhcCCCCEEEEccHHhcCCCCC-
Confidence            1 010  00    000011      11221  24555443 2233445555665655554 599999999998853321 


Q ss_pred             CCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEE
Q 035774          223 QRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIR  302 (357)
Q Consensus       223 ~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~r  302 (357)
                       ..+|.+++.++++.||.+|+++||+||+++|+++....               ...+.|..++++.|+.  +++.+|++
T Consensus       347 -~~~r~~ei~~isr~LK~lAkel~ipVi~LsQLnR~~e~---------------r~~krP~lsDLreSG~--IEqdAD~v  408 (464)
T PRK08840        347 -SDNRTLEIAEISRSLKALAKELNVPVVALSQLNRSLEQ---------------RADKRPVNSDLRESGS--IEQDADLI  408 (464)
T ss_pred             -CCchHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccc---------------cCCCCCchHhhhhccc--ccccCCEE
Confidence             23477889999999999999999999999999987552               1233445566776655  89999999


Q ss_pred             EEEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCceec
Q 035774          303 LVLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISLL  339 (357)
Q Consensus       303 l~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~  339 (357)
                      ++++++.         +.-.+.|.|+|.++.+.+.|.+...--.+.
T Consensus       409 ~~l~R~~~y~~~~~~~~~~elivaKnR~G~~G~v~l~f~~~~~~f~  454 (464)
T PRK08840        409 MFIYRDEVYNPDSPLKGTAEIIIGKQRNGPIGSVRLTFQGQYSRFD  454 (464)
T ss_pred             EEEecccccCCCcCCCCceEEEEecccCCCCceEEEEEecCccccc
Confidence            9999862         346789999999998888887765554444

>PRK05748 replicative DNA helicase; Provisional

Probab=99.96  E-value=1.8e-28  Score=235.64  Aligned_cols=233  Identities=16%  Similarity=0.148  Sum_probs=161.6

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHH-h
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMG-A  158 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~-~  158 (357)
                      ...+++||++.||.+++ |+++|++++|+|+||+|||+|+++++.+++..  .   +.+|+||++|++.... +.++. .
T Consensus       182 ~~~gi~TG~~~LD~~~~-G~~~G~livIaarpg~GKT~~al~ia~~~a~~--~---g~~v~~fSlEms~~~l-~~R~l~~  254 (448)
T PRK05748        182 DITGIPTGFTDLDKMTS-GLQPNDLIIVAARPSVGKTAFALNIAQNVATK--T---DKNVAIFSLEMGAESL-VMRMLCA  254 (448)
T ss_pred             CCCCccCChHHHHHhcC-CCCCCceEEEEeCCCCCchHHHHHHHHHHHHh--C---CCeEEEEeCCCCHHHH-HHHHHHH
Confidence            46789999999999986 79999999999999999999999999998752  1   4789999999964432 12221 1


Q ss_pred             -ccCchh-h-----cccc------hHHHhhc-CeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCC
Q 035774          159 -SSFPEI-F-----HSKG------MAQEMAG-RILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       159 -~~~~~~-~-----~~~~------~~~~~~~-~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~  223 (357)
                       ...+.. .     ....      ......+ ++++.+ .....+.++...+++...++ ++++||||||+.+.... ..
T Consensus       255 ~~~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~~~i~d-~~~~ti~~i~~~~r~~~~~~~~~~~vvIDyL~li~~~~-~~  332 (448)
T PRK05748        255 EGNIDAQRLRTGQLTDDDWPKLTIAMGSLSDAPIYIDD-TPGIKVTEIRARCRRLAQEHGGLGLILIDYLQLIQGSG-RS  332 (448)
T ss_pred             hcCCCHHHhhcCCCCHHHHHHHHHHHHHHhcCCEEEEC-CCCCCHHHHHHHHHHHHHhcCCCCEEEEccchhcCCCC-CC
Confidence             111100 0     0000      1111222 344433 32234455556666666666 79999999999885332 11


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                      ..+|...+.++++.||.+|++++|+||+++|+++....               ..+..+..++++.|+.  +++.+|+++
T Consensus       333 ~~~r~~~i~~i~~~LK~lAke~~i~vi~lsQlnr~~~~---------------r~~k~p~lsdlr~Sg~--Ieq~AD~v~  395 (448)
T PRK05748        333 GENRQQEVSEISRSLKALAKELKVPVIALSQLSRGVEQ---------------RQDKRPVMSDIRESGS--IEQDADIVA  395 (448)
T ss_pred             CcCHHHHHHHHHHHHHHHHHHhCCeEEEecccChhHhh---------------cCCCCCChHHHHhhcc--hhcCCCEEE
Confidence            23467889999999999999999999999999886431               1123344456665544  888899999


Q ss_pred             EEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          304 VLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       304 ~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      +|+++.         +.-.+.|.|+|.++.+.+.|.+...--.+
T Consensus       396 ~l~r~~~~~~~~~~~~~~e~~v~K~R~G~~g~~~~~~~~~~~~f  439 (448)
T PRK05748        396 FLYRDDYYDEETENKNTIEIIIAKQRNGPVGTVELAFQKEYNKF  439 (448)
T ss_pred             EEecccccCccccCCCceEEEEeccCCCCCceEEEEEeCCCCcc
Confidence            998753         24578999999999888887776554443

>PRK05636 replicative DNA helicase; Provisional

Probab=99.96  E-value=1.4e-28  Score=236.62  Aligned_cols=231  Identities=15%  Similarity=0.191  Sum_probs=162.1

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchH--HHHHHH
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSR--RMIEMG  157 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~--rl~~~~  157 (357)
                      ...+++||++.||.++ ||+.+|++++|+|+||+|||+|++++|.+++..  .   +.+|+||+.|++....  |+....
T Consensus       244 ~~~Gi~TG~~~LD~~t-~Gl~~G~Liiiaarpg~GKT~~al~~a~~~a~~--~---g~~v~~fSlEMs~~ql~~R~ls~~  317 (505)
T PRK05636        244 IATGIPTGFKDLDDLT-NGLRGGQMIIVAARPGVGKSTLALDFMRSASIK--H---NKASVIFSLEMSKSEIVMRLLSAE  317 (505)
T ss_pred             CCCceecChHHHhhhc-CCCCCCceEEEEeCCCCCHHHHHHHHHHHHHHh--C---CCeEEEEEeeCCHHHHHHHHHHHh
Confidence            3578999999999987 569999999999999999999999999988752  1   4789999999964332  221111


Q ss_pred             hc---------cCc--hhhcccchHHHhhc-CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC
Q 035774          158 AS---------SFP--EIFHSKGMAQEMAG-RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA  225 (357)
Q Consensus       158 ~~---------~~~--~~~~~~~~~~~~~~-~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~  225 (357)
                      ..         .+.  ++.........+.+ ++++.+ .....+.++...+++...++++++||||||+.+...  ....
T Consensus       318 s~v~~~~i~~g~l~~~e~~~~~~a~~~l~~~~l~I~d-~~~~ti~~I~~~~r~~~~~~~~~lvvIDYLql~~~~--~~~~  394 (505)
T PRK05636        318 AEVRLSDMRGGKMDEDAWEKLVQRLGKIAQAPIFIDD-SANLTMMEIRSKARRLKQKHDLKLIVVDYLQLMSSG--KRVE  394 (505)
T ss_pred             cCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEEC-CCCCCHHHHHHHHHHHHHhcCCCEEEEcchHhcCCC--CCCC
Confidence            00         000  00000011112222 345443 333345555566666666788999999999988532  1224


Q ss_pred             CChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEE
Q 035774          226 PGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVL  305 (357)
Q Consensus       226 ~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l  305 (357)
                      +|.+++.++++.||.||++++|+||+++|+++....               ..+..+..++++.|+.  +++.+|++++|
T Consensus       395 ~r~~ei~~isr~LK~lAkel~ipVi~lsQLnR~~e~---------------r~dkrP~lsDLreSG~--IEqdAD~vl~l  457 (505)
T PRK05636        395 SRQQEVSEFSRQLKLLAKELDVPLIAISQLNRGPES---------------RTDKRPQLADLRESGS--LEQDADMVMLL  457 (505)
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCeEEEEeecCccccc---------------cCCCCCcHHHHhhccc--ccccCCEEEEE
Confidence            477889999999999999999999999999987552               1223445566776655  88999999999


Q ss_pred             EEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCc
Q 035774          306 EAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGI  336 (357)
Q Consensus       306 ~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi  336 (357)
                      +++.         +.-.+.|.|+|.++.+.+.+.+..+--
T Consensus       458 ~R~~~y~~~~~~~g~~elivaK~RnG~~Gtv~l~f~~~~~  497 (505)
T PRK05636        458 YRPDSQDKDDERAGEADIILAKHRGGPIDTVQVAHQLHYS  497 (505)
T ss_pred             ecccccCCccCCCCceEEEEecCCCCCCceEEEEeecCcc
Confidence            8752         246799999999998887776655433

>PRK05595 replicative DNA helicase; Provisional

Probab=99.96  E-value=4.2e-28  Score=232.54  Aligned_cols=234  Identities=15%  Similarity=0.170  Sum_probs=164.9

Q ss_pred             cCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHH
Q 035774           79 HLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEM  156 (357)
Q Consensus        79 ~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~  156 (357)
                      ....+++||++.||.++ ||+.+|++++|+|+||+|||+|+++++.+++..  .   +.+|+||++|++...  .|+...
T Consensus       179 ~~~~gi~tg~~~ld~~~-~G~~~g~liviaarpg~GKT~~al~ia~~~a~~--~---g~~vl~fSlEms~~~l~~R~~a~  252 (444)
T PRK05595        179 GETTGVASGFRELDAKT-SGFQKGDMILIAARPSMGKTTFALNIAEYAALR--E---GKSVAIFSLEMSKEQLAYKLLCS  252 (444)
T ss_pred             CCCCcccCChHHHHHhc-CCCCCCcEEEEEecCCCChHHHHHHHHHHHHHH--c---CCcEEEEecCCCHHHHHHHHHHH
Confidence            33568999999999998 579999999999999999999999999987642  1   478999999995432  121111


Q ss_pred             HhccCc-hhhc-----ccc---h---HHHh-hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC
Q 035774          157 GASSFP-EIFH-----SKG---M---AQEM-AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       157 ~~~~~~-~~~~-----~~~---~---~~~~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~  223 (357)
                      .. ..+ ..+.     ...   +   ...+ ..++++.+..+ ..+.++...+++...++++++||||||+.+....  .
T Consensus       253 ~~-~v~~~~~~~~~l~~~e~~~~~~~~~~l~~~~l~i~d~~~-~t~~~i~~~~r~~~~~~~~~~vvIDylql~~~~~--~  328 (444)
T PRK05595        253 EA-NVDMLRLRTGNLEDKDWENIARASGPLAAAKIFIDDTAG-VSVMEMRSKCRRLKIEHGIDMILIDYLQLMSGGK--G  328 (444)
T ss_pred             hc-CCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCCC-CCHHHHHHHHHHHHHhcCCCEEEEeHHHhccCCC--C
Confidence            11 111 0000     000   1   1111 12455544433 3455556666666667889999999999885331  2


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                      ..+|..++.++++.||.+|++++|+|++++|+++....               ..+..|..++++.|++  +++.+|+++
T Consensus       329 ~~~r~~~v~~is~~LK~lAke~~i~vi~lsQLnR~~e~---------------r~~~rP~lsdlr~Sg~--Ieq~AD~vl  391 (444)
T PRK05595        329 SESRQQEVSEISRSIKALAKEMECPVIALSQLSRAPEQ---------------RADHRPMLSDLRESGS--IEQDADVVM  391 (444)
T ss_pred             CccHHHHHHHHHHHHHHHHHHhCCeEEEeeccCcchhc---------------cCCCCCchhhhhhhcc--cccCCCEEE
Confidence            24577889999999999999999999999999986542               1233455567776655  888999999


Q ss_pred             EEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCceec
Q 035774          304 VLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISLL  339 (357)
Q Consensus       304 ~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~  339 (357)
                      +++++.         +.-.+.|.|+|.++.+.+.|.....--.+.
T Consensus       392 ~l~r~~~~~~~~~~~~~~e~iv~K~R~G~~g~~~~~~~~~~~~f~  436 (444)
T PRK05595        392 FLYRDEYYNKETEDKNVAECIIAKQRNGPTGTVKLAWLGQYSKFG  436 (444)
T ss_pred             EEecccccccccCCCCceEEEEEccCCCCCceEEEEEecCCCccc
Confidence            998753         246899999999999888887766554443

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=99.96  E-value=9.4e-28  Score=237.22  Aligned_cols=210  Identities=24%  Similarity=0.285  Sum_probs=165.7

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ...++||++.||.+|+ ||+++|.+++|+|+||+|||+||++++.+++..      +++|+||++|+++.+.+..++...
T Consensus        38 v~~isTGi~~LD~lLg~GGip~GsiteI~G~~GsGKTtLal~~~~~a~~~------G~~v~yId~E~t~~~~~A~~lGvD  111 (790)
T PRK09519         38 ISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA------GGVAAFIDAEHALDPDYAKKLGVD  111 (790)
T ss_pred             CceecCCcHHHHHhhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCcEEEECCccchhHHHHHHcCCC
Confidence            6689999999999998 899999999999999999999999999988742      589999999999887655544321


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCCC------ChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRAP------GQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~~------r~~~~~  232 (357)
                                     .+++++..+.+.++....   +...+.+.++++|||||++++++ .++++...      +.+.+.
T Consensus       112 ---------------l~~llv~~~~~~E~~l~~---i~~lv~~~~~~LVVIDSI~aL~~r~E~~g~~g~~~~~~q~rl~~  173 (790)
T PRK09519        112 ---------------TDSLLVSQPDTGEQALEI---ADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMS  173 (790)
T ss_pred             ---------------hhHeEEecCCCHHHHHHH---HHHHhhcCCCeEEEEcchhhhcchhhccCCCCcccHHHHHHHHH
Confidence                           234567777777665443   44556667899999999999994 44433221      123345


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe----
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK----  308 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~----  308 (357)
                      .+++.|..+++++|+++|+|||+....+   .+|.                 ...+|.+|+.|.|...+||.+.+.    
T Consensus       174 q~L~~L~~~l~~~nvtvi~TNQv~~~~g---~~fg-----------------~p~~~~GG~~l~h~ss~Ri~lrk~~~ik  233 (790)
T PRK09519        174 QALRKMTGALNNSGTTAIFINQLRDKIG---VMFG-----------------SPETTTGGKALKFYASVRMDVRRVETLK  233 (790)
T ss_pred             HHHHHHHHHHHhCCCEEEEEecceecCC---CcCC-----------------CCCcCCCCcccceeccEEEEeeeccccc
Confidence            7888899999999999999999988655   1221                 123577888899999999999973    


Q ss_pred             ------CCeEEEEEEeCCCCCCceeEEEEcCC
Q 035774          309 ------SGQRFMNVEKSPTSPPLAFSFTINPS  334 (357)
Q Consensus       309 ------~~~R~l~v~K~r~~~~~~~~f~I~~~  334 (357)
                            +..|.++|+||++.|..+..|.++.+
T Consensus       234 ~~~~~~G~~~~~kv~ks~cLpe~e~v~~i~tG  265 (790)
T PRK09519        234 DGTNAVGNRTRVKVVKNKCLAEGTRIFDPVTG  265 (790)
T ss_pred             cCccccceEEEEEEEECCCCCCceEEEEecCC
Confidence                  56899999999999988889999743

>PRK06749 replicative DNA helicase; Provisional

Probab=99.96  E-value=1.1e-27  Score=226.87  Aligned_cols=229  Identities=14%  Similarity=0.160  Sum_probs=159.8

Q ss_pred             cCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh
Q 035774           79 HLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA  158 (357)
Q Consensus        79 ~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~  158 (357)
                      ....+++||++.||.+++ |+.+|++++|+|+||+|||+|+++++.+++..      +.+|+||+.|++.... ..++..
T Consensus       164 ~~~~Gi~TG~~~LD~~t~-Gl~~G~LiiIaarPgmGKTafal~ia~~~a~~------g~~v~~fSlEMs~~ql-~~R~ls  235 (428)
T PRK06749        164 KEITGIETGYTSLNKMTC-GLQEGDFVVLGARPSMGKTAFALNVGLHAAKS------GAAVGLFSLEMSSKQL-LKRMAS  235 (428)
T ss_pred             CCCCCccCCcHHHHHHhC-CCCCCcEEEEEeCCCCCchHHHHHHHHHHHhc------CCCEEEEEeeCCHHHH-HHHHHH
Confidence            346789999999999875 69999999999999999999999999999842      4789999999964331 112211


Q ss_pred             c--cCc--hh------hcccch------HHHhhc-CeEEeCCCCHHHHHHHHHHHHHHhhhcC--eeEEEEeccccccCC
Q 035774          159 S--SFP--EI------FHSKGM------AQEMAG-RILVLQPTSLSEFTESLEKIKVSLLQNQ--VKLLVIDSMEALVPG  219 (357)
Q Consensus       159 ~--~~~--~~------~~~~~~------~~~~~~-~i~~~~~~~~~~~~~~l~~l~~~~~~~~--~~lvvIDsl~~l~~~  219 (357)
                      .  .++  ..      +....+      ...+.+ ++++.+.. ...+.++...+++...+++  ..+||||||+.+...
T Consensus       236 ~~~~i~~~~l~~~~~~l~~~e~~~~~~a~~~l~~~~i~i~d~~-~~t~~~I~~~~r~~~~~~~~~~~lvvIDyLqli~~~  314 (428)
T PRK06749        236 CVGEVSGGRLKNPKHRFAMEDWEKVSKAFAEIGELPLEIYDNA-GVTVQDIWMQTRKLKRKHGDKKILIIVDYLQLITGD  314 (428)
T ss_pred             hccCCCHHHHhcCcccCCHHHHHHHHHHHHHHhcCCEEEECCC-CCCHHHHHHHHHHHHHhcCCCCcEEEEeChhhcCCC
Confidence            1  011  00      000111      111112 35555433 2344445555555555555  559999999987532


Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhc
Q 035774          220 VHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAV  299 (357)
Q Consensus       220 ~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~  299 (357)
                      . ....+|..++.++++.||.+|++++|+||+++|+++....               ..++.|..++++.|+.  +++.+
T Consensus       315 ~-~~~~~r~~ei~~isr~LK~lAkel~vpVi~lsQLnR~~e~---------------r~~krP~lsDLR~SG~--IEqdA  376 (428)
T PRK06749        315 P-KHKGNRFQEISEISRKLKLLARELNVCVVALSQLSRSVES---------------RQDKRPLLSDLRETGQ--IEQDA  376 (428)
T ss_pred             C-CCCCCHHHHHHHHHHHHHHHHHHhCCeEEEEEecCccccc---------------cCCCCCchHhhhhccc--ccccC
Confidence            1 1123477889999999999999999999999999987541               2234555667776655  88999


Q ss_pred             cEEEEEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCC
Q 035774          300 TIRLVLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPS  334 (357)
Q Consensus       300 ~~rl~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~  334 (357)
                      |++++++++.         +...+.|.|+|.++.+.+.+.+...
T Consensus       377 D~vl~l~R~~~y~~~~~~~~~~eliiaKnR~G~~G~v~~~f~~~  420 (428)
T PRK06749        377 DVIMLMYREDYYDKETMQKEMTEIHVAKHRNGPVGSFKLRFLKE  420 (428)
T ss_pred             CEEEEEeecccccccccCCCceEEEEecCCCCCCceEEEEEecC
Confidence            9999999863         2467899999999988877766544

>TIGR00665 DnaB replicative DNA helicase

Probab=99.96  E-value=8.4e-28  Score=230.83  Aligned_cols=232  Identities=17%  Similarity=0.182  Sum_probs=159.8

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHHH
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEMG  157 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~~  157 (357)
                      ...+++||++.||.+++ |+++|++++|+|+||+|||+|+++++.+++..  .   +.+|+||++|++...  .|+....
T Consensus       174 ~~~gi~tG~~~LD~~~~-G~~~G~l~vi~g~pg~GKT~~~l~~a~~~a~~--~---g~~vl~~SlEm~~~~i~~R~~~~~  247 (434)
T TIGR00665       174 GITGVPTGFTDLDKLTS-GLQPSDLIILAARPSMGKTAFALNIAENAAIK--E---GKPVAFFSLEMSAEQLAMRMLSSE  247 (434)
T ss_pred             CCCcccCCchhhHhhcC-CCCCCeEEEEEeCCCCChHHHHHHHHHHHHHh--C---CCeEEEEeCcCCHHHHHHHHHHHh
Confidence            46789999999999995 79999999999999999999999999998752  1   478999999996433  2222111


Q ss_pred             hccCc-hh-----hcccch------HHHhhc-CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC
Q 035774          158 ASSFP-EI-----FHSKGM------AQEMAG-RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR  224 (357)
Q Consensus       158 ~~~~~-~~-----~~~~~~------~~~~~~-~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~  224 (357)
                      .. .+ ..     +....+      .....+ ++++.+ ....++.++...++....++++++||||||+.+.....  .
T Consensus       248 ~~-v~~~~~~~g~l~~~~~~~~~~a~~~l~~~~l~i~d-~~~~~~~~i~~~i~~~~~~~~~~~vvID~l~~i~~~~~--~  323 (434)
T TIGR00665       248 SR-VDSQKLRTGKLSDEDWEKLTSAAGKLSEAPLYIDD-TPGLTITELRAKARRLKREHGLGLIVIDYLQLMSGSGR--S  323 (434)
T ss_pred             cC-CCHHHhccCCCCHHHHHHHHHHHHHHhcCCEEEEC-CCCCCHHHHHHHHHHHHHhcCCCEEEEcchHhcCCCCC--C
Confidence            11 10 00     000000      111222 344433 32234556666666676778899999999998853321  2


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEE
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLV  304 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~  304 (357)
                      ..|..++..+++.||.+|++++|+|++++|+++.....               .+..+..++++.+..  +++.+|+++.
T Consensus       324 ~~r~~~i~~i~~~Lk~lA~e~~i~vi~lsqlnr~~~~r---------------~~~~p~lsdlr~Sg~--ieq~aD~vi~  386 (434)
T TIGR00665       324 ENRQQEVSEISRSLKALAKELNVPVIALSQLSRSVEQR---------------EDKRPQLSDLRESGS--IEQDADIVMF  386 (434)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCCeEEEEeccCcchhcc---------------CCCCCChHHHhhccc--hhhcCCEEEE
Confidence            34667899999999999999999999999998864411               112233345554433  7888999999


Q ss_pred             EEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          305 LEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       305 l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      |+++.         +.-.+.|.|+|.++.+.+.|.....--.+
T Consensus       387 l~r~~~~~~~~~~~~~~~l~v~KnR~G~~g~~~l~~~~~~~~f  429 (434)
T TIGR00665       387 LYRDEYYNPDSEDKGIAEIIIAKQRNGPTGTVKLAFQGEYTRF  429 (434)
T ss_pred             eccccccCCCcCCCCceEEEEecCCCCCCCeEEEEEecCCCcc
Confidence            98753         34689999999999887777766544333

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.

>PRK08506 replicative DNA helicase; Provisional

Probab=99.96  E-value=2e-27  Score=228.32  Aligned_cols=230  Identities=17%  Similarity=0.190  Sum_probs=158.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh--
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA--  158 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~--  158 (357)
                      ..+++||++.||.++ ||+++|++++|+|+||+|||+|+++++.+++..      +.+|+||+.|++.... +.++..  
T Consensus       172 ~~Gi~TG~~~LD~~~-~G~~~G~LivIaarpg~GKT~fal~ia~~~~~~------g~~V~~fSlEMs~~ql-~~Rlla~~  243 (472)
T PRK08506        172 IIGLDTGFVELNKMT-KGFNKGDLIIIAARPSMGKTTLCLNMALKALNQ------DKGVAFFSLEMPAEQL-MLRMLSAK  243 (472)
T ss_pred             CCcccCChHHHHhhc-CCCCCCceEEEEcCCCCChHHHHHHHHHHHHhc------CCcEEEEeCcCCHHHH-HHHHHHHh
Confidence            568999999999998 579999999999999999999999999998742      4789999999954321 112211  


Q ss_pred             ccCc--h----------hhcccchHHHhh-cCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCC
Q 035774          159 SSFP--E----------IFHSKGMAQEMA-GRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQR  224 (357)
Q Consensus       159 ~~~~--~----------~~~~~~~~~~~~-~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~  224 (357)
                      ..++  .          +.........+. .++++.+. ....+.++...+++...++ ++++||||||+.+....  ..
T Consensus       244 s~v~~~~i~~~~l~~~e~~~~~~a~~~l~~~~l~I~d~-~~~ti~~I~~~~r~l~~~~~~~~lvvIDyLql~~~~~--~~  320 (472)
T PRK08506        244 TSIPLQNLRTGDLDDDEWERLSDACDELSKKKLFVYDS-GYVNIHQVRAQLRKLKSQHPEIGLAVIDYLQLMSGSG--NF  320 (472)
T ss_pred             cCCCHHHHhcCCCCHHHHHHHHHHHHHHHcCCeEEECC-CCCCHHHHHHHHHHHHHhCCCCCEEEEcChhhccCCC--CC
Confidence            1110  0          000001111222 24555443 2234555555555554443 69999999999875432  12


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEE
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLV  304 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~  304 (357)
                      ..|..++.++++.||.||++++|+||+++|+++....               ..+..|..++++.++.  +++.+|++++
T Consensus       321 ~~r~~ev~~isr~LK~lAkel~ipVi~lsQLnR~~e~---------------r~~krP~lsDLreSg~--IeqdAD~vl~  383 (472)
T PRK08506        321 KDRHLQISEISRGLKLLARELDIPIIALSQLNRSLES---------------RADKRPMLSDLRESGA--IEQDADIILF  383 (472)
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCCcEEEEeecCcchhh---------------ccCCCCChHHhhcchh--hhhcCCEEEE
Confidence            3477889999999999999999999999999986541               1223444566765555  8999999999


Q ss_pred             EEEeCC-------------------------------eEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          305 LEAKSG-------------------------------QRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       305 l~~~~~-------------------------------~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      ++++..                               .-.+.|.|+|.++.+.+.+.+..+--.+
T Consensus       384 l~R~~~y~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~eliiaKnR~G~~G~v~l~f~~~~~~f  448 (472)
T PRK08506        384 VYRDDVYKEREEKEKEKKAKKEGKEERRIHFQNKSIEEAEIIIGKNRNGPTGTVKLRFQKEFTRF  448 (472)
T ss_pred             EecccccccccccccccccccccccccccccccccccceEEEEecCCCCCCceEEEEEecCCccc
Confidence            987520                               1358899999999887776665544333

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=99.95  E-value=1.8e-26  Score=203.21  Aligned_cols=208  Identities=24%  Similarity=0.311  Sum_probs=142.5

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc-cC
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS-SF  161 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~-~~  161 (357)
                      +++||+++||++|+||+++|++++|.|+||+|||+|+++++.+.+.+      +.+|+||++|++..  .+.+.+.. .+
T Consensus         1 ri~tGi~~LD~~l~GGi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~------g~~~~~is~e~~~~--~i~~~~~~~g~   72 (229)
T TIGR03881         1 RLSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRD------GDPVIYVTTEESRE--SIIRQAAQFGM   72 (229)
T ss_pred             CcCCChhhHHHhhcCCCcCCeEEEEECCCCCChHHHHHHHHHHHHhc------CCeEEEEEccCCHH--HHHHHHHHhCC
Confidence            47999999999999999999999999999999999999999887742      47999999988643  33222211 11


Q ss_pred             chhhcccchHHHhhcCeEEeCCCC----------HHHHHHHHHHHHHHhhhc--CeeEEEEeccccccCCCCCCCCCChH
Q 035774          162 PEIFHSKGMAQEMAGRILVLQPTS----------LSEFTESLEKIKVSLLQN--QVKLLVIDSMEALVPGVHEQRAPGQH  229 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~~~~~----------~~~~~~~l~~l~~~~~~~--~~~lvvIDsl~~l~~~~~~~~~~r~~  229 (357)
                      .  ++  ...  ...++.+++...          ..++.++...++..+...  +.+++||||++.++...       ..
T Consensus        73 ~--~~--~~~--~~~~l~i~d~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~vvIDsl~~l~~~~-------~~  139 (229)
T TIGR03881        73 D--FE--KAI--EEGKLVIIDALMKEKEDEWSLRELSIEELLNKVIEAKKYLGYGHARLVIDSMSAFWLDK-------PA  139 (229)
T ss_pred             C--HH--HHh--hcCCEEEEEccccccccccccccCCHHHHHHHHHHHHHhhccCceEEEecCchhhhccC-------hH
Confidence            0  00  000  012333332110          123444555555555543  57899999999986531       12


Q ss_pred             HHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-
Q 035774          230 PLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-  308 (357)
Q Consensus       230 ~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-  308 (357)
                      ..++++..|+++++++|+|+++++|.......                  .  +...        .++.+|.++.|+.. 
T Consensus       140 ~~r~~~~~l~~~l~~~~~tvil~~~~~~~~~~------------------~--~~~~--------~~~l~D~vI~L~~~~  191 (229)
T TIGR03881       140 MARKYSYYLKRVLNRWNFTILLTSQYAITTSQ------------------A--FGFG--------IEHVADGIIRFRKVV  191 (229)
T ss_pred             HHHHHHHHHHHHHHhCCCEEEEEecccccCCC------------------C--cccc--------eEEEEeEEEEEEEec
Confidence            34567788999999999999999996432110                  0  0001        35678888888754 


Q ss_pred             ---CCeEEEEEEeCCCCC--CceeEEEEcC-CCceec
Q 035774          309 ---SGQRFMNVEKSPTSP--PLAFSFTINP-SGISLL  339 (357)
Q Consensus       309 ---~~~R~l~v~K~r~~~--~~~~~f~I~~-~Gi~~~  339 (357)
                         ...|+++|.|+|+++  ...++|+|++ .||+++
T Consensus       192 ~~~~~~R~i~i~K~R~~~~~~~~~~~~I~~~~Gi~v~  228 (229)
T TIGR03881       192 VDGELRRYLIVEKMRQTNHDKRAWEIDIVPGKGLVLK  228 (229)
T ss_pred             cCCcEEEEEEEEeccCCCCCCceeEEEEcCCCceEEe
Confidence               237999999999987  4778999995 799985

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.

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=99.95  E-value=2.4e-26  Score=205.92  Aligned_cols=230  Identities=20%  Similarity=0.292  Sum_probs=150.5

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHHHhcc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEMGASS  160 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~~~~~  160 (357)
                      +|+||++.||++++ |+.+|++++|+|+||+|||+|++++|.+++..     .+.+|+||+.|++...  .|+.......
T Consensus         1 Gi~TG~~~LD~~lg-G~~~g~L~vi~a~pg~GKT~~~l~ia~~~a~~-----~~~~vly~SlEm~~~~l~~R~la~~s~v   74 (259)
T PF03796_consen    1 GIPTGFPALDRLLG-GLRPGELTVIAARPGVGKTAFALQIALNAALN-----GGYPVLYFSLEMSEEELAARLLARLSGV   74 (259)
T ss_dssp             SB-SSTHHHHHHHS-SB-TT-EEEEEESTTSSHHHHHHHHHHHHHHT-----TSSEEEEEESSS-HHHHHHHHHHHHHTS
T ss_pred             CCCCChHHHHHHhc-CCCcCcEEEEEecccCCchHHHHHHHHHHHHh-----cCCeEEEEcCCCCHHHHHHHHHHHhhcc
Confidence            58999999999996 69999999999999999999999999999863     1389999999996433  2221111110


Q ss_pred             ---------Cc-hhh-cccchHHHhhc-CeEEeCCCCHHHHHHHHHHHHHHhhh-cCeeEEEEeccccccCCCCCCCCCC
Q 035774          161 ---------FP-EIF-HSKGMAQEMAG-RILVLQPTSLSEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPGVHEQRAPG  227 (357)
Q Consensus       161 ---------~~-~~~-~~~~~~~~~~~-~i~~~~~~~~~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~~~~~~~~r  227 (357)
                               +. ..+ ........+.+ .+++.+.. ...+.++...++..... .++++|||||++.+....  ....+
T Consensus        75 ~~~~i~~g~l~~~e~~~~~~~~~~l~~~~l~i~~~~-~~~~~~i~~~i~~~~~~~~~~~~v~IDyl~ll~~~~--~~~~~  151 (259)
T PF03796_consen   75 PYNKIRSGDLSDEEFERLQAAAEKLSDLPLYIEDTP-SLTIDDIESKIRRLKREGKKVDVVFIDYLQLLKSED--SSDNR  151 (259)
T ss_dssp             THHHHHCCGCHHHHHHHHHHHHHHHHTSEEEEEESS-S-BHHHHHHHHHHHHHHSTTEEEEEEEEGGGSBTSC--SSSCC
T ss_pred             hhhhhhccccCHHHHHHHHHHHHHHhhCcEEEECCC-CCCHHHHHHHHHHHHhhccCCCEEEechHHHhcCCC--CCCCH
Confidence                     00 000 00001111222 24443332 22444444445555445 789999999999887653  33447


Q ss_pred             hHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEE
Q 035774          228 QHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA  307 (357)
Q Consensus       228 ~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~  307 (357)
                      ...+..+++.||.+|++++|+||+++|+++.....               .+..+..++++.+.+  .++.+|+++.+.+
T Consensus       152 ~~~~~~i~~~Lk~lA~~~~i~vi~~sQlnr~~~~~---------------~~~~p~l~dl~~sg~--Ie~~AD~vl~l~r  214 (259)
T PF03796_consen  152 RQEIGEISRELKALAKELNIPVIALSQLNREAEDR---------------EDKRPSLSDLRESGA--IEQDADVVLFLHR  214 (259)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSEEEEEEEBSGGGGGS---------------SSCS--HHHHCSTSS--HHHH-SEEEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHcCCeEEEccccChhhhcc---------------cccccchhhhhhhHH--HHHHHhhhhhhcc
Confidence            78899999999999999999999999998864411               112223344544444  7788999999998


Q ss_pred             eC---------CeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          308 KS---------GQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       308 ~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      +.         ..-.+.|.|+|.++.+.+.+.+..+--.+
T Consensus       215 ~~~~~~~~~~~~~~~l~v~KnR~G~~g~v~~~f~~~~~~f  254 (259)
T PF03796_consen  215 DEKYDEDRDDKGEAELIVAKNRNGPTGTVPLRFNPETSRF  254 (259)
T ss_dssp             HCHCHCCSSCTTEEEEEEEEESSS--EEEEEEEETTTTEE
T ss_pred             chhhccccCCCCeEEEEEEecCCCCCceEEEEEECCCCeE
Confidence            53         25679999999999888877777654443

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=99.95  E-value=4.5e-26  Score=199.86  Aligned_cols=211  Identities=17%  Similarity=0.232  Sum_probs=142.4

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhc
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFH  166 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~  166 (357)
                      |+++||++|+||+++|++++|.|+||+|||+||++++.+.+..      +++|+||++|++  ...+.+.+... .  ++
T Consensus         1 Gi~~LD~~l~gGi~~g~~~li~G~~G~GKt~~~~~~~~~~~~~------g~~~~y~s~e~~--~~~l~~~~~~~-~--~~   69 (224)
T TIGR03880         1 GIPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKN------GEKAMYISLEER--EERILGYAKSK-G--WD   69 (224)
T ss_pred             CchhhHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHHhC------CCeEEEEECCCC--HHHHHHHHHHc-C--CC
Confidence            7899999999999999999999999999999999999998752      589999999985  44444433221 0  11


Q ss_pred             ccchHHHhhcCeEEeCCCCH---HHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHH-HHHHHHHHHH
Q 035774          167 SKGMAQEMAGRILVLQPTSL---SEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLS-WHISLITSLA  242 (357)
Q Consensus       167 ~~~~~~~~~~~i~~~~~~~~---~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~-~i~~~Lk~la  242 (357)
                      ..   +....++++.+..+.   ..+..+...+...+.+.+++++||||++.+.... ..    ....+ .+...++. .
T Consensus        70 ~~---~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~~i~~~~~~~vVIDsls~l~~~~-~~----~~~~r~~l~~l~~~-l  140 (224)
T TIGR03880        70 LE---DYIDKSLYIVRLDPSDFKTSLNRIKNELPILIKELGASRVVIDPISLLETLF-DD----DAERRTELFRFYSS-L  140 (224)
T ss_pred             hH---HHHhCCeEEEecCHHHHHhhHHHHHHHHHHHHHHhCCCEEEEcChHHHhhhc-CC----HHHHHHHHHHHHHH-H
Confidence            11   111224555543321   1244555566777777899999999999884321 11    12222 23333333 3


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC------CeEEEEE
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS------GQRFMNV  316 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~------~~R~l~v  316 (357)
                      +++|+++++++|........                ..    ..       ..++++|..+.|+...      ..|.++|
T Consensus       141 k~~~~tvll~s~~~~~~~~~----------------~~----~~-------~~~~l~D~vI~L~~~~~~~~~~~~r~l~v  193 (224)
T TIGR03880       141 RETGVTTILTSEADKTNVFA----------------SK----YG-------LIEYLADGVIILKYVRNSDLRDVRLAVEV  193 (224)
T ss_pred             HhCCCEEEEEEcccCCCCCc----------------cC----CC-------ceEEEEeEEEEEeeeecccCcceEEEEEE
Confidence            56899999999875421100                00    00       0256778888887432      2567999


Q ss_pred             EeCCCCC--CceeEEEEcCCCceeccCCCc
Q 035774          317 EKSPTSP--PLAFSFTINPSGISLLTDDGT  344 (357)
Q Consensus       317 ~K~r~~~--~~~~~f~I~~~Gi~~~~~~~~  344 (357)
                      .|+|+++  +.+++|+|+++||++++..++
T Consensus       194 ~K~Rg~~~~~~~~~~~i~~~Gi~v~~~~~~  223 (224)
T TIGR03880       194 VKMRRSKHSREIKPYEITDSGITVYSEAEI  223 (224)
T ss_pred             EEccCCCCCCceEEEEEcCCcEEEeccCCc
Confidence            9999987  578999999999999997765

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>KOG1433 consensus DNA repair protein RAD51/RHP55 [Replication, recombination and repair]

Probab=99.95  E-value=2e-28  Score=219.40  Aligned_cols=293  Identities=28%  Similarity=0.403  Sum_probs=216.9

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCC
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLP   85 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   85 (357)
                      .+..+++......|...++.+++++...+..++..+.+.+.....++...+....+        +++.+    .....++
T Consensus        27 ~~~~~ita~~v~~l~~~~l~~v~~l~~~~~~el~~i~~~s~~~~~k~~~~l~~~~~--------~~~~~----~~~~~l~   94 (326)
T KOG1433|consen   27 LLAGGITAEDVLLLSEGELSTVEGLAYAGKEELLLIIGLSEAKSGKTVLGLHKLVP--------MLQLR----SELGFLS   94 (326)
T ss_pred             hhcccccHhhhhhhcccceEEEeccccCcchhheeeeeecccccccHHHHHHHhhH--------HHHhh----ccceeec
Confidence            34455666667777777777777777777777777777766665555544433211        12222    2256899


Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhh
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF  165 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~  165 (357)
                      ||..+||++|+||++.|.+++|+||||+|||+||+.++..+      ||.+..++|||++..|..+++..+......+.+
T Consensus        95 Tg~~~lD~lL~gGi~~g~~TEi~G~p~~GKtQlc~~~~v~~------~gge~~~l~IDs~s~~~~~~~~~ia~~~~~~~~  168 (326)
T KOG1433|consen   95 TGSKALDKLLGGGIETGSLTELVGPPGSGKTQLCHTLAVTC------GGGEGKVLYIDTESTFRLERLTEIAGRSGLRGR  168 (326)
T ss_pred             cchhhhhHhhccCcccCceeEEecCCCccHHHHHHHHHHhc------cCCcceEEEEecchhcccchhhhhhhhhhhhhH
Confidence            99999999999999999999999999999999998888766      355799999999998888888887766433322


Q ss_pred             cccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC---CChHHHHHHHHHHHHHH
Q 035774          166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA---PGQHPLSWHISLITSLA  242 (357)
Q Consensus       166 ~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~---~r~~~~~~i~~~Lk~la  242 (357)
                      .       ..+++.+....+..+.......+...+.+....++++||.++.+.....+..   .+...+...++.|++++
T Consensus       169 ~-------~~~~l~~~~~~~~~~~l~~~~~a~~~~~~~~~~l~~vds~ta~~~~~~~g~~~~~a~~~~~~~~~~~l~~la  241 (326)
T KOG1433|consen  169 D-------TLSNLMLARAYNLDHQLQLIQEAEIMINQSRVKLLIVDSATALYRTTFKGRGELSARQMLLAKFLRSLKKLA  241 (326)
T ss_pred             H-------HHHHHHHHHHHhhHHHHHHHHHHHHHhhccceeEEEecccccccccccccccchHHHHHHHHHHHHHHHHHH
Confidence            2       2334443333334444444444455555668899999999999988665521   13445677888999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEE-eCCeEEEEEEeCCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA-KSGQRFMNVEKSPT  321 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~-~~~~R~l~v~K~r~  321 (357)
                      ++++++||++||++.+..+. .+|.                ....+|.+|..|+|.+++|+.+.+ .+..|..++.++|.
T Consensus       242 ~~~g~~vvitn~v~~~~d~~-~~f~----------------~~~~~~~~~~~~~H~~~tr~~~~~~~g~~~~~k~~~s~~  304 (326)
T KOG1433|consen  242 DEFGVAVVITNQVTAQVDGA-IMFG----------------SDPKKPIGGNIWAHAVTTRLGLRKGKGERRICKIADSPC  304 (326)
T ss_pred             HhcCceEEEecccccccccc-cccC----------------cccccccccchHHHHHHHHHHHHhccccchhhhhhcCCC
Confidence            99999999999999987743 2332                024678999999999999999988 66788999999999


Q ss_pred             CCCceeEEEEcCCCceecc
Q 035774          322 SPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       322 ~~~~~~~f~I~~~Gi~~~~  340 (357)
                      .|..+..|.|.+.|+....
T Consensus       305 l~e~~~~~~i~~~g~~~~~  323 (326)
T KOG1433|consen  305 LPEAEAVFAITEDGISDQR  323 (326)
T ss_pred             CCcchhHHHHHhhhhhhhh
Confidence            9999999999999997654

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=99.94  E-value=1.1e-25  Score=217.75  Aligned_cols=226  Identities=19%  Similarity=0.159  Sum_probs=157.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||+++||++|+||+++|++++|.|+||+|||+|++|++.+++.+      +++|+||++|++..  .+...+.. 
T Consensus       242 ~~~~~tGi~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~------ge~~~y~s~eEs~~--~i~~~~~~-  312 (484)
T TIGR02655       242 NVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACAN------KERAILFAYEESRA--QLLRNAYS-  312 (484)
T ss_pred             ccccCCChHhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHC------CCeEEEEEeeCCHH--HHHHHHHH-
Confidence            4579999999999999999999999999999999999999999999853      58999999999643  33332222 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCC-CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPT-SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLIT  239 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk  239 (357)
                      +.  ++..++  ...+++.+.... ....+.+.+..+...+.+.++++|||||++.+... ..     ..++++++..|.
T Consensus       313 lg--~~~~~~--~~~g~l~~~~~~p~~~~~~~~~~~i~~~i~~~~~~~vvIDsi~~~~~~-~~-----~~~~r~~~~~l~  382 (484)
T TIGR02655       313 WG--IDFEEM--EQQGLLKIICAYPESAGLEDHLQIIKSEIADFKPARIAIDSLSALARG-VS-----NNAFRQFVIGVT  382 (484)
T ss_pred             cC--CChHHH--hhCCcEEEEEcccccCChHHHHHHHHHHHHHcCCCEEEEcCHHHHHHh-cC-----HHHHHHHHHHHH
Confidence            11  111111  111235444322 11234566777777788889999999999998754 21     244566777888


Q ss_pred             HHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe---C-CeEEEE
Q 035774          240 SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK---S-GQRFMN  315 (357)
Q Consensus       240 ~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~---~-~~R~l~  315 (357)
                      +++++.+++++++++.....+.                 ...       +.  ...++.+|..+.|...   + -+|.+.
T Consensus       383 ~~lk~~~it~~~t~~~~~~~~~-----------------~~~-------~~--~~~s~l~D~ii~l~~~e~~g~~~r~i~  436 (484)
T TIGR02655       383 GYAKQEEITGFFTNTSDQFMGS-----------------HSI-------TD--SHISTITDTILMLQYVEIRGEMSRAIN  436 (484)
T ss_pred             HHHhhCCCeEEEeecccccccC-----------------Ccc-------CC--CCeeEeeeEEEEEEEEecCCEEEEEEE
Confidence            9999999999999875432110                 000       00  0024567777877643   2 368899


Q ss_pred             EEeCCCCC--CceeEEEEcCCCceeccCC----Cceeccccc
Q 035774          316 VEKSPTSP--PLAFSFTINPSGISLLTDD----GTEMVVPET  351 (357)
Q Consensus       316 v~K~r~~~--~~~~~f~I~~~Gi~~~~~~----~~~~~~~~~  351 (357)
                      |+|+|.++  ...++|+|+++||++.++.    ++-...|..
T Consensus       437 V~K~R~~~~~~~~~~~~It~~Gi~v~~~~~~~~~~~~g~~~~  478 (484)
T TIGR02655       437 VFKMRGSWHDKGIREFMISDKGPEIKDSFRNFERIISGSPTR  478 (484)
T ss_pred             EEEccCCCCCCceEEEEEcCCcEEEcccccCCcceEcCCCcc
Confidence            99999988  4678999999999998664    344455543

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=99.94  E-value=1.3e-25  Score=217.23  Aligned_cols=216  Identities=19%  Similarity=0.317  Sum_probs=146.6

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHH-hccC
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMG-ASSF  161 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~-~~~~  161 (357)
                      +++||+++||++|+||+|+|++++|.|+||+|||+||+||+.+.+.+     .+++++||++|++  +..+.+.+ .-.|
T Consensus         2 r~~TGI~gLD~il~GGlp~g~~~Li~G~pGsGKT~la~qfl~~g~~~-----~ge~~lyvs~eE~--~~~l~~~~~~~G~   74 (484)
T TIGR02655         2 KIRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIH-----FDEPGVFVTFEES--PQDIIKNARSFGW   74 (484)
T ss_pred             cCCCCchhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHh-----CCCCEEEEEEecC--HHHHHHHHHHcCC
Confidence            68999999999999999999999999999999999999999987752     1489999999974  34444333 2222


Q ss_pred             chhhcccchHHHhhcCeEEeCCCC---------HHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHH
Q 035774          162 PEIFHSKGMAQEMAGRILVLQPTS---------LSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLS  232 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~~~~~---------~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~  232 (357)
                      .    .....  ..+++.+.+...         ..++...+..+...+...+.++|+|||++.+.... +..   ...-.
T Consensus        75 ~----~~~~~--~~g~l~~~~~~~~~~~~~~~~~~~l~~~l~~i~~~ls~g~~qRVvIDSl~aL~~~~-~~~---~~~r~  144 (484)
T TIGR02655        75 D----LQKLV--DEGKLFILDASPDPEGQDVVGGFDLSALIERINYAIRKYKAKRVSIDSVTAVFQQY-DAV---SVVRR  144 (484)
T ss_pred             C----HHHHh--hcCceEEEecCchhccccccccCCHHHHHHHHHHHHHHhCCcEEEEeehhHhhhhc-Cch---HHHHH
Confidence            1    11111  123444443321         12455677777788888899999999999875431 110   11112


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhH-hhhccEEEEEEEe--C
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHW-AHAVTIRLVLEAK--S  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w-~~~~~~rl~l~~~--~  309 (357)
                      .+...+ +..++.++++++++|........                  ..+        +  + ++++|.++.|+..  +
T Consensus       145 ~l~~Li-~~L~~~g~TvLLtsh~~~~~~~~------------------~~~--------~--~~e~laDgVI~L~~~~~~  195 (484)
T TIGR02655       145 EIFRLV-ARLKQIGVTTVMTTERIEEYGPI------------------ARY--------G--VEEFVSDNVVILRNVLEG  195 (484)
T ss_pred             HHHHHH-HHHHHCCCEEEEEecCccccccc------------------ccC--------C--ceeEeeeeEEEEEEEecC
Confidence            233333 33356799999999875432100                  000        0  2 4667888888643  2


Q ss_pred             --CeEEEEEEeCCCCC--CceeEEEEcCCCceeccCCCc
Q 035774          310 --GQRFMNVEKSPTSP--PLAFSFTINPSGISLLTDDGT  344 (357)
Q Consensus       310 --~~R~l~v~K~r~~~--~~~~~f~I~~~Gi~~~~~~~~  344 (357)
                        ..|.++|.|+|+++  .+.++|+|+++||+++|....
T Consensus       196 ~~~~R~l~I~K~Rgs~~~~~~~~~~It~~Gi~v~p~~~~  234 (484)
T TIGR02655       196 ERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAM  234 (484)
T ss_pred             CEEEEEEEEEECCCCCcCCceEEEEEcCCcEEEEecccc
Confidence              26899999999988  477999999999999885443

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.

>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=99.94  E-value=1.3e-25  Score=202.27  Aligned_cols=214  Identities=27%  Similarity=0.344  Sum_probs=153.8

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ...+|||++.||..|+ ||+|+|.+++|+|++++|||+|++++++++...      +..|+|||.|..+++..+..+.- 
T Consensus        31 ~~~i~TG~~~LD~aLg~GG~p~G~ivEi~G~~ssGKttLaL~~ia~~q~~------g~~~a~ID~e~~ld~~~a~~lGv-  103 (322)
T PF00154_consen   31 IEVISTGSPALDYALGIGGLPRGRIVEIYGPESSGKTTLALHAIAEAQKQ------GGICAFIDAEHALDPEYAESLGV-  103 (322)
T ss_dssp             S-EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT------T-EEEEEESSS---HHHHHHTT--
T ss_pred             cceEecCCcccchhhccCccccCceEEEeCCCCCchhhhHHHHHHhhhcc------cceeEEecCcccchhhHHHhcCc-
Confidence            5689999999999999 999999999999999999999999999988642      58999999999999887766542 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC-CCCCCC------CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG-VHEQRA------PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~-~~~~~~------~r~~~~~  232 (357)
                                    .++++++++|.+.++..+++++   .++...+++|||||+.++.+. +.++..      .+...+.
T Consensus       104 --------------dl~rllv~~P~~~E~al~~~e~---lirsg~~~lVVvDSv~al~p~~E~e~~~~~~~~g~~Ar~ms  166 (322)
T PF00154_consen  104 --------------DLDRLLVVQPDTGEQALWIAEQ---LIRSGAVDLVVVDSVAALVPKAELEGEIGDQQVGLQARLMS  166 (322)
T ss_dssp             ---------------GGGEEEEE-SSHHHHHHHHHH---HHHTTSESEEEEE-CTT-B-HHHHTTSTSSTSSSHHHHHHH
T ss_pred             --------------cccceEEecCCcHHHHHHHHHH---HhhcccccEEEEecCcccCCHHHHhhccccccCcchHHHHH
Confidence                          2467888888887766555544   455677899999999999765 222211      1335677


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      .+++.|..++.+.||++|++||++.+.+   .+|.   +|             . ...+|..|.+...+|+.+.+.+   
T Consensus       167 ~~lr~lt~~l~~~~~~~i~INQ~R~~ig---~~~g---~~-------------~-~t~GG~alkfyas~rl~i~k~~~ik  226 (322)
T PF00154_consen  167 QALRKLTPLLSKSNTTLIFINQVRDKIG---VMFG---NP-------------E-TTPGGRALKFYASVRLEIRKKEQIK  226 (322)
T ss_dssp             HHHHHHHHHHHTTT-EEEEEEEESSSSS---SSSS---SS-------------S-CCTSHHHHHHHCSEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHhhceEEEEeehHHHHHh---hccC---CC-------------c-CCCCCchhhhhhhhHHhhhcccccc
Confidence            8888888899999999999999998765   2222   11             1 2347888999999999998642   


Q ss_pred             -------CeEEEEEEeCCCCCC-ceeEEEEc-CCCcee
Q 035774          310 -------GQRFMNVEKSPTSPP-LAFSFTIN-PSGISL  338 (357)
Q Consensus       310 -------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi~~  338 (357)
                             ..-.++|+||+..++ ...+|.|. +.||..
T Consensus       227 ~~~~~iG~~~~vkv~KnKva~P~k~a~~~i~y~~Gid~  264 (322)
T PF00154_consen  227 EGDEVIGNKIKVKVVKNKVAPPFKKAEFDIYYGRGIDR  264 (322)
T ss_dssp             ETTCECEEEEEEEEEEESSS-TTEEEEEEEETTTEE-H
T ss_pred             cCCcccccEEEEEEEEcccCCCcceeEEEEecCCeECc
Confidence                   256799999999986 55788876 677743

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 ....

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=99.94  E-value=1.7e-25  Score=202.11  Aligned_cols=236  Identities=16%  Similarity=0.170  Sum_probs=156.5

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHHHhc
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEMGAS  159 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~~~~  159 (357)
                      .+++||++.||.++ ||+++|++++|+|+||+|||+|+.+++.+++..     .+.+|+||++|++...  .|+......
T Consensus        11 ~~~~tg~~~Ld~~~-gG~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~-----~g~~vl~iS~E~~~~~~~~r~~~~~~~   84 (271)
T cd01122          11 EEVWWPFPVLNKLT-KGLRKGELIILTAGTGVGKTTFLREYALDLITQ-----HGVRVGTISLEEPVVRTARRLLGQYAG   84 (271)
T ss_pred             cCCCCCcceeeeee-EEEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh-----cCceEEEEEcccCHHHHHHHHHHHHhC
Confidence            48999999999999 689999999999999999999999999998752     1489999999985322  222121111


Q ss_pred             -cCch-----hhcc---cchHHHh--hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCCh
Q 035774          160 -SFPE-----IFHS---KGMAQEM--AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQ  228 (357)
Q Consensus       160 -~~~~-----~~~~---~~~~~~~--~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~  228 (357)
                       .+..     ....   ....+..  ..++++++.....++..++..++..+..+++++|||||++.+..... ....+.
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~i~d~~~~~~~~~i~~~i~~~~~~~~~~~vvID~l~~l~~~~~-~~~~~~  163 (271)
T cd01122          85 KRLHLPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMAVSHGIQHIIIDNLSIMVSDER-ASGDER  163 (271)
T ss_pred             CCcccCCccccccHHHHHHHHHHhcCCCcEEEEcCCCccCHHHHHHHHHHHHhcCCceEEEECCHHHHhccCC-CchhHH
Confidence             1100     0000   0011122  13566666554446667777777777778999999999999875421 112244


Q ss_pred             HHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe
Q 035774          229 HPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK  308 (357)
Q Consensus       229 ~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~  308 (357)
                      ..+..+++.|+.+|++++|+|++++|+++......            ...+..+..++++  ++..+.+.+|.++.|++.
T Consensus       164 ~~~~~~~~~L~~la~~~~vtvll~sq~~~~~~~~~------------~~~~~~~~~~d~~--gs~~i~~~aD~vi~l~r~  229 (271)
T cd01122         164 KALDEIMTKLRGFATEHGIHITLVSHLRRPDGDKT------------HEEGGEVSLSDFR--GSAAIGQLADNVIALERN  229 (271)
T ss_pred             HHHHHHHHHHHHHHHHhCCEEEEEecccCccCCCc------------cccCCCceEEecc--CcHhHhhhccEEEEEEec
Confidence            56788999999999999999999999987543110            0001111112222  223477888999999864


Q ss_pred             C-------CeEEEEEEeCCCC-CCce-eEEEEcCCCcee
Q 035774          309 S-------GQRFMNVEKSPTS-PPLA-FSFTINPSGISL  338 (357)
Q Consensus       309 ~-------~~R~l~v~K~r~~-~~~~-~~f~I~~~Gi~~  338 (357)
                      .       ..|.++|.|+|++ +.+. +.+.++.+--.+
T Consensus       230 ~~~e~~~~~~~~i~v~K~R~~~~~g~~~~~~~~~~t~~~  268 (271)
T cd01122         230 QQAELDERNTTYLRILKNRFTGGTGVAGPLEYDKETGRL  268 (271)
T ss_pred             CccccccCCcEEEEEEeeccCCCccceeeEEEECCCcee
Confidence            3       4688999999986 5443 456665443333

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=99.94  E-value=3.5e-25  Score=195.46  Aligned_cols=213  Identities=19%  Similarity=0.209  Sum_probs=146.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||++.||++|+||+|+|++++|.|+||+|||+|+.+++...+.+      +++|+|+++|++.. ..+.++....
T Consensus         4 ~~~~~tGi~~LD~~l~gG~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~------g~~~~y~~~e~~~~-~~~~~~~~~g   76 (234)
T PRK06067          4 KEIISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQ------GKKVYVITTENTSK-SYLKQMESVK   76 (234)
T ss_pred             ceEEecCCHHHHHhhCCCCcCCcEEEEECCCCCChHHHHHHHHHHHHhC------CCEEEEEEcCCCHH-HHHHHHHHCC
Confidence            4579999999999999999999999999999999999999999888742      58999999998643 3334443322


Q ss_pred             CchhhcccchHHHhhcCeEEeCC------CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQP------TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWH  234 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~------~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i  234 (357)
                      +.    .....  ..+.+.+...      ........++..+...+.+.+++++|||+++.+....      ....+..+
T Consensus        77 ~~----~~~~~--~~g~l~i~~~~~~~~~~~~~~~~~ll~~l~~~i~~~~~~~iviDs~t~~~~~~------~~~~~~~~  144 (234)
T PRK06067         77 ID----ISDFF--LWGYLRIFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVIIIDSLTIFATYA------EEDDILNF  144 (234)
T ss_pred             CC----hhHHH--hCCCceEEeccccccccCcchHHHHHHHHHHHHHhcCCCEEEEecHHHHHhcC------CHHHHHHH
Confidence            21    11100  0122222211      1123445566677777777789999999999874321      22446667


Q ss_pred             HHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC----C
Q 035774          235 ISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS----G  310 (357)
Q Consensus       235 ~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~----~  310 (357)
                      +..|+.+++ .+++++++.|......                         ..    .....+.+|.++.|+...    .
T Consensus       145 l~~l~~l~~-~g~tvllt~~~~~~~~-------------------------~~----~~~~~~l~DgvI~L~~~~~~~~~  194 (234)
T PRK06067        145 LTEAKNLVD-LGKTILITLHPYAFSE-------------------------EL----LSRIRSICDVYLKLRAEQIGGRY  194 (234)
T ss_pred             HHHHHHHHh-CCCEEEEEecCCcCCH-------------------------HH----HHHHHhheEEEEEEEeeccCCEE
Confidence            777776665 5889888887532111                         00    011356677778787542    3


Q ss_pred             eEEEEEEeCCCCC--C-ceeEEEEcC-CCceeccCC
Q 035774          311 QRFMNVEKSPTSP--P-LAFSFTINP-SGISLLTDD  342 (357)
Q Consensus       311 ~R~l~v~K~r~~~--~-~~~~f~I~~-~Gi~~~~~~  342 (357)
                      .|+++|.|+|+++  . .+++|+|++ .||+++|..
T Consensus       195 ~r~l~i~K~Rg~~~~~~~~~~~~I~~~~Gi~v~~~~  230 (234)
T PRK06067        195 VKVLEVVKLRGARKTTGNIISFDVDPAFGIKIIPLS  230 (234)
T ss_pred             eEEEEEEhhcCCCCCCCCEEEEEEcCCCCeEEEEee
Confidence            6889999999987  3 678999997 599999753

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=99.94  E-value=3.8e-25  Score=216.24  Aligned_cols=219  Identities=23%  Similarity=0.347  Sum_probs=153.0

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc-
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS-  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~-  159 (357)
                      ..+++||+++||++|+||+|+|++++|+|+||+|||+|++||+.+.+.+     .+++|+||++|++  ...+.+.+.. 
T Consensus        10 ~~ri~TGI~~LD~~l~GG~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~-----~ge~~lyis~ee~--~~~i~~~~~~~   82 (509)
T PRK09302         10 IEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKR-----FDEPGVFVTFEES--PEDIIRNVASF   82 (509)
T ss_pred             CccccCCchhHHHhhcCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh-----cCCCEEEEEccCC--HHHHHHHHHHc
Confidence            6799999999999999999999999999999999999999999988852     1489999999995  3344333222 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCC---------HHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTS---------LSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHP  230 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~---------~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~  230 (357)
                      .|    +.....  ..+.+.+.+...         ..++..++..+...+...++++|||||++.++... +    ....
T Consensus        83 g~----d~~~~~--~~g~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls~l~~~~-d----~~~~  151 (509)
T PRK09302         83 GW----DLQKLI--DEGKLFILDASPDPSEQEEAGEYDLEALFIRIEYAIDKIGAKRVVLDSIEALFSGF-S----NEAV  151 (509)
T ss_pred             CC----CHHHHh--hCCeEEEEecCcccccccccccccHHHHHHHHHHHHHhhCCCEEEECCHHHHHhhc-c----CHHH
Confidence            21    111110  112344433221         12455667777888888899999999999875431 1    2234


Q ss_pred             HHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-
Q 035774          231 LSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-  309 (357)
Q Consensus       231 ~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-  309 (357)
                      ++..+..|.+.+++.+++++++.|........                  .. . .+       -.+.+|..+.|+... 
T Consensus       152 ~r~~l~~L~~~Lk~~g~TvLlt~~~~~~~~~~------------------~~-~-~~-------~~~laDgVI~L~~~~~  204 (509)
T PRK09302        152 VRRELRRLFAWLKQKGVTAVITGERGDEYGPL------------------TR-Y-GV-------EEFVSDCVIILRNRLE  204 (509)
T ss_pred             HHHHHHHHHHHHHhCCCEEEEEECCccCcCCc------------------cc-c-Cc-------eEEEeeEEEEEeEEcc
Confidence            45566667777788999999998864421100                  00 0 00       135678888887532 


Q ss_pred             ---CeEEEEEEeCCCCC--CceeEEEEcCCCceeccCCCc
Q 035774          310 ---GQRFMNVEKSPTSP--PLAFSFTINPSGISLLTDDGT  344 (357)
Q Consensus       310 ---~~R~l~v~K~r~~~--~~~~~f~I~~~Gi~~~~~~~~  344 (357)
                         ..|+++|.|+|+++  .+.++|+|++.||+++|....
T Consensus       205 ~~~~~R~l~I~K~Rg~~~~~~~~~f~I~~~Gi~v~p~~~~  244 (509)
T PRK09302        205 GEKRTRTLRILKYRGTTHGKNEYPFTITEDGISVLPLTAM  244 (509)
T ss_pred             CCeEEEEEEEEECCCCCcCCccEEEEECCCcEEEEecccc
Confidence               36999999999988  467999999999999987543

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=99.93  E-value=7.4e-25  Score=214.22  Aligned_cols=225  Identities=20%  Similarity=0.206  Sum_probs=158.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||+++||++|+||+++|++++|.|+||+|||+|+++++.+.+..      +++|+||++|++  +..+.+.+.. 
T Consensus       252 ~~~~~tGi~~lD~~l~GG~~~g~~~li~G~~G~GKT~l~~~~~~~~~~~------g~~~~yis~e~~--~~~i~~~~~~-  322 (509)
T PRK09302        252 NERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKFAEAACRR------GERCLLFAFEES--RAQLIRNARS-  322 (509)
T ss_pred             cccccCCcHHHHHhhcCCCCCCcEEEEEcCCCCCHHHHHHHHHHHHHhC------CCcEEEEEecCC--HHHHHHHHHH-
Confidence            4579999999999999999999999999999999999999999988752      589999999985  3344333321 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCC-CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPT-SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLIT  239 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk  239 (357)
                      +.  ++.....  ..+.+.+.... ....+...+..+...+.++++++|||||++.+....      ....+++++..|.
T Consensus       323 ~g--~~~~~~~--~~g~l~i~~~~~~~~~~~~~~~~i~~~i~~~~~~~vVIDslt~l~~~~------~~~~~~~~l~~l~  392 (509)
T PRK09302        323 WG--IDLEKME--EKGLLKIICARPESYGLEDHLIIIKREIEEFKPSRVAIDPLSALARGG------SLNEFRQFVIRLT  392 (509)
T ss_pred             cC--CChHHHh--hcCCceeecCCcccCCHHHHHHHHHHHHHHcCCCEEEEcCHHHHHHhC------CHHHHHHHHHHHH
Confidence            11  1111110  11223232211 122344556667777777899999999999987532      1245677788899


Q ss_pred             HHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC----CeEEEE
Q 035774          240 SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS----GQRFMN  315 (357)
Q Consensus       240 ~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~----~~R~l~  315 (357)
                      ++++++|+++++|+|.....+..                ...    .      ..+++++|.+|.|+...    ..|+++
T Consensus       393 ~~~k~~~~t~l~t~~~~~~~g~~----------------~~~----~------~~~~~l~D~vI~L~~~~~~~~~~R~l~  446 (509)
T PRK09302        393 DYLKSEEITGLFTNLTPDFMGSH----------------SIT----E------SHISSLTDTWILLQYVEINGEMNRALY  446 (509)
T ss_pred             HHHHhCCCeEEEEeccccccCCC----------------CCC----c------CceEEeeeEEEEEEEeecCCeeEEEEE
Confidence            99999999999999875422100                000    0      01467788889998642    369999


Q ss_pred             EEeCCCCC--CceeEEEEcCCCceeccC----CCceecccc
Q 035774          316 VEKSPTSP--PLAFSFTINPSGISLLTD----DGTEMVVPE  350 (357)
Q Consensus       316 v~K~r~~~--~~~~~f~I~~~Gi~~~~~----~~~~~~~~~  350 (357)
                      |.|+|+++  ...++|+|+++||.+.++    .++....|.
T Consensus       447 I~K~Rg~~~~~~~~~f~It~~Gi~v~~~~~~~~~~~~g~~~  487 (509)
T PRK09302        447 VLKMRGSWHSNQIREFVITDKGIHIKDPFRGFEGILSGSPR  487 (509)
T ss_pred             EEEcCCCCCCCceEEEEEeCCcEEEcccccCCCccccCCCc
Confidence            99999887  578899999999999876    344444444

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=99.92  E-value=6.1e-24  Score=188.70  Aligned_cols=216  Identities=15%  Similarity=0.168  Sum_probs=144.3

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh--ccCchh-hc
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA--SSFPEI-FH  166 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~--~~~~~~-~~  166 (357)
                      +||.+++ |+++|++++|+|+||+|||+|+++++.+++.+     .+.+|+||++|++.... +.++..  ..++.. ..
T Consensus         2 ~LD~~~~-Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~-----~g~~vly~s~E~~~~~~-~~r~~~~~~~~~~~~~~   74 (242)
T cd00984           2 DLDNLTG-GLQPGDLIIIAARPSMGKTAFALNIAENIAKK-----QGKPVLFFSLEMSKEQL-LQRLLASESGISLSKLR   74 (242)
T ss_pred             chhhhhc-CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh-----CCCceEEEeCCCCHHHH-HHHHHHHhcCCCHHHHh
Confidence            6999996 89999999999999999999999999999863     14899999999954321 222211  111100 00


Q ss_pred             --------c---cchHHHh-hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHH
Q 035774          167 --------S---KGMAQEM-AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWH  234 (357)
Q Consensus       167 --------~---~~~~~~~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i  234 (357)
                              .   ....... ..++++.+.. ..++..+...+.....++++++|||||++.+....  ....+...+..+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~~~~~l~~~i~~~~~~~~~~~vvID~l~~l~~~~--~~~~~~~~~~~~  151 (242)
T cd00984          75 TGSLSDEDWERLAEAIGELKELPIYIDDSS-SLTVSDIRSRARRLKKEHGLGLIVIDYLQLMSGSK--KKGNRQQEVAEI  151 (242)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCEEEeCCC-CCCHHHHHHHHHHHHHhcCCCEEEEcCchhcCCCC--CCCCHHHHHHHH
Confidence                    0   0001111 1244444332 23455566666666667799999999999886442  223455778899


Q ss_pred             HHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-----
Q 035774          235 ISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-----  309 (357)
Q Consensus       235 ~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-----  309 (357)
                      ++.|+.+|+++||++++++|+++......               ...+...+++-+  ..+.+.+|.++.|.++.     
T Consensus       152 ~~~L~~la~~~~~~ii~~~q~~r~~~~~~---------------~~~~~~~~~~gS--~~i~~~aD~vi~l~~~~~~~~~  214 (242)
T cd00984         152 SRSLKLLAKELNVPVIALSQLSRGVESRA---------------DKRPMLSDLRES--GSIEQDADVVMFLYRDEYYNKE  214 (242)
T ss_pred             HHHHHHHHHHhCCeEEEecccChhhhccC---------------CCCCCHHHHhhh--cccccCCCEEEEEecccccccc
Confidence            99999999999999999999987533110               001111222222  23677889999998763     


Q ss_pred             ----CeEEEEEEeCCCCCCceeEEEEc
Q 035774          310 ----GQRFMNVEKSPTSPPLAFSFTIN  332 (357)
Q Consensus       310 ----~~R~l~v~K~r~~~~~~~~f~I~  332 (357)
                          +.-.+.|.|+|.++.+.+.+.+.
T Consensus       215 ~~~~~~~~l~v~KnR~G~~g~~~l~~~  241 (242)
T cd00984         215 SESKGIAEIIVAKNRNGPTGTVELRFD  241 (242)
T ss_pred             cCCCCceEEEEECCCCCCCeeEEEEee
Confidence                34689999999999887776554

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK07773 replicative DNA helicase; Validated

Probab=99.91  E-value=5.3e-24  Score=219.18  Aligned_cols=173  Identities=18%  Similarity=0.228  Sum_probs=123.9

Q ss_pred             ccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHH
Q 035774           78 EHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMG  157 (357)
Q Consensus        78 ~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~  157 (357)
                      .....+++||++.||.++ ||+++|++++|+|+||+|||+|++++|.+++..     .+.+|+||++||+.... +.++.
T Consensus       194 ~~~~~Gi~TG~~~LD~l~-~Gl~~G~livIagrPg~GKT~fal~ia~~~a~~-----~~~~V~~fSlEms~~ql-~~R~~  266 (886)
T PRK07773        194 GGLARGVPTGFTELDAMT-NGLHPGQLIIVAARPSMGKTTFGLDFARNCAIR-----HRLAVAIFSLEMSKEQL-VMRLL  266 (886)
T ss_pred             CCCCCCccCChhHhcccc-CCCCCCcEEEEEeCCCCCcHHHHHHHHHHHHHh-----cCCeEEEEecCCCHHHH-HHHHH
Confidence            334679999999999998 679999999999999999999999999999853     14789999999964431 12222


Q ss_pred             h--ccCc-hhh-----cccc---h---HHHhh-cCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCC
Q 035774          158 A--SSFP-EIF-----HSKG---M---AQEMA-GRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHE  222 (357)
Q Consensus       158 ~--~~~~-~~~-----~~~~---~---~~~~~-~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~  222 (357)
                      .  ..++ ...     ....   .   ...+. .++++ +......+.++...+++...++++++||||||+.+...  .
T Consensus       267 s~~~~i~~~~i~~g~l~~~~~~~~~~a~~~l~~~~i~i-~d~~~~~i~~i~~~~r~~~~~~~~~lvvIDyLql~~~~--~  343 (886)
T PRK07773        267 SAEAKIKLSDMRSGRMSDDDWTRLARAMGEISEAPIFI-DDTPNLTVMEIRAKARRLRQEANLGLIVVDYLQLMTSG--K  343 (886)
T ss_pred             HHhcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEE-ECCCCCCHHHHHHHHHHHHHhcCCCEEEEcchhhcCCC--C
Confidence            1  1110 000     0000   0   11111 23444 33333355666666677766788999999999988643  2


Q ss_pred             CCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCC
Q 035774          223 QRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSH  260 (357)
Q Consensus       223 ~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~  260 (357)
                      ...+|.+++.++++.||.||++++|+||+++|+++...
T Consensus       344 ~~~~r~~ei~~isr~LK~lAkel~vpvi~lsQLnR~~e  381 (886)
T PRK07773        344 KYENRQQEVSEISRHLKLLAKELEVPVVALSQLSRGVE  381 (886)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHCCcEEEecccCcchh
Confidence            23457789999999999999999999999999998754

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=99.89  E-value=8.5e-22  Score=176.58  Aligned_cols=218  Identities=23%  Similarity=0.378  Sum_probs=150.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh-c
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA-S  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~-~  159 (357)
                      ..++|||++.||++|+||+|+|.+++|+|+||+|||+|++|++.+.+..      +.+|+||+++++  +..+.+.+. .
T Consensus         2 ~~~~~TGI~glD~~l~GG~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~------ge~vlyvs~~e~--~~~l~~~~~~~   73 (260)
T COG0467           2 MERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGARE------GEPVLYVSTEES--PEELLENARSF   73 (260)
T ss_pred             CccccCCCcchHHHhcCCCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhc------CCcEEEEEecCC--HHHHHHHHHHc
Confidence            4579999999999999999999999999999999999999999999852      599999999884  444443332 2


Q ss_pred             cCchhhcccchHHHhhcCeEEeC------------CCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCC
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQ------------PTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPG  227 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~------------~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r  227 (357)
                      .|.  ++  ...+.  ..+.+.+            ..+..++..+...+...+...+...+||||++.+.....     .
T Consensus        74 g~d--~~--~~~~~--g~l~i~d~~~~~~~~~~~~~~~~~~~~~l~~~I~~~~~~~~~~~~ViDsi~~~~~~~~-----~  142 (260)
T COG0467          74 GWD--LE--VYIEK--GKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEKEGADRVVIDSITELTLYLN-----D  142 (260)
T ss_pred             CCC--HH--HHhhc--CCEEEEEccccccccccccccCCccHHHHHHHHHHHHHHhCCCEEEEeCCchHhhhcC-----c
Confidence            221  11  00000  1111111            111234555666777777777899999999997554321     1


Q ss_pred             hHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEE
Q 035774          228 QHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA  307 (357)
Q Consensus       228 ~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~  307 (357)
                      ....+.++..++++.++++++.+++.+........                      ..+       -...++..+.|..
T Consensus       143 ~~~~r~~~~~l~~~~~~~~~t~~~~~~~~~~~~~~----------------------~~~-------~~~~vdgvI~l~~  193 (260)
T COG0467         143 PALVRRILLLLKRFLKKLGVTSLLTTEAPVEERGE----------------------SGV-------EEYIVDGVIRLDL  193 (260)
T ss_pred             hHHHHHHHHHHHHHHHhCCCEEEEEecccccCCCc----------------------cce-------EEEEEEEEEEEee
Confidence            23336788899999999999999998764432210                      001       0125566676665


Q ss_pred             e----CCeE-EEEEEeCCCCC--CceeEEEEcC-CCceeccCCCcee
Q 035774          308 K----SGQR-FMNVEKSPTSP--PLAFSFTINP-SGISLLTDDGTEM  346 (357)
Q Consensus       308 ~----~~~R-~l~v~K~r~~~--~~~~~f~I~~-~Gi~~~~~~~~~~  346 (357)
                      .    ...| +++|.|+|..+  ...+.|+|++ +||.+++......
T Consensus       194 ~~~~~~~~r~~~~i~k~r~~~~~~~~~~~~i~~g~gi~i~~~~~~~~  240 (260)
T COG0467         194 KEIEGGGDRRYLRILKMRGTPHSLKVIPFEITDGEGIVVYPEGRIRL  240 (260)
T ss_pred             ecccCceEEEEEEEEeccccccCCceeceEEecCCcEEEecCccccc
Confidence            3    2345 99999999987  3678999999 7999999866544

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=99.88  E-value=4.9e-21  Score=167.75  Aligned_cols=210  Identities=17%  Similarity=0.246  Sum_probs=138.9

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFP  162 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~  162 (357)
                      .+.++++.||++++||+++|++++|.|+||+|||+||++++...+.+      +.+++|+++|++. ...++++....+ 
T Consensus         5 ~~~~~~~~ld~~l~ggi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~------g~~~~yi~~e~~~-~~~~~~~~~~g~-   76 (230)
T PRK08533          5 KIELSRDELHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQN------GYSVSYVSTQLTT-TEFIKQMMSLGY-   76 (230)
T ss_pred             EEEEEEeeeehhhCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhC------CCcEEEEeCCCCH-HHHHHHHHHhCC-
Confidence            57899999999999999999999999999999999999999987642      4899999998854 334444432221 


Q ss_pred             hhhcccchHHHhhcCeEEeCC----CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHH
Q 035774          163 EIFHSKGMAQEMAGRILVLQP----TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLI  238 (357)
Q Consensus       163 ~~~~~~~~~~~~~~~i~~~~~----~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~L  238 (357)
                         ..+..  ...+++.+.+.    ....+....+..+.......+++++|||+++.+.....+     .....++.+.|
T Consensus        77 ---~~~~~--~~~~~l~~~~~~~~~~~~~~~~~~l~~il~~~~~~~~~~lVIDe~t~~l~~~~d-----~~~~~~l~~~l  146 (230)
T PRK08533         77 ---DINKK--LISGKLLYIPVYPLLSGNSEKRKFLKKLMNTRRFYEKDVIIIDSLSSLISNDAS-----EVAVNDLMAFF  146 (230)
T ss_pred             ---chHHH--hhcCcEEEEEecccccChHHHHHHHHHHHHHHHhcCCCEEEEECccHHhcCCcc-----hHHHHHHHHHH
Confidence               11111  11123333221    122233444555555555568999999999987643111     12345567777


Q ss_pred             HHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC----CeEEE
Q 035774          239 TSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS----GQRFM  314 (357)
Q Consensus       239 k~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~----~~R~l  314 (357)
                      +.++++ +++++++++.......                 .    ...        ..+++|..+.|+...    ..|++
T Consensus       147 ~~l~~~-g~tvi~t~~~~~~~~~-----------------~----~~~--------~~~~~DgvI~L~~~~~~~~~~R~i  196 (230)
T PRK08533        147 KRISSL-NKVIILTANPKELDES-----------------V----LTI--------LRTAATMLIRLEVKVFGGDLKNSA  196 (230)
T ss_pred             HHHHhC-CCEEEEEecccccccc-----------------c----cee--------EEEeeeEEEEEEEeecCCEEEEEE
Confidence            777654 7788887764321110                 0    000        256678888887542    26899


Q ss_pred             EEEeCCCCCC---ceeEEEEcCC-Cceecc
Q 035774          315 NVEKSPTSPP---LAFSFTINPS-GISLLT  340 (357)
Q Consensus       315 ~v~K~r~~~~---~~~~f~I~~~-Gi~~~~  340 (357)
                      .|.|+|+.++   ..++|+|.++ ||.+..
T Consensus       197 ~V~KmR~~~~~~~~~~~f~i~~~~g~~~~~  226 (230)
T PRK08533        197 KIVKYNMAKGSFQKSIPFRVEPKIGLAVEI  226 (230)
T ss_pred             EEEEecCCccccCCEEEEEEcCCccEEEEE
Confidence            9999999774   3789999965 998753

>PRK05973 replicative DNA helicase; Provisional

Probab=99.85  E-value=1.6e-20  Score=163.19  Aligned_cols=143  Identities=17%  Similarity=0.178  Sum_probs=98.6

Q ss_pred             HHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHH-HHHhccCchhhcccc
Q 035774           91 LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMI-EMGASSFPEIFHSKG  169 (357)
Q Consensus        91 LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~-~~~~~~~~~~~~~~~  169 (357)
                      .|++. ||+++|++++|+|+||+|||+|+++++.+++..      +++|+||++|++.  ..+. ++....+.    .  
T Consensus        54 ~~~l~-GGl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~------Ge~vlyfSlEes~--~~i~~R~~s~g~d----~--  118 (237)
T PRK05973         54 AEELF-SQLKPGDLVLLGARPGHGKTLLGLELAVEAMKS------GRTGVFFTLEYTE--QDVRDRLRALGAD----R--  118 (237)
T ss_pred             HHHhc-CCCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc------CCeEEEEEEeCCH--HHHHHHHHHcCCC----h--
Confidence            78855 679999999999999999999999999999852      5899999999963  2332 22222111    1  


Q ss_pred             hHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeE
Q 035774          170 MAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPI  249 (357)
Q Consensus       170 ~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~v  249 (357)
                        ....+ .+.++..+......++.++   ...+++++||||||+.+....      +...+..+++.|+.+|+++|+||
T Consensus       119 --~~~~~-~~~~d~~d~~~~~~ii~~l---~~~~~~~lVVIDsLq~l~~~~------~~~el~~~~~~Lk~~Ak~~gitv  186 (237)
T PRK05973        119 --AQFAD-LFEFDTSDAICADYIIARL---ASAPRGTLVVIDYLQLLDQRR------EKPDLSVQVRALKSFARERGLII  186 (237)
T ss_pred             --HHhcc-ceEeecCCCCCHHHHHHHH---HHhhCCCEEEEEcHHHHhhcc------cchhHHHHHHHHHHHHHhCCCeE
Confidence              11112 2223222222222333333   334678999999999885321      22346778889999999999999


Q ss_pred             EEeccccccCC
Q 035774          250 VVTNQVRPQSH  260 (357)
Q Consensus       250 v~~~q~~~~~~  260 (357)
                      |+++|++...+
T Consensus       187 Il~sQl~r~~e  197 (237)
T PRK05973        187 VFISQIDRSFD  197 (237)
T ss_pred             EEEecCccccc
Confidence            99999988765

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=99.81  E-value=1.5e-19  Score=154.95  Aligned_cols=170  Identities=24%  Similarity=0.373  Sum_probs=95.8

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC----CCCeEEEEeCCCCCch--HHHHH
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG----LDGGVIYIDVESTFTS--RRMIE  155 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg----~~~~vl~i~~e~~~~~--~rl~~  155 (357)
                      ..++++++.+|.++.|++++|++++|+|+||+|||+|+++++...+....+=|    .+.+|+||++|++...  .|+..
T Consensus        12 ~~~~~~~~~~~~li~g~~~~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~~~~~~~rl~~   91 (193)
T PF13481_consen   12 EDLDTGFPPLDWLIDGLLPRGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDSESQIARRLRA   91 (193)
T ss_dssp             -HHHS------EEETTEE-TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-HHHHHHHHHH
T ss_pred             hhccCCCCCcceeECCcccCCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCCHHHHHHHHHH
Confidence            35889999999999999999999999999999999999999999986322211    3579999999997532  44444


Q ss_pred             HHhccCchhhcccchHH--HhhcCeEEeCCCCH-HHHHHHHHHHHHHhhh-cCeeEEEEeccccccCCCCCCCCCChHHH
Q 035774          156 MGASSFPEIFHSKGMAQ--EMAGRILVLQPTSL-SEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPGVHEQRAPGQHPL  231 (357)
Q Consensus       156 ~~~~~~~~~~~~~~~~~--~~~~~i~~~~~~~~-~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~~~~~~~~r~~~~  231 (357)
                      +... ... ........  .. ..+.++..... ......+..+.+.+.. +++++||||+++.+...    ..+....+
T Consensus        92 ~~~~-~~~-~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~lvviD~l~~~~~~----~~~~~~~~  164 (193)
T PF13481_consen   92 LLQD-YDD-DANLFFVDLSNW-GCIRLFEPDSGGPLLDEDLEELEAALKELYGPDLVVIDPLQSLHDG----DENSNSAV  164 (193)
T ss_dssp             HHTT-S-H-HHHHHHHHH--E--EE---TTS---TTSHHHHHHHHHHHTT----SEEEEE-GGGG--S-----TT-HHHH
T ss_pred             Hhcc-cCC-ccceEEeecccc-ccceeeecccccccchHHHHHHHHHHhhcCCCcEEEEcCHHHHhcC----CCCCHHHH
Confidence            4432 110 00000000  01 12222222211 1134456677777777 78999999999999876    12234555


Q ss_pred             HHHHHHHHHHHHHcCCeEEEecccccc
Q 035774          232 SWHISLITSLAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       232 ~~i~~~Lk~la~~~~~~vv~~~q~~~~  258 (357)
                      .++++.|+++|+++|++|++++|.++.
T Consensus       165 ~~~~~~l~~la~~~~~~vi~v~H~~K~  191 (193)
T PF13481_consen  165 AQLMQELKRLAKEYGVAVILVHHTNKS  191 (193)
T ss_dssp             HHHHHHHHHHHHHH--EEEEEEEE---
T ss_pred             HHHHHHHHHHHHHcCCEEEEEECCCCC
Confidence            889999999999999999999999774

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=99.80  E-value=6.1e-18  Score=140.61  Aligned_cols=210  Identities=18%  Similarity=0.259  Sum_probs=151.5

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFP  162 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~  162 (357)
                      -+++|-++||+-|+||+|-|++++|.|+.|+|||.|++++++-.+.+      +..+.|+++|.+. .+-+.+|..-.++
T Consensus         9 ii~~gndelDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~------g~~v~yvsTe~T~-refi~qm~sl~yd   81 (235)
T COG2874           9 IIKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMN------GYRVTYVSTELTV-REFIKQMESLSYD   81 (235)
T ss_pred             hccCCcHHHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHHHhC------CceEEEEEechhH-HHHHHHHHhcCCC
Confidence            48999999999999999999999999999999999999999988753      6899999999863 3455666543321


Q ss_pred             hhhcccchHHHhhcCeEEeCC------CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHH
Q 035774          163 EIFHSKGMAQEMAGRILVLQP------TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHIS  236 (357)
Q Consensus       163 ~~~~~~~~~~~~~~~i~~~~~------~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~  236 (357)
                          ..+  .-..+++.++..      ++......+++.+....+..+.+++||||++.+...+      ....+.+++.
T Consensus        82 ----v~~--~~l~G~l~~~~~~~~~~~~~~~~~~~~L~~l~~~~k~~~~dViIIDSls~~~~~~------~~~~vl~fm~  149 (235)
T COG2874          82 ----VSD--FLLSGRLLFFPVNLEPVNWGRRSARKLLDLLLEFIKRWEKDVIIIDSLSAFATYD------SEDAVLNFMT  149 (235)
T ss_pred             ----chH--HHhcceeEEEEecccccccChHHHHHHHHHHHhhHHhhcCCEEEEecccHHhhcc------cHHHHHHHHH
Confidence                111  112344444331      2345556667777676667789999999999987652      2357788999


Q ss_pred             HHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC----CeE
Q 035774          237 LITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS----GQR  312 (357)
Q Consensus       237 ~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~----~~R  312 (357)
                      .+++++.+ |-+|++|.|...-.+                        +.+.     -....+++-+.|+..+    ..+
T Consensus       150 ~~r~l~d~-gKvIilTvhp~~l~e------------------------~~~~-----rirs~~d~~l~L~~~~~Gg~~~~  199 (235)
T COG2874         150 FLRKLSDL-GKVIILTVHPSALDE------------------------DVLT-----RIRSACDVYLRLRLEELGGDLIK  199 (235)
T ss_pred             HHHHHHhC-CCEEEEEeChhhcCH------------------------HHHH-----HHHHhhheeEEEEhhhhCCeeeE
Confidence            99999986 667777766533111                        0111     1567788888887642    367


Q ss_pred             EEEEEeCCCCC---CceeEEEEcC-CCceeccC
Q 035774          313 FMNVEKSPTSP---PLAFSFTINP-SGISLLTD  341 (357)
Q Consensus       313 ~l~v~K~r~~~---~~~~~f~I~~-~Gi~~~~~  341 (357)
                      .+.|+|-++.+   ...++|++.+ -|+.+.+.
T Consensus       200 ~~~i~K~~ga~~s~~~~I~F~V~P~~Glkvep~  232 (235)
T COG2874         200 VLEIVKYRGARKSFQNIISFRVEPGFGLKVEPA  232 (235)
T ss_pred             EEEEeeecCchhhcCCceeEEecCCCceEEEEe
Confidence            89999998877   3568999994 78888764

>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=99.71  E-value=8.5e-16  Score=130.85  Aligned_cols=174  Identities=22%  Similarity=0.225  Sum_probs=106.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc-cCchhhcccchHHHhhcCeEEeC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS-SFPEIFHSKGMAQEMAGRILVLQ  182 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~-~~~~~~~~~~~~~~~~~~i~~~~  182 (357)
                      +++|.|+||+|||+|+++++...+..      +++|+|+++|++..  .+.+.+.. .+.    ...+  ...+.+.+.+
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~~~~~------g~~v~~~s~e~~~~--~~~~~~~~~g~~----~~~l--~~~g~l~~~d   66 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYAGLAR------GEPGLYVTLEESPE--ELIENAESLGWD----LERL--EDEGLLAIVD   66 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHHHHC------CCcEEEEECCCCHH--HHHHHHHHcCCC----hHHH--HhcCCeEEEe
Confidence            47899999999999999999998842      58999999998533  33322211 111    1100  0112233333


Q ss_pred             CCC----HHHH---HHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          183 PTS----LSEF---TESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       183 ~~~----~~~~---~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ...    ..+.   .+++..+...+...+++++|||+++.+...  +    .......+.+.++.+. +.|+++|+++|.
T Consensus        67 ~~~~~~s~~~~~~~~~~~~~i~~~~~~~~~~~lviD~~~~~~~~--~----~~~~~~~i~~l~~~l~-~~g~tvi~v~~~  139 (187)
T cd01124          67 ADPDEIGPAESSLRLELIQRLKDAIEEFKAKRVVIDSVSGLLLM--E----QSTARLEIRRLLFALK-RFGVTTLLTSEQ  139 (187)
T ss_pred             cCccccchhhhhhhHHHHHHHHHHHHHhCCCEEEEeCcHHHhhc--C----hHHHHHHHHHHHHHHH-HCCCEEEEEecc
Confidence            221    1111   134555666666678999999999998653  1    1122223344444444 459999999987


Q ss_pred             cccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe--CC--eEEEEEEeCCCCCCc
Q 035774          256 RPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK--SG--QRFMNVEKSPTSPPL  325 (357)
Q Consensus       256 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~--~~--~R~l~v~K~r~~~~~  325 (357)
                      ......                           +.....+.+.+|..+.++..  ++  .|+++|.|+|++++.
T Consensus       140 ~~~~~~---------------------------~~~~~~~~~~aD~ii~l~~~~~~~~~~r~l~i~K~R~~~~~  186 (187)
T cd01124         140 SGLEGT---------------------------GFGGGDVEYLVDGVIRLRLDEEGGRLRRSLSVVKMRGGPHD  186 (187)
T ss_pred             ccCCCc---------------------------ccCcCceeEeeeEEEEEEEEccCCEEEEEEEEEEccCCCCC
Confidence            553210                           00011256778888888865  22  688999999998753

A related protein is found in archaea.

>KOG2859 consensus DNA repair protein, member of the recA/RAD51 family [Replication, recombination and repair]

Probab=99.70  E-value=2.5e-16  Score=130.54  Aligned_cols=205  Identities=18%  Similarity=0.183  Sum_probs=148.8

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchh-------------hc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEI-------------FH  166 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~-------------~~  166 (357)
                      ..|++++|.||.++|||.+..|+++++.+|.++||.+..|+|||++..|+..|+.++.+.+..+.             ..
T Consensus        36 daG~~vEi~Gp~~sgKt~vL~ql~a~CilPk~~GGl~~~VLfidld~~fd~lrL~~~l~hrL~q~~~~e~~~~~c~te~~  115 (293)
T KOG2859|consen   36 DAGTLVEISGPGNSGKTLVLQQLVAHCILPKKFGGLQWSVLFIDLDHKFDRLRLAKSLRHRLKQYSVGEVIAAKCPTEEQ  115 (293)
T ss_pred             ccCcEEEEeCCCCccHHHHHHHHHHHeecccccCCceeEEEEEeccccccHHHHHHHHHHHHHHhhhhhhhhhcCCcHhH
Confidence            36899999999999999999999999999999999999999999999999999988776543211             12


Q ss_pred             ccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCC-CCC---hHHHHHHHHHHHHH
Q 035774          167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQR-APG---QHPLSWHISLITSL  241 (357)
Q Consensus       167 ~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~-~~r---~~~~~~i~~~Lk~l  241 (357)
                      .++.....+.+++++.|++..++...+..++..+.++ ++.++++||+++++|.+.... +.+   ...++.+...|+++
T Consensus       116 ~eEi~~~Cm~Rf~~v~C~~s~~ll~sL~~l~y~i~~~p~~cll~~DslsaFyW~Dr~~~le~~n~~~~~lr~~~q~LeKL  195 (293)
T KOG2859|consen  116 LEEIAGECMSRFRFVNCFASDDLLTSLIDLRYAIINDPGICLLAMDSLSAFYWLDRPKILEKRNSMYRHLRLLQQRLEKL  195 (293)
T ss_pred             HHHHHHHHHhhEEEEEeeccHHHHHHHHHHHHHHhcCCceeEEeecchhhheeecccchHhhhhhHHHHHHHHHHHHHHH
Confidence            2344556688999999999999988888888887765 489999999999999854332 112   23467788899999


Q ss_pred             HHHcCCeEEEeccccccCCCCCCccccccc-ccccccccccCCCcceecccchhHhhhccEEEEEEEeCC
Q 035774          242 AEFSRIPIVVTNQVRPQSHDESCLYPFQVQ-KMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSG  310 (357)
Q Consensus       242 a~~~~~~vv~~~q~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~~  310 (357)
                      .+.+-+.++.|.+.-....     |.++-+ |+-+...-- .......|.+-..|.+.+.+++.+++..+
T Consensus       196 ~~d~~lv~~aT~~ti~~e~-----y~~~En~P~~~gRsvC-llliky~~~~~k~~qq~v~h~l~~sks~d  259 (293)
T KOG2859|consen  196 CKDAILVGMATVETIFLEN-----YRFGENLPEAGGRSVC-LLLIKYHVRMQKIQQQIVLHGLPLSKSND  259 (293)
T ss_pred             HhhheeeeeeehhHHHHhc-----ccccccCcccccccee-eeeccccHHHHHHHHHHHHccCceecccc
Confidence            9999888888887644322     111111 111100000 00011123445579999999999987654

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=99.66  E-value=1.1e-14  Score=129.00  Aligned_cols=210  Identities=21%  Similarity=0.242  Sum_probs=124.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC------CCCeEEEEeCCCCCc--hHHHHHHHhccCchhhcccchH-H
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG------LDGGVIYIDVESTFT--SRRMIEMGASSFPEIFHSKGMA-Q  172 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg------~~~~vl~i~~e~~~~--~~rl~~~~~~~~~~~~~~~~~~-~  172 (357)
                      |.+.+|+|+||+|||+|++++|..++....+.|      .+++|+|+++|++..  ..|+..+....-.......... .
T Consensus         1 g~~~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed~~~~i~~Rl~~i~~~~~~~~~~~rl~~~~   80 (239)
T cd01125           1 GYVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRLEAILQHLEPDDAGDRLFIDS   80 (239)
T ss_pred             CceeEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCCCHHHHHHHHHHHHhhcCCcCcccceEEec
Confidence            678999999999999999999999887555444      357899999999755  3566655543100000000000 0


Q ss_pred             HhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEe
Q 035774          173 EMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       173 ~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                      .....+.+..... ......+..+...+...++++||||+++.+...    ..........++..|++++++++++|+++
T Consensus        81 g~~~~l~~~~~~~-~~~~~~~~~l~~~~~~~~~~lvviDpl~~~~~~----~~~d~~~~~~~~~~L~~~a~~~g~avl~v  155 (239)
T cd01125          81 GRIQPISIAREGR-IIVVPEFERIIEQLLIRRIDLVVIDPLVSFHGV----SENDNGAMDAVIKALRRIAAQTGAAILLV  155 (239)
T ss_pred             cCCCceecccCCc-ccccHHHHHHHHHHHhcCCCEEEECChHHhCCC----CcCCHHHHHHHHHHHHHHHHHhCCEEEEE
Confidence            0011111111110 011222333333344568999999999987322    12234567778999999999999999999


Q ss_pred             ccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-------------CeEE--EEEE
Q 035774          253 NQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-------------GQRF--MNVE  317 (357)
Q Consensus       253 ~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-------------~~R~--l~v~  317 (357)
                      +|..+.......                    ..-...+...|.+.++..+.+.+..             ..++  ..+.
T Consensus       156 ~H~~K~~~~~~~--------------------~~~~~rGssal~~~~r~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  215 (239)
T cd01125         156 HHVRKGSAKDGD--------------------TQEAARGASALVDGARWVRALTRMTSEEAEKMGVGKAQPGLFFRFGVS  215 (239)
T ss_pred             eccCcccccCcc--------------------cccccCcHHHHhcccceEEEEeeCCHHHHHhcCCChhhcceEEEeccc
Confidence            999875432110                    0001112345777788888887531             1223  3467


Q ss_pred             eCCCC-CC-ceeEEEEcCCCc
Q 035774          318 KSPTS-PP-LAFSFTINPSGI  336 (357)
Q Consensus       318 K~r~~-~~-~~~~f~I~~~Gi  336 (357)
                      |+.+. ++ ...-|+-.++|+
T Consensus       216 k~n~~~~~~~~~w~~~~~~~~  236 (239)
T cd01125         216 KKNNAAATEADRWYRRNSGGV  236 (239)
T ss_pred             ccccCCCCCCCeEEEEccCcc
Confidence            77776 54 334566566554

RepA is encoded by a plasmid, which is found in most Gram negative bacteria. RepA is a 5'-3' DNA helicase which can utilize ATP, GTP and CTP to a lesser extent.

>KOG2373 consensus Predicted mitochondrial DNA helicase twinkle [Replication, recombination and repair]

Probab=99.51  E-value=5.5e-14  Score=124.50  Aligned_cols=222  Identities=16%  Similarity=0.200  Sum_probs=143.7

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHH-HHhc----cC
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIE-MGAS----SF  161 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~-~~~~----~~  161 (357)
                      -++.|+++|.| .++|+++++.||.|+|||||+...+...+.+      +...+|=|+|.  +..|+.. |+..    ..
T Consensus       259 RFpvLNk~LkG-hR~GElTvlTGpTGsGKTTFlsEYsLDL~~Q------GVnTLwgSFEi--~n~rla~~mL~Qyagyrl  329 (514)
T KOG2373|consen  259 RFPVLNKYLKG-HRPGELTVLTGPTGSGKTTFLSEYSLDLFTQ------GVNTLWGSFEI--PNKRLAHWMLVQYAGYRL  329 (514)
T ss_pred             hhhHHHHHhcc-CCCCceEEEecCCCCCceeEehHhhHHHHhh------hhhheeeeeec--chHHHHHHHHHHHccCch
Confidence            47789999965 9999999999999999999999999888754      58899999987  3445543 2211    11


Q ss_pred             c-hhhcccchHHHhhc-CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHH
Q 035774          162 P-EIFHSKGMAQEMAG-RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLIT  239 (357)
Q Consensus       162 ~-~~~~~~~~~~~~~~-~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk  239 (357)
                      . .......+.+.... .+++..-..-..+...++.+...+--+++.-||||+++.|.....- ...|-..-..|+..++
T Consensus       330 ~drl~~y~HWadrFErlplyfmtfhgqq~~~~vi~~i~ha~yV~di~HViIDNLQFmmg~~~~-~~Drf~~QD~iig~fR  408 (514)
T KOG2373|consen  330 LDRLNSYKHWADRFERLPLYFMTFHGQQFMEKVINEIAHAIYVEDIQHVIIDNLQFMMGQGMM-ALDRFHLQDRIIGYFR  408 (514)
T ss_pred             HhhhhhhhHHHHHHhccchHhhhhcccchHHHHHHHHHHHHHHHhhhhhhhhhHHHHhccchh-ccchhhhHHHHHHHHH
Confidence            0 00011112222221 1222222233445566666666665678899999999998765321 1225555667889999


Q ss_pred             HHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEE-----eCCeEEE
Q 035774          240 SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA-----KSGQRFM  314 (357)
Q Consensus       240 ~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~-----~~~~R~l  314 (357)
                      ++|.++||.|-++-|..+..++..             .+....|++. +      -.+-+|.++.+..     +.+++++
T Consensus       409 ~fAT~nn~HvTlVvHPRKed~d~E-------------l~t~s~fGsA-k------atQEADNVliiQdkrl~~~rgkkyL  468 (514)
T KOG2373|consen  409 QFATQNNIHVTLVVHPRKEDGDTE-------------LDTQSFFGSA-K------ATQEADNVLIIQDKRLDRDRGKKYL  468 (514)
T ss_pred             HHhhccceeEEEEecccccCCCce-------------eeehhhcccc-c------cccccccEEEEeecccccccchhhh
Confidence            999999999999999988655311             1111111111 1      2344566677654     3468999


Q ss_pred             EEEeCCCCC-CceeEEEEcCCCcee
Q 035774          315 NVEKSPTSP-PLAFSFTINPSGISL  338 (357)
Q Consensus       315 ~v~K~r~~~-~~~~~f~I~~~Gi~~  338 (357)
                      .|.|+|+.+ -+..+.++...+...
T Consensus       469 qi~KNRy~Gdvg~~pLEf~kn~lty  493 (514)
T KOG2373|consen  469 QILKNRYYGDVGSDPLEFVKNPLTY  493 (514)
T ss_pred             hhhhhcccCcccccceeeccCCccc
Confidence            999999877 455677777666544

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=99.46  E-value=7.7e-13  Score=109.61  Aligned_cols=140  Identities=21%  Similarity=0.281  Sum_probs=88.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQP  183 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  183 (357)
                      +++|+|+||+|||+|+.+++...+..      +.+++|++.|......... ....      ..    ....+++.+...
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~~~~~------~~~v~~~~~e~~~~~~~~~-~~~~------~~----~~~~~~~~~~~~   63 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALNIATK------GGKVVYVDIEEEIEELTER-LIGE------SL----KGALDNLIIVFA   63 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHHHHhc------CCEEEEEECCcchHHHHHH-Hhhh------hh----ccccccEEEEEc
Confidence            47899999999999999999988642      5899999999865542211 1000      00    011233333332


Q ss_pred             CC-HHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCC
Q 035774          184 TS-LSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSH  260 (357)
Q Consensus       184 ~~-~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~  260 (357)
                      .. ..................+++++|||+++.+..............+.+.+..|...+++.++++|+++|......
T Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~lviDe~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~vv~~~~~~~~~~  141 (165)
T cd01120          64 TADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELLERARKGGVTVIFTLQVPSGDK  141 (165)
T ss_pred             CCCCCcHHHHHHHHHHHHhCCCCEEEEEEcHHHHHHHHHHHHhcCChHHHHHHHHHHHHHhcCCceEEEEEecCCccc
Confidence            22 112222222334444567899999999998875422100112345677888889899999999999999876543

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.

>COG3598 RepA RecA-family ATPase [DNA replication, recombination, and repair]

Probab=99.35  E-value=1.6e-11  Score=108.17  Aligned_cols=151  Identities=20%  Similarity=0.190  Sum_probs=103.6

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC----CCCeEEEEeCCCCCch--HHHHHHHhccCchhhcccch
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG----LDGGVIYIDVESTFTS--RRMIEMGASSFPEIFHSKGM  170 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg----~~~~vl~i~~e~~~~~--~rl~~~~~~~~~~~~~~~~~  170 (357)
                      +-+..|-.+.|+|++|+|||+++++++...+...+|-|    ..++|+|+++|..-+.  .|+..+...     +...+ 
T Consensus        84 ~~fr~g~~~~~~gdsg~GKttllL~l~IalaaG~~lfG~~v~epGkvlyvslEl~re~~L~Rl~~v~a~-----mgLsP-  157 (402)
T COG3598          84 EFFRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILERLEPVRAR-----MGLSP-  157 (402)
T ss_pred             HHhhcCeeEEEecCCcccHhHHHHHHHHHHHhhHHHhcccccCCCeEEEEEeccChHHHHHHHHHHHHH-----cCCCh-
Confidence            44677888999999999999999999988876555543    2589999999975332  333333221     11111 


Q ss_pred             HHHhhcCeEEeCCC------CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 035774          171 AQEMAGRILVLQPT------SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEF  244 (357)
Q Consensus       171 ~~~~~~~i~~~~~~------~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~  244 (357)
                        ....++...+..      +.... .+.++....+.+..+++||||++..++...    +...-+++.+++.++++|.+
T Consensus       158 --advrn~dltd~~Gaa~~~d~l~p-kl~rRfek~~~Q~rp~~vViDp~v~f~~G~----s~s~vqv~~fi~~~rkla~~  230 (402)
T COG3598         158 --ADVRNMDLTDVSGAADESDVLSP-KLYRRFEKILEQKRPDFVVIDPFVAFYEGK----SISDVQVKEFIKKTRKLARN  230 (402)
T ss_pred             --HhhhheeccccccCCCccccccH-HHHHHHHHHHHHhCCCeEEEcchhhhcCCc----cchhHHHHHHHHHHHHHHHh
Confidence              122334432211      11222 445555666667789999999999988652    22336789999999999999


Q ss_pred             cCCeEEEeccccccCC
Q 035774          245 SRIPIVVTNQVRPQSH  260 (357)
Q Consensus       245 ~~~~vv~~~q~~~~~~  260 (357)
                      ++|+|+.++|.++...
T Consensus       231 l~caIiy~hHtskss~  246 (402)
T COG3598         231 LECAIIYIHHTSKSSG  246 (402)
T ss_pred             cCCeEEEEeccccccC
Confidence            9999999999987654

>PF07088 GvpD: GvpD gas vesicle protein; InterPro: IPR009788 This family consists of several archaeal GvpD gas vesicle proteins

Probab=99.18  E-value=4.8e-10  Score=101.76  Aligned_cols=195  Identities=18%  Similarity=0.244  Sum_probs=120.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhc--
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAG--  176 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~--  176 (357)
                      -..|...+|-|.||+|||+|++.++.....       ...++|+++-  .++.++.++.... ..........+...+  
T Consensus         7 ~~~G~TLLIKG~PGTGKTtfaLelL~~l~~-------~~~v~YISTR--Vd~d~vy~~y~~~-~~~i~~~~vlDatQd~~   76 (484)
T PF07088_consen    7 QEPGQTLLIKGEPGTGKTTFALELLNSLKD-------HGNVMYISTR--VDQDTVYEMYPWI-EESIDPTNVLDATQDPF   76 (484)
T ss_pred             CCCCcEEEEecCCCCCceeeehhhHHHHhc-------cCCeEEEEec--cCHHHHHHhhhhh-ccccChhhhhhhccchh
Confidence            357999999999999999999999987753       4789999996  4566666543100 000000001111101  


Q ss_pred             -----CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEE
Q 035774          177 -----RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVV  251 (357)
Q Consensus       177 -----~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~  251 (357)
                           ...-........+.++++++..   .....+|++||.-+++..-... ......+..+...|-.+|++.++-+|+
T Consensus        77 ~~~~~~~vp~~~l~~ds~~~f~~~i~~---~~k~~iI~~DSWdaiieyla~~-~~~~ed~e~l~~dLv~lard~g~~LIl  152 (484)
T PF07088_consen   77 ELPLDKDVPFERLDIDSFRDFVDKINE---AGKKPIIAFDSWDAIIEYLAEE-HDEPEDIETLTNDLVELARDMGINLIL  152 (484)
T ss_pred             hccccccCcccccCHHHHHHHHHHhhh---cccCcEEEEecHHHHHHHhhhh-hcCcHHHHHHHHHHHHHHhhcCceEEE
Confidence                 1111122345566666665433   2456789999955544321111 112234566777888899999999999


Q ss_pred             eccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-----CCeEEEEEEeCCCCCC--
Q 035774          252 TNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-----SGQRFMNVEKSPTSPP--  324 (357)
Q Consensus       252 ~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-----~~~R~l~v~K~r~~~~--  324 (357)
                      +.+......                                  ++.++|.++-+...     ...|.+++.|.|+.+-  
T Consensus       153 VsEsa~~~~----------------------------------LdYivDGVVTL~v~~derGR~~R~L~LeKLRGV~I~q  198 (484)
T PF07088_consen  153 VSESAENEP----------------------------------LDYIVDGVVTLQVKNDERGRTRRYLRLEKLRGVRIKQ  198 (484)
T ss_pred             EEecCCCCc----------------------------------chheeeeEEEEEeccccCCceEEEEEehhhcCcccCC
Confidence            987644321                                  45667777777532     2368999999999884  


Q ss_pred             ceeEEEEcCCCceeccC
Q 035774          325 LAFSFTINPSGISLLTD  341 (357)
Q Consensus       325 ~~~~f~I~~~Gi~~~~~  341 (357)
                      ..+.|+..++-...+.+
T Consensus       199 ~~Y~fTL~nGrF~~f~p  215 (484)
T PF07088_consen  199 RLYPFTLANGRFRSFTP  215 (484)
T ss_pred             ccceEEeeCCEEEEecc
Confidence            44677777777776654

GvpD is thought to be involved in the regulation of gas vesicle formation [,].; GO: 0005524 ATP binding

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=98.83  E-value=4.9e-08  Score=81.22  Aligned_cols=122  Identities=13%  Similarity=0.212  Sum_probs=66.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQP  183 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  183 (357)
                      +++|.|++|||||+||.+++...         +.+++|+++...++.+.-..+....           ..-...+.... 
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~~---------~~~~~y~at~~~~d~em~~rI~~H~-----------~~R~~~w~t~E-   59 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAEL---------GGPVTYIATAEAFDDEMAERIARHR-----------KRRPAHWRTIE-   59 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHhc---------CCCeEEEEccCcCCHHHHHHHHHHH-----------HhCCCCceEee-
Confidence            47899999999999999998651         4789999999877654333322210           00011111111 


Q ss_pred             CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC-ChHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          184 TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP-GQHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       184 ~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~-r~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                       ...++.+.+.   ..   .+.+.|+||+++.+.......... ....+.+.+..|....++.++++|+++
T Consensus        60 -~~~~l~~~l~---~~---~~~~~VLIDclt~~~~n~l~~~~~~~~~~~~~~i~~l~~~l~~~~~~~viVs  123 (169)
T cd00544          60 -TPRDLVSALK---EL---DPGDVVLIDCLTLWVTNLLFADLEEWEAAIADEIDALLAAVRNKPGTLILVS  123 (169)
T ss_pred             -cHHHHHHHHH---hc---CCCCEEEEEcHhHHHHHhCCCccccchhHHHHHHHHHHHHHHcCCCcEEEEE
Confidence             1122222221   11   156789999999987764332110 002233333333333344677666654

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK04296 thymidine kinase; Provisional

Probab=98.79  E-value=2.1e-07  Score=79.22  Aligned_cols=115  Identities=13%  Similarity=0.145  Sum_probs=66.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC--CCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV--ESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~--e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      .|.+++++|++|+|||+++++++.++..      .+.+|+++..  +......+   +... ..    .      ....+
T Consensus         1 ~g~i~litG~~GsGKTT~~l~~~~~~~~------~g~~v~i~k~~~d~~~~~~~---i~~~-lg----~------~~~~~   60 (190)
T PRK04296          1 MAKLEFIYGAMNSGKSTELLQRAYNYEE------RGMKVLVFKPAIDDRYGEGK---VVSR-IG----L------SREAI   60 (190)
T ss_pred             CcEEEEEECCCCCHHHHHHHHHHHHHHH------cCCeEEEEeccccccccCCc---EecC-CC----C------cccce
Confidence            3789999999999999999999998864      2578888843  22111111   1110 00    0      00111


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+   ....++   +..+..  ...+.++||||.++.+..          .++.    .|.+.++..+++|+++.....
T Consensus        61 ~~---~~~~~~---~~~~~~--~~~~~dvviIDEaq~l~~----------~~v~----~l~~~l~~~g~~vi~tgl~~~  117 (190)
T PRK04296         61 PV---SSDTDI---FELIEE--EGEKIDCVLIDEAQFLDK----------EQVV----QLAEVLDDLGIPVICYGLDTD  117 (190)
T ss_pred             Ee---CChHHH---HHHHHh--hCCCCCEEEEEccccCCH----------HHHH----HHHHHHHHcCCeEEEEecCcc
Confidence            11   222233   333333  345789999999975411          1222    344555678999999876533

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=98.75  E-value=1.6e-07  Score=79.23  Aligned_cols=137  Identities=18%  Similarity=0.242  Sum_probs=75.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCc---hHHHHHHHhccCchhhcccchHHHhh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFT---SRRMIEMGASSFPEIFHSKGMAQEMA  175 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~---~~rl~~~~~~~~~~~~~~~~~~~~~~  175 (357)
                      +.+|+++.|+||+|||||||+.  |.|.+.+.     ...-++|+.+....   ..++++...-.+ +.|...+. ..++
T Consensus        25 v~~Gevv~iiGpSGSGKSTlLR--clN~LE~~-----~~G~I~i~g~~~~~~~~~~~~R~~vGmVF-Q~fnLFPH-lTvl   95 (240)
T COG1126          25 VEKGEVVVIIGPSGSGKSTLLR--CLNGLEEP-----DSGSITVDGEDVGDKKDILKLRRKVGMVF-QQFNLFPH-LTVL   95 (240)
T ss_pred             EcCCCEEEEECCCCCCHHHHHH--HHHCCcCC-----CCceEEECCEeccchhhHHHHHHhcCeec-cccccccc-chHH
Confidence            8899999999999999999998  44555543     35588888754322   222222111111 01111100 0112


Q ss_pred             cCeEE----eCCCCHHHHHHHHHHH---------------------------HHHhhhcCeeEEEEeccccccCCCCCCC
Q 035774          176 GRILV----LQPTSLSEFTESLEKI---------------------------KVSLLQNQVKLLVIDSMEALVPGVHEQR  224 (357)
Q Consensus       176 ~~i~~----~~~~~~~~~~~~l~~l---------------------------~~~~~~~~~~lvvIDsl~~l~~~~~~~~  224 (357)
                      +|+..    +...+..+..+...++                           .+.+ ..+++++..|..++-..      
T Consensus        96 eNv~lap~~v~~~~k~eA~~~A~~lL~~VGL~~ka~~yP~qLSGGQqQRVAIARAL-aM~P~vmLFDEPTSALD------  168 (240)
T COG1126          96 ENVTLAPVKVKKLSKAEAREKALELLEKVGLADKADAYPAQLSGGQQQRVAIARAL-AMDPKVMLFDEPTSALD------  168 (240)
T ss_pred             HHHHhhhHHHcCCCHHHHHHHHHHHHHHcCchhhhhhCccccCcHHHHHHHHHHHH-cCCCCEEeecCCcccCC------
Confidence            22211    1111111111111111                           0111 24688999998776543      


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                         ...+.+++..++.+|++ |.|.++++|-
T Consensus       169 ---PElv~EVL~vm~~LA~e-GmTMivVTHE  195 (240)
T COG1126         169 ---PELVGEVLDVMKDLAEE-GMTMIIVTHE  195 (240)
T ss_pred             ---HHHHHHHHHHHHHHHHc-CCeEEEEech
Confidence               36788999999999997 7888888763

>PF13479 AAA_24: AAA domain

Probab=98.69  E-value=6.3e-07  Score=77.82  Aligned_cols=122  Identities=22%  Similarity=0.286  Sum_probs=76.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      +--++|+|+||+|||+|+..+              .+++||++|.....  +..                   ..+.-.+
T Consensus         3 ~~~~lIyG~~G~GKTt~a~~~--------------~k~l~id~E~g~~~--~~~-------------------~~~~~~i   47 (213)
T PF13479_consen    3 PIKILIYGPPGSGKTTLAASL--------------PKPLFIDTENGSDS--LKF-------------------LDDGDVI   47 (213)
T ss_pred             ceEEEEECCCCCCHHHHHHhC--------------CCeEEEEeCCCccc--hhh-------------------hcCCCee
Confidence            345899999999999999855              35899999985321  110                   0112223


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC---C-C-------C--CC---CCChHHHH-HHHHHHHHHHHH
Q 035774          182 QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG---V-H-------E--QR---APGQHPLS-WHISLITSLAEF  244 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~---~-~-------~--~~---~~r~~~~~-~i~~~Lk~la~~  244 (357)
                      +..+..++.+.+..+...  ..+.+.|||||++.+...   . .       .  +.   ...+..+. ++.+.++++.+.
T Consensus        48 ~i~s~~~~~~~~~~l~~~--~~~y~tiVIDsis~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yg~~~~~~~~~i~~l~~~  125 (213)
T PF13479_consen   48 PITSWEDFLEALDELEED--EADYDTIVIDSISWLEDMCLEYICRQNKKKIKRSGDPDYGKGYGELQQEFMRFIDKLLNA  125 (213)
T ss_pred             CcCCHHHHHHHHHHHHhc--cCCCCEEEEECHHHHHHHHHHHHhhhhcccccccCCCcccchHHHHHHHHHHHHHHHHHH
Confidence            344667777766655443  468999999999886322   0 0       0  01   11223333 344455556667


Q ss_pred             cCCeEEEeccccccCC
Q 035774          245 SRIPIVVTNQVRPQSH  260 (357)
Q Consensus       245 ~~~~vv~~~q~~~~~~  260 (357)
                      .+..||+|.|......
T Consensus       126 ~~~~VI~tah~~~~~~  141 (213)
T PF13479_consen  126 LGKNVIFTAHAKEEED  141 (213)
T ss_pred             CCCcEEEEEEEEEEEc
Confidence            9999999999876544

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=98.68  E-value=1.4e-07  Score=78.62  Aligned_cols=123  Identities=13%  Similarity=0.238  Sum_probs=68.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQ  182 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~  182 (357)
                      .+++|.|+||||||+||.+++...         +.+++|+++...++.+...++.....          .. ...+..+.
T Consensus         2 ~~ili~G~~~sGKS~~a~~l~~~~---------~~~~~~iat~~~~~~e~~~ri~~h~~----------~R-~~~w~t~E   61 (170)
T PRK05800          2 MLILVTGGARSGKSRFAERLAAQS---------GLQVLYIATAQPFDDEMAARIAHHRQ----------RR-PAHWQTVE   61 (170)
T ss_pred             CEEEEECCCCccHHHHHHHHHHHc---------CCCcEeCcCCCCChHHHHHHHHHHHh----------cC-CCCCeEec
Confidence            478999999999999999998653         25689999876655543333222100          01 12222222


Q ss_pred             CCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          183 PTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       183 ~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                      +.  .++...+.   ...  .+.++|+||+++.+.........  ...+...+..|.+..++.++++|+++.
T Consensus        62 ~~--~~l~~~i~---~~~--~~~~~VlID~Lt~~~~n~l~~~~--~~~~~~~l~~li~~L~~~~~tvVlVs~  124 (170)
T PRK05800         62 EP--LDLAELLR---ADA--APGRCVLVDCLTTWVTNLLFEEG--EEAIAAEIDALLAALQQLPAKIILVTN  124 (170)
T ss_pred             cc--ccHHHHHH---hhc--CCCCEEEehhHHHHHHHHhcccc--hHHHHHHHHHHHHHHHcCCCCEEEEEc
Confidence            21  12322222   111  24678999999998754321110  022233333344444457888777754

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

Probab=98.66  E-value=3.5e-07  Score=81.72  Aligned_cols=123  Identities=19%  Similarity=0.240  Sum_probs=83.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE-eCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV-LQP  183 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~-~~~  183 (357)
                      .+|+|+++.|||+++.+|....-...+.++...+|+++.+-...+..++....-.                 .+.. +.+
T Consensus        64 lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~-----------------~lgaP~~~  126 (302)
T PF05621_consen   64 LLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILE-----------------ALGAPYRP  126 (302)
T ss_pred             eEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHH-----------------HhCcccCC
Confidence            8999999999999999999866433222222358999998766666665432211                 1111 111


Q ss_pred             CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          184 TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       184 ~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                      .  ......-.++...++..+++++|||.+..+...       ...+-+++++.||.|..++++++|++.
T Consensus       127 ~--~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaG-------s~~~qr~~Ln~LK~L~NeL~ipiV~vG  187 (302)
T PF05621_consen  127 R--DRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAG-------SYRKQREFLNALKFLGNELQIPIVGVG  187 (302)
T ss_pred             C--CCHHHHHHHHHHHHHHcCCcEEEeechHHHhcc-------cHHHHHHHHHHHHHHhhccCCCeEEec
Confidence            1  122223334455667789999999999998765       234567799999999999999999884

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

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=98.60  E-value=5e-07  Score=77.82  Aligned_cols=44  Identities=14%  Similarity=0.175  Sum_probs=34.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .++++|+-|.-+.-.         ....-.+++..|+.++++.|.|||+++|-
T Consensus       159 ~~P~iilADEPTgnL---------D~~t~~~V~~ll~~~~~~~g~tii~VTHd  202 (226)
T COG1136         159 NNPKIILADEPTGNL---------DSKTAKEVLELLRELNKERGKTIIMVTHD  202 (226)
T ss_pred             cCCCeEEeeCccccC---------ChHHHHHHHHHHHHHHHhcCCEEEEEcCC
Confidence            478999999766433         22445568899999999999999999885

>COG1135 AbcC ABC-type metal ion transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.59  E-value=9.7e-07  Score=78.36  Aligned_cols=151  Identities=15%  Similarity=0.263  Sum_probs=88.2

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC--CCchHHHHHHHhccCchh
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES--TFTSRRMIEMGASSFPEI  164 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~--~~~~~rl~~~~~~~~~~~  164 (357)
                      .+..||.+--- +++|+++.|.|.+|+|||||..  +.|.+..+.     ..-++++...  .++...+++.. ......
T Consensus        18 ~~~al~~vsL~-I~~GeI~GIIG~SGAGKSTLiR--~iN~Le~Pt-----sG~v~v~G~di~~l~~~~Lr~~R-~~IGMI   88 (339)
T COG1135          18 TVTALDDVSLE-IPKGEIFGIIGYSGAGKSTLLR--LINLLERPT-----SGSVFVDGQDLTALSEAELRQLR-QKIGMI   88 (339)
T ss_pred             ceeeeccceEE-EcCCcEEEEEcCCCCcHHHHHH--HHhccCCCC-----CceEEEcCEecccCChHHHHHHH-hhccEE
Confidence            46678876443 9999999999999999999998  555655433     4466677643  22332333222 122222


Q ss_pred             hcccchH--HHhhcCeEE---eCCCCHHHHHHHHHHHHHHh--------------------------hhcCeeEEEEecc
Q 035774          165 FHSKGMA--QEMAGRILV---LQPTSLSEFTESLEKIKVSL--------------------------LQNQVKLLVIDSM  213 (357)
Q Consensus       165 ~~~~~~~--~~~~~~i~~---~~~~~~~~~~~~l~~l~~~~--------------------------~~~~~~lvvIDsl  213 (357)
                      |+...+.  ..+.+|+.+   ....+..+..+...++...+                          --.++++++.|..
T Consensus        89 FQhFnLLssrTV~~NvA~PLeiag~~k~ei~~RV~elLelVgL~dk~~~yP~qLSGGQKQRVaIARALa~~P~iLL~DEa  168 (339)
T COG1135          89 FQHFNLLSSRTVFENVAFPLELAGVPKAEIKQRVAELLELVGLSDKADRYPAQLSGGQKQRVAIARALANNPKILLCDEA  168 (339)
T ss_pred             eccccccccchHHhhhhhhHhhcCCCHHHHHHHHHHHHHHcCChhhhccCchhcCcchhhHHHHHHHHhcCCCEEEecCc
Confidence            2222111  112233322   11112222222222221111                          0246999999988


Q ss_pred             ccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          214 EALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       214 ~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ++-..+         +.-..++..|+.+.+++|+|||+++|-
T Consensus       169 TSALDP---------~TT~sIL~LL~~In~~lglTIvlITHE  201 (339)
T COG1135         169 TSALDP---------ETTQSILELLKDINRELGLTIVLITHE  201 (339)
T ss_pred             cccCCh---------HHHHHHHHHHHHHHHHcCCEEEEEech
Confidence            876544         556678999999999999999999984

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

Probab=98.55  E-value=1.6e-07  Score=74.80  Aligned_cols=124  Identities=23%  Similarity=0.242  Sum_probs=73.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeE
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL  179 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~  179 (357)
                      +.+.++.|.|+||+|||+++.+++.......... ...+++|++.........+.+....             .+    .
T Consensus         2 ~~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~i~~-------------~l----~   63 (131)
T PF13401_consen    2 QSQRILVISGPPGSGKTTLIKRLARQLNAEAEIK-NHPDVIYVNCPSSRTPRDFAQEILE-------------AL----G   63 (131)
T ss_dssp             -----EEEEE-TTSSHHHHHHHHHHHHHHHHHHC-CCEEEEEEEHHHHSSHHHHHHHHHH-------------HH----T
T ss_pred             CCCcccEEEcCCCCCHHHHHHHHHHHhHHhhhcc-CCCcEEEEEeCCCCCHHHHHHHHHH-------------Hh----C
Confidence            3567899999999999999999998775310000 0367888887543333333221111             00    0


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          180 VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       180 ~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ... ........+...+.+.+...+..+||||.+..+. .            ..++..|+.+..+.++.+|++.+.
T Consensus        64 ~~~-~~~~~~~~l~~~~~~~l~~~~~~~lviDe~~~l~-~------------~~~l~~l~~l~~~~~~~vvl~G~~  125 (131)
T PF13401_consen   64 LPL-KSRQTSDELRSLLIDALDRRRVVLLVIDEADHLF-S------------DEFLEFLRSLLNESNIKVVLVGTP  125 (131)
T ss_dssp             -SS-SSTS-HHHHHHHHHHHHHHCTEEEEEEETTHHHH-T------------HHHHHHHHHHTCSCBEEEEEEESS
T ss_pred             ccc-cccCCHHHHHHHHHHHHHhcCCeEEEEeChHhcC-C------------HHHHHHHHHHHhCCCCeEEEEECh
Confidence            000 0112333444566666667777899999999874 1            246777888888999999998754

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=98.54  E-value=2.1e-06  Score=74.15  Aligned_cols=122  Identities=20%  Similarity=0.204  Sum_probs=71.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      ...++|+|+||+|||++|.+++             .+.++++.+...  .++.   ..             ...+-+.+-
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~-------------~~~~~~~~d~~~--~~l~---g~-------------~~~~v~~~d   60 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLP-------------GKTLVLSFDMSS--KVLI---GD-------------ENVDIADHD   60 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcC-------------CCCEEEeccccc--hhcc---CC-------------CCCceeecC
Confidence            4679999999999999998663             457778887642  1210   00             000001111


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC--------CCCC--CCCChHHH-HHHHHHHHHHHHHcCCeEE
Q 035774          182 QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG--------VHEQ--RAPGQHPL-SWHISLITSLAEFSRIPIV  250 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~--------~~~~--~~~r~~~~-~~i~~~Lk~la~~~~~~vv  250 (357)
                      .+.+...+.+.+..+...  ..+.+.||||+++.+...        ...+  ....+..+ .++++.|+.|.. ++..||
T Consensus        61 ~~~~~~~~~d~l~~~~~~--~~~ydtVVIDsI~~l~~~~~~~~~r~~k~~~~~~~~yg~~~~~fl~~l~~L~~-~g~nII  137 (220)
T TIGR01618        61 DMPPIQAMVEFYVMQNIQ--AVKYDNIVIDNISALQNLWLENIGRAAKNGQPELQHYQKLDLWFLDLLTVLKE-SNKNIY  137 (220)
T ss_pred             CCCCHHHHHHHHHHHHhc--cccCCEEEEecHHHHHHHHHHHHhhhcCCCCcccccHHHHHHHHHHHHHHHHh-CCCcEE
Confidence            233445555555443322  356899999999988652        0000  11122222 245566666644 899999


Q ss_pred             Eeccccc
Q 035774          251 VTNQVRP  257 (357)
Q Consensus       251 ~~~q~~~  257 (357)
                      +++|...
T Consensus       138 ~tAhe~~  144 (220)
T TIGR01618       138 ATAWELT  144 (220)
T ss_pred             EEEeecc
Confidence            9999854

This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.54  E-value=1e-06  Score=70.33  Aligned_cols=121  Identities=24%  Similarity=0.292  Sum_probs=67.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      +..++|.||||+|||+++..++......      ...++|++.+............ .             ....  ...
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~-~-------------~~~~--~~~   59 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPP------GGGVIYIDGEDILEEVLDQLLL-I-------------IVGG--KKA   59 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCC------CCCEEEECCEEccccCHHHHHh-h-------------hhhc--cCC
Confidence            6789999999999999999999877531      1369999987643332221110 0             0000  000


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHH---HHHHHHHHHHcCCeEEEeccc
Q 035774          182 QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWH---ISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i---~~~Lk~la~~~~~~vv~~~q~  255 (357)
                       ....   ......+...+....+.+|+||.+..+.....       ......   ...+.......+..+|++++.
T Consensus        60 -~~~~---~~~~~~~~~~~~~~~~~viiiDei~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  125 (148)
T smart00382       60 -SGSG---ELRLRLALALARKLKPDVLILDEITSLLDAEQ-------EALLLLLEELRLLLLLKSEKNLTVILTTND  125 (148)
T ss_pred             -CCCH---HHHHHHHHHHHHhcCCCEEEEECCcccCCHHH-------HHHHHhhhhhHHHHHHHhcCCCEEEEEeCC
Confidence             0111   11122333333344579999999998765411       111000   123455556677888888764

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.

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=98.46  E-value=1.4e-06  Score=76.60  Aligned_cols=44  Identities=11%  Similarity=0.120  Sum_probs=35.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++....         ..--+++..+++++++.|.+||++.|-
T Consensus       155 Q~~~iLLLDEPTs~LDi---------~~Q~evl~ll~~l~~~~~~tvv~vlHD  198 (258)
T COG1120         155 QETPILLLDEPTSHLDI---------AHQIEVLELLRDLNREKGLTVVMVLHD  198 (258)
T ss_pred             cCCCEEEeCCCccccCH---------HHHHHHHHHHHHHHHhcCCEEEEEecC
Confidence            47899999998876543         233468999999999999999999874

>COG1127 Ttg2A ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=98.46  E-value=2.3e-06  Score=73.40  Aligned_cols=141  Identities=19%  Similarity=0.252  Sum_probs=79.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC--CchHHHHHHHhccCchhhcccchHHH--h
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST--FTSRRMIEMGASSFPEIFHSKGMAQE--M  174 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~--~~~~rl~~~~~~~~~~~~~~~~~~~~--~  174 (357)
                      +++|+++.|.|++|+|||+|...++-.  +++     ...-++|+.+.-  .+..++.++. .++.-.|+...+...  +
T Consensus        31 V~~Gei~~iiGgSGsGKStlLr~I~Gl--l~P-----~~GeI~i~G~~i~~ls~~~~~~ir-~r~GvlFQ~gALFssltV  102 (263)
T COG1127          31 VPRGEILAILGGSGSGKSTLLRLILGL--LRP-----DKGEILIDGEDIPQLSEEELYEIR-KRMGVLFQQGALFSSLTV  102 (263)
T ss_pred             ecCCcEEEEECCCCcCHHHHHHHHhcc--CCC-----CCCeEEEcCcchhccCHHHHHHHH-hheeEEeeccccccccch
Confidence            899999999999999999999988743  333     355778887752  2333333332 223333433322211  2


Q ss_pred             hcCeEEe----CCCCHHHHHHHH-HHH-------------HHHh-------------hhcCeeEEEEeccccccCCCCCC
Q 035774          175 AGRILVL----QPTSLSEFTESL-EKI-------------KVSL-------------LQNQVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       175 ~~~i~~~----~~~~~~~~~~~l-~~l-------------~~~~-------------~~~~~~lvvIDsl~~l~~~~~~~  223 (357)
                      .+|+.+.    ...+...+.++. .++             +..+             ..-++++++.|.-++=..+    
T Consensus       103 ~eNVafplre~~~lp~~~i~~lv~~KL~~VGL~~~~~~~~PsELSGGM~KRvaLARAialdPell~~DEPtsGLDP----  178 (263)
T COG1127         103 FENVAFPLREHTKLPESLIRELVLMKLELVGLRGAAADLYPSELSGGMRKRVALARAIALDPELLFLDEPTSGLDP----  178 (263)
T ss_pred             hHhhheehHhhccCCHHHHHHHHHHHHHhcCCChhhhhhCchhhcchHHHHHHHHHHHhcCCCEEEecCCCCCCCc----
Confidence            3344331    011111111111 001             0000             0236888898876654433    


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                           -..+.+-..++++.+..++|+++++|--
T Consensus       179 -----I~a~~~~~LI~~L~~~lg~T~i~VTHDl  206 (263)
T COG1127         179 -----ISAGVIDELIRELNDALGLTVIMVTHDL  206 (263)
T ss_pred             -----chHHHHHHHHHHHHHhhCCEEEEEECCh
Confidence                 3344567778888889999999998853

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

Probab=98.43  E-value=2.3e-06  Score=73.64  Aligned_cols=44  Identities=14%  Similarity=0.158  Sum_probs=36.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      -+++++|.|..++....         ..-.++++.|..+.++++.+.++++|-
T Consensus       158 ~~PklLIlDEptSaLD~---------siQa~IlnlL~~l~~~~~lt~l~IsHd  201 (252)
T COG1124         158 PEPKLLILDEPTSALDV---------SVQAQILNLLLELKKERGLTYLFISHD  201 (252)
T ss_pred             cCCCEEEecCchhhhcH---------HHHHHHHHHHHHHHHhcCceEEEEeCc
Confidence            46999999988876543         344568999999999999999999985

>COG0410 LivF ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]

Probab=98.41  E-value=3.2e-06  Score=72.16  Aligned_cols=139  Identities=22%  Similarity=0.281  Sum_probs=79.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC--CCchHHHHHHHhccCch---hhcccchHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES--TFTSRRMIEMGASSFPE---IFHSKGMAQE  173 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~--~~~~~rl~~~~~~~~~~---~~~~~~~~~~  173 (357)
                      +++|+++.|.|++|+||||++..++-  +.+..     ...+.++.++  ..++.+..+..-...++   .|..-.    
T Consensus        26 v~~Geiv~llG~NGaGKTTlLkti~G--l~~~~-----~G~I~~~G~dit~~p~~~r~r~Gi~~VPegR~iF~~LT----   94 (237)
T COG0410          26 VERGEIVALLGRNGAGKTTLLKTIMG--LVRPR-----SGRIIFDGEDITGLPPHERARLGIAYVPEGRRIFPRLT----   94 (237)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC--CCCCC-----CeeEEECCeecCCCCHHHHHhCCeEeCcccccchhhCc----
Confidence            78999999999999999999998874  33222     2345555443  22333333322222221   111100    


Q ss_pred             hhcCeEE----eC-----CCCHHHHHHHHHHHHHHhh--------------------hcCeeEEEEeccccccCCCCCCC
Q 035774          174 MAGRILV----LQ-----PTSLSEFTESLEKIKVSLL--------------------QNQVKLLVIDSMEALVPGVHEQR  224 (357)
Q Consensus       174 ~~~~i~~----~~-----~~~~~~~~~~l~~l~~~~~--------------------~~~~~lvvIDsl~~l~~~~~~~~  224 (357)
                      +.+|+.+    ..     ....+++.+++..+.....                    -.+++++++|.-+.=..+     
T Consensus        95 VeENL~~g~~~~~~~~~~~~~~e~v~~lFP~Lker~~~~aG~LSGGEQQMLAiaRALm~~PklLLLDEPs~GLaP-----  169 (237)
T COG0410          95 VEENLLLGAYARRDKEAQERDLEEVYELFPRLKERRNQRAGTLSGGEQQMLAIARALMSRPKLLLLDEPSEGLAP-----  169 (237)
T ss_pred             HHHHHhhhhhcccccccccccHHHHHHHChhHHHHhcCcccCCChHHHHHHHHHHHHhcCCCEEEecCCccCcCH-----
Confidence            1112211    00     0113333333333322211                    236999999987654433     


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                          ..+.++.+.++.+.++.+++|+++.|-..
T Consensus       170 ----~iv~~I~~~i~~l~~~~g~tIlLVEQn~~  198 (237)
T COG0410         170 ----KIVEEIFEAIKELRKEGGMTILLVEQNAR  198 (237)
T ss_pred             ----HHHHHHHHHHHHHHHcCCcEEEEEeccHH
Confidence                67888999999999998999999988543

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=98.39  E-value=5.1e-06  Score=72.77  Aligned_cols=43  Identities=14%  Similarity=0.070  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-..=..         ......+++.|+++.++ |++|++++|-
T Consensus       156 ~~p~lllLDEP~~gvD---------~~~~~~i~~lL~~l~~e-g~tIl~vtHD  198 (254)
T COG1121         156 QNPDLLLLDEPFTGVD---------VAGQKEIYDLLKELRQE-GKTVLMVTHD  198 (254)
T ss_pred             cCCCEEEecCCcccCC---------HHHHHHHHHHHHHHHHC-CCEEEEEeCC
Confidence            4799999997654322         24455688899999999 9999999985

>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.37  E-value=1.7e-05  Score=66.06  Aligned_cols=41  Identities=37%  Similarity=0.566  Sum_probs=32.3

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      -+|+|.++.|.||+|+|||||..-++.-.-       .+...++|+.-
T Consensus        23 ~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~-------~d~G~i~i~g~   63 (252)
T COG4604          23 DIPKGGITSIIGPNGAGKSTLLSMMSRLLK-------KDSGEITIDGL   63 (252)
T ss_pred             eecCCceeEEECCCCccHHHHHHHHHHhcc-------ccCceEEEeee
Confidence            389999999999999999999876555432       24668888864

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.35  E-value=1.2e-05  Score=70.46  Aligned_cols=45  Identities=16%  Similarity=0.139  Sum_probs=33.1

Q ss_pred             CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       204 ~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      +++++++|.-++...         .....+++..|+++.++.+.++|+++|-..
T Consensus       156 ~P~iliLDEPta~LD---------~~~~~~l~~~l~~L~~~~~~tii~~tHd~~  200 (235)
T COG1122         156 GPEILLLDEPTAGLD---------PKGRRELLELLKKLKEEGGKTIIIVTHDLE  200 (235)
T ss_pred             CCCEEEEcCCCCCCC---------HHHHHHHHHHHHHHHhcCCCeEEEEeCcHH
Confidence            466666666555443         355667889999999999999999988533

>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=98.34  E-value=1.8e-06  Score=68.52  Aligned_cols=107  Identities=25%  Similarity=0.308  Sum_probs=61.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPT  184 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  184 (357)
                      ++|.||||+|||+++..++...         +.++++++...-.+.                              ....
T Consensus         1 ill~G~~G~GKT~l~~~la~~l---------~~~~~~i~~~~~~~~------------------------------~~~~   41 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL---------GFPFIEIDGSELISS------------------------------YAGD   41 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT---------TSEEEEEETTHHHTS------------------------------STTH
T ss_pred             CEEECcCCCCeeHHHHHHHhhc---------ccccccccccccccc------------------------------cccc
Confidence            5799999999999999999875         366788877431100                              0000


Q ss_pred             CHHHHHHHHHHHHHHhhhcC-eeEEEEeccccccCCCCCCCCC--ChHHHHHHHHHHHHHHHH-cCCeEEEeccc
Q 035774          185 SLSEFTESLEKIKVSLLQNQ-VKLLVIDSMEALVPGVHEQRAP--GQHPLSWHISLITSLAEF-SRIPIVVTNQV  255 (357)
Q Consensus       185 ~~~~~~~~l~~l~~~~~~~~-~~lvvIDsl~~l~~~~~~~~~~--r~~~~~~i~~~Lk~la~~-~~~~vv~~~q~  255 (357)
                      ....+..++.+    ..... +.+++||.+..+.... .....  ....+..++..+...... .++.+|+++..
T Consensus        42 ~~~~i~~~~~~----~~~~~~~~vl~iDe~d~l~~~~-~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~  111 (132)
T PF00004_consen   42 SEQKIRDFFKK----AKKSAKPCVLFIDEIDKLFPKS-QPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNS  111 (132)
T ss_dssp             HHHHHHHHHHH----HHHTSTSEEEEEETGGGTSHHC-STSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESS
T ss_pred             ccccccccccc----ccccccceeeeeccchhccccc-ccccccccccccceeeecccccccccccceeEEeeCC
Confidence            11122233332    22334 7999999999998764 11111  112344455555554443 34677777654

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 ....

>COG3845 ABC-type uncharacterized transport systems, ATPase components [General function prediction only]

Probab=98.31  E-value=3.8e-06  Score=79.04  Aligned_cols=152  Identities=18%  Similarity=0.244  Sum_probs=86.9

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC-CCc-hHHHHHHHhc
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES-TFT-SRRMIEMGAS  159 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~-~~~-~~rl~~~~~~  159 (357)
                      .+++ |+..+|.+--. +++|++..|.|++|+|||||+.-+.  ...++     ...-+|++... .+. +....+..  
T Consensus        12 K~f~-~~~And~V~l~-v~~GeIHaLLGENGAGKSTLm~iL~--G~~~P-----~~GeI~v~G~~v~~~sP~dA~~~G--   80 (501)
T COG3845          12 KRFP-GVVANDDVSLS-VKKGEIHALLGENGAGKSTLMKILF--GLYQP-----DSGEIRVDGKEVRIKSPRDAIRLG--   80 (501)
T ss_pred             EEcC-CEEecCceeee-ecCCcEEEEeccCCCCHHHHHHHHh--CcccC-----CcceEEECCEEeccCCHHHHHHcC--
Confidence            3566 88888887543 9999999999999999999998554  33333     34567777643 111 11111111  


Q ss_pred             cCchhhcccchHH--HhhcCeEEeCCC------CHHHHHH----------------------------HHHHHHHHhhhc
Q 035774          160 SFPEIFHSKGMAQ--EMAGRILVLQPT------SLSEFTE----------------------------SLEKIKVSLLQN  203 (357)
Q Consensus       160 ~~~~~~~~~~~~~--~~~~~i~~~~~~------~~~~~~~----------------------------~l~~l~~~~~~~  203 (357)
                       ....++...+++  .+.+|+.+-...      +.....+                            .++-++.+  -.
T Consensus        81 -IGMVhQHF~Lv~~lTV~ENiiLg~e~~~~~~~~~~~~~~~i~~l~~~yGl~vdp~~~V~dLsVG~qQRVEIlKaL--yr  157 (501)
T COG3845          81 -IGMVHQHFMLVPTLTVAENIILGLEPSKGGLIDRRQARARIKELSERYGLPVDPDAKVADLSVGEQQRVEILKAL--YR  157 (501)
T ss_pred             -CcEEeeccccccccchhhhhhhcCccccccccCHHHHHHHHHHHHHHhCCCCCccceeecCCcchhHHHHHHHHH--hc
Confidence             111111100000  011222211110      1111111                            11111111  24


Q ss_pred             CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       204 ~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      +.+++|+|.-++...+         +++.+++..|++++++ |.+||+++|--.
T Consensus       158 ~a~iLILDEPTaVLTP---------~E~~~lf~~l~~l~~~-G~tIi~ITHKL~  201 (501)
T COG3845         158 GARLLILDEPTAVLTP---------QEADELFEILRRLAAE-GKTIIFITHKLK  201 (501)
T ss_pred             CCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHC-CCEEEEEeccHH
Confidence            7999999999988765         7888899999988886 999999998544

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=98.31  E-value=1.5e-05  Score=64.65  Aligned_cols=64  Identities=22%  Similarity=0.311  Sum_probs=45.8

Q ss_pred             CCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC--CCchHHHHH
Q 035774           84 LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES--TFTSRRMIE  155 (357)
Q Consensus        84 i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~--~~~~~rl~~  155 (357)
                      ..++-+-||.+--. +.+|+.+.|.||+|+|||+|..++|.-...       ....+||..|.  ...++.+++
T Consensus        12 ~a~~a~il~~isl~-v~~Ge~iaitGPSG~GKStllk~va~Lisp-------~~G~l~f~Ge~vs~~~pea~Rq   77 (223)
T COG4619          12 LAGDAKILNNISLS-VRAGEFIAITGPSGCGKSTLLKIVASLISP-------TSGTLLFEGEDVSTLKPEAYRQ   77 (223)
T ss_pred             hcCCCeeecceeee-ecCCceEEEeCCCCccHHHHHHHHHhccCC-------CCceEEEcCccccccChHHHHH
Confidence            44556667765433 899999999999999999999988865532       35688888774  334444443

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=98.31  E-value=1.8e-05  Score=66.29  Aligned_cols=37  Identities=32%  Similarity=0.422  Sum_probs=31.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.+.|+||+|||+++.+++......      +.++++++++.
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~------g~~v~~i~~D~   38 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK------GKKVLLVAADT   38 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC------CCcEEEEEcCC
Confidence            68899999999999999999887642      47899999875

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

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

Probab=98.29  E-value=1.5e-05  Score=66.09  Aligned_cols=120  Identities=20%  Similarity=0.250  Sum_probs=68.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      +++|+++.|.|++|+|||||+.-++..  .++.     ..-++++...- .......                 .....+
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~i~G~--~~~~-----~G~v~~~g~~~-~~~~~~~-----------------~~~~~i   77 (163)
T cd03216          23 VRRGEVHALLGENGAGKSTLMKILSGL--YKPD-----SGEILVDGKEV-SFASPRD-----------------ARRAGI   77 (163)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCC--CCCC-----CeEEEECCEEC-CcCCHHH-----------------HHhcCe
Confidence            889999999999999999999977643  2222     33456655321 1000000                 011123


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .++...+..+.. .+.-.+.+  -.+++++++|....-...         .....+...|++++++ +.++|+++|-.
T Consensus        78 ~~~~qLS~G~~q-rl~laral--~~~p~illlDEP~~~LD~---------~~~~~l~~~l~~~~~~-~~tiii~sh~~  142 (163)
T cd03216          78 AMVYQLSVGERQ-MVEIARAL--ARNARLLILDEPTAALTP---------AEVERLFKVIRRLRAQ-GVAVIFISHRL  142 (163)
T ss_pred             EEEEecCHHHHH-HHHHHHHH--hcCCCEEEEECCCcCCCH---------HHHHHHHHHHHHHHHC-CCEEEEEeCCH
Confidence            332223443332 22222222  247899999987654432         3344566777777654 88999988753

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.

>PF05625 PAXNEB: PAXNEB protein; InterPro: IPR008728 The RNA polymerase II elongator complex is a major histone acetyltransferase component of the RNA polymerase II (RNAPII) holoenzyme and is involved in transcriptional elongation [, ]

Probab=98.28  E-value=2.2e-05  Score=73.45  Aligned_cols=222  Identities=16%  Similarity=0.188  Sum_probs=109.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCC-cHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCc----------
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGT-GKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFT----------  149 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~Gs-GKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~----------  149 (357)
                      ..-++||+++||.+||||+|-|++++|.-..-+ ==..|+.-|+++.+..      +..+++++....+-          
T Consensus        27 ~~~~STG~~sLD~lLGGGlPlGs~llIeEd~~t~ya~~LlkyF~AEGi~~------~h~v~v~~~~~~~~~~LP~~~~~~  100 (363)
T PF05625_consen   27 QPLTSTGIPSLDDLLGGGLPLGSILLIEEDGTTDYASVLLKYFAAEGIVH------GHHVLVASPPEAWLRELPGPVSES  100 (363)
T ss_dssp             SEEE--S-HHHHHHTTSSEETT-EEEEEE-SS--THHHHHHHHHHHHHHH-------EEEEEE-S-GGGGGG-EEE----
T ss_pred             CEEEecCChhHHHHhcCCcccccEEEEecCCcCHHHHHHHHHHHHhcccc------CCeEEEEeCChHHHhhCCCccCcc
Confidence            346899999999999999999999999633212 1223445555555543      47788887632110          


Q ss_pred             ----------------hHHHHHHHhc-----------------cCchhhcccchH--HHhhcCeEEeCCCCH-----HHH
Q 035774          150 ----------------SRRMIEMGAS-----------------SFPEIFHSKGMA--QEMAGRILVLQPTSL-----SEF  189 (357)
Q Consensus       150 ----------------~~rl~~~~~~-----------------~~~~~~~~~~~~--~~~~~~i~~~~~~~~-----~~~  189 (357)
                                      ...+ +|+..                 .+...|+.....  ......+.++.....     ..+
T Consensus       101 ~~~~~~~~~~~~~~~~~~~m-KIAWRY~~~~~~~~~~~~~~~~~fcH~FDLsk~~~~~~~~~~~~~~~~~~~~~~~~~~~  179 (363)
T PF05625_consen  101 EKKEKKSKIAEESSESDEDM-KIAWRYEKLPKFQSSVGSSSYPNFCHQFDLSKRMDPEPLSAEIIFIPPDQPPSSSSSPY  179 (363)
T ss_dssp             ------------------------------------------TTSS--EETTSE-SS---TTTEEEE-TTS--------H
T ss_pred             hhccccccccccCCCCccCC-eeEeecccCccccccccCCcccccccccccccccChhhccccceEecCCCCcchhHHHH
Confidence                            0000 11111                 011112211111  011122222222211     234


Q ss_pred             HHHHHHHHHHhhh------cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHH--HcCCeEEEeccccccCCC
Q 035774          190 TESLEKIKVSLLQ------NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAE--FSRIPIVVTNQVRPQSHD  261 (357)
Q Consensus       190 ~~~l~~l~~~~~~------~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~--~~~~~vv~~~q~~~~~~~  261 (357)
                      ..++..+.+.+..      ..+-.|+|-++....+....  ......+-.++..|+.|.+  ..+++++++--..-  - 
T Consensus       180 ~~ll~~i~~~i~~~~~~~~~~v~RI~I~sl~SP~w~~~~--~~~~~~ll~FL~~LR~LlR~~~s~~v~~iTlP~~L--~-  254 (363)
T PF05625_consen  180 RSLLQQIQQIISKSGFSPPSKVLRIVIPSLGSPLWYPPS--ASQPSELLRFLHSLRALLRKYSSNAVAMITLPSHL--Y-  254 (363)
T ss_dssp             HHHHHHHHHHHHH----TTTSEEEEEETTTT-TTTS-GG--GGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEEGTT--S-
T ss_pred             HHHHHHHHHHHHhhccCCCCceEEEEEcCCCCcccCCcc--cccHHHHHHHHHHHHHHHhccCCCEEEEEEECHHH--h-
Confidence            5566666665543      36889999999987765322  2223468889999999999  44555555532111  0 


Q ss_pred             CCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-------------CeEEEEEEeCCCC----C-
Q 035774          262 ESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-------------GQRFMNVEKSPTS----P-  323 (357)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-------------~~R~l~v~K~r~~----~-  323 (357)
                                             .. .+.+-..|.+.+|+++.|+--.             ..=.++|.|.+..    + 
T Consensus       255 -----------------------~~-~~~~~~~l~~l~D~vi~Le~F~~~~~~~~~~~~~~~~Gll~v~KLp~~~sl~~~  310 (363)
T PF05625_consen  255 -----------------------PR-SPSLVRRLEHLADGVIELESFAGSMEKETNPPFKDYHGLLHVHKLPRLNSLGPM  310 (363)
T ss_dssp             ---------------------------HHHHHHHHHHSSEEEEEEE--HHHHHTTT-GGG---EEEEEEE-TTHHHHT--
T ss_pred             -----------------------cc-ChHHHHHHHHhCCEEEEeecCCCccccccCCcCcCCcEEEEEEEeccccccCCC
Confidence                                   00 1334456899999999997522             1357889997641    1 


Q ss_pred             ---CceeEEEEcCCCcee
Q 035774          324 ---PLAFSFTINPSGISL  338 (357)
Q Consensus       324 ---~~~~~f~I~~~Gi~~  338 (357)
                         .....|++...-+.+
T Consensus       311 ~~~~~~laFKl~Rkkf~I  328 (363)
T PF05625_consen  311 TPDSSDLAFKLKRKKFVI  328 (363)
T ss_dssp             --EEEEEEEEE-SS-EEE
T ss_pred             CCCccceEEEeeeeeEEE
Confidence               134566665544333

It may also play some role in wobble uridine tRNA modification []. This entry represents the ELP4 subunit. ELP4 is not required for the association of the complex with nascent RNA transcript, but is required for complex integrity and histone acetyltransferase activity. It is also required for an early step in synthesis of 5-methoxycarbonylmethyl (mcm5) and 5-carbamoylmethyl (ncm5) groups present on uridines at the wobble position in tRNA in yeast species.; GO: 0006357 regulation of transcription from RNA polymerase II promoter, 0033588 Elongator holoenzyme complex; PDB: 4EJS_A 4A8J_A.

>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=98.25  E-value=8.3e-06  Score=69.85  Aligned_cols=156  Identities=15%  Similarity=0.250  Sum_probs=85.7

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC--CchHHHHHHHhcc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST--FTSRRMIEMGASS  160 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~--~~~~rl~~~~~~~  160 (357)
                      ..|-|-..|+.+=-- |++|+++.|.|++|+|||||...+..  +....     ..-+++..++.  .....++++. ..
T Consensus        12 ~yp~~~~aL~~Vnl~-I~~GE~VaiIG~SGaGKSTLLR~lng--l~d~t-----~G~i~~~g~~i~~~~~k~lr~~r-~~   82 (258)
T COG3638          12 TYPGGHQALKDVNLE-INQGEMVAIIGPSGAGKSTLLRSLNG--LVDPT-----SGEILFNGVQITKLKGKELRKLR-RD   82 (258)
T ss_pred             ecCCCceeeeeEeEE-eCCCcEEEEECCCCCcHHHHHHHHhc--ccCCC-----cceEEecccchhccchHHHHHHH-Hh
Confidence            455677777776443 99999999999999999999997775  33222     34666666432  1222222222 12


Q ss_pred             CchhhcccchHHH--hhcCeE-----E-------eCCCCHHHHHHHHHHHHH------Hh-------------------h
Q 035774          161 FPEIFHSKGMAQE--MAGRIL-----V-------LQPTSLSEFTESLEKIKV------SL-------------------L  201 (357)
Q Consensus       161 ~~~~~~~~~~~~~--~~~~i~-----~-------~~~~~~~~~~~~l~~l~~------~~-------------------~  201 (357)
                      ....|+...++..  +..|+.     +       +..++.++-...++.+.+      ..                   -
T Consensus        83 iGmIfQ~~nLv~r~sv~~NVl~grl~~~s~~~slfglfsk~dk~~Al~aLervgi~~~A~qra~~LSGGQQQRVaIARaL  162 (258)
T COG3638          83 IGMIFQQFNLVPRLSVLENVLLGRLGYTSTWRSLFGLFSKEDKAQALDALERVGILDKAYQRASTLSGGQQQRVAIARAL  162 (258)
T ss_pred             ceeEeccCCcccccHHHHHHHhhhcccchHHHHHhCCCCHHHHHHHHHHHHHcCcHHHHHHHhccCCcchhHHHHHHHHH
Confidence            2222222211111  111111     1       111222222222222211      00                   0


Q ss_pred             hcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          202 QNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       202 ~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      -.++++|.-|.-.+-..+         .....+|..|++++++.|+|||+.-|..
T Consensus       163 ~Q~pkiILADEPvasLDp---------~~a~~Vm~~l~~in~~~g~Tvi~nLH~v  208 (258)
T COG3638         163 VQQPKIILADEPVASLDP---------ESAKKVMDILKDINQEDGITVIVNLHQV  208 (258)
T ss_pred             hcCCCEEecCCcccccCh---------hhHHHHHHHHHHHHHHcCCEEEEEechH
Confidence            236888888865543332         3445689999999999999999988753

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=98.24  E-value=8.6e-05  Score=68.90  Aligned_cols=93  Identities=19%  Similarity=0.255  Sum_probs=57.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCc--hHHHHHHHhccCchhhcccchHHHhhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFT--SRRMIEMGASSFPEIFHSKGMAQEMAG  176 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~--~~rl~~~~~~~~~~~~~~~~~~~~~~~  176 (357)
                      +.+|.++.|+||+|+||||++..++......      +.+|.+|+++..-.  .+.+...+.               .. 
T Consensus       203 ~~~~~ii~lvGptGvGKTTt~akLA~~l~~~------g~~V~lItaDtyR~gAveQLk~yae---------------~l-  260 (407)
T PRK12726        203 LSNHRIISLIGQTGVGKTTTLVKLGWQLLKQ------NRTVGFITTDTFRSGAVEQFQGYAD---------------KL-  260 (407)
T ss_pred             ecCCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEEeCCccCccHHHHHHHHhh---------------cC-
Confidence            4578999999999999999999999876532      47899999864211  122222111               11 


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccc
Q 035774          177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL  216 (357)
Q Consensus       177 ~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l  216 (357)
                      .+.+....++.++...+..+.   ...+.++|+||..+..
T Consensus       261 gvpv~~~~dp~dL~~al~~l~---~~~~~D~VLIDTAGr~  297 (407)
T PRK12726        261 DVELIVATSPAELEEAVQYMT---YVNCVDHILIDTVGRN  297 (407)
T ss_pred             CCCEEecCCHHHHHHHHHHHH---hcCCCCEEEEECCCCC
Confidence            122222345555544443322   1246899999987754

>PRK10867 signal recognition particle protein; Provisional

Probab=98.24  E-value=0.00011  Score=70.12  Aligned_cols=40  Identities=25%  Similarity=0.267  Sum_probs=33.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..++.++|++|+||||++..+|......  .   +.+|++++++.
T Consensus       100 p~vI~~vG~~GsGKTTtaakLA~~l~~~--~---G~kV~lV~~D~  139 (433)
T PRK10867        100 PTVIMMVGLQGAGKTTTAGKLAKYLKKK--K---KKKVLLVAADV  139 (433)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHh--c---CCcEEEEEccc
Confidence            4799999999999999999999877641  1   47899999875

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=98.23  E-value=0.00012  Score=69.91  Aligned_cols=40  Identities=25%  Similarity=0.167  Sum_probs=33.2

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +..++.++|++|+||||.+..+|.....   .   +.+|++++++.
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~L~~---~---g~kV~lV~~D~  133 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARYFKK---K---GLKVGLVAADT  133 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHH---c---CCeEEEecCCC
Confidence            3568999999999999999999987653   1   47899998864

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=98.21  E-value=1.9e-05  Score=66.65  Aligned_cols=136  Identities=19%  Similarity=0.256  Sum_probs=71.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC--CCchHHHHHHHhccCchhhcccchHHHhhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES--TFTSRRMIEMGASSFPEIFHSKGMAQEMAG  176 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~--~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~  176 (357)
                      +.+|+++.|.|++|+|||||+.-++..  .++.     ...++++...  ..+..+...... ..++......+. ...+
T Consensus        22 i~~G~~~~l~G~nGsGKStLl~~i~G~--~~~~-----~G~v~~~g~~~~~~~~~~~~~~i~-~~~q~l~~~gl~-~~~~   92 (180)
T cd03214          22 IEAGEIVGILGPNGAGKSTLLKTLAGL--LKPS-----SGEILLDGKDLASLSPKELARKIA-YVPQALELLGLA-HLAD   92 (180)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCC--CCCC-----CcEEEECCEECCcCCHHHHHHHHh-HHHHHHHHcCCH-hHhc
Confidence            889999999999999999999977643  2222     3345665432  112222211100 000000000000 0111


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       177 ~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      +  .....+..+. ..+.-.+..  -.+++++++|..+.-...         .....+.+.|++++++++.++|+++|-.
T Consensus        93 ~--~~~~LS~G~~-qrl~laral--~~~p~llllDEP~~~LD~---------~~~~~~~~~l~~~~~~~~~tiii~sh~~  158 (180)
T cd03214          93 R--PFNELSGGER-QRVLLARAL--AQEPPILLLDEPTSHLDI---------AHQIELLELLRRLARERGKTVVMVLHDL  158 (180)
T ss_pred             C--CcccCCHHHH-HHHHHHHHH--hcCCCEEEEeCCccCCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            1  0112233332 222222222  247899999987754432         3445677788888777789999998753


Q ss_pred             c
Q 035774          257 P  257 (357)
Q Consensus       257 ~  257 (357)
                      .
T Consensus       159 ~  159 (180)
T cd03214         159 N  159 (180)
T ss_pred             H
Confidence            3

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=98.20  E-value=9.8e-05  Score=66.42  Aligned_cols=41  Identities=24%  Similarity=0.161  Sum_probs=34.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .++.++.++|++|+||||.+.++|.....   .   +.+|++++++.
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~---~---g~~V~li~~D~  110 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKK---Q---GKSVLLAAGDT  110 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHh---c---CCEEEEEeCCC
Confidence            34679999999999999999999987753   1   47899999874

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.20  E-value=1.9e-05  Score=71.50  Aligned_cols=45  Identities=9%  Similarity=0.144  Sum_probs=34.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....++..|++++++.+.+||+++|-.
T Consensus       157 ~~p~lLlLDEPt~~LD~---------~~~~~l~~~l~~l~~~~g~tilivtH~~  201 (279)
T PRK13650        157 MRPKIIILDEATSMLDP---------EGRLELIKTIKGIRDDYQMTVISITHDL  201 (279)
T ss_pred             cCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            47899999987765432         4455678889999888899999998753

>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment

Probab=98.19  E-value=1.7e-05  Score=66.81  Aligned_cols=133  Identities=17%  Similarity=0.192  Sum_probs=70.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC--Cc--hHHHHHHHhccCchhhcccchH--H
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST--FT--SRRMIEMGASSFPEIFHSKGMA--Q  172 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~--~~--~~rl~~~~~~~~~~~~~~~~~~--~  172 (357)
                      +++|+++.|.|++|+|||||+.-++..  .+..     ..-++++...-  .+  ......    .....++.....  .
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G~--~~~~-----~G~i~~~g~~~~~~~~~~~~~~~----~i~~~~q~~~~~~~~   91 (178)
T cd03229          23 IEAGEIVALLGPSGSGKSTLLRCIAGL--EEPD-----SGSILIDGEDLTDLEDELPPLRR----RIGMVFQDFALFPHL   91 (178)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC--CCCC-----ceEEEECCEEccccchhHHHHhh----cEEEEecCCccCCCC
Confidence            789999999999999999999987743  2222     33455554321  11  111111    000000000000  0


Q ss_pred             HhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEe
Q 035774          173 EMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       173 ~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                      ...+++.+.  .+..+.. .+.-++..  -.+++++++|...+-...         .....+...|++++++++.++|++
T Consensus        92 t~~~~l~~~--lS~G~~q-r~~la~al--~~~p~llilDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tiii~  157 (178)
T cd03229          92 TVLENIALG--LSGGQQQ-RVALARAL--AMDPDVLLLDEPTSALDP---------ITRREVRALLKSLQAQLGITVVLV  157 (178)
T ss_pred             CHHHheeec--CCHHHHH-HHHHHHHH--HCCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEE
Confidence            112222221  2222221 11112222  247899999987654422         344557777888888778999999


Q ss_pred             cccc
Q 035774          253 NQVR  256 (357)
Q Consensus       253 ~q~~  256 (357)
                      +|-.
T Consensus       158 sH~~  161 (178)
T cd03229         158 THDL  161 (178)
T ss_pred             eCCH
Confidence            8753

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.

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=98.19  E-value=1e-05  Score=73.59  Aligned_cols=47  Identities=15%  Similarity=0.227  Sum_probs=36.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~  258 (357)
                      ++++++++|.-+.=..         .....++.+.|+.++++.+++|++++|....
T Consensus       153 ~~P~lliLDEPt~GLD---------p~~~~~~~~~l~~l~~~g~~tvlissH~l~e  199 (293)
T COG1131         153 HDPELLILDEPTSGLD---------PESRREIWELLRELAKEGGVTILLSTHILEE  199 (293)
T ss_pred             cCCCEEEECCCCcCCC---------HHHHHHHHHHHHHHHhCCCcEEEEeCCcHHH
Confidence            5789999998765433         2455678889999999988999999997553

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=98.19  E-value=3.4e-05  Score=64.66  Aligned_cols=128  Identities=15%  Similarity=0.175  Sum_probs=67.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC--CchHHHHHHHhccCchhhcccchH-HHhh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST--FTSRRMIEMGASSFPEIFHSKGMA-QEMA  175 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~--~~~~rl~~~~~~~~~~~~~~~~~~-~~~~  175 (357)
                      +++|+++.|.|++|+|||||+.-++...  ++.     ...++++.+.-  .+...+...    ....++..... ..+.
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~~l~G~~--~~~-----~G~i~~~g~~~~~~~~~~~~~~----i~~~~q~~~~~~~tv~   93 (173)
T cd03246          25 IEPGESLAIIGPSGSGKSTLARLILGLL--RPT-----SGRVRLDGADISQWDPNELGDH----VGYLPQDDELFSGSIA   93 (173)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHhcc--CCC-----CCeEEECCEEcccCCHHHHHhh----eEEECCCCccccCcHH
Confidence            7899999999999999999999777532  222     23455554321  111111111    00000000000 0111


Q ss_pred             cCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          176 GRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       176 ~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      +++     .+..+. +.+.-++..  -.+++++++|..+.-...         .....+...|+++++ .+.++|+++|-
T Consensus        94 ~~l-----LS~G~~-qrv~la~al--~~~p~~lllDEPt~~LD~---------~~~~~l~~~l~~~~~-~~~tii~~sh~  155 (173)
T cd03246          94 ENI-----LSGGQR-QRLGLARAL--YGNPRILVLDEPNSHLDV---------EGERALNQAIAALKA-AGATRIVIAHR  155 (173)
T ss_pred             HHC-----cCHHHH-HHHHHHHHH--hcCCCEEEEECCccccCH---------HHHHHHHHHHHHHHh-CCCEEEEEeCC
Confidence            111     222221 111111222  247899999987755432         334456677777765 48899998874

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

>COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=98.18  E-value=2e-05  Score=70.80  Aligned_cols=44  Identities=14%  Similarity=0.150  Sum_probs=34.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++|-|.-+.-.         ....-.++++.|+++.+++++++|+++|-
T Consensus       170 ~~P~LlIADEPTTAL---------Dvt~QaqIl~Ll~~l~~e~~~aiilITHD  213 (316)
T COG0444         170 LNPKLLIADEPTTAL---------DVTVQAQILDLLKELQREKGTALILITHD  213 (316)
T ss_pred             CCCCEEEeCCCcchh---------hHHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            468888888766433         22445678999999999999999999984

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=98.18  E-value=1.4e-05  Score=70.32  Aligned_cols=45  Identities=13%  Similarity=0.166  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       162 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~~g~tvii~sH~~  206 (233)
T PRK11629        162 NNPRLVLADEPTGNLDA---------RNADSIFQLLGELNRLQGTAFLVVTHDL  206 (233)
T ss_pred             cCCCEEEEeCCCCCCCH---------HHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            47899999987654432         3444577778888777789999998853

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=98.17  E-value=2.9e-05  Score=68.95  Aligned_cols=145  Identities=17%  Similarity=0.189  Sum_probs=73.2

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC---CCeEEEEeCCCCC-chHHHHHHHhccCchhhcccchHH
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL---DGGVIYIDVESTF-TSRRMIEMGASSFPEIFHSKGMAQ  172 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~---~~~vl~i~~e~~~-~~~rl~~~~~~~~~~~~~~~~~~~  172 (357)
                      |=+.+|+++.|.|++|+|||||+.-++.  ..++..|..   +..+.|+.-+... ....+.+.................
T Consensus        20 ~~i~~Ge~~~i~G~NGsGKSTLlk~L~G--~~~p~~G~i~~~g~~i~~~~q~~~~~~~~tv~e~l~~~~~~~~~~~~~~~   97 (246)
T cd03237          20 GSISESEVIGILGPNGIGKTTFIKMLAG--VLKPDEGDIEIELDTVSYKPQYIKADYEGTVRDLLSSITKDFYTHPYFKT   97 (246)
T ss_pred             CCcCCCCEEEEECCCCCCHHHHHHHHhC--CCcCCCCeEEECCceEEEecccccCCCCCCHHHHHHHHhhhccccHHHHH
Confidence            4488999999999999999999997764  323233211   1244454433211 111111111100000000000011


Q ss_pred             HhhcCeEE-------eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHc
Q 035774          173 EMAGRILV-------LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS  245 (357)
Q Consensus       173 ~~~~~i~~-------~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~  245 (357)
                      .+++.+-+       ....+..+. +.+.-++.+  -.+++++++|..++-...         .....+...|++++++.
T Consensus        98 ~~l~~l~l~~~~~~~~~~LSgGe~-qrv~iaraL--~~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~  165 (246)
T cd03237          98 EIAKPLQIEQILDREVPELSGGEL-QRVAIAACL--SKDADIYLLDEPSAYLDV---------EQRLMASKVIRRFAENN  165 (246)
T ss_pred             HHHHHcCCHHHhhCChhhCCHHHH-HHHHHHHHH--hcCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhc
Confidence            11111111       011122221 111111222  247899999988765533         33445777888888888


Q ss_pred             CCeEEEeccc
Q 035774          246 RIPIVVTNQV  255 (357)
Q Consensus       246 ~~~vv~~~q~  255 (357)
                      +.+||+++|-
T Consensus       166 ~~tiiivsHd  175 (246)
T cd03237         166 EKTAFVVEHD  175 (246)
T ss_pred             CCEEEEEeCC
Confidence            9999999885

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=98.17  E-value=0.0002  Score=67.97  Aligned_cols=39  Identities=26%  Similarity=0.277  Sum_probs=32.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..++.++|++|+||||++..+|.....   .   +.+|+.++++.
T Consensus       100 ~~vi~lvG~~GvGKTTtaaKLA~~l~~---~---G~kV~lV~~D~  138 (429)
T TIGR01425       100 QNVIMFVGLQGSGKTTTCTKLAYYYQR---K---GFKPCLVCADT  138 (429)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH---C---CCCEEEEcCcc
Confidence            469999999999999999999987653   1   47899998863

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.

>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=98.17  E-value=1.5e-05  Score=69.41  Aligned_cols=44  Identities=18%  Similarity=0.182  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-...         .....+.+.|++++++.+.+||+++|-
T Consensus       157 ~~p~lllLDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~sH~  200 (218)
T cd03255         157 NDPKIILADEPTGNLDS---------ETGKEVMELLRELNKEAGTTIVVVTHD  200 (218)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            47899999987755432         344557778888887779999999885

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.

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=98.16  E-value=1.6e-05  Score=69.33  Aligned_cols=45  Identities=16%  Similarity=0.121  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       158 ~~p~illlDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~tH~~  202 (221)
T TIGR02211       158 NQPSLVLADEPTGNLDN---------NNAKIIFDLMLELNRELNTSFLVVTHDL  202 (221)
T ss_pred             CCCCEEEEeCCCCcCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            47899999987654432         3444577788888887889999998753

This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina.

>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.16  E-value=2.6e-05  Score=70.64  Aligned_cols=45  Identities=11%  Similarity=0.152  Sum_probs=34.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|++++++++++||+++|-.
T Consensus       157 ~~p~lllLDEPt~gLD~---------~~~~~l~~~l~~l~~~~~~tilivsH~~  201 (279)
T PRK13635        157 LQPDIIILDEATSMLDP---------RGRREVLETVRQLKEQKGITVLSITHDL  201 (279)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHcCCCEEEEEecCH
Confidence            47899999987755432         3445677888888888899999998753

>PRK11701 phnK phosphonate C-P lyase system protein PhnK; Provisional

Probab=98.16  E-value=2.8e-05  Score=69.57  Aligned_cols=45  Identities=11%  Similarity=0.138  Sum_probs=33.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|+.++++++.+||+++|-.
T Consensus       168 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tii~isH~~  212 (258)
T PRK11701        168 THPRLVFMDEPTGGLDV---------SVQARLLDLLRGLVRELGLAVVIVTHDL  212 (258)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHhcCcEEEEEeCCH
Confidence            47899999987754432         3445677788888888899999998753

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=98.16  E-value=1.9e-05  Score=69.28  Aligned_cols=45  Identities=11%  Similarity=0.052  Sum_probs=33.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-+.-...         .....+...|++++++++.+||+++|-.
T Consensus       163 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~sH~~  207 (228)
T PRK10584        163 GRPDVLFADEPTGNLDR---------QTGDKIADLLFSLNREHGTTLILVTHDL  207 (228)
T ss_pred             cCCCEEEEeCCCCCCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            47899999987654432         3445677788888888899999998753

>PRK09473 oppD oligopeptide transporter ATP-binding component; Provisional

Probab=98.15  E-value=2.3e-05  Score=72.68  Aligned_cols=46  Identities=15%  Similarity=0.114  Sum_probs=35.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .++++++.|.-++-...         .....++..|+++.++++.++|+++|--.
T Consensus       178 ~~P~llilDEPts~LD~---------~~~~~i~~lL~~l~~~~g~til~iTHdl~  223 (330)
T PRK09473        178 CRPKLLIADEPTTALDV---------TVQAQIMTLLNELKREFNTAIIMITHDLG  223 (330)
T ss_pred             cCCCEEEEeCCCccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEECCHH
Confidence            47899999987765432         34456788889998889999999988643

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=98.15  E-value=1.3e-05  Score=69.65  Aligned_cols=45  Identities=7%  Similarity=0.010  Sum_probs=34.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+...|++++++.+.+||+++|-.
T Consensus       147 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tvi~~sH~~  191 (213)
T cd03301         147 REPKVFLMDEPLSNLDA---------KLRVQMRAELKRLQQRLGTTTIYVTHDQ  191 (213)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            47899999987755432         4455678888888888899999998853

ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.

>COG0411 LivG ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]

Probab=98.14  E-value=2.5e-06  Score=73.45  Aligned_cols=45  Identities=22%  Similarity=0.212  Sum_probs=36.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|...+=..         ..+..++...++++.++.+++|+++.|--
T Consensus       166 ~~P~lLLLDEPaAGln---------~~e~~~l~~~i~~i~~~~g~tillIEHdM  210 (250)
T COG0411         166 TQPKLLLLDEPAAGLN---------PEETEELAELIRELRDRGGVTILLIEHDM  210 (250)
T ss_pred             cCCCEEEecCccCCCC---------HHHHHHHHHHHHHHHhcCCcEEEEEEecc
Confidence            4799999998775443         36677788899999999999999998853

>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=98.14  E-value=3.3e-05  Score=65.98  Aligned_cols=93  Identities=22%  Similarity=0.274  Sum_probs=53.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQ  182 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~  182 (357)
                      .++.+.||+|+||||.+..+|+.....      +.+|.+++++. +......++..           +.+ .+ ++-++.
T Consensus         2 ~vi~lvGptGvGKTTt~aKLAa~~~~~------~~~v~lis~D~-~R~ga~eQL~~-----------~a~-~l-~vp~~~   61 (196)
T PF00448_consen    2 KVIALVGPTGVGKTTTIAKLAARLKLK------GKKVALISADT-YRIGAVEQLKT-----------YAE-IL-GVPFYV   61 (196)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT------T--EEEEEEST-SSTHHHHHHHH-----------HHH-HH-TEEEEE
T ss_pred             EEEEEECCCCCchHhHHHHHHHHHhhc------cccceeecCCC-CCccHHHHHHH-----------HHH-Hh-ccccch
Confidence            478999999999999999999988753      48899999864 33222222211           111 11 233332


Q ss_pred             CCCHHHHHHHHHHHHHHhhhcCeeEEEEecccc
Q 035774          183 PTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEA  215 (357)
Q Consensus       183 ~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~  215 (357)
                      ..+..+..+++.+........+.++|+||..+.
T Consensus        62 ~~~~~~~~~~~~~~l~~~~~~~~D~vlIDT~Gr   94 (196)
T PF00448_consen   62 ARTESDPAEIAREALEKFRKKGYDLVLIDTAGR   94 (196)
T ss_dssp             SSTTSCHHHHHHHHHHHHHHTTSSEEEEEE-SS
T ss_pred             hhcchhhHHHHHHHHHHHhhcCCCEEEEecCCc
Confidence            222222333333333334456789999998653

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 ....

>TIGR02314 ABC_MetN D-methionine ABC transporter, ATP-binding protein

Probab=98.14  E-value=2e-05  Score=73.19  Aligned_cols=46  Identities=11%  Similarity=0.145  Sum_probs=35.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .++++++.|..++-...         ..-..++..|++++++.+++||+++|-..
T Consensus       157 ~~P~iLLlDEPts~LD~---------~t~~~i~~lL~~l~~~~g~tiiliTH~~~  202 (343)
T TIGR02314       157 SNPKVLLCDEATSALDP---------ATTQSILELLKEINRRLGLTILLITHEMD  202 (343)
T ss_pred             hCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47899999987765432         44556788899999989999999988543

Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.

>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=98.13  E-value=2.9e-05  Score=62.26  Aligned_cols=40  Identities=25%  Similarity=0.341  Sum_probs=32.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+..+.|.|+||+|||+++..++......      +.+++|++...
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~~i~~~~~~~------~~~v~~~~~~~   57 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANELFRP------GAPFLYLNASD   57 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhhcC------CCCeEEEehhh
Confidence            46689999999999999999999877521      47788888754

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.

>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.13  E-value=3.1e-05  Score=69.75  Aligned_cols=45  Identities=9%  Similarity=0.161  Sum_probs=33.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       159 ~~p~lllLDEPt~~LD~---------~~~~~l~~~L~~~~~~~~~tiiivtH~~  203 (269)
T PRK13648        159 LNPSVIILDEATSMLDP---------DARQNLLDLVRKVKSEHNITIISITHDL  203 (269)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCc
Confidence            47899999987765432         3445577778888877789999998753

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=98.13  E-value=0.00014  Score=66.84  Aligned_cols=41  Identities=24%  Similarity=0.162  Sum_probs=34.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+|.++.+.|++|+||||++..+|......      +++|++++++.
T Consensus       112 ~~~~vi~lvGpnGsGKTTt~~kLA~~l~~~------g~~V~Li~~D~  152 (318)
T PRK10416        112 KKPFVILVVGVNGVGKTTTIGKLAHKYKAQ------GKKVLLAAGDT  152 (318)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhc------CCeEEEEecCc
Confidence            468999999999999999999999887631      47899888753

>TIGR00959 ffh signal recognition particle protein

Probab=98.12  E-value=0.00028  Score=67.28  Aligned_cols=40  Identities=28%  Similarity=0.366  Sum_probs=33.3

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      -.++.++|++|+||||++.++|......  .   +.+|++++++.
T Consensus        99 p~vi~~vG~~GsGKTTtaakLA~~l~~~--~---g~kV~lV~~D~  138 (428)
T TIGR00959        99 PTVILMVGLQGSGKTTTCGKLAYYLKKK--Q---GKKVLLVACDL  138 (428)
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHh--C---CCeEEEEeccc
Confidence            4699999999999999999999886421  1   47899999975

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.

>PRK13633 cobalt transporter ATP-binding subunit; Provisional

Probab=98.12  E-value=1.6e-05  Score=72.08  Aligned_cols=46  Identities=13%  Similarity=0.127  Sum_probs=34.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         .....+...|++++++.+++||+++|-..
T Consensus       161 ~~p~llllDEPt~gLD~---------~~~~~l~~~l~~l~~~~g~tillvtH~~~  206 (280)
T PRK13633        161 MRPECIIFDEPTAMLDP---------SGRREVVNTIKELNKKYGITIILITHYME  206 (280)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecChH
Confidence            46899999987755432         34455777888888878999999987543

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=98.11  E-value=1.6e-05  Score=67.76  Aligned_cols=26  Identities=35%  Similarity=0.510  Sum_probs=23.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        15 i~~Ge~~~i~G~nGsGKSTLl~~i~G   40 (190)
T TIGR01166        15 AERGEVLALLGANGAGKSTLLLHLNG   40 (190)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999986663

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.

>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.11  E-value=2.9e-05  Score=70.58  Aligned_cols=45  Identities=16%  Similarity=0.143  Sum_probs=33.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|+++.++.+.+||+++|-.
T Consensus       162 ~~p~illlDEPt~~LD~---------~~~~~l~~~l~~l~~~~g~tvl~vtH~~  206 (286)
T PRK13646        162 MNPDIIVLDEPTAGLDP---------QSKRQVMRLLKSLQTDENKTIILVSHDM  206 (286)
T ss_pred             hCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHHhCCCEEEEEecCH
Confidence            47899999987765432         3445677788888877899999998753

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

Probab=98.11  E-value=3.1e-05  Score=68.07  Aligned_cols=139  Identities=18%  Similarity=0.205  Sum_probs=83.3

Q ss_pred             chhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC--Cc----hHHHHHHHhccC
Q 035774           88 LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST--FT----SRRMIEMGASSF  161 (357)
Q Consensus        88 ~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~--~~----~~rl~~~~~~~~  161 (357)
                      +..+|.+=-- +.+|++..|.|++||||||++.-++.-.  .+     ..+.+||+...-  ++    .+++.+++... 
T Consensus        26 v~avd~Vsf~-i~~ge~~glVGESG~GKSTlgr~i~~L~--~p-----t~G~i~f~g~~i~~~~~~~~~~~v~elL~~V-   96 (268)
T COG4608          26 VKAVDGVSFS-IKEGETLGLVGESGCGKSTLGRLILGLE--EP-----TSGEILFEGKDITKLSKEERRERVLELLEKV-   96 (268)
T ss_pred             eEEecceeEE-EcCCCEEEEEecCCCCHHHHHHHHHcCc--CC-----CCceEEEcCcchhhcchhHHHHHHHHHHHHh-
Confidence            4566765433 8999999999999999999999777432  22     245677775431  11    12233333210 


Q ss_pred             chhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHH
Q 035774          162 PEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSL  241 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~l  241 (357)
                             ......+.+  +....+..+. +.+.-.+..  .-+++++|.|-..+....         ..-.++++.|+.+
T Consensus        97 -------gl~~~~~~r--yPhelSGGQr-QRi~IARAL--al~P~liV~DEpvSaLDv---------SiqaqIlnLL~dl  155 (268)
T COG4608          97 -------GLPEEFLYR--YPHELSGGQR-QRIGIARAL--ALNPKLIVADEPVSALDV---------SVQAQILNLLKDL  155 (268)
T ss_pred             -------CCCHHHhhc--CCcccCchhh-hhHHHHHHH--hhCCcEEEecCchhhcch---------hHHHHHHHHHHHH
Confidence                   011111111  1112233332 222222222  247999999998877643         3334688899999


Q ss_pred             HHHcCCeEEEecccc
Q 035774          242 AEFSRIPIVVTNQVR  256 (357)
Q Consensus       242 a~~~~~~vv~~~q~~  256 (357)
                      .++++++.++++|--
T Consensus       156 q~~~~lt~lFIsHDL  170 (268)
T COG4608         156 QEELGLTYLFISHDL  170 (268)
T ss_pred             HHHhCCeEEEEEEEH
Confidence            999999999999853

>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.10  E-value=3e-05  Score=70.44  Aligned_cols=46  Identities=17%  Similarity=0.170  Sum_probs=34.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..+.-...         .....+...|++++++.+.+||+++|-..
T Consensus       158 ~~p~lLilDEPt~gLD~---------~~~~~l~~~l~~l~~~~g~tillvsH~~~  203 (283)
T PRK13636        158 MEPKVLVLDEPTAGLDP---------MGVSEIMKLLVEMQKELGLTIIIATHDID  203 (283)
T ss_pred             cCCCEEEEeCCccCCCH---------HHHHHHHHHHHHHHHhCCCEEEEEecCHH
Confidence            47899999987765432         34456778888888888999999987533

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=98.10  E-value=3.4e-05  Score=64.64  Aligned_cols=129  Identities=16%  Similarity=0.157  Sum_probs=67.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch-HHHHHHHhccCchhhcccchH--HHhh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS-RRMIEMGASSFPEIFHSKGMA--QEMA  175 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~-~rl~~~~~~~~~~~~~~~~~~--~~~~  175 (357)
                      +++|+++.|.|++|+|||||+.-++..  .++.     ..-++++.+..... ...++    .....++.....  ....
T Consensus        23 i~~Ge~~~i~G~nGsGKStLl~~l~G~--~~~~-----~G~i~~~g~~~~~~~~~~~~----~i~~~~q~~~~~~~~tv~   91 (173)
T cd03230          23 VEKGEIYGLLGPNGAGKTTLIKIILGL--LKPD-----SGEIKVLGKDIKKEPEEVKR----RIGYLPEEPSLYENLTVR   91 (173)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC--CCCC-----CeEEEECCEEcccchHhhhc----cEEEEecCCccccCCcHH
Confidence            789999999999999999999977643  2222     33455554321110 11111    000000100000  0011


Q ss_pred             cCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          176 GRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       176 ~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      +++.    .+..+. ..+.-.+..  -.+++++++|..++-...         .....+.+.|++++++ +.++|+++|-
T Consensus        92 ~~~~----LS~G~~-qrv~laral--~~~p~illlDEPt~~LD~---------~~~~~l~~~l~~~~~~-g~tiii~th~  154 (173)
T cd03230          92 ENLK----LSGGMK-QRLALAQAL--LHDPELLILDEPTSGLDP---------ESRREFWELLRELKKE-GKTILLSSHI  154 (173)
T ss_pred             HHhh----cCHHHH-HHHHHHHHH--HcCCCEEEEeCCccCCCH---------HHHHHHHHHHHHHHHC-CCEEEEECCC
Confidence            1111    122221 111111222  247999999987765432         3445577788888776 8899998875

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=98.10  E-value=1.7e-05  Score=66.55  Aligned_cols=25  Identities=24%  Similarity=0.497  Sum_probs=22.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+++.|.||+|+|||||...++
T Consensus        18 i~~G~~~~l~G~nG~GKSTLl~~il   42 (176)
T cd03238          18 IPLNVLVVVTGVSGSGKSTLVNEGL   42 (176)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHh
Confidence            8899999999999999999998653

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.

>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.09  E-value=2e-05  Score=71.79  Aligned_cols=46  Identities=13%  Similarity=0.092  Sum_probs=35.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..++-...         .....+.+.|+.++++.+.+||+++|-..
T Consensus       162 ~~P~llllDEPt~~LD~---------~~~~~l~~~L~~l~~~~g~tviiitHd~~  207 (290)
T PRK13634        162 MEPEVLVLDEPTAGLDP---------KGRKEMMEMFYKLHKEKGLTTVLVTHSME  207 (290)
T ss_pred             cCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47999999987765432         44556788889998888999999988533

>cd03298 ABC_ThiQ_thiamine_transporter ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP

Probab=98.09  E-value=3.6e-05  Score=66.71  Aligned_cols=45  Identities=11%  Similarity=0.152  Sum_probs=33.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+++||+++|-.
T Consensus       145 ~~p~llllDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~sH~~  189 (211)
T cd03298         145 RDKPVLLLDEPFAALDP---------ALRAEMLDLVLDLHAETKMTVLMVTHQP  189 (211)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            47899999987765432         3344577788888888899999998853

Probably responsible for the translocation of thiamine across the membrane. 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.

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=98.09  E-value=4.4e-05  Score=64.06  Aligned_cols=111  Identities=22%  Similarity=0.094  Sum_probs=64.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      +++|+++.|.|++|+|||||+.-++..  .++.     ...++++...         +.  ..   .+          ..
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl--~~p~-----~G~i~~~g~~---------i~--~~---~q----------~~   70 (177)
T cd03222          22 VKEGEVIGIVGPNGTGKTTAVKILAGQ--LIPN-----GDNDEWDGIT---------PV--YK---PQ----------YI   70 (177)
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcC--CCCC-----CcEEEECCEE---------EE--EE---cc----------cC
Confidence            799999999999999999999976643  2222     2234443311         00  00   00          00


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .    .+..+- +.+.-.+..  -.+++++++|..++-...         .....+...|++++++.+.+||+++|-.
T Consensus        71 ~----LSgGq~-qrv~laral--~~~p~lllLDEPts~LD~---------~~~~~l~~~l~~~~~~~~~tiiivsH~~  132 (177)
T cd03222          71 D----LSGGEL-QRVAIAAAL--LRNATFYLFDEPSAYLDI---------EQRLNAARAIRRLSEEGKKTALVVEHDL  132 (177)
T ss_pred             C----CCHHHH-HHHHHHHHH--hcCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHHcCCCEEEEEECCH
Confidence            0    222221 222222222  246899999987655432         3344567777777776558999998853

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.

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=98.09  E-value=6.4e-05  Score=61.87  Aligned_cols=120  Identities=22%  Similarity=0.258  Sum_probs=69.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      +++|+++.|.|++|+|||+|+..++..  .+.     ...-++++.+...... ..                  .....+
T Consensus        22 i~~g~~~~i~G~nGsGKStll~~l~g~--~~~-----~~G~i~~~~~~~~~~~-~~------------------~~~~~i   75 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLRAIAGL--LKP-----TSGEILIDGKDIAKLP-LE------------------ELRRRI   75 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC--CCC-----CccEEEECCEEcccCC-HH------------------HHHhce
Confidence            789999999999999999999977643  222     2345666654311100 00                  111223


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+....+..+.. .+.-.+..+  .+++++++|....-...         .....+.+.|+.+.+. +.++++++|-..
T Consensus        76 ~~~~qlS~G~~~-r~~l~~~l~--~~~~i~ilDEp~~~lD~---------~~~~~l~~~l~~~~~~-~~tii~~sh~~~  141 (157)
T cd00267          76 GYVPQLSGGQRQ-RVALARALL--LNPDLLLLDEPTSGLDP---------ASRERLLELLRELAEE-GRTVIIVTHDPE  141 (157)
T ss_pred             EEEeeCCHHHHH-HHHHHHHHh--cCCCEEEEeCCCcCCCH---------HHHHHHHHHHHHHHHC-CCEEEEEeCCHH
Confidence            332223433322 122222222  36899999987754432         3344566777777665 789999987643

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.

>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin

Probab=98.09  E-value=3.3e-05  Score=67.38  Aligned_cols=44  Identities=16%  Similarity=0.154  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+...|++++++++.+||+++|-
T Consensus       148 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tvi~~tH~  191 (220)
T cd03265         148 HRPEVLFLDEPTIGLDP---------QTRAHVWEYIEKLKEEFGMTILLTTHY  191 (220)
T ss_pred             cCCCEEEEcCCccCCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            47899999987755432         344557778888888889999999875

In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=98.09  E-value=4.3e-05  Score=66.19  Aligned_cols=26  Identities=31%  Similarity=0.480  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        24 i~~G~~~~l~G~nGsGKSTLl~~l~G   49 (211)
T cd03225          24 IKKGEFVLIVGPNGSGKSTLLRLLNG   49 (211)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997764

The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=98.09  E-value=8.3e-05  Score=64.54  Aligned_cols=52  Identities=31%  Similarity=0.395  Sum_probs=37.0

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +-..+|++--- ++.|+++++.||+||||||++.-+- ....+      ...-++|+.+.
T Consensus        13 ~~~av~~v~l~-I~~gef~vliGpSGsGKTTtLkMIN-rLiep------t~G~I~i~g~~   64 (309)
T COG1125          13 NKKAVDDVNLT-IEEGEFLVLIGPSGSGKTTTLKMIN-RLIEP------TSGEILIDGED   64 (309)
T ss_pred             CceeeeeeeEE-ecCCeEEEEECCCCCcHHHHHHHHh-cccCC------CCceEEECCee
Confidence            44455665333 8999999999999999999987433 33322      35578888875

>TIGR03415 ABC_choXWV_ATP choline ABC transporter, ATP-binding protein

Probab=98.08  E-value=2.4e-05  Score=73.59  Aligned_cols=46  Identities=9%  Similarity=-0.024  Sum_probs=34.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|...+-...         ..-.++.+.|.++.++++.++|+++|--.
T Consensus       181 ~~P~ILLlDEPts~LD~---------~~r~~l~~~L~~l~~~~~~TII~iTHdl~  226 (382)
T TIGR03415       181 MDADILLMDEPFSALDP---------LIRTQLQDELLELQAKLNKTIIFVSHDLD  226 (382)
T ss_pred             cCCCEEEEECCCccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47899999977654432         34456777888888888999999988644

Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines.

>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit

Probab=98.08  E-value=2.1e-05  Score=73.63  Aligned_cols=46  Identities=11%  Similarity=0.008  Sum_probs=33.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|...+-...         ..-..+...|.++.++.+.|||+++|-..
T Consensus       146 ~~p~iLLlDEP~saLD~---------~~r~~l~~~l~~l~~~~~~Tii~vTHd~~  191 (363)
T TIGR01186       146 AEPDILLMDEAFSALDP---------LIRDSMQDELKKLQATLQKTIVFITHDLD  191 (363)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47899999976654322         34455777788888888999999988654

This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. 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. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lact

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=98.08  E-value=3.4e-05  Score=64.95  Aligned_cols=131  Identities=14%  Similarity=0.102  Sum_probs=67.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchH-HHhhcC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMA-QEMAGR  177 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~-~~~~~~  177 (357)
                      +++|+++.|.|++|+|||||+..++...  ++.     ...++++... ..  .............++...+. ....++
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~~l~G~~--~~~-----~G~i~~~g~~-~~--~~~~~~~~~i~~~~q~~~~~~~tv~~~   94 (178)
T cd03247          25 LKQGEKIALLGRSGSGKSTLLQLLTGDL--KPQ-----QGEITLDGVP-VS--DLEKALSSLISVLNQRPYLFDTTLRNN   94 (178)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhccC--CCC-----CCEEEECCEE-HH--HHHHHHHhhEEEEccCCeeecccHHHh
Confidence            8899999999999999999999887543  222     2345565532 11  11100111000000000000 011122


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      +  ....+..+. +.+.-.+..  -.+++++++|..++-...         .....+.+.|++++ + +.+||+++|-
T Consensus        95 i--~~~LS~G~~-qrv~laral--~~~p~~lllDEP~~~LD~---------~~~~~l~~~l~~~~-~-~~tii~~sh~  156 (178)
T cd03247          95 L--GRRFSGGER-QRLALARIL--LQDAPIVLLDEPTVGLDP---------ITERQLLSLIFEVL-K-DKTLIWITHH  156 (178)
T ss_pred             h--cccCCHHHH-HHHHHHHHH--hcCCCEEEEECCcccCCH---------HHHHHHHHHHHHHc-C-CCEEEEEecC
Confidence            2  112222222 111112222  257899999987765432         33445666777764 3 7899988875

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.

>TIGR01184 ntrCD nitrate transport ATP-binding subunits C and D

Probab=98.07  E-value=3.1e-05  Score=68.09  Aligned_cols=44  Identities=11%  Similarity=0.083  Sum_probs=33.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-
T Consensus       131 ~~p~lllLDEPt~gLD~---------~~~~~l~~~l~~~~~~~~~tii~~sH~  174 (230)
T TIGR01184       131 IRPKVLLLDEPFGALDA---------LTRGNLQEELMQIWEEHRVTVLMVTHD  174 (230)
T ss_pred             cCCCEEEEcCCCcCCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            47899999987755432         344567788888888889999999885

This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase.

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=98.07  E-value=3.5e-05  Score=67.99  Aligned_cols=45  Identities=9%  Similarity=0.127  Sum_probs=33.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.++|+++|-.
T Consensus       149 ~~p~llllDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tiii~sH~~  193 (236)
T TIGR03864       149 HRPALLLLDEPTVGLDP---------ASRAAIVAHVRALCRDQGLSVLWATHLV  193 (236)
T ss_pred             cCCCEEEEcCCccCCCH---------HHHHHHHHHHHHHHHhCCCEEEEEecCh
Confidence            47899999987654432         3445677888888877789999998753

Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification.

>PRK11022 dppD dipeptide transporter ATP-binding subunit; Provisional

Probab=98.07  E-value=4.1e-05  Score=70.91  Aligned_cols=46  Identities=17%  Similarity=0.164  Sum_probs=35.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .++++++.|..++-...         ....++++.|+.+.++.+.++|+++|--.
T Consensus       170 ~~P~llilDEPts~LD~---------~~~~~il~lL~~l~~~~g~til~iTHdl~  215 (326)
T PRK11022        170 CRPKLLIADEPTTALDV---------TIQAQIIELLLELQQKENMALVLITHDLA  215 (326)
T ss_pred             hCCCEEEEeCCCCCCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47899999987765432         44456788899998888999999988643

>PRK13652 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.07  E-value=2.3e-05  Score=70.92  Aligned_cols=46  Identities=15%  Similarity=0.199  Sum_probs=33.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..+.-...         .....+.+.|++++++++++||+++|-..
T Consensus       154 ~~p~llilDEPt~gLD~---------~~~~~l~~~l~~l~~~~g~tvli~tH~~~  199 (277)
T PRK13652        154 MEPQVLVLDEPTAGLDP---------QGVKELIDFLNDLPETYGMTVIFSTHQLD  199 (277)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCHH
Confidence            47899999987754432         33445777888888888999999987533

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=98.06  E-value=4.8e-05  Score=67.38  Aligned_cols=44  Identities=14%  Similarity=0.170  Sum_probs=32.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..+.-...         .....+...|++++++.+.+||+++|-
T Consensus       148 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~g~tii~~sH~  191 (241)
T PRK14250        148 NNPEVLLLDEPTSALDP---------TSTEIIEELIVKLKNKMNLTVIWITHN  191 (241)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhCCCEEEEEecc
Confidence            47899999987755432         334457778888888779999999875

>PRK11308 dppF dipeptide transporter ATP-binding subunit; Provisional

Probab=98.06  E-value=4.1e-05  Score=70.85  Aligned_cols=46  Identities=11%  Similarity=0.041  Sum_probs=35.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++|.|..++-...         .....+++.|+++.++.++++|+++|--.
T Consensus       171 ~~P~lLilDEPts~LD~---------~~~~~i~~lL~~l~~~~g~til~iTHdl~  216 (327)
T PRK11308        171 LDPDVVVADEPVSALDV---------SVQAQVLNLMMDLQQELGLSYVFISHDLS  216 (327)
T ss_pred             cCCCEEEEECCCccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            46899999988765532         34456788899998889999999988643

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=98.06  E-value=2.7e-05  Score=68.92  Aligned_cols=44  Identities=18%  Similarity=0.194  Sum_probs=33.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-
T Consensus       161 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~tH~  204 (241)
T cd03256         161 QQPKLILADEPVASLDP---------ASSRQVMDLLKRINREEGITVIVSLHQ  204 (241)
T ss_pred             cCCCEEEEeCccccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            47899999987755432         445567788888888789999999875

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. 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.

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=98.05  E-value=3.1e-05  Score=71.08  Aligned_cols=34  Identities=32%  Similarity=0.289  Sum_probs=27.4

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .|+.+-- -+++|+++.|.||+|+|||||+..++.
T Consensus        22 ~l~~vsl-~i~~Gei~gllGpNGaGKSTLl~~l~G   55 (306)
T PRK13537         22 VVDGLSF-HVQRGECFGLLGPNGAGKTTTLRMLLG   55 (306)
T ss_pred             EEecceE-EEeCCcEEEEECCCCCCHHHHHHHHhc
Confidence            4444422 388999999999999999999998774

>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=98.05  E-value=4.8e-05  Score=67.07  Aligned_cols=44  Identities=18%  Similarity=0.055  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-
T Consensus       153 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tvi~vsH~  196 (235)
T cd03261         153 LDPELLLYDEPTAGLDP---------IASGVIDDLIRSLKKELGLTSIMVTHD  196 (235)
T ss_pred             cCCCEEEecCCcccCCH---------HHHHHHHHHHHHHHHhcCcEEEEEecC
Confidence            47899999987755432         344557778888887778999999875

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.

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=98.05  E-value=5.7e-05  Score=72.92  Aligned_cols=44  Identities=16%  Similarity=0.148  Sum_probs=36.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .++++||.|...+....         .....+++.|+++.+++|++.++++|-
T Consensus       446 ~~P~lli~DEp~SaLDv---------svqa~VlnLl~~lq~e~g~t~lfISHD  489 (539)
T COG1123         446 LEPKLLILDEPVSALDV---------SVQAQVLNLLKDLQEELGLTYLFISHD  489 (539)
T ss_pred             cCCCEEEecCCccccCH---------HHHHHHHHHHHHHHHHhCCEEEEEeCC
Confidence            36999999987765433         556678999999999999999999985

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=98.05  E-value=4.9e-05  Score=65.67  Aligned_cols=26  Identities=31%  Similarity=0.455  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G   50 (207)
T PRK13539         25 LAAGEALVLTGPNGSGKTTLLRLIAG   50 (207)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999987764

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=98.04  E-value=3.6e-05  Score=66.38  Aligned_cols=26  Identities=23%  Similarity=0.501  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++-
T Consensus        21 i~~Ge~~~i~G~nGsGKSTLl~~l~G   46 (206)
T TIGR03608        21 IEKGKMYAIIGESGSGKSTLLNIIGL   46 (206)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999999997774

A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.

>PRK10070 glycine betaine transporter ATP-binding subunit; Provisional

Probab=98.04  E-value=2.7e-05  Score=73.80  Aligned_cols=46  Identities=11%  Similarity=-0.012  Sum_probs=33.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|...+-...         .....+...|+++.++.+.+||+++|-..
T Consensus       181 ~~P~iLLLDEPts~LD~---------~~r~~l~~~L~~l~~~~g~TIIivTHd~~  226 (400)
T PRK10070        181 INPDILLMDEAFSALDP---------LIRTEMQDELVKLQAKHQRTIVFISHDLD  226 (400)
T ss_pred             cCCCEEEEECCCccCCH---------HHHHHHHHHHHHHHHHCCCeEEEEECCHH
Confidence            47899999987654432         34445777788888888999999988644

>cd03294 ABC_Pro_Gly_Bertaine This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea

Probab=98.03  E-value=3.3e-05  Score=69.63  Aligned_cols=44  Identities=11%  Similarity=-0.029  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-...         .....+...|+.++++.+.+||+++|-
T Consensus       177 ~~p~illLDEPt~~LD~---------~~~~~l~~~l~~~~~~~g~tiii~tH~  220 (269)
T cd03294         177 VDPDILLMDEAFSALDP---------LIRREMQDELLRLQAELQKTIVFITHD  220 (269)
T ss_pred             cCCCEEEEcCCCccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            47899999987654432         445567778888887778999999885

This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. 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.

>TIGR01188 drrA daunorubicin resistance ABC transporter ATP-binding subunit

Probab=98.03  E-value=5.4e-05  Score=69.42  Aligned_cols=45  Identities=18%  Similarity=0.146  Sum_probs=32.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-+.-...         .....+...|++++++ +.+||+++|-..
T Consensus       141 ~~p~lllLDEPt~gLD~---------~~~~~l~~~l~~~~~~-g~tvi~~sH~~~  185 (302)
T TIGR01188       141 HQPDVLFLDEPTTGLDP---------RTRRAIWDYIRALKEE-GVTILLTTHYME  185 (302)
T ss_pred             cCCCEEEEeCCCcCCCH---------HHHHHHHHHHHHHHhC-CCEEEEECCCHH
Confidence            47999999987765432         3344567777887755 899999998644

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.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=98.03  E-value=3.6e-05  Score=66.77  Aligned_cols=44  Identities=11%  Similarity=0.031  Sum_probs=33.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-...         .....+.+.|++++++.+.+||+++|-
T Consensus       147 ~~p~~lllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~sH~  190 (213)
T cd03259         147 REPSLLLLDEPLSALDA---------KLREELREELKELQRELGITTIYVTHD  190 (213)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEecC
Confidence            47899999987755432         344567788888888779999999885

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=98.03  E-value=6e-05  Score=65.12  Aligned_cols=26  Identities=31%  Similarity=0.396  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G   48 (208)
T cd03268          23 VKKGEIYGFLGPNGAGKTTTMKIILG   48 (208)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999998774

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.

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=98.03  E-value=3.5e-05  Score=68.63  Aligned_cols=142  Identities=18%  Similarity=0.126  Sum_probs=72.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC----CCCeEEEEeCCCCCch---HHHHHHHhccCchhhcccchH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG----LDGGVIYIDVESTFTS---RRMIEMGASSFPEIFHSKGMA  171 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg----~~~~vl~i~~e~~~~~---~rl~~~~~~~~~~~~~~~~~~  171 (357)
                      +++|+++.|.|++|+|||||+.-++..  .++..|.    ....+.|+..+..+..   ..+.+..... .. .. ....
T Consensus        27 i~~Ge~~~I~G~NGsGKSTLl~~i~Gl--~~p~~G~i~~~~~~~i~~v~q~~~~~~~l~~~~~~~~~~~-~~-~~-~~~~  101 (251)
T PRK09544         27 LKPGKILTLLGPNGAGKSTLVRVVLGL--VAPDEGVIKRNGKLRIGYVPQKLYLDTTLPLTVNRFLRLR-PG-TK-KEDI  101 (251)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC--CCCCceEEEECCccCEEEeccccccccccChhHHHHHhcc-cc-cc-HHHH
Confidence            889999999999999999999977643  2222220    0123455543322211   1121111000 00 00 0001


Q ss_pred             HHhhcCeEE-------eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHH
Q 035774          172 QEMAGRILV-------LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEF  244 (357)
Q Consensus       172 ~~~~~~i~~-------~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~  244 (357)
                      ...++.+-+       ....+..+. ..+.-.+..  -.+++++++|..+.-...         .....+.+.|++++++
T Consensus       102 ~~~l~~~gl~~~~~~~~~~LSgGq~-qrv~laral--~~~p~lllLDEPt~~LD~---------~~~~~l~~~L~~~~~~  169 (251)
T PRK09544        102 LPALKRVQAGHLIDAPMQKLSGGET-QRVLLARAL--LNRPQLLVLDEPTQGVDV---------NGQVALYDLIDQLRRE  169 (251)
T ss_pred             HHHHHHcCChHHHhCChhhCCHHHH-HHHHHHHHH--hcCCCEEEEeCCCcCCCH---------HHHHHHHHHHHHHHHh
Confidence            111111111       011122221 111111222  247899999987755432         3344577788888887


Q ss_pred             cCCeEEEeccccc
Q 035774          245 SRIPIVVTNQVRP  257 (357)
Q Consensus       245 ~~~~vv~~~q~~~  257 (357)
                      ++.+||+++|-..
T Consensus       170 ~g~tiiivsH~~~  182 (251)
T PRK09544        170 LDCAVLMVSHDLH  182 (251)
T ss_pred             cCCEEEEEecCHH
Confidence            7999999988644

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=98.03  E-value=7.1e-05  Score=62.56  Aligned_cols=27  Identities=33%  Similarity=0.527  Sum_probs=24.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        25 i~~G~~~~l~G~nGsGKstLl~~i~G~   51 (171)
T cd03228          25 IKPGEKVAIVGPSGSGKSTLLKLLLRL   51 (171)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcC
Confidence            889999999999999999999977653

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.

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=98.03  E-value=4.4e-05  Score=65.65  Aligned_cols=26  Identities=31%  Similarity=0.488  Sum_probs=23.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G   48 (201)
T cd03231          23 LAAGEALQVTGPNGSGKTTLLRILAG   48 (201)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999886664

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.

>PRK11153 metN DL-methionine transporter ATP-binding subunit; Provisional

Probab=98.02  E-value=2.7e-05  Score=72.65  Aligned_cols=46  Identities=13%  Similarity=0.151  Sum_probs=35.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+++||+++|-..
T Consensus       157 ~~p~iLlLDEPts~LD~---------~~~~~l~~~L~~l~~~~g~tiilvtH~~~  202 (343)
T PRK11153        157 SNPKVLLCDEATSALDP---------ATTRSILELLKDINRELGLTIVLITHEMD  202 (343)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47999999987755432         34456778888888888999999988654

>PRK12377 putative replication protein; Provisional

Probab=98.02  E-value=6.6e-05  Score=66.40  Aligned_cols=37  Identities=22%  Similarity=0.255  Sum_probs=31.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .-+.|.|+||+|||.|+..++......      +..|+|++..
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~------g~~v~~i~~~  138 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAK------GRSVIVVTVP  138 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc------CCCeEEEEHH
Confidence            468999999999999999999887642      4789999774

>TIGR02323 CP_lyasePhnK phosphonate C-P lyase system protein PhnK

Probab=98.02  E-value=7.6e-05  Score=66.58  Aligned_cols=44  Identities=9%  Similarity=0.154  Sum_probs=32.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+...|++++++.+.+||+++|-
T Consensus       165 ~~p~vlllDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tii~vsH~  208 (253)
T TIGR02323       165 TRPRLVFMDEPTGGLDV---------SVQARLLDLLRGLVRDLGLAVIIVTHD  208 (253)
T ss_pred             cCCCEEEEcCCCccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            47899999987654432         334456777888888789999999885

Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se.

>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively

Probab=98.02  E-value=6e-05  Score=65.72  Aligned_cols=44  Identities=5%  Similarity=-0.022  Sum_probs=33.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+.+.|+++.++.+.+||+++|-
T Consensus       148 ~~p~lllLDEPt~~LD~---------~~~~~~~~~l~~~~~~~~~tiii~sH~  191 (220)
T cd03293         148 VDPDVLLLDEPFSALDA---------LTREQLQEELLDIWRETGKTVLLVTHD  191 (220)
T ss_pred             cCCCEEEECCCCCCCCH---------HHHHHHHHHHHHHHHHcCCEEEEEecC
Confidence            47899999987754432         344567778888888788999999875

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.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=98.02  E-value=2.3e-05  Score=64.96  Aligned_cols=44  Identities=23%  Similarity=0.292  Sum_probs=36.8

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ...+.|-+.|+.+--- +++|+++-|.||+|+|||||..-+....
T Consensus         9 k~Y~~g~~aL~~vs~~-i~~Gef~fl~GpSGAGKSTllkLi~~~e   52 (223)
T COG2884           9 KAYPGGREALRDVSFH-IPKGEFVFLTGPSGAGKSTLLKLIYGEE   52 (223)
T ss_pred             hhcCCCchhhhCceEe-ecCceEEEEECCCCCCHHHHHHHHHhhh
Confidence            3577786689988654 9999999999999999999998776544

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=98.02  E-value=7.5e-05  Score=65.39  Aligned_cols=44  Identities=11%  Similarity=0.096  Sum_probs=33.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..+.-...         .....+.+.|+.++++.+.+||+++|-
T Consensus       154 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tvii~sh~  197 (225)
T PRK10247        154 FMPKVLLLDEITSALDE---------SNKHNVNEIIHRYVREQNIAVLWVTHD  197 (225)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEECC
Confidence            47899999987654432         345567788888888889999999875

>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.02  E-value=7e-05  Score=67.95  Aligned_cols=45  Identities=11%  Similarity=0.205  Sum_probs=33.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+...|++++++.+.+||+++|-.
T Consensus       160 ~~P~llllDEPt~gLD~---------~~~~~l~~~l~~l~~~~g~tvli~tH~~  204 (282)
T PRK13640        160 VEPKIIILDESTSMLDP---------AGKEQILKLIRKLKKKNNLTVISITHDI  204 (282)
T ss_pred             cCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            47899999987755432         3445677888888888899999998753

>TIGR00968 3a0106s01 sulfate ABC transporter, ATP-binding protein

Probab=98.01  E-value=4.3e-05  Score=67.51  Aligned_cols=46  Identities=11%  Similarity=0.067  Sum_probs=33.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..+.-...         .....+.+.|++++++.+++||+++|-..
T Consensus       147 ~~p~llllDEP~~~LD~---------~~~~~~~~~l~~~~~~~~~tvli~sH~~~  192 (237)
T TIGR00968       147 VEPQVLLLDEPFGALDA---------KVRKELRSWLRKLHDEVHVTTVFVTHDQE  192 (237)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            46899999987654332         44556777888888777899999988533

>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport

Probab=98.01  E-value=4.9e-05  Score=66.92  Aligned_cols=44  Identities=16%  Similarity=0.214  Sum_probs=32.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+.+.|+.++++.+.+||+++|-
T Consensus       157 ~~p~lllLDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tvii~sH~  200 (233)
T cd03258         157 NNPKVLLCDEATSALDP---------ETTQSILALLRDINRELGLTIVLITHE  200 (233)
T ss_pred             cCCCEEEecCCCCcCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCC
Confidence            47899999987654322         344557778888888889999999875

Other members of this system include the MetP permease and the MetQ substrate binding protein. 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.

>cd03300 ABC_PotA_N PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D

Probab=98.00  E-value=3.9e-05  Score=67.53  Aligned_cols=45  Identities=16%  Similarity=0.043  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|....-...         .....+...|+.++++.+++||+++|-.
T Consensus       147 ~~p~llllDEP~~gLD~---------~~~~~l~~~l~~~~~~~~~tiii~sh~~  191 (232)
T cd03300         147 NEPKVLLLDEPLGALDL---------KLRKDMQLELKRLQKELGITFVFVTHDQ  191 (232)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            47899999977654322         3444577788888887799999998753

PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. 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.

>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.00  E-value=5.5e-05  Score=68.46  Aligned_cols=45  Identities=7%  Similarity=0.142  Sum_probs=33.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+...|++++++++.+||+++|-.
T Consensus       157 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~l~~~~g~tiil~sH~~  201 (277)
T PRK13642        157 LRPEIIILDESTSMLDP---------TGRQEIMRVIHEIKEKYQLTVLSITHDL  201 (277)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            36899999987654432         4455677888888888899999998753

>PRK13647 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=98.00  E-value=6.5e-05  Score=67.87  Aligned_cols=44  Identities=11%  Similarity=0.126  Sum_probs=32.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|++++++ +++||+++|-.
T Consensus       155 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~-g~tili~tH~~  198 (274)
T PRK13647        155 MDPDVIVLDEPMAYLDP---------RGQETLMEILDRLHNQ-GKTVIVATHDV  198 (274)
T ss_pred             cCCCEEEEECCCcCCCH---------HHHHHHHHHHHHHHHC-CCEEEEEeCCH
Confidence            47899999987765432         3445677788888765 89999998753

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=97.99  E-value=0.00011  Score=65.70  Aligned_cols=45  Identities=16%  Similarity=0.095  Sum_probs=33.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-..         ......+...|++++++.+.+||+++|-.
T Consensus       150 ~~p~lllLDEPt~~LD---------~~~~~~l~~~L~~~~~~~~~tviivsHd~  194 (257)
T PRK11247        150 HRPGLLLLDEPLGALD---------ALTRIEMQDLIESLWQQHGFTVLLVTHDV  194 (257)
T ss_pred             cCCCEEEEeCCCCCCC---------HHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            4789999998765442         23445677788888888899999998853

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=97.99  E-value=4.9e-05  Score=65.95  Aligned_cols=45  Identities=9%  Similarity=0.074  Sum_probs=33.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|+++.++.+.+||+++|-.
T Consensus       145 ~~p~llllDEPt~~LD~---------~~~~~~~~~l~~~~~~~~~tii~vsh~~  189 (213)
T TIGR01277       145 RPNPILLLDEPFSALDP---------LLREEMLALVKQLCSERQRTLLMVTHHL  189 (213)
T ss_pred             cCCCEEEEcCCCccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            46899999987765432         3445677788888887799999998753

This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found.

>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=97.98  E-value=4e-05  Score=70.64  Aligned_cols=51  Identities=25%  Similarity=0.421  Sum_probs=36.9

Q ss_pred             chhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           88 LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        88 ~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ...+|.+=- -+++|+++.+.||+||||||++.-+|--.  ++     ...-++++.+.
T Consensus        18 ~~av~~isl-~i~~Gef~~lLGPSGcGKTTlLR~IAGfe--~p-----~~G~I~l~G~~   68 (352)
T COG3842          18 FTAVDDISL-DIKKGEFVTLLGPSGCGKTTLLRMIAGFE--QP-----SSGEILLDGED   68 (352)
T ss_pred             eeEEeccee-eecCCcEEEEECCCCCCHHHHHHHHhCCC--CC-----CCceEEECCEE
Confidence            555666422 39999999999999999999999777432  22     34467776653

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.98  E-value=6.5e-05  Score=63.52  Aligned_cols=28  Identities=36%  Similarity=0.630  Sum_probs=24.8

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .|+++.++.+.||+|||||||+..+-.-
T Consensus        29 ~i~~~~VTAlIGPSGcGKST~LR~lNRm   56 (253)
T COG1117          29 DIPKNKVTALIGPSGCGKSTLLRCLNRM   56 (253)
T ss_pred             eccCCceEEEECCCCcCHHHHHHHHHhh
Confidence            5999999999999999999999866543

>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.98  E-value=7e-05  Score=67.54  Aligned_cols=45  Identities=4%  Similarity=0.090  Sum_probs=32.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|....-...         .....+...|++++++.+.+||+++|-.
T Consensus       159 ~~p~lllLDEP~~gLD~---------~~~~~l~~~l~~~~~~~~~tiii~sH~~  203 (271)
T PRK13632        159 LNPEIIIFDESTSMLDP---------KGKREIKKIMVDLRKTRKKTLISITHDM  203 (271)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCcEEEEEEech
Confidence            47899999987654432         3445677888888877678999888753

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.97  E-value=0.00027  Score=66.05  Aligned_cols=44  Identities=32%  Similarity=0.502  Sum_probs=35.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +..|.++.|.||+|+||||++..++...+..  .|  ..+|.+|+++.
T Consensus       134 ~~~g~ii~lvGptGvGKTTtiakLA~~~~~~--~G--~~~V~lit~D~  177 (374)
T PRK14722        134 MERGGVFALMGPTGVGKTTTTAKLAARCVMR--FG--ASKVALLTTDS  177 (374)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHHh--cC--CCeEEEEeccc
Confidence            6778999999999999999999999887542  12  25788888764

>PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.97  E-value=3.7e-05  Score=69.92  Aligned_cols=45  Identities=16%  Similarity=0.150  Sum_probs=34.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+...|+.++++.+.+||+++|-.
T Consensus       161 ~~P~llllDEPt~gLD~---------~~~~~l~~~l~~l~~~~g~tvi~vtHd~  205 (287)
T PRK13637        161 MEPKILILDEPTAGLDP---------KGRDEILNKIKELHKEYNMTIILVSHSM  205 (287)
T ss_pred             cCCCEEEEECCccCCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            46899999987765432         3445677788888888899999998753

>PRK10771 thiQ thiamine transporter ATP-binding subunit; Provisional

Probab=97.97  E-value=9e-05  Score=65.21  Aligned_cols=46  Identities=7%  Similarity=0.151  Sum_probs=33.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|....-...         .....+.+.|+.++++.+.+||+++|-..
T Consensus       146 ~~p~lllLDEP~~gLD~---------~~~~~~~~~l~~~~~~~~~tiii~sH~~~  191 (232)
T PRK10771        146 REQPILLLDEPFSALDP---------ALRQEMLTLVSQVCQERQLTLLMVSHSLE  191 (232)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEECCHH
Confidence            47899999987654432         34445777888888878999999987533

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=97.97  E-value=5.1e-05  Score=67.11  Aligned_cols=44  Identities=11%  Similarity=0.046  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+...|++++++.+.+||+++|-
T Consensus       153 ~~p~llllDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tvii~sH~  196 (239)
T cd03296         153 VEPKVLLLDEPFGALDA---------KVRKELRRWLRRLHDELHVTTVFVTHD  196 (239)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCC
Confidence            47899999987755432         344557778888888778999999875

Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). 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.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=97.96  E-value=6.9e-05  Score=64.60  Aligned_cols=26  Identities=31%  Similarity=0.409  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G   48 (205)
T cd03226          23 LYAGEIIALTGKNGAGKTTLAKILAG   48 (205)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997764

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.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=97.96  E-value=6.3e-05  Score=65.23  Aligned_cols=26  Identities=35%  Similarity=0.635  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++-
T Consensus        23 i~~G~~~~l~G~nGsGKSTLl~~l~G   48 (213)
T cd03262          23 VKKGEVVVIIGPSGSGKSTLLRCINL   48 (213)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997774

Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM

>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family

Probab=97.95  E-value=0.00018  Score=62.80  Aligned_cols=44  Identities=18%  Similarity=0.183  Sum_probs=33.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..+.-...         .....+...|++++++.+.+||+++|-
T Consensus       158 ~~p~illlDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~sh~  201 (220)
T TIGR02982       158 HRPKLVLADEPTAALDS---------KSGRDVVELMQKLAREQGCTILIVTHD  201 (220)
T ss_pred             cCCCEEEEeCCCCcCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCC
Confidence            47899999987765432         344467788888888789999999875

Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts.

>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane

Probab=97.95  E-value=7.9e-05  Score=64.64  Aligned_cols=26  Identities=31%  Similarity=0.493  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        24 i~~G~~~~i~G~nGsGKSTLl~~l~G   49 (214)
T cd03292          24 ISAGEFVFLVGPSGAGKSTLLKLIYK   49 (214)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999999997774

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake

Probab=97.94  E-value=4.9e-05  Score=67.10  Aligned_cols=45  Identities=7%  Similarity=0.037  Sum_probs=33.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       170 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tiiivsH~~  214 (236)
T cd03267         170 HEPEILFLDEPTIGLDV---------VAQENIRNFLKEYNRERGTTVLLTSHYM  214 (236)
T ss_pred             cCCCEEEEcCCCCCCCH---------HHHHHHHHHHHHHHhcCCCEEEEEecCH
Confidence            47899999987755432         4455677888888887789999998853

NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.

>PF13173 AAA_14: AAA domain

Probab=97.94  E-value=0.00015  Score=57.43  Aligned_cols=98  Identities=20%  Similarity=0.274  Sum_probs=63.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      +.+++|.|+.|+|||+++.+++.....       +..++|++++..    +......                .+     
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~~-------~~~~~yi~~~~~----~~~~~~~----------------~~-----   49 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLLP-------PENILYINFDDP----RDRRLAD----------------PD-----   49 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhcc-------cccceeeccCCH----HHHHHhh----------------hh-----
Confidence            568999999999999999999987752       378999998762    1111000                00     


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHc-CCeEEEeccccc
Q 035774          182 QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS-RIPIVVTNQVRP  257 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~-~~~vv~~~q~~~  257 (357)
                             +.+.   +.+.. ..+..+|+||.++.+-               .+...++.+.... ++.++++.....
T Consensus        50 -------~~~~---~~~~~-~~~~~~i~iDEiq~~~---------------~~~~~lk~l~d~~~~~~ii~tgS~~~  100 (128)
T PF13173_consen   50 -------LLEY---FLELI-KPGKKYIFIDEIQYLP---------------DWEDALKFLVDNGPNIKIILTGSSSS  100 (128)
T ss_pred             -------hHHH---HHHhh-ccCCcEEEEehhhhhc---------------cHHHHHHHHHHhccCceEEEEccchH
Confidence                   1111   11111 1267889999998761               1455677777766 789998875433

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=97.94  E-value=5e-05  Score=67.30  Aligned_cols=44  Identities=11%  Similarity=0.147  Sum_probs=32.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+++||+++|-
T Consensus       162 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tiii~tH~  205 (243)
T TIGR02315       162 QQPDLILADEPIASLDP---------KTSKQVMDYLKRINKEDGITVIINLHQ  205 (243)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCC
Confidence            46899999987654432         334456778888887778999999875

Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.94  E-value=0.00011  Score=62.59  Aligned_cols=135  Identities=17%  Similarity=0.122  Sum_probs=66.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      +.+|+++.|.|++|+|||||+.-++-....+..     ..-++++.+.- . .++..... ...+....... ....+++
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~~l~G~~~~~~~-----~G~i~~~g~~~-~-~~~~~~i~-~~~q~~~~~~~-~tv~~~l  100 (192)
T cd03232          30 VKPGTLTALMGESGAGKTTLLDVLAGRKTAGVI-----TGEILINGRPL-D-KNFQRSTG-YVEQQDVHSPN-LTVREAL  100 (192)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhCCCcCCCc-----ceEEEECCEeh-H-HHhhhceE-EecccCccccC-CcHHHHH
Confidence            789999999999999999999987743211111     33456655421 1 11111000 00000000000 0000111


Q ss_pred             EE---eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          179 LV---LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       179 ~~---~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+   ....+..+.. .+.-.+..  -.+++++++|...+-...         .....+...|+++++ .+.++|+++|-
T Consensus       101 ~~~~~~~~LSgGe~q-rv~la~al--~~~p~vlllDEP~~~LD~---------~~~~~l~~~l~~~~~-~~~tiiivtH~  167 (192)
T cd03232         101 RFSALLRGLSVEQRK-RLTIGVEL--AAKPSILFLDEPTSGLDS---------QAAYNIVRFLKKLAD-SGQAILCTIHQ  167 (192)
T ss_pred             HHHHHHhcCCHHHhH-HHHHHHHH--hcCCcEEEEeCCCcCCCH---------HHHHHHHHHHHHHHH-cCCEEEEEEcC
Confidence            00   0012222211 11111122  247899999987755432         334456677777765 48999998875

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.94  E-value=0.00012  Score=62.97  Aligned_cols=26  Identities=31%  Similarity=0.491  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~l~G   49 (204)
T PRK13538         24 LNAGELVQIEGPNGAGKTSLLRILAG   49 (204)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997764

>COG4107 PhnK ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.94  E-value=0.00019  Score=58.69  Aligned_cols=41  Identities=29%  Similarity=0.305  Sum_probs=32.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.||++..|.|++|||||||...++.+..-  .    .+.+.|..-.
T Consensus        29 l~PGeVLgiVGESGSGKtTLL~~is~rl~p--~----~G~v~Y~~r~   69 (258)
T COG4107          29 LYPGEVLGIVGESGSGKTTLLKCISGRLTP--D----AGTVTYRMRD   69 (258)
T ss_pred             ecCCcEEEEEecCCCcHHhHHHHHhcccCC--C----CCeEEEEcCC
Confidence            789999999999999999999988876642  2    2567776644

>PRK10851 sulfate/thiosulfate transporter subunit; Provisional

Probab=97.94  E-value=4.1e-05  Score=71.56  Aligned_cols=46  Identities=11%  Similarity=0.052  Sum_probs=33.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-...         ..-..+.+.|+++.+++++++|+++|-..
T Consensus       153 ~~P~llLLDEP~s~LD~---------~~r~~l~~~L~~l~~~~g~tii~vTHd~~  198 (353)
T PRK10851        153 VEPQILLLDEPFGALDA---------QVRKELRRWLRQLHEELKFTSVFVTHDQE  198 (353)
T ss_pred             cCCCEEEEeCCCccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47899999976644322         33445677888888888999999988654

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.94  E-value=9.2e-05  Score=69.70  Aligned_cols=43  Identities=28%  Similarity=0.290  Sum_probs=34.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..++.++.|.|++|+||||++.++|......     .+.+|.+++++.
T Consensus       220 ~~~~~vi~lvGptGvGKTTtaaKLA~~~~~~-----~G~~V~Lit~Dt  262 (432)
T PRK12724        220 KNQRKVVFFVGPTGSGKTTSIAKLAAKYFLH-----MGKSVSLYTTDN  262 (432)
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHHHh-----cCCeEEEecccc
Confidence            4567899999999999999999999866321     247899998864

>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake

Probab=97.94  E-value=6.9e-05  Score=65.24  Aligned_cols=26  Identities=46%  Similarity=0.531  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~~l~G   53 (218)
T cd03266          28 VKPGEVTGLLGPNGAGKTTTLRMLAG   53 (218)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999987764

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.

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.93  E-value=9.8e-05  Score=62.39  Aligned_cols=27  Identities=30%  Similarity=0.421  Sum_probs=24.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G~   49 (182)
T cd03215          23 VRAGEIVGIAGLVGNGQTELAEALFGL   49 (182)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            889999999999999999999977643

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.

>TIGR03005 ectoine_ehuA ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Probab=97.93  E-value=7.7e-05  Score=66.51  Aligned_cols=45  Identities=11%  Similarity=0.197  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|++++++.+.++|+++|-.
T Consensus       163 ~~p~llllDEP~~~LD~---------~~~~~l~~~l~~~~~~~~~tiiivsH~~  207 (252)
T TIGR03005       163 MRPKVMLFDEVTSALDP---------ELVGEVLNVIRRLASEHDLTMLLVTHEM  207 (252)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCcEEEEEeCCH
Confidence            47899999987654422         3344577788888887899999998853

Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins.

>PRK11650 ugpC glycerol-3-phosphate transporter ATP-binding subunit; Provisional

Probab=97.93  E-value=6.2e-05  Score=70.46  Aligned_cols=46  Identities=7%  Similarity=-0.065  Sum_probs=33.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++++|+++|-..
T Consensus       151 ~~P~llLLDEP~s~LD---------~~~r~~l~~~l~~l~~~~g~tii~vTHd~~  196 (356)
T PRK11650        151 REPAVFLFDEPLSNLD---------AKLRVQMRLEIQRLHRRLKTTSLYVTHDQV  196 (356)
T ss_pred             cCCCEEEEeCCcccCC---------HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            4799999997664432         233445677788888889999999998643

>PRK14974 cell division protein FtsY; Provisional

Probab=97.92  E-value=0.0002  Score=66.18  Aligned_cols=39  Identities=31%  Similarity=0.248  Sum_probs=31.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++.++.++|+||+||||.+..++.....   .   +.+|++++++
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~~l~~---~---g~~V~li~~D  177 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAYYLKK---N---GFSVVIAAGD  177 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHH---c---CCeEEEecCC
Confidence            3579999999999999999999976542   1   4688888775

>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.92  E-value=6.4e-05  Score=68.49  Aligned_cols=45  Identities=16%  Similarity=0.070  Sum_probs=33.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       167 ~~p~lLlLDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tiiiisH~~  211 (289)
T PRK13645        167 MDGNTLVLDEPTGGLDP---------KGEEDFINLFERLNKEYKKRIIMVTHNM  211 (289)
T ss_pred             hCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            46899999987765432         3344577778888887899999998853

>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine

Probab=97.92  E-value=3.9e-05  Score=67.64  Aligned_cols=26  Identities=38%  Similarity=0.547  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G   48 (236)
T cd03219          23 VRPGEIHGLIGPNGAGKTTLFNLISG   48 (236)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHcC
Confidence            78999999999999999999997764

MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=97.92  E-value=6e-05  Score=65.39  Aligned_cols=26  Identities=31%  Similarity=0.455  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~~l~G   47 (213)
T cd03235          22 VKPGEFLAIVGPNGAGKSTLLKAILG   47 (213)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHcC
Confidence            88999999999999999999997764

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.

>PRK11432 fbpC ferric transporter ATP-binding subunit; Provisional

Probab=97.92  E-value=7.9e-05  Score=69.59  Aligned_cols=47  Identities=13%  Similarity=0.035  Sum_probs=34.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~  258 (357)
                      .+++++++|.-.+-..         .....++...|+++.++.++++|+++|-...
T Consensus       153 ~~P~lLLLDEP~s~LD---------~~~r~~l~~~l~~l~~~~g~tii~vTHd~~e  199 (351)
T PRK11432        153 LKPKVLLFDEPLSNLD---------ANLRRSMREKIRELQQQFNITSLYVTHDQSE  199 (351)
T ss_pred             cCCCEEEEcCCcccCC---------HHHHHHHHHHHHHHHHhcCCEEEEEcCCHHH
Confidence            3689999997654432         2334456778888888899999999986543

>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome

Probab=97.92  E-value=0.00036  Score=58.03  Aligned_cols=27  Identities=33%  Similarity=0.474  Sum_probs=24.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~G~   50 (166)
T cd03223          24 IKPGDRLLITGPSGTGKSSLFRALAGL   50 (166)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999999977643

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

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=97.91  E-value=0.0001  Score=63.02  Aligned_cols=26  Identities=31%  Similarity=0.523  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        32 i~~Ge~~~l~G~nGsGKStLl~~i~G   57 (194)
T cd03213          32 AKPGELTAIMGPSGAGKSTLLNALAG   57 (194)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997764

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.

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids

Probab=97.91  E-value=4.6e-05  Score=66.50  Aligned_cols=26  Identities=35%  Similarity=0.528  Sum_probs=23.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G   48 (222)
T cd03224          23 VPEGEIVALLGRNGAGKTTLLKTIMG   48 (222)
T ss_pred             EcCCeEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999986653

The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). 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.

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=97.91  E-value=7.1e-05  Score=69.63  Aligned_cols=46  Identities=20%  Similarity=0.215  Sum_probs=33.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~  258 (357)
                      ++++++++|.-++-...         .....+.+.|+++++ .+.+||+++|.-..
T Consensus       189 ~~P~lLiLDEPt~gLD~---------~~r~~l~~~l~~l~~-~g~tilisSH~l~e  234 (340)
T PRK13536        189 NDPQLLILDEPTTGLDP---------HARHLIWERLRSLLA-RGKTILLTTHFMEE  234 (340)
T ss_pred             cCCCEEEEECCCCCCCH---------HHHHHHHHHHHHHHh-CCCEEEEECCCHHH
Confidence            57999999987765432         344456777778766 49999999986543

>PRK15079 oligopeptide ABC transporter ATP-binding protein OppF; Provisional

Probab=97.91  E-value=3.5e-05  Score=71.40  Aligned_cols=46  Identities=11%  Similarity=0.095  Sum_probs=34.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .++++++.|.-++-...         ..-.++++.|+++.++++.++|+++|--.
T Consensus       178 ~~P~llilDEPts~LD~---------~~~~~i~~lL~~l~~~~~~til~iTHdl~  223 (331)
T PRK15079        178 LEPKLIICDEPVSALDV---------SIQAQVVNLLQQLQREMGLSLIFIAHDLA  223 (331)
T ss_pred             cCCCEEEEeCCCccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCCHH
Confidence            47899999987765432         33446778888888888999999988543

>cd03299 ABC_ModC_like Archeal protein closely related to ModC

Probab=97.91  E-value=6.8e-05  Score=66.14  Aligned_cols=44  Identities=7%  Similarity=-0.000  Sum_probs=32.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..+.-...         .....+...|+.++.++++++|+++|-
T Consensus       146 ~~p~llllDEPt~gLD~---------~~~~~l~~~l~~~~~~~~~tili~tH~  189 (235)
T cd03299         146 VNPKILLLDEPFSALDV---------RTKEKLREELKKIRKEFGVTVLHVTHD  189 (235)
T ss_pred             cCCCEEEECCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecC
Confidence            47899999987754432         344457777888888779999999874

ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. 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.

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

Probab=97.91  E-value=6.1e-05  Score=63.36  Aligned_cols=40  Identities=30%  Similarity=0.399  Sum_probs=30.3

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..+.-+.|.|+||+|||.||..++..++..      +.+|+|++..
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~~------g~~v~f~~~~   84 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIRK------GYSVLFITAS   84 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHHT------T--EEEEEHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhccC------CcceeEeecC
Confidence            346679999999999999999999888742      5889999763

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.

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.91  E-value=9.1e-05  Score=65.33  Aligned_cols=36  Identities=25%  Similarity=0.308  Sum_probs=30.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ..+.+.|+||+|||.|+..++......      +.+|+|++.
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~------g~~v~~it~  135 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLR------GKSVLIITV  135 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhc------CCeEEEEEH
Confidence            368999999999999999999887642      478999965

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=97.90  E-value=7.4e-05  Score=64.67  Aligned_cols=26  Identities=35%  Similarity=0.424  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~G~~~~i~G~nGsGKSTLl~~l~G   48 (210)
T cd03269          23 VEKGEIFGLLGPNGAGKTTTIRMILG   48 (210)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997774

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.

>PRK13651 cobalt transporter ATP-binding subunit; Provisional

Probab=97.90  E-value=0.00013  Score=66.92  Aligned_cols=34  Identities=29%  Similarity=0.497  Sum_probs=27.2

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .|+.+-- =+.+|+++.|.|++|+|||||+..++.
T Consensus        22 ~l~~vsl-~i~~Ge~v~iiG~nGsGKSTLl~~L~G   55 (305)
T PRK13651         22 ALDNVSV-EINQGEFIAIIGQTGSGKTTFIEHLNA   55 (305)
T ss_pred             ceeeeEE-EEeCCCEEEEECCCCCcHHHHHHHHhC
Confidence            4544322 288999999999999999999997774

>PRK13548 hmuV hemin importer ATP-binding subunit; Provisional

Probab=97.90  E-value=0.00016  Score=64.65  Aligned_cols=45  Identities=13%  Similarity=0.112  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|++++++.+.+||+++|-.
T Consensus       157 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tiii~sH~~  201 (258)
T PRK13548        157 GPPRWLLLDEPTSALDL---------AHQHHVLRLARQLAHERGLAVIVVLHDL  201 (258)
T ss_pred             CCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEECCH
Confidence            47899999987765432         3344567778888866789999998853

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=97.90  E-value=0.00011  Score=63.85  Aligned_cols=26  Identities=31%  Similarity=0.416  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~~l~G   51 (216)
T TIGR00960        26 ITKGEMVFLVGHSGAGKSTFLKLILG   51 (216)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997774

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=97.90  E-value=3.6e-05  Score=67.65  Aligned_cols=45  Identities=18%  Similarity=0.138  Sum_probs=32.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       148 ~~p~illlDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~sH~~  192 (230)
T TIGR03410       148 TRPKLLLLDEPTEGIQP---------SIIKDIGRVIRRLRAEGGMAILLVEQYL  192 (230)
T ss_pred             cCCCEEEecCCcccCCH---------HHHHHHHHHHHHHHHcCCcEEEEEeCCH
Confidence            47899999987654422         3344567778888877789999998753

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>TIGR01288 nodI ATP-binding ABC transporter family nodulation protein NodI

Probab=97.90  E-value=8.5e-05  Score=68.13  Aligned_cols=45  Identities=20%  Similarity=0.207  Sum_probs=32.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         .....+.+.|+++++ .+.+||+++|-..
T Consensus       152 ~~p~lllLDEPt~gLD~---------~~~~~l~~~l~~~~~-~g~til~~sH~~~  196 (303)
T TIGR01288       152 NDPQLLILDEPTTGLDP---------HARHLIWERLRSLLA-RGKTILLTTHFME  196 (303)
T ss_pred             cCCCEEEEeCCCcCCCH---------HHHHHHHHHHHHHHh-CCCEEEEECCCHH
Confidence            47999999987755432         344456777888766 4899999998654

This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=97.89  E-value=7.2e-05  Score=66.17  Aligned_cols=27  Identities=30%  Similarity=0.589  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~l~G~   50 (240)
T PRK09493         24 IDQGEVVVIIGPSGSGKSTLLRCINKL   50 (240)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999999977753

>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.89  E-value=0.0001  Score=66.46  Aligned_cols=26  Identities=38%  Similarity=0.567  Sum_probs=23.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~G   49 (271)
T PRK13638         24 FSLSPVTGLVGANGCGKSTLFMNLSG   49 (271)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHcC
Confidence            78999999999999999999997664

>PRK13643 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.89  E-value=0.00011  Score=66.97  Aligned_cols=26  Identities=35%  Similarity=0.502  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        29 i~~Ge~v~i~G~nGsGKSTLl~~l~G   54 (288)
T PRK13643         29 VKKGSYTALIGHTGSGKSTLLQHLNG   54 (288)
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhc
Confidence            88999999999999999999997774

>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids

Probab=97.89  E-value=0.00015  Score=63.72  Aligned_cols=26  Identities=35%  Similarity=0.506  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G   48 (232)
T cd03218          23 VKQGEIVGLLGPNGAGKTTTFYMIVG   48 (232)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997774

The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.

>PF05729 NACHT: NACHT domain

Probab=97.88  E-value=0.0001  Score=60.77  Aligned_cols=26  Identities=31%  Similarity=0.344  Sum_probs=23.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccc
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALP  129 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~  129 (357)
                      ++.|.|+||+|||+++..++......
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~   27 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEE   27 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhc
Confidence            68999999999999999999888754

>PRK11000 maltose/maltodextrin transporter ATP-binding protein; Provisional

Probab=97.88  E-value=7.1e-05  Score=70.49  Aligned_cols=46  Identities=7%  Similarity=-0.039  Sum_probs=33.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-...         ..-..+...|+++.++.+.++|+++|-..
T Consensus       150 ~~P~lLLLDEPts~LD~---------~~~~~l~~~L~~l~~~~g~tvI~vTHd~~  195 (369)
T PRK11000        150 AEPSVFLLDEPLSNLDA---------ALRVQMRIEISRLHKRLGRTMIYVTHDQV  195 (369)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHHhCCEEEEEeCCHH
Confidence            47999999987654422         33445677788888888999999988654

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=97.88  E-value=9.2e-05  Score=63.58  Aligned_cols=137  Identities=16%  Similarity=0.148  Sum_probs=68.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC--CchHHHHHHHhccCchhhc-cc-chHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST--FTSRRMIEMGASSFPEIFH-SK-GMAQEM  174 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~--~~~~rl~~~~~~~~~~~~~-~~-~~~~~~  174 (357)
                      +.+|+++.|.|++|+|||||+.-++.....++.     ..-++++.+.-  .+........-...++... .. ......
T Consensus        23 i~~Ge~~~i~G~nGsGKStLl~~l~G~~~~~p~-----~G~i~~~g~~~~~~~~~~~~~~~i~~v~q~~~~~~~~~~~~~   97 (200)
T cd03217          23 IKKGEVHALMGPNGSGKSTLAKTIMGHPKYEVT-----EGEILFKGEDITDLPPEERARLGIFLAFQYPPEIPGVKNADF   97 (200)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHHhCCCcCCCC-----ccEEEECCEECCcCCHHHHhhCcEEEeecChhhccCccHHHH
Confidence            789999999999999999999987754211212     23455655421  1111111100000000000 00 000111


Q ss_pred             hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          175 AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       175 ~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                      ...  +....+..+.. .+.-.+..  -.+++++++|.-+.-...         .....+...|+++++ .+.++|+++|
T Consensus        98 l~~--~~~~LS~G~~q-rv~laral--~~~p~illlDEPt~~LD~---------~~~~~l~~~L~~~~~-~~~tiii~sh  162 (200)
T cd03217          98 LRY--VNEGFSGGEKK-RNEILQLL--LLEPDLAILDEPDSGLDI---------DALRLVAEVINKLRE-EGKSVLIITH  162 (200)
T ss_pred             Hhh--ccccCCHHHHH-HHHHHHHH--hcCCCEEEEeCCCccCCH---------HHHHHHHHHHHHHHH-CCCEEEEEec
Confidence            100  01122222221 11111222  247899999987654422         344556777887765 4889999887


Q ss_pred             c
Q 035774          255 V  255 (357)
Q Consensus       255 ~  255 (357)
                      -
T Consensus       163 ~  163 (200)
T cd03217         163 Y  163 (200)
T ss_pred             C
Confidence            5

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.

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=97.88  E-value=0.00031  Score=62.77  Aligned_cols=44  Identities=11%  Similarity=0.098  Sum_probs=32.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-...         .....+...|++++++.+.+||+++|-
T Consensus       145 ~~p~lllLDEPt~~LD~---------~~~~~l~~~L~~~~~~~g~tviivsH~  188 (255)
T PRK11248        145 ANPQLLLLDEPFGALDA---------FTREQMQTLLLKLWQETGKQVLLITHD  188 (255)
T ss_pred             cCCCEEEEeCCCccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            47899999987654432         344557777888877679999999875

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.88  E-value=0.00027  Score=60.64  Aligned_cols=26  Identities=31%  Similarity=0.457  Sum_probs=23.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~i~G   49 (200)
T PRK13540         24 LPAGGLLHLKGSNGAGKTTLLKLIAG   49 (200)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999999997664

>TIGR03265 PhnT2 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein

Probab=97.88  E-value=7.3e-05  Score=69.93  Aligned_cols=47  Identities=11%  Similarity=0.087  Sum_probs=34.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~  258 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++|+|+++|-...
T Consensus       151 ~~P~llLLDEP~s~LD---------~~~r~~l~~~L~~l~~~~~~tvi~vTHd~~e  197 (353)
T TIGR03265       151 TSPGLLLLDEPLSALD---------ARVREHLRTEIRQLQRRLGVTTIMVTHDQEE  197 (353)
T ss_pred             cCCCEEEEcCCcccCC---------HHHHHHHHHHHHHHHHhcCCEEEEEcCCHHH
Confidence            4689999997664432         2334456778888889999999999986543

This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.

>PRK13639 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.87  E-value=7e-05  Score=67.70  Aligned_cols=26  Identities=31%  Similarity=0.579  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Ge~~~l~G~nGsGKSTLl~~i~G   50 (275)
T PRK13639         25 AEKGEMVALLGPNGAGKSTLFLHFNG   50 (275)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997764

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=97.87  E-value=6.2e-05  Score=69.55  Aligned_cols=45  Identities=20%  Similarity=0.233  Sum_probs=37.2

Q ss_pred             hcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          202 QNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       202 ~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ..+++++++|-+.++...         .....+++.+.++|++.++|++++.|-
T Consensus       523 aerpn~~~iDEF~AhLD~---------~TA~rVArkiselaRe~giTlivvThr  567 (593)
T COG2401         523 AERPNVLLIDEFAAHLDE---------LTAVRVARKISELAREAGITLIVVTHR  567 (593)
T ss_pred             hcCCCcEEhhhhhhhcCH---------HHHHHHHHHHHHHHHHhCCeEEEEecC
Confidence            357899999999888643         455668999999999999999998764

>PRK08181 transposase; Validated

Probab=97.87  E-value=0.00013  Score=65.23  Aligned_cols=40  Identities=23%  Similarity=0.355  Sum_probs=33.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +..+.-+.|+||||+|||.|+..++..++..      +.+|+|++.
T Consensus       103 ~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~------g~~v~f~~~  142 (269)
T PRK08181        103 LAKGANLLLFGPPGGGKSHLAAAIGLALIEN------GWRVLFTRT  142 (269)
T ss_pred             HhcCceEEEEecCCCcHHHHHHHHHHHHHHc------CCceeeeeH
Confidence            4467779999999999999999999877642      478999976

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.87  E-value=8.9e-05  Score=68.38  Aligned_cols=39  Identities=23%  Similarity=0.185  Sum_probs=32.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.-+.|+|++|+|||.|+..+|..++..      +..|+|++...
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~------g~~V~y~t~~~  221 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDR------GKSVIYRTADE  221 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHC------CCeEEEEEHHH
Confidence            4669999999999999999999888742      57899998743

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.87  E-value=0.00022  Score=68.95  Aligned_cols=44  Identities=32%  Similarity=0.382  Sum_probs=35.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +..|.++.|.|++|+||||++..++...+..    +.+.+|.+++++.
T Consensus       347 l~~G~vIaLVGPtGvGKTTtaakLAa~la~~----~~gkkVaLIdtDt  390 (559)
T PRK12727        347 LERGGVIALVGPTGAGKTTTIAKLAQRFAAQ----HAPRDVALVTTDT  390 (559)
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHHHHHHHh----cCCCceEEEeccc
Confidence            5678999999999999999999999877642    1136788998863

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=97.87  E-value=5.8e-05  Score=67.39  Aligned_cols=44  Identities=16%  Similarity=0.157  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..+.-...         .....+.+.|++++++.+++||+++|-
T Consensus       170 ~~p~llllDEPt~~LD~---------~~~~~l~~~L~~~~~~~~~tii~~sH~  213 (255)
T PRK11300        170 TQPEILMLDEPAAGLNP---------KETKELDELIAELRNEHNVTVLLIEHD  213 (255)
T ss_pred             cCCCEEEEcCCccCCCH---------HHHHHHHHHHHHHHhhcCCEEEEEeCC
Confidence            47899999987754432         344557778888888779999999875

>COG1118 CysA ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=97.87  E-value=0.00014  Score=64.90  Aligned_cols=50  Identities=22%  Similarity=0.389  Sum_probs=34.1

Q ss_pred             chhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           88 LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        88 ~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +..+|++-- -|+.|+++.+.||+|+||||++.-||  .+..++     ..-+++..+
T Consensus        15 ~~a~~di~l-~i~~Ge~vaLlGpSGaGKsTlLRiIA--GLe~p~-----~G~I~~~~~   64 (345)
T COG1118          15 FGALDDISL-DIKSGELVALLGPSGAGKSTLLRIIA--GLETPD-----AGRIRLNGR   64 (345)
T ss_pred             cccccccee-eecCCcEEEEECCCCCcHHHHHHHHh--CcCCCC-----CceEEECCE
Confidence            344554322 28899999999999999999999776  343333     335555554

>COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.86  E-value=0.00019  Score=62.88  Aligned_cols=46  Identities=11%  Similarity=0.112  Sum_probs=34.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      |+++++++|..+-=..-         ..-..+.+.|+....++++||++++|.-.
T Consensus       173 h~p~VLfLDEpTvgLDV---------~aq~~ir~Flke~n~~~~aTVllTTH~~~  218 (325)
T COG4586         173 HPPKVLFLDEPTVGLDV---------NAQANIREFLKEYNEERQATVLLTTHIFD  218 (325)
T ss_pred             CCCcEEEecCCccCcch---------hHHHHHHHHHHHHHHhhCceEEEEecchh
Confidence            68999999987743221         22234667899999999999999999744

>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional

Probab=97.86  E-value=0.00024  Score=63.96  Aligned_cols=44  Identities=16%  Similarity=0.104  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-+.-...         .....+.+.|++++++.+.+||+++|-
T Consensus       160 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~~g~tiiivsH~  203 (269)
T PRK11831        160 LEPDLIMFDEPFVGQDP---------ITMGVLVKLISELNSALGVTCVVVSHD  203 (269)
T ss_pred             cCCCEEEEcCCCccCCH---------HHHHHHHHHHHHHHHhcCcEEEEEecC
Confidence            46899999977654422         445567778888888778999999885

>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.86  E-value=0.00024  Score=58.48  Aligned_cols=41  Identities=24%  Similarity=0.387  Sum_probs=29.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      -..|+++-|.|.+|||||||+.  |.|.+..+.     ...+++..|+
T Consensus        29 A~~GdVisIIGsSGSGKSTfLR--CiN~LE~P~-----~G~I~v~gee   69 (256)
T COG4598          29 ANAGDVISIIGSSGSGKSTFLR--CINFLEKPS-----AGSIRVNGEE   69 (256)
T ss_pred             cCCCCEEEEecCCCCchhHHHH--HHHhhcCCC-----CceEEECCeE
Confidence            4679999999999999999987  455554433     3456666553

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.86  E-value=0.00012  Score=62.87  Aligned_cols=28  Identities=14%  Similarity=0.146  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +..|+++.|.||+|+|||||+..++...
T Consensus        22 l~~g~~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          22 MEKKNGILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             EcCCcEEEEECCCCCChHHHHHHHHHHH
Confidence            4557999999999999999999998655

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

>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=97.86  E-value=0.00024  Score=61.90  Aligned_cols=108  Identities=21%  Similarity=0.280  Sum_probs=62.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      ...+.|+|++|+|||.|+..++..+...    ..+.+|+|++.+. |...    +..              ....     
T Consensus        34 ~~~l~l~G~~G~GKTHLL~Ai~~~~~~~----~~~~~v~y~~~~~-f~~~----~~~--------------~~~~-----   85 (219)
T PF00308_consen   34 YNPLFLYGPSGLGKTHLLQAIANEAQKQ----HPGKRVVYLSAEE-FIRE----FAD--------------ALRD-----   85 (219)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHHHHH----CTTS-EEEEEHHH-HHHH----HHH--------------HHHT-----
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHHhc----cccccceeecHHH-HHHH----HHH--------------HHHc-----
Confidence            3457899999999999999888776532    1257899998753 1111    110              0101     


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          182 QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                        ....+   +.+.+      ...++++||.+..+...        .....++...+.. ..+.|..+|+++....
T Consensus        86 --~~~~~---~~~~~------~~~DlL~iDDi~~l~~~--------~~~q~~lf~l~n~-~~~~~k~li~ts~~~P  141 (219)
T PF00308_consen   86 --GEIEE---FKDRL------RSADLLIIDDIQFLAGK--------QRTQEELFHLFNR-LIESGKQLILTSDRPP  141 (219)
T ss_dssp             --TSHHH---HHHHH------CTSSEEEEETGGGGTTH--------HHHHHHHHHHHHH-HHHTTSEEEEEESS-T
T ss_pred             --ccchh---hhhhh------hcCCEEEEecchhhcCc--------hHHHHHHHHHHHH-HHhhCCeEEEEeCCCC
Confidence              11112   22221      36899999999887421        1122334444444 4456888888876543

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.

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=97.86  E-value=0.00029  Score=57.12  Aligned_cols=26  Identities=27%  Similarity=0.332  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 ~~~Ge~~~i~G~nGsGKStLl~~l~G   48 (144)
T cd03221          23 INPGDRIGLVGRNGAGKSTLLKLIAG   48 (144)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHcC
Confidence            88999999999999999999997764

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.

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=97.86  E-value=0.00013  Score=65.56  Aligned_cols=44  Identities=9%  Similarity=0.111  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+...|+.++++.+.+||+++|-
T Consensus       164 ~~p~lllLDEPt~~LD~---------~~~~~~~~~l~~l~~~~~~tiii~sH~  207 (265)
T PRK10575        164 QDSRCLLLDEPTSALDI---------AHQVDVLALVHRLSQERGLTVIAVLHD  207 (265)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            47899999987654422         344567778888888779999999875

>PRK10908 cell division protein FtsE; Provisional

Probab=97.86  E-value=0.00018  Score=62.80  Aligned_cols=26  Identities=23%  Similarity=0.307  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G   50 (222)
T PRK10908         25 MRPGEMAFLTGHSGAGKSTLLKLICG   50 (222)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999998773

>PRK11144 modC molybdate transporter ATP-binding protein; Provisional

Probab=97.86  E-value=6.7e-05  Score=70.25  Aligned_cols=46  Identities=20%  Similarity=0.146  Sum_probs=34.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-...         .....+...|++++++.+.++|+++|-..
T Consensus       145 ~~p~llLLDEPts~LD~---------~~~~~l~~~L~~l~~~~g~tii~vTHd~~  190 (352)
T PRK11144        145 TAPELLLMDEPLASLDL---------PRKRELLPYLERLAREINIPILYVSHSLD  190 (352)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHhcCCeEEEEecCHH
Confidence            47899999977654322         33445777888888888999999988654

>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]

Probab=97.85  E-value=0.00011  Score=67.41  Aligned_cols=40  Identities=28%  Similarity=0.430  Sum_probs=31.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +..|+++.|.||+|||||||+.-+|  .+...     ..+-++|+.+
T Consensus        26 i~~Gef~vllGPSGcGKSTlLr~IA--GLe~~-----~~G~I~i~g~   65 (338)
T COG3839          26 IEDGEFVVLLGPSGCGKSTLLRMIA--GLEEP-----TSGEILIDGR   65 (338)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHh--CCCCC-----CCceEEECCE
Confidence            7899999999999999999999777  33322     3557777765

>PRK09452 potA putrescine/spermidine ABC transporter ATPase protein; Reviewed

Probab=97.85  E-value=9.9e-05  Score=69.52  Aligned_cols=46  Identities=15%  Similarity=0.116  Sum_probs=33.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++++|+++|-..
T Consensus       161 ~~P~llLLDEP~s~LD---------~~~r~~l~~~L~~l~~~~g~tiI~vTHd~~  206 (375)
T PRK09452        161 NKPKVLLLDESLSALD---------YKLRKQMQNELKALQRKLGITFVFVTHDQE  206 (375)
T ss_pred             cCCCEEEEeCCCCcCC---------HHHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            3689999997654332         233345677888999999999999998654

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=97.85  E-value=0.00012  Score=63.98  Aligned_cols=26  Identities=35%  Similarity=0.475  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        45 i~~Ge~~~i~G~nGsGKSTLl~~l~G   70 (224)
T cd03220          45 VPRGERIGLIGRNGAGKSTLLRLLAG   70 (224)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997774

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.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=97.85  E-value=0.00014  Score=72.95  Aligned_cols=28  Identities=32%  Similarity=0.553  Sum_probs=24.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       366 i~~G~~~aIvG~sGsGKSTLl~ll~gl~  393 (582)
T PRK11176        366 IPAGKTVALVGRSGSGKSTIANLLTRFY  393 (582)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            7899999999999999999999777543

>PRK13644 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.84  E-value=9.8e-05  Score=66.70  Aligned_cols=26  Identities=27%  Similarity=0.514  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G   50 (274)
T PRK13644         25 IKKGEYIGIIGKNGSGKSTLALHLNG   50 (274)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997774

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

Probab=97.84  E-value=0.00014  Score=68.98  Aligned_cols=29  Identities=31%  Similarity=0.381  Sum_probs=25.9

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |++++.-++|+||||+|||+++..+|...
T Consensus       175 Gl~~pkgvLL~GppGTGKT~LAkalA~~l  203 (398)
T PTZ00454        175 GIDPPRGVLLYGPPGTGKTMLAKAVAHHT  203 (398)
T ss_pred             CCCCCceEEEECCCCCCHHHHHHHHHHhc
Confidence            58888889999999999999999888654

>PRK08727 hypothetical protein; Validated

Probab=97.84  E-value=0.00019  Score=63.24  Aligned_cols=38  Identities=34%  Similarity=0.467  Sum_probs=30.9

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ...+.|+|++|+|||.|+..++..+..+      +.+++|++.+
T Consensus        41 ~~~l~l~G~~G~GKThL~~a~~~~~~~~------~~~~~y~~~~   78 (233)
T PRK08727         41 SDWLYLSGPAGTGKTHLALALCAAAEQA------GRSSAYLPLQ   78 (233)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHc------CCcEEEEeHH
Confidence            3569999999999999999988876532      4789999753

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=97.84  E-value=0.00017  Score=65.04  Aligned_cols=28  Identities=25%  Similarity=0.382  Sum_probs=25.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+|+++.|.|++|+|||||+.-++...
T Consensus        27 I~~Ge~~~IvG~nGsGKSTLl~~L~gl~   54 (275)
T cd03289          27 ISPGQRVGLLGRTGSGKSTLLSAFLRLL   54 (275)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhhhc
Confidence            8899999999999999999999877554

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>PRK11607 potG putrescine transporter ATP-binding subunit; Provisional

Probab=97.84  E-value=9.5e-05  Score=69.72  Aligned_cols=47  Identities=13%  Similarity=0.110  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~  258 (357)
                      .+++++++|.-.+-...         ..-..+...|+++.++.++++|+++|-...
T Consensus       166 ~~P~lLLLDEP~s~LD~---------~~r~~l~~~l~~l~~~~g~tii~vTHd~~e  212 (377)
T PRK11607        166 KRPKLLLLDEPMGALDK---------KLRDRMQLEVVDILERVGVTCVMVTHDQEE  212 (377)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEcCCHHH
Confidence            47899999976544321         233345667888888889999999986543

>PRK15112 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional

Probab=97.84  E-value=0.00014  Score=65.46  Aligned_cols=45  Identities=22%  Similarity=0.129  Sum_probs=33.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|++++++++.+||+++|-.
T Consensus       166 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~~g~tviivsH~~  210 (267)
T PRK15112        166 LRPKVIIADEALASLDM---------SMRSQLINLMLELQEKQGISYIYVTQHL  210 (267)
T ss_pred             hCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHHHcCcEEEEEeCCH
Confidence            47899999987755432         3344577788888888899999998753

>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.84  E-value=0.00013  Score=67.38  Aligned_cols=34  Identities=15%  Similarity=0.258  Sum_probs=27.5

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .|+.+-- -+++|+++.|.|++|+|||||+.-++.
T Consensus        41 ~L~~vsl-~i~~Ge~~~I~G~nGsGKSTLl~~L~G   74 (320)
T PRK13631         41 ALNNISY-TFEKNKIYFIIGNSGSGKSTLVTHFNG   74 (320)
T ss_pred             ceeeeEE-EEcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            4555422 389999999999999999999997774

>PRK06526 transposase; Provisional

Probab=97.84  E-value=0.00011  Score=65.34  Aligned_cols=40  Identities=28%  Similarity=0.428  Sum_probs=32.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +..+.-+.|+||||+|||.++..++..++..      +.+|+|++.
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~al~~~a~~~------g~~v~f~t~  134 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAIGLGIRACQA------GHRVLFATA  134 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHHHHHHHHHHC------CCchhhhhH
Confidence            4556789999999999999999999887742      477887654

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=97.83  E-value=7.5e-05  Score=64.47  Aligned_cols=27  Identities=33%  Similarity=0.477  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        31 i~~G~~~~i~G~nGsGKSTLl~~l~Gl   57 (207)
T cd03369          31 VKAGEKIGIVGRTGAGKSTLILALFRF   57 (207)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            889999999999999999999977653

NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.

>TIGR03258 PhnT 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT

Probab=97.83  E-value=8.9e-05  Score=69.52  Aligned_cols=47  Identities=13%  Similarity=0.089  Sum_probs=33.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHc-CCeEEEecccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS-RIPIVVTNQVRPQ  258 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~-~~~vv~~~q~~~~  258 (357)
                      .+++++++|.-.+-..         ...-.++...|+++.+++ ++++|+++|-...
T Consensus       154 ~~P~llLLDEP~s~LD---------~~~r~~l~~~l~~l~~~~~g~til~vTHd~~e  201 (362)
T TIGR03258       154 IEPDVLLLDEPLSALD---------ANIRANMREEIAALHEELPELTILCVTHDQDD  201 (362)
T ss_pred             cCCCEEEEcCccccCC---------HHHHHHHHHHHHHHHHhCCCCEEEEEeCCHHH
Confidence            4799999997664432         233445677788888887 8999999886543

This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.82  E-value=0.00026  Score=67.78  Aligned_cols=41  Identities=39%  Similarity=0.430  Sum_probs=34.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhc-cccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAA-LPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~-~~~~~gg~~~~vl~i~~e~  146 (357)
                      .|.++.|.||+|+||||++..+|...+ ..     .+.+|.+|+++.
T Consensus       220 ~~~~i~~vGptGvGKTTt~~kLA~~~~~~~-----~g~~V~li~~D~  261 (424)
T PRK05703        220 QGGVVALVGPTGVGKTTTLAKLAARYALLY-----GKKKVALITLDT  261 (424)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhc-----CCCeEEEEECCc
Confidence            367999999999999999999998876 31     147899999864

>COG1129 MglA ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]

Probab=97.82  E-value=0.0001  Score=70.73  Aligned_cols=51  Identities=37%  Similarity=0.473  Sum_probs=37.6

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      |++.||.+--- +.+|+++.+.|++|+|||||+.-++--.  ++     ...-++++.+
T Consensus        20 gV~AL~~v~l~-v~~GEV~aL~GeNGAGKSTLmKiLsGv~--~p-----~~G~I~~~G~   70 (500)
T COG1129          20 GVKALDGVSLT-VRPGEVHALLGENGAGKSTLMKILSGVY--PP-----DSGEILIDGK   70 (500)
T ss_pred             CceeeccceeE-EeCceEEEEecCCCCCHHHHHHHHhCcc--cC-----CCceEEECCE
Confidence            56677776433 8999999999999999999999666433  32     2446777754

>PRK08116 hypothetical protein; Validated

Probab=97.82  E-value=0.00039  Score=62.48  Aligned_cols=37  Identities=27%  Similarity=0.262  Sum_probs=30.7

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +.-+.|.|+||+|||.|+..++......      +.+|+|++.
T Consensus       114 ~~gl~l~G~~GtGKThLa~aia~~l~~~------~~~v~~~~~  150 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAACIANELIEK------GVPVIFVNF  150 (268)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEEEH
Confidence            3458999999999999999999887642      478999975

>TIGR02142 modC_ABC molybdenum ABC transporter, ATP-binding protein

Probab=97.82  E-value=6.7e-05  Score=70.34  Aligned_cols=46  Identities=17%  Similarity=0.148  Sum_probs=34.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-...         .....+...|++++++.+.+||+++|-..
T Consensus       148 ~~p~lllLDEPts~LD~---------~~~~~l~~~L~~l~~~~g~tiiivtH~~~  193 (354)
T TIGR02142       148 SSPRLLLMDEPLAALDD---------PRKYEILPYLERLHAEFGIPILYVSHSLQ  193 (354)
T ss_pred             cCCCEEEEcCCCcCCCH---------HHHHHHHHHHHHHHHhcCCEEEEEecCHH
Confidence            46899999987655432         34445778888888888999999988654

This model represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulfate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulfate transporter rather than by a specific molybdate transporter.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.82  E-value=0.00035  Score=65.22  Aligned_cols=93  Identities=17%  Similarity=0.172  Sum_probs=55.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      +..+.|.|++|+||||++..+|.....      .+.+|.+++++. +....+.+...           +.+.  .++-++
T Consensus       241 ~~vI~LVGptGvGKTTTiaKLA~~L~~------~GkkVglI~aDt-~RiaAvEQLk~-----------yae~--lgipv~  300 (436)
T PRK11889        241 VQTIALIGPTGVGKTTTLAKMAWQFHG------KKKTVGFITTDH-SRIGTVQQLQD-----------YVKT--IGFEVI  300 (436)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHH------cCCcEEEEecCC-cchHHHHHHHH-----------Hhhh--cCCcEE
Confidence            468999999999999999999987653      247899999864 22212222111           0011  123233


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhcCeeEEEEecccccc
Q 035774          182 QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALV  217 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~  217 (357)
                      ...+..++...+..+   ....+.++|+||..+...
T Consensus       301 v~~d~~~L~~aL~~l---k~~~~~DvVLIDTaGRs~  333 (436)
T PRK11889        301 AVRDEAAMTRALTYF---KEEARVDYILIDTAGKNY  333 (436)
T ss_pred             ecCCHHHHHHHHHHH---HhccCCCEEEEeCccccC
Confidence            234555554433332   212368999999877543

>PRK15093 antimicrobial peptide ABC transporter ATP-binding protein; Provisional

Probab=97.82  E-value=0.00026  Score=65.67  Aligned_cols=46  Identities=20%  Similarity=0.213  Sum_probs=35.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         ....++++.|+++.+++++++|+++|--.
T Consensus       175 ~~P~llilDEPts~LD~---------~~~~~i~~lL~~l~~~~g~tii~itHdl~  220 (330)
T PRK15093        175 NQPRLLIADEPTNAMEP---------TTQAQIFRLLTRLNQNNNTTILLISHDLQ  220 (330)
T ss_pred             CCCCEEEEeCCCCcCCH---------HHHHHHHHHHHHHHHhcCCEEEEEECCHH
Confidence            46899999987765432         34456788888888888999999998643

>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment

Probab=97.81  E-value=0.00022  Score=63.16  Aligned_cols=44  Identities=14%  Similarity=-0.007  Sum_probs=32.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..+.-...         .....+.+.|++++++.+.+||+++|-
T Consensus       152 ~~p~llllDEPt~~LD~---------~~~~~l~~~L~~~~~~~g~tvii~sH~  195 (242)
T cd03295         152 ADPPLLLMDEPFGALDP---------ITRDQLQEEFKRLQQELGKTIVFVTHD  195 (242)
T ss_pred             cCCCEEEecCCcccCCH---------HHHHHHHHHHHHHHHHcCCEEEEEecC
Confidence            47899999987654322         334457778888888778999999875

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. 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.

>PRK13649 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.81  E-value=0.00016  Score=65.62  Aligned_cols=26  Identities=27%  Similarity=0.419  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~~i~G   55 (280)
T PRK13649         30 IEDGSYTAFIGHTGSGKSTIMQLLNG   55 (280)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997764

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=97.81  E-value=0.00016  Score=72.58  Aligned_cols=28  Identities=39%  Similarity=0.565  Sum_probs=25.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       373 i~~G~~vaIvG~SGsGKSTL~~lL~g~~  400 (588)
T PRK11174        373 LPAGQRIALVGPSGAGKTSLLNALLGFL  400 (588)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            7899999999999999999999777644

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=97.81  E-value=0.00011  Score=64.02  Aligned_cols=27  Identities=33%  Similarity=0.496  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        27 i~~Ge~~~i~G~nGsGKSTLl~~l~G~   53 (221)
T cd03244          27 IKPGEKVGIVGRTGSGKSSLLLALFRL   53 (221)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHcC
Confidence            889999999999999999999977743

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>PRK13641 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=97.80  E-value=0.00015  Score=65.92  Aligned_cols=26  Identities=27%  Similarity=0.485  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        30 i~~Ge~~~iiG~NGaGKSTLl~~l~G   55 (287)
T PRK13641         30 LEEGSFVALVGHTGSGKSTLMQHFNA   55 (287)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997774

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=97.80  E-value=0.00016  Score=62.02  Aligned_cols=26  Identities=31%  Similarity=0.446  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G   48 (198)
T TIGR01189        23 LNAGEALQVTGPNGIGKTTLLRILAG   48 (198)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997764

This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.80  E-value=0.00014  Score=63.20  Aligned_cols=25  Identities=28%  Similarity=0.558  Sum_probs=23.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +.+|+++.|.||+|||||||..-+|
T Consensus        26 v~~GEfvsilGpSGcGKSTLLriiA   50 (248)
T COG1116          26 VEKGEFVAILGPSGCGKSTLLRLIA   50 (248)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHh
Confidence            8899999999999999999998665

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=97.80  E-value=0.00016  Score=62.96  Aligned_cols=26  Identities=35%  Similarity=0.337  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G   50 (220)
T cd03263          25 VYKGEIFGLLGHNGAGKTTTLKMLTG   50 (220)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997774

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.79  E-value=0.00018  Score=65.19  Aligned_cols=43  Identities=37%  Similarity=0.471  Sum_probs=35.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..+.++.|+||+|+||||++..++......  .|  +.+|.+|+++.
T Consensus       192 ~~~~vi~~vGptGvGKTTt~~kLa~~~~~~--~g--~~~V~li~~D~  234 (282)
T TIGR03499       192 EQGGVIALVGPTGVGKTTTLAKLAARFVLE--HG--NKKVALITTDT  234 (282)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHH--cC--CCeEEEEECCc
Confidence            467899999999999999999999887641  11  36899999874

>PRK10418 nikD nickel transporter ATP-binding protein NikD; Provisional

Probab=97.79  E-value=0.0007  Score=60.43  Aligned_cols=44  Identities=7%  Similarity=0.124  Sum_probs=33.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+...|++++++.+.+||+++|-
T Consensus       157 ~~p~lLlLDEPt~~LD~---------~~~~~l~~~L~~~~~~~g~til~~sH~  200 (254)
T PRK10418        157 CEAPFIIADEPTTDLDV---------VAQARILDLLESIVQKRALGMLLVTHD  200 (254)
T ss_pred             cCCCEEEEeCCCcccCH---------HHHHHHHHHHHHHHHhcCcEEEEEecC
Confidence            47899999987755432         334457778888888889999999875

>PRK07721 fliI flagellum-specific ATP synthase; Validated

Probab=97.79  E-value=0.00038  Score=66.60  Aligned_cols=58  Identities=19%  Similarity=0.208  Sum_probs=44.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ...+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.... +      ...++.+..|..
T Consensus       139 ~~~l~tg~~vid~l~~--i~~Gq~i~I~G~sG~GKStLl~~I~~~~~-~------~~gvI~~~Gerg  196 (438)
T PRK07721        139 REPMEVGVRAIDSLLT--VGKGQRVGIFAGSGVGKSTLMGMIARNTS-A------DLNVIALIGERG  196 (438)
T ss_pred             ccccccchhhhheeee--ecCCcEEEEECCCCCCHHHHHHHHhcccC-C------CeEEEEEEecCC
Confidence            3478999999999965  99999999999999999999876664332 1      244566655543

>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]

Probab=97.78  E-value=0.00023  Score=68.79  Aligned_cols=44  Identities=14%  Similarity=0.139  Sum_probs=36.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++|.|.-+.....         ..-.+++..|+.+.+++|+++++++|.
T Consensus       171 ~~P~LLIaDEPTTaLDv---------t~q~qIL~llk~l~~e~g~a~l~ITHD  214 (539)
T COG1123         171 LKPKLLIADEPTTALDV---------TTQAQILDLLKDLQRELGMAVLFITHD  214 (539)
T ss_pred             CCCCEEEECCCccccCH---------HHHHHHHHHHHHHHHHcCcEEEEEcCC
Confidence            47999999987765432         455678999999999999999999995

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=97.78  E-value=0.00015  Score=62.96  Aligned_cols=26  Identities=35%  Similarity=0.402  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~G~~~~l~G~nGsGKSTLl~~i~G   50 (214)
T TIGR02673        25 IRKGEFLFLTGPSGAGKTTLLKLLYG   50 (214)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999987663

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.

>KOG0061 consensus Transporter, ABC superfamily (Breast cancer resistance protein) [Secondary metabolites biosynthesis, transport and catabolism]

Probab=97.78  E-value=0.00015  Score=72.74  Aligned_cols=32  Identities=28%  Similarity=0.425  Sum_probs=28.2

Q ss_pred             cCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           96 CGGVPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        96 ~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .|=+.+|+++.|.||+|+|||||..-++....
T Consensus        50 sg~~~~Gel~AimG~SGsGKtTLL~~Lagr~~   81 (613)
T KOG0061|consen   50 SGTAKPGELLAIMGPSGSGKTTLLNALAGRLN   81 (613)
T ss_pred             EEEEecCeEEEEECCCCCCHHHHHHHHhcccc
Confidence            35589999999999999999999998887664

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=97.78  E-value=0.00015  Score=74.21  Aligned_cols=27  Identities=26%  Similarity=0.364  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       488 i~~G~~iaIvG~sGsGKSTLlklL~gl  514 (694)
T TIGR03375       488 IRPGEKVAIIGRIGSGKSTLLKLLLGL  514 (694)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999999877643

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.

>PRK09984 phosphonate/organophosphate ester transporter subunit; Provisional

Probab=97.77  E-value=0.00014  Score=65.23  Aligned_cols=45  Identities=18%  Similarity=0.180  Sum_probs=33.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       169 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~g~tvii~tH~~  213 (262)
T PRK09984        169 QQAKVILADEPIASLDP---------ESARIVMDTLRDINQNDGITVVVTLHQV  213 (262)
T ss_pred             cCCCEEEecCccccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            46899999987755432         4455678888888887789999998753

>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE)

Probab=97.77  E-value=0.00022  Score=62.48  Aligned_cols=44  Identities=16%  Similarity=0.143  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+...|++++++.+.+||+++|-
T Consensus       162 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tii~~sH~  205 (228)
T cd03257         162 LNPKLLIADEPTSALDV---------SVQAQILDLLKKLQEELGLTLLFITHD  205 (228)
T ss_pred             cCCCEEEecCCCCCCCH---------HHHHHHHHHHHHHHHHcCCEEEEEeCC
Confidence            47899999987754422         334457788888888778999999885

The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.

>PRK11614 livF leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=97.77  E-value=0.0002  Score=63.19  Aligned_cols=26  Identities=31%  Similarity=0.468  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+..++.
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~~l~G   53 (237)
T PRK11614         28 INQGEIVTLIGANGAGKTTLLGTLCG   53 (237)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHcC
Confidence            88999999999999999999997763

>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein

Probab=97.77  E-value=0.00014  Score=74.37  Aligned_cols=40  Identities=25%  Similarity=0.504  Sum_probs=30.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+.+.|.|++|||||||+.-++....  +     ..+-++++..
T Consensus       476 i~~Ge~vaIvG~sGsGKSTLlklL~gl~~--p-----~~G~I~idg~  515 (686)
T TIGR03797       476 IEPGEFVAIVGPSGSGKSTLLRLLLGFET--P-----ESGSVFYDGQ  515 (686)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCC--C-----CCCEEEECCE
Confidence            88999999999999999999997775432  2     2345666653

Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif

>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD

Probab=97.76  E-value=0.0002  Score=62.96  Aligned_cols=45  Identities=11%  Similarity=0.067  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       142 ~~p~vllLDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tiii~sH~~  186 (230)
T TIGR02770       142 LEPPFLIADEPTTDLDV---------VNQARVLKLLRELRQLFGTGILLITHDL  186 (230)
T ss_pred             cCCCEEEEcCCccccCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            47899999987754422         3445577788888887899999998853

This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous.

>TIGR02769 nickel_nikE nickel import ATP-binding protein NikE

Probab=97.76  E-value=0.0001  Score=66.24  Aligned_cols=45  Identities=13%  Similarity=0.062  Sum_probs=33.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       167 ~~p~illLDEPt~~LD~---------~~~~~l~~~l~~~~~~~g~tiiivsH~~  211 (265)
T TIGR02769       167 VKPKLIVLDEAVSNLDM---------VLQAVILELLRKLQQAFGTAYLFITHDL  211 (265)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCcEEEEEeCCH
Confidence            47899999987654422         3344577888888888899999998853

This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase.

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=97.76  E-value=0.00025  Score=61.04  Aligned_cols=27  Identities=37%  Similarity=0.581  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        28 i~~G~~~~i~G~nG~GKSTLl~~i~G~   54 (204)
T cd03250          28 VPKGELVAIVGPVGSGKSSLLSALLGE   54 (204)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCc
Confidence            889999999999999999999987653

This family is also known as MRP (mulrtidrug resisitance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.

>TIGR02324 CP_lyasePhnL phosphonate C-P lyase system protein PhnL

Probab=97.76  E-value=0.00037  Score=60.91  Aligned_cols=26  Identities=35%  Similarity=0.528  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        31 i~~Ge~~~l~G~nGsGKSTLl~~i~G   56 (224)
T TIGR02324        31 VNAGECVALSGPSGAGKSTLLKSLYA   56 (224)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997764

Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se.

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=97.76  E-value=0.00019  Score=72.20  Aligned_cols=27  Identities=33%  Similarity=0.414  Sum_probs=24.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       364 i~~Ge~iaIvG~SGsGKSTLl~lL~gl  390 (592)
T PRK10790        364 VPSRGFVALVGHTGSGKSTLASLLMGY  390 (592)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999999977653

>PRK03695 vitamin B12-transporter ATPase; Provisional

Probab=97.75  E-value=0.00027  Score=62.83  Aligned_cols=26  Identities=35%  Similarity=0.621  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        19 i~~Gei~~l~G~nGsGKSTLl~~l~G   44 (248)
T PRK03695         19 VRAGEILHLVGPNGAGKSTLLARMAG   44 (248)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHcC
Confidence            78999999999999999999997764

>PRK10253 iron-enterobactin transporter ATP-binding protein; Provisional

Probab=97.75  E-value=0.00022  Score=64.11  Aligned_cols=45  Identities=7%  Similarity=0.044  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+.+.|++++++.+.+||+++|-.
T Consensus       160 ~~p~llllDEPt~gLD~---------~~~~~l~~~L~~l~~~~~~tiii~tH~~  204 (265)
T PRK10253        160 QETAIMLLDEPTTWLDI---------SHQIDLLELLSELNREKGYTLAAVLHDL  204 (265)
T ss_pred             cCCCEEEEeCccccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            47899999987654432         3444577788888877789999998753

>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters

Probab=97.75  E-value=0.00023  Score=62.06  Aligned_cols=26  Identities=23%  Similarity=0.399  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        27 i~~G~~~~i~G~nGsGKSTLl~~i~G   52 (220)
T cd03245          27 IRAGEKVAIIGRVGSGKSTLLKLLAG   52 (220)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999999997764

Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.

>PRK09536 btuD corrinoid ABC transporter ATPase; Reviewed

Probab=97.75  E-value=0.00013  Score=69.18  Aligned_cols=26  Identities=38%  Similarity=0.554  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.||+|+|||||+..++.
T Consensus        26 i~~Geiv~liGpNGaGKSTLLk~LaG   51 (402)
T PRK09536         26 VREGSLVGLVGPNGAGKTTLLRAING   51 (402)
T ss_pred             ECCCCEEEEECCCCchHHHHHHHHhc
Confidence            78999999999999999999997764

>cd01132 F1_ATPase_alpha F1 ATP synthase alpha, central domain

Probab=97.75  E-value=0.00014  Score=64.76  Aligned_cols=58  Identities=22%  Similarity=0.273  Sum_probs=46.0

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|-++.  +-+|+=..|.|++|+|||+|+++.+.+...      .+..++|.-.-+
T Consensus        50 ~e~L~TGI~~ID~l~p--igrGQr~~Ifg~~g~GKt~L~l~~i~~~~~------~~v~~V~~~iGe  107 (274)
T cd01132          50 NEPLQTGIKAIDAMIP--IGRGQRELIIGDRQTGKTAIAIDTIINQKG------KKVYCIYVAIGQ  107 (274)
T ss_pred             ccccccCCEEeeccCC--cccCCEEEeeCCCCCCccHHHHHHHHHhcC------CCeEEEEEeccc
Confidence            5689999999999987  889999999999999999998766655432      145567776544

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.

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

Probab=97.75  E-value=0.00032  Score=63.75  Aligned_cols=112  Identities=15%  Similarity=0.214  Sum_probs=66.5

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      ||.|-.=++++||||+|||.||...|...           .+-||-.-+   ++-+.+...                   
T Consensus       181 GI~PPKGVLLYGPPGTGKTLLAkAVA~~T-----------~AtFIrvvg---SElVqKYiG-------------------  227 (406)
T COG1222         181 GIDPPKGVLLYGPPGTGKTLLAKAVANQT-----------DATFIRVVG---SELVQKYIG-------------------  227 (406)
T ss_pred             CCCCCCceEeeCCCCCcHHHHHHHHHhcc-----------CceEEEecc---HHHHHHHhc-------------------
Confidence            58888889999999999999999776543           344554332   122211110                   


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHH----HHHHHHHHHHHHHHcCCeEEEe
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHP----LSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~----~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                                +=..++..+-.+.+++.+.+|+||.|-++-...++.......+    +-+++..|..+-..-|+-||+.
T Consensus       228 ----------EGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~~~nvKVI~A  296 (406)
T COG1222         228 ----------EGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKVIMA  296 (406)
T ss_pred             ----------cchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCCCCCeEEEEe
Confidence                      1112334444555678899999999999866544433322233    3334444444445556777654

>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=97.74  E-value=0.00016  Score=64.79  Aligned_cols=35  Identities=23%  Similarity=0.162  Sum_probs=25.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      |++|+|-||||||++|.++......      .+..|.+++.
T Consensus         3 Liil~G~P~SGKTt~a~~L~~~~~~------~~~~v~~i~~   37 (270)
T PF08433_consen    3 LIILCGLPCSGKTTRAKELKKYLEE------KGKEVVIISD   37 (270)
T ss_dssp             EEEEE--TTSSHHHHHHHHHHHHHH------TT--EEEE-T
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHHh------cCCEEEEEcc
Confidence            7899999999999999999987653      1477888874

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=97.74  E-value=0.00016  Score=71.65  Aligned_cols=27  Identities=33%  Similarity=0.666  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       358 i~~G~~vaIvG~SGsGKSTLl~lL~g~  384 (529)
T TIGR02868       358 LPPGERVAILGPSGSGKSTLLMLLTGL  384 (529)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999999876643

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.

>PRK10419 nikE nickel transporter ATP-binding protein NikE; Provisional

Probab=97.74  E-value=0.00013  Score=65.71  Aligned_cols=45  Identities=16%  Similarity=0.058  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-...         .....+...|+.++++++.++|+++|-.
T Consensus       168 ~~p~lllLDEPt~~LD~---------~~~~~~~~~l~~~~~~~~~tiiivsH~~  212 (268)
T PRK10419        168 VEPKLLILDEAVSNLDL---------VLQAGVIRLLKKLQQQFGTACLFITHDL  212 (268)
T ss_pred             cCCCEEEEeCCCcccCH---------HHHHHHHHHHHHHHHHcCcEEEEEECCH
Confidence            47899999987654422         3344577788888888899999998753

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.74  E-value=0.00024  Score=61.72  Aligned_cols=26  Identities=31%  Similarity=0.307  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        34 i~~Ge~~~i~G~nGsGKSTLl~~i~G   59 (214)
T PRK13543         34 VDAGEALLVQGDNGAGKTTLLRVLAG   59 (214)
T ss_pred             ECCCCEEEEEcCCCCCHHHHHHHHhC
Confidence            88999999999999999999998774

>PRK06921 hypothetical protein; Provisional

Probab=97.72  E-value=0.00045  Score=61.95  Aligned_cols=39  Identities=21%  Similarity=0.187  Sum_probs=31.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+.-+.|.|+||+|||.|+..++..+...  .   +..|+|++.
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~--~---g~~v~y~~~  154 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRK--K---GVPVLYFPF  154 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhh--c---CceEEEEEH
Confidence            36678999999999999999998877631  1   478999986

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=97.72  E-value=0.00015  Score=63.40  Aligned_cols=26  Identities=35%  Similarity=0.551  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~l~G   48 (223)
T TIGR03740        23 VPKNSVYGLLGPNGAGKSTLLKMITG   48 (223)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997764

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.

>PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional

Probab=97.72  E-value=0.00063  Score=60.17  Aligned_cols=27  Identities=33%  Similarity=0.503  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLl~~l~G~   52 (241)
T PRK10895         26 VNSGEIVGLLGPNGAGKTTTFYMVVGI   52 (241)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999999977753

>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=97.72  E-value=0.00012  Score=63.97  Aligned_cols=150  Identities=20%  Similarity=0.162  Sum_probs=71.3

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccc
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKG  169 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~  169 (357)
                      .|...+.+|  ++..+.|+||.|+|||+|+.+++...-.      .+..++|++.-.......+....... ........
T Consensus        10 ~l~~~l~~~--~~~~~~l~G~rg~GKTsLl~~~~~~~~~------~~~~~~y~~~~~~~~~~~~~~~~~~~-~~~~~l~~   80 (234)
T PF01637_consen   10 KLKELLESG--PSQHILLYGPRGSGKTSLLKEFINELKE------KGYKVVYIDFLEESNESSLRSFIEET-SLADELSE   80 (234)
T ss_dssp             HHHHCHHH----SSEEEEEESTTSSHHHHHHHHHHHCT--------EECCCHHCCTTBSHHHHHHHHHHHH-HHHCHCHH
T ss_pred             HHHHHHHhh--cCcEEEEEcCCcCCHHHHHHHHHHHhhh------cCCcEEEEecccchhhhHHHHHHHHH-HHHHHHHH
Confidence            344444432  4689999999999999999999876631      12467787765443333333331100 00000000


Q ss_pred             hHHHhhcC--e-EEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHc
Q 035774          170 MAQEMAGR--I-LVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS  245 (357)
Q Consensus       170 ~~~~~~~~--i-~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~  245 (357)
                      ........  + .+.. .........+..+...+... .--+||||.+..+. ....   .....+..+...+.......
T Consensus        81 ~~~~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~-~~~~---~~~~~~~~l~~~~~~~~~~~  155 (234)
T PF01637_consen   81 ALGISIPSITLEKISK-DLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLA-IASE---EDKDFLKSLRSLLDSLLSQQ  155 (234)
T ss_dssp             HHHHHCCTSTTEEEEC-TS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGG-BCTT---TTHHHHHHHHHHHHH----T
T ss_pred             HHhhhcccccchhhhh-cchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHh-hccc---chHHHHHHHHHHHhhccccC
Confidence            00111111  1 1111 11222223333333333333 23788999999987 2111   13355566666666666667


Q ss_pred             CCeEEEec
Q 035774          246 RIPIVVTN  253 (357)
Q Consensus       246 ~~~vv~~~  253 (357)
                      ++.+|++.
T Consensus       156 ~~~~v~~~  163 (234)
T PF01637_consen  156 NVSIVITG  163 (234)
T ss_dssp             TEEEEEEE
T ss_pred             CceEEEEC
Confidence            77777664

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

>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional

Probab=97.71  E-value=0.00036  Score=62.10  Aligned_cols=26  Identities=38%  Similarity=0.666  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        26 i~~Ge~~~i~G~nGsGKSTLl~~l~G   51 (250)
T PRK11264         26 VKPGEVVAIIGPSGSGKTTLLRCINL   51 (250)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997764

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=97.71  E-value=0.00025  Score=71.20  Aligned_cols=27  Identities=30%  Similarity=0.493  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       358 i~~G~~v~IvG~sGsGKSTLl~lL~gl  384 (588)
T PRK13657        358 AKPGQTVAIVGPTGAGKSTLINLLQRV  384 (588)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            779999999999999999999866643

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

Probab=97.71  E-value=0.00037  Score=61.72  Aligned_cols=37  Identities=19%  Similarity=0.186  Sum_probs=31.3

Q ss_pred             hhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           89 KGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        89 ~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ..+|-++.  +.+|+-+.|.|++|+|||+|+..++.+..
T Consensus         5 ~~id~~~~--i~~Gqr~~I~G~~G~GKTTLlr~I~n~l~   41 (249)
T cd01128           5 RVVDLFAP--IGKGQRGLIVAPPKAGKTTLLQSIANAIT   41 (249)
T ss_pred             hheeeecc--cCCCCEEEEECCCCCCHHHHHHHHHhccc
Confidence            45777765  77999999999999999999988887654

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.

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.71  E-value=0.00023  Score=69.19  Aligned_cols=31  Identities=26%  Similarity=0.203  Sum_probs=26.0

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      |+++..-++|+||||+|||+++..++.....
T Consensus       212 gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~  242 (512)
T TIGR03689       212 DLKPPKGVLLYGPPGCGKTLIAKAVANSLAQ  242 (512)
T ss_pred             cCCCCcceEEECCCCCcHHHHHHHHHHhhcc
Confidence            4666667999999999999999999877643

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.

>COG4175 ProV ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.70  E-value=0.0013  Score=59.10  Aligned_cols=154  Identities=16%  Similarity=0.198  Sum_probs=83.0

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC--CCchHHHHHHHhcc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES--TFTSRRMIEMGASS  160 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~--~~~~~rl~~~~~~~  160 (357)
                      +..-|....+-    -++.|++.+|.|-+|||||||...+-  -+..+.     ..-++++.++  ..+...++++....
T Consensus        39 g~vvGv~~~sl----~v~~GeIfViMGLSGSGKSTLvR~~N--rLiept-----~G~ilv~g~di~~~~~~~Lr~~Rr~~  107 (386)
T COG4175          39 GLVVGVNDASL----DVEEGEIFVIMGLSGSGKSTLVRLLN--RLIEPT-----RGEILVDGKDIAKLSAAELRELRRKK  107 (386)
T ss_pred             CcEEeecccee----eecCCeEEEEEecCCCCHHHHHHHHh--ccCCCC-----CceEEECCcchhcCCHHHHHHHHhhh
Confidence            45556554432    27889999999999999999998543  333333     3466777764  23445555554444


Q ss_pred             CchhhcccchH--HHhhcCeEE---eCCCCHHHHHHHH-HHH--------------------------HHHhhhcCeeEE
Q 035774          161 FPEIFHSKGMA--QEMAGRILV---LQPTSLSEFTESL-EKI--------------------------KVSLLQNQVKLL  208 (357)
Q Consensus       161 ~~~~~~~~~~~--~~~~~~i~~---~~~~~~~~~~~~l-~~l--------------------------~~~~~~~~~~lv  208 (357)
                      ....|+...+.  ..+++|+.|   +..-+..+-.+.. +.+                          .+.+ ..+++++
T Consensus       108 ~sMVFQ~FaLlPhrtVl~Nv~fGLev~Gv~~~er~~~a~~~l~~VgL~~~~~~yp~eLSGGMqQRVGLARAl-a~~~~Il  186 (386)
T COG4175         108 ISMVFQSFALLPHRTVLENVAFGLEVQGVPKAEREERALEALELVGLEGYADKYPNELSGGMQQRVGLARAL-ANDPDIL  186 (386)
T ss_pred             hhhhhhhhccccchhHhhhhhcceeecCCCHHHHHHHHHHHHHHcCchhhhhcCcccccchHHHHHHHHHHH-ccCCCEE
Confidence            43333322111  122333322   1111111111110 000                          0011 2368888


Q ss_pred             EEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          209 VIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       209 vIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      +.|..-+-..+         -.-.++-..|.+|-++++-|||+++|--.
T Consensus       187 LMDEaFSALDP---------LIR~~mQdeLl~Lq~~l~KTIvFitHDLd  226 (386)
T COG4175         187 LMDEAFSALDP---------LIRTEMQDELLELQAKLKKTIVFITHDLD  226 (386)
T ss_pred             EecCchhhcCh---------HHHHHHHHHHHHHHHHhCCeEEEEecCHH
Confidence            88865433322         12224556788889999999999998644

>TIGR03771 anch_rpt_ABC anchored repeat-type ABC transporter, ATP-binding subunit

Probab=97.70  E-value=0.00022  Score=62.29  Aligned_cols=27  Identities=33%  Similarity=0.469  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus         3 i~~Ge~~~l~G~nGsGKSTLl~~l~G~   29 (223)
T TIGR03771         3 ADKGELLGLLGPNGAGKTTLLRAILGL   29 (223)
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            678999999999999999999977753

This protein family is the ATP-binding cassette subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in an adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous ATP-binding subunits outside the scope of this family include manganese transporter MntA in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown.

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=97.70  E-value=0.00026  Score=71.66  Aligned_cols=41  Identities=29%  Similarity=0.388  Sum_probs=30.9

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      -+++|+.+.|.|++|||||||+.-+..-.  .+     ..+-+++|.-
T Consensus       495 ~I~~Ge~vaIvG~SGsGKSTL~KLL~gly--~p-----~~G~I~~dg~  535 (709)
T COG2274         495 EIPPGEKVAIVGRSGSGKSTLLKLLLGLY--KP-----QQGRILLDGV  535 (709)
T ss_pred             EeCCCCEEEEECCCCCCHHHHHHHHhcCC--CC-----CCceEEECCE
Confidence            39999999999999999999999666433  22     2446666654

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=97.70  E-value=0.00015  Score=73.19  Aligned_cols=46  Identities=13%  Similarity=0.046  Sum_probs=35.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         .....+.+.|++++++++.+||+++|--.
T Consensus       480 ~~p~llllDEPts~LD~---------~~~~~i~~ll~~l~~~~g~tvi~isHdl~  525 (623)
T PRK10261        480 LNPKVIIADEAVSALDV---------SIRGQIINLLLDLQRDFGIAYLFISHDMA  525 (623)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCHH
Confidence            47999999987765432         44556788889998888999999998543

>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB

Probab=97.70  E-value=0.00022  Score=61.84  Aligned_cols=45  Identities=13%  Similarity=0.152  Sum_probs=33.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..+.-..         ......+.+.|++++++.+.+||+++|-.
T Consensus       148 ~~p~llllDEPt~~LD---------~~~~~~l~~~l~~~~~~~~~tiii~sH~~  192 (214)
T cd03297         148 AQPELLLLDEPFSALD---------RALRLQLLPELKQIKKNLNIPVIFVTHDL  192 (214)
T ss_pred             cCCCEEEEcCCcccCC---------HHHHHHHHHHHHHHHHHcCcEEEEEecCH
Confidence            4789999998665432         24455677888888888899999998753

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.

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=97.69  E-value=0.00023  Score=65.18  Aligned_cols=26  Identities=23%  Similarity=0.415  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Gei~~l~G~NGaGKTTLl~~l~G   50 (301)
T TIGR03522        25 AQKGRIVGFLGPNGAGKSTTMKIITG   50 (301)
T ss_pred             EeCCeEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997764

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.

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=97.69  E-value=0.00028  Score=63.35  Aligned_cols=26  Identities=31%  Similarity=0.323  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        47 i~~Ge~~~liG~NGsGKSTLlk~L~G   72 (264)
T PRK13546         47 AYEGDVIGLVGINGSGKSTLSNIIGG   72 (264)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997774

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=97.69  E-value=0.00014  Score=62.45  Aligned_cols=28  Identities=32%  Similarity=0.348  Sum_probs=23.2

Q ss_pred             CCCC-cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFG-VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G-~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+| .++.|.||+|+|||||+..++...
T Consensus        24 i~~~~~~~~ltG~Ng~GKStll~~i~~~~   52 (200)
T cd03280          24 LGENKRVLVITGPNAGGKTVTLKTLGLLT   52 (200)
T ss_pred             ECCCceEEEEECCCCCChHHHHHHHHHHH
Confidence            4445 599999999999999999988444

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

>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD

Probab=97.69  E-value=0.0002  Score=63.45  Aligned_cols=27  Identities=30%  Similarity=0.438  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        25 i~~Ge~~~l~G~nGsGKSTLl~~l~G~   51 (242)
T TIGR03411        25 VDPGELRVIIGPNGAGKTTMMDVITGK   51 (242)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            889999999999999999999977753

Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.69  E-value=0.00066  Score=62.10  Aligned_cols=38  Identities=16%  Similarity=0.016  Sum_probs=31.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+.-+.|.|++|+|||.|+..++..++..      +.+|.|+..
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~------g~~v~~~~~  192 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKK------GVSSTLLHF  192 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHc------CCCEEEEEH
Confidence            34568999999999999999999888742      578999876

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=97.68  E-value=0.00036  Score=60.36  Aligned_cols=43  Identities=16%  Similarity=0.241  Sum_probs=31.1

Q ss_pred             chhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCC
Q 035774           88 LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYG  133 (357)
Q Consensus        88 ~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~g  133 (357)
                      +..|+++--- +.+|+.+.|.|++|+|||||+.-++  .+.+++.|
T Consensus        40 ~~aL~disf~-i~~Ge~vGiiG~NGaGKSTLlklia--Gi~~Pt~G   82 (249)
T COG1134          40 FWALKDISFE-IYKGERVGIIGHNGAGKSTLLKLIA--GIYKPTSG   82 (249)
T ss_pred             EEEecCceEE-EeCCCEEEEECCCCCcHHHHHHHHh--CccCCCCc
Confidence            4455555333 8999999999999999999998555  34444443

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=97.68  E-value=0.00032  Score=62.72  Aligned_cols=27  Identities=30%  Similarity=0.583  Sum_probs=24.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~i~G~   54 (257)
T PRK10619         28 ANAGDVISIIGSSGSGKSTFLRCINFL   54 (257)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            889999999999999999999977743

>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules

Probab=97.68  E-value=0.00068  Score=59.33  Aligned_cols=26  Identities=42%  Similarity=0.611  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        37 i~~Ge~~~i~G~nGsGKSTLl~~l~G   62 (226)
T cd03248          37 LHPGEVTALVGPSGSGKSTVVALLEN   62 (226)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997764

Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.

>PRK13547 hmuV hemin importer ATP-binding subunit; Provisional

Probab=97.67  E-value=0.00053  Score=61.84  Aligned_cols=44  Identities=11%  Similarity=0.069  Sum_probs=32.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-+.-...         .....+...|++++++++.+||+++|-
T Consensus       171 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tviiisH~  214 (272)
T PRK13547        171 QPPRYLLLDEPTAALDL---------AHQHRLLDTVRRLARDWNLGVLAIVHD  214 (272)
T ss_pred             CCCCEEEEcCccccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEECC
Confidence            37899999987654422         344457777888888789999999875

>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E

Probab=97.67  E-value=0.00044  Score=61.00  Aligned_cols=27  Identities=26%  Similarity=0.476  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (237)
T cd03252          25 IKPGEVVGIVGRSGSGKSTLTKLIQRF   51 (237)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999999977744

coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.67  E-value=0.00047  Score=60.75  Aligned_cols=38  Identities=13%  Similarity=0.147  Sum_probs=30.9

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +..+.|+||||+|||+|+..++......      +..+.|++.+
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~~~~~------~~~v~y~~~~   82 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAELSQR------GRAVGYVPLD   82 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhC------CCeEEEEEHH
Confidence            3578999999999999999888776531      4789998774

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=97.66  E-value=0.00038  Score=69.72  Aligned_cols=28  Identities=25%  Similarity=0.415  Sum_probs=24.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       355 i~~G~~v~IvG~sGsGKSTLl~lL~gl~  382 (571)
T TIGR02203       355 IEPGETVALVGRSGSGKSTLVNLIPRFY  382 (571)
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            7899999999999999999999777543

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>COG2087 CobU Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase [Coenzyme metabolism]

Probab=97.66  E-value=0.00049  Score=55.80  Aligned_cols=127  Identities=17%  Similarity=0.236  Sum_probs=70.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeE-EeC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL-VLQ  182 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~-~~~  182 (357)
                      ++.|.|+.-||||.+|-.++...         +.+++||.+-..++.+.-.++....-    +      . ..... +-.
T Consensus         2 ~ilvtGgaRSGKS~~AE~la~~~---------~~~v~YvAT~~a~D~Em~~RI~~Hr~----r------R-p~~W~tvE~   61 (175)
T COG2087           2 MILVTGGARSGKSSFAEALAGES---------GGQVLYVATGRAFDDEMQERIAHHRA----R------R-PEHWRTVEA   61 (175)
T ss_pred             eEEEecCccCCchHHHHHHHHhh---------CCceEEEEecCCCCHHHHHHHHHHHh----c------C-CCcceEEec
Confidence            68899999999999999999764         37899999988776544333332210    0      0 01111 111


Q ss_pred             CCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC---ChHHHHHHHHHHHH-HHHHcCCeEEEecccccc
Q 035774          183 PTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP---GQHPLSWHISLITS-LAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       183 ~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~---r~~~~~~i~~~Lk~-la~~~~~~vv~~~q~~~~  258 (357)
                      +.   ++...+..   .  ..+-++|+||+|+.+....+.....   ....+......|-. +....+-.|+++|++...
T Consensus        62 ~~---~l~~~L~~---~--~~~~~~VLvDcLt~wvtNll~~~e~~~~~~~~~~~~~~~L~~al~~~~~~~ilVsNEvG~G  133 (175)
T COG2087          62 PL---DLATLLEA---L--IEPGDVVLVDCLTLWVTNLLFAGEKDWSAEAAIEAEIEALLAALSRAPGTVVLVSNEVGLG  133 (175)
T ss_pred             cc---cHHHHHHh---c--ccCCCEEEEEcHHHHHHHHHhccccccchhhhHHHHHHHHHHHHhcCCccEEEEecCccCC
Confidence            22   22222222   1  1234899999999876653221110   02333333444433 333344577777776543

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=97.66  E-value=0.0003  Score=72.28  Aligned_cols=28  Identities=29%  Similarity=0.375  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|||||||+.-++...
T Consensus       502 i~~Ge~vaIvG~sGsGKSTLlklL~gl~  529 (710)
T TIGR03796       502 LQPGQRVALVGGSGSGKSTIAKLVAGLY  529 (710)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            7899999999999999999998666433

This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin.

>TIGR02857 CydD thiol reductant ABC exporter, CydD subunit

Probab=97.66  E-value=0.00034  Score=69.36  Aligned_cols=27  Identities=41%  Similarity=0.568  Sum_probs=24.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       345 i~~G~~~~ivG~sGsGKSTL~~ll~g~  371 (529)
T TIGR02857       345 VPPGERVALVGPSGAGKSTLLNLLLGF  371 (529)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999999977653

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

>TIGR03873 F420-0_ABC_ATP proposed F420-0 ABC transporter, ATP-binding protein

Probab=97.66  E-value=0.00032  Score=62.65  Aligned_cols=26  Identities=38%  Similarity=0.629  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~i~G   49 (256)
T TIGR03873        24 APPGSLTGLLGPNGSGKSTLLRLLAG   49 (256)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHcC
Confidence            78999999999999999999997764

This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter.

>TIGR00750 lao LAO/AO transport system ATPase

Probab=97.66  E-value=0.00038  Score=63.68  Aligned_cols=43  Identities=19%  Similarity=0.187  Sum_probs=35.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ..++.++.|.|+||+|||||+..++......      +.+|.+|+.+..
T Consensus        31 ~~~~~~i~i~G~~G~GKttl~~~l~~~~~~~------~~~v~~i~~D~~   73 (300)
T TIGR00750        31 TGNAHRVGITGTPGAGKSTLLEALGMELRRR------GLKVAVIAVDPS   73 (300)
T ss_pred             cCCceEEEEECCCCCCHHHHHHHHHHHHHHC------CCeEEEEecCCC
Confidence            4568999999999999999999999876531      478888888753

Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however.

>cd03271 ABC_UvrA_II The excision repair protein UvrA domain II; 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=97.65  E-value=0.00095  Score=59.58  Aligned_cols=28  Identities=32%  Similarity=0.553  Sum_probs=25.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ||.|.++.|+|.+|||||||+..+.+.+
T Consensus        18 ip~g~~~~vtGvSGsGKStL~~~~l~~~   45 (261)
T cd03271          18 IPLGVLTCVTGVSGSGKSSLINDTLYPA   45 (261)
T ss_pred             ccCCcEEEEECCCCCchHHHHHHHHHHH
Confidence            8999999999999999999999886443

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.

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=97.65  E-value=0.00033  Score=61.63  Aligned_cols=27  Identities=33%  Similarity=0.680  Sum_probs=24.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (234)
T cd03251          25 IPAGETVALVGPSGSGKSTLVNLIPRF   51 (234)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            889999999999999999999977643

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.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.65  E-value=0.00045  Score=64.42  Aligned_cols=44  Identities=16%  Similarity=0.088  Sum_probs=39.4

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      ..++|...+|-++.  +-+|+=.+|.|+||+|||+|+.+++.....
T Consensus       152 ~~~~~~rvID~l~P--IGkGQR~lIvgppGvGKTTLaK~Ian~I~~  195 (416)
T PRK09376        152 PEDLSTRIIDLIAP--IGKGQRGLIVAPPKAGKTVLLQNIANSITT  195 (416)
T ss_pred             Ccccceeeeeeecc--cccCceEEEeCCCCCChhHHHHHHHHHHHh
Confidence            47899999999987  778999999999999999999998887764

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=97.65  E-value=0.00032  Score=72.03  Aligned_cols=27  Identities=26%  Similarity=0.421  Sum_probs=24.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       497 i~~G~~vaIvG~SGsGKSTLlklL~gl  523 (708)
T TIGR01193       497 IKMNSKTTIVGMSGSGKSTLAKLLVGF  523 (708)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999999877653

This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.

>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]

Probab=97.65  E-value=0.00083  Score=55.52  Aligned_cols=41  Identities=29%  Similarity=0.557  Sum_probs=31.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.|+++.|.||+|+|||||..-+|-- ..|      ....++|..++
T Consensus        22 v~~ge~vAi~GpSGaGKSTLLnLIAGF-~~P------~~G~i~i~g~d   62 (231)
T COG3840          22 VPAGEIVAILGPSGAGKSTLLNLIAGF-ETP------ASGEILINGVD   62 (231)
T ss_pred             ecCCcEEEEECCCCccHHHHHHHHHhc-cCC------CCceEEEcCee
Confidence            889999999999999999998766543 333      34577777654

>TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase

Probab=97.65  E-value=0.00035  Score=66.71  Aligned_cols=44  Identities=25%  Similarity=0.298  Sum_probs=38.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++...
T Consensus       126 ~~~l~tG~~~id~l~~--i~~Gq~~~I~G~sG~GKStLl~~I~~~~  169 (422)
T TIGR02546       126 DQPLPTGVRAIDGLLT--CGEGQRIGIFAGAGVGKSTLLGMIARGA  169 (422)
T ss_pred             ccccCCCceeehhhcc--ccCCCEEEEECCCCCChHHHHHHHhCCC
Confidence            4579999999999965  8899999999999999999987776543

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.64  E-value=0.0019  Score=57.88  Aligned_cols=94  Identities=17%  Similarity=0.178  Sum_probs=56.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      +|+.+.+.|++|+|||+++..++.....      .+..+.+++++.. ......+....           ... . .+-+
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~------~~~~v~~i~~D~~-ri~~~~ql~~~-----------~~~-~-~~~~  133 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHG------KKKTVGFITTDHS-RIGTVQQLQDY-----------VKT-I-GFEV  133 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHH------cCCeEEEEecCCC-CHHHHHHHHHH-----------hhh-c-CceE
Confidence            6799999999999999999999887642      1478999988742 22222221110           011 1 1233


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEecccccc
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALV  217 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~  217 (357)
                      ....+..++.+.+..+   -...+.++|+||......
T Consensus       134 ~~~~~~~~l~~~l~~l---~~~~~~D~ViIDt~Gr~~  167 (270)
T PRK06731        134 IAVRDEAAMTRALTYF---KEEARVDYILIDTAGKNY  167 (270)
T ss_pred             EecCCHHHHHHHHHHH---HhcCCCCEEEEECCCCCc
Confidence            3334444554433332   122468999999887654

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=97.64  E-value=0.00039  Score=69.69  Aligned_cols=28  Identities=36%  Similarity=0.496  Sum_probs=25.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       363 i~~Ge~i~IvG~sGsGKSTLlklL~gl~  390 (576)
T TIGR02204       363 VRPGETVALVGPSGAGKSTLFQLLLRFY  390 (576)
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            8899999999999999999999887644

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>PF02283 CobU: Cobinamide kinase / cobinamide phosphate guanyltransferase; InterPro: IPR003203 This family is composed of a group of bifunctional cobalbumin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity

Probab=97.64  E-value=5.1e-05  Score=62.95  Aligned_cols=123  Identities=20%  Similarity=0.260  Sum_probs=60.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe-CC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL-QP  183 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~-~~  183 (357)
                      ++|.|...||||.||.+++...         +.+++|+.|-..++.+...++..+.      .    .. ...+..+ .+
T Consensus         1 ilv~GG~rSGKS~~Ae~la~~~---------~~~~~YiAT~~~~D~em~~RI~~H~------~----~R-~~~w~tiE~~   60 (167)
T PF02283_consen    1 ILVTGGARSGKSSFAERLALSF---------GGPVTYIATARPFDEEMRERIARHR------Q----RR-PKGWITIEEP   60 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHTS-----------SCEEEEESSHHHHHHHHHHHHHHH------H----HS-STCEEEEE-S
T ss_pred             CEEeCCCCcchHHHHHHHHHhc---------CCCcEEEeCCCCCCHHHHHHHHHHH------H----hC-CCCcEEEecc
Confidence            6799999999999999999322         3789999997655443333333221      0    01 1222222 22


Q ss_pred             CCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCCC-CChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          184 TSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQRA-PGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       184 ~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~~-~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+..+.   +       ... ..+.|+||+++.+....+.... .......++.+.+..+.+...-.||++|++..
T Consensus        61 ~~l~~~---~-------~~~~~~~~vLlDclt~wl~n~l~~~~~~~~~~~~~i~~~l~~l~~~~~~lViVsnEVG~  126 (167)
T PF02283_consen   61 RDLAEA---L-------EELSPGDVVLLDCLTLWLANLLFAEEDDEEDILEEIERLLEALRERNADLVIVSNEVGW  126 (167)
T ss_dssp             S-GGGT---S--------TTS-T-EEEEE-HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH--SEEEEEEE---S
T ss_pred             hhHHHH---H-------HHhccCCeEEEeCHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHccCCCEEEEEcCCCC
Confidence            322221   1       112 2589999999988755221110 01223344444555554444455556665543

The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape [].; GO: 0000166 nucleotide binding, 0043752 adenosylcobinamide kinase activity, 0051188 cofactor biosynthetic process; PDB: 1CBU_C 1C9K_B.

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=97.64  E-value=0.00073  Score=59.55  Aligned_cols=27  Identities=33%  Similarity=0.602  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        24 i~~Ge~~~l~G~nGsGKSTLl~~i~Gl   50 (236)
T cd03253          24 IPAGKKVAIVGPSGSGKSTILRLLFRF   50 (236)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            889999999999999999999988753

Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. 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.

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

Probab=97.63  E-value=0.00036  Score=66.79  Aligned_cols=29  Identities=31%  Similarity=0.356  Sum_probs=25.8

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+.++.-++|+||||+|||+++..++...
T Consensus       213 gi~~p~gVLL~GPPGTGKT~LAraIA~el  241 (438)
T PTZ00361        213 GIKPPKGVILYGPPGTGKTLLAKAVANET  241 (438)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            57788889999999999999999988754

>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]

Probab=97.63  E-value=0.00032  Score=65.70  Aligned_cols=141  Identities=20%  Similarity=0.211  Sum_probs=77.7

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC-----CCeEEEEeCCCCCchHHHH-HHHhccCchhhcccch
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL-----DGGVIYIDVESTFTSRRMI-EMGASSFPEIFHSKGM  170 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~-----~~~vl~i~~e~~~~~~rl~-~~~~~~~~~~~~~~~~  170 (357)
                      |.+..|+++.+.||+|.|||||+.-+|-  ...+..|+.     ..+--||+.+-.-..+.+. ......+.    ...+
T Consensus       362 G~i~~gEvigilGpNgiGKTTFvk~LAG--~ikPdeg~~~~~~vSyKPQyI~~~~~gtV~~~l~~~~~~~~~----~s~~  435 (591)
T COG1245         362 GEIYDGEVIGILGPNGIGKTTFVKLLAG--VIKPDEGSEEDLKVSYKPQYISPDYDGTVEDLLRSAIRSAFG----SSYF  435 (591)
T ss_pred             CeeecceEEEEECCCCcchHHHHHHHhc--cccCCCCCCccceEeecceeecCCCCCcHHHHHHHhhhhhcc----cchh
Confidence            6799999999999999999999997773  222233321     1233455554332222222 22211111    1101


Q ss_pred             HHHhhcCeEE-------eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHH
Q 035774          171 AQEMAGRILV-------LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAE  243 (357)
Q Consensus       171 ~~~~~~~i~~-------~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~  243 (357)
                      ..++...+.+       ++..+..++..+.   .........++-++|.-++....         .+--.+++.+++++.
T Consensus       436 ~~ei~~pl~l~~i~e~~v~~LSGGELQRva---Iaa~L~reADlYllDEPSA~LDv---------EqR~~vakvIRR~~e  503 (591)
T COG1245         436 KTEIVKPLNLEDLLERPVDELSGGELQRVA---IAAALSREADLYLLDEPSAYLDV---------EQRIIVAKVIRRFIE  503 (591)
T ss_pred             HHhhcCccchHHHHhcccccCCchhHHHHH---HHHHhccccCEEEecCchhhccH---------HHHHHHHHHHHHHHh
Confidence            1111111110       1222333432221   11122356899999998887643         122236788999999


Q ss_pred             HcCCeEEEeccc
Q 035774          244 FSRIPIVVTNQV  255 (357)
Q Consensus       244 ~~~~~vv~~~q~  255 (357)
                      +.+.+.+++.|-
T Consensus       504 ~~~kta~vVdHD  515 (591)
T COG1245         504 NNEKTALVVDHD  515 (591)
T ss_pred             hcCceEEEEecc
Confidence            999999999884

>TIGR00767 rho transcription termination factor Rho

Probab=97.63  E-value=0.00042  Score=64.87  Aligned_cols=40  Identities=23%  Similarity=0.184  Sum_probs=32.0

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      |+..+|-.+.  +.+|+.+.|.|+||+|||+++..++.....
T Consensus       155 ~~R~id~~~p--ig~Gq~~~IvG~~g~GKTtL~~~i~~~I~~  194 (415)
T TIGR00767       155 STRVLDLFAP--IGKGQRGLIVAPPKAGKTVLLQKIAQAITR  194 (415)
T ss_pred             ceeeeeeEEE--eCCCCEEEEECCCCCChhHHHHHHHHhhcc
Confidence            3344466665  789999999999999999999988876653

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

>PRK13409 putative ATPase RIL; Provisional

Probab=97.63  E-value=0.00051  Score=68.69  Aligned_cols=44  Identities=16%  Similarity=0.098  Sum_probs=34.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++....         .....+.+.|++++++.+.+||+++|-
T Consensus       470 ~~p~llLLDEPt~~LD~---------~~~~~l~~~l~~l~~~~g~tviivsHD  513 (590)
T PRK13409        470 RDADLYLLDEPSAHLDV---------EQRLAVAKAIRRIAEEREATALVVDHD  513 (590)
T ss_pred             cCCCEEEEeCCccCCCH---------HHHHHHHHHHHHHHHhCCCEEEEEeCC
Confidence            47999999987765532         445567888999999889999999885

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=97.63  E-value=0.00035  Score=60.09  Aligned_cols=27  Identities=22%  Similarity=0.290  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        30 i~~Ge~~~i~G~nGsGKSTLl~~l~G~   56 (202)
T cd03233          30 VKPGEMVLVLGRPGSGCSTLLKALANR   56 (202)
T ss_pred             ECCCcEEEEECCCCCCHHHHHHHhccc
Confidence            889999999999999999999977754

PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK06893 DNA replication initiation factor; Validated

Probab=97.62  E-value=0.00053  Score=60.22  Aligned_cols=37  Identities=22%  Similarity=0.231  Sum_probs=30.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..+.|+|+||+|||.|+..++..++..      +.++.|++.+
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~------~~~~~y~~~~   76 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLN------QRTAIYIPLS   76 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc------CCCeEEeeHH
Confidence            468999999999999999999887642      4678998874

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=97.62  E-value=0.00067  Score=60.04  Aligned_cols=26  Identities=38%  Similarity=0.664  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++-
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G   50 (242)
T PRK11124         25 CPQGETLVLLGPSGAGKSSLLRVLNL   50 (242)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997774

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=97.62  E-value=0.0013  Score=54.47  Aligned_cols=28  Identities=29%  Similarity=0.423  Sum_probs=24.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      .+.+++|.||+|+|||+++..++.....
T Consensus        20 ~~~~~~i~G~NgsGKS~~l~~i~~~~~~   47 (162)
T cd03227          20 EGSLTIITGPNGSGKSTILDAIGLALGG   47 (162)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3479999999999999999998776654

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.

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

Probab=97.62  E-value=0.00054  Score=61.14  Aligned_cols=58  Identities=28%  Similarity=0.239  Sum_probs=48.1

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+.+.||+..+|-++.  +-+|+=..|.|++|+|||+|+.+++.+...+.     ...++|.-.-
T Consensus        50 ~e~L~TGIr~ID~l~p--ig~GQr~~If~~~G~GKTtLa~~i~~~i~~~~-----~~~~V~~~iG  107 (274)
T cd01133          50 TEILETGIKVIDLLAP--YAKGGKIGLFGGAGVGKTVLIMELINNIAKAH-----GGYSVFAGVG  107 (274)
T ss_pred             CcccccCceeeeccCC--cccCCEEEEecCCCCChhHHHHHHHHHHHhcC-----CCEEEEEEec
Confidence            4689999999999987  88999999999999999999999999886431     2456666543

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.

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=97.62  E-value=0.00049  Score=60.32  Aligned_cols=27  Identities=33%  Similarity=0.521  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        26 i~~G~~~~i~G~nGsGKSTLl~~l~G~   52 (229)
T cd03254          26 IKPGETVAIVGPTGAGKTTLINLLMRF   52 (229)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            889999999999999999999988743

In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar 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.

>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]

Probab=97.61  E-value=0.0011  Score=61.20  Aligned_cols=141  Identities=16%  Similarity=0.171  Sum_probs=75.8

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC--CCchHHHHHHHhccCchhhc------ccc
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES--TFTSRRMIEMGASSFPEIFH------SKG  169 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~--~~~~~rl~~~~~~~~~~~~~------~~~  169 (357)
                      -+.+|+++-|.|.+||||||||+-+.  .+.++.     .+-++++.+.  ....++.++.....+.+++-      .+.
T Consensus       345 ~ikrGelvFliG~NGsGKST~~~LLt--GL~~Pq-----sG~I~ldg~pV~~e~ledYR~LfSavFsDyhLF~~ll~~e~  417 (546)
T COG4615         345 TIKRGELVFLIGGNGSGKSTLAMLLT--GLYQPQ-----SGEILLDGKPVSAEQLEDYRKLFSAVFSDYHLFDQLLGPEG  417 (546)
T ss_pred             EEecCcEEEEECCCCCcHHHHHHHHh--cccCCC-----CCceeECCccCCCCCHHHHHHHHHHHhhhHhhhHhhhCCcc
Confidence            38899999999999999999999555  443333     4467777653  11234444444332222111      110


Q ss_pred             -----hHHHhhcCe------------EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHH
Q 035774          170 -----MAQEMAGRI------------LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLS  232 (357)
Q Consensus       170 -----~~~~~~~~i------------~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~  232 (357)
                           .+...+.++            +....-+.. ....+..+...++  .-+++|.|..++=..+         .--+
T Consensus       418 ~as~q~i~~~LqrLel~~ktsl~d~~fs~~kLStG-QkKRlAll~AllE--eR~Ilv~DEWAADQDP---------aFRR  485 (546)
T COG4615         418 KASPQLIEKWLQRLELAHKTSLNDGRFSNLKLSTG-QKKRLALLLALLE--ERDILVLDEWAADQDP---------AFRR  485 (546)
T ss_pred             CCChHHHHHHHHHHHHhhhhcccCCcccccccccc-hHHHHHHHHHHHh--hCCeEEeehhhccCCh---------HHHH
Confidence                 011111111            000001111 1222333334443  3567899977643222         2234


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccc
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+.+.|--+.++.|.||++++|--.
T Consensus       486 ~FY~~lLp~LK~qGKTI~aIsHDd~  510 (546)
T COG4615         486 EFYQVLLPLLKEQGKTIFAISHDDH  510 (546)
T ss_pred             HHHHHHhHHHHHhCCeEEEEecCch
Confidence            5667777788889999999998644

>COG4674 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]

Probab=97.61  E-value=3.7e-05  Score=64.03  Aligned_cols=38  Identities=29%  Similarity=0.386  Sum_probs=31.0

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      |+..|..+--- +.+|++-.|.||+|+|||||+--|.-.
T Consensus        17 GF~Aln~ls~~-v~~Gelr~lIGpNGAGKTT~mD~ItGK   54 (249)
T COG4674          17 GFKALNDLSFS-VDPGELRVLIGPNGAGKTTLMDVITGK   54 (249)
T ss_pred             ceeeeeeeEEE-ecCCeEEEEECCCCCCceeeeeeeccc
Confidence            67777776543 899999999999999999998765543

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]

Probab=97.61  E-value=0.00086  Score=56.35  Aligned_cols=55  Identities=25%  Similarity=0.414  Sum_probs=38.9

Q ss_pred             CCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           84 LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        84 i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .++-...++++.-- ...|+++.|.|++|+||||++.-++.- +.|      ...+++|+.-.
T Consensus        11 y~~~v~AvrdVSF~-ae~Gei~GlLG~NGAGKTT~LRmiatl-L~P------~~G~v~idg~d   65 (245)
T COG4555          11 YGSKVQAVRDVSFE-AEEGEITGLLGENGAGKTTLLRMIATL-LIP------DSGKVTIDGVD   65 (245)
T ss_pred             ccCHHhhhhheeEE-eccceEEEEEcCCCCCchhHHHHHHHh-ccC------CCceEEEeecc
Confidence            33434466666543 789999999999999999998866643 333      35578887543

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=97.61  E-value=0.001  Score=56.76  Aligned_cols=26  Identities=19%  Similarity=0.247  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~l~G   48 (195)
T PRK13541         23 FLPSAITYIKGANGCGKSSLLRMIAG   48 (195)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999999997764

>PF13245 AAA_19: Part of AAA domain

Probab=97.61  E-value=0.00011  Score=52.34  Aligned_cols=43  Identities=19%  Similarity=0.102  Sum_probs=32.3

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+++|.|+||+|||+++.+.+.........  .+.++++++...
T Consensus        10 ~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~~--~~~~vlv~a~t~   52 (76)
T PF13245_consen   10 SPLFVVQGPPGTGKTTTLAARIAELLAARAD--PGKRVLVLAPTR   52 (76)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHHhcC--CCCeEEEECCCH
Confidence            5688899999999999999988887632111  157889887643

>PRK10261 glutathione transporter ATP-binding protein; Provisional

Probab=97.60  E-value=0.0006  Score=68.89  Aligned_cols=45  Identities=11%  Similarity=0.078  Sum_probs=35.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-...         .....+...|++++++++++||+++|--
T Consensus       185 ~~P~lLllDEPt~~LD~---------~~~~~l~~ll~~l~~~~g~tvi~itHdl  229 (623)
T PRK10261        185 CRPAVLIADEPTTALDV---------TIQAQILQLIKVLQKEMSMGVIFITHDM  229 (623)
T ss_pred             CCCCEEEEeCCCCccCH---------HHHHHHHHHHHHHHHhcCCEEEEEcCCH
Confidence            47999999988765533         4445677788888888899999999864

>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]

Probab=97.60  E-value=0.00055  Score=63.30  Aligned_cols=43  Identities=9%  Similarity=0.197  Sum_probs=34.3

Q ss_pred             CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       204 ~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ++++|++|.-++-.         ....-.+++..|+.|.++++.+-++++|-
T Consensus       444 kP~~i~LDEPTSAL---------D~SVQaQvv~LLr~LQ~k~~LsYLFISHD  486 (534)
T COG4172         444 KPELILLDEPTSAL---------DRSVQAQVLDLLRDLQQKHGLSYLFISHD  486 (534)
T ss_pred             CCcEEEecCCchHh---------hHHHHHHHHHHHHHHHHHhCCeEEEEecc
Confidence            68999999766433         22445678899999999999999999984

>PRK14271 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.59  E-value=0.00067  Score=61.34  Aligned_cols=27  Identities=44%  Similarity=0.744  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        44 i~~Ge~~~I~G~nGsGKSTLl~~l~Gl   70 (276)
T PRK14271         44 FPARAVTSLMGPTGSGKTTFLRTLNRM   70 (276)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999999988753

>PF09807 DUF2348: Uncharacterized conserved protein (DUF2348); InterPro: IPR018627 Members of this family of putative uncharacterised proteins have no known function

Probab=97.59  E-value=0.0039  Score=55.25  Aligned_cols=158  Identities=15%  Similarity=0.102  Sum_probs=96.9

Q ss_pred             chhHHhhhc---CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch-HHHHHHHhccCch
Q 035774           88 LKGLDAALC---GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS-RRMIEMGASSFPE  163 (357)
Q Consensus        88 ~~~LD~~l~---GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~-~rl~~~~~~~~~~  163 (357)
                      +++|+.+|.   +..++|.+++|... ++-=+.|..+++...+..      +.+|+|+++..++.- .++.+...-.+..
T Consensus         2 f~eln~ll~~~~~~~~~g~~ili~d~-~~dgsFLlh~~L~~~Lk~------~~~V~fv~~~q~~~HY~~v~~KLG~NL~~   74 (249)
T PF09807_consen    2 FPELNSLLNWSPDSVPPGKLILIEDC-ETDGSFLLHHFLSQYLKA------GCKVCFVAFSQSFSHYNNVAQKLGVNLSA   74 (249)
T ss_pred             chHHHHHhcCCCCCCCCCeEEEEEcC-CCCchhHHHHHHHHHhcC------CCcEEEEEccCCHHHHHHHHHhhEecchH
Confidence            467777774   45889999999999 888899999999988852      589999999887653 1111111111100


Q ss_pred             h-----hcccchHHHhhcC------------eEEeCCCCHHHHHHHHHHHHHHhhh---cCeeEEEEeccccccCCCCCC
Q 035774          164 I-----FHSKGMAQEMAGR------------ILVLQPTSLSEFTESLEKIKVSLLQ---NQVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       164 ~-----~~~~~~~~~~~~~------------i~~~~~~~~~~~~~~l~~l~~~~~~---~~~~lvvIDsl~~l~~~~~~~  223 (357)
                      .     +..-+......+.            +.+........+..+...+...+..   .+..+||||.++.+.....  
T Consensus        75 ~~~~gql~fiD~l~~~~~~l~~~~~~~~~~~~~~l~~~~~~~L~~L~~~I~~~l~~~~~~~~~~liIDdls~Ll~lG~--  152 (249)
T PF09807_consen   75 AKEKGQLVFIDGLKSSLDLLFDEDSSDEPNPLKFLREDNASSLRSLYEFIQEALSPADSNGSVVLIIDDLSVLLSLGV--  152 (249)
T ss_pred             hccCCcEEEeehhhhhhhhhhccccccCCccccccccCCcchHHHHHHHHHHHHhhccCCCCeEEEEeCHHHHHHcCC--
Confidence            0     0000000100000            1111111223455555666555543   3578999999999987422  


Q ss_pred             CCCChHHHHHHHHHHH-HHHHHcCCeEEEeccccc
Q 035774          224 RAPGQHPLSWHISLIT-SLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk-~la~~~~~~vv~~~q~~~  257 (357)
                         ....+-.+++.++ .++.+.++.+|++.|...
T Consensus       153 ---s~~~vldF~~ycra~l~~~~~~~lVvl~h~d~  184 (249)
T PF09807_consen  153 ---SSNDVLDFIHYCRATLCSESNGSLVVLVHCDI  184 (249)
T ss_pred             ---CHHHHHHHHHHHHHHhccccCCCEEEEEecCC
Confidence               2356667888888 678888888888877643

>PRK05642 DNA replication initiation factor; Validated

Probab=97.59  E-value=0.0005  Score=60.56  Aligned_cols=37  Identities=16%  Similarity=0.274  Sum_probs=29.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..+.|+|++|+|||.|+..++......      +.+|+|++.+
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~------~~~v~y~~~~   82 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQR------GEPAVYLPLA   82 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhC------CCcEEEeeHH
Confidence            467899999999999998887665431      4789999874

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

Probab=97.59  E-value=0.00012  Score=69.63  Aligned_cols=30  Identities=47%  Similarity=0.635  Sum_probs=24.9

Q ss_pred             hcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           95 LCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        95 l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |||-+|+|  +++.||||+|||.||..+|-.+
T Consensus       332 LGGKLPKG--VLLvGPPGTGKTlLARAvAGEA  361 (752)
T KOG0734|consen  332 LGGKLPKG--VLLVGPPGTGKTLLARAVAGEA  361 (752)
T ss_pred             ccCcCCCc--eEEeCCCCCchhHHHHHhhccc
Confidence            56779998  8899999999999999777433

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=97.58  E-value=0.00033  Score=69.08  Aligned_cols=45  Identities=20%  Similarity=0.232  Sum_probs=32.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..++-...         .....+...|++++++ +.+||+++|-..
T Consensus       157 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~-g~tiiivtHd~~  201 (510)
T PRK15439        157 RDSRILILDEPTASLTP---------AETERLFSRIRELLAQ-GVGIVFISHKLP  201 (510)
T ss_pred             cCCCEEEEECCCCCCCH---------HHHHHHHHHHHHHHHC-CCEEEEEeCCHH
Confidence            47999999987765433         3445567778887664 899999988643

>TIGR01194 cyc_pep_trnsptr cyclic peptide transporter

Probab=97.58  E-value=0.00074  Score=67.36  Aligned_cols=40  Identities=25%  Similarity=0.348  Sum_probs=30.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+.+.|.|++|+|||||+.-++...  ++     ..+.++++..
T Consensus       365 i~~G~~~aivG~sGsGKSTl~~ll~g~~--~p-----~~G~i~~~g~  404 (555)
T TIGR01194       365 IAQGDIVFIVGENGCGKSTLAKLFCGLY--IP-----QEGEILLDGA  404 (555)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCCC--CC-----CCcEEEECCE
Confidence            7899999999999999999999776433  22     2445666654

This model describes cyclic peptide transporter in bacteria. Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. Syringomycin is an amphipathic, cylclic lipodepsipeptide when inserted into host causes formation of channels, permeable to variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.

>PRK09700 D-allose transporter ATP-binding protein; Provisional

Probab=97.58  E-value=0.00038  Score=68.68  Aligned_cols=45  Identities=11%  Similarity=0.211  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         .....+.+.|++++++ +.+||+++|-..
T Consensus       162 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~l~~~-g~tiiivsHd~~  206 (510)
T PRK09700        162 LDAKVIIMDEPTSSLTN---------KEVDYLFLIMNQLRKE-GTAIVYISHKLA  206 (510)
T ss_pred             cCCCEEEEeCCCCCCCH---------HHHHHHHHHHHHHHhC-CCEEEEEeCCHH
Confidence            47899999987765432         4455677788888765 899999998643

>PRK09099 type III secretion system ATPase; Provisional

Probab=97.58  E-value=0.00024  Score=67.70  Aligned_cols=44  Identities=23%  Similarity=0.316  Sum_probs=39.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+.+++...
T Consensus       144 ~e~l~TGi~~ID~l~~--i~~Gq~~~I~G~sG~GKTtLl~~ia~~~  187 (441)
T PRK09099        144 EAPLPTGVRIVDGLMT--LGEGQRMGIFAPAGVGKSTLMGMFARGT  187 (441)
T ss_pred             ccccCCCceeccceee--ecCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4689999999999965  7899999999999999999998887654

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=97.58  E-value=0.00012  Score=62.98  Aligned_cols=169  Identities=16%  Similarity=0.197  Sum_probs=75.6

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc-
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS-  160 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~-  160 (357)
                      -.++.|.......+.--+....=++|+|.+|+|||+++..++...+.....  .+..+..+|.... .-..+....... 
T Consensus        18 ~~i~~g~~~~~~~v~~dl~~~~h~li~G~tgsGKS~~l~~ll~~l~~~~~p--~~~~l~iiD~k~~-~l~~~~~~~~~~~   94 (205)
T PF01580_consen   18 GPIPVGVDQRGDPVVLDLKKNPHLLIAGATGSGKSTLLRTLLLSLALTYSP--DDVQLYIIDPKGS-DLAPLADLPHVAA   94 (205)
T ss_dssp             TEEEEEEETTS-EEEEEGGGS-SEEEE--TTSSHHHHHHHHHHHHHTT--T--TTEEEEEE-TTSS-CCGGGTT-TTBSS
T ss_pred             eEEEecccCCCCEEEEEcCCCceEEEEcCCCCCccHHHHHHHHHHHHHhcC--CccEEEEEcCCcc-ccchhhhhhhhcc
Confidence            346666665444333234445579999999999999999999998873211  1356666776532 111111100000 


Q ss_pred             --C-chhhccc----chHHHhhcCeEEeC---CCCHHHHHHHHHHHHHH------hhhcCeeEEEEeccccccCCCCCCC
Q 035774          161 --F-PEIFHSK----GMAQEMAGRILVLQ---PTSLSEFTESLEKIKVS------LLQNQVKLLVIDSMEALVPGVHEQR  224 (357)
Q Consensus       161 --~-~~~~~~~----~~~~~~~~~i~~~~---~~~~~~~~~~l~~l~~~------~~~~~~~lvvIDsl~~l~~~~~~~~  224 (357)
                        . .......    .+..++..+..+..   ..+..............      ......-+++||.+..+........
T Consensus        95 ~~~~~~~~~~~~~l~~l~~em~~R~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~iDe~~~l~~~~~~~~  174 (205)
T PF01580_consen   95 VAVATDPEEILRLLEELVEEMERRQALLREAGVRNIDDYNEERGELPDDIFADPWLKELPPIFIVIDEFAALRDSAPDDS  174 (205)
T ss_dssp             -S-B-SHHHHHHHHHHHHHHHHHHHHHHHHCT-SSHHHHHHHHHHHHHTT----B-----EEEEEECTHHHHHHHHHHH-
T ss_pred             ccccccHHHHHHHHHHHHHHHHHHHHHHHHcCccchhhHHHHhhhhccccccccccccCchHHHHhhhHHHHHhhcchhh
Confidence              0 0000000    00011111111111   11111111111110000      0123567889999999875422111


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                         ...+...+..+-+.++..|+.+|+..|-.
T Consensus       175 ---~~~~~~~l~~i~~~gR~~Gi~li~~~Q~p  203 (205)
T PF01580_consen  175 ---KKEIMDLLARIARKGRAAGIHLILATQRP  203 (205)
T ss_dssp             ------HHHHHHHHHHHCGGGTEEEEEEESS-
T ss_pred             ---HHHHHHHHHHHHHHHHhcCEEEEEEeCCC
Confidence               23455566666677889999999998853

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

>cd03290 ABCC_SUR1_N The SUR domain 1

Probab=97.57  E-value=0.00063  Score=59.19  Aligned_cols=27  Identities=33%  Similarity=0.541  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~i~G~   50 (218)
T cd03290          24 IPTGQLTMIVGQVGCGKSSLLLAILGE   50 (218)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999999977744

The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>PRK15056 manganese/iron transporter ATP-binding protein; Provisional

Probab=97.57  E-value=0.00046  Score=62.27  Aligned_cols=26  Identities=38%  Similarity=0.556  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLl~~l~G   55 (272)
T PRK15056         30 VPGGSIAALVGVNGSGKSTLFKALMG   55 (272)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997764

>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=97.57  E-value=0.00023  Score=64.63  Aligned_cols=121  Identities=19%  Similarity=0.198  Sum_probs=65.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHH-HHHhccCchhhcccchHHHhhcCe
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMI-EMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~-~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      ....++.|.|.+|+|||+||.+++........    -..++|++.....+...+. ++...              +....
T Consensus        17 ~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~----f~~v~wv~~~~~~~~~~~~~~i~~~--------------l~~~~   78 (287)
T PF00931_consen   17 NEVRVVAIVGMGGIGKTTLARQVARDLRIKNR----FDGVIWVSLSKNPSLEQLLEQILRQ--------------LGEPD   78 (287)
T ss_dssp             TSSEEEEEEESTTSSHHHHHHHHHCHHHHCCC----CTEEEEEEEES-SCCHHHHHHHHHH--------------HTCC-
T ss_pred             CCeEEEEEEcCCcCCcceeeeecccccccccc----ccccccccccccccccccccccccc--------------ccccc
Confidence            77889999999999999999999976332211    2578899877655443332 22211              10000


Q ss_pred             E-EeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          179 L-VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       179 ~-~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      . .....+   .......+...+... .-++|+|.+....            .+..+...+.  ....++.||+|+...
T Consensus        79 ~~~~~~~~---~~~~~~~l~~~L~~~-~~LlVlDdv~~~~------------~~~~l~~~~~--~~~~~~kilvTTR~~  139 (287)
T PF00931_consen   79 SSISDPKD---IEELQDQLRELLKDK-RCLLVLDDVWDEE------------DLEELREPLP--SFSSGSKILVTTRDR  139 (287)
T ss_dssp             STSSCCSS---HHHHHHHHHHHHCCT-SEEEEEEEE-SHH------------HH-------H--CHHSS-EEEEEESCG
T ss_pred             cccccccc---cccccccchhhhccc-cceeeeeeecccc------------cccccccccc--ccccccccccccccc
Confidence            0 011222   333445555555443 7889999865332            2222222222  234588999987653

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.

>PRK09580 sufC cysteine desulfurase ATPase component; Reviewed

Probab=97.57  E-value=0.00082  Score=59.68  Aligned_cols=27  Identities=33%  Similarity=0.540  Sum_probs=24.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (248)
T PRK09580         24 VRPGEVHAIMGPNGSGKSTLSATLAGR   50 (248)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHcCC
Confidence            889999999999999999999977654

>COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]

Probab=97.57  E-value=0.00069  Score=55.44  Aligned_cols=44  Identities=11%  Similarity=0.074  Sum_probs=32.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ..+++++-|.-+--.         ....-..+...|..+.++++.|.|+++|-
T Consensus       163 ~~P~vLfADEPTGNL---------D~~Tg~~iaDLlF~lnre~G~TlVlVTHD  206 (228)
T COG4181         163 GRPDVLFADEPTGNL---------DRATGDKIADLLFALNRERGTTLVLVTHD  206 (228)
T ss_pred             CCCCEEeccCCCCCc---------chhHHHHHHHHHHHHhhhcCceEEEEeCC
Confidence            357888877544221         22444568888999999999999999885

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=97.56  E-value=0.00062  Score=64.66  Aligned_cols=29  Identities=31%  Similarity=0.369  Sum_probs=24.3

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+.+-.-++|+||||+|||++|..++...
T Consensus       161 g~~~p~gvLL~GppGtGKT~lAkaia~~~  189 (389)
T PRK03992        161 GIEPPKGVLLYGPPGTGKTLLAKAVAHET  189 (389)
T ss_pred             CCCCCCceEEECCCCCChHHHHHHHHHHh
Confidence            45666669999999999999999988754

>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient

Probab=97.56  E-value=0.00095  Score=58.45  Aligned_cols=28  Identities=39%  Similarity=0.715  Sum_probs=25.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+|+++.|.|++|+|||||+.-++...
T Consensus        23 i~~Ge~~~i~G~nGsGKSTLl~~i~G~~   50 (227)
T cd03260          23 IPKGEITALIGPSGCGKSTLLRLLNRLN   50 (227)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            8899999999999999999999777543

The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.56  E-value=0.00064  Score=58.24  Aligned_cols=121  Identities=19%  Similarity=0.213  Sum_probs=70.0

Q ss_pred             CCCCcE-EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           99 VPFGVV-TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        99 i~~G~l-~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      ...|-+ ++|.|||++||||++..+|...+-... +=...+|..||.-...     .... ...++        .....+
T Consensus       133 y~~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~-~~l~kkv~IiDersEI-----ag~~-~gvpq--------~~~g~R  197 (308)
T COG3854         133 YQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGIN-QFLPKKVGIIDERSEI-----AGCL-NGVPQ--------HGRGRR  197 (308)
T ss_pred             HhcCceeeEEecCCCCChHHHHHHHHHHhhcccc-ccCCceEEEEeccchh-----hccc-cCCch--------hhhhhh
Confidence            345777 999999999999999999998764211 1146889999874421     1100 00000        011223


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      +-+.++..-.      .-+..+++.+.+.++|||.+.....            ...    +.. |-+.|+-++.+.|-..
T Consensus       198 ~dVld~cpk~------~gmmmaIrsm~PEViIvDEIGt~~d------------~~A----~~t-a~~~GVkli~TaHG~~  254 (308)
T COG3854         198 MDVLDPCPKA------EGMMMAIRSMSPEVIIVDEIGTEED------------ALA----ILT-ALHAGVKLITTAHGNG  254 (308)
T ss_pred             hhhcccchHH------HHHHHHHHhcCCcEEEEeccccHHH------------HHH----HHH-HHhcCcEEEEeecccc
Confidence            3333332211      1223445567899999999885421            111    222 3346999999988543

>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=97.55  E-value=0.00049  Score=59.47  Aligned_cols=51  Identities=22%  Similarity=0.291  Sum_probs=42.3

Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ||++.+|-++.  +-+|+=+.|.|++|+|||+|+.+++.+...        ..++|+-..+
T Consensus         1 TGir~ID~l~P--ig~Gqr~~I~g~~g~GKt~Ll~~i~~~~~~--------d~~V~~~iGe   51 (215)
T PF00006_consen    1 TGIRAIDLLFP--IGRGQRIGIFGGAGVGKTVLLQEIANNQDA--------DVVVYALIGE   51 (215)
T ss_dssp             -SHHHHHHHSC--EETTSEEEEEESTTSSHHHHHHHHHHHCTT--------TEEEEEEESE
T ss_pred             CCCceeccccc--cccCCEEEEEcCcccccchhhHHHHhcccc--------cceeeeeccc
Confidence            89999999987  889999999999999999999999998842        3447766543

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 ....

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=97.55  E-value=0.00063  Score=58.88  Aligned_cols=25  Identities=36%  Similarity=0.557  Sum_probs=22.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++| ++.|.|++|+|||||+.-++.
T Consensus        23 i~~g-~~~i~G~nGsGKSTLl~~l~G   47 (211)
T cd03264          23 LGPG-MYGLLGPNGAGKTTLMRILAT   47 (211)
T ss_pred             EcCC-cEEEECCCCCCHHHHHHHHhC
Confidence            7789 999999999999999997764

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.55  E-value=0.00077  Score=63.48  Aligned_cols=43  Identities=28%  Similarity=0.382  Sum_probs=33.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.++.+.|++|+||||.+..+|........  ..+.+|.+++++.
T Consensus       174 ~~vi~lvGptGvGKTTT~aKLA~~~~~~~~--~~g~~V~lit~Dt  216 (388)
T PRK12723        174 KRVFILVGPTGVGKTTTIAKLAAIYGINSD--DKSLNIKIITIDN  216 (388)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhhhc--cCCCeEEEEeccC
Confidence            569999999999999999999987754211  1247888888874

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=97.55  E-value=0.00052  Score=68.72  Aligned_cols=28  Identities=25%  Similarity=0.335  Sum_probs=25.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       363 i~~G~~~aivG~sGsGKSTL~~ll~g~~  390 (574)
T PRK11160        363 IKAGEKVALLGRTGCGKSTLLQLLTRAW  390 (574)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            7899999999999999999999777543

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

Probab=97.55  E-value=0.00071  Score=67.18  Aligned_cols=121  Identities=18%  Similarity=0.271  Sum_probs=76.9

Q ss_pred             hhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHH
Q 035774           94 ALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQE  173 (357)
Q Consensus        94 ~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~  173 (357)
                      +++-|+.+.+=++++||||+|||.+|..+|-++.           --|++..+   ++-+ .|                 
T Consensus       697 LfssglrkRSGILLYGPPGTGKTLlAKAVATEcs-----------L~FlSVKG---PELL-NM-----------------  744 (953)
T KOG0736|consen  697 LFSSGLRKRSGILLYGPPGTGKTLLAKAVATECS-----------LNFLSVKG---PELL-NM-----------------  744 (953)
T ss_pred             hhhccccccceeEEECCCCCchHHHHHHHHhhce-----------eeEEeecC---HHHH-HH-----------------
Confidence            4566899999999999999999999998887764           33666654   2211 11                 


Q ss_pred             hhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC---ChHHHHHHHHHHHHHHHHcCCeEE
Q 035774          174 MAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP---GQHPLSWHISLITSLAEFSRIPIV  250 (357)
Q Consensus       174 ~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~---r~~~~~~i~~~Lk~la~~~~~~vv  250 (357)
                           ++  ..+.+.+.+++++.+.    -.+.+|+.|.|.++.+........   -...+.+++..|..+.....-.|+
T Consensus       745 -----YV--GqSE~NVR~VFerAR~----A~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VF  813 (953)
T KOG0736|consen  745 -----YV--GQSEENVREVFERARS----AAPCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVF  813 (953)
T ss_pred             -----Hh--cchHHHHHHHHHHhhc----cCCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceE
Confidence                 11  1233455556655443    468999999999998763221111   124566666677777664455666


Q ss_pred             Eeccccc
Q 035774          251 VTNQVRP  257 (357)
Q Consensus       251 ~~~q~~~  257 (357)
                      ++.-.++
T Consensus       814 ViGATNR  820 (953)
T KOG0736|consen  814 VIGATNR  820 (953)
T ss_pred             EEecCCC
Confidence            6655444

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

Probab=97.55  E-value=8.3e-05  Score=66.52  Aligned_cols=132  Identities=19%  Similarity=0.329  Sum_probs=78.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      +--..++++.||||+|||+||..+|-....+.  .+...+...|....    -++       +..+|..           
T Consensus       174 It~NRliLlhGPPGTGKTSLCKaLaQkLSIR~--~~~y~~~~liEins----hsL-------FSKWFsE-----------  229 (423)
T KOG0744|consen  174 ITWNRLILLHGPPGTGKTSLCKALAQKLSIRT--NDRYYKGQLIEINS----HSL-------FSKWFSE-----------  229 (423)
T ss_pred             eeeeeEEEEeCCCCCChhHHHHHHHHhheeee--cCccccceEEEEeh----hHH-------HHHHHhh-----------
Confidence            55678999999999999999999887664321  11123333333221    111       1111111           


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCC---CCCCCC--ChHHHHHHHHHHHHHHHHcCCeEEEe
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGV---HEQRAP--GQHPLSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~---~~~~~~--r~~~~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                            +..-+..+++++..++... ..=.|.||.+-++....   ..++..  .-..+..++..|.++.+..|+.++.|
T Consensus       230 ------SgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~T  303 (423)
T KOG0744|consen  230 ------SGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILAT  303 (423)
T ss_pred             ------hhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEec
Confidence                  1122334455555555543 45678899887764331   111111  12456778888999999999999999


Q ss_pred             ccccccCC
Q 035774          253 NQVRPQSH  260 (357)
Q Consensus       253 ~q~~~~~~  260 (357)
                      +.+....+
T Consensus       304 SNl~~siD  311 (423)
T KOG0744|consen  304 SNLTDSID  311 (423)
T ss_pred             cchHHHHH
Confidence            98876543

>TIGR01842 type_I_sec_PrtD type I secretion system ABC transporter, PrtD family

Probab=97.55  E-value=0.00069  Score=67.44  Aligned_cols=28  Identities=21%  Similarity=0.456  Sum_probs=24.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       341 i~~G~~~~ivG~sGsGKSTL~~ll~g~~  368 (544)
T TIGR01842       341 LQAGEALAIIGPSGSGKSTLARLIVGIW  368 (544)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            7899999999999999999999777543

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.

>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor

Probab=97.55  E-value=0.0014  Score=58.48  Aligned_cols=34  Identities=32%  Similarity=0.246  Sum_probs=27.4

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .|+.+-  -+.+|+++.|.|++|+|||||+.-++..
T Consensus        16 ~l~~i~--~i~~Ge~~~IvG~nGsGKSTLlk~l~Gl   49 (255)
T cd03236          16 KLHRLP--VPREGQVLGLVGPNGIGKSTALKILAGK   49 (255)
T ss_pred             hhhcCC--CCCCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            455543  2789999999999999999999866643

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.

>PRK11231 fecE iron-dicitrate transporter ATP-binding subunit; Provisional

Probab=97.54  E-value=0.00042  Score=61.88  Aligned_cols=26  Identities=35%  Similarity=0.675  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Ge~~~l~G~nGsGKSTLl~~l~G   50 (255)
T PRK11231         25 LPTGKITALIGPNGCGKSTLLKCFAR   50 (255)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997774

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

Probab=97.54  E-value=0.0013  Score=60.69  Aligned_cols=84  Identities=11%  Similarity=0.093  Sum_probs=52.8

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhc
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAG  176 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~  176 (357)
                      .|+++-.+++|.||||+|||.+|..++...         +...+.++.-+      +   ... |   .           
T Consensus       143 ~~ik~PlgllL~GPPGcGKTllAraiA~el---------g~~~i~vsa~e------L---~sk-~---v-----------  189 (413)
T PLN00020        143 PNIKVPLILGIWGGKGQGKSFQCELVFKKM---------GIEPIVMSAGE------L---ESE-N---A-----------  189 (413)
T ss_pred             cCCCCCeEEEeeCCCCCCHHHHHHHHHHHc---------CCCeEEEEHHH------h---hcC-c---C-----------
Confidence            458889999999999999999999888765         24455554421      1   000 0   0           


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHHh-hhcCeeEEEEeccccccCC
Q 035774          177 RILVLQPTSLSEFTESLEKIKVSL-LQNQVKLLVIDSMEALVPG  219 (357)
Q Consensus       177 ~i~~~~~~~~~~~~~~l~~l~~~~-~~~~~~lvvIDsl~~l~~~  219 (357)
                            -.+...+.+++....... .+..+.+|+||.|-++...
T Consensus       190 ------GEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~  227 (413)
T PLN00020        190 ------GEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGR  227 (413)
T ss_pred             ------CcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCC
Confidence                  011122333344333333 2456899999999998865

>TIGR03269 met_CoM_red_A2 methyl coenzyme M reductase system, component A2

Probab=97.53  E-value=0.00065  Score=67.20  Aligned_cols=46  Identities=13%  Similarity=0.112  Sum_probs=35.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         .....+...|++++++.+.+||+++|-..
T Consensus       185 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~l~~~~g~tviivtHd~~  230 (520)
T TIGR03269       185 KEPFLFLADEPTGTLDP---------QTAKLVHNALEEAVKASGISMVLTSHWPE  230 (520)
T ss_pred             cCCCEEEeeCCcccCCH---------HHHHHHHHHHHHHHHhcCcEEEEEeCCHH
Confidence            47899999987765533         44556778889998888999999998654

The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.

>PRK07594 type III secretion system ATPase SsaN; Validated

Probab=97.52  E-value=0.00023  Score=67.63  Aligned_cols=42  Identities=19%  Similarity=0.244  Sum_probs=37.1

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ...+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.
T Consensus       136 ~~~l~tGi~aID~ll~--i~~GqrigI~G~sG~GKSTLL~~I~~  177 (433)
T PRK07594        136 TQPLMTGIRAIDSVAT--CGEGQRVGIFSAPGVGKSTLLAMLCN  177 (433)
T ss_pred             hheeCCCceeeeeeee--cCCCCEEEEECCCCCCccHHHHHhcC
Confidence            3468899999999965  99999999999999999999976664

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=97.51  E-value=0.00068  Score=58.29  Aligned_cols=27  Identities=22%  Similarity=0.363  Sum_probs=23.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +|++++|.|++|+|||||+..++....
T Consensus        28 ~~~~~~l~G~Ng~GKStll~~i~~~~~   54 (202)
T cd03243          28 SGRLLLITGPNMGGKSTYLRSIGLAVL   54 (202)
T ss_pred             CCeEEEEECCCCCccHHHHHHHHHHHH
Confidence            469999999999999999999985543

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

>CHL00059 atpA ATP synthase CF1 alpha subunit

Probab=97.51  E-value=0.00056  Score=65.55  Aligned_cols=58  Identities=21%  Similarity=0.200  Sum_probs=47.9

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|.++.  +-+|+=..|.|++|+|||+||+.++.+...      .+..|+|.-.-+
T Consensus       122 ~epl~TGI~aID~l~p--igrGQR~~I~g~~g~GKt~Lal~~I~~q~~------~dv~cV~~~IGe  179 (485)
T CHL00059        122 YEPLQTGLIAIDSMIP--IGRGQRELIIGDRQTGKTAVATDTILNQKG------QNVICVYVAIGQ  179 (485)
T ss_pred             CcccccCceeeccccc--cccCCEEEeecCCCCCHHHHHHHHHHhccc------CCeEEEEEEecC
Confidence            5689999999999987  789999999999999999998887766542      245678887643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.51  E-value=0.00054  Score=70.58  Aligned_cols=29  Identities=34%  Similarity=0.377  Sum_probs=25.8

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+.++.-++|+||||+|||+|+..++...
T Consensus       208 gi~~~~giLL~GppGtGKT~laraia~~~  236 (733)
T TIGR01243       208 GIEPPKGVLLYGPPGTGKTLLAKAVANEA  236 (733)
T ss_pred             CCCCCceEEEECCCCCChHHHHHHHHHHh
Confidence            58888999999999999999999887654

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.

>PRK10762 D-ribose transporter ATP binding protein; Provisional

Probab=97.51  E-value=0.00079  Score=66.29  Aligned_cols=45  Identities=13%  Similarity=0.116  Sum_probs=32.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         .....+.+.|+++++ .+.+||+++|-..
T Consensus       158 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~l~~-~~~tvii~sHd~~  202 (501)
T PRK10762        158 FESKVIIMDEPTDALTD---------TETESLFRVIRELKS-QGRGIVYISHRLK  202 (501)
T ss_pred             cCCCEEEEeCCcCCCCH---------HHHHHHHHHHHHHHH-CCCEEEEEeCCHH
Confidence            47999999987765433         344456677777765 4889999988644

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

Probab=97.51  E-value=0.00026  Score=68.47  Aligned_cols=116  Identities=19%  Similarity=0.223  Sum_probs=69.3

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+.|-.=+++.||||||||.||..+|.+..         .+-+-|+.-+     -+..                      
T Consensus       219 Gv~PprGvLlHGPPGCGKT~lA~AiAgel~---------vPf~~isApe-----ivSG----------------------  262 (802)
T KOG0733|consen  219 GVRPPRGVLLHGPPGCGKTSLANAIAGELG---------VPFLSISAPE-----IVSG----------------------  262 (802)
T ss_pred             CCCCCCceeeeCCCCccHHHHHHHHhhhcC---------CceEeecchh-----hhcc----------------------
Confidence            688888899999999999999998886553         2322222211     1111                      


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCC---hHHHHHHHHHHHHHHHH--cCCeEEEe
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPG---QHPLSWHISLITSLAEF--SRIPIVVT  252 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r---~~~~~~i~~~Lk~la~~--~~~~vv~~  252 (357)
                         +...+-..+.+++++.    ....+.+|+||.|.++.+....  +.|   +..+.+++..+..+..+  .|-+|+++
T Consensus       263 ---vSGESEkkiRelF~~A----~~~aPcivFiDeIDAI~pkRe~--aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVI  333 (802)
T KOG0733|consen  263 ---VSGESEKKIRELFDQA----KSNAPCIVFIDEIDAITPKREE--AQREMERRIVAQLLTSMDELSNEKTKGDPVLVI  333 (802)
T ss_pred             ---cCcccHHHHHHHHHHH----hccCCeEEEeecccccccchhh--HHHHHHHHHHHHHHHhhhcccccccCCCCeEEE
Confidence               0111223344444432    3456899999999999765211  222   23345555555555433  46788888


Q ss_pred             cccccc
Q 035774          253 NQVRPQ  258 (357)
Q Consensus       253 ~q~~~~  258 (357)
                      .-.++.
T Consensus       334 gATnRP  339 (802)
T KOG0733|consen  334 GATNRP  339 (802)
T ss_pred             ecCCCC
Confidence            776654

>PLN03130 ABC transporter C family member; Provisional

Probab=97.51  E-value=0.00047  Score=76.49  Aligned_cols=40  Identities=25%  Similarity=0.310  Sum_probs=31.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+-+.|+|++|+|||||+.-+..-.-  .     ..+.++||..
T Consensus      1262 I~~GekVaIVGrSGSGKSTLl~lL~rl~~--p-----~~G~I~IDG~ 1301 (1622)
T PLN03130       1262 ISPSEKVGIVGRTGAGKSSMLNALFRIVE--L-----ERGRILIDGC 1301 (1622)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCcCC--C-----CCceEEECCE
Confidence            88999999999999999999987775432  1     2456777764

>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family

Probab=97.50  E-value=0.00075  Score=69.21  Aligned_cols=40  Identities=28%  Similarity=0.462  Sum_probs=30.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+.+.|.|++|+|||||+.-++....  +     ..+.++++..
T Consensus       480 i~~G~~vaivG~sGsGKSTL~~ll~g~~~--p-----~~G~I~idg~  519 (694)
T TIGR01846       480 IKPGEFIGIVGPSGSGKSTLTKLLQRLYT--P-----QHGQVLVDGV  519 (694)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCCC--C-----CCceEEECCE
Confidence            78999999999999999999997775432  1     2345666653

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.

>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1

Probab=97.50  E-value=0.0017  Score=57.25  Aligned_cols=27  Identities=33%  Similarity=0.551  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLl~~i~G~   52 (238)
T cd03249          26 IPPGKTVALVGSSGCGKSTVVSLLERF   52 (238)
T ss_pred             ecCCCEEEEEeCCCCCHHHHHHHHhcc
Confidence            889999999999999999999977753

In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=97.50  E-value=0.00085  Score=58.75  Aligned_cols=27  Identities=33%  Similarity=0.441  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        30 i~~Ge~~~l~G~nGsGKSTLlk~l~G~   56 (226)
T cd03234          30 VESGQVMAILGSSGSGKTTLLDAISGR   56 (226)
T ss_pred             EcCCeEEEEECCCCCCHHHHHHHHhCc
Confidence            889999999999999999999977754

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional

Probab=97.50  E-value=0.0014  Score=64.97  Aligned_cols=46  Identities=11%  Similarity=0.119  Sum_probs=35.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-...         .....+.+.|++++++++.+||+++|-..
T Consensus       173 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~l~~~~g~tvi~vtHd~~  218 (529)
T PRK15134        173 TRPELLIADEPTTALDV---------SVQAQILQLLRELQQELNMGLLFITHNLS  218 (529)
T ss_pred             cCCCEEEEcCCCCccCH---------HHHHHHHHHHHHHHHhcCCeEEEEcCcHH
Confidence            47999999987765433         45556778888888888999999988644

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.49  E-value=0.001  Score=63.36  Aligned_cols=41  Identities=24%  Similarity=0.263  Sum_probs=30.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ..+.|+|+||+|||+++..++......    +.+..++|+++...
T Consensus        56 ~~~lI~G~~GtGKT~l~~~v~~~l~~~----~~~~~~v~in~~~~   96 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVKKVFEELEEI----AVKVVYVYINCQID   96 (394)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHh----cCCcEEEEEECCcC
Confidence            346899999999999999999876431    11367889987543

>PRK08233 hypothetical protein; Provisional

Probab=97.49  E-value=0.00048  Score=57.96  Aligned_cols=25  Identities=20%  Similarity=0.292  Sum_probs=22.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +-++.|.|+|||||||||.+++...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~l   27 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhhC
Confidence            4689999999999999999999764

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.49  E-value=0.00095  Score=57.21  Aligned_cols=27  Identities=30%  Similarity=0.520  Sum_probs=24.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|++..|.||+|||||||+..++-+
T Consensus        27 v~~GEvhaiMGPNGsGKSTLa~~i~G~   53 (251)
T COG0396          27 VKEGEVHAIMGPNGSGKSTLAYTIMGH   53 (251)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999999988743

>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional

Probab=97.49  E-value=0.00066  Score=66.85  Aligned_cols=27  Identities=33%  Similarity=0.410  Sum_probs=24.5

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      -+++|+++.|.|++|+|||||+.-++.
T Consensus        26 ~i~~Ge~~~l~G~nGsGKSTLl~~l~G   52 (501)
T PRK11288         26 DCRAGQVHALMGENGAGKSTLLKILSG   52 (501)
T ss_pred             EEeCCcEEEEECCCCCCHHHHHHHHhC
Confidence            389999999999999999999997774

>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=97.48  E-value=0.00091  Score=66.93  Aligned_cols=28  Identities=21%  Similarity=0.381  Sum_probs=24.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       338 i~~G~~~~ivG~sGsGKSTLl~ll~g~~  365 (569)
T PRK10789        338 LKPGQMLGICGPTGSGKSTLLSLIQRHF  365 (569)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhccc
Confidence            7899999999999999999998776543

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=97.47  E-value=0.00084  Score=65.28  Aligned_cols=27  Identities=26%  Similarity=0.484  Sum_probs=24.5

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      -+++|+++.|.|++|+|||||+.-++.
T Consensus        46 sI~~GEivgIiGpNGSGKSTLLkiLaG   72 (549)
T PRK13545         46 EVPEGEIVGIIGLNGSGKSTLSNLIAG   72 (549)
T ss_pred             EEeCCCEEEEEcCCCCCHHHHHHHHhC
Confidence            388999999999999999999997774

>TIGR01192 chvA glucan exporter ATP-binding protein

Probab=97.47  E-value=0.00081  Score=67.49  Aligned_cols=27  Identities=33%  Similarity=0.524  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       358 i~~G~~~~ivG~sGsGKSTL~~ll~g~  384 (585)
T TIGR01192       358 AKAGQTVAIVGPTGAGKTTLINLLQRV  384 (585)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHccC
Confidence            789999999999999999999877643

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.

>PRK10522 multidrug transporter membrane component/ATP-binding component; Provisional

Probab=97.47  E-value=0.0009  Score=66.66  Aligned_cols=26  Identities=27%  Similarity=0.464  Sum_probs=23.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+.+.|.|++|+|||||+.-++.
T Consensus       346 i~~G~~~aivG~sGsGKSTL~~ll~g  371 (547)
T PRK10522        346 IKRGELLFLIGGNGSGKSTLAMLLTG  371 (547)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999986664

>PRK14258 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.46  E-value=0.0021  Score=57.61  Aligned_cols=27  Identities=33%  Similarity=0.577  Sum_probs=24.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        30 i~~Ge~~~I~G~nGsGKSTLl~~l~Gl   56 (261)
T PRK14258         30 IYQSKVTAIIGPSGCGKSTFLKCLNRM   56 (261)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhcc
Confidence            889999999999999999999988754

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.46  E-value=0.0002  Score=70.25  Aligned_cols=108  Identities=19%  Similarity=0.236  Sum_probs=58.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPT  184 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  184 (357)
                      ++|+||||+|||+++..++...         +.+.++++...      +.....                 +       .
T Consensus        91 iLL~GppGtGKT~la~alA~~~---------~~~~~~i~~~~------~~~~~~-----------------g-------~  131 (495)
T TIGR01241        91 VLLVGPPGTGKTLLAKAVAGEA---------GVPFFSISGSD------FVEMFV-----------------G-------V  131 (495)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc---------CCCeeeccHHH------HHHHHh-----------------c-------c
Confidence            8999999999999999988654         24555554321      111000                 0       0


Q ss_pred             CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC----CCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          185 SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR----APGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       185 ~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~----~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ....+..++..    .....+.+|+||.+..+........    ......+..++..+..+....++.||.+++-
T Consensus       132 ~~~~l~~~f~~----a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~aTn~  202 (495)
T TIGR01241       132 GASRVRDLFEQ----AKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNR  202 (495)
T ss_pred             cHHHHHHHHHH----HHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEecCC
Confidence            11122233322    2335678999999998875422111    1122334444444544445556666665543

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.

>PRK14269 phosphate ABC transporter ATP-binding protein; Provisional

Probab=97.46  E-value=0.001  Score=59.00  Aligned_cols=27  Identities=26%  Similarity=0.505  Sum_probs=24.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (246)
T PRK14269         25 IEQNKITALIGASGCGKSTFLRCFNRM   51 (246)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcc
Confidence            789999999999999999999977753

>PLN03232 ABC transporter C family member; Provisional

Probab=97.46  E-value=0.00054  Score=75.72  Aligned_cols=40  Identities=28%  Similarity=0.305  Sum_probs=31.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+-+.|+|++|+|||||+.-+..-.-  +     ..+-++||..
T Consensus      1259 I~~GekvaIVG~SGSGKSTL~~lL~rl~~--p-----~~G~I~IdG~ 1298 (1495)
T PLN03232       1259 VSPSEKVGVVGRTGAGKSSMLNALFRIVE--L-----EKGRIMIDDC 1298 (1495)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCc--C-----CCceEEECCE
Confidence            78999999999999999999997775432  1     2446777764

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=97.46  E-value=0.0029  Score=53.32  Aligned_cols=130  Identities=15%  Similarity=0.103  Sum_probs=75.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC---chHHHHHHHhccCchhhcccchHHHhhcC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF---TSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~---~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      ....+.|++.+|.|||+.|+-++.+++.      .+.+|+++-+--.-   ......+... .    +....    ....
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g------~G~~V~ivQFlKg~~~~GE~~~l~~l~-~----v~~~~----~g~~   85 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVG------HGKKVGVVQFIKGAWSTGERNLLEFGG-G----VEFHV----MGTG   85 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHH------CCCeEEEEEEecCCCccCHHHHHhcCC-C----cEEEE----CCCC
Confidence            3448899999999999999999999983      46899988764321   1111111100 0    00000    0011


Q ss_pred             eEEeCCCC---HHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          178 ILVLQPTS---LSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       178 i~~~~~~~---~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                      +.+.....   .......++.+...+.....++||+|.+.......+       -...+++..|+.  +.-++-||+|.+
T Consensus        86 ~~~~~~~~~e~~~~~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gl-------i~~eevi~~L~~--rp~~~evVlTGR  156 (191)
T PRK05986         86 FTWETQDRERDIAAAREGWEEAKRMLADESYDLVVLDELTYALKYGY-------LDVEEVLEALNA--RPGMQHVVITGR  156 (191)
T ss_pred             CcccCCCcHHHHHHHHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCC-------ccHHHHHHHHHc--CCCCCEEEEECC
Confidence            11111111   122333455566667778899999999987765422       223345566653  556788999865

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

Probab=97.46  E-value=0.0012  Score=59.37  Aligned_cols=29  Identities=21%  Similarity=0.189  Sum_probs=23.6

Q ss_pred             CCC-CcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPF-GVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~-G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +++ ..+++|.|++|+|||+++..++....
T Consensus        39 ~~~~~~~~~l~G~~G~GKTtl~~~l~~~l~   68 (269)
T TIGR03015        39 LSQREGFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             HhcCCCEEEEEcCCCCCHHHHHHHHHHhcC
Confidence            444 34899999999999999999976653

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.

>cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A

Probab=97.46  E-value=0.00092  Score=61.39  Aligned_cols=56  Identities=30%  Similarity=0.325  Sum_probs=46.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ...+.||+..+|.++.  +-+|+-..|.|++|+|||+++.+++.+.-        ..-++|+-+-+
T Consensus       138 ~~pL~TGirvID~l~P--i~kGqr~~I~G~~G~GKT~L~~~Iak~~~--------~dvvVyv~iGE  193 (369)
T cd01134         138 NEPLLTGQRVLDTLFP--VVKGGTAAIPGPFGCGKTVIQQSLSKYSN--------SDIVIYVGCGE  193 (369)
T ss_pred             CCchhccchhhhcccc--ccCCCEEEEECCCCCChHHHHHHHHhCCC--------CCEEEEEEeCC
Confidence            5679999999999987  88999999999999999999999887542        14577777643

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.

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

Probab=97.45  E-value=0.0017  Score=57.85  Aligned_cols=41  Identities=24%  Similarity=0.348  Sum_probs=34.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++.+.-+.++|+||+|||.|+..++..++.   .   +.+|+|+.+-
T Consensus       102 ~~~~~nl~l~G~~G~GKThLa~Ai~~~l~~---~---g~sv~f~~~~  142 (254)
T COG1484         102 FERGENLVLLGPPGVGKTHLAIAIGNELLK---A---GISVLFITAP  142 (254)
T ss_pred             hccCCcEEEECCCCCcHHHHHHHHHHHHHH---c---CCeEEEEEHH
Confidence            447888999999999999999999998883   2   5899999873

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.45  E-value=0.0015  Score=63.44  Aligned_cols=29  Identities=31%  Similarity=0.253  Sum_probs=25.4

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |++...-++++||||+|||.+|..+|...
T Consensus       255 gl~~pkGILL~GPpGTGKTllAkaiA~e~  283 (489)
T CHL00195        255 GLPTPRGLLLVGIQGTGKSLTAKAIANDW  283 (489)
T ss_pred             CCCCCceEEEECCCCCcHHHHHHHHHHHh
Confidence            57777789999999999999999888765

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.45  E-value=0.0011  Score=67.08  Aligned_cols=44  Identities=32%  Similarity=0.432  Sum_probs=34.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +++|.++.+.||+|+||||.+..++......  .|  ..+|.+++++.
T Consensus       182 ~~~g~Vi~lVGpnGvGKTTTiaKLA~~~~~~--~G--~kkV~lit~Dt  225 (767)
T PRK14723        182 LAQGGVLALVGPTGVGKTTTTAKLAARCVAR--EG--ADQLALLTTDS  225 (767)
T ss_pred             cCCCeEEEEECCCCCcHHHHHHHHHhhHHHH--cC--CCeEEEecCcc
Confidence            4468899999999999999999999876431  22  25788888763

>COG4161 ArtP ABC-type arginine transport system, ATPase component [Amino acid transport and metabolism]

Probab=97.44  E-value=0.002  Score=52.20  Aligned_cols=25  Identities=36%  Similarity=0.620  Sum_probs=22.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      .+.|+.+++.||+|+|||+|...+-
T Consensus        25 ~~~getlvllgpsgagkssllr~ln   49 (242)
T COG4161          25 CPEGETLVLLGPSGAGKSSLLRVLN   49 (242)
T ss_pred             CCCCCEEEEECCCCCchHHHHHHHH
Confidence            6889999999999999999987543

>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional

Probab=97.44  E-value=0.00086  Score=65.85  Aligned_cols=45  Identities=18%  Similarity=0.105  Sum_probs=32.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..++-...         .....+.+.|++++++ +.+||+++|-..
T Consensus       152 ~~p~lllLDEPt~~LD~---------~~~~~l~~~l~~~~~~-g~tvii~tH~~~  196 (490)
T PRK10938        152 SEPDLLILDEPFDGLDV---------ASRQQLAELLASLHQS-GITLVLVLNRFD  196 (490)
T ss_pred             cCCCEEEEcCCcccCCH---------HHHHHHHHHHHHHHhc-CCeEEEEeCCHH
Confidence            47899999987755432         4455677788888765 889999988643

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=97.44  E-value=0.0026  Score=52.07  Aligned_cols=128  Identities=16%  Similarity=0.144  Sum_probs=70.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC---CchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST---FTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~---~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      ++.|+.++|.|||+.|.-++..++.      .+.+|+++.+--.   .....+.+.... + ..+.       ......+
T Consensus         4 ~i~vy~g~G~Gkt~~a~g~~~ra~~------~g~~v~~vQFlKg~~~~gE~~~l~~l~~-v-~~~~-------~g~~~~~   68 (159)
T cd00561           4 LIQVYTGNGKGKTTAALGLALRALG------HGYRVGVVQFLKGGWKYGELKALERLPN-I-EIHR-------MGRGFFW   68 (159)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH------CCCeEEEEEEeCCCCccCHHHHHHhCCC-c-EEEE-------CCCCCcc
Confidence            7788888899999999999999984      3689999765322   111111111100 0 0000       0001111


Q ss_pred             eCCCCHH---HHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          181 LQPTSLS---EFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       181 ~~~~~~~---~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ......+   .....+......+.....++||+|.+........-       ...++...|++  +--++.||+|.+.
T Consensus        69 ~~~~~~~~~~~a~~~~~~a~~~~~~~~~dLlVLDEi~~a~~~gli-------~~~~v~~ll~~--rp~~~evIlTGr~  137 (159)
T cd00561          69 TTENDEEDIAAAAEGWAFAKEAIASGEYDLVILDEINYALGYGLL-------DVEEVVDLLKA--KPEDLELVLTGRN  137 (159)
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHhcCCCCEEEEechHhHhhCCCC-------CHHHHHHHHHc--CCCCCEEEEECCC
Confidence            1111111   22233444555666678999999999987554221       22334555543  4447888888643

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PRK13549 xylose transporter ATP-binding subunit; Provisional

Probab=97.43  E-value=0.00082  Score=66.28  Aligned_cols=26  Identities=35%  Similarity=0.457  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~l~G   53 (506)
T PRK13549         28 VRAGEIVSLCGENGAGKSTLMKVLSG   53 (506)
T ss_pred             EeCCeEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997774

>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit

Probab=97.43  E-value=0.00073  Score=65.57  Aligned_cols=58  Identities=22%  Similarity=0.279  Sum_probs=47.4

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|.++.  +.+|+=..|.|++|+|||+|+++++.+...      .+..|+|+-.-+
T Consensus       142 ~~pl~TGi~aID~l~p--igrGQr~~I~g~~g~GKt~Lal~~i~~~~~------~dv~~V~~~IGe  199 (501)
T TIGR00962       142 HEPLQTGIKAIDAMIP--IGRGQRELIIGDRQTGKTAVAIDTIINQKD------SDVYCVYVAIGQ  199 (501)
T ss_pred             CceeccCCceeeccCC--cccCCEEEeecCCCCCccHHHHHHHHhhcC------CCeEEEEEEccC
Confidence            5689999999999987  889999999999999999998777766542      245568887644

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=97.42  E-value=0.0012  Score=65.35  Aligned_cols=40  Identities=23%  Similarity=0.187  Sum_probs=31.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .-+.|+|++|+|||.|+..++..+...    ..+.+|+|++++.
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~----~~g~~V~Yitaee  354 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRL----YPGTRVRYVSSEE  354 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHh----CCCCeEEEeeHHH
Confidence            458999999999999999999877531    1147899998854

>PRK10982 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional

Probab=97.42  E-value=0.00083  Score=65.96  Aligned_cols=26  Identities=27%  Similarity=0.276  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++-
T Consensus        21 i~~Ge~~~liG~nGsGKSTLl~~l~G   46 (491)
T PRK10982         21 VRPHSIHALMGENGAGKSTLLKCLFG   46 (491)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHcC
Confidence            88999999999999999999997764

>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=97.42  E-value=0.013  Score=54.93  Aligned_cols=94  Identities=14%  Similarity=0.197  Sum_probs=57.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch---HHHHHHHhccCchhhcccchHHHhhc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS---RRMIEMGASSFPEIFHSKGMAQEMAG  176 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~---~rl~~~~~~~~~~~~~~~~~~~~~~~  176 (357)
                      .+-.+++++|--|+||||.|-.+|.....      .+.+|+.++++- +.+   +.|++++..              .  
T Consensus        98 ~~P~vImmvGLQGsGKTTt~~KLA~~lkk------~~~kvllVaaD~-~RpAA~eQL~~La~q--------------~--  154 (451)
T COG0541          98 KPPTVILMVGLQGSGKTTTAGKLAKYLKK------KGKKVLLVAADT-YRPAAIEQLKQLAEQ--------------V--  154 (451)
T ss_pred             CCCeEEEEEeccCCChHhHHHHHHHHHHH------cCCceEEEeccc-CChHHHHHHHHHHHH--------------c--
Confidence            34678999999999999999999988864      258999998874 333   333333322              1  


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccc
Q 035774          177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL  216 (357)
Q Consensus       177 ~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l  216 (357)
                      ++-++...+..+..++..+.....+....++||||....+
T Consensus       155 ~v~~f~~~~~~~Pv~Iak~al~~ak~~~~DvvIvDTAGRl  194 (451)
T COG0541         155 GVPFFGSGTEKDPVEIAKAALEKAKEEGYDVVIVDTAGRL  194 (451)
T ss_pred             CCceecCCCCCCHHHHHHHHHHHHHHcCCCEEEEeCCCcc
Confidence            1222222222223334444444445567888888876654

>cd03291 ABCC_CFTR1 The CFTR subfamily domain 1

Probab=97.42  E-value=0.0041  Score=56.35  Aligned_cols=26  Identities=23%  Similarity=0.422  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        60 i~~Ge~~~liG~NGsGKSTLl~~I~G   85 (282)
T cd03291          60 IEKGEMLAITGSTGSGKTSLLMLILG   85 (282)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997764

The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.

>PRK13343 F0F1 ATP synthase subunit alpha; Provisional

Probab=97.41  E-value=0.00081  Score=64.98  Aligned_cols=58  Identities=22%  Similarity=0.253  Sum_probs=47.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|.++.  +.+|+=..|.|++|+|||+|++.++.+...      .+..|+|.-.-+
T Consensus       143 ~epl~TGIkaID~l~p--igrGQR~~I~g~~g~GKt~Lal~~i~~~~~------~dv~~V~~~IGe  200 (502)
T PRK13343        143 TEPLQTGIKVVDALIP--IGRGQRELIIGDRQTGKTAIAIDAIINQKD------SDVICVYVAIGQ  200 (502)
T ss_pred             CcccccCCceeccccc--cccCCEEEeeCCCCCCccHHHHHHHHhhcC------CCEEEEEEEecc
Confidence            5689999999999997  889999999999999999998777766532      235568877644

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=97.41  E-value=0.001  Score=62.70  Aligned_cols=29  Identities=31%  Similarity=0.369  Sum_probs=24.4

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+.+..-++|+||||+|||+++..++...
T Consensus       152 g~~~p~gvLL~GppGtGKT~lakaia~~l  180 (364)
T TIGR01242       152 GIEPPKGVLLYGPPGTGKTLLAKAVAHET  180 (364)
T ss_pred             CCCCCceEEEECCCCCCHHHHHHHHHHhC
Confidence            46666669999999999999999988754

Many proteins may score above the trusted cutoff because an internal

>PRK06793 fliI flagellum-specific ATP synthase; Validated

Probab=97.41  E-value=0.00059  Score=64.88  Aligned_cols=57  Identities=23%  Similarity=0.256  Sum_probs=44.5

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ..+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.+...       ...++.+..|..
T Consensus       138 ~~l~TGiraID~ll~--I~~Gqri~I~G~sG~GKTtLl~~Ia~~~~~-------~~gvI~~iGerg  194 (432)
T PRK06793        138 DVFETGIKSIDSMLT--IGIGQKIGIFAGSGVGKSTLLGMIAKNAKA-------DINVISLVGERG  194 (432)
T ss_pred             hccCCCCEEEeccce--ecCCcEEEEECCCCCChHHHHHHHhccCCC-------CeEEEEeCCCCc
Confidence            468899999999875  889999999999999999999888765421       244555555543

>PRK09700 D-allose transporter ATP-binding protein; Provisional

Probab=97.41  E-value=0.0014  Score=64.64  Aligned_cols=26  Identities=27%  Similarity=0.296  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus       286 i~~Ge~~~l~G~NGsGKSTLlk~i~G  311 (510)
T PRK09700        286 VCRGEILGFAGLVGSGRTELMNCLFG  311 (510)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997774

>PRK06936 type III secretion system ATPase; Provisional

Probab=97.40  E-value=0.00044  Score=65.72  Aligned_cols=44  Identities=23%  Similarity=0.225  Sum_probs=39.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.+.
T Consensus       143 ~~~l~TGi~vid~l~~--i~~Gq~~~I~G~sG~GKStLl~~Ia~~~  186 (439)
T PRK06936        143 ETPLSLGVRVIDGLLT--CGEGQRMGIFAAAGGGKSTLLASLIRSA  186 (439)
T ss_pred             CCCCcCCcceeeeeEE--ecCCCEEEEECCCCCChHHHHHHHhcCC
Confidence            5689999999999965  8999999999999999999988777654

>TIGR01039 atpD ATP synthase, F1 beta subunit

Probab=97.40  E-value=0.001  Score=63.48  Aligned_cols=57  Identities=28%  Similarity=0.205  Sum_probs=47.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+.+.||+..+|-++.  +-+|+=+.|.|++|+|||+|+.+++.+.....     ..-++|.-.
T Consensus       124 ~e~l~TGiraID~l~p--ig~GQr~~If~~~G~GKt~L~~~~~~~~~~~~-----~~v~V~alI  180 (461)
T TIGR01039       124 VEILETGIKVIDLLAP--YAKGGKIGLFGGAGVGKTVLIQELINNIAKEH-----GGYSVFAGV  180 (461)
T ss_pred             ccccccCceeecccCC--cccCCEEEeecCCCCChHHHHHHHHHHHHhcC-----CCeEEEEEe
Confidence            5679999999999987  78999999999999999999999999886421     235666554

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.

>PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional

Probab=97.40  E-value=0.00051  Score=68.14  Aligned_cols=44  Identities=11%  Similarity=0.175  Sum_probs=34.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         .....+...|++++++++.+||+++|-
T Consensus       442 ~~p~llllDEPt~~LD~---------~~~~~l~~~l~~~~~~~~~tvi~vsHd  485 (529)
T PRK15134        442 LKPSLIILDEPTSSLDK---------TVQAQILALLKSLQQKHQLAYLFISHD  485 (529)
T ss_pred             CCCCEEEeeCCccccCH---------HHHHHHHHHHHHHHHhhCCEEEEEeCC
Confidence            47899999987765432         445567788888988889999999885

>PRK08472 fliI flagellum-specific ATP synthase; Validated

Probab=97.40  E-value=0.0011  Score=63.24  Aligned_cols=44  Identities=16%  Similarity=0.174  Sum_probs=38.5

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ...+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.+.
T Consensus       138 ~~~l~tgi~aid~l~~--i~~Gq~~~i~G~sG~GKStLl~~i~~~~  181 (434)
T PRK08472        138 DEVFSVGVKSIDGLLT--CGKGQKLGIFAGSGVGKSTLMGMIVKGC  181 (434)
T ss_pred             ceeccchhHHhhhcce--ecCCCEEEEECCCCCCHHHHHHHHhhcc
Confidence            4568899999999965  8999999999999999999998777554

>PTZ00243 ABC transporter; Provisional

Probab=97.39  E-value=0.0008  Score=74.54  Aligned_cols=40  Identities=23%  Similarity=0.389  Sum_probs=30.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+.+.|+|++|+|||||+.-+..-.-.       ..+.++||..
T Consensus      1333 I~~GekVaIVGrTGSGKSTLl~lLlrl~~p-------~~G~I~IDG~ 1372 (1560)
T PTZ00243       1333 IAPREKVGIVGRTGSGKSTLLLTFMRMVEV-------CGGEIRVNGR 1372 (1560)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCCC-------CCcEEEECCE
Confidence            779999999999999999999977654321       2345677754

>PRK00889 adenylylsulfate kinase; Provisional

Probab=97.39  E-value=0.00026  Score=59.32  Aligned_cols=40  Identities=25%  Similarity=0.210  Sum_probs=33.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++|.++.|.|.||+||||++..++......      +..+.+++.+
T Consensus         2 ~~g~~i~~~G~~GsGKST~a~~la~~l~~~------g~~v~~id~D   41 (175)
T PRK00889          2 QRGVTVWFTGLSGAGKTTIARALAEKLREA------GYPVEVLDGD   41 (175)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEEcCc
Confidence            579999999999999999999999876421      3578889875

>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]

Probab=97.39  E-value=0.002  Score=59.70  Aligned_cols=44  Identities=16%  Similarity=0.172  Sum_probs=34.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      ..++++|-|.-+.-..         ...-.+|+..|+.|-+++|+++++++|-
T Consensus       174 n~P~lLIADEPTTALD---------VtvQaQIL~Ll~~Lq~~~gMa~lfITHD  217 (534)
T COG4172         174 NEPDLLIADEPTTALD---------VTVQAQILDLLKELQAELGMAILFITHD  217 (534)
T ss_pred             CCCCeEeecCCcchhh---------hhhHHHHHHHHHHHHHHhCcEEEEEecc
Confidence            4688999887665432         2344578999999999999999999984

>cd03288 ABCC_SUR2 The SUR domain 2

Probab=97.39  E-value=0.0017  Score=58.10  Aligned_cols=27  Identities=22%  Similarity=0.439  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.|++|+|||||+.-++..
T Consensus        44 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl   70 (257)
T cd03288          44 IKPGQKVGICGRTGSGKSSLSLAFFRM   70 (257)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcc
Confidence            789999999999999999999987753

The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.

>PRK06820 type III secretion system ATPase; Validated

Probab=97.39  E-value=0.00053  Score=65.37  Aligned_cols=43  Identities=23%  Similarity=0.262  Sum_probs=38.1

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .+.+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++..
T Consensus       144 ~~~l~TGi~aID~l~~--i~~Gqri~I~G~sG~GKStLl~~I~~~  186 (440)
T PRK06820        144 EQMLTTGIRAIDGILS--CGEGQRIGIFAAAGVGKSTLLGMLCAD  186 (440)
T ss_pred             hhhccCCCceecceEE--ecCCCEEEEECCCCCChHHHHHHHhcc
Confidence            4579999999999976  899999999999999999998766643

>PRK13768 GTPase; Provisional

Probab=97.39  E-value=0.0008  Score=59.97  Aligned_cols=39  Identities=23%  Similarity=0.314  Sum_probs=32.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      .++.|.|++|+||||++.+++...+..      +.+|++|+.+..
T Consensus         3 ~~i~v~G~~G~GKTt~~~~~~~~l~~~------g~~v~~i~~D~~   41 (253)
T PRK13768          3 YIVFFLGTAGSGKTTLTKALSDWLEEQ------GYDVAIVNLDPA   41 (253)
T ss_pred             EEEEEECCCCccHHHHHHHHHHHHHhc------CCceEEEECCCc
Confidence            478999999999999999999877642      578999988753

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=97.38  E-value=0.0024  Score=62.82  Aligned_cols=142  Identities=15%  Similarity=0.138  Sum_probs=77.6

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC----CCeEEEEeCCCCCchHHHHHHHhcc-CchhhcccchHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL----DGGVIYIDVESTFTSRRMIEMGASS-FPEIFHSKGMAQ  172 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~----~~~vl~i~~e~~~~~~rl~~~~~~~-~~~~~~~~~~~~  172 (357)
                      .+++|+-++|.|++|+|||+|...++-  +-|-..|..    +...+|+.-..-++...+++..-.- ....+..+...+
T Consensus       415 ~v~~G~~llI~G~SG~GKTsLlRaiaG--LWP~g~G~I~~P~~~~~lflpQ~PY~p~GtLre~l~YP~~~~~~~d~~l~~  492 (604)
T COG4178         415 EVRPGERLLITGESGAGKTSLLRALAG--LWPWGSGRISMPADSALLFLPQRPYLPQGTLREALCYPNAAPDFSDAELVA  492 (604)
T ss_pred             eeCCCCEEEEECCCCCCHHHHHHHHhc--cCccCCCceecCCCCceEEecCCCCCCCccHHHHHhCCCCCCCCChHHHHH
Confidence            389999999999999999999997774  333222221    3457888877767766666554220 000111111111


Q ss_pred             H--------hhcCeEEeCCC----CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHH
Q 035774          173 E--------MAGRILVLQPT----SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS  240 (357)
Q Consensus       173 ~--------~~~~i~~~~~~----~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~  240 (357)
                      .        ..+++.-.+.+    +..+. +.+.-.+-.  -++++.+|+|..++-....             .-..|.+
T Consensus       493 vL~~vgL~~L~~rl~~~~~W~~vLS~GEq-QRlafARil--L~kP~~v~LDEATsALDe~-------------~e~~l~q  556 (604)
T COG4178         493 VLHKVGLGDLAERLDEEDRWDRVLSGGEQ-QRLAFARLL--LHKPKWVFLDEATSALDEE-------------TEDRLYQ  556 (604)
T ss_pred             HHHHcCcHHHHHHHhccCcHhhhcChhHH-HHHHHHHHH--HcCCCEEEEecchhccChH-------------HHHHHHH
Confidence            0        11111111111    11111 111111222  3689999999988655431             1123455


Q ss_pred             HHHH--cCCeEEEeccccc
Q 035774          241 LAEF--SRIPIVVTNQVRP  257 (357)
Q Consensus       241 la~~--~~~~vv~~~q~~~  257 (357)
                      +.++  .+++||-+.|-++
T Consensus       557 ~l~~~lp~~tvISV~Hr~t  575 (604)
T COG4178         557 LLKEELPDATVISVGHRPT  575 (604)
T ss_pred             HHHhhCCCCEEEEeccchh
Confidence            5555  7999999988644

>PRK05922 type III secretion system ATPase; Validated

Probab=97.38  E-value=0.00076  Score=64.11  Aligned_cols=44  Identities=23%  Similarity=0.320  Sum_probs=38.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.+.||+..+|.++.  +.+|+-+.|.|++|+|||+|+..++...
T Consensus       138 ~e~l~TGIr~ID~ll~--I~~GqrigI~G~nG~GKSTLL~~Ia~~~  181 (434)
T PRK05922        138 QEIFPTGIKAIDAFLT--LGKGQRIGVFSEPGSGKSSLLSTIAKGS  181 (434)
T ss_pred             ceecCCCceeecceEE--EcCCcEEEEECCCCCChHHHHHHHhccC
Confidence            4579999999999876  8999999999999999999987777543

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=97.37  E-value=0.00024  Score=55.45  Aligned_cols=23  Identities=30%  Similarity=0.527  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|+|+|||||||+|..++...
T Consensus         1 vI~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
Confidence            57899999999999999999764

...

>TIGR00957 MRP_assoc_pro multi drug resistance-associated protein (MRP)

Probab=97.36  E-value=0.001  Score=73.77  Aligned_cols=40  Identities=30%  Similarity=0.390  Sum_probs=31.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+.+.|+|++|+|||||+.-+..-.-  .     ..+.++||..
T Consensus      1309 I~~GekiaIVGrTGsGKSTL~~lL~rl~~--~-----~~G~I~IdG~ 1348 (1522)
T TIGR00957      1309 IHGGEKVGIVGRTGAGKSSLTLGLFRINE--S-----AEGEIIIDGL 1348 (1522)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCcc--C-----CCCeEEECCE
Confidence            88999999999999999999997765432  1     2446777754

This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.36  E-value=0.0021  Score=52.01  Aligned_cols=24  Identities=29%  Similarity=0.389  Sum_probs=21.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      =+.|+|+||+||||+++.++-...
T Consensus         7 ki~ITG~PGvGKtTl~~ki~e~L~   30 (179)
T COG1618           7 KIFITGRPGVGKTTLVLKIAEKLR   30 (179)
T ss_pred             EEEEeCCCCccHHHHHHHHHHHHH
Confidence            368999999999999999997664

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.35  E-value=0.0017  Score=60.43  Aligned_cols=42  Identities=19%  Similarity=0.214  Sum_probs=36.4

Q ss_pred             CCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           85 PTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        85 ~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      .+|...+|.++.  +-+|+=.+|.|+||+|||+++..++.+...
T Consensus       118 ~~~~RvID~l~P--iGkGQR~LIvG~pGtGKTTLl~~la~~i~~  159 (380)
T PRK12608        118 DLSMRVVDLVAP--IGKGQRGLIVAPPRAGKTVLLQQIAAAVAA  159 (380)
T ss_pred             chhHhhhhheee--cCCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            677888999886  558889999999999999999999987754

>TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR)

Probab=97.35  E-value=0.0011  Score=73.27  Aligned_cols=39  Identities=33%  Similarity=0.365  Sum_probs=31.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+-+.|+|++|+|||||+.-++.-..   .     .+.++||..
T Consensus      1242 I~~GekvaIvGrSGsGKSTLl~lL~rl~~---~-----~G~I~IdG~ 1280 (1490)
T TIGR01271      1242 VEGGQRVGLLGRTGSGKSTLLSALLRLLS---T-----EGEIQIDGV 1280 (1490)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhhhcC---C-----CcEEEECCE
Confidence            78999999999999999999998886542   1     345677754

The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.

>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=97.35  E-value=0.0024  Score=55.89  Aligned_cols=118  Identities=14%  Similarity=0.128  Sum_probs=62.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQP  183 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  183 (357)
                      -++|.|++|||||+|++.++.....       ....+|+-++.. . ....+.                 +..+ ++...
T Consensus        15 r~viIG~sGSGKT~li~~lL~~~~~-------~f~~I~l~t~~~-n-~~~~~~-----------------i~p~-~i~~~   67 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTLIKSLLYYLRH-------KFDHIFLITPEY-N-NEYYKY-----------------IWPD-HIFKV   67 (241)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhhcc-------cCCEEEEEecCC-c-hhhhhh-----------------cchh-hcccc
Confidence            4789999999999999999977543       234555554421 1 100000                 0000 11112


Q ss_pred             CCHHHHHHHHHH----HHHHhhh------cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          184 TSLSEFTESLEK----IKVSLLQ------NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       184 ~~~~~~~~~l~~----l~~~~~~------~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                      .+.+++...+..    +.+....      ...-+||+|.++.-        ..+.+    .+..+-.-.+.+++.++++.
T Consensus        68 ~~~e~le~~l~~~k~~I~k~~~k~~~~k~~~~~LiIlDD~~~~--------~~k~~----~l~~~~~~gRH~~is~i~l~  135 (241)
T PF04665_consen   68 FDKEELEYILIRQKEKIEKYIKKSPQKKNNPRFLIILDDLGDK--------KLKSK----ILRQFFNNGRHYNISIIFLS  135 (241)
T ss_pred             ccHHHHHHHHHHHHHHHHHHhhhhcccCCCCCeEEEEeCCCCc--------hhhhH----HHHHHHhcccccceEEEEEe
Confidence            223333333222    2222221      12468999987531        01222    23444456778999999999


Q ss_pred             cccccCC
Q 035774          254 QVRPQSH  260 (357)
Q Consensus       254 q~~~~~~  260 (357)
                      |......
T Consensus       136 Q~~~~lp  142 (241)
T PF04665_consen  136 QSYFHLP  142 (241)
T ss_pred             eecccCC
Confidence            9876543

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

>TIGR03497 FliI_clade2 flagellar protein export ATPase FliI

Probab=97.35  E-value=0.00059  Score=64.79  Aligned_cols=42  Identities=21%  Similarity=0.283  Sum_probs=36.8

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ..+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++..
T Consensus       119 ~~~~tGi~~iD~l~~--i~~Gqri~I~G~sG~GKTtLl~~i~~~  160 (413)
T TIGR03497       119 DPLETGIKAIDGLLT--IGKGQRVGIFAGSGVGKSTLLGMIARN  160 (413)
T ss_pred             hhccccceeeeeEEE--EcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            468899999999965  899999999999999999998766643

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.

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=97.35  E-value=0.0014  Score=64.25  Aligned_cols=140  Identities=18%  Similarity=0.145  Sum_probs=78.7

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCC----CCCCeEEEEeCCCCC--chHHHHHHHhccCchhhcccchH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYG----GLDGGVIYIDVESTF--TSRRMIEMGASSFPEIFHSKGMA  171 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~g----g~~~~vl~i~~e~~~--~~~rl~~~~~~~~~~~~~~~~~~  171 (357)
                      .+.+|+-+.|.||+|+|||||+.-++....-  ..|    |.+.++-||+-+...  ....+.+......+...  +..+
T Consensus       344 ~i~~g~riaiiG~NG~GKSTLlk~l~g~~~~--~~G~v~~g~~v~igyf~Q~~~~l~~~~t~~d~l~~~~~~~~--e~~~  419 (530)
T COG0488         344 RIDRGDRIAIVGPNGAGKSTLLKLLAGELGP--LSGTVKVGETVKIGYFDQHRDELDPDKTVLEELSEGFPDGD--EQEV  419 (530)
T ss_pred             EecCCCEEEEECCCCCCHHHHHHHHhhhccc--CCceEEeCCceEEEEEEehhhhcCccCcHHHHHHhhCcccc--HHHH
Confidence            5889999999999999999999988644321  122    234678899876521  22223332222221110  1222


Q ss_pred             HHhhcCeEEeCC--------CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHH
Q 035774          172 QEMAGRILVLQP--------TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAE  243 (357)
Q Consensus       172 ~~~~~~i~~~~~--------~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~  243 (357)
                      ...+.++.+...        .+..+-..+   ....+.-.++.++|+|.-+.....             +-...|.....
T Consensus       420 r~~L~~f~F~~~~~~~~v~~LSGGEk~Rl---~La~ll~~~pNvLiLDEPTNhLDi-------------~s~~aLe~aL~  483 (530)
T COG0488         420 RAYLGRFGFTGEDQEKPVGVLSGGEKARL---LLAKLLLQPPNLLLLDEPTNHLDI-------------ESLEALEEALL  483 (530)
T ss_pred             HHHHHHcCCChHHHhCchhhcCHhHHHHH---HHHHHhccCCCEEEEcCCCccCCH-------------HHHHHHHHHHH
Confidence            333444333211        111111111   111222358999999987755432             12455777778


Q ss_pred             HcCCeEEEeccccc
Q 035774          244 FSRIPIVVTNQVRP  257 (357)
Q Consensus       244 ~~~~~vv~~~q~~~  257 (357)
                      +|.-+||+++|-..
T Consensus       484 ~f~Gtvl~VSHDr~  497 (530)
T COG0488         484 DFEGTVLLVSHDRY  497 (530)
T ss_pred             hCCCeEEEEeCCHH
Confidence            89999999998643

>TIGR03269 met_CoM_red_A2 methyl coenzyme M reductase system, component A2

Probab=97.34  E-value=0.0025  Score=63.13  Aligned_cols=45  Identities=7%  Similarity=0.018  Sum_probs=34.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-...         .....+.+.|++++++++.+||+++|-.
T Consensus       444 ~~p~lLllDEPt~~LD~---------~~~~~l~~~l~~l~~~~g~tvi~vsHd~  488 (520)
T TIGR03269       444 KEPRIVILDEPTGTMDP---------ITKVDVTHSILKAREEMEQTFIIVSHDM  488 (520)
T ss_pred             cCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHHHcCcEEEEEeCCH
Confidence            47899999987765432         4455678888888888899999998853

The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.

>cd03114 ArgK-like The function of this protein family is unkown

Probab=97.34  E-value=0.0006  Score=55.49  Aligned_cols=36  Identities=17%  Similarity=0.238  Sum_probs=30.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+.|++|+|||+++.+++......      +.++++++.+.
T Consensus         2 i~~~G~~GsGKTt~~~~l~~~~~~~------g~~v~ii~~D~   37 (148)
T cd03114           2 IGITGVPGAGKSTLIDALITALRAR------GKRVAVLAIDP   37 (148)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHC------CCEEEEEEeCC
Confidence            6789999999999999999877532      47899998875

The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=97.34  E-value=0.0018  Score=61.96  Aligned_cols=40  Identities=20%  Similarity=0.189  Sum_probs=31.3

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +..+.|+|++|+|||.|+..++..+...    ..+..++|++.+
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~l~~~----~~~~~v~yi~~~  175 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNEILEN----NPNAKVVYVSSE  175 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHHHh----CCCCcEEEEEHH
Confidence            4578999999999999999888776532    124789999865

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).

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

Probab=97.33  E-value=0.00045  Score=65.58  Aligned_cols=28  Identities=25%  Similarity=0.460  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+|+...|.||+|||||||+.-+.--.
T Consensus       359 l~~G~~lgIIGPSgSGKSTLaR~lvG~w  386 (580)
T COG4618         359 LQAGEALGIIGPSGSGKSTLARLLVGIW  386 (580)
T ss_pred             ecCCceEEEECCCCccHHHHHHHHHccc
Confidence            7789999999999999999999777443

>PRK07165 F0F1 ATP synthase subunit alpha; Validated

Probab=97.33  E-value=0.0014  Score=63.05  Aligned_cols=58  Identities=21%  Similarity=0.271  Sum_probs=47.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|.++.  +-+|+=..|.|++|+|||++++..+.+...      .+..|+|...-.
T Consensus       124 ~epL~TGIkaID~l~p--igrGQR~~Ifg~~gtGKT~lal~~I~~q~~------~dv~~V~~~IGe  181 (507)
T PRK07165        124 NEQLYTGIIAIDLLIP--IGKGQRELIIGDRQTGKTHIALNTIINQKN------TNVKCIYVAIGQ  181 (507)
T ss_pred             CceeecCchhhhhcCC--cccCCEEEeecCCCCCccHHHHHHHHHhcC------CCeEEEEEEccC
Confidence            5689999999999987  789999999999999999998766655532      245678887644

>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.33  E-value=0.0014  Score=57.79  Aligned_cols=46  Identities=17%  Similarity=0.147  Sum_probs=32.5

Q ss_pred             CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccccc
Q 035774          204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQ  258 (357)
Q Consensus       204 ~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~  258 (357)
                      .++++..|.--+-...         ..=++++-.|.++.+|.+++|+.++|...+
T Consensus       146 ~P~LLLmDEPLaSLD~---------~RK~EilpylERL~~e~~IPIlYVSHS~~E  191 (352)
T COG4148         146 APELLLMDEPLASLDL---------PRKREILPYLERLRDEINIPILYVSHSLDE  191 (352)
T ss_pred             CCCeeeecCchhhccc---------chhhHHHHHHHHHHHhcCCCEEEEecCHHH
Confidence            5788888853322111         122457888999999999999999997554

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=97.33  E-value=0.0025  Score=61.63  Aligned_cols=40  Identities=20%  Similarity=0.112  Sum_probs=30.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .-+.|+|++|+|||.|+..++......    ..+..|+|++.+.
T Consensus       142 npl~i~G~~G~GKTHLl~Ai~~~l~~~----~~~~~v~yv~~~~  181 (450)
T PRK14087        142 NPLFIYGESGMGKTHLLKAAKNYIESN----FSDLKVSYMSGDE  181 (450)
T ss_pred             CceEEECCCCCcHHHHHHHHHHHHHHh----CCCCeEEEEEHHH
Confidence            347899999999999998877654321    1257899998854

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=97.32  E-value=0.0018  Score=64.87  Aligned_cols=28  Identities=32%  Similarity=0.488  Sum_probs=25.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++||||||++.-++.-.
T Consensus       352 i~~Ge~vaiVG~sGsGKSTl~~LL~r~~  379 (567)
T COG1132         352 IEPGEKVAIVGPSGSGKSTLIKLLLRLY  379 (567)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            8999999999999999999999777544

>PRK08972 fliI flagellum-specific ATP synthase; Validated

Probab=97.32  E-value=0.00072  Score=64.17  Aligned_cols=42  Identities=21%  Similarity=0.256  Sum_probs=38.4

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+.+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.
T Consensus       143 ~e~l~TGi~aID~ll~--i~~GqrigI~G~sG~GKSTLL~~I~~  184 (444)
T PRK08972        143 TEPLDVGVRAINAMLT--VGKGQRMGLFAGSGVGKSVLLGMMTR  184 (444)
T ss_pred             CCcccccceeecceEE--EcCCCEEEEECCCCCChhHHHHHhcc
Confidence            5689999999999976  89999999999999999999987774

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

Probab=97.32  E-value=0.0036  Score=61.83  Aligned_cols=118  Identities=19%  Similarity=0.258  Sum_probs=69.0

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      ++..| -++|.|++|+|||.|+..++...-.+     .-..|.|++++.. ...+                         
T Consensus       428 v~~~~-~Ill~G~~GsGKT~L~kal~~~~~k~-----~~~hv~~v~Cs~l-~~~~-------------------------  475 (952)
T KOG0735|consen  428 VFRHG-NILLNGPKGSGKTNLVKALFDYYSKD-----LIAHVEIVSCSTL-DGSS-------------------------  475 (952)
T ss_pred             ccccc-cEEEeCCCCCCHhHHHHHHHHHhccc-----cceEEEEEechhc-cchh-------------------------
Confidence            35555 56899999999999999999887642     2356778887541 1111                         


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCC---hHHHHHHH-HHHHHHHHHcC-CeEEEe
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPG---QHPLSWHI-SLITSLAEFSR-IPIVVT  252 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r---~~~~~~i~-~~Lk~la~~~~-~~vv~~  252 (357)
                              .+.+...+..+-.....+.+.+||+|.+..+.......+...   .+.+..++ ...+.+.+..+ +++|++
T Consensus       476 --------~e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat  547 (952)
T KOG0735|consen  476 --------LEKIQKFLNNVFSEALWYAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIAT  547 (952)
T ss_pred             --------HHHHHHHHHHHHHHHHhhCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEe
Confidence                    122223333333334467899999999999987422221111   12344444 33344444434 467776


Q ss_pred             ccc
Q 035774          253 NQV  255 (357)
Q Consensus       253 ~q~  255 (357)
                      .|-
T Consensus       548 ~qe  550 (952)
T KOG0735|consen  548 GQE  550 (952)
T ss_pred             chh
Confidence            654

>PRK09435 membrane ATPase/protein kinase; Provisional

Probab=97.30  E-value=0.0014  Score=60.47  Aligned_cols=94  Identities=13%  Similarity=0.175  Sum_probs=56.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch---------HHHHHHHhccCchhhcccchH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS---------RRMIEMGASSFPEIFHSKGMA  171 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~---------~rl~~~~~~~~~~~~~~~~~~  171 (357)
                      ..-++.|.|+||+|||||+..++.....      .+.+|..++.+..-+.         .|+.+..              
T Consensus        55 ~~~~igi~G~~GaGKSTl~~~l~~~l~~------~g~~v~vi~~Dp~s~~~~gallgd~~r~~~~~--------------  114 (332)
T PRK09435         55 NALRIGITGVPGVGKSTFIEALGMHLIE------QGHKVAVLAVDPSSTRTGGSILGDKTRMERLS--------------  114 (332)
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHHHHHH------CCCeEEEEEeCCCccccchhhhchHhHHHhhc--------------
Confidence            3458999999999999999999877753      1467888877653221         1111110              


Q ss_pred             HHhhcCeEEeCCC---CHHHHHHHHHHHHHHhhhcCeeEEEEeccccc
Q 035774          172 QEMAGRILVLQPT---SLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL  216 (357)
Q Consensus       172 ~~~~~~i~~~~~~---~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l  216 (357)
                        ....+++....   ....+...+......+...+.++|+||....-
T Consensus       115 --~~~~~~~r~~~~~~~l~~~a~~~~~~~~~~~~~g~d~viieT~Gv~  160 (332)
T PRK09435        115 --RHPNAFIRPSPSSGTLGGVARKTRETMLLCEAAGYDVILVETVGVG  160 (332)
T ss_pred             --CCCCeEEEecCCcccccchHHHHHHHHHHHhccCCCEEEEECCCCc
Confidence              01122332211   22233444555555566678999999987744

>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]

Probab=97.30  E-value=0.0028  Score=61.39  Aligned_cols=27  Identities=33%  Similarity=0.475  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+||||+..-++--
T Consensus       344 ~~~g~~talvG~SGaGKSTLl~lL~G~  370 (559)
T COG4988         344 IKAGQLTALVGASGAGKSTLLNLLLGF  370 (559)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHhCc
Confidence            889999999999999999999866643

>PRK12678 transcription termination factor Rho; Provisional

Probab=97.30  E-value=0.0021  Score=62.66  Aligned_cols=45  Identities=16%  Similarity=0.134  Sum_probs=39.9

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      ..+.||+..+|-++.  +-+|+=.+|.|+||+|||+|+..|+...+.
T Consensus       398 e~~~~giRvIDll~P--IGkGQR~LIvgpp~aGKTtLL~~IAn~i~~  442 (672)
T PRK12678        398 EPKKLTTRVIDLIMP--IGKGQRGLIVSPPKAGKTTILQNIANAITT  442 (672)
T ss_pred             Ccccccceeeeeecc--cccCCEeEEeCCCCCCHHHHHHHHHHHHhh
Confidence            478999999999987  778999999999999999999998876653

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

Probab=97.30  E-value=0.0041  Score=58.30  Aligned_cols=104  Identities=24%  Similarity=0.318  Sum_probs=63.1

Q ss_pred             HHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHH-HHHhccCchhhcccc
Q 035774           91 LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMI-EMGASSFPEIFHSKG  169 (357)
Q Consensus        91 LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~-~~~~~~~~~~~~~~~  169 (357)
                      |...+.|+.|..  +.|+|+||+|||..+..++...-....    +..++||.+...-.+.++. ++...          
T Consensus        33 l~~~~~~~~p~n--~~iyG~~GTGKT~~~~~v~~~l~~~~~----~~~~~yINc~~~~t~~~i~~~i~~~----------   96 (366)
T COG1474          33 LAPALRGERPSN--IIIYGPTGTGKTATVKFVMEELEESSA----NVEVVYINCLELRTPYQVLSKILNK----------   96 (366)
T ss_pred             HHHHhcCCCCcc--EEEECCCCCCHhHHHHHHHHHHHhhhc----cCceEEEeeeeCCCHHHHHHHHHHH----------
Confidence            666677776665  888999999999999998887753211    1238999987754443332 22221          


Q ss_pred             hHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhh-cCeeEEEEeccccccCC
Q 035774          170 MAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPG  219 (357)
Q Consensus       170 ~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~  219 (357)
                          + .    --+.+.....+++..+.+.+.. ...=+||+|.+..+...
T Consensus        97 ----~-~----~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~  138 (366)
T COG1474          97 ----L-G----KVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDK  138 (366)
T ss_pred             ----c-C----CCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccc
Confidence                0 0    1111112223334444444443 45678899999998764

>TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha

Probab=97.29  E-value=0.0015  Score=63.04  Aligned_cols=58  Identities=26%  Similarity=0.214  Sum_probs=46.5

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|.++.  +-+|+=..|.|++|+|||++++.++.+...      .+..|+|.-.-+
T Consensus       143 ~epl~TGI~aID~l~p--igrGQR~~Ifg~~g~GKT~Lal~~I~~q~~------~dv~~V~~~IGe  200 (497)
T TIGR03324       143 TVPLQTGLKVIDALIP--IGRGQRELILGDRQTGKTAIAIDTILNQKG------RNVLCIYCAIGQ  200 (497)
T ss_pred             CchhhcCCEEEeccCC--cccCCEEEeecCCCCCHHHHHHHHHHHhcC------CCcEEEEEEecc
Confidence            5689999999999987  789999999999999999998766655431      234578877543

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.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=97.29  E-value=0.0047  Score=53.81  Aligned_cols=30  Identities=20%  Similarity=0.406  Sum_probs=26.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      +..|+++.|.|++|+|||+++..++....+
T Consensus        28 ~~~g~~~~itG~N~~GKStll~~i~~~~~l   57 (222)
T cd03287          28 AEGGYCQIITGPNMGGKSSYIRQVALITIM   57 (222)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            567899999999999999999999886654

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

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=97.28  E-value=0.0016  Score=66.90  Aligned_cols=28  Identities=39%  Similarity=0.565  Sum_probs=25.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       504 i~~Ge~vaIvG~SGsGKSTLl~lL~gl~  531 (711)
T TIGR00958       504 LHPGEVVALVGPSGSGKSTVAALLQNLY  531 (711)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            7899999999999999999999777543

>CHL00176 ftsH cell division protein; Validated

Probab=97.28  E-value=0.00067  Score=68.07  Aligned_cols=33  Identities=33%  Similarity=0.317  Sum_probs=25.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .-++|+||||+|||+++..+|...         +.+.+++++
T Consensus       217 ~gVLL~GPpGTGKT~LAralA~e~---------~~p~i~is~  249 (638)
T CHL00176        217 KGVLLVGPPGTGKTLLAKAIAGEA---------EVPFFSISG  249 (638)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh---------CCCeeeccH
Confidence            349999999999999999998654         255666654

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.27  E-value=0.0021  Score=57.64  Aligned_cols=36  Identities=19%  Similarity=0.170  Sum_probs=25.8

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .|+.++..|  ...-+.|.|+||+|||||+..++....
T Consensus       101 ~l~~l~~~~--~~~~~~i~g~~g~GKttl~~~l~~~~~  136 (270)
T TIGR02858       101 LLPYLVRNN--RVLNTLIISPPQCGKTTLLRDLARILS  136 (270)
T ss_pred             HHHHHHhCC--CeeEEEEEcCCCCCHHHHHHHHhCccC
Confidence            445555322  115789999999999999998886553

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=97.27  E-value=0.0015  Score=62.47  Aligned_cols=57  Identities=28%  Similarity=0.218  Sum_probs=47.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+.+.||+..+|-++.  +-+|+=+.|.|++|+|||+|+.+++.+.....     ...++|.-.
T Consensus       125 ~~~l~TGiraID~l~p--igkGQR~gIfa~~GvGKt~Ll~~i~~~~~~~~-----~~v~V~~li  181 (463)
T PRK09280        125 TEILETGIKVIDLLAP--YAKGGKIGLFGGAGVGKTVLIQELINNIAKEH-----GGYSVFAGV  181 (463)
T ss_pred             cceeccCCeeecccCC--cccCCEEEeecCCCCChhHHHHHHHHHHHhcC-----CCEEEEEEe
Confidence            4579999999999987  88999999999999999999999999886421     235666654

>PTZ00265 multidrug resistance protein (mdr1); Provisional

Probab=97.27  E-value=0.002  Score=71.02  Aligned_cols=28  Identities=25%  Similarity=0.284  Sum_probs=25.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++||||||++.-++.-.
T Consensus      1191 i~~G~~vAIVG~SGsGKSTl~~LL~r~y 1218 (1466)
T PTZ00265       1191 CDSKKTTAIVGETGSGKSTVMSLLMRFY 1218 (1466)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            8899999999999999999998777654

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

Probab=97.27  E-value=0.0024  Score=62.05  Aligned_cols=113  Identities=19%  Similarity=0.279  Sum_probs=68.9

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+..-.=++++||||||||.||..+|..+           +.=||+..+   ++-+-.                      
T Consensus       541 Gi~~PsGvLL~GPPGCGKTLlAKAVANEa-----------g~NFisVKG---PELlNk----------------------  584 (802)
T KOG0733|consen  541 GIDAPSGVLLCGPPGCGKTLLAKAVANEA-----------GANFISVKG---PELLNK----------------------  584 (802)
T ss_pred             CCCCCCceEEeCCCCccHHHHHHHHhhhc-----------cCceEeecC---HHHHHH----------------------
Confidence            46666679999999999999999777544           234666654   222111                      


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC-CChHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA-PGQHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~-~r~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                       |+  ..+-..+.+++.    ..+...+.+|+.|.+.+|.+....+.. .....+.+++..|..+-.+.|+.||..+
T Consensus       585 -YV--GESErAVR~vFq----RAR~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaAT  654 (802)
T KOG0733|consen  585 -YV--GESERAVRQVFQ----RARASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAAT  654 (802)
T ss_pred             -Hh--hhHHHHHHHHHH----HhhcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeec
Confidence             00  001112222332    233456899999999999876322221 1234566777777777777888888654

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=97.26  E-value=0.0022  Score=61.85  Aligned_cols=39  Identities=26%  Similarity=0.256  Sum_probs=30.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .-..|+|+||+|||.|+..++......    +.+..|+|++.+
T Consensus       131 n~l~lyG~~G~GKTHLl~ai~~~l~~~----~~~~~v~yi~~~  169 (440)
T PRK14088        131 NPLFIYGGVGLGKTHLLQSIGNYVVQN----EPDLRVMYITSE  169 (440)
T ss_pred             CeEEEEcCCCCcHHHHHHHHHHHHHHh----CCCCeEEEEEHH
Confidence            358999999999999999888776532    124689999875

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.26  E-value=0.0016  Score=67.18  Aligned_cols=29  Identities=31%  Similarity=0.391  Sum_probs=24.3

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+.+..-++++||||+|||+++..+|...
T Consensus       483 g~~~~~giLL~GppGtGKT~lakalA~e~  511 (733)
T TIGR01243       483 GIRPPKGVLLFGPPGTGKTLLAKAVATES  511 (733)
T ss_pred             CCCCCceEEEECCCCCCHHHHHHHHHHhc
Confidence            45666668999999999999999998754

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.

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.25  E-value=0.0073  Score=58.43  Aligned_cols=43  Identities=33%  Similarity=0.444  Sum_probs=33.8

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..|.++.+.|++|+||||.+..++......  .|  ..+|.+++++.
T Consensus       254 ~~g~Vi~LvGpnGvGKTTTiaKLA~~~~~~--~G--~~kV~LI~~Dt  296 (484)
T PRK06995        254 DRGGVFALMGPTGVGKTTTTAKLAARCVMR--HG--ASKVALLTTDS  296 (484)
T ss_pred             cCCcEEEEECCCCccHHHHHHHHHHHHHHh--cC--CCeEEEEeCCc
Confidence            457899999999999999999999877532  22  24788888764

>PTZ00265 multidrug resistance protein (mdr1); Provisional

Probab=97.25  E-value=0.0028  Score=69.90  Aligned_cols=28  Identities=25%  Similarity=0.345  Sum_probs=25.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+.+.|.|++|+|||||+.-++...
T Consensus       408 i~~Ge~vaIvG~SGsGKSTLl~lL~gl~  435 (1466)
T PTZ00265        408 LTEGKTYAFVGESGCGKSTILKLIERLY  435 (1466)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            8999999999999999999998777544

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=97.25  E-value=0.0081  Score=51.36  Aligned_cols=25  Identities=36%  Similarity=0.699  Sum_probs=22.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+| ++.|.|++|+|||+|+..++.
T Consensus        20 ~~~g-~~~i~G~nGsGKStll~al~~   44 (197)
T cd03278          20 FPPG-LTAIVGPNGSGKSNIIDAIRW   44 (197)
T ss_pred             cCCC-cEEEECCCCCCHHHHHHHHHH
Confidence            6678 999999999999999987753

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>TIGR00955 3a01204 The Eye Pigment Precursor Transporter (EPP) Family protein

Probab=97.24  E-value=0.0021  Score=64.95  Aligned_cols=35  Identities=26%  Similarity=0.361  Sum_probs=28.6

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      -|+.+ .+-+++|+++.|.|++|+|||||+.-++..
T Consensus        40 iL~~v-s~~i~~Ge~~aI~G~sGsGKSTLL~~L~g~   74 (617)
T TIGR00955        40 LLKNV-SGVAKPGELLAVMGSSGAGKTTLMNALAFR   74 (617)
T ss_pred             cccCC-EEEEeCCeEEEEECCCCCCHHHHHHHHhCC
Confidence            35553 345999999999999999999999977754

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=97.24  E-value=0.001  Score=63.40  Aligned_cols=42  Identities=19%  Similarity=0.178  Sum_probs=36.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ...+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.
T Consensus       146 ~~~l~TGi~aID~L~~--I~~Gqri~I~G~SGsGKTTLL~~Ia~  187 (450)
T PRK06002        146 ETGLRTGVRVIDIFTP--LCAGQRIGIFAGSGVGKSTLLAMLAR  187 (450)
T ss_pred             eEEcCCCcEEeeeece--ecCCcEEEEECCCCCCHHHHHHHHhC
Confidence            4578899999999873  99999999999999999999876653

>TIGR01026 fliI_yscN ATPase FliI/YscN family

Probab=97.23  E-value=0.0011  Score=63.47  Aligned_cols=43  Identities=21%  Similarity=0.246  Sum_probs=37.9

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .+.+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++..
T Consensus       144 ~e~l~TGi~~iD~l~~--i~~Gq~~~I~G~sG~GKStLl~~I~~~  186 (440)
T TIGR01026       144 REILSTGVRSIDGLLT--VGKGQRIGIFAGSGVGKSTLLGMIARN  186 (440)
T ss_pred             cccccceeeeeeeccc--cCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            4579999999999965  899999999999999999998766644

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.

>PRK12597 F0F1 ATP synthase subunit beta; Provisional

Probab=97.23  E-value=0.0016  Score=62.46  Aligned_cols=57  Identities=28%  Similarity=0.336  Sum_probs=47.4

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+.+.||+..+|-++.  +-+|+=+.|.|++|+|||+|+..++.+...+.     ...++|.-.
T Consensus       124 ~e~l~TGir~ID~l~p--igkGQR~gIfa~~G~GKt~Ll~~~~~~~~~~~-----~dv~V~~li  180 (461)
T PRK12597        124 TEILETGIKVIDLLCP--IAKGGKTGLFGGAGVGKTVLMMELIFNISKQH-----SGSSVFAGV  180 (461)
T ss_pred             CcceecCCeeecccCc--cccCCEEEeecCCCCChhHHHHHHHHHHHhhC-----CCEEEEEcC
Confidence            5689999999999987  88999999999999999999999999887421     245566544

>PRK05688 fliI flagellum-specific ATP synthase; Validated

Probab=97.22  E-value=0.00095  Score=63.71  Aligned_cols=42  Identities=19%  Similarity=0.247  Sum_probs=38.1

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+.+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.
T Consensus       149 ~~~l~TGi~aID~l~~--I~~GqrigI~G~sG~GKSTLl~~I~g  190 (451)
T PRK05688        149 SEPLDVGIRSINGLLT--VGRGQRLGLFAGTGVGKSVLLGMMTR  190 (451)
T ss_pred             cCCcccceeeecceEE--ecCCcEEEEECCCCCCHHHHHHHHhC
Confidence            4689999999999976  99999999999999999999987764

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=97.22  E-value=0.0033  Score=62.05  Aligned_cols=26  Identities=31%  Similarity=0.425  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus       286 i~~Ge~~~l~G~NGsGKSTLl~~i~G  311 (510)
T PRK15439        286 VRAGEILGLAGVVGAGRTELAETLYG  311 (510)
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHcC
Confidence            78999999999999999999987764

>PRK09183 transposase/IS protein; Provisional

Probab=97.21  E-value=0.00042  Score=61.93  Aligned_cols=41  Identities=24%  Similarity=0.340  Sum_probs=33.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +..|+.+.|.||||+|||+|+..++..++..      +..|.|++..
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~------G~~v~~~~~~  139 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAIALGYEAVRA------GIKVRFTTAA  139 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc------CCeEEEEeHH
Confidence            6789999999999999999999997765531      4789998753

>cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein

Probab=97.21  E-value=0.0015  Score=60.02  Aligned_cols=43  Identities=23%  Similarity=0.296  Sum_probs=37.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ...+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++..
T Consensus        50 ~~~l~tGi~aiD~l~~--i~~Gqri~I~G~sG~GKTtLl~~Ia~~   92 (326)
T cd01136          50 DEVLPTGVRAIDGLLT--VGKGQRLGIFAGSGVGKSTLLGMIARG   92 (326)
T ss_pred             eeEcCCCcEEEeeeeE--EcCCcEEEEECCCCCChHHHHHHHhCC
Confidence            3478899999999965  899999999999999999997766643

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.

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

Probab=97.21  E-value=0.0025  Score=55.33  Aligned_cols=113  Identities=14%  Similarity=0.224  Sum_probs=63.1

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+.|-.-++++||||+|||.|+...|.+..           .-||-.-+   .+-+.+.+..                  
T Consensus       185 gidpprgvllygppg~gktml~kava~~t~-----------a~firvvg---sefvqkylge------------------  232 (408)
T KOG0727|consen  185 GIDPPRGVLLYGPPGTGKTMLAKAVANHTT-----------AAFIRVVG---SEFVQKYLGE------------------  232 (408)
T ss_pred             CCCCCcceEEeCCCCCcHHHHHHHHhhccc-----------hheeeecc---HHHHHHHhcc------------------
Confidence            577877899999999999999997775543           33443322   1111111110                  


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHH----HHHHHHHHHHHHcCCeEEEec
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLS----WHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~----~i~~~Lk~la~~~~~~vv~~~  253 (357)
                             .+..    +..+-++.++..+.+|+||.+.++....++....-..++.    +++..+..+-...|+-||+..
T Consensus       233 -------gprm----vrdvfrlakenapsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq~~nvkvimat  301 (408)
T KOG0727|consen  233 -------GPRM----VRDVFRLAKENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQTTNVKVIMAT  301 (408)
T ss_pred             -------CcHH----HHHHHHHHhccCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCcccceEEEEec
Confidence                   0111    1222233445678999999999887665443322223333    333333344455677776654

>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]

Probab=97.20  E-value=0.0089  Score=54.29  Aligned_cols=98  Identities=16%  Similarity=0.171  Sum_probs=63.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      +-.++++.|-+|+||||-.-.+|......      +.+|+...++ +|..-.+.|+..           |.+..  ++-+
T Consensus       138 ~p~Vil~vGVNG~GKTTTIaKLA~~l~~~------g~~VllaA~D-TFRAaAiEQL~~-----------w~er~--gv~v  197 (340)
T COG0552         138 KPFVILFVGVNGVGKTTTIAKLAKYLKQQ------GKSVLLAAGD-TFRAAAIEQLEV-----------WGERL--GVPV  197 (340)
T ss_pred             CcEEEEEEecCCCchHhHHHHHHHHHHHC------CCeEEEEecc-hHHHHHHHHHHH-----------HHHHh--CCeE
Confidence            46799999999999999999999888642      4777766664 666655555432           11222  2333


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP  218 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~  218 (357)
                      +......+...+.....+.....++++|+||....+..
T Consensus       198 I~~~~G~DpAaVafDAi~~Akar~~DvvliDTAGRLhn  235 (340)
T COG0552         198 ISGKEGADPAAVAFDAIQAAKARGIDVVLIDTAGRLHN  235 (340)
T ss_pred             EccCCCCCcHHHHHHHHHHHHHcCCCEEEEeCcccccC
Confidence            33223334444555544555567999999998887643

>TIGR02633 xylG D-xylose ABC transporter, ATP-binding protein

Probab=97.20  E-value=0.0017  Score=63.88  Aligned_cols=26  Identities=35%  Similarity=0.381  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus        24 i~~Ge~~~liG~nGsGKSTLl~~i~G   49 (500)
T TIGR02633        24 VRPGECVGLCGENGAGKSTLMKILSG   49 (500)
T ss_pred             EeCCcEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997774

Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (pfam00005).

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=97.19  E-value=0.0044  Score=61.52  Aligned_cols=36  Identities=31%  Similarity=0.382  Sum_probs=27.4

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -|+.+-- -++||+++.+.||+|+||||++.-+..-.
T Consensus       483 Vlk~lsf-ti~pGe~vALVGPSGsGKSTiasLL~rfY  518 (716)
T KOG0058|consen  483 VLKNLSF-TIRPGEVVALVGPSGSGKSTIASLLLRFY  518 (716)
T ss_pred             hhcCcee-eeCCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            3444433 39999999999999999999987555443

>PRK08927 fliI flagellum-specific ATP synthase; Validated

Probab=97.19  E-value=0.0014  Score=62.46  Aligned_cols=44  Identities=23%  Similarity=0.249  Sum_probs=39.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.+.||+..+|-++.  +.+|+.+.|.|++|+|||+|+.+++...
T Consensus       139 ~~~l~TGir~ID~l~~--i~~Gqri~I~G~sG~GKTtLL~~I~~~~  182 (442)
T PRK08927        139 GEPLDLGVRALNTFLT--CCRGQRMGIFAGSGVGKSVLLSMLARNA  182 (442)
T ss_pred             ccccccceEEEeeeeE--EcCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            5689999999999997  8999999999999999999998777554

>PRK09281 F0F1 ATP synthase subunit alpha; Validated

Probab=97.19  E-value=0.0019  Score=62.80  Aligned_cols=58  Identities=24%  Similarity=0.284  Sum_probs=47.4

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|.++.  +-+|+=..|.|++|+|||+||++++.+...      .+..|+|...-+
T Consensus       143 ~~~l~TGi~~ID~l~p--igrGQr~~Ifg~~g~GKt~lal~~i~~~~~------~dv~~V~~~IGe  200 (502)
T PRK09281        143 HEPLQTGIKAIDAMIP--IGRGQRELIIGDRQTGKTAIAIDTIINQKG------KDVICIYVAIGQ  200 (502)
T ss_pred             cceeecCCeeeecccc--cccCcEEEeecCCCCCchHHHHHHHHHhcC------CCeEEEEEEecC
Confidence            5689999999999987  889999999999999999998887766542      245568877543

>COG4559 ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.19  E-value=0.01  Score=50.53  Aligned_cols=29  Identities=31%  Similarity=0.436  Sum_probs=26.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +++|++..|.||+|+|||||...+.-...
T Consensus        24 ~~pGev~ailGPNGAGKSTlLk~LsGel~   52 (259)
T COG4559          24 LRPGEVLAILGPNGAGKSTLLKALSGELS   52 (259)
T ss_pred             ccCCcEEEEECCCCccHHHHHHHhhCccC
Confidence            89999999999999999999998886553

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

Probab=97.18  E-value=0.0046  Score=55.04  Aligned_cols=104  Identities=19%  Similarity=0.277  Sum_probs=65.2

Q ss_pred             CcccHHHHHHHHHhcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEE
Q 035774           63 PFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI  142 (357)
Q Consensus        63 ~~~~~~~~~~~~~~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i  142 (357)
                      +...|.+.+.+.       --+|--++.|   +.|+-.|=.-++++||||+|||-||...|-.+           ..-||
T Consensus       137 GLE~AKeALKEA-------VILPIKFPql---FtGkR~PwrgiLLyGPPGTGKSYLAKAVATEA-----------nSTFF  195 (439)
T KOG0739|consen  137 GLEGAKEALKEA-------VILPIKFPQL---FTGKRKPWRGILLYGPPGTGKSYLAKAVATEA-----------NSTFF  195 (439)
T ss_pred             cchhHHHHHHhh-------eeecccchhh---hcCCCCcceeEEEeCCCCCcHHHHHHHHHhhc-----------CCceE
Confidence            345555555542       2345555544   66777788889999999999999999777544           14455


Q ss_pred             eCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC
Q 035774          143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG  219 (357)
Q Consensus       143 ~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~  219 (357)
                      +...    ..+..   . |             +           .+-..++..+-.+.+++.+.+|+||.+.++...
T Consensus       196 SvSS----SDLvS---K-W-------------m-----------GESEkLVknLFemARe~kPSIIFiDEiDslcg~  240 (439)
T KOG0739|consen  196 SVSS----SDLVS---K-W-------------M-----------GESEKLVKNLFEMARENKPSIIFIDEIDSLCGS  240 (439)
T ss_pred             Eeeh----HHHHH---H-H-------------h-----------ccHHHHHHHHHHHHHhcCCcEEEeehhhhhccC
Confidence            5432    11110   0 0             0           011234445556667789999999999988765

>PRK10535 macrolide transporter ATP-binding /permease protein; Provisional

Probab=97.18  E-value=0.0013  Score=66.82  Aligned_cols=27  Identities=30%  Similarity=0.501  Sum_probs=24.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.|++|+|||||+.-++..
T Consensus        31 i~~Ge~~~l~G~nGsGKSTLl~~i~Gl   57 (648)
T PRK10535         31 IYAGEMVAIVGASGSGKSTLMNILGCL   57 (648)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999999977754

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.17  E-value=0.00062  Score=57.11  Aligned_cols=40  Identities=38%  Similarity=0.434  Sum_probs=32.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .++|.++.|.|+|||||||++..++.....+      +..++|++.
T Consensus         4 ~~~~~~I~i~G~~GsGKst~a~~l~~~l~~~------~~~~~~~~~   43 (176)
T PRK05541          4 KPNGYVIWITGLAGSGKTTIAKALYERLKLK------YSNVIYLDG   43 (176)
T ss_pred             CCCCCEEEEEcCCCCCHHHHHHHHHHHHHHc------CCcEEEEec
Confidence            5678999999999999999999988776421      355777764

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.17  E-value=0.0041  Score=62.73  Aligned_cols=29  Identities=17%  Similarity=0.171  Sum_probs=24.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      .....++|+|++|+|||+++..|+.....
T Consensus        36 RL~HAyLFtGPpGvGKTTlAriLAKaLnC   64 (830)
T PRK07003         36 RLHHAYLFTGTRGVGKTTLSRIFAKALNC   64 (830)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            34557899999999999999999987753

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=97.17  E-value=0.0038  Score=58.52  Aligned_cols=42  Identities=29%  Similarity=0.315  Sum_probs=32.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      .+++|.|.||||||.++++++......    ..+..++|+.....+
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l~~~----~~~~~~~~l~~n~~l   43 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKELQNS----EEGKKVLYLCGNHPL   43 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHhhcc----ccCCceEEEEecchH
Confidence            578999999999999999999988211    125778888876643

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PRK11147 ABC transporter ATPase component; Reviewed

Probab=97.17  E-value=0.0044  Score=62.88  Aligned_cols=26  Identities=35%  Similarity=0.429  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+..++.
T Consensus       342 i~~Ge~~~l~G~NGsGKSTLlk~l~G  367 (635)
T PRK11147        342 VQRGDKIALIGPNGCGKTTLLKLMLG  367 (635)
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhC
Confidence            78999999999999999999987774

>TIGR03498 FliI_clade3 flagellar protein export ATPase FliI

Probab=97.17  E-value=0.0012  Score=62.84  Aligned_cols=43  Identities=23%  Similarity=0.247  Sum_probs=37.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .+.+.||+..+|..+.  +.+|+.+.|.|++|+|||+|+..++..
T Consensus       121 ~~~l~tGi~aiD~~~~--i~~Gq~i~I~G~sG~GKTtLl~~I~~~  163 (418)
T TIGR03498       121 GEPLDTGVRVIDTFLP--LCRGQRLGIFAGSGVGKSTLLSMLARN  163 (418)
T ss_pred             ccccCCccEEEeeecc--ccCCcEEEEECCCCCChHHHHHHHhCC
Confidence            4689999999998765  899999999999999999998666543

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.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=97.17  E-value=0.0075  Score=55.71  Aligned_cols=29  Identities=21%  Similarity=0.082  Sum_probs=25.0

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      ....-+++.||+|+|||+++..++.....
T Consensus        19 r~~hA~Lf~G~~G~GK~~la~~~a~~llC   47 (325)
T PRK08699         19 RRPNAWLFAGKKGIGKTAFARFAAQALLC   47 (325)
T ss_pred             CcceEEEeECCCCCCHHHHHHHHHHHHcC
Confidence            44557999999999999999999988765

>TIGR00954 3a01203 Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protei

Probab=97.16  E-value=0.0059  Score=62.15  Aligned_cols=27  Identities=37%  Similarity=0.535  Sum_probs=24.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|+|||||+.-++..
T Consensus       475 i~~Ge~~~IvG~nGsGKSTLl~lL~Gl  501 (659)
T TIGR00954       475 VPSGNHLLICGPNGCGKSSLFRILGEL  501 (659)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999999877653

>COG1101 PhnK ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.15  E-value=0.0041  Score=52.90  Aligned_cols=42  Identities=21%  Similarity=0.277  Sum_probs=33.4

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      -++.|+++.|.|.+|+|||||+..++-....       ...-++|+...
T Consensus        28 ~I~~g~FvtViGsNGAGKSTlln~iaG~l~~-------t~G~I~Idg~d   69 (263)
T COG1101          28 EIAEGDFVTVIGSNGAGKSTLLNAIAGDLKP-------TSGQILIDGVD   69 (263)
T ss_pred             eecCCceEEEEcCCCccHHHHHHHhhCcccc-------CCceEEECcee
Confidence            3899999999999999999999988866543       24466777653

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

Probab=97.15  E-value=0.0028  Score=56.51  Aligned_cols=62  Identities=10%  Similarity=0.147  Sum_probs=48.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=+.|.|.+|+|||+|+.+++.+....++  +....|+|.-.-+
T Consensus        50 ~e~l~TGIkaID~l~p--ig~GQR~gIfgg~GvGKt~L~~~i~~~~~~~~~--~~~~v~V~~~IGe  111 (276)
T cd01135          50 EEMIQTGISAIDGMNT--LVRGQKIPIFSGSGLPHNELAAQIARQAGVVGE--EENFAVVFAAMGI  111 (276)
T ss_pred             ccccccCcEeeecccc--cccCCEEEeecCCCCChhHHHHHHHHhhhcccc--CCCCEEEEEEecc
Confidence            5689999999999987  789999999999999999999998876532110  1135677776533

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.

>TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta

Probab=97.15  E-value=0.0026  Score=60.79  Aligned_cols=57  Identities=23%  Similarity=0.261  Sum_probs=47.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+.+.||+..+|-++.  +.+|+=..|.|++|+|||+|+.+++.+....     ...-++|.-.
T Consensus       119 ~e~L~TGIr~ID~l~p--igkGQr~~Ifg~~G~GKt~l~~~~~~~~~~~-----~~~v~V~~~i  175 (449)
T TIGR03305       119 SEVFETGIKAIDVLVP--LERGGKAGLFGGAGVGKTVLLTEMIHNMVGQ-----HQGVSIFCGI  175 (449)
T ss_pred             CcccccCceeeccccc--cccCCEEEeecCCCCChhHHHHHHHHHHHhc-----CCCEEEEEEe
Confidence            5689999999999987  8899999999999999999999999987521     1245667654

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.

>PRK13695 putative NTPase; Provisional

Probab=97.14  E-value=0.0011  Score=55.60  Aligned_cols=23  Identities=39%  Similarity=0.670  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+.|.|+||+|||||+..++...
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36899999999999999887654

>TIGR03496 FliI_clade1 flagellar protein export ATPase FliI

Probab=97.14  E-value=0.0012  Score=62.77  Aligned_cols=42  Identities=17%  Similarity=0.246  Sum_probs=37.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ...+.||+..+|.++.  +.+|+.+.|.|++|+|||+|+..++.
T Consensus       118 ~~~~~tGi~~id~l~~--i~~Gq~~~I~G~sG~GKTtLl~~I~~  159 (411)
T TIGR03496       118 DEPLDVGVRAINGLLT--VGRGQRMGIFAGSGVGKSTLLGMMAR  159 (411)
T ss_pred             ceEeeeeEEeecceEE--EecCcEEEEECCCCCCHHHHHHHHhc
Confidence            4578899999999976  99999999999999999999876664

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.

>cd01131 PilT Pilus retraction ATPase PilT

Probab=97.14  E-value=0.0035  Score=53.72  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +++|+||+||||||++..++....
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            799999999999999988877654

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.

>PRK13409 putative ATPase RIL; Provisional

Probab=97.14  E-value=0.0042  Score=62.24  Aligned_cols=44  Identities=16%  Similarity=0.092  Sum_probs=32.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..++....         .....+.+.|+++++  +.+||+++|-..
T Consensus       229 ~~p~lllLDEPts~LD~---------~~~~~l~~~i~~l~~--g~tvIivsHd~~  272 (590)
T PRK13409        229 RDADFYFFDEPTSYLDI---------RQRLNVARLIRELAE--GKYVLVVEHDLA  272 (590)
T ss_pred             cCCCEEEEECCCCCCCH---------HHHHHHHHHHHHHHC--CCEEEEEeCCHH
Confidence            47999999988766543         445556777777765  899999998644

>PTZ00185 ATPase alpha subunit; Provisional

Probab=97.14  E-value=0.0027  Score=61.10  Aligned_cols=64  Identities=20%  Similarity=0.208  Sum_probs=47.5

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc-ccC-CCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL-PAH-YGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~-~~~-~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|.++.  +-+|+=..|.|++|+|||++++..+.+... ... ..+....|+|+..-+
T Consensus       170 ~epL~TGIkaID~LiP--IGRGQR~lIfGd~GtGKTtLAld~IinQ~~~~~~~~~~~~~v~VyvaIGe  235 (574)
T PTZ00185        170 NYNLLTGFKAVDTMIP--IGRGQRELIVGDRQTGKTSIAVSTIINQVRINQQILSKNAVISIYVSIGQ  235 (574)
T ss_pred             CCcCcCCceeeecccc--ccCCCEEEeecCCCCChHHHHHHHHHhhhhhccccccCCCCEEEEEEecc
Confidence            5689999999999987  889999999999999999998766655431 000 001135688887644

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	357
2dfl_A	324	Crystal Structure Of Left-Handed Rada Filament Leng		4e-18
1pzn_A	349	Rad51 (Rada) Length = 349		9e-18
2bke_A	324	Conformational Flexibility Revealed By The Crystal		1e-17
4a6p_A	231	Rada C-Terminal Atpase Domain From Pyrococcus Furio		7e-17
4b2i_A	231	Humanised Monomeric Rada In Complex With Indazole L		2e-15
1n0w_A	243	Crystal Structure Of A Rad51-Brca2 Brc Repeat Compl		1e-14
2zjb_A	343	Crystal Structure Of The Human Dmc1-M200v Polymorph		2e-12
1v5w_A	343	Crystal Structure Of The Human Dmc1 Protein Length		2e-12
3ntu_A	319	Rada Recombinase D302k Mutant In Complex With Amp-P		1e-11
2cvf_A	220	Crystal Structure Of The Radb Recombinase Length =		5e-11
1t4g_A	322	Atpase In Complex With Amp-pnp Length = 322		6e-11
4dc9_A	266	Hexameric Ring Of Methanococcus Voltae Rada Length		7e-11
2gdj_A	264	Delta-62 Rada Recombinase In Complex With Amp-Pnp A		8e-11
3etl_A	322	Rada Recombinase From Methanococcus Maripaludis In		1e-10
2f1h_A	322	Recombinase In Complex With Amp-pnp And Potassium L		1e-10
3lda_A	400	Yeast Rad51 H352y Filament Interface Mutant Length		3e-09
1szp_A	321	A Crystal Structure Of The Rad51 Filament Length =		4e-09

>pdb|2DFL|A Chain A, Crystal Structure Of Left-Handed Rada Filament Length = 324

Iteration: 1
 Score = 89.0 bits (219), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 85/299 (28%), Positives = 129/299 (43%), Gaps = 49/299 (16%)
Query: 46  LSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVT 105
           + E R AL +        F+TAL + ++R   + +     T  + LD  L GG+    +T
Sbjct: 62  IKEARDALDI-------RFKTALEVKKERMNVKKIS----TGSQALDGLLAGGIETRTMT 110
Query: 106 ELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF 165
           E  G  G+GKTQ C +LS+   LP   GGL G  +YID E TF   R+  M  +   +I 
Sbjct: 111 EFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKALGLDI- 169
Query: 166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSM----EALVPGV 220
                   +   I  ++  +       ++ ++  + ++  +KL+V+DS+     A  PG 
Sbjct: 170 ------DNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPG- 222
Query: 221 HEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILK 278
            E  A  Q  L+ H+  +T LAE   I +++TNQV  RP                D    
Sbjct: 223 RENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVMARP----------------DMFYG 266
Query: 279 DRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSG-QRFMNVEKSPTSPPLAFSFTINPSGI 336
           D T      VAV G    H   IR+ L+   G +R   V  +P  P     F +   GI
Sbjct: 267 DPT------VAVGGHTLYHVPGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGI 319

>pdb|1PZN|A Chain A, Rad51 (Rada) Length = 349

Iteration: 1
 Score = 87.8 bits (216), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 83/283 (29%), Positives = 130/283 (45%), Gaps = 42/283 (14%)
Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS 123
           F  A   +++RA      G + T  K LD  L GG+    +TE+ G  G+GKTQ    L+
Sbjct: 97  FXRADEYLKKRATI----GRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA 152
Query: 124 LLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMA-QEMAGRILVLQ 182
           +   LP   GGL+G VI+ID E+TF   R+         EI  ++G+   E+   I V +
Sbjct: 153 VXVQLPPEEGGLNGSVIWIDTENTFRPERI--------REIAQNRGLDPDEVLKHIYVAR 204
Query: 183 PTSLSE----FTESLEKIKVSLLQNQ-VKLLVIDSMEALVPGVHEQR---APGQHPLSWH 234
             + +       ++ +KIK  L  ++ VKLL++DS+ +     +  R   A  Q  L+ H
Sbjct: 205 AFNSNHQXLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKH 264
Query: 235 ISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFH 294
           ++ +  LA    I + VTNQV+ +               D    D TR       + G  
Sbjct: 265 LADLHRLANLYDIAVFVTNQVQARP--------------DAFFGDPTR------PIGGHI 304
Query: 295 WAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
            AH+ T+R+ L + K G+R   +  +P  P     F+I   GI
Sbjct: 305 LAHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGI 347

>pdb|2BKE|A Chain A, Conformational Flexibility Revealed By The Crystal Structure Of A Crenarchaeal Rada Length = 324

Iteration: 1
 Score = 87.0 bits (214), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 87/300 (29%), Positives = 129/300 (43%), Gaps = 51/300 (17%)
Query: 46  LSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVT 105
           + E R AL +        F+TAL + ++R   + +     T  + LD  L GG+     T
Sbjct: 62  IKEARDALDI-------RFKTALEVKKERXNVKKIS----TGSQALDGLLAGGIETRTXT 110
Query: 106 ELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF 165
           E  G  G+GKTQ C +LS+   LP   GGL G  +YID E TF   R IE  A +     
Sbjct: 111 EFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWER-IENXAKAL---- 165
Query: 166 HSKGMA-QEMAGRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSM----EALVPG 219
              G+    +   I  ++  +       ++ ++  + ++  +KL+V+DS+     A  PG
Sbjct: 166 ---GLDIDNVXNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPG 222
Query: 220 VHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRIL 277
             E  A  Q  L+ H+  +T LAE   I +++TNQV  RP                D   
Sbjct: 223 -RENLAVRQQKLNKHLHQLTRLAEVYDIAVIITNQVXARP----------------DXFY 265
Query: 278 KDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSG-QRFMNVEKSPTSPPLAFSFTINPSGI 336
            D T      VAV G    H   IR+ L+   G +R   V  +P  P     F +   GI
Sbjct: 266 GDPT------VAVGGHTLYHVPGIRIQLKKSRGNRRIARVVDAPHLPEGEVVFALTEEGI 319

>pdb|4A6P|A Chain A, Rada C-Terminal Atpase Domain From Pyrococcus Furiosus Length = 231

Iteration: 1
 Score = 84.7 bits (208), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 76/265 (28%), Positives = 120/265 (45%), Gaps = 50/265 (18%)
Query: 82  GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIY 141
           G + T  K LD  L GG+    +TE+ G  G+GKTQ    L+++  LP   GGL+G VI+
Sbjct: 5   GRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIW 64
Query: 142 IDVESTFTSRRMIEMGASSFPEIFHSKGMA-QEMAGRILVLQPTSLSE----FTESLEKI 196
           ID E+TF   R+         EI  ++G+   E+   I V +  + +       ++ +KI
Sbjct: 65  IDTENTFRPERI--------REIAQNRGLDPDEVLKHIYVARAFNSNHQMLLVQQAEDKI 116
Query: 197 KVSLLQNQ-VKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFSRIPIVVT 252
           K  L  ++ VKLL++DS+ +     +  R   A  Q  L+ H++ +  LA    I + VT
Sbjct: 117 KELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVT 176
Query: 253 NQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVL-EAKSGQ 311
           NQV+                             HI+       AH+ T+R+ L + K G+
Sbjct: 177 NQVQANG-------------------------GHIL-------AHSATLRVYLRKGKGGK 204
Query: 312 RFMNVEKSPTSPPLAFSFTINPSGI 336
           R   +  +P  P     F+I   GI
Sbjct: 205 RIARLIDAPHLPEGEAVFSITEKGI 229

>pdb|4B2I|A Chain A, Humanised Monomeric Rada In Complex With Indazole Length = 231

Iteration: 1
 Score = 80.1 bits (196), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/264 (27%), Positives = 112/264 (42%), Gaps = 48/264 (18%)
Query: 82  GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIY 141
           G + T  K LD  L GG+    +TE+ G  G+GKTQ    L+++  LP   GGL+G V++
Sbjct: 5   GRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVMW 64
Query: 142 IDVESTFTSRRMIEMGASSF---PEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKV 198
           ID E+TF   R+ E+  +      E+      A+       +L         +  E +  
Sbjct: 65  IDTENTFRPERIREIAQNRGLDPDEVLKHIAYARAFNSNHQML-------LVQQAEDMIK 117
Query: 199 SLLQNQ--VKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFSRIPIVVTN 253
            LL     VKLL++DS+ +     +  R   A  Q  L+ H++ +  LA    I + VTN
Sbjct: 118 ELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTN 177
Query: 254 QVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVL-EAKSGQR 312
           QV+                             HI+       AH+ T+R+ L + K G+R
Sbjct: 178 QVQANG-------------------------GHIL-------AHSATLRVYLRKGKGGKR 205
Query: 313 FMNVEKSPTSPPLAFSFTINPSGI 336
              +  +P  P     F+I   GI
Sbjct: 206 IARLIDAPHLPEGEAVFSITEKGI 229

>pdb|1N0W|A Chain A, Crystal Structure Of A Rad51-Brca2 Brc Repeat Complex Length = 243

Iteration: 1
 Score = 77.0 bits (188), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/264 (27%), Positives = 108/264 (40%), Gaps = 30/264 (11%)
Query: 83  HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
            + T  K LD  L GG+  G +TE  G   TGKTQ C  L++   LP   GG +G   YI
Sbjct: 5   QITTGSKELDKLLQGGIETGSITEXFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAXYI 64
Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E TF   R++     +  E +   G   ++   +   +  +    T+ L +     ++
Sbjct: 65  DTEGTFRPERLL-----AVAERYGLSG--SDVLDNVAYARAFNTDHQTQLLYQASAXXVE 117
Query: 203 NQVKLLVIDSMEAL----VPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQ 258
           ++  LL++DS  AL      G  E  A   H   +   L+    EF  + +V+TNQV  Q
Sbjct: 118 SRYALLIVDSATALYRTDYSGRGELSARQXHLARFLRXLLRLADEFG-VAVVITNQVVAQ 176
Query: 259 SHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQ-RFMNVE 317
             D +  +    +K                 + G   AHA T RL L    G+ R   + 
Sbjct: 177 V-DGAAXFAADPKK----------------PIGGNIIAHASTTRLYLRKGRGETRICKIY 219
Query: 318 KSPTSPPLAFSFTINPSGISLLTD 341
            SP  P     F IN  G+    D
Sbjct: 220 DSPCLPEAEAXFAINADGVGDAKD 243

>pdb|2ZJB|A Chain A, Crystal Structure Of The Human Dmc1-M200v Polymorphic Variant Length = 343

Iteration: 1
 Score = 70.5 bits (171), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 78/287 (27%), Positives = 119/287 (41%), Gaps = 34/287 (11%)
Query: 57  SEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKT 116
           ++++ P F TA    E+R     +  H+ T  +  D  L GG+    +TE  G   TGKT
Sbjct: 81  NKLIEPGFLTAFEYSEKR----KMVFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKT 136
Query: 117 QFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAG 176
           Q    L + A LP   G   G +I+ID E+TF   R+ ++ A  F  + H       +  
Sbjct: 137 QLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDI-ADRF-NVDHDA-----VLD 189
Query: 177 RILVLQPTSLSEFTESLEKIKVSLLQNQ--VKLLVIDSMEALVPGVHEQR---APGQHPL 231
            +L  +  +     E L+ +     +     KLL+IDS+ AL       R   A  Q  L
Sbjct: 190 NVLYARAYTSEHQVELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKL 249
Query: 232 SWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVL 291
           +  +S +  ++E   + + VTNQ+   + D      FQ      I         HI+   
Sbjct: 250 AQMLSRLQKISEEYNVAVFVTNQM---TADPGATMTFQADPKKPI-------GGHIL--- 296
Query: 292 GFHWAHAVTIRLVLEAKSGQ-RFMNVEKSPTSPPLAFSFTINPSGIS 337
               AHA T R+ L    G+ R   +  SP  P    +F I   GI 
Sbjct: 297 ----AHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIG 339

>pdb|1V5W|A Chain A, Crystal Structure Of The Human Dmc1 Protein Length = 343

Iteration: 1
 Score = 70.1 bits (170), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 78/287 (27%), Positives = 118/287 (41%), Gaps = 34/287 (11%)
Query: 57  SEIVCPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKT 116
           ++++ P F TA    E+R        H+ T  +  D  L GG+    +TE  G   TGKT
Sbjct: 81  NKLIEPGFLTAFEYSEKRKMV----FHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKT 136
Query: 117 QFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAG 176
           Q    L + A LP   G   G +I+ID E+TF   R+ ++ A  F  + H       +  
Sbjct: 137 QLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDI-ADRF-NVDHDA-----VLD 189
Query: 177 RILVLQPTSLSEFTESLEKIKVSLLQNQ--VKLLVIDSMEALVPGVHEQR---APGQHPL 231
            +L  +  +     E L+ +     +     KLL+IDS+ AL       R   A  Q  L
Sbjct: 190 NVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKL 249
Query: 232 SWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVL 291
           +  +S +  ++E   + + VTNQ+   + D      FQ      I         HI+   
Sbjct: 250 AQMLSRLQKISEEYNVAVFVTNQM---TADPGATMTFQADPKKPI-------GGHIL--- 296
Query: 292 GFHWAHAVTIRLVLEAKSGQ-RFMNVEKSPTSPPLAFSFTINPSGIS 337
               AHA T R+ L    G+ R   +  SP  P    +F I   GI 
Sbjct: 297 ----AHASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIG 339

>pdb|3NTU|A Chain A, Rada Recombinase D302k Mutant In Complex With Amp-Pnp Length = 319

Iteration: 1
 Score = 67.0 bits (162), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 119/296 (40%), Gaps = 62/296 (20%)
Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQF----C 119
           F++ + L++QR+        L T    LD+ L GG+    VTE  G  G+GKTQ     C
Sbjct: 61  FKSGIDLLKQRSTV----WKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSC 116
Query: 120 LKLSLLAALPAHYGGLDGG------VIYIDVESTFTSRRMIEM-------GASSFPEIFH 166
           + L     L      +  G       +YID E TF   R+++M       G +     F 
Sbjct: 117 VNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFV 176
Query: 167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHEQR 224
           ++    +M  ++L         F E +E     L+Q  N +KL+VIDS+ +     +  R
Sbjct: 177 ARAYNSDM--QML---------FAEKIE----DLIQEGNNIKLVVIDSLTSTFRNEYTGR 221
Query: 225 ---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRT 281
              A  Q  L  H++ +  LA+     ++VTNQV   S      +    Q +        
Sbjct: 222 GKLAERQQKLGRHMATLNKLADLFNCVVLVTNQV---SAKPDAFFGMAEQAIG------- 271
Query: 282 RYYSHIVAVLGFHWAHAVTIR-LVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
               HIV        HA T R  V + K  +R   + KSP  P     F I   GI
Sbjct: 272 ---GHIV-------GHAATFRFFVRKGKGDKRVAKLYKSPHLPDAEAIFRITEKGI 317

>pdb|2CVF|A Chain A, Crystal Structure Of The Radb Recombinase Length = 220

Iteration: 1
 Score = 65.5 bits (158), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 84/180 (46%), Gaps = 20/180 (11%)
Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           L T  K LD+ L GG   GV+T++ GP  +GKT   L+  LL+            V Y+D
Sbjct: 2   LSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSGKK---------VAYVD 52
Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMA-GRILVLQPTSLSEFTESLEKIKVSLLQ 202
            E  F+  R+++M          ++G+  E A  R ++  P+   E    +  +K ++  
Sbjct: 53  TEGGFSPERLVQMA--------ETRGLNPEEALSRFILFTPSDFKEQRRVIGSLKKTVDS 104
Query: 203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDE 262
           N   L+V+DS+ A      E R+     LS  + ++  +A    IP++V NQV   S  E
Sbjct: 105 N-FALVVVDSITAHYRA-EENRSGLIAELSRQLQVLLWIARKHNIPVIVINQVHFDSRTE 162

>pdb|1T4G|A Chain A, Atpase In Complex With Amp-pnp Length = 322

Iteration: 1
 Score = 65.1 bits (157), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 118/296 (39%), Gaps = 62/296 (20%)
Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQF----C 119
           F++ + L++QR+        L T    LD+ L GG+    VTE  G  G+GKTQ     C
Sbjct: 64  FKSGIDLLKQRSTV----WKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSC 119
Query: 120 LKLSLLAALPAHYGGLDGG------VIYIDVESTFTSRRMIEM-------GASSFPEIFH 166
           + L     L      +  G       +YID E TF   R+++M       G +     F 
Sbjct: 120 VNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFV 179
Query: 167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHEQR 224
           ++    +M  ++L         F E +E     L+Q  N +KL+VIDS+ +     +  R
Sbjct: 180 ARAYNSDM--QML---------FAEKIE----DLIQEGNNIKLVVIDSLTSTFRNEYTGR 224
Query: 225 ---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRT 281
              A  Q  L  H++ +  LA+     ++VTNQV   S      +    Q +        
Sbjct: 225 GKLAERQQKLGRHMATLNKLADLFNCVVLVTNQV---SAKPDAFFGMAEQAIG------- 274
Query: 282 RYYSHIVAVLGFHWAHAVTIR-LVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
               HIV        HA T R  V + K  +R   +  SP  P     F I   GI
Sbjct: 275 ---GHIV-------GHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGI 320

>pdb|4DC9|A Chain A, Hexameric Ring Of Methanococcus Voltae Rada Length = 266

Iteration: 1
 Score = 64.7 bits (156), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 118/296 (39%), Gaps = 62/296 (20%)
Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQF----C 119
           F++ + L++QR+        L T    LD+ L GG+    VTE  G  G+GKTQ     C
Sbjct: 8   FKSGIDLLKQRSTV----WKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSC 63
Query: 120 LKLSLLAALPAHYGGLDGG------VIYIDVESTFTSRRMIEM-------GASSFPEIFH 166
           + L     L      +  G       +YID E TF   R+++M       G +     F 
Sbjct: 64  VNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFV 123
Query: 167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHEQR 224
           ++    +M  ++L         F E +E     L+Q  N +KL+VIDS+ +     +  R
Sbjct: 124 ARAYNSDM--QML---------FAEKIE----DLIQEGNNIKLVVIDSLTSTFRNEYTGR 168
Query: 225 ---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRT 281
              A  Q  L  H++ +  LA+     ++VTNQV   S      +    Q +        
Sbjct: 169 GKLAERQQKLGRHMATLNKLADLFNCVVLVTNQV---SAKPDAFFGMAEQAIG------- 218
Query: 282 RYYSHIVAVLGFHWAHAVTIR-LVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
               HIV        HA T R  V + K  +R   +  SP  P     F I   GI
Sbjct: 219 ---GHIV-------GHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGI 264

>pdb|2GDJ|A Chain A, Delta-62 Rada Recombinase In Complex With Amp-Pnp And Magnesium Length = 264

Iteration: 1
 Score = 64.7 bits (156), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 79/296 (26%), Positives = 118/296 (39%), Gaps = 62/296 (20%)
Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQF----C 119
           F++ + L++QR+        L T    LD+ L GG+    VTE  G  G+GKTQ     C
Sbjct: 6   FKSGIDLLKQRSTV----WKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSC 61
Query: 120 LKLSLLAALPAHYGGLDGG------VIYIDVESTFTSRRMIEM-------GASSFPEIFH 166
           + L     L      +  G       +YID E TF   R+++M       G +     F 
Sbjct: 62  VNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDGQTVLDNTFV 121
Query: 167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHEQR 224
           ++    +M  ++L         F E +E     L+Q  N +KL+VIDS+ +     +  R
Sbjct: 122 ARAYNSDM--QML---------FAEKIE----DLIQEGNNIKLVVIDSLTSTFRNEYTGR 166
Query: 225 ---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRT 281
              A  Q  L  H++ +  LA+     ++VTNQV   S      +    Q +        
Sbjct: 167 GKLAERQQKLGRHMATLNKLADLFNCVVLVTNQV---SAKPDAFFGMAEQAIG------- 216
Query: 282 RYYSHIVAVLGFHWAHAVTIR-LVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
               HIV        HA T R  V + K  +R   +  SP  P     F I   GI
Sbjct: 217 ---GHIV-------GHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGI 262

>pdb|3ETL|A Chain A, Rada Recombinase From Methanococcus Maripaludis In Complex With Amppnp Length = 322

Iteration: 1
 Score = 64.3 bits (155), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 76/296 (25%), Positives = 120/296 (40%), Gaps = 62/296 (20%)
Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQF----C 119
           F++ + L++QR +   L     T    LD  L GG+    VTE  G  G+GKTQ     C
Sbjct: 64  FKSGVELLKQRQSVWRL----STGSTELDTVLAGGIESQSVTEFAGMFGSGKTQIMHQTC 119
Query: 120 LKLSLLAALPAHYGGLDG------GVIYIDVESTFTSRRMIEM-------GASSFPEIFH 166
           + L +   + A   G+          +YID E TF   R+++M       G +     F 
Sbjct: 120 VNLQMREKIFADLEGVVEEELEAPKAVYIDTEGTFRPERVVQMAEGAGIDGQTVLDNTFV 179
Query: 167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR-- 224
           ++    +M  ++L         F E +E +      N +KL++IDS+ +        R  
Sbjct: 180 ARAYNSDM--QML---------FAEKIEDLIKG--GNNIKLVIIDSLTSTFRNEFTGRGK 226
Query: 225 -APGQHPLSWHISLITSLAEFSRIPIVVTNQV--RPQSHDESCLYPFQVQKMDRILKDRT 281
            A  Q  L  H++ +  LA+     ++VTNQV  +P ++       F V +         
Sbjct: 227 LAERQQKLGRHMATLNKLADLYNCIVLVTNQVAAKPDAY-------FGVAEQ-------- 271
Query: 282 RYYSHIVAVLGFHWAHAVTIRLVL-EAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
                  A+ G    HA T R  L ++K  +R   +  SP  P     F I   GI
Sbjct: 272 -------AIGGHVVGHAATFRFFLRKSKGDKRVAKLYDSPHLPDSEAVFRITEKGI 320

>pdb|2F1H|A Chain A, Recombinase In Complex With Amp-pnp And Potassium Length = 322

Iteration: 1
 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 118/296 (39%), Gaps = 62/296 (20%)
Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQF----C 119
           F++ + L++QR+        L T    LD+ L GG+    VTE  G  G+GKTQ     C
Sbjct: 64  FKSGIDLLKQRSTV----WKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSC 119
Query: 120 LKLSLLAALPAHYGGLDGG------VIYIDVESTFTSRRMIEM-------GASSFPEIFH 166
           + L     L      +  G       +YID + TF   R+++M       G +     F 
Sbjct: 120 VNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTDGTFRPERIMQMAEHAGIDGQTVLDNTFV 179
Query: 167 SKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHEQR 224
           ++    +M  ++L         F E +E     L+Q  N +KL+VIDS+ +     +  R
Sbjct: 180 ARAYNSDM--QML---------FAEKIE----DLIQEGNNIKLVVIDSLTSTFRNEYTGR 224
Query: 225 ---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRT 281
              A  Q  L  H++ +  LA+     ++VTNQV   S      +    Q +        
Sbjct: 225 GKLAERQQKLGRHMATLNKLADLFNCVVLVTNQV---SAKPDAFFGMAEQAIG------- 274
Query: 282 RYYSHIVAVLGFHWAHAVTIR-LVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
               HIV        HA T R  V + K  +R   +  SP  P     F I   GI
Sbjct: 275 ---GHIV-------GHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGI 320

>pdb|3LDA|A Chain A, Yeast Rad51 H352y Filament Interface Mutant Length = 400

Iteration: 1
 Score = 59.3 bits (142), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 41/73 (56%)
Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           L T  K LD  L GGV  G +TEL G   TGK+Q C  L++   +P   GG +G  +YID
Sbjct: 160 LTTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID 219
Query: 144 VESTFTSRRMIEM 156
            E TF   R++ +
Sbjct: 220 TEGTFRPVRLVSI 232

>pdb|1SZP|A Chain A, A Crystal Structure Of The Rad51 Filament Length = 321

Iteration: 1
 Score = 59.3 bits (142), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 41/73 (56%)
Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           L T  K LD  L GGV  G +TEL G   TGK+Q C  L++   +P   GG +G  +YID
Sbjct: 81  LTTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYID 140
Query: 144 VESTFTSRRMIEM 156
            E TF   R++ +
Sbjct: 141 TEGTFRPVRLVSI 153

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	357
2z43_A	324	DNA repair and recombination protein RADA; archaea	1e-66
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	2e-62
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	5e-59
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	1e-58
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	5e-56
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	1e-54
2cvh_A	220	DNA repair and recombination protein RADB; filamen	2e-24
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	3e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-10
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	1e-09
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	4e-09
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	6e-09
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	3e-08
3io5_A	333	Recombination and repair protein; storage dimer, i	1e-05
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	3e-05

>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* Length = 324

 Score =  212 bits (541), Expect = 1e-66
 Identities = 78/331 (23%), Positives = 139/331 (41%), Gaps = 36/331 (10%)

Query: 11  LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLL 70
           + +++ N       ++ +     +  +L     + LS  +  +    + +   F+TAL +
Sbjct: 20  ISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARDALDIRFKTALEV 79

Query: 71  MEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPA 130
            ++R   + +     T  + LD  L GG+    +TE  G  G+GKTQ C +LS+   LP 
Sbjct: 80  KKERMNVKKI----STGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPP 135

Query: 131 HYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFT 190
             GGL G  +YID E TF   R+  M  +   +I         +   I  ++  +     
Sbjct: 136 EKGGLSGKAVYIDTEGTFRWERIENMAKALGLDI-------DNVMNNIYYIRAINTDHQI 188

Query: 191 ESLEKIKVSLLQNQ-VKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFSR 246
             ++ ++  + ++  +KL+V+DS+ +     +  R   A  Q  L+ H+  +T LAE   
Sbjct: 189 AIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQLTRLAEVYD 248

Query: 247 IPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE 306
           I +++TNQV                + D    D T       AV G    H   IR+ L+
Sbjct: 249 IAVIITNQVM--------------ARPDMFYGDPTV------AVGGHTLYHVPGIRIQLK 288

Query: 307 -AKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
            ++  +R   V  +P  P     F +   GI
Sbjct: 289 KSRGNRRIARVVDAPHLPEGEVVFALTEEGI 319

>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 Length = 343

 Score =  202 bits (514), Expect = 2e-62
 Identities = 76/333 (22%), Positives = 123/333 (36%), Gaps = 34/333 (10%)

Query: 11  LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLL 70
           +  +      +  I T K     T   L  +  +  ++V       ++++ P F TA   
Sbjct: 35  INVADIKKLKSVGICTIKGIQMTTRRALCNVKGLSEAKVDKIKEAANKLIEPGFLTAFEY 94

Query: 71  MEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPA 130
            E+R    H+     T  +  D  L GG+    +TE  G   TGKTQ    L + A LP 
Sbjct: 95  SEKRKMVFHI----TTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPG 150

Query: 131 HYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFT 190
             G   G +I+ID E+TF   R+ ++      +          +   +L  +  +     
Sbjct: 151 AGGYPGGKIIFIDTENTFRPDRLRDIADRFNVD-------HDAVLDNVLYARAYTSEHQM 203

Query: 191 ESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFS 245
           E L+ +     +     KLL+IDS+ AL       R   A  Q  L+  +S +  ++E  
Sbjct: 204 ELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLSRLQKISEEY 263

Query: 246 RIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVL 305
            + + VTNQ+                       D  +       + G   AHA T R+ L
Sbjct: 264 NVAVFVTNQMT-----------ADPGATMTFQADPKK------PIGGHILAHASTTRISL 306

Query: 306 E-AKSGQRFMNVEKSPTSPPLAFSFTINPSGIS 337
              +   R   +  SP  P    +F I   GI 
Sbjct: 307 RKGRGELRIAKIYDSPEMPENEATFAITAGGIG 339

>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 Length = 349

 Score =  193 bits (492), Expect = 5e-59
 Identities = 80/336 (23%), Positives = 138/336 (41%), Gaps = 41/336 (12%)

Query: 11  LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCP-PFQTALL 69
           +  + A         T +     + +EL ++  +        +    +      F  A  
Sbjct: 43  VGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKAANLGTFMRADE 102

Query: 70  LMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALP 129
            +++RA    +     T  K LD  L GG+    +TE+ G  G+GKTQ    L+++  LP
Sbjct: 103 YLKKRATIGRI----STGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLP 158

Query: 130 AHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEF 189
              GGL+G VI+ID E+TF   R+ E+  +   +         E+   I V +  + +  
Sbjct: 159 PEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDP-------DEVLKHIYVARAFNSNHQ 211

Query: 190 TESLEKIKVSLLQ-----NQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSL 241
              +++ +  + +       VKLL++DS+ +     +  R   A  Q  L+ H++ +  L
Sbjct: 212 MLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHRL 271

Query: 242 AEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTI 301
           A    I + VTNQV+               + D    D TR       + G   AH+ T+
Sbjct: 272 ANLYDIAVFVTNQVQ--------------ARPDAFFGDPTR------PIGGHILAHSATL 311

Query: 302 RLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
           R+ L   K G+R   +  +P  P     F+I   GI
Sbjct: 312 RVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGI 347

>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* Length = 400

 Score =  194 bits (493), Expect = 1e-58
 Identities = 76/339 (22%), Positives = 129/339 (38%), Gaps = 35/339 (10%)

Query: 6   ISEMRLP---KSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCP 62
           I ++++     +         + TA+        +L+++  +  ++    L   + +V  
Sbjct: 83  IEKLQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARLVPM 142

Query: 63  PFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKL 122
            F TA     +R+    L     T  K LD  L GGV  G +TEL G   TGK+Q C  L
Sbjct: 143 GFVTAADFHMRRSELICL----TTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTL 198

Query: 123 SLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQ 182
           ++   +P   GG +G  +YID E TF   R++ +      +         +    +   +
Sbjct: 199 AVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLVSIAQRFGLD-------PDDALNNVAYAR 251

Query: 183 PTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLIT 239
             +       L+     + +++  L+V+DS+ AL       R   +  Q  L+  +  + 
Sbjct: 252 AYNADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFSGRGELSARQMHLAKFMRALQ 311

Query: 240 SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAV 299
            LA+   + +VVTNQV  Q        P                      + G   A++ 
Sbjct: 312 RLADQFGVAVVVTNQVVAQVDGGMAFNP-----------------DPKKPIGGNIMAYSS 354

Query: 300 TIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGIS 337
           T RL  +  K  QR   V  SP  P     F I   G+ 
Sbjct: 355 TTRLGFKKGKGCQRLCKVVDSPCLPEAECVFAIYEDGVG 393

>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* Length = 322

 Score =  184 bits (469), Expect = 5e-56
 Identities = 76/351 (21%), Positives = 123/351 (35%), Gaps = 46/351 (13%)

Query: 1   MANKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV 60
           M + L     +  S A               + T  EL  +  +        +    ++ 
Sbjct: 1   MGDNLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLC 60

Query: 61  CPPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCL 120
              F++ + L++QR+    L     T    LD+ L GG+    VTE  G  G+GKTQ   
Sbjct: 61  DLGFKSGIDLLKQRSTVWKL----STSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMH 116

Query: 121 KLSLLAALPAHY----------GGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGM 170
           +  +    P                    +YID E TF   R+++M   +  +       
Sbjct: 117 QSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGID------- 169

Query: 171 AQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQ-VKLLVIDSMEALVPGVHEQR---AP 226
            Q +     V +  +        EKI+  + +   +KL+VIDS+ +     +  R   A 
Sbjct: 170 GQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAE 229

Query: 227 GQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSH 286
            Q  L  H++ +  LA+     ++VTNQV                K D       +    
Sbjct: 230 RQQKLGRHMATLNKLADLFNCVVLVTNQVS--------------AKPDAFFGMAEQ---- 271

Query: 287 IVAVLGFHWAHAVTIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
             A+ G    HA T R  +   K  +R   +  SP  P     F I   GI
Sbjct: 272 --AIGGHIVGHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGI 320

>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 Length = 243

 Score =  178 bits (453), Expect = 1e-54
 Identities = 65/263 (24%), Positives = 107/263 (40%), Gaps = 28/263 (10%)

Query: 83  HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
            + T  K LD  L GG+  G +TE+ G   TGKTQ C  L++   LP   GG +G  +YI
Sbjct: 5   QITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYI 64

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E TF   R++ +                ++   +   +  +    T+ L +    +++
Sbjct: 65  DTEGTFRPERLLAVAERYGLS-------GSDVLDNVAYARAFNTDHQTQLLYQASAMMVE 117

Query: 203 NQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQS 259
           ++  LL++DS  AL    +  R   +  Q  L+  + ++  LA+   + +V+TNQV    
Sbjct: 118 SRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQV---- 173

Query: 260 HDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE-AKSGQRFMNVEK 318
                        + ++             + G   AHA T RL L   +   R   +  
Sbjct: 174 -------------VAQVDGAAMFAADPKKPIGGNIIAHASTTRLYLRKGRGETRICKIYD 220

Query: 319 SPTSPPLAFSFTINPSGISLLTD 341
           SP  P     F IN  G+    D
Sbjct: 221 SPCLPEAEAMFAINADGVGDAKD 243

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A* Length = 220

 Score = 98.4 bits (246), Expect = 2e-24
 Identities = 62/260 (23%), Positives = 99/260 (38%), Gaps = 52/260 (20%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           L T  K LD+ L GG   GV+T++ GP  +GKT   L+  LL+            V Y+D
Sbjct: 2   LSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGLLSG---------KKVAYVD 52

Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGM-AQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
            E  F+  R +   A +        G+  +E   R ++  P+   E    +  +K   + 
Sbjct: 53  TEGGFSPER-LVQMAETR-------GLNPEEALSRFILFTPSDFKEQRRVIGSLK-KTVD 103

Query: 203 NQVKLLVIDSMEALVPGVHEQRAPG---QHPLSWHISLITSLAEFSRIPIVVTNQVRPQS 259
           +   L+V+DS+ A      E+   G   +  LS  + ++  +A    IP++V NQV    
Sbjct: 104 SNFALVVVDSITAHYRA--EENRSGLIAE--LSRQLQVLLWIARKHNIPVIVINQV---- 155

Query: 260 HDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE--AKSGQRFMNVE 317
                              + T+       V      +     L L+   K G R   +E
Sbjct: 156 -------------HFDSRTEMTK------PVAEQTLGYRCKDILRLDKLPKPGLRVAVLE 196

Query: 318 KSPTSPP-LAFSFTINPSGI 336
           +    P  L   F I   GI
Sbjct: 197 RHRFRPEGLMAYFRITERGI 216

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii} Length = 247

 Score = 58.9 bits (143), Expect = 3e-10
 Identities = 54/275 (19%), Positives = 88/275 (32%), Gaps = 64/275 (23%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VIY 141
           + T + G+D  L GG+P   V  L G  GTGKT F  +          + GL  G   IY
Sbjct: 5   VKTGIPGVDEILHGGIPERNVVLLSGGPGTGKTIFSQQFL--------WNGLKMGEPGIY 56

Query: 142 IDVEST------------FTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEF 189
           + +E              +  +   E G  +  + F +     +   + +V   T + EF
Sbjct: 57  VALEEHPVQVRQNMAQFGWDVKPYEEKGMFAMVDAFTAGIGKSKEYEKYIVHDLTDIREF 116

Query: 190 TESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ-RAPGQHPLSWHISLITSLAEFSRIP 248
            E L +    +     K +V+DS+  L        R+         I  +  +   +   
Sbjct: 117 IEVLRQAIRDI---NAKRVVVDSVTTLYINKPAMARS--------IILQLKRVLAGTGCT 165

Query: 249 IVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIV-AVLGFHWAHAVTIRLVLEA 307
            +  +QV   S  E       V               H V  ++           L    
Sbjct: 166 SIFVSQV---SVGERGFGGPGV--------------EHGVDGIIRL--------DLDEID 200

Query: 308 KSGQRFMNVEK---SPTSPPLAFSFTINPSGISLL 339
              +R + V K   +  S      F I   GI + 
Sbjct: 201 GELKRSLIVWKMRGTSHSMRR-HPFDITDKGIIVY 234

>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 = 60.3 bits (145), Expect = 4e-10
 Identities = 67/424 (15%), Positives = 133/424 (31%), Gaps = 116/424 (27%)

Query: 4   KLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALA--------- 54
           K + +M  PKSI +     +I  +KDA+S T      LL  +   V+  +          
Sbjct: 36  KDVQDM--PKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKF 93

Query: 55  LVSEIVCPPFQTAL---LLMEQRAATEHLGGHLP----TRLK---GLDAALCGGVPFGVV 104
           L+S I     Q ++   + +EQR    +          +RL+    L  AL    P   V
Sbjct: 94  LMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNV 153

Query: 105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEI 164
             + G  G+GKT   + L +  +       +D  + ++++++  +   ++EM      +I
Sbjct: 154 L-IDGVLGSGKT--WVALDVCLSYKVQ-CKMDFKIFWLNLKNCNSPETVLEMLQKLLYQI 209

Query: 165 FHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVK---LLVIDSMEALVPGVH 221
             +                +++     S++     LL+++     LLV+         V 
Sbjct: 210 DPN--------WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLL-------NV- 253

Query: 222 EQRAPGQHPLSWHIS--------LITS--------LAEFSRIPIVVTNQVRPQSHDES-- 263
                 Q+      +        L+T+        L+  +   I + +     + DE   
Sbjct: 254 ------QNA--KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305

Query: 264 ----CLY------PFQVQK-----------MDRILKDRTRYYSHIVAVLGFHWAHAVTIR 302
                L       P +V               R        + H+             I 
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHV-----NCDKLTTII- 359

Query: 303 LVLEAKSGQRFMNVEKSPTSPPLAFSFTINPSG-------ISLL----TDDGTEMVVPET 351
                   +  +NV +      +    ++ P         +SL+          +VV + 
Sbjct: 360 --------ESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKL 411

Query: 352 CNLS 355
              S
Sbjct: 412 HKYS 415

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2} Length = 235

 Score = 56.9 bits (138), Expect = 1e-09
 Identities = 43/142 (30%), Positives = 52/142 (36%), Gaps = 20/142 (14%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VIY 141
           L T +   D  + GG+P G    L G  GTGKT F L             GL  G   IY
Sbjct: 5   LSTGILDFDKLIQGGIPQGFFIALTGEPGTGKTIFSLHFI--------AKGLRDGDPCIY 56

Query: 142 IDVESTFTSRRMIEMGASSF---PEIFHSKGMAQEMAGRILVLQPTSLSEFT--ESLEKI 196
           +  E    SR  I   A  F    E +  K +    A         SL   T  E + K+
Sbjct: 57  VTTEE---SRDSIIRQAKQFNWDFEEYIEKKLIIIDALMKEKEDQWSLVNLTPEELVNKV 113

Query: 197 K--VSLLQNQVKLLVIDSMEAL 216
                 L      LVIDS+ AL
Sbjct: 114 IEAKQKLGYGKARLVIDSVSAL 135

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A* Length = 525

 Score = 56.9 bits (137), Expect = 4e-09
 Identities = 25/137 (18%), Positives = 57/137 (41%), Gaps = 11/137 (8%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGG--VIY 141
           + T ++G D    GG+P G  T + G +GTGKT F ++         + G ++     ++
Sbjct: 21  MRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQF-------LYNGIIEFDEPGVF 73

Query: 142 IDVESTFTS--RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVS 199
           +  E T     +     G      +   K    + +      +     + +  +E+I  +
Sbjct: 74  VTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYA 133

Query: 200 LLQNQVKLLVIDSMEAL 216
           + + + + + IDS+ ++
Sbjct: 134 IQKYRARRVSIDSVTSV 150

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A* Length = 525

 Score = 56.5 bits (136), Expect = 6e-09
 Identities = 29/134 (21%), Positives = 47/134 (35%), Gaps = 12/134 (8%)

Query: 83  HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
            + + +  LD    GG     +    G  GTGKT    +    A             I  
Sbjct: 262 RVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACA------NKERAILF 315

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
             E    SR  +   A S+      + M ++   +I+   P S     + L+ IK  +  
Sbjct: 316 AYE---ESRAQLLRNAYSWG--MDFEEMERQNLLKIVCAYPESAG-LEDHLQIIKSEIND 369

Query: 203 NQVKLLVIDSMEAL 216
            +   + IDS+ AL
Sbjct: 370 FKPARIAIDSLSAL 383

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4} Length = 333

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 28/143 (19%), Positives = 52/143 (36%), Gaps = 32/143 (22%)

Query: 84  LPTRLKGLDAAL----CGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGV 139
           + T++  ++ AL     GG+  G++  L GP+ + K+       L           D   
Sbjct: 7   VRTKIPMMNIALSGEITGGMQSGLLI-LAGPSKSFKSN----FGLTMVSSYMRQYPDAVC 61

Query: 140 IYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLS----EFTESLEK 195
           ++ D E   T            P    S G+  E   R++     SL     +    L+ 
Sbjct: 62  LFYDSEFGIT------------PAYLRSMGVDPE---RVIHTPVQSLEQLRIDMVNQLDA 106

Query: 196 IKVSLLQNQVKLLVIDSMEALVP 218
           I+    + +  ++ IDS+  L  
Sbjct: 107 IE----RGEKVVVFIDSLGNLAS 125

>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 Length = 279

 Score = 43.9 bits (103), Expect = 3e-05
 Identities = 28/131 (21%), Positives = 49/131 (37%), Gaps = 11/131 (8%)

Query: 95  LCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLD----GGVIYIDVESTFTS 150
           +   +  G V  LV P G GK+   L+L+   A       +     G VIY+  E   T+
Sbjct: 23  VLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTA 82

Query: 151 --RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLL 208
              R+  +GA    E   +      +   I  L      E+ + L++          +L+
Sbjct: 83  IHHRLHALGAHLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKR-----AAEGRRLM 137

Query: 209 VIDSMEALVPG 219
           V+D++      
Sbjct: 138 VLDTLRRFHIE 148

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	357
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	100.0
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	100.0
2z43_A	324	DNA repair and recombination protein RADA; archaea	100.0
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	100.0
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	100.0
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	100.0
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	100.0
2cvh_A	220	DNA repair and recombination protein RADB; filamen	99.98
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	99.97
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	99.97
3io5_A	333	Recombination and repair protein; storage dimer, i	99.97
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	99.97
1u94_A	356	RECA protein, recombinase A; homologous recombinat	99.97
1xp8_A	366	RECA protein, recombinase A; recombination, radior	99.97
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	99.97
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	99.96
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	99.96
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	99.96
4a74_A	231	DNA repair and recombination protein RADA; hydrola	99.96
2r6a_A	454	DNAB helicase, replicative helicase; replication,	99.96
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	99.95
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	99.95
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	99.94
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	99.94
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	99.93
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	99.92
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	99.9
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	99.89
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	99.82
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	99.82
3bs4_A	260	Uncharacterized protein PH0321; structural genomic	99.81
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	99.69
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	99.62
1b22_A	114	DNA repair protein RAD51; DNA binding, riken struc	99.07
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	98.8
2kz3_A	83	Putative uncharacterized protein RAD51L3; RAD51D,	98.46
4a8j_A	361	Elongator complex protein 4; transcription; 2.10A	98.46
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	98.42
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	98.39
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.37
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	98.34
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	98.32
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	98.3
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	98.29
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	98.28
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	98.23
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.21
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	98.21
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.21
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	98.2
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.12
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.1
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.1
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	98.09
1g6h_A	257	High-affinity branched-chain amino acid transport	98.09
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	98.09
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	98.07
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	98.06
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	98.05
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.04
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.04
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	98.03
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	97.99
1ji0_A	240	ABC transporter; ATP binding protein, structural g	97.99
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.98
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	97.97
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	97.97
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	97.96
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	97.95
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	97.95
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	97.93
1b0u_A	262	Histidine permease; ABC transporter, transport pro	97.91
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.91
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.91
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	97.91
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	97.9
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	97.9
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	97.87
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	97.87
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	97.86
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	97.86
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	97.86
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	97.85
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	97.85
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	97.85
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	97.84
3bos_A	242	Putative DNA replication factor; P-loop containing	97.84
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	97.84
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	97.83
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	97.83
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	97.83
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.82
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	97.81
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	97.8
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.79
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.77
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.77
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.76
3ice_A	422	Transcription termination factor RHO; transcriptio	97.75
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	97.75
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	97.75
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.75
1sgw_A	214	Putative ABC transporter; structural genomics, P p	97.73
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.73
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	97.72
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	97.72
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	97.72
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	97.67
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	97.67
2xxa_A	433	Signal recognition particle protein; protein trans	97.67
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	97.64
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	97.63
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.59
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	97.57
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	97.54
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	97.54
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	97.48
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.47
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	97.47
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	97.45
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	97.45
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	97.45
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	97.45
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	97.43
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	97.43
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	97.42
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	97.4
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	97.39
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.38
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.38
2fna_A	357	Conserved hypothetical protein; structural genomic	97.35
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	97.34
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	97.34
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	97.32
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.3
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	97.3
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	97.3
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	97.29
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	97.29
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.28
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.28
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	97.25
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	97.25
1z3e_B	73	DNA-directed RNA polymerase alpha chain; bacterial	97.24
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.23
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	97.23
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	97.22
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	97.21
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	97.21
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.21
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	97.21
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	97.2
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	97.19
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	97.19
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	97.18
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	97.18
1tue_A	212	Replication protein E1; helicase, replication, E1E	97.17
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	97.16
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	97.16
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.16
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	97.16
3k4g_A	86	DNA-directed RNA polymerase subunit alpha; bacteri	97.15
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	97.13
2og2_A	359	Putative signal recognition particle receptor; nuc	97.13
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	97.13
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	97.09
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	97.09
3gfk_B	79	DNA-directed RNA polymerase subunit alpha; protein	97.09
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.09
3ozx_A	538	RNAse L inhibitor; ATP binding cassette protein, h	97.08
1wcn_A	70	Transcription elongation protein NUSA; RNA-binding	97.05
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	97.05
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.02
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	97.01
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	97.0
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.99
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.98
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	96.97
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	96.96
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.94
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	96.94
3zq6_A	324	Putative arsenical pump-driving ATPase; tail-ancho	96.94
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	96.93
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.93
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.93
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	96.9
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	96.89
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	96.84
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	96.83
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	96.82
3pvs_A	447	Replication-associated recombination protein A; ma	96.82
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.82
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.81
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.79
4dzz_A	206	Plasmid partitioning protein PARF; deviant walker	96.79
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	96.78
1u9l_A	70	Transcription elongation protein NUSA; escherichia	96.78
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.78
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.77
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	96.77
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	96.76
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.76
3l0o_A	427	Transcription termination factor RHO; helicase, RH	96.75
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	96.75
2woj_A	354	ATPase GET3; tail-anchored, membrane protein, targ	96.75
1oft_A	161	SULA, hypothetical protein PA3008; bacterial cell	96.75
2eyu_A	261	Twitching motility protein PILT; pilus retraction	96.74
3kjh_A	254	CO dehydrogenase/acetyl-COA synthase complex, acce	96.74
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	96.74
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	96.73
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	96.72
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.72
3ug7_A	349	Arsenical pump-driving ATPase; tail-anchored, memb	96.69
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	96.66
4aby_A	415	DNA repair protein RECN; hydrolase, double strand	96.65
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	96.65
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.64
1hyq_A	263	MIND, cell division inhibitor (MIND-1); MINC, FTSZ	96.64
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.64
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.63
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	96.62
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	96.57
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.57
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.56
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	96.56
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	96.55
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	96.55
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.55
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.54
1coo_A	98	RNA polymerase alpha subunit; transcription regula	96.54
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	96.54
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.53
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	96.52
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.51
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.5
2ghi_A	260	Transport protein; multidrug resistance protein, M	96.49
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.49
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	96.48
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	96.43
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	96.43
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	96.43
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	96.42
2qgz_A	308	Helicase loader, putative primosome component; str	96.41
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.39
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.38
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	96.37
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	96.36
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	96.35
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	96.35
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	96.34
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.34
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.33
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	96.32
2woo_A	329	ATPase GET3; tail-anchored, membrane protein, targ	96.32
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	96.3
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.29
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	96.28
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	96.28
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.27
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	96.27
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.27
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.24
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.24
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	96.2
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	96.19
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.19
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	96.18
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.18
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.18
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	96.17
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	96.16
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	96.15
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.15
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.15
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.14
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.13
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	96.11
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.11
3fwy_A	314	Light-independent protochlorophyllide reductase I	96.11
3gqb_A	578	V-type ATP synthase alpha chain; A3B3, V-ATPase, A	96.11
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.1
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.1
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.07
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.06
2xj4_A	286	MIPZ; replication, cell division, ATPase, WACA; 1.	96.03
1p9r_A	418	General secretion pathway protein E; bacterial typ	96.02
3end_A	307	Light-independent protochlorophyllide reductase ir	96.02
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.01
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	95.99
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.98
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	95.98
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.98
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.97
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	95.96
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	95.95
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	95.95
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	95.94
2ewv_A	372	Twitching motility protein PILT; pilus retraction	95.92
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	95.88
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	95.87
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.87
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	95.84
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.83
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	95.82
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	95.82
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	95.81
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	95.81
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	95.79
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.76
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	95.74
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	95.73
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	95.73
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	95.73
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	95.71
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	95.71
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	95.68
1via_A	175	Shikimate kinase; structural genomics, transferase	95.67
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	95.66
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.65
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	95.65
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.63
3kta_A	182	Chromosome segregation protein SMC; structural mai	95.63
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	95.63
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.62
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.61
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	95.61
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	95.6
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	95.58
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.57
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.57
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	95.56
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	95.56
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.55
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	95.55
3bfv_A	271	CAPA1, CAPB2, membrane protein CAPA1, protein tyro	95.55
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	95.55
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.54
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	95.54
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.52
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	95.51
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	95.51
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	95.5
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.5
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.49
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	95.48
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	95.46
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.45
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	95.44
3cio_A	299	ETK, tyrosine-protein kinase ETK; WZC, escherichia	95.44
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	95.43
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	95.43
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	95.42
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	95.42
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	95.42
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	95.41
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	95.4
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.4
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.38
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	95.37
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	95.37
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.36
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	95.36
1ihu_A	589	Arsenical pump-driving ATPase; aluminum fluoride,	95.31
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	95.3
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.29
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	95.29
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	95.28
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	95.28
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	95.27
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.26
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	95.2
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	95.2
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.19
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	95.19
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	95.14
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.1
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	95.07
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.07
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.05
1t9h_A	307	YLOQ, probable GTPase ENGC; N-terminal beta-barrel	95.05
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	95.04
1g3q_A	237	MIND ATPase, cell division inhibitor; alpha-beta-a	95.04
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.03
2ph1_A	262	Nucleotide-binding protein; alpha-beta protein, st	95.03
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	95.03
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	95.0
2r44_A	331	Uncharacterized protein; putative ATPase, structur	95.0
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.97
3cwq_A	209	Para family chromosome partitioning protein; alpha	94.97
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.92
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	94.9
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.89
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.89
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	94.88
2chq_A	319	Replication factor C small subunit; DNA-binding pr	94.87
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	94.87
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.84
3ea0_A	245	ATPase, para family; alpha-beta-alpha sandwich, st	94.84
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.83
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	94.82
3la6_A	286	Tyrosine-protein kinase WZC; P-loop protein, nucle	94.82
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	94.81
3q9l_A	260	Septum site-determining protein MIND; ATPase, bact	94.81
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.8
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	94.79
3co5_A	143	Putative two-component system transcriptional RES	94.77
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	94.76
3k9g_A	267	PF-32 protein; ssgcid, SBRI, decode biostructures,	94.75
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	94.73
1wcv_1	257	SOJ, segregation protein; ATPase, bacterial, chrom	94.7
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	94.68
2oze_A	298	ORF delta'; para, walker type atpases, DNA segrega	94.67
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	94.67
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	94.66
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	94.66
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	94.57
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.54
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	94.53
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	94.47
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	94.43
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.34
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	94.29
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	94.28
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.26
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	94.24
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	94.17
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	94.16
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.15
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	94.13
3q3j_B	214	RHO-related GTP-binding protein RHO6; RAS-binding	94.13
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	94.12
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.11
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	94.06
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	94.04
3qxc_A	242	Dethiobiotin synthetase; DTBS, structural genomics	94.04
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	94.04
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.99
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	93.97
4gzl_A	204	RAS-related C3 botulinum toxin substrate 1; rossma	93.97
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	93.97
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	93.95
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	93.93
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	93.88
3qf7_A	365	RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.	93.87
3fgn_A	251	Dethiobiotin synthetase; biotin biosynthesis, BIOD	93.75
3pg5_A	361	Uncharacterized protein; structural genomics, PSI-	93.73
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	93.73
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	93.72
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.71
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	93.71
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	93.69
3euj_A	483	Chromosome partition protein MUKB, linker; MUKB, M	93.69
1byi_A	224	Dethiobiotin synthase; biotin synthesis, cyclo-lig	93.68
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	93.66
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.64
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	93.63
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.63
2wji_A	165	Ferrous iron transport protein B homolog; membrane	93.61
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	93.6
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	93.56
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	93.53
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	93.51
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	93.5
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.48
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.39
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.31
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	93.26
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.25
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	93.24
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	93.24
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	93.23
2vf7_A	842	UVRA2, excinuclease ABC, subunit A.; DNA-binding p	93.21
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	93.16
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	93.11
1e69_A	322	Chromosome segregation SMC protein; structural mai	93.08
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	93.03
2o5v_A	359	DNA replication and repair protein RECF; ABC ATPas	93.02
1w1w_A	430	Structural maintenance of chromosome 1; cohesin, c	92.99
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	92.94
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	92.93
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	92.92
3igf_A	374	ALL4481 protein; two-domained protein consisting o	92.89
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	92.88
3pih_A	916	Uvrabc system protein A; hydrolase, ABC ATPase, DN	92.87
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	92.86
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	92.81
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	92.78
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	92.76
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	92.74
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	92.69
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	92.66
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	92.66
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	92.63
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	92.63
2ged_A	193	SR-beta, signal recognition particle receptor beta	92.63
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	92.62
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	92.59
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	92.58
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	92.47
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	92.47

>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=100.00  E-value=3.5e-45  Score=339.24  Aligned_cols=308  Identities=24%  Similarity=0.292  Sum_probs=197.2

Q ss_pred             cccccC---CCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCC
Q 035774            5 LISEMR---LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLG   81 (357)
Q Consensus         5 ~~~~~~---l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (357)
                      +++.|+   +++.++.+|+++|+.|+++++..++.+|.++.+++++++.++++.+.+.+..++.++.++++.+.+    .
T Consensus        26 ~~~~l~~~g~~~~~~~~l~~~g~~t~~~~~~~~~~~l~~~~~is~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~----~  101 (343)
T 1v5w_A           26 DIDLLQKHGINVADIKKLKSVGICTIKGIQMTTRRALCNVKGLSEAKVDKIKEAANKLIEPGFLTAFEYSEKRKM----V  101 (343)
T ss_dssp             ------------------------------------------------------------CCSEEHHHHHHHGGG----C
T ss_pred             cHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHhhcccCCCcHHHHHhhhcc----c
Confidence            566665   999999999999999999999999999999999999999999998888788889999998876433    6


Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccC
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSF  161 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~  161 (357)
                      .+++||++.||.+|+||+++|++++|+|+||+|||+||++++.+++.+..+||.+++|+||++|+.++..++.+++... 
T Consensus       102 ~~i~TG~~~LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~~~l~~~~~~~-  180 (343)
T 1v5w_A          102 FHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRF-  180 (343)
T ss_dssp             CCBCCSCHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCHHHHHHHHHHT-
T ss_pred             ceeecCChhHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHc-
Confidence            7999999999999999999999999999999999999999999988876677778999999999998888887766431 


Q ss_pred             chhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhh--cCeeEEEEeccccccCCCCCC--C-CCChHHHHHHHH
Q 035774          162 PEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHEQ--R-APGQHPLSWHIS  236 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~--~~~~lvvIDsl~~l~~~~~~~--~-~~r~~~~~~i~~  236 (357)
                          ...  ...+++++++.++.+.+++.+++..+...+.+  .++++|||||++.+++....+  . ..|+..+.++++
T Consensus       181 ----g~~--~~~~l~~l~~~~~~~~e~~~~ll~~l~~~i~~~~~~~~lvVIDsl~~l~~~~~~~~g~~~~r~~~l~~~l~  254 (343)
T 1v5w_A          181 ----NVD--HDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLS  254 (343)
T ss_dssp             ----TCC--HHHHHHTEEEEECCSTTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGGHHHHCCGGGCHHHHHHHHHHHHH
T ss_pred             ----CCC--HHHHHhceeEeecCCHHHHHHHHHHHHHHHHhcCCCccEEEEechHHHHHHHhcccccHHHHHHHHHHHHH
Confidence                111  23456788888888888888888888888877  789999999999998654321  1 123456889999


Q ss_pred             HHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEE
Q 035774          237 LITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMN  315 (357)
Q Consensus       237 ~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~  315 (357)
                      .|+++++++|++||++||+++..+.. .+|.                .+..+|++|..|.+.+++|+.|++. +..|.++
T Consensus       255 ~L~~la~~~~~~Vi~~nq~~~~~~~~-~~~~----------------g~~~~~~gg~~i~~~ad~~l~l~r~~~~~r~~~  317 (343)
T 1v5w_A          255 RLQKISEEYNVAVFVTNQMTADPGAT-MTFQ----------------ADPKKPIGGHILAHASTTRISLRKGRGELRIAK  317 (343)
T ss_dssp             HHHHHHHHHTCEEEEEECC------------------------------------CCTTTTSSSEEEEEEESSTTEEEEE
T ss_pred             HHHHHHHHhCCEEEEEeeceecCCCc-cccC----------------CCCCcCCchHHHHHhCCEEEEEEEcCCCEEEEE
Confidence            99999999999999999998764410 0110                1245788999999999999999986 4579999


Q ss_pred             EEeCCCCCCceeEEEEcCCCceecc
Q 035774          316 VEKSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       316 v~K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      |+|+|+.|.+.+.|.|+++||.+..
T Consensus       318 v~K~r~~p~~~~~f~I~~~Gi~~~~  342 (343)
T 1v5w_A          318 IYDSPEMPENEATFAITAGGIGDAK  342 (343)
T ss_dssp             EEECTTCCSSCEEEEEETTEEEECC
T ss_pred             EEECCCCCCeeEEEEEeCCCccCCC
Confidence            9999999988899999999999865

>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=100.00  E-value=1.8e-44  Score=332.61  Aligned_cols=303  Identities=24%  Similarity=0.306  Sum_probs=250.3

Q ss_pred             ccccccC-CCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCC
Q 035774            4 KLISEMR-LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGG   82 (357)
Q Consensus         4 ~~~~~~~-l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (357)
                      +++..|+ +++++.++|+++|++|+++++..++.+|.++.+++++++.+++.++.+.+..++.++.++++++..    ..
T Consensus         3 ~~~~~l~gi~~~~~~kL~~~gi~t~~~~~~~~~~~L~~~~gis~~~a~~~i~~a~~~~~~~~~~~~~~~~~~~~----~~   78 (322)
T 2i1q_A            3 DNLTDLPGVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDLGFKSGIDLLKQRST----VW   78 (322)
T ss_dssp             --CTTSTTCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHHHHTTCSCCCTHHHHHHHTT----CC
T ss_pred             ccHhhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCcCHHHHHHHHHHHHHhhhhcCCcHHHHHHHhcc----CC
Confidence            4566675 999999999999999999999999999999999999999999999888888899999999875432    67


Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcccc---------CCCCCC-CeEEEEeCCCCCchHH
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPA---------HYGGLD-GGVIYIDVESTFTSRR  152 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~---------~~gg~~-~~vl~i~~e~~~~~~r  152 (357)
                      +++||++.||.+|+||+++|++++|+|+||+|||+||++++.+++++.         ..||.+ ++|+||++|+++++.+
T Consensus        79 ~i~TG~~~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~  158 (322)
T 2i1q_A           79 KLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPER  158 (322)
T ss_dssp             EECCSCHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHH
T ss_pred             eecCCChhHHHhcCCCccCCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCHHH
Confidence            899999999999999999999999999999999999999999876643         334443 7999999999988888


Q ss_pred             HHHHHhccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhh-cCeeEEEEeccccccCCCCCCC---CCCh
Q 035774          153 MIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPGVHEQR---APGQ  228 (357)
Q Consensus       153 l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~~~~~~---~~r~  228 (357)
                      +.+++...     ...  .+.+.+++++.++.+.+++.+++..+...+.+ .++++|||||++.++.....+.   ..|+
T Consensus       159 l~~~~~~~-----g~~--~~~~~~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~~~~~~~~~~~~r~  231 (322)
T 2i1q_A          159 IMQMAEHA-----GID--GQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQ  231 (322)
T ss_dssp             HHHHHHHH-----TCC--HHHHHHTEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSSHHHHHHCCCTTSHHHHH
T ss_pred             HHHHHHHc-----CCC--HHHHhcCEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcHHHHHHHhcCCccHHHHH
Confidence            87765431     111  23345788888888888888888888888877 7899999999999986533221   1234


Q ss_pred             HHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe
Q 035774          229 HPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK  308 (357)
Q Consensus       229 ~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~  308 (357)
                      ..+.++++.|++++++++++||++||+++..+.   +|                 ....+|++|..|.+.+++|+.|++.
T Consensus       232 ~~~~~~~~~L~~la~~~~~~vi~~nq~~~~~~~---~~-----------------g~~~~~~g~~~~~~~~d~~i~l~~~  291 (322)
T 2i1q_A          232 QKLGRHMATLNKLADLFNCVVLVTNQVSAKPDA---FF-----------------GMAEQAIGGHIVGHAATFRFFVRKG  291 (322)
T ss_dssp             HHHHHHHHHHHHHHHHTTCEEEEEECEECC---------------------------CCEESSHHHHHHHCSEEEEEEEC
T ss_pred             HHHHHHHHHHHHHHHHhCCEEEEECceeecCCC---CC-----------------CCCcCCCCcHHHHhcCcEEEEEEec
Confidence            568899999999999999999999999875431   11                 1234688999999999999999987


Q ss_pred             C-CeEEEEEEeCCCCCCceeEEEEcCCCce
Q 035774          309 S-GQRFMNVEKSPTSPPLAFSFTINPSGIS  337 (357)
Q Consensus       309 ~-~~R~l~v~K~r~~~~~~~~f~I~~~Gi~  337 (357)
                      . ..|.++|.|+|+.|.+.+.|.|+++||+
T Consensus       292 ~~~~r~~~v~k~~~~p~~~~~f~I~~~Gi~  321 (322)
T 2i1q_A          292 KGDKRVAKLYDSPHLPDAEAIFRITEKGIQ  321 (322)
T ss_dssp             STTEEEEEEEECSSSCCEEEEEEEETTEEE
T ss_pred             CCCeEEEEEEECCCCCCeEEEEEEeCCCcC
Confidence            4 5899999999999988899999999986

>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=100.00  E-value=3.2e-45  Score=337.37  Aligned_cols=306  Identities=25%  Similarity=0.379  Sum_probs=188.0

Q ss_pred             ccccccC-CCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCC
Q 035774            4 KLISEMR-LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGG   82 (357)
Q Consensus         4 ~~~~~~~-l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (357)
                      .+++.|+ ++++++++|+++|+.|+++++..++.+|.++.+++++++.++++++...+..++.++.++++++..    ..
T Consensus        12 ~~~~~l~g~~~~~~~~l~~~g~~t~~~~~~~~~~~l~~~~g~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~   87 (324)
T 2z43_A           12 KTINDLPGISQTVINKLIEAGYSSLETLAVASPQDLSVAAGIPLSTAQKIIKEARDALDIRFKTALEVKKERMN----VK   87 (324)
T ss_dssp             ------------------------------------------------------------CCCCHHHHHHHHCS----CC
T ss_pred             ccHHHcCCCCHHHHHHHHHcCCCcHHHHHcCCHHHHHHhhCCCHHHHHHHHHHHHhhcccCccchhhhhhhhcc----CC
Confidence            4678887 999999999999999999999999999999999999999999998888778889999998865322    67


Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFP  162 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~  162 (357)
                      +++||++.||.+|+||+++|++++|+|+||+|||+||++++.+++.+..+||.+++|+||++|++++..++.+++...  
T Consensus        88 ~i~TG~~~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~~~l~~~~~~~--  165 (324)
T 2z43_A           88 KISTGSQALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRWERIENMAKAL--  165 (324)
T ss_dssp             EECCSCHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHT--
T ss_pred             cccCCchhHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCHHHHHHHHHHh--
Confidence            899999999999999999999999999999999999999999988776677778999999999998888887766431  


Q ss_pred             hhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhh-cCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHH
Q 035774          163 EIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLI  238 (357)
Q Consensus       163 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~L  238 (357)
                         ...  ...+.+++++.++.+.+++.+++..+...+.+ .++++|||||++.++.....+.   ..|+..+.++++.|
T Consensus       166 ---g~~--~~~~~~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~~~~~~~g~~~~r~~~~~~~l~~L  240 (324)
T 2z43_A          166 ---GLD--IDNVMNNIYYIRAINTDHQIAIVDDLQELVSKDPSIKLIVVDSVTSHFRAEYPGRENLAVRQQKLNKHLHQL  240 (324)
T ss_dssp             ---TCC--HHHHHHTEEEEECCSHHHHHHHHHHHHHHHHHCTTEEEEEETTTTHHHHHHSCTTTSHHHHHHHHHHHHHHH
T ss_pred             ---CCC--HHHHhccEEEEeCCCHHHHHHHHHHHHHHHHhccCCCEEEEeCcHHHhhhhhcCcccHHHHHHHHHHHHHHH
Confidence               111  23345788888888888887888888888877 7899999999999986533211   12345688999999


Q ss_pred             HHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-CeEEEEEE
Q 035774          239 TSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-GQRFMNVE  317 (357)
Q Consensus       239 k~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-~~R~l~v~  317 (357)
                      +++++++|++||++||+++..+.   +|                 ....+|++|..|.+.+++|+.+++.. ..|.++|.
T Consensus       241 ~~la~~~~~~Vi~~nq~~~~~~~---~~-----------------~~~~~~~gg~~l~~~~d~~l~l~r~~~~~r~~~v~  300 (324)
T 2z43_A          241 TRLAEVYDIAVIITNQVMARPDM---FY-----------------GDPTVAVGGHTLYHVPGIRIQLKKSRGNRRIARVV  300 (324)
T ss_dssp             HHHHHHHTCEEEEEEEC--------------------------------------------CEEEEEEECSTTEEEEEEE
T ss_pred             HHHHHHhCCEEEEEcceeecCCC---cC-----------------CCCCCCCchHHHHhhCcEEEEEEEcCCCeEEEEEE
Confidence            99999999999999999875431   11                 12346888999999999999999874 58999999


Q ss_pred             eCCCCCCceeEEEEcCCCceecc
Q 035774          318 KSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       318 K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      |+|+.|.+.+.|.|+++||+++.
T Consensus       301 k~~~~p~~~~~f~I~~~Gi~~~~  323 (324)
T 2z43_A          301 DAPHLPEGEVVFALTEEGIRDAE  323 (324)
T ss_dssp             ECSSSCCEEEEEEEETTEEECCC
T ss_pred             ECCCCCceEEEEEEeCCCcccCC
Confidence            99999988899999999998764

>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=100.00  E-value=3e-43  Score=330.23  Aligned_cols=309  Identities=24%  Similarity=0.295  Sum_probs=247.5

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCC
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLP   85 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   85 (357)
                      +...|+++..+++|+++|++|+++++..++.+|.+++++++.++.++++++.+.++.++.+|.++++.+..    ..+++
T Consensus        86 l~~~gi~~~~~~~L~~ag~~tv~~~~~~~~~~L~~~~gis~~~~~~i~~~a~~~~~~~~~ta~~l~~~~~~----~~~i~  161 (400)
T 3lda_A           86 LQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARLVPMGFVTAADFHMRRSE----LICLT  161 (400)
T ss_dssp             GCCTTCCHHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHHHSCCSCCCHHHHHHHHHT----SCEEC
T ss_pred             HHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHhccccCCCHHHHHhhhcc----CCccc
Confidence            34467999999999999999999999999999999999999999999999999888899999999887544    67999


Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhh
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIF  165 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~  165 (357)
                      ||++.||++|+||+++|++++|+|+||+|||||+++++.+++.+...||.+++++||++|+.++..++.++....     
T Consensus       162 TG~~~LD~lLgGGI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~~~rl~~~a~~~-----  236 (400)
T 3lda_A          162 TGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRPVRLVSIAQRF-----  236 (400)
T ss_dssp             CSCHHHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHHHHHT-----
T ss_pred             cCChhHHHHhcCCcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccCHHHHHHHHHHc-----
Confidence            999999999999999999999999999999999999999998887777778999999999988888887765431     


Q ss_pred             cccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHHHHHHH
Q 035774          166 HSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISLITSLA  242 (357)
Q Consensus       166 ~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~Lk~la  242 (357)
                      ...  ...+++++++....+..+....+..+...+...++++||||+++.+++....+.   ..|+..+.++++.|++++
T Consensus       237 gl~--~~~vleni~~~~~~~~~~~~~~l~~~~~~l~~~~~~llVIDs~t~~~~~~~sg~g~l~~Rq~~l~~il~~L~~la  314 (400)
T 3lda_A          237 GLD--PDDALNNVAYARAYNADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFSGRGELSARQMHLAKFMRALQRLA  314 (400)
T ss_dssp             TCC--HHHHHHTEEEEECCSHHHHHHHHHHHHHHHHHSCEEEEEEETGGGGCC------CCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCC--hHhHhhcEEEeccCChHHHHHHHHHHHHHHHhcCCceEEecchhhhCchhhcCccchHHHHHHHHHHHHHHHHHH
Confidence            111  234567888888888777777777777777778999999999999987654421   124556788999999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCeEEEEEEeCCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQRFMNVEKSPT  321 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~R~l~v~K~r~  321 (357)
                      +++|++||+++|+....+.. .+|.                ....+|++|..|+|.+++|++|++. +..|.++|.|+|+
T Consensus       315 ke~gitVIlv~Hv~~~~~g~-~~~~----------------g~~~~p~gg~~l~~~ad~vl~L~~~~g~~R~l~v~K~R~  377 (400)
T 3lda_A          315 DQFGVAVVVTNQVVAQVDGG-MAFN----------------PDPKKPIGGNIMAYSSTTRLGFKKGKGCQRLCKVVDSPC  377 (400)
T ss_dssp             HHHCCEEEEEEEC-------------------------------------CHHHHHCSEEEEEEECSTTEEEEEEEECSS
T ss_pred             HHcCCEEEEEEeecccCCcc-cccc----------------CCCccCCchhHHHHhcceEEEEEecCCCcEEEEEEcCCC
Confidence            99999999999996644311 0110                0123588899999999999999986 4689999999999


Q ss_pred             CCCceeEEEEcCCCceeccCC
Q 035774          322 SPPLAFSFTINPSGISLLTDD  342 (357)
Q Consensus       322 ~~~~~~~f~I~~~Gi~~~~~~  342 (357)
                      .|+..+.|.|+++||...++.
T Consensus       378 ~p~~e~~F~It~~Gi~~~~~~  398 (400)
T 3lda_A          378 LPEAECVFAIYEDGVGDPREE  398 (400)
T ss_dssp             SCSCEEEEEEETTEEECCC--
T ss_pred             CCCCceEEEEeCCcccccccc
Confidence            998889999999999987653

>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=100.00  E-value=1.2e-40  Score=309.05  Aligned_cols=303  Identities=25%  Similarity=0.375  Sum_probs=243.2

Q ss_pred             ccccccC-CCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCC-CcccHHHHHHHHHhcccCC
Q 035774            4 KLISEMR-LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCP-PFQTALLLMEQRAATEHLG   81 (357)
Q Consensus         4 ~~~~~~~-l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   81 (357)
                      ++++.|+ ++++++++|+++|+.|+++++..++.+|.++.++++.++.++++++.+.+.. .+.++.++++++..    .
T Consensus        35 ~~l~~l~Gi~~~~~~kL~~ag~~t~~~~~~~~~~~L~~~~~~s~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~----~  110 (349)
T 1pzn_A           35 RSIEDLPGVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKAANLGTFMRADEYLKKRAT----I  110 (349)
T ss_dssp             CCSSCCTTCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHHCSTTSCEEHHHHHHHHHT----C
T ss_pred             ccHHHcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHhhcCCCHHHHHHHHHHHhhhccccCCccHHHHHhhhcc----C
Confidence            4677774 9999999999999999999999999999999999999999999998888877 89999999887543    6


Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccC
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSF  161 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~  161 (357)
                      .+++||++.||.+|+||+++|++++|+|+||+|||||+++++..++.++..||.+++|+||++++.+...++..+.+.. 
T Consensus       111 ~~isTG~~~LD~lL~ggi~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~~~~~~i~~i~q~~-  189 (349)
T 1pzn_A          111 GRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNR-  189 (349)
T ss_dssp             CEECCSCHHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHHHHHHHTT-
T ss_pred             CeecCCCHHHHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCCCCHHHHHHHHHHc-
Confidence            7899999999999999999999999999999999999999999887665666667889999999987777777766542 


Q ss_pred             chhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhh-----cCeeEEEEeccccccCCCCCCC---CCChHHHHH
Q 035774          162 PEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ-----NQVKLLVIDSMEALVPGVHEQR---APGQHPLSW  233 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~-----~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~  233 (357)
                          ...  ...+.+++.+....+.....+.+..+...+..     .++++||||++++++.....+.   ..|...+.+
T Consensus       190 ----~~~--~~~v~~ni~~~~~~~~~~~~~~l~~~~~~~~~lS~G~~~~~llIlDs~ta~ld~~~~~~~~~~~r~~~~~~  263 (349)
T 1pzn_A          190 ----GLD--PDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAK  263 (349)
T ss_dssp             ----TCC--HHHHGGGEEEEECCSHHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTTHHHHCCSTTTHHHHHHHHHH
T ss_pred             ----CCC--HHHHhhCEEEEecCChHHHHHHHHHHHHHHHHhccccCCCCEEEEeCchHhhhhhhcccccHHHHHHHHHH
Confidence                111  12556788887766666666667777777766     6899999999999986533221   113345788


Q ss_pred             HHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-CeE
Q 035774          234 HISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-GQR  312 (357)
Q Consensus       234 i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-~~R  312 (357)
                      +++.|+++++++|++||+++|.......   ++                 .....|++|..|+|.+++|+++++.. ..|
T Consensus       264 ~l~~L~~la~~~~~tvii~~h~~~~~~~---~~-----------------~~~~~~~~G~~l~~~~~~rL~l~~~~~~~R  323 (349)
T 1pzn_A          264 HLADLHRLANLYDIAVFVTNQVQARPDA---FF-----------------GDPTRPIGGHILAHSATLRVYLRKGKGGKR  323 (349)
T ss_dssp             HHHHHHHHHHHTTCEEEEEEECC-----------------------------------CCCCCTTCSEEEEEEECTTSEE
T ss_pred             HHHHHHHHHHHcCcEEEEEccccccccc---cc-----------------CCccccCCcceEeecCcEEEEEEEcCCCeE
Confidence            9999999999999999999998764320   10                 11346888999999999999999874 589


Q ss_pred             EEEEEeCCCCCCceeEEEEcCCCce
Q 035774          313 FMNVEKSPTSPPLAFSFTINPSGIS  337 (357)
Q Consensus       313 ~l~v~K~r~~~~~~~~f~I~~~Gi~  337 (357)
                      .+++.|+|+.|.+.+.|+|+++||+
T Consensus       324 i~k~~ks~~~~~~~~~f~It~~Gi~  348 (349)
T 1pzn_A          324 IARLIDAPHLPEGEAVFSITEKGIE  348 (349)
T ss_dssp             EEEESCSSSSCCSEEEEEEETTEEE
T ss_pred             EEEEEeCCCCCCeEEEEEEcCCCCC
Confidence            9999999999988899999999986

>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=100.00  E-value=1.3e-32  Score=242.99  Aligned_cols=236  Identities=28%  Similarity=0.382  Sum_probs=170.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||++.||++|+||+++|++++|+|+||+|||+|+.+++.+++.+...|+.+.+++||++++.++..++.++....
T Consensus         3 ~~~i~tG~~~LD~~l~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~~~~~~~~~~~~~   82 (243)
T 1n0w_A            3 IIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERY   82 (243)
T ss_dssp             CCEECCSCHHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             ceEecCCChHHHHhhcCCCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCcCHHHHHHHHHHc
Confidence            46899999999999999999999999999999999999999999877765555567899999999987777666554321


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC---CCChHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR---APGQHPLSWHISL  237 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~~i~~~  237 (357)
                           ..  ......+++.+..+.+..+....+..+...+..+++++||||+++.++.....+.   ..|+..+..++..
T Consensus        83 -----g~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lliiD~~~~~~~~~~~~~~~~~~r~~~~~~~~~~  155 (243)
T 1n0w_A           83 -----GL--SGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRM  155 (243)
T ss_dssp             -----TC--CHHHHHHTEEEEECCSHHHHHHHHHHHHHHHHHSCEEEEEEETSSGGGC-------CHHHHHHHHHHHHHH
T ss_pred             -----CC--CHHHHhhCeEEEecCCHHHHHHHHHHHHHHHhcCCceEEEEeCchHHHHHHhcCCccHHHHHHHHHHHHHH
Confidence                 11  1123456788877777777777777777777778999999999999886533221   1123347889999


Q ss_pred             HHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-CeEEEEE
Q 035774          238 ITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-GQRFMNV  316 (357)
Q Consensus       238 Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-~~R~l~v  316 (357)
                      |++++++++++||+++|..+..... ..|.                ....+|++|..|.+.++.++.+++.. ..|.++|
T Consensus       156 l~~~~~~~~~tvi~~~h~~~~~~~~-~~~~----------------~~~~~~~g~~~~~~~~d~vi~l~~~~~~~r~l~v  218 (243)
T 1n0w_A          156 LLRLADEFGVAVVITNQVVAQVDGA-AMFA----------------ADPKKPIGGNIIAHASTTRLYLRKGRGETRICKI  218 (243)
T ss_dssp             HHHHHHHHCCEEEEEC------------------------------------------CCTTCEEEEEEECSTTEEEEEE
T ss_pred             HHHHHHHcCCEEEEEeeeeecCCCc-cccC----------------CCcccCCccChhhhcCcEEEEEEEcCCCeEEEEE
Confidence            9999999999999999987754310 0000                12356888899999999999999854 5799999


Q ss_pred             EeCCCCCCceeEEEEcCCCceecc
Q 035774          317 EKSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       317 ~K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      .|+|+.+...+.|+|+++||+++.
T Consensus       219 ~K~r~~~~~~~~f~I~~~Gi~~~~  242 (243)
T 1n0w_A          219 YDSPCLPEAEAMFAINADGVGDAK  242 (243)
T ss_dssp             CCBTTBSCEEEEEEEETTEEECCC
T ss_pred             EECCCCCCCeEEEEEeCCccccCC
Confidence            999999987799999999999865

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=100.00  E-value=1.4e-32  Score=243.77  Aligned_cols=222  Identities=18%  Similarity=0.236  Sum_probs=153.7

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      +.++||||++.||++|+||+++|++++|+|+||+|||+||+|++.+++..     .+.+|+|+++|++  ..++.+.+..
T Consensus         8 ~i~ri~TGi~~LD~~l~GGl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~-----~~~~v~~~s~E~~--~~~~~~~~~~   80 (251)
T 2zts_A            8 PVRRVKSGIPGFDELIEGGFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEE-----YGEPGVFVTLEER--ARDLRREMAS   80 (251)
T ss_dssp             CCCEECCSCTTTGGGTTTSEETTCEEEEECCTTSSHHHHHHHHHHHHHHH-----HCCCEEEEESSSC--HHHHHHHHHT
T ss_pred             CCCeecCCcHHHHHhhcCCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHh-----cCCCceeecccCC--HHHHHHHHHH
Confidence            37799999999999999999999999999999999999999999987652     1478999999985  3344332222


Q ss_pred             -cCchhhcccchHHHhhcCeEEe---------------CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC
Q 035774          160 -SFPEIFHSKGMAQEMAGRILVL---------------QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       160 -~~~~~~~~~~~~~~~~~~i~~~---------------~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~  223 (357)
                       .+..    ...  ...+++.+.               ..........++..+...+..++++++|||+++.+....   
T Consensus        81 ~~~~~----~~~--~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vviD~~~~l~~~~---  151 (251)
T 2zts_A           81 FGWDF----EKY--EKEGKIAIVDGVSSVVGLPSEEKFVLEDRFNVDNFLRYIYRVVKAINAKRLVIDSIPSIALRL---  151 (251)
T ss_dssp             TTCCH----HHH--HHTTSEEEEC-------------------CCHHHHHHHHHHHHHHTTCSEEEEECHHHHHHHS---
T ss_pred             cCCCh----HHH--HhcCcchhhhhHHHHhhcccchhccccccccHHHHHHHHHHHHHhcCCcEEEEEcHHHHhhhc---
Confidence             1110    000  001111111               111122334556667777778899999999999886542   


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                        .+.+.+.+++..|+.+|+++||++++++|+.......                        +..  ...+.+.+|.++
T Consensus       152 --~~~~~~~~~~~~L~~~a~~~~i~vi~~~q~~~~~~~~------------------------~~~--~~~~~~~aD~vi  203 (251)
T 2zts_A          152 --EEERKIREVLLKLNTILLEMGVTTILTTEAPDPQHGK------------------------LSR--YGIEEFIARGVI  203 (251)
T ss_dssp             --SSGGGHHHHHHHHHHHHHHHCCEEEEEECCC----CC------------------------SSS--SSCGGGGCSEEE
T ss_pred             --cChHHHHHHHHHHHHHHHHcCCCeEEEEEEecccccc------------------------ccc--CCceeEEeeEEE
Confidence              2446678899999999999999999999986543210                        000  011567778888


Q ss_pred             EEEEeC----CeEEEEEEeCCCCC--CceeEEEEcCCCceeccCCCce
Q 035774          304 VLEAKS----GQRFMNVEKSPTSP--PLAFSFTINPSGISLLTDDGTE  345 (357)
Q Consensus       304 ~l~~~~----~~R~l~v~K~r~~~--~~~~~f~I~~~Gi~~~~~~~~~  345 (357)
                      .|++..    ..|.++|.|+|+++  ...++|+|+++||+++|+.++|
T Consensus       204 ~l~~~~~~~~~~R~l~I~K~R~~~~~~~~~~f~It~~Gi~v~p~~~if  251 (251)
T 2zts_A          204 VLDLQEKNIELKRYVLIRKMRETRHSMKKYPFEIGPNGIVVYPSGEIY  251 (251)
T ss_dssp             EEEEEECSSSEEEEEEEEEETTCCCCCBEEEEEEETTEEEECC-----
T ss_pred             EEEEEecCCeEEEEEEEEEcCCCCCCCEEEEEEEeCCcEEEeCccccC
Confidence            887642    36899999999988  4678999999999999988775

>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=99.98  E-value=1.9e-30  Score=225.54  Aligned_cols=216  Identities=26%  Similarity=0.360  Sum_probs=171.6

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFP  162 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~  162 (357)
                      +++||++.||.+++||+++|++++|+|+||+|||+|+.+++.  ..       +.+|+|+++++.++..++.++..... 
T Consensus         1 ri~tG~~~LD~~l~Ggi~~G~~~~i~G~~GsGKTtl~~~l~~--~~-------~~~v~~i~~~~~~~~~~~~~~~~~~~-   70 (220)
T 2cvh_A            1 MLSTGTKSLDSLLGGGFAPGVLTQVYGPYASGKTTLALQTGL--LS-------GKKVAYVDTEGGFSPERLVQMAETRG-   70 (220)
T ss_dssp             CBCCSCHHHHHHTTSSBCTTSEEEEECSTTSSHHHHHHHHHH--HH-------CSEEEEEESSCCCCHHHHHHHHHTTT-
T ss_pred             CcccCcHHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHH--Hc-------CCcEEEEECCCCCCHHHHHHHHHhcC-
Confidence            489999999999999999999999999999999999999998  21       47999999998777777776554311 


Q ss_pred             hhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHH
Q 035774          163 EIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLA  242 (357)
Q Consensus       163 ~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la  242 (357)
                          ..  .+...+++.+.++.+..+....+..++..+.. ++++||||+++.+...... ...+...+.++++.|++++
T Consensus        71 ----~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~lliiD~~~~~l~~~~~-~~~~~~~~~~~~~~L~~l~  142 (220)
T 2cvh_A           71 ----LN--PEEALSRFILFTPSDFKEQRRVIGSLKKTVDS-NFALVVVDSITAHYRAEEN-RSGLIAELSRQLQVLLWIA  142 (220)
T ss_dssp             ----CC--HHHHHHHEEEECCTTTSHHHHHHHHHHHHCCT-TEEEEEEECCCCCTTGGGG-SSTTHHHHHHHHHHHHHHH
T ss_pred             ----CC--hHHHhhcEEEEecCCHHHHHHHHHHHHHHhhc-CCCEEEEcCcHHHhhhcCc-hHHHHHHHHHHHHHHHHHH
Confidence                10  12344567777777666666667766666655 7999999999998754221 1235577888999999999


Q ss_pred             HHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe--CCeEEEEEEeCC
Q 035774          243 EFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK--SGQRFMNVEKSP  320 (357)
Q Consensus       243 ~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~--~~~R~l~v~K~r  320 (357)
                      ++++++||+++|.......                       ....|+++..|.+.+|.++.+++.  +..|.+.|.|+|
T Consensus       143 ~~~~~~vi~~~h~~~~~~~-----------------------~~~~p~~~~~~~~~~d~vi~l~~~~~~~~r~l~v~K~r  199 (220)
T 2cvh_A          143 RKHNIPVIVINQVHFDSRT-----------------------EMTKPVAEQTLGYRCKDILRLDKLPKPGLRVAVLERHR  199 (220)
T ss_dssp             HHHTCCEEEEECSSSSCTT-----------------------SSCCSCCCHHHHHTSSEEEEEEECSSTTEEEEEEEECS
T ss_pred             HHcCCEEEEEeeEEEcCCC-----------------------CccccCCCcceeecCcEEEEEEEecCCCEEEEEEEeCC
Confidence            9999999999998764331                       124577888899999999999987  568999999999


Q ss_pred             CCCCce-eEEEEcCCCceec
Q 035774          321 TSPPLA-FSFTINPSGISLL  339 (357)
Q Consensus       321 ~~~~~~-~~f~I~~~Gi~~~  339 (357)
                      +.+++. +.|+|+++||++.
T Consensus       200 ~~~~~~~~~f~I~~~Gi~~~  219 (220)
T 2cvh_A          200 FRPEGLMAYFRITERGIEDV  219 (220)
T ss_dssp             SSCTTCEEEEEEETTEEEEC
T ss_pred             CCCCCceEEEEEeCCceecC
Confidence            998654 8999999999874

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=99.97  E-value=1.3e-29  Score=232.15  Aligned_cols=231  Identities=17%  Similarity=0.147  Sum_probs=162.1

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch--HHHHHHH
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS--RRMIEMG  157 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~--~rl~~~~  157 (357)
                      ...+++||++.||.++ ||+++|++++|+|+||+|||+|+++++.+++.+      +.+|+||++|++...  .|+....
T Consensus        47 ~~~~i~TG~~~LD~~l-gGl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~------g~~vl~~slE~s~~~l~~R~~~~~  119 (315)
T 3bh0_A           47 NITGVPSGFTELDRMT-YGYKRRNFVLIAARPSMGKTAFALKQAKNMSDN------DDVVNLHSLEMGKKENIKRLIVTA  119 (315)
T ss_dssp             SCCSBCCSCHHHHHHH-SSBCTTCEEEEECCTTSSHHHHHHHHHHHHHTT------TCEEEEEESSSCHHHHHHHHHHHH
T ss_pred             CCCCccCChHHHHhhc-CCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc------CCeEEEEECCCCHHHHHHHHHHHH
Confidence            3679999999999999 789999999999999999999999999998863      379999999986432  2222211


Q ss_pred             hccCc--hh------hcccch------HHHh-hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCee--EEEEeccccccCCC
Q 035774          158 ASSFP--EI------FHSKGM------AQEM-AGRILVLQPTSLSEFTESLEKIKVSLLQNQVK--LLVIDSMEALVPGV  220 (357)
Q Consensus       158 ~~~~~--~~------~~~~~~------~~~~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~--lvvIDsl~~l~~~~  220 (357)
                      . .++  ..      .....+      ...+ ..++++.+... .++.++...++....+++++  +||||||+.+....
T Consensus       120 ~-~i~~~~l~~~~~~l~~~~~~~l~~a~~~l~~~~i~i~d~~~-~~~~~i~~~i~~l~~~~~~~~~lVVID~l~~l~~~~  197 (315)
T 3bh0_A          120 G-SINAQKIKAARRDFASEDWGKLSMAIGEISNSNINIFDKAG-QSVNYIWSKTRQTKRKNPGKRVIVMIDYLQLLEPAK  197 (315)
T ss_dssp             T-TCCHHHHHSCHHHHCSSCHHHHHHHHHHHHTSCEEEECCSC-CBHHHHHHHHHHHHHTSSSCCEEEEEECGGGSBCSC
T ss_pred             c-CCCHHHHhcCCCCCCHHHHHHHHHHHHHHhCCCEEEECCCC-CCHHHHHHHHHHHHHhcCCCCeEEEEeCchhcCCCC
Confidence            1 111  00      000000      0111 13556655432 23455556666666677889  99999999987532


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhcc
Q 035774          221 HEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVT  300 (357)
Q Consensus       221 ~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~  300 (357)
                        ....|.+.+.++++.|+.+|+++||+|++++|+++.....               .+..+..++++.+.  .+++.+|
T Consensus       198 --~~~~r~~~i~~~~~~Lk~lAk~~~i~vi~lsql~r~~e~r---------------~~~~p~l~dlr~sg--~ie~~aD  258 (315)
T 3bh0_A          198 --ANDSRTNQISQISRDLKKMARELDVVVIALSQLSRQVEQR---------------QDKRPMLSDLRESG--QLEQDAD  258 (315)
T ss_dssp             --TTSCHHHHHHHHHHHHHHHHHHHTCEEEEEECCCGGGTTS---------------SSCCCCGGGGTTTS--HHHHHCS
T ss_pred             --CCCCHHHHHHHHHHHHHHHHHHhCCeEEEEeecCcccccC---------------CCCCCCHHHhhhhh--hhHhhCC
Confidence              2234668899999999999999999999999998754411               11223334444432  4899999


Q ss_pred             EEEEEEEe---------CCeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          301 IRLVLEAK---------SGQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       301 ~rl~l~~~---------~~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      ++++|+++         .+.+.+.|.|+|+++.+.+.+.+..+--.+
T Consensus       259 ~vi~L~r~~~~~~~~~~~~~~~l~v~K~R~G~~g~~~l~f~~~~~~f  305 (315)
T 3bh0_A          259 IIEFLYRDDYYDKESESKNIVEVIIAKHRDGPVGTVSLAFIKEYGNF  305 (315)
T ss_dssp             EEEEEEEHHHHCTTCTTTTEEEEEEEEETTSCCEEEEEEEEGGGTEE
T ss_pred             EEEEEecccccCccccCCCcEEEEEECCcCCCCceEEEEEECCCCeE
Confidence            99999985         247899999999999887766666543333

>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=99.97  E-value=5.6e-30  Score=235.93  Aligned_cols=216  Identities=24%  Similarity=0.283  Sum_probs=168.3

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+++||++.||.+|+ ||+++|++++|+||||+||||||++++..++..      +++|+||++|+.+...+..++...
T Consensus        39 ~~~i~TG~~~LD~~Lg~GGi~~G~i~~I~GppGsGKSTLal~la~~~~~~------gg~VlyId~E~s~~~~ra~rlgv~  112 (356)
T 3hr8_A           39 VEVIPTGSLAIDIATGVGGYPRGRIVEIFGQESSGKTTLALHAIAEAQKM------GGVAAFIDAEHALDPVYAKNLGVD  112 (356)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTEEEEEEESTTSSHHHHHHHHHHHHHHT------TCCEEEEESSCCCCHHHHHHHTCC
T ss_pred             CceecCCCHHHHHHhccCCccCCcEEEEECCCCCCHHHHHHHHHHHHHhc------CCeEEEEecccccchHHHHHcCCc
Confidence            5689999999999999 999999999999999999999999999988742      478999999998887765554311


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCC-CC-----hHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRA-PG-----QHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~-~r-----~~~~~  232 (357)
                                     .+++.+..+.+.+++...+   ...+...++++|||||++.+++ ...++.. .+     ...+.
T Consensus       113 ---------------~~~l~i~~~~~~e~~l~~~---~~l~~~~~~dlvVIDSi~~l~~~~el~g~~G~~q~~~qar~la  174 (356)
T 3hr8_A          113 ---------------LKSLLISQPDHGEQALEIV---DELVRSGVVDLIVVDSVAALVPRAEIEGAMGDMQVGLQARLMS  174 (356)
T ss_dssp             ---------------GGGCEEECCSSHHHHHHHH---HHHHHTSCCSEEEEECTTTCCCHHHHTTCCCSSCSSHHHHHHH
T ss_pred             ---------------hhhhhhhhccCHHHHHHHH---HHHhhhcCCCeEEehHhhhhcChhhhcccchhhHHHHHHHHHH
Confidence                           2456777777766655444   4445557899999999999986 3333221 12     24567


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe----
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK----  308 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~----  308 (357)
                      .+++.|+.++++++++||++||++...+   .+|.                 ....|++|..|+|.+++|+.|++.    
T Consensus       175 ~~L~~L~~lak~~~~tVI~inqv~~k~g---~~fg-----------------~p~~~~GG~~l~h~~~~rl~l~k~~~~k  234 (356)
T 3hr8_A          175 QALRKIAGSVNKSKAVVIFTNQIRMKIG---VMFG-----------------SPETTTGGLALKFYATMRMEVRRGEPIK  234 (356)
T ss_dssp             HHHHHHHHHHHTSSCEEEEEEESSSCSS---SSSC-----------------SCSSCTHHHHHHHHCSEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHhcCCEEEEEeeeeeccc---cccC-----------------CcccCCCcchhhhhCcEEEEEEeccccc
Confidence            7888999999999999999999976544   2221                 122578899999999999999973    


Q ss_pred             ------CCeEEEEEEeCCCCCC-ceeEEEE-cCCCceecc
Q 035774          309 ------SGQRFMNVEKSPTSPP-LAFSFTI-NPSGISLLT  340 (357)
Q Consensus       309 ------~~~R~l~v~K~r~~~~-~~~~f~I-~~~Gi~~~~  340 (357)
                            +..|.++++|||..|+ ....|+| .++||....
T Consensus       235 ~g~~~~g~~~~vkvvKnr~~~~~~~~~f~i~~~~Gi~~~~  274 (356)
T 3hr8_A          235 EGKDVIGNVISVKIVKNKVAPPFKTAQTYIIYGKGIDREY  274 (356)
T ss_dssp             ETTEEEEEEEEEEEEEESSSCCCCEEEEEEETTTBSCHHH
T ss_pred             cCCcccccEEEEEEEeCCCCCCCceEEEEEeeCCCcChhc
Confidence                  2368999999999985 5689999 699987664

>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=99.97  E-value=5.5e-30  Score=228.81  Aligned_cols=216  Identities=20%  Similarity=0.249  Sum_probs=153.4

Q ss_pred             CCCCCCCchhHHhhhc----CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHH
Q 035774           81 GGHLPTRLKGLDAALC----GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEM  156 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~----GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~  156 (357)
                      ..+++||+++||.+|+    ||+++| +++|+|+||+|||+||+|++++++..    +.++.|+|||+|+++++.|..++
T Consensus         4 ~~risTGi~~LD~~LGg~~~GGl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~----g~g~~vlyId~E~s~~~~ra~~l   78 (333)
T 3io5_A            4 MDVVRTKIPMMNIALSGEITGGMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQ----YPDAVCLFYDSEFGITPAYLRSM   78 (333)
T ss_dssp             --CBCCSCHHHHHHHHSSTTCCBCSE-EEEEEESSSSSHHHHHHHHHHHHHHH----CTTCEEEEEESSCCCCHHHHHHT
T ss_pred             CCEecCCCHHHHHHhCCCCCCCCcCC-eEEEECCCCCCHHHHHHHHHHHHHhc----CCCceEEEEeccchhhHHHHHHh
Confidence            5689999999999999    999999 99999999999999999999998742    22589999999999988775554


Q ss_pred             HhccCchhhcccchHHHhhcCeEEeCCCCHHHH-HHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCC--------C
Q 035774          157 GASSFPEIFHSKGMAQEMAGRILVLQPTSLSEF-TESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRA--------P  226 (357)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~--------~  226 (357)
                      ...               .+++++..+.+.+++ .++++.+.. +.+..+++|||||++++++ .+.++..        .
T Consensus        79 Gvd---------------~d~llv~~~~~~E~~~l~i~~~l~~-i~~~~~~lvVIDSI~aL~~~~eieg~~gd~~~gsv~  142 (333)
T 3io5_A           79 GVD---------------PERVIHTPVQSLEQLRIDMVNQLDA-IERGEKVVVFIDSLGNLASKKETEDALNEKVVSDMT  142 (333)
T ss_dssp             TCC---------------GGGEEEEECSBHHHHHHHHHHHHHT-CCTTCCEEEEEECSTTCBCC--------------CT
T ss_pred             CCC---------------HHHeEEEcCCCHHHHHHHHHHHHHH-hhccCceEEEEecccccccchhccCccccccccHHH
Confidence            321               246778888887776 555544322 5667899999999999985 3333221        2


Q ss_pred             ChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEE
Q 035774          227 GQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE  306 (357)
Q Consensus       227 r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~  306 (357)
                      +.+.+...++.|..+|+++|++||+|||+++ .+   .+|.   +               ..+.+|..+ +...+|+.+.
T Consensus       143 qaR~~s~~LrkL~~~ak~~~i~vi~tNQV~k-~G---~~fg---~---------------p~~~GG~~l-~~ss~Rl~lr  199 (333)
T 3io5_A          143 RAKTMKSLFRIVTPYFSTKNIPCIAINHTYE-TQ---EMFS---K---------------TVMGGGTGP-MYSADTVFII  199 (333)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCEEEEEEEC-------------------------------------CCG-GGGSSEEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHhCCEEEEECCeee-cC---cccC---C---------------CCCCCccee-eeeeEEEEEE
Confidence            3345667777888899999999999999977 43   3332   1               123466778 8899999998


Q ss_pred             EeC----------CeEEEEEEeCCCCCC-ceeEEEEc-CCCceecc
Q 035774          307 AKS----------GQRFMNVEKSPTSPP-LAFSFTIN-PSGISLLT  340 (357)
Q Consensus       307 ~~~----------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi~~~~  340 (357)
                      +.+          ....+.++|++..++ ...+|.|. ++||.-..
T Consensus       200 k~~~ik~~~~~~G~~~~v~~~k~kv~k~k~~~~~~i~~~~Gi~~~~  245 (333)
T 3io5_A          200 GKRQIKDGSDLQGYQFVLNVEKSRTVKEKSKFFIDVKFDGGIDPYS  245 (333)
T ss_dssp             EEC----------CEEEEEEEECSSBCTTCEEEEEBCTTSCBCTTT
T ss_pred             eccccccCCccEEeEEEEeEEEEEEccCCcCCcEEEEecCCCChHH
Confidence            642          356788999998874 45678875 78886543

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=99.97  E-value=5.6e-30  Score=244.30  Aligned_cols=234  Identities=16%  Similarity=0.104  Sum_probs=166.3

Q ss_pred             CCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh-
Q 035774           80 LGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA-  158 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~-  158 (357)
                      ...+++||++.||.++ ||+++|++++|+|+||+|||+|+++++.+++.+      +.+|+||++|++......+-+.. 
T Consensus       176 ~~~gi~TG~~~LD~~l-gGl~~G~liiIaG~pG~GKTtlal~ia~~~a~~------g~~vl~fSlEms~~ql~~R~~~~~  248 (444)
T 3bgw_A          176 NITGVPSGFTELDRMT-YGYKRRNFVLIAARPSMGKTAFALKQAKNMSDN------DDVVNLHSLEMGKKENIKRLIVTA  248 (444)
T ss_dssp             SCCSBCCSCHHHHHHH-SSBCSSCEEEEEECSSSSHHHHHHHHHHHHHHT------TCEEEEECSSSCTTHHHHHHHHHH
T ss_pred             CCCCcCCCcHHHHhhc-CCCCCCcEEEEEeCCCCChHHHHHHHHHHHHHc------CCEEEEEECCCCHHHHHHHHHHHH
Confidence            3679999999999999 589999999999999999999999999999863      47999999999755422221111 


Q ss_pred             ccCc--hh------hcccch------HHHh-hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCee--EEEEeccccccCCCC
Q 035774          159 SSFP--EI------FHSKGM------AQEM-AGRILVLQPTSLSEFTESLEKIKVSLLQNQVK--LLVIDSMEALVPGVH  221 (357)
Q Consensus       159 ~~~~--~~------~~~~~~------~~~~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~--lvvIDsl~~l~~~~~  221 (357)
                      ..++  ..      .....+      ...+ ..++++.+.. ...+.++...+++...+++++  +||||||+.+.....
T Consensus       249 ~~i~~~~l~~g~~~l~~~~~~~l~~a~~~l~~~~l~i~d~~-~~s~~~i~~~ir~l~~~~~~~~~lIVID~Lq~~~~~~~  327 (444)
T 3bgw_A          249 GSINAQKIKAARRDFASEDWGKLSMAIGEISNSNINIFDKA-GQSVNYIWSKTRQTKRKNPGKRVIVMIDYLQLLEPAKA  327 (444)
T ss_dssp             SCCCHHHHHHTGGGTCCSCHHHHHHHHHHHHTSCEEEECCS-SCBHHHHHHHHHHHHHHSCSSCEEEEEECSTTSBCSCS
T ss_pred             cCCCHHHHhcccCCCCHHHHHHHHHHHHHHhcCCEEEECCC-CCCHHHHHHHHHHHHHHhCCCCeEEEEecHHhccCCCC
Confidence            1111  00      111111      1111 2355555543 234455555666666677899  999999999875421


Q ss_pred             CCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccE
Q 035774          222 EQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTI  301 (357)
Q Consensus       222 ~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~  301 (357)
                        ..+|.+.+.++++.|+.+|+++||+||+++|+++....               ..+..+..++++.+.+  +++.+|+
T Consensus       328 --~~~r~~~i~~i~~~Lk~lAke~~v~vi~lsql~r~~e~---------------r~~krp~lsdlr~Sg~--ieq~aD~  388 (444)
T 3bgw_A          328 --NDSRTNQISQISRDLKKMARELDVVVIALSQLSRQVEQ---------------RQDKRPMLSDLRESGQ--LEQDADI  388 (444)
T ss_dssp             --SSCHHHHHHHHHHHHHHHHHHHTCEEEEEEECCGGGGG---------------SSCCCCCGGGCCSCSH--HHHHCSE
T ss_pred             --CCCHHHHHHHHHHHHHHHHHHhCCeEEEEecCCccccc---------------cCCCCCchhhhhhhhh--HHhhCCE
Confidence              23467889999999999999999999999999875431               1122334456665543  8999999


Q ss_pred             EEEEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCceecc
Q 035774          302 RLVLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       302 rl~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      +++|+++.         +.+.+.|.|+|+++.+.+.+.+..+=-.+.+
T Consensus       389 Vi~L~r~~~~~~~~~~~~~~~l~i~K~R~G~~g~v~l~f~~~~~rf~~  436 (444)
T 3bgw_A          389 IEFLYRDDYYDKESESKNIVEVIIAKHRDGPVGTVSLAFIKEYGNFVN  436 (444)
T ss_dssp             EEECCBGGGTCTTCSSTTEEEEEEEEESSSCCEEEEEEEETTTTEEEC
T ss_pred             EEEEeccccccccccCCCeEEEEEEcccCCCCeEEEEEEEcCccEEec
Confidence            99998752         4689999999999988877777665444443

>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=99.97  E-value=2.7e-29  Score=232.37  Aligned_cols=215  Identities=22%  Similarity=0.280  Sum_probs=159.5

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+++||++.||.+|+ ||+++|++++|+|+||+|||+||++++.+++..      +.+|+||++|+++++.+...... 
T Consensus        41 ~~~i~TG~~~LD~~Lg~GGl~~G~ii~I~G~pGsGKTtLal~la~~~~~~------g~~vlyid~E~s~~~~~a~~~g~-  113 (356)
T 1u94_A           41 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE------GKTCAFIDAEHALDPIYARKLGV-  113 (356)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEESSCCCCHHHHHHTTC-
T ss_pred             CCcccCCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHC------CCeEEEEeCCCCccHHHHHHcCC-
Confidence            6789999999999999 999999999999999999999999999998752      47899999999888664322110 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCC------CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRA------PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~------~r~~~~~  232 (357)
                                    ..+++++.++.+.+++.+.+.   ..+...++++|||||++.+.. ...++..      .+.+.+.
T Consensus       114 --------------~~~~l~i~~~~~~e~~~~~~~---~l~~~~~~~lVVIDsl~~l~~~~e~~~~~g~~~~~~q~r~~~  176 (356)
T 1u94_A          114 --------------DIDNLLCSQPDTGEQALEICD---ALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMS  176 (356)
T ss_dssp             --------------CGGGCEEECCSSHHHHHHHHH---HHHHHTCCSEEEEECGGGCCCHHHHTTC------CHHHHHHH
T ss_pred             --------------ChhheeeeCCCCHHHHHHHHH---HHHhccCCCEEEEcCHHHhcchhhhccccccchhHHHHHHHH
Confidence                          124566777766666554443   344467899999999999985 2221111      0113578


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      ++++.|+.++++++|+||++||++...+.   +|.                 ...+|++|..|.+.+++|+.+++..   
T Consensus       177 ~~l~~L~~~a~~~~~~VI~~nq~~~~~~~---~fg-----------------~~~~~~gG~~l~~~advrl~l~r~~~~k  236 (356)
T 1u94_A          177 QAMRKLAGNLKQSNTLLIFINQIRMKIGV---MFG-----------------NPETTTGGNALKFYASVRLDIRRIGAVK  236 (356)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEEC----------------------------------CTTCSHHHHHCSEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHhCCEEEEEeccccccCc---ccC-----------------CCcccCCCcceeeeccEEEEEEEeeeec
Confidence            88999999999999999999999876441   111                 1235778889999999999998752   


Q ss_pred             -------CeEEEEEEeCCCCC-CceeEEEE-cCCCceec
Q 035774          310 -------GQRFMNVEKSPTSP-PLAFSFTI-NPSGISLL  339 (357)
Q Consensus       310 -------~~R~l~v~K~r~~~-~~~~~f~I-~~~Gi~~~  339 (357)
                             +.|.++|+|+|..| ...+.|.| .++||...
T Consensus       237 ~g~~~~g~~~~~~i~K~r~~p~~~~~~f~i~~~~Gi~~~  275 (356)
T 1u94_A          237 EGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFY  275 (356)
T ss_dssp             SSSSEEEEEEEEEEEEESSBCSCCEEEEEEETTTEECHH
T ss_pred             cCccccCcEEEEEECCCccCCCCCcEEEEEEcCCCcCcC
Confidence                   46899999999998 57889999 68998765

>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=99.97  E-value=2.2e-29  Score=233.71  Aligned_cols=215  Identities=23%  Similarity=0.307  Sum_probs=159.5

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+++||++.||.+|+ ||+++|++++|+|+||+|||+||++++.+++..      +.+|+||++|+++...+...+.. 
T Consensus        52 ~~~i~TG~~~LD~~Lg~GGl~~G~li~I~G~pGsGKTtlal~la~~~~~~------g~~vlyi~~E~s~~~~~a~~~g~-  124 (366)
T 1xp8_A           52 VQVVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKA------GGTCAFIDAEHALDPVYARALGV-  124 (366)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT------TCCEEEEESSCCCCHHHHHHTTC-
T ss_pred             CceecCCCHHHHHHhCCCCccCCcEEEEEcCCCCChHHHHHHHHHHHHHC------CCeEEEEECCCChhHHHHHHcCC-
Confidence            6789999999999999 999999999999999999999999999998752      47999999999887654322210 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCC------CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRA------PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~------~r~~~~~  232 (357)
                                    ..+++++.++.+.+++.+.   +...+...++++|||||++.++. ...++..      .+.+.+.
T Consensus       125 --------------d~~~l~i~~~~~~e~~l~~---l~~l~~~~~~~lVVIDsl~~l~~~~e~~g~~gd~~~~~~~r~~~  187 (366)
T 1xp8_A          125 --------------NTDELLVSQPDNGEQALEI---MELLVRSGAIDVVVVDSVAALTPRAEIEGDMGDSLPGLQARLMS  187 (366)
T ss_dssp             --------------CGGGCEEECCSSHHHHHHH---HHHHHTTTCCSEEEEECTTTCCCSTTC--------CCHHHHHHH
T ss_pred             --------------CHHHceeecCCcHHHHHHH---HHHHHhcCCCCEEEEeChHHhccccccccccccchhhHHHHHHH
Confidence                          1245677777766655444   44455567899999999999985 3322111      1224577


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      .+++.|+.++++++|+||++||++...+.   +|.                 ...+|++|..|.+.+++|+.+++..   
T Consensus       188 ~~lr~L~~~a~~~~~~VI~~nq~~~~~~~---~fg-----------------~p~~~~gg~al~~~a~~rl~L~r~~~~~  247 (366)
T 1xp8_A          188 QALRKLTAILSKTGTAAIFINQVREKIGV---MYG-----------------NPETTTGGRALKFYASVRLDVRKIGQPT  247 (366)
T ss_dssp             HHHHHHHHHHTTTCCEEEEEEEC-----------------------------------CHHHHHHHCSEEEEEEEESCCC
T ss_pred             HHHHHHHHHHHHcCCEEEEEEecccccCc---ccC-----------------CccccCCcchhhheeeEEEEEEecchhc
Confidence            88999999999999999999999876541   111                 1135778899999999999999864   


Q ss_pred             --------CeEEEEEEeCCCCCC-ceeEEEEc-CCCceec
Q 035774          310 --------GQRFMNVEKSPTSPP-LAFSFTIN-PSGISLL  339 (357)
Q Consensus       310 --------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi~~~  339 (357)
                              ..|.+.|+|+|..|+ ....|.|. ++||...
T Consensus       248 k~~~~~~g~~~~v~v~Knr~~p~~~~~~f~i~~~~Gi~~~  287 (366)
T 1xp8_A          248 KVGNDAVANTVKIKTVKNKVAAPFKEVELALVYGKGFDQL  287 (366)
T ss_dssp             ------CEEEEEEEEEEESSSCCCCEEEEEEETTTEECHH
T ss_pred             ccCccccCCEEEEEEEcCCCCCCCceEEEEEEeCCCcccc
Confidence                    368999999999995 66899997 8888765

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=99.97  E-value=5.5e-30  Score=245.48  Aligned_cols=233  Identities=18%  Similarity=0.204  Sum_probs=157.7

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHH--h
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMG--A  158 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~--~  158 (357)
                      ..+++||++.||.++ ||+++|++++|+|+||+|||+||++++.+++..     .+.+|+||++|++..... .++.  .
T Consensus       180 ~~~i~tG~~~LD~~l-gGl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~-----~g~~vl~~slE~~~~~l~-~R~~~~~  252 (444)
T 2q6t_A          180 VAGVRTGFKELDQLI-GTLGPGSLNIIAARPAMGKTAFALTIAQNAALK-----EGVGVGIYSLEMPAAQLT-LRMMCSE  252 (444)
T ss_dssp             ---CCCSCHHHHHHH-CCCCTTCEEEEEECTTSCHHHHHHHHHHHHHHT-----TCCCEEEEESSSCHHHHH-HHHHHHH
T ss_pred             CCcccCCCHhhhhhc-CCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh-----CCCeEEEEECCCCHHHHH-HHHHHHH
Confidence            578999999999999 789999999999999999999999999999852     147899999998643211 1111  1


Q ss_pred             ccCc--hh----hcccch------HHHh-hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCC-CCCC
Q 035774          159 SSFP--EI----FHSKGM------AQEM-AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGV-HEQR  224 (357)
Q Consensus       159 ~~~~--~~----~~~~~~------~~~~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~-~~~~  224 (357)
                      ..++  ..    .....+      ...+ ..++++.+.. ...+.++...++....++++++|||||++.+.... ....
T Consensus       253 ~~i~~~~l~~g~l~~~~~~~~~~a~~~l~~~~l~i~d~~-~~s~~~l~~~~~~l~~~~~~~lIvID~l~~~~~~~~~~~~  331 (444)
T 2q6t_A          253 ARIDMNRVRLGQLTDRDFSRLVDVASRLSEAPIYIDDTP-DLTLMEVRARARRLVSQNQVGLIIIDYLQLMSGPGSGKSG  331 (444)
T ss_dssp             TTCCTTTCCGGGCCHHHHHHHHHHHHHHHTSCEEEECCT-TCBHHHHHHHHHHHHHHSCCCEEEEECGGGCBCC------
T ss_pred             cCCCHHHHhCCCCCHHHHHHHHHHHHHHhcCCEEEECCC-CCCHHHHHHHHHHHHHHcCCCEEEEcChhhcCCCcCCCCC
Confidence            1111  00    000000      0111 2345555443 22344455566666667899999999999987531 1112


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEE
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLV  304 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~  304 (357)
                      .+|.+.+.++++.|+.+|++++|+||+++|+++.....               .+..+..++++.+.  .|++.+|++++
T Consensus       332 ~~r~~~i~~i~~~Lk~lAke~~v~vi~lsql~r~~e~r---------------~~~~p~l~dlr~Sg--~ie~~aD~vi~  394 (444)
T 2q6t_A          332 ENRQQEIAAISRGLKALARELGIPIIALSQLSRAVEAR---------------PNKRPMLSDLRESG--SIEQDADLVMF  394 (444)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHTSCEEEEEECCGGGGSS---------------SSCSCCGGGGGGGC--TTGGGCSEEEE
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCCeEEEEecCCcccccC---------------CCCCCChHHhcchh--HHHHhCCEEEE
Confidence            34678899999999999999999999999998754311               11222233444332  38899999999


Q ss_pred             EEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          305 LEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       305 l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      |+++.         +.|.+.|.|+|+++.+.+.+.+..+=-.+
T Consensus       395 L~r~~~~~~~~~~~~~~~l~i~K~R~g~~g~~~l~f~~~~~~f  437 (444)
T 2q6t_A          395 IYRDEYYNPHSEKAGIAEIIVGKQRNGPTGTVELQFHASHVRF  437 (444)
T ss_dssp             EEEGGGTCSSSSCCSEEEEEEEECSSSCCEEEEEEEETTTTEE
T ss_pred             EecccccCCcCCCCCeEEEEEEecCCCCceEEEEEEECCccEE
Confidence            99863         57899999999999887777766544443

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=99.96  E-value=1.5e-29  Score=231.41  Aligned_cols=238  Identities=16%  Similarity=0.155  Sum_probs=166.2

Q ss_pred             HHHHHHHh-cccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           69 LLMEQRAA-TEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        69 ~~~~~~~~-~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +.++++.+ ......+++||++.||.+++ |+++|++++|+|+||+|||+|+++++.+++..      +.+|+||++|++
T Consensus        13 ~~~~~~~~~~~~~~~gi~TG~~~LD~~~g-Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~------g~~Vl~fSlEms   85 (338)
T 4a1f_A           13 DLITENQRKGSLEVTGIPTGFVQLDNYTS-GFNKGSLVIIGARPSMGKTSLMMNMVLSALND------DRGVAVFSLEMS   85 (338)
T ss_dssp             HHHHHHHHHTTTCCCSBCCSCHHHHHHHC-SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHT------TCEEEEEESSSC
T ss_pred             HHHHHHHhcCCCCcCcccCCChHHHHHhc-CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc------CCeEEEEeCCCC
Confidence            34444433 34457899999999999995 79999999999999999999999999998862      589999999996


Q ss_pred             CchH--HHHHHHhccCc--hh----hcccc------hHHHh-hcCeEEeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEe
Q 035774          148 FTSR--RMIEMGASSFP--EI----FHSKG------MAQEM-AGRILVLQPTSLSEFTESLEKIKVSLLQN-QVKLLVID  211 (357)
Q Consensus       148 ~~~~--rl~~~~~~~~~--~~----~~~~~------~~~~~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvID  211 (357)
                      ....  |+..... .++  ..    .....      ....+ ..++++.+.. ...+.++...++....++ ++++||||
T Consensus        86 ~~ql~~Rlls~~~-~v~~~~l~~g~Ls~~e~~~l~~a~~~l~~~~l~I~d~~-~~si~~i~~~ir~l~~~~gg~~lIVID  163 (338)
T 4a1f_A           86 AEQLALRALSDLT-SINMHDLESGRLDDDQWENLAKCFDHLSQKKLFFYDKS-YVRIEQIRLQLRKLKSQHKELGIAFID  163 (338)
T ss_dssp             HHHHHHHHHHHHH-CCCHHHHHHTCCCHHHHHHHHHHHHHHHHSCEEEECCT-TCCHHHHHHHHHHHHHHCTTEEEEEEE
T ss_pred             HHHHHHHHHHHhh-CCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCeEEeCCC-CCcHHHHHHHHHHHHHhcCCCCEEEEe
Confidence            4432  2211110 010  00    00000      01111 2346665443 224555556666666677 89999999


Q ss_pred             ccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceeccc
Q 035774          212 SMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVL  291 (357)
Q Consensus       212 sl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pal  291 (357)
                      ||+.+.....  ..+|.+++.++++.||.+|++++|+||+++|+++....               ..++.|..++++.+.
T Consensus       164 yLqlm~~~~~--~~~r~~ei~~isr~LK~lAkel~vpVi~lsQl~R~~e~---------------r~dkrP~lsDLreSg  226 (338)
T 4a1f_A          164 YLQLMSGSKA--TKERHEQIAEISRELKTLARELEIPIIALVQLNRSLEN---------------RDDKRPILSDIKDSG  226 (338)
T ss_dssp             EEECCCTHHH--HHHCCCCHHHHHHHHHHHHHHHTSCEEEEEECCGGGGG---------------SSSCSCCGGGSEETT
T ss_pred             chHHhcCCCC--CCChHHHHHHHHHHHHHHHHHcCCeEEEEEecCccccc---------------cccCCCChHhcccch
Confidence            9999875421  12466789999999999999999999999999986541               123345556777655


Q ss_pred             chhHhhhccEEEEEEEeC-------------------------------------------CeEEEEEEeCCCCCCceeE
Q 035774          292 GFHWAHAVTIRLVLEAKS-------------------------------------------GQRFMNVEKSPTSPPLAFS  328 (357)
Q Consensus       292 g~~w~~~~~~rl~l~~~~-------------------------------------------~~R~l~v~K~r~~~~~~~~  328 (357)
                      .  +++.+|++++|+++.                                           +...+.|.|+|.+|.+.+.
T Consensus       227 ~--IeqdAD~Vl~l~R~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eiiiaK~R~G~~g~v~  304 (338)
T 4a1f_A          227 G--IEQDADIVLFLYRGYIYQMRAEDNKIDKLKKEGKIEEAQELYLKVNEERRIHKQNGSIEEAEIIVAKNRNGATGTVY  304 (338)
T ss_dssp             E--ECCCCSEEEEEECHHHHHHHHHHHHHHHHHGGGCHHHHHHHHHHHHHHHHHHHHTTSEEEEEEEEEEETTSCCEEEE
T ss_pred             h--hhhhCcEEEEEecchhcccccccccccccccccccccccchhhhhhhhhcccccccCCCceEEEEEeccCCCCceEE
Confidence            5  888899999998741                                           1357889999999988877


Q ss_pred             EEEcCC
Q 035774          329 FTINPS  334 (357)
Q Consensus       329 f~I~~~  334 (357)
                      +.+..+
T Consensus       305 l~f~~~  310 (338)
T 4a1f_A          305 TRFNAP  310 (338)
T ss_dssp             EEEEGG
T ss_pred             EEEccc
Confidence            666543

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=99.96  E-value=5.3e-28  Score=213.74  Aligned_cols=218  Identities=21%  Similarity=0.200  Sum_probs=153.9

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||++.||++|+||+++|++++|+|+||+|||+|+++++.+.+.+      +++|+|+++|++  ...+.+.... 
T Consensus         2 ~~~i~tG~~~LD~~l~gGl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~------~~~v~~~~~e~~--~~~~~~~~~~-   72 (247)
T 2dr3_A            2 TRRVKTGIPGVDEILHGGIPERNVVLLSGGPGTGKTIFSQQFLWNGLKM------GEPGIYVALEEH--PVQVRQNMAQ-   72 (247)
T ss_dssp             -CEECCCCTTHHHHTTTSEETTCEEEEEECTTSSHHHHHHHHHHHHHHT------TCCEEEEESSSC--HHHHHHHHHT-
T ss_pred             cccccCCchhHHHHcCCCCCCCcEEEEECCCCCCHHHHHHHHHHHHHhc------CCeEEEEEccCC--HHHHHHHHHH-
Confidence            3579999999999999999999999999999999999999999988742      478999999985  3333332221 


Q ss_pred             CchhhcccchHHHhhcCeEEeCC----------------CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQP----------------TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR  224 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~----------------~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~  224 (357)
                      ...  ......  ...++.+.+.                ....++.++...+.+.+...++++||||+++.+...+    
T Consensus        73 ~g~--~~~~~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~vviD~~~~l~~~~----  144 (247)
T 2dr3_A           73 FGW--DVKPYE--EKGMFAMVDAFTAGIGKSKEYEKYIVHDLTDIREFIEVLRQAIRDINAKRVVVDSVTTLYINK----  144 (247)
T ss_dssp             TTC--CCHHHH--HHTSEEEEECSTTTTCC--CCCSCBCSCCSSHHHHHHHHHHHHHHHTCCEEEEETSGGGTTTC----
T ss_pred             cCC--CHHHHh--hCCcEEEEecchhhcccccccccccccCccCHHHHHHHHHHHHHHhCCCEEEECCchHhhcCC----
Confidence            110  000000  0112222220                0122344555666666666789999999999987321    


Q ss_pred             CCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEE
Q 035774          225 APGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLV  304 (357)
Q Consensus       225 ~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~  304 (357)
                         .....+++..|+++++++|++|++++|..+....                        ...|    .|.+.+|.++.
T Consensus       145 ---~~~~~~~l~~l~~~~~~~~~~vi~~~h~~~~~~~------------------------~~~~----~~~~~~D~vi~  193 (247)
T 2dr3_A          145 ---PAMARSIILQLKRVLAGTGCTSIFVSQVSVGERG------------------------FGGP----GVEHGVDGIIR  193 (247)
T ss_dssp             ---GGGHHHHHHHHHHHHHHTTCEEEEEEECC----C------------------------CC-C----CHHHHSSEEEE
T ss_pred             ---HHHHHHHHHHHHHHHHHCCCeEEEEecCCCCccc------------------------cccc----ccceeEEEEEE
Confidence               1234567788899999999999999998764210                        0011    28888899999


Q ss_pred             EEEe--C--CeEEEEEEeCCCCCC--ceeEEEEcCCCceeccCCCcee
Q 035774          305 LEAK--S--GQRFMNVEKSPTSPP--LAFSFTINPSGISLLTDDGTEM  346 (357)
Q Consensus       305 l~~~--~--~~R~l~v~K~r~~~~--~~~~f~I~~~Gi~~~~~~~~~~  346 (357)
                      +++.  .  ..|.++|.|+|+++.  ..+.|+|+++||.+++...++.
T Consensus       194 L~~~~~~~~~~r~l~v~K~R~~~~~~~~~~f~i~~~Gi~~~~~~~~~~  241 (247)
T 2dr3_A          194 LDLDEIDGELKRSLIVWKMRGTSHSMRRHPFDITDKGIIVYPDKVLKR  241 (247)
T ss_dssp             EEEEEETTEEEEEEEEEEETTSCCCCBCEEEEEETTEEEECTTCCCCC
T ss_pred             EEEEccCCeeEEEEEEEECCCCCCCCceEEEEEcCCCEEEecCccccc
Confidence            9875  2  369999999999883  6789999999999999876654

>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=99.96  E-value=3e-28  Score=225.36  Aligned_cols=215  Identities=26%  Similarity=0.310  Sum_probs=160.6

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+++||++.||.+|+ ||+++|++++|+|+||+|||+||++++.+++.+      +++|+||++|+++...+...+.. 
T Consensus        39 ~~~i~TG~~~LD~~Lg~GGl~~G~iv~I~G~pGsGKTtLal~la~~~~~~------g~~vlyi~~E~~~~~~~a~~lG~-  111 (349)
T 2zr9_A           39 ISVIPTGSISLDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA------GGIAAFIDAEHALDPEYAKKLGV-  111 (349)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT------TCCEEEEESSCCCCHHHHHHTTC-
T ss_pred             CCccccCCHHHHHHhccCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhC------CCeEEEEECCCCcCHHHHHHcCC-
Confidence            5689999999999999 999999999999999999999999999988753      47899999999887654322210 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCC---C---CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQR---A---PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~---~---~r~~~~~  232 (357)
                                    ..+++++.++.+.+++.++   +...+...++++|||||+++++. ...++.   .   .+...+.
T Consensus       112 --------------~~~~l~i~~~~~~e~~l~~---~~~l~~~~~~~lIVIDsl~~l~~~~e~~~~~gd~~~~~q~r~~~  174 (349)
T 2zr9_A          112 --------------DTDSLLVSQPDTGEQALEI---ADMLVRSGALDIIVIDSVAALVPRAEIEGEMGDSHVGLQARLMS  174 (349)
T ss_dssp             --------------CGGGCEEECCSSHHHHHHH---HHHHHTTTCCSEEEEECGGGCCCHHHHTTC----CCCHHHHHHH
T ss_pred             --------------CHHHeEEecCCCHHHHHHH---HHHHHhcCCCCEEEEcChHhhcchhhhccccccchhhHHHHHHH
Confidence                          1245667777666655443   34445567899999999999984 221111   0   1123567


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe----
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK----  308 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~----  308 (357)
                      .+++.|+.+++++|++||++||++...+.   +|.                 ....|++|..|.+.+++|+.+++.    
T Consensus       175 ~~l~~L~~~a~~~~~tVI~inh~~~~~~~---~~~-----------------~p~~~~gg~~l~~~ad~~l~lrr~~~~k  234 (349)
T 2zr9_A          175 QALRKMTGALNNSGTTAIFINELREKIGV---MFG-----------------SPETTTGGKALKFYASVRLDVRRIETLK  234 (349)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEEECC-------------------------------CCSSHHHHHHHCSEEEEEEEEEEEC
T ss_pred             HHHHHHHHHHHHhCCEEEEEeccccccCc---ccC-----------------CCcccCCchHhhhccceEEEEEEeeeee
Confidence            88888999999999999999999875441   111                 112467788999999999999875    


Q ss_pred             ------CCeEEEEEEeCCCCC-CceeEEEE-cCCCceec
Q 035774          309 ------SGQRFMNVEKSPTSP-PLAFSFTI-NPSGISLL  339 (357)
Q Consensus       309 ------~~~R~l~v~K~r~~~-~~~~~f~I-~~~Gi~~~  339 (357)
                            +..|.++|+|+|..| .+...|.| .++||...
T Consensus       235 ~g~~~~g~~~~~~i~K~~~~p~~~~~~fdi~~~~Gi~~~  273 (349)
T 2zr9_A          235 DGTDAVGNRTRVKVVKNKVSPPFKQAEFDILYGQGISRE  273 (349)
T ss_dssp             SSSSCCEEEEEEEEEEESSSCCCCEEEEEEETTSCBCHH
T ss_pred             cCccccCCEEEEEeCCCccCCCCceEEEEEEeCCCcCcc
Confidence                  246899999999998 57789999 58998765

>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=99.96  E-value=5.2e-28  Score=211.63  Aligned_cols=218  Identities=31%  Similarity=0.465  Sum_probs=163.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      .++++||++.||++|+||+++|+++.|.||||+|||||+..++.....+...|+.+++++|++.+..+...++..+.+..
T Consensus         4 ~~~i~tG~~~LD~~l~ggi~~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~~~~~~~i~~~~~~~   83 (231)
T 4a74_A            4 IGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNR   83 (231)
T ss_dssp             CCEECCSCHHHHHHTTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CCccCCCChhHHhHhcCCCCCCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCCCCCHHHHHHHHHHc
Confidence            56899999999999999999999999999999999999999998877665555567889999999877766666655431


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhh-----hcCeeEEEEeccccccCCCCCCC---CCChHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLL-----QNQVKLLVIDSMEALVPGVHEQR---APGQHPLS  232 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~-----~~~~~lvvIDsl~~l~~~~~~~~---~~r~~~~~  232 (357)
                           ...  .....+++.+....+..+....+..+...+.     ..+++++++|+++..+.....+.   ..|...+.
T Consensus        84 -----~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llilDe~~~~l~~~~~~~~~~~~r~~~~~  156 (231)
T 4a74_A           84 -----GLD--PDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLA  156 (231)
T ss_dssp             -----TSC--HHHHHHTEEEEECCSHHHHHHHHHHHHHHHHHHTTSSSCEEEEEEETSSHHHHHHSCSTTHHHHHHHHHH
T ss_pred             -----CCC--HHHHhhcEEEEecCChHHHHHHHHHHHHHHHHhcccCCceeEEEECChHHHhccccCCCcchhHHHHHHH
Confidence                 111  1245667877777666555555555555555     67899999999999876543321   11233466


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-CCe
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-SGQ  311 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-~~~  311 (357)
                      +++..|+++++++|++||+++|..+.                                .|..|.+.++.++.+++. ...
T Consensus       157 ~~~~~l~~~~~~~g~tvi~vtH~~~~--------------------------------~g~~~~~~~d~~l~l~~~~~~~  204 (231)
T 4a74_A          157 KHLADLHRLANLYDIAVFVTNQVQAN--------------------------------GGHILAHSATLRVYLRKGKGGK  204 (231)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEEECC-----------------------------------------CCSEEEEEEECTTSC
T ss_pred             HHHHHHHHHHHHCCCeEEEEeecccC--------------------------------cchhhHhhceEEEEEEecCCCe
Confidence            88999999999999999999998663                                122388999999999885 458


Q ss_pred             EEEEEEeCCCCCCceeEEEEcCCCce
Q 035774          312 RFMNVEKSPTSPPLAFSFTINPSGIS  337 (357)
Q Consensus       312 R~l~v~K~r~~~~~~~~f~I~~~Gi~  337 (357)
                      |.+++.|+|+.|.+.+.|+|+++||+
T Consensus       205 r~l~~~K~r~~~~~~~~f~i~~~Gl~  230 (231)
T 4a74_A          205 RIARLIDAPHLPEGEAVFSITEKGIE  230 (231)
T ss_dssp             EEEEEESCC--CCSCEEEEEETTEEE
T ss_pred             EEEEEEeCCCCCCceEEEEEeccccc
Confidence            99999999999987789999999986

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=99.96  E-value=4.7e-28  Score=232.70  Aligned_cols=236  Identities=14%  Similarity=0.137  Sum_probs=159.7

Q ss_pred             cCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh
Q 035774           79 HLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA  158 (357)
Q Consensus        79 ~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~  158 (357)
                      ....+++||++.||.++ ||+++|++++|+|+||+|||+|+++++.+++..  .   +.+|+||++|++..... ..+..
T Consensus       181 ~~~~~i~tG~~~LD~~~-gGl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~--~---g~~Vl~~s~E~s~~~l~-~r~~~  253 (454)
T 2r6a_A          181 GEITGIPTGFTELDRMT-SGFQRSDLIIVAARPSVGKTAFALNIAQNVATK--T---NENVAIFSLEMSAQQLV-MRMLC  253 (454)
T ss_dssp             CCCCSBCCSCHHHHHHH-SSBCTTCEEEEECCTTSCHHHHHHHHHHHHHHH--S---SCCEEEEESSSCHHHHH-HHHHH
T ss_pred             CCCCCCCCCcHHHHhhc-CCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHh--C---CCcEEEEECCCCHHHHH-HHHHH
Confidence            34679999999999999 679999999999999999999999999998752  1   36899999998643211 11110


Q ss_pred             --ccCc--hh----hcccch------HHHh-hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC
Q 035774          159 --SSFP--EI----FHSKGM------AQEM-AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ  223 (357)
Q Consensus       159 --~~~~--~~----~~~~~~------~~~~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~  223 (357)
                        ..+.  ..    +....+      ...+ ..++++.+.. ...+.++...++..+..+++++|||||++.+..... .
T Consensus       254 ~~~~~~~~~l~~g~l~~~~~~~~~~a~~~l~~~~l~i~d~~-~~s~~~i~~~~~~l~~~~~~~livID~l~~~~~~~~-~  331 (454)
T 2r6a_A          254 AEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTP-SIRVSDIRAKCRRLKQESGLGMIVIDYLQLIQGSGR-S  331 (454)
T ss_dssp             HHHTCCHHHHHTSCCCHHHHHHHHHHHHHHHSSCEEEECCT-TCCHHHHHHHHHHHHTTTCCCEEEEECGGGSCCSCC--
T ss_pred             HHcCCCHHHHhcCCCCHHHHHHHHHHHHHHhcCCEEEECCC-CCCHHHHHHHHHHHHHHcCCCEEEEccHHHhccCCC-C
Confidence              0111  00    000000      0111 2345555432 123334445556666667899999999999875422 1


Q ss_pred             CCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEE
Q 035774          224 RAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRL  303 (357)
Q Consensus       224 ~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl  303 (357)
                      ...+.+.+.++++.|+.+|+++||+||+++|+++.....               .+..+..++++.+.  .+++.+|.++
T Consensus       332 ~~~~~~~i~~i~~~Lk~lAke~~i~vi~~sql~r~~e~~---------------~~~~p~lsdlr~Sg--~ie~~aD~vi  394 (454)
T 2r6a_A          332 KENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQR---------------QDKRPMMSDIRESG--SIEQDADIVA  394 (454)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHTCCEEEEECCCTTSTTC------------------CCCTHHHHTTC--SHHHHCSEEE
T ss_pred             CCCHHHHHHHHHHHHHHHHHHhCCeEEEEecCCcccccC---------------CCCCCcHHHhhccc--hhHhhCCEEE
Confidence            234778899999999999999999999999998765411               01112223333222  3788999999


Q ss_pred             EEEEeC---------CeEEEEEEeCCCCCCceeEEEEcCCCceecc
Q 035774          304 VLEAKS---------GQRFMNVEKSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       304 ~l~~~~---------~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      +++++.         +.+.+.|.|+|+++.+.+.+.+..+=-.+.+
T Consensus       395 ~l~r~~~~~~~~~~~~~~~l~i~K~R~G~~g~v~l~f~~~~~~f~~  440 (454)
T 2r6a_A          395 FLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVN  440 (454)
T ss_dssp             EEEETTC-------CCEEEEEEEEESSSCCEEEEEEEETTTTEEEC
T ss_pred             EEecccccCcccCCCCeEEEEEecccCCCCeEEEEEEEcCccEEeC
Confidence            998753         5689999999999988777777765545443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=99.95  E-value=3.8e-28  Score=260.72  Aligned_cols=215  Identities=22%  Similarity=0.274  Sum_probs=170.6

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+++||+++||++|+ ||+++|++++|+|+||+|||+||+++|.+++.+      +.+|+|||+|+++.+.+...+   
T Consensus       710 ~~~i~TG~~eLD~llggGGl~~G~lilIaG~PG~GKTtLalqlA~~~a~~------g~~VlyiS~Ees~~ql~A~rl---  780 (2050)
T 3cmu_A          710 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE------GKTCAFIDAEHALDPIYARKL---  780 (2050)
T ss_dssp             CCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTT------TCCEEEECTTSCCCHHHHHHT---
T ss_pred             cceeecCChHHHHHhccCCcCCCcEEEEEcCCCCCHHHHHHHHHHHHHhc------CCcEEEEECCCcHHHHHHHHc---
Confidence            6789999999999998 799999999999999999999999999999863      468999999999887642111   


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCC-CCChH-----HHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQR-APGQH-----PLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~-~~r~~-----~~~  232 (357)
                            ..      ..+++++.+..+..++.+.+.   +...+.++++||||||+.++. ....+. .++.+     ++.
T Consensus       781 ------G~------~~~~l~i~~~~~i~~i~~~~r---~l~~~~~~~LVIIDsLq~i~~~~~~~~~~Gs~~q~La~Reis  845 (2050)
T 3cmu_A          781 ------GV------DIDNLLCSQPDTGEQALEICD---ALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMS  845 (2050)
T ss_dssp             ------TC------CTTTCEEECCSSHHHHHHHHH---HHHHHTCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHH
T ss_pred             ------CC------CccceEEecCCCHHHHHHHHH---HHhhccCCCEEEEcchhhhcccccccCCCCchhhHHHHHHHH
Confidence                  11      125778877777666655554   444457899999999999987 321111 11222     578


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe----
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK----  308 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~----  308 (357)
                      ++++.|+++|+++||+||++||+++..+.   +                 |....+|++|..|+|.+++|++|++.    
T Consensus       846 ~ilr~Lk~lAke~~v~VI~l~Qv~r~~e~---~-----------------fgdp~~p~GG~~l~h~a~~Rl~Lrr~~~~~  905 (2050)
T 3cmu_A          846 QAMRKLAGNLKQSNTLLIFINQIRMKIGV---M-----------------FGNPETTTGGNALKFYASVRLDIRRIGAVK  905 (2050)
T ss_dssp             HHHHHHHHHHHTTTCEEEEEECCEECTTC---C-----------------SSCCEECSSHHHHHHHEEEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHhCCEEEEeccccccchh---h-----------------cCCCccccCCceeeeeeeEEEEEEeecccc
Confidence            89999999999999999999999987651   1                 11245799999999999999999875    


Q ss_pred             -C------CeEEEEEEeCCCCCCceeEEEE-cCCCceec
Q 035774          309 -S------GQRFMNVEKSPTSPPLAFSFTI-NPSGISLL  339 (357)
Q Consensus       309 -~------~~R~l~v~K~r~~~~~~~~f~I-~~~Gi~~~  339 (357)
                       +      ..|.++|.+++..|...+.|.| +++||...
T Consensus       906 ~g~~~~G~~~Rv~~v~~sp~lp~~e~~f~I~~~~Gi~~~  944 (2050)
T 3cmu_A          906 EGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFY  944 (2050)
T ss_dssp             ETTEEEEEEEEEEEEEESSSCSCCEEEEEEETTTEECHH
T ss_pred             ccccccCCcceEEEEecCCCCCCceEEEEEEcCCCcccH
Confidence             2      4788899999999988999999 99999854

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=99.95  E-value=2.4e-26  Score=223.86  Aligned_cols=231  Identities=11%  Similarity=0.090  Sum_probs=158.6

Q ss_pred             cCCCCCCC-CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHH-HH
Q 035774           79 HLGGHLPT-RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMI-EM  156 (357)
Q Consensus        79 ~~~~~i~T-G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~-~~  156 (357)
                      ....+++| |++.||.++ ||+++|++++|+|+||+|||+|++|++.+++.+     .+.+|+||++|++..  ++. ++
T Consensus       219 ~~~~~i~t~G~~~LD~~l-gGl~~G~l~li~G~pG~GKT~lal~~a~~~a~~-----~g~~vl~~s~E~s~~--~l~~r~  290 (503)
T 1q57_A          219 EESVGLLFSGCTGINDKT-LGARGGEVIMVTSGSGMVMSTFVRQQALQWGTA-----MGKKVGLAMLEESVE--ETAEDL  290 (503)
T ss_dssp             SCTTCSCCSSCTTHHHHH-CCCCTTCEEEEEESSCHHHHHHHHHHHHHHTTT-----SCCCEEEEESSSCHH--HHHHHH
T ss_pred             cccCCccccchhhhhHhh-cccCCCeEEEEeecCCCCchHHHHHHHHHHHHh-----cCCcEEEEeccCCHH--HHHHHH
Confidence            34679999 999999999 579999999999999999999999999999852     147899999999643  222 22


Q ss_pred             Hh--ccCc--h---h----hcccch---HHHh--hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCC
Q 035774          157 GA--SSFP--E---I----FHSKGM---AQEM--AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGV  220 (357)
Q Consensus       157 ~~--~~~~--~---~----~~~~~~---~~~~--~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~  220 (357)
                      ..  ..++  .   .    .....+   .+.+  ..++++.+.....++.+++..++..+.++++++||||||+.+....
T Consensus       291 ~~~~~~~~~~~~~~~~~g~l~~~~~~~~~~~~~~~~~l~i~~~~~~~~~~~i~~~i~~~~~~~~~~lvVID~l~~l~~~~  370 (503)
T 1q57_A          291 IGLHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHISIVVSAS  370 (503)
T ss_dssp             HHHHTTSCCTTCHHHHHHHHHTSHHHHHHHHHHTTTCEEEECCC---CHHHHHHHHHHHHHTTCCSEEEEECTTCCCSCC
T ss_pred             HHHHcCCChhhccccccCCCCHHHHHHHHHHHhccCCEEEECCCCCCCHHHHHHHHHHHHHhcCCCEEEEccchhcCCCC
Confidence            11  1111  0   0    000000   1111  2456666653334556666677777777899999999999886432


Q ss_pred             CCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhcc
Q 035774          221 HEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVT  300 (357)
Q Consensus       221 ~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~  300 (357)
                        ....+.+.+.++++.|+.+|+++||+||+++|+++ .....           +...+..+..++++.+  ..|++.+|
T Consensus       371 --~~~~~~~~~~~~~~~Lk~lak~~~i~vi~~~q~~r-~~~~~-----------~~~~~~~p~l~dlr~s--~~ie~~aD  434 (503)
T 1q57_A          371 --GESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKN-PDKGK-----------AHEEGRPVSITDLRGS--GALRQLSD  434 (503)
T ss_dssp             --SCCCHHHHHHHHHHHHHHHHHHHTCEEEEEEECCC-CSSSS-----------CSTTCCCCCSSSCSSS--SHHHHHCS
T ss_pred             --CCCCHHHHHHHHHHHHHHHHHHHCCeEEEEEcCCc-hhccC-----------ccccCCCCChhhhccc--hHhhecCc
Confidence              22346688999999999999999999999999987 22100           0001112222344433  34899999


Q ss_pred             EEEEEEEeC-----CeEEEEEEeCC-CCCCcee-EEEEcC
Q 035774          301 IRLVLEAKS-----GQRFMNVEKSP-TSPPLAF-SFTINP  333 (357)
Q Consensus       301 ~rl~l~~~~-----~~R~l~v~K~r-~~~~~~~-~f~I~~  333 (357)
                      +++.|+++.     ..|.++|.|+| .++.+.. .+.+..
T Consensus       435 ~vi~l~r~~~~~~~~~~~l~v~K~R~~G~~g~~~~l~f~~  474 (503)
T 1q57_A          435 TIIALERNQQGDMPNLVLVRILKCRFTGDTGIAGYMEYNK  474 (503)
T ss_dssp             EEEEEEECSSSSCTTEEEEEEEEETTTCCCEEEEEEEECT
T ss_pred             EEEEEEeCCcCCCCCeEEEEEEeccCCCCCCceEEEEEEc
Confidence            999999864     47999999999 6887765 545443

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=99.94  E-value=5.6e-26  Score=241.95  Aligned_cols=215  Identities=22%  Similarity=0.294  Sum_probs=165.9

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+++||++.||.+|+ ||+++|++++|+|+||+|||+||+|++.+++..      +++|+|||+|+++.+.+...+.. 
T Consensus       361 ~~~isTGi~~LD~lLg~GGl~~G~lilI~G~pGsGKTtLaLq~a~~~~~~------G~~vlyis~E~s~~~~~a~~lGv-  433 (1706)
T 3cmw_A          361 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE------GKTCAFIDAEHALDPIYARKLGV-  433 (1706)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEECTTSCCCHHHHHHTTC-
T ss_pred             CceeccCcHHHHHHhccCCcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh------CCCeEEEEccCchHHHHHHHcCC-
Confidence            6799999999999999 999999999999999999999999999999853      57999999999988765322110 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC-CCC---CCC---CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG-VHE---QRA---PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~-~~~---~~~---~r~~~~~  232 (357)
                                    ..+++++.++.+.+++.+.   +...+...++++|||||++.++.. ..+   +..   .+.+.+.
T Consensus       434 --------------d~~~L~i~~~~~~e~~l~~---l~~lv~~~~~~lVVIDSL~al~~~~e~e~~~g~~~~~~q~r~~s  496 (1706)
T 3cmw_A          434 --------------DIDNLLCSQPDTGEQALEI---CDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMS  496 (1706)
T ss_dssp             --------------CGGGCEEECCSSHHHHHHH---HHHHHHHTCCSEEEESCSTTCCCHHHHHSCTTCCCTTHHHHHHH
T ss_pred             --------------CHHHeEEcCCCCHHHHHHH---HHHHHHhcCCCEEEECCHHHhhccccccccccccchhHHHHHHH
Confidence                          1245677777776665544   444556678999999999999852 111   111   1334677


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      .+++.|+.+++++||+||++||+++..+.   +|.                 ...+|++|..|.+.+++|+.+++..   
T Consensus       497 ~~Lr~L~~~ak~~~v~VI~inQl~~~vg~---~fg-----------------~~~~p~gg~ale~~ADv~L~L~R~~~~~  556 (1706)
T 3cmw_A          497 QAMRKLAGNLKQSNTLLIFINQIRMKIGV---MFG-----------------NPETTTGGNALKFYASVRLDIRRIGAVK  556 (1706)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEECEEECTTC---CSS-----------------CCEEESSCSHHHHHEEEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHcCCEEEEEeeccccccc---ccC-----------------CCccCCCCcceeeeCCEEEEEEeccccc
Confidence            88999999999999999999999886541   111                 2346788889999999999998752   


Q ss_pred             -------CeEEEEEEeCCCCCC-ceeEEEE-cCCCceec
Q 035774          310 -------GQRFMNVEKSPTSPP-LAFSFTI-NPSGISLL  339 (357)
Q Consensus       310 -------~~R~l~v~K~r~~~~-~~~~f~I-~~~Gi~~~  339 (357)
                             ..|.++|+|+|.+|+ ....|.| .+.||...
T Consensus       557 ~g~~~~~~~~~l~V~KnR~gp~~~~~~F~I~~~~Gi~~~  595 (1706)
T 3cmw_A          557 EGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFY  595 (1706)
T ss_dssp             ETTEEEEEEEEEEEEEESSSCSCCEEEEEEETTTEECHH
T ss_pred             cCccccCcEEEEEEEecCCCCCCCeEEEEEecCCCcccc
Confidence                   357899999999985 4578986 57777643

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=99.94  E-value=7.3e-26  Score=243.16  Aligned_cols=215  Identities=22%  Similarity=0.307  Sum_probs=165.3

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+++||++.||++|+ ||+|+|++++|+|+||+|||+||+|++.+++.+      +++|+||++|++++..++..+.. 
T Consensus        12 ~~~i~TGi~~LD~lLg~GGip~G~vtlI~G~pGsGKT~lalq~a~~~~~~------Ge~vlYI~tEes~~~~ra~~lG~-   84 (2050)
T 3cmu_A           12 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE------GKTCAFIDAEHALDPIYARKLGV-   84 (2050)
T ss_dssp             CCEECCSCHHHHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTT------TCCEEEECTTSCCCHHHHHHTTC-
T ss_pred             CCeeccCcHHHHHHHhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHhhcc------CCceEEEEccCcchhhHHhhhcc-
Confidence            5789999999999998 999999999999999999999999999999863      58999999999988877543211 


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCC-CC------CCCChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVH-EQ------RAPGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~-~~------~~~r~~~~~  232 (357)
                                    .++++.++++...+++.+++..+.   ...++++|||||++.+++... +.      ...+...+.
T Consensus        85 --------------dl~~i~v~~p~~~e~ll~il~~L~---~~~~~~lVVIDSISaL~~~~e~~~e~~d~~~~~raR~l~  147 (2050)
T 3cmu_A           85 --------------DIDNLLCSQPDTGEQALEICDALA---RSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMS  147 (2050)
T ss_dssp             --------------CTTTCEEECCSSHHHHHHHHHHHH---HHTCCSEEEESCGGGCCCHHHHHSCSSSCCTTHHHHHHH
T ss_pred             --------------CcccceecCCCcHHHHHHHHHHHH---hccCCcEEEEcChHHhhhhcccccccccchhhHHHHHHH
Confidence                          123455666655555554444332   345799999999999987521 10      111234577


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe----
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK----  308 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~----  308 (357)
                      .++..|+.+++++|++||++||+....+   .+|                 .....|++|..|.+++++++.|++.    
T Consensus       148 ~~l~~L~~~ak~~gitVVlTNQv~~~~g---~~f-----------------g~~~~~~gG~~l~~iaD~VI~L~r~~~vk  207 (2050)
T 3cmu_A          148 QAMRKLAGNLKQSNTLLIFINQIRMKIG---VMF-----------------GNPETTTGGNALKFYASVRLDIRRIGAVK  207 (2050)
T ss_dssp             HHHHHHHHHHHTTTCEEEEEECCEECTT---CCS-----------------SCCEECSSHHHHHHHEEEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHhCCeEEEEEecccccc---ccc-----------------CcccccCCcchhhhhCcEEEEEEeccccc
Confidence            8899999999999999999999976433   111                 1224688899999999999999873    


Q ss_pred             ------CCeEEEEEEeCCCCCC-ceeEEEEc-CCCceec
Q 035774          309 ------SGQRFMNVEKSPTSPP-LAFSFTIN-PSGISLL  339 (357)
Q Consensus       309 ------~~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi~~~  339 (357)
                            +..|.++|.|+|..++ ..+.|.|. +.||.+.
T Consensus       208 ~ge~~~G~~Rrl~V~K~R~~~p~~~~~F~I~~g~GI~~~  246 (2050)
T 3cmu_A          208 EGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFY  246 (2050)
T ss_dssp             ETTEEEEEEEEEEEEEESSSCSCCEEEEEEETTTEECHH
T ss_pred             cccccccceEEEEEEeccCCCCCceEEEEEEcCCCeEEe
Confidence                  2469999999998875 56899995 7888776

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=99.93  E-value=2.6e-25  Score=236.88  Aligned_cols=217  Identities=22%  Similarity=0.275  Sum_probs=166.1

Q ss_pred             CCCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh
Q 035774           80 LGGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA  158 (357)
Q Consensus        80 ~~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~  158 (357)
                      ...+++||+++||++|+ ||+++|++++|+|+||+|||+|+++++.+++..      +++|+||++|++..+.+..... 
T Consensus       709 ~~~~i~TG~~eLD~lLg~GGl~~G~lVlI~G~PG~GKTtLal~lA~~aa~~------g~~VlyiS~Ees~~ql~A~~lG-  781 (1706)
T 3cmw_A          709 DVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE------GKTCAFIDAEHALDPIYARKLG-  781 (1706)
T ss_dssp             SCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEECTTSCCCHHHHHHTT-
T ss_pred             cccccccCcHHHHHHhccCCcCCCceEEEECCCCCCcHHHHHHHHHHHHHc------CCCeEEEeccchHHHHHHHHcC-
Confidence            36799999999999999 999999999999999999999999999998852      4789999999988765411110 


Q ss_pred             ccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCC---CCCC---CChHHH
Q 035774          159 SSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVH---EQRA---PGQHPL  231 (357)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~---~~~~---~r~~~~  231 (357)
                                    ...+++++.++.+..++.   ..++..+..+++++|||||++.+.. ...   .+..   .+.+.+
T Consensus       782 --------------vd~~~L~i~~~~~leei~---~~l~~lv~~~~~~lVVIDsLq~l~~~~e~~~~~G~~~~~~q~rei  844 (1706)
T 3cmw_A          782 --------------VDIDNLLCSQPDTGEQAL---EICDALARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMM  844 (1706)
T ss_dssp             --------------CCGGGCEEECCSSHHHHH---HHHHHHHHHTCCSEEEESCSTTCCCHHHHHSCTTCCCTTHHHHHH
T ss_pred             --------------CChhheEEecCCcHHHHH---HHHHHHHHccCCCEEEEechhhhccccccccccCccchhHHHHHH
Confidence                          112457777777665544   4445555667899999999999984 211   1110   123457


Q ss_pred             HHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC--
Q 035774          232 SWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS--  309 (357)
Q Consensus       232 ~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~--  309 (357)
                      ..+++.|+.+|+++|++||++||+++..+.   ++.           +      -.+|+++..|.+.+++++++++..  
T Consensus       845 s~~Lr~Lk~lAke~gi~VIlinql~r~~g~---~~G-----------d------p~~p~gs~~Leq~ADvvl~L~R~~~~  904 (1706)
T 3cmw_A          845 SQAMRKLAGNLKQSNTLLIFINQIRMKIGV---MFG-----------N------PETTTGGNALKFYASVRLDIRRIGAV  904 (1706)
T ss_dssp             HHHHHHHHHHHHHHTCEEEEEECEEECTTC---CSS-----------C------CEEESSCSHHHHHEEEEEEEEEEEEE
T ss_pred             HHHHHHHHHHHHHcCCEEEEEecCCCcccc---ccC-----------C------ccccCCcchhhheeeEEEEEEecccc
Confidence            788899999999999999999999886541   111           0      135777889999999999997642  


Q ss_pred             --------CeEEEEEEeCCCCCC-ceeEEEE-cCCCceecc
Q 035774          310 --------GQRFMNVEKSPTSPP-LAFSFTI-NPSGISLLT  340 (357)
Q Consensus       310 --------~~R~l~v~K~r~~~~-~~~~f~I-~~~Gi~~~~  340 (357)
                              ..|.++|+|+|.+|+ ....|+| .+.||....
T Consensus       905 ~~g~~~~g~~r~l~V~KnR~gp~~~~~~F~I~~~~Gi~~~g  945 (1706)
T 3cmw_A          905 KEGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGINFYG  945 (1706)
T ss_dssp             EETTEEEEEEEEEEEEEESSSCSCCEEEEEEETTTEECHHH
T ss_pred             cccccccCcEEEEEEEecCCCCCCceEEEEEEcCCCccccc
Confidence                    378999999999995 5579999 788987654

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=99.92  E-value=4.8e-24  Score=186.54  Aligned_cols=209  Identities=21%  Similarity=0.256  Sum_probs=143.7

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccC
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSF  161 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~  161 (357)
                      .+++||++.||.++.||+++|+++.|.|+||+|||+|+.+++...+..      +++|+|++.+..  ...+...... .
T Consensus         3 ~~i~tg~~~Ld~~~~ggi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~------~~~v~~~~~~~~--~~~~~~~~~~-~   73 (235)
T 2w0m_A            3 SRLSTGILDFDKLIQGGIPQGFFIALTGEPGTGKTIFSLHFIAKGLRD------GDPCIYVTTEES--RDSIIRQAKQ-F   73 (235)
T ss_dssp             CEECCSCHHHHGGGTTSEETTCEEEEECSTTSSHHHHHHHHHHHHHHH------TCCEEEEESSSC--HHHHHHHHHH-T
T ss_pred             ccccCCchHHHHHhcCCCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHC------CCeEEEEEcccC--HHHHHHHHHH-h
Confidence            579999999999999899999999999999999999999999877632      478999999874  3333222211 1


Q ss_pred             chhhcccchHHHhhcCeEEe-------------CCCCHHHHHHHHHHHHHHhhhcCee--EEEEeccccccCCCCCCCCC
Q 035774          162 PEIFHSKGMAQEMAGRILVL-------------QPTSLSEFTESLEKIKVSLLQNQVK--LLVIDSMEALVPGVHEQRAP  226 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~-------------~~~~~~~~~~~l~~l~~~~~~~~~~--lvvIDsl~~l~~~~~~~~~~  226 (357)
                      ...++  ..   ...++.+.             ...+..   ++...+...+...+++  +||||+++.+...+      
T Consensus        74 ~~~~~--~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~llilDe~~~~~~~d------  139 (235)
T 2w0m_A           74 NWDFE--EY---IEKKLIIIDALMKEKEDQWSLVNLTPE---ELVNKVIEAKQKLGYGKARLVIDSVSALFLDK------  139 (235)
T ss_dssp             TCCCG--GG---BTTTEEEEECCC----CTTBCSSCCHH---HHHHHHHHHHHHHCSSCEEEEEETGGGGSSSC------
T ss_pred             cchHH--HH---hhCCEEEEeccccccCceeeecCCCHH---HHHHHHHHHHHhhCCCceEEEEECchHhhcCC------
Confidence            00000  00   00011111             112333   3344444555556889  99999999886431      


Q ss_pred             ChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEE
Q 035774          227 GQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLE  306 (357)
Q Consensus       227 r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~  306 (357)
                       .....++++.|++++++++++||+++|..+....                        ..    +..|.+.+|.++.++
T Consensus       140 -~~~~~~~~~~l~~~~~~~~~~vi~~~h~~~~~~~------------------------~~----~~~~~~~~d~vi~l~  190 (235)
T 2w0m_A          140 -PAMARKISYYLKRVLNKWNFTIYATSQYAITTSQ------------------------AF----GFGVEHVADGIIRFR  190 (235)
T ss_dssp             -GGGHHHHHHHHHHHHHHTTEEEEEEEC---------------------------------------CHHHHCSEEEEEE
T ss_pred             -HHHHHHHHHHHHHHHHhCCCeEEEEeccCccccc------------------------cc----ccchheeeeEEEEEE
Confidence             1345678899999999999999999998642110                        00    012778889999998


Q ss_pred             EeC----CeEEEEEEeCCCCCC--ceeEEEEcCC-CceeccCC
Q 035774          307 AKS----GQRFMNVEKSPTSPP--LAFSFTINPS-GISLLTDD  342 (357)
Q Consensus       307 ~~~----~~R~l~v~K~r~~~~--~~~~f~I~~~-Gi~~~~~~  342 (357)
                      +..    ..|.++|.|+|+++.  ..+.|+|+++ ||.++++-
T Consensus       191 ~~~~~~~~~r~l~v~K~r~~~~~~~~~~f~i~~~~Gi~~~~~~  233 (235)
T 2w0m_A          191 RMIRNGELHRYILIEKMRQTDHDKHVWEIDIVNGKGIVLKGRL  233 (235)
T ss_dssp             EEEETTEEEEEEEEEEETTCCCCCSCEEEEEETTTEEEEEEEC
T ss_pred             EEecCCcEEEEEEEEeccCCcccceeEEEEEcCCCCeEEecCC
Confidence            752    369999999999874  6789999999 99998753

>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=99.89  E-value=1.9e-21  Score=176.54  Aligned_cols=248  Identities=10%  Similarity=0.093  Sum_probs=147.9

Q ss_pred             HHHHHHHhcccCCCCCCC-CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           69 LLMEQRAATEHLGGHLPT-RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        69 ~~~~~~~~~~~~~~~i~T-G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +.++++.+. ....+++| |++.||.++ +|+++|+++.|+|+||+|||||+.+++...+..  .   +.+|+|++.|++
T Consensus         3 ~~l~~~~~~-~~~~~i~t~g~~~Ld~i~-~~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~--~---G~~v~~~~~e~~   75 (296)
T 1cr0_A            3 ERIREHLSS-EESVGLLFSGCTGINDKT-LGARGGEVIMVTSGSGMGKSTFVRQQALQWGTA--M---GKKVGLAMLEES   75 (296)
T ss_dssp             HHHHHHHHH-CCCCCBCCCSCTTHHHHH-CSBCTTCEEEEEESTTSSHHHHHHHHHHHHHHT--S---CCCEEEEESSSC
T ss_pred             hHhhhhhcc-CCcCCcccCCHHHHHHHh-cCCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHH--c---CCeEEEEeCcCC
Confidence            344444332 33779999 999999998 679999999999999999999999999887642  1   358999999874


Q ss_pred             Cch--HHHHHHHhccCchh---h-----ccc---chHHHhh--cCeEEeCC---CCHHHHHHHHHHHHHHhhhcCeeEEE
Q 035774          148 FTS--RRMIEMGASSFPEI---F-----HSK---GMAQEMA--GRILVLQP---TSLSEFTESLEKIKVSLLQNQVKLLV  209 (357)
Q Consensus       148 ~~~--~rl~~~~~~~~~~~---~-----~~~---~~~~~~~--~~i~~~~~---~~~~~~~~~l~~l~~~~~~~~~~lvv  209 (357)
                      ...  .++...........   .     ...   .....++  .++++.+.   .+..++   ...+......+++++||
T Consensus        76 ~~~~~~r~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~l~i~~~~~~~~~~~l---~~~~~a~~~~~~p~lli  152 (296)
T 1cr0_A           76 VEETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRL---LAKLAYMRSGLGCDVII  152 (296)
T ss_dssp             HHHHHHHHHHHHTTCCGGGCHHHHHHHHHHTHHHHHHHHHHSSSCEEEECCCCSCCHHHH---HHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHHHHHHcCCChhhccccccCCCCHHHHHHHHHHHhccCCEEEECCCCCCCHHHH---HHHHHHHHHhcCCCEEE
Confidence            321  11111111100000   0     000   0111222  24555443   344444   34444444457899999


Q ss_pred             EeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceec
Q 035774          210 IDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVA  289 (357)
Q Consensus       210 IDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p  289 (357)
                      ||+++.+....  ....+...+.++++.|++++++++++||+++|..+.....            +...+..+..+.++.
T Consensus       153 lDept~~~~~~--~~~d~~~~~~~i~~~L~~la~~~~~~vi~vsh~~r~~~~~------------~~~~~~~p~l~dl~~  218 (296)
T 1cr0_A          153 LDHISIVVSAS--GESDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGK------------AHEEGRPVSITDLRG  218 (296)
T ss_dssp             EEEEC-------------CHHHHHHHHHHHHHHHHHCCEEEEEEECC-----------------------------CCC-
T ss_pred             EcCccccCCCC--CCCCHHHHHHHHHHHHHHHHHHhCCeEEEEEecCcccccc------------ccccCCCCCHHHhcc
Confidence            99999986431  1122446788899999999999999999999996411000            000111112223322


Q ss_pred             ccchhHhhhccEEEEEEEeC-----CeEEEEEEeCCC-CCCce---eEEEEcCCCceeccCC
Q 035774          290 VLGFHWAHAVTIRLVLEAKS-----GQRFMNVEKSPT-SPPLA---FSFTINPSGISLLTDD  342 (357)
Q Consensus       290 alg~~w~~~~~~rl~l~~~~-----~~R~l~v~K~r~-~~~~~---~~f~I~~~Gi~~~~~~  342 (357)
                      +  ..+.+.++.++++++..     ..|.+.|.|+|+ ++.+.   +.|.+...|+...+..
T Consensus       219 s--~~i~~~aD~vi~L~~~~~~~~~~~~~l~i~K~R~~g~~g~~~~~~f~~~~~~f~~~~~~  278 (296)
T 1cr0_A          219 S--GALRQLSDTIIALERNQQGDMPNLVLVRILKCRFTGDTGIAGYMEYNKETGWLEPSSYS  278 (296)
T ss_dssp             ----CHHHHCSEEEEEEEC-------CEEEEEEEETTTCCCEEEEEEEECTTTCCEEECCC-
T ss_pred             c--HHhHhhCcEEEEEecCcccCCCCeEEEEEEccccCCCCCceEEEEEEcCccEEecCCCC
Confidence            1  24788899999998753     468999999995 87654   4666778888776544

>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=99.82  E-value=5.1e-19  Score=159.19  Aligned_cols=223  Identities=18%  Similarity=0.187  Sum_probs=134.4

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC----CCCeEEEEeCCCCCchH--HHHHH
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG----LDGGVIYIDVESTFTSR--RMIEM  156 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg----~~~~vl~i~~e~~~~~~--rl~~~  156 (357)
                      .++||++.||.+++ |+++|++++|+|+||+|||||+++++..++....+.|    .+++|+|++.|+.....  ++..+
T Consensus        12 ~i~tg~~~ld~~lg-gl~~G~i~~i~G~~GsGKTtl~~~l~~~~~~g~~~~g~~~~~~~~v~~~~~e~~~~~~~~r~~~~   90 (279)
T 1nlf_A           12 AFAAAPPPLDYVLP-NMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHAL   90 (279)
T ss_dssp             HHHSCCCCCCEEET-TEETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSCHHHHHHHHHHH
T ss_pred             HhcCCCCChheeEC-CccCCCEEEEEcCCCCCHHHHHHHHHHHHhcCCCcCCCccCCCccEEEEECCCCHHHHHHHHHHH
Confidence            58899999999995 7999999999999999999999999986653110000    13679999999865321  33333


Q ss_pred             HhccCchhhcccchHHHhhcCeEEeCCC-------CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChH
Q 035774          157 GASSFPEIFHSKGMAQEMAGRILVLQPT-------SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQH  229 (357)
Q Consensus       157 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~-------~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~  229 (357)
                      ... +..     .......+++.+.+..       +..+    +..+...+  .++++||||+++++...+    .....
T Consensus        91 g~~-~~~-----~~~~~~~~~l~l~~~~~~~~~~ls~g~----~~~i~~l~--~~~~livlDe~~~~~~~d----~~~~~  154 (279)
T 1nlf_A           91 GAH-LSA-----EERQAVADGLLIQPLIGSLPNIMAPEW----FDGLKRAA--EGRRLMVLDTLRRFHIEE----ENASG  154 (279)
T ss_dssp             HTT-SCH-----HHHHHHHHHEEECCCTTSCCCTTSHHH----HHHHHHHH--TTCSEEEEECGGGGCCSC----TTCHH
T ss_pred             Hhh-cCh-----hhhhhccCceEEeecCCCCcccCCHHH----HHHHHHhc--CCCCEEEECCHHHhcCCC----cCchH
Confidence            211 110     0111223444443221       2222    22333333  268999999999987542    12345


Q ss_pred             HHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC
Q 035774          230 PLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS  309 (357)
Q Consensus       230 ~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~  309 (357)
                      .+..+++.|+.++++.|++||+++|..+.....              +..+.  .+..+  .+.++.+.+.....+++..
T Consensus       155 ~~~~~~~~L~~l~~~~g~tvi~i~H~~~~~~~~--------------g~~~~--~~~~~--g~~~l~d~v~~~~~~~~~~  216 (279)
T 1nlf_A          155 PMAQVIGRMEAIAADTGCSIVFLHHASKGAAMM--------------GAGDQ--QQASR--GSSVLVDNIRWQSYLSSMT  216 (279)
T ss_dssp             HHHHHHHHHHHHHHHHCCEEEEEEEC--------------------------------------CTGGGCSCEEEEEECC
T ss_pred             HHHHHHHHHHHHHHHcCCEEEEEecCCCccccc--------------CCchh--hhhcc--chhhhccchhhhhhccCCC
Confidence            678899999999999999999999987643210              00000  00011  1122344444444455432


Q ss_pred             -----------C----eEEEEEEeCCCCCCc-eeEEEEcCCCceecc
Q 035774          310 -----------G----QRFMNVEKSPTSPPL-AFSFTINPSGISLLT  340 (357)
Q Consensus       310 -----------~----~R~l~v~K~r~~~~~-~~~f~I~~~Gi~~~~  340 (357)
                                 .    ...+.|.|+|++|++ ...|.+.+.|+.+.+
T Consensus       217 ~~~~~~~gi~~~~~~~~~~~~v~K~~~~~~~~~~~~~~~~~G~l~~~  263 (279)
T 1nlf_A          217 SAEAEEWGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPA  263 (279)
T ss_dssp             HHHHHHTTCCTTSGGGEEEEEEEECSSSSCCCCEEEEECGGGCEEEC
T ss_pred             HHHHHHhCCChhhcCcEEEeeeccccCCCCCCceEEEEcCCeeEecc
Confidence                       1    234779999999864 356889999988773

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=99.82  E-value=6.3e-19  Score=172.17  Aligned_cols=215  Identities=19%  Similarity=0.167  Sum_probs=142.1

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||+++||.+|+||+++|+++.|.|+||+|||||+.+++.....   .   +++++|++++++  ...+...... 
T Consensus       260 ~~~l~~g~~~ld~vL~g~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~---~---G~~vi~~~~ee~--~~~l~~~~~~-  330 (525)
T 1tf7_A          260 NVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACA---N---KERAILFAYEES--RAQLLRNAYS-  330 (525)
T ss_dssp             CCEECCSCHHHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHT---T---TCCEEEEESSSC--HHHHHHHHHT-
T ss_pred             cceeecChHHHHHHhCCCCCCCcEEEEEeCCCCCHHHHHHHHHHHHHh---C---CCCEEEEEEeCC--HHHHHHHHHH-
Confidence            457899999999999999999999999999999999999999987653   2   367999999875  2333332221 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCC----CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPT----SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHIS  236 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~----~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~  236 (357)
                      +.  .....+.  ..+.+.+.+..    +..+.   ...+...+...+++++|||+++.+.... .    . .+.++.+.
T Consensus       331 ~g--~~~~~~~--~~g~~~~~~~~p~~LS~g~~---q~~~~a~~l~~~p~llilDp~~~Ld~~~-~----~-~~~~~~i~  397 (525)
T 1tf7_A          331 WG--MDFEEME--RQNLLKIVCAYPESAGLEDH---LQIIKSEINDFKPARIAIDSLSALARGV-S----N-NAFRQFVI  397 (525)
T ss_dssp             TS--CCHHHHH--HTTSEEECCCCGGGSCHHHH---HHHHHHHHHTTCCSEEEEECHHHHTSSS-C----H-HHHHHHHH
T ss_pred             cC--CCHHHHH--hCCCEEEEEeccccCCHHHH---HHHHHHHHHhhCCCEEEEcChHHHHhhC-C----h-HHHHHHHH
Confidence            11  0101110  11233333221    33332   2233333445689999999999886541 1    1 22444445


Q ss_pred             HHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe----CCeE
Q 035774          237 LITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK----SGQR  312 (357)
Q Consensus       237 ~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~----~~~R  312 (357)
                      .|.+.+++.|++||+++|.....+.               ...+           +..+.+++|.++.++..    ...|
T Consensus       398 ~ll~~l~~~g~tvilvsh~~~~~~~---------------~~~~-----------~~~l~~~~D~vi~L~~ge~~~~~~R  451 (525)
T 1tf7_A          398 GVTGYAKQEEITGLFTNTSDQFMGA---------------HSIT-----------DSHISTITDTIILLQYVEIRGEMSR  451 (525)
T ss_dssp             HHHHHHHHTTCEEEEEEECSSSSCC---------------CSSC-----------SSCCTTTCSEEEEEEEEEETTEEEE
T ss_pred             HHHHHHHhCCCEEEEEECcccccCc---------------cccc-----------CcccceeeeEEEEEEEEEeCCEEEE
Confidence            5555556789999999998643220               0000           01146778888888754    2379


Q ss_pred             EEEEEeCCCCCC--ceeEEEEcCCCceeccCCC
Q 035774          313 FMNVEKSPTSPP--LAFSFTINPSGISLLTDDG  343 (357)
Q Consensus       313 ~l~v~K~r~~~~--~~~~f~I~~~Gi~~~~~~~  343 (357)
                      .++|+|+|++++  ....|+|++.||++.++..
T Consensus       452 ~l~v~K~R~~~~~~~~~~f~i~~~Gi~v~~~~~  484 (525)
T 1tf7_A          452 AINVFKMRGSWHDKAIREFMISDKGPDIKDSFR  484 (525)
T ss_dssp             EEEEEEESSSCCCCBCEEEEECSSCEEEEEECT
T ss_pred             EEEEEECCCCCCCCCEEEEEEcCCCEEEecccc
Confidence            999999999985  5689999999999887653

>3bs4_A Uncharacterized protein PH0321; structural genomics, unknown function, PSI-2, protein struct initiative; 1.60A {Pyrococcus horikoshii}

Probab=99.81  E-value=1.8e-18  Score=152.12  Aligned_cols=202  Identities=10%  Similarity=-0.019  Sum_probs=119.1

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh-ccC
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA-SSF  161 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~-~~~  161 (357)
                      .++||+++||++|+||+++|++++|.|.||+|||+|++||+.+.+..      +++|+||+++++  +..+...+. ..|
T Consensus         2 ~i~tGi~~LD~~l~GGl~~gs~~li~g~p~~~~~~l~~qfl~~g~~~------Ge~~~~~~~~e~--~~~l~~~~~~~G~   73 (260)
T 3bs4_A            2 SLSWEIEELDREIGKIKKHSLILIHEEDASSRGKDILFYILSRKLKS------DNLVGMFSISYP--LQLIIRILSRFGV   73 (260)
T ss_dssp             CBCCSSHHHHHHHCCBCTTCEEEEEECSGGGCHHHHHHHHHHHHHHT------TCEEEEEECSSC--HHHHHHHHHHTTC
T ss_pred             cCccCcHHHHHHhCCCCCCCcEEEEEeCCCccHHHHHHHHHHHHHHC------CCcEEEEEEeCC--HHHHHHHHHHcCC
Confidence            48999999999999999999999999999999999999999999853      699999999885  333333222 222


Q ss_pred             chhhcccchHHHhhcCeEEe-------------------C-CCCHHHHHHHHHHHHHH------hhh-cC-ee-EEEEec
Q 035774          162 PEIFHSKGMAQEMAGRILVL-------------------Q-PTSLSEFTESLEKIKVS------LLQ-NQ-VK-LLVIDS  212 (357)
Q Consensus       162 ~~~~~~~~~~~~~~~~i~~~-------------------~-~~~~~~~~~~l~~l~~~------~~~-~~-~~-lvvIDs  212 (357)
                      .    .....+  .+++.++                   . ..++.++...+..+...      +.. .+ .+ ++|||+
T Consensus        74 d----l~~~~~--~g~l~i~d~~~~~~~~~~~~~~v~~~~~e~d~~~l~~~i~~iv~~~~~~~~i~~~~~~~rvv~vids  147 (260)
T 3bs4_A           74 D----VIKYLE--NHRLAIVDTFGSFHGIKATMPGVWYLEGMLSSETLPIKYAKAVEDHKKVWMDLNLFEGRELYGFAIS  147 (260)
T ss_dssp             C----HHHHHH--TTSEEEECHHHHHHTC---CTTEECCCSCCCTTTHHHHHHHHHHHHHHHHHHTTCSTTCCEEEEEET
T ss_pred             C----HHHHhh--CCcEEEEEcccccccccccccceecccccCCHHHHHHHHHHHHHhhccccchhhccCCceEEEEEee
Confidence            1    110000  0122222                   1 23444443334443333      122 23 45 358888


Q ss_pred             cccccCCCCCCCCCChHHHHHHHHHHHH------HHHH-cCCeEEEeccccccCCCCCCcccccccccccccccccCCCc
Q 035774          213 MEALVPGVHEQRAPGQHPLSWHISLITS------LAEF-SRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYS  285 (357)
Q Consensus       213 l~~l~~~~~~~~~~r~~~~~~i~~~Lk~------la~~-~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  285 (357)
                      +.++....      .......+...+..      +.++ .+++++++.+ .. ..                         
T Consensus       148 ldsl~~~~------~~~~~~~~~~~ll~~~~~~~~~~~~~~~ttil~~~-~~-~~-------------------------  194 (260)
T 3bs4_A          148 MSGYLEVF------TPEETLRYLETSAEVRYGHPAYKKYPRGTNFWLWE-GV-KD-------------------------  194 (260)
T ss_dssp             GGGGGGTS------CHHHHHHHHHHHHHHHHHCHHHHSSCCCEEEEEEE-SC-SC-------------------------
T ss_pred             cchHHHHh------ChhhHHHHHHHHHHhhhhHHHHhccCCcEEEEEEC-CC-cc-------------------------
Confidence            88776441      11222222222322      3333 6777777754 11 11                         


Q ss_pred             ceecccchhHhhhccEEEEEEEe----CCeEEEEEEeCCCCC--CceeEEEEcCC
Q 035774          286 HIVAVLGFHWAHAVTIRLVLEAK----SGQRFMNVEKSPTSP--PLAFSFTINPS  334 (357)
Q Consensus       286 ~~~palg~~w~~~~~~rl~l~~~----~~~R~l~v~K~r~~~--~~~~~f~I~~~  334 (357)
                         +.........+|.+|.++..    +..|.+.|.|+|.+.  +..++|.|+..
T Consensus       195 ---~~~~~~l~~laD~VI~lr~~e~~g~~rR~L~V~K~Rg~~~~~~~re~~i~~~  246 (260)
T 3bs4_A          195 ---KRVLLSVYRRADYVLKTRSSLGENGIKRELLVIKTPKPIEELVRFEYEFKGN  246 (260)
T ss_dssp             ---HHHHHHHHHHCSEEEEEEEEEETTEEEEEEEEEECCC-----CEEEEEEETT
T ss_pred             ---cccccceEEEeeEEEEEEEEecCCceEEEEEEEECCCCCcCCceEEEEEecC
Confidence               00011134567888888653    237999999999988  35666777743

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=99.69  E-value=2.2e-15  Score=147.04  Aligned_cols=217  Identities=18%  Similarity=0.279  Sum_probs=143.1

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+++||++.||.+..||+++|+++.|.|+||||||||+.+|+.+.+.+.     +.+++||+.++.  ...+.+.... 
T Consensus        18 ~~~~~~g~~~Ld~i~~G~i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~~~-----~~g~i~v~g~~~--~~~~~~~~~~-   89 (525)
T 1tf7_A           18 IAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF-----DEPGVFVTFEET--PQDIIKNARS-   89 (525)
T ss_dssp             CCEECCCCTTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHH-----CCCEEEEESSSC--HHHHHHHHGG-
T ss_pred             cccccCCchhHHHhcCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhC-----CCCEEEEEEeCC--HHHHHHHHHH-
Confidence            56799999999999988999999999999999999999999865555432     356999999873  3333332221 


Q ss_pred             CchhhcccchHHHhhcCeEEeCCC---------CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPT---------SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPL  231 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~---------~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~  231 (357)
                      +...++.  .  ....++......         ....+...+.++...+...++++|+||+++++.+..    .......
T Consensus        90 ~g~~~q~--~--~~~~~l~~~~~~~~~~~~~~l~~~~l~~~~~~~~~~LS~g~~~~lilDe~t~~~~~~----~lD~~~~  161 (525)
T 1tf7_A           90 FGWDLAK--L--VDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQY----DASSVVR  161 (525)
T ss_dssp             GTCCHHH--H--HHTTSEEEEECCCCSSCCSCCSSHHHHHHHHHHHHHHHHHTCSEEEEECSTTTSTTT----CCHHHHH
T ss_pred             cCCChHH--h--hccCcEEEEecCcccchhhhhcccCHHHHHHHHHHHHHHcCCCEEEECCHHHHHHhc----CCHHHHH
Confidence            1111111  0  011223332211         223455666777777777889999999999886541    1122333


Q ss_pred             HHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEE----
Q 035774          232 SWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA----  307 (357)
Q Consensus       232 ~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~----  307 (357)
                      ..+...++.+++ .|++||+++|........                 ..   ..+       .+.++|.++.++.    
T Consensus       162 ~~l~~ll~~l~~-~g~tvl~itH~~~~~~~~-----------------~~---~~i-------~~~laD~vi~L~~~~~~  213 (525)
T 1tf7_A          162 RELFRLVARLKQ-IGATTVMTTERIEEYGPI-----------------AR---YGV-------EEFVSDNVVILRNVLEG  213 (525)
T ss_dssp             HHHHHHHHHHHH-HTCEEEEEEECSSSSSCS-----------------ST---TSC-------HHHHCSEEEEEEEECST
T ss_pred             HHHHHHHHHHHH-CCCEEEEEecCCCCcccc-----------------cc---ccc-------eeeeeeEEEEEEEEccC
Confidence            455666666655 699999999875432200                 00   000       1455788888887    


Q ss_pred             eCCeEEEEEEeCCCCC--CceeEEEEcCCCceeccC
Q 035774          308 KSGQRFMNVEKSPTSP--PLAFSFTINPSGISLLTD  341 (357)
Q Consensus       308 ~~~~R~l~v~K~r~~~--~~~~~f~I~~~Gi~~~~~  341 (357)
                      ....|.+.+.|+|..+  ...+.|.|++.|+.+++.
T Consensus       214 G~~~r~l~~~k~r~~~~~~~~~~~~i~~~gi~v~p~  249 (525)
T 1tf7_A          214 ERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL  249 (525)
T ss_dssp             TCCEEEEEEEEETTSCCCCSEEEEEEETTEEEECCT
T ss_pred             CceeEEEEEEECCCCCCCCceEEEEEcCCCEEEEec
Confidence            3457899999999776  356899999999998763

>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=99.62  E-value=8.5e-16  Score=138.07  Aligned_cols=128  Identities=19%  Similarity=0.202  Sum_probs=91.4

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC--CCCCchHHHHHHHhc
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV--ESTFTSRRMIEMGAS  159 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~--e~~~~~~rl~~~~~~  159 (357)
                      ..++||++.||++| ||+++|.+++|+|+||+|||+||++++.+  .       +.+|+||++  ++.++.         
T Consensus       104 ~~i~TGi~~LD~lL-GGi~~gsviLI~GpPGsGKTtLAlqlA~~--~-------G~~VlyIs~~~eE~v~~---------  164 (331)
T 2vhj_A          104 GELVGCSPVVAEFG-GHRYASGMVIVTGKGNSGKTPLVHALGEA--L-------GGKDKYATVRFGEPLSG---------  164 (331)
T ss_dssp             TTCCSBCCEEEEET-TEEEESEEEEEECSCSSSHHHHHHHHHHH--H-------HTTSCCEEEEBSCSSTT---------
T ss_pred             hccccCcHHHHHHh-CCCCCCcEEEEEcCCCCCHHHHHHHHHHh--C-------CCCEEEEEecchhhhhh---------
Confidence            34789999999999 89999999999999999999999999986  1       478999998  332100         


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC--CCCChHHHHHHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ--RAPGQHPLSWHISL  237 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~--~~~r~~~~~~i~~~  237 (357)
                           +          .       .   +....+..+...+.+.+  +||||+++.+.......  .....+.+++++..
T Consensus       165 -----~----------~-------~---~le~~l~~i~~~l~~~~--LLVIDsI~aL~~~~~~~s~~G~v~~~lrqlL~~  217 (331)
T 2vhj_A          165 -----Y----------N-------T---DFNVFVDDIARAMLQHR--VIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSD  217 (331)
T ss_dssp             -----C----------B-------C---CHHHHHHHHHHHHHHCS--EEEEECCTTTC-----------CCHHHHHHHHH
T ss_pred             -----h----------h-------c---CHHHHHHHHHHHHhhCC--EEEEecccccccccccccccchHHHHHHHHHHH
Confidence                 0          0       1   22333444445555545  99999999986542210  01123568889999


Q ss_pred             HHHHHHHcCCeEEEeccc
Q 035774          238 ITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       238 Lk~la~~~~~~vv~~~q~  255 (357)
                      |..++++.+++++++++.
T Consensus       218 L~~~~k~~gvtVIlttnp  235 (331)
T 2vhj_A          218 IGAMAASRGCVVIASLNP  235 (331)
T ss_dssp             HHHHHHHHTCEEEEECCC
T ss_pred             HHHHHhhCCCEEEEEeCC
Confidence            999999999999987653

>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1

Probab=99.07  E-value=6.5e-11  Score=89.75  Aligned_cols=84  Identities=18%  Similarity=0.154  Sum_probs=52.4

Q ss_pred             cCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcccCCCCCCCCc
Q 035774            9 MRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQRAATEHLGGHLPTRL   88 (357)
Q Consensus         9 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~TG~   88 (357)
                      +|+.+....+|.++||.|++++...++.+|.++.|+++..+.+++.++.+....+|.+|.++++++.+    ..+|+||+
T Consensus        31 ~GIg~~~i~kL~eAG~~Tve~va~a~~~eL~~i~GIse~ka~kIi~aA~kl~~~gF~ta~e~~~~r~~----~~~itTGs  106 (114)
T 1b22_A           31 CGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVPMGFTTATEFHQRRSE----IIQITTGS  106 (114)
T ss_dssp             TTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHHSCCC-------------------------
T ss_pred             cCCCHHHHHHHHHcCcCcHHHHHhCCHHHHHHccCCCHHHHHHHHHHHHHHcccCCCcHHHHHHHhcC----CCeeccCc
Confidence            36999999999999999999999999999999999999999999999998888899999999998755    66899999


Q ss_pred             hhHHhhhc
Q 035774           89 KGLDAALC   96 (357)
Q Consensus        89 ~~LD~~l~   96 (357)
                      +.||.+|+
T Consensus       107 ~~lD~lLg  114 (114)
T 1b22_A          107 KELDKLLQ  114 (114)
T ss_dssp             --------
T ss_pred             HHHHhhhC
Confidence            99999985

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=98.80  E-value=3.4e-08  Score=84.84  Aligned_cols=118  Identities=15%  Similarity=0.139  Sum_probs=72.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeE
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL  179 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~  179 (357)
                      .+|.+++++|++|+||||++++++.++..      .+.+|+++..+.+..  -..++... .    ..      ....+.
T Consensus        10 ~~G~i~litG~mGsGKTT~ll~~~~r~~~------~g~kVli~~~~~d~r--~~~~i~sr-l----G~------~~~~~~   70 (223)
T 2b8t_A           10 KIGWIEFITGPMFAGKTAELIRRLHRLEY------ADVKYLVFKPKIDTR--SIRNIQSR-T----GT------SLPSVE   70 (223)
T ss_dssp             -CCEEEEEECSTTSCHHHHHHHHHHHHHH------TTCCEEEEEECCCGG--GCSSCCCC-C----CC------SSCCEE
T ss_pred             CCcEEEEEECCCCCcHHHHHHHHHHHHHh------cCCEEEEEEeccCch--HHHHHHHh-c----CC------Cccccc
Confidence            56899999999999999999999998874      257899997654211  00011110 0    00      001111


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          180 VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       180 ~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      +   .+.   .+++..+...+...++++|+||+++.+..              +++..|..++.. +++||++.+...
T Consensus        71 ~---~~~---~~i~~~i~~~~~~~~~dvViIDEaQ~l~~--------------~~ve~l~~L~~~-gi~Vil~Gl~~d  127 (223)
T 2b8t_A           71 V---ESA---PEILNYIMSNSFNDETKVIGIDEVQFFDD--------------RICEVANILAEN-GFVVIISGLDKN  127 (223)
T ss_dssp             E---SST---HHHHHHHHSTTSCTTCCEEEECSGGGSCT--------------HHHHHHHHHHHT-TCEEEEECCSBC
T ss_pred             c---CCH---HHHHHHHHHHhhCCCCCEEEEecCccCcH--------------HHHHHHHHHHhC-CCeEEEEecccc
Confidence            1   122   23334444444445689999999996421              134456666664 999999988654

>2kz3_A Putative uncharacterized protein RAD51L3; RAD51D, homologous recombination, unknown function; NMR {Homo sapiens}

Probab=98.46  E-value=1.4e-07  Score=66.97  Aligned_cols=73  Identities=12%  Similarity=0.062  Sum_probs=66.6

Q ss_pred             Cccccccc-cCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCcccHHHHHHH
Q 035774            1 MANKLISE-MRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPFQTALLLMEQ   73 (357)
Q Consensus         1 ~~~~~~~~-~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   73 (357)
                      |-++..+. .+|++.+.+.|+++++.|++|++..++.+|.++++++.+.+.++.+.+...+++.+.++.+++++
T Consensus         1 m~~l~~~~~p~Lse~~~~~L~~~~I~Tv~Dfl~~d~~eL~~~~~ls~~~v~~l~r~l~~~~s~~~~~~~~~~~~   74 (83)
T 2kz3_A            1 MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEE   74 (83)
T ss_dssp             CCCCCTTSSTTCCHHHHHHHHHTTCCCHHHHTTSCHHHHHHHHTCCHHHHHHHHHHHHHHHCSSCCCCCCCCCC
T ss_pred             CCccccccCCCCCHHHHHHHHHCCCCCHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCcCcHHHHHHH
Confidence            56677777 49999999999999999999999999999999999999999999999998888888888887765

>4a8j_A Elongator complex protein 4; transcription; 2.10A {Saccharomyces cerevisiae} PDB: 4ejs_A

Probab=98.46  E-value=1.2e-06  Score=79.59  Aligned_cols=119  Identities=13%  Similarity=0.090  Sum_probs=74.9

Q ss_pred             HHHHHHHHHHHhh--hcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHc--CCeEEEeccccccCCCCCC
Q 035774          189 FTESLEKIKVSLL--QNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS--RIPIVVTNQVRPQSHDESC  264 (357)
Q Consensus       189 ~~~~l~~l~~~~~--~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~--~~~vv~~~q~~~~~~~~~~  264 (357)
                      +..++.++.+.+.  ...+-+|+|=|+.+-.+..  ........+-.|+..||.|.+.+  +|+++++-...-  -    
T Consensus       200 y~~lL~~I~~~i~~~~~~ilRIvI~SLgSP~wy~--~~~~~~~~ll~FL~~LRaLlR~~~~~~v~~iTlP~~l--~----  271 (361)
T 4a8j_A          200 VSTILSQIEQTIKRNDKKLIRIVIPSLLHPAMYP--PKMFESSEIIGLMHGVRSLVKKYYERVVLFASISIDI--I----  271 (361)
T ss_dssp             HHHHHHHHHHHHHHTTTSEEEEEETTTTCTTTSC--GGGGBHHHHHHHHHHHHHHHHHTTTTEEEEEEEECTT--S----
T ss_pred             HHHHHHHHHHHHhcCCCceEEEEecCCCCcccCC--CcccCHHHHHHHHHHHHHHHhhcCCceEEEEEEChHH--c----
Confidence            4455666655553  3468889999998876642  22224577888999999999987  456666632211  0    


Q ss_pred             cccccccccccccccccCCCcceecccchhHhhhccEEEEEEEe-------------C-----CeEEEEEEeCCCC----
Q 035774          265 LYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAK-------------S-----GQRFMNVEKSPTS----  322 (357)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~-------------~-----~~R~l~v~K~r~~----  322 (357)
                                          .   +.+-..|++.+|+++.|+--             .     ..=.++|.|-+..    
T Consensus       272 --------------------~---~~l~~rle~l~D~vi~L~pF~~~~~~~~~~~yk~~p~~~~~GLl~V~KLP~l~~~g  328 (361)
T 4a8j_A          272 --------------------T---PPLLVLLRNMFDSVINLEPFNQEMTEFLERVYKSQPGKIQHGLVHILKLPVFTDRG  328 (361)
T ss_dssp             --------------------C---HHHHHHHHHHCSEEEEEEECCHHHHHHHHHHTTTCGGGCCCEEEEEEECTTHHHHT
T ss_pred             --------------------C---hHHHHHHHHhCcEEEEeeecCCchhhhcccccccCcccccceEEEEEecccccccC
Confidence                                0   12334589999999999852             1     2557889996531    


Q ss_pred             ---C-CceeEEEEcCCCcee
Q 035774          323 ---P-PLAFSFTINPSGISL  338 (357)
Q Consensus       323 ---~-~~~~~f~I~~~Gi~~  338 (357)
                         + .....|++...-+.+
T Consensus       329 ~~~~~~~dlaFKl~Rkkf~I  348 (361)
T 4a8j_A          329 EMRVLKSEWAFKNGRKKFEI  348 (361)
T ss_dssp             CCCCEEEEEEEEECSSCEEE
T ss_pred             CCCCCccceEEEecceeEEE
Confidence               1 134566666554433

>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=98.42  E-value=9.5e-08  Score=78.94  Aligned_cols=125  Identities=13%  Similarity=0.121  Sum_probs=64.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeC-
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQ-  182 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~-  182 (357)
                      +++|.|++|||||+||.+++..          +.+++|++++..++.+...++....      .    .. ......+. 
T Consensus         1 ~ilV~Gg~~SGKS~~A~~la~~----------~~~~~yiaT~~~~d~e~~~rI~~h~------~----~R-~~~w~tiE~   59 (180)
T 1c9k_A            1 MILVTGGARSGKSRHAEALIGD----------APQVLYIATSQILDDEMAARIQHHK------D----GR-PAHWRTAEC   59 (180)
T ss_dssp             CEEEEECTTSSHHHHHHHHHCS----------CSSEEEEECCCC------CHHHHHH------H----TS-CTTEEEECC
T ss_pred             CEEEECCCCCcHHHHHHHHHhc----------CCCeEEEecCCCCCHHHHHHHHHHH------h----cC-CCCcEEEEc
Confidence            4789999999999999999843          2579999998766554433333221      0    00 01222222 


Q ss_pred             CCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC-----CC--CC----hHHH-HHHHHHHHHHHHHcCCeEE
Q 035774          183 PTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ-----RA--PG----QHPL-SWHISLITSLAEFSRIPIV  250 (357)
Q Consensus       183 ~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~-----~~--~r----~~~~-~~i~~~Lk~la~~~~~~vv  250 (357)
                      +.+..+.   +..    . ..+.++|+||+++.+.......     ..  ..    ...+ .++...+..+.+...-.|+
T Consensus        60 p~~l~~~---l~~----~-~~~~~~VLvDclt~wl~n~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~vl  131 (180)
T 1c9k_A           60 WRHLDTL---ITA----D-LAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVL  131 (180)
T ss_dssp             SSCGGGT---SCT----T-SCTTCEEEEECHHHHHHHHHHHC----CTTSCCHHHHHHHHHHHHHHHHHHHHHCCSEEEE
T ss_pred             HhhHHHH---HHh----h-cccCCeEEEcCHHHHHHHHHhhcccccccccccchhhHHHHHHHHHHHHHHHHccCCCEEE
Confidence            2332222   110    0 1123699999999887552210     10  01    1112 2344445556555555666


Q ss_pred             Eeccccc
Q 035774          251 VTNQVRP  257 (357)
Q Consensus       251 ~~~q~~~  257 (357)
                      ++|++..
T Consensus       132 VsNEVG~  138 (180)
T 1c9k_A          132 VTNEVGM  138 (180)
T ss_dssp             ECCCCCS
T ss_pred             EEccccC
Confidence            6676644

>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=98.39  E-value=9.7e-07  Score=76.61  Aligned_cols=44  Identities=16%  Similarity=0.136  Sum_probs=34.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-..         ......+...|++++++.+.+||+++|-
T Consensus       162 ~~p~llllDEPts~LD---------~~~~~~i~~~l~~l~~~~g~tvi~vtHd  205 (235)
T 3tif_A          162 NNPPIILADQPTWALD---------SKTGEKIMQLLKKLNEEDGKTVVVVTHD  205 (235)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHHHCCEEEEECSC
T ss_pred             cCCCEEEEeCCcccCC---------HHHHHHHHHHHHHHHHHcCCEEEEEcCC
Confidence            4799999998776543         2455667888999988889999999885

>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=98.37  E-value=1.9e-06  Score=71.34  Aligned_cols=42  Identities=19%  Similarity=0.146  Sum_probs=32.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|..+.|.||||+|||+|+..++......  .   +..++|++..
T Consensus        35 ~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~--~---g~~~~~~~~~   76 (180)
T 3ec2_A           35 PEEGKGLTFVGSPGVGKTHLAVATLKAIYEK--K---GIRGYFFDTK   76 (180)
T ss_dssp             GGGCCEEEECCSSSSSHHHHHHHHHHHHHHH--S---CCCCCEEEHH
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHHHHHHHH--c---CCeEEEEEHH
Confidence            4568999999999999999999998876521  1   3578887653

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=98.34  E-value=2e-06  Score=79.07  Aligned_cols=45  Identities=11%  Similarity=0.163  Sum_probs=36.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .++++++.|.-++-..         ......++..|++++++.|+|||+++|--
T Consensus       180 ~~P~lLLlDEPTs~LD---------~~~~~~i~~lL~~l~~~~g~Tii~vTHdl  224 (366)
T 3tui_C          180 SNPKVLLCDQATSALD---------PATTRSILELLKDINRRLGLTILLITHEM  224 (366)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHHSCCEEEEEESCH
T ss_pred             cCCCEEEEECCCccCC---------HHHHHHHHHHHHHHHHhCCCEEEEEecCH
Confidence            4799999998776543         24556788899999999999999999853

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=98.32  E-value=1.3e-06  Score=72.76  Aligned_cols=111  Identities=16%  Similarity=0.181  Sum_probs=63.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      +|.+++++|++|+||||++++++.+....      +.+++++....+  . |.   ....+      ..........+.+
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~~~~~~~~~------g~~v~~~~~~~d--~-r~---~~~~i------~s~~g~~~~~~~~   63 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLSFVEIYKLG------KKKVAVFKPKID--S-RY---HSTMI------VSHSGNGVEAHVI   63 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHHHT------TCEEEEEEEC-----------CCCEE------CC----CEECEEE
T ss_pred             ccEEEEEECCCCCCHHHHHHHHHHHHHHC------CCeEEEEeeccc--c-cc---CcccE------EecCCCceeeEEE
Confidence            47899999999999999999999887632      478888865431  1 10   00000      0000000011111


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                         .+..++.   .    .+. .+.++|+||.++.+..              .+...|+.++.+ ++.|+++...
T Consensus        64 ---~~~~~~~---~----~~~-~~~dvviIDE~Q~~~~--------------~~~~~l~~l~~~-~~~Vi~~Gl~  112 (184)
T 2orw_A           64 ---ERPEEMR---K----YIE-EDTRGVFIDEVQFFNP--------------SLFEVVKDLLDR-GIDVFCAGLD  112 (184)
T ss_dssp             ---SSGGGGG---G----GCC-TTEEEEEECCGGGSCT--------------THHHHHHHHHHT-TCEEEEEEES
T ss_pred             ---CCHHHHH---H----Hhc-CCCCEEEEECcccCCH--------------HHHHHHHHHHHC-CCCEEEEeec
Confidence               1222221   1    111 3589999999997521              144567777776 9999988754

>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=98.30  E-value=5.1e-05  Score=71.43  Aligned_cols=95  Identities=14%  Similarity=0.094  Sum_probs=56.1

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      ++.++.++|++|+||||++..+|......      +.+|++++++. +.+....++...           . .. ..+-+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~------G~kVllv~~D~-~R~aa~eqL~~~-----------~-~~-~gvpv  158 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKR------GYKVGVVCSDT-WRPGAYHQLRQL-----------L-DR-YHIEV  158 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT------TCCEEEEECCC-SSTHHHHHHHHH-----------H-GG-GTCEE
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHC------CCeEEEEeCCC-cchhHHHHHHHH-----------H-Hh-cCCcE
Confidence            46899999999999999999999887642      58899999864 232222221110           0 00 12222


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEecccc
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEA  215 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~  215 (357)
                      +...+..+...++..........+.++||||....
T Consensus       159 ~~~~~~~dp~~i~~~al~~a~~~~~DvVIIDTaGr  193 (443)
T 3dm5_A          159 FGNPQEKDAIKLAKEGVDYFKSKGVDIIIVDTAGR  193 (443)
T ss_dssp             ECCTTCCCHHHHHHHHHHHHHHTTCSEEEEECCCC
T ss_pred             EecCCCCCHHHHHHHHHHHHHhCCCCEEEEECCCc
Confidence            22222222333333333344456789999997753

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=98.29  E-value=2.9e-06  Score=75.24  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=34.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-++-..         ......++..|++++++.|++||+++|--.
T Consensus       160 ~~P~lLlLDEPts~LD---------~~~~~~i~~~l~~l~~~~g~tvi~vtHdl~  205 (275)
T 3gfo_A          160 MEPKVLILDEPTAGLD---------PMGVSEIMKLLVEMQKELGITIIIATHDID  205 (275)
T ss_dssp             TCCSEEEEECTTTTCC---------HHHHHHHHHHHHHHHHHHCCEEEEEESCCS
T ss_pred             cCCCEEEEECccccCC---------HHHHHHHHHHHHHHHhhCCCEEEEEecCHH
Confidence            4799999998775443         244556788888888445999999988643

>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=98.28  E-value=3.9e-05  Score=68.80  Aligned_cols=54  Identities=26%  Similarity=0.184  Sum_probs=41.2

Q ss_pred             CchhHHhhhcCCCCC-------CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           87 RLKGLDAALCGGVPF-------GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        87 G~~~LD~~l~GGi~~-------G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..+.|+..++++...       +.++.+.|++|+||||++.+++...+..      +++|++++.+.
T Consensus        76 ~~~~l~~~~~~~~~~~i~~~~~~~vi~i~G~~G~GKTT~~~~la~~~~~~------g~~v~l~~~D~  136 (297)
T 1j8m_F           76 VYDELSNLFGGDKEPKVIPDKIPYVIMLVGVQGTGKTTTAGKLAYFYKKK------GFKVGLVGADV  136 (297)
T ss_dssp             HHHHHHHHTTCSCCCCCSCSSSSEEEEEECSSCSSTTHHHHHHHHHHHHT------TCCEEEEECCC
T ss_pred             HHHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHC------CCeEEEEecCC
Confidence            345555655543222       8899999999999999999999887642      47899999875

>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=98.23  E-value=3.4e-05  Score=72.61  Aligned_cols=40  Identities=25%  Similarity=0.248  Sum_probs=34.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.++.++|++|+||||++..++.....   .   +.+|++++++.
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~---~---G~kVllv~~D~  135 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKK---R---GYKVGLVAADV  135 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHH---T---TCCEEEEEECC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH---c---CCeEEEEecCc
Confidence            4789999999999999999999987763   2   58899999874

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.21  E-value=1e-05  Score=64.85  Aligned_cols=40  Identities=25%  Similarity=0.289  Sum_probs=33.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +|+.+.|.|++|+|||+|+..++.....   .   +.+++|++...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~---~---g~~~~~~~~~~   74 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALE---A---GKNAAYIDAAS   74 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHT---T---TCCEEEEETTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHh---c---CCcEEEEcHHH
Confidence            8999999999999999999998876652   1   35688988754

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=98.21  E-value=1e-05  Score=71.51  Aligned_cols=43  Identities=9%  Similarity=0.124  Sum_probs=33.9

Q ss_pred             CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       204 ~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      +++++++|.-++-..         ......+.+.|++++++.+++||+++|-
T Consensus       165 ~p~lLllDEPts~LD---------~~~~~~i~~~l~~l~~~~~~tvi~vtHd  207 (266)
T 4g1u_C          165 TPRWLFLDEPTSALD---------LYHQQHTLRLLRQLTRQEPLAVCCVLHD  207 (266)
T ss_dssp             CCEEEEECCCCSSCC---------HHHHHHHHHHHHHHHHHSSEEEEEECSC
T ss_pred             CCCEEEEeCccccCC---------HHHHHHHHHHHHHHHHcCCCEEEEEEcC
Confidence            799999998765443         2455667888999998888999999885

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.21  E-value=7.3e-06  Score=76.08  Aligned_cols=113  Identities=16%  Similarity=0.240  Sum_probs=66.6

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+++..=++++||||+|||.+|..+|...-         .+.+.++...-.+         . |                
T Consensus       178 gi~~prGvLL~GPPGTGKTllAkAiA~e~~---------~~f~~v~~s~l~s---------k-~----------------  222 (405)
T 4b4t_J          178 GIAQPKGVILYGPPGTGKTLLARAVAHHTD---------CKFIRVSGAELVQ---------K-Y----------------  222 (405)
T ss_dssp             TCCCCCCEEEESCSSSSHHHHHHHHHHHHT---------CEEEEEEGGGGSC---------S-S----------------
T ss_pred             CCCCCCceEEeCCCCCCHHHHHHHHHHhhC---------CCceEEEhHHhhc---------c-c----------------
Confidence            577777799999999999999999998763         5566665532110         0 0                


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCC----hHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPG----QHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r----~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                              ..+-...+..+-...+...+.+|+||.+-++...........    ...+..++..|..+....++.||.++
T Consensus       223 --------vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~V~vIaAT  294 (405)
T 4b4t_J          223 --------IGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFETSKNIKIIMAT  294 (405)
T ss_dssp             --------TTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTCCCCEEEEEEE
T ss_pred             --------cchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCCCCCeEEEecc
Confidence                    011112223333334456789999999999986532222111    12344455555544455566555544

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=98.20  E-value=3.7e-06  Score=72.39  Aligned_cols=43  Identities=16%  Similarity=0.139  Sum_probs=32.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-..         ......+.+.|++++++ +.+||+++|-
T Consensus       157 ~~p~lllLDEPt~~LD---------~~~~~~~~~~l~~l~~~-g~tvi~vtHd  199 (224)
T 2pcj_A          157 NEPILLFADEPTGNLD---------SANTKRVMDIFLKINEG-GTSIVMVTHE  199 (224)
T ss_dssp             TCCSEEEEESTTTTCC---------HHHHHHHHHHHHHHHHT-TCEEEEECSC
T ss_pred             cCCCEEEEeCCCCCCC---------HHHHHHHHHHHHHHHHC-CCEEEEEcCC
Confidence            4789999998775543         24455677788888777 9999999885

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.12  E-value=1.4e-05  Score=75.02  Aligned_cols=113  Identities=15%  Similarity=0.238  Sum_probs=67.8

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+++..-++++||||+|||.+|..+|...         +.+.+.++...-++.          +                
T Consensus       202 g~~~prGiLL~GPPGtGKT~lakAiA~~~---------~~~~~~v~~~~l~~~----------~----------------  246 (428)
T 4b4t_K          202 GIDPPRGVLLYGPPGTGKTMLVKAVANST---------KAAFIRVNGSEFVHK----------Y----------------  246 (428)
T ss_dssp             CCCCCCEEEEESCTTTTHHHHHHHHHHHH---------TCEEEEEEGGGTCCS----------S----------------
T ss_pred             CCCCCceEEEECCCCCCHHHHHHHHHHHh---------CCCeEEEecchhhcc----------c----------------
Confidence            57887889999999999999999999776         356666665321110          0                


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCC--CCC--hHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQR--APG--QHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~--~~r--~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                              ..+-...+..+-.......+.+|+||.+.++........  ..+  ...+..++..+..+....++.||+++
T Consensus       247 --------~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~aT  318 (428)
T 4b4t_K          247 --------LGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMAT  318 (428)
T ss_dssp             --------CSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEEEE
T ss_pred             --------cchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEEec
Confidence                    001111222222333446789999999999876532211  112  23355556666665556666666554

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.10  E-value=2.3e-05  Score=73.10  Aligned_cols=114  Identities=14%  Similarity=0.165  Sum_probs=65.1

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhc
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAG  176 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~  176 (357)
                      .|+++..=++++||||+|||.+|..+|...-         .+.+.++...-++         . +               
T Consensus       211 ~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~---------~~fi~v~~s~l~s---------k-~---------------  256 (437)
T 4b4t_I          211 MGIKPPKGVILYGAPGTGKTLLAKAVANQTS---------ATFLRIVGSELIQ---------K-Y---------------  256 (437)
T ss_dssp             HTCCCCSEEEEESSTTTTHHHHHHHHHHHHT---------CEEEEEESGGGCC---------S-S---------------
T ss_pred             CCCCCCCCCceECCCCchHHHHHHHHHHHhC---------CCEEEEEHHHhhh---------c-c---------------
Confidence            3688878899999999999999999998763         4566665422100         0 0               


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC--C--hHHHHHHHHHHHHHHHHcCCeEEEe
Q 035774          177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP--G--QHPLSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       177 ~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~--r--~~~~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                               ..+-...+..+-.......+.+|+||.+-++..........  +  ...+..++..+..+....++.||++
T Consensus       257 ---------vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~~~~ViVIaA  327 (437)
T 4b4t_I          257 ---------LGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMA  327 (437)
T ss_dssp             ---------SSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCCSSSEEEEEE
T ss_pred             ---------CchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCCCCCEEEEEe
Confidence                     00111222333333345678999999999988653222211  1  1223334444443334445555544


Q ss_pred             c
Q 035774          253 N  253 (357)
Q Consensus       253 ~  253 (357)
                      +
T Consensus       328 T  328 (437)
T 4b4t_I          328 T  328 (437)
T ss_dssp             E
T ss_pred             C
Confidence            3

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.10  E-value=1.7e-05  Score=74.66  Aligned_cols=79  Identities=16%  Similarity=0.273  Sum_probs=52.7

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+++-.=++++||||+|||.+|..+|...         +.+.++++...-++         . +                
T Consensus       211 g~~~prGvLL~GPPGtGKTllAkAiA~e~---------~~~~~~v~~s~l~s---------k-~----------------  255 (437)
T 4b4t_L          211 GIKPPKGVLLYGPPGTGKTLLAKAVAATI---------GANFIFSPASGIVD---------K-Y----------------  255 (437)
T ss_dssp             CCCCCCEEEEESCTTSSHHHHHHHHHHHH---------TCEEEEEEGGGTCC---------S-S----------------
T ss_pred             CCCCCCeEEEECCCCCcHHHHHHHHHHHh---------CCCEEEEehhhhcc---------c-c----------------
Confidence            68888889999999999999999999876         35666666532111         0 0                


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG  219 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~  219 (357)
                              ..+-...+..+-.......+.+|+||.+-++...
T Consensus       256 --------~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~  289 (437)
T 4b4t_L          256 --------IGESARIIREMFAYAKEHEPCIIFMDEVDAIGGR  289 (437)
T ss_dssp             --------SSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCC
T ss_pred             --------chHHHHHHHHHHHHHHhcCCceeeeecccccccc
Confidence                    0011122233333344567999999999998765

>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=98.09  E-value=9.8e-06  Score=71.38  Aligned_cols=43  Identities=16%  Similarity=0.224  Sum_probs=32.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-...         .....+.+.|++++++ +.+||+++|-
T Consensus       176 ~~p~lllLDEPts~LD~---------~~~~~~~~~l~~l~~~-g~tvi~vtHd  218 (263)
T 2olj_A          176 MEPKIMLFDEPTSALDP---------EMVGEVLSVMKQLANE-GMTMVVVTHE  218 (263)
T ss_dssp             TCCSEEEEESTTTTSCH---------HHHHHHHHHHHHHHHT-TCEEEEECSC
T ss_pred             CCCCEEEEeCCcccCCH---------HHHHHHHHHHHHHHhC-CCEEEEEcCC
Confidence            47899999987765432         4455677788888776 9999999885

>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=98.09  E-value=9.2e-06  Score=71.40  Aligned_cols=44  Identities=16%  Similarity=0.089  Sum_probs=33.1

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-..         ......+.+.|++++++ +.+||+++|-.
T Consensus       170 ~~p~lllLDEPts~LD---------~~~~~~l~~~l~~l~~~-g~tvi~vtHd~  213 (257)
T 1g6h_A          170 TNPKMIVMDEPIAGVA---------PGLAHDIFNHVLELKAK-GITFLIIEHRL  213 (257)
T ss_dssp             TCCSEEEEESTTTTCC---------HHHHHHHHHHHHHHHHT-TCEEEEECSCC
T ss_pred             cCCCEEEEeCCccCCC---------HHHHHHHHHHHHHHHHC-CCEEEEEecCH
Confidence            4799999998776543         24555677888888766 99999998853

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=98.09  E-value=1.3e-05  Score=65.87  Aligned_cols=23  Identities=35%  Similarity=0.645  Sum_probs=21.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLK  121 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~  121 (357)
                      +++|+++.|.|+||||||||+..
T Consensus         6 i~~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            6 IPELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             EESSEEEEEECCTTSCHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHH
Confidence            67899999999999999999995

>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=98.07  E-value=6.7e-06  Score=76.02  Aligned_cols=45  Identities=7%  Similarity=-0.032  Sum_probs=34.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-..         ...-.++...|+++.++.|+++|+++|--
T Consensus       150 ~~P~lLLLDEPts~LD---------~~~~~~l~~~l~~l~~~~g~tii~vTHd~  194 (381)
T 3rlf_A          150 AEPSVFLLDEPLSNLD---------AALRVQMRIEISRLHKRLGRTMIYVTHDQ  194 (381)
T ss_dssp             HCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHHHCCEEEEECSCH
T ss_pred             cCCCEEEEECCCcCCC---------HHHHHHHHHHHHHHHHhCCCEEEEEECCH
Confidence            4699999997665432         24445677888999999999999999854

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=98.06  E-value=1.7e-05  Score=69.48  Aligned_cols=144  Identities=14%  Similarity=0.153  Sum_probs=73.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC--CCeEEEEeCCCCCc-hHHHHHHHhccC-c--hhh-----cc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL--DGGVIYIDVESTFT-SRRMIEMGASSF-P--EIF-----HS  167 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~--~~~vl~i~~e~~~~-~~rl~~~~~~~~-~--~~~-----~~  167 (357)
                      +++|+++.|.||+|+|||||+..++.  ..++..|..  ...+.|+.-+..+. ...+.+...... .  ..+     ..
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~l~G--l~~p~~G~I~~~~~i~~v~q~~~~~~~~tv~enl~~~~~~~~~~~~~~~~~~  105 (253)
T 2nq2_C           28 LNKGDILAVLGQNGCGKSTLLDLLLG--IHRPIQGKIEVYQSIGFVPQFFSSPFAYSVLDIVLMGRSTHINTFAKPKSHD  105 (253)
T ss_dssp             EETTCEEEEECCSSSSHHHHHHHHTT--SSCCSEEEEEECSCEEEECSCCCCSSCCBHHHHHHGGGGGGSCTTCCCCHHH
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhC--CCCCCCcEEEEeccEEEEcCCCccCCCCCHHHHHHHhhhhhcccccCCCHHH
Confidence            88999999999999999999986663  333232210  12345655433221 111222111100 0  000     00


Q ss_pred             cchHHHhhcCeEE-------eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHH
Q 035774          168 KGMAQEMAGRILV-------LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITS  240 (357)
Q Consensus       168 ~~~~~~~~~~i~~-------~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~  240 (357)
                      .......++.+-+       ....+..+. +.+.-++..+  .+++++++|.-++-..         ......+.+.|++
T Consensus       106 ~~~~~~~l~~~~l~~~~~~~~~~LSgGq~-qrv~lAraL~--~~p~lllLDEPts~LD---------~~~~~~l~~~l~~  173 (253)
T 2nq2_C          106 YQVAMQALDYLNLTHLAKREFTSLSGGQR-QLILIARAIA--SECKLILLDEPTSALD---------LANQDIVLSLLID  173 (253)
T ss_dssp             HHHHHHHHHHTTCGGGTTSBGGGSCHHHH-HHHHHHHHHH--TTCSEEEESSSSTTSC---------HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCChHHhcCChhhCCHHHH-HHHHHHHHHH--cCCCEEEEeCCcccCC---------HHHHHHHHHHHHH
Confidence            0011111111111       111122222 2222222222  4799999998775443         2445567778888


Q ss_pred             HHHHcCCeEEEecccc
Q 035774          241 LAEFSRIPIVVTNQVR  256 (357)
Q Consensus       241 la~~~~~~vv~~~q~~  256 (357)
                      ++++.+.+||+++|-.
T Consensus       174 l~~~~g~tvi~vtHd~  189 (253)
T 2nq2_C          174 LAQSQNMTVVFTTHQP  189 (253)
T ss_dssp             HHHTSCCEEEEEESCH
T ss_pred             HHHhcCCEEEEEecCH
Confidence            8877799999998853

>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=98.05  E-value=8.2e-06  Score=74.90  Aligned_cols=45  Identities=9%  Similarity=0.010  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-.+-..         ...-.++...|+++.++.++|+|+++|--
T Consensus       155 ~~P~lLLLDEPts~LD---------~~~r~~l~~~l~~~~~~~g~tvi~vTHd~  199 (359)
T 3fvq_A          155 PDPELILLDEPFSALD---------EQLRRQIREDMIAALRANGKSAVFVSHDR  199 (359)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHHTTCEEEEECCCH
T ss_pred             cCCCEEEEeCCcccCC---------HHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            4799999997665432         23344556678888888999999999954

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.04  E-value=6.7e-05  Score=66.66  Aligned_cols=38  Identities=26%  Similarity=0.289  Sum_probs=30.7

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      |+.++.-++|+||||+|||+++..++...         +.++++++.
T Consensus        47 ~~~~~~~~ll~G~~GtGKT~la~~la~~~---------~~~~~~v~~   84 (285)
T 3h4m_A           47 GIEPPKGILLYGPPGTGKTLLAKAVATET---------NATFIRVVG   84 (285)
T ss_dssp             CCCCCSEEEEESSSSSSHHHHHHHHHHHT---------TCEEEEEEG
T ss_pred             CCCCCCeEEEECCCCCcHHHHHHHHHHHh---------CCCEEEEeh
Confidence            46677779999999999999999988664         356777765

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.04  E-value=1.1e-05  Score=76.02  Aligned_cols=38  Identities=21%  Similarity=0.317  Sum_probs=31.5

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      |+++..-++++||||+|||.+|..+|...         +.+.+.++.
T Consensus       211 g~~~prGvLLyGPPGTGKTllAkAiA~e~---------~~~f~~v~~  248 (434)
T 4b4t_M          211 GIRAPKGALMYGPPGTGKTLLARACAAQT---------NATFLKLAA  248 (434)
T ss_dssp             CCCCCCEEEEESCTTSSHHHHHHHHHHHH---------TCEEEEEEG
T ss_pred             CCCCCCeeEEECcCCCCHHHHHHHHHHHh---------CCCEEEEeh
Confidence            68888889999999999999999998776         355666655

>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=98.03  E-value=0.00037  Score=63.27  Aligned_cols=41  Identities=24%  Similarity=0.157  Sum_probs=32.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++|+++.|.|++|+||||++..++.....   .   ++.|.+.+.+-
T Consensus       127 ~~g~vi~lvG~nGaGKTTll~~Lag~l~~---~---~g~V~l~g~D~  167 (328)
T 3e70_C          127 EKPYVIMFVGFNGSGKTTTIAKLANWLKN---H---GFSVVIAASDT  167 (328)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHHHHH---T---TCCEEEEEECC
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHh---c---CCEEEEEeecc
Confidence            68999999999999999999999876542   1   36777776653

>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=97.99  E-value=2e-05  Score=69.13  Aligned_cols=25  Identities=36%  Similarity=0.547  Sum_probs=23.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+++.|.||+|+|||||+.-++
T Consensus        38 i~~Gei~~l~G~NGsGKSTLlk~l~   62 (256)
T 1vpl_A           38 IEEGEIFGLIGPNGAGKTTTLRIIS   62 (256)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHT
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHh
Confidence            8899999999999999999999666

>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=97.99  E-value=1.1e-05  Score=70.17  Aligned_cols=43  Identities=19%  Similarity=0.212  Sum_probs=31.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-..         ......+.+.|+++++ .+.+||+++|-
T Consensus       156 ~~p~lllLDEPts~LD---------~~~~~~l~~~l~~~~~-~g~tvi~vtHd  198 (240)
T 1ji0_A          156 SRPKLLMMDEPSLGLA---------PILVSEVFEVIQKINQ-EGTTILLVEQN  198 (240)
T ss_dssp             TCCSEEEEECTTTTCC---------HHHHHHHHHHHHHHHH-TTCCEEEEESC
T ss_pred             cCCCEEEEcCCcccCC---------HHHHHHHHHHHHHHHH-CCCEEEEEecC
Confidence            4799999998775443         2445567777888876 58999999875

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.98  E-value=2.9e-05  Score=73.08  Aligned_cols=79  Identities=16%  Similarity=0.180  Sum_probs=51.9

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+++-.-++++||||+|||.||..+|...-         .+.+.++...-++         . +                
T Consensus       239 Gi~pprGILLyGPPGTGKTlLAkAiA~e~~---------~~fi~vs~s~L~s---------k-~----------------  283 (467)
T 4b4t_H          239 GIDPPKGILLYGPPGTGKTLCARAVANRTD---------ATFIRVIGSELVQ---------K-Y----------------  283 (467)
T ss_dssp             TCCCCSEEEECSCTTSSHHHHHHHHHHHHT---------CEEEEEEGGGGCC---------C-S----------------
T ss_pred             CCCCCCceEeeCCCCCcHHHHHHHHHhccC---------CCeEEEEhHHhhc---------c-c----------------
Confidence            688888899999999999999999998763         4566665432100         0 0                


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG  219 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~  219 (357)
                              ..+-...+..+-.......+.+|+||.+-++...
T Consensus       284 --------vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~  317 (467)
T 4b4t_H          284 --------VGEGARMVRELFEMARTKKACIIFFDEIDAVGGA  317 (467)
T ss_dssp             --------SSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBC
T ss_pred             --------CCHHHHHHHHHHHHHHhcCCceEeeccccccccc
Confidence                    0011122223333334567899999999998765

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=97.97  E-value=1.3e-05  Score=71.25  Aligned_cols=45  Identities=16%  Similarity=0.162  Sum_probs=32.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeE--EEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPI--VVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~v--v~~~q~~~  257 (357)
                      .+++++++|.-++-..         ......+.+.|++++++ +.+|  |+++|-..
T Consensus       178 ~~p~lLlLDEPts~LD---------~~~~~~l~~~l~~l~~~-g~tv~~iivtHd~~  224 (279)
T 2ihy_A          178 GQPQVLILDEPAAGLD---------FIARESLLSILDSLSDS-YPTLAMIYVTHFIE  224 (279)
T ss_dssp             TCCSEEEEESTTTTCC---------HHHHHHHHHHHHHHHHH-CTTCEEEEEESCGG
T ss_pred             CCCCEEEEeCCccccC---------HHHHHHHHHHHHHHHHC-CCEEEEEEEecCHH
Confidence            4799999998775543         24455677788888877 8888  88888543

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=97.97  E-value=2.4e-05  Score=72.23  Aligned_cols=45  Identities=9%  Similarity=0.039  Sum_probs=33.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++++|+++|--
T Consensus       158 ~~P~lLLLDEP~s~LD---------~~~r~~l~~~l~~l~~~~g~tvi~vTHd~  202 (372)
T 1v43_A          158 VEPDVLLMDEPLSNLD---------AKLRVAMRAEIKKLQQKLKVTTIYVTHDQ  202 (372)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             cCCCEEEEcCCCccCC---------HHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            4689999997665432         24445577788889888899999999864

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=97.96  E-value=3.7e-05  Score=70.40  Aligned_cols=45  Identities=9%  Similarity=0.176  Sum_probs=34.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++++|+++|-.
T Consensus       144 ~~P~lLLLDEP~s~LD---------~~~~~~l~~~l~~l~~~~g~tii~vTHd~  188 (348)
T 3d31_A          144 TNPKILLLDEPLSALD---------PRTQENAREMLSVLHKKNKLTVLHITHDQ  188 (348)
T ss_dssp             SCCSEEEEESSSTTSC---------HHHHHHHHHHHHHHHHHTTCEEEEEESCH
T ss_pred             cCCCEEEEECccccCC---------HHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            4799999997665432         24445677788899888999999999864

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=97.95  E-value=1.8e-05  Score=73.20  Aligned_cols=45  Identities=4%  Similarity=0.023  Sum_probs=33.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++++|+++|--
T Consensus       156 ~~P~lLLLDEP~s~LD---------~~~r~~l~~~l~~l~~~~g~tvi~vTHd~  200 (372)
T 1g29_1          156 RKPQVFLMDEPLSNLD---------AKLRVRMRAELKKLQRQLGVTTIYVTHDQ  200 (372)
T ss_dssp             TCCSEEEEECTTTTSC---------HHHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             cCCCEEEECCCCccCC---------HHHHHHHHHHHHHHHHhcCCEEEEECCCH
Confidence            4799999997665432         24445577788888888899999999863

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=97.95  E-value=1.7e-05  Score=72.76  Aligned_cols=46  Identities=9%  Similarity=0.056  Sum_probs=34.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++++|+++|-..
T Consensus       162 ~~P~lLLLDEP~s~LD---------~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  207 (355)
T 1z47_A          162 PRPQVLLFDEPFAAID---------TQIRRELRTFVRQVHDEMGVTSVFVTHDQE  207 (355)
T ss_dssp             TCCSEEEEESTTCCSS---------HHHHHHHHHHHHHHHHHHTCEEEEECSCHH
T ss_pred             cCCCEEEEeCCcccCC---------HHHHHHHHHHHHHHHHhcCCEEEEECCCHH
Confidence            4799999997665432         244455777888998888999999998643

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=97.93  E-value=2.1e-05  Score=72.40  Aligned_cols=45  Identities=11%  Similarity=-0.000  Sum_probs=34.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-.+-...         ..-..+...|+++.++.++++|+++|--
T Consensus       150 ~~P~lLLLDEP~s~LD~---------~~r~~l~~~l~~l~~~~g~tvi~vTHd~  194 (362)
T 2it1_A          150 KEPEVLLLDEPLSNLDA---------LLRLEVRAELKRLQKELGITTVYVTHDQ  194 (362)
T ss_dssp             TCCSEEEEESGGGGSCH---------HHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             cCCCEEEEECccccCCH---------HHHHHHHHHHHHHHHhCCCEEEEECCCH
Confidence            47999999987765432         3445577788888888899999999864

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=97.91  E-value=2.2e-05  Score=69.16  Aligned_cols=43  Identities=16%  Similarity=0.190  Sum_probs=32.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-..         ......+...|++++++ +.+||+++|-
T Consensus       170 ~~p~lllLDEPts~LD---------~~~~~~~~~~l~~l~~~-g~tvi~vtHd  212 (262)
T 1b0u_A          170 MEPDVLLFDEPTSALD---------PELVGEVLRIMQQLAEE-GKTMVVVTHE  212 (262)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHT-TCCEEEECSC
T ss_pred             cCCCEEEEeCCCccCC---------HHHHHHHHHHHHHHHhC-CCEEEEEeCC
Confidence            4799999998775443         24455677788888776 9999999885

>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=97.91  E-value=9.5e-05  Score=68.54  Aligned_cols=119  Identities=26%  Similarity=0.225  Sum_probs=64.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHH-HHHhccCchhhcccchHHHhhcCeEEeC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMI-EMGASSFPEIFHSKGMAQEMAGRILVLQ  182 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~-~~~~~~~~~~~~~~~~~~~~~~~i~~~~  182 (357)
                      .+.|+|+||+|||+++..++......     .+..++|+++........+. .+...              +... .-..
T Consensus        46 ~~li~G~~G~GKTtl~~~l~~~~~~~-----~~~~~~~i~~~~~~~~~~~~~~l~~~--------------l~~~-~~~~  105 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTLRKLWELYKDK-----TTARFVYINGFIYRNFTAIIGEIARS--------------LNIP-FPRR  105 (389)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTTS-----CCCEEEEEETTTCCSHHHHHHHHHHH--------------TTCC-CCSS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHhhh-----cCeeEEEEeCccCCCHHHHHHHHHHH--------------hCcc-CCCC
Confidence            89999999999999999988766421     03578999875544332322 22211              0000 0000


Q ss_pred             CCCHHHHHHHHHHHHHHhhh-cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHH--cCCeEEEeccc
Q 035774          183 PTSLSEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEF--SRIPIVVTNQV  255 (357)
Q Consensus       183 ~~~~~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~--~~~~vv~~~q~  255 (357)
                      ..+..++   +..+...+.. .+..+|+||.+..+  .        ...+..+.+.+..+...  .++.+|++++.
T Consensus       106 ~~~~~~~---~~~l~~~l~~~~~~~vlilDE~~~l--~--------~~~~~~L~~~~~~~~~~~~~~~~iI~~~~~  168 (389)
T 1fnn_A          106 GLSRDEF---LALLVEHLRERDLYMFLVLDDAFNL--A--------PDILSTFIRLGQEADKLGAFRIALVIVGHN  168 (389)
T ss_dssp             CCCHHHH---HHHHHHHHHHTTCCEEEEEETGGGS--C--------HHHHHHHHHHTTCHHHHSSCCEEEEEEESS
T ss_pred             CCCHHHH---HHHHHHHHhhcCCeEEEEEECcccc--c--------hHHHHHHHHHHHhCCCCCcCCEEEEEEECC
Confidence            1122233   3333333332 45789999999877  1        12333333444333321  47888887653

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.91  E-value=4.4e-05  Score=68.39  Aligned_cols=82  Identities=12%  Similarity=0.137  Sum_probs=48.6

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |.++...++|+||||+|||++|..+|...         +.+++++++..         +... +         ..     
T Consensus        32 ~~~~p~~lLl~GppGtGKT~la~aiA~~l---------~~~~i~v~~~~---------l~~~-~---------~g-----   78 (293)
T 3t15_A           32 NIKVPLILGIWGGKGQGKSFQCELVFRKM---------GINPIMMSAGE---------LESG-N---------AG-----   78 (293)
T ss_dssp             TCCCCSEEEEEECTTSCHHHHHHHHHHHH---------TCCCEEEEHHH---------HHCC------------------
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHh---------CCCEEEEeHHH---------hhhc-c---------Cc-----
Confidence            45666688999999999999999998766         35677776521         1100 0         00     


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP  218 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~  218 (357)
                            .....+...+.......+...+.+|+||.+-.+..
T Consensus        79 ------~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD~~~~  113 (293)
T 3t15_A           79 ------EPAKLIRQRYREAAEIIRKGNMCCLFINDLDAGAG  113 (293)
T ss_dssp             ------HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC----
T ss_pred             ------hhHHHHHHHHHHHHHHHhcCCCeEEEEechhhhcC
Confidence                  01112233333333334456789999999988765

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=97.91  E-value=1.9e-05  Score=72.66  Aligned_cols=46  Identities=17%  Similarity=0.060  Sum_probs=34.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|.-.+-..         ...-..+...|+++.++.++++|+++|--.
T Consensus       150 ~~P~lLLLDEP~s~LD---------~~~r~~l~~~l~~l~~~~g~tvi~vTHd~~  195 (359)
T 2yyz_A          150 KQPKVLLFDEPLSNLD---------ANLRMIMRAEIKHLQQELGITSVYVTHDQA  195 (359)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHHHCCEEEEEESCHH
T ss_pred             cCCCEEEEECCcccCC---------HHHHHHHHHHHHHHHHhcCCEEEEEcCCHH
Confidence            4799999997665432         244455777888888888999999998643

>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=97.90  E-value=6.7e-05  Score=65.65  Aligned_cols=40  Identities=23%  Similarity=0.264  Sum_probs=30.8

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      |++...-++|+||||+|||+++..++...         +.+.++++...
T Consensus        35 g~~~~~~vll~G~~GtGKT~la~~la~~~---------~~~~~~~~~~~   74 (262)
T 2qz4_A           35 GAKVPKGALLLGPPGCGKTLLAKAVATEA---------QVPFLAMAGAE   74 (262)
T ss_dssp             -CCCCCEEEEESCTTSSHHHHHHHHHHHH---------TCCEEEEETTT
T ss_pred             CCCCCceEEEECCCCCCHHHHHHHHHHHh---------CCCEEEechHH
Confidence            35556668999999999999999998765         25677777643

>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=97.90  E-value=9.8e-05  Score=70.26  Aligned_cols=41  Identities=24%  Similarity=0.138  Sum_probs=32.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.+|.++.|.|++|+||||++..++.....   .   ++.|++.+.+
T Consensus       290 i~~GeVI~LVGpNGSGKTTLl~~LAgll~~---~---~G~V~l~g~D  330 (503)
T 2yhs_A          290 GKAPFVILMVGVNGVGKTTTIGKLARQFEQ---Q---GKSVMLAAGD  330 (503)
T ss_dssp             SCTTEEEEEECCTTSSHHHHHHHHHHHHHH---T---TCCEEEECCC
T ss_pred             ccCCeEEEEECCCcccHHHHHHHHHHHhhh---c---CCeEEEecCc
Confidence            678999999999999999999999876542   1   3566666554

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=97.87  E-value=7.8e-05  Score=67.72  Aligned_cols=41  Identities=24%  Similarity=0.243  Sum_probs=32.4

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      |+..+..-++|+||||+|||+++..++....        +.+.++++..
T Consensus        40 ~~~~~~~~iLL~GppGtGKT~la~ala~~~~--------~~~~~~i~~~   80 (322)
T 1xwi_A           40 GKRTPWRGILLFGPPGTGKSYLAKAVATEAN--------NSTFFSISSS   80 (322)
T ss_dssp             TTCCCCSEEEEESSSSSCHHHHHHHHHHHTT--------SCEEEEEECC
T ss_pred             CCCCCCceEEEECCCCccHHHHHHHHHHHcC--------CCcEEEEEhH
Confidence            4566777899999999999999999997652        2567777764

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=97.87  E-value=0.00024  Score=63.83  Aligned_cols=42  Identities=29%  Similarity=0.319  Sum_probs=35.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..+|.++.|.|++|+||||++..+|......      +++|++++.+.
T Consensus       101 ~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~------g~kV~lv~~D~  142 (306)
T 1vma_A          101 PEPPFVIMVVGVNGTGKTTSCGKLAKMFVDE------GKSVVLAAADT  142 (306)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHHHT------TCCEEEEEECT
T ss_pred             CCCCeEEEEEcCCCChHHHHHHHHHHHHHhc------CCEEEEEcccc
Confidence            4578999999999999999999999877531      47899998764

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=97.86  E-value=0.00014  Score=70.57  Aligned_cols=144  Identities=15%  Similarity=0.147  Sum_probs=74.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC---CCeEEEEeCCCCCc-hHHHHHHHhccCchhh-cccchHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL---DGGVIYIDVESTFT-SRRMIEMGASSFPEIF-HSKGMAQE  173 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~---~~~vl~i~~e~~~~-~~rl~~~~~~~~~~~~-~~~~~~~~  173 (357)
                      +++|+++.|.|++|+|||||+..++.  ..++..|..   +..+-|+..+.... ...+.+.......... ........
T Consensus       291 i~~Gei~~i~G~nGsGKSTLl~~l~G--l~~p~~G~i~~~~~~i~~~~q~~~~~~~~tv~~~l~~~~~~~~~~~~~~~~~  368 (538)
T 3ozx_A          291 AKEGEIIGILGPNGIGKTTFARILVG--EITADEGSVTPEKQILSYKPQRIFPNYDGTVQQYLENASKDALSTSSWFFEE  368 (538)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTT--SSCCSBCCEESSCCCEEEECSSCCCCCSSBHHHHHHHHCSSTTCTTSHHHHH
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhC--CCCCCCcEEEECCeeeEeechhcccccCCCHHHHHHHhhhhccchhHHHHHH
Confidence            57999999999999999999997663  333333311   23344544322110 0111111110000000 00011122


Q ss_pred             hhcCeEE-------eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcC
Q 035774          174 MAGRILV-------LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSR  246 (357)
Q Consensus       174 ~~~~i~~-------~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~  246 (357)
                      .++.+-+       ....+..+.. .+.-.+.+  -.+++++++|.-++-..         .....++.+.|++++++.+
T Consensus       369 ~l~~~~l~~~~~~~~~~LSGGq~Q-Rv~iAraL--~~~p~lLlLDEPT~gLD---------~~~~~~i~~~l~~l~~~~g  436 (538)
T 3ozx_A          369 VTKRLNLHRLLESNVNDLSGGELQ-KLYIAATL--AKEADLYVLDQPSSYLD---------VEERYIVAKAIKRVTRERK  436 (538)
T ss_dssp             TTTTTTGGGCTTSBGGGCCHHHHH-HHHHHHHH--HSCCSEEEEESTTTTCC---------HHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHcCCHHHhcCChhhCCHHHHH-HHHHHHHH--HcCCCEEEEeCCccCCC---------HHHHHHHHHHHHHHHHhCC
Confidence            2222211       1112223321 12111222  35799999998776543         2455568888999999999


Q ss_pred             CeEEEecccc
Q 035774          247 IPIVVTNQVR  256 (357)
Q Consensus       247 ~~vv~~~q~~  256 (357)
                      ++||+++|--
T Consensus       437 ~tvi~vsHdl  446 (538)
T 3ozx_A          437 AVTFIIDHDL  446 (538)
T ss_dssp             CEEEEECSCH
T ss_pred             CEEEEEeCCH
Confidence            9999998853

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=97.86  E-value=4.2e-05  Score=67.49  Aligned_cols=44  Identities=5%  Similarity=0.107  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-..         ......+...|++++++ +.+||+++|-.
T Consensus       155 ~~p~lllLDEPts~LD---------~~~~~~l~~~l~~l~~~-g~tii~vtHd~  198 (266)
T 2yz2_A          155 HEPDILILDEPLVGLD---------REGKTDLLRIVEKWKTL-GKTVILISHDI  198 (266)
T ss_dssp             TCCSEEEEESTTTTCC---------HHHHHHHHHHHHHHHHT-TCEEEEECSCC
T ss_pred             cCCCEEEEcCccccCC---------HHHHHHHHHHHHHHHHc-CCEEEEEeCCH
Confidence            4799999998775543         24455677788888777 99999998853

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=97.86  E-value=8.7e-05  Score=64.68  Aligned_cols=26  Identities=27%  Similarity=0.477  Sum_probs=23.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        32 i~~Ge~~~i~G~nGsGKSTLl~~l~G   57 (247)
T 2ff7_A           32 IKQGEVIGIVGRSGSGKSTLTKLIQR   57 (247)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999987653

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=97.85  E-value=5.4e-05  Score=66.08  Aligned_cols=25  Identities=36%  Similarity=0.704  Sum_probs=23.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+++.|.||+|+|||||+.-++
T Consensus        23 i~~Ge~~~liG~NGsGKSTLlk~l~   47 (249)
T 2qi9_C           23 VRAGEILHLVGPNGAGKSTLLARMA   47 (249)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHT
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHh
Confidence            8899999999999999999999665

>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=97.85  E-value=9.5e-05  Score=67.11  Aligned_cols=39  Identities=23%  Similarity=0.279  Sum_probs=30.3

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++..+..-++|+||||+|||++|..++...         +.+.++++.
T Consensus        46 ~~~~~~~~vLl~GppGtGKT~la~aia~~~---------~~~~~~v~~   84 (322)
T 3eie_A           46 GNRKPTSGILLYGPPGTGKSYLAKAVATEA---------NSTFFSVSS   84 (322)
T ss_dssp             TTCCCCCEEEEECSSSSCHHHHHHHHHHHH---------TCEEEEEEH
T ss_pred             cCCCCCCeEEEECCCCCcHHHHHHHHHHHH---------CCCEEEEch
Confidence            344556679999999999999999998764         356777754

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=97.85  E-value=0.0009  Score=64.21  Aligned_cols=39  Identities=28%  Similarity=0.316  Sum_probs=32.3

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..++.|+|+||+||||++..++......      +.+|++++.+.
T Consensus       101 ~~vI~ivG~~GvGKTTl~~kLA~~l~~~------G~kVllVd~D~  139 (504)
T 2j37_W          101 QNVIMFVGLQGSGKTTTCSKLAYYYQRK------GWKTCLICADT  139 (504)
T ss_dssp             -EEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC------CCeEEEEeccc
Confidence            5589999999999999999999887642      47899998864

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=97.84  E-value=7.9e-05  Score=64.65  Aligned_cols=44  Identities=16%  Similarity=0.128  Sum_probs=33.5

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-..         ......+.+.|++++++.+.+||+++|-
T Consensus       143 ~~p~lllLDEPts~LD---------~~~~~~~~~~l~~l~~~~g~tvi~vtHd  186 (240)
T 2onk_A          143 IQPRLLLLDEPLSAVD---------LKTKGVLMEELRFVQREFDVPILHVTHD  186 (240)
T ss_dssp             TCCSSBEEESTTSSCC---------HHHHHHHHHHHHHHHHHHTCCEEEEESC
T ss_pred             cCCCEEEEeCCcccCC---------HHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            4789999998775443         2445567788888888889999999885

>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=97.84  E-value=9e-05  Score=63.67  Aligned_cols=49  Identities=22%  Similarity=0.220  Sum_probs=36.4

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .|..+..++  .+..++|+|+||+|||+++..++......      +..++|++...
T Consensus        42 ~l~~~~~~~--~~~~~ll~G~~G~GKT~la~~l~~~~~~~------~~~~~~~~~~~   90 (242)
T 3bos_A           42 ALKSAASGD--GVQAIYLWGPVKSGRTHLIHAACARANEL------ERRSFYIPLGI   90 (242)
T ss_dssp             HHHHHHHTC--SCSEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEEGGG
T ss_pred             HHHHHHhCC--CCCeEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEEEHHH
Confidence            344444432  57789999999999999999999877532      46788887743

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=97.84  E-value=4.4e-05  Score=67.57  Aligned_cols=45  Identities=13%  Similarity=0.194  Sum_probs=33.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|..++-...         .....+...|++++++.+.+||+++|-.
T Consensus       173 ~~p~lllLDEPts~LD~---------~~~~~i~~~l~~~~~~~g~tviivtHd~  217 (271)
T 2ixe_A          173 RKPRLLILDNATSALDA---------GNQLRVQRLLYESPEWASRTVLLITQQL  217 (271)
T ss_dssp             TCCSEEEEESTTTTCCH---------HHHHHHHHHHHHCTTTTTSEEEEECSCH
T ss_pred             cCCCEEEEECCccCCCH---------HHHHHHHHHHHHHHhhcCCEEEEEeCCH
Confidence            47999999987755432         4445677778888776799999998853

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=97.83  E-value=1.8e-05  Score=72.69  Aligned_cols=45  Identities=11%  Similarity=0.109  Sum_probs=33.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-.+-...         ..-.++...|+++.++.++++|+++|--
T Consensus       157 ~~P~lLLLDEP~s~LD~---------~~r~~l~~~l~~l~~~~g~tvi~vTHd~  201 (353)
T 1oxx_K          157 KDPSLLLLDEPFSNLDA---------RMRDSARALVKEVQSRLGVTLLVVSHDP  201 (353)
T ss_dssp             TCCSEEEEESTTTTSCG---------GGHHHHHHHHHHHHHHHCCEEEEEESCH
T ss_pred             hCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            47999999987655432         2334566778888888899999999864

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=97.83  E-value=6e-05  Score=63.72  Aligned_cols=39  Identities=13%  Similarity=0.128  Sum_probs=33.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+|.+.+++|+.|+||||.+++.+.++..      .+.+|+++..
T Consensus        26 ~~G~l~vitG~MgsGKTT~lL~~a~r~~~------~g~kVli~k~   64 (214)
T 2j9r_A           26 QNGWIEVICGSMFSGKSEELIRRVRRTQF------AKQHAIVFKP   64 (214)
T ss_dssp             CSCEEEEEECSTTSCHHHHHHHHHHHHHH------TTCCEEEEEC
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHH------CCCEEEEEEe
Confidence            56899999999999999999999999874      2578988864

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=97.83  E-value=0.00012  Score=71.09  Aligned_cols=143  Identities=18%  Similarity=0.146  Sum_probs=76.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC--CCeEEEEeCCCCCc-hHHHHHHHhccCchhhcccchHHHhh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL--DGGVIYIDVESTFT-SRRMIEMGASSFPEIFHSKGMAQEMA  175 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~--~~~vl~i~~e~~~~-~~rl~~~~~~~~~~~~~~~~~~~~~~  175 (357)
                      +++|+++.|.|++|+|||||+..++.  ..++..|..  ...+.|+.-+.... ...+.+.........+.........+
T Consensus       309 i~~Ge~~~i~G~NGsGKSTLlk~l~G--l~~p~~G~i~~~~~i~~v~Q~~~~~~~~tv~~~~~~~~~~~~~~~~~~~~~l  386 (538)
T 1yqt_A          309 IKKGEVIGIVGPNGIGKTTFVKMLAG--VEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSKIDASKLNSNFYKTELL  386 (538)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHHT--SSCCSBCCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHTCHHHHHHTT
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHhC--CCCCCCeEEEECceEEEEecCCcCCCCCcHHHHHHhhhccCCCHHHHHHHHH
Confidence            46899999999999999999997763  333333321  23466766543211 10111111100000000011122233


Q ss_pred             cCeEEe-------CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCe
Q 035774          176 GRILVL-------QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIP  248 (357)
Q Consensus       176 ~~i~~~-------~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~  248 (357)
                      +.+-+.       ...+..+... +.-.+..  -.+++++++|.-+.-..         ......+...|++++++.+.+
T Consensus       387 ~~~~l~~~~~~~~~~LSGGe~qr-v~lAraL--~~~p~lLlLDEPt~~LD---------~~~~~~i~~~l~~l~~~~g~t  454 (538)
T 1yqt_A          387 KPLGIIDLYDREVNELSGGELQR-VAIAATL--LRDADIYLLDEPSAYLD---------VEQRLAVSRAIRHLMEKNEKT  454 (538)
T ss_dssp             TTTTCGGGTTSBGGGCCHHHHHH-HHHHHHH--TSCCSEEEEECTTTTCC---------HHHHHHHHHHHHHHHHHHTCE
T ss_pred             HHcCChhhhcCChhhCCHHHHHH-HHHHHHH--HhCCCEEEEeCCcccCC---------HHHHHHHHHHHHHHHHhCCCE
Confidence            322221       1122222221 1111222  35799999998775543         245566788889998888999


Q ss_pred             EEEeccc
Q 035774          249 IVVTNQV  255 (357)
Q Consensus       249 vv~~~q~  255 (357)
                      ||+++|-
T Consensus       455 vi~vsHd  461 (538)
T 1yqt_A          455 ALVVEHD  461 (538)
T ss_dssp             EEEECSC
T ss_pred             EEEEeCC
Confidence            9999885

>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=97.82  E-value=2.5e-05  Score=72.28  Aligned_cols=43  Identities=19%  Similarity=0.041  Sum_probs=31.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..+..+.|+|+||+|||+++..++......  .+ .+..++|+++.
T Consensus        43 ~~~~~vli~G~~G~GKTtl~~~l~~~~~~~--~~-~~~~~~~i~~~   85 (386)
T 2qby_A           43 EKPNNIFIYGLTGTGKTAVVKFVLSKLHKK--FL-GKFKHVYINTR   85 (386)
T ss_dssp             CCCCCEEEEECTTSSHHHHHHHHHHHHHHH--TC-SSCEEEEEEHH
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHHHHH--hc-CCceEEEEECC
Confidence            346789999999999999999998765421  10 03678888864

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=97.81  E-value=0.00013  Score=60.75  Aligned_cols=40  Identities=15%  Similarity=0.193  Sum_probs=33.7

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..|.+..|+|+.|+|||+.+++.+.+....      +.+|+|+..+
T Consensus        18 ~~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~------~~kvl~~kp~   57 (195)
T 1w4r_A           18 TRGQIQVILGPMFSGKSTELMRRVRRFQIA------QYKCLVIKYA   57 (195)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHHHHHHT------TCCEEEEEET
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHHHc------CCeEEEEccc
Confidence            358999999999999999999999888653      4889999865

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=97.80  E-value=0.00012  Score=72.18  Aligned_cols=143  Identities=18%  Similarity=0.142  Sum_probs=75.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC--CCeEEEEeCCCCCc-hHHHHHHHhccCchhhcccchHHHhh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL--DGGVIYIDVESTFT-SRRMIEMGASSFPEIFHSKGMAQEMA  175 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~--~~~vl~i~~e~~~~-~~rl~~~~~~~~~~~~~~~~~~~~~~  175 (357)
                      +++|+++.|.|++|+|||||+..++.  ..++..|..  ...+-|+.-+.... ...+.+.........+.........+
T Consensus       379 v~~Gei~~i~G~NGsGKSTLlk~l~G--l~~p~~G~I~~~~~i~~v~Q~~~~~~~~tv~e~~~~~~~~~~~~~~~~~~~l  456 (607)
T 3bk7_A          379 IRKGEVIGIVGPNGIGKTTFVKMLAG--VEEPTEGKVEWDLTVAYKPQYIKAEYEGTVYELLSKIDSSKLNSNFYKTELL  456 (607)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHHT--SSCCSBSCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHHCHHHHHHTH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHhc--CCCCCceEEEEeeEEEEEecCccCCCCCcHHHHHHhhhccCCCHHHHHHHHH
Confidence            46899999999999999999997764  333333322  23466665443211 10111111000000000001111222


Q ss_pred             cCeEE-------eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCe
Q 035774          176 GRILV-------LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIP  248 (357)
Q Consensus       176 ~~i~~-------~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~  248 (357)
                      +.+-+       +...+..+... +.-.+.+  -.+++++++|.-++-..         ......+.+.|++++++.+.+
T Consensus       457 ~~~~l~~~~~~~~~~LSGGe~QR-v~iAraL--~~~p~lLlLDEPt~~LD---------~~~~~~l~~~l~~l~~~~g~t  524 (607)
T 3bk7_A          457 KPLGIIDLYDRNVEDLSGGELQR-VAIAATL--LRDADIYLLDEPSAYLD---------VEQRLAVSRAIRHLMEKNEKT  524 (607)
T ss_dssp             HHHTCTTTTTSBGGGCCHHHHHH-HHHHHHH--TSCCSEEEEECTTTTCC---------HHHHHHHHHHHHHHHHHTTCE
T ss_pred             HHcCCchHhcCChhhCCHHHHHH-HHHHHHH--HhCCCEEEEeCCccCCC---------HHHHHHHHHHHHHHHHhCCCE
Confidence            11111       11123333221 1111222  35799999998776543         244556788889998888999


Q ss_pred             EEEeccc
Q 035774          249 IVVTNQV  255 (357)
Q Consensus       249 vv~~~q~  255 (357)
                      ||+++|-
T Consensus       525 vi~vsHd  531 (607)
T 3bk7_A          525 ALVVEHD  531 (607)
T ss_dssp             EEEECSC
T ss_pred             EEEEeCC
Confidence            9999885

>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=97.79  E-value=5.6e-05  Score=76.35  Aligned_cols=114  Identities=19%  Similarity=0.248  Sum_probs=68.7

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+.+-.-++++||||+|||+|+..+|...         +...++++...         +... +                
T Consensus       234 g~~~p~GILL~GPPGTGKT~LAraiA~el---------g~~~~~v~~~~---------l~sk-~----------------  278 (806)
T 3cf2_A          234 GVKPPRGILLYGPPGTGKTLIARAVANET---------GAFFFLINGPE---------IMSK-L----------------  278 (806)
T ss_dssp             CCCCCCEEEEECCTTSCHHHHHHHHHTTT---------TCEEEEEEHHH---------HHSS-C----------------
T ss_pred             CCCCCCeEEEECCCCCCHHHHHHHHHHHh---------CCeEEEEEhHH---------hhcc-c----------------
Confidence            57777779999999999999999888543         35666665421         1100 0                


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC-ChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP-GQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~-r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                              ..+-...+..+-.....+.+.+|+||.+-++.......... ....+..++..+..+....++.||.++.
T Consensus       279 --------~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~~~~V~VIaaTN  348 (806)
T 3cf2_A          279 --------AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATN  348 (806)
T ss_dssp             --------TTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCGGGCEEEEEECS
T ss_pred             --------chHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccccCCEEEEEecC
Confidence                    01112222333333445678999999999998653222211 2234555666666665666777776544

>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=97.77  E-value=5.3e-05  Score=68.09  Aligned_cols=116  Identities=16%  Similarity=0.231  Sum_probs=64.7

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |++++..++|+||||+|||+++..++...         +.+.+++++.      .+....       +          + 
T Consensus        45 ~~~~~~~vLL~Gp~GtGKT~la~ala~~~---------~~~~i~v~~~------~l~~~~-------~----------g-   91 (301)
T 3cf0_A           45 GMTPSKGVLFYGPPGCGKTLLAKAIANEC---------QANFISIKGP------ELLTMW-------F----------G-   91 (301)
T ss_dssp             CCCCCSEEEEECSSSSSHHHHHHHHHHHT---------TCEEEEECHH------HHHHHH-------H----------T-
T ss_pred             CCCCCceEEEECCCCcCHHHHHHHHHHHh---------CCCEEEEEhH------HHHhhh-------c----------C-
Confidence            57888999999999999999999888754         2456666431      111100       0          0 


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCC----CCCCChHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHE----QRAPGQHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~----~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                            .....+..++..    .....+.+|+||.+..+......    ........+..++..|..+....++.||+++
T Consensus        92 ------~~~~~~~~~f~~----a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~at  161 (301)
T 3cf0_A           92 ------ESEANVREIFDK----ARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGAT  161 (301)
T ss_dssp             ------TCTTHHHHHHHH----HHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEEEE
T ss_pred             ------chHHHHHHHHHH----HHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEEec
Confidence                  001112222222    22346789999999987643110    0111223344555555444444567777666


Q ss_pred             ccc
Q 035774          254 QVR  256 (357)
Q Consensus       254 q~~  256 (357)
                      +..
T Consensus       162 n~~  164 (301)
T 3cf0_A          162 NRP  164 (301)
T ss_dssp             SCG
T ss_pred             CCc
Confidence            543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.77  E-value=0.00026  Score=60.28  Aligned_cols=41  Identities=24%  Similarity=0.115  Sum_probs=33.8

Q ss_pred             CCcE-EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          101 FGVV-TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       101 ~G~l-~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +|.+ +.+.|+||+|||+++++++...+..      +.+|++++.+..
T Consensus         4 ~g~l~I~~~~kgGvGKTt~a~~la~~l~~~------G~~V~v~d~D~q   45 (228)
T 2r8r_A            4 RGRLKVFLGAAPGVGKTYAMLQAAHAQLRQ------GVRVMAGVVETH   45 (228)
T ss_dssp             CCCEEEEEESSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCCT
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHHHC------CCCEEEEEeCCC
Confidence            4666 7789999999999999999988752      478998888763

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.76  E-value=0.00013  Score=59.96  Aligned_cols=26  Identities=27%  Similarity=0.319  Sum_probs=22.7

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +..++|+|+||+|||+++..++....
T Consensus        43 ~~~vll~G~~G~GKT~la~~~~~~~~   68 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIVEGLAIKIV   68 (187)
T ss_dssp             SCEEEEESCGGGCHHHHHHHHHHHHH
T ss_pred             CCceEEECCCCCCHHHHHHHHHHHHH
Confidence            45679999999999999999988764

>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=97.75  E-value=0.00018  Score=66.06  Aligned_cols=59  Identities=19%  Similarity=0.144  Sum_probs=47.5

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+.||+..+|-++.  +.+|+-+.|.|++|+|||+|+.+++..+...    +.+..|+|+-..+
T Consensus       156 ~~~~tGiraID~~~p--i~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~----~~~v~~I~~lIGE  214 (422)
T 3ice_A          156 STEDLTARVLDLASP--IGRGQRGLIVAPPKAGKTMLLQNIAQSIAYN----HPDCVLMVLLIDE  214 (422)
T ss_dssp             CTTHHHHHHHHHHSC--CBTTCEEEEECCSSSSHHHHHHHHHHHHHHH----CTTSEEEEEEESS
T ss_pred             Ccccccceeeeeeee--ecCCcEEEEecCCCCChhHHHHHHHHHHhhc----CCCeeEEEEEecC
Confidence            467899999999987  8899999999999999999999998877542    1245677775543

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=97.75  E-value=6.6e-05  Score=62.71  Aligned_cols=39  Identities=21%  Similarity=0.244  Sum_probs=33.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+|.+..++|+.|+||||.+++++.++..      .+.+|+++..
T Consensus         6 ~~g~i~v~~G~mgsGKTT~ll~~a~r~~~------~g~kV~v~k~   44 (191)
T 1xx6_A            6 DHGWVEVIVGPMYSGKSEELIRRIRRAKI------AKQKIQVFKP   44 (191)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHH------TTCCEEEEEE
T ss_pred             CCCEEEEEECCCCCcHHHHHHHHHHHHHH------CCCEEEEEEe
Confidence            46889999999999999999999999863      2578888863

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=97.75  E-value=0.00022  Score=64.60  Aligned_cols=42  Identities=26%  Similarity=0.137  Sum_probs=35.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..+|.++.|.|++|+||||++..++...+..      +++|++++.+.
T Consensus       102 ~~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~------g~kVllid~D~  143 (320)
T 1zu4_A          102 ENRLNIFMLVGVNGTGKTTSLAKMANYYAEL------GYKVLIAAADT  143 (320)
T ss_dssp             TTSCEEEEEESSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCC
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHC------CCeEEEEeCCC
Confidence            4678999999999999999999999877632      47899999864

>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=97.75  E-value=0.00015  Score=69.26  Aligned_cols=113  Identities=17%  Similarity=0.187  Sum_probs=61.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      +++|  ++|+||||+|||+++..++...         +.+.++++...-..         . +   ..      .     
T Consensus        48 ~p~g--vLL~GppGtGKT~Laraia~~~---------~~~f~~is~~~~~~---------~-~---~g------~-----   92 (476)
T 2ce7_A           48 MPKG--ILLVGPPGTGKTLLARAVAGEA---------NVPFFHISGSDFVE---------L-F---VG------V-----   92 (476)
T ss_dssp             CCSE--EEEECCTTSSHHHHHHHHHHHH---------TCCEEEEEGGGTTT---------C-C---TT------H-----
T ss_pred             CCCe--EEEECCCCCCHHHHHHHHHHHc---------CCCeeeCCHHHHHH---------H-H---hc------c-----
Confidence            4555  8899999999999999888755         25677776532100         0 0   00      0     


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC----CCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ----RAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~----~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                            ....+..++.    ......+.+|+||.+..+.......    ...+.+.+..++..+..+....++.||.+++
T Consensus        93 ------~~~~~r~lf~----~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaTn  162 (476)
T 2ce7_A           93 ------GAARVRDLFA----QAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATN  162 (476)
T ss_dssp             ------HHHHHHHHHH----HHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEES
T ss_pred             ------cHHHHHHHHH----HHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEecC
Confidence                  0111222222    2223568999999999886542110    1111223444444444333445777777766


Q ss_pred             cc
Q 035774          255 VR  256 (357)
Q Consensus       255 ~~  256 (357)
                      ..
T Consensus       163 ~~  164 (476)
T 2ce7_A          163 RP  164 (476)
T ss_dssp             CG
T ss_pred             Ch
Confidence            54

>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=97.73  E-value=9e-05  Score=63.09  Aligned_cols=25  Identities=36%  Similarity=0.583  Sum_probs=23.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+++.|.||+|+|||||+.-++
T Consensus        32 i~~Ge~~~iiG~NGsGKSTLlk~l~   56 (214)
T 1sgw_A           32 IEKGNVVNFHGPNGIGKTTLLKTIS   56 (214)
T ss_dssp             EETTCCEEEECCTTSSHHHHHHHHT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHh
Confidence            8899999999999999999998665

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.73  E-value=5.7e-05  Score=69.89  Aligned_cols=50  Identities=24%  Similarity=0.117  Sum_probs=34.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS  150 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~  150 (357)
                      .+..+.|+||||+|||+++..++..........+.+..++|+++....+.
T Consensus        43 ~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~   92 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRETP   92 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCSH
T ss_pred             CCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCCH
Confidence            45689999999999999999998766321000012367889987654443

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=97.72  E-value=0.00021  Score=70.28  Aligned_cols=144  Identities=16%  Similarity=0.160  Sum_probs=74.2

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC--CCeEEEEeCCCC--CchHHHHHHHhccCchhhcccchHH
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL--DGGVIYIDVEST--FTSRRMIEMGASSFPEIFHSKGMAQ  172 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~--~~~vl~i~~e~~--~~~~rl~~~~~~~~~~~~~~~~~~~  172 (357)
                      |-+..|+++.|.|++|+|||||+..++  .+.++..|..  ...+.|+..+..  ++. .+.+.....+...+.......
T Consensus       373 G~~~~GEiv~iiG~NGsGKSTLlk~l~--Gl~~p~~G~~~~~~~i~~~~q~~~~~~~~-tv~e~~~~~~~~~~~~~~~~~  449 (608)
T 3j16_B          373 GEFSDSEILVMMGENGTGKTTLIKLLA--GALKPDEGQDIPKLNVSMKPQKIAPKFPG-TVRQLFFKKIRGQFLNPQFQT  449 (608)
T ss_dssp             EECCTTCEEEEESCTTSSHHHHHHHHH--TSSCCSBCCCCCSCCEEEECSSCCCCCCS-BHHHHHHHHCSSTTTSHHHHH
T ss_pred             CccccceEEEEECCCCCcHHHHHHHHh--cCCCCCCCcCccCCcEEEecccccccCCc-cHHHHHHHHhhcccccHHHHH
Confidence            346777999999999999999999776  3443333310  123555543311  110 111111100000000001111


Q ss_pred             HhhcCeE-------EeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHc
Q 035774          173 EMAGRIL-------VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS  245 (357)
Q Consensus       173 ~~~~~i~-------~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~  245 (357)
                      ..++.+-       .....+..+... +. +...+ -.+++++++|.-++-..         ......+++.|++++++.
T Consensus       450 ~~l~~l~l~~~~~~~~~~LSGGqkQR-v~-iAraL-~~~p~lLlLDEPT~gLD---------~~~~~~i~~ll~~l~~~~  517 (608)
T 3j16_B          450 DVVKPLRIDDIIDQEVQHLSGGELQR-VA-IVLAL-GIPADIYLIDEPSAYLD---------SEQRIICSKVIRRFILHN  517 (608)
T ss_dssp             HTHHHHTSTTTSSSBSSSCCHHHHHH-HH-HHHHT-TSCCSEEEECCTTTTCC---------HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCChhhhcCChhhCCHHHHHH-HH-HHHHH-HhCCCEEEEECCCCCCC---------HHHHHHHHHHHHHHHHhC
Confidence            1111110       111223333221 11 11222 35799999998765443         244556788899998888


Q ss_pred             CCeEEEeccc
Q 035774          246 RIPIVVTNQV  255 (357)
Q Consensus       246 ~~~vv~~~q~  255 (357)
                      +.+||+++|-
T Consensus       518 g~tviivtHd  527 (608)
T 3j16_B          518 KKTAFIVEHD  527 (608)
T ss_dssp             TCEEEEECSC
T ss_pred             CCEEEEEeCC
Confidence            9999999885

>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=97.72  E-value=0.0004  Score=63.88  Aligned_cols=39  Identities=23%  Similarity=0.279  Sum_probs=29.9

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++..+..-++|+||||+|||++|..++...         +.+.++++.
T Consensus        79 ~~~~~~~~iLL~GppGtGKT~la~ala~~~---------~~~~~~v~~  117 (355)
T 2qp9_X           79 GNRKPTSGILLYGPPGTGKSYLAKAVATEA---------NSTFFSVSS  117 (355)
T ss_dssp             SSCCCCCCEEEECSTTSCHHHHHHHHHHHH---------TCEEEEEEH
T ss_pred             cCCCCCceEEEECCCCCcHHHHHHHHHHHh---------CCCEEEeeH
Confidence            445566668999999999999999998765         255666654

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=97.72  E-value=0.00014  Score=65.45  Aligned_cols=26  Identities=38%  Similarity=0.468  Sum_probs=23.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.||+|+|||||+.-++.
T Consensus        77 i~~Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           77 VMPGQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             ECTTCEEEEESSSCHHHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCchHHHHHHHHHc
Confidence            88999999999999999999986653

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=97.67  E-value=0.00036  Score=62.29  Aligned_cols=36  Identities=22%  Similarity=0.272  Sum_probs=28.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++.-++|+||||+|||+++..++...         +.+.+++++.
T Consensus        53 ~~~~vll~Gp~GtGKT~la~~la~~~---------~~~~~~i~~~   88 (297)
T 3b9p_A           53 PAKGLLLFGPPGNGKTLLARAVATEC---------SATFLNISAA   88 (297)
T ss_dssp             CCSEEEEESSSSSCHHHHHHHHHHHT---------TCEEEEEEST
T ss_pred             CCCeEEEECcCCCCHHHHHHHHHHHh---------CCCeEEeeHH
Confidence            46679999999999999999888754         2566677653

>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=97.67  E-value=0.00018  Score=64.67  Aligned_cols=39  Identities=28%  Similarity=0.283  Sum_probs=31.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +|+++.|.|++|+||||++..++.....   .   +++|.+.+.+
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~~---~---~g~V~l~g~D  139 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQN---L---GKKVMFCAGD  139 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHT---T---TCCEEEECCC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHHh---c---CCEEEEEeec
Confidence            6899999999999999999999876642   1   3567766654

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=97.67  E-value=0.0019  Score=60.80  Aligned_cols=41  Identities=22%  Similarity=0.193  Sum_probs=34.1

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +..++.++|++|+||||++.++|...+..  .   +.+|+.++++.
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~l~~~--~---G~kVllvd~D~  139 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKFLREK--H---KKKVLVVSADV  139 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHHHHT--S---CCCEEEEECCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHh--c---CCeEEEEecCC
Confidence            34688889999999999999999888741  1   48999999975

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=97.64  E-value=0.00038  Score=57.16  Aligned_cols=27  Identities=26%  Similarity=0.242  Sum_probs=23.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .+..++|+|+||+|||+++..++....
T Consensus        42 ~~~~~ll~G~~G~GKT~l~~~~~~~~~   68 (195)
T 1jbk_A           42 TKNNPVLIGEPGVGKTAIVEGLAQRII   68 (195)
T ss_dssp             SSCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCceEEECCCCCCHHHHHHHHHHHHH
Confidence            345689999999999999999988764

>3b5x_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; 5.50A {Vibrio cholerae}

Probab=97.63  E-value=0.00016  Score=71.21  Aligned_cols=27  Identities=30%  Similarity=0.572  Sum_probs=24.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.||+|+|||||+.-++..
T Consensus       366 i~~G~~~~ivG~sGsGKSTll~~l~g~  392 (582)
T 3b5x_A          366 IPQGKTVALVGRSGSGKSTIANLFTRF  392 (582)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999999999977643

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.59  E-value=0.00016  Score=63.26  Aligned_cols=32  Identities=31%  Similarity=0.345  Sum_probs=25.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++|+||||+|||+++..++...         +.+.++++..
T Consensus        48 vll~G~~GtGKT~la~~la~~~---------~~~~~~i~~~   79 (257)
T 1lv7_A           48 VLMVGPPGTGKTLLAKAIAGEA---------KVPFFTISGS   79 (257)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH---------TCCEEEECSC
T ss_pred             EEEECcCCCCHHHHHHHHHHHc---------CCCEEEEeHH
Confidence            8899999999999999888754         2456777653

>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=97.57  E-value=0.00075  Score=63.33  Aligned_cols=40  Identities=25%  Similarity=0.223  Sum_probs=34.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.++.|+|++|+||||++..++......      +++|++++.+.
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~------g~~Vllvd~D~  136 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK------GRRPLLVAADT  136 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT------TCCEEEEECCS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEeeccc
Confidence            68899999999999999999999887642      47899999864

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=97.54  E-value=0.00058  Score=60.41  Aligned_cols=36  Identities=28%  Similarity=0.379  Sum_probs=27.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|  ++|+||||+|||+|+..++...         +...++++..
T Consensus        43 ~~~G--vlL~Gp~GtGKTtLakala~~~---------~~~~i~i~g~   78 (274)
T 2x8a_A           43 TPAG--VLLAGPPGCGKTLLAKAVANES---------GLNFISVKGP   78 (274)
T ss_dssp             CCSE--EEEESSTTSCHHHHHHHHHHHT---------TCEEEEEETT
T ss_pred             CCCe--EEEECCCCCcHHHHHHHHHHHc---------CCCEEEEEcH
Confidence            4556  9999999999999999888654         2346667654

>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=97.54  E-value=0.00033  Score=62.69  Aligned_cols=40  Identities=25%  Similarity=0.223  Sum_probs=34.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +|.++.|.|++|+||||++..++......      +++|++++.+.
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~~~------~~~v~l~~~d~  136 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGK------GRRPLLVAADT  136 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHHHT------TCCEEEEECCS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEecCCc
Confidence            68899999999999999999999877632      47899999865

>3b60_A Lipid A export ATP-binding/permease protein MSBA; ABC transporter, lipid flippase, hydrolase, inner membrane, lipid transport, membrane; HET: ANP; 3.70A {Salmonella typhimurium} SCOP: c.37.1.12 f.37.1.1 PDB: 3b5y_A* 3b5z_A* 3b5w_A

Probab=97.48  E-value=0.00016  Score=71.17  Aligned_cols=26  Identities=31%  Similarity=0.594  Sum_probs=23.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+.+.|.||+|+|||||+.-++.
T Consensus       366 i~~G~~~~ivG~sGsGKSTLl~~l~g  391 (582)
T 3b60_A          366 IPAGKTVALVGRSGSGKSTIASLITR  391 (582)
T ss_dssp             ECTTCEEEEEECTTSSHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhh
Confidence            78999999999999999999997664

>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=97.47  E-value=0.00051  Score=65.89  Aligned_cols=37  Identities=27%  Similarity=0.199  Sum_probs=29.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .++..-++|+|+||+|||+++..++...         +.+.+++++
T Consensus       235 ~~~~~~vLL~GppGtGKT~lAraia~~~---------~~~fv~vn~  271 (489)
T 3hu3_A          235 VKPPRGILLYGPPGTGKTLIARAVANET---------GAFFFLING  271 (489)
T ss_dssp             CCCCCEEEEECSTTSSHHHHHHHHHHHC---------SSEEEEEEH
T ss_pred             CCCCCcEEEECcCCCCHHHHHHHHHHHh---------CCCEEEEEc
Confidence            5666679999999999999999887654         367777775

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=97.47  E-value=0.00096  Score=64.80  Aligned_cols=44  Identities=11%  Similarity=0.073  Sum_probs=33.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-...         .....+...|+++++ .+++||+++|-.
T Consensus       175 ~~P~lLlLDEPTs~LD~---------~~~~~l~~~L~~l~~-~g~tvi~vsHd~  218 (538)
T 1yqt_A          175 RNATFYFFDEPSSYLDI---------RQRLNAARAIRRLSE-EGKSVLVVEHDL  218 (538)
T ss_dssp             SCCSEEEEESTTTTCCH---------HHHHHHHHHHHHHHH-TTCEEEEECSCH
T ss_pred             cCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHh-cCCEEEEEeCCH
Confidence            57999999987765432         455567778888876 599999999853

>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=97.45  E-value=0.00093  Score=64.66  Aligned_cols=114  Identities=11%  Similarity=0.133  Sum_probs=63.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeE
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL  179 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~  179 (357)
                      ++...++|+||||+|||+++..++...         +..+++++.........+......              ......
T Consensus        75 ~~~~~lLL~GppGtGKTtla~~la~~l---------~~~~i~in~s~~~~~~~~~~~i~~--------------~~~~~~  131 (516)
T 1sxj_A           75 GVFRAAMLYGPPGIGKTTAAHLVAQEL---------GYDILEQNASDVRSKTLLNAGVKN--------------ALDNMS  131 (516)
T ss_dssp             TSCSEEEEECSTTSSHHHHHHHHHHHT---------TCEEEEECTTSCCCHHHHHHTGGG--------------GTTBCC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHc---------CCCEEEEeCCCcchHHHHHHHHHH--------------Hhcccc
Confidence            456789999999999999999888765         367888877553332222211110              000000


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          180 VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       180 ~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      +.....  ....      ......+..+|+||.+..+....       ..    .+..|.++.++.++++|++...
T Consensus       132 ~~~~~~--~~~~------~~~~~~~~~vliIDEid~l~~~~-------~~----~l~~L~~~l~~~~~~iIli~~~  188 (516)
T 1sxj_A          132 VVGYFK--HNEE------AQNLNGKHFVIIMDEVDGMSGGD-------RG----GVGQLAQFCRKTSTPLILICNE  188 (516)
T ss_dssp             STTTTT--C----------CCSSTTSEEEEECSGGGCCTTS-------TT----HHHHHHHHHHHCSSCEEEEESC
T ss_pred             HHHHHh--hhhh------hhhccCCCeEEEEECCCccchhh-------HH----HHHHHHHHHHhcCCCEEEEEcC
Confidence            000000  0000      01123457899999999876431       11    2345666666778888877643

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=97.45  E-value=0.00097  Score=62.05  Aligned_cols=37  Identities=24%  Similarity=0.293  Sum_probs=29.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.-++|+|+||+|||+++..++...         +.+++++++..
T Consensus       147 ~~~~vLL~GppGtGKT~la~aia~~~---------~~~~~~v~~~~  183 (389)
T 3vfd_A          147 PARGLLLFGPPGNGKTMLAKAVAAES---------NATFFNISAAS  183 (389)
T ss_dssp             CCSEEEEESSTTSCHHHHHHHHHHHT---------TCEEEEECSCC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHhh---------cCcEEEeeHHH
Confidence            46689999999999999999987653         36788887643

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=97.45  E-value=0.00028  Score=59.56  Aligned_cols=126  Identities=12%  Similarity=0.063  Sum_probs=62.1

Q ss_pred             CCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCch
Q 035774           84 LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPE  163 (357)
Q Consensus        84 i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~  163 (357)
                      -++|+-.--.++.+--..|.+.+|+|+-|+||||.+++.+.+....      +.+|+.+...-+-... ...+... .. 
T Consensus        10 ~~~~~~~~~~~m~~~~~~G~I~vitG~M~sGKTT~Llr~~~r~~~~------g~kvli~kp~~D~R~~-~~~I~Sr-~G-   80 (219)
T 3e2i_A           10 HSSGLVPRGSHMYETYHSGWIECITGSMFSGKSEELIRRLRRGIYA------KQKVVVFKPAIDDRYH-KEKVVSH-NG-   80 (219)
T ss_dssp             -----------------CCEEEEEEECTTSCHHHHHHHHHHHHHHT------TCCEEEEEEC------------CB-TT-
T ss_pred             cccCcccCCceEeeccCCceEEEEECCCCCCHHHHHHHHHHHHHHc------CCceEEEEeccCCcch-hhhHHHh-cC-
Confidence            3455544444554434668999999999999999888888777532      4678777653211100 0111111 00 


Q ss_pred             hhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHH
Q 035774          164 IFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAE  243 (357)
Q Consensus       164 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~  243 (357)
                               ...+.+.+.   +..++.+.+        ..+.++|+||..+.+-.              ++...|..++ 
T Consensus        81 ---------~~~~a~~v~---~~~di~~~i--------~~~~dvV~IDEaQFf~~--------------~~v~~l~~la-  125 (219)
T 3e2i_A           81 ---------NAIEAINIS---KASEIMTHD--------LTNVDVIGIDEVQFFDD--------------EIVSIVEKLS-  125 (219)
T ss_dssp             ---------BCCEEEEES---SGGGGGGSC--------CTTCSEEEECCGGGSCT--------------HHHHHHHHHH-
T ss_pred             ---------CceeeEEeC---CHHHHHHHH--------hcCCCEEEEechhcCCH--------------HHHHHHHHHH-
Confidence                     000111111   122221111        24689999999996531              2566778888 


Q ss_pred             HcCCeEEEec
Q 035774          244 FSRIPIVVTN  253 (357)
Q Consensus       244 ~~~~~vv~~~  253 (357)
                      +.|++|++..
T Consensus       126 ~~gi~Vi~~G  135 (219)
T 3e2i_A          126 ADGHRVIVAG  135 (219)
T ss_dssp             HTTCEEEEEE
T ss_pred             HCCCEEEEee
Confidence            6899988764

>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=97.45  E-value=0.00065  Score=62.48  Aligned_cols=37  Identities=24%  Similarity=0.199  Sum_probs=29.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+..-++|+|+||+|||+++..++...         +.+.++++..
T Consensus       115 ~~~~~vLl~GppGtGKT~la~aia~~~---------~~~~~~i~~~  151 (357)
T 3d8b_A          115 GPPKGILLFGPPGTGKTLIGKCIASQS---------GATFFSISAS  151 (357)
T ss_dssp             SCCSEEEEESSTTSSHHHHHHHHHHHT---------TCEEEEEEGG
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHc---------CCeEEEEehH
Confidence            345679999999999999999998654         3567777663

>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=97.43  E-value=0.00084  Score=63.47  Aligned_cols=57  Identities=28%  Similarity=0.180  Sum_probs=46.0

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+.+.||++.+|.+..  +-+|+.+.|.|+||+|||+|+..++.+....  .   +.-++|...
T Consensus       132 ~e~l~TGir~ID~L~p--i~kGq~~~i~G~sGvGKTtL~~~l~~~~~~~--~---~~i~V~~~i  188 (473)
T 1sky_E          132 VEILETGIKVVDLLAP--YIKGGKIGLFGGAGVGKTVLIQELIHNIAQE--H---GGISVFAGV  188 (473)
T ss_dssp             CCEECCSCHHHHHHSC--EETTCEEEEECCSSSCHHHHHHHHHHHHHHH--T---CCCEEEEEE
T ss_pred             CccccccchHHHHHhh--hccCCEEEEECCCCCCccHHHHHHHhhhhhc--c---CcEEEEeee
Confidence            5679999999999876  7789999999999999999999999887642  1   244566543

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=97.43  E-value=0.00066  Score=62.47  Aligned_cols=33  Identities=24%  Similarity=0.366  Sum_probs=28.1

Q ss_pred             hcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           95 LCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        95 l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +..|..+|..++|+||||+|||+++..++....
T Consensus        63 ~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~   95 (368)
T 3uk6_A           63 IREGKIAGRAVLIAGQPGTGKTAIAMGMAQALG   95 (368)
T ss_dssp             HHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHC
T ss_pred             HHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            335567788999999999999999999998764

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=97.40  E-value=0.00025  Score=65.91  Aligned_cols=39  Identities=28%  Similarity=0.347  Sum_probs=30.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+++.|.||+|||||||+..++.  ..+ .     ..-++|+..
T Consensus        44 i~~Ge~~~llGpsGsGKSTLLr~iaG--l~~-~-----~G~I~i~G~   82 (390)
T 3gd7_A           44 ISPGQRVGLLGRTGSGKSTLLSAFLR--LLN-T-----EGEIQIDGV   82 (390)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHHT--CSE-E-----EEEEEESSC
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhC--CCC-C-----CeEEEECCE
Confidence            88999999999999999999987763  332 2     345666654

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=97.39  E-value=0.00035  Score=58.14  Aligned_cols=127  Identities=16%  Similarity=0.134  Sum_probs=70.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC-C--chHHHHHHHhccCchhhcccchHHHhhcCeE
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST-F--TSRRMIEMGASSFPEIFHSKGMAQEMAGRIL  179 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~-~--~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~  179 (357)
                      .++.|++.+|.||||.|.-++..++-      .+.+|+++.+-.. .  ....+.+...  +    ....    ....+.
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g------~G~rV~~vQF~Kg~~~~gE~~~l~~L~--v----~~~~----~g~gf~   92 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVG------HGKNVGVVQFIKGTWPNGERNLLEPHG--V----EFQV----MATGFT   92 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHH------TTCCEEEEESSCCSSCCHHHHHHGGGT--C----EEEE----CCTTCC
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHH------CCCeEEEEEeeCCCCCccHHHHHHhCC--c----EEEE----cccccc
Confidence            36778888899999999999999983      4699999977542 1  1122211110  0    0000    000111


Q ss_pred             EeCCCC----HHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          180 VLQPTS----LSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       180 ~~~~~~----~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                       .+...    .......+..+...+.....++||+|.++......+       -...+++..|.+  +-.+..||+|...
T Consensus        93 -~~~~~~~~~~~~a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~-------l~~~ev~~~l~~--Rp~~~~vIlTGr~  162 (196)
T 1g5t_A           93 -WETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDY-------LPLEEVISALNA--RPGHQTVIITGRG  162 (196)
T ss_dssp             -CCGGGHHHHHHHHHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTS-------SCHHHHHHHHHT--SCTTCEEEEECSS
T ss_pred             -cCCCCcHHHHHHHHHHHHHHHHHHhcCCCCEEEEeCCCccccCCC-------CCHHHHHHHHHh--CcCCCEEEEECCC
Confidence             11111    122233445556666667899999999987544311       112234444432  3346788887643

>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=97.38  E-value=0.00094  Score=60.41  Aligned_cols=39  Identities=26%  Similarity=0.204  Sum_probs=31.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+..+.|+||||+|||+++..++......      +.+++|++.+
T Consensus        36 ~~~~lll~G~~GtGKT~la~~i~~~~~~~------~~~~~~i~~~   74 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHLLQAAGNEAKKR------GYRVIYSSAD   74 (324)
T ss_dssp             SCSSEEEECSSSSSHHHHHHHHHHHHHHT------TCCEEEEEHH
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHHHC------CCEEEEEEHH
Confidence            46679999999999999999998876531      3789999864

>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=97.38  E-value=0.0016  Score=54.67  Aligned_cols=23  Identities=35%  Similarity=0.417  Sum_probs=21.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+|+||+|||+++..++....
T Consensus        41 ~ll~G~~G~GKT~l~~~l~~~~~   63 (226)
T 2chg_A           41 LLFSGPPGTGKTATAIALARDLF   63 (226)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            89999999999999999987754

>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=97.35  E-value=0.0011  Score=60.32  Aligned_cols=35  Identities=23%  Similarity=0.173  Sum_probs=29.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+++|.|++|+|||+|+.+++....         ..++|++...
T Consensus        31 ~~v~i~G~~G~GKT~L~~~~~~~~~---------~~~~~~~~~~   65 (357)
T 2fna_A           31 PITLVLGLRRTGKSSIIKIGINELN---------LPYIYLDLRK   65 (357)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHT---------CCEEEEEGGG
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhcC---------CCEEEEEchh
Confidence            5999999999999999999987652         3478998753

>2px0_A Flagellar biosynthesis protein FLHF; SRP GTPase, flagellum, protein transport, biosynthetic protein; HET: GNP; 3.00A {Bacillus subtilis} PDB: 2px3_A* 3syn_A*

Probab=97.34  E-value=0.00071  Score=60.52  Aligned_cols=42  Identities=24%  Similarity=0.352  Sum_probs=34.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+|.++.|.|++|+||||++..++......  .   +.+|++++.+.
T Consensus       103 ~~g~vi~lvG~~GsGKTTl~~~LA~~l~~~--~---G~~V~lv~~D~  144 (296)
T 2px0_A          103 IHSKYIVLFGSTGAGKTTTLAKLAAISMLE--K---HKKIAFITTDT  144 (296)
T ss_dssp             CCSSEEEEEESTTSSHHHHHHHHHHHHHHT--T---CCCEEEEECCC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHHh--c---CCEEEEEecCc
Confidence            368899999999999999999999877531  2   46899999865

>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=97.34  E-value=0.00071  Score=59.57  Aligned_cols=37  Identities=27%  Similarity=0.177  Sum_probs=28.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .++..-++|+||||+|||++|..++...         +.+.+++++
T Consensus        61 ~~~~~~vLl~G~~GtGKT~la~~ia~~~---------~~~~~~i~~   97 (272)
T 1d2n_A           61 RTPLVSVLLEGPPHSGKTALAAKIAEES---------NFPFIKICS   97 (272)
T ss_dssp             SCSEEEEEEECSTTSSHHHHHHHHHHHH---------TCSEEEEEC
T ss_pred             CCCCeEEEEECCCCCcHHHHHHHHHHHh---------CCCEEEEeC
Confidence            4556679999999999999999998764         255666654

>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=97.32  E-value=0.00064  Score=62.83  Aligned_cols=44  Identities=18%  Similarity=0.118  Sum_probs=30.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccC-CCCC-CCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAH-YGGL-DGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~-~gg~-~~~vl~i~~e  145 (357)
                      +..+.|+|+||+|||+++..++........ ..+. +..++|+++.
T Consensus        45 ~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~   90 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCR   90 (384)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECc
Confidence            458999999999999999999876532100 0011 3678888864

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=97.30  E-value=0.0026  Score=54.20  Aligned_cols=39  Identities=15%  Similarity=0.184  Sum_probs=33.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .|.+..++|+.|+||||-+++.+.++..      .+.+|+++...
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~------~g~kvli~kp~   56 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQI------AQYKCLVIKYA   56 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHT------TTCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH------CCCeEEEEeec
Confidence            5899999999999999999999999874      35888888743

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=97.30  E-value=0.00072  Score=66.49  Aligned_cols=40  Identities=23%  Similarity=0.382  Sum_probs=29.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+++.|.||+|+|||||+.-++...  ++     ....++++..
T Consensus       366 i~~Ge~~~ivG~sGsGKSTll~~l~g~~--~~-----~~G~i~i~g~  405 (587)
T 3qf4_A          366 VKPGSLVAVLGETGSGKSTLMNLIPRLI--DP-----ERGRVEVDEL  405 (587)
T ss_dssp             ECTTCEEEEECSSSSSHHHHHHTTTTSS--CC-----SEEEEEESSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCc--cC-----CCcEEEECCE
Confidence            7899999999999999999998665322  21     2456666654

>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=97.29  E-value=0.00022  Score=67.23  Aligned_cols=38  Identities=29%  Similarity=0.253  Sum_probs=32.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .++.|+|+||+||||++..++...+..      +.+|++++++.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~------G~kVllv~~D~  137 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKR------GLKPALIAADT  137 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHH------HCCEEEECCSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEEeccc
Confidence            589999999999999999999887642      47899999874

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=97.29  E-value=0.0012  Score=59.98  Aligned_cols=34  Identities=24%  Similarity=0.151  Sum_probs=28.0

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      |.+++|.|++|+|||+|+.+++...           +++|+++..
T Consensus        31 ~~~v~i~G~~G~GKT~Ll~~~~~~~-----------~~~~~~~~~   64 (350)
T 2qen_A           31 YPLTLLLGIRRVGKSSLLRAFLNER-----------PGILIDCRE   64 (350)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHHS-----------SEEEEEHHH
T ss_pred             CCeEEEECCCcCCHHHHHHHHHHHc-----------CcEEEEeec
Confidence            3699999999999999999988642           188998743

>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=97.28  E-value=0.00045  Score=65.54  Aligned_cols=41  Identities=24%  Similarity=0.243  Sum_probs=31.2

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      |+..+..-++|+||||+|||+++..++....        +.+.++++..
T Consensus       162 ~~~~~~~~vLL~GppGtGKT~lA~aia~~~~--------~~~~~~v~~~  202 (444)
T 2zan_A          162 GKRTPWRGILLFGPPGTGKSYLAKAVATEAN--------NSTFFSISSS  202 (444)
T ss_dssp             GGGCCCSEEEEECSTTSSHHHHHHHHHHHCC--------SSEEEEECCC
T ss_pred             ccCCCCceEEEECCCCCCHHHHHHHHHHHcC--------CCCEEEEeHH
Confidence            3455667899999999999999999987652        2566666654

>1zp6_A Hypothetical protein ATU3015; alpha-beta protein., structural genomics, PSI, protein struc initiative; 3.20A {Agrobacterium tumefaciens str} SCOP: c.37.1.25

Probab=97.28  E-value=0.00014  Score=60.42  Aligned_cols=38  Identities=21%  Similarity=0.184  Sum_probs=30.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|.++.|.|+|||||||++..++..  .       +.+.++++.+
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~~La~~--~-------~~g~i~i~~d   43 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAEALANL--P-------GVPKVHFHSD   43 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHHHHHTC--S-------SSCEEEECTT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHhc--c-------CCCeEEEccc
Confidence            889999999999999999999988753  1       2456777764

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=97.25  E-value=0.0011  Score=65.48  Aligned_cols=26  Identities=38%  Similarity=0.526  Sum_probs=23.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.||+|+|||||+.-++.
T Consensus       378 i~~G~~~~ivG~sGsGKSTll~~l~g  403 (598)
T 3qf4_B          378 IKPGQKVALVGPTGSGKTTIVNLLMR  403 (598)
T ss_dssp             CCTTCEEEEECCTTSSTTHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhc
Confidence            78999999999999999999986653

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=97.25  E-value=0.0013  Score=62.43  Aligned_cols=58  Identities=22%  Similarity=0.280  Sum_probs=47.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=..|.|++|+|||++++..+.+.+.      .+..|+|+-.-+
T Consensus       143 ~epl~TGiraID~l~P--igrGQR~~Ifg~~g~GKT~Lal~~I~~~~~------~dv~~V~~~iGe  200 (502)
T 2qe7_A          143 HEPLQTGIKAIDSMIP--IGRGQRELIIGDRQTGKTTIAIDTIINQKG------QDVICIYVAIGQ  200 (502)
T ss_dssp             CSBCCCSCHHHHHSSC--CBTTCBCEEEECSSSCHHHHHHHHHHGGGS------CSEEEEEEEESC
T ss_pred             CCccccceeecccccc--cccCCEEEEECCCCCCchHHHHHHHHHhhc------CCcEEEEEECCC
Confidence            5679999999999987  889999999999999999998877776652      134677877644

>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B

Probab=97.24  E-value=0.00088  Score=46.05  Aligned_cols=56  Identities=21%  Similarity=0.250  Sum_probs=51.7

Q ss_pred             cccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            3 NKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      ..++++|+|+....+.|.++||+|+.|++..++.++.++-++..+.+.++...+.+
T Consensus         8 ~~~Ie~L~LS~Ra~NcLkragI~Tv~dL~~~s~~dLlki~n~G~kSl~EI~~~L~~   63 (73)
T 1z3e_B            8 EMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   63 (73)
T ss_dssp             TCBGGGSCCBHHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             cCcHHHhCCCHHHHHHHHHcCCCcHHHHHcCCHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            36899999999999999999999999999999999999999999999888877654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.23  E-value=0.0015  Score=58.77  Aligned_cols=62  Identities=11%  Similarity=-0.061  Sum_probs=39.3

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC-CCeEEEEeCCCCCchHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL-DGGVIYIDVESTFTSRRM  153 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~-~~~vl~i~~e~~~~~~rl  153 (357)
                      .|...+.+|  ++..+.|+|+||+|||+++..++.........++. ...++|+.+....+...+
T Consensus        35 ~L~~~i~~~--~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~   97 (318)
T 3te6_A           35 PIYDSLMSS--QNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDAL   97 (318)
T ss_dssp             HHHHHHHTT--CCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHH
T ss_pred             HHHHHhcCC--CCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHH
Confidence            355556554  55677999999999999999998876432111111 246888887654444333

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=97.23  E-value=0.0028  Score=56.69  Aligned_cols=42  Identities=24%  Similarity=0.267  Sum_probs=29.1

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++.-++|+||||+|||+++..++.........  ...++++++.
T Consensus        66 ~~~~vll~G~~GtGKT~la~~la~~l~~~~~~--~~~~~~~~~~  107 (309)
T 3syl_A           66 PTLHMSFTGNPGTGKTTVALKMAGLLHRLGYV--RKGHLVSVTR  107 (309)
T ss_dssp             CCCEEEEEECTTSSHHHHHHHHHHHHHHTTSS--SSCCEEEECG
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHhcCCc--CCCcEEEEcH
Confidence            45569999999999999999888766431100  1246777764

>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=97.22  E-value=0.00073  Score=62.36  Aligned_cols=32  Identities=16%  Similarity=0.199  Sum_probs=26.9

Q ss_pred             hcCCCCC--CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           95 LCGGVPF--GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        95 l~GGi~~--G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.--+.+  |+.+.|.|++|+|||||+..++...
T Consensus       161 v~~~v~~~lg~k~~IvG~nGsGKSTLlk~L~gl~  194 (365)
T 1lw7_A          161 IPKEARPFFAKTVAILGGESSGKSVLVNKLAAVF  194 (365)
T ss_dssp             SCTTTGGGTCEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             CCHHHHHhhhCeEEEECCCCCCHHHHHHHHHHHh
Confidence            3334677  9999999999999999999888654

>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=97.21  E-value=0.00043  Score=63.61  Aligned_cols=28  Identities=18%  Similarity=0.150  Sum_probs=24.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..+|.++.|+||+||||||++..++...
T Consensus       120 ~~~~g~i~I~GptGSGKTTlL~~l~g~~  147 (356)
T 3jvv_A          120 DVPRGLVLVTGPTGSGKSTTLAAMLDYL  147 (356)
T ss_dssp             HCSSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             hCCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            3677799999999999999999887655

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=97.21  E-value=0.00039  Score=63.63  Aligned_cols=44  Identities=16%  Similarity=0.191  Sum_probs=37.6

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ...+.||+..||.++.  +.+|+.+.|.|++|+|||||+..++...
T Consensus        52 ~~~~~tg~~ald~ll~--i~~Gq~~gIiG~nGaGKTTLl~~I~g~~   95 (347)
T 2obl_A           52 DQPFILGVRAIDGLLT--CGIGQRIGIFAGSGVGKSTLLGMICNGA   95 (347)
T ss_dssp             CSEECCSCHHHHHHSC--EETTCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             ceecCCCCEEEEeeee--ecCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3456789999999965  9999999999999999999977777654

>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=97.21  E-value=0.00098  Score=63.12  Aligned_cols=41  Identities=24%  Similarity=0.212  Sum_probs=31.7

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.-+.|+|+||+|||+|+..++......    ..+.+++|++.+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~----~~~~~v~~v~~~~  170 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQN----EPDLRVMYITSEK  170 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHH----CCSSCEEEEEHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHh----CCCCeEEEeeHHH
Confidence            5689999999999999999988766432    1146789988653

>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=97.21  E-value=0.0013  Score=62.36  Aligned_cols=58  Identities=21%  Similarity=0.263  Sum_probs=47.4

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=..|.|++|+|||++++..+.+.+.      .+..|+|+-.-+
T Consensus       156 ~epl~TGiraID~l~P--igrGQR~~I~g~~g~GKT~Lal~~I~~~~~------~dv~~V~~~IGe  213 (515)
T 2r9v_A          156 DTPLQTGIKAIDSMIP--IGRGQRELIIGDRQTGKTAIAIDTIINQKG------QGVYCIYVAIGQ  213 (515)
T ss_dssp             CSEECCSCHHHHHHSC--EETTCBEEEEEETTSSHHHHHHHHHHTTTT------TTEEEEEEEESC
T ss_pred             CcchhcCccccccccc--cccCCEEEEEcCCCCCccHHHHHHHHHhhc------CCcEEEEEEcCC
Confidence            4679999999999987  889999999999999999998877766652      234677877654

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=97.20  E-value=0.00054  Score=64.77  Aligned_cols=56  Identities=23%  Similarity=0.189  Sum_probs=43.4

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ...+.||...||.++.  +.+|+.+.|.|++|+|||||+..++.... +      ...++.+..+
T Consensus       138 ~~~~~tg~~vld~vl~--i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~-~------~~G~i~~~G~  193 (438)
T 2dpy_A          138 EHVLDTGVRAINALLT--VGRGQRMGLFAGSGVGKSVLLGMMARYTR-A------DVIVVGLIGE  193 (438)
T ss_dssp             CSBCCCSCHHHHHHSC--CBTTCEEEEEECTTSSHHHHHHHHHHHSC-C------SEEEEEEESC
T ss_pred             ceecCCCceEEeeeEE--ecCCCEEEEECCCCCCHHHHHHHHhcccC-C------CeEEEEEece
Confidence            3456678999999954  99999999999999999999777766542 1      3456666665

>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=97.19  E-value=0.002  Score=61.31  Aligned_cols=64  Identities=17%  Similarity=0.171  Sum_probs=48.0

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCC--CCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYG--GLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~g--g~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=..|.|++|+|||++++..+.+.+.....|  +.+..|+|+-.-+
T Consensus       143 ~epl~TGiraID~l~P--igrGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGe  208 (510)
T 2ck3_A          143 REPMQTGIKAVDSLVP--IGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQ  208 (510)
T ss_dssp             CSBCCCSCHHHHHHSC--CBTTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESC
T ss_pred             Cccccccceeeccccc--cccCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCC
Confidence            5679999999999987  88999999999999999999887776665310000  0134578877644

>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=97.19  E-value=0.0032  Score=59.41  Aligned_cols=59  Identities=27%  Similarity=0.229  Sum_probs=48.5

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|-++.  +-+|+=..|.|++|+|||+|+.+++.+.+...     +.-++|.-.-+
T Consensus       134 ~e~l~TGir~ID~l~p--igkGQr~~Ifgg~G~GKT~L~~~i~~~~~~~~-----~~v~V~~~iGE  192 (482)
T 2ck3_D          134 QEILVTGIKVVDLLAP--YAKGGKIGLFGGAGVGKTVLIMELINNVAKAH-----GGYSVFAGVGE  192 (482)
T ss_dssp             CCEECCSCHHHHHHSC--EETTCEEEEEECTTSSHHHHHHHHHHHTTTTC-----SSEEEEEEESC
T ss_pred             CcCCccceEEEecccc--cccCCeeeeecCCCCChHHHHHHHHHhhHhhC-----CCEEEEEECCC
Confidence            4689999999999987  88999999999999999999999999876421     24567765443

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=97.18  E-value=0.0029  Score=62.19  Aligned_cols=44  Identities=9%  Similarity=0.046  Sum_probs=32.2

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-...         .....+.+.|++++++ +.+||+++|--
T Consensus       238 ~~p~llllDEPts~LD~---------~~~~~l~~~l~~l~~~-g~tvi~vtHdl  281 (608)
T 3j16_B          238 QEADVYMFDEPSSYLDV---------KQRLNAAQIIRSLLAP-TKYVICVEHDL  281 (608)
T ss_dssp             SCCSEEEEECTTTTCCH---------HHHHHHHHHHHGGGTT-TCEEEEECSCH
T ss_pred             hCCCEEEEECcccCCCH---------HHHHHHHHHHHHHHhC-CCEEEEEeCCH
Confidence            57999999987765432         4455567777777654 88999998853

>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=97.18  E-value=0.0017  Score=61.68  Aligned_cols=58  Identities=24%  Similarity=0.210  Sum_probs=47.8

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=..|.|++|+|||++++..+.+.+.      .+..|+|.-.-+
T Consensus       144 ~epl~TGiraID~l~P--igrGQR~~Ifg~~g~GKT~Lal~~I~~~~~------~dv~~V~~~iGe  201 (507)
T 1fx0_A          144 YEPLQTGLIAIDAMIP--VGRGQRELIIGDRQTGKTAVATDTILNQQG------QNVICVYVAIGQ  201 (507)
T ss_dssp             CSBCCCSCTTTTTTSC--CBTTCBCBEEESSSSSHHHHHHHHHHTCCT------TTCEEEEEEESC
T ss_pred             CCcccccceecccccc--cccCCEEEEecCCCCCccHHHHHHHHHhhc------CCcEEEEEEcCC
Confidence            4679999999999987  889999999999999999998877776652      245678887654

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=97.17  E-value=0.00024  Score=59.48  Aligned_cols=42  Identities=29%  Similarity=0.409  Sum_probs=34.3

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.. +..|...+.| +|+..-++|+||||+|||++|..++...
T Consensus        41 ~~~f-~~~l~~~~~~-iPkkn~ili~GPPGtGKTt~a~ala~~l   82 (212)
T 1tue_A           41 FITF-LGALKSFLKG-TPKKNCLVFCGPANTGKSYFGMSFIHFI   82 (212)
T ss_dssp             HHHH-HHHHHHHHHT-CTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHHHhc-CCcccEEEEECCCCCCHHHHHHHHHHHh
Confidence            3434 6677777765 8988889999999999999999888765

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=97.16  E-value=0.0013  Score=67.56  Aligned_cols=29  Identities=21%  Similarity=0.328  Sum_probs=25.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +++|+++.|.||+|+|||||+.+++....
T Consensus       670 ~~~g~i~~ItGPNGaGKSTlLr~i~~i~~  698 (918)
T 3thx_B          670 EDSERVMIITGPNMGGKSSYIKQVALITI  698 (918)
T ss_dssp             TTSCCEEEEESCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCchHHHHHHHHHHHH
Confidence            67899999999999999999998875443

>3bk7_A ABC transporter ATP-binding protein; ABC ATPase, iron-sulfur cluster, adenosine diphosphate, nucleotide-binding; HET: ADP; 2.80A {Pyrococcus abyssi} PDB: 3j15_B*

Probab=97.16  E-value=0.0019  Score=63.52  Aligned_cols=44  Identities=11%  Similarity=0.055  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-...         .....+.+.|++++++ +.+||+++|-.
T Consensus       245 ~~P~lLlLDEPTs~LD~---------~~~~~l~~~L~~l~~~-g~tvIivsHdl  288 (607)
T 3bk7_A          245 RKAHFYFFDEPSSYLDI---------RQRLKVARVIRRLANE-GKAVLVVEHDL  288 (607)
T ss_dssp             SCCSEEEEECTTTTCCH---------HHHHHHHHHHHHHHHT-TCEEEEECSCH
T ss_pred             cCCCEEEEECCcccCCH---------HHHHHHHHHHHHHHhc-CCEEEEEecCh
Confidence            57999999987765432         4455677788888764 99999999853

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.16  E-value=0.0006  Score=65.41  Aligned_cols=36  Identities=33%  Similarity=0.416  Sum_probs=28.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|  ++|+||||+|||+|+..++...         +.+.++++..
T Consensus        63 ip~G--vLL~GppGtGKTtLaraIa~~~---------~~~~i~i~g~   98 (499)
T 2dhr_A           63 IPKG--VLLVGPPGVGKTHLARAVAGEA---------RVPFITASGS   98 (499)
T ss_dssp             CCSE--EEEECSSSSSHHHHHHHHHHHT---------TCCEEEEEGG
T ss_pred             CCce--EEEECCCCCCHHHHHHHHHHHh---------CCCEEEEehh
Confidence            5666  9999999999999999888654         2567777663

>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=97.16  E-value=0.0026  Score=60.23  Aligned_cols=58  Identities=19%  Similarity=0.243  Sum_probs=47.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|.++.  +-+|+=..|.|++|+|||+++++.+.+...      .+..|+|+-.-+
T Consensus       143 ~epl~TGikaID~l~P--igrGQR~~Ifg~~g~GKT~l~l~~I~n~~~------~dv~~V~~~IGe  200 (513)
T 3oaa_A          143 DQPVQTGYKAVDSMIP--IGRGQRELIIGDRQTGKTALAIDAIINQRD------SGIKCIYVAIGQ  200 (513)
T ss_dssp             CCBCCCSCHHHHHHSC--CBTTCBCEEEESSSSSHHHHHHHHHHTTSS------SSCEEEEEEESC
T ss_pred             Ccccccceeeeccccc--cccCCEEEeecCCCCCcchHHHHHHHhhcc------CCceEEEEEecC
Confidence            5689999999999987  889999999999999999998877666431      245678887644

>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} SCOP: a.60.3.1 PDB: 3n4m_B* 1lb2_B* 3n97_B* 1xs9_D

Probab=97.15  E-value=0.0011  Score=46.96  Aligned_cols=56  Identities=18%  Similarity=0.253  Sum_probs=51.6

Q ss_pred             cccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            3 NKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      +.++++|.|+....+-|.++||+|+.+++..++.++.++-++..+.+.++...+.+
T Consensus        11 ~~~I~~L~LSvRa~NcLkragI~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~   66 (86)
T 3k4g_A           11 LRPVDDLELTVRSANCLXAEAIHYIGDLVQRTEVELLXTPNLGXXSLTEIXDVLAS   66 (86)
T ss_dssp             GSBGGGGCCCHHHHHHHHHTTCCBHHHHHHSCHHHHHTSTTCCHHHHHHHHHHHHT
T ss_pred             hCcHHHhCCCHHHHHHHHHcCCCcHHHHHhCCHHHHhhccccCcccHHHHHHHHHH
Confidence            46899999999999999999999999999999999999999999999888876654

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=97.13  E-value=0.0003  Score=58.02  Aligned_cols=29  Identities=21%  Similarity=0.258  Sum_probs=24.3

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |-.+|.++.|.||+|+|||||+..++...
T Consensus         1 ~~~~g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            1 GSHMRKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             --CCCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            35679999999999999999999888653

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=97.13  E-value=0.008  Score=55.06  Aligned_cols=41  Identities=24%  Similarity=0.117  Sum_probs=32.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+++.|.|++|+||||++..++.....   .   ++.|.+...+
T Consensus       154 ~~~g~vi~lvG~nGsGKTTll~~Lag~l~~---~---~G~V~l~g~D  194 (359)
T 2og2_A          154 FRKPAVIMIVGVNGGGKTTSLGKLAHRLKN---E---GTKVLMAAGD  194 (359)
T ss_dssp             SSSSEEEEEECCTTSCHHHHHHHHHHHHHH---T---TCCEEEECCC
T ss_pred             cCCCeEEEEEcCCCChHHHHHHHHHhhccc---c---CCEEEEeccc
Confidence            578999999999999999999999876542   1   3566666544

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=97.13  E-value=0.0072  Score=54.09  Aligned_cols=41  Identities=24%  Similarity=0.117  Sum_probs=32.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.+|+++.|.|++|+||||++..++.....   .   ++.|.+...+
T Consensus        97 ~~~g~vi~lvG~nGsGKTTll~~Lag~l~~---~---~g~V~l~g~d  137 (302)
T 3b9q_A           97 FRKPAVIMIVGVNGGGKTTSLGKLAHRLKN---E---GTKVLMAAGD  137 (302)
T ss_dssp             SSSCEEEEEECCTTSCHHHHHHHHHHHHHH---T---TCCEEEECCC
T ss_pred             cCCCcEEEEEcCCCCCHHHHHHHHHHHHHH---c---CCeEEEEeec
Confidence            678999999999999999999999876642   1   3566665543

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=97.09  E-value=0.00056  Score=56.50  Aligned_cols=47  Identities=30%  Similarity=0.372  Sum_probs=32.9

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .||.-..  ..+|.++.|.|.|||||||++..++......      +..+.+++.
T Consensus         3 ~~~~~~~--~~~~~~i~l~G~~GsGKsT~~~~L~~~l~~~------~~~~~~~~~   49 (186)
T 2yvu_A            3 ALTTYKC--IEKGIVVWLTGLPGSGKTTIATRLADLLQKE------GYRVEVLDG   49 (186)
T ss_dssp             -----CC--CSCCEEEEEECCTTSSHHHHHHHHHHHHHHT------TCCEEEEEH
T ss_pred             ccccccc--cCCCcEEEEEcCCCCCHHHHHHHHHHHHHhc------CCeEEEeeH
Confidence            4666444  3578999999999999999999998766421      356778764

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=97.09  E-value=0.0009  Score=64.19  Aligned_cols=46  Identities=20%  Similarity=0.099  Sum_probs=33.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +..+.-++|+|.+|||||+++..++...+.....+  .-.++.+|..+
T Consensus       164 L~~~pHlLIaG~TGSGKSt~L~~li~sLl~~~~p~--~v~l~liDpK~  209 (512)
T 2ius_A          164 LAKMPHLLVAGTTGSGASVGVNAMILSMLYKAQPE--DVRFIMIDPKM  209 (512)
T ss_dssp             GGGSCSEEEECCTTSSHHHHHHHHHHHHHTTCCTT--TEEEEEECCSS
T ss_pred             cccCceEEEECCCCCCHHHHHHHHHHHHHHhCCCc--eEEEEEECCch
Confidence            55677899999999999999999988766532221  24555666553

>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} SCOP: a.60.3.1

Probab=97.09  E-value=0.00084  Score=46.75  Aligned_cols=56  Identities=21%  Similarity=0.250  Sum_probs=51.3

Q ss_pred             cccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            3 NKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      +.++++|.|+....+.|.++||+|+.+++..++.++.++-++..+.+.++...+.+
T Consensus        15 ~~~Ie~L~LS~Ra~NcLk~agI~Tv~dL~~~se~dLlki~n~G~kSl~EI~~~L~e   70 (79)
T 3gfk_B           15 EMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   70 (79)
T ss_dssp             GCBGGGSCCBHHHHHHHHHTTCCBHHHHTTCCHHHHTTSTTCHHHHHHHHHHHHHH
T ss_pred             cCcHHHhCCCHHHHHHHHHhCCCCHHHHHhCCHHHHHHcCCCCHhHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999988888776654

>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=97.09  E-value=0.002  Score=58.78  Aligned_cols=23  Identities=39%  Similarity=0.527  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+||||+|||+++..++....
T Consensus        39 ~ll~Gp~G~GKTtl~~~la~~l~   61 (354)
T 1sxj_E           39 LLLYGPNGTGKKTRCMALLESIF   61 (354)
T ss_dssp             EEEECSTTSSHHHHHHTHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Confidence            89999999999999999888654

>3ozx_A RNAse L inhibitor; ATP binding cassette protein, hydrolase, translation; HET: ADP; 2.05A {Sulfolobus solfataricus}

Probab=97.08  E-value=0.0036  Score=60.71  Aligned_cols=43  Identities=9%  Similarity=0.086  Sum_probs=31.6

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .+++++++|.-++-...         .....+.+.|+++.+  +.+||+++|--
T Consensus       155 ~~p~illlDEPts~LD~---------~~~~~l~~~l~~l~~--g~tii~vsHdl  197 (538)
T 3ozx_A          155 READVYIFDQPSSYLDV---------RERMNMAKAIRELLK--NKYVIVVDHDL  197 (538)
T ss_dssp             SCCSEEEEESTTTTCCH---------HHHHHHHHHHHHHCT--TSEEEEECSCH
T ss_pred             cCCCEEEEECCcccCCH---------HHHHHHHHHHHHHhC--CCEEEEEEeCh
Confidence            57999999987765432         445556777777754  89999999853

>1wcn_A Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B

Probab=97.05  E-value=0.0014  Score=44.78  Aligned_cols=49  Identities=14%  Similarity=0.137  Sum_probs=46.3

Q ss_pred             CCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774           10 RLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus        10 ~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      |+++....+|.++|++|++++...+..+|..+.+++++++.+++.++.+
T Consensus        14 Gi~~~~~~kL~e~Gi~TvedlA~~~~~eL~~i~gise~kA~~ii~aAr~   62 (70)
T 1wcn_A           14 GVDRDLAFKLAARGVCTLEDLAEQGIDDLADIEGLTDEKAGALIMAARN   62 (70)
T ss_dssp             TCCHHHHHHHHTTTCCSHHHHHTSCHHHHHTSSSCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999999999999999999999999987765

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=97.05  E-value=0.0012  Score=64.77  Aligned_cols=25  Identities=24%  Similarity=0.408  Sum_probs=22.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+++.|.||+|+|||||+.-++
T Consensus       364 i~~G~~~~ivG~sGsGKSTll~~l~  388 (578)
T 4a82_A          364 IEKGETVAFVGMSGGGKSTLINLIP  388 (578)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHTTTT
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHh
Confidence            7899999999999999999998555

>2rhm_A Putative kinase; P-loop containing nucleoside triphosphate hydrolases fold, S genomics, joint center for structural genomics, JCSG; HET: MSE; 1.70A {Chloroflexus aurantiacus}

Probab=97.02  E-value=0.00044  Score=57.29  Aligned_cols=29  Identities=24%  Similarity=0.277  Sum_probs=25.7

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |++++.++.|.|+|||||||++..++...
T Consensus         1 ~~~~~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            1 GMQTPALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CCSCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            47788999999999999999999988654

>3iqw_A Tail-anchored protein targeting factor GET3; ATPase, Zn binding, protein transport; HET: ANP; 3.00A {Chaetomium thermophilum} PDB: 3iqx_A* 3ibg_A*

Probab=97.01  E-value=0.0022  Score=58.27  Aligned_cols=50  Identities=20%  Similarity=0.155  Sum_probs=39.6

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      .|+.++..  +.-.++.+.|..|+||||++.++|...+..      +.+|+.||++..
T Consensus         6 ~l~~~l~~--~~~~i~~~sgkGGvGKTt~a~~lA~~la~~------g~~vllid~D~~   55 (334)
T 3iqw_A            6 TLQSILDQ--RSLRWIFVGGKGGVGKTTTSCSLAIQLAKV------RRSVLLLSTDPA   55 (334)
T ss_dssp             SSHHHHHC--TTCCEEEEECSTTSSHHHHHHHHHHHHTTS------SSCEEEEECCSS
T ss_pred             cHHHHhcC--CCeEEEEEeCCCCccHHHHHHHHHHHHHhC------CCcEEEEECCCC
Confidence            35555654  234688999999999999999999988752      589999999853

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=97.00  E-value=0.0004  Score=58.18  Aligned_cols=27  Identities=22%  Similarity=0.278  Sum_probs=23.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|+++.|.||+||||||++..++..
T Consensus         4 m~~g~ii~l~Gp~GsGKSTl~~~L~~~   30 (205)
T 3tr0_A            4 MNKANLFIISAPSGAGKTSLVRALVKA   30 (205)
T ss_dssp             -CCCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCCcEEEEECcCCCCHHHHHHHHHhh
Confidence            467999999999999999999988765

>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=96.99  E-value=0.00078  Score=72.35  Aligned_cols=40  Identities=38%  Similarity=0.530  Sum_probs=30.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+.+.|+|++|||||||+.-+..-.  .+     ..+.++||..
T Consensus      1102 I~~Ge~vaIVG~SGsGKSTL~~lL~rl~--~p-----~~G~I~iDG~ 1141 (1321)
T 4f4c_A         1102 VEPGQTLALVGPSGCGKSTVVALLERFY--DT-----LGGEIFIDGS 1141 (1321)
T ss_dssp             ECTTCEEEEECSTTSSTTSHHHHHTTSS--CC-----SSSEEEETTE
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHhcCc--cC-----CCCEEEECCE
Confidence            8899999999999999999998665432  11     2446777654

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.98  E-value=0.00077  Score=56.46  Aligned_cols=41  Identities=20%  Similarity=0.205  Sum_probs=31.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .++|.++.|.|++||||||++..++...-.   .   +..++|++.+
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~La~~l~~---~---G~~~~~~d~d   62 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACALNQMLYQ---K---GKLCYILDGD   62 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHHHHHHHHH---T---TCCEEEEEHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHh---c---CceEEEecCc
Confidence            368999999999999999999998876532   1   2445678753

>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=96.97  E-value=0.0012  Score=71.00  Aligned_cols=27  Identities=33%  Similarity=0.416  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+.+.|.|++|||||||+.-++..
T Consensus       441 i~~G~~vaivG~sGsGKSTll~ll~~~  467 (1321)
T 4f4c_A          441 VNAGQTVALVGSSGCGKSTIISLLLRY  467 (1321)
T ss_dssp             ECTTCEEEEEECSSSCHHHHHHHHTTS
T ss_pred             ecCCcEEEEEecCCCcHHHHHHHhccc
Confidence            899999999999999999999866543

>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=96.96  E-value=0.00051  Score=55.41  Aligned_cols=28  Identities=21%  Similarity=0.202  Sum_probs=25.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+++.|.||+|+|||||+..++...
T Consensus        30 i~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           30 TEKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             CSSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            7899999999999999999999888654

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.94  E-value=0.00095  Score=59.42  Aligned_cols=37  Identities=30%  Similarity=0.307  Sum_probs=29.2

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..+.+++|+|+|||||||++..++...         +...++||.+
T Consensus        31 ~~~~livl~G~sGsGKSTla~~L~~~~---------~~~~~~Is~D   67 (287)
T 1gvn_B           31 ESPTAFLLGGQPGSGKTSLRSAIFEET---------QGNVIVIDND   67 (287)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHT---------TTCCEEECTH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh---------CCCeEEEech
Confidence            457899999999999999999988653         1346777763

>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=96.94  E-value=0.00048  Score=58.13  Aligned_cols=28  Identities=29%  Similarity=0.356  Sum_probs=23.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+++.|.||+|||||||+..++...
T Consensus        17 i~~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           17 AAVGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             --CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            8899999999999999999999887543

>3zq6_A Putative arsenical pump-driving ATPase; tail-anchored, membrane protein; HET: ADP; 2.11A {Methanothermobacter thermautotrophicusorganism_taxid}

Probab=96.94  E-value=0.0023  Score=57.97  Aligned_cols=39  Identities=21%  Similarity=0.270  Sum_probs=34.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      .++++.|.+|+||||++.++|...+..      +.+|+.||++..
T Consensus        15 ~i~v~sgKGGvGKTTvA~~LA~~lA~~------G~rVLlvD~D~~   53 (324)
T 3zq6_A           15 TFVFIGGKGGVGKTTISAATALWMARS------GKKTLVISTDPA   53 (324)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHT------TCCEEEEECCSS
T ss_pred             EEEEEeCCCCchHHHHHHHHHHHHHHC------CCcEEEEeCCCC
Confidence            789999999999999999999988852      589999999863

>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=96.93  E-value=0.00087  Score=62.50  Aligned_cols=46  Identities=22%  Similarity=0.179  Sum_probs=31.6

Q ss_pred             CCcEEEE--EcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTEL--VGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I--~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+..++|  +|+||+|||+++..++..........+.+..++|+++..
T Consensus        49 ~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~   96 (412)
T 1w5s_A           49 SDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFN   96 (412)
T ss_dssp             CCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGG
T ss_pred             CCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCC
Confidence            4568888  999999999999999876532100001135789998643

>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=96.93  E-value=0.00089  Score=54.90  Aligned_cols=39  Identities=23%  Similarity=0.176  Sum_probs=29.6

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++|.++.|.|++||||||++..++.....   .   +.++++++.
T Consensus         3 ~~g~~i~l~G~~GsGKST~~~~L~~~l~~---~---g~~~i~~d~   41 (179)
T 2pez_A            3 MRGCTVWLTGLSGAGKTTVSMALEEYLVC---H---GIPCYTLDG   41 (179)
T ss_dssp             -CCEEEEEECCTTSSHHHHHHHHHHHHHH---T---TCCEEEEEH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHhh---C---CCcEEEECC
Confidence            67999999999999999999988875421   1   356777763

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.93  E-value=0.00052  Score=57.55  Aligned_cols=28  Identities=25%  Similarity=0.326  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|.++.|.|++||||||++..++...
T Consensus         3 i~~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            3 NEKGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             -CCCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            5789999999999999999999887543

>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=96.90  E-value=0.00054  Score=58.47  Aligned_cols=29  Identities=21%  Similarity=0.319  Sum_probs=23.6

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+++|+++.|.||+|+|||||+..++...
T Consensus        12 ~~~~G~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           12 HMAQGTLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             ---CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cCCCCcEEEEECCCCCCHHHHHHHHhccC
Confidence            38999999999999999999999877643

>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=96.89  E-value=0.0058  Score=58.54  Aligned_cols=56  Identities=29%  Similarity=0.289  Sum_probs=46.2

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||+..+|.++.  +-+|+=..|.|++|+|||+++.+++.+.-        ..-++|+-.-+
T Consensus       208 ~epl~TGirvID~l~P--igkGqr~~I~g~~g~GKT~L~~~ia~~~~--------~~~~V~~~iGE  263 (588)
T 3mfy_A          208 EVPLITGQRVIDTFFP--QAKGGTAAIPGPAGSGKTVTQHQLAKWSD--------AQVVIYIGCGE  263 (588)
T ss_dssp             CSEECCSCHHHHHHSC--EETTCEEEECSCCSHHHHHHHHHHHHHSS--------CSEEEEEECCS
T ss_pred             CcccccCcchhhccCC--cccCCeEEeecCCCCCHHHHHHHHHhccC--------CCEEEEEEecc
Confidence            4678899999999987  78999999999999999999999876532        24677776654

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=96.84  E-value=0.0011  Score=55.42  Aligned_cols=36  Identities=22%  Similarity=0.134  Sum_probs=29.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ..+.|+|+||+|||+|+..++......      +.+++|+++
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~------~~~~~~~~~   90 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKR------NVSSLIVYV   90 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTT------TCCEEEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc------CCeEEEEEh
Confidence            578999999999999999998877532      467888876

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=96.83  E-value=0.00056  Score=58.28  Aligned_cols=28  Identities=25%  Similarity=0.195  Sum_probs=23.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+++.|.||+|+|||||+..++...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            7889999999999999999999887643

>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=96.82  E-value=0.00059  Score=68.96  Aligned_cols=112  Identities=13%  Similarity=0.156  Sum_probs=60.3

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhc
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAG  176 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~  176 (357)
                      .|+.+..-++++||||+|||.+|..+|...-         .+  ||....    .   .+....                
T Consensus       506 ~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~---------~~--f~~v~~----~---~l~s~~----------------  551 (806)
T 3cf2_A          506 FGMTPSKGVLFYGPPGCGKTLLAKAIANECQ---------AN--FISIKG----P---ELLTMW----------------  551 (806)
T ss_dssp             SCCCCCSCCEEESSTTSSHHHHHHHHHHTTT---------CE--EEECCH----H---HHHTTT----------------
T ss_pred             cCCCCCceEEEecCCCCCchHHHHHHHHHhC---------Cc--eEEecc----c---hhhccc----------------
Confidence            4677777799999999999999998886542         33  333311    1   111110                


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC----CCCChHHHHHHHHHHHHHHHHcCCeEEE
Q 035774          177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ----RAPGQHPLSWHISLITSLAEFSRIPIVV  251 (357)
Q Consensus       177 ~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~----~~~r~~~~~~i~~~Lk~la~~~~~~vv~  251 (357)
                           -..+...+.+++    ...+...+.+|+||.+-++.......    .......+.+++..|..+....++.||.
T Consensus       552 -----vGese~~vr~lF----~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~  621 (806)
T 3cf2_A          552 -----FGESEANVREIF----DKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIG  621 (806)
T ss_dssp             -----CSSCHHHHHHHH----HHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEEC
T ss_pred             -----cchHHHHHHHHH----HHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEE
Confidence                 001222233333    33345578999999999997652111    1112234556666666555555555553

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=96.82  E-value=0.0068  Score=57.40  Aligned_cols=24  Identities=38%  Similarity=0.461  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..++|+||||+|||+++..++...
T Consensus        51 ~~vLL~GppGtGKTtlAr~ia~~~   74 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLAEVIARYA   74 (447)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHh
Confidence            469999999999999999888764

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.82  E-value=0.00065  Score=57.32  Aligned_cols=28  Identities=25%  Similarity=0.356  Sum_probs=24.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .++|.++.|.|++|||||||+..++...
T Consensus        19 ~~~g~~v~I~G~sGsGKSTl~~~l~~~~   46 (208)
T 3c8u_A           19 QPGRQLVALSGAPGSGKSTLSNPLAAAL   46 (208)
T ss_dssp             CCSCEEEEEECCTTSCTHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4689999999999999999999887654

>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=96.81  E-value=0.0078  Score=54.20  Aligned_cols=36  Identities=17%  Similarity=0.231  Sum_probs=28.9

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..+++++||||+|||+++..++...         +..+++++...
T Consensus        48 ~~~~L~~G~~G~GKT~la~~la~~l---------~~~~~~i~~~~   83 (324)
T 3u61_B           48 PHIILHSPSPGTGKTTVAKALCHDV---------NADMMFVNGSD   83 (324)
T ss_dssp             CSEEEECSSTTSSHHHHHHHHHHHT---------TEEEEEEETTT
T ss_pred             CeEEEeeCcCCCCHHHHHHHHHHHh---------CCCEEEEcccc
Confidence            3589999999999999999988654         36788887643

>3tau_A Guanylate kinase, GMP kinase; structural genomics, center for structural genomics of infec diseases, csgid, putative guanylate kinase; HET: MSE; 2.05A {Listeria monocytogenes}

Probab=96.79  E-value=0.00076  Score=56.95  Aligned_cols=27  Identities=26%  Similarity=0.316  Sum_probs=24.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.++.|.||+|+||||++..++...
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHST
T ss_pred             CCCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            579999999999999999999888643

>4dzz_A Plasmid partitioning protein PARF; deviant walker BOX, DNA segregation, unknown function; HET: ADP; 1.80A {Escherichia coli} PDB: 4e03_A* 4e07_A* 4e09_A*

Probab=96.79  E-value=0.0033  Score=52.44  Aligned_cols=37  Identities=16%  Similarity=0.249  Sum_probs=30.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      .+..+..|+||||++.++|...+..      +.+|++||++..
T Consensus         5 ~v~s~kgG~GKTt~a~~la~~la~~------g~~vlliD~D~~   41 (206)
T 4dzz_A            5 SFLNPKGGSGKTTAVINIATALSRS------GYNIAVVDTDPQ   41 (206)
T ss_dssp             EECCSSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCTT
T ss_pred             EEEeCCCCccHHHHHHHHHHHHHHC------CCeEEEEECCCC
Confidence            3445788999999999999988752      589999999853

>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=96.78  E-value=0.0019  Score=61.20  Aligned_cols=59  Identities=24%  Similarity=0.162  Sum_probs=48.8

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=..|.|++|+|||+|+.+++.+.+..  .   +.-++|.-.-+
T Consensus       146 ~e~l~TGirvID~l~p--igkGqr~gIfgg~GvGKT~L~~~l~~~~a~~--~---~~v~V~~~iGE  204 (498)
T 1fx0_B          146 LSIFETGIKVVNLLAP--YRRGGKIGLFGGAGVGKTVLIMELINNIAKA--H---GGVSVFGGVGE  204 (498)
T ss_dssp             CCCCCCSCTTHHHHSC--CCTTCCEEEEECSSSSHHHHHHHHHHHTTTT--C---SSCEEEEEESC
T ss_pred             ccccccceeEeeeecc--cccCCeEEeecCCCCCchHHHHHHHHHHHhh--C---CCEEEEEEccc
Confidence            5689999999999987  8899999999999999999999999997642  1   24567765433

>1u9l_A Transcription elongation protein NUSA; escherichia coli NUSA, phage lambda protein N, regulation of RNA binding, transcription antitermination, X-RAY crystallography; 1.90A {Escherichia coli} SCOP: a.60.4.2 PDB: 1wcl_A

Probab=96.78  E-value=0.0026  Score=43.36  Aligned_cols=54  Identities=9%  Similarity=0.172  Sum_probs=49.3

Q ss_pred             ccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 035774            6 ISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEI   59 (357)
Q Consensus         6 ~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   59 (357)
                      ...|+.++....+|.++|++|++.+.+.+..+|..+.|++++.+.++...+.+.
T Consensus         9 ~~~lgI~e~~a~~L~~~Gf~tve~vA~~~~~eL~~I~G~dE~~a~~l~~~A~~~   62 (70)
T 1u9l_A            9 TKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNA   62 (70)
T ss_dssp             HHHHTCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHhCCCCHHHHHHHHHcCcCcHHHHHcCCHHHHhhccCCCHHHHHHHHHHHHHH
Confidence            456899999999999999999999999999999999999999999998876553

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.78  E-value=0.0009  Score=56.04  Aligned_cols=36  Identities=17%  Similarity=0.281  Sum_probs=28.7

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++|.++.|.|+|||||||++..++...           ..++++.+.
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~-----------g~~~i~~d~   62 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET-----------GLEFAEADA   62 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH-----------CCEEEEGGG
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh-----------CCeEEcccc
Confidence            679999999999999999999887543           256777654

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=96.77  E-value=0.0028  Score=61.36  Aligned_cols=45  Identities=18%  Similarity=0.209  Sum_probs=33.8

Q ss_pred             eEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          206 KLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       206 ~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      -+||||.+..++...       ...+...+..|-+.++.+|+.+|+.+|-..
T Consensus       345 ivvVIDE~~~L~~~~-------~~~~~~~L~~Iar~GRa~GIhLIlaTQRPs  389 (574)
T 2iut_A          345 IVVVVDEFADMMMIV-------GKKVEELIARIAQKARAAGIHLILATQRPS  389 (574)
T ss_dssp             EEEEESCCTTHHHHT-------CHHHHHHHHHHHHHCTTTTEEEEEEESCCC
T ss_pred             EEEEEeCHHHHhhhh-------hHHHHHHHHHHHHHHhhCCeEEEEEecCcc
Confidence            479999999886531       134556667777788899999999998654

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=96.77  E-value=0.0021  Score=64.31  Aligned_cols=42  Identities=14%  Similarity=0.107  Sum_probs=30.1

Q ss_pred             eeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          205 VKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       205 ~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      ++++++|.-++-...         .....+...|+++++ .+++||+++|-.
T Consensus       223 ~~lLlLDEPtsgLD~---------~~~~~l~~~l~~l~~-~g~tvi~vtHd~  264 (670)
T 3ux8_A          223 GVLYVLDEPSIGLHQ---------RDNDRLIATLKSMRD-LGNTLIVVEHDE  264 (670)
T ss_dssp             SCEEEEECTTTTCCG---------GGHHHHHHHHHHHHH-TTCEEEEECCCH
T ss_pred             CCEEEEECCccCCCH---------HHHHHHHHHHHHHHH-cCCEEEEEeCCH
Confidence            349999988765543         334456777777765 499999999863

>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=96.76  E-value=0.001  Score=59.59  Aligned_cols=36  Identities=31%  Similarity=0.513  Sum_probs=29.9

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .|+.+.- .+++|+++.|.||+|+|||||+.-++...
T Consensus       115 vL~~vsl-~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          115 ALKLWLK-GIPKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             HHHHHHH-TCTTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             hhccceE-EecCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            4555444 49999999999999999999999888665

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.76  E-value=0.00096  Score=55.82  Aligned_cols=28  Identities=25%  Similarity=0.128  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|.++.|.|+|||||||++..++...
T Consensus        22 ~~~~~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           22 SNAMVRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            6788999999999999999999998654

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=96.75  E-value=0.0013  Score=60.49  Aligned_cols=59  Identities=17%  Similarity=0.048  Sum_probs=47.7

Q ss_pred             CCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           82 GHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        82 ~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+.||+..+|-++.  +-+|+=..|.|++|+|||+++.+++.++...    +.+..|+|+-..+
T Consensus       157 e~~~tGiraID~l~P--igrGQR~lIfg~~g~GKT~Ll~~Ia~~i~~~----~~dv~~V~~lIGE  215 (427)
T 3l0o_A          157 DPKIYSTRLIDLFAP--IGKGQRGMIVAPPKAGKTTILKEIANGIAEN----HPDTIRIILLIDE  215 (427)
T ss_dssp             STTCHHHHHHHHHSC--CBTTCEEEEEECTTCCHHHHHHHHHHHHHHH----CTTSEEEEEECSC
T ss_pred             cchhccchhhhhccc--ccCCceEEEecCCCCChhHHHHHHHHHHhhc----CCCeEEEEEEecc
Confidence            467899999999987  7799999999999999999999998877542    1145677776543

>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=96.75  E-value=0.0063  Score=62.66  Aligned_cols=29  Identities=14%  Similarity=0.247  Sum_probs=25.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +.+|+++.|.||+|+||||++.+++....
T Consensus       659 ~~~g~i~~ItGpNGsGKSTlLr~ial~~~  687 (934)
T 3thx_A          659 KDKQMFHIITGPNMGGKSTYIRQTGVIVL  687 (934)
T ss_dssp             TTTBCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            56799999999999999999999865543

>2woj_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; HET: ADP; 1.99A {Saccharomyces cerevisiae} PDB: 3h84_A 3zs8_A 3zs9_A* 3sja_A 3sjb_A 3sjc_A 3sjd_A* 3idq_A 3a36_A 3a37_A*

Probab=96.75  E-value=0.006  Score=55.90  Aligned_cols=51  Identities=18%  Similarity=0.252  Sum_probs=40.7

Q ss_pred             hhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc--cccCCCCCCCeEEEEeCCCC
Q 035774           89 KGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAA--LPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        89 ~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~--~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +.|+.++..  +.-.+++..|..|+||||++.++|...+  ..      +.+|+.||++..
T Consensus         7 ~~l~~l~~~--~~~~i~v~sgKGGvGKTTvaanLA~~lA~~~~------G~rVLLvD~D~~   59 (354)
T 2woj_A            7 PNLHSLITS--TTHKWIFVGGKGGVGKTTSSCSIAIQMALSQP------NKQFLLISTDPA   59 (354)
T ss_dssp             SSCHHHHTC--SSCCEEEEEESTTSSHHHHHHHHHHHHHHHCT------TSCEEEEECCSS
T ss_pred             ccHHHHhcC--CCcEEEEEeCCCCCcHHHHHHHHHHHHHHhcC------CCeEEEEECCCC
Confidence            346666653  2346888899999999999999999887  53      589999999874

>1oft_A SULA, hypothetical protein PA3008; bacterial cell division inhibitor, FTSZ, SULA protein; 2.9A {Pseudomonas aeruginosa} SCOP: c.37.1.22

Probab=96.75  E-value=0.027  Score=44.93  Aligned_cols=134  Identities=13%  Similarity=0.006  Sum_probs=73.0

Q ss_pred             CCCCCCchhHHhhh-cCCCCCCcEEEEE-cCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           82 GHLPTRLKGLDAAL-CGGVPFGVVTELV-GPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        82 ~~i~TG~~~LD~~l-~GGi~~G~l~~I~-G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      ..+|.|.+.+|..+ +||++.|.++||. ..+|.|=..|+.-++......    ..+..++||.-.......-+.+..  
T Consensus        23 ~~~p~~~~~~~~~~~~~~~~~G~l~Ell~~~~g~gel~LL~P~La~l~~~----~~~r~vlwI~Pp~~l~~~~L~~~G--   96 (161)
T 1oft_A           23 NGAPLLDDVIDSPSSASIEEPAAFSELSLSGLPGHCLTLLAPILRELSEE----QDARWLTLIAPPASLTHEWLRRAG--   96 (161)
T ss_dssp             --------------------CCSEEEEEEESCHHHHHHHHHHHHHHHHTC----SSSSEEEEESCCTTSCHHHHHHTT--
T ss_pred             ccCCCCcccccccCCCCCCCCcceEEEccCCCcHHHHHHHHHHHHHhccc----ccCccEEEECCCCCCCHHHHHHcC--
Confidence            47899999999988 6789999999997 457778776777666654320    014789999876655544443322  


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLIT  239 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk  239 (357)
                                   ...+++.++++.+..+..   ..+++.++......||.. +..+          +..    -.+.|.
T Consensus        97 -------------l~~~rll~v~~~~~~daL---wa~EqALrsG~~~aVl~W-l~~l----------~~~----~~RRLq  145 (161)
T 1oft_A           97 -------------LNRERILLLQAKDNAAAL---ALSCEALRLGRSHTVVSW-LEPL----------SRA----ARKQLS  145 (161)
T ss_dssp             -------------CCGGGEEEECCSSTTHHH---HHHHHHHHTTCEEEEEEC-CSSC----------CHH----HHHHHH
T ss_pred             -------------CCHHHEEEEECCChHHHH---HHHHHHHhcCCccEEEEC-CCcC----------ChH----HHHHHH
Confidence                         124678888887765554   445566767788888864 2211          111    356777


Q ss_pred             HHHHHcCCeEEEe
Q 035774          240 SLAEFSRIPIVVT  252 (357)
Q Consensus       240 ~la~~~~~~vv~~  252 (357)
                      --|++-++..+++
T Consensus       146 lAAe~g~~~~fll  158 (161)
T 1oft_A          146 RAAQLGQAQSLNI  158 (161)
T ss_dssp             HHHHHTTCEEEEE
T ss_pred             HHHHhCCCeEEEe
Confidence            7778777777765

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=96.74  E-value=0.0013  Score=57.63  Aligned_cols=35  Identities=14%  Similarity=0.076  Sum_probs=29.7

Q ss_pred             hhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           89 KGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        89 ~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.|+.+.   +++|+++.|.||+||||||++..++...
T Consensus        15 ~vl~~i~---i~~g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           15 DKVLELC---HRKMGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             THHHHGG---GCSSEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             HHHHHHh---hCCCCEEEEECCCCccHHHHHHHHHHhC
Confidence            4566654   8999999999999999999999887654

>3kjh_A CO dehydrogenase/acetyl-COA synthase complex, accessory protein COOC; Zn-bound dimer, nickel binding protein, ATPase; 1.90A {Carboxydothermus hydrogenoformans} PDB: 3kjg_A* 3kje_A 3kji_A*

Probab=96.74  E-value=0.0022  Score=55.38  Aligned_cols=37  Identities=22%  Similarity=0.273  Sum_probs=31.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +.|.|..|+||||++.++|...+..      +.+|+.||++..
T Consensus         3 I~vs~kGGvGKTt~a~~LA~~la~~------g~~VlliD~D~~   39 (254)
T 3kjh_A            3 LAVAGKGGVGKTTVAAGLIKIMASD------YDKIYAVDGDPD   39 (254)
T ss_dssp             EEEECSSSHHHHHHHHHHHHHHTTT------CSCEEEEEECTT
T ss_pred             EEEecCCCCCHHHHHHHHHHHHHHC------CCeEEEEeCCCC
Confidence            4458999999999999999988752      589999999864

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=96.74  E-value=0.00067  Score=56.83  Aligned_cols=28  Identities=29%  Similarity=0.285  Sum_probs=21.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|.++.|.||+|+|||||+..++...
T Consensus         1 m~~g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            1 MAGPRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             ----CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3578999999999999999999887654

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=96.73  E-value=0.0044  Score=60.80  Aligned_cols=54  Identities=20%  Similarity=0.211  Sum_probs=35.0

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc-ccCCCCCCCeEEEEeCCC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL-PAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~-~~~~gg~~~~vl~i~~e~  146 (357)
                      .|...|..+-....++.|.|++|+|||+|+.+++..... ...   ....++|++...
T Consensus       135 ~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~---f~~~v~wv~~~~  189 (591)
T 1z6t_A          135 AIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGC---FPGGVHWVSVGK  189 (591)
T ss_dssp             HHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHH---CTTCEEEEEEES
T ss_pred             HHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhh---CCCceEEEECCC
Confidence            355555432234679999999999999999998753210 000   124688988654

>3p32_A Probable GTPase RV1496/MT1543; structural genomics, seattle structural genomics center for infectious disease, ssgcid, MEAB, MMAA; HET: GDP PGE; 1.90A {Mycobacterium tuberculosis} PDB: 3md0_A* 4gt1_A* 3nxs_A* 3tk1_A*

Probab=96.72  E-value=0.011  Score=54.25  Aligned_cols=40  Identities=18%  Similarity=0.165  Sum_probs=32.5

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..-.+.|+|.||+|||||+.+++...+..      +.+|..++.+.
T Consensus        78 ~~~~I~i~G~~G~GKSTl~~~L~~~l~~~------g~kV~vi~~Dp  117 (355)
T 3p32_A           78 NAHRVGITGVPGVGKSTAIEALGMHLIER------GHRVAVLAVDP  117 (355)
T ss_dssp             CSEEEEEECCTTSSHHHHHHHHHHHHHTT------TCCEEEEEEC-
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHHhC------CCceEEEecCC
Confidence            34589999999999999999999877632      57888888864

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.72  E-value=0.0021  Score=53.84  Aligned_cols=42  Identities=19%  Similarity=0.135  Sum_probs=32.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .++|.++.|.|++||||||++..++.....   .   +..+.+++.+.
T Consensus        19 ~~~~~~i~i~G~~GsGKstl~~~l~~~~~~---~---~~~v~~~~~d~   60 (201)
T 1rz3_A           19 TAGRLVLGIDGLSRSGKTTLANQLSQTLRE---Q---GISVCVFHMDD   60 (201)
T ss_dssp             CSSSEEEEEEECTTSSHHHHHHHHHHHHHH---T---TCCEEEEEGGG
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHhh---c---CCeEEEeccCc
Confidence            567899999999999999999988865421   1   35677776543

>3ug7_A Arsenical pump-driving ATPase; tail-anchored, membrane protein, targeting factor, ATP-bindi TRC40, ARSA, nucleotide-binding; HET: ADP; 2.90A {Methanocaldococcus jannaschii} PDB: 3ug6_A*

Probab=96.69  E-value=0.0017  Score=59.58  Aligned_cols=43  Identities=16%  Similarity=0.130  Sum_probs=36.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      -+...++++.|.+|+||||++.++|...+..      +.+|+.+|++..
T Consensus        23 ~~~~~i~v~sgKGGvGKTTvA~~LA~~lA~~------G~rVLlvD~D~~   65 (349)
T 3ug7_A           23 KDGTKYIMFGGKGGVGKTTMSAATGVYLAEK------GLKVVIVSTDPA   65 (349)
T ss_dssp             SCSCEEEEEECSSSTTHHHHHHHHHHHHHHS------SCCEEEEECCTT
T ss_pred             cCCCEEEEEeCCCCccHHHHHHHHHHHHHHC------CCeEEEEeCCCC
Confidence            4556788899999999999999999988852      589999999863

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=96.66  E-value=0.012  Score=59.80  Aligned_cols=28  Identities=25%  Similarity=0.409  Sum_probs=25.0

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+++.|.||+|+|||||+.+++....
T Consensus       605 ~~g~i~~ItGpNGsGKSTlLr~iagl~~  632 (800)
T 1wb9_A          605 PQRRMLIITGPNMGGKSTYMRQTALIAL  632 (800)
T ss_dssp             SSSCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCChHHHHHHHHHHHH
Confidence            6799999999999999999999887543

>4aby_A DNA repair protein RECN; hydrolase, double strand break repair, ATPase, nucleotide binding domain; HET: DNA; 3.00A {Deinococcus radiodurans}

Probab=96.65  E-value=0.0079  Score=56.22  Aligned_cols=39  Identities=18%  Similarity=0.194  Sum_probs=29.6

Q ss_pred             eEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          206 KLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       206 ~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      +++++|..++-...         .....+...|++++ + +++||+++|.
T Consensus       317 ~~LlLDEpt~~LD~---------~~~~~l~~~L~~l~-~-~~~vi~itH~  355 (415)
T 4aby_A          317 PSVVFDEVDAGIGG---------AAAIAVAEQLSRLA-D-TRQVLVVTHL  355 (415)
T ss_dssp             SEEEESSTTTTCCH---------HHHHHHHHHHHHHT-T-TSEEEEECSC
T ss_pred             CEEEEECCCCCCCH---------HHHHHHHHHHHHHh-C-CCEEEEEeCc
Confidence            89999988765432         45566777888877 3 8999999885

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=96.65  E-value=0.0057  Score=65.53  Aligned_cols=26  Identities=31%  Similarity=0.406  Sum_probs=23.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+.+.|.|++|||||||+.-++.
T Consensus       413 i~~G~~~~ivG~sGsGKSTl~~ll~g  438 (1284)
T 3g5u_A          413 VKSGQTVALVGNSGCGKSTTVQLMQR  438 (1284)
T ss_dssp             ECTTCEEEEECCSSSSHHHHHHHTTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999986653

>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=96.64  E-value=0.00087  Score=57.90  Aligned_cols=26  Identities=31%  Similarity=0.556  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.||+|+|||||+.-++.
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~~l~G   53 (237)
T 2cbz_A           28 IPEGALVAVVGQVGCGKSSLLSALLA   53 (237)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhc
Confidence            89999999999999999999997663

>1hyq_A MIND, cell division inhibitor (MIND-1); MINC, FTSZ, bacterial cell division, cell cycle; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.10

Probab=96.64  E-value=0.0072  Score=52.63  Aligned_cols=37  Identities=30%  Similarity=0.375  Sum_probs=31.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+..+..|+||||++.++|...+..      +.+|++||.+.
T Consensus         5 I~v~s~kgGvGKTt~a~~LA~~la~~------g~~VlliD~D~   41 (263)
T 1hyq_A            5 ITVASGKGGTGKTTITANLGVALAQL------GHDVTIVDADI   41 (263)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHHHHHT------TCCEEEEECCC
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHhC------CCcEEEEECCC
Confidence            45567899999999999999988752      48999999976

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.64  E-value=0.0012  Score=55.51  Aligned_cols=28  Identities=21%  Similarity=0.172  Sum_probs=25.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+|.+++|+|+|||||||++..++...
T Consensus         9 ~~~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A            9 MARIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             cccCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            5688999999999999999999988754

>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=96.63  E-value=0.0014  Score=53.45  Aligned_cols=26  Identities=19%  Similarity=0.259  Sum_probs=23.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .+|.++.|.|+|||||||++..++..
T Consensus         6 ~~g~~i~l~G~~GsGKSTl~~~l~~~   31 (175)
T 1knq_A            6 HDHHIYVLMGVSGSGKSAVASEVAHQ   31 (175)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHh
Confidence            46889999999999999999988754

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=96.62  E-value=0.0031  Score=67.59  Aligned_cols=26  Identities=35%  Similarity=0.445  Sum_probs=23.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+.+.|.|++|+|||||+.-++.
T Consensus      1056 i~~Ge~v~ivG~sGsGKSTl~~~l~g 1081 (1284)
T 3g5u_A         1056 VKKGQTLALVGSSGCGKSTVVQLLER 1081 (1284)
T ss_dssp             ECSSSEEEEECSSSTTHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999999987664

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=96.57  E-value=0.0012  Score=58.06  Aligned_cols=26  Identities=35%  Similarity=0.586  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        43 i~~Ge~~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           43 VHPGEVHAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997764

>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=96.57  E-value=0.0015  Score=53.25  Aligned_cols=25  Identities=20%  Similarity=0.177  Sum_probs=22.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.++.|+|+|||||||++..++...
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            5689999999999999999988754

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=96.56  E-value=0.0017  Score=56.89  Aligned_cols=38  Identities=24%  Similarity=0.279  Sum_probs=28.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++.+++|+|.|||||||++..++.....   .   +..+++++.
T Consensus         3 ~~~lIvl~G~pGSGKSTla~~La~~L~~---~---g~~~i~~~~   40 (260)
T 3a4m_A            3 DIMLIILTGLPGVGKSTFSKNLAKILSK---N---NIDVIVLGS   40 (260)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHH---T---TCCEEEECT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHHHh---C---CCEEEEECc
Confidence            4679999999999999999999876431   1   355665664

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=96.56  E-value=0.001  Score=57.63  Aligned_cols=26  Identities=23%  Similarity=0.388  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           25 AQPNSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997663

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=96.55  E-value=0.00079  Score=57.75  Aligned_cols=27  Identities=37%  Similarity=0.473  Sum_probs=19.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH-HH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS-LL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia-~~  125 (357)
                      +++|.++.|.||+||||||++..++ ..
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~~~L~~~~   51 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVANKLLEKQ   51 (231)
T ss_dssp             EECCCEEEEECSCC----CHHHHHHC--
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            6789999999999999999999887 54

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=96.55  E-value=0.0012  Score=57.57  Aligned_cols=26  Identities=42%  Similarity=0.641  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           26 VPKGEVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999997774

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=96.55  E-value=0.00099  Score=57.23  Aligned_cols=26  Identities=23%  Similarity=0.425  Sum_probs=23.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.||+|+|||||+.-++.
T Consensus        31 i~~Ge~~~i~G~nGsGKSTLl~~l~G   56 (229)
T 2pze_A           31 IERGQLLAVAGSTGAGKTSLLMMIMG   56 (229)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            88999999999999999999986663

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.54  E-value=0.0014  Score=53.23  Aligned_cols=25  Identities=32%  Similarity=0.347  Sum_probs=22.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .|.++.|.|+|||||||++..++..
T Consensus         3 ~~~~i~l~G~~GsGKSTl~~~La~~   27 (173)
T 1kag_A            3 EKRNIFLVGPMGAGKSTIGRQLAQQ   27 (173)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999999999988754

>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli} SCOP: a.60.3.1 PDB: 2jzb_A

Probab=96.54  E-value=0.003  Score=45.86  Aligned_cols=55  Identities=20%  Similarity=0.277  Sum_probs=51.0

Q ss_pred             ccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            4 KLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      .++++|.|+....+-|.++||+|+.+++..++.+|.++-++..+.+.++...+.+
T Consensus        24 ~~Ie~L~LSvRs~NcLkragI~Tv~dL~~~se~dLlki~n~G~KSl~EI~~~L~~   78 (98)
T 1coo_A           24 RPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS   78 (98)
T ss_dssp             SBGGGGTCCTTTHHHHHTTTCCBHHHHHTSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             CcHHHhCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999999999999888876654

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=96.54  E-value=0.013  Score=53.12  Aligned_cols=23  Identities=35%  Similarity=0.417  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -++|+|+||+|||+++..++...
T Consensus        57 ~vll~G~~GtGKT~la~~ia~~~   79 (338)
T 3pfi_A           57 HILFSGPAGLGKTTLANIISYEM   79 (338)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHT
T ss_pred             eEEEECcCCCCHHHHHHHHHHHh
Confidence            48999999999999999997654

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.53  E-value=0.0014  Score=53.86  Aligned_cols=27  Identities=26%  Similarity=0.422  Sum_probs=23.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+|.++.|.|+|||||||++..++...
T Consensus         2 ~~g~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            2 DVGQAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             -CEEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            357899999999999999999988643

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=96.52  E-value=0.0015  Score=56.63  Aligned_cols=35  Identities=20%  Similarity=0.300  Sum_probs=24.0

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .|+.+-- -+++|.++.|.|++||||||++..++..
T Consensus        14 ~l~~isl-~i~~g~iigI~G~~GsGKSTl~k~L~~~   48 (245)
T 2jeo_A           14 GTENLYF-QSMRPFLIGVSGGTASGKSTVCEKIMEL   48 (245)
T ss_dssp             ----------CCSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eecceec-cCCCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            4555432 3788999999999999999999988764

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=96.51  E-value=0.0015  Score=54.91  Aligned_cols=38  Identities=16%  Similarity=0.162  Sum_probs=30.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +++|.++.|.|+|||||||++..++...          ..+.|++.+.
T Consensus        18 ~~~~~~i~i~G~~GsGKSTl~~~L~~~~----------~~~~~i~~D~   55 (207)
T 2qt1_A           18 GSKTFIIGISGVTNSGKTTLAKNLQKHL----------PNCSVISQDD   55 (207)
T ss_dssp             SCCCEEEEEEESTTSSHHHHHHHHHTTS----------TTEEEEEGGG
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHhc----------CCcEEEeCCc
Confidence            7789999999999999999999877421          1467777764

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.50  E-value=0.0015  Score=56.98  Aligned_cols=38  Identities=24%  Similarity=0.260  Sum_probs=29.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ...+.++.|.|+|||||||++..++...         +..+++++.+
T Consensus        29 ~~~~~~i~l~G~~GsGKSTla~~L~~~l---------~~~~~~~~~D   66 (253)
T 2p5t_B           29 SKQPIAILLGGQSGAGKTTIHRIKQKEF---------QGNIVIIDGD   66 (253)
T ss_dssp             CSSCEEEEEESCGGGTTHHHHHHHHHHT---------TTCCEEECGG
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHhc---------CCCcEEEecH
Confidence            3557899999999999999999988654         1346677765

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=96.49  E-value=0.0013  Score=57.74  Aligned_cols=26  Identities=35%  Similarity=0.566  Sum_probs=24.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.||+|+|||||+.-++.
T Consensus        43 i~~Ge~~~i~G~nGsGKSTLl~~l~G   68 (260)
T 2ghi_A           43 IPSGTTCALVGHTGSGKSTIAKLLYR   68 (260)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhc
Confidence            88999999999999999999997764

>2bdt_A BH3686; alpha-beta protein, structural genomics, PSI, protein struct initiative, northeast structural genomics consortium, NESG, function; 2.40A {Bacillus halodurans} SCOP: c.37.1.25

Probab=96.49  E-value=0.0013  Score=54.32  Aligned_cols=23  Identities=35%  Similarity=0.660  Sum_probs=21.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      |.++.|.|+||+||||++..++.
T Consensus         2 g~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            2 KKLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHhc
Confidence            67999999999999999998874

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=96.48  E-value=0.0015  Score=55.07  Aligned_cols=38  Identities=21%  Similarity=0.317  Sum_probs=28.7

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++|.++.|.|++|||||||+..++...-         ..+.|++.+.
T Consensus         4 ~~~~~i~i~G~~GsGKSTl~~~l~~~~~---------~~i~~v~~d~   41 (211)
T 3asz_A            4 PKPFVIGIAGGTASGKTTLAQALARTLG---------ERVALLPMDH   41 (211)
T ss_dssp             -CCEEEEEEESTTSSHHHHHHHHHHHHG---------GGEEEEEGGG
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhC---------CCeEEEecCc
Confidence            5789999999999999999998876431         1366776543

>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=96.43  E-value=0.0053  Score=59.06  Aligned_cols=55  Identities=22%  Similarity=0.260  Sum_probs=45.9

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+.+.||+..+|-++.  +-+|+=..|.|++|+|||+++.+++.+..        ..-++|+-.-
T Consensus       213 ~epl~TGirvID~l~P--igrGqr~~Ifgg~g~GKT~L~~~ia~~~~--------~~v~V~~~iG  267 (600)
T 3vr4_A          213 DVPMITGQRVIDTFFP--VTKGGAAAVPGPFGAGKTVVQHQIAKWSD--------VDLVVYVGCG  267 (600)
T ss_dssp             CSBCCCCCHHHHHHSC--CBTTCEEEEECCTTSCHHHHHHHHHHHSS--------CSEEEEEEEE
T ss_pred             CceecccchhhhccCC--ccCCCEEeeecCCCccHHHHHHHHHhccC--------CCEEEEEEec
Confidence            5689999999999987  88999999999999999999999887642        2457776553

>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=96.43  E-value=0.0028  Score=55.02  Aligned_cols=26  Identities=42%  Similarity=0.657  Sum_probs=22.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|  +.|+||||+|||+++..++...
T Consensus        48 ~~~g--~ll~G~~G~GKTtl~~~i~~~~   73 (254)
T 1ixz_A           48 IPKG--VLLVGPPGVGKTHLARAVAGEA   73 (254)
T ss_dssp             CCSE--EEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCCe--EEEECCCCCCHHHHHHHHHHHh
Confidence            5566  9999999999999999888654

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=96.43  E-value=0.00097  Score=56.38  Aligned_cols=27  Identities=26%  Similarity=0.453  Sum_probs=24.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+++.|.||+|+|||||+..++..
T Consensus        19 i~~Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           19 IDTNTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             HHHCSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHhcC
Confidence            588999999999999999999987755

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=96.42  E-value=0.0018  Score=58.25  Aligned_cols=45  Identities=18%  Similarity=0.176  Sum_probs=33.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +++|.++.|.|++|||||||+..++.....  ..|  ...+.|+..+..
T Consensus        87 ~~~g~ivgI~G~sGsGKSTL~~~L~gll~~--~~G--~~~v~~v~qd~~  131 (312)
T 3aez_A           87 RPVPFIIGVAGSVAVGKSTTARVLQALLAR--WDH--HPRVDLVTTDGF  131 (312)
T ss_dssp             SCCCEEEEEECCTTSCHHHHHHHHHHHHHT--STT--CCCEEEEEGGGG
T ss_pred             CCCCEEEEEECCCCchHHHHHHHHHhhccc--cCC--CCeEEEEecCcc
Confidence            688999999999999999999987754421  122  145778877654

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=96.41  E-value=0.0031  Score=56.65  Aligned_cols=37  Identities=14%  Similarity=0.082  Sum_probs=31.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhc-cccCCCCCCCeEEEEeC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAA-LPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~-~~~~~gg~~~~vl~i~~  144 (357)
                      +.-+.|+|+||+|||+|+..++.... ..      +.+|+|++.
T Consensus       152 ~~~lll~G~~GtGKT~La~aia~~~~~~~------g~~v~~~~~  189 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLAAMAHELSEKK------GVSTTLLHF  189 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHHHHS------CCCEEEEEH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHhc------CCcEEEEEH
Confidence            57899999999999999999998776 42      478888876

>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=96.39  E-value=0.0022  Score=52.79  Aligned_cols=25  Identities=20%  Similarity=0.078  Sum_probs=22.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |.++.|.|+|||||||++..++...
T Consensus         3 ~~~I~i~G~~GsGKsT~~~~L~~~l   27 (192)
T 1kht_A            3 NKVVVVTGVPGVGSTTSSQLAMDNL   27 (192)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            5689999999999999999998754

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.38  E-value=0.002  Score=52.58  Aligned_cols=22  Identities=18%  Similarity=0.382  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 035774          103 VVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .++.|.|+|||||||++..++.
T Consensus         3 ~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            3 KIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEecCCCCCHHHHHHHHHh
Confidence            4789999999999999999886

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=96.37  E-value=0.019  Score=59.53  Aligned_cols=60  Identities=18%  Similarity=0.241  Sum_probs=38.8

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRM  153 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl  153 (357)
                      .|...|.. .....++.|.|++|.|||+||.+++.........   +..++|++.....+...+
T Consensus       139 eL~elL~~-~d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~F---d~gV~WVsVs~~~d~~~I  198 (1221)
T 1vt4_I          139 KLRQALLE-LRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKM---DFKIFWLNLKNCNSPETV  198 (1221)
T ss_dssp             HHHHHHHH-CCSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHH---SSCEEEEECCCSSSHHHH
T ss_pred             HHHHHHhc-cCCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhC---CCcEEEEEeCCCCCHHHH
Confidence            34444432 2335799999999999999999988532111111   246999998766555443

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=96.36  E-value=0.0033  Score=56.47  Aligned_cols=43  Identities=19%  Similarity=0.263  Sum_probs=32.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhcc-ccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAAL-PAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~-~~~~gg~~~~vl~i~~e~  146 (357)
                      ..+|.++.|.|++|||||||+..++...-. + .    .+.+.++++++
T Consensus        77 ~~~g~iigI~G~~GsGKSTl~~~L~~~l~~~~-~----~G~i~vi~~d~  120 (308)
T 1sq5_A           77 QRIPYIISIAGSVAVGKSTTARVLQALLSRWP-E----HRRVELITTDG  120 (308)
T ss_dssp             CCCCEEEEEEECTTSSHHHHHHHHHHHHTTST-T----CCCEEEEEGGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHhhCC-C----CCeEEEEecCC
Confidence            367899999999999999999988764421 1 1    25677777664

>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=96.35  E-value=0.0027  Score=58.67  Aligned_cols=28  Identities=29%  Similarity=0.345  Sum_probs=25.8

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++++|.++.|.||||+|||||+..++..
T Consensus       165 ~i~~~~~i~l~G~~GsGKSTl~~~l~~~  192 (377)
T 1svm_A          165 NIPKKRYWLFKGPIDSGKTTLAAALLEL  192 (377)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            5999999999999999999999988864

>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=96.35  E-value=0.0035  Score=59.11  Aligned_cols=61  Identities=13%  Similarity=0.238  Sum_probs=48.0

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+.+.||+..+|-++.  +-+|+=..|.|++|+|||+|+.++|.+....++  +.+..++|.-.-
T Consensus       133 ~e~l~TGir~ID~l~p--igrGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~--~~~~~~V~~~iG  193 (469)
T 2c61_A          133 KDFIQTGISTIDGTNT--LVRGQKLPIFSASGLPHNEIALQIARQASVPGS--ESAFAVVFAAMG  193 (469)
T ss_dssp             CSBCBCSCHHHHTTSC--CBTTCBCCEEECTTSCHHHHHHHHHHHCBCTTC--SSCEEEEEEEEE
T ss_pred             ccccceeeEeeeeeec--cccCCEEEEECCCCCCHHHHHHHHHHHHhhccC--CCCcEEEEEEcc
Confidence            4679999999999987  788999999999999999999999988765321  112356676553

>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=96.34  E-value=0.0026  Score=53.16  Aligned_cols=27  Identities=19%  Similarity=0.188  Sum_probs=23.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+|.++.|.||+|+|||||+..++...
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCCEEEEECcCCCCHHHHHHHHHhhC
Confidence            368999999999999999999888654

>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=96.34  E-value=0.0028  Score=52.18  Aligned_cols=27  Identities=30%  Similarity=0.447  Sum_probs=23.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .++|..+.|+|+|||||||++..++..
T Consensus         7 ~~~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            7 QPKGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             CCSSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHh
Confidence            456889999999999999999988865

>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=96.33  E-value=0.0023  Score=51.72  Aligned_cols=23  Identities=30%  Similarity=0.208  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|+|||||||++..++...
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            78999999999999999988654

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=96.32  E-value=0.017  Score=53.20  Aligned_cols=40  Identities=18%  Similarity=0.226  Sum_probs=32.5

Q ss_pred             CCCcEEEEE-cCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELV-GPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~-G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .++.++.|+ |..|+||||++.++|...+..      +.+|++||++
T Consensus       141 ~~~kvIav~s~KGGvGKTT~a~nLA~~La~~------g~rVlliD~D  181 (373)
T 3fkq_A          141 DKSSVVIFTSPCGGVGTSTVAAACAIAHANM------GKKVFYLNIE  181 (373)
T ss_dssp             TSCEEEEEECSSTTSSHHHHHHHHHHHHHHH------TCCEEEEECC
T ss_pred             CCceEEEEECCCCCChHHHHHHHHHHHHHhC------CCCEEEEECC
Confidence            345666665 599999999999999988752      5899999988

>2woo_A ATPase GET3; tail-anchored, membrane protein, targeting factor, endoplasmic reticulum, TRC40, ATP-binding, golgi apparatus; 3.01A {Schizosaccharomyces pombe}

Probab=96.32  E-value=0.012  Score=53.21  Aligned_cols=40  Identities=20%  Similarity=0.209  Sum_probs=34.9

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      -.++++.|.+|+||||++.++|...+..      +.+|+.+|++..
T Consensus        19 ~~i~v~sgkGGvGKTTva~~LA~~lA~~------G~rVllvD~D~~   58 (329)
T 2woo_A           19 LKWIFVGGKGGVGKTTTSCSLAIQMSKV------RSSVLLISTDPA   58 (329)
T ss_dssp             CCEEEEECSSSSSHHHHHHHHHHHHHTS------SSCEEEEECCTT
T ss_pred             CEEEEEeCCCCCcHHHHHHHHHHHHHHC------CCeEEEEECCCC
Confidence            4688899999999999999999988852      589999999864

>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=96.30  E-value=0.011  Score=60.82  Aligned_cols=113  Identities=16%  Similarity=0.194  Sum_probs=51.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCC-CCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGG-LDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg-~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      .-++|+|+||+|||+++..++.......-... .+..+++++...-..        ..             ..       
T Consensus       192 ~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~--------g~-------------~~-------  243 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLA--------GA-------------KY-------  243 (854)
T ss_dssp             CCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-------------------------------------
T ss_pred             CceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhc--------cC-------------cc-------
Confidence            34789999999999999999987642100000 135677776532100        00             00       


Q ss_pred             CCCCHHHHHHHHHHHHHHhhh-cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          182 QPTSLSEFTESLEKIKVSLLQ-NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~-~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                          ..++...+..+...+.. .+..+++||.+..+......      ..-..+...|+.+..+.++.+|.+.
T Consensus       244 ----~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~------~g~~~~~~~L~~~l~~~~i~~I~at  306 (854)
T 1qvr_A          244 ----RGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKA------EGAVDAGNMLKPALARGELRLIGAT  306 (854)
T ss_dssp             ------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------------HHHHHTTCCCEEEEE
T ss_pred             ----chHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCc------cchHHHHHHHHHHHhCCCeEEEEec
Confidence                00112222222222222 35679999999988644211      1112234556666666777777654

>3llm_A ATP-dependent RNA helicase A; alpha-beta-alpha, structural genomics, structural genomics consortium, SGC, activator, ATP-binding, DNA-binding; HET: ADP; 2.80A {Homo sapiens}

Probab=96.28  E-value=0.012  Score=50.30  Aligned_cols=45  Identities=16%  Similarity=0.200  Sum_probs=29.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +..|+.+++.|++|||||++...++......... +.+..+++..-
T Consensus        73 i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~-~~~~~~l~~~p  117 (235)
T 3llm_A           73 ISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR-AAECNIVVTQP  117 (235)
T ss_dssp             HHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC-GGGCEEEEEES
T ss_pred             HhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC-CCceEEEEecc
Confidence            4457899999999999998877776654332111 01235666654

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.27  E-value=0.0032  Score=53.45  Aligned_cols=29  Identities=28%  Similarity=0.316  Sum_probs=25.6

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+.+..++.|.|||||||+|.|..++...
T Consensus        25 ~~~k~kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           25 KLAKAKVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             CTTSCEEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             hccCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            36778899999999999999999998765

>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=96.27  E-value=0.0079  Score=62.68  Aligned_cols=47  Identities=11%  Similarity=0.131  Sum_probs=32.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+..+|++|.++.-...        ......+...|+.++++.++++|+++|...
T Consensus       867 ~~~sLlLLDEp~~Gtd~--------~dg~~~~~~il~~L~~~~g~~vl~~TH~~e  913 (1022)
T 2o8b_B          867 TAHSLVLVDELGRGTAT--------FDGTAIANAVVKELAETIKCRTLFSTHYHS  913 (1022)
T ss_dssp             CTTCEEEEECTTTTSCH--------HHHHHHHHHHHHHHHHTSCCEEEEECCCHH
T ss_pred             CCCcEEEEECCCCCCCh--------HHHHHHHHHHHHHHHhcCCCEEEEEeCCHH
Confidence            46899999988754322        112333556677777777999999998643

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.27  E-value=0.0044  Score=51.02  Aligned_cols=35  Identities=17%  Similarity=0.152  Sum_probs=27.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++.|.|+|||||||++..++...-.      .+..+.+++.
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~------~g~~~~~~~~   37 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDN------QGINNKIINY   37 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHT------TTCCEEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh------cCceEEEEEC
Confidence            6899999999999999999876531      1355777753

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.24  E-value=0.003  Score=52.90  Aligned_cols=26  Identities=27%  Similarity=0.314  Sum_probs=23.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +|.++.|.|+|||||||++..++...
T Consensus         3 ~~~~I~i~G~~GsGKsT~~~~L~~~l   28 (213)
T 2plr_A            3 KGVLIAFEGIDGSGKSSQATLLKDWI   28 (213)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            46799999999999999999998765

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=96.24  E-value=0.0034  Score=52.93  Aligned_cols=41  Identities=17%  Similarity=0.156  Sum_probs=31.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +++|.++.|.|++|+||||++..++...-.  ..   +.++++++.
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~l~~~l~~--~~---g~~~~~~~~   62 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVELEHQLVR--DR---RVHAYRLDG   62 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHH--HH---CCCEEEECH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHhcc--cc---CCcEEEECC
Confidence            678899999999999999999998875421  01   245777763

>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=96.20  E-value=0.0064  Score=52.83  Aligned_cols=40  Identities=23%  Similarity=0.408  Sum_probs=34.0

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.-++.+.|.+|+||||++.+++...+ .      +.+|+.++.+.
T Consensus        12 ~~~~i~~~~GkgGvGKTTl~~~La~~l~-~------g~~v~vvd~D~   51 (262)
T 1yrb_A           12 MASMIVVFVGTAGSGKTTLTGEFGRYLE-D------NYKVAYVNLDT   51 (262)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHT-T------TSCEEEEECCS
T ss_pred             cceEEEEEeCCCCCCHHHHHHHHHHHHH-C------CCeEEEEeCCC
Confidence            4567899999999999999999998776 3      47899999775

>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=96.19  E-value=0.0046  Score=58.00  Aligned_cols=61  Identities=11%  Similarity=0.164  Sum_probs=47.1

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+.+.||+..+|-++.  +-+|+=..|.|++|+|||+|+.+++..+....  ++.+..++|.-.-
T Consensus       132 ~e~l~TGiraID~l~p--igrGQr~~Ifgg~G~GKt~L~~~Ia~~~~~~~--d~~~~~~V~~~iG  192 (465)
T 3vr4_D          132 DEFIQTGISAIDHLNT--LVRGQKLPVFSGSGLPHKELAAQIARQATVLD--SSDDFAVVFAAIG  192 (465)
T ss_dssp             CCBCBCSCHHHHTTSC--CBTTCBCCEEECTTSCHHHHHHHHHHHCBCSS--CSSCEEEEEEEEE
T ss_pred             ccccccCceEEecccc--cccCCEEEEeCCCCcChHHHHHHHHHHHHhcc--CCCceEEEEEEec
Confidence            5679999999999987  78899999999999999999999887764310  0123366776553

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.19  E-value=0.0029  Score=52.32  Aligned_cols=27  Identities=26%  Similarity=0.297  Sum_probs=23.6

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .++.++.|.|+|||||||++..++...
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            7 KKTNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             TTSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            456799999999999999999998654

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=96.18  E-value=0.0021  Score=57.17  Aligned_cols=25  Identities=24%  Similarity=0.501  Sum_probs=23.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+++.|.|++|+|||||+..++
T Consensus        61 i~~Ge~~~i~G~NGsGKSTLlk~l~   85 (290)
T 2bbs_A           61 IERGQLLAVAGSTGAGKTSLLMMIM   85 (290)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHT
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHh
Confidence            8899999999999999999998665

>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=96.18  E-value=0.0034  Score=51.38  Aligned_cols=28  Identities=25%  Similarity=0.227  Sum_probs=23.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +..+.++.|.|+||+||||++..++...
T Consensus         8 ~~~~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A            8 FMLLPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             TCCCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cccCCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            3456789999999999999999988654

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.18  E-value=0.0032  Score=51.93  Aligned_cols=25  Identities=24%  Similarity=0.396  Sum_probs=22.0

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.++.|.|+|||||||++..++...
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            5689999999999999999888653

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=96.17  E-value=0.0046  Score=54.51  Aligned_cols=26  Identities=42%  Similarity=0.657  Sum_probs=22.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|  +.|+||||+|||+|+..++...
T Consensus        72 ~~~g--vll~Gp~GtGKTtl~~~i~~~~   97 (278)
T 1iy2_A           72 IPKG--VLLVGPPGVGKTHLARAVAGEA   97 (278)
T ss_dssp             CCCE--EEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCCe--EEEECCCcChHHHHHHHHHHHc
Confidence            5566  8999999999999999888654

>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=96.16  E-value=0.0053  Score=53.64  Aligned_cols=36  Identities=22%  Similarity=0.116  Sum_probs=29.3

Q ss_pred             HHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           91 LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        91 LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |...+.|..++..-++|+||||+|||.|+..+|...
T Consensus        93 l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A           93 FLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhh
Confidence            555666644767789999999999999999888754

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=96.15  E-value=0.0036  Score=49.41  Aligned_cols=37  Identities=19%  Similarity=0.200  Sum_probs=26.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.-++|.|+||+|||++|..++.....      .+.+.+ +++.
T Consensus        24 ~~~vll~G~~GtGKt~lA~~i~~~~~~------~~~~~v-~~~~   60 (145)
T 3n70_A           24 DIAVWLYGAPGTGRMTGARYLHQFGRN------AQGEFV-YREL   60 (145)
T ss_dssp             CSCEEEESSTTSSHHHHHHHHHHSSTT------TTSCCE-EEEC
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHhCCc------cCCCEE-EECC
Confidence            345899999999999999988764432      135555 6654

>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=96.15  E-value=0.0027  Score=51.27  Aligned_cols=19  Identities=37%  Similarity=0.627  Sum_probs=18.1

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKL  122 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~i  122 (357)
                      ++.|+|+|||||||++..+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            7899999999999999988

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.15  E-value=0.0037  Score=52.49  Aligned_cols=28  Identities=18%  Similarity=0.063  Sum_probs=25.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..+|.++.|.|+|||||||++..++...
T Consensus         7 ~~~~~~I~l~G~~GsGKST~~~~L~~~l   34 (212)
T 2wwf_A            7 KKKGKFIVFEGLDRSGKSTQSKLLVEYL   34 (212)
T ss_dssp             CBCSCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             hhcCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            5578899999999999999999998764

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.14  E-value=0.0031  Score=54.91  Aligned_cols=24  Identities=21%  Similarity=0.504  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+++|+|+|||||||++..++...
T Consensus         2 ~li~I~G~~GSGKSTla~~La~~~   25 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQET   25 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHhcC
Confidence            378999999999999999998754

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.13  E-value=0.0038  Score=51.22  Aligned_cols=25  Identities=32%  Similarity=0.343  Sum_probs=22.2

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +..+.|.|+|||||||++..++...
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            5689999999999999999998654

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=96.11  E-value=0.0053  Score=54.82  Aligned_cols=40  Identities=25%  Similarity=0.284  Sum_probs=31.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +...++|.||||+|||+++..++......      +.+++++++..
T Consensus        46 ~~~~~ll~G~~GtGKt~la~~la~~~~~~------~~~~~~~~~~~   85 (311)
T 4fcw_A           46 PIGSFLFLGPTGVGKTELAKTLAATLFDT------EEAMIRIDMTE   85 (311)
T ss_dssp             CSEEEEEESCSSSSHHHHHHHHHHHHHSC------GGGEEEEEGGG
T ss_pred             CceEEEEECCCCcCHHHHHHHHHHHHcCC------CcceEEeeccc
Confidence            34579999999999999999998876431      36788888754

>1nn5_A Similar to deoxythymidylate kinase (thymidylate K; P-loop, D4TMP, transferase; HET: 2DT ANP; 1.50A {Homo sapiens} SCOP: c.37.1.1 PDB: 1e2e_A* 1e2d_A* 1e2g_A* 1e2q_A* 1e99_A* 1e9a_A* 1e9b_A* 1nmx_A* 1nmz_A* 1nn0_A* 1nn1_A* 1e2f_A* 1nn3_A* 2xx3_A* 1e9c_A* 1e9d_A* 1e9e_A* 1e98_A* 1nmy_A* 1e9f_A*

Probab=96.11  E-value=0.0038  Score=52.45  Aligned_cols=27  Identities=26%  Similarity=0.196  Sum_probs=24.2

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+|.++.|.|+|||||||++..++...
T Consensus         7 ~~~~~I~l~G~~GsGKsT~~~~L~~~l   33 (215)
T 1nn5_A            7 RRGALIVLEGVDRAGKSTQSRKLVEAL   33 (215)
T ss_dssp             CCCCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            467899999999999999999998765

>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=96.11  E-value=0.025  Score=50.76  Aligned_cols=42  Identities=21%  Similarity=0.255  Sum_probs=35.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +..-.++.|+|.-|+||||.+.++++..+..      +.+|+.||++-
T Consensus        45 i~~aKVIAIaGKGGVGKTTtavNLA~aLA~~------GkkVllID~Dp   86 (314)
T 3fwy_A           45 ITGAKVFAVYGKGGIGKSTTSSNLSAAFSIL------GKRVLQIGCDP   86 (314)
T ss_dssp             --CCEEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEEESS
T ss_pred             CCCceEEEEECCCccCHHHHHHHHHHHHHHC------CCeEEEEecCC
Confidence            5567899999999999999999999988752      58999999984

>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=96.11  E-value=0.0054  Score=58.70  Aligned_cols=55  Identities=24%  Similarity=0.341  Sum_probs=45.8

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+.+.||+..+|.++.  +-+|+=..|.|++|+|||+++.+++.+..        ..-++|+-.-
T Consensus       202 ~epl~TGirvID~l~P--igrGqr~~Ifg~~g~GKT~l~~~ia~~~~--------~~v~V~~~iG  256 (578)
T 3gqb_A          202 NTPFLTGMRILDVLFP--VAMGGTAAIPGPFGSGKSVTQQSLAKWSN--------ADVVVYVGSG  256 (578)
T ss_dssp             CSEECCSCHHHHTTSC--EETTCEEEECCCTTSCHHHHHHHHHHHSS--------CSEEEEEEEE
T ss_pred             CCcccccchhhhhccc--ccCCCEEeeeCCCCccHHHHHHHHHhccC--------CCEEEEEEec
Confidence            5688999999999986  88999999999999999999999887642        2456776553

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=96.10  E-value=0.004  Score=51.92  Aligned_cols=27  Identities=22%  Similarity=0.350  Sum_probs=23.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+|.++.|.|++||||||++..++...
T Consensus         2 ~~~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            2 SRGALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            357899999999999999999888643

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=96.10  E-value=0.0033  Score=54.35  Aligned_cols=26  Identities=23%  Similarity=0.468  Sum_probs=23.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.++.|.|+|||||||++..++...
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            46899999999999999999988654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.07  E-value=0.003  Score=51.64  Aligned_cols=26  Identities=27%  Similarity=0.262  Sum_probs=18.2

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.++.|.|.|||||||++..++...
T Consensus         4 ~~~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             -CCEEEEECCC----CHHHHHHHHHS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            46799999999999999999987653

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.06  E-value=0.0038  Score=52.13  Aligned_cols=25  Identities=16%  Similarity=0.213  Sum_probs=21.9

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..++.|+|+|||||||++..++...
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999888654

>2xj4_A MIPZ; replication, cell division, ATPase, WACA; 1.60A {Caulobacter vibrioides} PDB: 2xj9_A* 2xit_A

Probab=96.03  E-value=0.025  Score=50.03  Aligned_cols=37  Identities=19%  Similarity=0.224  Sum_probs=30.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+..+..|+||||++.+++...+..      +.+|+.||++.
T Consensus         7 I~v~s~KGGvGKTT~a~nLA~~La~~------G~~VlliD~D~   43 (286)
T 2xj4_A            7 IVVGNEKGGAGKSTIAVHLVTALLYG------GAKVAVIDLDL   43 (286)
T ss_dssp             EEECCSSSCTTHHHHHHHHHHHHHHT------TCCEEEEECCT
T ss_pred             EEEEcCCCCCCHHHHHHHHHHHHHHC------CCcEEEEECCC
Confidence            33445788999999999999988752      58999999986

>1p9r_A General secretion pathway protein E; bacterial type II secretion system cytoplasmic protein - GSPE, putative ATPase/ ATP binding protein; 2.50A {Vibrio cholerae} SCOP: c.37.1.11 PDB: 1p9w_A*

Probab=96.02  E-value=0.0075  Score=56.47  Aligned_cols=39  Identities=13%  Similarity=0.143  Sum_probs=29.8

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+|.++.|.||+||||||++..++.....  .    .+.++++..
T Consensus       165 ~~ggii~I~GpnGSGKTTlL~allg~l~~--~----~g~I~~~ed  203 (418)
T 1p9r_A          165 RPHGIILVTGPTGSGKSTTLYAGLQELNS--S----ERNILTVED  203 (418)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHCC--T----TSCEEEEES
T ss_pred             hcCCeEEEECCCCCCHHHHHHHHHhhcCC--C----CCEEEEecc
Confidence            67999999999999999999988865532  1    245666543

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.01  E-value=0.0027  Score=52.72  Aligned_cols=27  Identities=26%  Similarity=0.297  Sum_probs=23.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.++.|.|+|||||||++..++...
T Consensus        10 ~~~~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           10 RKCKIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             HHSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            456799999999999999999998754

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=95.99  E-value=0.0031  Score=55.24  Aligned_cols=25  Identities=36%  Similarity=0.537  Sum_probs=22.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++ |+++.|.|++|+|||||+.-++-
T Consensus        28 i~-Ge~~~i~G~NGsGKSTLlk~l~G   52 (263)
T 2pjz_A           28 VN-GEKVIILGPNGSGKTTLLRAISG   52 (263)
T ss_dssp             EC-SSEEEEECCTTSSHHHHHHHHTT
T ss_pred             EC-CEEEEEECCCCCCHHHHHHHHhC
Confidence            88 99999999999999999997764

>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=95.98  E-value=0.0049  Score=52.25  Aligned_cols=26  Identities=27%  Similarity=0.333  Sum_probs=22.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +|.++.|.|+|||||||++..++...
T Consensus         3 ~~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            46789999999999999999998754

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=95.98  E-value=0.0072  Score=55.01  Aligned_cols=41  Identities=20%  Similarity=0.198  Sum_probs=31.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.+|.++.|.|+||+|||||+..++.....   .   ++.+.++..+
T Consensus        52 ~~~g~~v~i~G~~GaGKSTLl~~l~g~~~~---~---~g~v~i~~~d   92 (337)
T 2qm8_A           52 TGRAIRVGITGVPGVGKSTTIDALGSLLTA---A---GHKVAVLAVD   92 (337)
T ss_dssp             CCCSEEEEEECCTTSCHHHHHHHHHHHHHH---T---TCCEEEEEEC
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHhhhh---C---CCEEEEEEEc
Confidence            678999999999999999999988865432   1   3566666543

>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=95.98  E-value=0.0051  Score=51.29  Aligned_cols=27  Identities=30%  Similarity=0.361  Sum_probs=23.2

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..+.++.|.|+|||||||++..++...
T Consensus        18 ~~~~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           18 GSHMRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CSCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            345689999999999999999998754

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.97  E-value=0.0042  Score=52.95  Aligned_cols=28  Identities=14%  Similarity=0.218  Sum_probs=22.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..++.++.|.|+|||||||++..++...
T Consensus         4 ~~~~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            4 SARLLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             ---CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             cccCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4566799999999999999999988643

>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=95.96  E-value=0.093  Score=50.57  Aligned_cols=39  Identities=23%  Similarity=0.145  Sum_probs=28.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ...+++++|.||+||||++..++...-..      +..+..|+.+
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~~L~~~------~~d~~v~s~D   72 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTRYLNWI------GVPTKVFNVG   72 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHHHT------TCCEEEEEHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhhc------CCCeEEeccc
Confidence            34689999999999999999998765321      2456666653

>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=95.95  E-value=0.037  Score=49.47  Aligned_cols=25  Identities=16%  Similarity=0.173  Sum_probs=22.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ...++++||||+|||+++..++..+
T Consensus        18 ~~~~Lf~Gp~G~GKtt~a~~la~~~   42 (305)
T 2gno_A           18 GISILINGEDLSYPREVSLELPEYV   42 (305)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhC
Confidence            4589999999999999999998753

>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=95.95  E-value=0.007  Score=53.87  Aligned_cols=35  Identities=29%  Similarity=0.503  Sum_probs=27.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.-++|+||||+|||+++..++...         +.+++++++.
T Consensus        50 ~~~vll~G~~GtGKT~la~~la~~l---------~~~~~~i~~~   84 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIARRLAKLA---------NAPFIKVEAT   84 (310)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHH---------TCCEEEEEGG
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHh---------CCCEEEEcch
Confidence            3467899999999999999988765         2567777764

>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=95.94  E-value=0.021  Score=55.51  Aligned_cols=43  Identities=16%  Similarity=0.127  Sum_probs=31.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHH--hccccCCCCCCCeEEEEeCCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLL--AALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~--~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ...++.|.|.+|+|||+||.+++..  ....    +.-..++|++....
T Consensus       151 ~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~----~~F~~~~wv~vs~~  195 (549)
T 2a5y_B          151 DSFFLFLHGRAGSGKSVIASQALSKSDQLIG----INYDSIVWLKDSGT  195 (549)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHHCSSTBT----TTBSEEEEEECCCC
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHhhhHHHh----ccCCcEEEEEECCC
Confidence            4579999999999999999988851  1111    11257889987654

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=95.92  E-value=0.0053  Score=56.71  Aligned_cols=29  Identities=17%  Similarity=0.150  Sum_probs=25.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +++|.++.|.|++||||||++..++....
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            67899999999999999999998887553

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=95.88  E-value=0.005  Score=53.52  Aligned_cols=27  Identities=30%  Similarity=0.529  Sum_probs=24.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.++.|.|++||||||++..++...
T Consensus        25 ~~g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           25 AIAPVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             TTSCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhc
Confidence            678999999999999999999888543

>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=95.87  E-value=0.011  Score=56.19  Aligned_cols=29  Identities=34%  Similarity=0.445  Sum_probs=24.7

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |..++.-++++||||+|||++|..++...
T Consensus        59 ~~~~~~~iLl~GppGtGKT~la~ala~~l   87 (456)
T 2c9o_A           59 KKMAGRAVLLAGPPGTGKTALALAIAQEL   87 (456)
T ss_dssp             TCCTTCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCCCeEEEECCCcCCHHHHHHHHHHHh
Confidence            45566678999999999999999998875

>4eaq_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MTBI, transferase; HET: ATM; 1.85A {Staphylococcus aureus subsp} PDB: 4dwj_A* 4f4i_A

Probab=95.87  E-value=0.0062  Score=52.14  Aligned_cols=28  Identities=21%  Similarity=0.312  Sum_probs=25.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+|.++.|.|+||+||||++..++...
T Consensus        23 ~~~g~~i~i~G~~GsGKsT~~~~l~~~l   50 (229)
T 4eaq_A           23 NAMSAFITFEGPEGSGKTTVINEVYHRL   50 (229)
T ss_dssp             CCCCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCeEEEEEcCCCCCHHHHHHHHHHHH
Confidence            6689999999999999999999888765

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=95.84  E-value=0.0045  Score=51.40  Aligned_cols=25  Identities=36%  Similarity=0.414  Sum_probs=22.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+.+.|.|++|+||||++..++...
T Consensus         1 G~~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            1 ARHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCChHHHHHHHHHhhc
Confidence            6789999999999999999888765

>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=95.83  E-value=0.005  Score=51.25  Aligned_cols=26  Identities=27%  Similarity=0.514  Sum_probs=22.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .|..++|.|++|+|||+++..++...
T Consensus        33 ~g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhC
Confidence            36789999999999999999998654

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=95.82  E-value=0.24  Score=38.75  Aligned_cols=23  Identities=17%  Similarity=0.377  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+.|.|++|+|||+|+..++...
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            37899999999999999888654

>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=95.82  E-value=0.0059  Score=51.40  Aligned_cols=31  Identities=26%  Similarity=0.471  Sum_probs=25.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|.|||||||+|.|..++...           ...+||+.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~-----------g~~~istG   32 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK-----------GFVHISTG   32 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH-----------CCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH-----------CCeEEcHH
Confidence            57899999999999999999754           35678774

>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=95.81  E-value=0.0071  Score=52.80  Aligned_cols=38  Identities=24%  Similarity=0.402  Sum_probs=29.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .-++|+|+||+|||++|..++.....      .+.+.+++++..
T Consensus        30 ~~vll~G~~GtGKt~la~~i~~~~~~------~~~~~~~v~~~~   67 (265)
T 2bjv_A           30 KPVLIIGERGTGKELIASRLHYLSSR------WQGPFISLNCAA   67 (265)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHHTSTT------TTSCEEEEEGGG
T ss_pred             CCEEEECCCCCcHHHHHHHHHHhcCc------cCCCeEEEecCC
Confidence            46889999999999999988865431      146788998754

>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=95.81  E-value=0.011  Score=47.88  Aligned_cols=38  Identities=24%  Similarity=0.086  Sum_probs=28.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .++.|+|++|+||||++..++.....   .   +.+|..|..+.
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~---~---g~~v~~ik~~~   42 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVR---E---GWRVGTVKHHG   42 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHH---T---TCCEEEEECCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHh---c---CCeeeEEEeCC
Confidence            37899999999999999999876542   1   35666666543

>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=95.79  E-value=0.0067  Score=51.46  Aligned_cols=25  Identities=24%  Similarity=0.187  Sum_probs=22.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ..++|+|+||+|||+++..++....
T Consensus        46 ~~~ll~G~~G~GKT~l~~~~~~~~~   70 (250)
T 1njg_A           46 HAYLFSGTRGVGKTSIARLLAKGLN   70 (250)
T ss_dssp             SEEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4899999999999999999987664

>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=95.76  E-value=0.0072  Score=51.27  Aligned_cols=25  Identities=28%  Similarity=0.563  Sum_probs=21.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.++.|.|+|||||||++..++...
T Consensus         5 ~~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            5 APVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999888643

>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=95.74  E-value=0.0056  Score=50.18  Aligned_cols=24  Identities=29%  Similarity=0.372  Sum_probs=21.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .++.|+|+|||||||++..++...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            468999999999999999998754

>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=95.73  E-value=0.005  Score=57.79  Aligned_cols=46  Identities=11%  Similarity=0.153  Sum_probs=40.9

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      .+.+.||++.+|.++.  +-+|+=..|.|++|+|||+|+.+++..+..
T Consensus       128 ~e~l~TGiraID~l~p--igrGQr~~Ifgg~G~GKt~L~~~Ia~~~~a  173 (464)
T 3gqb_B          128 EQFIQTGISTIDVMNT--LVRGQKLPIFSGSGLPANEIAAQIARQATV  173 (464)
T ss_dssp             CCBCBCSCHHHHTTSC--CBTTCBCCEEEETTSCHHHHHHHHHHHCBC
T ss_pred             cccccCcceeeecccc--cccCCEEEEecCCCCCchHHHHHHHHHHHh
Confidence            5689999999999987  888999999999999999999998877643

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=95.73  E-value=0.013  Score=47.92  Aligned_cols=29  Identities=24%  Similarity=0.162  Sum_probs=23.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ...-.++.|+|++|+|||||+..++....
T Consensus         3 ~~~~~~i~i~G~sGsGKTTl~~~l~~~l~   31 (174)
T 1np6_A            3 KTMIPLLAFAAWSGTGKTTLLKKLIPALC   31 (174)
T ss_dssp             --CCCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCcceEEEEEeCCCCCHHHHHHHHHHhcc
Confidence            44456899999999999999999987643

>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=95.73  E-value=0.019  Score=58.22  Aligned_cols=28  Identities=29%  Similarity=0.241  Sum_probs=23.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ..+.-++|+|+||+|||+++..++....
T Consensus       205 ~~~~~vlL~G~~GtGKT~la~~la~~l~  232 (758)
T 1r6b_X          205 RRKNNPLLVGESGVGKTAIAEGLAWRIV  232 (758)
T ss_dssp             SSSCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cCCCCeEEEcCCCCCHHHHHHHHHHHHH
Confidence            3566789999999999999999987764

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=95.71  E-value=0.01  Score=49.57  Aligned_cols=24  Identities=21%  Similarity=0.295  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+++|+|+||+|||++|..++...
T Consensus         6 mi~l~tG~pGsGKT~~a~~~~~~~   29 (199)
T 2r2a_A            6 EICLITGTPGSGKTLKMVSMMAND   29 (199)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHH
Confidence            489999999999999999887655

>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=95.71  E-value=0.0059  Score=50.09  Aligned_cols=23  Identities=26%  Similarity=0.317  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.||+|+|||||+..++...
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999888654

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=95.68  E-value=0.3  Score=38.13  Aligned_cols=22  Identities=27%  Similarity=0.451  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+.|++|+|||+|+..++...
T Consensus         6 i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            6 LVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHHhCc
Confidence            7899999999999999998653

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=95.67  E-value=0.0063  Score=49.48  Aligned_cols=23  Identities=22%  Similarity=0.286  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|+|||||||++..++...
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58899999999999999998654

>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=95.66  E-value=0.02  Score=51.93  Aligned_cols=24  Identities=29%  Similarity=0.346  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+.|+||||+|||||+..++...
T Consensus        52 ~~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           52 DHVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             CCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHh
Confidence            578999999999999999998765

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.65  E-value=0.0082  Score=50.02  Aligned_cols=24  Identities=33%  Similarity=0.357  Sum_probs=21.3

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ..++.|.|+|||||||++..++..
T Consensus        15 ~~~I~l~G~~GsGKsT~~~~L~~~   38 (203)
T 1ukz_A           15 VSVIFVLGGPGAGKGTQCEKLVKD   38 (203)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999999988864

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=95.65  E-value=0.016  Score=52.97  Aligned_cols=49  Identities=18%  Similarity=0.194  Sum_probs=39.9

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc--cccCCCCCCCeEEEEeCCC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAA--LPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~--~~~~~gg~~~~vl~i~~e~  146 (357)
                      .|+.++..  +.-.++.+.|..|+||||++.++|...+  ..      +.+|+.||++.
T Consensus         8 ~L~~~l~~--~~~~i~~~~gkGGvGKTt~a~~lA~~la~~~~------g~~vllid~D~   58 (348)
T 3io3_A            8 TLESIVQH--DSLKWIFVGGKGGVGKTTTSSSVAVQLALAQP------NEQFLLISTDP   58 (348)
T ss_dssp             SSHHHHTC--TTCSEEEEECSTTSSHHHHHHHHHHHHHHHCT------TSCEEEEECCS
T ss_pred             hHHHHhcC--CCcEEEEEeCCCCCcHHHHHHHHHHHHHHhcC------CCeEEEEECCC
Confidence            45666653  2347999999999999999999999887  53      58999999984

>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=95.63  E-value=0.0083  Score=51.81  Aligned_cols=26  Identities=23%  Similarity=0.202  Sum_probs=22.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++-+++|.|+|||||||++..++...
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            56689999999999999999998654

>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=95.63  E-value=0.0078  Score=49.19  Aligned_cols=26  Identities=27%  Similarity=0.493  Sum_probs=22.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+| +++|+|++|+|||+++..+...
T Consensus        24 ~~~g-~~~i~G~NGsGKStll~ai~~~   49 (182)
T 3kta_A           24 FSKG-FTAIVGANGSGKSNIGDAILFV   49 (182)
T ss_dssp             CCSS-EEEEEECTTSSHHHHHHHHHHH
T ss_pred             cCCC-cEEEECCCCCCHHHHHHHHHHH
Confidence            5567 9999999999999999876643

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=95.63  E-value=0.0041  Score=57.21  Aligned_cols=39  Identities=31%  Similarity=0.377  Sum_probs=29.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +++|+++.|.|++|||||||+..++...  +.     ....+.++.
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~l~~~~--~~-----~~g~I~ie~  210 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKALMQEI--PF-----DQRLITIED  210 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHHHHTTS--CT-----TSCEEEEES
T ss_pred             HhcCCEEEEECCCCCCHHHHHHHHHhcC--CC-----CceEEEECC
Confidence            6789999999999999999999777533  21     245666763

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.62  E-value=0.0076  Score=50.98  Aligned_cols=27  Identities=22%  Similarity=0.218  Sum_probs=23.2

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+|..+.|.|+|||||||++..++...
T Consensus         3 ~~~~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            3 SKKHNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             GGCCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHh
Confidence            356689999999999999999998754

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.61  E-value=0.0071  Score=51.31  Aligned_cols=26  Identities=15%  Similarity=0.169  Sum_probs=22.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.++.|.|+|||||||++..++...
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45689999999999999999998754

>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=95.61  E-value=0.0038  Score=54.60  Aligned_cols=22  Identities=45%  Similarity=0.561  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|+||||+|||+++..++...
T Consensus        47 vll~G~~GtGKT~la~~la~~~   68 (268)
T 2r62_A           47 VLLVGPPGTGKTLLAKAVAGEA   68 (268)
T ss_dssp             CCCBCSSCSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHh
Confidence            7899999999999999998765

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=95.60  E-value=0.012  Score=51.47  Aligned_cols=39  Identities=13%  Similarity=0.176  Sum_probs=32.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      ++.|.|..|+||||++.++|...+..      +.+|++||++...
T Consensus         3 vI~vs~KGGvGKTT~a~nLA~~la~~------G~~VlliD~D~q~   41 (269)
T 1cp2_A            3 QVAIYGKGGIGKSTTTQNLTSGLHAM------GKTIMVVGCDPKA   41 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTT------TCCEEEEEECTTS
T ss_pred             EEEEecCCCCcHHHHHHHHHHHHHHC------CCcEEEEcCCCCC
Confidence            45668999999999999999988742      5899999998543

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=95.58  E-value=0.28  Score=38.57  Aligned_cols=22  Identities=27%  Similarity=0.401  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+..++...
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            6889999999999999988654

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.57  E-value=0.0083  Score=49.83  Aligned_cols=23  Identities=22%  Similarity=0.387  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|++||||||++..++...
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            68899999999999999998754

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.57  E-value=0.013  Score=52.80  Aligned_cols=40  Identities=18%  Similarity=0.154  Sum_probs=29.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      -++.|.|++|||||||+..++.......    .+..+.+++.+.
T Consensus        93 ~iigI~GpsGSGKSTl~~~L~~ll~~~~----~~~~v~~i~~D~  132 (321)
T 3tqc_A           93 YIIGIAGSVAVGKSTTSRVLKALLSRWP----DHPNVEVITTDG  132 (321)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTST----TCCCEEEEEGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhcccC----CCCeEEEEeecc
Confidence            3899999999999999988775543100    135678888765

>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=95.56  E-value=0.0053  Score=52.51  Aligned_cols=27  Identities=19%  Similarity=0.207  Sum_probs=23.4

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ..++|.++.|.|++||||||++..++.
T Consensus        16 ~~~~g~~i~i~G~~GsGKSTl~~~L~~   42 (230)
T 2vp4_A           16 EGTQPFTVLIEGNIGSGKTTYLNHFEK   42 (230)
T ss_dssp             TTCCCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CCCCceEEEEECCCCCCHHHHHHHHHh
Confidence            357899999999999999999986653

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=95.56  E-value=0.011  Score=58.08  Aligned_cols=52  Identities=19%  Similarity=0.130  Sum_probs=41.1

Q ss_pred             hhHHhhhcC-CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           89 KGLDAALCG-GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        89 ~~LD~~l~G-Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.||.++.+ +-....++++.|.+|+|||+++.++|...+..      +.+|+++|++.
T Consensus       313 ~~l~~~~~~~~~~~~~~~~~~~~~g~Gktt~a~~lA~~l~~~------g~~vllvD~Dp  365 (589)
T 1ihu_A          313 PSLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADM------GFDVHLTTSDP  365 (589)
T ss_dssp             CCHHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEESCC
T ss_pred             chhhhhhhhhhccCCeEEEEecCCCCChhhHHHHHHHHHHHC------CCcEEEEeCCC
Confidence            567776654 23345688889999999999999999988752      58999999985

>1odf_A YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser2 intergenic region; yeast protein, ATP binding protein; 2.25A {Saccharomyces cerevisiae} SCOP: c.37.1.6

Probab=95.55  E-value=0.009  Score=53.10  Aligned_cols=29  Identities=17%  Similarity=0.235  Sum_probs=24.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      -.++.++.|+|++|||||||+..++....
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            35678999999999999999998876553

>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=95.55  E-value=0.0057  Score=55.62  Aligned_cols=23  Identities=35%  Similarity=0.408  Sum_probs=21.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+||||+|||+++..++....
T Consensus        49 ~ll~Gp~G~GKTtla~~la~~l~   71 (340)
T 1sxj_C           49 LLFYGPPGTGKTSTIVALAREIY   71 (340)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHc
Confidence            89999999999999999988764

>3bfv_A CAPA1, CAPB2, membrane protein CAPA1, protein tyrosine kinase; chimerical protein, P-loop protein, capsule biogenesis/degradation; HET: ADP; 1.80A {Staphylococcus aureus} PDB: 2ved_A*

Probab=95.55  E-value=0.015  Score=51.04  Aligned_cols=41  Identities=15%  Similarity=0.165  Sum_probs=33.2

Q ss_pred             CCcEEEEEc-CCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          101 FGVVTELVG-PAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       101 ~G~l~~I~G-~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +..++.|++ .+|.|||+++.++|...+..      +.+|++||++..
T Consensus        81 ~~kvI~vts~kgG~GKTt~a~nLA~~lA~~------G~rVLLID~D~~  122 (271)
T 3bfv_A           81 AVQSIVITSEAPGAGKSTIAANLAVAYAQA------GYKTLIVDGDMR  122 (271)
T ss_dssp             CCCEEEEECSSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCSS
T ss_pred             CCeEEEEECCCCCCcHHHHHHHHHHHHHhC------CCeEEEEeCCCC
Confidence            345777775 58999999999999988852      589999999864

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=95.55  E-value=0.18  Score=40.44  Aligned_cols=23  Identities=26%  Similarity=0.421  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -++|.|++|+|||+|+..++...
T Consensus        14 ki~v~G~~~~GKSsli~~l~~~~   36 (181)
T 2efe_B           14 KLVLLGDVGAGKSSLVLRFVKDQ   36 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            37899999999999999988653

>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=95.54  E-value=0.0081  Score=49.35  Aligned_cols=25  Identities=24%  Similarity=0.311  Sum_probs=21.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..++.|.|+|||||||++..++...
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999988653

>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=95.54  E-value=0.017  Score=51.81  Aligned_cols=25  Identities=28%  Similarity=0.278  Sum_probs=21.7

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ...++|+|+||+|||+++..++...
T Consensus        38 ~~~vll~G~~GtGKT~la~~i~~~~   62 (324)
T 1hqc_A           38 LEHLLLFGPPGLGKTTLAHVIAHEL   62 (324)
T ss_dssp             CCCCEEECCTTCCCHHHHHHHHHHH
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHh
Confidence            3468999999999999999998755

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.52  E-value=0.0087  Score=50.40  Aligned_cols=23  Identities=22%  Similarity=0.174  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|+|||||||++..++...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999988654

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=95.51  E-value=0.012  Score=58.55  Aligned_cols=40  Identities=25%  Similarity=0.276  Sum_probs=31.6

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ....+.+|.||||+|||+.+.+++.....+      +.+++..+..
T Consensus       203 ~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~------~~~ILv~a~T  242 (646)
T 4b3f_X          203 SQKELAIIHGPPGTGKTTTVVEIILQAVKQ------GLKVLCCAPS  242 (646)
T ss_dssp             HCSSEEEEECCTTSCHHHHHHHHHHHHHHT------TCCEEEEESS
T ss_pred             cCCCceEEECCCCCCHHHHHHHHHHHHHhC------CCeEEEEcCc
Confidence            345699999999999999999998887653      4677776654

>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=95.51  E-value=0.012  Score=53.51  Aligned_cols=53  Identities=23%  Similarity=0.228  Sum_probs=33.0

Q ss_pred             chhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           88 LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        88 ~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +..|-..+..|-.+.  ++|+||||+|||+++..++.....+...   ...+++++..
T Consensus        46 ~~~l~~~l~~~~~~~--~ll~G~~G~GKT~la~~la~~l~~~~~~---~~~~~~~~~~   98 (353)
T 1sxj_D           46 VTVLKKTLKSANLPH--MLFYGPPGTGKTSTILALTKELYGPDLM---KSRILELNAS   98 (353)
T ss_dssp             HHHHHHHTTCTTCCC--EEEECSTTSSHHHHHHHHHHHHHHHHHH---TTSEEEECSS
T ss_pred             HHHHHHHHhcCCCCE--EEEECCCCCCHHHHHHHHHHHhCCCccc---ccceEEEccc
Confidence            344555554442222  8999999999999999998775321000   2456666554

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=95.50  E-value=0.014  Score=52.84  Aligned_cols=33  Identities=24%  Similarity=0.392  Sum_probs=26.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .++.|+|++|||||+|+..++...           ++.+|+.+.
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l-----------~~~iis~Ds   40 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKF-----------NGEIISGDS   40 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT-----------TEEEEECCS
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHc-----------CCceecccc
Confidence            489999999999999999998754           155677654

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.50  E-value=0.0092  Score=49.10  Aligned_cols=23  Identities=30%  Similarity=0.328  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|+|||||||++..++...
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l   24 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYL   24 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68899999999999999998765

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=95.49  E-value=0.0079  Score=49.69  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .++|+||+|+||||++..++...
T Consensus         3 pIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            58999999999999999888653

>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=95.48  E-value=0.024  Score=60.30  Aligned_cols=56  Identities=20%  Similarity=0.210  Sum_probs=36.5

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      .|...|..+=....++.|.|++|+|||+||.+++......  .+.....++|++....
T Consensus       135 ~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~--~~~~~~~~~~v~~~~~  190 (1249)
T 3sfz_A          135 AIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDHSLL--EGCFSGGVHWVSIGKQ  190 (1249)
T ss_dssp             HHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCHHHH--TTTSTTCEEEEECCSC
T ss_pred             HHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcChhHH--HhhCCCeEEEEEECCc
Confidence            4555553222345689999999999999999887653110  0012467889997654

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=95.46  E-value=0.009  Score=53.46  Aligned_cols=32  Identities=31%  Similarity=0.562  Sum_probs=26.1

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      ++|+++.  +..|.++.|.|++|+|||||+..++
T Consensus       155 gi~~L~~--~l~G~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          155 GIDELVD--YLEGFICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             THHHHHH--HTTTCEEEEECSTTSSHHHHHHHHH
T ss_pred             CHHHHHh--hccCcEEEEECCCCCCHHHHHHHHH
Confidence            3555554  4568899999999999999999888

>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=95.45  E-value=0.0082  Score=48.48  Aligned_cols=24  Identities=25%  Similarity=0.220  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .++.|.|+|||||||++..++...
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            368999999999999999988754

>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=95.44  E-value=0.013  Score=52.32  Aligned_cols=38  Identities=21%  Similarity=0.195  Sum_probs=27.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++|+|+||+|||+++..++.....+ .   ....+++++...
T Consensus        45 ~ll~G~~G~GKt~la~~l~~~l~~~-~---~~~~~~~~~~~~   82 (323)
T 1sxj_B           45 MIISGMPGIGKTTSVHCLAHELLGR-S---YADGVLELNASD   82 (323)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHGG-G---HHHHEEEECTTS
T ss_pred             EEEECcCCCCHHHHHHHHHHHhcCC-c---ccCCEEEecCcc
Confidence            8999999999999999999875321 0   123466666543

>3cio_A ETK, tyrosine-protein kinase ETK; WZC, escherichia coli tyrosine kinase domain, signaling protein, transferase, inner membrane, membrane; 2.50A {Escherichia coli}

Probab=95.44  E-value=0.016  Score=51.74  Aligned_cols=41  Identities=24%  Similarity=0.349  Sum_probs=33.1

Q ss_pred             CCcEEEEEcC-CCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          101 FGVVTELVGP-AGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       101 ~G~l~~I~G~-~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ++.++.|++. +|.|||+++.++|...+..      +.+|++||++..
T Consensus       103 ~~kvI~vts~kgG~GKTtva~nLA~~lA~~------G~rVLLID~D~r  144 (299)
T 3cio_A          103 ENNILMITGATPDSGKTFVSSTLAAVIAQS------DQKVLFIDADLR  144 (299)
T ss_dssp             SCCEEEEEESSSSSCHHHHHHHHHHHHHHT------TCCEEEEECCTT
T ss_pred             CCeEEEEECCCCCCChHHHHHHHHHHHHhC------CCcEEEEECCCC
Confidence            3457777664 8999999999999988752      589999999863

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=95.43  E-value=0.01  Score=47.82  Aligned_cols=24  Identities=29%  Similarity=0.421  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.+.|.|.|||||||++..++...
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            578999999999999999888654

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=95.43  E-value=0.011  Score=53.95  Aligned_cols=34  Identities=32%  Similarity=0.435  Sum_probs=26.9

Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .|++.|...+     +|+++.|.|+||+|||||+..++-
T Consensus       204 ~gl~~L~~~~-----~G~~~~lvG~sG~GKSTLln~L~g  237 (358)
T 2rcn_A          204 DGLKPLEEAL-----TGRISIFAGQSGVGKSSLLNALLG  237 (358)
T ss_dssp             BTHHHHHHHH-----TTSEEEEECCTTSSHHHHHHHHHC
T ss_pred             cCHHHHHHhc-----CCCEEEEECCCCccHHHHHHHHhc
Confidence            3556666543     678999999999999999987763

>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=95.42  E-value=0.17  Score=40.73  Aligned_cols=22  Identities=27%  Similarity=0.439  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+..++...
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            6899999999999999998644

>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=95.42  E-value=0.0086  Score=50.06  Aligned_cols=21  Identities=29%  Similarity=0.426  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++.|.|++||||||++..++.
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            688999999999999998864

>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=95.41  E-value=0.0047  Score=56.03  Aligned_cols=40  Identities=23%  Similarity=0.426  Sum_probs=29.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+++.|.|++|||||||+.-++...  +.     ....+.++..
T Consensus       168 i~~g~~v~i~G~~GsGKTTll~~l~g~~--~~-----~~g~i~i~~~  207 (330)
T 2pt7_A          168 IAIGKNVIVCGGTGSGKTTYIKSIMEFI--PK-----EERIISIEDT  207 (330)
T ss_dssp             HHHTCCEEEEESTTSCHHHHHHHGGGGS--CT-----TSCEEEEESS
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHhCCC--cC-----CCcEEEECCe
Confidence            4679999999999999999988766433  21     2456666643

>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=95.40  E-value=0.014  Score=53.77  Aligned_cols=37  Identities=27%  Similarity=0.285  Sum_probs=28.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+..-++|+||||+|||++|..++...         +.+.+++++.
T Consensus        70 ~~~~~ill~Gp~GtGKT~la~~la~~l---------~~~~~~~~~~  106 (376)
T 1um8_A           70 LSKSNILLIGPTGSGKTLMAQTLAKHL---------DIPIAISDAT  106 (376)
T ss_dssp             CCCCCEEEECCTTSSHHHHHHHHHHHT---------TCCEEEEEGG
T ss_pred             cCCCCEEEECCCCCCHHHHHHHHHHHh---------CCCEEEecch
Confidence            344568999999999999999988754         2567777653

>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=95.40  E-value=0.0099  Score=50.08  Aligned_cols=23  Identities=22%  Similarity=0.157  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|+|||||||++..++...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999987643

>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=95.38  E-value=0.013  Score=53.74  Aligned_cols=35  Identities=31%  Similarity=0.348  Sum_probs=27.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++.-++|+||||+|||++|..++...         +.+.+.+++
T Consensus        50 ~~~~vll~GppGtGKT~la~~ia~~~---------~~~~~~~~~   84 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLAETLARLL---------DVPFTMADA   84 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHT---------TCCEEEEEH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHc---------CCCEEEech
Confidence            45568999999999999999998765         245666654

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=95.37  E-value=0.086  Score=43.10  Aligned_cols=23  Identities=30%  Similarity=0.457  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -++|.|++|+|||+|+..++...
T Consensus         9 ki~v~G~~~~GKSsli~~l~~~~   31 (208)
T 3clv_A            9 KTVLLGESSVGKSSIVLRLTKDT   31 (208)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            37899999999999999998653

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=95.37  E-value=0.07  Score=53.57  Aligned_cols=39  Identities=28%  Similarity=0.300  Sum_probs=30.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .|..++|+||+|+|||+.+...+......  .   +.+++|+.-
T Consensus        45 ~~~~~lv~apTGsGKT~~~~l~il~~~~~--~---~~~il~i~P   83 (715)
T 2va8_A           45 EGNRLLLTSPTGSGKTLIAEMGIISFLLK--N---GGKAIYVTP   83 (715)
T ss_dssp             TTCCEEEECCTTSCHHHHHHHHHHHHHHH--S---CSEEEEECS
T ss_pred             CCCcEEEEcCCCCcHHHHHHHHHHHHHHH--C---CCeEEEEeC
Confidence            46789999999999999998777765431  1   368888864

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.36  E-value=0.0099  Score=53.76  Aligned_cols=26  Identities=27%  Similarity=0.441  Sum_probs=22.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .++.+++|.||+|+|||+|+..+|..
T Consensus        38 ~~~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           38 RKEKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             cCCceEEEECCCCCCHHHHHHHHHHH
Confidence            45679999999999999999999854

>2afh_E Nitrogenase iron protein 1; nitrogen fixation, iron-sulfur, metal-binding, molybdenum, oxidoreductase; HET: HCA CFN CLF PGE PG4 P6G 1PE; 2.10A {Azotobacter vinelandii} SCOP: c.37.1.10 PDB: 1g1m_A 1g5p_A 1m1y_E* 1m34_E* 1n2c_E* 1nip_A* 1fp6_A* 2afi_E* 2afk_E* 2nip_A 1de0_A 1xcp_A* 1xdb_A 1xd8_A 1xd9_A* 1g20_E* 1g21_E* 2c8v_A* 1rw4_A

Probab=95.36  E-value=0.014  Score=51.71  Aligned_cols=38  Identities=18%  Similarity=0.231  Sum_probs=32.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ++.|.|..|+||||++.++|...+..      +.+|+.||++..
T Consensus         4 vIavs~KGGvGKTT~a~nLA~~La~~------G~rVlliD~D~q   41 (289)
T 2afh_E            4 QCAIYGKGGIGKSTTTQNLVAALAEM------GKKVMIVGCDPK   41 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHT------TCCEEEEEECSS
T ss_pred             EEEEeCCCcCcHHHHHHHHHHHHHHC------CCeEEEEecCCC
Confidence            56668999999999999999988752      589999999854

>1ihu_A Arsenical pump-driving ATPase; aluminum fluoride, ADP, ARSA ATPase, ATP binding site, hydro; HET: ADP; 2.15A {Escherichia coli} SCOP: c.37.1.10 c.37.1.10 PDB: 1f48_A* 1ii0_A* 1ii9_A*

Probab=95.31  E-value=0.017  Score=56.65  Aligned_cols=40  Identities=18%  Similarity=0.232  Sum_probs=35.2

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ...++.+.|.+|+||||++.++|...+..      +.+|++||++.
T Consensus         7 ~~~i~~~sgkGGvGKTT~a~~lA~~lA~~------G~rVLlvd~D~   46 (589)
T 1ihu_A            7 IPPYLFFTGKGGVGKTSISCATAIRLAEQ------GKRVLLVSTDP   46 (589)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCT
T ss_pred             CCEEEEEeCCCcCHHHHHHHHHHHHHHHC------CCcEEEEECCC
Confidence            35789999999999999999999988852      58999999985

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=95.30  E-value=0.0086  Score=56.84  Aligned_cols=28  Identities=32%  Similarity=0.260  Sum_probs=24.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++|+++.|.|++|||||||+.-++...
T Consensus       135 i~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          135 NFEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SSSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            6789999999999999999999777543

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.29  E-value=0.008  Score=52.20  Aligned_cols=37  Identities=27%  Similarity=0.170  Sum_probs=28.6

Q ss_pred             hhHHhhhcCCCCC---CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           89 KGLDAALCGGVPF---GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        89 ~~LD~~l~GGi~~---G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .-|+.+--- +.+   |..+.|.|++|+||||++..++...
T Consensus        33 ~~l~~~~~~-i~~~l~g~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           33 QILKKKAEE-VKPYLNGRSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             HHHHHHHHT-THHHHTTCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             hhhhhhhhh-hhhhcCCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            345554332 666   9999999999999999999888654

>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=95.29  E-value=0.017  Score=52.53  Aligned_cols=42  Identities=21%  Similarity=0.258  Sum_probs=33.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ...|.++.|.|+||+||||++..++......      ++++..++.+.
T Consensus        53 ~~~~~~i~i~G~~g~GKSTl~~~l~~~~~~~------~~~v~v~~~d~   94 (341)
T 2p67_A           53 CGNTLRLGVTGTPGAGKSTFLEAFGMLLIRE------GLKVAVIAVDP   94 (341)
T ss_dssp             CSCSEEEEEEECTTSCHHHHHHHHHHHHHHT------TCCEEEEEECC
T ss_pred             cCCCEEEEEEcCCCCCHHHHHHHHHHHHHhc------CCeEEEEeecC
Confidence            3568899999999999999999998766421      46777777654

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=95.28  E-value=0.16  Score=39.89  Aligned_cols=22  Identities=36%  Similarity=0.404  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.|.|++|+|||+|+..++...
T Consensus         3 i~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6799999999999999998654

>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=95.28  E-value=0.27  Score=39.43  Aligned_cols=23  Identities=26%  Similarity=0.445  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -++|.|++|+|||+|+..++...
T Consensus        20 ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           20 KVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            47899999999999999988644

>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=95.27  E-value=0.0094  Score=55.75  Aligned_cols=34  Identities=24%  Similarity=0.141  Sum_probs=26.7

Q ss_pred             HHhhhcCCCCCCcE--EEEEcCCCCcHHHHHHHHHHH
Q 035774           91 LDAALCGGVPFGVV--TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        91 LD~~l~GGi~~G~l--~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      |+.+-- -+++|.+  +.|.|++|+|||||+..++..
T Consensus        30 L~~vsl-~i~~Gei~~vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           30 DQLVNK-SVSQGFCFNILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             HHHHHH-SCC-CCEEEEEEECSTTSSSHHHHHHHHTS
T ss_pred             cCCCce-EecCCCeeEEEEECCCCCCHHHHHHHHhCc
Confidence            555432 2899999  999999999999999887643

>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=95.26  E-value=0.0094  Score=49.68  Aligned_cols=21  Identities=24%  Similarity=0.311  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++.|.|++||||||++..++.
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            688999999999999998885

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=95.20  E-value=0.025  Score=52.48  Aligned_cols=40  Identities=25%  Similarity=0.213  Sum_probs=30.5

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..+.-+.|.|++|+|||+++..++.....   .   +..++++|..
T Consensus        33 ~~~~~~~i~G~~G~GKs~~~~~~~~~~~~---~---~~~~~~~D~~   72 (392)
T 4ag6_A           33 RTNSNWTILAKPGAGKSFTAKMLLLREYM---Q---GSRVIIIDPE   72 (392)
T ss_dssp             BCCCCEEEECCTTSSHHHHHHHHHHHHHT---T---TCCEEEEESS
T ss_pred             cccCceEEEcCCCCCHHHHHHHHHHHHHH---C---CCEEEEEeCC
Confidence            35667899999999999999999877653   2   3566677754

>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=95.20  E-value=0.012  Score=49.59  Aligned_cols=24  Identities=21%  Similarity=0.375  Sum_probs=21.1

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+-++.|.|++||||||++..++.
T Consensus         3 ~~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            3 LRYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999998874

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.19  E-value=0.013  Score=47.01  Aligned_cols=23  Identities=26%  Similarity=0.137  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|.|||||||++..++...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999888654

>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=95.19  E-value=0.015  Score=49.78  Aligned_cols=26  Identities=38%  Similarity=0.464  Sum_probs=22.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++..+.|.|+|||||||++..++...
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            34689999999999999999998764

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=95.14  E-value=0.016  Score=51.93  Aligned_cols=40  Identities=20%  Similarity=0.244  Sum_probs=30.9

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.-++|+|+||+|||++|..++.....      .+.+.+++++..
T Consensus        24 ~~~~vLi~Ge~GtGKt~lAr~i~~~~~~------~~~~~v~v~~~~   63 (304)
T 1ojl_A           24 SDATVLIHGDSGTGKELVARALHACSAR------SDRPLVTLNCAA   63 (304)
T ss_dssp             TTSCEEEESCTTSCHHHHHHHHHHHSSC------SSSCCCEEECSS
T ss_pred             CCCcEEEECCCCchHHHHHHHHHHhCcc------cCCCeEEEeCCC
Confidence            3456899999999999999988875532      146788888764

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.10  E-value=0.014  Score=49.56  Aligned_cols=23  Identities=22%  Similarity=0.175  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|+|||||||++..++...
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~~l   24 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKDKY   24 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            58899999999999999998654

>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=95.07  E-value=0.014  Score=56.73  Aligned_cols=26  Identities=31%  Similarity=0.475  Sum_probs=23.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +|..++|+||||+|||+++..++...
T Consensus       107 ~g~~vll~Gp~GtGKTtlar~ia~~l  132 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLAKSIAKSL  132 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhc
Confidence            78999999999999999999888654

>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=95.07  E-value=0.18  Score=45.44  Aligned_cols=27  Identities=15%  Similarity=0.075  Sum_probs=23.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      ...++++||||+|||+++..++.....
T Consensus        24 ~~a~L~~G~~G~GKt~~a~~la~~l~~   50 (334)
T 1a5t_A           24 HHALLIQALPGMGDDALIYALSRYLLC   50 (334)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             ceeEEEECCCCchHHHHHHHHHHHHhC
Confidence            457999999999999999999987754

>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=95.05  E-value=0.015  Score=49.85  Aligned_cols=25  Identities=36%  Similarity=0.522  Sum_probs=21.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .-++.|.|+|||||||++..++...
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4589999999999999999888654

>1t9h_A YLOQ, probable GTPase ENGC; N-terminal beta-barrel domain with oligonucleotide binding fold, central GTP binding domain; 1.60A {Bacillus subtilis} SCOP: b.40.4.5 c.37.1.8

Probab=95.05  E-value=0.0041  Score=55.71  Aligned_cols=26  Identities=23%  Similarity=0.234  Sum_probs=23.0

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|+||+|||||+..++.
T Consensus       170 ~~~G~~~~lvG~sG~GKSTLln~L~g  195 (307)
T 1t9h_A          170 HFQDKTTVFAGQSGVGKSSLLNAISP  195 (307)
T ss_dssp             GGTTSEEEEEESHHHHHHHHHHHHCC
T ss_pred             hcCCCEEEEECCCCCCHHHHHHHhcc
Confidence            56789999999999999999987763

>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*

Probab=95.04  E-value=0.06  Score=54.12  Aligned_cols=133  Identities=17%  Similarity=0.162  Sum_probs=67.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh--c-cC--chh---hcccchHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA--S-SF--PEI---FHSKGMAQ  172 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~--~-~~--~~~---~~~~~~~~  172 (357)
                      .|.-++|+||+|+|||..+...+......  .   +.+++|+.-....-.+....+..  . ..  ...   ...... .
T Consensus        38 ~~~~~lv~apTGsGKT~~~~l~il~~~~~--~---~~~~l~i~P~raLa~q~~~~~~~l~~~g~~v~~~~G~~~~~~~-~  111 (720)
T 2zj8_A           38 EGKNALISIPTASGKTLIAEIAMVHRILT--Q---GGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDE-W  111 (720)
T ss_dssp             GTCEEEEECCGGGCHHHHHHHHHHHHHHH--H---CSEEEEECSSGGGHHHHHHHTGGGGGGTCCEEEECSCSSCCCG-G
T ss_pred             CCCcEEEEcCCccHHHHHHHHHHHHHHHh--C---CCEEEEEcCcHHHHHHHHHHHHHHHhcCCEEEEecCCCCcccc-c
Confidence            35789999999999999886666544431  1   37899987543333333333210  0 00  000   000000 0


Q ss_pred             HhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEe
Q 035774          173 EMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       173 ~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                      .....+.+.   +++.+..++..-  ...-.++++||||.+..+...      .|...+..++..++    . ++.+|++
T Consensus       112 ~~~~~Iiv~---Tpe~l~~~~~~~--~~~l~~~~~vIiDE~H~l~~~------~r~~~~~~ll~~l~----~-~~~ii~l  175 (720)
T 2zj8_A          112 LGKYDIIIA---TAEKFDSLLRHG--SSWIKDVKILVADEIHLIGSR------DRGATLEVILAHML----G-KAQIIGL  175 (720)
T ss_dssp             GGGCSEEEE---CHHHHHHHHHHT--CTTGGGEEEEEEETGGGGGCT------TTHHHHHHHHHHHB----T-TBEEEEE
T ss_pred             cCCCCEEEE---CHHHHHHHHHcC--hhhhhcCCEEEEECCcccCCC------cccHHHHHHHHHhh----c-CCeEEEE
Confidence            001233333   344444433321  111236899999999977432      24455555555554    1 6666666


Q ss_pred             ccc
Q 035774          253 NQV  255 (357)
Q Consensus       253 ~q~  255 (357)
                      +-.
T Consensus       176 SAT  178 (720)
T 2zj8_A          176 SAT  178 (720)
T ss_dssp             ECC
T ss_pred             cCC
Confidence            543

>1g3q_A MIND ATPase, cell division inhibitor; alpha-beta-alpha layered, protein-ADP complex, cell cycle, hydrolase; HET: ADP; 2.00A {Pyrococcus furiosus} SCOP: c.37.1.10 PDB: 1g3r_A* 1ion_A*

Probab=95.04  E-value=0.021  Score=48.63  Aligned_cols=37  Identities=27%  Similarity=0.345  Sum_probs=30.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+..+..|+|||+++.++|...+..      +.+|++||.+.
T Consensus         5 i~v~s~kgGvGKTt~a~~LA~~la~~------g~~VlliD~D~   41 (237)
T 1g3q_A            5 ISIVSGKGGTGKTTVTANLSVALGDR------GRKVLAVDGDL   41 (237)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCT
T ss_pred             EEEecCCCCCCHHHHHHHHHHHHHhc------CCeEEEEeCCC
Confidence            34456788999999999999988752      58999999975

>1gtv_A TMK, thymidylate kinase; transferase, transferase (ATP:TMP phosphotransferase); HET: TYD TMP; 1.55A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1g3u_A* 1gsi_A* 1mrn_A* 1mrs_A* 1n5i_A* 1n5j_A* 1n5k_A* 1n5l_A* 1w2g_A* 1w2h_A*

Probab=95.03  E-value=0.0072  Score=50.71  Aligned_cols=24  Identities=29%  Similarity=0.328  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++.|.|++||||||++..++...-
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            689999999999999999987653

>2ph1_A Nucleotide-binding protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; 2.70A {Archaeoglobus fulgidus dsm 4304} PDB: 3kb1_A*

Probab=95.03  E-value=0.021  Score=49.69  Aligned_cols=39  Identities=21%  Similarity=0.209  Sum_probs=32.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      +.+..+..|+||||++.++|...+..      +.+|++||++...
T Consensus        21 I~v~s~kGGvGKTT~a~nLA~~la~~------G~~VlliD~D~~~   59 (262)
T 2ph1_A           21 IAVMSGKGGVGKSTVTALLAVHYARQ------GKKVGILDADFLG   59 (262)
T ss_dssp             EEEECSSSCTTHHHHHHHHHHHHHHT------TCCEEEEECCSSC
T ss_pred             EEEEcCCCCCCHHHHHHHHHHHHHHC------CCeEEEEeCCCCC
Confidence            55567888999999999999988752      5899999998654

>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=95.03  E-value=0.57  Score=38.25  Aligned_cols=23  Identities=26%  Similarity=0.445  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -++|.|++|+|||+|+..+....
T Consensus        16 ki~v~G~~~~GKSsli~~l~~~~   38 (206)
T 2bov_A           16 KVIMVGSGGVGKSALTLQFMYDE   38 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999988654

>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=95.00  E-value=0.028  Score=47.42  Aligned_cols=38  Identities=24%  Similarity=0.142  Sum_probs=28.8

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      .+|.++.|.|++|+||||++..++.....      .+.+|+...
T Consensus         4 m~g~~i~~eG~~gsGKsT~~~~l~~~l~~------~~~~v~~~~   41 (213)
T 4edh_A            4 MTGLFVTLEGPEGAGKSTNRDYLAERLRE------RGIEVQLTR   41 (213)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHHHT------TTCCEEEEE
T ss_pred             CCceEEEEEcCCCCCHHHHHHHHHHHHHH------cCCCccccc
Confidence            46889999999999999999998876642      135665443

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=95.00  E-value=0.026  Score=50.91  Aligned_cols=25  Identities=28%  Similarity=0.139  Sum_probs=21.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |.-++|+|+||+|||+++..++...
T Consensus        46 ~~~vll~G~pGtGKT~la~~la~~~   70 (331)
T 2r44_A           46 GGHILLEGVPGLAKTLSVNTLAKTM   70 (331)
T ss_dssp             TCCEEEESCCCHHHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHh
Confidence            3468999999999999999988754

>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=94.97  E-value=0.016  Score=48.10  Aligned_cols=23  Identities=22%  Similarity=0.426  Sum_probs=20.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ..++.|+|++||||||++..++.
T Consensus         8 ~~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            8 PIIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999998875

>3cwq_A Para family chromosome partitioning protein; alpha-beta protein, structural genomics, PSI-2, protein STRU initiative; HET: ADP; 2.47A {Synechocystis SP}

Probab=94.97  E-value=0.027  Score=47.26  Aligned_cols=38  Identities=29%  Similarity=0.297  Sum_probs=31.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      +.+..+..|+||||++.++|...+..      + +|+.||++...
T Consensus         3 I~v~s~KGGvGKTT~a~~LA~~la~~------g-~VlliD~D~q~   40 (209)
T 3cwq_A            3 ITVASFKGGVGKTTTAVHLSAYLALQ------G-ETLLIDGDPNR   40 (209)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHTT------S-CEEEEEECTTC
T ss_pred             EEEEcCCCCCcHHHHHHHHHHHHHhc------C-CEEEEECCCCC
Confidence            45567899999999999999988752      5 89999998643

>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=94.92  E-value=0.018  Score=51.34  Aligned_cols=25  Identities=28%  Similarity=0.489  Sum_probs=22.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..+++|+||+|+|||+|+..++...
T Consensus        10 ~~~i~i~GptgsGKt~la~~La~~~   34 (316)
T 3foz_A           10 PKAIFLMGPTASGKTALAIELRKIL   34 (316)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECCCccCHHHHHHHHHHhC
Confidence            4689999999999999999998653

>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=94.90  E-value=0.017  Score=50.12  Aligned_cols=43  Identities=19%  Similarity=0.275  Sum_probs=29.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      -++.|+|++||||||++..++...-.+.-. ..+..+++++++.
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~lg~~~~d-~~~~~~~~i~~D~   65 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLLGQNEVD-YRQKQVVILSQDS   65 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTGGGSC-GGGCSEEEEEGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhhhhccc-ccCCceEEEecCc
Confidence            489999999999999999888753211000 0124577888865

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.89  E-value=0.014  Score=51.87  Aligned_cols=41  Identities=10%  Similarity=0.122  Sum_probs=27.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      ++-++.|+|++||||||++..++...-.      .+..+.+|+++.-
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~~lg~------~~~~~~vI~~D~~   44 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQIFRR------EGVKAVSIEGDAF   44 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHHHHHH------HTCCEEEEEGGGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHhh------cCCCeeEeecchh
Confidence            3458999999999999999998864311      1245778887753

>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=94.89  E-value=0.017  Score=51.63  Aligned_cols=24  Identities=29%  Similarity=0.469  Sum_probs=21.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+++|+||+|+|||+|+..++..
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~~   26 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAKR   26 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHT
T ss_pred             CcEEEEECCCcCCHHHHHHHHHHh
Confidence            458999999999999999999864

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=94.88  E-value=0.016  Score=52.06  Aligned_cols=24  Identities=29%  Similarity=0.447  Sum_probs=21.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+++|+|++|+|||+++..++...
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l   29 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADAL   29 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            489999999999999999998653

>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=94.87  E-value=0.022  Score=50.78  Aligned_cols=23  Identities=35%  Similarity=0.417  Sum_probs=20.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+||||+|||+++..++....
T Consensus        41 ~ll~G~~G~GKt~la~~l~~~l~   63 (319)
T 2chq_A           41 LLFSGPPGTGKTATAIALARDLF   63 (319)
T ss_dssp             EEEESSSSSSHHHHHHHHHHHHH
T ss_pred             EEEECcCCcCHHHHHHHHHHHhc
Confidence            89999999999999999988753

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=94.87  E-value=0.017  Score=46.84  Aligned_cols=26  Identities=23%  Similarity=0.210  Sum_probs=22.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .|.-++|.|+||+|||++++.++...
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~rG   40 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALIDRG   40 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHHTT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHcC
Confidence            36679999999999999999998753

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.84  E-value=0.018  Score=49.32  Aligned_cols=28  Identities=18%  Similarity=0.170  Sum_probs=23.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..+|.++.|.|++||||||++..++...
T Consensus        13 ~~~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           13 KMKTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             -CCCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4678899999999999999999887643

>3ea0_A ATPase, para family; alpha-beta-alpha sandwich, structural genomics, PSI-2, prote structure initiative; HET: ATP; 2.20A {Chlorobium tepidum}

Probab=94.84  E-value=0.036  Score=47.41  Aligned_cols=41  Identities=15%  Similarity=0.150  Sum_probs=31.6

Q ss_pred             CcEE-EEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          102 GVVT-ELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       102 G~l~-~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +.++ +..+..|+||||++.++|...+..  .   +.+|++||++..
T Consensus         4 ~~vI~v~s~kGGvGKTt~a~~LA~~la~~--~---g~~VlliD~D~~   45 (245)
T 3ea0_A            4 KRVFGFVSAKGGDGGSCIAANFAFALSQE--P---DIHVLAVDISLP   45 (245)
T ss_dssp             CEEEEEEESSTTSSHHHHHHHHHHHHTTS--T---TCCEEEEECCTT
T ss_pred             CeEEEEECCCCCcchHHHHHHHHHHHHhC--c---CCCEEEEECCCC
Confidence            3444 445778999999999999988742  1   489999999854

>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=94.83  E-value=0.016  Score=51.95  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=21.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+||||+|||+++..++....
T Consensus        49 ~ll~G~~G~GKT~la~~l~~~l~   71 (327)
T 1iqp_A           49 LLFAGPPGVGKTTAALALARELF   71 (327)
T ss_dssp             EEEESCTTSSHHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHhc
Confidence            89999999999999999998753

>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=94.82  E-value=0.012  Score=52.55  Aligned_cols=33  Identities=18%  Similarity=0.339  Sum_probs=26.2

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+|+++.  +..|+++.|.|+||+|||||+..++.
T Consensus       159 gv~~lf~--~l~geiv~l~G~sG~GKSTll~~l~g  191 (301)
T 1u0l_A          159 GIEELKE--YLKGKISTMAGLSGVGKSSLLNAINP  191 (301)
T ss_dssp             THHHHHH--HHSSSEEEEECSTTSSHHHHHHHHST
T ss_pred             CHHHHHH--HhcCCeEEEECCCCCcHHHHHHHhcc
Confidence            3555554  55688999999999999999987763

>3la6_A Tyrosine-protein kinase WZC; P-loop protein, nucleotide binding domain, walker A motif, B protein kinase, oligomerization; HET: ADP; 3.20A {Escherichia coli}

Probab=94.82  E-value=0.033  Score=49.29  Aligned_cols=39  Identities=21%  Similarity=0.276  Sum_probs=31.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      -+.+..+.+|.|||+++.++|...+..      +.+|++||++..
T Consensus        94 vI~vts~kgG~GKTtva~nLA~~lA~~------G~rVLLID~D~~  132 (286)
T 3la6_A           94 VLMMTGVSPSIGMTFVCANLAAVISQT------NKRVLLIDCDMR  132 (286)
T ss_dssp             EEEEEESSSSSSHHHHHHHHHHHHHTT------TCCEEEEECCTT
T ss_pred             EEEEECCCCCCcHHHHHHHHHHHHHhC------CCCEEEEeccCC
Confidence            344555678999999999999988852      589999999864

>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=94.81  E-value=0.016  Score=48.75  Aligned_cols=23  Identities=17%  Similarity=0.017  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|+|||||||++..++...
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999998754

>3q9l_A Septum site-determining protein MIND; ATPase, bacterial cell division inhibitor, MINC, MINE, cell hydrolase; HET: ATP; 2.34A {Escherichia coli} PDB: 3r9i_A* 3r9j_A*

Probab=94.81  E-value=0.026  Score=48.77  Aligned_cols=37  Identities=22%  Similarity=0.219  Sum_probs=30.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.+..+..|+||||++.++|...+..      +.+|++||++.
T Consensus         5 i~v~s~kgGvGKTt~a~~LA~~la~~------g~~VlliD~D~   41 (260)
T 3q9l_A            5 IVVTSGKGGVGKTTSSAAIATGLAQK------GKKTVVIDFAI   41 (260)
T ss_dssp             EEEECSSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCC
T ss_pred             EEEECCCCCCcHHHHHHHHHHHHHhC------CCcEEEEECCC
Confidence            34446788999999999999988752      58999999986

>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=94.80  E-value=0.015  Score=54.59  Aligned_cols=24  Identities=29%  Similarity=0.307  Sum_probs=21.5

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ...+++|+|+|||||||++..++.
T Consensus       257 ~~~lIil~G~pGSGKSTla~~L~~  280 (416)
T 3zvl_A          257 NPEVVVAVGFPGAGKSTFIQEHLV  280 (416)
T ss_dssp             SCCEEEEESCTTSSHHHHHHHHTG
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999998874

>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=94.79  E-value=0.017  Score=51.42  Aligned_cols=23  Identities=17%  Similarity=0.335  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .+++|.|+|||||||++..++..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~   25 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAK   25 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHh
Confidence            47999999999999999998863

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=94.77  E-value=0.0061  Score=47.93  Aligned_cols=21  Identities=19%  Similarity=0.113  Sum_probs=17.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 035774          103 VVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      .-++|.|+||+|||++|..++
T Consensus        28 ~~vll~G~~GtGKt~lA~~i~   48 (143)
T 3co5_A           28 SPVFLTGEAGSPFETVARYFH   48 (143)
T ss_dssp             SCEEEEEETTCCHHHHHGGGC
T ss_pred             CcEEEECCCCccHHHHHHHHH
Confidence            348899999999999988555

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=94.76  E-value=0.47  Score=38.41  Aligned_cols=23  Identities=26%  Similarity=0.388  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      =++|.|++|+|||+|+..++...
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            37899999999999999988644

>3k9g_A PF-32 protein; ssgcid, SBRI, decode biostructures, UW, NIH, niaid, borellia burgdorferi, plasmid partition protein, iodide; 2.25A {Borrelia burgdorferi} PDB: 3k9h_A

Probab=94.75  E-value=0.023  Score=49.53  Aligned_cols=40  Identities=20%  Similarity=0.331  Sum_probs=32.2

Q ss_pred             CcEEEE-EcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          102 GVVTEL-VGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       102 G~l~~I-~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      +.++.| .+..|+||||++.++|...+ .      +.+|++||++...
T Consensus        27 ~~vI~v~s~kGGvGKTT~a~~LA~~la-~------g~~VlliD~D~~~   67 (267)
T 3k9g_A           27 PKIITIASIKGGVGKSTSAIILATLLS-K------NNKVLLIDMDTQA   67 (267)
T ss_dssp             CEEEEECCSSSSSCHHHHHHHHHHHHT-T------TSCEEEEEECTTC
T ss_pred             CeEEEEEeCCCCchHHHHHHHHHHHHH-C------CCCEEEEECCCCC
Confidence            445554 78889999999999998887 3      5899999998643

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=94.73  E-value=0.035  Score=50.68  Aligned_cols=40  Identities=23%  Similarity=0.404  Sum_probs=29.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.+.++.|.|+||+|||||...++......      ++++..+..+
T Consensus        72 ~~~~~v~lvG~pgaGKSTLln~L~~~~~~~------~~~v~V~~~d  111 (349)
T 2www_A           72 PLAFRVGLSGPPGAGKSTFIEYFGKMLTER------GHKLSVLAVD  111 (349)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHHHHHT------TCCEEEEECC
T ss_pred             cCceEEEEEcCCCCCHHHHHHHHHHHhhhc------CCeEEEEeec
Confidence            457799999999999999999998654321      2455555544

>1wcv_1 SOJ, segregation protein; ATPase, bacterial, chromosome segregation; 1.6A {Thermus thermophilus} PDB: 2bej_A* 2bek_A*

Probab=94.70  E-value=0.025  Score=49.06  Aligned_cols=40  Identities=23%  Similarity=0.280  Sum_probs=32.2

Q ss_pred             CcEEEEE-cCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          102 GVVTELV-GPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       102 G~l~~I~-G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +.++.|+ +..|+||||++.++|...+..      +.+|++||++..
T Consensus         6 ~~vI~v~s~kGGvGKTt~a~~LA~~la~~------g~~VlliD~D~~   46 (257)
T 1wcv_1            6 VRRIALANQKGGVGKTTTAINLAAYLARL------GKRVLLVDLDPQ   46 (257)
T ss_dssp             CCEEEECCSSCCHHHHHHHHHHHHHHHHT------TCCEEEEECCTT
T ss_pred             CEEEEEEeCCCCchHHHHHHHHHHHHHHC------CCCEEEEECCCC
Confidence            4556664 788999999999999988752      589999999863

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=94.68  E-value=0.14  Score=47.99  Aligned_cols=38  Identities=21%  Similarity=0.027  Sum_probs=26.8

Q ss_pred             CCcEEEEEcCCCCcHHHHH-HHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFC-LKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~-~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +|+.+++.|++|+|||..+ ..++..+..   .   +..++|+.-
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~---~---g~~~lvl~P   39 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK---K---RLRTVILAP   39 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH---T---TCCEEEEES
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh---C---CCCEEEECc
Confidence            4788999999999999986 444434432   1   367888864

>2oze_A ORF delta'; para, walker type atpases, DNA segregation, PSM19035, plasmid, DNA binding protein; HET: AGS EPE; 1.83A {Streptococcus pyogenes}

Probab=94.67  E-value=0.025  Score=50.19  Aligned_cols=40  Identities=18%  Similarity=0.277  Sum_probs=32.2

Q ss_pred             CcEEEEEc---CCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          102 GVVTELVG---PAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       102 G~l~~I~G---~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      +.++.|++   ..|+||||++.++|...+..      +.+|+.||++..
T Consensus        34 ~~~i~v~~~s~KGGvGKTT~a~nLA~~la~~------G~rVlliD~D~q   76 (298)
T 2oze_A           34 NEAIVILNNYFKGGVGKSKLSTMFAYLTDKL------NLKVLMIDKDLQ   76 (298)
T ss_dssp             CSCEEEEECCSSSSSSHHHHHHHHHHHHHHT------TCCEEEEEECTT
T ss_pred             CcEEEEEeccCCCCchHHHHHHHHHHHHHhC------CCeEEEEeCCCC
Confidence            44566664   99999999999999887742      589999999864

>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=94.67  E-value=0.022  Score=47.29  Aligned_cols=24  Identities=33%  Similarity=0.491  Sum_probs=21.3

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      -.++.|+|.+||||||++..++..
T Consensus        12 ~~iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           12 HMVIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            458899999999999999988864

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=94.66  E-value=0.01  Score=57.11  Aligned_cols=39  Identities=23%  Similarity=0.371  Sum_probs=28.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++.|..+.|+|++||||||++..++...  +.     ..+.+.|..
T Consensus       257 v~~g~~i~I~GptGSGKTTlL~aL~~~i--~~-----~~giitied  295 (511)
T 2oap_1          257 IEHKFSAIVVGETASGKTTTLNAIMMFI--PP-----DAKVVSIED  295 (511)
T ss_dssp             HHTTCCEEEEESTTSSHHHHHHHHGGGS--CT-----TCCEEEEES
T ss_pred             HhCCCEEEEECCCCCCHHHHHHHHHhhC--CC-----CCCEEEEcC
Confidence            3678999999999999999998766433  21     345666653

>2jlq_A Serine protease subunit NS3; ribonucleoprotein, nucleotide-binding, viral nucleoprotein, endoplasmic reticulum, helicase, hydrolase; 1.67A {Dengue virus 4} PDB: 2jly_A* 2jls_A* 2jlu_A 2jlv_A* 2jlw_A 2jlx_A* 2jlz_A* 2jlr_A* 2bmf_A 2bhr_A

Probab=94.66  E-value=0.084  Score=49.90  Aligned_cols=39  Identities=18%  Similarity=0.049  Sum_probs=29.1

Q ss_pred             CCCcEEEEEcCCCCcHHH-HHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          100 PFGVVTELVGPAGTGKTQ-FCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~-l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ..++++++.|++|||||. ++..++......      +..++|+.-
T Consensus        17 ~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~------~~~~lvl~P   56 (451)
T 2jlq_A           17 RKKRLTIMDLHPGAGKTKRILPSIVREALLR------RLRTLILAP   56 (451)
T ss_dssp             STTCEEEECCCTTSSCCTTHHHHHHHHHHHT------TCCEEEEES
T ss_pred             hcCCeEEEECCCCCCHhhHHHHHHHHHHHhc------CCcEEEECC
Confidence            347889999999999999 577776655431      367888863

>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=94.57  E-value=0.0095  Score=49.70  Aligned_cols=32  Identities=19%  Similarity=0.274  Sum_probs=26.3

Q ss_pred             hhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           89 KGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        89 ~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      ..|+. +.  +.+|..+.|.|++|+|||||+..++
T Consensus        16 ~~l~~-~~--~~~~~~v~lvG~~g~GKSTLl~~l~   47 (210)
T 1pui_A           16 PDIRH-LP--SDTGIEVAFAGRSNAGKSSALNTLT   47 (210)
T ss_dssp             SSGGG-SS--CSCSEEEEEEECTTSSHHHHHTTTC
T ss_pred             CCHhH-CC--CCCCcEEEEECCCCCCHHHHHHHHh
Confidence            45555 43  7889999999999999999998765

>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=94.54  E-value=0.024  Score=47.09  Aligned_cols=23  Identities=17%  Similarity=0.466  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|++||||||++..++...
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            89999999999999999888643

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=94.53  E-value=0.023  Score=48.52  Aligned_cols=29  Identities=21%  Similarity=0.171  Sum_probs=21.6

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+.+|.++.|.|++|+||||++..++...
T Consensus        21 ~m~~g~~I~~eG~~GsGKsT~~~~l~~~l   49 (227)
T 3v9p_A           21 SMARGKFITFEGIDGAGKTTHLQWFCDRL   49 (227)
T ss_dssp             --CCCCEEEEECCC---CHHHHHHHHHHH
T ss_pred             cccCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35689999999999999999999888665

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=94.47  E-value=0.018  Score=55.94  Aligned_cols=42  Identities=21%  Similarity=0.267  Sum_probs=31.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|.++.|.|++||||||++..++...-.   .+  +..+.|++.+
T Consensus       366 ~~~G~iI~LiG~sGSGKSTLar~La~~L~~---~~--G~~i~~lDgD  407 (552)
T 3cr8_A          366 ERQGFTVFFTGLSGAGKSTLARALAARLME---MG--GRCVTLLDGD  407 (552)
T ss_dssp             GGSCEEEEEEESSCHHHHHHHHHHHHHHHT---TC--SSCEEEESSH
T ss_pred             cccceEEEEECCCCChHHHHHHHHHHhhcc---cC--CceEEEECCc
Confidence            568999999999999999999988876532   11  1346667763

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=94.43  E-value=0.14  Score=56.26  Aligned_cols=142  Identities=15%  Similarity=0.126  Sum_probs=76.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHh---ccCc----hhhcccch-H
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGA---SSFP----EIFHSKGM-A  171 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~---~~~~----~~~~~~~~-~  171 (357)
                      ..++-++|++|+|||||..+.-.+.+.....    .+.+++|+.--..+..++......   ....    ........ .
T Consensus       940 ~~~~nvlv~APTGSGKTliaelail~~l~~~----~~~kavyi~P~raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~ 1015 (1724)
T 4f92_B          940 NSDDNVFVGAPTGSGKTICAEFAILRMLLQS----SEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDL 1015 (1724)
T ss_dssp             SCCSCEEEECCTTSCCHHHHHHHHHHHHHHC----TTCCEEEECSCHHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHHH
T ss_pred             cCCCcEEEEeCCCCCchHHHHHHHHHHHHhC----CCCEEEEEcChHHHHHHHHHHHHHHhchhcCCEEEEEECCCCcch
Confidence            3467899999999999998766665555421    246899997644333333332211   1000    00000000 0


Q ss_pred             HH-hhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHc--CCe
Q 035774          172 QE-MAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS--RIP  248 (357)
Q Consensus       172 ~~-~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~--~~~  248 (357)
                      .. ....+.+.   +++.+..++........-.++++||||.+..+-.       .|...+..++..|+.++...  ++-
T Consensus      1016 ~~~~~~~IiV~---TPEkld~llr~~~~~~~l~~v~lvViDE~H~l~d-------~rg~~le~il~rl~~i~~~~~~~~r 1085 (1724)
T 4f92_B         1016 KLLGKGNIIIS---TPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGG-------ENGPVLEVICSRMRYISSQIERPIR 1085 (1724)
T ss_dssp             HHHHHCSEEEE---CHHHHHHHHTTTTTCHHHHSCSEEEECCGGGGGS-------TTHHHHHHHHHHHHHHHHTTSSCCE
T ss_pred             hhcCCCCEEEE---CHHHHHHHHhCcccccccceeeEEEeechhhcCC-------CCCccHHHHHHHHHHHHhhcCCCce
Confidence            00 11234443   4444444332211100013699999999996631       14456667777788777643  566


Q ss_pred             EEEeccc
Q 035774          249 IVVTNQV  255 (357)
Q Consensus       249 vv~~~q~  255 (357)
                      +|+++-.
T Consensus      1086 iI~lSAT 1092 (1724)
T 4f92_B         1086 IVALSSS 1092 (1724)
T ss_dssp             EEEEESC
T ss_pred             EEEEeCC
Confidence            7776644

>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=94.34  E-value=0.024  Score=50.02  Aligned_cols=22  Identities=32%  Similarity=0.460  Sum_probs=20.2

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      ..++.|+|++||||||++..++
T Consensus        75 ~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           75 LYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHH
Confidence            4589999999999999999888

>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=94.29  E-value=0.2  Score=40.65  Aligned_cols=24  Identities=29%  Similarity=0.267  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      --++|.|++|+|||+|+..++...
T Consensus        23 ~ki~v~G~~~~GKSsli~~l~~~~   46 (188)
T 1zd9_A           23 MELTLVGLQYSGKTTFVNVIASGQ   46 (188)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHcCC
Confidence            357899999999999999998643

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=94.28  E-value=0.052  Score=45.56  Aligned_cols=37  Identities=16%  Similarity=0.135  Sum_probs=28.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      -.+.|.|.+|+|||||+..++.....       ..++..++.+.
T Consensus        31 ~~i~i~G~~g~GKTTl~~~l~~~~~~-------~~~~~~i~~d~   67 (221)
T 2wsm_A           31 VAVNIMGAIGSGKTLLIERTIERIGN-------EVKIGAMLGDV   67 (221)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTT-------TSCEEEEECSC
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhcc-------CCeEEEEecCC
Confidence            37899999999999999999977532       24566666654

>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=94.26  E-value=0.042  Score=53.69  Aligned_cols=38  Identities=24%  Similarity=0.111  Sum_probs=30.2

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.+++|.|+||+|||+++..++......      +.++++....
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~~------g~~Vl~~ApT  241 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAESL------GLEVGLCAPT  241 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHHT------TCCEEEEESS
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHhc------CCeEEEecCc
Confidence            5799999999999999999988766532      4678877653

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=94.24  E-value=0.018  Score=46.86  Aligned_cols=25  Identities=20%  Similarity=0.456  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .++.|.|++|||||||+..++....
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4789999999999999998887654

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=94.17  E-value=0.019  Score=57.31  Aligned_cols=43  Identities=9%  Similarity=0.132  Sum_probs=31.6

Q ss_pred             CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       204 ~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      +++++++|.-++-..         ......+...|++++++ +.|||+++|--
T Consensus       564 ~p~llllDEPt~~LD---------~~~~~~i~~~l~~l~~~-g~tvi~vtHd~  606 (670)
T 3ux8_A          564 GRTLYILDEPTTGLH---------VDDIARLLDVLHRLVDN-GDTVLVIEHNL  606 (670)
T ss_dssp             SCEEEEEESTTTTCC---------HHHHHHHHHHHHHHHHT-TCEEEEECCCH
T ss_pred             CCcEEEEeCCCCCCC---------HHHHHHHHHHHHHHHHC-CCEEEEEeCCH
Confidence            467999998775443         24556677788888765 99999998853

>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal helicase, DNA repair,, DNA binding protein/DNA complex; 3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2 c.37.1.19 c.37.1.19 PDB: 2p6u_A

Probab=94.16  E-value=0.076  Score=53.17  Aligned_cols=133  Identities=14%  Similarity=0.180  Sum_probs=68.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchh-hccc------chHHH-
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEI-FHSK------GMAQE-  173 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~-~~~~------~~~~~-  173 (357)
                      |.-++|+||+|+|||+.+...+......      +.+++|+.--..+-.+..... . .+... ....      ..... 
T Consensus        40 ~~~~lv~apTGsGKT~~~~l~il~~~~~------~~~~l~i~P~r~La~q~~~~~-~-~~~~~g~~v~~~~G~~~~~~~~  111 (702)
T 2p6r_A           40 GKNLLLAMPTAAGKTLLAEMAMVREAIK------GGKSLYVVPLRALAGEKYESF-K-KWEKIGLRIGISTGDYESRDEH  111 (702)
T ss_dssp             CSCEEEECSSHHHHHHHHHHHHHHHHHT------TCCEEEEESSHHHHHHHHHHH-T-TTTTTTCCEEEECSSCBCCSSC
T ss_pred             CCcEEEEcCCccHHHHHHHHHHHHHHHh------CCcEEEEeCcHHHHHHHHHHH-H-HHHhcCCEEEEEeCCCCcchhh
Confidence            5789999999999999987777665432      368899874322222222222 1 11000 0000      00000 


Q ss_pred             h-hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEe
Q 035774          174 M-AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       174 ~-~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                      . ...+.+.   +++.+..++..-...  -.++++||||.+..+...      .|...+..++..++.+  ..++-+|++
T Consensus       112 ~~~~~Iiv~---Tpe~l~~~l~~~~~~--l~~~~~vIiDE~H~l~~~------~r~~~~~~ll~~l~~~--~~~~~ii~l  178 (702)
T 2p6r_A          112 LGDCDIIVT---TSEKADSLIRNRASW--IKAVSCLVVDEIHLLDSE------KRGATLEILVTKMRRM--NKALRVIGL  178 (702)
T ss_dssp             STTCSEEEE---EHHHHHHHHHTTCSG--GGGCCEEEETTGGGGGCT------TTHHHHHHHHHHHHHH--CTTCEEEEE
T ss_pred             ccCCCEEEE---CHHHHHHHHHcChhH--HhhcCEEEEeeeeecCCC------CcccHHHHHHHHHHhc--CcCceEEEE
Confidence            0 1123332   344444333321001  236899999999977432      2445566666666543  235667766


Q ss_pred             ccc
Q 035774          253 NQV  255 (357)
Q Consensus       253 ~q~  255 (357)
                      +-.
T Consensus       179 SAT  181 (702)
T 2p6r_A          179 SAT  181 (702)
T ss_dssp             ECC
T ss_pred             CCC
Confidence            543

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.15  E-value=0.031  Score=47.93  Aligned_cols=26  Identities=19%  Similarity=0.110  Sum_probs=22.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +|.++.|.|.+|+||||++..++...
T Consensus         1 ~~~~i~~~G~~g~GKtt~~~~l~~~l   26 (241)
T 2ocp_A            1 GPRRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHc
Confidence            36789999999999999999988764

>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=94.13  E-value=0.035  Score=50.74  Aligned_cols=25  Identities=24%  Similarity=0.187  Sum_probs=22.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ..++|+|+||+|||+++..++....
T Consensus        39 ~~~ll~G~~G~GKT~la~~la~~l~   63 (373)
T 1jr3_A           39 HAYLFSGTRGVGKTSIARLLAKGLN   63 (373)
T ss_dssp             SEEEEESCTTSSHHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4789999999999999999987664

>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=94.13  E-value=0.085  Score=44.16  Aligned_cols=23  Identities=30%  Similarity=0.225  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      =++|.|++|+|||+|+..++...
T Consensus        29 ki~vvG~~~vGKSsL~~~l~~~~   51 (214)
T 3q3j_B           29 KLVLVGDVQCGKTAMLQVLAKDC   51 (214)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            48899999999999999998654

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=94.12  E-value=0.037  Score=46.79  Aligned_cols=27  Identities=30%  Similarity=0.220  Sum_probs=24.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+|.++.|.|++|+||||.+..++...
T Consensus         3 ~~g~~i~~eG~~g~GKst~~~~l~~~l   29 (216)
T 3tmk_A            3 GRGKLILIEGLDRTGKTTQCNILYKKL   29 (216)
T ss_dssp             CCCCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            468899999999999999999988765

>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=94.11  E-value=0.04  Score=52.27  Aligned_cols=37  Identities=27%  Similarity=0.370  Sum_probs=28.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .++|.|+||+|||+++..++......   |  ...++.+...
T Consensus        47 ~~li~G~aGTGKT~ll~~~~~~l~~~---~--~~~il~~a~T   83 (459)
T 3upu_A           47 HVTINGPAGTGATTLTKFIIEALIST---G--ETGIILAAPT   83 (459)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT---T--CCCEEEEESS
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhc---C--CceEEEecCc
Confidence            99999999999999999998877642   1  1356666554

>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=94.06  E-value=0.036  Score=47.55  Aligned_cols=31  Identities=13%  Similarity=0.047  Sum_probs=24.2

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +.-.+|.++.|.|++|+||||++..++....
T Consensus        22 ~~~~~~~~i~~eG~~GsGKsT~~~~l~~~l~   52 (236)
T 3lv8_A           22 SNAMNAKFIVIEGLEGAGKSTAIQVVVETLQ   52 (236)
T ss_dssp             ----CCCEEEEEESTTSCHHHHHHHHHHHHH
T ss_pred             cCCCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3445688999999999999999999887654

>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=94.04  E-value=0.047  Score=51.34  Aligned_cols=22  Identities=41%  Similarity=0.747  Sum_probs=20.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++++||||+|||+++..+|...
T Consensus        53 iLl~GppGtGKT~lar~lA~~l   74 (444)
T 1g41_A           53 ILMIGPTGVGKTEIARRLAKLA   74 (444)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEcCCCCCHHHHHHHHHHHc
Confidence            8899999999999999998765

>3qxc_A Dethiobiotin synthetase; DTBS, structural genomics, ATP BIND biology, protein structure initiative, midwest center for S genomics, MCSG; HET: ATP; 1.34A {Helicobacter pylori} PDB: 3mle_A* 3qxh_A* 3qxj_A* 3qxs_A* 3qxx_A* 3qy0_A* 2qmo_A

Probab=94.04  E-value=1  Score=38.54  Aligned_cols=49  Identities=14%  Similarity=0.026  Sum_probs=27.6

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      .-++|-+.|-.+.      ..+++..-.+|+|||+++..++......      +.+|.||-
T Consensus         9 ~~~~~~~~~~~m~------k~i~ItgT~t~vGKT~vs~gL~~~L~~~------G~~V~~fK   57 (242)
T 3qxc_A            9 HHSSGRENLYFQG------HMLFISATNTNAGKTTCARLLAQYCNAC------GVKTILLK   57 (242)
T ss_dssp             ----------CCC------EEEEEEESSTTSSHHHHHHHHHHHHHHT------TCCEEEEC
T ss_pred             cccchhhHHhhcC------cEEEEEeCCCCCcHHHHHHHHHHHHHhC------CCceEEEe
Confidence            3455665554431      2345555569999999999999877642      57888885

>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=94.04  E-value=0.11  Score=52.74  Aligned_cols=29  Identities=24%  Similarity=0.344  Sum_probs=23.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +..|+.++|.|++|+|||+++-.++....
T Consensus       106 l~~~~~vii~gpTGSGKTtllp~ll~~~~  134 (773)
T 2xau_A          106 YQNNQIMVFVGETGSGKTTQIPQFVLFDE  134 (773)
T ss_dssp             HHHCSEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             HhCCCeEEEECCCCCCHHHHHHHHHHHhc
Confidence            45578999999999999997777765443

>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation, ATP-binding, cytoplasm, mitochondrion, nucleotide-binding, nucleus; 2.95A {Saccharomyces cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*

Probab=93.99  E-value=0.034  Score=51.49  Aligned_cols=24  Identities=29%  Similarity=0.494  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+++|+||+|+|||+|+..++...
T Consensus         3 ~~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHHHC
Confidence            478999999999999999999764

>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=93.97  E-value=0.019  Score=52.08  Aligned_cols=22  Identities=32%  Similarity=0.404  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|+|+||+|||+++..++...
T Consensus        48 vLl~G~~GtGKT~la~~la~~~   69 (350)
T 1g8p_A           48 VLVFGDRGTGKSTAVRALAALL   69 (350)
T ss_dssp             EEEECCGGGCTTHHHHHHHHHS
T ss_pred             EEEECCCCccHHHHHHHHHHhC
Confidence            9999999999999999988754

>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=93.97  E-value=0.093  Score=43.48  Aligned_cols=25  Identities=24%  Similarity=0.291  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      --++|.|++|+|||+|+..++.+..
T Consensus        31 ~ki~vvG~~~~GKSsLi~~l~~~~~   55 (204)
T 4gzl_A           31 IKCVVVGDGAVGKTCLLISYTTNAF   55 (204)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSCC
T ss_pred             EEEEEECcCCCCHHHHHHHHHhCCC
Confidence            3578999999999999999886544

>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=93.97  E-value=0.02  Score=53.50  Aligned_cols=21  Identities=29%  Similarity=0.450  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++.|.|++|+|||||+..++.
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            999999999999999987764

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=93.95  E-value=0.037  Score=50.36  Aligned_cols=27  Identities=26%  Similarity=0.348  Sum_probs=22.0

Q ss_pred             CCCcE--EEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVV--TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l--~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+|+.  +.|.|+||+||||++..++...
T Consensus        20 ~~g~~~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A           20 EDNYRVCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             TTCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ccCCeeEEEEECCCCCcHHHHHHHHHHHh
Confidence            34555  8999999999999998887654

>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=93.93  E-value=0.033  Score=44.92  Aligned_cols=24  Identities=21%  Similarity=0.331  Sum_probs=20.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +|.-+.|.|+||+|||+|...++.
T Consensus         3 ~~~ki~ivG~~g~GKStLl~~l~~   26 (172)
T 2gj8_A            3 HGMKVVIAGRPNAGKSSLLNALAG   26 (172)
T ss_dssp             -CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            567799999999999999998874

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=93.88  E-value=0.029  Score=57.90  Aligned_cols=26  Identities=19%  Similarity=0.326  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +++|+++.|.|++|+|||||+.-++.
T Consensus       458 I~~Ge~v~LiGpNGsGKSTLLk~Lag  483 (986)
T 2iw3_A          458 LKRARRYGICGPNGCGKSTLMRAIAN  483 (986)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHH
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999998873

>3qf7_A RAD50; ABC-ATPase, ATPase, hydrolase; HET: ANP; 1.90A {Thermotoga maritima} PDB: 3qg5_A 3tho_A*

Probab=93.87  E-value=0.038  Score=50.75  Aligned_cols=43  Identities=14%  Similarity=0.074  Sum_probs=29.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-..         ......++..|+++.+ .|.+||+++|.
T Consensus       302 ~~p~~lllDEpt~~LD---------~~~~~~~~~~l~~l~~-~g~tvi~itH~  344 (365)
T 3qf7_A          302 GRLDAFFIDEGFSSLD---------TENKEKIASVLKELER-LNKVIVFITHD  344 (365)
T ss_dssp             TTCCEEEEESCCTTSC---------HHHHHHHHHHHHGGGG-SSSEEEEEESC
T ss_pred             CCCCEEEEeCCCccCC---------HHHHHHHHHHHHHHHh-CCCEEEEEecc
Confidence            4688888887665432         2445566777777754 48899888875

>3fgn_A Dethiobiotin synthetase; biotin biosynthesis, BIOD, ATP-BIND ligase, magnesium, nucleotide-binding; 1.85A {Mycobacterium tuberculosis} PDB: 3fmf_A* 3fmi_A* 3fpa_A*

Probab=93.75  E-value=0.48  Score=40.87  Aligned_cols=54  Identities=20%  Similarity=0.225  Sum_probs=28.9

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      .-++|..+--+.+.+ -....+++-.-.+|+|||+++..++......      +.+|.||-
T Consensus         9 ~~~~~~~~~~~~~~~-~~m~~i~Itgt~t~vGKT~vt~gL~~~l~~~------G~~V~~fK   62 (251)
T 3fgn_A            9 HHSSGLQGTENLYFQ-SHMTILVVTGTGTGVGKTVVCAALASAARQA------GIDVAVCK   62 (251)
T ss_dssp             -------------CC-SSCEEEEEEESSTTSCHHHHHHHHHHHHHHT------TCCEEEEE
T ss_pred             cccchhhHHHHHhcc-cCCCEEEEEeCCCCCcHHHHHHHHHHHHHHC------CCeEEEEe
Confidence            345566554444443 2233455556677999999999999877642      57888885

>3pg5_A Uncharacterized protein; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; 3.30A {Corynebacterium diphtheriae}

Probab=93.73  E-value=0.031  Score=51.25  Aligned_cols=39  Identities=23%  Similarity=0.414  Sum_probs=31.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      +.+..+..|+||||++.++|...+..      +.+|++||++...
T Consensus         4 Iav~s~KGGvGKTT~a~nLA~~LA~~------G~rVLlID~D~q~   42 (361)
T 3pg5_A            4 ISFFNNKGGVGKTTLSTNVAHYFALQ------GKRVLYVDCDPQC   42 (361)
T ss_dssp             EEBCCSSCCHHHHHHHHHHHHHHHHT------TCCEEEEECCTTC
T ss_pred             EEEEcCCCCCcHHHHHHHHHHHHHhC------CCcEEEEEcCCCC
Confidence            34455889999999999999988752      5899999998643

>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=93.73  E-value=0.2  Score=40.74  Aligned_cols=24  Identities=29%  Similarity=0.232  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      --++|.|++|+|||+|+..++...
T Consensus        22 ~ki~v~G~~~~GKSsli~~l~~~~   45 (190)
T 2h57_A           22 VHVLCLGLDNSGKTTIINKLKPSN   45 (190)
T ss_dssp             EEEEEEECTTSSHHHHHHHTSCGG
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCC
Confidence            358899999999999999887554

>1oix_A RAS-related protein RAB-11A; small G protein, intracellular trafficking, GTP-binding, lipoprotein, prenylation, protein transport; HET: GDP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1oiw_A* 1oiv_A* 3rwo_B* 3rwm_B*

Probab=93.72  E-value=0.033  Score=45.84  Aligned_cols=23  Identities=22%  Similarity=0.414  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|++|+|||+|+..++...
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            68999999999999999888643

>1f2t_A RAD50 ABC-ATPase; DNA double-strand break repair, replication; 1.60A {Pyrococcus furiosus} SCOP: c.37.1.12 PDB: 1f2u_A* 1us8_A*

Probab=93.71  E-value=0.047  Score=43.20  Aligned_cols=22  Identities=18%  Similarity=0.421  Sum_probs=19.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHH
Q 035774          103 VVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+++|+||+|+|||++.-.+..
T Consensus        24 g~~~I~G~NGsGKStil~Ai~~   45 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDAILV   45 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3999999999999999876654

>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=93.71  E-value=0.036  Score=45.79  Aligned_cols=22  Identities=23%  Similarity=0.433  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      -+.|.|++|+|||+|+..++..
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            4789999999999999988864

>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=93.69  E-value=0.3  Score=39.58  Aligned_cols=20  Identities=30%  Similarity=0.243  Sum_probs=16.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|++|+|||+|+ +++..
T Consensus        17 i~vvG~~~~GKssL~-~~l~~   36 (198)
T 3t1o_A           17 IVYYGPGLSGKTTNL-KWIYS   36 (198)
T ss_dssp             EEEECSTTSSHHHHH-HHHHH
T ss_pred             EEEECCCCCCHHHHH-HHHHh
Confidence            789999999999999 55543

>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=93.69  E-value=0.04  Score=52.37  Aligned_cols=26  Identities=27%  Similarity=0.289  Sum_probs=23.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++ +++.|.||+|+|||||+..++..
T Consensus        27 i~~-e~~~liG~nGsGKSTLl~~l~Gl   52 (483)
T 3euj_A           27 FDE-LVTTLSGGNGAGKSTTMAGFVTA   52 (483)
T ss_dssp             CCS-SEEEEECCTTSSHHHHHHHHHHH
T ss_pred             Ecc-ceEEEECCCCCcHHHHHHHHhcC
Confidence            778 99999999999999999977754

>1byi_A Dethiobiotin synthase; biotin synthesis, cyclo-ligase, ligase; 0.97A {Escherichia coli} SCOP: c.37.1.10 PDB: 1bs1_A* 1a82_A 1dad_A* 1dae_A* 1daf_A* 1dag_A* 1dah_A* 1dai_A* 1dak_A* 1dam_A* 1dbs_A 1dts_A

Probab=93.68  E-value=0.063  Score=45.23  Aligned_cols=34  Identities=15%  Similarity=-0.142  Sum_probs=27.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      +.+..+.+|+|||+++.++|...+..      +.+|++++
T Consensus         4 I~v~s~kgGvGKTt~a~nLa~~la~~------G~rVll~d   37 (224)
T 1byi_A            4 YFVTGTDTEVGKTVASCALLQAAKAA------GYRTAGYK   37 (224)
T ss_dssp             EEEEESSTTSCHHHHHHHHHHHHHHT------TCCEEEEC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC------CCCEEEEc
Confidence            44555579999999999999988752      57899987

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=93.66  E-value=0.07  Score=54.00  Aligned_cols=36  Identities=28%  Similarity=0.358  Sum_probs=27.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .++|+||||+|||++|..++.....      .+.+.+++++.
T Consensus       523 ~~Ll~Gp~GtGKT~lA~ala~~l~~------~~~~~i~i~~s  558 (758)
T 3pxi_A          523 SFIFLGPTGVGKTELARALAESIFG------DEESMIRIDMS  558 (758)
T ss_dssp             EEEEESCTTSSHHHHHHHHHHHHHS------CTTCEEEEEGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcC------CCcceEEEech
Confidence            6899999999999999999887642      13566666653

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.64  E-value=0.028  Score=55.35  Aligned_cols=28  Identities=25%  Similarity=0.281  Sum_probs=24.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +..|..++|.||||+|||+++..++...
T Consensus        57 i~~g~~vll~Gp~GtGKTtlar~ia~~l   84 (604)
T 3k1j_A           57 ANQKRHVLLIGEPGTGKSMLGQAMAELL   84 (604)
T ss_dssp             HHTTCCEEEECCTTSSHHHHHHHHHHTS
T ss_pred             ccCCCEEEEEeCCCCCHHHHHHHHhccC
Confidence            4566899999999999999999888643

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=93.63  E-value=0.89  Score=43.90  Aligned_cols=53  Identities=13%  Similarity=0.001  Sum_probs=30.9

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccC-CCCCCCeEEEEeCC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAH-YGGLDGGVIYIDVE  145 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~-~gg~~~~vl~i~~e  145 (357)
                      .++.++.|   .|.-+++.+|+|+|||...+-.+...+.... .++.+..++|+.-.
T Consensus       102 ~i~~~l~~---~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lil~Pt  155 (563)
T 3i5x_A          102 TIKPILSS---EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPT  155 (563)
T ss_dssp             HHHHHHSS---SSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECSS
T ss_pred             HHHHHhcC---CCCeEEEECCCCCCccHHHHHHHHHHHHhccccccCCeeEEEEcCc
Confidence            45555532   5778999999999999764443333332111 11112468888643

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.63  E-value=0.055  Score=45.98  Aligned_cols=40  Identities=20%  Similarity=0.162  Sum_probs=30.2

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhcc-ccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAAL-PAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~-~~~~gg~~~~vl~i~~e  145 (357)
                      .+|.++.|.|.+|+||||++..++..... .      +.+|+++.-|
T Consensus        19 ~~~~~i~~~G~~g~GKst~~~~l~~~l~~~~------g~~v~~~tre   59 (223)
T 3ld9_A           19 PGSMFITFEGIDGSGKTTQSHLLAEYLSEIY------GVNNVVLTRE   59 (223)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHHHHH------CGGGEEEEES
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhhcc------CceeeEeeeC
Confidence            46889999999999999999988876532 1      3567664444

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=93.61  E-value=0.04  Score=44.01  Aligned_cols=21  Identities=24%  Similarity=0.322  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+.|.|+||+|||+|+..++.
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~   25 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTG   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            578999999999999998874

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=93.60  E-value=0.12  Score=42.97  Aligned_cols=23  Identities=22%  Similarity=0.160  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -++|.|++|+|||+|+..++...
T Consensus        11 ki~i~G~~~~GKTsli~~l~~~~   33 (212)
T 2j0v_A           11 KCVTVGDGAVGKTCMLICYTSNK   33 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            47899999999999999888543

>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=93.56  E-value=0.071  Score=52.64  Aligned_cols=39  Identities=26%  Similarity=0.290  Sum_probs=29.7

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.+++|.||||+|||+++..++......     .+.++++....
T Consensus       195 ~~~~li~GppGTGKT~~~~~~i~~l~~~-----~~~~ilv~a~t  233 (624)
T 2gk6_A          195 RPLSLIQGPPGTGKTVTSATIVYHLARQ-----GNGPVLVCAPS  233 (624)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHTS-----SSCCEEEEESS
T ss_pred             CCCeEEECCCCCCHHHHHHHHHHHHHHc-----CCCeEEEEeCc
Confidence            4589999999999999999988776531     13567766654

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=93.53  E-value=0.052  Score=45.77  Aligned_cols=27  Identities=19%  Similarity=0.038  Sum_probs=23.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +|.++.|.|++|+||||.+..++....
T Consensus         2 ~g~~i~~eG~~gsGKsT~~~~l~~~l~   28 (213)
T 4tmk_A            2 RSKYIVIEGLEGAGKTTARNVVVETLE   28 (213)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999998887654

>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=93.51  E-value=0.089  Score=44.01  Aligned_cols=35  Identities=26%  Similarity=0.302  Sum_probs=27.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      |.++.|-|..||||||.+..++.....       +.+|++..
T Consensus         2 ~kFI~~EG~dGsGKsTq~~~L~~~L~~-------~~~v~~~~   36 (205)
T 4hlc_A            2 SAFITFEGPEGSGKTTVINEVYHRLVK-------DYDVIMTR   36 (205)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHTT-------TSCEEEEE
T ss_pred             CCEEEEECCCCCcHHHHHHHHHHHHHC-------CCCEEEee
Confidence            568999999999999999888876531       35666554

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=93.50  E-value=0.061  Score=50.54  Aligned_cols=38  Identities=21%  Similarity=0.275  Sum_probs=28.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..=+.|.|++|+|||+++..++.+.+.   +   +.+++.+|..
T Consensus        53 ~~h~~i~G~tGsGKs~~~~~li~~~~~---~---g~~viv~Dpk   90 (437)
T 1e9r_A           53 PRHLLVNGATGTGKSVLLRELAYTGLL---R---GDRMVIVDPN   90 (437)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHH---T---TCEEEEEEET
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHHHH---C---CCcEEEEeCC
Confidence            346899999999999998888877764   2   3566666654

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.48  E-value=0.039  Score=48.40  Aligned_cols=23  Identities=26%  Similarity=0.297  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|++|+|||||+..++...
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            47899999999999999888654

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=93.39  E-value=0.036  Score=45.13  Aligned_cols=20  Identities=35%  Similarity=0.509  Sum_probs=18.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.|.|++|+|||+|+..++.
T Consensus         5 v~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            5 LMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEESCTTSSHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            78999999999999998874

>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=93.31  E-value=0.047  Score=43.22  Aligned_cols=23  Identities=17%  Similarity=0.199  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+.|.|++|+|||+|+..++...
T Consensus         7 ~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            7 KMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            36889999999999999988643

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=93.26  E-value=0.049  Score=42.85  Aligned_cols=20  Identities=25%  Similarity=0.383  Sum_probs=18.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++|.|++|+|||+|+..++.
T Consensus         4 i~v~G~~~~GKSsli~~l~~   23 (161)
T 2dyk_A            4 VVIVGRPNVGKSSLFNRLLK   23 (161)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999998884

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.25  E-value=0.053  Score=45.70  Aligned_cols=24  Identities=29%  Similarity=0.335  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .+.|.|.+|+|||+|+.+++....
T Consensus        40 ~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           40 AFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHhc
Confidence            688889999999999999998754

>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=93.24  E-value=0.027  Score=49.09  Aligned_cols=26  Identities=23%  Similarity=0.197  Sum_probs=22.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .++.++.|.|.+|+||||++..++..
T Consensus        22 ~~~~~I~ieG~~GsGKST~~~~L~~~   47 (263)
T 1p5z_B           22 TRIKKISIEGNIAAGKSTFVNILKQL   47 (263)
T ss_dssp             -CCEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHh
Confidence            56789999999999999999877753

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=93.24  E-value=0.058  Score=51.29  Aligned_cols=27  Identities=26%  Similarity=0.256  Sum_probs=22.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ...-++|+|+||+|||+++..++....
T Consensus       200 ~~~~~LL~G~pG~GKT~la~~la~~l~  226 (468)
T 3pxg_A          200 TKNNPVLIGEPGVGKTAIAEGLAQQII  226 (468)
T ss_dssp             SSCEEEEESCTTTTTHHHHHHHHHHHH
T ss_pred             CCCCeEEECCCCCCHHHHHHHHHHHHH
Confidence            344568999999999999999998764

>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=93.23  E-value=0.038  Score=49.68  Aligned_cols=24  Identities=33%  Similarity=0.246  Sum_probs=21.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      =.++.|.|++|+|||||+..++..
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            358999999999999999988864

>2vf7_A UVRA2, excinuclease ABC, subunit A.; DNA-binding protein, nucleotide-binding, zinc-binding domain, SOS response, metal-binding; HET: ADP; 2.30A {Deinococcus radiodurans} PDB: 2vf8_A*

Probab=93.21  E-value=0.03  Score=56.94  Aligned_cols=26  Identities=23%  Similarity=0.455  Sum_probs=23.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ||+|.+++|+|.+|||||+|+...++
T Consensus        33 iP~~~l~viTGvSGSGKSSLafdtl~   58 (842)
T 2vf7_A           33 VPRDALVVFTGVSGSGKSSLAFGTLY   58 (842)
T ss_dssp             EESSSEEEEESSTTSSHHHHHTTTHH
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHH
Confidence            89999999999999999999986654

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=93.11  E-value=0.023  Score=54.49  Aligned_cols=26  Identities=27%  Similarity=0.405  Sum_probs=21.9

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .|.-++|+||||+|||++|..++...
T Consensus        40 ~~~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           40 SGESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             HTCEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             cCCeeEeecCchHHHHHHHHHHHHHH
Confidence            34578999999999999999888644

>1e69_A Chromosome segregation SMC protein; structural maintenance of chromosomes, coiled coil; 3.1A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.08  E-value=0.051  Score=48.91  Aligned_cols=25  Identities=32%  Similarity=0.518  Sum_probs=21.5

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+| ++.|.|++|+|||+|+--+..
T Consensus        22 ~~~g-~~~i~G~NGsGKS~ll~ai~~   46 (322)
T 1e69_A           22 FSDR-VTAIVGPNGSGKSNIIDAIKW   46 (322)
T ss_dssp             CCSS-EEEEECCTTTCSTHHHHHHHH
T ss_pred             cCCC-cEEEECCCCCcHHHHHHHHHH
Confidence            5667 999999999999999887663

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=93.03  E-value=0.059  Score=45.27  Aligned_cols=24  Identities=25%  Similarity=0.432  Sum_probs=20.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.++.|.|++|||||+++..++..
T Consensus         3 ~~~i~i~G~~gsGkst~~~~l~~~   26 (219)
T 2h92_A            3 AINIALDGPAAAGKSTIAKRVASE   26 (219)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHh
Confidence            357899999999999999988764

>2o5v_A DNA replication and repair protein RECF; ABC ATPase, walker A motif, P-loop, signature motif, replication/recombination complex; HET: DNA; 1.61A {Deinococcus radiodurans}

Probab=93.02  E-value=0.059  Score=49.30  Aligned_cols=25  Identities=40%  Similarity=0.553  Sum_probs=22.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+| ++.|.|++|+|||++...+..
T Consensus        24 ~~~g-~~~i~G~nG~GKttll~ai~~   48 (359)
T 2o5v_A           24 FPEG-VTGIYGENGAGKTNLLEAAYL   48 (359)
T ss_dssp             CCSE-EEEEECCTTSSHHHHHHHHHH
T ss_pred             EcCC-eEEEECCCCCChhHHHHHHHH
Confidence            6678 999999999999999887765

>1w1w_A Structural maintenance of chromosome 1; cohesin, chromosome segregation, cell adhesion, kleisin, MIT cell cycle; HET: ATG; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.12

Probab=92.99  E-value=0.062  Score=50.43  Aligned_cols=27  Identities=26%  Similarity=0.502  Sum_probs=23.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.+|.++.|.||+|+|||+|+..++..
T Consensus        23 ~~~~~~~~i~G~nG~GKstll~ai~~~   49 (430)
T 1w1w_A           23 FGESNFTSIIGPNGSGKSNMMDAISFV   49 (430)
T ss_dssp             CTTCSEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHHhh
Confidence            556889999999999999999877653

>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=92.94  E-value=0.058  Score=42.56  Aligned_cols=22  Identities=27%  Similarity=0.490  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.|.|++|+|||+|+..++...
T Consensus         7 i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            7 VIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCc
Confidence            6889999999999999988644

>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=92.93  E-value=0.057  Score=43.10  Aligned_cols=20  Identities=30%  Similarity=0.438  Sum_probs=18.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.|.|++|+|||+|+..++.
T Consensus         7 i~i~G~~~vGKSsl~~~l~~   26 (175)
T 2nzj_A            7 VVLLGDPGVGKTSLASLFAG   26 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCccHHHHHHHHhc
Confidence            78999999999999998874

>1x6v_B Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthethase 1; transferase, ATP sulfurylase, APS kinase, PAPS; HET: ADP; 1.75A {Homo sapiens} SCOP: b.122.1.3 c.26.1.5 c.37.1.4 PDB: 1xjq_B* 1xnj_B* 2qjf_A* 2ofx_A* 2ofw_A*

Probab=92.92  E-value=0.088  Score=51.69  Aligned_cols=37  Identities=24%  Similarity=0.247  Sum_probs=28.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      +|.++.|.|.|||||||++..++......      +.+++++|
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~~~------G~~~v~lD   87 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLVCH------GIPCYTLD   87 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEES
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHhc------CCeEEEec
Confidence            67899999999999999999998765311      24566665

>3igf_A ALL4481 protein; two-domained protein consisting of the N-terminal alpha-beta the C-terminal all beta domain., structural genomics; 2.00A {Nostoc SP}

Probab=92.89  E-value=0.058  Score=49.63  Aligned_cols=36  Identities=17%  Similarity=0.354  Sum_probs=31.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .++.+.|..|+||||++.++|...+..      +.+|++||+
T Consensus         3 ~i~~~~gkGG~GKTt~a~~la~~la~~------g~~vllvd~   38 (374)
T 3igf_A            3 LILTFLGKSGVARTKIAIAAAKLLASQ------GKRVLLAGL   38 (374)
T ss_dssp             EEEEEECSBHHHHHHHHHHHHHHHHHT------TCCEEEEEC
T ss_pred             EEEEEeCCCCCcHHHHHHHHHHHHHHC------CCCeEEEeC
Confidence            467899999999999999999988752      589999999

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=92.88  E-value=1.4  Score=42.89  Aligned_cols=52  Identities=13%  Similarity=0.001  Sum_probs=30.0

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccC-CCCCCCeEEEEeC
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAH-YGGLDGGVIYIDV  144 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~-~gg~~~~vl~i~~  144 (357)
                      .++.++.+   .|.-+++.+|+|+|||...+-.+...+.... .++.+..++++.-
T Consensus        51 ~i~~il~~---~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~~~~~~~~lvl~P  103 (579)
T 3sqw_A           51 TIKPILSS---EDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAP  103 (579)
T ss_dssp             HHHHHHCS---SSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTSSTTSCCEEEECS
T ss_pred             HHHHHHcc---CCCeEEEEcCCCcHHHHHHHHHHHHHHHhccccccCCCeEEEEcc
Confidence            34555533   4678899999999999754433333322111 1111346888764

>3pih_A Uvrabc system protein A; hydrolase, ABC ATPase, DNA repair, nucleotide excision repai hydrolase-DNA complex; HET: DNA; 2.90A {Thermotoga maritima}

Probab=92.87  E-value=0.05  Score=55.85  Aligned_cols=42  Identities=10%  Similarity=0.147  Sum_probs=31.0

Q ss_pred             CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       204 ~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      +++++|+|.-++-..         ......+...|+++++ .|.|||+++|-
T Consensus       826 ~p~LLILDEPTsGLD---------~~~~~~L~~lL~~L~~-~G~TVIvI~Hd  867 (916)
T 3pih_A          826 GRTLYILDEPTVGLH---------FEDVRKLVEVLHRLVD-RGNTVIVIEHN  867 (916)
T ss_dssp             SSEEEEEESTTTTCC---------HHHHHHHHHHHHHHHH-TTCEEEEECCC
T ss_pred             CCCEEEEECCCCCCC---------HHHHHHHHHHHHHHHh-cCCEEEEEeCC
Confidence            468999998775442         2556667788888865 48999999885

>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=92.86  E-value=0.06  Score=42.73  Aligned_cols=19  Identities=32%  Similarity=0.546  Sum_probs=17.5

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia  123 (357)
                      +.|.|++|+|||+|+..++
T Consensus         5 i~ivG~~~~GKSsli~~l~   23 (169)
T 3q85_A            5 VMLVGESGVGKSTLAGTFG   23 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            6899999999999999886

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=92.81  E-value=0.07  Score=52.03  Aligned_cols=41  Identities=20%  Similarity=0.199  Sum_probs=30.7

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.|.++.|.|.|||||||++..++......   |  +.++++++.+
T Consensus       394 q~~~~I~l~GlsGSGKSTiA~~La~~L~~~---G--~~~~~~lD~D  434 (573)
T 1m8p_A          394 TQGFTIFLTGYMNSGKDAIARALQVTLNQQ---G--GRSVSLLLGD  434 (573)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHH---C--SSCEEEEEHH
T ss_pred             ccceEEEeecCCCCCHHHHHHHHHHHhccc---C--CceEEEECcH
Confidence            357899999999999999999998765321   1  1457777753

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=92.78  E-value=0.061  Score=43.64  Aligned_cols=22  Identities=23%  Similarity=0.265  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      -+.|.|++|+|||+|+..++..
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            5889999999999999998853

>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein biosynthesis, nucleotide-binding, phosphorylation, RNA- binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A

Probab=92.76  E-value=0.032  Score=57.50  Aligned_cols=26  Identities=23%  Similarity=0.434  Sum_probs=23.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.+|+++.|.|++|+|||||+.-++.
T Consensus       696 I~~GeivaIiGpNGSGKSTLLklLaG  721 (986)
T 2iw3_A          696 CSLSSRIAVIGPNGAGKSTLINVLTG  721 (986)
T ss_dssp             EETTCEEEECSCCCHHHHHHHHHHTT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999999997764

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=92.74  E-value=0.064  Score=42.57  Aligned_cols=21  Identities=24%  Similarity=0.487  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.|.|++|+|||+|+..++..
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            689999999999999988853

>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=92.69  E-value=0.065  Score=42.92  Aligned_cols=21  Identities=24%  Similarity=0.368  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.|.|++|+|||+|+..++..
T Consensus        10 i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A           10 VILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            689999999999999998754

>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=92.66  E-value=0.066  Score=42.48  Aligned_cols=23  Identities=26%  Similarity=0.319  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+.|.|++|+|||+|+..++...
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            8 KVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            36899999999999999988653

>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=92.66  E-value=0.061  Score=42.63  Aligned_cols=21  Identities=24%  Similarity=0.404  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.|.|++|+|||+|+..++..
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            689999999999999998854

>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=92.63  E-value=0.066  Score=42.97  Aligned_cols=23  Identities=22%  Similarity=0.288  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+.|.|++|+|||+|+..++...
T Consensus        10 ~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A           10 KVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCc
Confidence            37899999999999999888643

>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=92.63  E-value=0.068  Score=42.22  Aligned_cols=21  Identities=19%  Similarity=0.404  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.|.|++|+|||+|+..+...
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            688999999999999998864

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=92.63  E-value=0.066  Score=43.72  Aligned_cols=24  Identities=25%  Similarity=0.300  Sum_probs=20.6

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .--++|.|++|+|||+|+..++..
T Consensus        48 ~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           48 QPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            346899999999999999988754

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=92.62  E-value=0.077  Score=45.21  Aligned_cols=22  Identities=23%  Similarity=0.187  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..|.|+|||||||+|..++...
T Consensus        11 ~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A           11 LILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             eeeECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999998755

>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=92.59  E-value=0.068  Score=42.34  Aligned_cols=23  Identities=22%  Similarity=0.336  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -++|.|++|+|||+|+..++...
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            37899999999999999988654

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=92.58  E-value=0.077  Score=51.42  Aligned_cols=50  Identities=18%  Similarity=0.165  Sum_probs=35.0

Q ss_pred             hHHhhhcCCCC----CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           90 GLDAALCGGVP----FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        90 ~LD~~l~GGi~----~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +....+.-..+    .+.++.|+|.+||||||++..++.....   .   +..+.+++.+
T Consensus       356 eV~~~lr~~~~~~~~~~~~I~l~G~~GsGKSTia~~La~~L~~---~---G~~~~~ld~D  409 (546)
T 2gks_A          356 EVAEILAETYVPKHKQGFCVWLTGLPCAGKSTIAEILATMLQA---R---GRKVTLLDGD  409 (546)
T ss_dssp             HHHHHHHHHSCCGGGCCEEEEEECSTTSSHHHHHHHHHHHHHH---T---TCCEEEECHH
T ss_pred             hHHHHHHHhhccccccceEEEccCCCCCCHHHHHHHHHHHhhh---c---CCeEEEECch
Confidence            44444443342    3789999999999999999999876432   1   3567787753

>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=92.47  E-value=0.1  Score=53.55  Aligned_cols=38  Identities=26%  Similarity=0.359  Sum_probs=30.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..++|+||||+|||++|..++.....      .+.+.+++++..
T Consensus       589 ~~vLl~Gp~GtGKT~lA~~la~~~~~------~~~~~i~i~~~~  626 (854)
T 1qvr_A          589 GSFLFLGPTGVGKTELAKTLAATLFD------TEEAMIRIDMTE  626 (854)
T ss_dssp             EEEEEBSCSSSSHHHHHHHHHHHHHS------SGGGEEEECTTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhcC------CCCcEEEEechh
Confidence            47899999999999999999887642      146788888754

>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=92.47  E-value=0.13  Score=51.88  Aligned_cols=35  Identities=26%  Similarity=0.364  Sum_probs=28.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .-++|+||||+|||+++..++...         +.+.+++++..
T Consensus       489 ~~~ll~G~~GtGKT~la~~la~~l---------~~~~~~i~~s~  523 (758)
T 1r6b_X          489 GSFLFAGPTGVGKTEVTVQLSKAL---------GIELLRFDMSE  523 (758)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH---------TCEEEEEEGGG
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHh---------cCCEEEEechh
Confidence            368999999999999999888765         25788888643

---

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	357
d1pzna2	254	c.37.1.11 (A:96-349) DNA repair protein Rad51, cat	3e-32
d1szpa2	251	c.37.1.11 (A:145-395) DNA repair protein Rad51, ca	5e-31
d1v5wa_	258	c.37.1.11 (A:) Meiotic recombination protein DMC1/	1e-30
d1n0wa_	242	c.37.1.11 (A:) DNA repair protein Rad51, catalytic	2e-25
d2i1qa2	258	c.37.1.11 (A:65-322) DNA repair protein Rad51, cat	3e-25
d1mo6a1	269	c.37.1.11 (A:1-269) RecA protein, ATPase-domain {M	5e-19
d1u94a1	263	c.37.1.11 (A:6-268) RecA protein, ATPase-domain {E	7e-19
d1xp8a1	268	c.37.1.11 (A:15-282) RecA protein, ATPase-domain {	5e-17
d1tf7a1	242	c.37.1.11 (A:14-255) Circadian clock protein KaiC	9e-16
d1tf7a2	242	c.37.1.11 (A:256-497) Circadian clock protein KaiC	6e-13
d1cr2a_	277	c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase),	1e-04
d1nlfa_	274	c.37.1.11 (A:) Hexameric replicative helicase repA	0.001
d1doqa_	69	a.60.3.1 (A:) C-terminal domain of RNA polymerase	0.003

>d1pzna2 c.37.1.11 (A:96-349) DNA repair protein Rad51, catalytic domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 254

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]

 Score =  119 bits (298), Expect = 3e-32
 Identities = 66/277 (23%), Positives = 110/277 (39%), Gaps = 30/277 (10%)

Query: 64  FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLS 123
           F  A   +++RA    +     T  K LD  L GG+    +TE+ G  G+GKTQ    L+
Sbjct: 2   FMRADEYLKKRATIGRI----STGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLA 57

Query: 124 LLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQP 183
           ++  LP   GGL+G VI+ID E+TF   R+ E+  +   +                  Q 
Sbjct: 58  VMVQLPPEEGGLNGSVIWIDTENTFRPERIREIAQNRGLDPDEVLKHIYVARAFNSNHQM 117

Query: 184 TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLI---TS 240
             + +  + ++++  +     VKLL++DS+ +     +  R             +     
Sbjct: 118 LLVQQAEDKIKELLNT--DRPVKLLIVDSLTSHFRSEYIGRGALAERQQKLAKHLADLHR 175

Query: 241 LAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVT 300
           LA    I + VTNQV+                     +    +      + G   AH+ T
Sbjct: 176 LANLYDIAVFVTNQVQ--------------------ARPDAFFGDPTRPIGGHILAHSAT 215

Query: 301 IRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
           +R+ L   K G+R   +  +P  P     F+I   GI
Sbjct: 216 LRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGI 252

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 251

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]

 Score =  115 bits (289), Expect = 5e-31
 Identities = 60/272 (22%), Positives = 94/272 (34%), Gaps = 26/272 (9%)

Query: 66  TALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLL 125
           TA     +R+    L     T  K LD  L GGV  G +TEL G   TGK+Q C  L++ 
Sbjct: 2   TAADFHMRRSELICL----TTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVT 57

Query: 126 AALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTS 185
             +P   GG +G  +YID E TF   R++ +      +         +    +   +  +
Sbjct: 58  CQIPLDIGGGEGKCLYIDTEGTFRPVRLVSIAQRFGLDPD-------DALNNVAYARAYN 110

Query: 186 LSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFS 245
                  L+     + +++  L+V+DS+ AL       R             + +L    
Sbjct: 111 ADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFSGRGELSARQMHLAKFMRALQRL- 169

Query: 246 RIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVL 305
                        +           Q + ++               G   AH+ T RL  
Sbjct: 170 -------------ADQFGVAVVVTNQVVAQVDGGMAFNPDPKKPTGGNIMAHSSTTRLGF 216

Query: 306 E-AKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
           +  K  QR   V  SP  P     F I   G+
Sbjct: 217 KKGKGCQRLCKVVDSPCLPEAECVFAIYEDGV 248

>d1v5wa_ c.37.1.11 (A:) Meiotic recombination protein DMC1/LIM15 homolog {Human (Homo sapiens) [TaxId: 9606]} Length = 258

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]

 Score =  115 bits (287), Expect = 1e-30
 Identities = 69/282 (24%), Positives = 105/282 (37%), Gaps = 34/282 (12%)

Query: 62  PPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLK 121
           P F TA    E+R    H+     T  +  D  L GG+    +TE  G   TGKTQ    
Sbjct: 1   PGFLTAFEYSEKRKMVFHI----TTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHT 56

Query: 122 LSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL 181
           L + A LP   G   G +I+ID E+TF   R+ ++      +          +   +L  
Sbjct: 57  LCVTAQLPGAGGYPGGKIIFIDTENTFRPDRLRDIADRFNVDHD-------AVLDNVLYA 109

Query: 182 QPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPGVHE---QRAPGQHPLSWHIS 236
           +  +     E L+ +     +     KLL+IDS+ AL         + A  Q  L+  +S
Sbjct: 110 RAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRVDFSGRGELAERQQKLAQMLS 169

Query: 237 LITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWA 296
            +  ++E   + + VTNQ+                         T        + G   A
Sbjct: 170 RLQKISEEYNVAVFVTNQMTADPGATM-----------------TFQADPKKPIGGHILA 212

Query: 297 HAVTIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGIS 337
           HA T R+ L   +   R   +  SP  P    +F I   GI 
Sbjct: 213 HASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIG 254

>d1n0wa_ c.37.1.11 (A:) DNA repair protein Rad51, catalytic domain {Human (Homo sapiens) [TaxId: 9606]} Length = 242

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  100 bits (249), Expect = 2e-25
 Identities = 65/259 (25%), Positives = 106/259 (40%), Gaps = 28/259 (10%)

Query: 83  HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYI 142
            + T  K LD  L GG+  G +TE+ G   TGKTQ C  L++   LP   GG +G  +YI
Sbjct: 4   QITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYI 63

Query: 143 DVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ 202
           D E TF   R++ +                ++   +   +  +    T+ L +    +++
Sbjct: 64  DTEGTFRPERLLAVAERYGLSG-------SDVLDNVAYARAFNTDHQTQLLYQASAMMVE 116

Query: 203 NQVKLLVIDSMEALVP---GVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQS 259
           ++  LL++DS  AL         + +  Q  L+  + ++  LA+   + +V+TNQV  Q 
Sbjct: 117 SRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRMLLRLADEFGVAVVITNQVVAQV 176

Query: 260 HDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQ-RFMNVEK 318
              +       + +                  G   AHA T RL L    G+ R   +  
Sbjct: 177 DGAAMFAADPKKPIG-----------------GNIIAHASTTRLYLRKGRGETRICKIYD 219

Query: 319 SPTSPPLAFSFTINPSGIS 337
           SP  P     F IN  G+ 
Sbjct: 220 SPCLPEAEAMFAINADGVG 238

>d2i1qa2 c.37.1.11 (A:65-322) DNA repair protein Rad51, catalytic domain {Archaeon Methanococcus voltae [TaxId: 2188]} Length = 258

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]

 Score =  100 bits (249), Expect = 3e-25
 Identities = 62/287 (21%), Positives = 99/287 (34%), Gaps = 46/287 (16%)

Query: 65  QTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL 124
           ++ + L++QR+    L     T    LD+ L GG+    VTE  G  G+GKTQ   +  +
Sbjct: 1   KSGIDLLKQRSTVWKL----STSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCV 56

Query: 125 LAALPAHYGGL----------DGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEM 174
               P                    +YID E TF   R+++M   +  +        Q +
Sbjct: 57  NLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGIDG-------QTV 109

Query: 175 AGRILVLQPTSLSEFTESLEKIKVSLLQN----QVKLLVIDSMEALVPGVHEQRAPGQHP 230
                V +  +        EKI+  + +      V +  + S          + A  Q  
Sbjct: 110 LDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRGKLAERQQK 169

Query: 231 LSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAV 290
           L  H++ +  LA+     ++VTNQV                      K    +     A+
Sbjct: 170 LGRHMATLNKLADLFNCVVLVTNQVS--------------------AKPDAFFGMAEQAI 209

Query: 291 LGFHWAHAVTIRLVLE-AKSGQRFMNVEKSPTSPPLAFSFTINPSGI 336
            G    HA T R  +   K  +R   +  SP  P     F I   GI
Sbjct: 210 GGHIVGHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGI 256

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {Mycobacterium tuberculosis [TaxId: 1773]} Length = 269

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]

 Score = 83.4 bits (206), Expect = 5e-19
 Identities = 53/260 (20%), Positives = 85/260 (32%), Gaps = 62/260 (23%)

Query: 83  HLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIY 141
            +PT    LD AL  GG+P G V E+ GP  +GKT   L         A+     G   +
Sbjct: 40  VIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAV------ANAQAAGGVAAF 93

Query: 142 IDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLL 201
           ID E         ++G  +                 +LV QP +  +  E  + +   + 
Sbjct: 94  IDAEHALDPDYAKKLGVDT---------------DSLLVSQPDTGEQALEIADML---IR 135

Query: 202 QNQVKLLVIDSMEALVP-----GVHEQRAPG--QHPLSWHISLITSLAEFSRIPIVVTNQ 254
              + ++VIDS+ ALVP     G       G     +S  +  +T     S    +  NQ
Sbjct: 136 SGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFINQ 195

Query: 255 VRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS----- 309
           +R               K+  +               G       ++R+ +         
Sbjct: 196 LR--------------DKIGVMFGSPETTTG------GKALKFYASVRMDVRRVETLKDG 235

Query: 310 ----GQRF-MNVEKSPTSPP 324
               G R  + V K+    P
Sbjct: 236 TNAVGNRTRVKVVKNKCLAP 255

>d1u94a1 c.37.1.11 (A:6-268) RecA protein, ATPase-domain {Escherichia coli [TaxId: 562]} Length = 263

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]

 Score = 83.1 bits (205), Expect = 7e-19
 Identities = 49/256 (19%), Positives = 86/256 (33%), Gaps = 54/256 (21%)

Query: 83  HLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIY 141
            + T    LD AL  GG+P G + E+ GP  +GKT   L++   A              +
Sbjct: 34  TISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKT------CAF 87

Query: 142 IDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLL 201
           ID E         ++G                    +L  QP +  +  E  + +     
Sbjct: 88  IDAEHALDPIYARKLGVDI---------------DNLLCSQPDTGEQALEICDAL---AR 129

Query: 202 QNQVKLLVIDSMEALVP-----GVHEQRAPGQHP--LSWHISLITSLAEFSRIPIVVTNQ 254
              V ++V+DS+ AL P     G       G     +S  +  +    + S   ++  NQ
Sbjct: 130 SGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFINQ 189

Query: 255 VRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRF- 313
           +R               K+  +  +           L F+ +  + IR +   K G+   
Sbjct: 190 IR--------------MKIGVMFGNPETTTGGN--ALKFYASVRLDIRRIGAVKEGENVV 233

Query: 314 -----MNVEKSPTSPP 324
                + V K+  + P
Sbjct: 234 GSETRVKVVKNKIAAP 249

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]} Length = 268

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]

 Score = 77.6 bits (191), Expect = 5e-17
 Identities = 47/261 (18%), Positives = 84/261 (32%), Gaps = 63/261 (24%)

Query: 83  HLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIY 141
            + T    LD AL  GG+P G +TE+ GP   GKT   L +   A          G   +
Sbjct: 37  VVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKA------GGTCAF 90

Query: 142 IDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLL 201
           ID E                P    + G+  +    +LV QP +  +  E +E +   + 
Sbjct: 91  IDAEHALD------------PVYARALGVNTD---ELLVSQPDNGEQALEIMELL---VR 132

Query: 202 QNQVKLLVIDSMEALVP-------GVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ 254
              + ++V+DS+ AL P                   +S  +  +T++   +    +  NQ
Sbjct: 133 SGAIDVVVVDSVAALTPRAEIEGDMGDSLPGLQARLMSQALRKLTAILSKTGTAAIFINQ 192

Query: 255 VRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEA------- 307
           VR    ++  +     +                    G       ++RL +         
Sbjct: 193 VR----EKIGVMYGNPETTT----------------GGRALKFYASVRLDVRKIGQPTKV 232

Query: 308 ---KSGQRF-MNVEKSPTSPP 324
                     +   K+  + P
Sbjct: 233 GNDAVANTVKIKTVKNKVAAP 253

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]} Length = 242

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

 Score = 73.9 bits (180), Expect = 9e-16
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 37/260 (14%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           + T ++G D    GG+P G  T + G +GTGKT F ++      +           +++ 
Sbjct: 8   MRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE-----PGVFVT 62

Query: 144 VESTFTS--RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLL 201
            E T     +     G      +   K    + +      +     + +  +E+I  ++ 
Sbjct: 63  FEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQ 122

Query: 202 QNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHD 261
           + + + + IDS+ ++      Q+      +   +  + +  +      V+T +   +   
Sbjct: 123 KYRARRVSIDSVTSV-----FQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGP 177

Query: 262 ESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKSGQRFMNVEKSPT 321
            +                          V  F   + V +R VLE +  +R + + K   
Sbjct: 178 IA-----------------------RYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRG 214

Query: 322 SP--PLAFSFTINPSGISLL 339
           +      + FTI   GI++ 
Sbjct: 215 TSHMKGEYPFTITDHGINIF 234

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]} Length = 242

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

 Score = 65.3 bits (158), Expect = 6e-13
 Identities = 39/258 (15%), Positives = 66/258 (25%), Gaps = 44/258 (17%)

Query: 84  LPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID 143
           + + +  LD    GG     +    G  GTGKT    +    A            +   +
Sbjct: 8   VSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKER----AILFAYE 63

Query: 144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQN 203
                  R     G         +           +V      +   + L+ IK  +   
Sbjct: 64  ESRAQLLRNAYSWGMDFEEMERQNL--------LKIVCAYPESAGLEDHLQIIKSEINDF 115

Query: 204 QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDES 263
           +   + IDS+ AL  GV              +  +T  A+   I  + TN          
Sbjct: 116 KPARIAIDSLSALARGVSNNA------FRQFVIGVTGYAKQEEITGLFTNTS-------- 161

Query: 264 CLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAV-TIRLVLEAKSGQRFMNVEKSPTS 322
                        + D                   +  ++ V       R +NV K   S
Sbjct: 162 -----DQFMGAHSITDSHIS----------TITDTIILLQYVEIRGEMSRAINVFKMRGS 206

Query: 323 P--PLAFSFTINPSGISL 338
                   F I+  G  +
Sbjct: 207 WHDKAIREFMISDKGPDI 224

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]} Length = 277

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]

 Score = 41.2 bits (95), Expect = 1e-04
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 71  MEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL 124
           + +  ++E   G L +   G++    G    G V  +   +G GK+ F  + +L
Sbjct: 5   IREHLSSEESVGLLFSGCTGINDKTLGARG-GEVIMVTSGSGMGKSTFVRQQAL 57

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {Escherichia coli [TaxId: 562]} Length = 274

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]

 Score = 37.7 bits (86), Expect = 0.001
 Identities = 33/170 (19%), Positives = 60/170 (35%), Gaps = 19/170 (11%)

Query: 95  LCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL----DGGVIYIDVESTFTS 150
           +   +  G V  LV P G GK+   L+L+   A       +     G VIY+  E   T+
Sbjct: 22  VLPNMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTA 81

Query: 151 --RRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVK 206
              R+  +GA       H     ++     L++QP   S       +    L +     +
Sbjct: 82  IHHRLHALGA-------HLSAEERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRAAEGRR 134

Query: 207 LLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR 256
           L+V+D++            P    +      + ++A  +   IV  +   
Sbjct: 135 LMVLDTLRRFHIEEENASGPMAQVIGR----MEAIAADTGCSIVFLHHAS 180

>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Length = 69

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Thermus thermophilus [TaxId: 274]

 Score = 33.8 bits (78), Expect = 0.003
 Identities = 10/55 (18%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 3  NKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDV---ELSEVRSALA 54
          +  + E+ L   + +      I + +  L+L   +L  +  +    L E++ AL 
Sbjct: 7  DLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALE 61

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	357
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	100.0
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	100.0
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	100.0
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	100.0
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	100.0
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	100.0
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	99.97
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	99.97
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	99.97
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	99.97
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	99.95
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	99.85
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	98.72
d2awna2	232	Maltose transport protein MalK, N-terminal domain	98.63
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	98.61
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	98.55
d1g2912	240	Maltose transport protein MalK, N-terminal domain	98.5
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	98.5
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	98.44
d1okkd2	207	GTPase domain of the signal recognition particle r	98.4
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	98.36
d2qy9a2	211	GTPase domain of the signal recognition particle r	98.35
d1ls1a2	207	GTPase domain of the signal sequence recognition p	98.32
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	98.31
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	98.3
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	98.3
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	98.26
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	98.23
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	98.22
d1vmaa2	213	GTPase domain of the signal recognition particle r	98.22
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	98.21
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	98.2
d1j8yf2	211	GTPase domain of the signal sequence recognition p	98.18
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.17
d1szpa1	64	DNA repair protein Rad51, N-terminal domain {Baker	98.11
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	98.07
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.06
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.06
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	98.05
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.03
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	98.02
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	97.91
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.8
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.8
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	97.69
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	97.51
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.5
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	97.47
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	97.46
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.42
d1lb2b_	72	C-terminal domain of RNA polymerase alpha subunit	97.35
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.34
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	97.32
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	97.32
d1doqa_	69	C-terminal domain of RNA polymerase alpha subunit	97.31
d1b22a_	70	DNA repair protein Rad51, N-terminal domain {Human	97.31
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.24
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.23
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.22
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.19
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.14
d1c9ka_	180	Adenosylcobinamide kinase/adenosylcobinamide phosp	97.14
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	97.14
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	97.12
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.1
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.1
d1z3eb1	67	C-terminal domain of RNA polymerase alpha subunit	97.1
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.08
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.05
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.04
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.98
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	96.96
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	96.96
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.94
d2i1qa1	60	DNA repair protein Rad51, N-terminal domain {Archa	96.91
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	96.9
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	96.89
d1xpua3	289	Transcription termination factor Rho, ATPase domai	96.88
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.86
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.8
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.78
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.77
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.77
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.76
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.75
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	96.73
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	96.71
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.66
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.65
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	96.65
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	96.63
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.61
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.56
d1pzna1	61	DNA repair protein Rad51, N-terminal domain {Archa	96.53
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	96.52
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.51
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.47
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.44
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.43
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.39
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.36
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	96.35
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.34
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.34
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.31
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.31
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.25
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.25
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	96.2
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	96.18
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.16
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.16
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	96.13
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.13
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	96.11
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	96.11
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.11
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.07
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	96.06
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	96.05
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	96.05
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	96.05
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.02
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	96.01
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	96.01
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	95.98
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	95.92
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.92
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.91
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	95.89
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.87
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	95.85
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.77
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	95.75
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	95.75
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	95.71
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	95.68
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	95.67
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	95.66
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	95.63
d1tuea_	205	Replication protein E1 helicase domain {Human papi	95.47
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	95.43
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.42
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.4
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	95.38
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	95.33
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	95.25
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	95.19
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	95.19
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	95.16
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	95.16
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	95.1
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.05
d1y88a1	59	Hypothetical protein AF1548, C-terminal domain {Ar	95.03
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	94.98
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	94.97
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	94.95
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.94
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	94.93
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	94.76
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	94.76
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	94.7
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	94.67
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	94.55
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	94.52
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	94.52
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	94.4
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.3
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	94.28
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	94.28
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	94.21
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.18
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.17
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	94.03
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.01
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.0
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.87
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	93.81
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	93.73
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	93.66
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.64
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	93.64
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	93.63
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	93.63
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	93.56
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	93.55
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.52
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.5
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	93.45
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.41
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	93.41
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	93.4
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.4
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.4
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	93.39
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	93.36
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.3
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.29
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	93.25
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	93.24
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.21
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.18
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	93.16
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	93.13
d2fh5b1	207	Signal recognition particle receptor beta-subunit	93.08
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	93.06
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	93.02
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	93.0
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	92.96
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	92.95
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	92.94
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	92.94
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	92.93
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	92.92
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.92
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	92.91
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.89
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	92.86
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	92.83
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.79
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	92.79
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	92.78
d1nrjb_	209	Signal recognition particle receptor beta-subunit	92.73
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.72
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	92.71
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	92.7
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	92.65
d1u9la_	68	Transcription elongation protein NusA {Escherichia	92.48
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	92.45
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	92.19
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	92.09
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	92.09
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	92.09
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	92.08
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.02
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	91.94
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	91.79
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.79
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	91.72
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	91.59
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	91.58
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	91.37
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.35
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	91.35
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	91.26
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	91.2
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	91.13
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	90.97
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	90.85
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	90.67
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	90.38
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	90.1
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	89.98
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	89.97
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	89.9
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.74
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	89.64
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	89.4
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	89.35
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	89.35
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	89.06
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	88.98
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	88.79
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	87.69
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.57
d1ii2a1	323	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	87.0
d1n0ua2	341	Elongation factor 2 (eEF-2), N-terminal (G) domain	86.46
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	86.19
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	85.78
d2q0zx1	176	Protein pro2281 {Human (Homo sapiens) [TaxId: 9606	85.71
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	83.34
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	82.49
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	80.86

>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=100.00  E-value=4e-34  Score=252.19  Aligned_cols=252  Identities=27%  Similarity=0.328  Sum_probs=189.6

Q ss_pred             CCcccHHHHHHHHHhcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEE
Q 035774           62 PPFQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIY  141 (357)
Q Consensus        62 ~~~~~~~~~~~~~~~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~  141 (357)
                      ++|.++.++.+++..    ..+||||++.||++|+||+|+|++++|+|+||+|||+||+|++.+++.....++....++|
T Consensus         1 ~~~~~~~~~~~~~~~----~~ri~TGi~~LD~~lgGGip~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~   76 (258)
T d1v5wa_           1 PGFLTAFEYSEKRKM----VFHITTGSQEFDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIF   76 (258)
T ss_dssp             CCSEEHHHHHHHGGG----CCCBCCSCHHHHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEE
T ss_pred             CCcccHHHHHHhhcC----CceecCCCHHHHHhhcCCCcCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEE
Confidence            468899999987544    6789999999999999999999999999999999999999999998875444445678999


Q ss_pred             EeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhh--cCeeEEEEeccccccCC
Q 035774          142 IDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQ--NQVKLLVIDSMEALVPG  219 (357)
Q Consensus       142 i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~--~~~~lvvIDsl~~l~~~  219 (357)
                      ++.+..+...+...+.....       ........++.+.++.+..++...+..+......  ..++++++|++.+++..
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vid~~~~~~~~  149 (258)
T d1v5wa_          77 IDTENTFRPDRLRDIADRFN-------VDHDAVLDNVLYARAYTSEHQMELLDYVAAKFHEEAGIFKLLIIDSIMALFRV  149 (258)
T ss_dssp             EESSSCCCHHHHHHHHHHTT-------CCHHHHHHTEEEEECCSTTHHHHHHHHHHHHHHHSCSSEEEEEEETSGGGHHH
T ss_pred             echHHHHHHHHHHHHHhhhc-------ccchhhhhcccccccCcHHHHHHHHHHHHHHhhhhccCceEEEeeehhhhhhc
Confidence            99999988888777654321       1112345678888888877777777666555433  45799999999998765


Q ss_pred             CCCCCC---CChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHh
Q 035774          220 VHEQRA---PGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWA  296 (357)
Q Consensus       220 ~~~~~~---~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~  296 (357)
                      ......   .+...++.++..|++++.++++++++++|.+.........                 ......|++|..|.
T Consensus       150 ~~~~~~~~~~~~~~l~~~~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~g~~~~  212 (258)
T d1v5wa_         150 DFSGRGELAERQQKLAQMLSRLQKISEEYNVAVFVTNQMTADPGATMTF-----------------QADPKKPIGGHILA  212 (258)
T ss_dssp             HCCGGGCHHHHHHHHHHHHHHHHHHHHHHTCEEEEEECC------------------------------------CCTTT
T ss_pred             cccCCcchhHHHHHHHHHHHHHHHHHHhcCCEEEEeeeEeecccccccc-----------------cCCceeecccceeh
Confidence            332221   1335678889999999999999999999987654411100                 01234578889999


Q ss_pred             hhccEEEEEEEe-CCeEEEEEEeCCCCCCceeEEEEcCCCceeccC
Q 035774          297 HAVTIRLVLEAK-SGQRFMNVEKSPTSPPLAFSFTINPSGISLLTD  341 (357)
Q Consensus       297 ~~~~~rl~l~~~-~~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~~~~  341 (357)
                      +.+++++.+++. +..|.++|.|+|+.++..++|+|+++||+++++
T Consensus       213 ~~~~~~l~l~~~~~~~R~l~i~K~r~~~~~~~~F~It~~GI~~~~~  258 (258)
T d1v5wa_         213 HASTTRISLRKGRGELRIAKIYDSPEMPENEATFAITAGGIGDAKE  258 (258)
T ss_dssp             TSSSEEEEEEESSTTEEEEEEEECTTCCSSCEEEEEETTEEEECCC
T ss_pred             heeEEEEEEEEcCCCEEEEEEEeCCCCCCcEEEEEEcCCCcccCCC
Confidence            999999999875 568999999999999888899999999998763

>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=100.00  E-value=1e-33  Score=248.59  Aligned_cols=212  Identities=23%  Similarity=0.300  Sum_probs=163.0

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      .++||||+..||.+|+ ||+++|.+++|+|+||+|||+||++++++++.+      +..|+|||+|+++++++++.+..+
T Consensus        32 ~~~isTG~~~lD~~Lg~GGi~~g~itei~G~~gsGKTtl~l~~~~~~q~~------g~~~vyidtE~~~~~~~a~~~Gvd  105 (263)
T d1u94a1          32 VETISTGSLSLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE------GKTCAFIDAEHALDPIYARKLGVD  105 (263)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEESSCCCCHHHHHHTTCC
T ss_pred             CCeEccCCHHHHHHhcCCCccCceEEEEecCCCcHHHHHHHHHHHHHHcC------CCEEEEEccccccCHHHHHHhCCC
Confidence            6789999999999997 999999999999999999999999999999863      588999999999999887665421


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCC-CCCCC------CCChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPG-VHEQR------APGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~-~~~~~------~~r~~~~~  232 (357)
                                     .+++++.++.+.++..+.++.   +++..++++|||||++++++. +.+..      ..+.+.+.
T Consensus       106 ---------------~d~v~~~~~~~~E~~~~~i~~---l~~~~~~~liViDSi~al~~~~e~~~~~~~~~~~~~a~~l~  167 (263)
T d1u94a1         106 ---------------IDNLLCSQPDTGEQALEICDA---LARSGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMS  167 (263)
T ss_dssp             ---------------GGGCEEECCSSHHHHHHHHHH---HHHHTCCSEEEEECGGGCCCHHHHTTC------CHHHHHHH
T ss_pred             ---------------HHHEEEecCCCHHHHHHHHHH---HHhcCCCCEEEEECccccccchhcccccccchHHHHHHHHH
Confidence                           357888888888777665554   445578999999999999853 11111      11234577


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      .+++.|..++.++++++|++||++...+   .+|                 ....+|++|..|.|.+++|+.+.+..   
T Consensus       168 ~~~~~l~~~~~~~~~~vi~~NQv~~~~~---~~~-----------------g~~~~~~GG~al~~~~~~rl~l~k~~~~k  227 (263)
T d1u94a1         168 QAMRKLAGNLKQSNTLLIFINQIRMKIG---VMF-----------------GNPETTTGGNALKFYASVRLDIRRIGAVK  227 (263)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEEC----------------------------------CTTCSHHHHHCSEEEEEEEEEEEE
T ss_pred             HHHHHHHHhhhccCceEEEEEEEEeccc---ccc-----------------CCCccccccchhheeeEEEEEEEeccccc
Confidence            8889999999999999999999977654   111                 12236889999999999999997631   


Q ss_pred             -------CeEEEEEEeCCCCCC-ceeEEEEc-CCCc
Q 035774          310 -------GQRFMNVEKSPTSPP-LAFSFTIN-PSGI  336 (357)
Q Consensus       310 -------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi  336 (357)
                             ..+.++++|+|..|+ ..+.|.|+ ++||
T Consensus       228 ~g~~~iG~~~r~~v~Knr~~~p~~~~~f~i~~~~GI  263 (263)
T d1u94a1         228 EGENVVGSETRVKVVKNKIAAPFKQAEFQILYGEGI  263 (263)
T ss_dssp             SSSSEEEEEEEEEEEEESSBCSCCEEEEEEETTTEE
T ss_pred             cCCceeeeEEEEEEEeCCCCCCCCEEEEEEEcCCCC
Confidence                   244689999998886 57899998 8886

>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=100.00  E-value=3.5e-33  Score=244.82  Aligned_cols=245  Identities=28%  Similarity=0.331  Sum_probs=184.0

Q ss_pred             cHHHHHHHHHhcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           66 TALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++.|+.+++..    ..+||||++.||.+|+||+|+|++++|+|+||+|||+||+|++++++.....+..+.+++|++++
T Consensus         2 ~~~~~~~~~~~----~~~i~TGi~~LD~ll~GGi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2           2 TAADFHMRRSE----LICLTTGSKNLDTLLGGGVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             CHHHHHHHHHS----SCEECCSCHHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             CHHHHHHHhcC----CCeecCCCHHHHhhhCCCCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            67777777544    67899999999999999999999999999999999999999999987765555567899999999


Q ss_pred             CCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCC
Q 035774          146 STFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRA  225 (357)
Q Consensus       146 ~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~  225 (357)
                      ..+...++........     ..  ......++.+.+.............+...+......++++|++..+.........
T Consensus        78 ~~~~~~~~~~~~~~~~-----~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~  150 (251)
T d1szpa2          78 GTFRPVRLVSIAQRFG-----LD--PDDALNNVAYARAYNADHQLRLLDAAAQMMSESRFSLIVVDSVMALYRTDFSGRG  150 (251)
T ss_dssp             SCCCGGGGHHHHHHTC-----CC--HHHHGGGEEEEECCSTTTHHHHHHHTHHHHHHSCEEEEEEETGGGGGSCC-----
T ss_pred             chHHHHHHHHHHHhcC-----Cc--hhhhhcceEEEeccchhHHHHHHHHHHHHhhccccceeeehhhhhhhhhhhcccc
Confidence            9888777766544321     11  1234566777777766666666666677777788999999999998866433222


Q ss_pred             C---ChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEE
Q 035774          226 P---GQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIR  302 (357)
Q Consensus       226 ~---r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~r  302 (357)
                      .   +......++..|.+++..+++++++++|.+.......                 ........|++|..|.+.+++|
T Consensus       151 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~gg~~~~~~~~~~  213 (251)
T d1szpa2         151 ELSARQMHLAKFMRALQRLADQFGVAVVVTNQVVAQVDGGM-----------------AFNPDPKKPTGGNIMAHSSTTR  213 (251)
T ss_dssp             CTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECC---------------------------------CHHHHHHHHCSEE
T ss_pred             chhhHHHHHHHHHHHHHhhhhhcceEEEEEEEEEeccCccc-----------------cccCcceeccCccchhhheeEE
Confidence            2   2345667888899999999999999999987644210                 0111345688999999999999


Q ss_pred             EEEEEe-CCeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          303 LVLEAK-SGQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       303 l~l~~~-~~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      +.+++. +..|.++|.|+|+.|+..+.|+|+++||+.
T Consensus       214 i~l~~~~~~~r~l~i~K~r~~~~~~~~f~It~~Gi~~  250 (251)
T d1szpa2         214 LGFKKGKGCQRLCKVVDSPCLPEAECVFAIYEDGVGD  250 (251)
T ss_dssp             EEEEECSTTEEEEECCSCSSSCCCCCCEEEETTEEEC
T ss_pred             EEEEecCCcEEEEEEEECCCCCCeeEEEEEcCCCccC
Confidence            999885 468999999999999888899999999974

>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=100.00  E-value=6.1e-32  Score=237.90  Aligned_cols=244  Identities=29%  Similarity=0.427  Sum_probs=176.0

Q ss_pred             cccHHHHHHHHHhcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774           64 FQTALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      |.++.+.++.+..    ..+||||++.||.+|+||+|+|++++|+|+||+|||+|++|++.+++.+....+.+..++|++
T Consensus         2 ~~~~~~~~~~~~~----i~ri~TGi~~LD~ll~GGlp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~   77 (254)
T d1pzna2           2 FMRADEYLKKRAT----IGRISTGSKSLDKLLGGGIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWID   77 (254)
T ss_dssp             CEEHHHHHHHHHT----CCEECCSCHHHHHHHTSSEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEE
T ss_pred             cccHHHHHHhhcC----CCeECCCCHHHHHhhcCCccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEe
Confidence            5678888887654    679999999999999999999999999999999999999999999987655556678999999


Q ss_pred             CCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHh-----hhcCeeEEEEeccccccC
Q 035774          144 VESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSL-----LQNQVKLLVIDSMEALVP  218 (357)
Q Consensus       144 ~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~-----~~~~~~lvvIDsl~~l~~  218 (357)
                      ++......++.......     ...  .+.......+............+.......     ....++++++|+++.++.
T Consensus        78 ~~~~~~~~~~~~~~~~~-----~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viDs~~~~~~  150 (254)
T d1pzna2          78 TENTFRPERIREIAQNR-----GLD--PDEVLKHIYVARAFNSNHQMLLVQQAEDKIKELLNTDRPVKLLIVDSLTSHFR  150 (254)
T ss_dssp             SSSCCCHHHHHHHHHTT-----TCC--HHHHGGGEEEEECCSHHHHHHHHHHHHHHHHHSSSSSSCEEEEEEETSSTTHH
T ss_pred             ccchhHHHHHHHHHHhc-----CCC--hHHhhhhhhhhhhccchhHHHHHHhhhhhhHHHHhhccCceeEeecchhheee
Confidence            99988887777655431     111  122233444555555544444443322221     234689999999999876


Q ss_pred             CCCCCCCC---ChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhH
Q 035774          219 GVHEQRAP---GQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHW  295 (357)
Q Consensus       219 ~~~~~~~~---r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w  295 (357)
                      ........   ....+...+..++.++...++++++++|.+......   +                 .....+++|..|
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~---~-----------------~~~~~~~~~~~~  210 (254)
T d1pzna2         151 SEYIGRGALAERQQKLAKHLADLHRLANLYDIAVFVTNQVQARPDAF---F-----------------GDPTRPIGGHIL  210 (254)
T ss_dssp             HHCCSTTTHHHHHHHHHHHHHHHHHHHHHTTCEEEEEEECC-----------------------------------CCCC
T ss_pred             hhhcccchhhhhHHHHHHHHHHHHHHhhccceEEEecceEeeccCcc---c-----------------CCceeecCceee
Confidence            54322221   234566778888899999999999999987654310   0                 112345677789


Q ss_pred             hhhccEEEEEEEeC-CeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          296 AHAVTIRLVLEAKS-GQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       296 ~~~~~~rl~l~~~~-~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      ++.+++++.+++.. ..|+++|.|+|++|++.++|+|+++||+.
T Consensus       211 ~~~~~~~l~l~~~~~~~R~~~v~K~R~~~~~~~~f~It~~Gi~~  254 (254)
T d1pzna2         211 AHSATLRVYLRKGKGGKRIARLIDAPHLPEGEAVFSITEKGIED  254 (254)
T ss_dssp             CTTCSEEEEEEECTTSEEEEEESCSSSSCCSEEEEEEETTEEEC
T ss_pred             hhhceEEEEEEecCCCeEEEEEEECCCCCCeEEEEEECCCCccC
Confidence            99999999999864 58999999999999999999999999973

>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=100.00  E-value=7e-32  Score=236.66  Aligned_cols=212  Identities=25%  Similarity=0.329  Sum_probs=165.4

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      .+.||||+..||.+|+ ||+|+|.+++|+|+||+|||+||++++++++..      +..|+|||+|+.++++++.++..+
T Consensus        38 ~~~i~TG~~~lD~~lg~gG~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~------g~~~vyIDtE~~~~~e~a~~~GvD  111 (269)
T d1mo6a1          38 ISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQAA------GGVAAFIDAEHALDPDYAKKLGVD  111 (269)
T ss_dssp             SCCBCCSCHHHHHHTSSSSBCSSSEEEEECSSSSSHHHHHHHHHHHHHHT------TCEEEEEESSCCCCHHHHHHHTCC
T ss_pred             cceEccCCHHHHHhhccCCcccceeEEEecCCCcHHHHHHHHHHHHHhcC------CCEEEEEECCccCCHHHHHHhCCC
Confidence            6789999999999998 999999999999999999999999999988753      589999999999999998776422


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCC------CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRA------PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~------~r~~~~~  232 (357)
                                     .++++++++.+.++..++++.+   +.+..+++|||||++++++ .+.+...      .+.+.+.
T Consensus       112 ---------------~d~il~~~~~~~E~~~~~~~~l---~~~~~~~liIiDSi~al~~~~E~e~~~~~~~~~~~a~~l~  173 (269)
T d1mo6a1         112 ---------------TDSLLVSQPDTGEQALEIADML---IRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMS  173 (269)
T ss_dssp             ---------------GGGCEEECCSSHHHHHHHHHHH---HHTTCEEEEEEECSTTCCCHHHHC-------CCHHHHHHH
T ss_pred             ---------------HHHeEEecCCCHHHHHHHHHHH---HhcCCCCEEEEecccccccHHHhccccccchHHHHHHHHH
Confidence                           2568889998888877666544   5567899999999999985 3332221      1335677


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      .+++.|..++.+++++++++||+..+.+   .+|.                 ...+|.+|..|.|.+++|+.+.+..   
T Consensus       174 ~~l~~l~~~~~~~~~~vi~~NQv~~~~~---~~~g-----------------~~~~~~GG~al~~~ss~rl~l~k~~~~k  233 (269)
T d1mo6a1         174 QALRKMTGALNNSGTTAIFINQLRDKIG---VMFG-----------------SPETTTGGKALKFYASVRMDVRRVETLK  233 (269)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEECC---------------------------------CTTHHHHHHHCSEEEEEEEEECCB
T ss_pred             HHHHHHHHHHhhcCchhhhhheeeccCc---cccC-----------------CceecccccceeeeeeEEEEEEecceec
Confidence            8888999999999999999999987654   1211                 2235778999999999999997642   


Q ss_pred             -------CeEEEEEEeCCCCCC-ceeEEEEc-CCCc
Q 035774          310 -------GQRFMNVEKSPTSPP-LAFSFTIN-PSGI  336 (357)
Q Consensus       310 -------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi  336 (357)
                             ..+.++|.|||..|+ ..+.|.|+ +.||
T Consensus       234 dg~~~iG~~~~~kv~Knr~~~p~~~a~f~I~~~~GI  269 (269)
T d1mo6a1         234 DGTNAVGNRTRVKVVKNKCLAPFKQAEFDILYGKGI  269 (269)
T ss_dssp             CSSSBCEEEEEEEEEEESSSCSCEEEEEEEETTTEE
T ss_pred             cCCceEEEEEEEEEEECCCCCCCCEEEEEEEeCCcC
Confidence                   245699999999987 57899998 8886

>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=100.00  E-value=3.9e-32  Score=238.63  Aligned_cols=212  Identities=23%  Similarity=0.314  Sum_probs=162.8

Q ss_pred             CCCCCCCchhHHhhhc-CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALC-GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGAS  159 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~-GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~  159 (357)
                      .+.||||+..||.+|+ ||+|.|.+++|+|+||+|||+||++++++++.+      ++.|+|||+|.+++++++.++.-+
T Consensus        35 ~~~i~TGs~~lD~~Lg~GGip~g~itei~G~~~sGKT~l~l~~~~~aqk~------g~~v~yiDtE~~~~~~~a~~~Gvd  108 (268)
T d1xp8a1          35 VQVVSTGSLSLDLALGVGGIPRGRITEIYGPESGGKTTLALAIVAQAQKA------GGTCAFIDAEHALDPVYARALGVN  108 (268)
T ss_dssp             CCEECCSCHHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHT------TCCEEEEESSCCCCHHHHHHTTCC
T ss_pred             CCeEcCCCHHHHHHhcCCCccCceEEEEecCCccchHHHHHHHHHHHHhC------CCEEEEEECCccCCHHHHHHhCCC
Confidence            6789999999999997 999999999999999999999999999998753      578999999999999877665321


Q ss_pred             cCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccC-CCCCCCC------CChHHHH
Q 035774          160 SFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVP-GVHEQRA------PGQHPLS  232 (357)
Q Consensus       160 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~-~~~~~~~------~r~~~~~  232 (357)
                                     .+++++.++.+.++..++++.   ++.+..+++|||||++++++ .+.+...      .+.+.+.
T Consensus       109 ---------------~d~i~~~~~~~~E~~~~~~~~---l~~~~~~~liIiDSi~al~~r~e~~~~~~~~~~~~~a~~l~  170 (268)
T d1xp8a1         109 ---------------TDELLVSQPDNGEQALEIMEL---LVRSGAIDVVVVDSVAALTPRAEIEGDMGDSLPGLQARLMS  170 (268)
T ss_dssp             ---------------GGGCEEECCSSHHHHHHHHHH---HHTTTCCSEEEEECTTTCCCSTTC--------CCHHHHHHH
T ss_pred             ---------------chhEEEEcCCCHHHHHHHHHH---HHhcCCCcEEEEecccccccHHHHcccccchhHHHHHHHHH
Confidence                           357888899888877665544   45567899999999999984 4443321      1345678


Q ss_pred             HHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC---
Q 035774          233 WHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS---  309 (357)
Q Consensus       233 ~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~---  309 (357)
                      .+++.|..++.++++++|+|||+....+   .+|.                 ...+|.+|..|.|..++|+.+++..   
T Consensus       171 ~~lr~l~~~~~~~~~~vi~tNQv~~~~g---~~~g-----------------~~~~~~GG~al~~~ss~rl~l~k~~~~~  230 (268)
T d1xp8a1         171 QALRKLTAILSKTGTAAIFINQVREKIG---VMYG-----------------NPETTTGGRALKFYASVRLDVRKIGQPT  230 (268)
T ss_dssp             HHHHHHHHHHTTTCCEEEEEEEC-----------------------------------CHHHHHHHCSEEEEEEEESCCC
T ss_pred             HHHHHHHhhhhhcCCeEEEEeEEeeccc---cccC-----------------cceeecccchhhhceeEEEEEEecCccc
Confidence            8899999999999999999999987654   1111                 1235778999999999999998753   


Q ss_pred             --------CeEEEEEEeCCCCCC-ceeEEEEc-CCCc
Q 035774          310 --------GQRFMNVEKSPTSPP-LAFSFTIN-PSGI  336 (357)
Q Consensus       310 --------~~R~l~v~K~r~~~~-~~~~f~I~-~~Gi  336 (357)
                              ....++++|||.+|+ ..+.|.|. +.||
T Consensus       231 k~~~~~iG~~v~~kv~Knr~~~p~~~~~~~i~~~~Gi  267 (268)
T d1xp8a1         231 KVGNDAVANTVKIKTVKNKVAAPFKEVELALVYGKGF  267 (268)
T ss_dssp             ------CEEEEEEEEEEESSSCCCCEEEEEEETTTEE
T ss_pred             ccCCceEEEEEEEEEEECCcCCCCCEEEEEEecCCCC
Confidence                    234689999999986 57899988 7887

>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=99.97  E-value=1.5e-30  Score=228.25  Aligned_cols=242  Identities=27%  Similarity=0.315  Sum_probs=180.9

Q ss_pred             cHHHHHHHHHhcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCC----------CC
Q 035774           66 TALLLMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYG----------GL  135 (357)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~g----------g~  135 (357)
                      ++.++++++..    ..+||||+++||++|+||+++|++++|+|+||+|||+||+++|++++.+..+.          ..
T Consensus         2 ~~~~~~~~~~~----~~~i~TG~~~LD~ll~GGl~~G~l~~i~G~~G~GKT~~~l~~a~~~~~~~~~~~~~~~~~~~~~~   77 (258)
T d2i1qa2           2 SGIDLLKQRST----VWKLSTSSSELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVA   77 (258)
T ss_dssp             CTHHHHHHHTT----CCEECCSCHHHHHHTTSSEETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTS
T ss_pred             CHHHHHHhhCC----CceecCCCHHHHHhcCCCccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCCceEEeecccchhc
Confidence            45677777433    67899999999999999999999999999999999999999999998643211          01


Q ss_pred             CCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHh-hhcCeeEEEEeccc
Q 035774          136 DGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSL-LQNQVKLLVIDSME  214 (357)
Q Consensus       136 ~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~-~~~~~~lvvIDsl~  214 (357)
                      ..+++||++|..++......+......       .......++.+..+....++...+......+ ......++++|++.
T Consensus        78 ~~~~~~i~~e~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vid~i~  150 (258)
T d2i1qa2          78 QPKAVYIDTEGTFRPERIMQMAEHAGI-------DGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLT  150 (258)
T ss_dssp             SEEEEEEESSSCCCHHHHHHHHHHHTC-------CHHHHHHTEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSS
T ss_pred             CceEEEEEecCCcCHHHHHHHHhhcch-------hhhhhhhcceeeccCchhhHHHHHHHHHHHHHHhcccceeeeeEEE
Confidence            357999999988887776655543211       1233456777777777767666665544433 34568899999999


Q ss_pred             cccCCCCCCCCC---ChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceeccc
Q 035774          215 ALVPGVHEQRAP---GQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVL  291 (357)
Q Consensus       215 ~l~~~~~~~~~~---r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pal  291 (357)
                      .+..........   +......+++.++.++..+++++++++|.+......                    ......+++
T Consensus       151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~~~~~~~  210 (258)
T d2i1qa2         151 STFRNEYTGRGKLAERQQKLGRHMATLNKLADLFNCVVLVTNQVSAKPDAF--------------------FGMAEQAIG  210 (258)
T ss_dssp             HHHHHHCCCTTSHHHHHHHHHHHHHHHHHHHHHTTCEEEEEECEECC---------------------------CCEESS
T ss_pred             EeechhccccccchhhHHHHHHHHHHHHHhhhhcceEEEeecceEeccccc--------------------cCCcccccC
Confidence            887653332221   234456788899999999999999999877654311                    001235778


Q ss_pred             chhHhhhccEEEEEEEe-CCeEEEEEEeCCCCCCceeEEEEcCCCcee
Q 035774          292 GFHWAHAVTIRLVLEAK-SGQRFMNVEKSPTSPPLAFSFTINPSGISL  338 (357)
Q Consensus       292 g~~w~~~~~~rl~l~~~-~~~R~l~v~K~r~~~~~~~~f~I~~~Gi~~  338 (357)
                      |..|++.+++++.+++. +..|+++|.|+|++|++++.|+|+++||+.
T Consensus       211 ~~~~~~~~~~~i~l~~~~~~~r~l~v~K~R~~~~~~~~f~I~~~Gi~~  258 (258)
T d2i1qa2         211 GHIVGHAATFRFFVRKGKGDKRVAKLYDSPHLPDAEAIFRITEKGIQD  258 (258)
T ss_dssp             HHHHHHHCSEEEEEEECSTTEEEEEEEECSSSCCEEEEEEEETTEEEC
T ss_pred             cchhhhhceEEEEEEEcCCCEEEEEEEECCCCCCceEEEEECCCCccC
Confidence            89999999999999985 579999999999999999999999999873

>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=99.97  E-value=2.4e-29  Score=216.54  Aligned_cols=236  Identities=28%  Similarity=0.359  Sum_probs=163.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+||||++.||.+|+||+++|++++|+|+||+|||+||+|+|++++.+...++....+.+++.+.......+.......
T Consensus         2 ~~ri~TG~~~LD~ll~GGi~~G~v~~i~G~~GsGKT~l~l~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (242)
T d1n0wa_           2 IIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERY   81 (242)
T ss_dssp             CCEECCSCHHHHHHTTTSEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCCHHHHHHHHHHT
T ss_pred             CCEEcCCCHHHHHhhcCCCcCCEEEEEEeCCCCCHHHHHHHHHHHHHHhhccccccceehhhhhhhhhHHHHHHHHHhhc
Confidence            46899999999999999999999999999999999999999999998765555556788888888776666655444321


Q ss_pred             CchhhcccchHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC---ChHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP---GQHPLSWHISL  237 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~---r~~~~~~i~~~  237 (357)
                      .       ........++.+..........................++.+|++..+..........   +......+...
T Consensus        82 ~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (242)
T d1n0wa_          82 G-------LSGSDVLDNVAYARAFNTDHQTQLLYQASAMMVESRYALLIVDSATALYRTDYSGRGELSARQMHLARFLRM  154 (242)
T ss_dssp             T-------CCHHHHHHTEEEEECCSHHHHHHHHHHHHHHHHHSCEEEEEEETSSGGGC-------CHHHHHHHHHHHHHH
T ss_pred             c-------cchhhhhhhhhhhhhhchhhhhhhhhhhhhhhhhhhheeecccceeeeehhhhhcccchhhhHHHHHHHHHH
Confidence            1       1112233456666666666666666666666666778899999998876653322221   23456678888


Q ss_pred             HHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC-CeEEEEE
Q 035774          238 ITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS-GQRFMNV  316 (357)
Q Consensus       238 Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~-~~R~l~v  316 (357)
                      |+.+++..++++++++|++.........                 ......|++|..|.+.++.|+.|++++ ..|.++|
T Consensus       155 l~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~l~~~~~~~i~l~~~~~~~r~~~i  217 (242)
T d1n0wa_         155 LLRLADEFGVAVVITNQVVAQVDGAAMF-----------------AADPKKPIGGNIIAHASTTRLYLRKGRGETRICKI  217 (242)
T ss_dssp             HHHHHHHHCCEEEEEC------------------------------------------CCTTCEEEEEEECSTTEEEEEE
T ss_pred             HHHhhhhcceeEEEEEEEecccccccee-----------------ecccccccchhhHHHhCcEEEEEEEcCCcEEEEEE
Confidence            9999999999999999987654421100                 112345778888999999999999864 6899999


Q ss_pred             EeCCCCCCceeEEEEcCCCceecc
Q 035774          317 EKSPTSPPLAFSFTINPSGISLLT  340 (357)
Q Consensus       317 ~K~r~~~~~~~~f~I~~~Gi~~~~  340 (357)
                      .|+|+.|+.+++|+|+++||+...
T Consensus       218 ~K~r~~~~~~~~f~I~~~Gi~~~~  241 (242)
T d1n0wa_         218 YDSPCLPEAEAMFAINADGVGDAK  241 (242)
T ss_dssp             CCBTTBSCEEEEEEEETTEEECCC
T ss_pred             EeCCCCCCeEEEEEEcCCceEcCC
Confidence            999999999999999999998764

>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=99.97  E-value=2.1e-29  Score=219.21  Aligned_cols=222  Identities=16%  Similarity=0.216  Sum_probs=161.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..+|+||++.||++|+||+++|++++|+|+||+|||+||+|++.+.+.+.     +.+++|+++|++..  .+.......
T Consensus         5 ~~~i~TGi~~LD~~l~GGi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~-----~~~~~~~s~e~~~~--~~~~~~~~~   77 (242)
T d1tf7a1           5 IAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF-----DEPGVFVTFEETPQ--DIIKNARSF   77 (242)
T ss_dssp             CCEECCCCTTHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHHH-----CCCEEEEESSSCHH--HHHHHHGGG
T ss_pred             CCcccCCcHHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-----CCCcccccccCCHH--HHHHHHHHc
Confidence            67899999999999999999999999999999999999999999877631     46899999998543  333222211


Q ss_pred             CchhhcccchHHHhhcCeEE---------eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILV---------LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPL  231 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~---------~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~  231 (357)
                      -   +......  ...+...         .......+...+++.+...+.+++++++|||+++.++...     ......
T Consensus        78 ~---~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~i~~~~~~~viiD~~~~l~~~~-----~~~~~~  147 (242)
T d1tf7a1          78 G---WDLAKLV--DEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQY-----DASSVV  147 (242)
T ss_dssp             T---CCHHHHH--HTTSEEEEECCCCSSCCSCCSSHHHHHHHHHHHHHHHHHTCSEEEEECSTTTSTTT-----CCHHHH
T ss_pred             C---CChHHHH--HhcchhhhhhccchhhhhhhccccHHHHHHHHHHHHHhhccchhhhhHHHHHHHhc-----cChhHH
Confidence            0   0000000  0111111         1112234566677888888888999999999999887542     234666


Q ss_pred             HHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC--
Q 035774          232 SWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS--  309 (357)
Q Consensus       232 ~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~--  309 (357)
                      ..++..+.+++++.++++++++|.....+...                           ....+.+.++..+.++...  
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------------------------~~~~~~~~~d~i~~~~~~~~~  200 (242)
T d1tf7a1         148 RRELFRLVARLKQIGATTVMTTERIEEYGPIA---------------------------RYGVEEFVSDNVVILRNVLEG  200 (242)
T ss_dssp             HHHHHHHHHHHHHHTCEEEEEEECSSSSSCSS---------------------------TTSCHHHHCSEEEEEEEECST
T ss_pred             HHHHHHHHHHHHhcCCceEEeecccccccccc---------------------------cCcceeeeccEEEEEEEeeeC
Confidence            77888899999999999999999876543110                           0011567788888887642  


Q ss_pred             --CeEEEEEEeCCCCC--CceeEEEEcCCCceeccCCCcee
Q 035774          310 --GQRFMNVEKSPTSP--PLAFSFTINPSGISLLTDDGTEM  346 (357)
Q Consensus       310 --~~R~l~v~K~r~~~--~~~~~f~I~~~Gi~~~~~~~~~~  346 (357)
                        ..|+++|.|+|+++  ...+.|+|+++||+++|....+|
T Consensus       201 ~~~~r~l~v~K~R~~~~~~~~~~f~I~~~Gi~v~p~~~~~~  241 (242)
T d1tf7a1         201 ERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRL  241 (242)
T ss_dssp             TCCEEEEEEEEETTSCCCCSEEEEEEETTEEEECCTTTCCS
T ss_pred             CeeEEEEEEEEcCCCCCCCeEEEEEEeCCcEEEeCCCcccc
Confidence              47999999999888  46678999999999999877654

>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=99.97  E-value=4.5e-29  Score=218.13  Aligned_cols=218  Identities=19%  Similarity=0.168  Sum_probs=160.0

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhcc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASS  160 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~  160 (357)
                      ..++|||++.||++|+||+++|++++|+|+||+|||+||+|++.+++.+      +.+|+||++|++  ...+.+.....
T Consensus         5 ~~ri~TG~~~LD~~l~GGi~~gsl~li~G~pGsGKT~l~~qia~~~~~~------~~~~~~is~e~~--~~~~~~~~~~~   76 (242)
T d1tf7a2           5 NVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACAN------KERAILFAYEES--RAQLLRNAYSW   76 (242)
T ss_dssp             CCEECCSCHHHHHHTTSSEESSCEEEEEECTTSSHHHHHHHHHHHHHTT------TCCEEEEESSSC--HHHHHHHHHTT
T ss_pred             CCccCCCcHHHHHhhcCCCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHh------ccccceeeccCC--HHHHHHHHHHc
Confidence            4579999999999999999999999999999999999999999998753      588999999984  44444433321


Q ss_pred             CchhhcccchHHHhhcCeEEeCCC-CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHH
Q 035774          161 FPEIFHSKGMAQEMAGRILVLQPT-SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLIT  239 (357)
Q Consensus       161 ~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk  239 (357)
                       .  ......  .....+.+.+.. ....+.+.+..+...+...+++++||||++.++...      ....+..++..|.
T Consensus        77 -~--~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~i~~~i~~~~~~~vviDs~~~~~~~~------~~~~~~~~~~~l~  145 (242)
T d1tf7a2          77 -G--MDFEEM--ERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGV------SNNAFRQFVIGVT  145 (242)
T ss_dssp             -S--CCHHHH--HHTTSEEECCCCGGGSCHHHHHHHHHHHHHTTCCSEEEEECHHHHTSSS------CHHHHHHHHHHHH
T ss_pred             -C--CChHHH--hhcCceEEEEeecchhhHHHHHHHHHHHHHhcCCceeeeecchhhhcCC------CHHHHHHHHHHHH
Confidence             0  011111  112233333322 223455566777777788899999999999987642      3467778889999


Q ss_pred             HHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC----CeEEEE
Q 035774          240 SLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS----GQRFMN  315 (357)
Q Consensus       240 ~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~----~~R~l~  315 (357)
                      ++++++++++++++|........                          ++.+..|.+.+|.++.+++..    ..|+++
T Consensus       146 ~~~~~~~~~~i~~~~~~~~~~~~--------------------------~~~~~~~~~~ad~vi~l~~~~~~~~~~R~i~  199 (242)
T d1tf7a2         146 GYAKQEEITGLFTNTSDQFMGAH--------------------------SITDSHISTITDTIILLQYVEIRGEMSRAIN  199 (242)
T ss_dssp             HHHHHTTCEEEEEEECSSSSCCC--------------------------SSCSSCCTTTCSEEEEEEEEEETTEEEEEEE
T ss_pred             HHHHHcCCeEEEEEeeEeecccc--------------------------ccCCcceeeecceEEEEEEeecCCceEEEEE
Confidence            99999999999999975532210                          111122678888888887642    268999


Q ss_pred             EEeCCCCCC--ceeEEEEcCCCceeccCCC
Q 035774          316 VEKSPTSPP--LAFSFTINPSGISLLTDDG  343 (357)
Q Consensus       316 v~K~r~~~~--~~~~f~I~~~Gi~~~~~~~  343 (357)
                      |.|+|++++  ..++|+|+++||++.++..
T Consensus       200 v~K~R~~~~~~~~~~f~I~~~Gi~i~~~~~  229 (242)
T d1tf7a2         200 VFKMRGSWHDKAIREFMISDKGPDIKDSFR  229 (242)
T ss_dssp             EEEESSSCCCCBCEEEEECSSCEEEEEECT
T ss_pred             EEecCCCCCCCeEEEEEEeCCcEEEcCccc
Confidence            999999884  5579999999999987654

>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=99.95  E-value=2.3e-26  Score=204.88  Aligned_cols=242  Identities=12%  Similarity=0.128  Sum_probs=149.2

Q ss_pred             HHHHHHhcccCCCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCc
Q 035774           70 LMEQRAATEHLGGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFT  149 (357)
Q Consensus        70 ~~~~~~~~~~~~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~  149 (357)
                      .+++....+....+|+||++.||+++ ||+.+|++++|+|+||+|||+|+++++.+++..     .+.+|+||++|++..
T Consensus         4 ~~~~~~~~~~~~~~i~TG~~~lD~~~-~G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~-----~g~~v~~~s~E~~~~   77 (277)
T d1cr2a_           4 RIREHLSSEESVGLLFSGCTGINDKT-LGARGGEVIMVTSGSGMGKSTFVRQQALQWGTA-----MGKKVGLAMLEESVE   77 (277)
T ss_dssp             HHHHHHTSCCCSCBCCCSCTTHHHHH-CSBCTTCEEEEECSTTSSHHHHHHHHHHHHHHT-----SCCCEEEEESSSCHH
T ss_pred             HHHHHHhCCCCccccCCCchhHHHHh-cCCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhh-----cccceeEeeeccchh
Confidence            34444444555689999999999999 679999999999999999999999999987642     258999999998644


Q ss_pred             h--HHHHHHHhcc-Cc--hh-----hcc---cchHHHh--hcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccc
Q 035774          150 S--RRMIEMGASS-FP--EI-----FHS---KGMAQEM--AGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSME  214 (357)
Q Consensus       150 ~--~rl~~~~~~~-~~--~~-----~~~---~~~~~~~--~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~  214 (357)
                      .  .|+..+.... ..  ..     ...   ..+.+..  ...++++..........++..+......+++++||||+++
T Consensus        78 ~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vvID~l~  157 (277)
T d1cr2a_          78 ETAEDLIGLHNRVRLRQSDSLKREIIENGKFDQWFDELFGNDTFHLYDSFAEAETDRLLAKLAYMRSGLGCDVIILDHIS  157 (277)
T ss_dssp             HHHHHHHHHHTTCCGGGCHHHHHHHHHTSHHHHHHHHHHSSSCEEEECCC-CCCHHHHHHHHHHHHHTTCCSEEEEEEEE
T ss_pred             hHHhHHHHHhhcCCchhhcccccchhhhHHHHHHHHHhhccceeeeeccccchhHHHHHHHhhhhhhccCcceEEEcccc
Confidence            3  2222221110 00  00     000   0111111  2345555444334445555566666667899999999999


Q ss_pred             cccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchh
Q 035774          215 ALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFH  294 (357)
Q Consensus       215 ~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~  294 (357)
                      .+......  ......+.+++..|+.+|+++||+|++++|+++...+...            .....+...++  ..+..
T Consensus       158 ~l~~~~~~--~~~~~~~~~~~~~l~~lA~~~~i~vi~~~q~~r~~~~~~~------------~~~~~~~~~~~--~gS~~  221 (277)
T d1cr2a_         158 IVVSASGE--SDERKMIDNLMTKLKGFAKSTGVVLVVICHLKNPDKGKAH------------EEGRPVSITDL--RGSGA  221 (277)
T ss_dssp             C------------CHHHHHHHHHHHHHHHHHCCEEEEEEECC-----------------------------------CHH
T ss_pred             cccccccc--cchhHHHHHHHHHHHHHhhhccccceeecccccccccccc------------cccccchhhhc--ccccc
Confidence            87654222  2244678889999999999999999999999876432110            00111111222  24456


Q ss_pred             HhhhccEEEEEEEe-----CCeEEEEEEeCCCC-CCce-eEEEEcC
Q 035774          295 WAHAVTIRLVLEAK-----SGQRFMNVEKSPTS-PPLA-FSFTINP  333 (357)
Q Consensus       295 w~~~~~~rl~l~~~-----~~~R~l~v~K~r~~-~~~~-~~f~I~~  333 (357)
                      |.+.++..+.++++     .+.+.+.|.|+|.. +.+. +.+..+.
T Consensus       222 i~~~ad~vl~l~r~~~~~~~~~~~l~v~KnR~~G~~G~~~~l~~d~  267 (277)
T d1cr2a_         222 LRQLSDTIIALERNQQGDMPNLVLVRILKCRFTGDTGIAGYMEYNK  267 (277)
T ss_dssp             HHHHCSEEEEEECC------CEEEEEEEEETTTCCCEEEEEEEECT
T ss_pred             hhhhCcEEEEEEecCccCCCCeEEEEEEccCCCCCCCCEEEEEEeC
Confidence            99999999999764     24689999999974 4443 3455553

>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=99.85  E-value=5.5e-21  Score=169.35  Aligned_cols=225  Identities=19%  Similarity=0.184  Sum_probs=141.0

Q ss_pred             CCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC----CCCeEEEEeCCCCCch--HHHHHHHh
Q 035774           85 PTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG----LDGGVIYIDVESTFTS--RRMIEMGA  158 (357)
Q Consensus        85 ~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg----~~~~vl~i~~e~~~~~--~rl~~~~~  158 (357)
                      ..+.+.+|.+++| +.+|++++|+|+||+|||+|++++|.+++....+.+    .+.+|+|+++|+....  .|+..+..
T Consensus        13 ~~~~p~~d~li~G-~~pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~~~~~~~~Rl~~~~~   91 (274)
T d1nlfa_          13 AAAPPPLDYVLPN-MVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGA   91 (274)
T ss_dssp             HSCCCCCCEEETT-EETTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSSCHHHHHHHHHHHHT
T ss_pred             cCCCCCHHHHhCC-ccCCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccchHHHHHHHHHHHhh
Confidence            3456789999965 667999999999999999999999998875332211    2468999999986443  33433332


Q ss_pred             ccCchhhcccchHHHhhcCeEEeCCC---CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHH
Q 035774          159 SSFPEIFHSKGMAQEMAGRILVLQPT---SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHI  235 (357)
Q Consensus       159 ~~~~~~~~~~~~~~~~~~~i~~~~~~---~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~  235 (357)
                      .. .    .. .......++.+....   ........+..+...  .+++++||||+++.+...    ..++...+..++
T Consensus        92 ~~-~----~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~lvviD~l~~~~~~----~~~~~~~~~~~~  159 (274)
T d1nlfa_          92 HL-S----AE-ERQAVADGLLIQPLIGSLPNIMAPEWFDGLKRA--AEGRRLMVLDTLRRFHIE----EENASGPMAQVI  159 (274)
T ss_dssp             TS-C----HH-HHHHHHHHEEECCCTTSCCCTTSHHHHHHHHHH--HTTCSEEEEECGGGGCCS----CTTCHHHHHHHH
T ss_pred             cc-C----hh-hhhcccccceeccccCccchhHHHHHHHHHHHh--ccCccEEecCchhhhccc----cccchhhHHHHH
Confidence            21 1    00 011122233332211   111112222222222  257899999999988654    233567788999


Q ss_pred             HHHHHHHHHcCCeEEEeccccccCCCCCCcccccccccccccccccCCCcceecccchhHhhhccEEEEEEEeC------
Q 035774          236 SLITSLAEFSRIPIVVTNQVRPQSHDESCLYPFQVQKMDRILKDRTRYYSHIVAVLGFHWAHAVTIRLVLEAKS------  309 (357)
Q Consensus       236 ~~Lk~la~~~~~~vv~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~palg~~w~~~~~~rl~l~~~~------  309 (357)
                      +.|+.++++++|+|++++|+++.....+..              .    ..-...++..|.+.+++++.|.+..      
T Consensus       160 ~~l~~la~~~~~~vi~v~H~~K~~~~~~~~--------------~----~~~~~~Gssai~~~a~~v~~l~r~~~~~~~~  221 (274)
T d1nlfa_         160 GRMEAIAADTGCSIVFLHHASKGAAMMGAG--------------D----QQQASRGSSVLVDNIRWQSYLSSMTSAEAEE  221 (274)
T ss_dssp             HHHHHHHHHHCCEEEEEEEC--------------------------------------CTGGGCSCEEEEEECCHHHHHH
T ss_pred             HHHHHHhhcCCCceehhhhccccccccCCc--------------c----cccccccHHHHHhhccEEEEEEecchhhhhh
Confidence            999999999999999999998753311100              0    0011223456899999999998742      


Q ss_pred             ---------CeEEEEEEeCCCCCC-ceeEEEEcCCCceecc
Q 035774          310 ---------GQRFMNVEKSPTSPP-LAFSFTINPSGISLLT  340 (357)
Q Consensus       310 ---------~~R~l~v~K~r~~~~-~~~~f~I~~~Gi~~~~  340 (357)
                               ..+.++|.|+|++++ ....|+..+.|+-.-.
T Consensus       222 ~~~~~~~~~~~~~~~v~K~~~~~~~~~~~~~~~~~g~~~~~  262 (274)
T d1nlfa_         222 WGVDDDQRRFFVRFGVSKANYGAPFADRWFRRHDGGVLKPA  262 (274)
T ss_dssp             TTCCTTSGGGEEEEEEEECSSSSCCCCEEEEECGGGCEEEC
T ss_pred             ccCcccccCcEEEEEEEeeCCCCCCceEEEEEeCCcCCchH
Confidence                     247899999999985 4467888888866543

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.72  E-value=2.4e-08  Score=83.78  Aligned_cols=44  Identities=16%  Similarity=0.167  Sum_probs=35.8

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .++++++.|.-++-..         ...-.+++..|+++.+++|+|||+++|-
T Consensus       162 ~~P~lLllDEPTs~LD---------~~~~~~i~~~l~~l~~~~g~tii~vTHd  205 (230)
T d1l2ta_         162 NNPPIILADQPTGALD---------SKTGEKIMQLLKKLNEEDGKTVVVVTHD  205 (230)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHTTCCEEEEECSC
T ss_pred             cCCCEEEecCCccccC---------HHHHHHHHHHHHHHHHhhCCEEEEECCC
Confidence            5799999998775443         3555678899999999999999999984

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=98.63  E-value=7.3e-08  Score=80.81  Aligned_cols=44  Identities=7%  Similarity=-0.044  Sum_probs=35.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .++++++.|.-++-..         ...-.++...|+++.++.|+|||+++|-
T Consensus       147 ~~P~illlDEPts~LD---------~~~~~~i~~~l~~l~~~~g~tii~vTHd  190 (232)
T d2awna2         147 AEPSVFLLDEPLSNLD---------AALRVQMRIEISRLHKRLGRTMIYVTHD  190 (232)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHHSCCEEEEEESC
T ss_pred             cCCCEEEEcCCCCCCC---------HHHHHHHHHHHHHHHHhcCCEEEEEeCC
Confidence            4799999998765443         2455668889999999999999999985

>d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Methionine import ATP-binding protein MetN
species: Escherichia coli [TaxId: 562]

Probab=98.61  E-value=4.7e-08  Score=82.45  Aligned_cols=44  Identities=11%  Similarity=0.169  Sum_probs=36.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .++++++.|.-++-...         ..-.++++.|+++.+++|+|||+++|-
T Consensus       157 ~~P~lLllDEPt~~LD~---------~~~~~i~~~l~~l~~~~g~tvi~vTHd  200 (240)
T d3dhwc1         157 SNPKVLLCDEATSALDP---------ATTRSILELLKDINRRLGLTILLITHE  200 (240)
T ss_dssp             TCCSEEEEESGGGSSCH---------HHHHHHHHHHHHHHHHHCCEEEEEBSC
T ss_pred             cCCCeEEeccccccCCH---------HHhhHHHHHHHHHHhccCCEEEEEcCC
Confidence            57999999988765432         455678899999999999999999985

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=98.55  E-value=1.2e-07  Score=79.80  Aligned_cols=45  Identities=9%  Similarity=0.045  Sum_probs=35.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .++++++.|.-++-..+         ..-.++.+.|+++.+++|+|||+++|--
T Consensus       153 ~~P~iLllDEPts~LD~---------~~~~~i~~ll~~l~~~~g~tii~vTHd~  197 (239)
T d1v43a3         153 VEPDVLLMDEPLSNLDA---------KLRVAMRAEIKKLQQKLKVTTIYVTHDQ  197 (239)
T ss_dssp             TCCSEEEEESTTTTSCH---------HHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             cCCCceeecCCcccCCH---------HHHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            47999999987755432         4556688889999999999999999853

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=98.50  E-value=4.7e-08  Score=82.45  Aligned_cols=45  Identities=4%  Similarity=0.023  Sum_probs=36.3

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .++++++.|.-++-..         ...-..+.+.|+++.+++|+|||+++|--
T Consensus       156 ~~P~iLllDEPt~~LD---------~~~~~~i~~~l~~l~~~~g~tvi~vTHd~  200 (240)
T d1g2912         156 RKPQVFLMDEPLSNLD---------AKLRVRMRAELKKLQRQLGVTTIYVTHDQ  200 (240)
T ss_dssp             TCCSEEEEECTTTTSC---------HHHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             cCCCEEEecCCCcccC---------HHHHHHHHHHHHHHHhccCCEEEEEcCCH
Confidence            5799999998776543         24556688899999999999999999853

>d3d31a2 c.37.1.12 (A:1-229) Sulfate/molybdate ABC transporter, ATP-binding protein {Methanosarcina acetivorans [TaxId: 2214]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Sulfate/molybdate ABC transporter, ATP-binding protein
species: Methanosarcina acetivorans [TaxId: 2214]

Probab=98.50  E-value=1.5e-07  Score=78.57  Aligned_cols=45  Identities=9%  Similarity=0.176  Sum_probs=35.9

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      .++++++.|.-++-..         .....++.+.|+++.++.++|||+++|--
T Consensus       144 ~~P~iLllDEPts~LD---------~~~~~~i~~~l~~l~~~~g~tii~vtHd~  188 (229)
T d3d31a2         144 TNPKILLLDEPLSALD---------PRTQENAREMLSVLHKKNKLTVLHITHDQ  188 (229)
T ss_dssp             SCCSEEEEESSSTTSC---------HHHHHHHHHHHHHHHHHTTCEEEEEESCH
T ss_pred             ccCCceeecCCCcCCC---------HHHHHHHHHHHHHHHhcCCcEEEEEcCCH
Confidence            5899999998765443         35556788899999999999999999853

>d1oxxk2 c.37.1.12 (K:1-242) Glucose transport protein GlcV, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Glucose transport protein GlcV, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=98.44  E-value=3.4e-08  Score=83.29  Aligned_cols=44  Identities=11%  Similarity=0.118  Sum_probs=35.4

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .++++++.|.-++-..+         ....++.+.|+++.+++|+|||+++|-
T Consensus       157 ~~P~llllDEPt~~LD~---------~~~~~i~~~i~~l~~~~g~tvi~vTHd  200 (242)
T d1oxxk2         157 KDPSLLLLDEPFSNLDA---------RMRDSARALVKEVQSRLGVTLLVVSHD  200 (242)
T ss_dssp             TCCSEEEEESTTTTSCG---------GGHHHHHHHHHHHHHHHCCEEEEEESC
T ss_pred             hcccceeecCCccCCCH---------HHHHHHHHHHHHHHhccCCEEEEEECC
Confidence            47999999987765533         344567888999999999999999985

>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=98.40  E-value=1.1e-06  Score=72.31  Aligned_cols=96  Identities=20%  Similarity=0.202  Sum_probs=58.7

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      .+.++.++||+|+||||.+..+|+....   .   +.+|.+|+++. +..--..|+..           +.+. + ++-+
T Consensus         5 ~~~vi~lvGptGvGKTTTiaKLA~~~~~---~---g~kV~lit~Dt-~R~gA~eQL~~-----------~a~~-l-~i~~   64 (207)
T d1okkd2           5 KGRVVLVVGVNGVGKTTTIAKLGRYYQN---L---GKKVMFCAGDT-FRAAGGTQLSE-----------WGKR-L-SIPV   64 (207)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHHT---T---TCCEEEECCCC-SSTTHHHHHHH-----------HHHH-H-TCCE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHH---C---CCcEEEEEecc-ccccchhhHhh-----------cccc-c-CceE
Confidence            5779999999999999999999987753   2   47899998864 23222222211           1111 1 2333


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccc
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL  216 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l  216 (357)
                      +...+..++...+..........+.++|+||.....
T Consensus        65 ~~~~~~~d~~~~~~~~~~~~~~~~~d~ilIDTaGr~  100 (207)
T d1okkd2          65 IQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRL  100 (207)
T ss_dssp             ECCCTTCCHHHHHHHHHHHHHHHTCSEEEECCCCCC
T ss_pred             EeccCCccHHHHHHHHHHHHHHCCCCEEEcCccccc
Confidence            333333445555544444444457899999987744

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=98.36  E-value=3.6e-07  Score=77.28  Aligned_cols=43  Identities=19%  Similarity=0.180  Sum_probs=33.7

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-..         .....++.+.|++++++ |++||+++|-
T Consensus       156 ~~P~lLllDEPt~gLD---------~~~~~~i~~~i~~l~~~-g~til~~tH~  198 (240)
T d1ji0a_         156 SRPKLLMMDEPSLGLA---------PILVSEVFEVIQKINQE-GTTILLVEQN  198 (240)
T ss_dssp             TCCSEEEEECTTTTCC---------HHHHHHHHHHHHHHHHT-TCCEEEEESC
T ss_pred             hCCCEeeecCCCcCCC---------HHHHHHHHHHHHHHHhC-CCEEEEEeCC
Confidence            5799999998775443         35566788889998776 9999999874

>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=98.35  E-value=4.4e-06  Score=68.66  Aligned_cols=95  Identities=18%  Similarity=0.196  Sum_probs=61.2

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEe
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVL  181 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~  181 (357)
                      -.++.+.||+|+||||.+..+|+....   .   +.+|..|+++. +..--..|+..           +.+.  -++-+.
T Consensus         9 p~vi~lvGptGvGKTTTiAKLA~~~~~---~---g~kV~lit~Dt-~R~gA~eQL~~-----------~a~~--l~v~~~   68 (211)
T d2qy9a2           9 PFVILMVGVNGVGKTTTIGKLARQFEQ---Q---GKSVMLAAGDT-FRAAAVEQLQV-----------WGQR--NNIPVI   68 (211)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHHHHT---T---TCCEEEECCCT-TCHHHHHHHHH-----------HHHH--TTCCEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH---C---CCcEEEEeccc-ccccchhhhhh-----------hhhh--cCCccc
Confidence            458999999999999999999987653   2   47899998864 44333333221           1111  123334


Q ss_pred             CCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccc
Q 035774          182 QPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL  216 (357)
Q Consensus       182 ~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l  216 (357)
                      ...+..++..++..........+.++|+||.....
T Consensus        69 ~~~~~~d~~~~l~~~~~~a~~~~~d~ilIDTaGr~  103 (211)
T d2qy9a2          69 AQHTGADSASVIFDAIQAAKARNIDVLIADTAGRL  103 (211)
T ss_dssp             CCSTTCCHHHHHHHHHHHHHHTTCSEEEECCCCCG
T ss_pred             ccccCCCHHHHHHHHHHHHHHcCCCEEEeccCCCc
Confidence            44455566666666555555578999999986643

>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=98.32  E-value=3.7e-06  Score=69.14  Aligned_cols=98  Identities=14%  Similarity=0.142  Sum_probs=59.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      .....++.+.||+|+||||.+..+|......      +.+|.+++++. +...-..++..           +.+.+.-.+
T Consensus         7 ~~~~~vi~lvGp~GvGKTTTiaKLA~~~~~~------g~kV~lit~Dt-~R~gA~eQL~~-----------~a~~l~v~~   68 (207)
T d1ls1a2           7 LKDRNLWFLVGLQGSGKTTTAAKLALYYKGK------GRRPLLVAADT-QRPAAREQLRL-----------LGEKVGVPV   68 (207)
T ss_dssp             CCSSEEEEEECCTTTTHHHHHHHHHHHHHHT------TCCEEEEECCS-SCHHHHHHHHH-----------HHHHHTCCE
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHHC------CCcEEEEeccc-ccchHHHHHHH-----------HHHhcCCcc
Confidence            3456799999999999999999999887642      47899999864 44433333221           111221122


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccc
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEAL  216 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l  216 (357)
                      +..  .+..++.+............+.++|+||.....
T Consensus        69 ~~~--~~~~~~~~~~~~~~~~~~~~~~d~vlIDTaGr~  104 (207)
T d1ls1a2          69 LEV--MDGESPESIRRRVEEKARLEARDLILVDTAGRL  104 (207)
T ss_dssp             EEC--CTTCCHHHHHHHHHHHHHHHTCCEEEEECCCCS
T ss_pred             ccc--cccchhhHHHHHHHHHHhhccCcceeecccccc
Confidence            322  223334444444334444567899999987754

>d1g6ha_ c.37.1.12 (A:) MJ1267 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ1267
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=98.31  E-value=7.3e-07  Score=76.05  Aligned_cols=50  Identities=34%  Similarity=0.528  Sum_probs=34.9

Q ss_pred             chhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           88 LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        88 ~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+.||.+-- -+++|+++.|.||+|+|||||+..++-  ..++     ...-++++.+
T Consensus        17 ~~aL~~vs~-~v~~Gei~~liG~nGaGKSTLl~~i~G--l~~p-----~~G~I~~~g~   66 (254)
T d1g6ha_          17 FKALDGVSI-SVNKGDVTLIIGPNGSGKSTLINVITG--FLKA-----DEGRVYFENK   66 (254)
T ss_dssp             EEEEEEECC-EEETTCEEEEECSTTSSHHHHHHHHTT--SSCC-----SEEEEEETTE
T ss_pred             eEEEcceEE-EECCCCEEEEECCCCCcHHHHHHHHHC--CCcC-----CCcEEEECCE
Confidence            334555422 389999999999999999999996663  3332     3456666654

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=98.30  E-value=9e-07  Score=74.70  Aligned_cols=40  Identities=25%  Similarity=0.415  Sum_probs=30.3

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+.+.|.|++|||||||+.-++.  ..++     ....++|+..
T Consensus        26 i~~Ge~vaIvG~sGsGKSTLl~ll~g--l~~p-----~~G~I~i~g~   65 (241)
T d2pmka1          26 IKQGEVIGIVGRSGSGKSTLTKLIQR--FYIP-----ENGQVLIDGH   65 (241)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTT--SSCC-----SEEEEEETTE
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHh--cCCC-----CCCEEEECCE
Confidence            89999999999999999999996664  3222     2446666643

>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=98.30  E-value=1.1e-06  Score=74.93  Aligned_cols=43  Identities=16%  Similarity=0.190  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .++++++.|.-++-..         .....++.+.|++++++ |+|||+++|-
T Consensus       166 ~~P~llilDEPT~gLD---------~~~~~~i~~ll~~l~~~-g~til~vtHd  208 (258)
T d1b0ua_         166 MEPDVLLFDEPTSALD---------PELVGEVLRIMQQLAEE-GKTMVVVTHE  208 (258)
T ss_dssp             TCCSEEEEESTTTTSC---------HHHHHHHHHHHHHHHHT-TCCEEEECSC
T ss_pred             cCCCEEEeccccccCC---------HHHHHHHHHhhhhhccc-CCceEEEeCC
Confidence            4799999998775543         24556678888888776 8999999874

>d1vpla_ c.37.1.12 (A:) Putative ABC transporter TM0544 {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter TM0544
species: Thermotoga maritima [TaxId: 2336]

Probab=98.26  E-value=1.4e-06  Score=73.37  Aligned_cols=45  Identities=9%  Similarity=0.034  Sum_probs=33.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVRP  257 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~~  257 (357)
                      .+++++++|..++-...         .....+...++.++++ |.+||+++|.-.
T Consensus       150 ~~p~illLDEPt~gLD~---------~~~~~i~~~i~~~~~~-g~tii~~tH~l~  194 (238)
T d1vpla_         150 VNPRLAILDEPTSGLDV---------LNAREVRKILKQASQE-GLTILVSSHNML  194 (238)
T ss_dssp             TCCSEEEEESTTTTCCH---------HHHHHHHHHHHHHHHT-TCEEEEEECCHH
T ss_pred             cCCCEEEecCCCCCCCH---------HHHHHHHHHHHHHHhc-CCEEEEEeCCHH
Confidence            57999999987754432         3445577778887766 999999998644

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.23  E-value=2.2e-06  Score=72.77  Aligned_cols=44  Identities=11%  Similarity=0.096  Sum_probs=34.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|..++-...         ..-..+...|+++.++++.|||+++|-
T Consensus       168 ~~p~ililDEpTs~LD~---------~~~~~i~~~l~~l~~~~~~Tvi~itH~  211 (251)
T d1jj7a_         168 RKPCVLILDDATSALDA---------NSQLQVEQLLYESPERYSRSVLLITQH  211 (251)
T ss_dssp             TCCSEEEEESTTTTCCH---------HHHHHHHHHHHTCGGGGGCEEEEECSC
T ss_pred             cCCcEEEecCcCcccCh---------hhHHHHHHHHHHHhhhcCCEEEEEeCC
Confidence            47999999988765432         344567788888888899999999884

>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=98.22  E-value=8.3e-07  Score=74.44  Aligned_cols=44  Identities=16%  Similarity=0.128  Sum_probs=35.0

Q ss_pred             cCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEeccc
Q 035774          203 NQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQV  255 (357)
Q Consensus       203 ~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~  255 (357)
                      .+++++++|.-++-..         ......+...+++++++++++||+++|-
T Consensus       143 ~~P~illlDEPts~LD---------~~~~~~i~~~i~~l~~~~g~tvi~vtHd  186 (240)
T d2onka1         143 IQPRLLLLDEPLSAVD---------LKTKGVLMEELRFVQREFDVPILHVTHD  186 (240)
T ss_dssp             TCCSSBEEESTTSSCC---------HHHHHHHHHHHHHHHHHHTCCEEEEESC
T ss_pred             ccCCceEecCccccCC---------HHHHHHHHHHHHHHHHhcCCeEEEEeCC
Confidence            4799999997665432         3555668889999999999999999885

>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=98.22  E-value=1.3e-05  Score=66.02  Aligned_cols=95  Identities=18%  Similarity=0.213  Sum_probs=58.9

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      +..++.++||+|+||||.+..+|+.....      +.+|.+|+++. +..-...|+..           +.+ .+ ++-+
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~~~~~------~~kV~lit~Dt-~R~gA~eQL~~-----------~a~-~l-~i~~   69 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKMFVDE------GKSVVLAAADT-FRAAAIEQLKI-----------WGE-RV-GATV   69 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHT------TCCEEEEEECT-TCHHHHHHHHH-----------HHH-HH-TCEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHC------CCceEEEeecc-cccchhHHHHH-----------Hhh-hc-Cccc
Confidence            45688999999999999999999887532      47899998864 33322222221           111 12 2333


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEecccc
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEA  215 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~  215 (357)
                      +...+..++..++..........+.++|+||....
T Consensus        70 ~~~~~~~d~~~~~~~~~~~~~~~~~d~ilIDTaGr  104 (213)
T d1vmaa2          70 ISHSEGADPAAVAFDAVAHALARNKDVVIIDTAGR  104 (213)
T ss_dssp             ECCSTTCCHHHHHHHHHHHHHHTTCSEEEEEECCC
T ss_pred             cccCCCCcHHHHHHHHHHHHHHcCCCEEEEecccc
Confidence            33344444555454444444456789999997763

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=98.21  E-value=4.5e-06  Score=70.86  Aligned_cols=25  Identities=32%  Similarity=0.647  Sum_probs=23.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+.+.|.|++|||||||+.-++
T Consensus        38 i~~Ge~iaivG~sGsGKSTLl~ll~   62 (253)
T d3b60a1          38 IPAGKTVALVGRSGSGKSTIASLIT   62 (253)
T ss_dssp             ECTTCEEEEEECTTSSHHHHHHHHT
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHh
Confidence            8999999999999999999998665

>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=98.20  E-value=2.5e-06  Score=71.57  Aligned_cols=27  Identities=33%  Similarity=0.588  Sum_probs=24.2

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      -+++|+++.|.|++|+|||||...++.
T Consensus        21 ~I~~Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          21 EVRAGEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             EEETTCEEECBCCTTSSHHHHHHHHHT
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhC
Confidence            489999999999999999999886664

>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=98.18  E-value=1.5e-05  Score=65.42  Aligned_cols=95  Identities=16%  Similarity=0.230  Sum_probs=54.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      ...++.+.||+|+||||.+..+|+....   .   +.+|.+|+++. +..--..|+..           +.+.+  ++-+
T Consensus        11 ~p~vi~lvGptGvGKTTTiAKLA~~~~~---~---g~kV~lit~Dt-~R~ga~eQL~~-----------~a~~l--~v~~   70 (211)
T d1j8yf2          11 IPYVIMLVGVQGTGKATTAGKLAYFYKK---K---GFKVGLVGADV-YRPAALEQLQQ-----------LGQQI--GVPV   70 (211)
T ss_dssp             SSEEEEEECSCCC----HHHHHHHHHHH---T---TCCEEEEECCC-SSHHHHHHHHH-----------HHHHH--TCCE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHH---C---CCceEEEEeec-cccchhHHHHH-----------hcccc--Ccce
Confidence            4568999999999999999999987753   2   47899998864 33322222211           11111  2233


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhcCeeEEEEecccc
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEA  215 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~  215 (357)
                      ....+..++...+.+........+.++|+||..+.
T Consensus        71 ~~~~~~~~~~~~~~~a~~~~~~~~~d~IlIDTaGr  105 (211)
T d1j8yf2          71 YGEPGEKDVVGIAKRGVEKFLSEKMEIIIVDTAGR  105 (211)
T ss_dssp             ECCTTCCCHHHHHHHHHHHHHHTTCSEEEEECCCS
T ss_pred             eecccchhhhHHHHHHHHHhhccCCceEEEecCCc
Confidence            33344445555554433333456799999997663

>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=98.17  E-value=2.7e-06  Score=72.52  Aligned_cols=112  Identities=16%  Similarity=0.149  Sum_probs=63.6

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCe
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRI  178 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i  178 (357)
                      +....-++++||||+|||+++..+|...         +.++++++...-.+.          +                 
T Consensus        42 ~~~~~~iLL~GppGtGKT~la~~iA~~~---------~~~~~~i~~~~l~~~----------~-----------------   85 (256)
T d1lv7a_          42 GKIPKGVLMVGPPGTGKTLLAKAIAGEA---------KVPFFTISGSDFVEM----------F-----------------   85 (256)
T ss_dssp             -CCCCEEEEECCTTSCHHHHHHHHHHHH---------TCCEEEECSCSSTTS----------C-----------------
T ss_pred             CCCCCeEEeeCCCCCCccHHHHHHHHHc---------CCCEEEEEhHHhhhc----------c-----------------
Confidence            4445568999999999999999999765         367888877542110          0                 


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCC--C--hHHHHHHHHHHHHHHHHcCCeEEEec
Q 035774          179 LVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAP--G--QHPLSWHISLITSLAEFSRIPIVVTN  253 (357)
Q Consensus       179 ~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~--r--~~~~~~i~~~Lk~la~~~~~~vv~~~  253 (357)
                         -..+...+..++.    ....+.+.+|+||.+-.+..........  .  .+.+..++..+..+....++.||.++
T Consensus        86 ---~g~~~~~l~~~f~----~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIatT  157 (256)
T d1lv7a_          86 ---VGVGASRVRDMFE----QAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAAT  157 (256)
T ss_dssp             ---CCCCHHHHHHHHH----HHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEEE
T ss_pred             ---hhHHHHHHHHHHH----HHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeC
Confidence               0012222333333    3345678899999999887642222111  1  12233444444433344556666554

>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=98.11  E-value=3.4e-06  Score=55.05  Aligned_cols=60  Identities=12%  Similarity=0.159  Sum_probs=53.5

Q ss_pred             ccccc---CCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCc
Q 035774            5 LISEM---RLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPPF   64 (357)
Q Consensus         5 ~~~~~---~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~   64 (357)
                      |++.|   |+.+...++|.++||.|++++...++.+|.++.|++++.+.+++.++.+.++.+|
T Consensus         2 pi~~L~~~Gig~~~~~kL~~aG~~Tve~ia~~t~~~L~~i~Gi~e~~a~KIi~~A~k~~~~gf   64 (64)
T d1szpa1           2 PIEKLQVNGITMADVKKLRESGLHTAEAVAYAPRKDLLEIKGISEAKADKLLNEAARLVPMGF   64 (64)
T ss_dssp             CGGGGCCTTCCHHHHHHHHTTSCCSHHHHHHSCSHHHHTSTTCCHHHHHHHHHHHHHHSCCSC
T ss_pred             CHHHHhHCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHcCCCCHHHHHHHHHHHHHHcCCCC
Confidence            45555   8999999999999999999999999999999999999999999999887766543

>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=98.07  E-value=3e-06  Score=69.44  Aligned_cols=27  Identities=33%  Similarity=0.511  Sum_probs=24.3

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      -+++|+++.|.||+|+|||||+.-++.
T Consensus        23 ~i~~Gei~~l~G~NGsGKSTLl~~i~g   49 (200)
T d1sgwa_          23 TIEKGNVVNFHGPNGIGKTTLLKTIST   49 (200)
T ss_dssp             EEETTCCEEEECCTTSSHHHHHHHHTT
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhc
Confidence            389999999999999999999997753

>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=98.06  E-value=3.2e-06  Score=72.60  Aligned_cols=120  Identities=13%  Similarity=0.120  Sum_probs=66.4

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhc
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAG  176 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~  176 (357)
                      .|+++..-++++||||+|||+|+..+|...         +.+.++++..      .+   ... +               
T Consensus        36 ~g~~~~~giLL~Gp~GtGKT~l~~ala~~~---------~~~~~~~~~~------~l---~~~-~---------------   81 (265)
T d1r7ra3          36 FGMTPSKGVLFYGPPGCGKTLLAKAIANEC---------QANFISIKGP------EL---LTM-W---------------   81 (265)
T ss_dssp             CCCCCCCEEEEBCCTTSSHHHHHHHHHHHT---------TCEEEEECHH------HH---HTS-C---------------
T ss_pred             CCCCCCCeEEEECCCCCcchhHHHHHHHHh---------CCcEEEEEHH------Hh---hhc-c---------------
Confidence            468888889999999999999999998766         3566666431      11   100 0               


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCCh----HHHHHHHHHHHHHHHHcCCeEEEe
Q 035774          177 RILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQ----HPLSWHISLITSLAEFSRIPIVVT  252 (357)
Q Consensus       177 ~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~----~~~~~i~~~Lk~la~~~~~~vv~~  252 (357)
                           .......+..++    .....+.+.+|+||.+-.++...........    +.+..++..|..+....++.||.+
T Consensus        82 -----~~~~~~~l~~~f----~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~t  152 (265)
T d1r7ra3          82 -----FGESEANVREIF----DKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGA  152 (265)
T ss_dssp             -----TTTHHHHHHHHH----HHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEEC
T ss_pred             -----ccchHHHHHHHH----HHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEe
Confidence                 000111222222    2234467899999999988764211111111    123445555555556667888887


Q ss_pred             ccccccC
Q 035774          253 NQVRPQS  259 (357)
Q Consensus       253 ~q~~~~~  259 (357)
                      ++.....
T Consensus       153 tn~~~~l  159 (265)
T d1r7ra3         153 TNRPDII  159 (265)
T ss_dssp             CBSCTTT
T ss_pred             CCCchhC
Confidence            6654433

>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=98.06  E-value=3.4e-06  Score=71.59  Aligned_cols=33  Identities=30%  Similarity=0.260  Sum_probs=27.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .-++++||||+|||+++..++...         +.++++++.
T Consensus        43 ~giLl~GppGtGKT~la~aia~~~---------~~~~~~i~~   75 (247)
T d1ixza_          43 KGVLLVGPPGVGKTHLARAVAGEA---------RVPFITASG   75 (247)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHT---------TCCEEEEEH
T ss_pred             ceEEEecCCCCChhHHHHHHHHHc---------CCCEEEEEh
Confidence            348999999999999999999654         367888765

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=98.05  E-value=1.4e-05  Score=67.33  Aligned_cols=25  Identities=24%  Similarity=0.433  Sum_probs=23.2

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+++.|.|++|||||||+.-++
T Consensus        25 i~~Ge~vaivG~sGsGKSTLl~ll~   49 (242)
T d1mv5a_          25 AQPNSIIAFAGPSGGGKSTIFSLLE   49 (242)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHHHHT
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHH
Confidence            8999999999999999999998665

>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=98.03  E-value=6.1e-06  Score=70.49  Aligned_cols=114  Identities=19%  Similarity=0.241  Sum_probs=62.1

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGR  177 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~  177 (357)
                      |+++-.-++++||||+|||+++..++...         +.++++++...      +   ... +                
T Consensus        34 g~~~~~giLL~GppGtGKT~l~~ala~~~---------~~~~~~i~~~~------l---~~~-~----------------   78 (258)
T d1e32a2          34 GVKPPRGILLYGPPGTGKTLIARAVANET---------GAFFFLINGPE------I---MSK-L----------------   78 (258)
T ss_dssp             CCCCCCEEEEECCTTSSHHHHHHHHHHHT---------TCEEEEECHHH------H---TTS-C----------------
T ss_pred             CCCCCceeEEecCCCCCchHHHHHHHHHh---------CCeEEEEEchh------h---ccc-c----------------
Confidence            45555568999999999999999888765         35677665321      0   000 0                


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCC-hHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          178 ILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPG-QHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       178 i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r-~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                              ..+-...+..+-.....+.+.+|+||.+-.+........... ...+..+...+.......++.||+++.
T Consensus        79 --------~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~tTn  148 (258)
T d1e32a2          79 --------AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATN  148 (258)
T ss_dssp             --------TTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEEEES
T ss_pred             --------cccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEEeCC
Confidence                    000011122222233456789999999999876522221111 122333333343333444566665543

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=98.02  E-value=2.5e-06  Score=72.48  Aligned_cols=25  Identities=24%  Similarity=0.408  Sum_probs=22.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +++|+.+.|.|++|||||||+.-++
T Consensus        41 i~~Ge~vaivG~sGsGKSTLl~ll~   65 (255)
T d2hyda1          41 IEKGETVAFVGMSGGGKSTLINLIP   65 (255)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHTTTT
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHH
Confidence            8999999999999999999987554

>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=97.91  E-value=3.2e-06  Score=67.58  Aligned_cols=45  Identities=16%  Similarity=0.242  Sum_probs=31.6

Q ss_pred             hhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          201 LQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       201 ~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      ...+++++++|.++.....       .    ..+...|.++.++.+++++++.|..
T Consensus        96 ~~~~~~vlllDE~~~~~~~-------~----~~~~~~l~~~l~~~~~~il~~~h~~  140 (178)
T d1ye8a1          96 KKDRRKVIIIDEIGKMELF-------S----KKFRDLVRQIMHDPNVNVVATIPIR  140 (178)
T ss_dssp             HHCTTCEEEECCCSTTGGG-------C----HHHHHHHHHHHTCTTSEEEEECCSS
T ss_pred             HhcCCCceeecCCCccchh-------h----HHHHHHHHHHhccCCCEEEEEEccH
Confidence            3568999999997543321       1    2345667777778899999998853

>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=97.80  E-value=0.00011  Score=60.48  Aligned_cols=102  Identities=20%  Similarity=0.213  Sum_probs=61.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQPT  184 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  184 (357)
                      +.|+|++|+|||.|+..++.....+      +..++|++...-     ...+..              ....       .
T Consensus        39 l~l~G~~G~GKTHLl~A~~~~~~~~------~~~~~~~~~~~~-----~~~~~~--------------~~~~-------~   86 (213)
T d1l8qa2          39 IFIYGSVGTGKTHLLQAAGNEAKKR------GYRVIYSSADDF-----AQAMVE--------------HLKK-------G   86 (213)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHHHT------TCCEEEEEHHHH-----HHHHHH--------------HHHH-------T
T ss_pred             EEEECCCCCcHHHHHHHHHHHhccC------ccceEEechHHH-----HHHHHH--------------HHHc-------c
Confidence            6799999999999999999887642      478999976431     111110              0000       0


Q ss_pred             CHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecccc
Q 035774          185 SLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQVR  256 (357)
Q Consensus       185 ~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q~~  256 (357)
                      ...++.+   .    +  ...++++||.+..+...         ......+-.+-..+.+.+..+|+++...
T Consensus        87 ~~~~~~~---~----~--~~~dll~iDDi~~i~~~---------~~~~~~lf~lin~~~~~~~~iiits~~~  140 (213)
T d1l8qa2          87 TINEFRN---M----Y--KSVDLLLLDDVQFLSGK---------ERTQIEFFHIFNTLYLLEKQIILASDRH  140 (213)
T ss_dssp             CHHHHHH---H----H--HTCSEEEEECGGGGTTC---------HHHHHHHHHHHHHHHHTTCEEEEEESSC
T ss_pred             chhhHHH---H----H--hhccchhhhhhhhhcCc---------hHHHHHHHHHHHHHhhccceEEEecCCc
Confidence            1112211   1    1  26899999999987532         2222223334455667899999987653

>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=97.80  E-value=3.6e-05  Score=65.00  Aligned_cols=33  Identities=30%  Similarity=0.299  Sum_probs=26.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .-++++||||+|||++|..+|...         +.+.+.+++
T Consensus        41 ~~vLL~GppGtGKT~la~alA~~~---------~~~~~~i~~   73 (246)
T d1d2na_          41 VSVLLEGPPHSGKTALAAKIAEES---------NFPFIKICS   73 (246)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHH---------TCSEEEEEC
T ss_pred             eEEEEECcCCCCHHHHHHHHhhcc---------ccccccccc
Confidence            358899999999999999998764         356666654

>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=97.69  E-value=0.00017  Score=62.69  Aligned_cols=122  Identities=11%  Similarity=0.013  Sum_probs=68.6

Q ss_pred             hhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhccc
Q 035774           89 KGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSK  168 (357)
Q Consensus        89 ~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~  168 (357)
                      +.+...++. -.+..+.+++||||+|||.++..+|..+..       +.+-+.++..+-++                   
T Consensus       111 ~~~~~~~~~-~~~~g~~l~~G~pG~GKT~la~ala~~~~~-------~~~~~~~~~~~~~~-------------------  163 (321)
T d1w44a_         111 PVVAEFGGH-RYASGMVIVTGKGNSGKTPLVHALGEALGG-------KDKYATVRFGEPLS-------------------  163 (321)
T ss_dssp             CEEEEETTE-EEESEEEEEECSSSSCHHHHHHHHHHHHHT-------TSCCEEEEBSCSST-------------------
T ss_pred             hHHHHHhhc-ccCCceEEEECCCCccHHHHHHHHHHHhcC-------CCCeEEEEhhHhhh-------------------
Confidence            444555532 344556778999999999999999987632       12223333322111                   


Q ss_pred             chHHHhhcCeEEeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCC--CCCChHHHHHHHHHHHHHHHHcC
Q 035774          169 GMAQEMAGRILVLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQ--RAPGQHPLSWHISLITSLAEFSR  246 (357)
Q Consensus       169 ~~~~~~~~~i~~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~--~~~r~~~~~~i~~~Lk~la~~~~  246 (357)
                              .   +.......+..++...+    .  ..+|+||.+.++......+  .....+.+.+++..+..+....+
T Consensus       164 --------~---~~G~~e~~~~~~f~~a~----~--~~ilf~DEid~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~  226 (321)
T d1w44a_         164 --------G---YNTDFNVFVDDIARAML----Q--HRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRG  226 (321)
T ss_dssp             --------T---CBCCHHHHHHHHHHHHH----H--CSEEEEECCTTTC-----------CCHHHHHHHHHHHHHHHHHT
T ss_pred             --------c---ccchHHHHHHHHHHHHh----h--ccEEEeehhhhhccccccCCCCCcchhhhhhhhhhccccccCCC
Confidence                    0   00111223334444332    2  4699999999987652111  11123567777888888888888


Q ss_pred             CeEEEecc
Q 035774          247 IPIVVTNQ  254 (357)
Q Consensus       247 ~~vv~~~q  254 (357)
                      +.||..+.
T Consensus       227 v~viaatN  234 (321)
T d1w44a_         227 CVVIASLN  234 (321)
T ss_dssp             CEEEEECC
T ss_pred             eEEEEeCC
Confidence            88887653

>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=97.51  E-value=0.00054  Score=57.36  Aligned_cols=45  Identities=16%  Similarity=0.124  Sum_probs=32.8

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRM  153 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl  153 (357)
                      .....++|+||||+|||+++..+|...         +..+.+++..+......+
T Consensus        50 ~~~~~lll~GPpG~GKTt~a~~la~~~---------~~~~~~~~~~~~~~~~~~   94 (253)
T d1sxja2          50 GVFRAAMLYGPPGIGKTTAAHLVAQEL---------GYDILEQNASDVRSKTLL   94 (253)
T ss_dssp             TSCSEEEEECSTTSSHHHHHHHHHHHT---------TCEEEEECTTSCCCHHHH
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHHH---------HhhhhccccccchhhHHH
Confidence            344578999999999999999988765         356777776554443333

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.50  E-value=8.9e-05  Score=58.87  Aligned_cols=24  Identities=33%  Similarity=0.387  Sum_probs=21.3

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      +.-.+++++|+||||||||+.+++
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~   35 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHL   35 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHH
Confidence            556799999999999999998775

>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=97.47  E-value=0.00028  Score=60.02  Aligned_cols=58  Identities=24%  Similarity=0.210  Sum_probs=46.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=+.|.|++|+|||+|+.+++.+...      ....++|.-.-+
T Consensus        48 ~~~l~TGi~~ID~l~p--ig~GQr~~Ifg~~g~GKt~l~~~~~~~~~~------~~~v~V~~~iGe  105 (276)
T d1fx0a3          48 YEPLQTGLIAIDAMIP--VGRGQRELIIGDRQTGKTAVATDTILNQQG------QNVICVYVAIGQ  105 (276)
T ss_dssp             CSBCCCSCTTTTTTSC--CBTTCBCBEEESSSSSHHHHHHHHHHTCCT------TTCEEEEEEESC
T ss_pred             CccccccceEEecccc--ccCCceEeeccCCCCChHHHHHHHHhhhcc------cCceeeeeeecc
Confidence            4579999999999987  889999999999999999999987765432      134667765433

>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=97.46  E-value=0.00025  Score=60.62  Aligned_cols=45  Identities=20%  Similarity=0.279  Sum_probs=41.3

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .+.+.||++.+|-++.  +-+|+=+.|.|++|+|||+++.+++.+..
T Consensus        49 ~e~l~TGIraID~l~p--ig~GQr~~If~~~g~GKt~ll~~~~~~~~   93 (285)
T d2jdia3          49 REPMQTGIKAVDSLVP--IGRGQRELIIGDRQTGKTSIAIDTIINQK   93 (285)
T ss_dssp             CSBCCCSCHHHHHHSC--CBTTCBCEEEESTTSSHHHHHHHHHHHTH
T ss_pred             CcccccCceEEecccC--ccCCCEEEeecCCCCChHHHHHHHHHhHH
Confidence            5689999999999987  88999999999999999999999998764

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.42  E-value=3.5e-05  Score=60.91  Aligned_cols=36  Identities=22%  Similarity=0.266  Sum_probs=28.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .|.++.|.|+|||||||+|..++...         +.+.++++.+
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~~l---------g~~~~~~~~d   38 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALANLP---------GVPKVHFHSD   38 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCS---------SSCEEEECTT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh---------CCCEEEecHH
Confidence            47899999999999999998776422         4667777664

>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Escherichia coli [TaxId: 562]

Probab=97.35  E-value=0.00039  Score=45.99  Aligned_cols=56  Identities=20%  Similarity=0.255  Sum_probs=51.8

Q ss_pred             cccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            3 NKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      ++++++|+|+....+.|+++|+.|+.|+...++.+|.++-+...+.+.++.+.+.+
T Consensus         5 ~k~I~~L~lS~R~~N~L~~~gI~tvgdL~~~s~~dLl~~~n~G~KSl~EI~~~L~~   60 (72)
T d1lb2b_           5 LRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS   60 (72)
T ss_dssp             TSBGGGGCCCHHHHHHHHHTTCCBHHHHHTCCHHHHHHSTTCCHHHHHHHHHHHHH
T ss_pred             cCcHHHhCCCHHHHHHHhHcCCcCHHHHHhCCHHHHHhCCCCcHhHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999988888776654

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.34  E-value=0.0012  Score=53.29  Aligned_cols=36  Identities=22%  Similarity=0.197  Sum_probs=27.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+++++|.|||||||++..++...-..      +.++.-++.
T Consensus         3 ~li~l~GlpgsGKSTla~~L~~~l~~~------~~~~~~~~~   38 (213)
T d1bifa1           3 TLIVMVGLPARGKTYISKKLTRYLNFI------GVPTREFNV   38 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHT------TCCEEEEEH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHhc------CCCCeEEcc
Confidence            478999999999999999999765321      345555554

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=97.32  E-value=9.8e-05  Score=57.84  Aligned_cols=37  Identities=22%  Similarity=0.080  Sum_probs=29.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.|+|+||||||||+.+++.....+      +.++.++..+.
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~------g~~v~v~~~d~   40 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCAR------GIRPGLIKHTH   40 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT------TCCEEEEEECC
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHC------CCeEEEecccc
Confidence            78999999999999999999876532      46666665543

>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=97.32  E-value=0.00014  Score=61.71  Aligned_cols=59  Identities=27%  Similarity=0.223  Sum_probs=48.9

Q ss_pred             CCCCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774           81 GGHLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus        81 ~~~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.+.||++.+|-++.  +-+|+=..|.|++|+|||+|+.+++.+.+..     ....++|.-.-+
T Consensus        49 ~~~l~TGIraID~l~p--igkGQr~~If~~~g~GKt~l~~~i~~~~~~~-----~~~v~V~~~iGe  107 (276)
T d2jdid3          49 QEILVTGIKVVDLLAP--YAKGGKIGLFGGAGVGKTVLIMELINNVAKA-----HGGYSVFAGVGE  107 (276)
T ss_dssp             CCEECCSCHHHHHHSC--EETTCEEEEEECTTSSHHHHHHHHHHHHTTT-----CSSEEEEEEESC
T ss_pred             CcccccCceeeeeecc--ccCCCEEEeeCCCCCCHHHHHHHHHHHHHhh-----CCCeEEEEEecc
Confidence            4679999999999987  7899999999999999999999999987542     134677776544

>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Thermus thermophilus [TaxId: 274]

Probab=97.31  E-value=0.00018  Score=47.25  Aligned_cols=56  Identities=11%  Similarity=0.200  Sum_probs=52.1

Q ss_pred             cccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            3 NKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      +.|+++|+|+....+.|.++|+.|+.|++..++.+|.++-++....+.++.+.+.+
T Consensus         7 ~~~I~~L~LS~R~~N~L~~~gI~tv~dL~~~s~~dLl~i~n~G~ksl~EI~~~L~~   62 (69)
T d1doqa_           7 DLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEK   62 (69)
T ss_dssp             CCCHHHHTCCHHHHHHHHHTTCCSHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHH
T ss_pred             CCcHHHcCCCHHHHHHHHHcCCccHHHHHHCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999988877654

>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.31  E-value=9.2e-05  Score=48.93  Aligned_cols=57  Identities=14%  Similarity=0.161  Sum_probs=50.9

Q ss_pred             ccccc---CCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcC
Q 035774            5 LISEM---RLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVC   61 (357)
Q Consensus         5 ~~~~~---~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~   61 (357)
                      +++.|   |+.+...++|.++||.|+++++..++.+|.++.|+++..+.++++++.+.++
T Consensus         9 ~i~~L~~~Gig~~~i~kL~~aG~~Tv~~i~~at~~~L~~i~G~~e~~A~KIi~~a~k~~~   68 (70)
T d1b22a_           9 PISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAKADKILAEAAKLVP   68 (70)
T ss_dssp             CHHHHHHTTCSHHHHHHHHTTCCSSGGGBTSSBHHHHHTTTTCSTTHHHHHHHHHHHHSC
T ss_pred             cHHHHhhCCCCHHHHHHHHHcCcchHHHHHhCCHHHHHHcCCCCHHHHHHHHHHHHHHcC
Confidence            44544   8999999999999999999999999999999999999999999998876543

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.24  E-value=0.00011  Score=58.18  Aligned_cols=36  Identities=31%  Similarity=0.215  Sum_probs=27.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+.|+|+||+|||+|+.+++......      +..+.++.+.
T Consensus         3 ~v~ItG~~GtGKTtl~~~i~~~l~~~------~~~v~~~~~~   38 (189)
T d2i3ba1           3 HVFLTGPPGVGKTTLIHKASEVLKSS------GVPVDGFYTE   38 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHHHT------TCCCEEEECC
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHC------CCEEEEEEec
Confidence            47899999999999999999877532      3455555443

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.23  E-value=9.2e-05  Score=58.09  Aligned_cols=24  Identities=33%  Similarity=0.609  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+++|+|+|||||||+|..++...
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            589999999999999999998754

>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=97.22  E-value=0.00017  Score=61.12  Aligned_cols=36  Identities=31%  Similarity=0.280  Sum_probs=27.4

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .....++++||||+|||++|..+|...-         ...+.+++
T Consensus        30 ~~P~~ilL~GpPGtGKT~la~~la~~~~---------~~~~~i~~   65 (273)
T d1gvnb_          30 ESPTAFLLGGQPGSGKTSLRSAIFEETQ---------GNVIVIDN   65 (273)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHHHTT---------TCCEEECT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhh---------cceEEEec
Confidence            3344699999999999999998887652         44666665

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=97.19  E-value=0.0001  Score=56.75  Aligned_cols=23  Identities=17%  Similarity=0.335  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHH
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .+++|+|+|||||||+|..++..
T Consensus         3 klIii~G~pGsGKTTla~~L~~~   25 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAK   25 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            47899999999999999988653

>d1x6va3 c.37.1.4 (A:34-228) Adenosine-5'phosphosulfate kinase (APS kinase) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.14  E-value=8.8e-05  Score=59.62  Aligned_cols=30  Identities=33%  Similarity=0.492  Sum_probs=26.0

Q ss_pred             CCCCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           97 GGVPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        97 GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +|+ +|.++.|+|+|||||||+|..++...-
T Consensus        15 ~~~-~g~vI~L~G~pGSGKTTiAk~La~~l~   44 (195)
T d1x6va3          15 GGF-RGCTVWLTGLSGAGKTTVSMALEEYLV   44 (195)
T ss_dssp             CSC-CCEEEEEESSCHHHHHHHHHHHHHHHH
T ss_pred             cCC-CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            355 788999999999999999999987764

>d1c9ka_ c.37.1.11 (A:) Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.14  E-value=5.1e-05  Score=60.47  Aligned_cols=37  Identities=22%  Similarity=0.261  Sum_probs=27.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCch
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTS  150 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~  150 (357)
                      +++|.|...||||.+|.+++.   .       ..+++||.|-..++.
T Consensus         1 iiLVtGGarSGKS~~AE~l~~---~-------~~~~~YiAT~~~~D~   37 (180)
T d1c9ka_           1 MILVTGGARSGKSRHAEALIG---D-------APQVLYIATSQILDD   37 (180)
T ss_dssp             CEEEEECTTSSHHHHHHHHHC---S-------CSSEEEEECCCC---
T ss_pred             CEEEECCCCccHHHHHHHHHh---c-------CCCcEEEEccCCCCH
Confidence            579999999999999998751   1       367999998765554

>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=97.14  E-value=0.00016  Score=64.34  Aligned_cols=39  Identities=23%  Similarity=0.370  Sum_probs=33.0

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      |.|.+..++++||||+|||+||..+|...         +.+++.|+..
T Consensus       150 ~~~~~~~~~~~g~~~~gk~~~~~~~~~~~---------~~~~i~in~s  188 (362)
T d1svma_         150 NIPKKRYWLFKGPIDSGKTTLAAALLELC---------GGKALNVNLP  188 (362)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHH---------CCEEECCSSC
T ss_pred             CCCCcCeEEEECCCCCCHHHHHHHHHHHc---------CCCEEEEECc
Confidence            59999999999999999999999998766         3667766543

>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=97.12  E-value=0.00038  Score=57.91  Aligned_cols=22  Identities=32%  Similarity=0.451  Sum_probs=20.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++++||||+|||++|..++...
T Consensus        38 ~L~~GPpGtGKT~lA~~la~~~   59 (238)
T d1in4a2          38 VLLAGPPGLGKTTLAHIIASEL   59 (238)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHhcc
Confidence            7899999999999999888776

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=97.10  E-value=0.00016  Score=56.79  Aligned_cols=27  Identities=30%  Similarity=0.450  Sum_probs=24.2

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+|-.+.|+|+|||||||+|..++...
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            678899999999999999999998764

>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=97.10  E-value=0.0035  Score=50.03  Aligned_cols=116  Identities=19%  Similarity=0.185  Sum_probs=64.1

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC-CCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL-DGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL  179 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~-~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~  179 (357)
                      ...-.++.|+||+|||+++..+|.......-.... +..++.+|.      .++..                        
T Consensus        42 ~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~------~~LiA------------------------   91 (195)
T d1jbka_          42 TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM------GALVA------------------------   91 (195)
T ss_dssp             SSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECH------HHHHT------------------------
T ss_pred             CCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeH------HHHhc------------------------
Confidence            45568899999999999999999887642100000 123332222      11110                        


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          180 VLQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       180 ~~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                        ......++.+.+..+...+..+ +--+++||.+..++.........      .+...||-+..+-.+.+|..+-
T Consensus        92 --g~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~~------d~~~~Lkp~L~rg~l~~IgatT  159 (195)
T d1jbka_          92 --GAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAM------DAGNMLKPALARGELHCVGATT  159 (195)
T ss_dssp             --TTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CC------CCHHHHHHHHHTTSCCEEEEEC
T ss_pred             --cCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCcc------cHHHHHHHHHhCCCceEEecCC
Confidence              0112335555555554444333 34578999999998653221111      1345677776667788887653

>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: SAM domain-like
superfamily: C-terminal domain of RNA polymerase alpha subunit
family: C-terminal domain of RNA polymerase alpha subunit
domain: C-terminal domain of RNA polymerase alpha subunit
species: Bacillus subtilis [TaxId: 1423]

Probab=97.10  E-value=0.00075  Score=43.87  Aligned_cols=56  Identities=21%  Similarity=0.250  Sum_probs=51.5

Q ss_pred             cccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            3 NKLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         3 ~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      +.++++|+|+....+.|.++|+.|+.|+...++.+|.++-+.....+.++.+.+.+
T Consensus         6 ~~~I~~L~LS~R~~N~Lk~~~I~tv~dL~~~s~~dLl~~~nfG~kSl~EIk~~L~~   61 (67)
T d1z3eb1           6 EMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE   61 (67)
T ss_dssp             TCBGGGSCCBHHHHHHHHHTTCCBHHHHHTSCHHHHHTSTTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHhcCCHHHHHHHHHcCCcCHHHHHHCCHHHHHhCCCCchhhHHHHHHHHHH
Confidence            46899999999999999999999999999999999999999999999888876654

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=97.08  E-value=0.00018  Score=56.44  Aligned_cols=27  Identities=19%  Similarity=0.235  Sum_probs=24.0

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..+.+++|+|+|||||||++..++...
T Consensus         4 ~~~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           4 HDHHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             TTSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            457899999999999999999998765

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=97.05  E-value=0.00053  Score=51.43  Aligned_cols=41  Identities=22%  Similarity=0.120  Sum_probs=28.9

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +.+|..++|.+++|+|||..+...+......     .+..++++.-
T Consensus         4 l~~~~~~il~~~tGsGKT~~~~~~~~~~~~~-----~~~~vli~~p   44 (140)
T d1yksa1           4 LKKGMTTVLDFHPGAGKTRRFLPQILAECAR-----RRLRTLVLAP   44 (140)
T ss_dssp             TSTTCEEEECCCTTSSTTTTHHHHHHHHHHH-----TTCCEEEEES
T ss_pred             HHcCCcEEEEcCCCCChhHHHHHHHHHHhhh-----cCceeeeeec
Confidence            5679999999999999997776554444321     1356777654

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.04  E-value=0.0002  Score=56.45  Aligned_cols=28  Identities=21%  Similarity=0.241  Sum_probs=24.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .+|.++.|+|.|||||||++..++....
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La~~L~   31 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQVTLN   31 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4688999999999999999999987663

>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=96.98  E-value=0.00037  Score=54.64  Aligned_cols=25  Identities=20%  Similarity=0.177  Sum_probs=22.2

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..++.|+|+|||||||+|..++...
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            4689999999999999999988764

>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=96.96  E-value=0.0019  Score=54.98  Aligned_cols=53  Identities=15%  Similarity=0.078  Sum_probs=37.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMI  154 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~  154 (357)
                      ....++.|+|.+|.||||||.+++......  .+.....++|++....++...+.
T Consensus        42 ~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~--~~~~f~~~~Wv~vs~~~~~~~l~   94 (277)
T d2a5yb3          42 LDSFFLFLHGRAGSGKSVIASQALSKSDQL--IGINYDSIVWLKDSGTAPKSTFD   94 (277)
T ss_dssp             SSSEEEEEECSTTSSHHHHHHHHHHHCSST--BTTTBSEEEEEECCCCSTTHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHhhhhh--hhhcCceEEEEEecCCCCHHHHH
Confidence            346689999999999999999988764311  11123578899876666655443

>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=96.96  E-value=0.0011  Score=56.07  Aligned_cols=117  Identities=19%  Similarity=0.212  Sum_probs=67.9

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC-CCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG-LDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL  179 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg-~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~  179 (357)
                      ...-+++.|+||+|||+++..+|.......-... .+..++.+|...      +                          
T Consensus        38 ~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~------l--------------------------   85 (268)
T d1r6bx2          38 RKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGS------L--------------------------   85 (268)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC----------------------------------
T ss_pred             ccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeech------H--------------------------
Confidence            3456789999999999999999988764210000 012233222211      0                          


Q ss_pred             EeCCCCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          180 VLQPTSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       180 ~~~~~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                      +.......++.+.+..+...+...+--+++||.+..++.......  .   -..+...||-+..+-++.+|..+-
T Consensus        86 iag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g--~---~~d~a~~Lkp~L~rg~i~vIgatT  155 (268)
T d1r6bx2          86 LAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASG--G---QVDAANLIKPLLSSGKIRVIGSTT  155 (268)
T ss_dssp             -CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSS--C---HHHHHHHHSSCSSSCCCEEEEEEC
T ss_pred             hccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCC--c---cccHHHHhhHHHhCCCCeEEEeCC
Confidence            000111234555555555555566667899999999987532111  1   123566677666667788887653

>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=96.94  E-value=0.00023  Score=55.75  Aligned_cols=22  Identities=32%  Similarity=0.419  Sum_probs=19.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|+|+|||||||+|..++...
T Consensus         7 I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           7 ILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6799999999999999998765

>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.91  E-value=0.0013  Score=41.83  Aligned_cols=54  Identities=9%  Similarity=-0.020  Sum_probs=47.6

Q ss_pred             CCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCC
Q 035774           10 RLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIVCPP   63 (357)
Q Consensus        10 ~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~   63 (357)
                      |+-+...++|.++|+.|++++...++++|.++-+++...+.++++++.+....+
T Consensus         6 GIG~~~a~~L~~~G~~tv~~l~~a~~eeL~~i~Gi~~~~A~~i~~~ar~~~d~g   59 (60)
T d2i1qa1           6 GVGPSTAEKLVEAGYIDFMKIATATVGELTDIEGISEKAAAKMIMGARDLCDLG   59 (60)
T ss_dssp             TCCHHHHHHHHHHTCCSHHHHHTCCHHHHHTSTTCCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCHHHHHHHHHccCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHHHcCCC
Confidence            567888999999999999999999999999999999999999988877655433

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=96.90  E-value=0.0015  Score=56.81  Aligned_cols=102  Identities=14%  Similarity=0.164  Sum_probs=57.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      +.-.+.|+|+||+|||||.-.++......    |..-.|+-+|...+++-..+   +..    ..+....  ....++++
T Consensus        50 ~~~~igitG~pGaGKSTli~~l~~~~~~~----g~~vaViavDpss~~~gg~l---lgd----r~rm~~~--~~~~~~~i  116 (323)
T d2qm8a1          50 RAIRVGITGVPGVGKSTTIDALGSLLTAA----GHKVAVLAVDPSSTRTGGSI---LGD----KTRMARL--AIDRNAFI  116 (323)
T ss_dssp             CSEEEEEECCTTSCHHHHHHHHHHHHHHT----TCCEEEEEECGGGGSSCCCS---SCC----GGGSTTG--GGCTTEEE
T ss_pred             CceEEeeeCCCCCCHHHHHHHHHHHHhhc----CCceeeeecccccHHHHhcc---ccc----hhhHHHH--hcccceee
Confidence            45679999999999999999999776532    23345566665443321111   000    0000000  11234555


Q ss_pred             eCCCC---HHHHHHHHHHHHHHhhhcCeeEEEEecccc
Q 035774          181 LQPTS---LSEFTESLEKIKVSLLQNQVKLLVIDSMEA  215 (357)
Q Consensus       181 ~~~~~---~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~  215 (357)
                      ....+   ...+..........+...+.++|+|-.+..
T Consensus       117 r~~~~~~~~gg~~~~~~~~i~~~~~~g~d~iiiETVG~  154 (323)
T d2qm8a1         117 RPSPSSGTLGGVAAKTRETMLLCEAAGFDVILVETVGV  154 (323)
T ss_dssp             ECCCCCSSHHHHHHHHHHHHHHHHHTTCCEEEEEECSS
T ss_pred             ccccccccccchhHHHHHHHHhhccCCCCeEEEeehhh
Confidence            44332   344444455555556667889999888754

>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=96.89  E-value=0.00052  Score=53.61  Aligned_cols=37  Identities=24%  Similarity=0.128  Sum_probs=29.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.|+|.+|||||||+..++.....+      +.+|..|..+.
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~------g~~v~vik~d~   39 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVRE------GWRVGTVKHHG   39 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT------TCCEEEEECCC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhC------CCeEEEEEecc
Confidence            68899999999999999999877632      46777776543

>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=96.88  E-value=0.0011  Score=56.47  Aligned_cols=44  Identities=23%  Similarity=0.169  Sum_probs=39.2

Q ss_pred             CCCCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774           83 HLPTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus        83 ~i~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      ...+|...+|-++.  +-+|+=..|.|++|+|||+|+.+++.+...
T Consensus        26 ~~~~~~r~ID~l~P--igrGQr~~I~g~~g~GKT~l~~~i~~~~~~   69 (289)
T d1xpua3          26 TEDLTARVLDLASP--IGRGQRGLIVAPPKAGKTMLLQNIAQSIAY   69 (289)
T ss_dssp             STHHHHHHHHHHSC--CBTTCEEEEEECSSSSHHHHHHHHHHHHHH
T ss_pred             cccccceeeeeccc--ccCCCeeeEeCCCCCCHHHHHHHHHHHHhh
Confidence            45678899999987  889999999999999999999999988764

>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=96.86  E-value=0.00028  Score=55.76  Aligned_cols=24  Identities=21%  Similarity=0.351  Sum_probs=21.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..++|.|+||+||||||..++...
T Consensus         8 K~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           8 KTVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999998764

>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=96.80  E-value=0.0015  Score=53.14  Aligned_cols=25  Identities=16%  Similarity=0.126  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      -++++||||+|||+++..+|.....
T Consensus        26 ~lLl~Gp~G~GKtt~a~~~a~~l~~   50 (207)
T d1a5ta2          26 ALLIQALPGMGDDALIYALSRYLLC   50 (207)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTC
T ss_pred             EEEEECCCCCcHHHHHHHHHHhccc
Confidence            4899999999999999999987764

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.78  E-value=0.00061  Score=53.83  Aligned_cols=36  Identities=14%  Similarity=-0.001  Sum_probs=27.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .++.|.|+|||||||++..++......      +.++..++.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~------~~~~~~~~~   37 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE------GVNYKMVSF   37 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT------TCCCEEEEH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc------CCCeEEEec
Confidence            589999999999999999998776431      345555543

>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=96.77  E-value=0.00077  Score=56.16  Aligned_cols=25  Identities=24%  Similarity=0.187  Sum_probs=21.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ..++|+||||+|||++|..++....
T Consensus        35 ~~~Ll~Gp~G~GKtt~a~~~~~~l~   59 (239)
T d1njfa_          35 HAYLFSGTRGVGKTSIARLLAKGLN   59 (239)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eeEEEECCCCCcHHHHHHHHHHHhc
Confidence            4688999999999999998887664

>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=96.77  E-value=0.0086  Score=49.35  Aligned_cols=28  Identities=21%  Similarity=0.387  Sum_probs=25.0

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccc
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALP  129 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~  129 (357)
                      +.+++|+||+.+|||+++.+++....+.
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~la   68 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMA   68 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHH
Confidence            5789999999999999999999887653

>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=96.76  E-value=0.00042  Score=55.68  Aligned_cols=26  Identities=23%  Similarity=0.257  Sum_probs=22.4

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +..++.|.|||||||||+|..++...
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999998654

>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=96.75  E-value=0.00061  Score=59.21  Aligned_cols=36  Identities=31%  Similarity=0.484  Sum_probs=26.8

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .|++ -++++||||+|||.||..+|...-         .+.+.+++
T Consensus        47 ~~~~-~iLl~GPpG~GKT~lAkalA~~~~---------~~~~~i~~   82 (309)
T d1ofha_          47 VTPK-NILMIGPTGVGKTEIARRLAKLAN---------APFIKVEA   82 (309)
T ss_dssp             CCCC-CEEEECCTTSSHHHHHHHHHHHHT---------CCEEEEEG
T ss_pred             CCCc-eEEEECCCCCCHHHHHHHHhhccc---------cchhcccc
Confidence            3454 346899999999999999987652         45666665

>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=96.73  E-value=0.00067  Score=57.43  Aligned_cols=43  Identities=21%  Similarity=0.215  Sum_probs=27.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.|+||||+|||+++..++...............++|+....
T Consensus        48 ~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~   90 (287)
T d1w5sa2          48 IYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFN   90 (287)
T ss_dssp             EEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGG
T ss_pred             EEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeecccc
Confidence            4567899999999999999876531100011134566666543

>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=96.71  E-value=0.0014  Score=54.33  Aligned_cols=22  Identities=32%  Similarity=0.440  Sum_probs=19.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++++||||+|||+++.-++...
T Consensus        38 ~Ll~GPpG~GKTtla~~la~~~   59 (239)
T d1ixsb2          38 LLLFGPPGLGKTTLAHVIAHEL   59 (239)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6799999999999999888765

>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=96.66  E-value=0.00048  Score=53.13  Aligned_cols=23  Identities=35%  Similarity=0.460  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|+||+||||++..++...
T Consensus         4 ~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           4 NIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            46777999999999999999764

>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=96.65  E-value=0.00063  Score=54.41  Aligned_cols=27  Identities=41%  Similarity=0.540  Sum_probs=22.8

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |+|-=++|.|||||||||.|..+|...
T Consensus         1 p~~~riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           1 PKGVRAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCccEEEEECCCCCCHHHHHHHHHHHh
Confidence            466667789999999999999998654

>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=96.65  E-value=0.0011  Score=55.82  Aligned_cols=35  Identities=23%  Similarity=0.167  Sum_probs=28.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+..++|.|++|+|||+|+.+++...         +....|++.
T Consensus        28 ~~~~i~i~G~~G~GKTsLl~~~~~~~---------~~~~~~i~~   62 (283)
T d2fnaa2          28 RAPITLVLGLRRTGKSSIIKIGINEL---------NLPYIYLDL   62 (283)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHHHH---------TCCEEEEEG
T ss_pred             cCCEEEEEcCCCCcHHHHHHHHHHHC---------CCCeEEEEe
Confidence            45789999999999999999988765         255777765

>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=96.63  E-value=0.00059  Score=54.26  Aligned_cols=25  Identities=32%  Similarity=0.392  Sum_probs=22.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |.+++|.||||+||||++..++...
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhC
Confidence            7899999999999999999887654

>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=96.61  E-value=0.00046  Score=55.54  Aligned_cols=35  Identities=23%  Similarity=0.298  Sum_probs=28.3

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ..+.++.|.|||||||||.|..++...           +..+|++.
T Consensus         6 ~~~~iI~l~G~pGSGKsT~a~~La~~~-----------g~~~is~g   40 (194)
T d3adka_           6 KKSKIIFVVGGPGSGKGTQCEKIVQKY-----------GYTHLSTG   40 (194)
T ss_dssp             HTSCEEEEEECTTSSHHHHHHHHHHHT-----------CCEEEEHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHh-----------CCeeEecc
Confidence            457899999999999999999888643           35677764

>d1rz3a_ c.37.1.6 (A:) Hypothetical protein rbstp0775 {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein rbstp0775
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.56  E-value=0.00061  Score=54.42  Aligned_cols=36  Identities=22%  Similarity=0.204  Sum_probs=26.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++.|+|++||||||||..++......      +..+..++..
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~l~~~------~~~~~~~~~~   59 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQTLREQ------GISVCVFHMD   59 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHT------TCCEEEEEGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhccc------cccceecccc
Confidence            57799999999999999998765421      3455555544

>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: DNA repair protein Rad51, N-terminal domain
domain: DNA repair protein Rad51, N-terminal domain
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=96.53  E-value=0.0071  Score=38.40  Aligned_cols=51  Identities=8%  Similarity=0.071  Sum_probs=46.6

Q ss_pred             CCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhc
Q 035774           10 RLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEIV   60 (357)
Q Consensus        10 ~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   60 (357)
                      |+-+...++|.++|+.+++++...++.+|.++-+++.+.+.++++.+.+.+
T Consensus         8 GIG~~~a~~L~~~g~~sv~~l~~a~~~eL~~i~Gi~~~~A~~i~~~ar~~~   58 (61)
T d1pzna1           8 GVGPATAEKLREAGYDTLEAIAVASPIELKEVAGISEGTALKIIQAARKAA   58 (61)
T ss_dssp             TCCHHHHHHHHTTTCCSHHHHHTCCHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHhcCCCHHHHHhCCHHHHHHCCCCCHHHHHHHHHHHHHHc
Confidence            778899999999999999999999999999999999999999988776543

>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=96.52  E-value=0.0036  Score=52.33  Aligned_cols=42  Identities=29%  Similarity=0.178  Sum_probs=30.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCc
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFT  149 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~  149 (357)
                      ..++|+||||+|||+++..++......     ....++|+.......
T Consensus        44 ~~lll~GppGtGKT~l~~~l~~~l~~~-----~~~~~~~~~~~~~~~   85 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLRKLWELYKDK-----TTARFVYINGFIYRN   85 (276)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTTS-----CCCEEEEEETTTCCS
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHhcc-----cCCcEEEecchhhhh
Confidence            468899999999999999988876421     146677777654433

>d1r0wa_ c.37.1.12 (A:) Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cystic fibrosis transmembrane conductance regulator, CFTR, nucleotide-binding domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.51  E-value=0.00062  Score=58.20  Aligned_cols=46  Identities=26%  Similarity=0.328  Sum_probs=31.7

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCC--CCCeEEEEeCCC
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGG--LDGGVIYIDVES  146 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg--~~~~vl~i~~e~  146 (357)
                      +++|+++.|.||+|+|||||+.-++.  ..++..|.  .++++.|+.-+.
T Consensus        59 i~~Ge~vaivG~nGsGKSTLl~~i~G--l~~p~~G~I~~~g~i~~v~Q~~  106 (281)
T d1r0wa_          59 IEKGEMLAITGSTGSGKTSLLMLILG--ELEASEGIIKHSGRVSFCSQFS  106 (281)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHHT--SSCCSEEEEECCSCEEEECSSC
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhC--CCcCCCcEEEECCEEEEEeccc
Confidence            89999999999999999999987663  33222221  124566665543

>d1m7ga_ c.37.1.4 (A:) Adenosine-5'phosphosulfate kinase (APS kinase) {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Adenosine-5'phosphosulfate kinase (APS kinase)
domain: Adenosine-5'phosphosulfate kinase (APS kinase)
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.47  E-value=0.00059  Score=55.68  Aligned_cols=41  Identities=17%  Similarity=0.187  Sum_probs=32.3

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .+|.++.|+|.|||||||++..++......  .   +..+++++.+
T Consensus        22 ~kg~vIwltGlsGsGKTTia~~L~~~l~~~--~---~~~~~~ldgD   62 (208)
T d1m7ga_          22 QRGLTIWLTGLSASGKSTLAVELEHQLVRD--R---RVHAYRLDGD   62 (208)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHHHHH--H---CCCEEEECHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHh--c---CceEEEEcch
Confidence            678899999999999999999988765321  1   3578888765

>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=96.44  E-value=0.00097  Score=53.54  Aligned_cols=35  Identities=23%  Similarity=0.231  Sum_probs=28.0

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.-.++.|.|||||||||+|..++...           ...||++.
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~-----------g~~~is~g   40 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDY-----------SFVHLSAG   40 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS-----------SCEEEEHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh-----------CCeEEehh
Confidence            345689999999999999999998644           36788863

>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=96.43  E-value=0.00084  Score=53.04  Aligned_cols=22  Identities=27%  Similarity=0.280  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+|||||||+|..++...
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6799999999999999888754

>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=96.39  E-value=0.0067  Score=53.93  Aligned_cols=115  Identities=17%  Similarity=0.202  Sum_probs=53.1

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCC-CCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEE
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGL-DGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILV  180 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~-~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~  180 (357)
                      ..-.+|.|+||+|||+++..+|..+....-.... +..++.+|...      +..-                        
T Consensus        43 k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~------l~ag------------------------   92 (387)
T d1qvra2          43 KNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGS------LLAG------------------------   92 (387)
T ss_dssp             CCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC------------------------------------
T ss_pred             CCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhh------hhcc------------------------
Confidence            3445777999999999999998876542100001 23444444321      1100                        


Q ss_pred             eCCCCHHHHHHHHHHHHHHhhhc-CeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          181 LQPTSLSEFTESLEKIKVSLLQN-QVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       181 ~~~~~~~~~~~~l~~l~~~~~~~-~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                        .....++.+.+..+...+... +.-+++||.+..++.......      -..+...||-+..+-.+.+|..+-
T Consensus        93 --~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g------~~d~a~~Lkp~L~rg~~~~I~~tT  159 (387)
T d1qvra2          93 --AKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEG------AVDAGNMLKPALARGELRLIGATT  159 (387)
T ss_dssp             -------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------------HHHHHTTCCCEEEEEC
T ss_pred             --cCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCC------cccHHHHHHHHHhCCCcceeeecC
Confidence              001123334444444444343 345689999999986532111      123567788887777888887754

>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=96.36  E-value=0.001  Score=53.19  Aligned_cols=23  Identities=26%  Similarity=0.427  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|||||||||.|..++...
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68999999999999999988654

>d2bmfa2 c.37.1.14 (A:178-482) Dengue virus helicase {Dengue virus type 2 [TaxId: 11060]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: Dengue virus helicase
species: Dengue virus type 2 [TaxId: 11060]

Probab=96.35  E-value=0.0063  Score=51.92  Aligned_cols=40  Identities=15%  Similarity=0.035  Sum_probs=29.2

Q ss_pred             CCCCcEEEEEcCCCCcHHH-HHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           99 VPFGVVTELVGPAGTGKTQ-FCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~-l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +.+|..++|.|++|||||. ++..++..+..+      +..++|+.-
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~------~~~~lvi~P   46 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR------GLRTLILAP   46 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH------TCCEEEEES
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc------CCEEEEEcc
Confidence            6789999999999999995 544555444321      367888853

>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=96.34  E-value=0.00094  Score=53.32  Aligned_cols=23  Identities=17%  Similarity=0.253  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|||||||||+|..++...
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            36799999999999999887655

>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=96.34  E-value=0.001  Score=52.66  Aligned_cols=22  Identities=36%  Similarity=0.536  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+|||||||+|..++...
T Consensus         3 I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           3 VLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6788999999999999999765

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.31  E-value=0.0019  Score=51.02  Aligned_cols=36  Identities=17%  Similarity=0.146  Sum_probs=27.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+++|.|+||+||||++..++...-.+      +..+..++.
T Consensus         2 kiivi~G~~GsGKTT~~~~La~~L~~~------~~~~~~~~~   37 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKEILDNQ------GINNKIINY   37 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHHTT------TCCEEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc------CCCEEEEEC
Confidence            378899999999999999998766431      356666653

>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=96.31  E-value=0.0011  Score=52.54  Aligned_cols=22  Identities=23%  Similarity=0.228  Sum_probs=19.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.|.|+|||||||+|..++...
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6789999999999999999765

>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=96.25  E-value=0.0012  Score=52.90  Aligned_cols=31  Identities=13%  Similarity=0.260  Sum_probs=24.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      -++|.|+|||||||+|..++...           ...+||+.
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~-----------g~~~is~g   38 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHF-----------ELKHLSSG   38 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHB-----------CCEEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH-----------CCeEEcHH
Confidence            46678999999999999999754           26677763

>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=96.25  E-value=0.0013  Score=53.67  Aligned_cols=23  Identities=30%  Similarity=0.631  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|||||||||.|..++.+.
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            89999999999999999999876

>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=96.20  E-value=0.0025  Score=53.95  Aligned_cols=39  Identities=21%  Similarity=0.190  Sum_probs=34.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..+++++|.-|+||||++.++|...+..      +.+|++||++.
T Consensus        20 ~~iii~sGKGGVGKTT~a~nLA~~lA~~------G~rVllvD~Dp   58 (279)
T d1ihua2          20 HGLIMLMGKGGVGKTTMAAAIAVRLADM------GFDVHLTTSDP   58 (279)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEESCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHC------CCcEEEEeCCC
Confidence            6788999999999999999999988752      58999999985

>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=96.18  E-value=0.0013  Score=54.15  Aligned_cols=38  Identities=21%  Similarity=0.253  Sum_probs=27.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++|+||||+|||+++..+|.......    ....++.++...
T Consensus        48 lll~Gp~G~GKTtla~~iak~l~~~~----~~~~~~e~n~s~   85 (231)
T d1iqpa2          48 LLFAGPPGVGKTTAALALARELFGEN----WRHNFLELNASD   85 (231)
T ss_dssp             EEEESCTTSSHHHHHHHHHHHHHGGG----HHHHEEEEETTC
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHhcc----cCCCeeEEecCc
Confidence            78999999999999999987664210    124566676543

>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=96.16  E-value=0.0014  Score=51.78  Aligned_cols=22  Identities=32%  Similarity=0.430  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+|||||||+|..++...
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5678999999999999998654

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=96.16  E-value=0.0093  Score=48.79  Aligned_cols=26  Identities=31%  Similarity=0.498  Sum_probs=23.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhcc
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      ++++|+||+.+|||+++.+++....+
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~il   61 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALL   61 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHHHHHH
Confidence            48999999999999999999988765

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.13  E-value=0.0017  Score=52.68  Aligned_cols=25  Identities=24%  Similarity=0.397  Sum_probs=22.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |.+++|+||+|+|||+|...++...
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhC
Confidence            7899999999999999999888763

>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=96.13  E-value=0.0023  Score=52.62  Aligned_cols=23  Identities=39%  Similarity=0.452  Sum_probs=20.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+||||+|||+++..++....
T Consensus        36 lll~Gp~G~GKTtl~~~i~~~l~   58 (237)
T d1sxjd2          36 MLFYGPPGTGKTSTILALTKELY   58 (237)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHHc
Confidence            78999999999999999998753

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=96.11  E-value=0.0028  Score=47.43  Aligned_cols=37  Identities=19%  Similarity=0.138  Sum_probs=26.5

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +..+..+|.+|+|+|||.++..++..      .   +.+++++.-.
T Consensus         6 ~~~~~~ll~apTGsGKT~~~~~~~~~------~---~~~vli~~P~   42 (136)
T d1a1va1           6 QSFQVAHLHAPTGSGKSTKVPAAYAA------Q---GYKVLVLNPS   42 (136)
T ss_dssp             SSCEEEEEECCTTSCTTTHHHHHHHT------T---TCCEEEEESC
T ss_pred             cCCCEEEEEeCCCCCHHHHHHHHHHH------c---CCcEEEEcCh
Confidence            34578899999999999887655432      1   4678877653

>d1yrba1 c.37.1.10 (A:1-244) ATP(GTP)-binding protein PAB0955 {Pyrococcus abyssi [TaxId: 29292]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: ATP(GTP)-binding protein PAB0955
species: Pyrococcus abyssi [TaxId: 29292]

Probab=96.11  E-value=0.0031  Score=51.96  Aligned_cols=33  Identities=27%  Similarity=0.427  Sum_probs=25.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      ++.|.|++|+|||||+..+..+...       +..+..|+
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~~~~~-------~~~~~ivn   34 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGRYLED-------NYKVAYVN   34 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTT-------TSCEEEEE
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHHhh-------CCeEEEEe
Confidence            6899999999999999999865432       34566664

>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=96.11  E-value=0.0015  Score=51.60  Aligned_cols=22  Identities=18%  Similarity=0.048  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+|||||||.|..++...
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999888654

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=96.07  E-value=0.0037  Score=50.25  Aligned_cols=47  Identities=19%  Similarity=0.262  Sum_probs=31.6

Q ss_pred             chhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           88 LKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        88 ~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ...++.++.|     .-++|++|+|+|||+.+.-.+......      +.+++|+.-.
T Consensus        31 ~~ai~~l~~~-----~~~il~apTGsGKT~~a~l~i~~~~~~------~~~vl~l~P~   77 (202)
T d2p6ra3          31 AEAVEKVFSG-----KNLLLAMPTAAGKTLLAEMAMVREAIK------GGKSLYVVPL   77 (202)
T ss_dssp             HHHHHHHTTC-----SCEEEECSSHHHHHHHHHHHHHHHHHT------TCCEEEEESS
T ss_pred             HHHHHHHHcC-----CCEEEEcCCCCchhHHHHHHHHHHhhc------cCcceeeccc
Confidence            4557777654     246799999999998875444444321      3678888653

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=96.06  E-value=0.0027  Score=54.64  Aligned_cols=43  Identities=16%  Similarity=0.208  Sum_probs=32.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      --++.|+|++||||||||..+......   + ..+.+|..|++++-+
T Consensus        80 P~iIGIaG~sgSGKSTla~~L~~lL~~---~-~~~~~v~~Is~D~F~  122 (308)
T d1sq5a_          80 PYIISIAGSVAVGKSTTARVLQALLSR---W-PEHRRVELITTDGFL  122 (308)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHHTT---S-TTCCCEEEEEGGGGB
T ss_pred             CEEEEEeCCCCCCCcHHHHHHHHHHhh---h-cCCCceEEEeeeeeE
Confidence            358999999999999999988866542   1 114678889987643

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.05  E-value=0.0018  Score=52.61  Aligned_cols=42  Identities=19%  Similarity=0.281  Sum_probs=27.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.|+|++|||||||+..++.......-. -....+..++++.
T Consensus         4 iIgI~G~~gSGKSTla~~L~~~l~~~~~~-~~~~~~~vi~~D~   45 (213)
T d1uj2a_           4 LIGVSGGTASGKSSVCAKIVQLLGQNEVD-YRQKQVVILSQDS   45 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTGGGSC-GGGCSEEEEEGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhchhccc-cCCCceEEEeccc
Confidence            67899999999999999888765321000 0023566777653

>d2p67a1 c.37.1.10 (A:1-327) LAO/AO transport system kinase ArgK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: LAO/AO transport system kinase ArgK
species: Escherichia coli [TaxId: 562]

Probab=96.05  E-value=0.0061  Score=52.95  Aligned_cols=39  Identities=23%  Similarity=0.288  Sum_probs=29.3

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +.-.+.|+|+||+|||||...++......      +.+|..+..+
T Consensus        53 ~~~~IgitG~pGaGKSTLi~~l~~~~~~~------g~~vavlavD   91 (327)
T d2p67a1          53 NTLRLGVTGTPGAGKSTFLEAFGMLLIRE------GLKVAVIAVD   91 (327)
T ss_dssp             CSEEEEEEECTTSCHHHHHHHHHHHHHHT------TCCEEEEEEC
T ss_pred             CceEEEeeCCCCCCHHHHHHHHHHHHHhc------CCceeeecCC
Confidence            46689999999999999999999776532      3455555443

>d2eyqa3 c.37.1.19 (A:546-778) Transcription-repair coupling factor, TRCF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Transcription-repair coupling factor, TRCF
species: Escherichia coli [TaxId: 562]

Probab=96.05  E-value=0.014  Score=47.92  Aligned_cols=49  Identities=16%  Similarity=0.232  Sum_probs=38.1

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIE  155 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~  155 (357)
                      .-...+|+|..|||||..++..+..++..      +..|+++.-+..+..+....
T Consensus        75 ~~~~~LL~GdvGsGKT~V~~~a~~~~~~~------g~qv~~l~Pt~~La~Q~~~~  123 (233)
T d2eyqa3          75 LAMDRLVCGDVGFGKTEVAMRAAFLAVDN------HKQVAVLVPTTLLAQQHYDN  123 (233)
T ss_dssp             SCCEEEEECCCCTTTHHHHHHHHHHHHTT------TCEEEEECSSHHHHHHHHHH
T ss_pred             CccCeEEEcCCCCCcHHHHHHHHHHHHHc------CCceEEEccHHHhHHHHHHH
Confidence            44688999999999999999999988852      58899988766555444433

>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=96.02  E-value=0.016  Score=46.37  Aligned_cols=27  Identities=15%  Similarity=0.112  Sum_probs=23.5

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .+.-++++|+||+|||++|..++....
T Consensus        14 ~~~~~l~~G~~g~gk~~~a~~l~~~i~   40 (198)
T d2gnoa2          14 EGISILINGEDLSYPREVSLELPEYVE   40 (198)
T ss_dssp             SSEEEEEECSSSSHHHHHHHHHHHHHH
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHh
Confidence            466899999999999999999997653

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.01  E-value=0.0034  Score=50.92  Aligned_cols=39  Identities=18%  Similarity=0.101  Sum_probs=31.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      .+|-++.|.|+.||||||++..++.....      .+.+|+++..
T Consensus         1 ~rG~lI~ieG~dGsGKsT~~~~L~~~L~~------~g~~v~~~~~   39 (209)
T d1nn5a_           1 RRGALIVLEGVDRAGKSTQSRKLVEALCA------AGHRAELLRF   39 (209)
T ss_dssp             CCCCEEEEEESTTSSHHHHHHHHHHHHHH------TTCCEEEEES
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHHHHHHH------CCCcEEEEeC
Confidence            46889999999999999999988876542      1467877764

>d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=96.01  E-value=0.0029  Score=53.59  Aligned_cols=127  Identities=16%  Similarity=0.185  Sum_probs=60.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQP  183 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  183 (357)
                      -+.|.|..|+|||||+-.++...-...+.|.........|.+.   .++-+.+.-......+..      -...+.+++.
T Consensus         8 ni~i~gh~~~GKTtL~e~ll~~~g~~~~~g~v~~~~~~~D~~~---~E~~r~~si~~~~~~~~~------~~~~~n~iDt   78 (276)
T d2bv3a2           8 NIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFME---QERERGITITAAVTTCFW------KDHRINIIDA   78 (276)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHTSSCC----------------------CCCCCCCSEEEEEE------TTEEEEEECC
T ss_pred             EEEEEeCCCCCHHHHHHHHHHhcCccccccceecCceEEeccH---HHHhcCCccccceeeecc------CCeEEEEecC
Confidence            3789999999999999999887654333332222222333221   111111110000000000      0124556665


Q ss_pred             CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeE-EEeccccc
Q 035774          184 TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPI-VVTNQVRP  257 (357)
Q Consensus       184 ~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~v-v~~~q~~~  257 (357)
                      ....++..   .....+..-...++|||....+..               ....+-+.+++++++. +++|.+-+
T Consensus        79 PG~~dF~~---e~~~~l~~~D~avlVvda~~Gv~~---------------~T~~~w~~a~~~~lP~i~fINKmDr  135 (276)
T d2bv3a2          79 PGHVDFTI---EVERSMRVLDGAIVVFDSSQGVEP---------------QSETVWRQAEKYKVPRIAFANKMDK  135 (276)
T ss_dssp             CSSSSCST---THHHHHHHCCEEEEEEETTTSSCH---------------HHHHHHHHHHTTTCCEEEEEECTTS
T ss_pred             CchhhhHH---HHHHHHHhhhheEEeccccCCcch---------------hHHHHHHHHHHcCCCEEEEEecccc
Confidence            54333321   222233345788999997664422               2345667788889885 46676644

>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=95.98  E-value=0.0016  Score=54.32  Aligned_cols=23  Identities=39%  Similarity=0.527  Sum_probs=21.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++|+||||+|||+++..++....
T Consensus        36 lll~Gp~G~GKTt~~~~la~~l~   58 (252)
T d1sxje2          36 LLLYGPNGTGKKTRCMALLESIF   58 (252)
T ss_dssp             EEEECSTTSSHHHHHHTHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhhc
Confidence            78999999999999999998764

>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=95.92  E-value=0.003  Score=51.76  Aligned_cols=23  Identities=35%  Similarity=0.408  Sum_probs=20.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++++||||+|||+++..++....
T Consensus        38 lLl~Gp~G~GKttl~~~la~~l~   60 (227)
T d1sxjc2          38 LLFYGPPGTGKTSTIVALAREIY   60 (227)
T ss_dssp             EEEECSSSSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCChhHHHHHHHHHhh
Confidence            67999999999999999998754

>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=95.92  E-value=0.0023  Score=52.18  Aligned_cols=23  Identities=22%  Similarity=0.284  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++.|.|||||||||.|..++...
T Consensus         5 ~IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           5 QIAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            45688999999999999999876

>d1odfa_ c.37.1.6 (A:) Hypothetical protein Ygr205W {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Hypothetical protein Ygr205W
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.91  E-value=0.0021  Score=54.72  Aligned_cols=42  Identities=19%  Similarity=0.358  Sum_probs=30.2

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      -=++.|+|++|||||||+..+.......  .+ ....|+.++.++
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~~L~~~--~~-~~~~v~~iS~Dd   68 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYNHLMEK--YG-GEKSIGYASIDD   68 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHH--HG-GGSCEEEEEGGG
T ss_pred             CEEEEeECCCCCCHHHHHHHHHHHHHHH--hC-CCcceEeeccCC
Confidence            3488899999999999999887655321  10 124688888775

>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=95.89  E-value=0.0032  Score=51.53  Aligned_cols=23  Identities=26%  Similarity=0.173  Sum_probs=20.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++++||||+|||++|.-++....
T Consensus        39 ~ll~Gp~G~GKTt~a~~la~~l~   61 (224)
T d1sxjb2          39 MIISGMPGIGKTTSVHCLAHELL   61 (224)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCchhhHHHHHHHHh
Confidence            68999999999999999887654

>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=95.87  E-value=0.0024  Score=49.89  Aligned_cols=23  Identities=26%  Similarity=0.257  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|.|+|||||||++..+|...
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~~L   26 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELARAL   26 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh
Confidence            45678999999999999998765

>d1g3qa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.85  E-value=0.0044  Score=50.79  Aligned_cols=39  Identities=31%  Similarity=0.419  Sum_probs=32.1

Q ss_pred             CcEEEEE-cCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELV-GPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~-G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      |.++.|+ +..|+||||++.++|...+..      +.+|+++|++.
T Consensus         2 ~~vIav~~~kGGvGKTtia~nLA~~la~~------g~~VlliD~D~   41 (237)
T d1g3qa_           2 GRIISIVSGKGGTGKTTVTANLSVALGDR------GRKVLAVDGDL   41 (237)
T ss_dssp             CEEEEEECSSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCT
T ss_pred             CeEEEEECCCCCCcHHHHHHHHHHHHHhC------CCCEEEEeCCC
Confidence            5566555 889999999999999988742      58999999874

>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=95.77  E-value=0.0028  Score=49.07  Aligned_cols=22  Identities=23%  Similarity=0.332  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.|.|+||+||||++..+|...
T Consensus         3 I~liG~~GsGKsTi~k~La~~l   24 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAKDL   24 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5667999999999999998765

>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=95.75  E-value=0.0028  Score=49.21  Aligned_cols=22  Identities=32%  Similarity=0.459  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+||+||||++..++...
T Consensus         4 IvliG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4455999999999999998765

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=95.75  E-value=0.0039  Score=50.46  Aligned_cols=27  Identities=19%  Similarity=0.038  Sum_probs=24.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +|.+++|.|+.||||||++..++....
T Consensus         1 rgkfIviEG~dGsGKsT~~~~L~~~L~   27 (210)
T d4tmka_           1 RSKYIVIEGLEGAGKTTARNVVVETLE   27 (210)
T ss_dssp             CCCEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHH
Confidence            588999999999999999999887654

>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=95.71  E-value=0.0047  Score=51.96  Aligned_cols=37  Identities=14%  Similarity=0.205  Sum_probs=32.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+.|+|.-|+||||++.+++...+..      +.+|+.||++.
T Consensus         3 ~Iai~gKGGvGKTT~a~nLA~~LA~~------G~rVllID~D~   39 (269)
T d1cp2a_           3 QVAIYGKGGIGKSTTTQNLTSGLHAM------GKTIMVVGCDP   39 (269)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHTT------TCCEEEEEECT
T ss_pred             EEEEECCCcCCHHHHHHHHHHHHHhC------CCcEEEEecCC
Confidence            46789999999999999999998852      58999999974

>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=95.68  E-value=0.11  Score=39.58  Aligned_cols=22  Identities=27%  Similarity=0.401  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+.++...-
T Consensus         6 i~vvG~~~vGKTsLi~~~~~~~   27 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5788999999999999998653

>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=95.67  E-value=0.0055  Score=50.06  Aligned_cols=39  Identities=31%  Similarity=0.391  Sum_probs=31.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTF  148 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~  148 (357)
                      +.+..|..|+||||++.++|...+..      +.+|++||++...
T Consensus         4 Iav~s~KGGvGKTtia~nlA~~la~~------g~~VlliD~D~~~   42 (232)
T d1hyqa_           4 ITVASGKGGTGKTTITANLGVALAQL------GHDVTIVDADITM   42 (232)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHHHHHT------TCCEEEEECCCSS
T ss_pred             EEEECCCCCChHHHHHHHHHHHHHhC------CCCEEEEeCCCCC
Confidence            45566999999999999999988742      5899999997543

>d1htwa_ c.37.1.18 (A:) Hypothetical protein HI0065 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: YjeE-like
domain: Hypothetical protein HI0065
species: Haemophilus influenzae [TaxId: 727]

Probab=95.66  E-value=0.0043  Score=47.71  Aligned_cols=29  Identities=21%  Similarity=0.201  Sum_probs=26.1

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .++|.++.+.|+=|+|||+|+..++....
T Consensus        30 ~~~g~ii~L~G~LGaGKTtfvr~~~~~lg   58 (158)
T d1htwa_          30 TEKAIMVYLNGDLGAGKTTLTRGMLQGIG   58 (158)
T ss_dssp             CSSCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCCCeEEEEecCCCccHHHHHHHHHhhcc
Confidence            47899999999999999999999997653

>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=95.63  E-value=0.0054  Score=52.13  Aligned_cols=37  Identities=19%  Similarity=0.272  Sum_probs=33.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.+.|.-|+||||++.++|...+..      +.+|+.||++.
T Consensus        10 ~i~~sGKGGVGKTTvaa~lA~~lA~~------G~rVLlvD~Dp   46 (296)
T d1ihua1          10 YLFFTGKGGVGKTSISCATAIRLAEQ------GKRVLLVSTDP   46 (296)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEECCT
T ss_pred             EEEEECCCcChHHHHHHHHHHHHHHC------CCCEEEEeCCC
Confidence            77899999999999999999988853      58999999985

>d1tuea_ c.37.1.20 (A:) Replication protein E1 helicase domain {Human papillomavirus type 18 [TaxId: 333761]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Replication protein E1 helicase domain
species: Human papillomavirus type 18 [TaxId: 333761]

Probab=95.47  E-value=0.0042  Score=49.56  Aligned_cols=39  Identities=31%  Similarity=0.408  Sum_probs=32.7

Q ss_pred             CchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           87 RLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        87 G~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      -+..|-.+|. |.|+-..++|.|||++|||.||..++...
T Consensus        39 Fl~~l~~~l~-~~PKkn~i~~~GP~~TGKS~f~~sl~~~l   77 (205)
T d1tuea_          39 FLGALKSFLK-GTPKKNCLVFCGPANTGKSYFGMSFIHFI   77 (205)
T ss_dssp             HHHHHHHHHH-TCTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCceEEEEECCCCccHHHHHHHHHHHh
Confidence            3566777785 48999999999999999999999887654

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=95.43  E-value=0.023  Score=42.70  Aligned_cols=41  Identities=22%  Similarity=0.259  Sum_probs=33.1

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..|.|.+|+||=.||||+-+++.+.+....      +.+|+.|.-..
T Consensus         5 ~~G~l~lI~GpMfSGKTteLi~~~~~~~~~------g~~vl~i~~~~   45 (141)
T d1xx6a1           5 DHGWVEVIVGPMYSGKSEELIRRIRRAKIA------KQKIQVFKPEI   45 (141)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHT------TCCEEEEEEC-
T ss_pred             cceeEEEEEeccccHHHHHHHHHHHHhhhc------CCcEEEEEecc
Confidence            369999999999999999999999877542      47888886543

>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=95.42  E-value=0.0043  Score=49.26  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .++|+||||+|||+++..++...
T Consensus         3 pIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           3 PIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHC
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            47899999999999999998764

>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=95.40  E-value=0.0043  Score=49.42  Aligned_cols=23  Identities=35%  Similarity=0.446  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .++|+||||+|||+++..++...
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHhC
Confidence            37899999999999999988764

>d1yzqa1 c.37.1.8 (A:14-177) Rab6 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.38  E-value=0.11  Score=39.46  Aligned_cols=22  Identities=18%  Similarity=0.295  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.++..+-
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~~   24 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYDS   24 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5788999999999999998644

>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=95.33  E-value=0.0049  Score=46.93  Aligned_cols=22  Identities=36%  Similarity=0.404  Sum_probs=19.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+||+|||+|+..++.+-
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhcCC
Confidence            5799999999999999998664

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.25  E-value=0.0037  Score=53.11  Aligned_cols=37  Identities=11%  Similarity=0.214  Sum_probs=26.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++.|+|++||||||++..+....-.      .+.+++.|+.+.
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~------~~v~~~iI~~Ds   42 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRR------EGVKAVSIEGDA   42 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHH------HTCCEEEEEGGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhh------cCCCeEEEeCCC
Confidence            8999999999999999988765432      135788888875

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=95.19  E-value=0.0063  Score=51.89  Aligned_cols=40  Identities=15%  Similarity=0.095  Sum_probs=27.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      .+|.|+||||||+.+.+-+...+..  .+....++++++...
T Consensus        17 ~lI~g~aGTGKTt~l~~rv~~ll~~--~~~~~~~ILvlt~tn   56 (306)
T d1uaaa1          17 CLVLAGAGSGKTRVITNKIAHLIRG--CGYQARHIAAVTFTN   56 (306)
T ss_dssp             EEECCCTTSCHHHHHHHHHHHHHHH--HCCCGGGEEEEESSH
T ss_pred             EEEEeeCCccHHHHHHHHHHHHHHh--cCCChhHEEEEeCcH
Confidence            5688999999999887766555421  111246799998753

>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=95.19  E-value=0.0078  Score=51.17  Aligned_cols=38  Identities=18%  Similarity=0.231  Sum_probs=32.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST  147 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~  147 (357)
                      .+.|.|.-|+||||++.++|...+..      +.+|+.||++..
T Consensus         4 ~IaisgKGGVGKTT~a~NLA~~LA~~------G~rVLlID~DpQ   41 (289)
T d2afhe1           4 QCAIYGKGGIGKSTTTQNLVAALAEM------GKKVMIVGCDPK   41 (289)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHT------TCCEEEEEECSS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC------CCCEEEEecCCC
Confidence            45679999999999999999888752      589999999753

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=95.16  E-value=0.023  Score=42.61  Aligned_cols=39  Identities=18%  Similarity=0.153  Sum_probs=32.0

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      |.+.+|+||=.||||+-+++.+.+....      +.+|+.|-...
T Consensus         2 G~L~~i~GpMfsGKTteLi~~~~~~~~~------~~kv~~ikp~~   40 (139)
T d2b8ta1           2 GWIEFITGPMFAGKTAELIRRLHRLEYA------DVKYLVFKPKI   40 (139)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT------TCCEEEEEECC
T ss_pred             cEEEEEEccccCHHHHHHHHHHHHHHHC------CCcEEEEEEcc
Confidence            7899999999999999999888777532      57888887654

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=95.16  E-value=0.0079  Score=51.69  Aligned_cols=40  Identities=15%  Similarity=0.091  Sum_probs=27.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ++|.|+||||||+.+.+-++..+...  +-....+++++...
T Consensus        27 ~lV~g~aGSGKTt~l~~ri~~ll~~~--~~~p~~il~lt~t~   66 (318)
T d1pjra1          27 LLIMAGAGSGKTRVLTHRIAYLMAEK--HVAPWNILAITFTN   66 (318)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHTT--CCCGGGEEEEESSH
T ss_pred             EEEEecCCccHHHHHHHHHHHHHHcC--CCCHHHeEeEeccH
Confidence            67889999999999887665554321  11236788888754

>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=95.10  E-value=0.012  Score=50.71  Aligned_cols=36  Identities=25%  Similarity=0.287  Sum_probs=27.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +...++++||||+|||.||..+|...         +.+.+.+++.
T Consensus        51 p~~~~lf~Gp~GvGKT~lak~la~~l---------~~~~i~~d~s   86 (315)
T d1r6bx3          51 PVGSFLFAGPTGVGKTEVTVQLSKAL---------GIELLRFDMS   86 (315)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHHHH---------TCEEEEEEGG
T ss_pred             CceEEEEECCCcchhHHHHHHHHhhc---------cCCeeEeccc
Confidence            33467899999999999999999754         2566667743

>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=95.05  E-value=0.0076  Score=47.43  Aligned_cols=25  Identities=20%  Similarity=0.218  Sum_probs=21.5

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..+++|.||+|+|||+++..++...
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhC
Confidence            3589999999999999999888653

>d1y88a1 a.60.4.3 (A:128-186) Hypothetical protein AF1548, C-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: Hypothetical protein AF1548, C-terminal domain
domain: Hypothetical protein AF1548, C-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.03  E-value=0.062  Score=31.04  Aligned_cols=54  Identities=17%  Similarity=0.247  Sum_probs=46.7

Q ss_pred             ccccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 035774            4 KLISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSE   58 (357)
Q Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   58 (357)
                      +|+..|.+++.++..|.++|.--+.|+....++.+. ..+++-+.+.+++.++.+
T Consensus         1 ypitilridkevldelvraglvfcrdvvsageeklr-eiglsakkareviaeakk   54 (59)
T d1y88a1           1 YPITILRIDKEVLDELVRAGLVFCRDVVSAGEEKLR-EIGLSAKKAREVIAEAKK   54 (59)
T ss_dssp             CBGGGSSCCHHHHHHHHHTTCCBHHHHHHHCHHHHH-HTTCCHHHHHHHHHHHHH
T ss_pred             CCeeeeeecHHHHHHHHHhchhhhHHHHhhhHHHHH-HhccchHHHHHHHHHHHh
Confidence            588999999999999999999999999999988874 578998888888766544

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=94.98  E-value=0.017  Score=48.45  Aligned_cols=126  Identities=17%  Similarity=0.231  Sum_probs=62.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHHHHHHHhccCchhhcccchHHHhhcCeEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRRMIEMGASSFPEIFHSKGMAQEMAGRILVLQP  183 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  183 (357)
                      -+.|.|..|+|||||+-.++...-.....|.......+.|.   .+.++.+++....-...+..      -..++.+++.
T Consensus         4 Nv~iiGh~~~GKTtL~e~ll~~~g~~~~~g~v~~g~~~~D~---~~~E~~r~~ti~~~~~~~~~------~~~~~n~iDt   74 (267)
T d2dy1a2           4 TVALVGHAGSGKTTLTEALLYKTGAKERRGRVEEGTTTTDY---TPEAKLHRTTVRTGVAPLLF------RGHRVFLLDA   74 (267)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHTTSSSSCCCGGGTCCSSCC---SHHHHHTTSCCSCEEEEEEE------TTEEEEEEEC
T ss_pred             EEEEEcCCCCcHHHHHHHHHHHcCCchhhccchhccccccc---hHHHHHhCCeEEeecccccc------cccceeEEcc
Confidence            36789999999999999998765332222211111111111   11222222211100000000      0124566766


Q ss_pred             CCHHHHHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEE-Eecccc
Q 035774          184 TSLSEFTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIV-VTNQVR  256 (357)
Q Consensus       184 ~~~~~~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv-~~~q~~  256 (357)
                      ....++.   ......+..-+.-++|||....+..               ....+-+++++++++.+ ++|.+-
T Consensus        75 PGh~dF~---~e~~~al~~~D~avlvvda~~Gv~~---------------~t~~~~~~~~~~~~p~~i~iNk~D  130 (267)
T d2dy1a2          75 PGYGDFV---GEIRGALEAADAALVAVSAEAGVQV---------------GTERAWTVAERLGLPRMVVVTKLD  130 (267)
T ss_dssp             CCSGGGH---HHHHHHHHHCSEEEEEEETTTCSCH---------------HHHHHHHHHHHTTCCEEEEEECGG
T ss_pred             Cchhhhh---hhhhhhhcccCceEEEeeccCCccc---------------hhHHHHHhhhhccccccccccccc
Confidence            6544443   2333344445788999996543321               12334556777777665 455543

>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=94.97  E-value=0.0098  Score=48.48  Aligned_cols=35  Identities=20%  Similarity=0.357  Sum_probs=28.1

Q ss_pred             CCCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           85 PTRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        85 ~TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ..|++.|-..|     +|..+++.|+||+|||||...+.-
T Consensus        83 ~~g~~~L~~~l-----~~kt~~~~G~SGVGKSTLiN~L~~  117 (225)
T d1u0la2          83 GMGIEELKEYL-----KGKISTMAGLSGVGKSSLLNAINP  117 (225)
T ss_dssp             CTTHHHHHHHH-----SSSEEEEECSTTSSHHHHHHHHST
T ss_pred             chhHhhHHHHh-----cCCeEEEECCCCCCHHHHHHhhcc
Confidence            35667777766     467999999999999999987753

>d1kkma_ c.91.1.2 (A:) HPr kinase HprK C-terminal domain {Lactobacillus casei [TaxId: 1582]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Lactobacillus casei [TaxId: 1582]

Probab=94.95  E-value=0.0071  Score=47.37  Aligned_cols=25  Identities=28%  Similarity=0.466  Sum_probs=21.8

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      |.-++|.|+||+|||++++.++...
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~g   38 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQRG   38 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHTT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHcC
Confidence            6679999999999999999888654

>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=94.94  E-value=0.0059  Score=48.42  Aligned_cols=20  Identities=25%  Similarity=0.499  Sum_probs=17.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia  123 (357)
                      ++.|+|++||||||+|..+.
T Consensus         5 IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           5 IIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            67899999999999998663

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=94.93  E-value=0.02  Score=45.96  Aligned_cols=22  Identities=27%  Similarity=0.430  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +.|.|.+++|||||+-++....
T Consensus         6 i~iiGhvd~GKSTL~~~Ll~~~   27 (204)
T d2c78a3           6 VGTIGHVDHGKTTLTAALTYVA   27 (204)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHHHHh
Confidence            6789999999999999987654

>d1knxa2 c.91.1.2 (A:133-309) HPr kinase HprK C-terminal domain {Mycoplasma pneumoniae [TaxId: 2104]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Mycoplasma pneumoniae [TaxId: 2104]

Probab=94.76  E-value=0.0063  Score=47.71  Aligned_cols=26  Identities=38%  Similarity=0.535  Sum_probs=22.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .|.-++|.|++|+|||++++.++.+.
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~~~G   39 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLINKN   39 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHTTT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHcC
Confidence            36678999999999999999987543

>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=94.76  E-value=0.012  Score=53.24  Aligned_cols=33  Identities=30%  Similarity=0.550  Sum_probs=26.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +=+++.||||+|||.||..+|...         +.|-+.+|+
T Consensus        50 sNILliGPTGvGKTlLAr~LAk~l---------~VPFv~~da   82 (443)
T d1g41a_          50 KNILMIGPTGVGKTEIARRLAKLA---------NAPFIKVEA   82 (443)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHT---------TCCEEEEEG
T ss_pred             ccEEEECCCCCCHHHHHHHHHHHh---------CCCEEEeec
Confidence            358899999999999999999754         366666664

>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=94.70  E-value=0.011  Score=47.49  Aligned_cols=35  Identities=17%  Similarity=-0.038  Sum_probs=29.2

Q ss_pred             EEEEEcC-CCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          104 VTELVGP-AGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       104 l~~I~G~-~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      -+-|+|- +|+|||+++.++|...+..      +.+|++|+.
T Consensus         3 ~~~i~gt~~GVGKTtvs~~La~aLa~~------G~rVl~id~   38 (224)
T d1byia_           3 RYFVTGTDTEVGKTVASCALLQAAKAA------GYRTAGYKP   38 (224)
T ss_dssp             EEEEEESSTTSCHHHHHHHHHHHHHHT------TCCEEEECS
T ss_pred             eEEEEECCCCccHHHHHHHHHHHHHHC------CCeEEEECc
Confidence            3567888 5999999999999988753      589999985

>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=94.67  E-value=0.0095  Score=48.66  Aligned_cols=34  Identities=29%  Similarity=0.236  Sum_probs=25.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      +++|+|.-|||||||..+++.+.     .   +.++..|..|
T Consensus         5 v~iitGFLGaGKTTll~~lL~~~-----~---~~riaVI~Ne   38 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILNEQ-----H---GYKIAVIENE   38 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHSC-----C---CCCEEEECSS
T ss_pred             EEEEeeCCCCCHHHHHHHHHhcC-----C---CCcEEEEEec
Confidence            78999999999999999887631     1   3566666544

>d1gm5a3 c.37.1.19 (A:286-549) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.55  E-value=0.04  Score=45.91  Aligned_cols=45  Identities=18%  Similarity=0.087  Sum_probs=34.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCCCchHH
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVESTFTSRR  152 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~~~~~r  152 (357)
                      ....+|.|..|||||..+...+..++..      +..|+++.-+..+..+.
T Consensus       104 ~m~rLL~GdvGSGKT~Va~~a~~~~~~~------g~q~~~m~Pt~~La~Qh  148 (264)
T d1gm5a3         104 PMNRLLQGDVGSGKTVVAQLAILDNYEA------GFQTAFMVPTSILAIQH  148 (264)
T ss_dssp             CCCCEEECCSSSSHHHHHHHHHHHHHHH------TSCEEEECSCHHHHHHH
T ss_pred             cceeeeeccccccccHHHHHHHHHHHhc------ccceeEEeehHhhhHHH
Confidence            3457899999999999999988887742      57888887665444433

>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=94.52  E-value=0.016  Score=49.96  Aligned_cols=40  Identities=25%  Similarity=0.263  Sum_probs=30.2

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      .|...++++||+|+|||.+|..+|....-      .+.+.+.+++.
T Consensus        51 kp~~~~lf~Gp~G~GKt~lak~la~~l~~------~~~~~~~~~~~   90 (315)
T d1qvra3          51 RPIGSFLFLGPTGVGKTELAKTLAATLFD------TEEAMIRIDMT   90 (315)
T ss_dssp             SCSEEEEEBSCSSSSHHHHHHHHHHHHHS------SGGGEEEECTT
T ss_pred             CCceEEEEECCCcchHHHHHHHHHHHhcC------CCcceEEEecc
Confidence            34446789999999999999999987642      23567777754

>d1ko7a2 c.91.1.2 (A:130-298) HPr kinase HprK C-terminal domain {Staphylococcus xylosus [TaxId: 1288]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: HPr kinase HprK C-terminal domain
domain: HPr kinase HprK C-terminal domain
species: Staphylococcus xylosus [TaxId: 1288]

Probab=94.52  E-value=0.0097  Score=46.26  Aligned_cols=26  Identities=31%  Similarity=0.510  Sum_probs=22.6

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .|.-++|.|++|+|||++++.++.+.
T Consensus        14 ~g~gvli~G~sg~GKS~la~~l~~~g   39 (169)
T d1ko7a2          14 YGVGVLITGDSGIGKSETALELIKRG   39 (169)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHcC
Confidence            36679999999999999999988765

>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=94.40  E-value=0.013  Score=51.57  Aligned_cols=41  Identities=24%  Similarity=0.186  Sum_probs=27.4

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +.+++|.|+||+|||+.+..++........  +.+.+++....
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~--~~~~~I~l~Ap  203 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALIQMAD--GERCRIRLAAP  203 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCS--SCCCCEEEEBS
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHHHHHh--ccCCeEEEecC
Confidence            569999999999999998877655432111  12345555544

>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=94.30  E-value=0.011  Score=45.07  Aligned_cols=22  Identities=27%  Similarity=0.433  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+||+|||+|...+...-
T Consensus         8 I~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           8 ILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7899999999999999987643

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=94.28  E-value=0.017  Score=51.94  Aligned_cols=36  Identities=22%  Similarity=0.346  Sum_probs=29.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +.|.|++|+|||+++..++.+.+.   +   +.+++.||..+
T Consensus        53 ~~I~G~tGsGKT~~l~~li~~~~~---~---g~~~iiiD~kg   88 (433)
T d1e9ra_          53 LLVNGATGTGKSVLLRELAYTGLL---R---GDRMVIVDPNG   88 (433)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHH---T---TCEEEEEEETT
T ss_pred             EEEEeCCCCcHHHHHHHHHHHHHh---C---CCCEEEEeCCh
Confidence            799999999999999888887764   2   46777777654

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.28  E-value=0.023  Score=45.34  Aligned_cols=35  Identities=23%  Similarity=0.220  Sum_probs=27.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      ++.|.|..||||||++..++.....   .   +.+|+++..
T Consensus         2 lI~ieG~dGsGKST~~~~L~~~l~~---~---g~~v~~~~~   36 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSGAFRA---A---GRSVATLAF   36 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH---T---TCCEEEEES
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH---C---CCCEEEEec
Confidence            6889999999999999998876532   1   366777654

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.21  E-value=0.18  Score=38.19  Aligned_cols=129  Identities=16%  Similarity=0.170  Sum_probs=69.1

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCCC-CchHHHHHHHhccCchhhcccchHHHhhcCeE
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVEST-FTSRRMIEMGASSFPEIFHSKGMAQEMAGRIL  179 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~~-~~~~rl~~~~~~~~~~~~~~~~~~~~~~~~i~  179 (357)
                      +|-+. |+=.+|=||||-|+-+|.+++      |.+.+|+++.+--. ....- .......... +.       ....-+
T Consensus         2 kG~i~-vytG~GKGKTTAAlG~alRA~------G~G~rV~ivQFlKg~~~~ge-~~~~~~~~~~-~~-------~~~~~~   65 (157)
T d1g5ta_           2 RGIII-VFTGNGKGKTTAAFGTAARAV------GHGKNVGVVQFIKGTWPNGE-RNLLEPHGVE-FQ-------VMATGF   65 (157)
T ss_dssp             CCCEE-EEESSSSCHHHHHHHHHHHHH------HTTCCEEEEESSCCSSCCHH-HHHHGGGTCE-EE-------ECCTTC
T ss_pred             CcEEE-EEeCCCCCcHHHHHHHHHHHh------cCCCEEEEEEEecCCcccch-hhhhcccCcE-EE-------EecCCC
Confidence            45444 444579999999999999998      45799999987432 11111 1111110000 00       000001


Q ss_pred             EeCCCCHHH----HHHHHHHHHHHhhhcCeeEEEEeccccccCCCCCCCCCChHHHHHHHHHHHHHHHHcCCeEEEecc
Q 035774          180 VLQPTSLSE----FTESLEKIKVSLLQNQVKLLVIDSMEALVPGVHEQRAPGQHPLSWHISLITSLAEFSRIPIVVTNQ  254 (357)
Q Consensus       180 ~~~~~~~~~----~~~~l~~l~~~~~~~~~~lvvIDsl~~l~~~~~~~~~~r~~~~~~i~~~Lk~la~~~~~~vv~~~q  254 (357)
                      +....+.+.    ....++.....+.....++||+|.+.......+=       ...++...|+.  +-.++-||+|..
T Consensus        66 ~~~~~~~e~~~~~a~~~~~~a~~~~~~~~~dllILDEi~~Ai~~gli-------~~~~v~~ll~~--rp~~~evVlTGr  135 (157)
T d1g5ta_          66 TWETQNREADTAACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYL-------PLEEVISALNA--RPGHQTVIITGR  135 (157)
T ss_dssp             CCCGGGHHHHHHHHHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSS-------CHHHHHHHHHT--SCTTCEEEEECS
T ss_pred             cccCCChHHHHHHHHHHHHHHHHHhhcCccCEEeHHHHHHHHHcCCC-------CHHHHHHHHHh--CCCCCEEEEECC
Confidence            111111121    2223344455566778999999999877654221       12334555543  446788888853

>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=94.18  E-value=0.012  Score=46.59  Aligned_cols=19  Identities=32%  Similarity=0.482  Sum_probs=18.0

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia  123 (357)
                      +.|.|+||+|||||...+.
T Consensus        26 I~lvG~~n~GKSTLin~L~   44 (195)
T d1svia_          26 IALAGRSNVGKSSFINSLI   44 (195)
T ss_dssp             EEEEEBTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHhc
Confidence            9999999999999999886

>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=94.17  E-value=0.011  Score=45.75  Aligned_cols=21  Identities=29%  Similarity=0.431  Sum_probs=18.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      =++|.|.||+|||+|+.++..
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            478999999999999998874

>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=94.03  E-value=0.014  Score=44.85  Aligned_cols=21  Identities=19%  Similarity=0.257  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++.|+||+|||+|+.++...
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999999864

>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=94.00  E-value=0.014  Score=44.15  Aligned_cols=21  Identities=24%  Similarity=0.181  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|+|++|||+|+..+...
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            568999999999999988754

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=93.87  E-value=0.035  Score=49.48  Aligned_cols=28  Identities=18%  Similarity=0.119  Sum_probs=24.3

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      .++.+++|+||+||||||.+..++....
T Consensus       156 ~~~GliLvtGpTGSGKSTTl~~~l~~~~  183 (401)
T d1p9ra_         156 RPHGIILVTGPTGSGKSTTLYAGLQELN  183 (401)
T ss_dssp             SSSEEEEEECSTTSCHHHHHHHHHHHHC
T ss_pred             hhhceEEEEcCCCCCccHHHHHHhhhhc
Confidence            3566999999999999999999988764

>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=93.81  E-value=0.016  Score=44.92  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+||+|||+|+..++..-
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDKR   27 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHhcCC
Confidence            5789999999999999988653

>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=93.73  E-value=0.016  Score=44.43  Aligned_cols=20  Identities=25%  Similarity=0.283  Sum_probs=17.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++|.|++|+|||+|...+..
T Consensus         5 i~ivG~~~~GKTsLi~~l~~   24 (165)
T d1ksha_           5 LLMLGLDNAGKTTILKKFNG   24 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHcC
Confidence            67999999999999998753

>d1f6ba_ c.37.1.8 (A:) SAR1 {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: SAR1
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=93.66  E-value=0.013  Score=45.52  Aligned_cols=21  Identities=24%  Similarity=0.227  Sum_probs=18.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 035774          103 VVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      -=++|.|+||+|||+|...+.
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~   34 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLK   34 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            347799999999999998875

>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=93.64  E-value=0.018  Score=44.29  Aligned_cols=21  Identities=19%  Similarity=0.430  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|++|+|||+|+.+++..
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999999864

>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=93.64  E-value=0.018  Score=44.25  Aligned_cols=22  Identities=18%  Similarity=0.309  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++.+-
T Consensus         7 ivlvG~~~vGKTsli~~~~~~~   28 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEKK   28 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6788999999999999998653

>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=93.63  E-value=0.012  Score=50.85  Aligned_cols=36  Identities=25%  Similarity=0.418  Sum_probs=26.0

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +.-++|+|++|||||||+..++...  +     .+.+++.|..
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i--~-----~~~rivtiEd  201 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFI--P-----KEERIISIED  201 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGS--C-----TTCCEEEEES
T ss_pred             CCCEEEEeeccccchHHHHHHhhhc--c-----cccceeeccc
Confidence            4458999999999999998766433  2     1466777643

>d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Initiation factor IF2/eIF5b, N-terminal (G) domain
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.63  E-value=0.046  Score=44.47  Aligned_cols=24  Identities=21%  Similarity=0.284  Sum_probs=20.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHhc
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      ++.|.|.|.+|||||+-.+.....
T Consensus         7 ~IaIiGh~d~GKSTL~~~L~~~~~   30 (227)
T d1g7sa4           7 IVSVLGHVDHGKTTLLDHIRGSAV   30 (227)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEeCCCccHHHHHHHHHhhcc
Confidence            588999999999999988876543

>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=93.56  E-value=0.02  Score=46.03  Aligned_cols=20  Identities=25%  Similarity=0.517  Sum_probs=17.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia  123 (357)
                      ++.|+|.+||||||+|..|.
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            78899999999999997554

>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=93.55  E-value=0.018  Score=44.34  Aligned_cols=22  Identities=27%  Similarity=0.451  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+.+++.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~~   27 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6788999999999999998653

>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=93.52  E-value=0.019  Score=44.31  Aligned_cols=20  Identities=30%  Similarity=0.426  Sum_probs=18.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia  123 (357)
                      .+.|.|+||+|||+|+.+++
T Consensus         2 ~V~liG~~n~GKSsLi~~L~   21 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLV   21 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47899999999999999886

>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=93.50  E-value=0.02  Score=43.93  Aligned_cols=22  Identities=32%  Similarity=0.295  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+.++...-
T Consensus         5 i~i~G~~~~GKTsLl~~l~~~~   26 (164)
T d1zd9a1           5 LTLVGLQYSGKTTFVNVIASGQ   26 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            5688999999999999987543

>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=93.45  E-value=0.02  Score=44.37  Aligned_cols=22  Identities=23%  Similarity=0.345  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|+||+|||+|+.+++.+.
T Consensus         9 I~vvG~~~vGKSSli~~~~~~~   30 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTNK   30 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            7899999999999999998643

>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=93.41  E-value=0.019  Score=44.39  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++...
T Consensus         8 i~lvG~~~vGKTsLi~r~~~~~   29 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQSY   29 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            7889999999999999998643

>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=93.41  E-value=0.021  Score=45.80  Aligned_cols=19  Identities=32%  Similarity=0.515  Sum_probs=16.8

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKL  122 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~i  122 (357)
                      ++.|+|.+||||||+|..+
T Consensus         4 iIgITG~igSGKStv~~~l   22 (205)
T d1jjva_           4 IVGLTGGIGSGKTTIANLF   22 (205)
T ss_dssp             EEEEECSTTSCHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            6789999999999998755

>d1gkub1 c.37.1.16 (B:1-250) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.40  E-value=0.023  Score=46.61  Aligned_cols=44  Identities=30%  Similarity=0.290  Sum_probs=31.7

Q ss_pred             HHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774           91 LDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus        91 LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++.+|.     |+-++|.+|+|+|||..++..+...+.+      +.+++|+.-.
T Consensus        52 i~~~l~-----g~~~~i~apTGsGKT~~~~~~~~~~~~~------~~rvliv~Pt   95 (237)
T d1gkub1          52 AKRILR-----KESFAATAPTGVGKTSFGLAMSLFLALK------GKRCYVIFPT   95 (237)
T ss_dssp             HHHHHT-----TCCEECCCCBTSCSHHHHHHHHHHHHTT------SCCEEEEESC
T ss_pred             HHHHHC-----CCCEEEEecCCChHHHHHHHHHHHHHHh------cCeEEEEecc
Confidence            556554     4568888999999998877666655532      4689998754

>d1ky3a_ c.37.1.8 (A:) Rab-related protein ypt7p {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-related protein ypt7p
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=93.40  E-value=0.021  Score=44.24  Aligned_cols=22  Identities=23%  Similarity=0.327  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+.++...-
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~~   26 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVNDK   26 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHcCC
Confidence            6799999999999999988643

>d2atva1 c.37.1.8 (A:5-172) Ras-like estrogen-regulated growth inhibitor, RERG {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ras-like estrogen-regulated growth inhibitor, RERG
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.40  E-value=0.021  Score=44.05  Aligned_cols=22  Identities=23%  Similarity=0.453  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|++|+|||+|+.+++..-
T Consensus         5 i~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            5789999999999999998643

>d1z08a1 c.37.1.8 (A:17-183) Rab21 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab21
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.39  E-value=0.021  Score=43.93  Aligned_cols=22  Identities=27%  Similarity=0.359  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++.+-
T Consensus         6 ivlvG~~~vGKTsLi~r~~~~~   27 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCENK   27 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5799999999999999988643

>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=93.36  E-value=0.021  Score=44.01  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++..-
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5789999999999999998643

>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=93.30  E-value=0.022  Score=43.93  Aligned_cols=21  Identities=24%  Similarity=0.487  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|.+|+|||+|+.+++.+
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578899999999999998854

>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=93.29  E-value=0.022  Score=44.66  Aligned_cols=20  Identities=30%  Similarity=0.469  Sum_probs=17.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++|.|++|+|||+|+.+++.
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            67899999999999998874

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.25  E-value=0.059  Score=39.87  Aligned_cols=40  Identities=15%  Similarity=0.193  Sum_probs=33.0

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      +|.|.+|+||=.||||+-+++.+.+....      +.+|+.|.-..
T Consensus         1 ~G~L~li~GpMfsGKTt~Li~~~~~~~~~------g~~v~~ikp~~   40 (133)
T d1xbta1           1 RGQIQVILGPMFSGKSTELMRRVRRFQIA------QYKCLVIKYAK   40 (133)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTT------TCCEEEEEETT
T ss_pred             CcEEEEEEecccCHHHHHHHHHHHHHHHc------CCcEEEEeccc
Confidence            68999999999999999999999887642      47788886543

>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=93.24  E-value=0.014  Score=46.20  Aligned_cols=24  Identities=21%  Similarity=0.288  Sum_probs=20.5

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.-++.|.|..||||||++..++.
T Consensus         8 kp~~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1           8 QPFTVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            345899999999999999997764

>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=93.21  E-value=0.023  Score=43.76  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|++|+|||+|+..++.+-
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~~   29 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADDS   29 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHcCC
Confidence            6899999999999999998653

>d1vg8a_ c.37.1.8 (A:) Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab7
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=93.18  E-value=0.023  Score=44.45  Aligned_cols=21  Identities=24%  Similarity=0.343  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|.+|+|||+|+.+++..
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999998753

>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=93.16  E-value=0.014  Score=50.76  Aligned_cols=21  Identities=29%  Similarity=0.327  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      =++|.|+||+|||+++..++.
T Consensus        30 ~vLl~G~pG~GKT~lar~~~~   50 (333)
T d1g8pa_          30 GVLVFGDRGTGKSTAVRALAA   50 (333)
T ss_dssp             CEEEECCGGGCTTHHHHHHHH
T ss_pred             eEEEECCCCccHHHHHHHHHH
Confidence            379999999999999998885

>d1t9ha2 c.37.1.8 (A:68-298) Probable GTPase EngC (YjeQ), C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngC (YjeQ), C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=93.13  E-value=0.014  Score=47.65  Aligned_cols=34  Identities=21%  Similarity=0.275  Sum_probs=26.2

Q ss_pred             CCchhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHH
Q 035774           86 TRLKGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus        86 TG~~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .|++.|-..|     .|..+++.|+||+|||+|...+.-
T Consensus        86 ~gl~~L~~~l-----~~~~~vl~G~SGVGKSSLiN~L~~  119 (231)
T d1t9ha2          86 DSLADIIPHF-----QDKTTVFAGQSGVGKSSLLNAISP  119 (231)
T ss_dssp             TTCTTTGGGG-----TTSEEEEEESHHHHHHHHHHHHCC
T ss_pred             hHHHHHHHhh-----ccceEEEECCCCccHHHHHHhhcc
Confidence            4566666655     356889999999999999987764

>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=93.08  E-value=0.024  Score=45.24  Aligned_cols=22  Identities=27%  Similarity=0.330  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      -++|.|+||+|||+|+..+...
T Consensus         2 ~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           2 AVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            4789999999999999998864

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=93.06  E-value=0.046  Score=45.71  Aligned_cols=37  Identities=22%  Similarity=0.083  Sum_probs=30.4

Q ss_pred             hHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           90 GLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        90 ~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .|=.+|.|+.++-..+.+.|+|++|||+|+..++...
T Consensus        92 ~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          92 VFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3445577889999999999999999999998776543

>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=93.02  E-value=0.024  Score=43.98  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++.+-
T Consensus         9 v~lvG~~~vGKTsLi~r~~~~~   30 (173)
T d2fn4a1           9 LVVVGGGGVGKSALTIQFIQSY   30 (173)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999988643

>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=93.00  E-value=0.026  Score=43.15  Aligned_cols=22  Identities=18%  Similarity=0.289  Sum_probs=19.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|.+|+|||+|+.+++..-
T Consensus         5 v~liG~~~vGKTsLl~~~~~~~   26 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAGR   26 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999998653

>d1xtqa1 c.37.1.8 (A:3-169) GTP-binding protein RheB {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: GTP-binding protein RheB
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.96  E-value=0.025  Score=43.46  Aligned_cols=22  Identities=14%  Similarity=0.277  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+.+++.+.
T Consensus         7 v~liG~~~vGKTsLl~~~~~~~   28 (167)
T d1xtqa1           7 IAILGYRSVGKSSLTIQFVEGQ   28 (167)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6788999999999999988643

>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=92.95  E-value=0.036  Score=43.86  Aligned_cols=36  Identities=25%  Similarity=0.399  Sum_probs=25.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCC
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVE  145 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e  145 (357)
                      ++|++|+|+|||..+..++...+..  .   +.+++|+.-.
T Consensus        26 ~lv~~pTGsGKT~i~~~~~~~~~~~--~---~~~il~i~P~   61 (200)
T d1wp9a1          26 CLIVLPTGLGKTLIAMMIAEYRLTK--Y---GGKVLMLAPT   61 (200)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHH--S---CSCEEEECSS
T ss_pred             eEEEeCCCCcHHHHHHHHHHHHHHh--c---CCcEEEEcCc
Confidence            5688999999998777666555432  1   3678888653

>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=92.94  E-value=0.025  Score=43.68  Aligned_cols=22  Identities=32%  Similarity=0.425  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++.+.
T Consensus         8 i~lvG~~~vGKTsLi~~l~~~~   29 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQGL   29 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6789999999999999998643

>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=92.94  E-value=0.027  Score=43.40  Aligned_cols=21  Identities=33%  Similarity=0.439  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|++|+|||+|+.+++..
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998864

>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=92.93  E-value=0.027  Score=43.24  Aligned_cols=22  Identities=18%  Similarity=0.374  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++..-
T Consensus         6 ivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHcCC
Confidence            6789999999999999998653

>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=92.92  E-value=0.027  Score=43.64  Aligned_cols=21  Identities=24%  Similarity=0.480  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|++|+|||+|+..+...
T Consensus         7 i~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            689999999999999998764

>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=92.92  E-value=0.025  Score=43.77  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|.+|+|||+|+.++...-
T Consensus         8 I~lvG~~~vGKTsll~~~~~~~   29 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEKK   29 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6899999999999999998643

>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=92.91  E-value=0.025  Score=43.34  Aligned_cols=21  Identities=24%  Similarity=0.404  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++.|.+|+|||+|+.+++..
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578999999999999998754

>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=92.89  E-value=0.045  Score=47.97  Aligned_cols=28  Identities=29%  Similarity=0.407  Sum_probs=23.1

Q ss_pred             CCCCCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774           98 GVPFGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus        98 Gi~~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ..|+++ +++.||+|+|||.+|..+|...
T Consensus        65 ~~p~~n-iLfiGPTGvGKTElAk~LA~~~   92 (364)
T d1um8a_          65 ELSKSN-ILLIGPTGSGKTLMAQTLAKHL   92 (364)
T ss_dssp             TCCCCC-EEEECCTTSSHHHHHHHHHHHT
T ss_pred             cCCCcc-eeeeCCCCccHHHHHHHHHhhc
Confidence            467776 5667999999999999998754

>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=92.86  E-value=0.025  Score=44.72  Aligned_cols=22  Identities=32%  Similarity=0.445  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+.+++...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~~   30 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDDT   30 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHhhCC
Confidence            6789999999999999998643

>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=92.83  E-value=0.028  Score=43.90  Aligned_cols=23  Identities=26%  Similarity=0.304  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      =++|.|.+|+|||+|+.+++...
T Consensus         7 KivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999998654

>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=92.79  E-value=0.027  Score=42.77  Aligned_cols=20  Identities=20%  Similarity=0.335  Sum_probs=17.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia  123 (357)
                      =+.|.|+|++|||+|+.++.
T Consensus         3 kI~lvG~~nvGKSsLin~l~   22 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALA   22 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            36899999999999998887

>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=92.79  E-value=0.025  Score=43.74  Aligned_cols=20  Identities=30%  Similarity=0.380  Sum_probs=17.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia  123 (357)
                      =++|.|+||+|||+|+.++.
T Consensus        18 kI~vvG~~~vGKSsLi~~l~   37 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLA   37 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47899999999999998774

>d1tmka_ c.37.1.1 (A:) Thymidylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=92.78  E-value=0.036  Score=44.70  Aligned_cols=26  Identities=31%  Similarity=0.249  Sum_probs=23.2

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +|.++.|.|.-||||||++..++...
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~~L   27 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYKKL   27 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHHHH
Confidence            68999999999999999999887654

>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=92.73  E-value=0.032  Score=44.36  Aligned_cols=22  Identities=27%  Similarity=0.369  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      .++|.|+|++|||+|...+...
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            5899999999999999988753

>d1kmqa_ c.37.1.8 (A:) RhoA {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.72  E-value=0.028  Score=43.67  Aligned_cols=22  Identities=27%  Similarity=0.211  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++...
T Consensus         5 ivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            4678999999999999988654

>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=92.71  E-value=0.031  Score=43.08  Aligned_cols=21  Identities=29%  Similarity=0.514  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|.+|+|||+|+.+++..
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578999999999999998854

>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=92.70  E-value=0.03  Score=43.06  Aligned_cols=20  Identities=25%  Similarity=0.403  Sum_probs=17.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++|.|.+|+|||+|+.++..
T Consensus         4 i~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCcCHHHHHHHHhC
Confidence            57899999999999998864

>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=92.65  E-value=0.031  Score=42.89  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=19.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++..-
T Consensus         7 i~lvG~~~vGKTsli~rl~~~~   28 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVEDS   28 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5788999999999999998644

>d1u9la_ a.60.4.2 (A:) Transcription elongation protein NusA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: SAM domain-like
superfamily: Rad51 N-terminal domain-like
family: NusA extra C-terminal domains
domain: Transcription elongation protein NusA
species: Escherichia coli [TaxId: 562]

Probab=92.48  E-value=0.095  Score=33.38  Aligned_cols=55  Identities=9%  Similarity=0.181  Sum_probs=48.5

Q ss_pred             cccccCCCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHh
Q 035774            5 LISEMRLPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALVSEI   59 (357)
Q Consensus         5 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   59 (357)
                      ....|.++..+...|..-|+.+++++.+.+..+|..+-|...+.+..+...+.+.
T Consensus         8 F~~~LdVDe~lA~lLv~EGF~siEeIAyv~~~eL~~IegfDee~a~eL~~RA~~~   62 (68)
T d1u9la_           8 FTKYLDIDEDFATVLVEEGFSTLEELAYVPMKELLEIEGLDEPTVEALRERAKNA   62 (68)
T ss_dssp             HHHHHTCCHHHHHHHHHTTCCCHHHHHHSCHHHHTTSTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHcCCcHHHHHHHHHhccCcHHHHhcCCHHHHHHhcccCHHHHHHHHHHHHHH
Confidence            3567899999999999999999999999999999999999999888887766543

>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=92.45  E-value=0.034  Score=42.82  Aligned_cols=22  Identities=23%  Similarity=0.404  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|.+|+|||+|+.+++...
T Consensus         7 i~lvG~~~vGKTsll~~~~~~~   28 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQKI   28 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            4678999999999999998643

>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=92.19  E-value=0.039  Score=42.81  Aligned_cols=22  Identities=23%  Similarity=0.472  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|.+|+|||+|...+..+-
T Consensus        10 i~vvG~~~vGKTsli~~l~~~~   31 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDDT   31 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6799999999999999988644

>d1p5zb_ c.37.1.1 (B:) Deoxycytidine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxycytidine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.09  E-value=0.022  Score=46.46  Aligned_cols=25  Identities=24%  Similarity=0.203  Sum_probs=21.8

Q ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++.++.|.|+.||||||++..++..
T Consensus         1 ~~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           1 RIKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999999999987754

>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=92.09  E-value=0.035  Score=43.10  Aligned_cols=20  Identities=20%  Similarity=0.441  Sum_probs=17.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia  123 (357)
                      -+.|.|+|++|||+|...+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~   21 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLT   21 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            47899999999999998876

>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=92.09  E-value=0.04  Score=42.54  Aligned_cols=20  Identities=25%  Similarity=0.419  Sum_probs=17.9

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++|.|.+|+|||+|+.++..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            67899999999999998874

>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=92.08  E-value=0.022  Score=44.13  Aligned_cols=19  Identities=32%  Similarity=0.447  Sum_probs=17.2

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia  123 (357)
                      ++|.|+||+|||+|..+++
T Consensus        15 IvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_          15 ILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             EEEEEETTSSHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6789999999999999875

>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=91.94  E-value=0.047  Score=42.32  Aligned_cols=21  Identities=24%  Similarity=0.320  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+.|.|.||+|||+|+..++.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~   27 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLG   27 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            699999999999999988763

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=91.79  E-value=0.051  Score=48.12  Aligned_cols=24  Identities=29%  Similarity=0.510  Sum_probs=19.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      ..+.+++|.|++|+|||++.-.|.
T Consensus        23 ~~~~l~~i~G~NGsGKS~ileAi~   46 (427)
T d1w1wa_          23 GESNFTSIIGPNGSGKSNMMDAIS   46 (427)
T ss_dssp             TTCSEEEEECSTTSSHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH
Confidence            335599999999999999977664

>d1m7ba_ c.37.1.8 (A:) RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: RhoE (RND3)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.79  E-value=0.042  Score=42.79  Aligned_cols=22  Identities=23%  Similarity=0.224  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|.+|+|||+|+.+++...
T Consensus         5 ivliG~~~vGKTsli~r~~~~~   26 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKDC   26 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            5789999999999999998754

>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=91.72  E-value=0.043  Score=43.16  Aligned_cols=22  Identities=23%  Similarity=0.302  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|++|+|||+|+.+++..-
T Consensus         6 vvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6788999999999999998654

>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=91.59  E-value=0.045  Score=42.83  Aligned_cols=22  Identities=27%  Similarity=0.297  Sum_probs=19.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|..+++.+.
T Consensus        12 i~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            7899999999999999988643

>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=91.58  E-value=0.03  Score=43.62  Aligned_cols=25  Identities=24%  Similarity=0.333  Sum_probs=20.4

Q ss_pred             CCCCcEEEEEcCCCCcHHHHHHHHH
Q 035774           99 VPFGVVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus        99 i~~G~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      -.+.-=++|.|++|+|||+|..++.
T Consensus        14 ~~k~~KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          14 SNKELRILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             CSSCEEEEEEEETTSSHHHHHHHTC
T ss_pred             CCceEEEEEECCCCCCHHHHHHHHh
Confidence            4555557899999999999998764

>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=91.37  E-value=0.039  Score=43.06  Aligned_cols=19  Identities=32%  Similarity=0.389  Sum_probs=16.8

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia  123 (357)
                      +.|.|+|++|||+|+..+.
T Consensus         4 VaiiG~~nvGKSSLin~L~   22 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVS   22 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSE
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6799999999999998764

>d1i2ma_ c.37.1.8 (A:) Ran {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Ran
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.35  E-value=0.025  Score=43.70  Aligned_cols=21  Identities=43%  Similarity=0.476  Sum_probs=17.0

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      ++|.|++|+|||+|+.+++..
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            578899999999999887654

>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=91.35  E-value=0.05  Score=42.78  Aligned_cols=19  Identities=26%  Similarity=0.515  Sum_probs=17.4

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia  123 (357)
                      ++|.|.+|+|||+|+.++.
T Consensus         5 ivllG~~~vGKTsll~r~~   23 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQMR   23 (200)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            5789999999999999994

>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=91.26  E-value=0.033  Score=43.05  Aligned_cols=22  Identities=36%  Similarity=0.449  Sum_probs=8.1

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      ++|.|.+|+|||+|+.+++.+-
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~~   30 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSEDA   30 (173)
T ss_dssp             EEEECCCCC-------------
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            6788999999999999888543

>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=91.20  E-value=0.058  Score=41.83  Aligned_cols=22  Identities=18%  Similarity=0.286  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|.+|+|||+|+.+++..-
T Consensus         8 i~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           8 LGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEECCTTTTHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHHhCC
Confidence            6789999999999999998654

>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=91.13  E-value=0.068  Score=43.56  Aligned_cols=21  Identities=19%  Similarity=0.086  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      ++.|+|..||||||+|..|+.
T Consensus         3 iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            789999999999999987764

>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=90.85  E-value=0.069  Score=41.09  Aligned_cols=21  Identities=29%  Similarity=0.344  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~  124 (357)
                      .+.|.|.|++|||+|...+..
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999998874

>d1qhla_ c.37.1.12 (A:) Cell division protein MukB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Cell division protein MukB
species: Escherichia coli [TaxId: 562]

Probab=90.67  E-value=0.011  Score=46.65  Aligned_cols=22  Identities=32%  Similarity=0.392  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +++|+|++|+|||+++-.+...
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~   47 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTA   47 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            7899999999999998866543

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.38  E-value=0.063  Score=45.40  Aligned_cols=21  Identities=38%  Similarity=0.675  Sum_probs=17.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHH
Q 035774          103 VVTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia  123 (357)
                      .+++|+|++|||||++...+.
T Consensus        25 ~lnvlvG~NgsGKS~iL~Ai~   45 (308)
T d1e69a_          25 RVTAIVGPNGSGKSNIIDAIK   45 (308)
T ss_dssp             SEEEEECCTTTCSTHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHH
Confidence            399999999999999975443

>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=90.10  E-value=0.055  Score=41.96  Aligned_cols=19  Identities=26%  Similarity=0.459  Sum_probs=17.2

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia  123 (357)
                      +.|.|.|++|||+|...+.
T Consensus         4 VaivG~~nvGKSTLin~L~   22 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMT   22 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            6789999999999998875

>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=89.98  E-value=0.094  Score=42.27  Aligned_cols=24  Identities=21%  Similarity=0.445  Sum_probs=20.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhcc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAAL  128 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~  128 (357)
                      ++|.|.+|+|||+|+.++...--.
T Consensus         9 illlG~~~vGKTsll~~~~~~~~~   32 (221)
T d1azta2           9 LLLLGAGESGKSTIVKQMRILHVV   32 (221)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHhcCCcC
Confidence            689999999999999999765543

>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=89.97  E-value=0.085  Score=40.91  Aligned_cols=20  Identities=20%  Similarity=0.325  Sum_probs=17.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSL  124 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~  124 (357)
                      +.|.|.+|+|||+|...++.
T Consensus        11 V~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2          11 VAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEECSTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHC
Confidence            68999999999999987763

>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=89.90  E-value=0.093  Score=42.62  Aligned_cols=24  Identities=21%  Similarity=0.213  Sum_probs=21.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHHHHh
Q 035774          103 VVTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       103 ~l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+++|.|.-||||||++..++...
T Consensus         3 k~IviEG~~GsGKST~~~~L~~~l   26 (241)
T d2ocpa1           3 RRLSIEGNIAVGKSTFVKLLTKTY   26 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHC
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHH
Confidence            478999999999999999988764

>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=89.74  E-value=0.094  Score=40.94  Aligned_cols=22  Identities=23%  Similarity=0.510  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|.+|+|||+|+.++....
T Consensus         5 iv~lG~~~vGKTsll~r~~~~~   26 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRIIH   26 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            5789999999999999997654

>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=89.64  E-value=0.18  Score=41.30  Aligned_cols=39  Identities=18%  Similarity=0.227  Sum_probs=26.9

Q ss_pred             CcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeCCC
Q 035774          102 GVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDVES  146 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~e~  146 (357)
                      ..-++|.|++|+|||.+|..+......      .....+-+++..
T Consensus        23 ~~pvlI~Ge~GtGK~~~A~~ih~~s~~------~~~~~~~~~~~~   61 (247)
T d1ny5a2          23 ECPVLITGESGVGKEVVARLIHKLSDR------SKEPFVALNVAS   61 (247)
T ss_dssp             CSCEEEECSTTSSHHHHHHHHHHHSTT------TTSCEEEEETTT
T ss_pred             CCCEEEECCCCcCHHHHHHHHHHhcCC------cccccccchhhh
Confidence            344799999999999999877654321      135566666643

>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=89.40  E-value=0.048  Score=42.19  Aligned_cols=20  Identities=20%  Similarity=0.306  Sum_probs=17.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia  123 (357)
                      -+.|.|+|++|||+|...+.
T Consensus        18 ~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          18 EVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             EEEEEECTTSSHHHHHTTTC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            38899999999999997653

>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=89.35  E-value=0.036  Score=42.02  Aligned_cols=21  Identities=24%  Similarity=0.287  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      +.|.|+|++|||+|...+...
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            579999999999999998754

>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=89.35  E-value=0.19  Score=39.86  Aligned_cols=42  Identities=21%  Similarity=0.208  Sum_probs=29.1

Q ss_pred             hhHHhhhcCCCCCCcEEEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEeC
Q 035774           89 KGLDAALCGGVPFGVVTELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYIDV  144 (357)
Q Consensus        89 ~~LD~~l~GGi~~G~l~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~~  144 (357)
                      +.++.++.+    + -.+|.+++|+|||.++..++...         +.+++++.-
T Consensus        77 eav~~~~~~----~-~~ll~~~tG~GKT~~a~~~~~~~---------~~~~Liv~p  118 (206)
T d2fz4a1          77 KALERWLVD----K-RGCIVLPTGSGKTHVAMAAINEL---------STPTLIVVP  118 (206)
T ss_dssp             HHHHHHTTT----S-EEEEEESSSTTHHHHHHHHHHHS---------CSCEEEEES
T ss_pred             HHHHHHHhC----C-CcEEEeCCCCCceehHHhHHHHh---------cCceeEEEc
Confidence            455666543    2 34678899999999888776543         367888875

>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=88.98  E-value=0.11  Score=40.30  Aligned_cols=22  Identities=18%  Similarity=0.443  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHh
Q 035774          105 TELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      +++.|..|+|||+|+.++....
T Consensus         5 ivllG~~~vGKTsl~~r~~~~~   26 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKIIH   26 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhhCC
Confidence            5789999999999999987654

>d1h65a_ c.37.1.8 (A:) Chloroplast protein translocon GTPase Toc34 {Garden pea (Pisum sativum) [TaxId: 3888]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Chloroplast protein translocon GTPase Toc34
species: Garden pea (Pisum sativum) [TaxId: 3888]

Probab=88.79  E-value=0.1  Score=43.17  Aligned_cols=22  Identities=18%  Similarity=0.203  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 035774          104 VTELVGPAGTGKTQFCLKLSLL  125 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~  125 (357)
                      -++|.|.||+|||+|+-.++..
T Consensus        34 ~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          34 TILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCcHHHHHHHHhCC
Confidence            4889999999999999988754

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=87.69  E-value=0.14  Score=43.22  Aligned_cols=21  Identities=38%  Similarity=0.504  Sum_probs=18.8

Q ss_pred             CCCcEEEEEcCCCCcHHHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCL  120 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~  120 (357)
                      ..|++.++.|-+|+|||||..
T Consensus        12 ~~~~~alfFGLSGTGKTTLs~   32 (313)
T d2olra1          12 EKGDVAVFFGLSGTGKTTLST   32 (313)
T ss_dssp             TTSCEEEEECSTTSSHHHHHC
T ss_pred             CCCCEEEEEccCCCCccccee
Confidence            468999999999999999874

>d1ii2a1 c.91.1.1 (A:201-523) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Trypanosoma cruzi [TaxId: 5693]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Trypanosoma cruzi [TaxId: 5693]

Probab=87.00  E-value=0.16  Score=43.07  Aligned_cols=21  Identities=43%  Similarity=0.545  Sum_probs=18.9

Q ss_pred             CCCcEEEEEcCCCCcHHHHHH
Q 035774          100 PFGVVTELVGPAGTGKTQFCL  120 (357)
Q Consensus       100 ~~G~l~~I~G~~GsGKT~l~~  120 (357)
                      ..|++.++.|-+|+|||||..
T Consensus        12 ~~gd~alfFGLSGTGKTTLs~   32 (323)
T d1ii2a1          12 KQGDVTVFFGLSGTGKTTLSA   32 (323)
T ss_dssp             TTCCEEEEECCTTSSHHHHHC
T ss_pred             CCCCEEEEEccCCCCccccee
Confidence            468999999999999999984

>d1n0ua2 c.37.1.8 (A:3-343) Elongation factor 2 (eEF-2), N-terminal (G) domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor 2 (eEF-2), N-terminal (G) domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.46  E-value=0.7  Score=39.57  Aligned_cols=23  Identities=17%  Similarity=0.216  Sum_probs=20.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhc
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAA  127 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~  127 (357)
                      +.|.|..++|||||+-.++...-
T Consensus        20 I~iiGhvd~GKTTL~d~Ll~~~g   42 (341)
T d1n0ua2          20 MSVIAHVDHGKSTLTDSLVQRAG   42 (341)
T ss_dssp             EEEECCGGGTHHHHHHHHHHHHB
T ss_pred             EEEEeCCCCcHHHHHHHHHHHCC
Confidence            88999999999999999987653

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=86.19  E-value=0.17  Score=43.00  Aligned_cols=20  Identities=40%  Similarity=0.527  Sum_probs=18.2

Q ss_pred             CCcEEEEEcCCCCcHHHHHH
Q 035774          101 FGVVTELVGPAGTGKTQFCL  120 (357)
Q Consensus       101 ~G~l~~I~G~~GsGKT~l~~  120 (357)
                      .|++.++.|-+|+|||||..
T Consensus        13 ~~~valffGLSGTGKTTLs~   32 (318)
T d1j3ba1          13 EGDVAVFFGLSGTGKTTLST   32 (318)
T ss_dssp             TCCEEEEEECTTSCHHHHTC
T ss_pred             CCCEEEEEccCCCCcccccc
Confidence            57899999999999999875

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=85.78  E-value=0.2  Score=38.59  Aligned_cols=19  Identities=26%  Similarity=0.377  Sum_probs=17.5

Q ss_pred             EEEEcCCCCcHHHHHHHHH
Q 035774          105 TELVGPAGTGKTQFCLKLS  123 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia  123 (357)
                      +.|.|.|.+|||||.-.+.
T Consensus         8 IaiiG~~naGKSTL~n~L~   26 (179)
T d1wb1a4           8 LGIFGHIDHGKTTLSKVLT   26 (179)
T ss_dssp             EEEEECTTSSHHHHHHHHH
T ss_pred             EEEEeCCCCcHHHHHHHHH
Confidence            7899999999999998876

>d2q0zx1 a.289.1.1 (X:33-208) Protein pro2281 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Sec63 N-terminal domain-like
superfamily: Sec63 N-terminal domain-like
family: Sec63 N-terminal domain
domain: Protein pro2281
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.71  E-value=1.2  Score=33.85  Aligned_cols=54  Identities=9%  Similarity=0.203  Sum_probs=47.1

Q ss_pred             cccccccC-CCHHHHHHHHhCCCCCHHHHhcCCHHHHHHHhCCCHHHHHHHHHHH
Q 035774            3 NKLISEMR-LPKSIANIFAARNITTAKDALSLTELELMKLLDVELSEVRSALALV   56 (357)
Q Consensus         3 ~~~~~~~~-l~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~   56 (357)
                      ..|+.|++ +++...+++.+.|+.+..++...++.++...++++..+..++.+.+
T Consensus       118 ~~~L~Qlp~~~~~~~~kl~~~~i~sl~~l~~~~~~e~~~ll~~~~~~~~~i~~~~  172 (176)
T d2q0zx1         118 DSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQIADVARFC  172 (176)
T ss_dssp             SCGGGGSTTCCHHHHHHHHHTTCCSHHHHHHSCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             CCCccCCCcCCHHHHHHHHHCCCCCHHHHHhCCHHHHHHHHcCCHHHHHHHHHHH
Confidence            34678885 9999999999999999999999999999999999998887776654

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=83.34  E-value=1.2  Score=35.01  Aligned_cols=19  Identities=32%  Similarity=0.228  Sum_probs=15.4

Q ss_pred             CcEEEEEcCCCCcHHHHHH
Q 035774          102 GVVTELVGPAGTGKTQFCL  120 (357)
Q Consensus       102 G~l~~I~G~~GsGKT~l~~  120 (357)
                      |.=+++.+++|+|||.-..
T Consensus        47 g~dvl~~a~TGsGKT~a~~   65 (212)
T d1qdea_          47 GHDVLAQAQSGTGKTGTFS   65 (212)
T ss_dssp             TCCEEEECCTTSSHHHHHH
T ss_pred             CCCEEeecccccchhhhhH
Confidence            4568999999999997544

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=82.49  E-value=0.36  Score=41.34  Aligned_cols=33  Identities=24%  Similarity=0.256  Sum_probs=25.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHhccccCCCCCCCeEEEEe
Q 035774          105 TELVGPAGTGKTQFCLKLSLLAALPAHYGGLDGGVIYID  143 (357)
Q Consensus       105 ~~I~G~~GsGKT~l~~~ia~~~~~~~~~gg~~~~vl~i~  143 (357)
                      +.|-|.-|+||||++..++......      +.+++|+.
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~~~------g~~v~~~~   40 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFAIT------PNRILLIG   40 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTTTS------GGGEEEEC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhhc------CCceEEEe
Confidence            7899999999999999888765421      35666664

>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=80.86  E-value=0.57  Score=40.05  Aligned_cols=23  Identities=26%  Similarity=0.156  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHh
Q 035774          104 VTELVGPAGTGKTQFCLKLSLLA  126 (357)
Q Consensus       104 l~~I~G~~GsGKT~l~~~ia~~~  126 (357)
                      .+.|-|.-|+||||++..++...
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l   30 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAA   30 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGG
T ss_pred             EEEEECCccCCHHHHHHHHHHHh
Confidence            47789999999999999888654