Citrus Sinensis ID: 041007

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------580-------590-------
Protein Sequence
MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccEEEccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccEEcccccccccccccccccccccccccHHHHHHHHHHHHcccccccccccccccEEEEEccccccHHHHHHHHHccHHHHHcccccEEEEEcccccHHHHHHHHHHccccccHHHHHHHHHHHHcccccccccHHHHHHHHHHHccccEEEEEEccccccccccHHHHHHHHHcccccccEEEEEccccHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHcccccccccccHHHHHHHHHHHccccHHHHHHHHHHHcccccHHHHHHHHccccccccHHHHHHccccccccHHHHccccccccHHHHHHHHHccccccccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHcccccccccccccccEEEEEEccHHHHHHHHHHcccEEEEEEcccccccccccccccEEEEEEEEccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccEcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccEEcccccHHHHHHHHHccccccccccccccEEEEEEccccccHHHHHHHHHccHHHHHcccEEEEEEEcccccHHHHHHHHHHHcccccccHHHHHHHHHHcccccccccHHHHHHHHHHHHccccEEEEEEcccccccHHHHHHHHccccccccccEEEEEEccHHHHHHHccccccccccccccEEEcccccHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccHHHHHHHHHHHHccccHHHHHHHHHHcccccccccccccccHHcHHHHHHccHHcccHHHHHHHHEEEEcccccEEcHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHccccEEcccccccccEEEEEEHHHHHHHHHHHccccEEEEEEcccccccccccccccEEEEEEEEcccccccccHHHHHHHHcccc
Coil and Loop (DISEMBL)
MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLAnetdhkaskvRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMsgsgeggimttssavidplefhgrnAEKQKILQLLkgessdeesgskptlpviwilgnegigktALARqvfddsdvkanfdkriwvsasyprdeirVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLksgsegsrilvtrsggkngtnmteiglgekngtnmmeiglgelsEEECRSLFRQIAFhgrssdyrekfepigrrvvgkckgLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICkragvgyeclsplllsyfdlspalkKCFLYCSIFPKNYEIEKDRLIKLWMAQgylksqeskdMELVGEEyfgnlssrslFQDFqksefdgriircqmhPIVHEFAQLLSKshnfnaevkgsdqecqsksshEKFRHLMIMFETdhgafpnsvynqkklrslv
Flexible Loop (DISEMBL)
MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIRevlddaekrqvkdvkdkAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLanetdhkaskvRSFTCHLRIALRFDIGCKLKNLSRRvdaiagkkdgFVIKLMsgsgeggiMTTSSAVIDPLEFHGRNAEKQKILQLLKgessdeesgskptLPVIWILGNEGIGKTALARQVFDdsdvkanfdkriwvsasyprdeirvardeisvardrdeiRVAKAILeslkgsvssqvEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVtrsggkngtnmteiglgekngtNMMEIGLGELSEEECRSLFRQIafhgrssdyrekfepigrrvvgkckgLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETdhgafpnsvynqkklrslv
Low Complexity Region (SEG)
MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKgessdeesgsKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV
Disordered region (IsUnstruct)
*********VLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEF****************************LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLK************************************IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKS*****MELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLS*************************RHLMIMFETDHGAF**************
Disordered Region (DISOPRED)
MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAI*******************TCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGF*********************DPLEFHGRNAEKQKILQLLKGESS****GSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAIL***************VLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGR**DYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICK*AGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQE**DMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSD******SSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV
Disordered Region (DISEMBL)
********TVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLL************PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNA**************HEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV
Disordered Region (DISPRO)
MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLL*N***HKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIK*************SSAVIDPLEFHGRNAEKQKILQLLKGESSD****SKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDxxxxxxxxxxxxxxxxxxxxxQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV
Positional Conservation
no confident homologs detected

---

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	597	2.2.26 [Sep-21-2011]
Q7XA42	979	Putative disease resistan	N/A	no	0.827	0.504	0.323	3e-69
Q7XA40	992	Putative disease resistan	N/A	no	0.785	0.472	0.333	1e-66
Q7XBQ9	970	Disease resistance protei	N/A	no	0.845	0.520	0.325	2e-66
Q7XA39	988	Putative disease resistan	N/A	no	0.792	0.478	0.320	1e-60
Q9LRR4	1054	Putative disease resistan	yes	no	0.767	0.434	0.295	2e-57
Q9LRR5	1424	Putative disease resistan	no	no	0.804	0.337	0.272	6e-39
Q9M667	835	Disease resistance protei	no	no	0.817	0.584	0.279	1e-38
Q38834	852	Disease resistance RPP13-	no	no	0.824	0.577	0.263	2e-38
Q39214	926	Disease resistance protei	no	no	0.825	0.532	0.256	4e-37
Q9STE5	847	Putative disease resistan	no	no	0.817	0.576	0.266	5e-37

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

 Score =  263 bits (672), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 179/554 (32%), Positives = 287/554 (51%), Gaps = 60/554 (10%)

Query: 1   MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDV 60
           MAE   +  VLD L+S    + G  +L+ G   + ++L S    I+ VL+DA+++Q+ D 
Sbjct: 1   MAEAF-IQVVLDNLTSF---LKGELVLLFGFQDEFQRLSSMFSTIQAVLEDAQEKQLND- 55

Query: 61  KDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFD 120
             K +E+WL++L    Y VDD LDE+ T   + L  +E      KV        I  R  
Sbjct: 56  --KPLENWLQKLNAATYEVDDILDEYKTKATRFL-QSEYGRYHPKV--------IPFRHK 104

Query: 121 IGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQ 180
           +G ++  + ++++AIA ++  F ++      +     T S + +P + +GR+ EK +I++
Sbjct: 105 VGKRMDQVMKKLNAIAEERKKFHLQEKIIERQAATRETGSVLTEP-QVYGRDKEKDEIVK 163

Query: 181 LLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD 240
           +L   +SD +      L V+ ILG  G+GKT L++ VF+D  V   F  +IW        
Sbjct: 164 ILINTASDAQK-----LSVLPILGMGGLGKTTLSQMVFNDQRVTERFYPKIW-------- 210

Query: 241 EIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDD 300
                   I ++ D +E R+ KAI+ES++G   S +++  + + + E + GK+  LVLDD
Sbjct: 211 --------ICISDDFNEKRLIKAIVESIEGKSLSDMDLAPLQKKLQELLNGKRYFLVLDD 262

Query: 301 LWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGEL 360
           +W N     W  L   LK G+ G+ +L T    K G+ M         GT +    L  L
Sbjct: 263 VW-NEDQHKWANLRAVLKVGASGAFVLTTTRLEKVGSIM---------GT-LQPYELSNL 311

Query: 361 SEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQ 420
           S E+C  LF Q AF G   +       IG+ +V KC G+P A K LG +LRFK   +EW+
Sbjct: 312 SPEDCWFLFMQRAF-GHQEEINPNLMAIGKEIVKKCGGVPLAAKTLGGILRFKREEREWE 370

Query: 421 SVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRL 480
            V DS IWNL  +           L  L LSY  L   L++CF+YC++FPK+ ++ K+ L
Sbjct: 371 HVRDSPIWNLPQD-------ESSILPALRLSYHHLPLDLRQCFVYCAVFPKDTKMAKENL 423

Query: 481 IKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFA 540
           I  WMA G+L S+ + ++E VG E +  L  RS FQ+    E +      +MH ++H+ A
Sbjct: 424 IAFWMAHGFLLSKGNLELEDVGNEVWNELYLRSFFQEI---EVESGKTYFKMHDLIHDLA 480

Query: 541 QLLSKSHNFNAEVK 554
             L  ++  ++ ++
Sbjct: 481 TSLFSANTSSSNIR 494

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

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

 Score =  254 bits (649), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 183/549 (33%), Positives = 284/549 (51%), Gaps = 80/549 (14%)

Query: 1   MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDV 60
           MAE   +  +LD L+   Q   G   LV G   + +KL S    I+ VL+DA+++Q+K  
Sbjct: 1   MAEAF-LQVLLDNLTFFIQ---GELGLVFGFEKEFKKLSSMFSMIQAVLEDAQEKQLKY- 55

Query: 61  KDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLR-IALRF 119
             KA+++WL++L    Y VDD LD+  T   +         K + +  +  H R I   +
Sbjct: 56  --KAIKNWLQKLNVAAYEVDDILDDCKTEAARF--------KQAVLGRY--HPRTITFCY 103

Query: 120 DIGCKLKNLSRRVDAIAGKKDGF-----VIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAE 174
            +G ++K +  ++DAIA ++  F     +I+  +   + G + T   V      +GR  E
Sbjct: 104 KVGKRMKEMMEKLDAIAEERRNFHLDERIIERQAARRQTGFVLTEPKV------YGREKE 157

Query: 175 KQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS 234
           + +I+++L    S  E      +PV+ ILG  G+GKT LA+ VF+D  +  +F+ +IWV 
Sbjct: 158 EDEIVKILINNVSYSEE-----VPVLPILGMGGLGKTTLAQMVFNDQRITEHFNLKIWVC 212

Query: 235 ASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKV 294
                           V+ D DE R+ KAI+ES++G     +++  + + + E + GK+ 
Sbjct: 213 ----------------VSDDFDEKRLIKAIVESIEGKSLGDMDLAPLQKKLQELLNGKRY 256

Query: 295 LLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME 354
            LVLDD+W N     W+ L   LK G+ G+ IL+T    K G+ M  + L +        
Sbjct: 257 FLVLDDVW-NEDQEKWDNLRAVLKIGASGASILITTRLEKIGSIMGTLQLYQ-------- 307

Query: 355 IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKT 414
             L  LS+E+C  LF+Q AF    ++   K   IG+ +V KC G+P A K LG LLRFK 
Sbjct: 308 --LSNLSQEDCWLLFKQRAF-CHQTETSPKLMEIGKEIVKKCGGVPLAAKTLGGLLRFKR 364

Query: 415 SIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYE 474
              EW+ V DSEIWNL  +           L  L LSY  L   L++CF YC++FPK+ +
Sbjct: 365 EESEWEHVRDSEIWNLPQD-------ENSVLPALRLSYHHLPLDLRQCFAYCAVFPKDTK 417

Query: 475 IEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQ----KSEFDGRIIRC 530
           IEK+ LI LWMA  +L S+ + ++E VG E +  L  RS FQ+ +    K+ F       
Sbjct: 418 IEKEYLIALWMAHSFLLSKGNMELEDVGNEVWNELYLRSFFQEIEVKSGKTYF------- 470

Query: 531 QMHPIVHEF 539
           +MH ++H+ 
Sbjct: 471 KMHDLIHDL 479

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

Solanum bulbocastanum (taxid: 147425)

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

 Score =  254 bits (648), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 187/574 (32%), Positives = 296/574 (51%), Gaps = 69/574 (12%)

Query: 1   MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDV 60
           MAE   +  +LD L+S    + G  +L+ G   + ++L S    I+ VL+DA+++Q+ + 
Sbjct: 1   MAEAF-IQVLLDNLTSF---LKGELVLLFGFQDEFQRLSSMFSTIQAVLEDAQEKQLNN- 55

Query: 61  KDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFD 120
             K +E+WL++L    Y VDD LDE+ T   +    +E      KV        I  R  
Sbjct: 56  --KPLENWLQKLNAATYEVDDILDEYKTKATRFS-QSEYGRYHPKV--------IPFRHK 104

Query: 121 IGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQ 180
           +G ++  + +++ AIA ++  F +       +     T S + +P + +GR+ EK +I++
Sbjct: 105 VGKRMDQVMKKLKAIAEERKNFHLHEKIVERQAVRRETGSVLTEP-QVYGRDKEKDEIVK 163

Query: 181 LLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD 240
           +L    SD +      L V+ ILG  G+GKT LA+ VF+D  V  +F  +IW        
Sbjct: 164 ILINNVSDAQH-----LSVLPILGMGGLGKTTLAQMVFNDQRVTEHFHSKIW-------- 210

Query: 241 EIRVARDEISVARDRDEIRVAKAILESLKG-SVSSQVEMETVLQYINEFVQGKKVLLVLD 299
                   I V+ D DE R+ KAI+ES++G  +  ++++  + + + E + GK+ LLVLD
Sbjct: 211 --------ICVSEDFDEKRLIKAIVESIEGRPLLGEMDLAPLQKKLQELLNGKRYLLVLD 262

Query: 300 DLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGE 359
           D+W N   + W  L   LK G+ G+ +L T    K G+ M         GT +    L  
Sbjct: 263 DVW-NEDQQKWANLRAVLKVGASGASVLTTTRLEKVGSIM---------GT-LQPYELSN 311

Query: 360 LSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEW 419
           LS+E+C  LF Q AF G   +       IG+ +V K  G+P A K LG +L FK   + W
Sbjct: 312 LSQEDCWLLFMQRAF-GHQEEINPNLVAIGKEIVKKSGGVPLAAKTLGGILCFKREERAW 370

Query: 420 QSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDR 479
           + V DS IWNL  +           L  L LSY  L   LK+CF YC++FPK+ ++EK++
Sbjct: 371 EHVRDSPIWNLPQD-------ESSILPALRLSYHQLPLDLKQCFAYCAVFPKDAKMEKEK 423

Query: 480 LIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEF 539
           LI LWMA G+L S+ + ++E VG+E +  L  RS FQ+ +    DG+    +MH ++H+ 
Sbjct: 424 LISLWMAHGFLLSKGNMELEDVGDEVWKELYLRSFFQEIEVK--DGKTY-FKMHDLIHDL 480

Query: 540 AQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLM 573
           A  L     F+A    S+    +K S   + H+M
Sbjct: 481 ATSL-----FSANTSSSNIREINKHS---YTHMM 506

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

Solanum bulbocastanum (taxid: 147425)

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

 Score =  234 bits (598), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 171/533 (32%), Positives = 271/533 (50%), Gaps = 60/533 (11%)

Query: 14  LSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELT 73
           L ++T  +    +L+ G   + EKL S    I+ VL DA+++Q+KD   KA+E+WL++L 
Sbjct: 10  LENLTSFIGDKLVLIFGFEKECEKLSSVFSTIQAVLQDAQEKQLKD---KAIENWLQKLN 66

Query: 74  DTCYAVDDALDEW-NTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRV 132
              Y VDD L E  N AI+          + S++  +   + I  R  IG ++K +  ++
Sbjct: 67  SAAYEVDDILGECKNEAIR---------FEQSRLGFYHPGI-INFRHKIGRRMKEIMEKL 116

Query: 133 DAIAG--KKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEE 190
           DAI+   +K  F+ K+           T   + +P + +GR+ E+ +I+++L    +  E
Sbjct: 117 DAISEERRKFHFLEKITERQAAAATRETGFVLTEP-KVYGRDKEEDEIVKILINNVNVAE 175

Query: 191 SGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEIS 250
                 LPV  I+G  G+GKT LA+ +F+D  V  +F+ +IWV                 
Sbjct: 176 E-----LPVFPIIGMGGLGKTTLAQMIFNDERVTKHFNPKIWVC---------------- 214

Query: 251 VARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYW 310
           V+ D DE R+ K I+ +++ S     ++ +  + + E + GK+ LLVLDD+W N     W
Sbjct: 215 VSDDFDEKRLIKTIIGNIERSSPHVEDLASFQKKLQELLNGKRYLLVLDDVW-NDDLEKW 273

Query: 311 EQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFR 370
            +L   L  G+ G+ IL T    K G+ M         GT +    L  LS  +   LF 
Sbjct: 274 AKLRAVLTVGARGASILATTRLEKVGSIM---------GT-LQPYHLSNLSPHDSLLLFM 323

Query: 371 QIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNL 430
           Q AF G+  +       IG+ +V KC G+P A K LG LLRFK    EW+ V D+EIW+L
Sbjct: 324 QRAF-GQQKEANPNLVAIGKEIVKKCGGVPLAAKTLGGLLRFKREESEWEHVRDNEIWSL 382

Query: 431 DSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYL 490
             +           L  L LSY  L   L++CF YC++FPK+ ++ K+ LI LWMA G+L
Sbjct: 383 PQD-------ESSILPALRLSYHHLPLDLRQCFAYCAVFPKDTKMIKENLITLWMAHGFL 435

Query: 491 KSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLL 543
            S+ + ++E VG E +  L  RS FQ+ +    +      ++H ++H+ A  L
Sbjct: 436 LSKGNLELEDVGNEVWNELYLRSFFQEIEAKSGNTYF---KIHDLIHDLATSL 485

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

Solanum bulbocastanum (taxid: 147425)

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

 Score =  224 bits (570), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 153/518 (29%), Positives = 263/518 (50%), Gaps = 60/518 (11%)

Query: 35  VEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLL 94
           +E+L + L  I  VL DAE++Q+ +     VE W+ EL D  Y  +DALD+  T   +L 
Sbjct: 39  LERLSTALLTITAVLIDAEEKQITN---PVVEKWVNELRDVVYHAEDALDDIATEALRLN 95

Query: 95  LANETDHKASKVRSFTCHLRIALRFD-----IGCKLKNLSRRVDAIAGKKDGFVIKLMSG 149
           +  E+   ++++R     + +    D     +  +L+ ++ R++ +A +++   +K ++ 
Sbjct: 96  IGAESS-SSNRLRQLRGRMSLGDFLDGNSEHLETRLEKVTIRLERLASQRNILGLKELTA 154

Query: 150 SGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIG 209
                 + T+S ++D  E  GR+ +K +I++ L       E+G    + V+ I+G  G+G
Sbjct: 155 MIPKQRLPTTS-LVDESEVFGRDDDKDEIMRFLI-----PENGKDNGITVVAIVGIGGVG 208

Query: 210 KTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLK 269
           KT L++ +++D  V++ F  ++W                  V+ + D  ++ K + ES+ 
Sbjct: 209 KTTLSQLLYNDQHVRSYFGTKVWAH----------------VSEEFDVFKITKKVYESVT 252

Query: 270 GSVSSQVEMETVLQYINEFVQGK--KVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRIL 327
                  +++ +   + E + G     LLVLDDLW   +   W+ L       ++GS+IL
Sbjct: 253 SRPCEFTDLDVLQVKLKERLTGTGLPFLLVLDDLWNENFAD-WDLLRQPFIHAAQGSQIL 311

Query: 328 VTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEP 387
           VT    +  + M  + +            L  LS+ +C SLF +  F  +      +   
Sbjct: 312 VTTRSQRVASIMCAVHVH----------NLQPLSDGDCWSLFMKTVFGNQEPCLNREIGD 361

Query: 388 IGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSP 447
           +  R+V KC+GLP AVK LG +LRF+  + EW+ VL S IW+L ++           L  
Sbjct: 362 LAERIVHKCRGLPLAVKTLGGVLRFEGKVIEWERVLSSRIWDLPAD-------KSNLLPV 414

Query: 448 LLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYL-KSQESKDMELVGEEYF 506
           L +SY+ L   LK+CF YCSIFPK +  EKD+++ LWMA+G+L +++ SK++E +G EYF
Sbjct: 415 LRVSYYYLPAHLKRCFAYCSIFPKGHAFEKDKVVLLWMAEGFLQQTRSSKNLEELGNEYF 474

Query: 507 GNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLS 544
             L SRSL Q  +         R  MH  ++E AQ  S
Sbjct: 475 SELESRSLLQKTK--------TRYIMHDFINELAQFAS 504

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  162 bits (410), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 148/543 (27%), Positives = 249/543 (45%), Gaps = 63/543 (11%)

Query: 35  VEKLRSHLEAIREVLDDAEKR--QVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQK 92
           +++L+  L     VL DA++R   V++VK      WL  + D  +  +D LDE  T   +
Sbjct: 36  LKRLKVALVTANPVLADADQRAEHVREVKH-----WLTGIKDAFFQAEDILDELQTEALR 90

Query: 93  LLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGE 152
             +  E        ++     R A++  I  K++ + R ++      +   +K  S + E
Sbjct: 91  RRVVAEAGGLGGLFQNLMAG-REAIQKKIEPKMEKVVRLLEHHVKHIEVIGLKEYSETRE 149

Query: 153 GGIMTTSSAVIDPLE---FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIG 209
                 S +  D L      GR  +K  ++ LL   S DE S  KP   VI ++G  G+G
Sbjct: 150 PQWRQASRSRPDDLPQGRLVGRVEDKLALVNLLL--SDDEISIGKPA--VISVVGMPGVG 205

Query: 210 KTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLK 269
           KT L   VF+D  V  +F+ ++W+SA                  + +   V KA+L+ + 
Sbjct: 206 KTTLTEIVFNDYRVTEHFEVKMWISAGI----------------NFNVFTVTKAVLQDIT 249

Query: 270 GSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVT 329
            S  +  ++ ++   + + + GK+ LLVLDD +W+     WE    +     EGS+I++T
Sbjct: 250 SSAVNTEDLPSLQIQLKKTLSGKRFLLVLDD-FWSESDSEWESFQVAFTDAEEGSKIVLT 308

Query: 330 RSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRS-SDYREKFEPI 388
                     +EI         + ++ L  ++ EEC  L  + AF   S     ++ E I
Sbjct: 309 --------TRSEIVSTVAKAEKIYQMKL--MTNEECWELISRFAFGNISVGSINQELEGI 358

Query: 389 GRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPL 448
           G+R+  +CKGLP A + + S LR K +  +W +V             K        + P+
Sbjct: 359 GKRIAEQCKGLPLAARAIASHLRSKPNPDDWYAV------------SKNFSSYTNSILPV 406

Query: 449 L-LSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYL-KSQESKDMELVGEEYF 506
           L LSY  L P LK+CF  CSIFPK +  +++ L+ LWMA   L + + S+ +E +G +Y 
Sbjct: 407 LKLSYDSLPPQLKRCFALCSIFPKGHVFDREELVLLWMAIDLLYQPRSSRRLEDIGNDYL 466

Query: 507 GNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSH 566
           G+L ++S FQ       D  +    MH ++++ A+ +S    F  E   +  E  S + H
Sbjct: 467 GDLVAQSFFQ-----RLDITMTSFVMHDLMNDLAKAVSGDFCFRLE-DDNIPEIPSTTRH 520

Query: 567 EKF 569
             F
Sbjct: 521 FSF 523

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M667|RPP13_ARATH Disease resistance protein RPP13 OS=Arabidopsis thaliana GN=RPP13 PE=2 SV=2

 Score =  161 bits (408), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 156/559 (27%), Positives = 265/559 (47%), Gaps = 71/559 (12%)

Query: 30  GVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTA 89
            V  D+E+L++ L  I   L D E R+ +D   +  ++W + + D  Y V+D LD ++  
Sbjct: 26  AVKEDLEELKTELTCIHGYLKDVEARERED---EVSKEWSKLVLDFAYDVEDVLDTYH-- 80

Query: 90  IQKLLLANETDHKASKVRSFTCHL-RIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMS 148
                L  E   +   +R  T  + R    + I   ++ L RR+  I  K++ + I  + 
Sbjct: 81  -----LKLEERSQRRGLRRLTNKIGRKMDAYSIVDDIRILKRRILDITRKRETYGIGGLK 135

Query: 149 GSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESS-------DEESGSKPTLPVIW 201
               GG   TSS  +  L    R+ ++++++  L+ ++        D E  ++    +I 
Sbjct: 136 EPQGGG--NTSSLRVRQLR-RARSVDQEEVVVGLEDDAKILLEKLLDYEEKNRF---IIS 189

Query: 202 ILGNEGIGKTALARQVFDDSDVKANFDKRIW--VSASYPRDEI--RVARDEISVARDRDE 257
           I G  G+GKTALAR++++  DVK  F+ R W  VS  Y   +I  R+ R     + +   
Sbjct: 190 IFGMGGLGKTALARKLYNSRDVKERFEYRAWTYVSQEYKTGDILMRIIRSLGMTSGEE-- 247

Query: 258 IRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSL 317
                  LE ++     ++E+     Y+   ++GKK L+V+DD+W       W+ L  +L
Sbjct: 248 -------LEKIRKFAEEELEV-----YLYGLLEGKKYLVVVDDIWEREA---WDSLKRAL 292

Query: 318 KSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHG- 376
               EGSR+++T       T +  +  G        ++    L+ EE   LF Q AF   
Sbjct: 293 PCNHEGSRVIIT-------TRIKAVAEGVDGRFYAHKLRF--LTFEESWELFEQRAFRNI 343

Query: 377 RSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICK 436
           +  D  E     G+ +V KC+GLP  + +L  LL  KT   EW  V +S    L  +   
Sbjct: 344 QRKD--EDLLKTGKEMVQKCRGLPLCIVVLAGLLSRKTP-SEWNDVCNSLWRRLKDDSIH 400

Query: 437 RAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESK 496
            A + ++      LS+ +L    K CFLY SIFP++YEI+ ++LI L +A+G+++  E  
Sbjct: 401 VAPIVFD------LSFKELRHESKLCFLYLSIFPEDYEIDLEKLIHLLVAEGFIQGDEEM 454

Query: 497 DMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNF----NAE 552
            ME V   Y   L  RSL +  ++    G+++ C++H ++ + A   SK  NF    N  
Sbjct: 455 MMEDVARYYIEELIDRSLLEAVRRER--GKVMSCRIHDLLRDVAIKKSKELNFVNVYNDH 512

Query: 553 V-KGSDQECQSKSSHEKFR 570
           V + S   C+ +  H +F+
Sbjct: 513 VAQHSSTTCRREVVHHQFK 531

Disease resistance protein. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. In contrast to other resistance proteins, it works independently of ESD1 and NSD1 proteins and does not require the accumulation of salicylic acid, suggesting the existence of an independent signaling pathway. The specificity to avirulence proteins differs in the different cultivars.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  160 bits (405), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 147/558 (26%), Positives = 273/558 (48%), Gaps = 66/558 (11%)

Query: 29  GGVVTD----VEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALD 84
           G  V+D    +E L+S L+ ++  L DAE+++  +   + +   LREL    Y  +D L 
Sbjct: 21  GRTVSDYRKQLEDLQSELKYMQSFLKDAERQKRTNETLRTLVADLRELV---YEAEDILV 77

Query: 85  EWNTAIQKLLLANETDHKASKVRSFTCH-LRIALRFDIGCKLKNLSRRVDAIAGKKDGFV 143
           +   A       +  + ++S       H  R+ L++    +L+ ++ R+  I  + + + 
Sbjct: 78  DCQLADGD----DGNEQRSSNAWLSRLHPARVPLQYKKSKRLQEINERITKIKSQVEPY- 132

Query: 144 IKLMSGSGEG---GIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVI 200
            + ++ S  G   G    SS V D  +  G   +K+KI + L   S+D +      L ++
Sbjct: 133 FEFITPSNVGRDNGTDRWSSPVYDHTQVVGLEGDKRKIKEWL-FRSNDSQ------LLIM 185

Query: 201 WILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRV 260
             +G  G+GKT +A++VF+D +++  F++RIWVS                V++   E ++
Sbjct: 186 AFVGMGGLGKTTIAQEVFNDKEIEHRFERRIWVS----------------VSQTFTEEQI 229

Query: 261 AKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG 320
            ++IL +L G  S   ++ T+L+ I +++ GK+ L+V+DD+W +    +W+++   L  G
Sbjct: 230 MRSILRNL-GDASVGDDIGTLLRKIQQYLLGKRYLIVMDDVW-DKNLSWWDKIYQGLPRG 287

Query: 321 SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSD 380
             GS I+ TRS      ++ +      + T+  E+    LS +    LF  +AF      
Sbjct: 288 QGGSVIVTTRS-----ESVAKRVQARDDKTHRPEL----LSPDNSWLLFCNVAFAANDGT 338

Query: 381 Y-REKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSI-KEWQSVLDSEIWNLDSEICKRA 438
             R + E +G+ +V KCKGLP  +K +G LL  K  +  EW+ + +    +   E+    
Sbjct: 339 CERPELEDVGKEIVTKCKGLPLTIKAVGGLLLCKDHVYHEWRRIAE----HFQDELRGNT 394

Query: 439 GVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDM 498
                 +S L LSY +L   LK C L  S++P++  I K +L+  W+ +G++  +  +  
Sbjct: 395 SETDNVMSSLQLSYDELPSHLKSCILTLSLYPEDCVIPKQQLVHGWIGEGFVMWRNGRSA 454

Query: 499 ELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNF-NAE----- 552
              GE+ F  L++R L +   K+ + G II C++H +V +    ++K  +F N E     
Sbjct: 455 TESGEDCFSGLTNRCLIEVVDKT-YSGTIITCKIHDMVRDLVIDIAKKDSFSNPEGLNCR 513

Query: 553 ---VKGSDQECQSKSSHE 567
              + G+  E Q K +H+
Sbjct: 514 HLGISGNFDEKQIKVNHK 531

Disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

>sp|Q39214|RPM1_ARATH Disease resistance protein RPM1 OS=Arabidopsis thaliana GN=RPM1 PE=1 SV=1

 Score =  156 bits (395), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 145/566 (25%), Positives = 251/566 (44%), Gaps = 73/566 (12%)

Query: 8   STVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVED 67
           +TV   +  I   +    LL+ GV  +++K++  L  ++  L+D  K           + 
Sbjct: 4   ATVDFGIGRILSVLENETLLLSGVHGEIDKMKKELLIMKSFLEDTHKHGGNGSTTTTTQL 63

Query: 68  WLRELTDT---CYAVDDALDEWNTAIQKLLLANETDHKASKV-RSFTCHLRIALRFDIGC 123
           +   + +T    Y ++D LDE+   I             +K+ R+F     +  R  I  
Sbjct: 64  FQTFVANTRDLAYQIEDILDEFGYHIHGY-------RSCAKIWRAFHFPRYMWARHSIAQ 116

Query: 124 KLKNLSRRVDAIAG------KKDGFVIKLMSGSGEGGI-----MTTSSAVIDPLEFHGRN 172
           KL  ++  + +I+         + +   L+    +G       ++ SS         G +
Sbjct: 117 KLGMVNVMIQSISDSMKRYYHSENYQAALLPPIDDGDAKWVNNISESSLFFSENSLVGID 176

Query: 173 AEKQKIL-QLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRI 231
           A K K++ +LL  E         P   V+ ++G  G GKT L+  +F    V+ +F+   
Sbjct: 177 APKGKLIGRLLSPE---------PQRIVVAVVGMGGSGKTTLSANIFKSQSVRRHFESYA 227

Query: 232 WVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMET-------VLQY 284
           WV+ S           +  V  D     V + +++       +Q+  E        +++ 
Sbjct: 228 WVTIS-----------KSYVIED-----VFRTMIKEFYKEADTQIPAELYSLGYRELVEK 271

Query: 285 INEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGL 344
           + E++Q K+ ++VLDD+W       W ++  +L  G  GSR+++T        N+     
Sbjct: 272 LVEYLQSKRYIVVLDDVWTTGL---WREISIALPDGIYGSRVMMT----TRDMNVASFPY 324

Query: 345 GEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYR-EKFEPIGRRVVGKCKGLPFAV 403
           G   G+   EI L  L E+E   LF   AF       R +  EPI R++V +C+GLP A+
Sbjct: 325 GI--GSTKHEIEL--LKEDEAWVLFSNKAFPASLEQCRTQNLEPIARKLVERCQGLPLAI 380

Query: 404 KILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCF 463
             LGS++  K    EW+ V  +  W L++    +        S + LS+ DL   LK+CF
Sbjct: 381 ASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKI-----VRSIMFLSFNDLPYPLKRCF 435

Query: 464 LYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEF 523
           LYCS+FP NY +++ RLI++WMAQ +++       E V + Y   L  R++ Q    + F
Sbjct: 436 LYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKAEEVADSYLNELVYRNMLQVILWNPF 495

Query: 524 DGRIIRCQMHPIVHEFAQLLSKSHNF 549
            GR    +MH ++ E A  +SK   F
Sbjct: 496 -GRPKAFKMHDVIWEIALSVSKLERF 520

Disease resistance (R) protein that specifically recognizes the AvrRpm1 type III effector avirulence protein from Pseudomonas syringae. Resistance proteins guard the plant against pathogens that contain an appropriate avirulence protein via an indirect interaction with this avirulence protein. That triggers a defense system including the hypersensitive response, which restricts the pathogen growth. Acts via its interaction with RIN4, and probably triggers the plant resistance when RIN4 is phosphorylated by AvrRpm1. It is then degraded at the onset of the hypersensitive response.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9STE5|R13L2_ARATH Putative disease resistance RPP13-like protein 2 OS=Arabidopsis thaliana GN=RPP13L2 PE=3 SV=1

 Score =  156 bits (394), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 147/551 (26%), Positives = 270/551 (49%), Gaps = 63/551 (11%)

Query: 30  GVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTA 89
           GV  D+E+L++ L  I+  L + E   V D +D+  ++W + + D  Y V+D LD +   
Sbjct: 26  GVKDDLEELKTELTCIQVYLKNVE---VCDKEDEVSKEWTKLVLDIAYDVEDVLDTYFLK 82

Query: 90  IQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSG 149
           ++K L      H+   +R           ++I   +K L RR   +  K + + I     
Sbjct: 83  LEKRL------HRLGLMRLTNIISDKKDAYNILDDIKTLKRRTLDVTRKLEMYGI---GN 133

Query: 150 SGEGGIMTTSSAVIDPLEFHGRNAEKQKI-----LQLLKGESSDEESGSKPTLPVIWILG 204
             E  ++ ++S V +       + E++ +      ++L  +  D++  +K  + +I I G
Sbjct: 134 FNEHRVVASTSRVREVRRARSDDQEERVVGLTDDAKVLLTKLLDDDGDNK--IYMISIFG 191

Query: 205 NEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAI 264
            EG+GKT+LAR++F+ SDVK +F+ R+W + S   +     RD +        +R+  ++
Sbjct: 192 MEGLGKTSLARKLFNSSDVKESFEYRVWTNVSGECN----TRDIL--------MRIISSL 239

Query: 265 LESLKGSVS--SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSE 322
            E+ +G +   +Q E+E    Y+++ +Q K+ L+V+DD+W +      E L  +L    +
Sbjct: 240 EETSEGELEKMAQQELEV---YLHDILQEKRYLVVVDDIWES---EALESLKRALPCSYQ 293

Query: 323 GSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYR 382
           GSR+++T       T++  +  G         I    L+ +E  +LF + AF        
Sbjct: 294 GSRVIIT-------TSIRVVAEGRDKRVYTHNIRF--LTFKESWNLFEKKAFR-YILKVD 343

Query: 383 EKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGY 442
           ++ + IG+ +V KC GLP    +L  L+  K    EW     +++W+  S   K   +  
Sbjct: 344 QELQKIGKEMVQKCGGLPRTTVVLAGLMSRKKP-NEW-----NDVWS--SLRVKDDNIHV 395

Query: 443 ECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVG 502
             L  L  S+ D+   LK CFLY S+FP++YE++ ++LI+L +A+G+++  E   ME V 
Sbjct: 396 SSLFDL--SFKDMGHELKLCFLYLSVFPEDYEVDVEKLIQLLVAEGFIQEDEEMTMEDVA 453

Query: 503 EEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQS 562
             Y  +L   SL +  ++ +  G+++  ++H +V EF   + KS   N      +Q   +
Sbjct: 454 RYYIEDLVYISLVEVVKRKK--GKLMSFRIHDLVREFT--IKKSKELNFVNVYDEQHSST 509

Query: 563 KSSHEKFRHLM 573
            S  E   HLM
Sbjct: 510 TSRREVVHHLM 520

Potential disease resistance protein.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	597
224122712	945	cc-nbs-lrr resistance protein [Populus t	0.924	0.584	0.425	1e-115
224115620	963	cc-nbs-lrr resistance protein [Populus t	0.927	0.575	0.410	1e-112
224115686	938	cc-nbs-lrr resistance protein [Populus t	0.924	0.588	0.407	1e-110
225463558	928	PREDICTED: putative disease resistance p	0.921	0.592	0.411	1e-109
147860109	699	hypothetical protein VITISV_033138 [Viti	0.906	0.773	0.412	1e-107
224114824	941	cc-nbs-lrr resistance protein [Populus t	0.886	0.562	0.408	1e-107
224114794	742	cc-nbs-lrr resistance protein [Populus t	0.874	0.703	0.407	1e-107
359482800	1006	PREDICTED: putative disease resistance p	0.916	0.543	0.416	1e-106
224134406	987	cc-nbs-lrr resistance protein [Populus t	0.904	0.547	0.389	1e-106
225470202	910	PREDICTED: putative disease resistance p	0.914	0.6	0.409	1e-104

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

 Score =  421 bits (1081), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 259/609 (42%), Positives = 370/609 (60%), Gaps = 57/609 (9%)

Query: 1   MAEEITVSTVLDQLSSIT-QQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKD 59
           MAE + +S +L+QL++I  QQ+     LV GV   V+KL+S+L  I+ VL+DA+++QVKD
Sbjct: 1   MAEAL-LSPILEQLTTIVAQQVQEEVNLVVGVKKQVDKLKSNLLDIQSVLEDADRKQVKD 59

Query: 60  VKDKAVEDWLRELTDTCYAVDDALDEWNTAIQ--KLLLANETDHKASKVR-SFT-----C 111
              KAV DW+ +L D CY +DD LDEW+TAI   K+  A E  H   K+R SF      C
Sbjct: 60  ---KAVRDWVDKLKDACYDMDDVLDEWSTAILRWKMEEAEENTHSRQKIRCSFLGSPCFC 116

Query: 112 HLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGR 171
             ++  R DI  K+K +S +VD IA ++  +   L  G+ E   +TT+S V D     GR
Sbjct: 117 FNQVVRRRDIALKIKEVSEKVDDIAKERAKYGFDLYKGTDELQRLTTTSFV-DESSVIGR 175

Query: 172 NAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRI 231
           + EK+ ++  L  ESS E       + VI ++G  GIGKT LA+  F+DS+V A+F+K+I
Sbjct: 176 DGEKRNVVSKLLAESSHEARD----VDVISLVGLGGIGKTTLAQLAFNDSEVTAHFEKKI 231

Query: 232 WVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQG 291
           WV  S P DEIR+A                KAILE L+G  ++ VE++++LQ ++E + G
Sbjct: 232 WVCVSEPFDEIRIA----------------KAILEQLEGRPTNLVELQSLLQGVSESITG 275

Query: 292 KKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN 351
           K++LLVLDD+W   + + WEQL  SL   + GSRILVT       T M         GT+
Sbjct: 276 KRLLLVLDDVWTENHGQ-WEQLKPSLTGCARGSRILVTTRKDAVATMM---------GTD 325

Query: 352 MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLR 411
              I + +LS+E CRS+F  +AF  RS D RE+   IG ++  KCKGLP A K+LG L++
Sbjct: 326 H-RINIEKLSDEICRSIFNHVAFQERSEDERERLTDIGDKIANKCKGLPLAAKVLGGLMQ 384

Query: 412 FKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPK 471
            K + +EW+ VL SE+W LD     R  V      PLLLSY+DL   +++CFLYC++FPK
Sbjct: 385 SKRTREEWERVLSSELWRLDE--VDRDQVESRIFIPLLLSYYDLPSVVRRCFLYCAMFPK 442

Query: 472 NYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQ 531
           +YE+ K  L+K+WMAQGY+K     DMELVGE YF  L++RS FQDF+   F+G  ++ +
Sbjct: 443 DYEMGKYELVKMWMAQGYIKETSGGDMELVGERYFHVLAARSFFQDFETDIFEG--MKFK 500

Query: 532 MHPIVHEFAQLLSKSHNFNAEVK---GSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVY 588
           MH IVH+FAQ ++K+     +V    G+  E    +S E+ RHL +M  ++  +FP S++
Sbjct: 501 MHDIVHDFAQYMTKNECLTVDVNTLGGATVE----TSIERVRHLSMMV-SEETSFPVSIH 555

Query: 589 NQKKLRSLV 597
             K LRSL+
Sbjct: 556 KAKGLRSLL 564

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224115620|ref|XP_002332101.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222874921|gb|EEF12052.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  411 bits (1056), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 249/606 (41%), Positives = 359/606 (59%), Gaps = 52/606 (8%)

Query: 1   MAEEITVSTVLDQLSSIT-QQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKD 59
           MA+ + VS VL+QLSSI  Q++     LV GV  +V+KL S+ +AI+ +  DAE+RQ+KD
Sbjct: 1   MADAL-VSVVLEQLSSIIIQEVQREVRLVVGVENEVKKLTSNFQAIQAMFADAEERQLKD 59

Query: 60  VKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRS------FTCHL 113
              + V+ WL +L D  Y +DD LDEW T I K   +   +H     R       F+C  
Sbjct: 60  ---QLVKHWLDQLKDVSYDMDDVLDEWGTEIAKSQ-SKVNEHPRKNTRKVCSFMIFSCFR 115

Query: 114 --RIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGR 171
              + LR DI  K+K L+ R+D IA +K+ F  K      +      + + ID  E  GR
Sbjct: 116 FREVGLRRDIALKIKELNERIDGIAIEKNRFHFKSSEVVIKQHDHRKTVSFIDAAEVKGR 175

Query: 172 NAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRI 231
             +K ++  +L  ESS       P L  I ++G  GIGKT LA+ V++D +V+ +FDKRI
Sbjct: 176 ETDKGRVRNMLLTESS-----QGPALRTISLVGMGGIGKTTLAQLVYNDHEVEIHFDKRI 230

Query: 232 WVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQG 291
           WV  S P DE ++A                KAILE+LKGS S  +E++T+L+ I   ++G
Sbjct: 231 WVCVSDPFDETKIA----------------KAILEALKGSASDLIELQTLLENIQPLIRG 274

Query: 292 KKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN 351
           KK LLVLDD+W N     WEQL YSL  G  GS ILVT       + M        + T+
Sbjct: 275 KKFLLVLDDVW-NEDSTKWEQLKYSLMCGLPGSSILVTTRKRNVASRMG------SSPTD 327

Query: 352 MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLR 411
           ++E+GL  LS +EC SLF ++AF  ++S  R   E IGR++  KCKGLP A K LGSLLR
Sbjct: 328 ILELGL--LSTDECWSLFSRLAFFEKNSRERGDLEDIGRQIAAKCKGLPLAAKSLGSLLR 385

Query: 412 FKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPK 471
           FK+ I+EW+SVL+S +W    E         + L+PL LSY+DL   +++CF YC++FPK
Sbjct: 386 FKSRIEEWESVLNSHVWESAEE------AESKILAPLWLSYYDLPSDMRRCFSYCAVFPK 439

Query: 472 NYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQ 531
           ++  E+D L+KLWMAQG+L+   +K+ME++G + F  L++RS FQDFQK   DG I  C+
Sbjct: 440 DFTFERDTLVKLWMAQGFLRETHNKEMEVIGRQCFEALAARSFFQDFQKETGDGSIYACK 499

Query: 532 MHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQK 591
           MH +VH+ AQ L+K+   + ++ G   E +  S     RH M++F  ++ +FP ++++ K
Sbjct: 500 MHDMVHDLAQNLTKNECSSVDIDGP-TELKIDSFSINARHSMVVFR-NYNSFPATIHSLK 557

Query: 592 KLRSLV 597
           KLRSL+
Sbjct: 558 KLRSLI 563

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  405 bits (1042), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 248/609 (40%), Positives = 359/609 (58%), Gaps = 57/609 (9%)

Query: 1   MAEEITVSTVLDQLSSI-TQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKD 59
           MA+ + V  V++QLS I  Q++     LV GV  +V+KL ++ + I+ VL DAE+R++KD
Sbjct: 1   MADAL-VFVVMEQLSLIFAQEVQQEVRLVVGVKNEVQKLTNNFQTIQAVLADAEERELKD 59

Query: 60  VKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLL-ANETDHKASK-----VRSFTCHL 113
               +++ W+ +L    Y +DD LDEW TAI K  +  NE   K ++     + S  C  
Sbjct: 60  ---GSIKRWIDQLKGVSYDMDDVLDEWGTAIAKSQMKVNEHPRKTARKVCSMIFSCLCFR 116

Query: 114 RIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGI----MTTSSAVIDPLEFH 169
            + LR DI  K+K L+ R+D I  +KD F  K    S E GI       +++VID  E  
Sbjct: 117 EVGLRRDIAHKIKELNERIDGIVIEKDRFHFK----SSEVGIKQLEHQKTTSVIDAAEVK 172

Query: 170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDK 229
           GR  +K ++  +L  ESS       P L  I ++G  GIGKT LA+ V++D DV  +FDK
Sbjct: 173 GRENDKDRVKNMLLSESS-----QGPALRTISLVGMGGIGKTTLAKLVYNDHDVTTHFDK 227

Query: 230 RIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFV 289
           RIWV  S P +EI +A                KAILE L GS  +  E++T+++++ E +
Sbjct: 228 RIWVCVSDPFNEITIA----------------KAILEDLTGSAPNLNELQTLVKHVQESI 271

Query: 290 QGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNG 349
           + KK LLVLDD+W N     WEQL  SLK G  GSRI+VT       ++M     G    
Sbjct: 272 REKKFLLVLDDVW-NEDSTKWEQLKDSLKCGLPGSRIMVTTRKTNVASSM-----GSSPS 325

Query: 350 TNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSL 409
           T+++E+GL  LS ++C SLF Q+AF  ++S  R   E IGR++  KCKGLP A K LGSL
Sbjct: 326 TDILELGL--LSTDKCWSLFSQLAFFEKNSRERGDLEDIGRQIAAKCKGLPLAAKSLGSL 383

Query: 410 LRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIF 469
           LRFK    EW+SVL++ +W +     K        L+PL LSY DL   +++CF YC++F
Sbjct: 384 LRFKRIRAEWESVLNNHVWEIKEAESK-------ILAPLWLSYNDLPSDMRRCFSYCAVF 436

Query: 470 PKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIR 529
           PK++  E+D LIKLWMAQG+L+  ++K+ME++G E F  L++RS FQDF+  E DG I  
Sbjct: 437 PKDFTFERDTLIKLWMAQGFLRETQNKEMEVMGRECFEALAARSFFQDFEIDEDDGSIYA 496

Query: 530 CQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFET-DHGAFPNSVY 588
           C+MH +VH+FAQ L+K+  F+ ++ G   E +  S     RH M++F      +FP +++
Sbjct: 497 CKMHDMVHDFAQSLTKNECFSVDIDGV-SESKIDSFSRDTRHSMVVFRNYRTTSFPATIH 555

Query: 589 NQKKLRSLV 597
           + KKLRSL+
Sbjct: 556 SLKKLRSLI 564

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225463558|ref|XP_002267795.1| PREDICTED: putative disease resistance protein RGA3-like [Vitis vinifera]

 Score =  402 bits (1033), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 248/603 (41%), Positives = 364/603 (60%), Gaps = 53/603 (8%)

Query: 1   MAEEITVSTVLDQLSSIT-QQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKD 59
           MA+ + VS VL++L+S+  QQ+     LV GV ++V+ L+S L++IR VL DAEKRQ   
Sbjct: 1   MADAL-VSIVLERLASVLEQQIRQQVTLVVGVESEVDNLKSTLQSIRAVLGDAEKRQ--- 56

Query: 60  VKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDH-KASKVRS-----FTCHL 113
             ++ V+ WL  L D  Y +DD +D W+TA+ KL +A E       K+ S       C  
Sbjct: 57  FTEELVKVWLERLKDISYQMDDVVDGWSTALLKLQIAAENPGIPKPKISSCLPSPCVCFK 116

Query: 114 RIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNA 173
           +++LR DI  ++K++ ++++AIA +++ F   + S   +      +S+VID  +F GR+A
Sbjct: 117 QVSLRHDIALQIKDIKKQLNAIANERNQFNF-VSSSIIQQPHRRITSSVIDVSQFCGRDA 175

Query: 174 EKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWV 233
           +   I+  L G S  E S    +L ++ I+G  GIGKT LA+  ++   VK+ F +R+WV
Sbjct: 176 DINIIIGKLLGGSCQESS----SLYIVSIVGMGGIGKTTLAQLAYNHEKVKSYFHERMWV 231

Query: 234 SASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKK 293
             S P D +R++R                AILE+L+   S   ++E V Q I   +  +K
Sbjct: 232 CVSDPFDPMRISR----------------AILEALQKKSSGFHDLEAVQQKICTLIADEK 275

Query: 294 VLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM 353
            LLVLDD+W   Y   WEQ+  SLK G+ GSRILVT    +N    T +G   K+     
Sbjct: 276 FLLVLDDVWTENY-ELWEQVESSLKGGAPGSRILVTT---RNENVSTMMGTTYKH----- 326

Query: 354 EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFK 413
              LGELS+E+C SLF  IAF+GRS +  E+ E IGR++  KC+GLP A K+LGSL+R K
Sbjct: 327 --PLGELSKEQCWSLFSNIAFYGRSREKVEELENIGRKIADKCRGLPLAAKVLGSLMRLK 384

Query: 414 TSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNY 473
            + ++W+S+L++EIW LD        +     +PLLLSY+DLSPA+K+CF YC++FPK+ 
Sbjct: 385 DNKEDWESILNNEIWQLDV-------IEKHLSTPLLLSYYDLSPAVKRCFSYCAVFPKDQ 437

Query: 474 EIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMH 533
            I KDRLIKLWMA  YL S+ES +ME  G +YF +L SRSLFQDF + + +G II C+MH
Sbjct: 438 IIRKDRLIKLWMANSYLNSRESIEMEKTGGDYFEDLVSRSLFQDFDRDD-EGNIISCKMH 496

Query: 534 PIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKL 593
            IVH+ AQ L+K+  F  E+   ++E +  SS +K RH   +  T    FP++++N K L
Sbjct: 497 DIVHDLAQYLTKNECFILEID-DEKEVRMASSFQKARH-ATLISTPGAGFPSTIHNLKYL 554

Query: 594 RSL 596
            +L
Sbjct: 555 HTL 557

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147860109|emb|CAN82921.1| hypothetical protein VITISV_033138 [Vitis vinifera]

 Score =  396 bits (1017), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 244/591 (41%), Positives = 360/591 (60%), Gaps = 50/591 (8%)

Query: 7   VSTVLDQLSSI-TQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAV 65
           VS VL++L+S+  QQ+     LV GV ++V+ L+S L++IR VL DAEKRQ     ++ V
Sbjct: 6   VSIVLERLASVLKQQIRQQVTLVVGVKSEVDNLKSTLQSIRAVLGDAEKRQ---FTEELV 62

Query: 66  EDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKL 125
           + WL  L D  Y +DD +D WNTA+ KL +A E +    K +  +C     + F    ++
Sbjct: 63  KVWLERLKDISYQMDDMVDGWNTALLKLQIAAE-NPGIPKPKISSCLPSPCVCFK---QI 118

Query: 126 KNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGE 185
           K++ ++++AIA +++ F   + S + +      +S+VID  +F GR+A+   I+  L G 
Sbjct: 119 KDIKKQLNAIANERNQFNF-VSSSTIQQPHRRITSSVIDVSQFCGRDADINIIIGKLLGG 177

Query: 186 SSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA 245
           S  E S    +L ++ I+G EGIGKT LA+  ++   VK+ F +R+WV    P D +R++
Sbjct: 178 SCQESS----SLYIVSIVGMEGIGKTTLAQLAYNHEKVKSYFHERMWVCVFDPFDPMRIS 233

Query: 246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNA 305
           R                AILE+L+   S   ++E V Q I   +  KK LLVLDD+W   
Sbjct: 234 R----------------AILEALQKESSGFHDLEAVQQKICTLIADKKFLLVLDDVWTEN 277

Query: 306 YPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEEC 365
           Y   WEQ+  SLK G+ GSRILVT    +N +  T +G   K+        LGELS+E+C
Sbjct: 278 Y-ELWEQVESSLKGGAPGSRILVT---TRNESVSTMMGTTYKH-------PLGELSKEQC 326

Query: 366 RSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDS 425
           RSLF  IAF+GRS +  E+ E IGR++  +C+GLP A K+LGSL+R K + ++W+S+L++
Sbjct: 327 RSLFSNIAFYGRSREKVEELENIGRKIADECRGLPLAAKVLGSLMRLKDNKEDWESILNN 386

Query: 426 EIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWM 485
           EIW LD        +      PLLLSY+DLSPA+K+CF YC++FPK+  I KDRLIKLWM
Sbjct: 387 EIWQLDV-------IEKHLSPPLLLSYYDLSPAVKRCFSYCAVFPKDQIISKDRLIKLWM 439

Query: 486 AQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSK 545
           A  YL S+ES +ME  G +YF +L SRSLFQDF++ + +G II C+MH IVH+ AQ L+K
Sbjct: 440 ANSYLNSRESIEMEKTGGDYFEDLVSRSLFQDFRRDD-EGNIISCKMHDIVHDLAQYLTK 498

Query: 546 SHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSL 596
           +  F  E+   ++E +  SS +K RH  ++     G FP++++N K L +L
Sbjct: 499 NECFILEI-DDEKEVRMASSFQKARHATLISARRVG-FPSTIHNLKYLHTL 547

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  395 bits (1016), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 236/578 (40%), Positives = 346/578 (59%), Gaps = 49/578 (8%)

Query: 27  LVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEW 86
           LVGGV   V+KL+++L AI+ VL+DA+++QVKD   KA+ DW+ +L D CY +DD LDEW
Sbjct: 23  LVGGVKKQVDKLKNNLLAIQSVLEDADRKQVKD---KALRDWVDKLKDVCYDMDDVLDEW 79

Query: 87  NTAIQ--KLLLANETDHKASKVR------SFTCHLRIALRFDIGCKLKNLSRRVDAIAGK 138
           +TAI   K+  A E      K+R       F C  ++  R DI  K+K +  +VD IA +
Sbjct: 80  STAILRWKMEEAEENTPSRKKIRCSFLGSPFFCLNQVVQRRDIALKIKEVCEKVDDIAKE 139

Query: 139 KDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLP 198
           +  +  +L   + E   +T++S ++D     GR+ +++ ++  L GES  +E+G    + 
Sbjct: 140 RAMYGFELYRATDELQRITSTS-LVDESSVIGRDDKREAVVSKLLGESI-QEAGD---VE 194

Query: 199 VIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEI 258
           VI ++G  GIGKT LA+  F+D +V A+F+K+IWV  S P DE+R+              
Sbjct: 195 VISLVGMGGIGKTTLAQLAFNDDEVTAHFEKKIWVCVSDPFDEVRIG------------- 241

Query: 259 RVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLK 318
              KAILE L+G     VE++++LQ ++E ++G++ LLVLDD+W   + R WEQL  SL 
Sbjct: 242 ---KAILEQLEGRAPDLVELQSLLQRVSESIKGERFLLVLDDVWTENH-RQWEQLKPSLT 297

Query: 319 SGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRS 378
             + GSRILVT       T M         GT  + I L +LS+E CRS+F  +AF  RS
Sbjct: 298 GCARGSRILVTTRKHSVATMM---------GTGHV-INLEKLSDEVCRSIFNHVAFQQRS 347

Query: 379 SDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRA 438
            D RE+    G ++  KCKGLP A K+LG L++ K + +EW+ V  SE+W LD     R 
Sbjct: 348 KDERERLTDTGDKIANKCKGLPLAAKVLGGLMQSKRTREEWERVFCSELWGLDE--VDRD 405

Query: 439 GVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDM 498
            V      PLLLSY+DL   +++CFLYC++FPK+YE+ K  L+K+W+AQGYLK     DM
Sbjct: 406 QVERGIFLPLLLSYYDLPSMVRRCFLYCAMFPKDYEMRKYELVKMWIAQGYLKETSGGDM 465

Query: 499 ELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQ 558
           E VGE+YF  L++RS FQDF+   +D   +R +MH IVH+FAQ ++K+     +V    +
Sbjct: 466 EAVGEQYFQVLAARSFFQDFKT--YDREDVRFKMHDIVHDFAQYMTKNECLTVDVNNL-R 522

Query: 559 ECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSL 596
           E   ++S E+ RHL +M  +    FP S++  K LRSL
Sbjct: 523 EATVETSIERVRHLSMML-SKETYFPVSIHKAKGLRSL 559

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  395 bits (1014), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 234/574 (40%), Positives = 343/574 (59%), Gaps = 52/574 (9%)

Query: 27  LVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEW 86
           LV GV    +KL+S+L  I+ VL+DA+++QVKD   KAV DW+ +L D CY +DD LDEW
Sbjct: 14  LVVGVKKQCDKLKSNLLDIQSVLEDADRKQVKD---KAVRDWVDKLKDACYDMDDVLDEW 70

Query: 87  NTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKL 146
           +TAI +  +    ++  S+ +     +R +    +      +S +VD IA ++  +   L
Sbjct: 71  STAILRWKMEEAEENTPSRQK-----IRRSFLISLLLSQSKVSEKVDDIAKERVVYGFDL 125

Query: 147 MSGSGEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNE 206
              + E     TS++ +D     GR+ EK+ I+  L GESS E       + VI ++G  
Sbjct: 126 YRATYELQ-RPTSTSFVDESSVIGRDVEKKTIVSKLVGESSQEARD----VDVITLVGLG 180

Query: 207 GIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILE 266
           GIGKT LA+  + D++V A+F+K+IWV  S P DE+R+A                KAILE
Sbjct: 181 GIGKTTLAQLAYKDAEVTAHFEKKIWVCVSEPFDEVRIA----------------KAILE 224

Query: 267 SLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRI 326
            L+GS  + +E++++LQ ++E ++GK++LLVLDD+W + + R WEQL  S    + GSRI
Sbjct: 225 QLEGSAPNLIELQSLLQMVSESIKGKRLLLVLDDVWTDNH-RQWEQLKPSFTGCARGSRI 283

Query: 327 LVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFE 386
           LVT   G   T M         GT+  +I + +LS+E CRS+F  +AF  RS D RE+  
Sbjct: 284 LVTTRKGTVATIM---------GTDH-QINVEKLSDEICRSIFNHVAFQERSKDERERLT 333

Query: 387 PIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLS 446
            IG ++  KCKGLP A K+LG L++FK + +EW+ VL SE+W LD     R  V      
Sbjct: 334 DIGDKIANKCKGLPLAAKVLGGLMQFKRTREEWERVLSSELWGLDE--VDRDQVERGIFL 391

Query: 447 PLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYF 506
           PLLLSY+DL   +++CFLYC++FPK+YE+ K  L+K+W+AQGYLK     DME VGEEYF
Sbjct: 392 PLLLSYYDLPSVVRRCFLYCAMFPKDYEMRKYELVKMWIAQGYLKETSGGDMEAVGEEYF 451

Query: 507 GNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVK---GSDQECQSK 563
             L++R+ FQDF+   +    IR +MH IVH+FAQ ++K+     +V    G+  E    
Sbjct: 452 QVLAARAFFQDFKT--YGREDIRFKMHDIVHDFAQYMTKNECLTVDVNTLGGATVE---- 505

Query: 564 SSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV 597
           +S E+ RHL IM   +  +FP S++  K LRSL+
Sbjct: 506 TSIERVRHLSIML-PNETSFPVSIHKAKGLRSLL 538

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359482800|ref|XP_003632842.1| PREDICTED: putative disease resistance protein RGA4-like [Vitis vinifera]

 Score =  393 bits (1009), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 251/602 (41%), Positives = 353/602 (58%), Gaps = 55/602 (9%)

Query: 1   MAEEITVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDV 60
           MA+ + VS VL++L+S+ +Q      LV GV ++V+ L S L++IR VL DAEKRQ  + 
Sbjct: 1   MADAL-VSIVLERLASVLEQQVT---LVVGVGSEVDNLNSTLQSIRAVLADAEKRQFSE- 55

Query: 61  KDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKAS-KVRSF-----TCHLR 114
             + V+ WL  L D  Y +DD +D WNTA+ KL +  E       K+ S       C  +
Sbjct: 56  --ELVKVWLERLKDISYQMDDVVDGWNTALLKLQIGAENPCIPKLKISSCLPSPCVCFKQ 113

Query: 115 IALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRNAE 174
           + LR DIG K+K++ +++DAIA +++ F   + S + +      +S+VID  +F GR+A+
Sbjct: 114 VLLRCDIGIKIKDIRKQLDAIANERNQFNF-VSSSTIQQPHRRMTSSVIDVSQFCGRDAD 172

Query: 175 KQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS 234
              I+  L G SS E S    +L +I I+G  GIGKT LA+  ++D  VKA F +R+WV 
Sbjct: 173 MDVIIDKLLGGSSQESS----SLYIISIVGMGGIGKTTLAQLAYNDDRVKAYFHERMWVC 228

Query: 235 ASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKV 294
            S P D + ++R                AILE+L+       E+E V Q I   +  KK 
Sbjct: 229 VSDPFDPVTISR----------------AILEALQKESCDFHELENVEQKICTLIADKKF 272

Query: 295 LLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME 354
           LLVLDD+W   Y   WE++  SLK G+ GSRILVT       T M         GT    
Sbjct: 273 LLVLDDVWTENY-ELWEKVESSLKGGAPGSRILVTTRKDDVSTMM---------GTTYKH 322

Query: 355 IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKT 414
             L ELSE +C SLF  IAF GRS +  E+ E IGR++  KC+GLP A K+LGSL+R K 
Sbjct: 323 -PLRELSEGQCWSLFSNIAFCGRSREKVEELENIGRKIADKCRGLPLAAKVLGSLMRLKD 381

Query: 415 SIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYE 474
           + + W+S+L++EIW LD        +     +PLLLSY+DLSPA+K+CF YC++FPK+  
Sbjct: 382 NKENWESILNNEIWQLDV-------IEKHLSTPLLLSYYDLSPAVKRCFSYCAVFPKDQI 434

Query: 475 IEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHP 534
           I KDRLIKLWMA  YL S+ S +ME  G +YF +L SRSLFQDF++   D  II C+MH 
Sbjct: 435 ISKDRLIKLWMANSYLNSRGSIEMEKTGGDYFEDLVSRSLFQDFRRDNEDN-IISCKMHD 493

Query: 535 IVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLR 594
           IVH+ AQ L+K+  F  E    ++E +  SS +K RH  ++  T    FP++++N K L 
Sbjct: 494 IVHDLAQSLTKNECFILEFD-DEKEVRMASSFQKARHATLII-TPWAGFPSTIHNLKYLH 551

Query: 595 SL 596
           +L
Sbjct: 552 TL 553

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134406|ref|XP_002321815.1| cc-nbs-lrr resistance protein [Populus trichocarpa] gi|222868811|gb|EEF05942.1| cc-nbs-lrr resistance protein [Populus trichocarpa]

 Score =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 246/631 (38%), Positives = 362/631 (57%), Gaps = 91/631 (14%)

Query: 7   VSTVLDQLSSITQ-QMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAV 65
           VST+L+Q+ +I + Q+     LV GV  +++ L+++ +AIR+VL+DAE++Q+KD    AV
Sbjct: 6   VSTILEQIITIARHQVEHEVKLVVGVEKEIQHLKNNFQAIRDVLEDAERKQLKDT---AV 62

Query: 66  EDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASK-------------------- 105
           + WL  L D  Y +DD LDEW+TA+ K  +    +  A K                    
Sbjct: 63  KHWLNNLKDVSYDMDDVLDEWSTAVLKWEMEEAENALAPKSVVFSFLRSCCFCFRRAEQA 122

Query: 106 ---------VRSFTCHL-----RIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSG-S 150
                    V SF C       R+A R DI  K+  + ++++ IA +K  F  +L     
Sbjct: 123 ENALAPKSVVSSFLCSFCCSFRRVARRHDIAHKIIEVGQKLEDIAKRKAMFGFELHKAIE 182

Query: 151 GEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGK 210
            E    TTS   +D    HGR  EK+ ++  L  +SS E  G K  + VI I+G  G+GK
Sbjct: 183 KEPDRQTTS--FVDVSRVHGREDEKKNVISKLLCDSSQE--GRK--VQVISIVGMGGLGK 236

Query: 211 TALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKG 270
           T LA+  ++  ++K  F+KRIWV  S+P DE  VA                KAI+E L G
Sbjct: 237 TTLAQLAYNADEIKTYFEKRIWVCVSHPFDENTVA----------------KAIIEDLSG 280

Query: 271 SVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTR 330
           +  + VE+E + + I+E ++GKK LLVLDD+W +  PR WE L  SLK G+ GSRILVT 
Sbjct: 281 AAPNLVELEPLCKRISESIEGKKFLLVLDDVWEDN-PRKWEPLKESLKCGAPGSRILVTT 339

Query: 331 SGGKNGTNMTEIGLGEKNGTNMME----IGLGELSEEECRSLFRQIAFHGRSSDYREKFE 386
                          +     MME    + LG+L++EEC S+F Q+AF+GRS D  E F 
Sbjct: 340 R--------------KDTVAKMMESDYSLLLGKLTDEECWSVFSQVAFYGRSQDACEMFT 385

Query: 387 PIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLS 446
            IGR++V +CKGLP A K LG L++ KT+ ++W ++L +E+W ++        V      
Sbjct: 386 EIGRQIVYRCKGLPLAAKTLGGLMQSKTTTEDWDNILSNELWEIEE-------VEKGIFP 438

Query: 447 PLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYF 506
           PLLLSY+DL  A++ CF YC++FPK++ +E+ +LIK+WMAQGYLK+  SK+MELVG+ YF
Sbjct: 439 PLLLSYYDLPVAIRSCFTYCAMFPKDHVMERGKLIKMWMAQGYLKASPSKEMELVGKGYF 498

Query: 507 GNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSH 566
             L++R+ FQDFQ+++ D   I+ +MH IVH+FAQ L K   F  E     ++ +++S +
Sbjct: 499 EILATRAFFQDFQETDEDS--IKFKMHDIVHDFAQFLMKDECFTVETDVLKRQ-KTESFY 555

Query: 567 EKFRHLMIMFETDHGAFPNSVYNQKKLRSLV 597
           E+ RH  IM  ++   FP S+Y   KLRSL+
Sbjct: 556 ERARH-AIMTVSNWARFPQSIYKAGKLRSLL 585

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225470202|ref|XP_002269053.1| PREDICTED: putative disease resistance protein RGA3-like [Vitis vinifera]

 Score =  385 bits (989), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 249/608 (40%), Positives = 353/608 (58%), Gaps = 62/608 (10%)

Query: 1   MAEEITVSTVLDQLSS-ITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKD 59
           MA+ + +S VLD+L+S I QQ +    LV GV  +++ L + L+ +R V+ DAEKRQV +
Sbjct: 1   MADAL-LSIVLDRLASLIQQQFHHEVCLVVGVKREIQSLTNTLQIVRAVVADAEKRQVNE 59

Query: 60  VKDKAVEDWLRELTDTCYAVDDALDEWNTA-----IQKLLLANETDHKASKV--RSFTCH 112
              + V+ WL  L D  Y +DD LDEW+TA     I+++   +    K S        C 
Sbjct: 60  ---EPVKVWLERLKDIAYQMDDVLDEWSTAFLKSQIERVESPSMPKKKVSSCIPSPCICF 116

Query: 113 LRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMTTSSAVIDPLEFHGRN 172
            R+A R DI  K+K + + VD IA +++ F  K  +      I+T S+  +D  E +GR+
Sbjct: 117 KRVARRRDIALKIKGIKQEVDDIANERNQFDFKSTNNEELQRIITISA--VDTTEVYGRD 174

Query: 173 AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIW 232
            ++  IL+ L G S ++  G    L  I + G  GIGKT LA+  F+  DVKA+F+ RIW
Sbjct: 175 RDEGIILRQLLGTSCEQSLG----LYTISVFGMGGIGKTTLAQLAFNHYDVKAHFEIRIW 230

Query: 233 VSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGK 292
           V  S P   IR+ R                AILE+L+G  S   + E + Q I + + GK
Sbjct: 231 VCVSDPFVPIRILR----------------AILEALQGQSSDLHDPEALQQKIQKSIYGK 274

Query: 293 KVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM 352
           K LLVLDD+W   Y + WEQL   LK G  GSRILVT         M          T M
Sbjct: 275 KFLLVLDDVWTEDY-QLWEQLKNCLKCGGGGSRILVTTHNESVARMM--------RSTYM 325

Query: 353 MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRF 412
               LG L  E+ ++LF QIAF G+S+D  E+ E IG+++  KCKGLP AVK LGSL++ 
Sbjct: 326 H--SLGSLPLEQSQALFSQIAFCGKSTDKIEELEEIGKKIADKCKGLPLAVKALGSLMQS 383

Query: 413 KTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSP-LLLSYFDLSPALKKCFLYCSIFPK 471
           K + ++W++VL+S++W LD        V  + LSP LLLSY+DL P +K+CF YC++FPK
Sbjct: 384 KNNKEDWENVLNSKMWELD--------VFEKKLSPALLLSYYDLPPPIKQCFSYCAVFPK 435

Query: 472 NYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQ 531
           ++ IE+D LIKLWMAQ YL S+  ++ME VG EYF NL++RS FQDF+K +  G I+RC+
Sbjct: 436 DHSIERDDLIKLWMAQSYLNSKAGREMETVGREYFENLAARSFFQDFEKDD-KGNIVRCK 494

Query: 532 MHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGA--FPNSVYN 589
           MH IVH+FAQ L  +HN    ++   +  ++    +K RH  +M    HG+  FP S  N
Sbjct: 495 MHDIVHDFAQFL--THNECLNLEDDSENLKTNLYLQKGRHASLMV---HGSTKFPFSDNN 549

Query: 590 QKKLRSLV 597
            + LR+L+
Sbjct: 550 VRNLRTLL 557

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	597
TAIR|locus:2078012	852	ZAR1 "HOPZ-ACTIVATED RESISTANC	0.524	0.367	0.278	1.9e-38
TAIR|locus:2075170	835	RPP13 "RECOGNITION OF PERONOSP	0.333	0.238	0.330	5.9e-37
TAIR|locus:2091672	1054	AT3G14470 [Arabidopsis thalian	0.448	0.254	0.346	8.8e-35
TAIR|locus:2102857	847	AT3G46710 [Arabidopsis thalian	0.333	0.234	0.308	3.3e-34
TAIR|locus:504956483	847	AT3G46730 [Arabidopsis thalian	0.338	0.238	0.313	5.8e-34
TAIR|locus:2011982	857	AT1G50180 [Arabidopsis thalian	0.447	0.311	0.280	8.9e-33
TAIR|locus:2077572	926	RPM1 "RESISTANCE TO P. SYRINGA	0.467	0.301	0.318	5.4e-32
TAIR|locus:2091662	1424	AT3G14460 [Arabidopsis thalian	0.321	0.134	0.323	2.1e-29
UNIPROTKB|O48647	1802	O48647 "XA1" [Oryza sativa (ta	0.510	0.169	0.280	2.9e-29
TAIR|locus:504956186	1138	AT1G58602 [Arabidopsis thalian	0.614	0.322	0.280	2.9e-26

TAIR|locus:2078012 ZAR1 "HOPZ-ACTIVATED RESISTANCE 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 334 (122.6 bits), Expect = 1.9e-38, Sum P(2) = 1.9e-38
 Identities = 95/341 (27%), Positives = 173/341 (50%)

Query:   249 ISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPR 308
             +SV++   E ++ ++IL +L G  S   ++ T+L+ I +++ GK+ L+V+DD+W +    
Sbjct:   218 VSVSQTFTEEQIMRSILRNL-GDASVGDDIGTLLRKIQQYLLGKRYLIVMDDVW-DKNLS 275

Query:   309 YWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSL 368
             +W+++   L  G  GS I+ TRS      ++ +      + T+  E+    LS +    L
Sbjct:   276 WWDKIYQGLPRGQGGSVIVTTRS-----ESVAKRVQARDDKTHRPEL----LSPDNSWLL 326

Query:   369 FRQIAFHGRSSDY-REKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSI-KEWQSVLDSE 426
             F  +AF        R + E +G+ +V KCKGLP  +K +G LL  K  +  EW+ + +  
Sbjct:   327 FCNVAFAANDGTCERPELEDVGKEIVTKCKGLPLTIKAVGGLLLCKDHVYHEWRRIAE-- 384

Query:   427 IWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMA 486
               +   E+          +S L LSY +L   LK C L  S++P++  I K +L+  W+ 
Sbjct:   385 --HFQDELRGNTSETDNVMSSLQLSYDELPSHLKSCILTLSLYPEDCVIPKQQLVHGWIG 442

Query:   487 QGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKS 546
             +G++  +  +     GE+ F  L++R L +   K+ + G II C++H +V +    ++K 
Sbjct:   443 EGFVMWRNGRSATESGEDCFSGLTNRCLIEVVDKT-YSGTIITCKIHDMVRDLVIDIAKK 501

Query:   547 HNF-NAE--------VKGSDQECQSKSSHEKFRHLMIMFET 578
              +F N E        + G+  E Q K +H K R ++   +T
Sbjct:   502 DSFSNPEGLNCRHLGISGNFDEKQIKVNH-KLRGVVSTTKT 541

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2075170 RPP13 "RECOGNITION OF PERONOSPORA PARASITICA 13" [Arabidopsis thaliana (taxid:3702)]

 Score = 259 (96.2 bits), Expect = 5.9e-37, Sum P(2) = 5.9e-37
 Identities = 72/218 (33%), Positives = 113/218 (51%)

Query:   360 LSEEECRSLFRQIAFHG-RSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKE 418
             L+ EE   LF Q AF   +  D  E     G+ +V KC+GLP  + +L  LL  KT   E
Sbjct:   326 LTFEESWELFEQRAFRNIQRKD--EDLLKTGKEMVQKCRGLPLCIVVLAGLLSRKTP-SE 382

Query:   419 WQSVLDSEIWN-LDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEK 477
             W  V +S +W  L  +    A + ++      LS+ +L    K CFLY SIFP++YEI+ 
Sbjct:   383 WNDVCNS-LWRRLKDDSIHVAPIVFD------LSFKELRHESKLCFLYLSIFPEDYEIDL 435

Query:   478 DRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVH 537
             ++LI L +A+G+++  E   ME V   Y   L  RSL +  ++    G+++ C++H ++ 
Sbjct:   436 EKLIHLLVAEGFIQGDEEMMMEDVARYYIEELIDRSLLEAVRRER--GKVMSCRIHDLLR 493

Query:   538 EFAQLLSKSHNF----NAEV-KGSDQECQSKSSHEKFR 570
             + A   SK  NF    N  V + S   C+ +  H +F+
Sbjct:   494 DVAIKKSKELNFVNVYNDHVAQHSSTTCRREVVHHQFK 531

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=TAS

GO:0009814 "defense response, incompatible interaction" evidence=IMP

GO:0005886 "plasma membrane" evidence=IDA

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

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

 Score = 403 (146.9 bits), Expect = 8.8e-35, P = 8.8e-35
 Identities = 103/297 (34%), Positives = 161/297 (54%)

Query:   251 VARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKV--LLVLDDLWWNAYPR 308
             V+ + D  ++ K + ES+        +++ +   + E + G  +  LLVLDDLW N    
Sbjct:   234 VSEEFDVFKITKKVYESVTSRPCEFTDLDVLQVKLKERLTGTGLPFLLVLDDLW-NENFA 292

Query:   309 YWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSL 368
              W+ L       ++GS+ILVT    +  + M  + +            L  LS+ +C SL
Sbjct:   293 DWDLLRQPFIHAAQGSQILVTTRSQRVASIMCAVHVHN----------LQPLSDGDCWSL 342

Query:   369 FRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIW 428
             F +  F  +      +   +  R+V KC+GLP AVK LG +LRF+  + EW+ VL S IW
Sbjct:   343 FMKTVFGNQEPCLNREIGDLAERIVHKCRGLPLAVKTLGGVLRFEGKVIEWERVLSSRIW 402

Query:   429 NLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQG 488
             +L ++   ++ +    L  L +SY+ L   LK+CF YCSIFPK +  EKD+++ LWMA+G
Sbjct:   403 DLPAD---KSNL----LPVLRVSYYYLPAHLKRCFAYCSIFPKGHAFEKDKVVLLWMAEG 455

Query:   489 YLK-SQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLS 544
             +L+ ++ SK++E +G EYF  L SRSL Q   K++   R I   MH  ++E AQ  S
Sbjct:   456 FLQQTRSSKNLEELGNEYFSELESRSLLQ---KTKT--RYI---MHDFINELAQFAS 504

GO:0005576 "extracellular region" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0009627 "systemic acquired resistance" evidence=RCA

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

TAIR|locus:2102857 AT3G46710 [Arabidopsis thaliana (taxid:3702)]

 Score = 228 (85.3 bits), Expect = 3.3e-34, Sum P(2) = 3.3e-34
 Identities = 66/214 (30%), Positives = 110/214 (51%)

Query:   360 LSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEW 419
             L+ +E  +LF + AF        ++ + IG+ +V KC GLP    +L  L+  K    EW
Sbjct:   322 LTFKESWNLFEKKAFR-YILKVDQELQKIGKEMVQKCGGLPRTTVVLAGLMSRKKP-NEW 379

Query:   420 QSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDR 479
                  +++W+  S   K   +    L  L  S+ D+   LK CFLY S+FP++YE++ ++
Sbjct:   380 -----NDVWS--SLRVKDDNIHVSSLFDL--SFKDMGHELKLCFLYLSVFPEDYEVDVEK 430

Query:   480 LIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEF 539
             LI+L +A+G+++  E   ME V   Y  +L   SL +  ++ +  G+++  ++H +V EF
Sbjct:   431 LIQLLVAEGFIQEDEEMTMEDVARYYIEDLVYISLVEVVKRKK--GKLMSFRIHDLVREF 488

Query:   540 AQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLM 573
                 SK  NF   V   +Q   + S  E   HLM
Sbjct:   489 TIKKSKELNF-VNVY-DEQHSSTTSRREVVHHLM 520

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:504956483 AT3G46730 [Arabidopsis thaliana (taxid:3702)]

 Score = 240 (89.5 bits), Expect = 5.8e-34, Sum P(2) = 5.8e-34
 Identities = 67/214 (31%), Positives = 106/214 (49%)

Query:   360 LSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEW 419
             L+ EE  +LF + AF        E  +  G+ +V KC GLP A+ +L  LL  K +  EW
Sbjct:   327 LTFEESWTLFERKAF-SNIEKVDEDLQRTGKEMVKKCGGLPLAIVVLSGLLSRKRT-NEW 384

Query:   420 QSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDR 479
               V  S +W    +        ++      LS+ ++   LK CFLY S+FP++YEI+ ++
Sbjct:   385 HEVCAS-LWRRLKDNSIHISTVFD------LSFKEMRHELKLCFLYFSVFPEDYEIKVEK 437

Query:   480 LIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEF 539
             LI L +A+G+++  E   ME V   Y   L  RSL +  ++ E  G+++ C++H ++ + 
Sbjct:   438 LIHLLVAEGFIQEDEEMMMEDVARCYIDELVDRSLVKA-ERIE-RGKVMSCRIHDLLRDL 495

Query:   540 AQLLSKSHNFNAEVKGSDQECQSKSSHEKFRHLM 573
             A   +K  NF   V    Q        E   HLM
Sbjct:   496 AIKKAKELNF-VNVYNEKQHSSDICRREVVHHLM 528

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

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2011982 AT1G50180 [Arabidopsis thaliana (taxid:3702)]

 Score = 267 (99.0 bits), Expect = 8.9e-33, Sum P(2) = 8.9e-33
 Identities = 81/289 (28%), Positives = 141/289 (48%)

Query:   279 ETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTN 338
             E + + ++ F++  K L+VLDD+W       W+ L +     + GS I++T       T 
Sbjct:   255 EQLGEELHRFLKRNKCLIVLDDIWGKDA---WDCLKHVFPHET-GSEIILT-------TR 303

Query:   339 MTEIGL-GEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYR---EKFEPIGRRVVG 394
               E+ L  +  G  + E  L  L+ EE   L  +I+  GR +      +K E IG+++V 
Sbjct:   304 NKEVALYADPRGV-LHEPQL--LTCEESWELLEKISLSGRENIEPMLVKKMEEIGKQIVV 360

Query:   395 KCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFD 454
             +C GLP A+ +LG LL  K++  EWQ V ++    + +               L LSY  
Sbjct:   361 RCGGLPLAITVLGGLLATKSTWNEWQRVCENIKSYVSNGGSSNGSKNMLVADVLCLSYEY 420

Query:   455 LSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYL---KSQES-KDMELVGEEYFGNLS 510
             L P +K+CFLY + +P++YE+    L+   +A+G +   K  E+   +E VG++Y   L 
Sbjct:   421 LPPHVKQCFLYFAHYPEDYEVHVGTLVSYCIAEGMVMPVKHTEAGTTVEDVGQDYLEELV 480

Query:   511 SRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQE 559
              RS+    ++      ++ C+MH ++ E     +K  +F   +   DQ+
Sbjct:   481 KRSMVMVGRRDIVTSEVMTCRMHDLMREVCLQKAKQESFVQVIDSRDQD 529

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

GO:0043531 "ADP binding" evidence=IEA

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2077572 RPM1 "RESISTANCE TO P. SYRINGAE PV MACULICOLA 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 358 (131.1 bits), Expect = 5.4e-32, Sum P(2) = 5.4e-32
 Identities = 96/301 (31%), Positives = 153/301 (50%)

Query:   281 VLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMT 340
             +++ + E++Q K+ ++VLDD+W       W ++  +L  G  GSR+++T        N+ 
Sbjct:   268 LVEKLVEYLQSKRYIVVLDDVWTTGL---WREISIALPDGIYGSRVMMTT----RDMNVA 320

Query:   341 EIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYR-EKFEPIGRRVVGKCKGL 399
                 G   G+   EI L  L E+E   LF   AF       R +  EPI R++V +C+GL
Sbjct:   321 SFPYGI--GSTKHEIEL--LKEDEAWVLFSNKAFPASLEQCRTQNLEPIARKLVERCQGL 376

Query:   400 PFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPAL 459
             P A+  LGS++  K    EW+ V  +  W L++    +        S + LS+ DL   L
Sbjct:   377 PLAIASLGSMMSTKKFESEWKKVYSTLNWELNNNHELKI-----VRSIMFLSFNDLPYPL 431

Query:   460 KKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQ 519
             K+CFLYCS+FP NY +++ RLI++WMAQ +++       E V + Y   L  R++ Q   
Sbjct:   432 KRCFLYCSLFPVNYRMKRKRLIRMWMAQRFVEPIRGVKAEEVADSYLNELVYRNMLQVIL 491

Query:   520 KSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQECQSKS-SHEKF--RHLMIMF 576
              + F GR    +MH ++ E A  +SK   F  +V   D +    + + E +  RHL I  
Sbjct:   492 WNPF-GRPKAFKMHDVIWEIALSVSKLERF-CDVYNDDSDGDDAAETMENYGSRHLCIQK 549

Query:   577 E 577
             E
Sbjct:   550 E 550

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

GO:0043531 "ADP binding" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA

GO:0000166 "nucleotide binding" evidence=ISS

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

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

 Score = 250 (93.1 bits), Expect = 2.1e-29, Sum P(2) = 2.1e-29
 Identities = 69/213 (32%), Positives = 109/213 (51%)

Query:   360 LSEEECRSLFRQIAFHGRS-SDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKE 418
             ++ EEC  L  + AF   S     ++ E IG+R+  +CKGLP A + + S LR K +  +
Sbjct:   329 MTNEECWELISRFAFGNISVGSINQELEGIGKRIAEQCKGLPLAARAIASHLRSKPNPDD 388

Query:   419 WQSVLDSEIWNLDSEICKRAGVGYECLSPLL-LSYFDLSPALKKCFLYCSIFPKNYEIEK 477
             W +V  S+  N  S            + P+L LSY  L P LK+CF  CSIFPK +  ++
Sbjct:   389 WYAV--SK--NFSSYT--------NSILPVLKLSYDSLPPQLKRCFALCSIFPKGHVFDR 436

Query:   478 DRLIKLWMAQGYL-KSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIV 536
             + L+ LWMA   L + + S+ +E +G +Y G+L ++S FQ       D  +    MH ++
Sbjct:   437 EELVLLWMAIDLLYQPRSSRRLEDIGNDYLGDLVAQSFFQ-----RLDITMTSFVMHDLM 491

Query:   537 HEFAQLLSKSHNFNAEVKGSDQECQSKSSHEKF 569
             ++ A+ +S    F  E   +  E  S + H  F
Sbjct:   492 NDLAKAVSGDFCFRLE-DDNIPEIPSTTRHFSF 523

GO:0005634 "nucleus" evidence=ISM

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

GO:0043531 "ADP binding" evidence=IEA

UNIPROTKB|O48647 O48647 "XA1" [Oryza sativa (taxid:4530)]

 Score = 349 (127.9 bits), Expect = 2.9e-29, Sum P(2) = 2.9e-29
 Identities = 91/324 (28%), Positives = 159/324 (49%)

Query:   256 DEIRVAKAILESLKGSVSSQVE-METVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLM 314
             D +++ + IL+ +       +  ++T+ Q + E ++ KK L+VLDD+W       W++L+
Sbjct:   362 DVVKITRQILDHVSNQSHEGISNLDTLQQDLEEQMKSKKFLIVLDDVW-EIRTDDWKKLL 420

Query:   315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAF 374
               L+   + +      +G           + +  GT +  I L  L +++  SLF+  AF
Sbjct:   421 APLRPNDQVNSSQEEATGNMIILTTRIQSIAKSLGT-VQSIKLEALKDDDIWSLFKVHAF 479

Query:   375 HGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEI 434
                  D     + +G+++  + KG P A K +GSLL    +I  W S++ SE W      
Sbjct:   480 GNDKHDSSPGLQVLGKQIASELKGNPLAAKTVGSLLGTNLTIDHWDSIIKSEEW------ 533

Query:   435 CKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQE 494
              K     Y  +  L LSY  LS  L++C  YCS+FPK Y   K +LI++W+AQG+++ + 
Sbjct:   534 -KSLQQAYGIMQALKLSYDHLSNPLQQCVSYCSLFPKGYSFSKAQLIQIWIAQGFVE-ES 591

Query:   495 SKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVK 554
             S+ +E  G +Y   L +    Q  + + F        MH ++H+ AQ +S++    A + 
Sbjct:   592 SEKLEQKGWKYLAELVNSGFLQQVESTRFSSEYF--VMHDLMHDLAQKVSQTEY--ATID 647

Query:   555 GSDQECQSKSSHEKFRHLMIMFET 578
             GS  EC   +     RHL I+ ++
Sbjct:   648 GS--ECTELAP--SIRHLSIVTDS 667

GO:0006915 "apoptotic process" evidence=IGI

GO:0006952 "defense response" evidence=IGI

TAIR|locus:504956186 AT1G58602 [Arabidopsis thaliana (taxid:3702)]

 Score = 302 (111.4 bits), Expect = 2.9e-26, Sum P(2) = 2.9e-26
 Identities = 116/413 (28%), Positives = 193/413 (46%)

Query:   199 VIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEI 258
             V+ I G  G+GKT LARQVF+   V   FDK  WVS S       V ++ +   + ++E 
Sbjct:   184 VVSITGMGGLGKTTLARQVFNHDMVTKKFDKLAWVSVSQDFTLKNVWQNILGDLKPKEE- 242

Query:   259 RVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLK 318
                    E  K  +    E  T+ + + + ++  K L+VLDD+W       WE ++  + 
Sbjct:   243 ----ETKEEEK-KILEMTEY-TLQRELYQLLEMSKSLIVLDDIWKK---EDWE-VIKPIF 292

Query:   319 SGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFH-GR 377
               ++G ++L+T    +N     E  +   N T         L  ++   LF++IAF    
Sbjct:   293 PPTKGWKLLLT---SRN-----ESIVAPTN-TKYFNFKPECLKTDDSWKLFQRIAFPIND 343

Query:   378 SSDYR--EKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEIC 435
             +S++   E+ E +G +++  C GLP A+K+LG +L  K +  +W+ +  SE  N+ S + 
Sbjct:   344 ASEFEIDEEMEKLGEKMIEHCGGLPLAIKVLGGMLAEKYTSHDWRRL--SE--NIGSHLV 399

Query:   436 K-RAGVGYE----CLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYL 490
               R     +    C   L LS+ +L   LK CFLY + FP++YEI+ + L   W A+   
Sbjct:   400 GGRTNFNDDNNNSCNYVLSLSFEELPSYLKHCFLYLAHFPEDYEIKVENLSYYWAAEEIF 459

Query:   491 KSQESKDMEL---VGEEYFGNLSSRSLF---QDFQKSEFDGRIIRCQMHPIVHEFAQLLS 544
             + +   D E+   VG+ Y   L  R++    +D + S F+     C +H ++ E   L +
Sbjct:   460 QPRHY-DGEIIRDVGDVYIEELVRRNMVISERDVKTSRFE----TCHLHDMMREVCLLKA 514

Query:   545 KSHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV 597
             K  NF  ++  +     +  S    R L+  + T          N  KLRSLV
Sbjct:   515 KEENF-LQITSNPPSTANFQSTVTSRRLVYQYPTT--LHVEKDINNPKLRSLV 564

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

GO:0043531 "ADP binding" 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

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh4_pg.C_LG_XII001317 cc-nbs-lrr resistance protein (945 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	597
pfam00931	285	pfam00931, NB-ARC, NB-ARC domain	1e-52
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	5e-10
pfam01637	223	pfam01637, Arch_ATPase, Archaeal ATPase	1e-04

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

 Score =  180 bits (460), Expect = 1e-52
 Identities = 101/304 (33%), Positives = 148/304 (48%), Gaps = 40/304 (13%)

Query: 191 SGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEIS 250
                 L V+ I+G  G+GKT LA+Q+++D  V  +FD   WV                 
Sbjct: 13  LEMSDNLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVV---------------- 56

Query: 251 VARDRDEIRVAKAILESLKGSVSSQVEMET-VLQ-YINEFVQGKKVLLVLDDLW--WNAY 306
           V++   E R+ K IL+ L    S  VE     L   I E +  K+ LLVLDD+W   +  
Sbjct: 57  VSKTYTEFRLQKDILQELGLDDSDWVEKNESELAVKIKEALLRKRFLLVLDDVWEKND-- 114

Query: 307 PRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECR 366
              W+++      G  GSR++VT       T    +       +   E+    L  EE  
Sbjct: 115 ---WDKIGVPFPDGENGSRVIVT-------TRSESVAGRMGGTSKPHEVES--LEPEESW 162

Query: 367 SLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSE 426
            LF    F        E  E + + +V KCKGLP A+K+LG LL FK++++EW+ VL+  
Sbjct: 163 ELFSNKVFEKELPPCPE-LEEVAKEIVEKCKGLPLALKVLGGLLAFKSTVQEWEHVLEQL 221

Query: 427 IWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMA 486
              L            E LS L LSY +L   LK+CFLY ++FP++Y I K++LIKLW+A
Sbjct: 222 NNELAGRDGL-----NEVLSILSLSYDNLPMHLKRCFLYLALFPEDYNIRKEQLIKLWIA 276

Query: 487 QGYL 490
           +G++
Sbjct: 277 EGFV 280

Length = 285

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

 Score = 58.0 bits (140), Expect = 5e-10
 Identities = 27/138 (19%), Positives = 51/138 (36%), Gaps = 9/138 (6%)

Query: 167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK-A 225
              GR  E +++L  L               P + + G  G GKT+L R++ +   V   
Sbjct: 1   RLVGREEELERLLDAL-------RRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAG 53

Query: 226 NFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYI 285
             D+            +R    ++       E+ + +  L +  G+   +   + V    
Sbjct: 54  KCDQAERNPPYAFSQALRELLRQLLRELA-AELLLLREALLAALGAELIEGLQDLVELLE 112

Query: 286 NEFVQGKKVLLVLDDLWW 303
               + + ++LVLDDL W
Sbjct: 113 RLLARARPLVLVLDDLQW 130

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

>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase

 Score = 43.4 bits (103), Expect = 1e-04
 Identities = 23/118 (19%), Positives = 52/118 (44%), Gaps = 16/118 (13%)

Query: 189 EESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDE 248
           EE   + T P+I + G    GKTAL R+      ++   +    V    P       +  
Sbjct: 12  EEWAERGTYPIIVVYGPRRCGKTALLREF-----LEELRELGYRVIYYDPLRREFEEK-- 64

Query: 249 ISVARDRDEIRVAKAILESLKGSVSSQVE-----METVLQYINEFVQGKKVLLVLDDL 301
             + R  +  R+A+A+ ++L     ++ +     +  + + +    +GKK+ +++D++
Sbjct: 65  --LDRFEEAKRLAEALGDALPKIGIAKSKLAFLSLTLLFELLKR--KGKKIAIIIDEV 118

This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family. Length = 223

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	597
KOG4658	889	consensus Apoptotic ATPase [Signal transduction me	100.0
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	100.0
PLN03210	1153	Resistant to P. syringae 6; Provisional	100.0
PRK04841	903	transcriptional regulator MalT; Provisional	99.69
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	99.58
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.52
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.41
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.29
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.29
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.28
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.28
COG3899	849	Predicted ATPase [General function prediction only	99.26
PF05729	166	NACHT: NACHT domain	99.06
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.03
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.98
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.88
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	98.84
PRK13342	413	recombination factor protein RarA; Reviewed	98.82
PRK06893	229	DNA replication initiation factor; Validated	98.81
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.81
PF13173	128	AAA_14: AAA domain	98.79
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	98.76
COG3903	414	Predicted ATPase [General function prediction only	98.76
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	98.76
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	98.73
PRK12402	337	replication factor C small subunit 2; Reviewed	98.71
PRK04195	482	replication factor C large subunit; Provisional	98.7
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.68
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.65
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	98.65
PLN03025	319	replication factor C subunit; Provisional	98.64
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.64
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.64
PRK05564	313	DNA polymerase III subunit delta'; Validated	98.62
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.61
PRK00440	319	rfc replication factor C small subunit; Reviewed	98.61
PTZ00202	550	tuzin; Provisional	98.61
PRK08727	233	hypothetical protein; Validated	98.6
PRK09112	351	DNA polymerase III subunit delta'; Validated	98.6
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	98.59
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.58
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	98.57
PRK08084	235	DNA replication initiation factor; Provisional	98.56
PRK07471	365	DNA polymerase III subunit delta'; Validated	98.56
PRK05642	234	DNA replication initiation factor; Validated	98.55
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.53
KOG2028	554	consensus ATPase related to the helicase subunit o	98.53
PF14516	331	AAA_35: AAA-like domain	98.52
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.5
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	98.5
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	98.49
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.48
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	98.48
PRK08903	227	DnaA regulatory inactivator Hda; Validated	98.48
PRK13341	725	recombination factor protein RarA/unknown domain f	98.48
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	98.45
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	98.45
cd01128	249	rho_factor Transcription termination factor rho is	98.42
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	98.42
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.41
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	98.39
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.38
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.37
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	98.36
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	98.36
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.36
PRK14087	450	dnaA chromosomal replication initiation protein; P	98.33
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	98.31
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	98.3
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	98.3
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	98.29
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.28
PRK09087	226	hypothetical protein; Validated	98.28
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	98.27
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	98.26
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.25
PRK09376	416	rho transcription termination factor Rho; Provisio	98.23
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.22
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	98.17
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.17
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	98.16
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	98.16
PRK14086	617	dnaA chromosomal replication initiation protein; P	98.14
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.14
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	98.14
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	98.13
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.1
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.08
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	98.08
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	98.07
TIGR00767	415	rho transcription termination factor Rho. Members	98.07
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	98.07
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	98.07
CHL00181	287	cbbX CbbX; Provisional	98.06
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	98.06
PRK06620	214	hypothetical protein; Validated	98.05
PRK14088	440	dnaA chromosomal replication initiation protein; P	98.05
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.05
PHA02544	316	44 clamp loader, small subunit; Provisional	98.04
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	98.02
PRK00149	450	dnaA chromosomal replication initiation protein; R	98.02
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	98.0
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.98
PRK05707	328	DNA polymerase III subunit delta'; Validated	97.97
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.97
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.97
PF00004	132	AAA: ATPase family associated with various cellula	97.95
PRK12422	445	chromosomal replication initiation protein; Provis	97.94
COG0593	408	DnaA ATPase involved in DNA replication initiation	97.93
PRK10536	262	hypothetical protein; Provisional	97.91
CHL00095	821	clpC Clp protease ATP binding subunit	97.91
smart00382	148	AAA ATPases associated with a variety of cellular	97.9
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	97.89
PRK10865	857	protein disaggregation chaperone; Provisional	97.84
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.84
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	97.82
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	97.82
PRK08116	268	hypothetical protein; Validated	97.81
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.81
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.79
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	97.77
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.73
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	97.72
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	97.69
PRK08181	269	transposase; Validated	97.69
PRK08769	319	DNA polymerase III subunit delta'; Validated	97.63
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.62
KOG1514	767	consensus Origin recognition complex, subunit 1, a	97.61
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.59
CHL00176	638	ftsH cell division protein; Validated	97.59
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.58
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.58
PRK12377	248	putative replication protein; Provisional	97.57
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	97.55
PRK06871	325	DNA polymerase III subunit delta'; Validated	97.54
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	97.51
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	97.5
PRK10865	857	protein disaggregation chaperone; Provisional	97.5
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	97.5
PRK08939	306	primosomal protein DnaI; Reviewed	97.47
PRK06526	254	transposase; Provisional	97.46
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	97.46
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.43
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.43
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	97.42
PRK07993	334	DNA polymerase III subunit delta'; Validated	97.4
PRK06921	266	hypothetical protein; Provisional	97.38
PRK06090	319	DNA polymerase III subunit delta'; Validated	97.38
PRK07952	244	DNA replication protein DnaC; Validated	97.38
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.37
PRK06835	329	DNA replication protein DnaC; Validated	97.35
PRK09183	259	transposase/IS protein; Provisional	97.34
PRK06964	342	DNA polymerase III subunit delta'; Validated	97.33
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	97.33
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.33
PRK05541	176	adenylylsulfate kinase; Provisional	97.32
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.31
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.3
PRK04296	190	thymidine kinase; Provisional	97.29
PRK04132	846	replication factor C small subunit; Provisional	97.27
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	97.23
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	97.22
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.21
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.21
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	97.2
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.18
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	97.18
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.17
CHL00095	821	clpC Clp protease ATP binding subunit	97.17
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.16
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	97.15
PRK12608	380	transcription termination factor Rho; Provisional	97.14
PRK08118	167	topology modulation protein; Reviewed	97.12
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.12
CHL00195	489	ycf46 Ycf46; Provisional	97.1
PHA00729	226	NTP-binding motif containing protein	97.07
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	97.03
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	97.02
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	97.01
PTZ00494	664	tuzin-like protein; Provisional	97.01
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	97.01
PRK06067	234	flagellar accessory protein FlaH; Validated	97.0
cd01394	218	radB RadB. The archaeal protein radB shares simila	96.99
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	96.99
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	96.99
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	96.96
PRK08699	325	DNA polymerase III subunit delta'; Validated	96.96
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	96.94
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	96.94
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	96.93
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	96.92
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.91
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.91
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	96.91
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	96.89
PRK07261	171	topology modulation protein; Provisional	96.86
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	96.85
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	96.84
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.84
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.83
KOG1969	877	consensus DNA replication checkpoint protein CHL12	96.82
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.82
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	96.8
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	96.79
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	96.79
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	96.78
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.77
cd01133	274	F1-ATPase_beta F1 ATP synthase beta subunit, nucle	96.76
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.76
cd03246	173	ABCC_Protease_Secretion This family represents the	96.75
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.75
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	96.74
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	96.73
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	96.72
cd03369	207	ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-ty	96.72
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	96.72
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	96.71
PRK06696	223	uridine kinase; Validated	96.71
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	96.71
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.71
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.71
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.69
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	96.67
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	96.67
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	96.65
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	96.65
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.64
PRK08533	230	flagellar accessory protein FlaH; Reviewed	96.64
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.64
cd00983	325	recA RecA is a bacterial enzyme which has roles in	96.63
COG1066	456	Sms Predicted ATP-dependent serine protease [Postt	96.63
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.62
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	96.62
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.62
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	96.58
COG0468	279	RecA RecA/RadA recombinase [DNA replication, recom	96.54
cd03244	221	ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.	96.54
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.53
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	96.53
cd03269	210	ABC_putative_ATPase This subfamily is involved in	96.52
PRK05973	237	replicative DNA helicase; Provisional	96.52
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	96.5
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.5
PRK09354	349	recA recombinase A; Provisional	96.5
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.5
cd03263	220	ABC_subfamily_A The ABCA subfamily mediates the tr	96.49
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.48
PHA02244	383	ATPase-like protein	96.46
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.46
PRK13538	204	cytochrome c biogenesis protein CcmA; Provisional	96.44
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	96.44
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	96.43
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.43
COG2884	223	FtsE Predicted ATPase involved in cell division [C	96.42
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.39
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	96.38
PRK11247	257	ssuB aliphatic sulfonates transport ATP-binding su	96.38
PRK08233	182	hypothetical protein; Provisional	96.38
PRK13695	174	putative NTPase; Provisional	96.36
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	96.35
cd03231	201	ABC_CcmA_heme_exporter CcmA, the ATP-binding compo	96.34
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	96.34
PF00154	322	RecA: recA bacterial DNA recombination protein; In	96.32
cd03254	229	ABCC_Glucan_exporter_like Glucan exporter ATP-bind	96.32
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.32
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.31
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.3
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	96.3
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	96.29
PRK14974	336	cell division protein FtsY; Provisional	96.28
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	96.28
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.27
cd03297	214	ABC_ModC_molybdenum_transporter ModC is an ABC-typ	96.27
cd03235	213	ABC_Metallic_Cations ABC component of the metal-ty	96.27
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	96.27
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	96.26
cd03220	224	ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transpo	96.26
cd03245	220	ABCC_bacteriocin_exporters ABC-type bacteriocin ex	96.25
PRK07667	193	uridine kinase; Provisional	96.25
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	96.25
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	96.25
cd03255	218	ABC_MJ0796_Lo1CDE_FtsE This family is comprised of	96.24
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	96.24
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.24
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	96.24
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	96.23
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.22
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	96.22
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.21
cd03215	182	ABC_Carb_Monos_II This family represents domain II	96.21
cd03259	213	ABC_Carb_Solutes_like ABC Carbohydrate and Solute	96.21
PRK11248	255	tauB taurine transporter ATP-binding subunit; Prov	96.21
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	96.19
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	96.18
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.17
TIGR01166	190	cbiO cobalt transport protein ATP-binding subunit.	96.17
cd03225	211	ABC_cobalt_CbiO_domain1 Domain I of the ABC compon	96.17
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	96.17
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	96.15
PF00485	194	PRK: Phosphoribulokinase / Uridine kinase family;	96.15
TIGR00960	216	3a0501s02 Type II (General) Secretory Pathway (IIS	96.14
PRK14247	250	phosphate ABC transporter ATP-binding protein; Pro	96.12
PRK00889	175	adenylylsulfate kinase; Provisional	96.11
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.11
PRK15455	644	PrkA family serine protein kinase; Provisional	96.1
PRK14269	246	phosphate ABC transporter ATP-binding protein; Pro	96.1
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	96.1
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.1
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	96.1
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.09
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	96.09
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	96.08
cd03300	232	ABC_PotA_N PotA is an ABC-type transporter and the	96.08
cd03252	237	ABCC_Hemolysin The ABC-transporter hemolysin B is	96.08
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.07
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	96.07
TIGR01277	213	thiQ thiamine ABC transporter, ATP-binding protein	96.06
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	96.05
PRK09544	251	znuC high-affinity zinc transporter ATPase; Review	96.05
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	96.05
cd03298	211	ABC_ThiQ_thiamine_transporter ABC-type thiamine tr	96.05
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	96.04
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.04
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	96.04
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	96.04
cd03253	236	ABCC_ATM1_transporter ATM1 is an ABC transporter t	96.03
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	96.03
TIGR02673	214	FtsE cell division ATP-binding protein FtsE. This	96.02
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.02
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.02
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	96.01
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	96.01
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	96.01
PRK13531	498	regulatory ATPase RavA; Provisional	96.0
PRK04328	249	hypothetical protein; Provisional	96.0
PTZ00035	337	Rad51 protein; Provisional	95.99
cd02025	220	PanK Pantothenate kinase (PanK) catalyzes the phos	95.99
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	95.99
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	95.99
KOG0736	953	consensus Peroxisome assembly factor 2 containing	95.99
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	95.98
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.98
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	95.98
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	95.98
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	95.97
TIGR03005	252	ectoine_ehuA ectoine/hydroxyectoine ABC transporte	95.97
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	95.97
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.97
PRK00771	437	signal recognition particle protein Srp54; Provisi	95.97
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	95.96
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	95.96
cd03292	214	ABC_FtsE_transporter FtsE is a hydrophilic nucleot	95.95
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	95.95
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	95.95
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	95.94
TIGR01188	302	drrA daunorubicin resistance ABC transporter ATP-b	95.93
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	95.92
PTZ00301	210	uridine kinase; Provisional	95.92
TIGR03873	256	F420-0_ABC_ATP proposed F420-0 ABC transporter, AT	95.91
TIGR01189	198	ccmA heme ABC exporter, ATP-binding protein CcmA.	95.91
TIGR02211	221	LolD_lipo_ex lipoprotein releasing system, ATP-bin	95.9
cd03224	222	ABC_TM1139_LivF_branched LivF (TM1139) is part of	95.9
cd03267	236	ABC_NatA_like Similar in sequence to NatA, this is	95.9
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.89
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	95.88
TIGR03411	242	urea_trans_UrtD urea ABC transporter, ATP-binding	95.87
COG0572	218	Udk Uridine kinase [Nucleotide transport and metab	95.87
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	95.86
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	95.85
PRK10418	254	nikD nickel transporter ATP-binding protein NikD;	95.84
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	95.84
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	95.83
PRK05439	311	pantothenate kinase; Provisional	95.83
PRK10867	433	signal recognition particle protein; Provisional	95.83
cd03294	269	ABC_Pro_Gly_Bertaine This family comprises the gly	95.82
PRK10908	222	cell division protein FtsE; Provisional	95.82
cd03249	238	ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6)	95.82
PRK11264	250	putative amino-acid ABC transporter ATP-binding pr	95.81
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	95.81
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	95.8
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	95.8
TIGR00064	272	ftsY signal recognition particle-docking protein F	95.8
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	95.79
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	95.78
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.78
TIGR00235	207	udk uridine kinase. Model contains a number of lon	95.78
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	95.77
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	95.76
TIGR00968	237	3a0106s01 sulfate ABC transporter, ATP-binding pro	95.75
PRK14256	252	phosphate ABC transporter ATP-binding protein; Pro	95.75
TIGR00554	290	panK_bact pantothenate kinase, bacterial type. Sho	95.75
cd03251	234	ABCC_MsbA MsbA is an essential ABC transporter, cl	95.75
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	95.74
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	95.74
PRK10771	232	thiQ thiamine transporter ATP-binding subunit; Pro	95.74
cd03299	235	ABC_ModC_like Archeal protein closely related to M	95.73
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	95.73
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	95.73
PRK14267	253	phosphate ABC transporter ATP-binding protein; Pro	95.73
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	95.73
TIGR02315	243	ABC_phnC phosphonate ABC transporter, ATP-binding	95.73
PRK05480	209	uridine/cytidine kinase; Provisional	95.72
TIGR00959	428	ffh signal recognition particle protein. This mode	95.71
TIGR01184	230	ntrCD nitrate transport ATP-binding subunits C and	95.71
PRK03846	198	adenylylsulfate kinase; Provisional	95.71
PRK11823	446	DNA repair protein RadA; Provisional	95.7
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	95.69
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	95.69
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	95.67
PRK13650	279	cbiO cobalt transporter ATP-binding subunit; Provi	95.66
PRK11144	352	modC molybdate transporter ATP-binding protein; Pr	95.65
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	95.65
cd03290	218	ABCC_SUR1_N The SUR domain 1. The sulfonylurea rec	95.65
cd03289	275	ABCC_CFTR2 The CFTR subfamily domain 2. The cystic	95.64
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	95.63
cd03240	204	ABC_Rad50 The catalytic domains of Rad50 are simil	95.63
PRK13537	306	nodulation ABC transporter NodI; Provisional	95.63
PTZ00088	229	adenylate kinase 1; Provisional	95.62
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	95.62
PRK14272	252	phosphate ABC transporter ATP-binding protein; Pro	95.61
cd03260	227	ABC_PstB_phosphate_transporter Phosphate uptake is	95.61
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	95.61
PRK13546	264	teichoic acids export protein ATP-binding subunit;	95.61
PRK14261	253	phosphate ABC transporter ATP-binding protein; Pro	95.6
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	95.59
COG1703	323	ArgK Putative periplasmic protein kinase ArgK and	95.59
TIGR03771	223	anch_rpt_ABC anchored repeat-type ABC transporter,	95.58
PRK10895	241	lipopolysaccharide ABC transporter ATP-binding pro	95.57
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	95.56
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	95.56
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	95.56
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	95.56
PRK10744	260	pstB phosphate transporter ATP-binding protein; Pr	95.56
PRK06762	166	hypothetical protein; Provisional	95.56
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	95.55
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	95.55
PRK14235	267	phosphate transporter ATP-binding protein; Provisi	95.54
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	95.53
KOG1532	366	consensus GTPase XAB1, interacts with DNA repair p	95.51
PF03308	266	ArgK: ArgK protein; InterPro: IPR005129 Bacterial	95.51
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	95.5
TIGR03410	230	urea_trans_UrtE urea ABC transporter, ATP-binding	95.48
PRK14268	258	phosphate ABC transporter ATP-binding protein; Pro	95.48
cd03291	282	ABCC_CFTR1 The CFTR subfamily domain 1. The cystic	95.48
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	95.47
PRK14246	257	phosphate ABC transporter ATP-binding protein; Pro	95.47
PRK14257	329	phosphate ABC transporter ATP-binding protein; Pro	95.45
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	95.44
TIGR02770	230	nickel_nikD nickel import ATP-binding protein NikD	95.44
PRK11153	343	metN DL-methionine transporter ATP-binding subunit	95.44
PRK14271	276	phosphate ABC transporter ATP-binding protein; Pro	95.43
PRK11160	574	cysteine/glutathione ABC transporter membrane/ATP-	95.43
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	95.42
PRK11831	269	putative ABC transporter ATP-binding protein YrbF;	95.42
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	95.41
PRK13632	271	cbiO cobalt transporter ATP-binding subunit; Provi	95.4
PRK06547	172	hypothetical protein; Provisional	95.38
PRK14244	251	phosphate ABC transporter ATP-binding protein; Pro	95.38
PRK13648	269	cbiO cobalt transporter ATP-binding subunit; Provi	95.36
TIGR00972	247	3a0107s01c2 phosphate ABC transporter, ATP-binding	95.36
PRK07132	299	DNA polymerase III subunit delta'; Validated	95.36
PRK14262	250	phosphate ABC transporter ATP-binding protein; Pro	95.35
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	95.35
TIGR01288	303	nodI ATP-binding ABC transporter family nodulation	95.33
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	95.33
PRK14259	269	phosphate ABC transporter ATP-binding protein; Pro	95.32
PRK11231	255	fecE iron-dicitrate transporter ATP-binding subuni	95.31
PRK09302	509	circadian clock protein KaiC; Reviewed	95.3
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	95.3
PRK14258	261	phosphate ABC transporter ATP-binding protein; Pro	95.3
TIGR02314	343	ABC_MetN D-methionine ABC transporter, ATP-binding	95.29
PRK13638	271	cbiO cobalt transporter ATP-binding subunit; Provi	95.29
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	95.29
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	95.28
PRK13647	274	cbiO cobalt transporter ATP-binding subunit; Provi	95.28
PRK06002	450	fliI flagellum-specific ATP synthase; Validated	95.27
PRK14265	274	phosphate ABC transporter ATP-binding protein; Pro	95.27
PRK14245	250	phosphate ABC transporter ATP-binding protein; Pro	95.26
PRK14236	272	phosphate transporter ATP-binding protein; Provisi	95.26
TIGR00958	711	3a01208 Conjugate Transporter-2 (CT2) Family prote	95.26
PRK09270	229	nucleoside triphosphate hydrolase domain-containin	95.26
PRK14249	251	phosphate ABC transporter ATP-binding protein; Pro	95.25
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.24
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	95.24
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	95.24
PRK14242	253	phosphate transporter ATP-binding protein; Provisi	95.24
PRK13548	258	hmuV hemin importer ATP-binding subunit; Provision	95.22
PF00625	183	Guanylate_kin: Guanylate kinase; InterPro: IPR0081	95.21
PRK09580	248	sufC cysteine desulfurase ATPase component; Review	95.19
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	95.18
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	95.18
TIGR02142	354	modC_ABC molybdenum ABC transporter, ATP-binding p	95.18
cd03236	255	ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 o	95.15
PF07726	131	AAA_3: ATPase family associated with various cellu	95.15
PRK15112	267	antimicrobial peptide ABC system ATP-binding prote	95.15
PRK14274	259	phosphate ABC transporter ATP-binding protein; Pro	95.15
PRK13536	340	nodulation factor exporter subunit NodI; Provision	95.14
PRK15424	538	propionate catabolism operon regulatory protein Pr	95.14
PF03193	161	DUF258: Protein of unknown function, DUF258; Inter	95.13
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	95.13

>KOG4658 consensus Apoptotic ATPase [Signal transduction mechanisms]

Probab=100.00  E-value=5e-68  Score=588.24  Aligned_cols=526  Identities=25%  Similarity=0.412  Sum_probs=417.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHhccccccCCcHHHHHHHHHHHhhhhhhhhHHHH
Q 041007            6 TVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDE   85 (597)
Q Consensus         6 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~i~~~l~~a~~~~~~~~~~~~~~~Wl~~l~~~ayd~ed~ld~   85 (597)
                      .++..++++.++   +.++...+.|.++.+..|++.|..+++++.++++++.   ....+..|.+.+++++|+++|.++.
T Consensus         4 ~~s~~~~~~~~~---l~~~~~~~~~~~~~i~~Lk~~L~~l~~~l~d~~a~~~---~~~~~~~~~e~~~~~~~~~e~~~~~   77 (889)
T KOG4658|consen    4 CVSFGVEKLDQL---LNRESECLDGKDNYILELKENLKALQSALEDLDAKRD---DLERRVNWEEDVGDLVYLAEDIIWL   77 (889)
T ss_pred             EEEEehhhHHHH---HHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHhhcc---hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            566677788886   7888889999999999999999999999999999887   6778899999999999999999999


Q ss_pred             HHHHHHHHHhhcccc---cccCceeeccccchhhhhhhHHHHHHHHHHHHHHHHccccccCccc----cCC-CCCCCccc
Q 041007           86 WNTAIQKLLLANETD---HKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKL----MSG-SGEGGIMT  157 (597)
Q Consensus        86 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~r~~~~~~i~~l~~~l~~i~~~~~~~~~~~----~~~-~~~~~~~~  157 (597)
                      |.......+......   ...+..    |..  ..++..+..+..+.+++-.+......+....    ... ..+.....
T Consensus        78 ~~v~~~~~~~~~~l~~~~~~~~~~----c~~--~~~~~~~~~~~~~~~rv~~~l~~ve~l~~~~~~~~~~~~~~~~~~~e  151 (889)
T KOG4658|consen   78 FLVEEIERKANDLLSTRSVERQRL----CLC--GFCSKNVSDSYKYGKRVSKVLREVESLGSKGVFEVVGESLDPREKVE  151 (889)
T ss_pred             HHHHHHHHHHhHHhhhhHHHHHHH----hhh--hhHhHhhhhhHhHHHHHHHHHHHHHHhccccceecccccccchhhcc
Confidence            987765543321110   011111    111  3444555555555555555544444443222    111 11111122


Q ss_pred             CCccccCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChh-hhccCCeeEEEEec
Q 041007          158 TSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSD-VKANFDKRIWVSAS  236 (597)
Q Consensus       158 ~~~~~~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~-~~~~F~~~~wv~~~  236 (597)
                      +.+ ..+... ||.+..++++...|..++          ..+++|+||||+||||||++++|+.. ++.+|+.++||.+|
T Consensus       152 ~~~-~~~~~~-VG~e~~~~kl~~~L~~d~----------~~iv~i~GMGGvGKTTL~~qi~N~~~~v~~~Fd~~iWV~VS  219 (889)
T KOG4658|consen  152 TRP-IQSESD-VGLETMLEKLWNRLMEDD----------VGIVGIYGMGGVGKTTLARQIFNKFDEVGNHFDGVIWVVVS  219 (889)
T ss_pred             cCC-CCcccc-ccHHHHHHHHHHHhccCC----------CCEEEEECCCcccHHHHHHHHhcccchhcccCceEEEEEEc
Confidence            222 333344 999999999999999543          38999999999999999999999977 99999999999999


Q ss_pred             CCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc--hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHH
Q 041007          237 YPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS--QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~--~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                      +.++.                ..++.+|+..++.....  ..+.+.+...|.+.|+++||||||||||...   .|+.+.
T Consensus       220 k~f~~----------------~~iq~~Il~~l~~~~~~~~~~~~~~~~~~i~~~L~~krfllvLDDIW~~~---dw~~I~  280 (889)
T KOG4658|consen  220 KEFTT----------------RKIQQTILERLGLLDEEWEDKEEDELASKLLNLLEGKRFLLVLDDIWEEV---DWDKIG  280 (889)
T ss_pred             ccccH----------------HhHHHHHHHHhccCCcccchhhHHHHHHHHHHHhccCceEEEEecccccc---cHHhcC
Confidence            99999                99999999998874433  2334788999999999999999999999888   799999


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ce----eecCCCChHHHHHHHHHHhccCCCCCCccchHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-ME----IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIG  389 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~----~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~  389 (597)
                      .++|...+||+|++|||+.              .++.. ++    +++..|+++|||.||++.++.... ..++.++++|
T Consensus       281 ~~~p~~~~g~KvvlTTRs~--------------~V~~~~m~~~~~~~v~~L~~~eaW~LF~~~v~~~~~-~~~~~i~~la  345 (889)
T KOG4658|consen  281 VPFPSRENGSKVVLTTRSE--------------EVCGRAMGVDYPIEVECLTPEEAWDLFQKKVGPNTL-GSHPDIEELA  345 (889)
T ss_pred             CCCCCccCCeEEEEEeccH--------------hhhhccccCCccccccccCccccHHHHHHhhccccc-cccccHHHHH
Confidence            9999999999999999999              77766 33    999999999999999999986533 3334589999


Q ss_pred             HHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHHHhhcC
Q 041007          390 RRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIF  469 (597)
Q Consensus       390 ~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~~ls~F  469 (597)
                      ++|+++|+|+|||++++|+.|+.+.+.++|.++++...+......   .+....++++|.+||++||+++|.||+|||+|
T Consensus       346 k~v~~kC~GLPLAl~viG~~ma~K~t~~eW~~~~~~l~s~~~~~~---~~~~~~i~~iLklSyd~L~~~lK~CFLycalF  422 (889)
T KOG4658|consen  346 KEVAEKCGGLPLALNVLGGLLACKKTVQEWRRALNVLKSSLAADF---SGMEESILPILKLSYDNLPEELKSCFLYCALF  422 (889)
T ss_pred             HHHHHHhCChHHHHHHHHHHhcCCCcHHHHHHHHccccccccCCC---CchhhhhHHhhhccHhhhhHHHHHHHHhhccC
Confidence            999999999999999999999999999999999998766533332   23367889999999999999999999999999


Q ss_pred             CCCcccChhHHHHHHHHcCCccc-CCCCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEEeChHHHHHHHHhhc---
Q 041007          470 PKNYEIEKDRLIKLWMAQGYLKS-QESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSK---  545 (597)
Q Consensus       470 p~~~~i~~~~Li~~W~aeg~i~~-~~~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~mH~lv~~~a~~~~~---  545 (597)
                      |+||.|+++.||.+|+||||+.+ ..+.+++++|+.|+.+|+++||++.....   ++..+|+|||+||++|.++++   
T Consensus       423 PED~~I~~e~Li~yWiaEGfi~~~~~~~~~~d~G~~~i~~LV~~~Ll~~~~~~---~~~~~~kmHDvvRe~al~ias~~~  499 (889)
T KOG4658|consen  423 PEDYEIKKEKLIEYWIAEGFIDPLDGGETAEDVGYDYIEELVRASLLIEERDE---GRKETVKMHDVVREMALWIASDFG  499 (889)
T ss_pred             CcccccchHHHHHHHHhccCcCccccccchhcchHHHHHHHHHHHHHhhcccc---cceeEEEeeHHHHHHHHHHhcccc
Confidence            99999999999999999999998 45778999999999999999999876543   346789999999999999999   


Q ss_pred             --cccEEEeecCCcccccccCCCCCeEEEEEEecCCCCCCccccCCCCCccccC
Q 041007          546 --SHNFNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVYNQKKLRSLV  597 (597)
Q Consensus       546 --~~~~~~~~~~~~~~~~~~~~~~~~r~ls~~~~~~~~~~~~~~~~~~~lr~l~  597 (597)
                        .+++++..+......+....+..+||+|++++..  +......++++|+||+
T Consensus       500 ~~~e~~iv~~~~~~~~~~~~~~~~~~rr~s~~~~~~--~~~~~~~~~~~L~tLl  551 (889)
T KOG4658|consen  500 KQEENQIVSDGVGLSEIPQVKSWNSVRRMSLMNNKI--EHIAGSSENPKLRTLL  551 (889)
T ss_pred             ccccceEEECCcCccccccccchhheeEEEEeccch--hhccCCCCCCccceEE
Confidence              7776666542221334455668899999998764  2333335567888874

>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=100.00  E-value=5.7e-45  Score=365.91  Aligned_cols=277  Identities=38%  Similarity=0.581  Sum_probs=219.2

Q ss_pred             chhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhh
Q 041007          171 RNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEIS  250 (597)
Q Consensus       171 R~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~  250 (597)
                      ||.++++|.+.|....        .+.++|+|+|+||+||||||.+++++..++.+|+.++|+.++...+.         
T Consensus         1 re~~~~~l~~~L~~~~--------~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~---------   63 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNS--------NEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSL---------   63 (287)
T ss_dssp             -HHHHHHHHHHHHTTT--------TSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCC---------
T ss_pred             CHHHHHHHHHHhhCCC--------CCeEEEEEEcCCcCCcceeeeeccccccccccccccccccccccccc---------
Confidence            7899999999999643        26899999999999999999999997668999999999999998888         


Q ss_pred             hcccchHHHHHHHHHHhccCCCC---chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEE
Q 041007          251 VARDRDEIRVAKAILESLKGSVS---SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRIL  327 (597)
Q Consensus       251 ~~~~~~~~~~~~~il~~l~~~~~---~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~II  327 (597)
                             ..++..|+..++....   ...+.+.....+.+.|.++++||||||||+..   .|+.+...++....|++||
T Consensus        64 -------~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~---~~~~l~~~~~~~~~~~kil  133 (287)
T PF00931_consen   64 -------EQLLEQILRQLGEPDSSISDPKDIEELQDQLRELLKDKRCLLVLDDVWDEE---DLEELREPLPSFSSGSKIL  133 (287)
T ss_dssp             -------HHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHHHCCTSEEEEEEEE-SHH---HH-------HCHHSS-EEE
T ss_pred             -------ccccccccccccccccccccccccccccccchhhhccccceeeeeeecccc---ccccccccccccccccccc
Confidence                   8899999999988743   45667779999999999999999999998665   8888888888878899999


Q ss_pred             EEccCCCCCCCcccccccccCcccc-----ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          328 VTRSGGKNGTNMTEIGLGEKNGTNM-----MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       328 vTtR~~~~~~~~~~~~~~~~~~~~~-----~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                      ||||+.              .++..     ..+++++|+.+++++||.+.++... ...++...+.+++|+++|+|+|||
T Consensus       134 vTTR~~--------------~v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~-~~~~~~~~~~~~~i~~~c~glPLa  198 (287)
T PF00931_consen  134 VTTRDR--------------SVAGSLGGTDKVIELEPLSEEEALELFKKRAGRKE-SESPEDLEDLAKEIVEKCGGLPLA  198 (287)
T ss_dssp             EEESCG--------------GGGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS-----TTSCTHHHHHHHHTTT-HHH
T ss_pred             cccccc--------------ccccccccccccccccccccccccccccccccccc-cccccccccccccccccccccccc
Confidence            999998              54432     2399999999999999999987544 223345567889999999999999


Q ss_pred             HHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHHHhhcCCCCcccChhHHHH
Q 041007          403 VKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIK  482 (597)
Q Consensus       403 i~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~~ls~Fp~~~~i~~~~Li~  482 (597)
                      |+++|++|+.+.+..+|..+++...+.....    .+....+..++.+||+.||+++|+||+|||+||+++.|+++.|++
T Consensus       199 l~~~a~~l~~~~~~~~w~~~~~~l~~~~~~~----~~~~~~~~~~l~~s~~~L~~~~~~~f~~L~~f~~~~~i~~~~li~  274 (287)
T PF00931_consen  199 LKLIASYLRSKSTVDEWEEALEELENSLRES----RDYDRSVFSALELSYDSLPDELRRCFLYLSIFPEGVPIPRERLIR  274 (287)
T ss_dssp             HHHHHHHHHHHHSSSSHHHHHHHHHHCHTCS----SGSCHHHHHHHHHHHHSSHTCCHHHHHHGGGSGTTS-EEHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccc----ccccccccccceechhcCCccHHHHHhhCcCCCCCceECHHHHHH
Confidence            9999999976667788999887755443221    112567889999999999999999999999999999999999999


Q ss_pred             HHHHcCCcccC
Q 041007          483 LWMAQGYLKSQ  493 (597)
Q Consensus       483 ~W~aeg~i~~~  493 (597)
                      +|++||||...
T Consensus       275 lW~~e~~i~~~  285 (287)
T PF00931_consen  275 LWVAEGFISSK  285 (287)
T ss_dssp             HHTT-HHTC--
T ss_pred             HHHHCCCCccc
Confidence            99999998753

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

>PLN03210 Resistant to P

Probab=100.00  E-value=2.8e-39  Score=377.85  Aligned_cols=369  Identities=21%  Similarity=0.268  Sum_probs=258.1

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      .+...+|||+.+++++..+|....        ..+++|+|+||||+||||||+.+|+  ++..+|+..+|+.........
T Consensus       181 ~~~~~~vG~~~~l~~l~~lL~l~~--------~~~~vvgI~G~gGiGKTTLA~~l~~--~l~~~F~g~vfv~~~~v~~~~  250 (1153)
T PLN03210        181 NDFEDFVGIEDHIAKMSSLLHLES--------EEVRMVGIWGSSGIGKTTIARALFS--RLSRQFQSSVFIDRAFISKSM  250 (1153)
T ss_pred             cccccccchHHHHHHHHHHHcccc--------CceEEEEEEcCCCCchHHHHHHHHH--HHhhcCCeEEEeeccccccch
Confidence            345679999999999999986443        3689999999999999999999999  688899998887521000000


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCC
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSE  322 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~  322 (597)
                      ...... ..........+...++..+.........   ....+++.+.++|+||||||||+..   .|+.+.......++
T Consensus       251 ~~~~~~-~~~~~~~~~~l~~~~l~~il~~~~~~~~---~~~~~~~~L~~krvLLVLDdv~~~~---~l~~L~~~~~~~~~  323 (1153)
T PLN03210        251 EIYSSA-NPDDYNMKLHLQRAFLSEILDKKDIKIY---HLGAMEERLKHRKVLIFIDDLDDQD---VLDALAGQTQWFGS  323 (1153)
T ss_pred             hhcccc-cccccchhHHHHHHHHHHHhCCCCcccC---CHHHHHHHHhCCeEEEEEeCCCCHH---HHHHHHhhCccCCC
Confidence            000000 0000000123334444443322111100   0145677789999999999998655   88888876666788


Q ss_pred             CcEEEEEccCCCCCCCcccccccccCccccc----eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCC
Q 041007          323 GSRILVTRSGGKNGTNMTEIGLGEKNGTNMM----EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKG  398 (597)
Q Consensus       323 gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~----~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~G  398 (597)
                      |++||||||+.              .++...    .|++..|++++|++||+++||...  .++.++.+++++|+++|+|
T Consensus       324 GsrIIiTTrd~--------------~vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~~--~~~~~~~~l~~~iv~~c~G  387 (1153)
T PLN03210        324 GSRIIVITKDK--------------HFLRAHGIDHIYEVCLPSNELALEMFCRSAFKKN--SPPDGFMELASEVALRAGN  387 (1153)
T ss_pred             CcEEEEEeCcH--------------HHHHhcCCCeEEEecCCCHHHHHHHHHHHhcCCC--CCcHHHHHHHHHHHHHhCC
Confidence            99999999998              554332    399999999999999999998653  3445688999999999999


Q ss_pred             chHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCCh-hHhHHHHHhhcCCCCcccCh
Q 041007          399 LPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSP-ALKKCFLYCSIFPKNYEIEK  477 (597)
Q Consensus       399 lPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~-~~k~cf~~ls~Fp~~~~i~~  477 (597)
                      +||||+++|+.|+.+ +..+|..++.++....          ..++..+|++||+.|++ ..|.||+++|+|+.+..++ 
T Consensus       388 LPLAl~vlgs~L~~k-~~~~W~~~l~~L~~~~----------~~~I~~~L~~SYd~L~~~~~k~~Fl~ia~ff~~~~~~-  455 (1153)
T PLN03210        388 LPLGLNVLGSYLRGR-DKEDWMDMLPRLRNGL----------DGKIEKTLRVSYDGLNNKKDKAIFRHIACLFNGEKVN-  455 (1153)
T ss_pred             CcHHHHHHHHHHcCC-CHHHHHHHHHHHHhCc----------cHHHHHHHHHhhhccCccchhhhhheehhhcCCCCHH-
Confidence            999999999999865 6899999998865433          34688999999999987 5999999999999986553 


Q ss_pred             hHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEEeChHHHHHHHHhhcccc-------EE
Q 041007          478 DRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHN-------FN  550 (597)
Q Consensus       478 ~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~mH~lv~~~a~~~~~~~~-------~~  550 (597)
                        .+..|++.+...          ++..++.|+++|||+...    +    +++|||++|+|++.+++.+.       +.
T Consensus       456 --~v~~~l~~~~~~----------~~~~l~~L~~ksLi~~~~----~----~~~MHdLl~~~~r~i~~~~~~~~~~r~~l  515 (1153)
T PLN03210        456 --DIKLLLANSDLD----------VNIGLKNLVDKSLIHVRE----D----IVEMHSLLQEMGKEIVRAQSNEPGEREFL  515 (1153)
T ss_pred             --HHHHHHHhcCCC----------chhChHHHHhcCCEEEcC----C----eEEhhhHHHHHHHHHHHhhcCCCCcceeE
Confidence              467788876532          233489999999997532    1    38999999999999986653       22


Q ss_pred             EeecCCcccccccCCCCCeEEEEEEecCCCC--CCccccCCCCCcccc
Q 041007          551 AEVKGSDQECQSKSSHEKFRHLMIMFETDHG--AFPNSVYNQKKLRSL  596 (597)
Q Consensus       551 ~~~~~~~~~~~~~~~~~~~r~ls~~~~~~~~--~~~~~~~~~~~lr~l  596 (597)
                      ....+............+++++++..+....  -....+.+|++||+|
T Consensus       516 ~~~~di~~vl~~~~g~~~v~~i~l~~~~~~~~~i~~~aF~~m~~L~~L  563 (1153)
T PLN03210        516 VDAKDICDVLEDNTGTKKVLGITLDIDEIDELHIHENAFKGMRNLLFL  563 (1153)
T ss_pred             eCHHHHHHHHHhCcccceeeEEEeccCccceeeecHHHHhcCccccEE
Confidence            2211111011123455678998887544311  112345566666654

syringae 6; Provisional

>PRK04841 transcriptional regulator MalT; Provisional

Probab=99.69  E-value=3.8e-15  Score=173.54  Aligned_cols=299  Identities=16%  Similarity=0.200  Sum_probs=179.5

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRV  244 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  244 (597)
                      +..+|-|+.-++.|    ...         ...+++.|+|++|.||||++.++.+.      ++.++|+++....+..  
T Consensus        13 ~~~~~~R~rl~~~l----~~~---------~~~~~~~v~apaG~GKTtl~~~~~~~------~~~~~w~~l~~~d~~~--   71 (903)
T PRK04841         13 LHNTVVRERLLAKL----SGA---------NNYRLVLVTSPAGYGKTTLISQWAAG------KNNLGWYSLDESDNQP--   71 (903)
T ss_pred             ccccCcchHHHHHH----hcc---------cCCCeEEEECCCCCCHHHHHHHHHHh------CCCeEEEecCcccCCH--
Confidence            34567776554444    321         24789999999999999999998862      2268999987554332  


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccCCCC-------------chhhHHHHHHHHHHHhc--CceEEEEEecccCCCCcch
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKGSVS-------------SQVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAYPRY  309 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~~~~-------------~~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~~~~  309 (597)
                                   ..++..++..+.....             ...+...+...+...+.  +.+++|||||+++.+....
T Consensus        72 -------------~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~~~  138 (903)
T PRK04841         72 -------------ERFASYLIAALQQATNGHCSKSEALAQKRQYASLSSLFAQLFIELADWHQPLYLVIDDYHLITNPEI  138 (903)
T ss_pred             -------------HHHHHHHHHHHHHhcCcccchhhhhhccCCcCCHHHHHHHHHHHHhcCCCCEEEEEeCcCcCCChHH
Confidence                         3333344444321100             00122233333333333  6799999999998874433


Q ss_pred             HHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecC----CCChHHHHHHHHHHhccCCCCCCccch
Q 041007          310 WEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLG----ELSEEECRSLFRQIAFHGRSSDYREKF  385 (597)
Q Consensus       310 ~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~----~Ls~~es~~Lf~~~~~~~~~~~~~~~~  385 (597)
                      .+.+...+.....+.++|||||..+.... ...     ..... ...+.    +|+.+|+.+||....+...       .
T Consensus       139 ~~~l~~l~~~~~~~~~lv~~sR~~~~~~~-~~l-----~~~~~-~~~l~~~~l~f~~~e~~~ll~~~~~~~~-------~  204 (903)
T PRK04841        139 HEAMRFFLRHQPENLTLVVLSRNLPPLGI-ANL-----RVRDQ-LLEIGSQQLAFDHQEAQQFFDQRLSSPI-------E  204 (903)
T ss_pred             HHHHHHHHHhCCCCeEEEEEeCCCCCCch-HhH-----HhcCc-ceecCHHhCCCCHHHHHHHHHhccCCCC-------C
Confidence            44555555556778899999998532210 000     00111 13344    9999999999987653211       1


Q ss_pred             HHHHHHHHHhcCCchHHHHHHHhhhccCCC-HHHHHHHHhhhcccCChhhhhhcCCCCCcccchh-ccccCCChhHhHHH
Q 041007          386 EPIGRRVVGKCKGLPFAVKILGSLLRFKTS-IKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLL-LSYFDLSPALKKCF  463 (597)
Q Consensus       386 ~~~~~~I~~~~~GlPLai~~~~~~l~~~~~-~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~-~sy~~L~~~~k~cf  463 (597)
                      .+.+..|.+.|+|+|+++..++..++.... .......+.    ...         ...+...|. ..|+.||+..+..+
T Consensus       205 ~~~~~~l~~~t~Gwp~~l~l~~~~~~~~~~~~~~~~~~~~----~~~---------~~~~~~~l~~~v~~~l~~~~~~~l  271 (903)
T PRK04841        205 AAESSRLCDDVEGWATALQLIALSARQNNSSLHDSARRLA----GIN---------ASHLSDYLVEEVLDNVDLETRHFL  271 (903)
T ss_pred             HHHHHHHHHHhCChHHHHHHHHHHHhhCCCchhhhhHhhc----CCC---------chhHHHHHHHHHHhcCCHHHHHHH
Confidence            455789999999999999999877754332 111110000    000         112223322 23789999999999


Q ss_pred             HHhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEEeChHHHHHHHHh
Q 041007          464 LYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLL  543 (597)
Q Consensus       464 ~~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~mH~lv~~~a~~~  543 (597)
                      ..+|+++.   ++.+ +..     .+..       .+.+...+++|.+.++|.....+ .+   .+|+.|++++++++..
T Consensus       272 ~~~a~~~~---~~~~-l~~-----~l~~-------~~~~~~~L~~l~~~~l~~~~~~~-~~---~~yr~H~L~r~~l~~~  331 (903)
T PRK04841        272 LRCSVLRS---MNDA-LIV-----RVTG-------EENGQMRLEELERQGLFIQRMDD-SG---EWFRYHPLFASFLRHR  331 (903)
T ss_pred             HHhccccc---CCHH-HHH-----HHcC-------CCcHHHHHHHHHHCCCeeEeecC-CC---CEEehhHHHHHHHHHH
Confidence            99999973   4433 222     1111       12357889999999997532211 11   2588999999999876


Q ss_pred             h
Q 041007          544 S  544 (597)
Q Consensus       544 ~  544 (597)
                      .
T Consensus       332 l  332 (903)
T PRK04841        332 C  332 (903)
T ss_pred             H
Confidence            4

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=99.58  E-value=5.2e-13  Score=142.59  Aligned_cols=303  Identities=19%  Similarity=0.215  Sum_probs=195.1

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRV  244 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  244 (597)
                      +.+.|-|..    |.+.|...         ...+.+.|..|+|.|||||+.++..  + ...-..+.|.++.+..+..  
T Consensus        18 ~~~~v~R~r----L~~~L~~~---------~~~RL~li~APAGfGKttl~aq~~~--~-~~~~~~v~Wlslde~dndp--   79 (894)
T COG2909          18 PDNYVVRPR----LLDRLRRA---------NDYRLILISAPAGFGKTTLLAQWRE--L-AADGAAVAWLSLDESDNDP--   79 (894)
T ss_pred             cccccccHH----HHHHHhcC---------CCceEEEEeCCCCCcHHHHHHHHHH--h-cCcccceeEeecCCccCCH--
Confidence            455666654    44445432         3589999999999999999999975  1 1223458999998766542  


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccCCCC-------------chhhHHHHHHHHHHHhc--CceEEEEEecccCCCCcch
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKGSVS-------------SQVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAYPRY  309 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~~~~-------------~~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~~~~  309 (597)
                                   ..+...++..++.-.+             ...+...+.+.+...+.  .++..|||||.+-..++.-
T Consensus        80 -------------~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~~l  146 (894)
T COG2909          80 -------------ARFLSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLDDYHLISDPAL  146 (894)
T ss_pred             -------------HHHHHHHHHHHHHhCccccHHHHHHHHhcccccHHHHHHHHHHHHHhhcCceEEEeccccccCcccH
Confidence                         5555555555543221             12234445555555444  5689999999877665555


Q ss_pred             HHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc---eeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          310 WEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM---EIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       310 ~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~---~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      -..+...+...+.+..+|||||+.+...-.      ...+.+..   +-+.-.|+.+|+.+||.......-       ..
T Consensus       147 ~~~l~fLl~~~P~~l~lvv~SR~rP~l~la------~lRlr~~llEi~~~~Lrf~~eE~~~fl~~~~~l~L-------d~  213 (894)
T COG2909         147 HEALRFLLKHAPENLTLVVTSRSRPQLGLA------RLRLRDELLEIGSEELRFDTEEAAAFLNDRGSLPL-------DA  213 (894)
T ss_pred             HHHHHHHHHhCCCCeEEEEEeccCCCCccc------ceeehhhHHhcChHhhcCChHHHHHHHHHcCCCCC-------Ch
Confidence            566666677788999999999998432110      00111110   133346899999999987752111       13


Q ss_pred             HHHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHHHh
Q 041007          387 PIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYC  466 (597)
Q Consensus       387 ~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~~l  466 (597)
                      ..++.|++.++|.+-|+..++=.++.+.+.+.-...+.-....+.+             -...--++.||+++|..++-|
T Consensus       214 ~~~~~L~~~teGW~~al~L~aLa~~~~~~~~q~~~~LsG~~~~l~d-------------YL~eeVld~Lp~~l~~FLl~~  280 (894)
T COG2909         214 ADLKALYDRTEGWAAALQLIALALRNNTSAEQSLRGLSGAASHLSD-------------YLVEEVLDRLPPELRDFLLQT  280 (894)
T ss_pred             HHHHHHHhhcccHHHHHHHHHHHccCCCcHHHHhhhccchHHHHHH-------------HHHHHHHhcCCHHHHHHHHHH
Confidence            4578999999999999999998887444444433333211000000             012234679999999999999


Q ss_pred             hcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcc-cccccCCCCeeeEEEeChHHHHHHHHhhc
Q 041007          467 SIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQ-DFQKSEFDGRIIRCQMHPIVHEFAQLLSK  545 (597)
Q Consensus       467 s~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~-~~~~~~~~~~~~~~~mH~lv~~~a~~~~~  545 (597)
                      |+++.-    ...|+..-..            ++.+..++++|.+++||- +.+..  +   .+|+.|.++.+|.+....
T Consensus       281 svl~~f----~~eL~~~Ltg------------~~ng~amLe~L~~~gLFl~~Ldd~--~---~WfryH~LFaeFL~~r~~  339 (894)
T COG2909         281 SVLSRF----NDELCNALTG------------EENGQAMLEELERRGLFLQRLDDE--G---QWFRYHHLFAEFLRQRLQ  339 (894)
T ss_pred             HhHHHh----hHHHHHHHhc------------CCcHHHHHHHHHhCCCceeeecCC--C---ceeehhHHHHHHHHhhhc
Confidence            999763    2334443222            235778999999999884 43322  2   369999999999987644

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.52  E-value=6.4e-12  Score=131.97  Aligned_cols=333  Identities=13%  Similarity=0.087  Sum_probs=182.0

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..|..|+||++++++|...|...-.      +.....+.|+|++|+|||++++.++++.......-..+++++....+. 
T Consensus        27 ~~P~~l~~Re~e~~~l~~~l~~~~~------~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~~-   99 (394)
T PRK00411         27 YVPENLPHREEQIEELAFALRPALR------GSRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRTR-   99 (394)
T ss_pred             CcCCCCCCHHHHHHHHHHHHHHHhC------CCCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCCH-
Confidence            3567899999999999999864322      124567889999999999999999985332221233556666555444 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCC-CC-chhhHHHHHHHHHHHhc--CceEEEEEecccCCCC---cchHHHHHH
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGS-VS-SQVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAY---PRYWEQLMY  315 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~-~~-~~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~---~~~~~~l~~  315 (597)
                                     ..++..++.++... .+ ...+.+.+...+.+.+.  +++.+||||+++....   ...+..+..
T Consensus       100 ---------------~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~~~~l~~l~~  164 (394)
T PRK00411        100 ---------------YAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEGNDVLYSLLR  164 (394)
T ss_pred             ---------------HHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCCchHHHHHHH
Confidence                           67788888888652 21 22345566666777665  4578999999976431   122333333


Q ss_pred             hhcCCC-CCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCC--CCCCccchHHHHHHH
Q 041007          316 SLKSGS-EGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGR--SSDYREKFEPIGRRV  392 (597)
Q Consensus       316 ~l~~~~-~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~--~~~~~~~~~~~~~~I  392 (597)
                      .+.... .+..+|.++......... .....  .......+.+.|++.++..+++..++....  ....+..++.+++..
T Consensus       165 ~~~~~~~~~v~vI~i~~~~~~~~~l-~~~~~--s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~  241 (394)
T PRK00411        165 AHEEYPGARIGVIGISSDLTFLYIL-DPRVK--SVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLT  241 (394)
T ss_pred             hhhccCCCeEEEEEEECCcchhhhc-CHHHH--hcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHH
Confidence            222221 123355555443110000 00000  001112389999999999999998764221  111212222233333


Q ss_pred             HHhcCCchHHHHHHHhhh--c--c-CC--CHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHHH
Q 041007          393 VGKCKGLPFAVKILGSLL--R--F-KT--SIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLY  465 (597)
Q Consensus       393 ~~~~~GlPLai~~~~~~l--~--~-~~--~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~~  465 (597)
                      ....|..+.|+.++-.+.  .  . ..  +.++...++....                 ...+.-.+..||.+.|..+..
T Consensus       242 ~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~-----------------~~~~~~~~~~L~~~~k~~L~a  304 (394)
T PRK00411        242 AREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSE-----------------IVHLSEVLRTLPLHEKLLLRA  304 (394)
T ss_pred             HHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHH-----------------HHHHHHHHhcCCHHHHHHHHH
Confidence            333466777877664322  1  1 11  4555555555421                 112334578999998887776


Q ss_pred             hhcCCC--CcccChhHHHHH--HHHcCCcccCCCCCHHHHHHHHHHHHhhCCCccccccc-CCCCeeeEEEeChHHHHHH
Q 041007          466 CSIFPK--NYEIEKDRLIKL--WMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKS-EFDGRIIRCQMHPIVHEFA  540 (597)
Q Consensus       466 ls~Fp~--~~~i~~~~Li~~--W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~-~~~~~~~~~~mH~lv~~~a  540 (597)
                      ++..-+  ...+....+...  .+++.+-  ....+ ......|++.|...|||.....+ +..++.+.++++.---++.
T Consensus       305 i~~~~~~~~~~~~~~~i~~~y~~l~~~~~--~~~~~-~~~~~~~l~~L~~~glI~~~~~~~g~~g~~~~~~~~~~~~~~~  381 (394)
T PRK00411        305 IVRLLKKGGDEVTTGEVYEEYKELCEELG--YEPRT-HTRFYEYINKLDMLGIINTRYSGKGGRGRTRLISLSYDPEDVL  381 (394)
T ss_pred             HHHHHhcCCCcccHHHHHHHHHHHHHHcC--CCcCc-HHHHHHHHHHHHhcCCeEEEEecCCCCCCeEEEEecCCHHHHH
Confidence            653321  123555555432  2222110  00011 23456799999999999865321 2234455565544333333

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.41  E-value=7.7e-11  Score=122.50  Aligned_cols=311  Identities=13%  Similarity=0.120  Sum_probs=170.8

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh-ccC---CeeEEEEecCCC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK-ANF---DKRIWVSASYPR  239 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~-~~F---~~~~wv~~~~~~  239 (597)
                      -|..|+||+.++++|...|.....      +.....+.|+|++|+|||++++.+++..... ...   -..+|+++....
T Consensus        13 ~p~~l~gRe~e~~~l~~~l~~~~~------~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~   86 (365)
T TIGR02928        13 VPDRIVHRDEQIEELAKALRPILR------GSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILD   86 (365)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHc------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCC
Confidence            456799999999999999874322      1245679999999999999999999842211 111   135677776555


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhcc---CCCC-chhhHHHHHHHHHHHhc--CceEEEEEecccCCCC--cchHH
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLK---GSVS-SQVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAY--PRYWE  311 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~---~~~~-~~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~--~~~~~  311 (597)
                      +.                ..++..++.++.   ...+ ...+..+....+.+.+.  +++++||||+++....  .....
T Consensus        87 ~~----------------~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~~~L~  150 (365)
T TIGR02928        87 TL----------------YQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLY  150 (365)
T ss_pred             CH----------------HHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCcHHHH
Confidence            54                677788888773   2211 11233444555555553  5689999999976621  11122


Q ss_pred             HHHHhh-cCCC--CCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccC-CCCCCccchHH
Q 041007          312 QLMYSL-KSGS--EGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHG-RSSDYREKFEP  387 (597)
Q Consensus       312 ~l~~~l-~~~~--~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~-~~~~~~~~~~~  387 (597)
                      .+.... ....  .+..+|.++.... ..........  .......+.+.|++.++..+++..++... ......++..+
T Consensus       151 ~l~~~~~~~~~~~~~v~lI~i~n~~~-~~~~l~~~~~--s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~~l~  227 (365)
T TIGR02928       151 QLSRARSNGDLDNAKVGVIGISNDLK-FRENLDPRVK--SSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDGVIP  227 (365)
T ss_pred             hHhccccccCCCCCeEEEEEEECCcc-hHhhcCHHHh--ccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChhHHH
Confidence            222211 1111  2334444443321 1000000000  00011228899999999999999887421 11122233344


Q ss_pred             HHHHHHHhcCCchH-HHHHHHhhh----c-cC--CCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhH
Q 041007          388 IGRRVVGKCKGLPF-AVKILGSLL----R-FK--TSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPAL  459 (597)
Q Consensus       388 ~~~~I~~~~~GlPL-ai~~~~~~l----~-~~--~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~  459 (597)
                      .+..++..+.|.|- |+.++-...    . ..  -+.++...+++...                 ...+.-++..||.+.
T Consensus       228 ~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~-----------------~~~~~~~i~~l~~~~  290 (365)
T TIGR02928       228 LCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE-----------------KDRLLELIRGLPTHS  290 (365)
T ss_pred             HHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH-----------------HHHHHHHHHcCCHHH
Confidence            55667777778874 333322111    1 11  13444444444321                 112334567899988


Q ss_pred             hHHHHHhhcCC--CCcccChhHHHHHHH--HcCCcccCCCCCHHHHHHHHHHHHhhCCCccccc
Q 041007          460 KKCFLYCSIFP--KNYEIEKDRLIKLWM--AQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQ  519 (597)
Q Consensus       460 k~cf~~ls~Fp--~~~~i~~~~Li~~W~--aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~  519 (597)
                      +..+..+...-  ++..+....+...+-  ++.+ ..  ..-......++++.|...|||....
T Consensus       291 ~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~-~~--~~~~~~~~~~~l~~l~~~gli~~~~  351 (365)
T TIGR02928       291 KLVLLAIANLAANDEDPFRTGEVYEVYKEVCEDI-GV--DPLTQRRISDLLNELDMLGLVEAEE  351 (365)
T ss_pred             HHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhc-CC--CCCcHHHHHHHHHHHHhcCCeEEEE
Confidence            87776655321  333466666665332  1111 11  1122457788999999999998653

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

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

Probab=99.29  E-value=2.6e-10  Score=113.22  Aligned_cols=190  Identities=19%  Similarity=0.198  Sum_probs=112.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ...+.|+|++|+|||||++.+++.... ..+ ..+|+. ....+.                .+++..++..++.+.....
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~-~~~-~~~~~~-~~~~~~----------------~~~l~~i~~~lG~~~~~~~  103 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQ-ERV-VAAKLV-NTRVDA----------------EDLLRMVAADFGLETEGRD  103 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCC-CCe-EEeeee-CCCCCH----------------HHHHHHHHHHcCCCCCCCC
Confidence            468999999999999999999985321 111 122332 222233                6677788888766533221


Q ss_pred             h---HHHHHHHHHHHh-cCceEEEEEecccCCCCcchHHHHHHhhcCC---CCCcEEEEEccCCCCCC-CcccccccccC
Q 041007          277 E---METVLQYINEFV-QGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG---SEGSRILVTRSGGKNGT-NMTEIGLGEKN  348 (597)
Q Consensus       277 ~---~~~~~~~l~~~L-~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~---~~gs~IIvTtR~~~~~~-~~~~~~~~~~~  348 (597)
                      .   ...+...+.... .+++.+||+||+|+.+ ...++.+.......   .....|++|........ .....    ..
T Consensus       104 ~~~~~~~l~~~l~~~~~~~~~~vliiDe~~~l~-~~~~~~l~~l~~~~~~~~~~~~vvl~g~~~~~~~l~~~~~----~~  178 (269)
T TIGR03015       104 KAALLRELEDFLIEQFAAGKRALLVVDEAQNLT-PELLEELRMLSNFQTDNAKLLQIFLVGQPEFRETLQSPQL----QQ  178 (269)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCeEEEEECcccCC-HHHHHHHHHHhCcccCCCCeEEEEEcCCHHHHHHHcCchh----HH
Confidence            1   122333333322 5788999999998876 44566655332221   22334566654331000 00000    00


Q ss_pred             ccc--cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhh
Q 041007          349 GTN--MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLL  410 (597)
Q Consensus       349 ~~~--~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l  410 (597)
                      ...  ...+.+.+|+.+|..+++...+...+......-..+..+.|++.|+|.|..|+.++..+
T Consensus       179 l~~r~~~~~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~  242 (269)
T TIGR03015       179 LRQRIIASCHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRL  242 (269)
T ss_pred             HHhheeeeeeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHH
Confidence            111  12288999999999999988774332211112235788999999999999999988776

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.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=99.29  E-value=1.2e-11  Score=119.90  Aligned_cols=218  Identities=20%  Similarity=0.215  Sum_probs=101.2

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhh
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARD  247 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~  247 (597)
                      |+||+.|+++|.+++...          ..+.+.|+|+.|+|||+|++.+.+.  .+..-..++|+..............
T Consensus         1 F~gR~~el~~l~~~l~~~----------~~~~~~l~G~rg~GKTsLl~~~~~~--~~~~~~~~~y~~~~~~~~~~~~~~~   68 (234)
T PF01637_consen    1 FFGREKELEKLKELLESG----------PSQHILLYGPRGSGKTSLLKEFINE--LKEKGYKVVYIDFLEESNESSLRSF   68 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH------------SSEEEEEESTTSSHHHHHHHHHHH--CT--EECCCHHCCTTBSHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhh----------cCcEEEEEcCCcCCHHHHHHHHHHH--hhhcCCcEEEEecccchhhhHHHHH
Confidence            799999999999999743          3579999999999999999999883  3221113344433332221000000


Q ss_pred             hhhhcccchHHHHHHHHHHhccCCC------CchhhHHHHHHHHHHHhc--CceEEEEEecccCCC-C----cchHHHHH
Q 041007          248 EISVARDRDEIRVAKAILESLKGSV------SSQVEMETVLQYINEFVQ--GKKVLLVLDDLWWNA-Y----PRYWEQLM  314 (597)
Q Consensus       248 ~~~~~~~~~~~~~~~~il~~l~~~~------~~~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~-~----~~~~~~l~  314 (597)
                       ..  .......+...+...+....      ............+.+.+.  +++++||+||++... .    ......+.
T Consensus        69 -~~--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~  145 (234)
T PF01637_consen   69 -IE--ETSLADELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLR  145 (234)
T ss_dssp             -HH--HHHHHCHCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHH
T ss_pred             -HH--HHHHHHHHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHH
Confidence             00  00000011111222221110      011122222222223332  345999999997654 1    12223344


Q ss_pred             HhhcC---CCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHH
Q 041007          315 YSLKS---GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRR  391 (597)
Q Consensus       315 ~~l~~---~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~  391 (597)
                      ..+..   ..+-+.|+++|..... ....  ............+.++||+.+++++++...+... . .. +.-.+..++
T Consensus       146 ~~~~~~~~~~~~~~v~~~S~~~~~-~~~~--~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~-~-~~-~~~~~~~~~  219 (234)
T PF01637_consen  146 SLLDSLLSQQNVSIVITGSSDSLM-EEFL--DDKSPLFGRFSHIELKPLSKEEAREFLKELFKEL-I-KL-PFSDEDIEE  219 (234)
T ss_dssp             HHHHH----TTEEEEEEESSHHHH-HHTT---TTSTTTT---EEEE----HHHHHHHHHHHHHCC---------HHHHHH
T ss_pred             HHHhhccccCCceEEEECCchHHH-HHhh--cccCccccccceEEEeeCCHHHHHHHHHHHHHHh-h-cc-cCCHHHHHH
Confidence            43433   3333444444432100 0000  0000011122229999999999999999876432 1 11 122556699


Q ss_pred             HHHhcCCchHHHHHH
Q 041007          392 VVGKCKGLPFAVKIL  406 (597)
Q Consensus       392 I~~~~~GlPLai~~~  406 (597)
                      |+..+||+|..|..+
T Consensus       220 i~~~~gG~P~~l~~~  234 (234)
T PF01637_consen  220 IYSLTGGNPRYLQEL  234 (234)
T ss_dssp             HHHHHTT-HHHHHHH
T ss_pred             HHHHhCCCHHHHhcC
Confidence            999999999988653

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

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.28  E-value=1.2e-10  Score=117.85  Aligned_cols=264  Identities=16%  Similarity=0.144  Sum_probs=139.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+|+|+++.+++|..++.....     ....+..+.|+|++|+|||+||+.+++.  ....+   ..+..+....     
T Consensus         4 ~~~iG~~~~~~~l~~~l~~~~~-----~~~~~~~~ll~Gp~G~GKT~la~~ia~~--~~~~~---~~~~~~~~~~-----   68 (305)
T TIGR00635         4 AEFIGQEKVKEQLQLFIEAAKM-----RQEALDHLLLYGPPGLGKTTLAHIIANE--MGVNL---KITSGPALEK-----   68 (305)
T ss_pred             HHHcCHHHHHHHHHHHHHHHHh-----cCCCCCeEEEECCCCCCHHHHHHHHHHH--hCCCE---EEeccchhcC-----
Confidence            4699999999999998864321     0124567899999999999999999883  32222   1111110000     


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhc-------
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLK-------  318 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~-------  318 (597)
                                  ...+...+..+                      +...+|+||+++... ....+.+...+.       
T Consensus        69 ------------~~~l~~~l~~~----------------------~~~~vl~iDEi~~l~-~~~~e~l~~~~~~~~~~~v  113 (305)
T TIGR00635        69 ------------PGDLAAILTNL----------------------EEGDVLFIDEIHRLS-PAVEELLYPAMEDFRLDIV  113 (305)
T ss_pred             ------------chhHHHHHHhc----------------------ccCCEEEEehHhhhC-HHHHHHhhHHHhhhheeee
Confidence                        11111111111                      123355555554332 111111211111       


Q ss_pred             ------------CCCCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccc
Q 041007          319 ------------SGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREK  384 (597)
Q Consensus       319 ------------~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~  384 (597)
                                  ...+.+-|..||+......          .....+  .+.+.+++.++..+++.+.+...+..    -
T Consensus       114 ~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~----------~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~~----~  179 (305)
T TIGR00635       114 IGKGPSARSVRLDLPPFTLVGATTRAGMLTS----------PLRDRFGIILRLEFYTVEELAEIVSRSAGLLNVE----I  179 (305)
T ss_pred             eccCccccceeecCCCeEEEEecCCccccCH----------HHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCCC----c
Confidence                        1112344455555431100          111112  27899999999999999887533221    1


Q ss_pred             hHHHHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHH
Q 041007          385 FEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFL  464 (597)
Q Consensus       385 ~~~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~  464 (597)
                      ..+.+..|++.|+|.|-.+..++..+        |...............      -......+...|..|+++.+..|.
T Consensus       180 ~~~al~~ia~~~~G~pR~~~~ll~~~--------~~~a~~~~~~~it~~~------v~~~l~~l~~~~~~l~~~~~~~L~  245 (305)
T TIGR00635       180 EPEAALEIARRSRGTPRIANRLLRRV--------RDFAQVRGQKIINRDI------ALKALEMLMIDELGLDEIDRKLLS  245 (305)
T ss_pred             CHHHHHHHHHHhCCCcchHHHHHHHH--------HHHHHHcCCCCcCHHH------HHHHHHHhCCCCCCCCHHHHHHHH
Confidence            24567899999999997665444432        1110000000000000      001112245678889998887776


Q ss_pred             -HhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHH-HHhhCCCccccc
Q 041007          465 -YCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFG-NLSSRSLFQDFQ  519 (597)
Q Consensus       465 -~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~-~Lv~rsli~~~~  519 (597)
                       .+..|+.+ .+..+.+....   |-        ....++..++ .|++++||....
T Consensus       246 al~~~~~~~-~~~~~~ia~~l---g~--------~~~~~~~~~e~~Li~~~li~~~~  290 (305)
T TIGR00635       246 VLIEQFQGG-PVGLKTLAAAL---GE--------DADTIEDVYEPYLLQIGFLQRTP  290 (305)
T ss_pred             HHHHHhCCC-cccHHHHHHHh---CC--------CcchHHHhhhHHHHHcCCcccCC
Confidence             55777654 44444433321   11        2235677788 699999997443

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.28  E-value=2.2e-10  Score=116.72  Aligned_cols=265  Identities=18%  Similarity=0.168  Sum_probs=144.4

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRV  244 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  244 (597)
                      -.+|+|++..++.+..++.....     .+...+.+.|+|++|+|||+||+.+++.  ....+   .++... ....   
T Consensus        24 ~~~~vG~~~~~~~l~~~l~~~~~-----~~~~~~~~ll~GppG~GKT~la~~ia~~--l~~~~---~~~~~~-~~~~---   89 (328)
T PRK00080         24 LDEFIGQEKVKENLKIFIEAAKK-----RGEALDHVLLYGPPGLGKTTLANIIANE--MGVNI---RITSGP-ALEK---   89 (328)
T ss_pred             HHHhcCcHHHHHHHHHHHHHHHh-----cCCCCCcEEEECCCCccHHHHHHHHHHH--hCCCe---EEEecc-cccC---
Confidence            35699999999999888864221     0124568899999999999999999984  33221   111111 0110   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-----
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-----  319 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-----  319 (597)
                                   ...+..++..+                      ++..+|+||+++... ....+.+...+..     
T Consensus        90 -------------~~~l~~~l~~l----------------------~~~~vl~IDEi~~l~-~~~~e~l~~~~e~~~~~~  133 (328)
T PRK00080         90 -------------PGDLAAILTNL----------------------EEGDVLFIDEIHRLS-PVVEEILYPAMEDFRLDI  133 (328)
T ss_pred             -------------hHHHHHHHHhc----------------------ccCCEEEEecHhhcc-hHHHHHHHHHHHhcceee
Confidence                         11111222211                      223466666665432 1111112111110     


Q ss_pred             --------------CCCCcEEEEEccCCCCCCCcccccccccCcccc--ceeecCCCChHHHHHHHHHHhccCCCCCCcc
Q 041007          320 --------------GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM--MEIGLGELSEEECRSLFRQIAFHGRSSDYRE  383 (597)
Q Consensus       320 --------------~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~--~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~  383 (597)
                                    ..+.+-|..|++......          ...+.  ..+.+.+++.++..+++...+...+..    
T Consensus       134 ~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~----------~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~----  199 (328)
T PRK00080        134 MIGKGPAARSIRLDLPPFTLIGATTRAGLLTS----------PLRDRFGIVQRLEFYTVEELEKIVKRSARILGVE----  199 (328)
T ss_pred             eeccCccccceeecCCCceEEeecCCcccCCH----------HHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCC----
Confidence                          112334555555441100          11111  228899999999999999887543222    


Q ss_pred             chHHHHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHH
Q 041007          384 KFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCF  463 (597)
Q Consensus       384 ~~~~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf  463 (597)
                      -..+.+..|++.|+|.|-.+..+...+      ..|......  .......      -......+...+..|++..+..+
T Consensus       200 ~~~~~~~~ia~~~~G~pR~a~~~l~~~------~~~a~~~~~--~~I~~~~------v~~~l~~~~~~~~~l~~~~~~~l  265 (328)
T PRK00080        200 IDEEGALEIARRSRGTPRIANRLLRRV------RDFAQVKGD--GVITKEI------ADKALDMLGVDELGLDEMDRKYL  265 (328)
T ss_pred             cCHHHHHHHHHHcCCCchHHHHHHHHH------HHHHHHcCC--CCCCHHH------HHHHHHHhCCCcCCCCHHHHHHH
Confidence            124578899999999996555444432      112111100  0010000      11122345667788998888877


Q ss_pred             H-HhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHH-HHhhCCCccccc
Q 041007          464 L-YCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFG-NLSSRSLFQDFQ  519 (597)
Q Consensus       464 ~-~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~-~Lv~rsli~~~~  519 (597)
                      . .+..|+.+ .+..+.+....   |        ...+.+++.++ .|++.+||+...
T Consensus       266 ~~~~~~~~~~-~~~~~~~a~~l---g--------~~~~~~~~~~e~~Li~~~li~~~~  311 (328)
T PRK00080        266 RTIIEKFGGG-PVGLDTLAAAL---G--------EERDTIEDVYEPYLIQQGFIQRTP  311 (328)
T ss_pred             HHHHHHcCCC-ceeHHHHHHHH---C--------CCcchHHHHhhHHHHHcCCcccCC
Confidence            6 77778766 46665554332   1        12235566677 999999997543

>COG3899 Predicted ATPase [General function prediction only]

Probab=99.26  E-value=1.1e-10  Score=131.81  Aligned_cols=333  Identities=18%  Similarity=0.199  Sum_probs=189.4

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec---C--CCch
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS---Y--PRDE  241 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~---~--~~~~  241 (597)
                      .++||+.+++.|...+.....       +...++.|.|.+|||||+|+++|..  .+.+.+...+--.+.   .  +...
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~-------g~~~~~lv~G~sGIGKsalv~ev~~--~i~~~~~~~i~~~f~q~~~~ipl~~   71 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSK-------GRGEVVLVAGESGIGKSALVNEVHK--PITQQRGYFIKGKFDQFERNIPLSP   71 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhC-------CCeEEEEEeecCCCcHHHHHHHHHH--HHhccceeeeHhhcccccCCCchHH
Confidence            378999999999999986653       4567999999999999999999988  444432221111111   1  1111


Q ss_pred             hh-hhhh---hhhhcccchHHHHHHHHHHhccCCCCc----------------------h---hh--HHHHHHHHHHHhc
Q 041007          242 IR-VARD---EISVARDRDEIRVAKAILESLKGSVSS----------------------Q---VE--METVLQYINEFVQ  290 (597)
Q Consensus       242 ~~-~~~~---~~~~~~~~~~~~~~~~il~~l~~~~~~----------------------~---~~--~~~~~~~l~~~L~  290 (597)
                      .. .+++   .+..............++..++.....                      .   .+  .......+.....
T Consensus        72 lvq~~r~l~~~ll~~~~~~~~~~~~~il~~~g~~~~~~~~vip~L~~i~g~~~~~~el~~~~~~~r~n~~~~~~i~~~~~  151 (849)
T COG3899          72 LVQAFRDLMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQNRFNLAFLRFIQVFTA  151 (849)
T ss_pred             HHHHHHHHHHHHhhccchHHHHHHHHHHHHhcccchhHHhhhHHHHhhcCCCcchhhcccchhHHHHHHHHHHHHHHHHh
Confidence            11 1111   111222333344444455544432110                      0   00  0113344444444


Q ss_pred             -CceEEEEEecccCCCCcchHHHHHHhhcCCC----CCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHH
Q 041007          291 -GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS----EGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEEC  365 (597)
Q Consensus       291 -~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~----~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es  365 (597)
                       .++.++|+||++|.| ..+.+-+........    ....|..+..........      .........|.|.||+..+.
T Consensus       152 ~~~plVi~leDlhWaD-~~SL~lL~~lm~~~~~~~~~~n~v~~~h~~~~~~~~~------~~~~~~i~~I~L~PL~~~d~  224 (849)
T COG3899         152 EEHPLVIVLEDLHWAD-SASLKLLQLLMDRIAIGAYRDNEVLLLHPLRPTLGEI------LKSATNITTITLAPLSRADT  224 (849)
T ss_pred             ccCCeEEEEecccccC-hhHHHHHHHHHHhcchhhhhccccccCCCccchhhHH------hhcCCceeEEecCcCchhhH
Confidence             459999999999998 555555544433222    011222222221100000      00112223399999999999


Q ss_pred             HHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhhccC------CCHHHHHHHHhhhcccCChhhhhhcC
Q 041007          366 RSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFK------TSIKEWQSVLDSEIWNLDSEICKRAG  439 (597)
Q Consensus       366 ~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~------~~~~~w~~~l~~~~~~~~~~~~~~~~  439 (597)
                      ..+.........     ....+..+.|+++..|+|+.+..+-..+..+      .+...|..-....         ...+
T Consensus       225 ~~lV~~~l~~~~-----~~~~p~~~~i~~kt~GnPfFi~e~lk~l~~~~~i~f~~~~~~w~~~~~~i---------~~~~  290 (849)
T COG3899         225 NQLVAATLGCTK-----LLPAPLLELIFEKTKGNPFFIEEFLKALYEEGLLVFNFDTGAWQCSIASL---------GILA  290 (849)
T ss_pred             HHHHHHHhCCcc-----cccchHHHHHHHHhcCCCccHHHHHHHHHhCCeeEecCCCcceeccHHhc---------CCch
Confidence            999998874322     2235678999999999999999998888653      2334444322211         1111


Q ss_pred             CCCCcccchhccccCCChhHhHHHHHhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCccccc
Q 041007          440 VGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQ  519 (597)
Q Consensus       440 ~~~~~~~~l~~sy~~L~~~~k~cf~~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~  519 (597)
                      ..+++...+..-.+.||...|+.+-..|++...  |+.+.|...|-.          .....+....+.|....++-..+
T Consensus       291 ~~~~vv~~l~~rl~kL~~~t~~Vl~~AA~iG~~--F~l~~La~l~~~----------~~~~~a~~l~~al~e~lI~~~~~  358 (849)
T COG3899         291 TTDAVVEFLAARLQKLPGTTREVLKAAACIGNR--FDLDTLAALAED----------SPALEAAALLDALQEGLILPLSE  358 (849)
T ss_pred             hhHHHHHHHHHHHhcCCHHHHHHHHHHHHhCcc--CCHHHHHHHHhh----------chHHHHHHHHHHhHhhceecccc
Confidence            122344457778999999999999999999765  566666666532          34456666666666655554322


Q ss_pred             ccCCCCeeeE--E-EeChHHHHHHH
Q 041007          520 KSEFDGRIIR--C-QMHPIVHEFAQ  541 (597)
Q Consensus       520 ~~~~~~~~~~--~-~mH~lv~~~a~  541 (597)
                      ....+..+..  | -.|+.|++.|-
T Consensus       359 ~yr~~~~~~~~~Y~F~H~~vqqaaY  383 (849)
T COG3899         359 TYRFGSNVDIATYKFLHDRVQQAAY  383 (849)
T ss_pred             ccccccccchhhHHhhHHHHHHHHh
Confidence            2222111111  2 35777777663

>PF05729 NACHT: NACHT domain

Probab=99.06  E-value=1.5e-09  Score=99.20  Aligned_cols=150  Identities=22%  Similarity=0.284  Sum_probs=85.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhcc----CCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKAN----FDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      +++.|+|.+|+||||+++.++........    +...+|++..........             ..+...+.........
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------------~~l~~~l~~~~~~~~~   67 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNS-------------RSLADLLFDQLPESIA   67 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhcccc-------------chHHHHHHHhhccchh
Confidence            58999999999999999999875332222    345667766554332000             1233333333322211


Q ss_pred             chhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcc------hHHHHHH-hhcC-CCCCcEEEEEccCCCCCCCcccccc
Q 041007          274 SQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPR------YWEQLMY-SLKS-GSEGSRILVTRSGGKNGTNMTEIGL  344 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~------~~~~l~~-~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~  344 (597)
                      ..   ..   .+... ...++++||||+++......      .+..+.. .+.. ..+++++|||+|........     
T Consensus        68 ~~---~~---~~~~~~~~~~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~~~~-----  136 (166)
T PF05729_consen   68 PI---EE---LLQELLEKNKRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQALPPGVKLIITSRPRAFPDLR-----  136 (166)
T ss_pred             hh---HH---HHHHHHHcCCceEEEEechHhcccchhhhHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHHHHH-----
Confidence            11   11   12122 24789999999996544211      1233333 3333 36789999999987210000     


Q ss_pred             cccCccccceeecCCCChHHHHHHHHHHh
Q 041007          345 GEKNGTNMMEIGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       345 ~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~  373 (597)
                        ........+.+.+|++++..+++.+..
T Consensus       137 --~~~~~~~~~~l~~~~~~~~~~~~~~~f  163 (166)
T PF05729_consen  137 --RRLKQAQILELEPFSEEDIKQYLRKYF  163 (166)
T ss_pred             --HhcCCCcEEEECCCCHHHHHHHHHHHh
Confidence              011112238999999999999998765

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.03  E-value=4.5e-08  Score=106.24  Aligned_cols=308  Identities=10%  Similarity=0.069  Sum_probs=161.5

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhh---hccCC--eeEEEEecCCC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV---KANFD--KRIWVSASYPR  239 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~---~~~F~--~~~wv~~~~~~  239 (597)
                      |..+.|||+|+++|...|...-..     .+...++.|+|++|.|||++++.|.+....   +...+  .+++|.+....
T Consensus       754 PD~LPhREeEIeeLasfL~paIkg-----sgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Ls  828 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQ-----SGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVV  828 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhc-----CCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccC
Confidence            567899999999999998754321     123357789999999999999999874321   11222  25667765544


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHHhc---CceEEEEEecccCCCCcchHHHHHH
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEFVQ---GKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~L~---~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                      ..                ..++..|..++....+. ..........+...+.   ....+||||+++..... .-+.|..
T Consensus       829 tp----------------~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK-~QDVLYn  891 (1164)
T PTZ00112        829 HP----------------NAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITK-TQKVLFT  891 (1164)
T ss_pred             CH----------------HHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCcc-HHHHHHH
Confidence            44                66777777777543322 2222334444444432   23468999999755421 1122333


Q ss_pred             hhcC-CCCCcEEEE--EccCCCCCCCcccccccccCccccc---eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHH
Q 041007          316 SLKS-GSEGSRILV--TRSGGKNGTNMTEIGLGEKNGTNMM---EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIG  389 (597)
Q Consensus       316 ~l~~-~~~gs~IIv--TtR~~~~~~~~~~~~~~~~~~~~~~---~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~  389 (597)
                      .+.. ...+++|+|  ++... ..+....-     .+...+   .+...|++.++..+++..++........+..++-+|
T Consensus       892 LFR~~~~s~SKLiLIGISNdl-DLperLdP-----RLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELIA  965 (1164)
T PTZ00112        892 LFDWPTKINSKLVLIAISNTM-DLPERLIP-----RCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLCA  965 (1164)
T ss_pred             HHHHhhccCCeEEEEEecCch-hcchhhhh-----hhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHHH
Confidence            3322 234455444  23211 11100000     111111   177899999999999999885432222223333344


Q ss_pred             HHHHHhcCCchHHHHHHHhhhccCC----CHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHHH
Q 041007          390 RRVVGKCKGLPFAVKILGSLLRFKT----SIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLY  465 (597)
Q Consensus       390 ~~I~~~~~GlPLai~~~~~~l~~~~----~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~~  465 (597)
                      +.++...|-.-.||.++-.+.....    ..++-..+.....                 ...+.-....||.+.|-.|..
T Consensus       966 rkVAq~SGDARKALDILRrAgEikegskVT~eHVrkAleeiE-----------------~srI~e~IktLPlHqKLVLlA 1028 (1164)
T PTZ00112        966 RKVANVSGDIRKALQICRKAFENKRGQKIVPRDITEATNQLF-----------------DSPLTNAINYLPWPFKMFLTC 1028 (1164)
T ss_pred             HhhhhcCCHHHHHHHHHHHHHhhcCCCccCHHHHHHHHHHHH-----------------hhhHHHHHHcCCHHHHHHHHH
Confidence            4444445556777766654442211    2233333322210                 011223446889887776654


Q ss_pred             hhcCCC---CcccChhHHHHHH--HHcCCcccCCCCCHHHHHHHHHHHHhhCCCccc
Q 041007          466 CSIFPK---NYEIEKDRLIKLW--MAQGYLKSQESKDMELVGEEYFGNLSSRSLFQD  517 (597)
Q Consensus       466 ls~Fp~---~~~i~~~~Li~~W--~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~  517 (597)
                      +...-+   ...++...+....  +++..-..-+....-....+|+.+|...|+|..
T Consensus      1029 LIlLlk~tg~~~i~TGEVYerYk~Lce~~Gk~iGv~plTqRV~d~L~eL~~LGIIl~ 1085 (1164)
T PTZ00112       1029 LIVELRMLNDFIIPYKKVLNRYKVLVETSGKYIGMCSNNELFKIMLDKLVKMGILLI 1085 (1164)
T ss_pred             HHHHHhhcCCCceeHHHHHHHHHHHHHhhhhhcCCCCcHHHHHHHHHHHHhcCeEEe
Confidence            433211   2235555544322  222000000111111267889999999998864

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

Probab=98.98  E-value=6.4e-09  Score=102.95  Aligned_cols=177  Identities=17%  Similarity=0.211  Sum_probs=103.3

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      +...+++|.+..+.++++             .+.+....+|||+|+||||||+.+..  .....|.     .++-..+. 
T Consensus        27 vGQ~HLlg~~~~lrr~v~-------------~~~l~SmIl~GPPG~GKTTlA~liA~--~~~~~f~-----~~sAv~~g-   85 (436)
T COG2256          27 VGQEHLLGEGKPLRRAVE-------------AGHLHSMILWGPPGTGKTTLARLIAG--TTNAAFE-----ALSAVTSG-   85 (436)
T ss_pred             cChHhhhCCCchHHHHHh-------------cCCCceeEEECCCCCCHHHHHHHHHH--hhCCceE-----Eecccccc-
Confidence            334455555555554443             34678899999999999999999988  4555442     22222222 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHH-HHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCC
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYI-NEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS  321 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l-~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~  321 (597)
                                     ..                 ++..+.+.- +....+++.+|++|.|+.-+    -.+.-..||...
T Consensus        86 ---------------vk-----------------dlr~i~e~a~~~~~~gr~tiLflDEIHRfn----K~QQD~lLp~vE  129 (436)
T COG2256          86 ---------------VK-----------------DLREIIEEARKNRLLGRRTILFLDEIHRFN----KAQQDALLPHVE  129 (436)
T ss_pred             ---------------HH-----------------HHHHHHHHHHHHHhcCCceEEEEehhhhcC----hhhhhhhhhhhc
Confidence                           22                 222222222 22234889999999997665    223334556667


Q ss_pred             CCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCCCCCC--ccch-HHHHHHHHHhcCC
Q 041007          322 EGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDY--REKF-EPIGRRVVGKCKG  398 (597)
Q Consensus       322 ~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~--~~~~-~~~~~~I~~~~~G  398 (597)
                      +|..|+|-+..+.+.+....-     -..+...+.++||+.++...++.+.+........  ...+ ++..+.|+..++|
T Consensus       130 ~G~iilIGATTENPsF~ln~A-----LlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~G  204 (436)
T COG2256         130 NGTIILIGATTENPSFELNPA-----LLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNG  204 (436)
T ss_pred             CCeEEEEeccCCCCCeeecHH-----HhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCc
Confidence            788888755555333322211     1111222999999999999999984432211111  1112 4466778888888


Q ss_pred             chH
Q 041007          399 LPF  401 (597)
Q Consensus       399 lPL  401 (597)
                      ---
T Consensus       205 D~R  207 (436)
T COG2256         205 DAR  207 (436)
T ss_pred             hHH
Confidence            653

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

Probab=98.88  E-value=6e-09  Score=97.08  Aligned_cols=47  Identities=30%  Similarity=0.533  Sum_probs=32.6

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|+||++++++|...|....       ....+.+.|+|++|+|||+|+++++..
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~-------~~~~~~~ll~G~~G~GKT~ll~~~~~~   47 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQ-------SGSPRNLLLTGESGSGKTSLLRALLDR   47 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTS-------S-----EEE-B-TTSSHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHH-------cCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            48999999999999996222       245799999999999999999999884

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=98.84  E-value=1.2e-07  Score=102.46  Aligned_cols=197  Identities=12%  Similarity=0.153  Sum_probs=116.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .++||.+..++.|..++....         -...+.++|+.|+||||+|+.+.+.......+..   ..+..        
T Consensus        16 dEVIGQe~Vv~~L~~aL~~gR---------L~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~---~PCG~--------   75 (830)
T PRK07003         16 ASLVGQEHVVRALTHALDGGR---------LHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTS---QPCGV--------   75 (830)
T ss_pred             HHHcCcHHHHHHHHHHHhcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCC---CCCcc--------
Confidence            468999999999999987432         2456689999999999999988773211111100   00000        


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-----ccCCCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-----LKGSVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-----l~~~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -.....|...     +..........+++.+.+...    ..++.-++|||+++..+ ...++.++..
T Consensus        76 ------------C~sCr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT-~~A~NALLKt  142 (830)
T PRK07003         76 ------------CRACREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLT-NHAFNAMLKT  142 (830)
T ss_pred             ------------cHHHHHHhcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCC-HHHHHHHHHH
Confidence                        0000111000     000000011122222222211    12455689999998886 5678888888


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +..-..+.++|+||.+......         -+...|. +.+++++.++..+.+.+.+...+...    ..+....|++.
T Consensus       143 LEEPP~~v~FILaTtd~~KIp~---------TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~EgI~i----d~eAL~lIA~~  209 (830)
T PRK07003        143 LEEPPPHVKFILATTDPQKIPV---------TVLSRCLQFNLKQMPAGHIVSHLERILGEERIAF----EPQALRLLARA  209 (830)
T ss_pred             HHhcCCCeEEEEEECChhhccc---------hhhhheEEEecCCcCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            8777778888888877632111         1222222 99999999999999988775432211    24567889999


Q ss_pred             cCCch-HHHHHHHh
Q 041007          396 CKGLP-FAVKILGS  408 (597)
Q Consensus       396 ~~GlP-Lai~~~~~  408 (597)
                      ++|.. -++.++-.
T Consensus       210 A~GsmRdALsLLdQ  223 (830)
T PRK07003        210 AQGSMRDALSLTDQ  223 (830)
T ss_pred             cCCCHHHHHHHHHH
Confidence            98855 56665443

>PRK13342 recombination factor protein RarA; Reviewed

Probab=98.82  E-value=8.8e-08  Score=100.71  Aligned_cols=179  Identities=17%  Similarity=0.181  Sum_probs=102.6

Q ss_pred             CccccchhhHHH---HHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQK---ILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~---l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      .+|||++..+..   |..++..          .....+.|+|++|+||||||+.+++.  ....|     +.++..... 
T Consensus        12 ~d~vGq~~~v~~~~~L~~~i~~----------~~~~~ilL~GppGtGKTtLA~~ia~~--~~~~~-----~~l~a~~~~-   73 (413)
T PRK13342         12 DEVVGQEHLLGPGKPLRRMIEA----------GRLSSMILWGPPGTGKTTLARIIAGA--TDAPF-----EALSAVTSG-   73 (413)
T ss_pred             HHhcCcHHHhCcchHHHHHHHc----------CCCceEEEECCCCCCHHHHHHHHHHH--hCCCE-----EEEeccccc-
Confidence            468888877665   7777753          24567889999999999999999883  32222     222211111 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHhhcCCC
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS  321 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~  321 (597)
                                     ....+.++.                 ..... ..+++.+|+||+++... ....+.+...+.   
T Consensus        74 ---------------~~~ir~ii~-----------------~~~~~~~~g~~~vL~IDEi~~l~-~~~q~~LL~~le---  117 (413)
T PRK13342         74 ---------------VKDLREVIE-----------------EARQRRSAGRRTILFIDEIHRFN-KAQQDALLPHVE---  117 (413)
T ss_pred             ---------------HHHHHHHHH-----------------HHHHhhhcCCceEEEEechhhhC-HHHHHHHHHHhh---
Confidence                           111112221                 11111 13578899999998765 334455554443   


Q ss_pred             CCcEEEEE--ccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCC
Q 041007          322 EGSRILVT--RSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKG  398 (597)
Q Consensus       322 ~gs~IIvT--tR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~G  398 (597)
                      .+..+++.  |.+..  .....      .+... ..+.+.+++.++...++.+.+....... ..-..+....|++.|+|
T Consensus       118 ~~~iilI~att~n~~--~~l~~------aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~~~-i~i~~~al~~l~~~s~G  188 (413)
T PRK13342        118 DGTITLIGATTENPS--FEVNP------ALLSRAQVFELKPLSEEDIEQLLKRALEDKERGL-VELDDEALDALARLANG  188 (413)
T ss_pred             cCcEEEEEeCCCChh--hhccH------HHhccceeeEeCCCCHHHHHHHHHHHHHHhhcCC-CCCCHHHHHHHHHhCCC
Confidence            24444443  33321  00000      11111 2289999999999999998653211100 01224567889999999


Q ss_pred             chHHHHHHH
Q 041007          399 LPFAVKILG  407 (597)
Q Consensus       399 lPLai~~~~  407 (597)
                      .|..+.-+.
T Consensus       189 d~R~aln~L  197 (413)
T PRK13342        189 DARRALNLL  197 (413)
T ss_pred             CHHHHHHHH
Confidence            997664443

>PRK06893 DNA replication initiation factor; Validated

Probab=98.81  E-value=3.7e-08  Score=94.81  Aligned_cols=162  Identities=17%  Similarity=0.207  Sum_probs=95.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      .+.+.|+|++|+|||+|++.+++.  .......+.|+++....                   .....             
T Consensus        39 ~~~l~l~G~~G~GKThL~~ai~~~--~~~~~~~~~y~~~~~~~-------------------~~~~~-------------   84 (229)
T PRK06893         39 QPFFYIWGGKSSGKSHLLKAVSNH--YLLNQRTAIYIPLSKSQ-------------------YFSPA-------------   84 (229)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEeeHHHhh-------------------hhhHH-------------
Confidence            467899999999999999999984  43333455666643110                   00001             


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHH-HHHhhcCC-CCCcEEE-EEccCCCCCCCcccccccccCcccc-
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQ-LMYSLKSG-SEGSRIL-VTRSGGKNGTNMTEIGLGEKNGTNM-  352 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~-l~~~l~~~-~~gs~II-vTtR~~~~~~~~~~~~~~~~~~~~~-  352 (597)
                              +.+.+. +.-+|||||+|.......|+. +...+... ..|..+| +|+...+.......-     .+... 
T Consensus        85 --------~~~~~~-~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~-----~L~sRl  150 (229)
T PRK06893         85 --------VLENLE-QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPHALSIKLP-----DLASRL  150 (229)
T ss_pred             --------HHhhcc-cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChHHccccch-----hHHHHH
Confidence                    111111 235999999987543446664 33334332 3455554 455443221111100     22221 


Q ss_pred             ---ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhh
Q 041007          353 ---MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLL  410 (597)
Q Consensus       353 ---~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l  410 (597)
                         ..+++.++++++.++++.+.+...+.. .   -.+...-|++++.|..-.+..+-..+
T Consensus       151 ~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~-l---~~~v~~~L~~~~~~d~r~l~~~l~~l  207 (229)
T PRK06893        151 TWGEIYQLNDLTDEQKIIVLQRNAYQRGIE-L---SDEVANFLLKRLDRDMHTLFDALDLL  207 (229)
T ss_pred             hcCCeeeCCCCCHHHHHHHHHHHHHHcCCC-C---CHHHHHHHHHhccCCHHHHHHHHHHH
Confidence               128999999999999999988643321 1   15677889999998777665554433

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

Probab=98.81  E-value=1.3e-08  Score=88.97  Aligned_cols=117  Identities=21%  Similarity=0.303  Sum_probs=79.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhcc-----CCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKAN-----FDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKG  270 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-----F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~  270 (597)
                      +.+++.|+|++|+|||+++..+.+.  ....     -..++|+.+....+.                ..+...++..++.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~~~i~~~l~~   64 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQ--LNAEAEIKNHPDVIYVNCPSSRTP----------------RDFAQEILEALGL   64 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHH--HHHHHHHCCCEEEEEEEHHHHSSH----------------HHHHHHHHHHHT-
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHH--hHHhhhccCCCcEEEEEeCCCCCH----------------HHHHHHHHHHhCc
Confidence            3578999999999999999999884  2221     345678888766665                8999999999988


Q ss_pred             CCCchhhHHHHHHHHHHHhcCc-eEEEEEecccCC-CCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          271 SVSSQVEMETVLQYINEFVQGK-KVLLVLDDLWWN-AYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       271 ~~~~~~~~~~~~~~l~~~L~~k-r~LLVLDdv~~~-~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      ......+...+.+.+.+.+... ..+||||+++.. . ...++.+.....  ..+..+|+..+..
T Consensus        65 ~~~~~~~~~~l~~~~~~~l~~~~~~~lviDe~~~l~~-~~~l~~l~~l~~--~~~~~vvl~G~~~  126 (131)
T PF13401_consen   65 PLKSRQTSDELRSLLIDALDRRRVVLLVIDEADHLFS-DEFLEFLRSLLN--ESNIKVVLVGTPE  126 (131)
T ss_dssp             SSSSTS-HHHHHHHHHHHHHHCTEEEEEEETTHHHHT-HHHHHHHHHHTC--SCBEEEEEEESST
T ss_pred             cccccCCHHHHHHHHHHHHHhcCCeEEEEeChHhcCC-HHHHHHHHHHHh--CCCCeEEEEEChh
Confidence            7666556666777777777754 459999999765 3 344444544333  6677777776644

>PF13173 AAA_14: AAA domain

Probab=98.79  E-value=2e-08  Score=87.36  Aligned_cols=125  Identities=23%  Similarity=0.341  Sum_probs=78.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      .+++.|.|+.|+|||||+++++.+..   ....++++++......                ..                .
T Consensus         2 ~~~~~l~G~R~vGKTtll~~~~~~~~---~~~~~~yi~~~~~~~~----------------~~----------------~   46 (128)
T PF13173_consen    2 RKIIILTGPRGVGKTTLLKQLAKDLL---PPENILYINFDDPRDR----------------RL----------------A   46 (128)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhc---ccccceeeccCCHHHH----------------HH----------------h
Confidence            36899999999999999999987422   3344666665432211                00                0


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-ee
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EI  355 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~  355 (597)
                      +.+ +.+.+.+....++.+|+||+++...   .|......+....++.+|++|+.+........    . ...++.. .+
T Consensus        47 ~~~-~~~~~~~~~~~~~~~i~iDEiq~~~---~~~~~lk~l~d~~~~~~ii~tgS~~~~l~~~~----~-~~l~gr~~~~  117 (128)
T PF13173_consen   47 DPD-LLEYFLELIKPGKKYIFIDEIQYLP---DWEDALKFLVDNGPNIKIILTGSSSSLLSKDI----A-ESLAGRVIEI  117 (128)
T ss_pred             hhh-hHHHHHHhhccCCcEEEEehhhhhc---cHHHHHHHHHHhccCceEEEEccchHHHhhcc----c-ccCCCeEEEE
Confidence            000 2233333334478899999997766   78887777776667789999998773221100    0 0122222 28


Q ss_pred             ecCCCChHHH
Q 041007          356 GLGELSEEEC  365 (597)
Q Consensus       356 ~l~~Ls~~es  365 (597)
                      ++.||+..|.
T Consensus       118 ~l~Plsf~E~  127 (128)
T PF13173_consen  118 ELYPLSFREF  127 (128)
T ss_pred             EECCCCHHHh
Confidence            9999998773

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.76  E-value=8.5e-07  Score=94.81  Aligned_cols=196  Identities=11%  Similarity=0.113  Sum_probs=111.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc--CCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN--FDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~--F~~~~wv~~~~~~~~~~  243 (597)
                      .++||.+.-++.|..++....         -...+.++|+.|+||||+|+.+.+...-...  -.....-.+..      
T Consensus        16 ddVIGQe~vv~~L~~al~~gR---------LpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~------   80 (700)
T PRK12323         16 TTLVGQEHVVRALTHALEQQR---------LHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQ------   80 (700)
T ss_pred             HHHcCcHHHHHHHHHHHHhCC---------CceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcc------
Confidence            468999999999999998433         2456789999999999999999773111000  00000000000      


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHh-----ccCCCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHH
Q 041007          244 VARDEISVARDRDEIRVAKAILES-----LKGSVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~-----l~~~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                                    -.....|...     +..........+++.+.+...    ..++.-++|||+++..+ ...++.++
T Consensus        81 --------------C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls-~~AaNALL  145 (700)
T PRK12323         81 --------------CRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLT-NHAFNAML  145 (700)
T ss_pred             --------------cHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcC-HHHHHHHH
Confidence                          0000111000     000000111122222222221    13566799999998876 66778888


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      ..|..-..++++|++|.+......         -+...|. +.+.+++.++..+.+.+.+...+...    ..+..+.|+
T Consensus       146 KTLEEPP~~v~FILaTtep~kLlp---------TIrSRCq~f~f~~ls~eei~~~L~~Il~~Egi~~----d~eAL~~IA  212 (700)
T PRK12323        146 KTLEEPPEHVKFILATTDPQKIPV---------TVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAH----EVNALRLLA  212 (700)
T ss_pred             HhhccCCCCceEEEEeCChHhhhh---------HHHHHHHhcccCCCChHHHHHHHHHHHHHcCCCC----CHHHHHHHH
Confidence            877766667777766665421110         1112222 99999999999999887764322211    134568899


Q ss_pred             HhcCCchHHHH
Q 041007          394 GKCKGLPFAVK  404 (597)
Q Consensus       394 ~~~~GlPLai~  404 (597)
                      +.++|.|.-..
T Consensus       213 ~~A~Gs~RdAL  223 (700)
T PRK12323        213 QAAQGSMRDAL  223 (700)
T ss_pred             HHcCCCHHHHH
Confidence            99999886443

>COG3903 Predicted ATPase [General function prediction only]

Probab=98.76  E-value=1.7e-08  Score=100.71  Aligned_cols=299  Identities=18%  Similarity=0.121  Sum_probs=181.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeE-EEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRI-WVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~-wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ..+.+.++|+|||||||++-++.+   ++..|..-. ++.+....+.                ..+.-.....++....+
T Consensus        13 ~~RlvtL~g~ggvgkttl~~~~a~---~~~~~~~~v~~vdl~pitD~----------------~~v~~~~ag~~gl~~~~   73 (414)
T COG3903          13 ALRLVTLTGAGGVGKTTLALQAAH---AASEYADGVAFVDLAPITDP----------------ALVFPTLAGALGLHVQP   73 (414)
T ss_pred             hhheeeeeccCccceehhhhhhHh---HhhhcccceeeeeccccCch----------------hHhHHHHHhhccccccc
Confidence            468999999999999999999988   566776544 4544433333                33333333334443322


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME  354 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~  354 (597)
                      .   +.....+.....+++.++|+||....  .+.-..+...+..+...-.|+.|+|...             .+.....
T Consensus        74 g---~~~~~~~~~~~~~rr~llvldncehl--~~~~a~~i~all~~~~~~~~~atsre~~-------------l~~ge~~  135 (414)
T COG3903          74 G---DSAVDTLVRRIGDRRALLVLDNCEHL--LDACAALIVALLGACPRLAILATSREAI-------------LVAGEVH  135 (414)
T ss_pred             c---hHHHHHHHHHHhhhhHHHHhcCcHHH--HHHHHHHHHHHHccchhhhhHHHhHhhh-------------ccccccc
Confidence            1   12233445556688999999998322  1233335555666777778999999873             3334444


Q ss_pred             eecCCCChH-HHHHHHHHHhccCCCC-CCccchHHHHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCCh
Q 041007          355 IGLGELSEE-ECRSLFRQIAFHGRSS-DYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDS  432 (597)
Q Consensus       355 ~~l~~Ls~~-es~~Lf~~~~~~~~~~-~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~  432 (597)
                      ..+.+|+.. ++.++|...+...... .........+.+|+++..|.|++|..+++..+.- .+.+....|+.....+..
T Consensus       136 ~~~~~L~~~d~a~~lf~~ra~~~~~~f~l~~~~~a~v~~icr~ldg~~laielaaarv~sl-~~~~i~~~L~drf~ll~~  214 (414)
T COG3903         136 RRVPSLSLFDEAIELFVCRAVLVALSFWLTDDNAAAVAEICRRLDGIPLAIELAAARVRSL-SPDEIAAGLRDRFRLLTG  214 (414)
T ss_pred             ccCCccccCCchhHHHHHHHHHhccceeecCCchHHHHHHHHHhhcchHHHHHHHHHHHhc-CHHHHHHHHhhHHHHHhc
Confidence            677777765 7888888776432221 2223346678999999999999999999887643 233333333221111110


Q ss_pred             hhhhhcCCCCCcccchhccccCCChhHhHHHHHhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhC
Q 041007          433 EICKRAGVGYECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSR  512 (597)
Q Consensus       433 ~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~r  512 (597)
                      .......-.......+.+||.-|..-.+-.|..++.|...|...    ...|.+-|-..    ..+.-..-.-+..|+++
T Consensus       215 ~~r~a~~~~qtl~asl~ws~~lLtgwe~~~~~rLa~~~g~f~~~----l~~~~a~g~~~----~~~~y~~~~a~~ll~~k  286 (414)
T COG3903         215 GARLAVLRQQTLRASLDWSYALLTGWERALFGRLAVFVGGFDLG----LALAVAAGADV----DVPRYLVLLALTLLVDK  286 (414)
T ss_pred             ccccchhHHHhccchhhhhhHhhhhHHHHHhcchhhhhhhhccc----HHHHHhcCCcc----ccchHHHHHHHHHHhhc
Confidence            00000011345678899999999999999999999998886544    34455544311    11222344556778899


Q ss_pred             CCcccccccCCCCeeeEEEeChHHHHHHHHhh
Q 041007          513 SLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLS  544 (597)
Q Consensus       513 sli~~~~~~~~~~~~~~~~mH~lv~~~a~~~~  544 (597)
                      |++........    ..|+.-+-++.|+..+.
T Consensus       287 slv~a~~~~~~----a~~Rl~eT~r~YalaeL  314 (414)
T COG3903         287 SLVVALDLLGR----ARYRLLETGRRYALAEL  314 (414)
T ss_pred             cchhhhhhhhH----HHHHHHHHHHHHHHHHH
Confidence            98864433221    23666666666665543

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

Probab=98.76  E-value=3e-07  Score=93.97  Aligned_cols=212  Identities=19%  Similarity=0.202  Sum_probs=132.6

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCC--eeEEEEecCCCchh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFD--KRIWVSASYPRDEI  242 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~  242 (597)
                      |..+.+|+++++++...|...-.      +..+..+.|+|++|+|||+.++.+++  +++....  ..++|++...... 
T Consensus        16 P~~l~~Re~ei~~l~~~l~~~~~------~~~p~n~~iyG~~GTGKT~~~~~v~~--~l~~~~~~~~~~yINc~~~~t~-   86 (366)
T COG1474          16 PEELPHREEEINQLASFLAPALR------GERPSNIIIYGPTGTGKTATVKFVME--ELEESSANVEVVYINCLELRTP-   86 (366)
T ss_pred             cccccccHHHHHHHHHHHHHHhc------CCCCccEEEECCCCCCHhHHHHHHHH--HHHhhhccCceEEEeeeeCCCH-
Confidence            44588999999999998875544      22344599999999999999999999  4444322  2688888877777 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhc--CceEEEEEecccCCCCcchHHHHHHhhcCC
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAYPRYWEQLMYSLKSG  320 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~  320 (597)
                                     .+++..|+..++..........+....+.+.+.  ++.+++|||++........ +.+...+...
T Consensus        87 ---------------~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~-~~LY~L~r~~  150 (366)
T COG1474          87 ---------------YQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDG-EVLYSLLRAP  150 (366)
T ss_pred             ---------------HHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccc-hHHHHHHhhc
Confidence                           899999999987554444555666666776665  5789999999976653333 3444444332


Q ss_pred             CC-CcEEEEE-ccCCCCCCCcccccccccCccccc---eeecCCCChHHHHHHHHHHhccCC-CCCCccchHHHHHHHHH
Q 041007          321 SE-GSRILVT-RSGGKNGTNMTEIGLGEKNGTNMM---EIGLGELSEEECRSLFRQIAFHGR-SSDYREKFEPIGRRVVG  394 (597)
Q Consensus       321 ~~-gs~IIvT-tR~~~~~~~~~~~~~~~~~~~~~~---~~~l~~Ls~~es~~Lf~~~~~~~~-~~~~~~~~~~~~~~I~~  394 (597)
                      .. .++|++- .-+.......     ....+....   .+...|-+.+|-.+.+..++-.+- .....+..-+.+..++.
T Consensus       151 ~~~~~~v~vi~i~n~~~~~~~-----ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a  225 (366)
T COG1474         151 GENKVKVSIIAVSNDDKFLDY-----LDPRVKSSLGPSEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVA  225 (366)
T ss_pred             cccceeEEEEEEeccHHHHHH-----hhhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHH
Confidence            22 3444332 2222100000     000111111   278999999999999998874322 22333444455555555


Q ss_pred             hcC-CchHHHHHH
Q 041007          395 KCK-GLPFAVKIL  406 (597)
Q Consensus       395 ~~~-GlPLai~~~  406 (597)
                      .-+ ---.||..+
T Consensus       226 ~~~GDAR~aidil  238 (366)
T COG1474         226 AESGDARKAIDIL  238 (366)
T ss_pred             HcCccHHHHHHHH
Confidence            555 455565544

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=98.73  E-value=2.5e-07  Score=89.18  Aligned_cols=178  Identities=16%  Similarity=0.130  Sum_probs=103.2

Q ss_pred             chhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhh
Q 041007          171 RNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEIS  250 (597)
Q Consensus       171 R~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~  250 (597)
                      .+..++++..++..          .....+.|+|++|+|||+||+.+++.  ........++++++.....         
T Consensus        22 ~~~~~~~l~~~~~~----------~~~~~lll~G~~G~GKT~la~~~~~~--~~~~~~~~~~i~~~~~~~~---------   80 (226)
T TIGR03420        22 NAELLAALRQLAAG----------KGDRFLYLWGESGSGKSHLLQAACAA--AEERGKSAIYLPLAELAQA---------   80 (226)
T ss_pred             cHHHHHHHHHHHhc----------CCCCeEEEECCCCCCHHHHHHHHHHH--HHhcCCcEEEEeHHHHHHh---------
Confidence            45567777777642          23578999999999999999999984  3333334556654321110         


Q ss_pred             hcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchH-HHHHHhhcC-CCCCcEEEE
Q 041007          251 VARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYW-EQLMYSLKS-GSEGSRILV  328 (597)
Q Consensus       251 ~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~-~~l~~~l~~-~~~gs~IIv  328 (597)
                                   .              ..    +...+.+ .-+|||||++.......| +.+...+.. ...+..+|+
T Consensus        81 -------------~--------------~~----~~~~~~~-~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIi  128 (226)
T TIGR03420        81 -------------D--------------PE----VLEGLEQ-ADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLI  128 (226)
T ss_pred             -------------H--------------HH----HHhhccc-CCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEE
Confidence                         0              00    1111222 248999999876533233 334444332 223457888


Q ss_pred             EccCCCCCCCcccccccccCccc----cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHH
Q 041007          329 TRSGGKNGTNMTEIGLGEKNGTN----MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       329 TtR~~~~~~~~~~~~~~~~~~~~----~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~  404 (597)
                      |++.........     ......    ...+++.|++.++...++...+...+. .   --.+....|++.+.|+|.-+.
T Consensus       129 ts~~~~~~~~~~-----~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~-~---~~~~~l~~L~~~~~gn~r~L~  199 (226)
T TIGR03420       129 AGRAAPAQLPLR-----LPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAARRGL-Q---LPDEVADYLLRHGSRDMGSLM  199 (226)
T ss_pred             ECCCChHHCCcc-----cHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHHHcCC-C---CCHHHHHHHHHhccCCHHHHH
Confidence            888652111000     001111    123899999999999998876532221 1   124566788888999998887


Q ss_pred             HHHhhh
Q 041007          405 ILGSLL  410 (597)
Q Consensus       405 ~~~~~l  410 (597)
                      -+...+
T Consensus       200 ~~l~~~  205 (226)
T TIGR03420       200 ALLDAL  205 (226)
T ss_pred             HHHHHH
Confidence            664443

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.71  E-value=7e-07  Score=91.76  Aligned_cols=204  Identities=14%  Similarity=0.087  Sum_probs=109.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CC-eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN-FD-KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~-~~~wv~~~~~~~~~~  243 (597)
                      ..++|++..++.|..++...          ..+.+.|+|++|+||||+|+.+++.  ...+ +. ..+.++++.......
T Consensus        15 ~~~~g~~~~~~~L~~~~~~~----------~~~~lll~Gp~GtGKT~la~~~~~~--l~~~~~~~~~~~i~~~~~~~~~~   82 (337)
T PRK12402         15 EDILGQDEVVERLSRAVDSP----------NLPHLLVQGPPGSGKTAAVRALARE--LYGDPWENNFTEFNVADFFDQGK   82 (337)
T ss_pred             HHhcCCHHHHHHHHHHHhCC----------CCceEEEECCCCCCHHHHHHHHHHH--hcCcccccceEEechhhhhhcch
Confidence            56889999999999988732          3456889999999999999999873  3222 21 233444332111000


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCC-CCchhhHHHHHHHHHHHh--cCceEEEEEecccCCCCcchHHHHHHhhcCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGS-VSSQVEMETVLQYINEFV--QGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG  320 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~-~~~~~~~~~~~~~l~~~L--~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~  320 (597)
                      .   ...  .+   .... .+....... .........+........  ...+-+|||||++... ......+...+...
T Consensus        83 ~---~~~--~~---~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~-~~~~~~L~~~le~~  152 (337)
T PRK12402         83 K---YLV--ED---PRFA-HFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALR-EDAQQALRRIMEQY  152 (337)
T ss_pred             h---hhh--cC---cchh-hhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCC-HHHHHHHHHHHHhc
Confidence            0   000  00   0000 000000000 000111111222222211  1344589999997654 33445566555555


Q ss_pred             CCCcEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCc
Q 041007          321 SEGSRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGL  399 (597)
Q Consensus       321 ~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~Gl  399 (597)
                      ...+++|+|+........         .+.. ...+.+.|++.++...++...+...+..    -..+....|++.++|.
T Consensus       153 ~~~~~~Il~~~~~~~~~~---------~L~sr~~~v~~~~~~~~~~~~~l~~~~~~~~~~----~~~~al~~l~~~~~gd  219 (337)
T PRK12402        153 SRTCRFIIATRQPSKLIP---------PIRSRCLPLFFRAPTDDELVDVLESIAEAEGVD----YDDDGLELIAYYAGGD  219 (337)
T ss_pred             cCCCeEEEEeCChhhCch---------hhcCCceEEEecCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHcCCC
Confidence            556778887754421110         1111 1238899999999999998876433222    1245678899999987


Q ss_pred             hHHHH
Q 041007          400 PFAVK  404 (597)
Q Consensus       400 PLai~  404 (597)
                      +-.+.
T Consensus       220 lr~l~  224 (337)
T PRK12402        220 LRKAI  224 (337)
T ss_pred             HHHHH
Confidence            65543

>PRK04195 replication factor C large subunit; Provisional

Probab=98.70  E-value=1.2e-06  Score=93.97  Aligned_cols=184  Identities=15%  Similarity=0.159  Sum_probs=108.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+..+++|..|+.....      +...+.+.|+|++|+||||+|+.+++..    .|+. +-++++....     
T Consensus        14 ~dlvg~~~~~~~l~~~l~~~~~------g~~~~~lLL~GppG~GKTtla~ala~el----~~~~-ielnasd~r~-----   77 (482)
T PRK04195         14 SDVVGNEKAKEQLREWIESWLK------GKPKKALLLYGPPGVGKTSLAHALANDY----GWEV-IELNASDQRT-----   77 (482)
T ss_pred             HHhcCCHHHHHHHHHHHHHHhc------CCCCCeEEEECCCCCCHHHHHHHHHHHc----CCCE-EEEccccccc-----
Confidence            5689999999999999975432      1236889999999999999999998842    1322 2233332111     


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC---cchHHHHHHhhcCCCC
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY---PRYWEQLMYSLKSGSE  322 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~---~~~~~~l~~~l~~~~~  322 (597)
                                  ......++.......              .....++-+||||+++....   ...+..+...+..  .
T Consensus        78 ------------~~~i~~~i~~~~~~~--------------sl~~~~~kvIiIDEaD~L~~~~d~~~~~aL~~~l~~--~  129 (482)
T PRK04195         78 ------------ADVIERVAGEAATSG--------------SLFGARRKLILLDEVDGIHGNEDRGGARAILELIKK--A  129 (482)
T ss_pred             ------------HHHHHHHHHHhhccC--------------cccCCCCeEEEEecCcccccccchhHHHHHHHHHHc--C
Confidence                        122222222211100              00113678999999976542   1234555555542  3


Q ss_pred             CcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchH
Q 041007          323 GSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       323 gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPL  401 (597)
                      +..||+|+.+......        ..+... ..+.+.+++.++....+...+...+...    ..+....|++.++|..-
T Consensus       130 ~~~iIli~n~~~~~~~--------k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~~egi~i----~~eaL~~Ia~~s~GDlR  197 (482)
T PRK04195        130 KQPIILTANDPYDPSL--------RELRNACLMIEFKRLSTRSIVPVLKRICRKEGIEC----DDEALKEIAERSGGDLR  197 (482)
T ss_pred             CCCEEEeccCccccch--------hhHhccceEEEecCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCCHH
Confidence            3456666644311100        011111 2289999999999998888775433221    14567899999999665


Q ss_pred             HHHH
Q 041007          402 AVKI  405 (597)
Q Consensus       402 ai~~  405 (597)
                      .+..
T Consensus       198 ~ain  201 (482)
T PRK04195        198 SAIN  201 (482)
T ss_pred             HHHH
Confidence            5543

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.68  E-value=1.5e-07  Score=100.30  Aligned_cols=198  Identities=14%  Similarity=0.100  Sum_probs=113.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-.+.|..++....         -...+.++|++|+||||+|+.+++.....+.+...+|.|.+...-.    
T Consensus        14 ~dvvGq~~v~~~L~~~i~~~~---------l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~----   80 (504)
T PRK14963         14 DEVVGQEHVKEVLLAALRQGR---------LGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVR----   80 (504)
T ss_pred             HHhcChHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHh----
Confidence            458999999999988887432         2346799999999999999999874322222333344432210000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCC-CCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGS-VSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~-~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                           ...+.        -+..+... .....+..++...+... ..+++-++|||+++... ...++.+...+......
T Consensus        81 -----~~~h~--------dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls-~~a~naLLk~LEep~~~  146 (504)
T PRK14963         81 -----RGAHP--------DVLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMS-KSAFNALLKTLEEPPEH  146 (504)
T ss_pred             -----cCCCC--------ceEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccC-HHHHHHHHHHHHhCCCC
Confidence                 00000        00000000 01111222222222211 22456799999997665 55677787777766566


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                      +.+|+++........         .+...+ .+++.+++.++....+.+.+...+...    ..+.+..|++.++|.+--
T Consensus       147 t~~Il~t~~~~kl~~---------~I~SRc~~~~f~~ls~~el~~~L~~i~~~egi~i----~~~Al~~ia~~s~GdlR~  213 (504)
T PRK14963        147 VIFILATTEPEKMPP---------TILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREA----EPEALQLVARLADGAMRD  213 (504)
T ss_pred             EEEEEEcCChhhCCh---------HHhcceEEEEecCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCCHHH
Confidence            666666643311000         111112 299999999999999998775333211    245678899999998854


Q ss_pred             H
Q 041007          403 V  403 (597)
Q Consensus       403 i  403 (597)
                      +
T Consensus       214 a  214 (504)
T PRK14963        214 A  214 (504)
T ss_pred             H
Confidence            4

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.65  E-value=9.5e-07  Score=97.55  Aligned_cols=194  Identities=13%  Similarity=0.160  Sum_probs=114.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCe-eEEEEecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDK-RIWVSASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~  244 (597)
                      .++||.+.-++.|..++....         -...+.++|+.|+||||+|+.+++...-...... -+..|          
T Consensus        16 ddIIGQe~Iv~~LknaI~~~r---------l~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C----------   76 (944)
T PRK14949         16 EQMVGQSHVLHALTNALTQQR---------LHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVC----------   76 (944)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC---------CCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCc----------
Confidence            468999999999999887432         2345689999999999999999884211111000 00000          


Q ss_pred             hhhhhhhcccchHHHHHHHHHH-------hccCC-CCchhhHHHHHHHHHH-HhcCceEEEEEecccCCCCcchHHHHHH
Q 041007          245 ARDEISVARDRDEIRVAKAILE-------SLKGS-VSSQVEMETVLQYINE-FVQGKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~-------~l~~~-~~~~~~~~~~~~~l~~-~L~~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                                    .....+..       .+... .....+...+...+.. -..++.-++|||+++... ....+.++.
T Consensus        77 --------------~sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT-~eAqNALLK  141 (944)
T PRK14949         77 --------------SSCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLS-RSSFNALLK  141 (944)
T ss_pred             --------------hHHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcC-HHHHHHHHH
Confidence                          00000000       00000 0111122222222221 123667799999998886 667788888


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCcc-ccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGT-NMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVG  394 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~-~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~  394 (597)
                      .+.......++|++|.+......         -+. +...+.+.+|+.++....+.+.+...+.    ....+.+..|++
T Consensus       142 tLEEPP~~vrFILaTTe~~kLl~---------TIlSRCq~f~fkpLs~eEI~~~L~~il~~EgI----~~edeAL~lIA~  208 (944)
T PRK14949        142 TLEEPPEHVKFLLATTDPQKLPV---------TVLSRCLQFNLKSLTQDEIGTQLNHILTQEQL----PFEAEALTLLAK  208 (944)
T ss_pred             HHhccCCCeEEEEECCCchhchH---------HHHHhheEEeCCCCCHHHHHHHHHHHHHHcCC----CCCHHHHHHHHH
Confidence            88776777788777665521110         111 1223999999999999999887643221    112456788999


Q ss_pred             hcCCchH-HHHHH
Q 041007          395 KCKGLPF-AVKIL  406 (597)
Q Consensus       395 ~~~GlPL-ai~~~  406 (597)
                      .++|.|- |+.++
T Consensus       209 ~S~Gd~R~ALnLL  221 (944)
T PRK14949        209 AANGSMRDALSLT  221 (944)
T ss_pred             HcCCCHHHHHHHH
Confidence            9999885 44443

>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=98.65  E-value=3.6e-07  Score=81.18  Aligned_cols=124  Identities=18%  Similarity=0.177  Sum_probs=72.5

Q ss_pred             ccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhh
Q 041007          169 HGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDE  248 (597)
Q Consensus       169 vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~  248 (597)
                      +|++..+..+...+...          ..+.+.|+|++|+|||++++.+++.  ....-..++++........       
T Consensus         1 ~~~~~~~~~i~~~~~~~----------~~~~v~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~~~~~~~-------   61 (151)
T cd00009           1 VGQEEAIEALREALELP----------PPKNLLLYGPPGTGKTTLARAIANE--LFRPGAPFLYLNASDLLEG-------   61 (151)
T ss_pred             CchHHHHHHHHHHHhCC----------CCCeEEEECCCCCCHHHHHHHHHHH--hhcCCCCeEEEehhhhhhh-------
Confidence            47888899998888632          3468999999999999999999984  3222234566665433222       


Q ss_pred             hhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC------CC
Q 041007          249 ISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG------SE  322 (597)
Q Consensus       249 ~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~------~~  322 (597)
                               ......+ ...           ............++.+||+||++... ......+...+...      ..
T Consensus        62 ---------~~~~~~~-~~~-----------~~~~~~~~~~~~~~~~lilDe~~~~~-~~~~~~~~~~i~~~~~~~~~~~  119 (151)
T cd00009          62 ---------LVVAELF-GHF-----------LVRLLFELAEKAKPGVLFIDEIDSLS-RGAQNALLRVLETLNDLRIDRE  119 (151)
T ss_pred             ---------hHHHHHh-hhh-----------hHhHHHHhhccCCCeEEEEeChhhhh-HHHHHHHHHHHHhcCceeccCC
Confidence                     0000000 000           00111112233567899999997652 12233344333332      46


Q ss_pred             CcEEEEEccCC
Q 041007          323 GSRILVTRSGG  333 (597)
Q Consensus       323 gs~IIvTtR~~  333 (597)
                      +..+|+||...
T Consensus       120 ~~~ii~~~~~~  130 (151)
T cd00009         120 NVRVIGATNRP  130 (151)
T ss_pred             CeEEEEecCcc
Confidence            78888888876

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.

>PLN03025 replication factor C subunit; Provisional

Probab=98.64  E-value=9.2e-07  Score=89.81  Aligned_cols=182  Identities=13%  Similarity=0.136  Sum_probs=104.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh-ccCCe-eEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK-ANFDK-RIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~-~~F~~-~~wv~~~~~~~~~~  243 (597)
                      .+++|.++.++.|..++...          ..+.+.++|++|+||||+|..+++.  .. ..|.. ++-++.+....   
T Consensus        13 ~~~~g~~~~~~~L~~~~~~~----------~~~~lll~Gp~G~GKTtla~~la~~--l~~~~~~~~~~eln~sd~~~---   77 (319)
T PLN03025         13 DDIVGNEDAVSRLQVIARDG----------NMPNLILSGPPGTGKTTSILALAHE--LLGPNYKEAVLELNASDDRG---   77 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhcC----------CCceEEEECCCCCCHHHHHHHHHHH--HhcccCccceeeeccccccc---
Confidence            45789998888888877632          3456789999999999999999883  21 12221 11111111111   


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                    .+..+.++..+.....             ....++.-+++||+++... ......+...+......
T Consensus        78 --------------~~~vr~~i~~~~~~~~-------------~~~~~~~kviiiDE~d~lt-~~aq~aL~~~lE~~~~~  129 (319)
T PLN03025         78 --------------IDVVRNKIKMFAQKKV-------------TLPPGRHKIVILDEADSMT-SGAQQALRRTMEIYSNT  129 (319)
T ss_pred             --------------HHHHHHHHHHHHhccc-------------cCCCCCeEEEEEechhhcC-HHHHHHHHHHHhcccCC
Confidence                          1122222211110000             0002356799999998776 44445565555544566


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                      +++|+++........         .+...+ .+++.++++++....+...+...+....    .+....|++.++|..-.
T Consensus       130 t~~il~~n~~~~i~~---------~L~SRc~~i~f~~l~~~~l~~~L~~i~~~egi~i~----~~~l~~i~~~~~gDlR~  196 (319)
T PLN03025        130 TRFALACNTSSKIIE---------PIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYV----PEGLEAIIFTADGDMRQ  196 (319)
T ss_pred             ceEEEEeCCccccch---------hHHHhhhcccCCCCCHHHHHHHHHHHHHHcCCCCC----HHHHHHHHHHcCCCHHH
Confidence            777777654311100         111122 2899999999999998887754332211    45678899999986643


Q ss_pred             H
Q 041007          403 V  403 (597)
Q Consensus       403 i  403 (597)
                      +
T Consensus       197 a  197 (319)
T PLN03025        197 A  197 (319)
T ss_pred             H
Confidence            3

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.64  E-value=1e-06  Score=91.04  Aligned_cols=192  Identities=15%  Similarity=0.168  Sum_probs=108.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-++.|...+....         -...+.++|+.|+||||+|+.+++..........       .+...    
T Consensus        16 ~~iiGq~~~~~~l~~~~~~~~---------~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~-------~pc~~----   75 (363)
T PRK14961         16 RDIIGQKHIVTAISNGLSLGR---------IHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITS-------NPCRK----   75 (363)
T ss_pred             hhccChHHHHHHHHHHHHcCC---------CCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCC-------CCCCC----
Confidence            468999999999999887432         2456789999999999999999873211111100       00000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhc-------cCCC-CchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESL-------KGSV-SSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l-------~~~~-~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -.....+....       .... ....+...+.+.+... ..+++-++|+|+++... ...++.+...
T Consensus        76 ------------c~~c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~-~~a~naLLk~  142 (363)
T PRK14961         76 ------------CIICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLS-RHSFNALLKT  142 (363)
T ss_pred             ------------CHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcC-HHHHHHHHHH
Confidence                        00000000000       0000 0111111222211111 12455699999998776 4457777777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +...+....+|++|.+......         .+... ..+++.|++.++..+.+...+...+...    ..+.+..|++.
T Consensus       143 lEe~~~~~~fIl~t~~~~~l~~---------tI~SRc~~~~~~~l~~~el~~~L~~~~~~~g~~i----~~~al~~ia~~  209 (363)
T PRK14961        143 LEEPPQHIKFILATTDVEKIPK---------TILSRCLQFKLKIISEEKIFNFLKYILIKESIDT----DEYALKLIAYH  209 (363)
T ss_pred             HhcCCCCeEEEEEcCChHhhhH---------HHHhhceEEeCCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            7766667778877754311000         11111 2299999999999998888664322111    24567889999


Q ss_pred             cCCchHHH
Q 041007          396 CKGLPFAV  403 (597)
Q Consensus       396 ~~GlPLai  403 (597)
                      ++|.|--+
T Consensus       210 s~G~~R~a  217 (363)
T PRK14961        210 AHGSMRDA  217 (363)
T ss_pred             cCCCHHHH
Confidence            99988543

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

Probab=98.64  E-value=7e-07  Score=82.94  Aligned_cols=182  Identities=20%  Similarity=0.236  Sum_probs=95.7

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRV  244 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  244 (597)
                      -.+|||.++-+..+.-++.....     .+.....+.+|||+|+||||||.-+++  .....|.   +.+... ...   
T Consensus        23 L~efiGQ~~l~~~l~i~i~aa~~-----r~~~l~h~lf~GPPG~GKTTLA~IIA~--e~~~~~~---~~sg~~-i~k---   88 (233)
T PF05496_consen   23 LDEFIGQEHLKGNLKILIRAAKK-----RGEALDHMLFYGPPGLGKTTLARIIAN--ELGVNFK---ITSGPA-IEK---   88 (233)
T ss_dssp             CCCS-S-HHHHHHHHHHHHHHHC-----TTS---EEEEESSTTSSHHHHHHHHHH--HCT--EE---EEECCC---S---
T ss_pred             HHHccCcHHHHhhhHHHHHHHHh-----cCCCcceEEEECCCccchhHHHHHHHh--ccCCCeE---eccchh-hhh---
Confidence            46799999988887665543211     013577899999999999999999998  4444442   222210 000   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC----
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG----  320 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~----  320 (597)
                                                       ..++...+.. + +++-+|++|+++..+ ...-+.+...+.++    
T Consensus        89 ---------------------------------~~dl~~il~~-l-~~~~ILFIDEIHRln-k~~qe~LlpamEd~~idi  132 (233)
T PF05496_consen   89 ---------------------------------AGDLAAILTN-L-KEGDILFIDEIHRLN-KAQQEILLPAMEDGKIDI  132 (233)
T ss_dssp             ---------------------------------CHHHHHHHHT----TT-EEEECTCCC---HHHHHHHHHHHHCSEEEE
T ss_pred             ---------------------------------HHHHHHHHHh-c-CCCcEEEEechhhcc-HHHHHHHHHHhccCeEEE
Confidence                                             0111111111 2 245688899998776 44444455544321    


Q ss_pred             ----CCC-----------cEEEEEccCCCCCCCcccccccccCccccce--eecCCCChHHHHHHHHHHhccCCCCCCcc
Q 041007          321 ----SEG-----------SRILVTRSGGKNGTNMTEIGLGEKNGTNMME--IGLGELSEEECRSLFRQIAFHGRSSDYRE  383 (597)
Q Consensus       321 ----~~g-----------s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~--~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~  383 (597)
                          +.+           +.|=.|||......          ......+  .++...+.+|-.++..+.+..-..    +
T Consensus       133 iiG~g~~ar~~~~~l~~FTligATTr~g~ls~----------pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i----~  198 (233)
T PF05496_consen  133 IIGKGPNARSIRINLPPFTLIGATTRAGLLSS----------PLRDRFGIVLRLEFYSEEELAKIVKRSARILNI----E  198 (233)
T ss_dssp             EBSSSSS-BEEEEE----EEEEEESSGCCTSH----------CCCTTSSEEEE----THHHHHHHHHHCCHCTT-----E
T ss_pred             EeccccccceeeccCCCceEeeeeccccccch----------hHHhhcceecchhcCCHHHHHHHHHHHHHHhCC----C
Confidence                111           12335677652111          1122222  579999999999999877642221    2


Q ss_pred             chHHHHHHHHHhcCCchHHHHHHHhhh
Q 041007          384 KFEPIGRRVVGKCKGLPFAVKILGSLL  410 (597)
Q Consensus       384 ~~~~~~~~I~~~~~GlPLai~~~~~~l  410 (597)
                      -..+.+.+|+++|.|-|--..-+-...
T Consensus       199 i~~~~~~~Ia~rsrGtPRiAnrll~rv  225 (233)
T PF05496_consen  199 IDEDAAEEIARRSRGTPRIANRLLRRV  225 (233)
T ss_dssp             E-HHHHHHHHHCTTTSHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHhcCCChHHHHHHHHHH
Confidence            235678999999999997655444433

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

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=98.62  E-value=1.6e-06  Score=87.74  Aligned_cols=182  Identities=15%  Similarity=0.148  Sum_probs=113.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCCh----hhhccCCeeEEEEecCCCch
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDS----DVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~----~~~~~F~~~~wv~~~~~~~~  241 (597)
                      .+++|.+.-++.|..++....         -.....++|+.|+||||+|+.+++..    ....|++...|.........
T Consensus         4 ~~i~g~~~~~~~l~~~~~~~~---------~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~~~~i~   74 (313)
T PRK05564          4 HTIIGHENIKNRIKNSIIKNR---------FSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIG   74 (313)
T ss_pred             hhccCcHHHHHHHHHHHHcCC---------CCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEeccccCCCCC
Confidence            357899889999999987432         34677899999999999999987731    12234454444332111000


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCC
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS  321 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~  321 (597)
                                      .+-.+++.+.+...                -..+++-++|+|+++..+ ...++.+...+...+
T Consensus        75 ----------------v~~ir~~~~~~~~~----------------p~~~~~kv~iI~~ad~m~-~~a~naLLK~LEepp  121 (313)
T PRK05564         75 ----------------VDDIRNIIEEVNKK----------------PYEGDKKVIIIYNSEKMT-EQAQNAFLKTIEEPP  121 (313)
T ss_pred             ----------------HHHHHHHHHHHhcC----------------cccCCceEEEEechhhcC-HHHHHHHHHHhcCCC
Confidence                            11122222222110                012456688888887665 667889999998888


Q ss_pred             CCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCch
Q 041007          322 EGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLP  400 (597)
Q Consensus       322 ~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlP  400 (597)
                      .++.+|++|.+......         .+...+. +++.++++++....+.+...+    .    ..+.++.++..++|.|
T Consensus       122 ~~t~~il~~~~~~~ll~---------TI~SRc~~~~~~~~~~~~~~~~l~~~~~~----~----~~~~~~~l~~~~~g~~  184 (313)
T PRK05564        122 KGVFIILLCENLEQILD---------TIKSRCQIYKLNRLSKEEIEKFISYKYND----I----KEEEKKSAIAFSDGIP  184 (313)
T ss_pred             CCeEEEEEeCChHhCcH---------HHHhhceeeeCCCcCHHHHHHHHHHHhcC----C----CHHHHHHHHHHcCCCH
Confidence            88999988865411100         1111122 999999999998888665421    1    1334678899999998


Q ss_pred             HHHHHH
Q 041007          401 FAVKIL  406 (597)
Q Consensus       401 Lai~~~  406 (597)
                      .-+...
T Consensus       185 ~~a~~~  190 (313)
T PRK05564        185 GKVEKF  190 (313)
T ss_pred             HHHHHH
Confidence            765433

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.61  E-value=1e-06  Score=94.46  Aligned_cols=193  Identities=15%  Similarity=0.184  Sum_probs=111.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+...+.|..++....         -...+.++|+.|+||||+|+.+++.  .....    ++... +...    
T Consensus        15 ddVIGQe~vv~~L~~aI~~gr---------l~HAyLF~GPpGvGKTTlAriLAK~--LnC~~----~~~~~-pCg~----   74 (702)
T PRK14960         15 NELVGQNHVSRALSSALERGR---------LHHAYLFTGTRGVGKTTIARILAKC--LNCET----GVTST-PCEV----   74 (702)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHH--hCCCc----CCCCC-CCcc----
Confidence            468999999999999998432         2467899999999999999998773  21100    11000 0000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-------ccCC-CCchhhHHHHHHHHHH-HhcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-------LKGS-VSSQVEMETVLQYINE-FVQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-------l~~~-~~~~~~~~~~~~~l~~-~L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -...+.+...       +... .....+...+...+.. -..++.-++|||+++..+ ....+.+...
T Consensus        75 ------------C~sC~~I~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS-~~A~NALLKt  141 (702)
T PRK14960         75 ------------CATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLS-THSFNALLKT  141 (702)
T ss_pred             ------------CHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcC-HHHHHHHHHH
Confidence                        0000000000       0000 0011111112221111 123566799999998776 5567778777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhc
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKC  396 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~  396 (597)
                      +.....+..+|++|.+.......        -..+...+++.+++.++....+.+.+...+...    -.+....|++.+
T Consensus       142 LEEPP~~v~FILaTtd~~kIp~T--------IlSRCq~feFkpLs~eEI~k~L~~Il~kEgI~i----d~eAL~~IA~~S  209 (702)
T PRK14960        142 LEEPPEHVKFLFATTDPQKLPIT--------VISRCLQFTLRPLAVDEITKHLGAILEKEQIAA----DQDAIWQIAESA  209 (702)
T ss_pred             HhcCCCCcEEEEEECChHhhhHH--------HHHhhheeeccCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHc
Confidence            77666777888877654211100        111122299999999999999988775433221    245678899999


Q ss_pred             CCchHHH
Q 041007          397 KGLPFAV  403 (597)
Q Consensus       397 ~GlPLai  403 (597)
                      +|.+-.+
T Consensus       210 ~GdLRdA  216 (702)
T PRK14960        210 QGSLRDA  216 (702)
T ss_pred             CCCHHHH
Confidence            9977433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=98.61  E-value=2.1e-06  Score=87.44  Aligned_cols=183  Identities=13%  Similarity=0.115  Sum_probs=105.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|+++.++.+..++...          ..+.+.|+|++|+||||+|+.+++.. ....+.. .++.+......    
T Consensus        17 ~~~~g~~~~~~~l~~~i~~~----------~~~~~ll~G~~G~GKt~~~~~l~~~l-~~~~~~~-~~i~~~~~~~~----   80 (319)
T PRK00440         17 DEIVGQEEIVERLKSYVKEK----------NMPHLLFAGPPGTGKTTAALALAREL-YGEDWRE-NFLELNASDER----   80 (319)
T ss_pred             HHhcCcHHHHHHHHHHHhCC----------CCCeEEEECCCCCCHHHHHHHHHHHH-cCCcccc-ceEEecccccc----
Confidence            45889999999999998732          34567999999999999999998731 1111211 12222111000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcE
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSR  325 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~  325 (597)
                                + .......+..+....+              .....+-+|++|+++... ......+...+......+.
T Consensus        81 ----------~-~~~~~~~i~~~~~~~~--------------~~~~~~~vviiDe~~~l~-~~~~~~L~~~le~~~~~~~  134 (319)
T PRK00440         81 ----------G-IDVIRNKIKEFARTAP--------------VGGAPFKIIFLDEADNLT-SDAQQALRRTMEMYSQNTR  134 (319)
T ss_pred             ----------c-hHHHHHHHHHHHhcCC--------------CCCCCceEEEEeCcccCC-HHHHHHHHHHHhcCCCCCe
Confidence                      0 1111111111100000              001235689999996654 3345566666665556677


Q ss_pred             EEEEccCCCCCCCcccccccccCcc-ccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHH
Q 041007          326 ILVTRSGGKNGTNMTEIGLGEKNGT-NMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAV  403 (597)
Q Consensus       326 IIvTtR~~~~~~~~~~~~~~~~~~~-~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai  403 (597)
                      +|+++........         ... ....+++.+++.++....+...+...+...    ..+.+..|++.++|.+--+
T Consensus       135 lIl~~~~~~~l~~---------~l~sr~~~~~~~~l~~~ei~~~l~~~~~~~~~~i----~~~al~~l~~~~~gd~r~~  200 (319)
T PRK00440        135 FILSCNYSSKIID---------PIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEI----TDDALEAIYYVSEGDMRKA  200 (319)
T ss_pred             EEEEeCCccccch---------hHHHHhheeeeCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCCHHHH
Confidence            7777654311100         111 111289999999999999888775332211    2456788999999987654

>PTZ00202 tuzin; Provisional

Probab=98.61  E-value=2e-06  Score=87.15  Aligned_cols=170  Identities=13%  Similarity=0.136  Sum_probs=100.5

Q ss_pred             ccCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          162 VIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       162 ~~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      +.++..|+||+.++.+|...|...+.       ..++++.|+|++|+|||||++.+.....    +. .++++..   ..
T Consensus       258 Pa~~~~FVGReaEla~Lr~VL~~~d~-------~~privvLtG~~G~GKTTLlR~~~~~l~----~~-qL~vNpr---g~  322 (550)
T PTZ00202        258 PAVIRQFVSREAEESWVRQVLRRLDT-------AHPRIVVFTGFRGCGKSSLCRSAVRKEG----MP-AVFVDVR---GT  322 (550)
T ss_pred             CCCccCCCCcHHHHHHHHHHHhccCC-------CCceEEEEECCCCCCHHHHHHHHHhcCC----ce-EEEECCC---CH
Confidence            56678899999999999999975432       2346999999999999999999987422    21 2222222   33


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCch--hhHHHHHHHHHHHh-c-CceEEEEEecccCCCCcchHHHHH---
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSSQ--VEMETVLQYINEFV-Q-GKKVLLVLDDLWWNAYPRYWEQLM---  314 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~--~~~~~~~~~l~~~L-~-~kr~LLVLDdv~~~~~~~~~~~l~---  314 (597)
                                      .+++..++.+|+.+....  .-...+.+.+.+.- . +++.+||+-=- ..+   ++..+.   
T Consensus       323 ----------------eElLr~LL~ALGV~p~~~k~dLLrqIqeaLl~~~~e~GrtPVLII~lr-eg~---~l~rvyne~  382 (550)
T PTZ00202        323 ----------------EDTLRSVVKALGVPNVEACGDLLDFISEACRRAKKMNGETPLLVLKLR-EGS---SLQRVYNEV  382 (550)
T ss_pred             ----------------HHHHHHHHHHcCCCCcccHHHHHHHHHHHHHHHHHhCCCCEEEEEEec-CCC---cHHHHHHHH
Confidence                            899999999999743221  22334444444332 2 55666665321 112   222221   


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHh
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~  373 (597)
                      ..|.....-|+|++----+  ...+....++..+.     |.+.+++.++|.++-.+..
T Consensus       383 v~la~drr~ch~v~evple--slt~~~~~lprldf-----~~vp~fsr~qaf~y~~h~~  434 (550)
T PTZ00202        383 VALACDRRLCHVVIEVPLE--SLTIANTLLPRLDF-----YLVPNFSRSQAFAYTQHAI  434 (550)
T ss_pred             HHHHccchhheeeeeehHh--hcchhcccCcccee-----EecCCCCHHHHHHHHhhcc
Confidence            1333445567777653322  11111111111111     8899999999988766543

>PRK08727 hypothetical protein; Validated

Probab=98.60  E-value=9.8e-07  Score=85.14  Aligned_cols=159  Identities=18%  Similarity=0.117  Sum_probs=91.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ...+.|+|++|+|||+|++.+++.  .......+.++++...                      ...+            
T Consensus        41 ~~~l~l~G~~G~GKThL~~a~~~~--~~~~~~~~~y~~~~~~----------------------~~~~------------   84 (233)
T PRK08727         41 SDWLYLSGPAGTGKTHLALALCAA--AEQAGRSSAYLPLQAA----------------------AGRL------------   84 (233)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEeHHHh----------------------hhhH------------
Confidence            356999999999999999999884  3333345566653211                      0000            


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHH-HHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccccce
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQ-LMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME  354 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~-l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~  354 (597)
                           ...+. .+ .+.-+|||||++.......|.. +...+.. ..++..||+|++..+.......-++.+ .......
T Consensus        85 -----~~~~~-~l-~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~~~~~~~~vI~ts~~~p~~l~~~~~dL~S-Rl~~~~~  156 (233)
T PRK08727         85 -----RDALE-AL-EGRSLVALDGLESIAGQREDEVALFDFHNRARAAGITLLYTARQMPDGLALVLPDLRS-RLAQCIR  156 (233)
T ss_pred             -----HHHHH-HH-hcCCEEEEeCcccccCChHHHHHHHHHHHHHHHcCCeEEEECCCChhhhhhhhHHHHH-HHhcCce
Confidence                 01111 11 1335899999976543334443 3332222 234677999998763322111111100 0001123


Q ss_pred             eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHH
Q 041007          355 IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAV  403 (597)
Q Consensus       355 ~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai  403 (597)
                      +++.+++.++-.+++.+.+...+..    --.+....|++.++|..-.+
T Consensus       157 ~~l~~~~~e~~~~iL~~~a~~~~l~----l~~e~~~~La~~~~rd~r~~  201 (233)
T PRK08727        157 IGLPVLDDVARAAVLRERAQRRGLA----LDEAAIDWLLTHGERELAGL  201 (233)
T ss_pred             EEecCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHhCCCCHHHH
Confidence            8999999999999999877532221    12556788888888766554

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=98.60  E-value=2.6e-06  Score=86.79  Aligned_cols=198  Identities=13%  Similarity=0.166  Sum_probs=115.6

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc----CCeeEEEEecCC
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN----FDKRIWVSASYP  238 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~  238 (597)
                      .....++|.++..+.|...+....         .+..+.|+|+.|+||||+|..+.+.  +-.+    +...   ....+
T Consensus        20 ~~~~~l~Gh~~a~~~L~~a~~~gr---------l~ha~L~~G~~G~GKttlA~~lA~~--Llc~~~~~~~~~---~~~~~   85 (351)
T PRK09112         20 SENTRLFGHEEAEAFLAQAYREGK---------LHHALLFEGPEGIGKATLAFHLANH--ILSHPDPAEAPE---TLADP   85 (351)
T ss_pred             CchhhccCcHHHHHHHHHHHHcCC---------CCeeEeeECCCCCCHHHHHHHHHHH--HcCCCccccCcc---ccCCC
Confidence            344668999999999999997432         3457999999999999999988773  2211    1110   00000


Q ss_pred             CchhhhhhhhhhhcccchHHHHHHHHHHh-------ccCC-------CCchhhHHHHHHHHHHHhc-----CceEEEEEe
Q 041007          239 RDEIRVARDEISVARDRDEIRVAKAILES-------LKGS-------VSSQVEMETVLQYINEFVQ-----GKKVLLVLD  299 (597)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~il~~-------l~~~-------~~~~~~~~~~~~~l~~~L~-----~kr~LLVLD  299 (597)
                      ...                ....+.+...       +..+       .......+++. .+.+++.     ++.-++|+|
T Consensus        86 ~~~----------------c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR-~l~~~l~~~~~~g~~rVviID  148 (351)
T PRK09112         86 DPA----------------SPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIR-RVGHFLSQTSGDGNWRIVIID  148 (351)
T ss_pred             CCC----------------CHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHH-HHHHHhhhccccCCceEEEEE
Confidence            000                1111111111       0000       01112233322 3333332     566799999


Q ss_pred             cccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCC
Q 041007          300 DLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRS  378 (597)
Q Consensus       300 dv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~  378 (597)
                      +++..+ ....+.+...+.....+..+|++|........         .+... ..+.+.|++.++..+++.+....   
T Consensus       149 eAd~l~-~~aanaLLk~LEEpp~~~~fiLit~~~~~llp---------tIrSRc~~i~l~pl~~~~~~~~L~~~~~~---  215 (351)
T PRK09112        149 PADDMN-RNAANAILKTLEEPPARALFILISHSSGRLLP---------TIRSRCQPISLKPLDDDELKKALSHLGSS---  215 (351)
T ss_pred             chhhcC-HHHHHHHHHHHhcCCCCceEEEEECChhhccH---------HHHhhccEEEecCCCHHHHHHHHHHhhcc---
Confidence            999887 66677788777665556665555544311110         11112 23999999999999999874321   


Q ss_pred             CCCccchHHHHHHHHHhcCCchHHHHHHH
Q 041007          379 SDYREKFEPIGRRVVGKCKGLPFAVKILG  407 (597)
Q Consensus       379 ~~~~~~~~~~~~~I~~~~~GlPLai~~~~  407 (597)
                        .. -..+.+..|++.++|.|.....+.
T Consensus       216 --~~-~~~~~~~~i~~~s~G~pr~Al~ll  241 (351)
T PRK09112        216 --QG-SDGEITEALLQRSKGSVRKALLLL  241 (351)
T ss_pred             --cC-CCHHHHHHHHHHcCCCHHHHHHHH
Confidence              11 114456789999999998665443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=98.59  E-value=1.8e-06  Score=93.43  Aligned_cols=196  Identities=11%  Similarity=0.142  Sum_probs=111.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+..++.|..++....         -...+.++|+.|+||||+|+.+.+.........   +..+....      
T Consensus        16 ddIIGQe~vv~~L~~ai~~~r---------l~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~---~~pCg~C~------   77 (709)
T PRK08691         16 ADLVGQEHVVKALQNALDEGR---------LHHAYLLTGTRGVGKTTIARILAKSLNCENAQH---GEPCGVCQ------   77 (709)
T ss_pred             HHHcCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCcHHHHHHHHHHHhcccCCCC---CCCCcccH------
Confidence            468999999999999998432         245789999999999999999977311111100   00011000      


Q ss_pred             hhhhhhcccchHHHHHHHHHH-------hccC-CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILE-------SLKG-SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~-------~l~~-~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                    ....+..       .+.. ......++..++...... ..+++-++|||+++..+ ....+.++..
T Consensus        78 --------------sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls-~~A~NALLKt  142 (709)
T PRK08691         78 --------------SCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLS-KSAFNAMLKT  142 (709)
T ss_pred             --------------HHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccC-HHHHHHHHHH
Confidence                          0000000       0000 000111122222221111 12566799999997665 4456667777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhc
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKC  396 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~  396 (597)
                      +......+.+|++|.+.......        -..+...+.+.+++.++....+.+.+...+...    ..+....|++.+
T Consensus       143 LEEPp~~v~fILaTtd~~kL~~T--------IrSRC~~f~f~~Ls~eeI~~~L~~Il~kEgi~i----d~eAL~~Ia~~A  210 (709)
T PRK08691        143 LEEPPEHVKFILATTDPHKVPVT--------VLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAY----EPPALQLLGRAA  210 (709)
T ss_pred             HHhCCCCcEEEEEeCCccccchH--------HHHHHhhhhcCCCCHHHHHHHHHHHHHHcCCCc----CHHHHHHHHHHh
Confidence            76655667777777554211100        011122289999999999999988775433221    245678899999


Q ss_pred             CCchHHH-HHH
Q 041007          397 KGLPFAV-KIL  406 (597)
Q Consensus       397 ~GlPLai-~~~  406 (597)
                      +|.+.-+ ..+
T Consensus       211 ~GslRdAlnLL  221 (709)
T PRK08691        211 AGSMRDALSLL  221 (709)
T ss_pred             CCCHHHHHHHH
Confidence            9988544 444

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.58  E-value=2.1e-06  Score=91.86  Aligned_cols=185  Identities=17%  Similarity=0.218  Sum_probs=110.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-------------------c
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-------------------N  226 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-------------------~  226 (597)
                      .+++|.+..++.|...+....         -...+.++|+.|+||||+|+.+++...-..                   .
T Consensus        16 ~diiGq~~~v~~L~~~i~~~r---------l~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~~~   86 (546)
T PRK14957         16 AEVAGQQHALNSLVHALETQK---------VHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNS   86 (546)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhcCC
Confidence            468899999999999887432         235678999999999999999976211000                   1


Q ss_pred             CCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCC
Q 041007          227 FDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNA  305 (597)
Q Consensus       227 F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~  305 (597)
                      |...+++.....                                  ....+...+.+.+... ..+++-++|+|+++..+
T Consensus        87 ~~dlieidaas~----------------------------------~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls  132 (546)
T PRK14957         87 FIDLIEIDAASR----------------------------------TGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLS  132 (546)
T ss_pred             CCceEEeecccc----------------------------------cCHHHHHHHHHHHHhhhhcCCcEEEEEechhhcc
Confidence            111111111000                                  0111222233322221 23566799999998776


Q ss_pred             CcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccc
Q 041007          306 YPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREK  384 (597)
Q Consensus       306 ~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~  384 (597)
                       ...++.+...+......+.+|++|.+......         .+...+ .+++.+++.++....+.+.+...+.    .-
T Consensus       133 -~~a~naLLK~LEepp~~v~fIL~Ttd~~kil~---------tI~SRc~~~~f~~Ls~~eI~~~L~~il~~egi----~~  198 (546)
T PRK14957        133 -KQSFNALLKTLEEPPEYVKFILATTDYHKIPV---------TILSRCIQLHLKHISQADIKDQLKIILAKENI----NS  198 (546)
T ss_pred             -HHHHHHHHHHHhcCCCCceEEEEECChhhhhh---------hHHHheeeEEeCCCCHHHHHHHHHHHHHHcCC----CC
Confidence             55677788888776667777765543311000         111112 2999999999998888876543221    11


Q ss_pred             hHHHHHHHHHhcCCch-HHHHHHH
Q 041007          385 FEPIGRRVVGKCKGLP-FAVKILG  407 (597)
Q Consensus       385 ~~~~~~~I~~~~~GlP-Lai~~~~  407 (597)
                      .......|++.++|.+ -|+..+-
T Consensus       199 e~~Al~~Ia~~s~GdlR~alnlLe  222 (546)
T PRK14957        199 DEQSLEYIAYHAKGSLRDALSLLD  222 (546)
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHHH
Confidence            2456678999999966 4555553

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=98.57  E-value=2.4e-06  Score=92.83  Aligned_cols=195  Identities=13%  Similarity=0.157  Sum_probs=113.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .++||.+.-++.|...+....         -...+.++|+.|+||||+|+.+++...-...+..   -.+..        
T Consensus        16 ~divGQe~vv~~L~~~l~~~r---------l~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~---~pCg~--------   75 (647)
T PRK07994         16 AEVVGQEHVLTALANALDLGR---------LHHAYLFSGTRGVGKTTIARLLAKGLNCETGITA---TPCGE--------   75 (647)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCC---CCCCC--------
Confidence            468999999999999887432         2345789999999999999999874211110000   00000        


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-------ccCC-CCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-------LKGS-VSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-------l~~~-~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -.....|...       +... .....+...+...+... ..++.-++|||+++... ....+.++..
T Consensus        76 ------------C~~C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls-~~a~NALLKt  142 (647)
T PRK07994         76 ------------CDNCREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLS-RHSFNALLKT  142 (647)
T ss_pred             ------------CHHHHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCC-HHHHHHHHHH
Confidence                        1111111100       0000 01111222222222211 23567799999998876 6677888888


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCcc-ccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGT-NMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~-~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +..-....++|++|.+......         -+. +...+.+.+++.++....+.+.+...+..    ........|++.
T Consensus       143 LEEPp~~v~FIL~Tt~~~kLl~---------TI~SRC~~~~f~~Ls~~ei~~~L~~il~~e~i~----~e~~aL~~Ia~~  209 (647)
T PRK07994        143 LEEPPEHVKFLLATTDPQKLPV---------TILSRCLQFHLKALDVEQIRQQLEHILQAEQIP----FEPRALQLLARA  209 (647)
T ss_pred             HHcCCCCeEEEEecCCccccch---------HHHhhheEeeCCCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHH
Confidence            8776777777777666521110         111 12229999999999999998876332211    124556789999


Q ss_pred             cCCchH-HHHHH
Q 041007          396 CKGLPF-AVKIL  406 (597)
Q Consensus       396 ~~GlPL-ai~~~  406 (597)
                      ++|.+- |+.++
T Consensus       210 s~Gs~R~Al~ll  221 (647)
T PRK07994        210 ADGSMRDALSLT  221 (647)
T ss_pred             cCCCHHHHHHHH
Confidence            999776 44443

>PRK08084 DNA replication initiation factor; Provisional

Probab=98.56  E-value=1.4e-06  Score=84.20  Aligned_cols=162  Identities=17%  Similarity=0.136  Sum_probs=93.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      .+.+.|+|++|+|||+|++.+++.  ....-..+.++++.....                   .                
T Consensus        45 ~~~l~l~Gp~G~GKThLl~a~~~~--~~~~~~~v~y~~~~~~~~-------------------~----------------   87 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLLHAACAE--LSQRGRAVGYVPLDKRAW-------------------F----------------   87 (235)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEEHHHHhh-------------------h----------------
Confidence            468999999999999999999984  333333455665431100                   0                


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHH-HhhcCC-CCC-cEEEEEccCCCCCCCcccccccccCcccc-
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLM-YSLKSG-SEG-SRILVTRSGGKNGTNMTEIGLGEKNGTNM-  352 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~-~~l~~~-~~g-s~IIvTtR~~~~~~~~~~~~~~~~~~~~~-  352 (597)
                       ...+.+.+.     +--+|+|||++.......|+... ..+... ..| .++|+||+..+.......-     ..... 
T Consensus        88 -~~~~~~~~~-----~~dlliiDdi~~~~~~~~~~~~lf~l~n~~~e~g~~~li~ts~~~p~~l~~~~~-----~L~SRl  156 (235)
T PRK08084         88 -VPEVLEGME-----QLSLVCIDNIECIAGDELWEMAIFDLYNRILESGRTRLLITGDRPPRQLNLGLP-----DLASRL  156 (235)
T ss_pred             -hHHHHHHhh-----hCCEEEEeChhhhcCCHHHHHHHHHHHHHHHHcCCCeEEEeCCCChHHcCcccH-----HHHHHH
Confidence             001111111     12489999997654334555432 333221 233 4799999866322111000     11121 


Q ss_pred             ---ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhh
Q 041007          353 ---MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLL  410 (597)
Q Consensus       353 ---~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l  410 (597)
                         ..+++.++++++-.+++.+.+...+- .   --++...-|++.+.|..-.+..+-..+
T Consensus       157 ~~g~~~~l~~~~~~~~~~~l~~~a~~~~~-~---l~~~v~~~L~~~~~~d~r~l~~~l~~l  213 (235)
T PRK08084        157 DWGQIYKLQPLSDEEKLQALQLRARLRGF-E---LPEDVGRFLLKRLDREMRTLFMTLDQL  213 (235)
T ss_pred             hCCceeeecCCCHHHHHHHHHHHHHHcCC-C---CCHHHHHHHHHhhcCCHHHHHHHHHHH
Confidence               22899999999999998886643221 1   125677889999998776665544433

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=98.56  E-value=5.5e-06  Score=84.93  Aligned_cols=199  Identities=14%  Similarity=0.098  Sum_probs=114.6

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeE----EEEecCCC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRI----WVSASYPR  239 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~----wv~~~~~~  239 (597)
                      ...+++|.+...+.|.+.+....         -...+.++|+.|+||+++|..+.+..--........    -.++.. .
T Consensus        17 ~~~~iiGq~~~~~~L~~~~~~~r---------l~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~-~   86 (365)
T PRK07471         17 ETTALFGHAAAEAALLDAYRSGR---------LHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAI-D   86 (365)
T ss_pred             chhhccChHHHHHHHHHHHHcCC---------CCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccC-C
Confidence            34568999999999999988432         245789999999999999988866311111000000    000000 0


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccC--------------CCCchhhHHHHHHHHHHHhc-----CceEEEEEec
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKG--------------SVSSQVEMETVLQYINEFVQ-----GKKVLLVLDD  300 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~--------------~~~~~~~~~~~~~~l~~~L~-----~kr~LLVLDd  300 (597)
                      ..                -...+.+...-..              .......+++ ++.+.+.+.     +++.++|+|+
T Consensus        87 ~~----------------c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~Vdq-iR~l~~~~~~~~~~~~~kVviIDe  149 (365)
T PRK07471         87 PD----------------HPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDE-VRELISFFGLTAAEGGWRVVIVDT  149 (365)
T ss_pred             CC----------------ChHHHHHHccCCCCeEEEecccccccccccccccHHH-HHHHHHHhCcCcccCCCEEEEEec
Confidence            00                0011111100000              0001122333 223333332     5567999999


Q ss_pred             ccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCC
Q 041007          301 LWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSS  379 (597)
Q Consensus       301 v~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~  379 (597)
                      +++.+ ......+...+..-..++.+|++|.+......         .+...+ .+.+.+++.++..+++......    
T Consensus       150 ad~m~-~~aanaLLK~LEepp~~~~~IL~t~~~~~llp---------ti~SRc~~i~l~~l~~~~i~~~L~~~~~~----  215 (365)
T PRK07471        150 ADEMN-ANAANALLKVLEEPPARSLFLLVSHAPARLLP---------TIRSRCRKLRLRPLAPEDVIDALAAAGPD----  215 (365)
T ss_pred             hHhcC-HHHHHHHHHHHhcCCCCeEEEEEECCchhchH---------HhhccceEEECCCCCHHHHHHHHHHhccc----
Confidence            99887 67778888888776667777777766521110         111222 2999999999999999876421    


Q ss_pred             CCccchHHHHHHHHHhcCCchHHHHHHH
Q 041007          380 DYREKFEPIGRRVVGKCKGLPFAVKILG  407 (597)
Q Consensus       380 ~~~~~~~~~~~~I~~~~~GlPLai~~~~  407 (597)
                       ..   ......+++.++|.|+....+.
T Consensus       216 -~~---~~~~~~l~~~s~Gsp~~Al~ll  239 (365)
T PRK07471        216 -LP---DDPRAALAALAEGSVGRALRLA  239 (365)
T ss_pred             -CC---HHHHHHHHHHcCCCHHHHHHHh
Confidence             11   1223678999999998665543

>PRK05642 DNA replication initiation factor; Validated

Probab=98.55  E-value=1.7e-06  Score=83.52  Aligned_cols=162  Identities=16%  Similarity=0.183  Sum_probs=95.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ...+.|+|+.|+|||.|++.+++.  ....-..++|++...                      +...             
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~--~~~~~~~v~y~~~~~----------------------~~~~-------------   87 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLR--FEQRGEPAVYLPLAE----------------------LLDR-------------   87 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHhCCCcEEEeeHHH----------------------HHhh-------------
Confidence            367899999999999999999873  332223456665421                      1110             


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHH-HHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccc--
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQ-LMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM--  352 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~-l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~--  352 (597)
                       ...    +.+.+.+- =+||+||++.......|.. +...+.. ..+|..+|+|+...+........     .....  
T Consensus        88 -~~~----~~~~~~~~-d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~-----~L~SRl~  156 (234)
T PRK05642         88 -GPE----LLDNLEQY-ELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLP-----DLKSRLT  156 (234)
T ss_pred             -hHH----HHHhhhhC-CEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCc-----cHHHHHh
Confidence             011    22222222 2788999975543345554 4444433 24567889998876332211100     11111  


Q ss_pred             --ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhh
Q 041007          353 --MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLL  410 (597)
Q Consensus       353 --~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l  410 (597)
                        ..+++.++++++-.+++..++...+. ..   -.++..-|++.+.|..-.+..+-..|
T Consensus       157 ~gl~~~l~~~~~e~~~~il~~ka~~~~~-~l---~~ev~~~L~~~~~~d~r~l~~~l~~l  212 (234)
T PRK05642        157 LALVFQMRGLSDEDKLRALQLRASRRGL-HL---TDEVGHFILTRGTRSMSALFDLLERL  212 (234)
T ss_pred             cCeeeecCCCCHHHHHHHHHHHHHHcCC-CC---CHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence              22889999999999999966643221 11   15677889999988876665554443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.53  E-value=5.2e-07  Score=93.95  Aligned_cols=199  Identities=10%  Similarity=0.063  Sum_probs=112.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-+..|..++....         -...+.++|+.|+||||+|+.+++.  +....... ...+.....-    
T Consensus        18 ~dvVGQe~iv~~L~~~i~~~r---------i~ha~Lf~GP~GtGKTTlAriLAk~--Lnce~~~~-~~pCg~C~sC----   81 (484)
T PRK14956         18 RDVIHQDLAIGALQNALKSGK---------IGHAYIFFGPRGVGKTTIARILAKR--LNCENPIG-NEPCNECTSC----   81 (484)
T ss_pred             HHHhChHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHh--cCcccccC-ccccCCCcHH----
Confidence            468999999999999887432         2346899999999999999999874  22110000 0001100000    


Q ss_pred             hhhhhhcccchHHHHHHHHHH---hccC-CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHhhcCC
Q 041007          246 RDEISVARDRDEIRVAKAILE---SLKG-SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG  320 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~---~l~~-~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~  320 (597)
                                  ..+...+..   .+.. ......+...+.+.+... ..++.-++|||+++... ...++.++..+...
T Consensus        82 ------------~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls-~~A~NALLKtLEEP  148 (484)
T PRK14956         82 ------------LEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLT-DQSFNALLKTLEEP  148 (484)
T ss_pred             ------------HHHHccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcC-HHHHHHHHHHhhcC
Confidence                        000000000   0000 001112222222222221 23566799999998776 66788887777665


Q ss_pred             CCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCc
Q 041007          321 SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGL  399 (597)
Q Consensus       321 ~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~Gl  399 (597)
                      .....+|++|........         .+...+. |.+.+++.++..+.+.+.+...+..    -..+....|++.++|.
T Consensus       149 p~~viFILaTte~~kI~~---------TI~SRCq~~~f~~ls~~~i~~~L~~i~~~Egi~----~e~eAL~~Ia~~S~Gd  215 (484)
T PRK14956        149 PAHIVFILATTEFHKIPE---------TILSRCQDFIFKKVPLSVLQDYSEKLCKIENVQ----YDQEGLFWIAKKGDGS  215 (484)
T ss_pred             CCceEEEeecCChhhccH---------HHHhhhheeeecCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHcCCh
Confidence            566666666654311110         1122222 9999999999999888876433221    1255678899999998


Q ss_pred             hH-HHHHH
Q 041007          400 PF-AVKIL  406 (597)
Q Consensus       400 PL-ai~~~  406 (597)
                      +- |+..+
T Consensus       216 ~RdAL~lL  223 (484)
T PRK14956        216 VRDMLSFM  223 (484)
T ss_pred             HHHHHHHH
Confidence            84 33333

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

Probab=98.53  E-value=2.5e-06  Score=83.32  Aligned_cols=163  Identities=15%  Similarity=0.128  Sum_probs=95.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ...+.+.+||++|+||||||+.+....+...    ..||..+-....                ..-.+.|+++-.     
T Consensus       160 ~~ipSmIlWGppG~GKTtlArlia~tsk~~S----yrfvelSAt~a~----------------t~dvR~ife~aq-----  214 (554)
T KOG2028|consen  160 NRIPSMILWGPPGTGKTTLARLIASTSKKHS----YRFVELSATNAK----------------TNDVRDIFEQAQ-----  214 (554)
T ss_pred             CCCCceEEecCCCCchHHHHHHHHhhcCCCc----eEEEEEeccccc----------------hHHHHHHHHHHH-----
Confidence            3678899999999999999999988422222    556766654433                333444443311     


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME  354 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~  354 (597)
                                =...+.++|.+|++|.|+.-+    -.+.-.+||...+|..++|-...+.+.+...     ..-+.+...
T Consensus       215 ----------~~~~l~krkTilFiDEiHRFN----ksQQD~fLP~VE~G~I~lIGATTENPSFqln-----~aLlSRC~V  275 (554)
T KOG2028|consen  215 ----------NEKSLTKRKTILFIDEIHRFN----KSQQDTFLPHVENGDITLIGATTENPSFQLN-----AALLSRCRV  275 (554)
T ss_pred             ----------HHHhhhcceeEEEeHHhhhhh----hhhhhcccceeccCceEEEecccCCCccchh-----HHHHhccce
Confidence                      112245789999999996543    2233345666777887776443332222221     111112222


Q ss_pred             eecCCCChHHHHHHHHHHhc---cCCC---CCCcc---chHHHHHHHHHhcCCchH
Q 041007          355 IGLGELSEEECRSLFRQIAF---HGRS---SDYRE---KFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       355 ~~l~~Ls~~es~~Lf~~~~~---~~~~---~~~~~---~~~~~~~~I~~~~~GlPL  401 (597)
                      +-|++|+.++...++.+..-   ....   +.+.+   -...+.+-++..|.|-.-
T Consensus       276 fvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR  331 (554)
T KOG2028|consen  276 FVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDAR  331 (554)
T ss_pred             eEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCchHH
Confidence            89999999999998887432   1111   11111   123456667788888653

>PF14516 AAA_35: AAA-like domain

Probab=98.52  E-value=5e-05  Score=77.30  Aligned_cols=217  Identities=16%  Similarity=0.183  Sum_probs=119.3

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      +.+..|.|...-+++.+.|..           ....+.|.|+-.+|||+|...+.+.  .+..=..++++++........
T Consensus         9 ~~~~Yi~R~~~e~~~~~~i~~-----------~G~~~~I~apRq~GKTSll~~l~~~--l~~~~~~~v~id~~~~~~~~~   75 (331)
T PF14516_consen    9 DSPFYIERPPAEQECYQEIVQ-----------PGSYIRIKAPRQMGKTSLLLRLLER--LQQQGYRCVYIDLQQLGSAIF   75 (331)
T ss_pred             CCCcccCchHHHHHHHHHHhc-----------CCCEEEEECcccCCHHHHHHHHHHH--HHHCCCEEEEEEeecCCCccc
Confidence            345567898666677777763           2469999999999999999999884  332223355777765322100


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCc-------hhhHHHHHHHHHHHh-c--CceEEEEEecccCCCCc-chHHH
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSS-------QVEMETVLQYINEFV-Q--GKKVLLVLDDLWWNAYP-RYWEQ  312 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-------~~~~~~~~~~l~~~L-~--~kr~LLVLDdv~~~~~~-~~~~~  312 (597)
                      .....+       ...+...+..+++....-       ..........+.+.+ .  +++.+|+||+++..... ...+.
T Consensus        76 ~~~~~f-------~~~~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~~~~d  148 (331)
T PF14516_consen   76 SDLEQF-------LRWFCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQIADD  148 (331)
T ss_pred             CCHHHH-------HHHHHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcchHHH
Confidence            000000       033444444444433210       011223344444432 2  68999999999654421 12223


Q ss_pred             HHHhhc---CC-C-----CCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCc
Q 041007          313 LMYSLK---SG-S-----EGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYR  382 (597)
Q Consensus       313 l~~~l~---~~-~-----~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~  382 (597)
                      +...+.   .. .     ...++++....+. . ...+..  . ..-+. ..+.|.+|+.+|...|+..+-..     ..
T Consensus       149 F~~~LR~~~~~~~~~~~~~~L~li~~~~t~~-~-~~~~~~--~-SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~-----~~  218 (331)
T PF14516_consen  149 FFGLLRSWYEQRKNNPIWQKLRLILAGSTED-Y-IILDIN--Q-SPFNIGQPIELPDFTPEEVQELAQRYGLE-----FS  218 (331)
T ss_pred             HHHHHHHHHHhcccCcccceEEEEEecCccc-c-cccCCC--C-CCcccccceeCCCCCHHHHHHHHHhhhcc-----CC
Confidence            333332   11 1     1122333222211 0 000000  0 11111 12999999999999998876421     11


Q ss_pred             cchHHHHHHHHHhcCCchHHHHHHHhhhccC
Q 041007          383 EKFEPIGRRVVGKCKGLPFAVKILGSLLRFK  413 (597)
Q Consensus       383 ~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~  413 (597)
                         ....+.|...+||+|.-+..++..+...
T Consensus       219 ---~~~~~~l~~~tgGhP~Lv~~~~~~l~~~  246 (331)
T PF14516_consen  219 ---QEQLEQLMDWTGGHPYLVQKACYLLVEE  246 (331)
T ss_pred             ---HHHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence               2337999999999999999999999654

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.50  E-value=4.5e-06  Score=86.26  Aligned_cols=198  Identities=12%  Similarity=0.092  Sum_probs=107.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|-+.-++.|..++......-...+.+-...+.++|++|+|||++|..+.+.  .......  +.++...       
T Consensus         5 ~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~--l~c~~~~--~~~Cg~C-------   73 (394)
T PRK07940          5 DDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAA--LQCTDPD--EPGCGEC-------   73 (394)
T ss_pred             hhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHH--hCCCCCC--CCCCCCC-------
Confidence            3578999999999999985431000000113457889999999999999998662  1111000  0000000       


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccC------CCCchhhHHH---HHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHH
Q 041007          246 RDEISVARDRDEIRVAKAILESLKG------SVSSQVEMET---VLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~------~~~~~~~~~~---~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                                   .....+...-..      +.......++   +.+.+... ..+++-++|+|+++..+ ....+.+..
T Consensus        74 -------------~~C~~~~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~-~~aanaLLk  139 (394)
T PRK07940         74 -------------RACRTVLAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLT-ERAANALLK  139 (394)
T ss_pred             -------------HHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcC-HHHHHHHHH
Confidence                         000000000000      0000011122   22211110 12455688899998876 455566777


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVG  394 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~  394 (597)
                      .+.....++.+|++|.+......         .+...+ .+.+.+++.++..+.+.....     ..    .+.+..+++
T Consensus       140 ~LEep~~~~~fIL~a~~~~~llp---------TIrSRc~~i~f~~~~~~~i~~~L~~~~~-----~~----~~~a~~la~  201 (394)
T PRK07940        140 AVEEPPPRTVWLLCAPSPEDVLP---------TIRSRCRHVALRTPSVEAVAEVLVRRDG-----VD----PETARRAAR  201 (394)
T ss_pred             HhhcCCCCCeEEEEECChHHChH---------HHHhhCeEEECCCCCHHHHHHHHHHhcC-----CC----HHHHHHHHH
Confidence            77666667777777666421110         111112 299999999999988875421     11    345678999


Q ss_pred             hcCCchHHHHHH
Q 041007          395 KCKGLPFAVKIL  406 (597)
Q Consensus       395 ~~~GlPLai~~~  406 (597)
                      .++|.|.....+
T Consensus       202 ~s~G~~~~A~~l  213 (394)
T PRK07940        202 ASQGHIGRARRL  213 (394)
T ss_pred             HcCCCHHHHHHH
Confidence            999999755443

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=98.50  E-value=4.2e-06  Score=88.96  Aligned_cols=195  Identities=14%  Similarity=0.125  Sum_probs=110.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCe-eEEEEecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDK-RIWVSASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~  244 (597)
                      .+++|-+.-++.|...+....         -...+.++|+.|+||||+|+.+++.......... ..+..+....     
T Consensus        21 ~dliGq~~vv~~L~~ai~~~r---------i~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~-----   86 (507)
T PRK06645         21 AELQGQEVLVKVLSYTILNDR---------LAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCT-----   86 (507)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCCh-----
Confidence            457899999999888776432         3468899999999999999999874211111000 0000010000     


Q ss_pred             hhhhhhhcccchHHHHHHHHHHh-------ccC-CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHH
Q 041007          245 ARDEISVARDRDEIRVAKAILES-------LKG-SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~-------l~~-~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                                     ....+...       +.. ......+...+.+..... +.+++-++|+|+++... ...++.+..
T Consensus        87 ---------------~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls-~~a~naLLk  150 (507)
T PRK06645         87 ---------------NCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLS-KGAFNALLK  150 (507)
T ss_pred             ---------------HHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcC-HHHHHHHHH
Confidence                           00000000       000 001112222222222111 23567799999998776 567888888


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVG  394 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~  394 (597)
                      .+......+.+|++|........         .+...+. +++.+++.++....+...+...+...    ..+....|++
T Consensus       151 ~LEepp~~~vfI~aTte~~kI~~---------tI~SRc~~~ef~~ls~~el~~~L~~i~~~egi~i----e~eAL~~Ia~  217 (507)
T PRK06645        151 TLEEPPPHIIFIFATTEVQKIPA---------TIISRCQRYDLRRLSFEEIFKLLEYITKQENLKT----DIEALRIIAY  217 (507)
T ss_pred             HHhhcCCCEEEEEEeCChHHhhH---------HHHhcceEEEccCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHH
Confidence            88776667777665533210000         1111222 89999999999999998875433211    1456678999


Q ss_pred             hcCCchHHH
Q 041007          395 KCKGLPFAV  403 (597)
Q Consensus       395 ~~~GlPLai  403 (597)
                      .++|.+--+
T Consensus       218 ~s~GslR~a  226 (507)
T PRK06645        218 KSEGSARDA  226 (507)
T ss_pred             HcCCCHHHH
Confidence            999977433

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=98.49  E-value=6.6e-06  Score=90.37  Aligned_cols=218  Identities=14%  Similarity=0.111  Sum_probs=118.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC---CeeEEEEecCCC---
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF---DKRIWVSASYPR---  239 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F---~~~~wv~~~~~~---  239 (597)
                      +.++|++..+..+...+..          +....+.|+|++|+||||||+.+++.......+   ...-|+.+....   
T Consensus       154 ~~iiGqs~~~~~l~~~ia~----------~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l~~  223 (615)
T TIGR02903       154 SEIVGQERAIKALLAKVAS----------PFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRW  223 (615)
T ss_pred             HhceeCcHHHHHHHHHHhc----------CCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhccC
Confidence            4588999999988877742          234679999999999999999998753333333   123455443211   


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccCC------------------CCchhhHHHHHHHHHHHhcCceEEEEEecc
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKGS------------------VSSQVEMETVLQYINEFVQGKKVLLVLDDL  301 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~------------------~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv  301 (597)
                      +........+.. .+..........+...+..                  .....+ ...+..+.+.++++++.++.|+.
T Consensus       224 d~~~i~~~llg~-~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld-~~~Q~~Ll~~Le~~~v~~~~~~~  301 (615)
T TIGR02903       224 DPREVTNPLLGS-VHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELD-PLLQNKLLKVLEDKRVEFSSSYY  301 (615)
T ss_pred             CHHHHhHHhcCC-ccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCC-HHHHHHHHHHHhhCeEEeeccee
Confidence            110000000000 0000001111112221110                  000111 23466777788888888886666


Q ss_pred             cCCCCcchHHHHHHhhcCCCCCcEEEE--EccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCC
Q 041007          302 WWNAYPRYWEQLMYSLKSGSEGSRILV--TRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRS  378 (597)
Q Consensus       302 ~~~~~~~~~~~l~~~l~~~~~gs~IIv--TtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~  378 (597)
                      |..+ ...|+.+...+....+...+++  ||++......         .+... ..+.+.|++.++.+.++.+.+.....
T Consensus       302 ~~~~-~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~---------aLrSR~~~i~~~pls~edi~~Il~~~a~~~~v  371 (615)
T TIGR02903       302 DPDD-PNVPKYIKKLFEEGAPADFVLIGATTRDPEEINP---------ALRSRCAEVFFEPLTPEDIALIVLNAAEKINV  371 (615)
T ss_pred             ccCC-cccchhhhhhcccCccceEEEEEeccccccccCH---------HHHhceeEEEeCCCCHHHHHHHHHHHHHHcCC
Confidence            5544 5567777766665555544555  4554311000         11111 22889999999999999997743211


Q ss_pred             CCCccchHHHHHHHHHhcCCchHHHHHHHhh
Q 041007          379 SDYREKFEPIGRRVVGKCKGLPFAVKILGSL  409 (597)
Q Consensus       379 ~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~  409 (597)
                       ..   ..+..+.|.+.+..-+-++..++..
T Consensus       372 -~l---s~eal~~L~~ys~~gRraln~L~~~  398 (615)
T TIGR02903       372 -HL---AAGVEELIARYTIEGRKAVNILADV  398 (615)
T ss_pred             -CC---CHHHHHHHHHCCCcHHHHHHHHHHH
Confidence             11   1345566666666557777766544

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.48  E-value=4e-06  Score=88.79  Aligned_cols=213  Identities=16%  Similarity=0.178  Sum_probs=112.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-...|...+....         -+..+.++|++|+||||+|+.+++.........   +.++..        
T Consensus        14 ~divGq~~i~~~L~~~i~~~~---------l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~---~~pc~~--------   73 (472)
T PRK14962         14 SEVVGQDHVKKLIINALKKNS---------ISHAYIFAGPRGTGKTTVARILAKSLNCENRKG---VEPCNE--------   73 (472)
T ss_pred             HHccCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhccccCCC---CCCCcc--------
Confidence            568999988888888776322         234689999999999999999977311110000   000000        


Q ss_pred             hhhhhhcccchHHHHHHHHHH-------hccCC-CCchhhHHHHHHHHHH-HhcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILE-------SLKGS-VSSQVEMETVLQYINE-FVQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~-------~l~~~-~~~~~~~~~~~~~l~~-~L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -.....+..       .+... .....+...+.+.+.. -..+++-++|+|+++... ....+.+...
T Consensus        74 ------------c~~c~~i~~g~~~dv~el~aa~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt-~~a~~~LLk~  140 (472)
T PRK14962         74 ------------CRACRSIDEGTFMDVIELDAASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLT-KEAFNALLKT  140 (472)
T ss_pred             ------------cHHHHHHhcCCCCccEEEeCcccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhH-HHHHHHHHHH
Confidence                        000000000       00000 0011111111111111 122466799999997654 3345666666


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +........+|++|.+......         .+...+ .+.+.+++.++....+...+...+...    ..+....|++.
T Consensus       141 LE~p~~~vv~Ilattn~~kl~~---------~L~SR~~vv~f~~l~~~el~~~L~~i~~~egi~i----~~eal~~Ia~~  207 (472)
T PRK14962        141 LEEPPSHVVFVLATTNLEKVPP---------TIISRCQVIEFRNISDELIIKRLQEVAEAEGIEI----DREALSFIAKR  207 (472)
T ss_pred             HHhCCCcEEEEEEeCChHhhhH---------HHhcCcEEEEECCccHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            6554445555555543210000         111122 289999999999999888774322211    14567788887


Q ss_pred             cCC-chHHHHHHHhhhcc--C-CCHHHHHHHHh
Q 041007          396 CKG-LPFAVKILGSLLRF--K-TSIKEWQSVLD  424 (597)
Q Consensus       396 ~~G-lPLai~~~~~~l~~--~-~~~~~w~~~l~  424 (597)
                      ++| .+.++..+-.+...  . -+.+....++.
T Consensus       208 s~GdlR~aln~Le~l~~~~~~~It~e~V~~~l~  240 (472)
T PRK14962        208 ASGGLRDALTMLEQVWKFSEGKITLETVHEALG  240 (472)
T ss_pred             hCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHc
Confidence            865 57777777654321  1 24555555443

>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=98.48  E-value=2.6e-06  Score=81.22  Aligned_cols=174  Identities=13%  Similarity=0.172  Sum_probs=96.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCC--eeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFD--KRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      ....+.|+|+.|+|||.|.+.+++  ......+  .++++++                      .+....+...+...  
T Consensus        33 ~~~~l~l~G~~G~GKTHLL~Ai~~--~~~~~~~~~~v~y~~~----------------------~~f~~~~~~~~~~~--   86 (219)
T PF00308_consen   33 RYNPLFLYGPSGLGKTHLLQAIAN--EAQKQHPGKRVVYLSA----------------------EEFIREFADALRDG--   86 (219)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHHH--HHHHHCTTS-EEEEEH----------------------HHHHHHHHHHHHTT--
T ss_pred             CCCceEEECCCCCCHHHHHHHHHH--HHHhccccccceeecH----------------------HHHHHHHHHHHHcc--
Confidence            455689999999999999999999  4443322  3556653                      44444444444331  


Q ss_pred             chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHH-HHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccc
Q 041007          274 SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQL-MYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN  351 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l-~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~  351 (597)
                         .    ...+.+.+. .-=+|+|||++.......|... ...+.. ...|.+||+|+...+........++.+ ....
T Consensus        87 ---~----~~~~~~~~~-~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l~~~~~~L~S-Rl~~  157 (219)
T PF00308_consen   87 ---E----IEEFKDRLR-SADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSELSGLLPDLRS-RLSW  157 (219)
T ss_dssp             ---S----HHHHHHHHC-TSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTTTTS-HHHHH-HHHC
T ss_pred             ---c----chhhhhhhh-cCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccccccChhhhh-hHhh
Confidence               1    122333333 3458899999876644455543 333322 245678999997764322211111000 0111


Q ss_pred             cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHh
Q 041007          352 MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGS  408 (597)
Q Consensus       352 ~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~  408 (597)
                      ...+++.+++.++-.+++.+.+...+..    --++++.-|++.+.+..-.+..+-.
T Consensus       158 Gl~~~l~~pd~~~r~~il~~~a~~~~~~----l~~~v~~~l~~~~~~~~r~L~~~l~  210 (219)
T PF00308_consen  158 GLVVELQPPDDEDRRRILQKKAKERGIE----LPEEVIEYLARRFRRDVRELEGALN  210 (219)
T ss_dssp             SEEEEE----HHHHHHHHHHHHHHTT------S-HHHHHHHHHHTTSSHHHHHHHHH
T ss_pred             cchhhcCCCCHHHHHHHHHHHHHHhCCC----CcHHHHHHHHHhhcCCHHHHHHHHH
Confidence            1229999999999999999988543322    1255677788887776665554433

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.

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=98.48  E-value=4.1e-06  Score=80.76  Aligned_cols=157  Identities=15%  Similarity=0.135  Sum_probs=89.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      ..+.+.|+|++|+|||+||+.+++.  ....-....++++....                      .. +          
T Consensus        41 ~~~~~~l~G~~G~GKT~La~ai~~~--~~~~~~~~~~i~~~~~~----------------------~~-~----------   85 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLLQALVAD--ASYGGRNARYLDAASPL----------------------LA-F----------   85 (227)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHH--HHhCCCcEEEEehHHhH----------------------HH-H----------
Confidence            3468899999999999999999884  22211233444432110                      00 0          


Q ss_pred             hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCc-EEEEEccCCCCCCCcccccccccCcc-c-
Q 041007          276 VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGS-RILVTRSGGKNGTNMTEIGLGEKNGT-N-  351 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs-~IIvTtR~~~~~~~~~~~~~~~~~~~-~-  351 (597)
                                 ... ...-+||+||++..+ ...-..+...+... ..+. .+|+|++.......     +. .... . 
T Consensus        86 -----------~~~-~~~~~liiDdi~~l~-~~~~~~L~~~~~~~~~~~~~~vl~~~~~~~~~~~-----l~-~~L~sr~  146 (227)
T PRK08903         86 -----------DFD-PEAELYAVDDVERLD-DAQQIALFNLFNRVRAHGQGALLVAGPAAPLALP-----LR-EDLRTRL  146 (227)
T ss_pred             -----------hhc-ccCCEEEEeChhhcC-chHHHHHHHHHHHHHHcCCcEEEEeCCCCHHhCC-----CC-HHHHHHH
Confidence                       011 234479999997654 22333344444331 2333 46666664311110     00 0111 1 


Q ss_pred             --cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhh
Q 041007          352 --MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLL  410 (597)
Q Consensus       352 --~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l  410 (597)
                        ...+.+.|+++++-..++.+.+-..+. .   --.+....|++.+.|++..+..+...+
T Consensus       147 ~~~~~i~l~pl~~~~~~~~l~~~~~~~~v-~---l~~~al~~L~~~~~gn~~~l~~~l~~l  203 (227)
T PRK08903        147 GWGLVYELKPLSDADKIAALKAAAAERGL-Q---LADEVPDYLLTHFRRDMPSLMALLDAL  203 (227)
T ss_pred             hcCeEEEecCCCHHHHHHHHHHHHHHcCC-C---CCHHHHHHHHHhccCCHHHHHHHHHHH
Confidence              123899999998877777765432221 1   124577888999999999887776655

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

Probab=98.48  E-value=3.8e-06  Score=93.14  Aligned_cols=177  Identities=17%  Similarity=0.244  Sum_probs=95.3

Q ss_pred             CccccchhhHH---HHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQ---KILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~---~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      .+|+|.+..+.   .|...+..          .....+.|+|++|+||||||+.+++  ....+|.   .+++.  ... 
T Consensus        28 dd~vGQe~ii~~~~~L~~~i~~----------~~~~slLL~GPpGtGKTTLA~aIA~--~~~~~f~---~lna~--~~~-   89 (725)
T PRK13341         28 EEFVGQDHILGEGRLLRRAIKA----------DRVGSLILYGPPGVGKTTLARIIAN--HTRAHFS---SLNAV--LAG-   89 (725)
T ss_pred             HHhcCcHHHhhhhHHHHHHHhc----------CCCceEEEECCCCCCHHHHHHHHHH--HhcCcce---eehhh--hhh-
Confidence            46889888774   45566652          2456789999999999999999998  3444431   11111  000 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHh--cCceEEEEEecccCCCCcchHHHHHHhhcCC
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFV--QGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG  320 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L--~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~  320 (597)
                                     ..                 +...........+  .+++.+|||||++..+ ...++.+...+   
T Consensus        90 ---------------i~-----------------dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln-~~qQdaLL~~l---  133 (725)
T PRK13341         90 ---------------VK-----------------DLRAEVDRAKERLERHGKRTILFIDEVHRFN-KAQQDALLPWV---  133 (725)
T ss_pred             ---------------hH-----------------HHHHHHHHHHHHhhhcCCceEEEEeChhhCC-HHHHHHHHHHh---
Confidence                           00                 0111111111111  2467899999997665 33444454433   


Q ss_pred             CCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCC---CCCCccchHHHHHHHHHhcC
Q 041007          321 SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGR---SSDYREKFEPIGRRVVGKCK  397 (597)
Q Consensus       321 ~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~---~~~~~~~~~~~~~~I~~~~~  397 (597)
                      ..+..+++++........... .    -..+...+.+.+|+.++...++.+.+....   ......-..+....|++.+.
T Consensus       134 E~g~IiLI~aTTenp~~~l~~-a----L~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~  208 (725)
T PRK13341        134 ENGTITLIGATTENPYFEVNK-A----LVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVAN  208 (725)
T ss_pred             cCceEEEEEecCCChHhhhhh-H----hhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCC
Confidence            235555554333211110000 0    001112289999999999999988764100   00011112456678888888


Q ss_pred             CchH
Q 041007          398 GLPF  401 (597)
Q Consensus       398 GlPL  401 (597)
                      |.--
T Consensus       209 GD~R  212 (725)
T PRK13341        209 GDAR  212 (725)
T ss_pred             CCHH
Confidence            8643

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=98.45  E-value=7.2e-06  Score=76.50  Aligned_cols=91  Identities=11%  Similarity=0.052  Sum_probs=62.7

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf  369 (597)
                      +.+-++|+||++... ....+.+...+...+..+.+|++|.+......         .+... ..+++.+++.++..+.+
T Consensus        95 ~~~kviiide~~~l~-~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~---------~i~sr~~~~~~~~~~~~~~~~~l  164 (188)
T TIGR00678        95 SGRRVVIIEDAERMN-EAAANALLKTLEEPPPNTLFILITPSPEKLLP---------TIRSRCQVLPFPPLSEEALLQWL  164 (188)
T ss_pred             CCeEEEEEechhhhC-HHHHHHHHHHhcCCCCCeEEEEEECChHhChH---------HHHhhcEEeeCCCCCHHHHHHHH
Confidence            556789999997766 55677788888776667777777764411100         11111 22999999999999888


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPL  401 (597)
                      .+.    +  .    ..+.+..|++.++|.|.
T Consensus       165 ~~~----g--i----~~~~~~~i~~~~~g~~r  186 (188)
T TIGR00678       165 IRQ----G--I----SEEAAELLLALAGGSPG  186 (188)
T ss_pred             HHc----C--C----CHHHHHHHHHHcCCCcc
Confidence            876    1  1    14568899999999885

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.45  E-value=5.4e-06  Score=89.89  Aligned_cols=196  Identities=13%  Similarity=0.140  Sum_probs=109.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc--CCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN--FDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~--F~~~~wv~~~~~~~~~~  243 (597)
                      .++||-+.-++.|..++....         -...+.++|+.|+||||+|+.+.+...-...  ......-.+..      
T Consensus        16 ~dviGQe~vv~~L~~~l~~~r---------l~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~------   80 (618)
T PRK14951         16 SEMVGQEHVVQALTNALTQQR---------LHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGV------   80 (618)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCc------
Confidence            468999998999999987432         2456789999999999999999652110000  00000000000      


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhc-----cCCCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHH
Q 041007          244 VARDEISVARDRDEIRVAKAILESL-----KGSVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l-----~~~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                                    -.....|...-     ..........+++.+.+...    ..++.-++|||+++..+ ...++.+.
T Consensus        81 --------------C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls-~~a~NaLL  145 (618)
T PRK14951         81 --------------CQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLT-NTAFNAML  145 (618)
T ss_pred             --------------cHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCC-HHHHHHHH
Confidence                          11111110000     00000011122222222211    12445689999998876 66777788


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      ..+......+.+|++|.+......         .+...+ .+++++++.++..+.+.+.+...+...    ..+....|+
T Consensus       146 KtLEEPP~~~~fIL~Ttd~~kil~---------TIlSRc~~~~f~~Ls~eei~~~L~~i~~~egi~i----e~~AL~~La  212 (618)
T PRK14951        146 KTLEEPPEYLKFVLATTDPQKVPV---------TVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPA----EPQALRLLA  212 (618)
T ss_pred             HhcccCCCCeEEEEEECCchhhhH---------HHHHhceeeecCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHH
Confidence            777766667777766644311000         111122 299999999999999988765433221    145678899


Q ss_pred             HhcCCchHHHH
Q 041007          394 GKCKGLPFAVK  404 (597)
Q Consensus       394 ~~~~GlPLai~  404 (597)
                      +.++|.+--+.
T Consensus       213 ~~s~GslR~al  223 (618)
T PRK14951        213 RAARGSMRDAL  223 (618)
T ss_pred             HHcCCCHHHHH
Confidence            99999775443

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

Probab=98.42  E-value=7.4e-07  Score=86.09  Aligned_cols=90  Identities=17%  Similarity=0.179  Sum_probs=59.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC--CchhhhhhhhhhhcccchHHHHHHHHHHhccCCC-
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP--RDEIRVARDEISVARDRDEIRVAKAILESLKGSV-  272 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~-  272 (597)
                      ....++|.|++|+|||||++.++++.... +|+..+|+.+.+.  .+.                .++++.+...+-... 
T Consensus        15 ~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~-~fdv~~~v~vI~er~~ev----------------~el~~~I~~~~v~~~~   77 (249)
T cd01128          15 KGQRGLIVAPPKAGKTTLLQSIANAITKN-HPEVYLIVLLIDERPEEV----------------TDMQRSVKGEVIASTF   77 (249)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhccccc-cCCeEEEEEEccCCCccH----------------HHHHHHhccEEEEecC
Confidence            45789999999999999999999974433 8999999997766  455                777777733222111 


Q ss_pred             --Cchh---hHHHHHHHHHHH-hcCceEEEEEeccc
Q 041007          273 --SSQV---EMETVLQYINEF-VQGKKVLLVLDDLW  302 (597)
Q Consensus       273 --~~~~---~~~~~~~~l~~~-L~~kr~LLVLDdv~  302 (597)
                        +...   -..........+ -.+++.+|++|++.
T Consensus        78 ~~~~~~~~~~~~~~~~~a~~~~~~G~~vll~iDei~  113 (249)
T cd01128          78 DEPPERHVQVAEMVLEKAKRLVEHGKDVVILLDSIT  113 (249)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHH
Confidence              1111   111222222222 24789999999994

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.

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.42  E-value=7.9e-06  Score=88.07  Aligned_cols=184  Identities=15%  Similarity=0.156  Sum_probs=108.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-------------------c
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-------------------N  226 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-------------------~  226 (597)
                      .+++|.+.-++.|..++....         -...+.++|+.|+||||+|+.+.+...-..                   .
T Consensus        16 ~divGq~~v~~~L~~~i~~~~---------~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~~~   86 (527)
T PRK14969         16 SELVGQEHVVRALTNALEQQR---------LHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGR   86 (527)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCC
Confidence            468899999999999987432         234678999999999999999976311100                   0


Q ss_pred             CCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHH-HhcCceEEEEEecccCCC
Q 041007          227 FDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINE-FVQGKKVLLVLDDLWWNA  305 (597)
Q Consensus       227 F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~-~L~~kr~LLVLDdv~~~~  305 (597)
                      |...+++..+.                                  .....+...+...+.. -..+++-++|+|+++...
T Consensus        87 ~~d~~ei~~~~----------------------------------~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls  132 (527)
T PRK14969         87 FVDLIEVDAAS----------------------------------NTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLS  132 (527)
T ss_pred             CCceeEeeccc----------------------------------cCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCC
Confidence            11111111110                                  0011111111111111 013566799999998766


Q ss_pred             CcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccc
Q 041007          306 YPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREK  384 (597)
Q Consensus       306 ~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~  384 (597)
                       ....+.+...+......+.+|++|.+......         .+...+. +++.+++.++....+.+.+...+..    .
T Consensus       133 -~~a~naLLK~LEepp~~~~fIL~t~d~~kil~---------tI~SRc~~~~f~~l~~~~i~~~L~~il~~egi~----~  198 (527)
T PRK14969        133 -KSAFNAMLKTLEEPPEHVKFILATTDPQKIPV---------TVLSRCLQFNLKQMPPPLIVSHLQHILEQENIP----F  198 (527)
T ss_pred             -HHHHHHHHHHHhCCCCCEEEEEEeCChhhCch---------hHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCC----C
Confidence             45567777777776667777766644311100         1111122 9999999999998888776432211    1


Q ss_pred             hHHHHHHHHHhcCCchH-HHHHH
Q 041007          385 FEPIGRRVVGKCKGLPF-AVKIL  406 (597)
Q Consensus       385 ~~~~~~~I~~~~~GlPL-ai~~~  406 (597)
                      .......|++.++|.+- |+..+
T Consensus       199 ~~~al~~la~~s~Gslr~al~ll  221 (527)
T PRK14969        199 DATALQLLARAAAGSMRDALSLL  221 (527)
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHH
Confidence            24556889999999775 44444

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.41  E-value=9.6e-06  Score=85.58  Aligned_cols=182  Identities=14%  Similarity=0.157  Sum_probs=110.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc--------------------
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA--------------------  225 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~--------------------  225 (597)
                      .++||.+.-++.|...+....         -...+.++|+.|+||||+|+.+++.  ...                    
T Consensus        13 ~dliGQe~vv~~L~~a~~~~r---------i~ha~Lf~Gp~G~GKTT~ArilAk~--LnC~~~~~~~pCg~C~~C~~i~~   81 (491)
T PRK14964         13 KDLVGQDVLVRILRNAFTLNK---------IPQSILLVGASGVGKTTCARIISLC--LNCSNGPTSDPCGTCHNCISIKN   81 (491)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCceEEEECCCCccHHHHHHHHHHH--HcCcCCCCCCCccccHHHHHHhc
Confidence            468999999998888887432         2458999999999999999988762  111                    


Q ss_pred             -cCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH-hcCceEEEEEecccC
Q 041007          226 -NFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWW  303 (597)
Q Consensus       226 -~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~  303 (597)
                       .+..++.++.+....                                  .++...+.+..... ..++.-++|+|+++.
T Consensus        82 ~~~~Dv~eidaas~~~----------------------------------vddIR~Iie~~~~~P~~~~~KVvIIDEah~  127 (491)
T PRK14964         82 SNHPDVIEIDAASNTS----------------------------------VDDIKVILENSCYLPISSKFKVYIIDEVHM  127 (491)
T ss_pred             cCCCCEEEEecccCCC----------------------------------HHHHHHHHHHHHhccccCCceEEEEeChHh
Confidence             111122222211111                                  11111122111111 124566899999977


Q ss_pred             CCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCc
Q 041007          304 NAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYR  382 (597)
Q Consensus       304 ~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~  382 (597)
                      .. ....+.+...+..-.+.+.+|++|........         .+...+. +++.+++.++....+...+...+...  
T Consensus       128 Ls-~~A~NaLLK~LEePp~~v~fIlatte~~Kl~~---------tI~SRc~~~~f~~l~~~el~~~L~~ia~~Egi~i--  195 (491)
T PRK14964        128 LS-NSAFNALLKTLEEPAPHVKFILATTEVKKIPV---------TIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEH--  195 (491)
T ss_pred             CC-HHHHHHHHHHHhCCCCCeEEEEEeCChHHHHH---------HHHHhheeeecccccHHHHHHHHHHHHHHcCCCC--
Confidence            65 55677788888776777877777643310000         1111122 89999999999999988775433221  


Q ss_pred             cchHHHHHHHHHhcCCchH-HHHHH
Q 041007          383 EKFEPIGRRVVGKCKGLPF-AVKIL  406 (597)
Q Consensus       383 ~~~~~~~~~I~~~~~GlPL-ai~~~  406 (597)
                        ..+.+..|++.++|.+- ++..+
T Consensus       196 --~~eAL~lIa~~s~GslR~alslL  218 (491)
T PRK14964        196 --DEESLKLIAENSSGSMRNALFLL  218 (491)
T ss_pred             --CHHHHHHHHHHcCCCHHHHHHHH
Confidence              24566789999999875 33433

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=98.39  E-value=7.5e-06  Score=87.76  Aligned_cols=197  Identities=14%  Similarity=0.167  Sum_probs=110.0

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|++.-++.|..++....         ....+.++|+.|+||||+|+.+++...-..      |.... +...    
T Consensus        16 ~dIIGQe~iv~~L~~aI~~~r---------l~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~------~~~~~-~Cg~----   75 (605)
T PRK05896         16 KQIIGQELIKKILVNAILNNK---------LTHAYIFSGPRGIGKTSIAKIFAKAINCLN------PKDGD-CCNS----   75 (605)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCceEEEECCCCCCHHHHHHHHHHHhcCCC------CCCCC-CCcc----
Confidence            468899999999999886432         246789999999999999999977311111      11100 0000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-------ccCCC-CchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-------LKGSV-SSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-------l~~~~-~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -...+.+...       +.+.. ....+...+...+... ..+++-++|+|+++... ...+..+...
T Consensus        76 ------------C~sCr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt-~~A~NaLLKt  142 (605)
T PRK05896         76 ------------CSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLS-TSAWNALLKT  142 (605)
T ss_pred             ------------cHHHHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCC-HHHHHHHHHH
Confidence                        0111111100       00000 0111122222222211 11334479999997765 5567778877


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +...+..+.+|++|........         .+...+ .+++.+++.++....+...+...+...    ..+.+..|++.
T Consensus       143 LEEPp~~tvfIL~Tt~~~KLl~---------TI~SRcq~ieF~~Ls~~eL~~~L~~il~kegi~I----s~eal~~La~l  209 (605)
T PRK05896        143 LEEPPKHVVFIFATTEFQKIPL---------TIISRCQRYNFKKLNNSELQELLKSIAKKEKIKI----EDNAIDKIADL  209 (605)
T ss_pred             HHhCCCcEEEEEECCChHhhhH---------HHHhhhhhcccCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            7666666677666643310000         111112 299999999999998888764322111    14567889999


Q ss_pred             cCCchH-HHHHHHh
Q 041007          396 CKGLPF-AVKILGS  408 (597)
Q Consensus       396 ~~GlPL-ai~~~~~  408 (597)
                      ++|.+- |+..+-.
T Consensus       210 S~GdlR~AlnlLek  223 (605)
T PRK05896        210 ADGSLRDGLSILDQ  223 (605)
T ss_pred             cCCcHHHHHHHHHH
Confidence            999664 5555444

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.38  E-value=8e-06  Score=82.70  Aligned_cols=221  Identities=18%  Similarity=0.183  Sum_probs=124.4

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      .+...+||+.|+..+..++...-.      ....+.+-|.|.+|.|||.+...++.+..-...-..++++++..-...  
T Consensus       148 ~p~~l~gRe~e~~~v~~F~~~hle------~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~--  219 (529)
T KOG2227|consen  148 PPGTLKGRELEMDIVREFFSLHLE------LNTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEA--  219 (529)
T ss_pred             CCCCccchHHHHHHHHHHHHhhhh------cccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccch--
Confidence            457789999999999999975543      235678999999999999999999885322222234567766544444  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcC--ceEEEEEecccCCCCcchHHHHHHhhcC-C
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQG--KKVLLVLDDLWWNAYPRYWEQLMYSLKS-G  320 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~--kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~  320 (597)
                                    ..++..|...+........+..+....+.++..+  ..+|+|||..+... ...-..+...|.+ .
T Consensus       220 --------------~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~-tr~~~vLy~lFewp~  284 (529)
T KOG2227|consen  220 --------------SAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLI-TRSQTVLYTLFEWPK  284 (529)
T ss_pred             --------------HHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHh-hcccceeeeehhccc
Confidence                          6677777766622111111114445555555553  36899999984432 1111222222322 3


Q ss_pred             CCCcEEEEEccCCCCCCCcccccccccCccccce---eecCCCChHHHHHHHHHHhccCCCC-CCccchHHHHHHHHHhc
Q 041007          321 SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME---IGLGELSEEECRSLFRQIAFHGRSS-DYREKFEPIGRRVVGKC  396 (597)
Q Consensus       321 ~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~---~~l~~Ls~~es~~Lf~~~~~~~~~~-~~~~~~~~~~~~I~~~~  396 (597)
                      -+++++|+..--.  ..++.+..++.......+.   +...|.+.++..++|..+.-..... ..+..++-.|++++.-.
T Consensus       285 lp~sr~iLiGiAN--slDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~S  362 (529)
T KOG2227|consen  285 LPNSRIILIGIAN--SLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPS  362 (529)
T ss_pred             CCcceeeeeeehh--hhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCc
Confidence            3455555432111  1111122222222211111   7889999999999999987432222 22223344455555555


Q ss_pred             CCchHHHHHHHhh
Q 041007          397 KGLPFAVKILGSL  409 (597)
Q Consensus       397 ~GlPLai~~~~~~  409 (597)
                      |.+--|+.+.-+.
T Consensus       363 GDlRkaLdv~R~a  375 (529)
T KOG2227|consen  363 GDLRKALDVCRRA  375 (529)
T ss_pred             hhHHHHHHHHHHH
Confidence            5555666555433

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.37  E-value=9.4e-06  Score=84.86  Aligned_cols=197  Identities=14%  Similarity=0.129  Sum_probs=109.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE-ecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS-ASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~-~~~~~~~~~~  244 (597)
                      .+++|.+.-++.|..++....         -...+.++|++|+||||+|..+++...-...+...-|.. ...+...   
T Consensus        16 ~eiiGq~~~~~~L~~~~~~~~---------~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~---   83 (397)
T PRK14955         16 ADITAQEHITRTIQNSLRMGR---------VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGE---   83 (397)
T ss_pred             hhccChHHHHHHHHHHHHhCC---------cceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCC---
Confidence            568899999999999887432         234588999999999999999877321111111000110 0000000   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccC-----CCCchhhHHHHHHHHHHHh-----cCceEEEEEecccCCCCcchHHHHH
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKG-----SVSSQVEMETVLQYINEFV-----QGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~-----~~~~~~~~~~~~~~l~~~L-----~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                                   -...+.+......     ........+++.+ +.+.+     .+++-++|+|+++... ...++.+.
T Consensus        84 -------------c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~-l~~~~~~~p~~~~~kvvIIdea~~l~-~~~~~~LL  148 (397)
T PRK14955         84 -------------CESCRDFDAGTSLNISEFDAASNNSVDDIRL-LRENVRYGPQKGRYRVYIIDEVHMLS-IAAFNAFL  148 (397)
T ss_pred             -------------CHHHHHHhcCCCCCeEeecccccCCHHHHHH-HHHHHhhchhcCCeEEEEEeChhhCC-HHHHHHHH
Confidence                         0111111110000     0000111222222 22222     2456688999997765 45677888


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccc----cce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN----MME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIG  389 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~----~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~  389 (597)
                      ..+......+.+|++|....             .+..    .+. +++.+++.++....+...+-..+..    -..+.+
T Consensus       149 k~LEep~~~t~~Il~t~~~~-------------kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~~~g~~----i~~~al  211 (397)
T PRK14955        149 KTLEEPPPHAIFIFATTELH-------------KIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGIS----VDADAL  211 (397)
T ss_pred             HHHhcCCCCeEEEEEeCChH-------------HhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHcCCC----CCHHHH
Confidence            88776666777766653321             2211    111 8999999999998888776322211    125577


Q ss_pred             HHHHHhcCCchH-HHHHH
Q 041007          390 RRVVGKCKGLPF-AVKIL  406 (597)
Q Consensus       390 ~~I~~~~~GlPL-ai~~~  406 (597)
                      ..|++.++|.+- ++..+
T Consensus       212 ~~l~~~s~g~lr~a~~~L  229 (397)
T PRK14955        212 QLIGRKAQGSMRDAQSIL  229 (397)
T ss_pred             HHHHHHcCCCHHHHHHHH
Confidence            899999999775 44433

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

Probab=98.36  E-value=9.5e-06  Score=76.55  Aligned_cols=111  Identities=15%  Similarity=0.220  Sum_probs=70.9

Q ss_pred             ccCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          162 VIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       162 ~~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      .+....++|-|.+++.|.+.....-.      .....-+.+||..|+|||+|++.+.+.  ....= . --|.+..    
T Consensus        23 ~~~l~~L~Gie~Qk~~l~~Nt~~Fl~------G~pannvLL~G~rGtGKSSlVkall~~--y~~~G-L-RlIev~k----   88 (249)
T PF05673_consen   23 PIRLDDLIGIERQKEALIENTEQFLQ------GLPANNVLLWGARGTGKSSLVKALLNE--YADQG-L-RLIEVSK----   88 (249)
T ss_pred             CCCHHHhcCHHHHHHHHHHHHHHHHc------CCCCcceEEecCCCCCHHHHHHHHHHH--HhhcC-c-eEEEECH----
Confidence            45567899999999999876654433      224567889999999999999999883  22211 1 1122211    


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS  319 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~  319 (597)
                                                     ....++..+.+.++.  ...+|+|++||+--.........+...|..
T Consensus        89 -------------------------------~~L~~l~~l~~~l~~--~~~kFIlf~DDLsFe~~d~~yk~LKs~LeG  133 (249)
T PF05673_consen   89 -------------------------------EDLGDLPELLDLLRD--RPYKFILFCDDLSFEEGDTEYKALKSVLEG  133 (249)
T ss_pred             -------------------------------HHhccHHHHHHHHhc--CCCCEEEEecCCCCCCCcHHHHHHHHHhcC
Confidence                                           111223334444442  357999999999655555667777777754

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=98.36  E-value=1.5e-05  Score=82.44  Aligned_cols=184  Identities=13%  Similarity=0.126  Sum_probs=107.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh--ccCC---------------
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK--ANFD---------------  228 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~--~~F~---------------  228 (597)
                      ..++|.+..++.|..++....         -...+.++|++|+|||++|+.+.....-.  ..+.               
T Consensus        14 ~~iig~~~~~~~l~~~~~~~~---------~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~   84 (355)
T TIGR02397        14 EDVIGQEHIVQTLKNAIKNGR---------IAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGS   84 (355)
T ss_pred             hhccCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhcCC
Confidence            467999999999999997432         24578899999999999998887631100  0110               


Q ss_pred             --eeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCC
Q 041007          229 --KRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNA  305 (597)
Q Consensus       229 --~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~  305 (597)
                        ..+++.....                                  ....+...+...+... ..+++-++|+|++....
T Consensus        85 ~~~~~~~~~~~~----------------------------------~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~  130 (355)
T TIGR02397        85 SLDVIEIDAASN----------------------------------NGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLS  130 (355)
T ss_pred             CCCEEEeecccc----------------------------------CCHHHHHHHHHHHhcCcccCCceEEEEeChhhcC
Confidence              0111111000                                  0011112222222111 12455688999986654


Q ss_pred             CcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccc
Q 041007          306 YPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREK  384 (597)
Q Consensus       306 ~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~  384 (597)
                       ....+.+...+......+.+|++|.+......         .+.. ...+++.+++.++..+++...+-..+...    
T Consensus       131 -~~~~~~Ll~~le~~~~~~~lIl~~~~~~~l~~---------~l~sr~~~~~~~~~~~~~l~~~l~~~~~~~g~~i----  196 (355)
T TIGR02397       131 -KSAFNALLKTLEEPPEHVVFILATTEPHKIPA---------TILSRCQRFDFKRIPLEDIVERLKKILDKEGIKI----  196 (355)
T ss_pred             -HHHHHHHHHHHhCCccceeEEEEeCCHHHHHH---------HHHhheeEEEcCCCCHHHHHHHHHHHHHHcCCCC----
Confidence             34566677777655566777777644310000         1111 12288999999999999888764322211    


Q ss_pred             hHHHHHHHHHhcCCchHHHHHH
Q 041007          385 FEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       385 ~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      ..+.+..|++.++|.|..+...
T Consensus       197 ~~~a~~~l~~~~~g~~~~a~~~  218 (355)
T TIGR02397       197 EDEALELIARAADGSLRDALSL  218 (355)
T ss_pred             CHHHHHHHHHHcCCChHHHHHH
Confidence            1457788999999998765444

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.36  E-value=1e-05  Score=86.64  Aligned_cols=195  Identities=11%  Similarity=0.115  Sum_probs=109.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .++||-+.-++.|..++....         -...+.++|+.|+||||+|+.+.+..--...+..   -++..        
T Consensus        16 ~divGq~~v~~~L~~~~~~~~---------l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~---~pCg~--------   75 (509)
T PRK14958         16 QEVIGQAPVVRALSNALDQQY---------LHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSA---NPCND--------   75 (509)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC---------CCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCc---ccCCC--------
Confidence            468999999999999997432         2346789999999999999998773111111100   00000        


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-------ccC-CCCchhhHHHHHHHHHH-HhcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-------LKG-SVSSQVEMETVLQYINE-FVQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-------l~~-~~~~~~~~~~~~~~l~~-~L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -.....|...       +.. ......+...+.+.+.- -..++.-++|+|+++... ....+.+...
T Consensus        76 ------------C~~C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls-~~a~naLLk~  142 (509)
T PRK14958         76 ------------CENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLS-GHSFNALLKT  142 (509)
T ss_pred             ------------CHHHHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcC-HHHHHHHHHH
Confidence                        0000000000       000 00011111112211111 112556689999998776 5677778887


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +......+++|++|.+......         .+...+. +++.+++.++....+.+.+...+...    ..+....|++.
T Consensus       143 LEepp~~~~fIlattd~~kl~~---------tI~SRc~~~~f~~l~~~~i~~~l~~il~~egi~~----~~~al~~ia~~  209 (509)
T PRK14958        143 LEEPPSHVKFILATTDHHKLPV---------TVLSRCLQFHLAQLPPLQIAAHCQHLLKEENVEF----ENAALDLLARA  209 (509)
T ss_pred             HhccCCCeEEEEEECChHhchH---------HHHHHhhhhhcCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            7776677877776644311000         1111122 89999999998887777664332211    13456789999


Q ss_pred             cCCchHHH-HHH
Q 041007          396 CKGLPFAV-KIL  406 (597)
Q Consensus       396 ~~GlPLai-~~~  406 (597)
                      ++|.+--+ ..+
T Consensus       210 s~GslR~al~lL  221 (509)
T PRK14958        210 ANGSVRDALSLL  221 (509)
T ss_pred             cCCcHHHHHHHH
Confidence            99987544 444

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=98.33  E-value=1.2e-05  Score=84.95  Aligned_cols=177  Identities=15%  Similarity=0.158  Sum_probs=100.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccC--CeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANF--DKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ...+.|+|..|+|||+|++.+++.  .....  ..+++++.                      ..+...+...+....  
T Consensus       141 ~npl~i~G~~G~GKTHLl~Ai~~~--l~~~~~~~~v~yv~~----------------------~~f~~~~~~~l~~~~--  194 (450)
T PRK14087        141 YNPLFIYGESGMGKTHLLKAAKNY--IESNFSDLKVSYMSG----------------------DEFARKAVDILQKTH--  194 (450)
T ss_pred             cCceEEECCCCCcHHHHHHHHHHH--HHHhCCCCeEEEEEH----------------------HHHHHHHHHHHHHhh--
Confidence            456899999999999999999883  33222  23445543                      444555554443210  


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchH-HHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccc
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYW-EQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM  352 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~-~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~  352 (597)
                           .....+.+.+. ..-+|||||++.......+ +.+...+.. ...+..||+|+...+.......-++.+ .....
T Consensus       195 -----~~~~~~~~~~~-~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~S-R~~~G  267 (450)
T PRK14087        195 -----KEIEQFKNEIC-QNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLIT-RFNMG  267 (450)
T ss_pred             -----hHHHHHHHHhc-cCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHH-HHhCC
Confidence                 11222333333 3448899999765422233 334444433 234557888877653211100000000 00111


Q ss_pred             ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHh
Q 041007          353 MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGS  408 (597)
Q Consensus       353 ~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~  408 (597)
                      ..+.+.+++.++-.+++.+.+-..+..  ..-..++..-|++.++|.|-.+.-+..
T Consensus       268 l~~~L~~pd~e~r~~iL~~~~~~~gl~--~~l~~evl~~Ia~~~~gd~R~L~gaL~  321 (450)
T PRK14087        268 LSIAIQKLDNKTATAIIKKEIKNQNIK--QEVTEEAINFISNYYSDDVRKIKGSVS  321 (450)
T ss_pred             ceeccCCcCHHHHHHHHHHHHHhcCCC--CCCCHHHHHHHHHccCCCHHHHHHHHH
Confidence            227899999999999999988532210  112256788999999999987765543

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=98.31  E-value=2.1e-05  Score=85.63  Aligned_cols=197  Identities=11%  Similarity=0.091  Sum_probs=112.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCC--eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFD--KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~  243 (597)
                      .+++|.+..++.|..++....         -...+.++|+.|+||||+|+.+++.........  ...+-.+..      
T Consensus        24 ~dliGq~~~v~~L~~~~~~gr---------i~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~------   88 (598)
T PRK09111         24 DDLIGQEAMVRTLTNAFETGR---------IAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGV------   88 (598)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcc------
Confidence            468999999999999997432         245789999999999999999987421111100  000000000      


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccC--------CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHH
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKG--------SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~--------~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                                    -.....|...-..        ......+..++.+.+... ..+++-++|+|+++... ....+.+.
T Consensus        89 --------------c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls-~~a~naLL  153 (598)
T PRK09111         89 --------------GEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLS-TAAFNALL  153 (598)
T ss_pred             --------------cHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCC-HHHHHHHH
Confidence                          0111111111100        001112222222222211 12455689999997766 45677788


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      ..+..-..++.+|++|........         .+...+. +++.+++.++....+.+.+...+...    ..+....|+
T Consensus       154 KtLEePp~~~~fIl~tte~~kll~---------tI~SRcq~~~f~~l~~~el~~~L~~i~~kegi~i----~~eAl~lIa  220 (598)
T PRK09111        154 KTLEEPPPHVKFIFATTEIRKVPV---------TVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEV----EDEALALIA  220 (598)
T ss_pred             HHHHhCCCCeEEEEEeCChhhhhH---------HHHhheeEEEecCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHH
Confidence            777776677777766633210000         1112222 89999999999999988774332211    145678899


Q ss_pred             HhcCCchHHHHH
Q 041007          394 GKCKGLPFAVKI  405 (597)
Q Consensus       394 ~~~~GlPLai~~  405 (597)
                      +.++|.+.-+..
T Consensus       221 ~~a~Gdlr~al~  232 (598)
T PRK09111        221 RAAEGSVRDGLS  232 (598)
T ss_pred             HHcCCCHHHHHH
Confidence            999998865543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.30  E-value=2.1e-05  Score=84.79  Aligned_cols=199  Identities=14%  Similarity=0.190  Sum_probs=112.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|-+..++.|...+....         -...+.++|+.|+||||+|+.+.+...-.......       .++.    
T Consensus        16 ~dIiGQe~v~~~L~~ai~~~r---------i~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~-------pCg~----   75 (624)
T PRK14959         16 AEVAGQETVKAILSRAAQENR---------VAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGE-------PCNT----   75 (624)
T ss_pred             HHhcCCHHHHHHHHHHHHcCC---------CCceEEEECCCCCCHHHHHHHHHHhccccCCCCCC-------CCcc----
Confidence            467899888888888887432         24678899999999999999998742111100000       0000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhcc-------C-CCCchhhHHHHHHHHHH-HhcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESLK-------G-SVSSQVEMETVLQYINE-FVQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~-------~-~~~~~~~~~~~~~~l~~-~L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -...+.|.....       . ......+...+.+.+.. -..+++-++|||+++..+ ....+.+...
T Consensus        76 ------------C~sC~~i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt-~~a~naLLk~  142 (624)
T PRK14959         76 ------------CEQCRKVTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLT-REAFNALLKT  142 (624)
T ss_pred             ------------cHHHHHHhcCCCCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCC-HHHHHHHHHH
Confidence                        001111111000       0 00011111222222211 123566799999998776 5566777777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +........+|++|........         .+...+ .+++.+++.++....+...+...+...    ..+.+..|++.
T Consensus       143 LEEP~~~~ifILaTt~~~kll~---------TI~SRcq~i~F~pLs~~eL~~~L~~il~~egi~i----d~eal~lIA~~  209 (624)
T PRK14959        143 LEEPPARVTFVLATTEPHKFPV---------TIVSRCQHFTFTRLSEAGLEAHLTKVLGREGVDY----DPAAVRLIARR  209 (624)
T ss_pred             hhccCCCEEEEEecCChhhhhH---------HHHhhhhccccCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            7654456666666654311100         011111 289999999999999888764332211    24567889999


Q ss_pred             cCCch-HHHHHHHhhh
Q 041007          396 CKGLP-FAVKILGSLL  410 (597)
Q Consensus       396 ~~GlP-Lai~~~~~~l  410 (597)
                      ++|.+ .|+..+..++
T Consensus       210 s~GdlR~Al~lLeqll  225 (624)
T PRK14959        210 AAGSVRDSMSLLGQVL  225 (624)
T ss_pred             cCCCHHHHHHHHHHHH
Confidence            99954 6777776554

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=98.30  E-value=2.3e-05  Score=88.20  Aligned_cols=192  Identities=11%  Similarity=0.074  Sum_probs=109.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .++||.+..++.|..++....         -...+.++|+.|+||||+|+.+.+...-.......   .|...       
T Consensus        15 ~eiiGqe~v~~~L~~~i~~~r---------i~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~---pCg~C-------   75 (824)
T PRK07764         15 AEVIGQEHVTEPLSTALDSGR---------INHAYLFSGPRGCGKTSSARILARSLNCVEGPTST---PCGEC-------   75 (824)
T ss_pred             HHhcCcHHHHHHHHHHHHhCC---------CCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCC---CCccc-------
Confidence            468999999999999997432         23468899999999999999997742111111000   00000       


Q ss_pred             hhhhhhcccchHHHHHHHHHHh---------ccC-CCCchhhHHHHHHHHH-HHhcCceEEEEEecccCCCCcchHHHHH
Q 041007          246 RDEISVARDRDEIRVAKAILES---------LKG-SVSSQVEMETVLQYIN-EFVQGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~---------l~~-~~~~~~~~~~~~~~l~-~~L~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                                   ...+.+...         +.. .....++...+.+.+. .-..++.-++|||+++... ....+.|+
T Consensus        76 -------------~sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt-~~a~NaLL  141 (824)
T PRK07764         76 -------------DSCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVT-PQGFNALL  141 (824)
T ss_pred             -------------HHHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcC-HHHHHHHH
Confidence                         000000000         000 0001111222221111 1123556689999998877 66778888


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      ..+..-...+.+|++|.+......         .+...+. |++.+++.++..+++.+.+-..+...    ..+....|+
T Consensus       142 K~LEEpP~~~~fIl~tt~~~kLl~---------TIrSRc~~v~F~~l~~~~l~~~L~~il~~EGv~i----d~eal~lLa  208 (824)
T PRK07764        142 KIVEEPPEHLKFIFATTEPDKVIG---------TIRSRTHHYPFRLVPPEVMRGYLERICAQEGVPV----EPGVLPLVI  208 (824)
T ss_pred             HHHhCCCCCeEEEEEeCChhhhhH---------HHHhheeEEEeeCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHH
Confidence            888877777777766643310000         1111222 99999999999988887663322211    144567899


Q ss_pred             HhcCCchHHH
Q 041007          394 GKCKGLPFAV  403 (597)
Q Consensus       394 ~~~~GlPLai  403 (597)
                      +.++|.+..+
T Consensus       209 ~~sgGdlR~A  218 (824)
T PRK07764        209 RAGGGSVRDS  218 (824)
T ss_pred             HHcCCCHHHH
Confidence            9999988433

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.29  E-value=4e-05  Score=79.62  Aligned_cols=186  Identities=11%  Similarity=0.171  Sum_probs=104.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh------ccCCeeEEEEecCCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK------ANFDKRIWVSASYPR  239 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~------~~F~~~~wv~~~~~~  239 (597)
                      .+++|.+...+.+...+....         -.+.+.++|++|+|||++|..+.+.....      ..|...+ +......
T Consensus        17 ~~iig~~~~~~~l~~~i~~~~---------~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~-~~l~~~~   86 (367)
T PRK14970         17 DDVVGQSHITNTLLNAIENNH---------LAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNI-FELDAAS   86 (367)
T ss_pred             HhcCCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcce-EEecccc
Confidence            457899999999999997432         34588999999999999999997731110      0111111 0000000


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS  319 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~  319 (597)
                      .              .+ ......+++.+...                -..+++-++++|+++... ...++.+...+..
T Consensus        87 ~--------------~~-~~~i~~l~~~~~~~----------------p~~~~~kiviIDE~~~l~-~~~~~~ll~~le~  134 (367)
T PRK14970         87 N--------------NS-VDDIRNLIDQVRIP----------------PQTGKYKIYIIDEVHMLS-SAAFNAFLKTLEE  134 (367)
T ss_pred             C--------------CC-HHHHHHHHHHHhhc----------------cccCCcEEEEEeChhhcC-HHHHHHHHHHHhC
Confidence            0              00 11111111111000                012455689999996554 3456667666655


Q ss_pred             CCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCC
Q 041007          320 GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKG  398 (597)
Q Consensus       320 ~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~G  398 (597)
                      ....+.+|+++........         .+...+ .+++.++++++....+...+...+...    ..+.+..|+..++|
T Consensus       135 ~~~~~~~Il~~~~~~kl~~---------~l~sr~~~v~~~~~~~~~l~~~l~~~~~~~g~~i----~~~al~~l~~~~~g  201 (367)
T PRK14970        135 PPAHAIFILATTEKHKIIP---------TILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKF----EDDALHIIAQKADG  201 (367)
T ss_pred             CCCceEEEEEeCCcccCCH---------HHHhcceeEecCCccHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHhCCC
Confidence            4455666665543311100         111111 289999999999988888764332211    14577889999998


Q ss_pred             chH-HHHHH
Q 041007          399 LPF-AVKIL  406 (597)
Q Consensus       399 lPL-ai~~~  406 (597)
                      .+- ++..+
T Consensus       202 dlr~~~~~l  210 (367)
T PRK14970        202 ALRDALSIF  210 (367)
T ss_pred             CHHHHHHHH
Confidence            665 43433

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.28  E-value=8.6e-06  Score=84.34  Aligned_cols=191  Identities=12%  Similarity=0.062  Sum_probs=98.8

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCC---cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDE---ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~---~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      +....+.|++..+++|.+.+...-...   ..-+-..++-+.|+|++|+|||+||+.+++.  ....|     +.+..  
T Consensus       119 ~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~--l~~~~-----~~v~~--  189 (364)
T TIGR01242       119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE--TNATF-----IRVVG--  189 (364)
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh--CCCCE-----Eecch--
Confidence            334568999999999988875321100   0000123566999999999999999999983  33332     22111  


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC----------cch
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY----------PRY  309 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~----------~~~  309 (597)
                                        ..+.....   +      .....+...+...-...+.+|+||+++....          ...
T Consensus       190 ------------------~~l~~~~~---g------~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~  242 (364)
T TIGR01242       190 ------------------SELVRKYI---G------EGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREV  242 (364)
T ss_pred             ------------------HHHHHHhh---h------HHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHH
Confidence                              11111100   0      0001111112222234678999999864310          111


Q ss_pred             HHHHHHhh---cC--CCCCcEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCcc
Q 041007          310 WEQLMYSL---KS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYRE  383 (597)
Q Consensus       310 ~~~l~~~l---~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~  383 (597)
                      ...+...+   ..  ...+..||.||........    .+.  .... ...+.+.+.+.++..++|..+....... ...
T Consensus       243 ~~~l~~ll~~ld~~~~~~~v~vI~ttn~~~~ld~----al~--r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~-~~~  315 (364)
T TIGR01242       243 QRTLMQLLAELDGFDPRGNVKVIAATNRPDILDP----ALL--RPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLA-EDV  315 (364)
T ss_pred             HHHHHHHHHHhhCCCCCCCEEEEEecCChhhCCh----hhc--CcccCceEEEeCCcCHHHHHHHHHHHHhcCCCC-ccC
Confidence            22232222   21  2346678888765411100    000  0000 1128899999999999999877432211 111


Q ss_pred             chHHHHHHHHHhcCCch
Q 041007          384 KFEPIGRRVVGKCKGLP  400 (597)
Q Consensus       384 ~~~~~~~~I~~~~~GlP  400 (597)
                      .    ...+++.+.|..
T Consensus       316 ~----~~~la~~t~g~s  328 (364)
T TIGR01242       316 D----LEAIAKMTEGAS  328 (364)
T ss_pred             C----HHHHHHHcCCCC
Confidence            2    356777777654

Many proteins may score above the trusted cutoff because an internal

>PRK09087 hypothetical protein; Validated

Probab=98.28  E-value=8.7e-06  Score=77.93  Aligned_cols=153  Identities=15%  Similarity=0.133  Sum_probs=87.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      .+.+.|+|++|+|||+|++.++...       ...+++..                      .+...++.          
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~-------~~~~i~~~----------------------~~~~~~~~----------   84 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKS-------DALLIHPN----------------------EIGSDAAN----------   84 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhc-------CCEEecHH----------------------HcchHHHH----------
Confidence            4679999999999999999988732       11244321                      00011111          


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccccee
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEI  355 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~  355 (597)
                                 .+.+  -+|+|||++....  .-+.+...+.. ...|..+|+|++..+........++.+ .......+
T Consensus        85 -----------~~~~--~~l~iDDi~~~~~--~~~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~S-Rl~~gl~~  148 (226)
T PRK09087         85 -----------AAAE--GPVLIEDIDAGGF--DETGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKS-RLKAATVV  148 (226)
T ss_pred             -----------hhhc--CeEEEECCCCCCC--CHHHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHH-HHhCCcee
Confidence                       0111  2788899965321  11234433332 234678999988653322110000000 01111229


Q ss_pred             ecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHh
Q 041007          356 GLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGS  408 (597)
Q Consensus       356 ~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~  408 (597)
                      ++++++.++-.+++.+.+....-.    --+++..-|++.+.|..-++..+..
T Consensus       149 ~l~~pd~e~~~~iL~~~~~~~~~~----l~~ev~~~La~~~~r~~~~l~~~l~  197 (226)
T PRK09087        149 EIGEPDDALLSQVIFKLFADRQLY----VDPHVVYYLVSRMERSLFAAQTIVD  197 (226)
T ss_pred             ecCCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHhhhhHHHHHHHHH
Confidence            999999999999999888542211    1256778899999988877765433

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.27  E-value=2.5e-05  Score=85.73  Aligned_cols=196  Identities=12%  Similarity=0.103  Sum_probs=110.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-++.|..++....         -...+.++|+.|+||||+|+.+++.  +.......-+-.+    ..    
T Consensus        16 ~eiiGq~~~~~~L~~~i~~~~---------i~~a~Lf~Gp~G~GKTtlA~~lA~~--l~c~~~~~~~~~c----~~----   76 (585)
T PRK14950         16 AELVGQEHVVQTLRNAIAEGR---------VAHAYLFTGPRGVGKTSTARILAKA--VNCTTNDPKGRPC----GT----   76 (585)
T ss_pred             HHhcCCHHHHHHHHHHHHhCC---------CceEEEEECCCCCCHHHHHHHHHHH--hcCCCCCCCCCCC----cc----
Confidence            468999999999998887432         2356789999999999999999873  2111000000000    00    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCC--------CCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGS--------VSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~--------~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  ....+.+.......        .....+..++.+.+... ..+++-++|||+++... ....+.+...
T Consensus        77 ------------c~~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~-~~a~naLLk~  143 (585)
T PRK14950         77 ------------CEMCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLS-TAAFNALLKT  143 (585)
T ss_pred             ------------CHHHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCC-HHHHHHHHHH
Confidence                        11122222111110        01111222222222211 12456799999997665 4456777777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +......+.+|+++.+......         .+... ..+.+.+++..+....+...+...+...    ..+.+..|++.
T Consensus       144 LEepp~~tv~Il~t~~~~kll~---------tI~SR~~~i~f~~l~~~el~~~L~~~a~~egl~i----~~eal~~La~~  210 (585)
T PRK14950        144 LEEPPPHAIFILATTEVHKVPA---------TILSRCQRFDFHRHSVADMAAHLRKIAAAEGINL----EPGALEAIARA  210 (585)
T ss_pred             HhcCCCCeEEEEEeCChhhhhH---------HHHhccceeeCCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            7665566777766643310000         11111 2288999999999988888764332211    14567899999


Q ss_pred             cCCchHHHHHH
Q 041007          396 CKGLPFAVKIL  406 (597)
Q Consensus       396 ~~GlPLai~~~  406 (597)
                      ++|.+..+...
T Consensus       211 s~Gdlr~al~~  221 (585)
T PRK14950        211 ATGSMRDAENL  221 (585)
T ss_pred             cCCCHHHHHHH
Confidence            99988655433

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=98.26  E-value=1.4e-05  Score=90.93  Aligned_cols=45  Identities=22%  Similarity=0.315  Sum_probs=38.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.++.++++.|....          ...+.++|++|+|||++|+.+++.
T Consensus       187 d~~iGr~~ei~~~i~~l~r~~----------~~n~lLvG~pGvGKTal~~~La~~  231 (852)
T TIGR03345       187 DPVLGRDDEIRQMIDILLRRR----------QNNPILTGEAGVGKTAVVEGLALR  231 (852)
T ss_pred             CcccCCHHHHHHHHHHHhcCC----------cCceeEECCCCCCHHHHHHHHHHH
Confidence            568999999999999997433          346679999999999999999883

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.25  E-value=4.1e-05  Score=82.87  Aligned_cols=197  Identities=13%  Similarity=0.089  Sum_probs=111.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-++.|..++....         -...+.++|+.|+||||+|+.+++...-.....   +-.+...       
T Consensus        13 ~eivGq~~i~~~L~~~i~~~r---------~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~---~~pCg~C-------   73 (584)
T PRK14952         13 AEVVGQEHVTEPLSSALDAGR---------INHAYLFSGPRGCGKTSSARILARSLNCAQGPT---ATPCGVC-------   73 (584)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhccccCCC---CCccccc-------
Confidence            468999999999999997432         234578999999999999999987311111100   0000000       


Q ss_pred             hhhhhhcccchHHHHHHHHHHh---------ccC-CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHH
Q 041007          246 RDEISVARDRDEIRVAKAILES---------LKG-SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~---------l~~-~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                                   .....+...         +.. .....++..++.+.+... ..+++-++|+|+++... ....+.++
T Consensus        74 -------------~~C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt-~~A~NALL  139 (584)
T PRK14952         74 -------------ESCVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVT-TAGFNALL  139 (584)
T ss_pred             -------------HHHHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCC-HHHHHHHH
Confidence                         000000000         000 001112222222222211 12456689999998776 66777788


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      ..+......+.+|++|........         .+...+ .+++.+++.++..+.+...+...+...    ..+....|+
T Consensus       140 K~LEEpp~~~~fIL~tte~~kll~---------TI~SRc~~~~F~~l~~~~i~~~L~~i~~~egi~i----~~~al~~Ia  206 (584)
T PRK14952        140 KIVEEPPEHLIFIFATTEPEKVLP---------TIRSRTHHYPFRLLPPRTMRALIARICEQEGVVV----DDAVYPLVI  206 (584)
T ss_pred             HHHhcCCCCeEEEEEeCChHhhHH---------HHHHhceEEEeeCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHH
Confidence            888776677777766643310000         111112 299999999999988887764332211    134567788


Q ss_pred             HhcCCchH-HHHHHHh
Q 041007          394 GKCKGLPF-AVKILGS  408 (597)
Q Consensus       394 ~~~~GlPL-ai~~~~~  408 (597)
                      +.++|.+- ++..+-.
T Consensus       207 ~~s~GdlR~aln~Ldq  222 (584)
T PRK14952        207 RAGGGSPRDTLSVLDQ  222 (584)
T ss_pred             HHcCCCHHHHHHHHHH
Confidence            99999774 4444433

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=98.23  E-value=3e-06  Score=85.42  Aligned_cols=90  Identities=17%  Similarity=0.199  Sum_probs=58.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC--chhhhhhhhhhhcccchHHHHHHHHHHhccCCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR--DEIRVARDEISVARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      ......|+|++|+||||||+.++++...+ +|+.++||.+.+..  ..                .++++.+...+-....
T Consensus       168 kGQR~lIvgppGvGKTTLaK~Ian~I~~n-hFDv~~~VvLIgER~~EV----------------tdiqrsIlg~vv~st~  230 (416)
T PRK09376        168 KGQRGLIVAPPKAGKTVLLQNIANSITTN-HPEVHLIVLLIDERPEEV----------------TDMQRSVKGEVVASTF  230 (416)
T ss_pred             cCceEEEeCCCCCChhHHHHHHHHHHHhh-cCCeEEEEEEeCCchhHH----------------HHHHHHhcCcEEEECC
Confidence            45688999999999999999999964333 89999999998876  33                5666666532221111


Q ss_pred             -c-hhh----HHHHHHHHHHH-hcCceEEEEEeccc
Q 041007          274 -S-QVE----METVLQYINEF-VQGKKVLLVLDDLW  302 (597)
Q Consensus       274 -~-~~~----~~~~~~~l~~~-L~~kr~LLVLDdv~  302 (597)
                       . ...    .......-+.+ -.++++||++|++.
T Consensus       231 d~~~~~~~~~a~~~ie~Ae~~~e~G~dVlL~iDsIt  266 (416)
T PRK09376        231 DEPAERHVQVAEMVIEKAKRLVEHGKDVVILLDSIT  266 (416)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEEChH
Confidence             1 111    01112222222 25789999999994

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

Probab=98.22  E-value=3.1e-05  Score=75.57  Aligned_cols=204  Identities=17%  Similarity=0.180  Sum_probs=118.3

Q ss_pred             hhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh--c--cCCeeEEEEecCCCchhhhhhhh
Q 041007          173 AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK--A--NFDKRIWVSASYPRDEIRVARDE  248 (597)
Q Consensus       173 ~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~--~--~F~~~~wv~~~~~~~~~~~~~~~  248 (597)
                      .-+++|.++|....       ....+.+.|+|.+|+|||++++.+.+..-..  .  .--.++.|.+...++.       
T Consensus        44 ~~L~~L~~Ll~~P~-------~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~-------  109 (302)
T PF05621_consen   44 EALDRLEELLEYPK-------RHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDE-------  109 (302)
T ss_pred             HHHHHHHHHHhCCc-------ccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCCh-------
Confidence            34566666666443       3567889999999999999999998641111  0  1113566677677777       


Q ss_pred             hhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcC-ceEEEEEecccCCC--CcchHHHHHHhhc---CCCC
Q 041007          249 ISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQG-KKVLLVLDDLWWNA--YPRYWEQLMYSLK---SGSE  322 (597)
Q Consensus       249 ~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~-kr~LLVLDdv~~~~--~~~~~~~l~~~l~---~~~~  322 (597)
                               ..++..|+.+++.+.........+.......++. +--+||+|++++.-  ....-..+...+.   +.-.
T Consensus       110 ---------~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~  180 (302)
T PF05621_consen  110 ---------RRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQ  180 (302)
T ss_pred             ---------HHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccC
Confidence                     9999999999999876665666655555555653 34589999997642  1112222333332   2223


Q ss_pred             CcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChH-HHHHHHHHHh--ccCCCCCCccchHHHHHHHHHhcCC
Q 041007          323 GSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEE-ECRSLFRQIA--FHGRSSDYREKFEPIGRRVVGKCKG  398 (597)
Q Consensus       323 gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~-es~~Lf~~~~--~~~~~~~~~~~~~~~~~~I~~~~~G  398 (597)
                      =+-|.+-|+........+      .+.++... +.+.+...+ +...|+....  ..-+. ...-...+++..|...++|
T Consensus       181 ipiV~vGt~~A~~al~~D------~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~-~S~l~~~~la~~i~~~s~G  253 (302)
T PF05621_consen  181 IPIVGVGTREAYRALRTD------PQLASRFEPFELPRWELDEEFRRLLASFERALPLRK-PSNLASPELARRIHERSEG  253 (302)
T ss_pred             CCeEEeccHHHHHHhccC------HHHHhccCCccCCCCCCCcHHHHHHHHHHHhCCCCC-CCCCCCHHHHHHHHHHcCC
Confidence            344555555432111110      02222222 566666544 4455554432  11111 1112346789999999999


Q ss_pred             chHHHHHH
Q 041007          399 LPFAVKIL  406 (597)
Q Consensus       399 lPLai~~~  406 (597)
                      +.=-+..+
T Consensus       254 ~iG~l~~l  261 (302)
T PF05621_consen  254 LIGELSRL  261 (302)
T ss_pred             chHHHHHH
Confidence            87655433

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

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=98.17  E-value=9.6e-05  Score=78.86  Aligned_cols=192  Identities=11%  Similarity=0.068  Sum_probs=109.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCe-eEEEEecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDK-RIWVSASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~  244 (597)
                      .+++|-+.-.+.|...+....         -.....++|+.|+||||+|+.+.+..--....+. -+-.|          
T Consensus        14 deiiGqe~v~~~L~~~I~~gr---------l~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C----------   74 (535)
T PRK08451         14 DELIGQESVSKTLSLALDNNR---------LAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTC----------   74 (535)
T ss_pred             HHccCcHHHHHHHHHHHHcCC---------CCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCccc----------
Confidence            468999999999999987432         2456789999999999999988663100000000 00000          


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhcc-----CCCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHHH
Q 041007          245 ARDEISVARDRDEIRVAKAILESLK-----GSVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~-----~~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                                    .....+.....     .........+.+.+.+...    ..+++-++|+|+++..+ ....+.+..
T Consensus        75 --------------~~C~~~~~~~h~dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt-~~A~NALLK  139 (535)
T PRK08451         75 --------------IQCQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLT-KEAFNALLK  139 (535)
T ss_pred             --------------HHHHHHhhcCCCeEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC-HHHHHHHHH
Confidence                          00000000000     0000000122222222110    12456689999998776 566777877


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVG  394 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~  394 (597)
                      .+...+..+.+|++|.+......         .+...+ .+++.+++.++....+.+.+...+...    ..+.+..|++
T Consensus       140 ~LEEpp~~t~FIL~ttd~~kL~~---------tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~EGi~i----~~~Al~~Ia~  206 (535)
T PRK08451        140 TLEEPPSYVKFILATTDPLKLPA---------TILSRTQHFRFKQIPQNSIISHLKTILEKEGVSY----EPEALEILAR  206 (535)
T ss_pred             HHhhcCCceEEEEEECChhhCch---------HHHhhceeEEcCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHH
Confidence            77766677787777755311110         111122 299999999999998887764333211    2456788999


Q ss_pred             hcCCchHHHH
Q 041007          395 KCKGLPFAVK  404 (597)
Q Consensus       395 ~~~GlPLai~  404 (597)
                      .++|.+--+.
T Consensus       207 ~s~GdlR~al  216 (535)
T PRK08451        207 SGNGSLRDTL  216 (535)
T ss_pred             HcCCcHHHHH
Confidence            9999885443

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

Probab=98.17  E-value=2.3e-05  Score=75.30  Aligned_cols=190  Identities=16%  Similarity=0.099  Sum_probs=115.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeE-EEEecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRI-WVSASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~-wv~~~~~~~~~~~  244 (597)
                      .+++|.+..++.|...+..          ...+....+||+|.|||+-|..+++..--.+-|++.+ -.++|.....   
T Consensus        36 de~~gQe~vV~~L~~a~~~----------~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGi---  102 (346)
T KOG0989|consen   36 DELAGQEHVVQVLKNALLR----------RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGI---  102 (346)
T ss_pred             HhhcchHHHHHHHHHHHhh----------cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhhcccccccc---
Confidence            5688999999999999985          2478999999999999999998887422234454433 2333332222   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhc--Cce-EEEEEecccCCCCcchHHHHHHhhcCCC
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQ--GKK-VLLVLDDLWWNAYPRYWEQLMYSLKSGS  321 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~--~kr-~LLVLDdv~~~~~~~~~~~l~~~l~~~~  321 (597)
                                   . +.+.          ...+.+.+.........  -++ -++|||+++.+. .+.|..+...+....
T Consensus       103 -------------s-vvr~----------Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmt-sdaq~aLrr~mE~~s  157 (346)
T KOG0989|consen  103 -------------S-VVRE----------KIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMT-SDAQAALRRTMEDFS  157 (346)
T ss_pred             -------------c-chhh----------hhcCHHHHhhccccccCCCCCcceEEEEechhhhh-HHHHHHHHHHHhccc
Confidence                         0 0000          00011111111100000  123 488899998887 789999999998877


Q ss_pred             CCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCc-
Q 041007          322 EGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGL-  399 (597)
Q Consensus       322 ~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~Gl-  399 (597)
                      ..++.|+.+..-.+...         .+...+. +..++|.+++...-+...+..++....    .+..+.|++.++|. 
T Consensus       158 ~~trFiLIcnylsrii~---------pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d----~~al~~I~~~S~GdL  224 (346)
T KOG0989|consen  158 RTTRFILICNYLSRIIR---------PLVSRCQKFRFKKLKDEDIVDRLEKIASKEGVDID----DDALKLIAKISDGDL  224 (346)
T ss_pred             cceEEEEEcCChhhCCh---------HHHhhHHHhcCCCcchHHHHHHHHHHHHHhCCCCC----HHHHHHHHHHcCCcH
Confidence            77776655443211110         1222233 999999999999888887754443322    45668899999984 


Q ss_pred             hHHHHHH
Q 041007          400 PFAVKIL  406 (597)
Q Consensus       400 PLai~~~  406 (597)
                      --|+..+
T Consensus       225 R~Ait~L  231 (346)
T KOG0989|consen  225 RRAITTL  231 (346)
T ss_pred             HHHHHHH
Confidence            4444444

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.16  E-value=7.1e-05  Score=81.65  Aligned_cols=202  Identities=12%  Similarity=0.134  Sum_probs=108.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe-cCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA-SYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~-~~~~~~~~~  244 (597)
                      .+++|.+.-+..|..++....         -...+.++|+.|+||||+|+.+.+...-...++...|..- ..+...   
T Consensus        16 ~eivGQe~i~~~L~~~i~~~r---------i~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~---   83 (620)
T PRK14954         16 ADITAQEHITHTIQNSLRMDR---------VGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGE---   83 (620)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCcc---
Confidence            468999999999999887432         2345889999999999999998773211111110011100 000000   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccC-----CCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHHH
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKG-----SVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~-----~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                                   -...+.+...-..     ........+++...+...    ..+++-++|+|+++... ....+.+..
T Consensus        84 -------------C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt-~~a~naLLK  149 (620)
T PRK14954         84 -------------CESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLS-TAAFNAFLK  149 (620)
T ss_pred             -------------CHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcC-HHHHHHHHH
Confidence                         1111111110000     000111122222222221    23455688999997765 445677777


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVG  394 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~  394 (597)
                      .+..-...+.+|++|........         .+...+ .+++.+++.++....+.+.+...+...    ..+.++.|++
T Consensus       150 ~LEePp~~tv~IL~t~~~~kLl~---------TI~SRc~~vef~~l~~~ei~~~L~~i~~~egi~I----~~eal~~La~  216 (620)
T PRK14954        150 TLEEPPPHAIFIFATTELHKIPA---------TIASRCQRFNFKRIPLDEIQSQLQMICRAEGIQI----DADALQLIAR  216 (620)
T ss_pred             HHhCCCCCeEEEEEeCChhhhhH---------HHHhhceEEecCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHH
Confidence            77666566666655533210000         111112 299999999999888887664322111    1456788999


Q ss_pred             hcCCchH-HHHHH
Q 041007          395 KCKGLPF-AVKIL  406 (597)
Q Consensus       395 ~~~GlPL-ai~~~  406 (597)
                      .++|..- ++..+
T Consensus       217 ~s~Gdlr~al~eL  229 (620)
T PRK14954        217 KAQGSMRDAQSIL  229 (620)
T ss_pred             HhCCCHHHHHHHH
Confidence            9999554 44443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=98.16  E-value=9.2e-05  Score=78.39  Aligned_cols=195  Identities=13%  Similarity=0.103  Sum_probs=106.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc----CCeeEEE-----Eec
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN----FDKRIWV-----SAS  236 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv-----~~~  236 (597)
                      .+++|.+..+..|..++....         -...+.++|+.|+||||+|+.+.+...-...    -.+..-.     ...
T Consensus        17 ~diiGq~~~v~~L~~~i~~~~---------i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~~~   87 (451)
T PRK06305         17 SEILGQDAVVAVLKNALRFNR---------AAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSG   87 (451)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHhcC
Confidence            568999999999999997432         2456889999999999999998763111000    0000000     000


Q ss_pred             CCCchhhhhhhhhhhcccchHHHHHHHHHHhccC-CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHH
Q 041007          237 YPRDEIRVARDEISVARDRDEIRVAKAILESLKG-SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       237 ~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~-~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                      ...+.                        ..+.+ ......+...+.+.+.-. ..+++-++|+|+++... ....+.+.
T Consensus        88 ~~~d~------------------------~~i~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt-~~~~n~LL  142 (451)
T PRK06305         88 TSLDV------------------------LEIDGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLT-KEAFNSLL  142 (451)
T ss_pred             CCCce------------------------EEeeccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhC-HHHHHHHH
Confidence            00000                        00000 000011111122111111 12566789999997665 34556677


Q ss_pred             HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          315 YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       315 ~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      ..+.....++.+|++|........         .+...+. +++.+++.++....+...+...+...    ..+.+..|+
T Consensus       143 k~lEep~~~~~~Il~t~~~~kl~~---------tI~sRc~~v~f~~l~~~el~~~L~~~~~~eg~~i----~~~al~~L~  209 (451)
T PRK06305        143 KTLEEPPQHVKFFLATTEIHKIPG---------TILSRCQKMHLKRIPEETIIDKLALIAKQEGIET----SREALLPIA  209 (451)
T ss_pred             HHhhcCCCCceEEEEeCChHhcch---------HHHHhceEEeCCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHH
Confidence            777665566677766633210000         1111222 99999999999988887664322111    245678899


Q ss_pred             HhcCCch-HHHHHHH
Q 041007          394 GKCKGLP-FAVKILG  407 (597)
Q Consensus       394 ~~~~GlP-Lai~~~~  407 (597)
                      +.++|.+ .|+..+-
T Consensus       210 ~~s~gdlr~a~~~Le  224 (451)
T PRK06305        210 RAAQGSLRDAESLYD  224 (451)
T ss_pred             HHcCCCHHHHHHHHH
Confidence            9999966 4555443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=98.14  E-value=4.6e-05  Score=81.93  Aligned_cols=168  Identities=11%  Similarity=0.127  Sum_probs=94.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccC--CeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANF--DKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      ..+.|+|..|+|||.|++.+++  .....+  ..+++++.                      ..+...+...+...    
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~--~a~~~~~g~~V~Yita----------------------eef~~el~~al~~~----  366 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGH--YARRLYPGTRVRYVSS----------------------EEFTNEFINSIRDG----  366 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeH----------------------HHHHHHHHHHHHhc----
Confidence            4589999999999999999999  443322  23456653                      23333333332211    


Q ss_pred             hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHH-HHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccccc
Q 041007          276 VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQ-LMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM  353 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~-l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~  353 (597)
                       ..    ..+++.+.+ -=+|||||++.......|.. +...+.. ...+..|||||...+.......-++.+ ......
T Consensus       367 -~~----~~f~~~y~~-~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~S-Rf~~GL  439 (617)
T PRK14086        367 -KG----DSFRRRYRE-MDILLVDDIQFLEDKESTQEEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRN-RFEWGL  439 (617)
T ss_pred             -cH----HHHHHHhhc-CCEEEEehhccccCCHHHHHHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHh-hhhcCc
Confidence             11    122233332 35889999976643344433 3333332 234567888887653222111111110 111112


Q ss_pred             eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHH
Q 041007          354 EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       354 ~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~  404 (597)
                      .+.+.+.+.+.-.+++.+.+.......    -.+++.-|++++.+..-.|.
T Consensus       440 vv~I~~PD~EtR~aIL~kka~~r~l~l----~~eVi~yLa~r~~rnvR~Le  486 (617)
T PRK14086        440 ITDVQPPELETRIAILRKKAVQEQLNA----PPEVLEFIASRISRNIRELE  486 (617)
T ss_pred             eEEcCCCCHHHHHHHHHHHHHhcCCCC----CHHHHHHHHHhccCCHHHHH
Confidence            289999999999999998875432211    15667778888776654443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.14  E-value=1.6e-05  Score=87.02  Aligned_cols=200  Identities=13%  Similarity=0.169  Sum_probs=109.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-++.|..++....         -...+.++|+.|+||||+|+.+++.  +-..-....+-++.......   
T Consensus        18 ~dIiGQe~~v~~L~~aI~~~r---------l~HAYLF~GP~GtGKTt~AriLAk~--LnC~~~~~~~~pC~~C~~~~---   83 (725)
T PRK07133         18 DDIVGQDHIVQTLKNIIKSNK---------ISHAYLFSGPRGTGKTSVAKIFANA--LNCSHKTDLLEPCQECIENV---   83 (725)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCcHHHHHHHHHHH--hcccccCCCCCchhHHHHhh---
Confidence            457899999999999997432         2456789999999999999999763  21100000000000000000   


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccC-CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          246 RDEISVARDRDEIRVAKAILESLKG-SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~-~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                            ..+   ..    ++ .+.+ ......+...+.+.+... ..+++-++|+|+++... ...+..+...+...+..
T Consensus        84 ------~~~---~D----vi-eidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT-~~A~NALLKtLEEPP~~  148 (725)
T PRK07133         84 ------NNS---LD----II-EMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLS-KSAFNALLKTLEEPPKH  148 (725)
T ss_pred             ------cCC---Cc----EE-EEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCC-HHHHHHHHHHhhcCCCc
Confidence                  000   00    00 0000 000111222333322221 12566699999997765 55777787777665566


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchH-
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPF-  401 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPL-  401 (597)
                      +.+|++|........         .+...+ .+++.+++.++....+...+...+...    ..+.+..|++.++|.+- 
T Consensus       149 tifILaTte~~KLl~---------TI~SRcq~ieF~~L~~eeI~~~L~~il~kegI~i----d~eAl~~LA~lS~GslR~  215 (725)
T PRK07133        149 VIFILATTEVHKIPL---------TILSRVQRFNFRRISEDEIVSRLEFILEKENISY----EKNALKLIAKLSSGSLRD  215 (725)
T ss_pred             eEEEEEcCChhhhhH---------HHHhhceeEEccCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCCHHH
Confidence            666655543311000         111122 299999999999988887654322111    13457889999999664 


Q ss_pred             HHHHHH
Q 041007          402 AVKILG  407 (597)
Q Consensus       402 ai~~~~  407 (597)
                      |+..+-
T Consensus       216 AlslLe  221 (725)
T PRK07133        216 ALSIAE  221 (725)
T ss_pred             HHHHHH
Confidence            554443

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.14  E-value=9.3e-05  Score=78.88  Aligned_cols=192  Identities=11%  Similarity=0.076  Sum_probs=104.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhh--hcc-CCeeEEEE-----ecC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV--KAN-FDKRIWVS-----ASY  237 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~--~~~-F~~~~wv~-----~~~  237 (597)
                      ..++|.+.-.+.|..++....         -...+.++|+.|+||||+|+.++....-  ... .+|..-.+     -+.
T Consensus        16 ~diiGq~~i~~~L~~~i~~~~---------i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~g~   86 (486)
T PRK14953         16 KEVIGQEIVVRILKNAVKLQR---------VSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGS   86 (486)
T ss_pred             HHccChHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhcCC
Confidence            457899999999999997432         2346778999999999999998763110  000 00000000     000


Q ss_pred             CCchhhhhhhhhhhcccchHHHHHHHHHHhccC-CCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHH
Q 041007          238 PRDEIRVARDEISVARDRDEIRVAKAILESLKG-SVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~-~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                      ..+.                       . .+.. ......+...+.+.+... ..+++-++|+|+++... ....+.+..
T Consensus        87 ~~d~-----------------------~-eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt-~~a~naLLk  141 (486)
T PRK14953         87 FPDL-----------------------I-EIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLT-KEAFNALLK  141 (486)
T ss_pred             CCcE-----------------------E-EEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcC-HHHHHHHHH
Confidence            0000                       0 0000 001111122222222211 13566799999997665 445667777


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVG  394 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~  394 (597)
                      .+........+|++|........         .+...+ .+.+.+++.++....+...+-..+...    ..+.+..|++
T Consensus       142 ~LEepp~~~v~Il~tt~~~kl~~---------tI~SRc~~i~f~~ls~~el~~~L~~i~k~egi~i----d~~al~~La~  208 (486)
T PRK14953        142 TLEEPPPRTIFILCTTEYDKIPP---------TILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEY----EEKALDLLAQ  208 (486)
T ss_pred             HHhcCCCCeEEEEEECCHHHHHH---------HHHHhceEEEcCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHH
Confidence            77665556666655532210000         111112 289999999999988888764322211    2456678899


Q ss_pred             hcCCchHHHH
Q 041007          395 KCKGLPFAVK  404 (597)
Q Consensus       395 ~~~GlPLai~  404 (597)
                      .++|.+..+.
T Consensus       209 ~s~G~lr~al  218 (486)
T PRK14953        209 ASEGGMRDAA  218 (486)
T ss_pred             HcCCCHHHHH
Confidence            9999775443

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

Probab=98.13  E-value=0.00013  Score=72.37  Aligned_cols=211  Identities=16%  Similarity=0.194  Sum_probs=119.0

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRV  244 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~  244 (597)
                      .+.|.+|+.++..+..++.....       .-+..|.|+|-+|.|||.+.+++++..  ..   ..+|+++-+.+..   
T Consensus         5 ~~~v~~Re~qi~~L~~Llg~~~~-------~~PS~~~iyG~sgTGKT~~~r~~l~~~--n~---~~vw~n~~ecft~---   69 (438)
T KOG2543|consen    5 EPNVPCRESQIRRLKSLLGNNSC-------TIPSIVHIYGHSGTGKTYLVRQLLRKL--NL---ENVWLNCVECFTY---   69 (438)
T ss_pred             ccCccchHHHHHHHHHHhCCCCc-------ccceeEEEeccCCCchhHHHHHHHhhc--CC---cceeeehHHhccH---
Confidence            45688999999999999975542       234566999999999999999999954  22   3589999999988   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhcc-CCCCc------hhhHHHHHHHHHHH--hc--CceEEEEEecccCCCCc--chHH
Q 041007          245 ARDEISVARDRDEIRVAKAILESLK-GSVSS------QVEMETVLQYINEF--VQ--GKKVLLVLDDLWWNAYP--RYWE  311 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~-~~~~~------~~~~~~~~~~l~~~--L~--~kr~LLVLDdv~~~~~~--~~~~  311 (597)
                                   ..++..|+..++ .+.+.      ..+.......+.++  ..  ++.++||||+++...+.  .-+.
T Consensus        70 -------------~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~~a~ll~  136 (438)
T KOG2543|consen   70 -------------AILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDMDAILLQ  136 (438)
T ss_pred             -------------HHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhccchHHHH
Confidence                         888999998885 22221      12233334444442  22  45899999998543211  1122


Q ss_pred             HHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCCCCC-CccchHHHHH
Q 041007          312 QLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSD-YREKFEPIGR  390 (597)
Q Consensus       312 ~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~-~~~~~~~~~~  390 (597)
                      .+...-.-......+|+++....+......  .   .......+....-+.+|...++.+.--+..... ...-+.-+..
T Consensus       137 ~l~~L~el~~~~~i~iils~~~~e~~y~~n--~---g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~r~~~~ya~fl~v~l~  211 (438)
T KOG2543|consen  137 CLFRLYELLNEPTIVIILSAPSCEKQYLIN--T---GTLEIVVLHFPQYSVEETQVILSRDNPGKRKLDVYAQFLHVLLQ  211 (438)
T ss_pred             HHHHHHHHhCCCceEEEEeccccHHHhhcc--c---CCCCceEEecCCCCHHHHHHHHhcCCccccchHHHHHHHHHHHH
Confidence            222211122333455555543311110000  0   000111166777888998888875431111000 0111222334


Q ss_pred             HHHHhcCCchHHHHHHHhh
Q 041007          391 RVVGKCKGLPFAVKILGSL  409 (597)
Q Consensus       391 ~I~~~~~GlPLai~~~~~~  409 (597)
                      -....|+ -+-.+..++..
T Consensus       212 vF~~~cr-d~~eL~~~~~~  229 (438)
T KOG2543|consen  212 VFYMACR-DVNELRSLISL  229 (438)
T ss_pred             HHHHHhC-CHHHHHHHHHH
Confidence            4556666 66666655543

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.10  E-value=1.7e-05  Score=82.49  Aligned_cols=57  Identities=18%  Similarity=0.202  Sum_probs=39.6

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCC---cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDE---ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~---~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....+.|++..+++|.+.+...-...   ..-+-..++-|.|+|++|+|||++|+.+++.
T Consensus       129 ~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~  188 (389)
T PRK03992        129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHE  188 (389)
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHH
Confidence            34568899999999988774211100   0000124567999999999999999999883

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.08  E-value=4.3e-05  Score=75.22  Aligned_cols=53  Identities=23%  Similarity=0.244  Sum_probs=34.4

Q ss_pred             ccccchhhHHHHHHHhhCC---C--CCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLKGE---S--SDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~---~--~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|.+..+++|.+.....   .  ...+-...+....+.++|++|+||||+|+.+++
T Consensus         7 ~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~   64 (261)
T TIGR02881         7 RMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK   64 (261)
T ss_pred             HhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHH
Confidence            4788887777665443211   0  000111134556789999999999999999987

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

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=98.08  E-value=8.2e-05  Score=78.30  Aligned_cols=169  Identities=17%  Similarity=0.191  Sum_probs=93.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccC--CeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANF--DKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F--~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ...+.|+|++|+|||+|++.+++.  .....  ..++++++                      ..+...+...+...   
T Consensus       136 ~n~l~l~G~~G~GKThL~~ai~~~--l~~~~~~~~v~yi~~----------------------~~~~~~~~~~~~~~---  188 (405)
T TIGR00362       136 YNPLFIYGGVGLGKTHLLHAIGNE--ILENNPNAKVVYVSS----------------------EKFTNDFVNALRNN---  188 (405)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HHHhCCCCcEEEEEH----------------------HHHHHHHHHHHHcC---
Confidence            456899999999999999999984  43333  23555543                      22333333333221   


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchH-HHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccc
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYW-EQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM  352 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~-~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~  352 (597)
                        ..+..    .+.+.+ .-+|||||++.......+ +.+...+.. ...+..+|+|+...+.......-.+.+ .....
T Consensus       189 --~~~~~----~~~~~~-~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~S-Rl~~g  260 (405)
T TIGR00362       189 --KMEEF----KEKYRS-VDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRS-RFEWG  260 (405)
T ss_pred             --CHHHH----HHHHHh-CCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhh-hccCC
Confidence              11222    222322 348999999754322222 223333332 134566888876542211110000000 11111


Q ss_pred             ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHH
Q 041007          353 MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       353 ~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~  404 (597)
                      ..+.+.+.+.++-..++.+.+...+...    -.++...|++.+.|..-.+.
T Consensus       261 ~~v~i~~pd~~~r~~il~~~~~~~~~~l----~~e~l~~ia~~~~~~~r~l~  308 (405)
T TIGR00362       261 LVVDIEPPDLETRLAILQKKAEEEGLEL----PDEVLEFIAKNIRSNVRELE  308 (405)
T ss_pred             eEEEeCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHhcCCCHHHHH
Confidence            2388999999999999998875432211    25677888888888776543

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).

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

Probab=98.07  E-value=5.2e-05  Score=85.58  Aligned_cols=45  Identities=27%  Similarity=0.355  Sum_probs=38.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+++++++.+.|...          ...-+.++|++|+|||++|+.+++.
T Consensus       182 ~~~igr~~ei~~~~~~L~~~----------~~~n~lL~G~pG~GKT~l~~~la~~  226 (731)
T TIGR02639       182 DPLIGREDELERTIQVLCRR----------KKNNPLLVGEPGVGKTAIAEGLALR  226 (731)
T ss_pred             CcccCcHHHHHHHHHHHhcC----------CCCceEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999743          3356789999999999999999883

>TIGR00767 rho transcription termination factor Rho

Probab=98.07  E-value=1.3e-05  Score=81.43  Aligned_cols=90  Identities=14%  Similarity=0.168  Sum_probs=59.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC--CchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP--RDEIRVARDEISVARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      ....++|+|++|+|||||++.+++... ..+|+..+|+.+.+.  .+.                .++++.++..+-....
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~~~i~~~I~-~nhfdv~v~VlLIgER~~EV----------------tDLqrsIlg~Vvast~  229 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLLQKIAQAIT-RNHPEVELIVLLIDERPEEV----------------TDMQRSVKGEVVASTF  229 (415)
T ss_pred             CCCEEEEECCCCCChhHHHHHHHHhhc-ccCCceEEEEEEcCCCCccH----------------HHHHHHhhceEEEecC
Confidence            457899999999999999999999532 337999999998865  444                7777777443322211


Q ss_pred             c--hhh---H-HHHHHHHHHH-hcCceEEEEEeccc
Q 041007          274 S--QVE---M-ETVLQYINEF-VQGKKVLLVLDDLW  302 (597)
Q Consensus       274 ~--~~~---~-~~~~~~l~~~-L~~kr~LLVLDdv~  302 (597)
                      +  ...   . ..+.+..... -.+++++|++|++.
T Consensus       230 d~p~~~~~~va~~v~e~Ae~~~~~GkdVVLlIDEit  265 (415)
T TIGR00767       230 DEPASRHVQVAEMVIEKAKRLVEHKKDVVILLDSIT  265 (415)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHHcCCCeEEEEEChh
Confidence            1  111   1 1222222222 24889999999994

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

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

Probab=98.07  E-value=1.6e-05  Score=81.97  Aligned_cols=64  Identities=19%  Similarity=0.083  Sum_probs=51.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      .+.++.+..++.+...|..            .+.|.++|++|+|||++|+.+++.......|..+.||.++...+.
T Consensus       175 ~d~~i~e~~le~l~~~L~~------------~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySY  238 (459)
T PRK11331        175 NDLFIPETTIETILKRLTI------------KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSY  238 (459)
T ss_pred             hcccCCHHHHHHHHHHHhc------------CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccH
Confidence            4577889999999998873            357888999999999999999885433446777889998876655

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.07  E-value=0.00016  Score=79.27  Aligned_cols=183  Identities=11%  Similarity=0.123  Sum_probs=107.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh---------------------
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK---------------------  224 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~---------------------  224 (597)
                      .+++|.+..++.|..++....         -...+.++|+.|+||||+|+.+.....-.                     
T Consensus        17 ~~viGq~~~~~~L~~~i~~~~---------l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~~~   87 (614)
T PRK14971         17 ESVVGQEALTTTLKNAIATNK---------LAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFNEQ   87 (614)
T ss_pred             HHhcCcHHHHHHHHHHHHcCC---------CCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHhcC
Confidence            468999999999999997432         24568899999999999998887631100                     


Q ss_pred             ccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH-hcCceEEEEEecccC
Q 041007          225 ANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWW  303 (597)
Q Consensus       225 ~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~  303 (597)
                      .+|+. ..+.....                                  ....+...+...+... ..+++-++|+|+++.
T Consensus        88 ~~~n~-~~ld~~~~----------------------------------~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~  132 (614)
T PRK14971         88 RSYNI-HELDAASN----------------------------------NSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHM  132 (614)
T ss_pred             CCCce-EEeccccc----------------------------------CCHHHHHHHHHHHhhCcccCCcEEEEEECccc
Confidence            01111 11111000                                  0011111122111111 124556889999987


Q ss_pred             CCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCc
Q 041007          304 NAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYR  382 (597)
Q Consensus       304 ~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~  382 (597)
                      .. ...++.+...+..-..++.+|++|........         .+...+. +++.+++.++....+...+...+...  
T Consensus       133 Ls-~~a~naLLK~LEepp~~tifIL~tt~~~kIl~---------tI~SRc~iv~f~~ls~~ei~~~L~~ia~~egi~i--  200 (614)
T PRK14971        133 LS-QAAFNAFLKTLEEPPSYAIFILATTEKHKILP---------TILSRCQIFDFNRIQVADIVNHLQYVASKEGITA--  200 (614)
T ss_pred             CC-HHHHHHHHHHHhCCCCCeEEEEEeCCchhchH---------HHHhhhheeecCCCCHHHHHHHHHHHHHHcCCCC--
Confidence            76 55677788888776667777665543310000         1111122 99999999999998887764332211  


Q ss_pred             cchHHHHHHHHHhcCCchH-HHHHH
Q 041007          383 EKFEPIGRRVVGKCKGLPF-AVKIL  406 (597)
Q Consensus       383 ~~~~~~~~~I~~~~~GlPL-ai~~~  406 (597)
                        ..+.+..|++.++|..- ++..+
T Consensus       201 --~~~al~~La~~s~gdlr~al~~L  223 (614)
T PRK14971        201 --EPEALNVIAQKADGGMRDALSIF  223 (614)
T ss_pred             --CHHHHHHHHHHcCCCHHHHHHHH
Confidence              13467889999999665 44433

>CHL00181 cbbX CbbX; Provisional

Probab=98.06  E-value=7.4e-05  Score=74.21  Aligned_cols=143  Identities=10%  Similarity=0.089  Sum_probs=71.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ...+.++|++|+|||++|+.+++.....+.-...-|+.++.                    ..+..    ...+..    
T Consensus        59 ~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~--------------------~~l~~----~~~g~~----  110 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTR--------------------DDLVG----QYIGHT----  110 (287)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecH--------------------HHHHH----HHhccc----
Confidence            34588999999999999999977311111111112333331                    11111    111110    


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCC--------CcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccC
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNA--------YPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKN  348 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~--------~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~  348 (597)
                       .......+.+.   ..-+|+||++....        .....+.+...+.....+..||+++.....    ..+......
T Consensus       111 -~~~~~~~l~~a---~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~~~----~~~~~~np~  182 (287)
T CHL00181        111 -APKTKEVLKKA---MGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQRDDLVVIFAGYKDRM----DKFYESNPG  182 (287)
T ss_pred             -hHHHHHHHHHc---cCCEEEEEccchhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHH----HHHHhcCHH
Confidence             01111222222   23499999996431        012233344445455556677777754310    000000001


Q ss_pred             ccccc--eeecCCCChHHHHHHHHHHhcc
Q 041007          349 GTNMM--EIGLGELSEEECRSLFRQIAFH  375 (597)
Q Consensus       349 ~~~~~--~~~l~~Ls~~es~~Lf~~~~~~  375 (597)
                      ..+..  .+.+.+++.+|..+++...+..
T Consensus       183 L~sR~~~~i~F~~~t~~el~~I~~~~l~~  211 (287)
T CHL00181        183 LSSRIANHVDFPDYTPEELLQIAKIMLEE  211 (287)
T ss_pred             HHHhCCceEEcCCcCHHHHHHHHHHHHHH
Confidence            12222  2899999999999998888743

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=98.06  E-value=0.00024  Score=77.36  Aligned_cols=192  Identities=13%  Similarity=0.097  Sum_probs=107.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+...+.|..++....         -...+.++|+.|+|||++|+.+.+..--...-+.       .+.+.    
T Consensus        16 ~~viGq~~v~~~L~~~i~~~~---------~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~-------~pC~~----   75 (559)
T PRK05563         16 EDVVGQEHITKTLKNAIKQGK---------ISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDG-------EPCNE----   75 (559)
T ss_pred             HhccCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC-------CCCCc----
Confidence            468999999999999998532         2456788999999999999998763110000000       00000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccC-------C-CCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESLKG-------S-VSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~-------~-~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -.....+......       . ....++..++...+... ..++.-++|+|+++... ...+..+...
T Consensus        76 ------------C~~C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt-~~a~naLLKt  142 (559)
T PRK05563         76 ------------CEICKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLS-TGAFNALLKT  142 (559)
T ss_pred             ------------cHHHHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC-HHHHHHHHHH
Confidence                        1111111111000       0 01111222222222211 13566788999997765 5567777777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +......+.+|++|........         .+...+ .+++.+++.++....+...+...+...    -.+.+..|++.
T Consensus       143 LEepp~~~ifIlatt~~~ki~~---------tI~SRc~~~~f~~~~~~ei~~~L~~i~~~egi~i----~~~al~~ia~~  209 (559)
T PRK05563        143 LEEPPAHVIFILATTEPHKIPA---------TILSRCQRFDFKRISVEDIVERLKYILDKEGIEY----EDEALRLIARA  209 (559)
T ss_pred             hcCCCCCeEEEEEeCChhhCcH---------HHHhHheEEecCCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHH
Confidence            7665556666666543311100         111112 288999999999988887764322111    14567788889


Q ss_pred             cCCchHHH
Q 041007          396 CKGLPFAV  403 (597)
Q Consensus       396 ~~GlPLai  403 (597)
                      ++|.+.-+
T Consensus       210 s~G~~R~a  217 (559)
T PRK05563        210 AEGGMRDA  217 (559)
T ss_pred             cCCCHHHH
Confidence            98877543

>PRK06620 hypothetical protein; Validated

Probab=98.05  E-value=6e-05  Score=71.54  Aligned_cols=102  Identities=11%  Similarity=0.011  Sum_probs=57.7

Q ss_pred             EEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHH
Q 041007          294 VLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQI  372 (597)
Q Consensus       294 ~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~  372 (597)
                      -+|++||++...   . ..+...+.. ...|..||+|++..+......  ++.+ .......++++++++++-..++.+.
T Consensus        87 d~lliDdi~~~~---~-~~lf~l~N~~~e~g~~ilits~~~p~~l~l~--~L~S-Rl~~gl~~~l~~pd~~~~~~~l~k~  159 (214)
T PRK06620         87 NAFIIEDIENWQ---E-PALLHIFNIINEKQKYLLLTSSDKSRNFTLP--DLSS-RIKSVLSILLNSPDDELIKILIFKH  159 (214)
T ss_pred             CEEEEeccccch---H-HHHHHHHHHHHhcCCEEEEEcCCCccccchH--HHHH-HHhCCceEeeCCCCHHHHHHHHHHH
Confidence            478899996322   1 123222222 245678999998775432110  0000 1111112999999999988888877


Q ss_pred             hccCCCCCCccchHHHHHHHHHhcCCchHHHHHH
Q 041007          373 AFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       373 ~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      +...+- .   --+++.+-|++.+.|.--.+.-+
T Consensus       160 ~~~~~l-~---l~~ev~~~L~~~~~~d~r~l~~~  189 (214)
T PRK06620        160 FSISSV-T---ISRQIIDFLLVNLPREYSKIIEI  189 (214)
T ss_pred             HHHcCC-C---CCHHHHHHHHHHccCCHHHHHHH
Confidence            643211 1   11567788888888766555433

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=98.05  E-value=6.9e-05  Score=79.18  Aligned_cols=170  Identities=16%  Similarity=0.175  Sum_probs=92.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccC-C-eeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANF-D-KRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F-~-~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ...+.|+|++|+|||+|++.+++  ...... . .++|++.                      .++...+...+...   
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~--~l~~~~~~~~v~yi~~----------------------~~f~~~~~~~~~~~---  182 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYITS----------------------EKFLNDLVDSMKEG---  182 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHH--HHHHhCCCCeEEEEEH----------------------HHHHHHHHHHHhcc---
Confidence            44699999999999999999999  444433 2 3566653                      33344444443221   


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchH-HHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccc
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYW-EQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM  352 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~-~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~  352 (597)
                        ..+    .+.+.+..+.-+|+|||++.......+ +.+...+.. ...|..||+||...+.......-.+.+ .....
T Consensus       183 --~~~----~f~~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~S-R~~~g  255 (440)
T PRK14088        183 --KLN----EFREKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVS-RFQMG  255 (440)
T ss_pred             --cHH----HHHHHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhh-HHhcC
Confidence              111    122233334568999999754212222 233333322 123457888876432111000000000 00111


Q ss_pred             ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHH
Q 041007          353 MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       353 ~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~  404 (597)
                      ..+.+.+.+.+.-.+++.+.+...... .   -.++...|++.+.|.--.+.
T Consensus       256 l~v~i~~pd~e~r~~IL~~~~~~~~~~-l---~~ev~~~Ia~~~~~~~R~L~  303 (440)
T PRK14088        256 LVAKLEPPDEETRKKIARKMLEIEHGE-L---PEEVLNFVAENVDDNLRRLR  303 (440)
T ss_pred             ceEeeCCCCHHHHHHHHHHHHHhcCCC-C---CHHHHHHHHhccccCHHHHH
Confidence            127899999999999999887532221 1   15567888888887654443

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

Probab=98.05  E-value=0.00037  Score=66.55  Aligned_cols=177  Identities=18%  Similarity=0.223  Sum_probs=101.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+|+|.+.-+++|.=.+.....     .+..+--|.++||+|.||||||.-+++.  ...++.    ++  +.+..    
T Consensus        26 ~efiGQ~~vk~~L~ifI~AAk~-----r~e~lDHvLl~GPPGlGKTTLA~IIA~E--mgvn~k----~t--sGp~l----   88 (332)
T COG2255          26 DEFIGQEKVKEQLQIFIKAAKK-----RGEALDHVLLFGPPGLGKTTLAHIIANE--LGVNLK----IT--SGPAL----   88 (332)
T ss_pred             HHhcChHHHHHHHHHHHHHHHh-----cCCCcCeEEeeCCCCCcHHHHHHHHHHH--hcCCeE----ec--ccccc----
Confidence            5799999998888777764432     1235778999999999999999999994  333221    11  11111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC------
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS------  319 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~------  319 (597)
                                                    ....++...+.. | ...=+|++|.++... ...-+.+...+..      
T Consensus        89 ------------------------------eK~gDlaaiLt~-L-e~~DVLFIDEIHrl~-~~vEE~LYpaMEDf~lDI~  135 (332)
T COG2255          89 ------------------------------EKPGDLAAILTN-L-EEGDVLFIDEIHRLS-PAVEEVLYPAMEDFRLDII  135 (332)
T ss_pred             ------------------------------cChhhHHHHHhc-C-CcCCeEEEehhhhcC-hhHHHHhhhhhhheeEEEE
Confidence                                          011111222211 2 234577889987665 3333333333321      


Q ss_pred             --CCCCcE-----------EEEEccCCCCCCCcccccccccCccccce--eecCCCChHHHHHHHHHHhccCCCCCCccc
Q 041007          320 --GSEGSR-----------ILVTRSGGKNGTNMTEIGLGEKNGTNMME--IGLGELSEEECRSLFRQIAFHGRSSDYREK  384 (597)
Q Consensus       320 --~~~gs~-----------IIvTtR~~~~~~~~~~~~~~~~~~~~~~~--~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~  384 (597)
                        .+++++           |=-|||...-.          .......+  .++.-.+.+|-.++..+.+..-..    +-
T Consensus       136 IG~gp~Arsv~ldLppFTLIGATTr~G~lt----------~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i----~i  201 (332)
T COG2255         136 IGKGPAARSIRLDLPPFTLIGATTRAGMLT----------NPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGI----EI  201 (332)
T ss_pred             EccCCccceEeccCCCeeEeeecccccccc----------chhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCC----CC
Confidence              123333           23467665110          01111111  677778889998888887732221    11


Q ss_pred             hHHHHHHHHHhcCCchHHHHHH
Q 041007          385 FEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       385 ~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      ..+.+.+|+++..|-|--..-+
T Consensus       202 ~~~~a~eIA~rSRGTPRIAnRL  223 (332)
T COG2255         202 DEEAALEIARRSRGTPRIANRL  223 (332)
T ss_pred             ChHHHHHHHHhccCCcHHHHHH
Confidence            2567899999999999654433

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=98.04  E-value=3.5e-05  Score=78.32  Aligned_cols=150  Identities=17%  Similarity=0.169  Sum_probs=83.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+...+.+..++....         .+.++.++|++|+|||++|+.+++.  ....   ...++.+. ...    
T Consensus        21 ~~~~~~~~~~~~l~~~~~~~~---------~~~~lll~G~~G~GKT~la~~l~~~--~~~~---~~~i~~~~-~~~----   81 (316)
T PHA02544         21 DECILPAADKETFKSIVKKGR---------IPNMLLHSPSPGTGKTTVAKALCNE--VGAE---VLFVNGSD-CRI----   81 (316)
T ss_pred             HHhcCcHHHHHHHHHHHhcCC---------CCeEEEeeCcCCCCHHHHHHHHHHH--hCcc---ceEeccCc-ccH----
Confidence            568999999999999987422         3457777999999999999999873  2211   22333332 111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcE
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSR  325 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~  325 (597)
                                  ..+ +..+...             ....  .+.+.+-+||+|+++..........+...+.....++.
T Consensus        82 ------------~~i-~~~l~~~-------------~~~~--~~~~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~  133 (316)
T PHA02544         82 ------------DFV-RNRLTRF-------------ASTV--SLTGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCS  133 (316)
T ss_pred             ------------HHH-HHHHHHH-------------HHhh--cccCCCeEEEEECcccccCHHHHHHHHHHHHhcCCCce
Confidence                        111 1101000             0000  01134568999999766323333445444555567788


Q ss_pred             EEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHH
Q 041007          326 ILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQ  371 (597)
Q Consensus       326 IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~  371 (597)
                      +|+||........         .+...+ .+.+...+.++..+++..
T Consensus       134 ~Ilt~n~~~~l~~---------~l~sR~~~i~~~~p~~~~~~~il~~  171 (316)
T PHA02544        134 FIITANNKNGIIE---------PLRSRCRVIDFGVPTKEEQIEMMKQ  171 (316)
T ss_pred             EEEEcCChhhchH---------HHHhhceEEEeCCCCHHHHHHHHHH
Confidence            8888864411000         111111 266777777777665543

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.02  E-value=0.0002  Score=78.49  Aligned_cols=196  Identities=14%  Similarity=0.092  Sum_probs=108.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.+.-...|..++....         -...+.++|+.|+||||+|+.+++...-. .......-.+..        
T Consensus        16 ~~liGq~~i~~~L~~~l~~~r---------l~~a~Lf~Gp~G~GKttlA~~lAk~L~c~-~~~~~~~~~Cg~--------   77 (620)
T PRK14948         16 DELVGQEAIATTLKNALISNR---------IAPAYLFTGPRGTGKTSSARILAKSLNCL-NSDKPTPEPCGK--------   77 (620)
T ss_pred             hhccChHHHHHHHHHHHHcCC---------CCceEEEECCCCCChHHHHHHHHHHhcCC-CcCCCCCCCCcc--------
Confidence            467899999999999988432         23578899999999999999998742111 110000000000        


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccC-----C---CCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESLKG-----S---VSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~-----~---~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -...+.+......     .   ........++...+... ..+++-++|+|+++... ...++.+...
T Consensus        78 ------------C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt-~~a~naLLK~  144 (620)
T PRK14948         78 ------------CELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLS-TAAFNALLKT  144 (620)
T ss_pred             ------------cHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccC-HHHHHHHHHH
Confidence                        1111111111110     0   01111222222221110 12455689999998776 5567778777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +..-...+.+|++|.+......         .+...+. +++.+++.++....+...+...+...    ..+.+..|++.
T Consensus       145 LEePp~~tvfIL~t~~~~~llp---------TIrSRc~~~~f~~l~~~ei~~~L~~ia~kegi~i----s~~al~~La~~  211 (620)
T PRK14948        145 LEEPPPRVVFVLATTDPQRVLP---------TIISRCQRFDFRRIPLEAMVQHLSEIAEKESIEI----EPEALTLVAQR  211 (620)
T ss_pred             HhcCCcCeEEEEEeCChhhhhH---------HHHhheeEEEecCCCHHHHHHHHHHHHHHhCCCC----CHHHHHHHHHH
Confidence            7765556666665544311000         1111222 88889999998888877664322111    13567889999


Q ss_pred             cCCchHHHHH
Q 041007          396 CKGLPFAVKI  405 (597)
Q Consensus       396 ~~GlPLai~~  405 (597)
                      ++|.+..+..
T Consensus       212 s~G~lr~A~~  221 (620)
T PRK14948        212 SQGGLRDAES  221 (620)
T ss_pred             cCCCHHHHHH
Confidence            9998764433

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=98.02  E-value=6.8e-05  Score=79.94  Aligned_cols=169  Identities=15%  Similarity=0.165  Sum_probs=94.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCC--eeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFD--KRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ...+.|+|++|+|||+|++.+++  .....++  .++++++                      ..+...+...+...   
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~--~~~~~~~~~~v~yi~~----------------------~~~~~~~~~~~~~~---  200 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGN--YILEKNPNAKVVYVTS----------------------EKFTNDFVNALRNN---  200 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEEEH----------------------HHHHHHHHHHHHcC---
Confidence            45789999999999999999999  4544432  3556653                      22333333333211   


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchH-HHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccc
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYW-EQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM  352 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~-~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~  352 (597)
                        ..+    .+.+.++ +.-+|||||++.......+ +.+...+.. ...+..+|+|+...+.........+.+ .....
T Consensus       201 --~~~----~~~~~~~-~~dlLiiDDi~~l~~~~~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~S-Rl~~g  272 (450)
T PRK00149        201 --TME----EFKEKYR-SVDVLLIDDIQFLAGKERTQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRS-RFEWG  272 (450)
T ss_pred             --cHH----HHHHHHh-cCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHh-HhcCC
Confidence              111    2223333 3448999999754322222 233333322 223456888876542111100000000 11111


Q ss_pred             ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHH
Q 041007          353 MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       353 ~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~  404 (597)
                      ..+++.+.+.++-..++.+.+...+..    --.++...|++.+.|..-.+.
T Consensus       273 l~v~i~~pd~~~r~~il~~~~~~~~~~----l~~e~l~~ia~~~~~~~R~l~  320 (450)
T PRK00149        273 LTVDIEPPDLETRIAILKKKAEEEGID----LPDEVLEFIAKNITSNVRELE  320 (450)
T ss_pred             eeEEecCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHcCcCCCHHHHH
Confidence            238999999999999999987532211    125678889999998776543

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=98.00  E-value=0.00023  Score=77.12  Aligned_cols=192  Identities=10%  Similarity=0.111  Sum_probs=109.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|-+.-++.|..++....         -...+.++|+.|+||||+|+.+++..--......   .++....      
T Consensus        16 ~diiGqe~iv~~L~~~i~~~~---------i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~---~pC~~C~------   77 (563)
T PRK06647         16 NSLEGQDFVVETLKHSIESNK---------IANAYIFSGPRGVGKTSSARAFARCLNCVNGPTP---MPCGECS------   77 (563)
T ss_pred             HHccCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHhhccccCCCC---CCCccch------
Confidence            468999999999999997432         3457889999999999999999874211111000   0000000      


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-------ccCCC-CchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-------LKGSV-SSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-------l~~~~-~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                    ..+.+...       +.+.. ....+..++.+.+... ..+++-++|+|+++... ...++.+...
T Consensus        78 --------------~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls-~~a~naLLK~  142 (563)
T PRK06647         78 --------------SCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLS-NSAFNALLKT  142 (563)
T ss_pred             --------------HHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcC-HHHHHHHHHh
Confidence                          00000000       00000 1111121222211111 23566689999998776 5567778777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +...+..+.+|++|.......         ..+...+. +++.+++.++....+...+...+..    -..+.+..|++.
T Consensus       143 LEepp~~~vfI~~tte~~kL~---------~tI~SRc~~~~f~~l~~~el~~~L~~i~~~egi~----id~eAl~lLa~~  209 (563)
T PRK06647        143 IEEPPPYIVFIFATTEVHKLP---------ATIKSRCQHFNFRLLSLEKIYNMLKKVCLEDQIK----YEDEALKWIAYK  209 (563)
T ss_pred             hccCCCCEEEEEecCChHHhH---------HHHHHhceEEEecCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHH
Confidence            776666777777664321000         01112222 8999999999998888876433221    124567789999


Q ss_pred             cCCchHHH
Q 041007          396 CKGLPFAV  403 (597)
Q Consensus       396 ~~GlPLai  403 (597)
                      ++|.+-.+
T Consensus       210 s~GdlR~a  217 (563)
T PRK06647        210 STGSVRDA  217 (563)
T ss_pred             cCCCHHHH
Confidence            99987544

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.98  E-value=0.00019  Score=78.38  Aligned_cols=197  Identities=11%  Similarity=0.152  Sum_probs=109.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+.-.+.|..++....         -...+.++|+.|+||||+|+.+++..--......   -.+..        
T Consensus        16 ~~iiGq~~v~~~L~~~i~~~~---------~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~---~~c~~--------   75 (576)
T PRK14965         16 SDLTGQEHVSRTLQNAIDTGR---------VAHAFLFTGARGVGKTSTARILAKALNCEQGLTA---EPCNV--------   75 (576)
T ss_pred             HHccCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC---CCCCc--------
Confidence            468999999999999987432         2356789999999999999998773111111000   00000        


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-------ccCC-CCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-------LKGS-VSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-------l~~~-~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -.....|...       +.+. .....+...+...+... ..++.-++|+|+++..+ ....+.+...
T Consensus        76 ------------c~~c~~i~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt-~~a~naLLk~  142 (576)
T PRK14965         76 ------------CPPCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLS-TNAFNALLKT  142 (576)
T ss_pred             ------------cHHHHHHhcCCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCC-HHHHHHHHHH
Confidence                        0000000000       0000 01111222222222211 12455689999997766 5567778888


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +......+.+|++|.+......         .+...+. +++.+++.++....+...+...+...    -.+.+..|++.
T Consensus       143 LEepp~~~~fIl~t~~~~kl~~---------tI~SRc~~~~f~~l~~~~i~~~L~~i~~~egi~i----~~~al~~la~~  209 (576)
T PRK14965        143 LEEPPPHVKFIFATTEPHKVPI---------TILSRCQRFDFRRIPLQKIVDRLRYIADQEGISI----SDAALALVARK  209 (576)
T ss_pred             HHcCCCCeEEEEEeCChhhhhH---------HHHHhhhhhhcCCCCHHHHHHHHHHHHHHhCCCC----CHHHHHHHHHH
Confidence            8766667777766643310000         1111122 88999999999888877654322211    14566789999


Q ss_pred             cCCch-HHHHHHHh
Q 041007          396 CKGLP-FAVKILGS  408 (597)
Q Consensus       396 ~~GlP-Lai~~~~~  408 (597)
                      ++|.. .++..+-.
T Consensus       210 a~G~lr~al~~Ldq  223 (576)
T PRK14965        210 GDGSMRDSLSTLDQ  223 (576)
T ss_pred             cCCCHHHHHHHHHH
Confidence            99865 55555533

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=97.97  E-value=0.00023  Score=72.06  Aligned_cols=98  Identities=14%  Similarity=0.041  Sum_probs=66.1

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|+|+++.++ ....+.+...+..-+.++.+|+||.+......         -+...+. +.+.+++.+++.+.+
T Consensus       105 ~~~kv~iI~~a~~m~-~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~---------TI~SRc~~~~~~~~~~~~~~~~L  174 (328)
T PRK05707        105 GGRKVVLIEPAEAMN-RNAANALLKSLEEPSGDTVLLLISHQPSRLLP---------TIKSRCQQQACPLPSNEESLQWL  174 (328)
T ss_pred             CCCeEEEECChhhCC-HHHHHHHHHHHhCCCCCeEEEEEECChhhCcH---------HHHhhceeeeCCCcCHHHHHHHH
Confidence            344456789998887 66778888888776677888888876622111         1111222 999999999999988


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      .....  .  .    ..+.+..++..++|.|+....+
T Consensus       175 ~~~~~--~--~----~~~~~~~~l~la~Gsp~~A~~l  203 (328)
T PRK05707        175 QQALP--E--S----DERERIELLTLAGGSPLRALQL  203 (328)
T ss_pred             HHhcc--c--C----ChHHHHHHHHHcCCCHHHHHHH
Confidence            76531  0  1    1334567889999999865544

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.97  E-value=0.00037  Score=70.09  Aligned_cols=197  Identities=14%  Similarity=0.205  Sum_probs=110.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhh-------------hccCCeeEE
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV-------------KANFDKRIW  232 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~-------------~~~F~~~~w  232 (597)
                      .+++|.+..++.|...+....         -.....++|+.|+||+++|..+.+..--             ...++...|
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~r---------l~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~   74 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNR---------IAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLW   74 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCC---------CCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEE
Confidence            357899999999999997432         2578999999999999999887653100             112233344


Q ss_pred             EEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhcc--CCCCchhhHHHHHHHHHHHhc-----CceEEEEEecccCCC
Q 041007          233 VSASYPRDEIRVARDEISVARDRDEIRVAKAILESLK--GSVSSQVEMETVLQYINEFVQ-----GKKVLLVLDDLWWNA  305 (597)
Q Consensus       233 v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~--~~~~~~~~~~~~~~~l~~~L~-----~kr~LLVLDdv~~~~  305 (597)
                      +.-......                ..+....+...+  .........+++ +.+.+.+.     +++-++|+|+++.++
T Consensus        75 i~p~~~~~g----------------~~~~~~~~~~~~~~~~~~~~I~id~i-r~i~~~l~~~p~~~~~kVvII~~ae~m~  137 (314)
T PRK07399         75 VEPTYQHQG----------------KLITASEAEEAGLKRKAPPQIRLEQI-REIKRFLSRPPLEAPRKVVVIEDAETMN  137 (314)
T ss_pred             Eeccccccc----------------cccchhhhhhccccccccccCcHHHH-HHHHHHHccCcccCCceEEEEEchhhcC
Confidence            421100000                000001111111  111112222222 22333332     556799999997776


Q ss_pred             CcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccc
Q 041007          306 YPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREK  384 (597)
Q Consensus       306 ~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~  384 (597)
                       ....+.+...+..-+ .+.+|++|.+......         -+...+. +++.+++.++..+.+.+.....       .
T Consensus       138 -~~aaNaLLK~LEEPp-~~~fILi~~~~~~Ll~---------TI~SRcq~i~f~~l~~~~~~~~L~~~~~~~-------~  199 (314)
T PRK07399        138 -EAAANALLKTLEEPG-NGTLILIAPSPESLLP---------TIVSRCQIIPFYRLSDEQLEQVLKRLGDEE-------I  199 (314)
T ss_pred             -HHHHHHHHHHHhCCC-CCeEEEEECChHhCcH---------HHHhhceEEecCCCCHHHHHHHHHHhhccc-------c
Confidence             556777887776545 4556655544311110         1112222 9999999999999998764211       1


Q ss_pred             hHHHHHHHHHhcCCchHHHHHH
Q 041007          385 FEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       385 ~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      .......++..++|.|..+..+
T Consensus       200 ~~~~~~~l~~~a~Gs~~~al~~  221 (314)
T PRK07399        200 LNINFPELLALAQGSPGAAIAN  221 (314)
T ss_pred             chhHHHHHHHHcCCCHHHHHHH
Confidence            1111367899999999766543

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.97  E-value=0.00052  Score=64.73  Aligned_cols=187  Identities=18%  Similarity=0.159  Sum_probs=107.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC-CchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP-RDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      +.+++.|+|.-|+|||.+.+.....  ..+  +.++-+.+..+ ...                ..+...++..+..+...
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s--~~~--d~~~~v~i~~~~~s~----------------~~~~~ai~~~l~~~p~~  109 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLAS--LNE--DQVAVVVIDKPTLSD----------------ATLLEAIVADLESQPKV  109 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHh--cCC--CceEEEEecCcchhH----------------HHHHHHHHHHhccCccc
Confidence            3469999999999999999944331  111  11121222221 222                67777777777763221


Q ss_pred             --hhhHHHHHHHHHHHhc-Cce-EEEEEecccCCCCcchHHHHHHhhcC---CCCCcEEEEEccCCCCCCCccccccccc
Q 041007          275 --QVEMETVLQYINEFVQ-GKK-VLLVLDDLWWNAYPRYWEQLMYSLKS---GSEGSRILVTRSGGKNGTNMTEIGLGEK  347 (597)
Q Consensus       275 --~~~~~~~~~~l~~~L~-~kr-~LLVLDdv~~~~~~~~~~~l~~~l~~---~~~gs~IIvTtR~~~~~~~~~~~~~~~~  347 (597)
                        ....+...+.+....+ +++ ..+++|+.+... ....+.+......   ....-+|+.....+....-    .++..
T Consensus       110 ~~~~~~e~~~~~L~al~~~g~r~v~l~vdEah~L~-~~~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~l----r~~~l  184 (269)
T COG3267         110 NVNAVLEQIDRELAALVKKGKRPVVLMVDEAHDLN-DSALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRL----RLPVL  184 (269)
T ss_pred             hhHHHHHHHHHHHHHHHHhCCCCeEEeehhHhhhC-hhHHHHHHHHHhhcccccCceeeeecCCcccchhh----chHHH
Confidence              2223444444444443 566 899999997765 4455555543322   2222345554443311100    00000


Q ss_pred             -Ccc-ccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHh
Q 041007          348 -NGT-NMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGS  408 (597)
Q Consensus       348 -~~~-~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~  408 (597)
                       +.. +... |++.|++.++...++..+..+...+ .+--..+....|.....|.|.+|..++.
T Consensus       185 ~e~~~R~~ir~~l~P~~~~~t~~yl~~~Le~a~~~-~~l~~~~a~~~i~~~sqg~P~lin~~~~  247 (269)
T COG3267         185 RELEQRIDIRIELPPLTEAETGLYLRHRLEGAGLP-EPLFSDDALLLIHEASQGIPRLINNLAT  247 (269)
T ss_pred             HhhhheEEEEEecCCcChHHHHHHHHHHHhccCCC-cccCChhHHHHHHHHhccchHHHHHHHH
Confidence             111 1112 8999999999999999888665332 2222356678899999999999987754

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.95  E-value=4e-05  Score=66.69  Aligned_cols=21  Identities=43%  Similarity=0.585  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |.|+|++|+|||++|+.+++.
T Consensus         1 ill~G~~G~GKT~l~~~la~~   21 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQY   21 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhh
Confidence            579999999999999999984

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 ....

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=97.94  E-value=0.00017  Score=76.10  Aligned_cols=164  Identities=18%  Similarity=0.200  Sum_probs=87.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ...+.|+|+.|+|||+|++.+++.  .......+++++.                      ..+...+...+...     
T Consensus       141 ~npl~L~G~~G~GKTHLl~Ai~~~--l~~~~~~v~yi~~----------------------~~f~~~~~~~l~~~-----  191 (445)
T PRK12422        141 FNPIYLFGPEGSGKTHLMQAAVHA--LRESGGKILYVRS----------------------ELFTEHLVSAIRSG-----  191 (445)
T ss_pred             CceEEEEcCCCCCHHHHHHHHHHH--HHHcCCCEEEeeH----------------------HHHHHHHHHHHhcc-----
Confidence            456889999999999999999984  4333233455542                      22333333333211     


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchH-HHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccccce
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYW-EQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME  354 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~-~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~  354 (597)
                      .    ...++..+. ..-+|++||++.......+ +.+...+.. ...|..||+||...+........++.+ .......
T Consensus       192 ~----~~~f~~~~~-~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~S-R~~~Gl~  265 (445)
T PRK12422        192 E----MQRFRQFYR-NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLIS-RFEWGIA  265 (445)
T ss_pred             h----HHHHHHHcc-cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHh-hhcCCeE
Confidence            1    112333333 3458889999765422122 223333322 124567888886542111111000000 0111123


Q ss_pred             eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCc
Q 041007          355 IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGL  399 (597)
Q Consensus       355 ~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~Gl  399 (597)
                      +++.+++.++-..++.+.+...+.. .   -.++..-|+..+.|.
T Consensus       266 ~~l~~pd~e~r~~iL~~k~~~~~~~-l---~~evl~~la~~~~~d  306 (445)
T PRK12422        266 IPLHPLTKEGLRSFLERKAEALSIR-I---EETALDFLIEALSSN  306 (445)
T ss_pred             EecCCCCHHHHHHHHHHHHHHcCCC-C---CHHHHHHHHHhcCCC
Confidence            8899999999999999887543211 1   144556676666654

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

Probab=97.93  E-value=0.00047  Score=70.68  Aligned_cols=148  Identities=18%  Similarity=0.181  Sum_probs=84.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      ....+.|+|+.|.|||.|++++.+  ......+....+.++.                    +.....++..+..     
T Consensus       112 ~~nplfi~G~~GlGKTHLl~Aign--~~~~~~~~a~v~y~~s--------------------e~f~~~~v~a~~~-----  164 (408)
T COG0593         112 AYNPLFIYGGVGLGKTHLLQAIGN--EALANGPNARVVYLTS--------------------EDFTNDFVKALRD-----  164 (408)
T ss_pred             cCCcEEEECCCCCCHHHHHHHHHH--HHHhhCCCceEEeccH--------------------HHHHHHHHHHHHh-----
Confidence            467899999999999999999999  5555555333333322                    3333333333221     


Q ss_pred             hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHH-HHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccccc
Q 041007          276 VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQ-LMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM  353 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~-l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~  353 (597)
                          .-...+++..  .-=++++||++.....+.|+. +...|.. ...|..||+|++..+.......-++.+ ......
T Consensus       165 ----~~~~~Fk~~y--~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~S-R~~~Gl  237 (408)
T COG0593         165 ----NEMEKFKEKY--SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRS-RLEWGL  237 (408)
T ss_pred             ----hhHHHHHHhh--ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHH-HHhcee
Confidence                1123344444  334889999976543333433 3444433 234448999987663322211111100 011112


Q ss_pred             eeecCCCChHHHHHHHHHHhccCC
Q 041007          354 EIGLGELSEEECRSLFRQIAFHGR  377 (597)
Q Consensus       354 ~~~l~~Ls~~es~~Lf~~~~~~~~  377 (597)
                      .+.+.|.+.+.-..++.+.+....
T Consensus       238 ~~~I~~Pd~e~r~aiL~kka~~~~  261 (408)
T COG0593         238 VVEIEPPDDETRLAILRKKAEDRG  261 (408)
T ss_pred             EEeeCCCCHHHHHHHHHHHHHhcC
Confidence            299999999999999998775433

>PRK10536 hypothetical protein; Provisional

Probab=97.91  E-value=0.00043  Score=66.35  Aligned_cols=54  Identities=20%  Similarity=0.362  Sum_probs=40.0

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCe
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDK  229 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~  229 (597)
                      +...+.+|......+..+|..            ..+|.++|++|+|||+||..+..+.-..+.|..
T Consensus        53 ~~~~i~p~n~~Q~~~l~al~~------------~~lV~i~G~aGTGKT~La~a~a~~~l~~~~~~k  106 (262)
T PRK10536         53 DTSPILARNEAQAHYLKAIES------------KQLIFATGEAGCGKTWISAAKAAEALIHKDVDR  106 (262)
T ss_pred             CCccccCCCHHHHHHHHHHhc------------CCeEEEECCCCCCHHHHHHHHHHHHHhcCCeeE
Confidence            334567888899999998862            359999999999999999998774222334443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.91  E-value=0.00012  Score=83.64  Aligned_cols=45  Identities=27%  Similarity=0.434  Sum_probs=38.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++++.+.|....          ...+.++|++|+|||++|..++..
T Consensus       179 ~~~igr~~ei~~~~~~L~r~~----------~~n~lL~G~pGvGKTal~~~la~~  223 (821)
T CHL00095        179 DPVIGREKEIERVIQILGRRT----------KNNPILIGEPGVGKTAIAEGLAQR  223 (821)
T ss_pred             CCCCCcHHHHHHHHHHHcccc----------cCCeEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999998432          346679999999999999999874

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.90  E-value=9.2e-05  Score=64.90  Aligned_cols=38  Identities=32%  Similarity=0.433  Sum_probs=27.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ..+.|+|++|+||||+++.++..  .......++++..+.
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~--~~~~~~~~~~~~~~~   40 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARE--LGPPGGGVIYIDGED   40 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhc--cCCCCCCEEEECCEE
Confidence            68999999999999999999884  333223455555443

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.

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=97.89  E-value=0.00016  Score=71.86  Aligned_cols=141  Identities=13%  Similarity=0.093  Sum_probs=71.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhh
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVE  277 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~  277 (597)
                      .-+.++|++|+|||++|+.+++.....+......|+.++.                    .++    +..+.+..  .  
T Consensus        59 ~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~--------------------~~l----~~~~~g~~--~--  110 (284)
T TIGR02880        59 LHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR--------------------DDL----VGQYIGHT--A--  110 (284)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH--------------------HHH----hHhhcccc--h--
Confidence            3688999999999999977766311111111112343331                    111    11111111  1  


Q ss_pred             HHHHHHHHHHHhcCceEEEEEecccCCC--------CcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCc
Q 041007          278 METVLQYINEFVQGKKVLLVLDDLWWNA--------YPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNG  349 (597)
Q Consensus       278 ~~~~~~~l~~~L~~kr~LLVLDdv~~~~--------~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~  349 (597)
                       ......+.+.   ..-+|+||++....        ....++.+...+.....+.+||+++......    .+.......
T Consensus       111 -~~~~~~~~~a---~~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~~~~----~~~~~np~L  182 (284)
T TIGR02880       111 -PKTKEILKRA---MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMD----SFFESNPGF  182 (284)
T ss_pred             -HHHHHHHHHc---cCcEEEEechhhhccCCCccchHHHHHHHHHHHHhcCCCCEEEEEeCCcHHHH----HHHhhCHHH
Confidence             1112222222   23689999996431        0123344555555555666777776543000    000000011


Q ss_pred             cc--cceeecCCCChHHHHHHHHHHhc
Q 041007          350 TN--MMEIGLGELSEEECRSLFRQIAF  374 (597)
Q Consensus       350 ~~--~~~~~l~~Ls~~es~~Lf~~~~~  374 (597)
                      ..  ...+.+.+++.+|..+++...+-
T Consensus       183 ~sR~~~~i~fp~l~~edl~~I~~~~l~  209 (284)
T TIGR02880       183 SSRVAHHVDFPDYSEAELLVIAGLMLK  209 (284)
T ss_pred             HhhCCcEEEeCCcCHHHHHHHHHHHHH
Confidence            11  12389999999999999888764

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

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.84  E-value=0.00015  Score=82.99  Aligned_cols=45  Identities=24%  Similarity=0.406  Sum_probs=38.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++++++.|....          ...+.++|++|+|||+||..+...
T Consensus       178 ~~vigr~~ei~~~i~iL~r~~----------~~n~lL~G~pGvGKT~l~~~la~~  222 (857)
T PRK10865        178 DPVIGRDEEIRRTIQVLQRRT----------KNNPVLIGEPGVGKTAIVEGLAQR  222 (857)
T ss_pred             CcCCCCHHHHHHHHHHHhcCC----------cCceEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999998533          356779999999999999999873

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.84  E-value=0.00026  Score=77.19  Aligned_cols=51  Identities=16%  Similarity=0.272  Sum_probs=40.8

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.++.++++..++......     ....+++.|+|++|+||||+++.++..
T Consensus        83 ldel~~~~~ki~~l~~~l~~~~~~-----~~~~~illL~GP~GsGKTTl~~~la~~  133 (637)
T TIGR00602        83 QHELAVHKKKIEEVETWLKAQVLE-----NAPKRILLITGPSGCGKSTTIKILSKE  133 (637)
T ss_pred             HHHhcCcHHHHHHHHHHHHhcccc-----cCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            467899999999999999754321     123468999999999999999999874

This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

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

Probab=97.82  E-value=0.0024  Score=59.62  Aligned_cols=125  Identities=14%  Similarity=0.263  Sum_probs=80.2

Q ss_pred             ccCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          162 VIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       162 ~~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      .++-..++|-|...+.|.+.......      .....-|.+||.-|+|||+|++++.+  .+.......+  -+..    
T Consensus        56 ~i~L~~l~Gvd~qk~~L~~NT~~F~~------G~pANnVLLwGaRGtGKSSLVKA~~~--e~~~~glrLV--EV~k----  121 (287)
T COG2607          56 PIDLADLVGVDRQKEALVRNTEQFAE------GLPANNVLLWGARGTGKSSLVKALLN--EYADEGLRLV--EVDK----  121 (287)
T ss_pred             CcCHHHHhCchHHHHHHHHHHHHHHc------CCcccceEEecCCCCChHHHHHHHHH--HHHhcCCeEE--EEcH----
Confidence            34456789999999988876654433      22345789999999999999999998  4544433322  2211    


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-  320 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-  320 (597)
                                                     .+..+...+.+.|+.  ..++|+|..||+--+........+...|..+ 
T Consensus       122 -------------------------------~dl~~Lp~l~~~Lr~--~~~kFIlFcDDLSFe~gd~~yK~LKs~LeG~v  168 (287)
T COG2607         122 -------------------------------EDLATLPDLVELLRA--RPEKFILFCDDLSFEEGDDAYKALKSALEGGV  168 (287)
T ss_pred             -------------------------------HHHhhHHHHHHHHhc--CCceEEEEecCCCCCCCchHHHHHHHHhcCCc
Confidence                                           011122233333332  3679999999997766677888888888643 


Q ss_pred             --CCCcEEEEEccCC
Q 041007          321 --SEGSRILVTRSGG  333 (597)
Q Consensus       321 --~~gs~IIvTtR~~  333 (597)
                        .+...++..|.++
T Consensus       169 e~rP~NVl~YATSNR  183 (287)
T COG2607         169 EGRPANVLFYATSNR  183 (287)
T ss_pred             ccCCCeEEEEEecCC
Confidence              3444555556555

>TIGR03689 pup_AAA proteasome ATPase

Probab=97.82  E-value=0.00016  Score=76.88  Aligned_cols=55  Identities=18%  Similarity=0.227  Sum_probs=37.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.|.+..+++|.+.+...-.+ +  ..-+-..++-+.++|++|+|||++|+.+++.
T Consensus       182 ~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~e  239 (512)
T TIGR03689       182 ADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANS  239 (512)
T ss_pred             HHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHh
Confidence            45678999999998876421100 0  0000123466899999999999999999984

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.

>PRK08116 hypothetical protein; Validated

Probab=97.81  E-value=0.00011  Score=72.19  Aligned_cols=104  Identities=23%  Similarity=0.253  Sum_probs=59.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhh
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVE  277 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~  277 (597)
                      ..+.|+|.+|+|||.||..+++.  .......++++++                      ..++..+........  ..+
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~--l~~~~~~v~~~~~----------------------~~ll~~i~~~~~~~~--~~~  168 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANE--LIEKGVPVIFVNF----------------------PQLLNRIKSTYKSSG--KED  168 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEH----------------------HHHHHHHHHHHhccc--ccc
Confidence            46899999999999999999994  4333344566653                      334444443332211  111


Q ss_pred             HHHHHHHHHHHhcCceEEEEEecccCCCCcchHHH--HHHhhcC-CCCCcEEEEEccCC
Q 041007          278 METVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQ--LMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       278 ~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~--l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      ...    +.+.+.+-. ||||||+.... ...|..  +...+.. ...+..+|+||...
T Consensus       169 ~~~----~~~~l~~~d-lLviDDlg~e~-~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        169 ENE----IIRSLVNAD-LLILDDLGAER-DTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             HHH----HHHHhcCCC-EEEEecccCCC-CCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            112    223333333 89999995433 234443  4333333 24566799998644

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

Probab=97.81  E-value=0.00014  Score=81.37  Aligned_cols=45  Identities=27%  Similarity=0.347  Sum_probs=37.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++++.+.|....          ...+.++|++|+|||++|+.+++.
T Consensus       186 ~~liGR~~ei~~~i~iL~r~~----------~~n~LLvGppGvGKT~lae~la~~  230 (758)
T PRK11034        186 DPLIGREKELERAIQVLCRRR----------KNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_pred             CcCcCCCHHHHHHHHHHhccC----------CCCeEEECCCCCCHHHHHHHHHHH
Confidence            458999999999999998532          245578999999999999999873

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

Probab=97.79  E-value=0.00049  Score=71.76  Aligned_cols=124  Identities=23%  Similarity=0.253  Sum_probs=73.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhH
Q 041007          199 VIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEM  278 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~  278 (597)
                      ++.|.|+-++||||+++.+...  ..+.   .+++...+....                ..                 ..
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~--~~~~---~iy~~~~d~~~~----------------~~-----------------~l   80 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKG--LLEE---IIYINFDDLRLD----------------RI-----------------EL   80 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhh--CCcc---eEEEEecchhcc----------------hh-----------------hH
Confidence            9999999999999999776663  2222   444443221111                00                 00


Q ss_pred             HHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecC
Q 041007          279 ETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLG  358 (597)
Q Consensus       279 ~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~  358 (597)
                      .+....+.+.-..++..++||.|+...   .|......+....+. +|++|+.+.........    +.-..+...+++.
T Consensus        81 ~d~~~~~~~~~~~~~~yifLDEIq~v~---~W~~~lk~l~d~~~~-~v~itgsss~ll~~~~~----~~L~GR~~~~~l~  152 (398)
T COG1373          81 LDLLRAYIELKEREKSYIFLDEIQNVP---DWERALKYLYDRGNL-DVLITGSSSSLLSKEIS----ESLAGRGKDLELY  152 (398)
T ss_pred             HHHHHHHHHhhccCCceEEEecccCch---hHHHHHHHHHccccc-eEEEECCchhhhccchh----hhcCCCceeEEEC
Confidence            111111111111277899999997766   899988888776666 88888777632211110    0011122239999


Q ss_pred             CCChHHHHHH
Q 041007          359 ELSEEECRSL  368 (597)
Q Consensus       359 ~Ls~~es~~L  368 (597)
                      |||..|-..+
T Consensus       153 PlSF~Efl~~  162 (398)
T COG1373         153 PLSFREFLKL  162 (398)
T ss_pred             CCCHHHHHhh
Confidence            9999998664

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

Probab=97.77  E-value=9.2e-05  Score=81.24  Aligned_cols=141  Identities=19%  Similarity=0.286  Sum_probs=87.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.++.+..+.+.+......-. .++....+....||.|||||.||++++..  .-+.=+..+-+++|         
T Consensus       491 ~rViGQd~AV~avs~aIrraRaGL~-dp~rPigsFlF~GPTGVGKTELAkaLA~~--Lfg~e~aliR~DMS---------  558 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRARAGLG-DPNRPIGSFLFLGPTGVGKTELAKALAEA--LFGDEQALIRIDMS---------  558 (786)
T ss_pred             cceeChHHHHHHHHHHHHHHhcCCC-CCCCCceEEEeeCCCcccHHHHHHHHHHH--hcCCCccceeechH---------
Confidence            5688999999999998875543221 12345668888999999999999998762  21111333444444         


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceE-EEEEecccCCCCcchHHHHHHhhcCC----
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKV-LLVLDDLWWNAYPRYWEQLMYSLKSG----  320 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~-LLVLDdv~~~~~~~~~~~l~~~l~~~----  320 (597)
                                  +-..+.-...|-+..+.-...++ -..|-+..+.++| +|.||++...+ ++..+.+...|..+    
T Consensus       559 ------------Ey~EkHsVSrLIGaPPGYVGyee-GG~LTEaVRr~PySViLlDEIEKAH-pdV~nilLQVlDdGrLTD  624 (786)
T COG0542         559 ------------EYMEKHSVSRLIGAPPGYVGYEE-GGQLTEAVRRKPYSVILLDEIEKAH-PDVFNLLLQVLDDGRLTD  624 (786)
T ss_pred             ------------HHHHHHHHHHHhCCCCCCceecc-ccchhHhhhcCCCeEEEechhhhcC-HHHHHHHHHHhcCCeeec
Confidence                        22233334444444443222222 2334455667877 88899998776 77888888888653    


Q ss_pred             C-------CCcEEEEEccC
Q 041007          321 S-------EGSRILVTRSG  332 (597)
Q Consensus       321 ~-------~gs~IIvTtR~  332 (597)
                      +       +++-||+||--
T Consensus       625 ~~Gr~VdFrNtiIImTSN~  643 (786)
T COG0542         625 GQGRTVDFRNTIIIMTSNA  643 (786)
T ss_pred             CCCCEEecceeEEEEeccc
Confidence            2       24567777743

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.73  E-value=0.00051  Score=78.91  Aligned_cols=45  Identities=24%  Similarity=0.396  Sum_probs=37.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.++++++..|....          ...+.++|++|+|||++|..+.+.
T Consensus       173 ~~~igr~~ei~~~~~~l~r~~----------~~n~lL~G~pGvGKT~l~~~la~~  217 (852)
T TIGR03346       173 DPVIGRDEEIRRTIQVLSRRT----------KNNPVLIGEPGVGKTAIVEGLAQR  217 (852)
T ss_pred             CcCCCcHHHHHHHHHHHhcCC----------CCceEEEcCCCCCHHHHHHHHHHH
Confidence            458999999999999997432          356678999999999999998873

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

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

Probab=97.72  E-value=0.00077  Score=70.04  Aligned_cols=55  Identities=25%  Similarity=0.270  Sum_probs=37.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.|-+..+++|.+.+...-.. +  ...+-..++-|.++|++|+|||+||+.+++.
T Consensus       145 ~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~  202 (398)
T PTZ00454        145 SDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHH  202 (398)
T ss_pred             HHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            45789999998888776421100 0  0000124578999999999999999999983

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

Probab=97.69  E-value=0.00027  Score=73.92  Aligned_cols=55  Identities=22%  Similarity=0.276  Sum_probs=37.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.|.+..+++|.+.+...-.+ +  ..-+-..++.|.|+|++|+|||+||+.+++.
T Consensus       183 ~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~e  240 (438)
T PTZ00361        183 ADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANE  240 (438)
T ss_pred             HHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHh
Confidence            34678999999998877522110 0  0000123467889999999999999999983

>PRK08181 transposase; Validated

Probab=97.69  E-value=0.0003  Score=68.88  Aligned_cols=102  Identities=20%  Similarity=0.236  Sum_probs=55.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhh
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVE  277 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~  277 (597)
                      ..+.|+|++|+|||.||..+.+.  .......++|+++                      .++...+.....     ..+
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~--a~~~g~~v~f~~~----------------------~~L~~~l~~a~~-----~~~  157 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTRT----------------------TDLVQKLQVARR-----ELQ  157 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHH--HHHcCCceeeeeH----------------------HHHHHHHHHHHh-----CCc
Confidence            46999999999999999999883  3333334556543                      233333322211     011


Q ss_pred             HHHHHHHHHHHhcCceEEEEEecccCCCCcchHH-HHHHhhcCCCCCcEEEEEccCC
Q 041007          278 METVLQYINEFVQGKKVLLVLDDLWWNAYPRYWE-QLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       278 ~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~-~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .......    + .+.-||||||+........+. .+...+.....+..+||||...
T Consensus       158 ~~~~l~~----l-~~~dLLIIDDlg~~~~~~~~~~~Lf~lin~R~~~~s~IiTSN~~  209 (269)
T PRK08181        158 LESAIAK----L-DKFDLLILDDLAYVTKDQAETSVLFELISARYERRSILITANQP  209 (269)
T ss_pred             HHHHHHH----H-hcCCEEEEeccccccCCHHHHHHHHHHHHHHHhCCCEEEEcCCC
Confidence            1222222    2 234599999996554333332 2344443322234688888755

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=97.63  E-value=0.0022  Score=64.40  Aligned_cols=97  Identities=10%  Similarity=0.033  Sum_probs=65.5

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|||+++.++ ...-+.+...+..-..++.+|++|.+......         -+...+. +.+.+++.+++.+.+
T Consensus       112 g~~kV~iI~~ae~m~-~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLp---------TIrSRCq~i~~~~~~~~~~~~~L  181 (319)
T PRK08769        112 GIAQVVIVDPADAIN-RAACNALLKTLEEPSPGRYLWLISAQPARLPA---------TIRSRCQRLEFKLPPAHEALAWL  181 (319)
T ss_pred             CCcEEEEeccHhhhC-HHHHHHHHHHhhCCCCCCeEEEEECChhhCch---------HHHhhheEeeCCCcCHHHHHHHH
Confidence            456799999998776 55667788788777778888777765521111         1112222 899999999998888


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILG  407 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~  407 (597)
                      ....      ..    ...+..++..++|.|+....+.
T Consensus       182 ~~~~------~~----~~~a~~~~~l~~G~p~~A~~~~  209 (319)
T PRK08769        182 LAQG------VS----ERAAQEALDAARGHPGLAAQWL  209 (319)
T ss_pred             HHcC------CC----hHHHHHHHHHcCCCHHHHHHHh
Confidence            6531      11    2235678999999998765543

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=97.62  E-value=0.003  Score=58.52  Aligned_cols=44  Identities=20%  Similarity=0.314  Sum_probs=36.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++||-++.+++|.-.-.          .++.+-+.|.||+|+||||-+..+++
T Consensus        27 ~dIVGNe~tv~rl~via~----------~gnmP~liisGpPG~GKTTsi~~LAr   70 (333)
T KOG0991|consen   27 QDIVGNEDTVERLSVIAK----------EGNMPNLIISGPPGTGKTTSILCLAR   70 (333)
T ss_pred             HHhhCCHHHHHHHHHHHH----------cCCCCceEeeCCCCCchhhHHHHHHH
Confidence            468999999988877665          34678999999999999998887777

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=97.61  E-value=0.002  Score=68.98  Aligned_cols=214  Identities=17%  Similarity=0.174  Sum_probs=123.8

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChh---hhc---cCCeeEEEEecCC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSD---VKA---NFDKRIWVSASYP  238 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~---~~~---~F~~~~wv~~~~~  238 (597)
                      |..+-+|+.|..+|...+...-..     ......+-|.|.+|+|||..+..|.+...   .++   .|++ +.|+.-.-
T Consensus       395 p~sLpcRe~E~~~I~~f~~~~i~~-----~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~y-veINgm~l  468 (767)
T KOG1514|consen  395 PESLPCRENEFSEIEDFLRSFISD-----QGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDY-VEINGLRL  468 (767)
T ss_pred             cccccchhHHHHHHHHHHHhhcCC-----CCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccE-EEEcceee
Confidence            344669999999999988755442     13445999999999999999999988532   122   2332 22333222


Q ss_pred             CchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhc-----CceEEEEEecccCCCCcchHHHH
Q 041007          239 RDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQ-----GKKVLLVLDDLWWNAYPRYWEQL  313 (597)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~-----~kr~LLVLDdv~~~~~~~~~~~l  313 (597)
                      ...                .+++..|...+.+.....   ....+.|..+..     .+.++|++|+++..- ...-+.+
T Consensus       469 ~~~----------------~~~Y~~I~~~lsg~~~~~---~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lv-tr~QdVl  528 (767)
T KOG1514|consen  469 ASP----------------REIYEKIWEALSGERVTW---DAALEALNFRFTVPKPKRSTTVVLIDELDILV-TRSQDVL  528 (767)
T ss_pred             cCH----------------HHHHHHHHHhcccCcccH---HHHHHHHHHhhccCCCCCCCEEEEeccHHHHh-cccHHHH
Confidence            223                889999999988764322   222333444433     346899999884332 1123445


Q ss_pred             HHhhcC-CCCCcEEEEEccCC-CCCCCcccccccccCccccce---eecCCCChHHHHHHHHHHhccCCCCCCccchHHH
Q 041007          314 MYSLKS-GSEGSRILVTRSGG-KNGTNMTEIGLGEKNGTNMME---IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPI  388 (597)
Q Consensus       314 ~~~l~~-~~~gs~IIvTtR~~-~~~~~~~~~~~~~~~~~~~~~---~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~  388 (597)
                      ...|.+ ..++++++|-+-.. ...+. .   +....+....+   +...|.+.++-.++...++.+. ........+-+
T Consensus       529 Yn~fdWpt~~~sKLvvi~IaNTmdlPE-r---~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~-~~f~~~aielv  603 (767)
T KOG1514|consen  529 YNIFDWPTLKNSKLVVIAIANTMDLPE-R---LLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGL-DAFENKAIELV  603 (767)
T ss_pred             HHHhcCCcCCCCceEEEEecccccCHH-H---HhccchhhhccceeeecCCCCHHHHHHHHHHhhcch-hhcchhHHHHH
Confidence            555554 56777766553322 11110 0   00001222222   8888889888888888777543 22222334445


Q ss_pred             HHHHHHhcCCchHHHHHHHhh
Q 041007          389 GRRVVGKCKGLPFAVKILGSL  409 (597)
Q Consensus       389 ~~~I~~~~~GlPLai~~~~~~  409 (597)
                      +++|+.-.|-.-.|+.+.-++
T Consensus       604 arkVAavSGDaRraldic~RA  624 (767)
T KOG1514|consen  604 ARKVAAVSGDARRALDICRRA  624 (767)
T ss_pred             HHHHHhccccHHHHHHHHHHH
Confidence            666666666666666555443

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=97.59  E-value=0.0031  Score=64.57  Aligned_cols=127  Identities=11%  Similarity=0.071  Sum_probs=74.9

Q ss_pred             eEEEEEecccCCCCc--chHHHHHHhh--cCCCCCcEEEEEccCCCCCCCcccccccccCccc--cceeecCCCChHHHH
Q 041007          293 KVLLVLDDLWWNAYP--RYWEQLMYSL--KSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN--MMEIGLGELSEEECR  366 (597)
Q Consensus       293 r~LLVLDdv~~~~~~--~~~~~l~~~l--~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~--~~~~~l~~Ls~~es~  366 (597)
                      +-+|||||.......  ..|+.+..--  ....+=.+||++|-+....... ..     ...+  ...+.|.-.+++-|.
T Consensus       149 ~PVVVIdnF~~k~~~~~~iy~~laeWAa~Lv~~nIAHVIFlT~dv~~~k~L-sk-----aLPn~vf~tI~L~Das~~~Ak  222 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEENDFIYDKLAEWAASLVQNNIAHVIFLTDDVSYSKPL-SK-----ALPNRVFKTISLSDASPESAK  222 (431)
T ss_pred             CCEEEEcchhccCcccchHHHHHHHHHHHHHhcCccEEEEECCCCchhhhH-HH-----hCCCCceeEEeecCCCHHHHH
Confidence            568999998543321  1222222111  1133456788888765211100 00     1111  112899999999999


Q ss_pred             HHHHHHhccCCCC------------CC----ccchHHHHHHHHHhcCCchHHHHHHHhhhccCCCHH-HHHHHHhh
Q 041007          367 SLFRQIAFHGRSS------------DY----REKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIK-EWQSVLDS  425 (597)
Q Consensus       367 ~Lf~~~~~~~~~~------------~~----~~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~-~w~~~l~~  425 (597)
                      .+...++......            ..    ......-....+..+||--.=+..+++.++.+.+++ ...++..+
T Consensus       223 ~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~LGGRltDLe~lvrRiksGe~p~~Av~~iI~q  298 (431)
T PF10443_consen  223 QYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPLGGRLTDLEFLVRRIKSGESPEEAVEEIISQ  298 (431)
T ss_pred             HHHHHHhcccccccccccccccccccccccccccchHHHHHHHHHcCCcHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence            9999988542110            00    012344567788999999999999999999887765 34444443

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>CHL00176 ftsH cell division protein; Validated

Probab=97.59  E-value=0.00081  Score=73.96  Aligned_cols=186  Identities=13%  Similarity=0.132  Sum_probs=92.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCc--CCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEE--SGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~--~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      .++.|.++..+++.+.+......+.  .-+...++-|.++|++|+|||+||+.+++.  ...     -|+.++.      
T Consensus       183 ~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e--~~~-----p~i~is~------  249 (638)
T CHL00176        183 RDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGE--AEV-----PFFSISG------  249 (638)
T ss_pred             HhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHH--hCC-----CeeeccH------
Confidence            4577887766666555422111000  000123567999999999999999999873  221     2233221      


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCC---------CcchHHH--
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNA---------YPRYWEQ--  312 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~---------~~~~~~~--  312 (597)
                                    ..+....   .+      .....+...+.......+++|+|||++...         .......  
T Consensus       250 --------------s~f~~~~---~g------~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L  306 (638)
T CHL00176        250 --------------SEFVEMF---VG------VGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTL  306 (638)
T ss_pred             --------------HHHHHHh---hh------hhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHH
Confidence                          1110000   00      011223334444556788999999995331         0112222  


Q ss_pred             --HHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccchHH
Q 041007          313 --LMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEP  387 (597)
Q Consensus       313 --l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~  387 (597)
                        +...+..  ...+..||.||.... ..+   ..+.  ...+ ...+.+.+.+.++-.+++..++.....     ....
T Consensus       307 ~~LL~~~dg~~~~~~ViVIaaTN~~~-~LD---~ALl--RpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~-----~~d~  375 (638)
T CHL00176        307 NQLLTEMDGFKGNKGVIVIAATNRVD-ILD---AALL--RPGRFDRQITVSLPDREGRLDILKVHARNKKL-----SPDV  375 (638)
T ss_pred             HHHHhhhccccCCCCeeEEEecCchH-hhh---hhhh--ccccCceEEEECCCCHHHHHHHHHHHHhhccc-----chhH
Confidence              2222221  234555666665431 000   0000  0000 112788888888888888887743111     1123


Q ss_pred             HHHHHHHhcCC
Q 041007          388 IGRRVVGKCKG  398 (597)
Q Consensus       388 ~~~~I~~~~~G  398 (597)
                      ....|++.+.|
T Consensus       376 ~l~~lA~~t~G  386 (638)
T CHL00176        376 SLELIARRTPG  386 (638)
T ss_pred             HHHHHHhcCCC
Confidence            45678888887

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.58  E-value=0.0025  Score=62.71  Aligned_cols=22  Identities=36%  Similarity=0.445  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..|.|.|++|+|||+||+.+++
T Consensus        22 ~~vLL~G~~GtGKT~lA~~la~   43 (262)
T TIGR02640        22 YPVHLRGPAGTGKTTLAMHVAR   43 (262)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHH
Confidence            4677999999999999999986

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.58  E-value=0.0016  Score=66.36  Aligned_cols=162  Identities=11%  Similarity=0.064  Sum_probs=88.3

Q ss_pred             ccc-chhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhh
Q 041007          168 FHG-RNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVAR  246 (597)
Q Consensus       168 ~vG-R~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~  246 (597)
                      ++| -+.-++.|...+....         -+....++|+.|+|||++|..+.+..--.......   .+..         
T Consensus         7 i~~~q~~~~~~L~~~~~~~~---------l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~---~cg~---------   65 (329)
T PRK08058          7 LTALQPVVVKMLQNSIAKNR---------LSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVE---PCGT---------   65 (329)
T ss_pred             HHhhHHHHHHHHHHHHHcCC---------CCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCC---CCCc---------
Confidence            556 6667778888776332         35577999999999999999886531100100000   0000         


Q ss_pred             hhhhhcccchHHHHHHHHHHhccC------CCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          247 DEISVARDRDEIRVAKAILESLKG------SVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       247 ~~~~~~~~~~~~~~~~~il~~l~~------~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                 -...+.+...-..      ........+++.+.+...    ..+.+-++|+|+++..+ ....+.+...
T Consensus        66 -----------C~~c~~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~-~~a~NaLLK~  133 (329)
T PRK08058         66 -----------CTNCKRIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMT-ASAANSLLKF  133 (329)
T ss_pred             -----------CHHHHHHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhC-HHHHHHHHHH
Confidence                       0000000000000      000111223332222211    23455689999997776 5566778888


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHH
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQ  371 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~  371 (597)
                      +..-+.++.+|++|.+......         -+...+. +++.+++.++..+.+..
T Consensus       134 LEEPp~~~~~Il~t~~~~~ll~---------TIrSRc~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        134 LEEPSGGTTAILLTENKHQILP---------TILSRCQVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             hcCCCCCceEEEEeCChHhCcH---------HHHhhceeeeCCCCCHHHHHHHHHH
Confidence            8777778888888766521110         1112222 99999999999888765

>PRK12377 putative replication protein; Provisional

Probab=97.57  E-value=0.00044  Score=66.85  Aligned_cols=37  Identities=24%  Similarity=0.213  Sum_probs=28.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      ...+.|+|++|+|||+||..+++.  .......++++++
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~--l~~~g~~v~~i~~  137 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNR--LLAKGRSVIVVTV  137 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCeEEEEH
Confidence            367999999999999999999994  4444444566654

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

Probab=97.55  E-value=0.00084  Score=75.95  Aligned_cols=136  Identities=14%  Similarity=0.188  Sum_probs=75.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.+..++.+...+......-. .++....++.++|++|+|||+||+.++..  .   +...+.++++.....    
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~~~g~~-~~~~p~~~~lf~Gp~GvGKT~lA~~la~~--l---~~~~~~~d~se~~~~----  523 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRSRAGLG-NPNKPVGSFLFTGPTGVGKTELAKQLAEA--L---GVHLERFDMSEYMEK----  523 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHHhcCCC-CCCCCceeEEEECCCCccHHHHHHHHHHH--h---cCCeEEEeCchhhhc----
Confidence            4578888888888888764321000 01123446899999999999999999873  3   223344554432111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCC--chhhHHHHHHHHHHHhcC-ceEEEEEecccCCCCcchHHHHHHhhcCC--
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVS--SQVEMETVLQYINEFVQG-KKVLLVLDDLWWNAYPRYWEQLMYSLKSG--  320 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~--~~~~~~~~~~~l~~~L~~-kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--  320 (597)
                                  .    .+...++.+..  .......+    .+.++. ..-+|+||+++..+ .+.++.+...+..+  
T Consensus       524 ------------~----~~~~lig~~~gyvg~~~~~~l----~~~~~~~p~~VvllDEieka~-~~~~~~Ll~~ld~g~~  582 (731)
T TIGR02639       524 ------------H----TVSRLIGAPPGYVGFEQGGLL----TEAVRKHPHCVLLLDEIEKAH-PDIYNILLQVMDYATL  582 (731)
T ss_pred             ------------c----cHHHHhcCCCCCcccchhhHH----HHHHHhCCCeEEEEechhhcC-HHHHHHHHHhhccCee
Confidence                        0    01111221111  01111122    233333 34599999998776 67777777776543  


Q ss_pred             ---------CCCcEEEEEccC
Q 041007          321 ---------SEGSRILVTRSG  332 (597)
Q Consensus       321 ---------~~gs~IIvTtR~  332 (597)
                               -.++.||+||..
T Consensus       583 ~d~~g~~vd~~~~iii~Tsn~  603 (731)
T TIGR02639       583 TDNNGRKADFRNVILIMTSNA  603 (731)
T ss_pred             ecCCCcccCCCCCEEEECCCc
Confidence                     124557777744

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=97.54  E-value=0.0045  Score=62.32  Aligned_cols=94  Identities=7%  Similarity=-0.048  Sum_probs=65.3

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|+|+++.+. ....+.+...+..-+.++.+|++|.+......         -+...+. +.+.+++.++..+.+
T Consensus       106 g~~KV~iI~~a~~m~-~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llp---------TI~SRC~~~~~~~~~~~~~~~~L  175 (325)
T PRK06871        106 GGNKVVYIQGAERLT-EAAANALLKTLEEPRPNTYFLLQADLSAALLP---------TIYSRCQTWLIHPPEEQQALDWL  175 (325)
T ss_pred             CCceEEEEechhhhC-HHHHHHHHHHhcCCCCCeEEEEEECChHhCch---------HHHhhceEEeCCCCCHHHHHHHH
Confidence            556688899998887 66778888888887788888888776521111         1111222 999999999999888


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAV  403 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai  403 (597)
                      .....   .  .    ...+...++.++|.|+..
T Consensus       176 ~~~~~---~--~----~~~~~~~~~l~~g~p~~A  200 (325)
T PRK06871        176 QAQSS---A--E----ISEILTALRINYGRPLLA  200 (325)
T ss_pred             HHHhc---c--C----hHHHHHHHHHcCCCHHHH
Confidence            87541   1  1    113566788999999644

>TIGR00763 lon ATP-dependent protease La

Probab=97.51  E-value=0.0086  Score=68.30  Aligned_cols=51  Identities=25%  Similarity=0.447  Sum_probs=37.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|.+.-+++|.+++......    .....+++.++|++|+|||++|+.+++.
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~----~~~~~~~lll~GppG~GKT~lAk~iA~~  370 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLR----GKMKGPILCLVGPPGVGKTSLGKSIAKA  370 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhh----cCCCCceEEEECCCCCCHHHHHHHHHHH
Confidence            44789999999988876422110    0123458999999999999999999883

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=97.50  E-value=0.0005  Score=78.46  Aligned_cols=140  Identities=19%  Similarity=0.251  Sum_probs=77.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.+..++.+.+.+......-. .++....++.++|++|+|||.||+.+...  .-+.....+-++++....     
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~gl~-~~~~p~~~~lf~Gp~GvGKT~lA~~La~~--l~~~~~~~~~~dmse~~~-----  637 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAGLE-DPRKPLGVFLLVGPSGVGKTETALALAEL--LYGGEQNLITINMSEFQE-----  637 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcCCC-CCCCCceEEEEECCCCCCHHHHHHHHHHH--HhCCCcceEEEeHHHhhh-----
Confidence            4678999999999888864321000 01234457899999999999999988762  212112222222221110     


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCch---hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCC-
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQ---VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS-  321 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~---~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~-  321 (597)
                                      ..-...+.+..+..   .....+...+++   ....+|+||++...+ ...++.+...+..+. 
T Consensus       638 ----------------~~~~~~l~g~~~gyvg~~~~g~L~~~v~~---~p~svvllDEieka~-~~v~~~Llq~ld~g~l  697 (852)
T TIGR03345       638 ----------------AHTVSRLKGSPPGYVGYGEGGVLTEAVRR---KPYSVVLLDEVEKAH-PDVLELFYQVFDKGVM  697 (852)
T ss_pred             ----------------hhhhccccCCCCCcccccccchHHHHHHh---CCCcEEEEechhhcC-HHHHHHHHHHhhccee
Confidence                            00111121211111   111122233322   445799999997665 667777777775542 


Q ss_pred             ----------CCcEEEEEccCC
Q 041007          322 ----------EGSRILVTRSGG  333 (597)
Q Consensus       322 ----------~gs~IIvTtR~~  333 (597)
                                .++.||+||...
T Consensus       698 ~d~~Gr~vd~~n~iiI~TSNlg  719 (852)
T TIGR03345       698 EDGEGREIDFKNTVILLTSNAG  719 (852)
T ss_pred             ecCCCcEEeccccEEEEeCCCc
Confidence                      456777887543

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=97.50  E-value=0.00066  Score=77.75  Aligned_cols=53  Identities=17%  Similarity=0.340  Sum_probs=37.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.+..++.+...+......-. .++....++.++|++|+|||+||+.+++
T Consensus       568 ~~viGQ~~ai~~l~~~i~~~~~gl~-~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~  620 (857)
T PRK10865        568 HRVIGQNEAVEAVSNAIRRSRAGLS-DPNRPIGSFLFLGPTGVGKTELCKALAN  620 (857)
T ss_pred             CeEeCCHHHHHHHHHHHHHHHhccc-CCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            4578999999998888864321000 0112235788999999999999999986

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

Probab=97.50  E-value=0.0004  Score=64.70  Aligned_cols=144  Identities=23%  Similarity=0.240  Sum_probs=63.5

Q ss_pred             cchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhh
Q 041007          170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEI  249 (597)
Q Consensus       170 GR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~  249 (597)
                      .+..+-....+.|.            ...++.+.|++|.|||.||.+..-+.-..+.|+.++++.-.-+.....-++..-
T Consensus         4 p~~~~Q~~~~~al~------------~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g~~~kiii~Rp~v~~~~~lGflpG~   71 (205)
T PF02562_consen    4 PKNEEQKFALDALL------------NNDLVIVNGPAGTGKTFLALAAALELVKEGEYDKIIITRPPVEAGEDLGFLPGD   71 (205)
T ss_dssp             --SHHHHHHHHHHH------------H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT----SS---
T ss_pred             CCCHHHHHHHHHHH------------hCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCcEEEEEecCCCCccccccCCCC
Confidence            34555666667676            246999999999999999998876644457788877764322110000000000


Q ss_pred             hhcccchHHHHHHHHHHhccCCCCchhhHHHHHHH------HHHHhcCc---eEEEEEecccCCCCcchHHHHHHhhcCC
Q 041007          250 SVARDRDEIRVAKAILESLKGSVSSQVEMETVLQY------INEFVQGK---KVLLVLDDLWWNAYPRYWEQLMYSLKSG  320 (597)
Q Consensus       250 ~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~------l~~~L~~k---r~LLVLDdv~~~~~~~~~~~l~~~l~~~  320 (597)
                      ...+-.....-+.+.+..+...    ...+.+...      --.+++|+   ..++|+|++++.. ..+   +...+-..
T Consensus        72 ~~eK~~p~~~p~~d~l~~~~~~----~~~~~~~~~~~Ie~~~~~~iRGrt~~~~~iIvDEaQN~t-~~~---~k~ilTR~  143 (205)
T PF02562_consen   72 LEEKMEPYLRPIYDALEELFGK----EKLEELIQNGKIEIEPLAFIRGRTFDNAFIIVDEAQNLT-PEE---LKMILTRI  143 (205)
T ss_dssp             ------TTTHHHHHHHTTTS-T----TCHHHHHHTTSEEEEEGGGGTT--B-SEEEEE-SGGG---HHH---HHHHHTTB
T ss_pred             HHHHHHHHHHHHHHHHHHHhCh----HhHHHHhhcCeEEEEehhhhcCccccceEEEEecccCCC-HHH---HHHHHccc
Confidence            0000000011122222222211    111111110      01233443   4699999998775 444   44445556


Q ss_pred             CCCcEEEEEccCC
Q 041007          321 SEGSRILVTRSGG  333 (597)
Q Consensus       321 ~~gs~IIvTtR~~  333 (597)
                      +.||++|++--..
T Consensus       144 g~~skii~~GD~~  156 (205)
T PF02562_consen  144 GEGSKIIITGDPS  156 (205)
T ss_dssp             -TT-EEEEEE---
T ss_pred             CCCcEEEEecCce
Confidence            7899999996544

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

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.47  E-value=0.00087  Score=67.13  Aligned_cols=123  Identities=15%  Similarity=0.217  Sum_probs=68.4

Q ss_pred             cchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhh
Q 041007          170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEI  249 (597)
Q Consensus       170 GR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~  249 (597)
                      +|..-.....+++.....      ....+-+.|+|+.|+|||.||..+++.  ....-..+.++++              
T Consensus       135 ~~~~~~~~~~~fi~~~~~------~~~~~gl~L~G~~G~GKThLa~Aia~~--l~~~g~~v~~~~~--------------  192 (306)
T PRK08939        135 DRLDALMAALDFLEAYPP------GEKVKGLYLYGDFGVGKSYLLAAIANE--LAKKGVSSTLLHF--------------  192 (306)
T ss_pred             HHHHHHHHHHHHHHHhhc------cCCCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEEEH--------------
Confidence            455555555666653321      123467999999999999999999995  3222233455554              


Q ss_pred             hhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHH--HHHhh-cCC-CCCcE
Q 041007          250 SVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQ--LMYSL-KSG-SEGSR  325 (597)
Q Consensus       250 ~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~--l~~~l-~~~-~~gs~  325 (597)
                              ..++..+-......     +....   +.. + .+-=||||||+.... ...|..  +...+ ... ..+..
T Consensus       193 --------~~l~~~lk~~~~~~-----~~~~~---l~~-l-~~~dlLiIDDiG~e~-~s~~~~~~ll~~Il~~R~~~~~~  253 (306)
T PRK08939        193 --------PEFIRELKNSISDG-----SVKEK---IDA-V-KEAPVLMLDDIGAEQ-MSSWVRDEVLGVILQYRMQEELP  253 (306)
T ss_pred             --------HHHHHHHHHHHhcC-----cHHHH---HHH-h-cCCCEEEEecCCCcc-ccHHHHHHHHHHHHHHHHHCCCe
Confidence                    23333333332211     11222   222 2 245699999997654 445653  44443 322 35667


Q ss_pred             EEEEccCC
Q 041007          326 ILVTRSGG  333 (597)
Q Consensus       326 IIvTtR~~  333 (597)
                      +|+||--.
T Consensus       254 ti~TSNl~  261 (306)
T PRK08939        254 TFFTSNFD  261 (306)
T ss_pred             EEEECCCC
Confidence            88888533

>PRK06526 transposase; Provisional

Probab=97.46  E-value=0.00027  Score=68.79  Aligned_cols=24  Identities=33%  Similarity=0.264  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+.|+|++|+|||+||..+.+.
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~  121 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIR  121 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHH
Confidence            357899999999999999999874

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=97.46  E-value=0.00063  Score=78.16  Aligned_cols=142  Identities=17%  Similarity=0.235  Sum_probs=78.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.+..++.+...+......-. .++....++.++|++|+|||++|+.+...  ....-...+.++++.....    
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~-~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~--l~~~~~~~i~~d~s~~~~~----  637 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLS-DPNRPIGSFLFLGPTGVGKTELAKALAEF--LFDDEDAMVRIDMSEYMEK----  637 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCC-CCCCCCeEEEEEcCCCCCHHHHHHHHHHH--hcCCCCcEEEEechhhccc----
Confidence            4588999999999998875421000 01123457889999999999999999873  2222223344444432111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCc-eEEEEEecccCCCCcchHHHHHHhhcCC----
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGK-KVLLVLDDLWWNAYPRYWEQLMYSLKSG----  320 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~k-r~LLVLDdv~~~~~~~~~~~l~~~l~~~----  320 (597)
                                  .. .   ...++.+ +.....++ ...+.+.++.+ ..+|+||++...+ ...+..+...+..+    
T Consensus       638 ------------~~-~---~~l~g~~-~g~~g~~~-~g~l~~~v~~~p~~vlllDeieka~-~~v~~~Ll~~l~~g~l~d  698 (852)
T TIGR03346       638 ------------HS-V---ARLIGAP-PGYVGYEE-GGQLTEAVRRKPYSVVLFDEVEKAH-PDVFNVLLQVLDDGRLTD  698 (852)
T ss_pred             ------------ch-H---HHhcCCC-CCccCccc-ccHHHHHHHcCCCcEEEEeccccCC-HHHHHHHHHHHhcCceec
Confidence                        00 0   1111211 11100000 01122222223 3589999998776 77888888877543    


Q ss_pred             -------CCCcEEEEEccCC
Q 041007          321 -------SEGSRILVTRSGG  333 (597)
Q Consensus       321 -------~~gs~IIvTtR~~  333 (597)
                             -.++.||+||...
T Consensus       699 ~~g~~vd~rn~iiI~TSn~g  718 (852)
T TIGR03346       699 GQGRTVDFRNTVIIMTSNLG  718 (852)
T ss_pred             CCCeEEecCCcEEEEeCCcc
Confidence                   1345588887654

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=97.43  E-value=0.0023  Score=57.87  Aligned_cols=119  Identities=17%  Similarity=0.233  Sum_probs=72.6

Q ss_pred             cchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh------------------ccCCeeE
Q 041007          170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK------------------ANFDKRI  231 (597)
Q Consensus       170 GR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~------------------~~F~~~~  231 (597)
                      |-+...+.|...+....         -+..+.++|+.|+||+++|..+.+..--.                  ...+...
T Consensus         1 gq~~~~~~L~~~~~~~~---------l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~   71 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGR---------LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFI   71 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC-----------SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEE
T ss_pred             CcHHHHHHHHHHHHcCC---------cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceE
Confidence            45666777777776432         35578999999999999999886631111                  1122233


Q ss_pred             EEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhc-----CceEEEEEecccCCCC
Q 041007          232 WVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQ-----GKKVLLVLDDLWWNAY  306 (597)
Q Consensus       232 wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~-----~kr~LLVLDdv~~~~~  306 (597)
                      |+.-.....                                  ....+++. .+.+.+.     ++.=++||||++.+. 
T Consensus        72 ~~~~~~~~~----------------------------------~i~i~~ir-~i~~~~~~~~~~~~~KviiI~~ad~l~-  115 (162)
T PF13177_consen   72 IIKPDKKKK----------------------------------SIKIDQIR-EIIEFLSLSPSEGKYKVIIIDEADKLT-  115 (162)
T ss_dssp             EEETTTSSS----------------------------------SBSHHHHH-HHHHHCTSS-TTSSSEEEEEETGGGS--
T ss_pred             EEecccccc----------------------------------hhhHHHHH-HHHHHHHHHHhcCCceEEEeehHhhhh-
Confidence            333222100                                  11222222 2222222     356699999998887 


Q ss_pred             cchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          307 PRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       307 ~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      ......++..+..-+.++.+|++|.+.
T Consensus       116 ~~a~NaLLK~LEepp~~~~fiL~t~~~  142 (162)
T PF13177_consen  116 EEAQNALLKTLEEPPENTYFILITNNP  142 (162)
T ss_dssp             HHHHHHHHHHHHSTTTTEEEEEEES-G
T ss_pred             HHHHHHHHHHhcCCCCCEEEEEEECCh
Confidence            778888999998888899999998876

...

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=97.43  E-value=0.00045  Score=72.99  Aligned_cols=189  Identities=14%  Similarity=0.165  Sum_probs=112.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ++++|-+.-...|...+....         -..--...|+-|+||||+|+.++.-.--...       ....++..    
T Consensus        16 ~evvGQe~v~~~L~nal~~~r---------i~hAYlfsG~RGvGKTt~Ari~AkalNC~~~-------~~~ePC~~----   75 (515)
T COG2812          16 DDVVGQEHVVKTLSNALENGR---------IAHAYLFSGPRGVGKTTIARILAKALNCENG-------PTAEPCGK----   75 (515)
T ss_pred             HHhcccHHHHHHHHHHHHhCc---------chhhhhhcCCCCcCchhHHHHHHHHhcCCCC-------CCCCcchh----
Confidence            457999999999999998543         2456678999999999999988763111100       00001111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhc--------cCCCCchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESL--------KGSVSSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l--------~~~~~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  -...+.|...-        .......++...+.+.+.-. ..++.=+.|+|+|+-.. ...|..++..
T Consensus        76 ------------C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS-~~afNALLKT  142 (515)
T COG2812          76 ------------CISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLS-KQAFNALLKT  142 (515)
T ss_pred             ------------hhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhh-HHHHHHHhcc
Confidence                        11112222110        00111122222222222111 12455589999998665 7788998888


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +..-......|+.|.+....+.         -+...+. |.++.++.++....+...+.......    ..+...-|++.
T Consensus       143 LEEPP~hV~FIlATTe~~Kip~---------TIlSRcq~f~fkri~~~~I~~~L~~i~~~E~I~~----e~~aL~~ia~~  209 (515)
T COG2812         143 LEEPPSHVKFILATTEPQKIPN---------TILSRCQRFDFKRLDLEEIAKHLAAILDKEGINI----EEDALSLIARA  209 (515)
T ss_pred             cccCccCeEEEEecCCcCcCch---------hhhhccccccccCCCHHHHHHHHHHHHHhcCCcc----CHHHHHHHHHH
Confidence            8887888888888887743332         1222233 99999999999998888875433222    24455677777


Q ss_pred             cCCch
Q 041007          396 CKGLP  400 (597)
Q Consensus       396 ~~GlP  400 (597)
                      ..|..
T Consensus       210 a~Gs~  214 (515)
T COG2812         210 AEGSL  214 (515)
T ss_pred             cCCCh
Confidence            77744

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=97.42  E-value=0.0022  Score=69.39  Aligned_cols=56  Identities=18%  Similarity=0.262  Sum_probs=35.2

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -.+++|-+..++++.+++......+  ...+...++-+.++|++|+|||+||+.+++.
T Consensus        54 ~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~  111 (495)
T TIGR01241        54 FKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGE  111 (495)
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHH
Confidence            3567888877766655443111000  0000123456899999999999999999873

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=97.40  E-value=0.0067  Score=61.61  Aligned_cols=95  Identities=12%  Similarity=-0.024  Sum_probs=65.0

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|+|+++.++ ...-+.+...|..-+.++.+|++|.+......         -+...+. +.+.+++.+++.+.+
T Consensus       107 g~~kV~iI~~ae~m~-~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLp---------TIrSRCq~~~~~~~~~~~~~~~L  176 (334)
T PRK07993        107 GGAKVVWLPDAALLT-DAAANALLKTLEEPPENTWFFLACREPARLLA---------TLRSRCRLHYLAPPPEQYALTWL  176 (334)
T ss_pred             CCceEEEEcchHhhC-HHHHHHHHHHhcCCCCCeEEEEEECChhhChH---------HHHhccccccCCCCCHHHHHHHH
Confidence            566799999998877 66778888888877778888887776521110         1111122 899999999998887


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~  404 (597)
                      .....     ..    .+.+..+++.++|.|....
T Consensus       177 ~~~~~-----~~----~~~a~~~~~la~G~~~~Al  202 (334)
T PRK07993        177 SREVT-----MS----QDALLAALRLSAGAPGAAL  202 (334)
T ss_pred             HHccC-----CC----HHHHHHHHHHcCCCHHHHH
Confidence            65421     11    2346788999999996443

>PRK06921 hypothetical protein; Provisional

Probab=97.38  E-value=0.0011  Score=65.13  Aligned_cols=37  Identities=22%  Similarity=0.240  Sum_probs=28.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CCeeEEEEe
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKAN-FDKRIWVSA  235 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~~~~wv~~  235 (597)
                      ...+.++|++|+|||.||..+++.  .... -..+++++.
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~--l~~~~g~~v~y~~~  154 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANE--LMRKKGVPVLYFPF  154 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHH--HhhhcCceEEEEEH
Confidence            467999999999999999999984  3333 344566653

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=97.38  E-value=0.0053  Score=61.62  Aligned_cols=94  Identities=10%  Similarity=0.010  Sum_probs=65.6

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf  369 (597)
                      ++.-++|+|+++.++ ....+.+...+..-+.++.+|++|.+......         -+...+. +.+.+++.+++.+.+
T Consensus       107 ~~~kV~iI~~ae~m~-~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLp---------TI~SRCq~~~~~~~~~~~~~~~L  176 (319)
T PRK06090        107 NGYRLFVIEPADAMN-ESASNALLKTLEEPAPNCLFLLVTHNQKRLLP---------TIVSRCQQWVVTPPSTAQAMQWL  176 (319)
T ss_pred             CCceEEEecchhhhC-HHHHHHHHHHhcCCCCCeEEEEEECChhhChH---------HHHhcceeEeCCCCCHHHHHHHH
Confidence            445689999998877 67788888888877778888777766521111         1112222 899999999999888


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      ....   .  .       ....+++.++|.|+....+
T Consensus       177 ~~~~---~--~-------~~~~~l~l~~G~p~~A~~~  201 (319)
T PRK06090        177 KGQG---I--T-------VPAYALKLNMGSPLKTLAM  201 (319)
T ss_pred             HHcC---C--c-------hHHHHHHHcCCCHHHHHHH
Confidence            6531   1  1       1356789999999977655

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.38  E-value=0.0013  Score=63.54  Aligned_cols=36  Identities=17%  Similarity=0.309  Sum_probs=26.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS  234 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~  234 (597)
                      ...+.++|.+|+|||+||..+++.  ....-..+++++
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~--l~~~g~~v~~it  134 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNE--LLLRGKSVLIIT  134 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEE
Confidence            457899999999999999999984  333333455554

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

Probab=97.37  E-value=0.0021  Score=62.48  Aligned_cols=81  Identities=19%  Similarity=0.300  Sum_probs=51.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhh--ccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVK--ANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~--~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      -.++|.++||+|.|||+|.+.+++...++  +.|....-+-++.                    ..++...+.+      
T Consensus       176 ~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins--------------------hsLFSKWFsE------  229 (423)
T KOG0744|consen  176 WNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS--------------------HSLFSKWFSE------  229 (423)
T ss_pred             eeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh--------------------hHHHHHHHhh------
Confidence            35789999999999999999999975443  3444444343322                    3333333322      


Q ss_pred             chhhHHHHHHHHHHHhcCce--EEEEEeccc
Q 041007          274 SQVEMETVLQYINEFVQGKK--VLLVLDDLW  302 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L~~kr--~LLVLDdv~  302 (597)
                      +...+..+.+.|++.+.++.  +++.+|.|.
T Consensus       230 SgKlV~kmF~kI~ELv~d~~~lVfvLIDEVE  260 (423)
T KOG0744|consen  230 SGKLVAKMFQKIQELVEDRGNLVFVLIDEVE  260 (423)
T ss_pred             hhhHHHHHHHHHHHHHhCCCcEEEEEeHHHH
Confidence            22345666777778777655  455689884

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.35  E-value=0.00071  Score=68.32  Aligned_cols=36  Identities=25%  Similarity=0.342  Sum_probs=27.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      ..+.++|++|+|||.||..+++.  ....-..++++++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~--l~~~g~~V~y~t~  219 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKE--LLDRGKSVIYRTA  219 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHH--HHHCCCeEEEEEH
Confidence            67999999999999999999984  3333335666654

>PRK09183 transposase/IS protein; Provisional

Probab=97.34  E-value=0.0011  Score=65.01  Aligned_cols=24  Identities=38%  Similarity=0.416  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+.|+|++|+|||+||..+.+.
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~  125 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYE  125 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHH
Confidence            357889999999999999999773

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=97.33  E-value=0.0061  Score=61.83  Aligned_cols=95  Identities=13%  Similarity=0.082  Sum_probs=64.3

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf  369 (597)
                      ++.-++|+|+++.++ ....+.+...+..-.+++.+|++|.+......         -+...+ .+.+.+++.++..+.+
T Consensus       131 ~~~kV~iI~~ae~m~-~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLp---------TI~SRcq~i~~~~~~~~~~~~~L  200 (342)
T PRK06964        131 GGARVVVLYPAEALN-VAAANALLKTLEEPPPGTVFLLVSARIDRLLP---------TILSRCRQFPMTVPAPEAAAAWL  200 (342)
T ss_pred             CCceEEEEechhhcC-HHHHHHHHHHhcCCCcCcEEEEEECChhhCcH---------HHHhcCEEEEecCCCHHHHHHHH
Confidence            455688999998887 77888899888877778877777666521111         111122 2999999999999888


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILG  407 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~  407 (597)
                      ....   .  .  +     ...++..++|.|+....+.
T Consensus       201 ~~~~---~--~--~-----~~~~l~~~~Gsp~~Al~~~  226 (342)
T PRK06964        201 AAQG---V--A--D-----ADALLAEAGGAPLAALALA  226 (342)
T ss_pred             HHcC---C--C--h-----HHHHHHHcCCCHHHHHHHH
Confidence            7641   1  1  1     1346788999997554443

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

Probab=97.33  E-value=0.0021  Score=66.43  Aligned_cols=148  Identities=20%  Similarity=0.228  Sum_probs=81.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      .....+.+.|++|+|||+||..++.    ...|+.+--++..   ++                          ++-  +.
T Consensus       536 s~lvSvLl~Gp~~sGKTaLAA~iA~----~S~FPFvKiiSpe---~m--------------------------iG~--sE  580 (744)
T KOG0741|consen  536 SPLVSVLLEGPPGSGKTALAAKIAL----SSDFPFVKIISPE---DM--------------------------IGL--SE  580 (744)
T ss_pred             CcceEEEEecCCCCChHHHHHHHHh----hcCCCeEEEeChH---Hc--------------------------cCc--cH
Confidence            4677889999999999999999976    3567764433311   11                          000  11


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCC---------cchHHHHHHhhcCC-CCCcE--EEEEccCCCCCCCcccc
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAY---------PRYWEQLMYSLKSG-SEGSR--ILVTRSGGKNGTNMTEI  342 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~---------~~~~~~l~~~l~~~-~~gs~--IIvTtR~~~~~~~~~~~  342 (597)
                      ......+...+...-+..--+||+||+...-+         ......+...|... .+|-+  |+-||...         
T Consensus       581 saKc~~i~k~F~DAYkS~lsiivvDdiErLiD~vpIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~---------  651 (744)
T KOG0741|consen  581 SAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRR---------  651 (744)
T ss_pred             HHHHHHHHHHHHHhhcCcceEEEEcchhhhhcccccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHH---------
Confidence            12233344444555556678999999843320         11223344444332 23333  44454444         


Q ss_pred             cccccCccccce--------eecCCCCh-HHHHHHHHHHhccCCCCCCccchHHHHHHHHHhc
Q 041007          343 GLGEKNGTNMME--------IGLGELSE-EECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKC  396 (597)
Q Consensus       343 ~~~~~~~~~~~~--------~~l~~Ls~-~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~  396 (597)
                           .+...++        |.+..++. ++..+.++..-     ...+...+.++.+...+|
T Consensus       652 -----~vL~~m~i~~~F~~~i~Vpnl~~~~~~~~vl~~~n-----~fsd~~~~~~~~~~~~~~  704 (744)
T KOG0741|consen  652 -----EVLQEMGILDCFSSTIHVPNLTTGEQLLEVLEELN-----IFSDDEVRAIAEQLLSKK  704 (744)
T ss_pred             -----HHHHHcCHHHhhhheeecCccCchHHHHHHHHHcc-----CCCcchhHHHHHHHhccc
Confidence                 4444433        88888887 66677666542     122334455666666666

>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=97.33  E-value=0.00054  Score=65.32  Aligned_cols=37  Identities=24%  Similarity=0.432  Sum_probs=30.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      +-.++|.|..|+|||||+..+..  .....|..+++++-
T Consensus        13 ~fr~viIG~sGSGKT~li~~lL~--~~~~~f~~I~l~t~   49 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTTLIKSLLY--YLRHKFDHIFLITP   49 (241)
T ss_pred             CceEEEECCCCCCHHHHHHHHHH--hhcccCCEEEEEec
Confidence            34788999999999999999987  47778877776643

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

>PRK05541 adenylylsulfate kinase; Provisional

Probab=97.32  E-value=0.00073  Score=62.19  Aligned_cols=36  Identities=33%  Similarity=0.690  Sum_probs=29.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEE
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWV  233 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  233 (597)
                      ...+|.|.|++|+||||+|+.++.  .....+...+++
T Consensus         6 ~~~~I~i~G~~GsGKst~a~~l~~--~l~~~~~~~~~~   41 (176)
T PRK05541          6 NGYVIWITGLAGSGKTTIAKALYE--RLKLKYSNVIYL   41 (176)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHH--HHHHcCCcEEEE
Confidence            567999999999999999999998  555556555555

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.31  E-value=0.0014  Score=62.10  Aligned_cols=41  Identities=17%  Similarity=0.190  Sum_probs=33.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      +...++.|+|++|+|||+++.+++..  ....-..++|++...
T Consensus        10 ~~g~i~~i~G~~GsGKT~l~~~~~~~--~~~~g~~v~yi~~e~   50 (209)
T TIGR02237        10 ERGTITQIYGPPGSGKTNICMILAVN--AARQGKKVVYIDTEG   50 (209)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCC
Confidence            45689999999999999999998873  333456789998865

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

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.30  E-value=0.0021  Score=69.67  Aligned_cols=44  Identities=32%  Similarity=0.422  Sum_probs=36.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+++|.+..++.+...+...          ....|.|+|++|+|||++|+.+++
T Consensus        65 ~~iiGqs~~i~~l~~al~~~----------~~~~vLi~Ge~GtGKt~lAr~i~~  108 (531)
T TIGR02902        65 DEIIGQEEGIKALKAALCGP----------NPQHVIIYGPPGVGKTAAARLVLE  108 (531)
T ss_pred             HHeeCcHHHHHHHHHHHhCC----------CCceEEEECCCCCCHHHHHHHHHH
Confidence            35899999999998876532          345778999999999999999976

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>PRK04296 thymidine kinase; Provisional

Probab=97.29  E-value=0.00071  Score=63.06  Aligned_cols=112  Identities=14%  Similarity=0.065  Sum_probs=59.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc--h
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS--Q  275 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~--~  275 (597)
                      .++.|+|+.|.||||++..+...  ...+-..++.+.-  .++.                ......++..++.....  .
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~--~~~~g~~v~i~k~--~~d~----------------~~~~~~i~~~lg~~~~~~~~   62 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYN--YEERGMKVLVFKP--AIDD----------------RYGEGKVVSRIGLSREAIPV   62 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHH--HHHcCCeEEEEec--cccc----------------cccCCcEecCCCCcccceEe
Confidence            47889999999999999998873  3333333333321  1111                11111222333221111  1


Q ss_pred             hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          276 VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .....+...+.+ ..++.-+||+|.++..+ .+....+...+  ...|..||+|.+..
T Consensus        63 ~~~~~~~~~~~~-~~~~~dvviIDEaq~l~-~~~v~~l~~~l--~~~g~~vi~tgl~~  116 (190)
T PRK04296         63 SSDTDIFELIEE-EGEKIDCVLIDEAQFLD-KEQVVQLAEVL--DDLGIPVICYGLDT  116 (190)
T ss_pred             CChHHHHHHHHh-hCCCCCEEEEEccccCC-HHHHHHHHHHH--HHcCCeEEEEecCc
Confidence            223344444444 33445689999996543 12222233222  35678999998876

>PRK04132 replication factor C small subunit; Provisional

Probab=97.27  E-value=0.006  Score=68.72  Aligned_cols=156  Identities=13%  Similarity=0.011  Sum_probs=93.9

Q ss_pred             Ec--CCCCcHHHHHHHHhCChhhhccCC-eeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHH
Q 041007          203 LG--NEGIGKTALARQVFDDSDVKANFD-KRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEME  279 (597)
Q Consensus       203 ~G--~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~  279 (597)
                      .|  |.++||||+|..++++. ....+. ..+-++++.....                 +..+.++..+....+.     
T Consensus       570 ~G~lPh~lGKTT~A~ala~~l-~g~~~~~~~lElNASd~rgi-----------------d~IR~iIk~~a~~~~~-----  626 (846)
T PRK04132        570 GGNLPTVLHNTTAALALAREL-FGENWRHNFLELNASDERGI-----------------NVIREKVKEFARTKPI-----  626 (846)
T ss_pred             cCCCCCcccHHHHHHHHHHhh-hcccccCeEEEEeCCCcccH-----------------HHHHHHHHHHHhcCCc-----
Confidence            36  88999999999999842 112222 2455666643332                 2333333322111000     


Q ss_pred             HHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecC
Q 041007          280 TVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLG  358 (597)
Q Consensus       280 ~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~  358 (597)
                               -..+.-++|||+++..+ ....+.+...+......+++|+++.+......         .+...|. +.+.
T Consensus       627 ---------~~~~~KVvIIDEaD~Lt-~~AQnALLk~lEep~~~~~FILi~N~~~kIi~---------tIrSRC~~i~F~  687 (846)
T PRK04132        627 ---------GGASFKIIFLDEADALT-QDAQQALRRTMEMFSSNVRFILSCNYSSKIIE---------PIQSRCAIFRFR  687 (846)
T ss_pred             ---------CCCCCEEEEEECcccCC-HHHHHHHHHHhhCCCCCeEEEEEeCChhhCch---------HHhhhceEEeCC
Confidence                     01245799999998886 56677777777666667788777665521110         1122232 9999


Q ss_pred             CCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHH
Q 041007          359 ELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       359 ~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~  404 (597)
                      +++.++....+...+...+...    ..+....|++.|+|.+-.+.
T Consensus       688 ~ls~~~i~~~L~~I~~~Egi~i----~~e~L~~Ia~~s~GDlR~AI  729 (846)
T PRK04132        688 PLRDEDIAKRLRYIAENEGLEL----TEEGLQAILYIAEGDMRRAI  729 (846)
T ss_pred             CCCHHHHHHHHHHHHHhcCCCC----CHHHHHHHHHHcCCCHHHHH
Confidence            9999999988877664322111    14567899999999885443

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

Probab=97.23  E-value=0.014  Score=57.92  Aligned_cols=59  Identities=25%  Similarity=0.349  Sum_probs=40.6

Q ss_pred             ccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC
Q 041007          167 EFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF  227 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F  227 (597)
                      .+=|-++.+++|.+.+.-.-.+ +  ..-+-..++=|.++|++|.|||-||++|++  +....|
T Consensus       152 dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~--~T~AtF  213 (406)
T COG1222         152 DIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVAN--QTDATF  213 (406)
T ss_pred             hccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHh--ccCceE
Confidence            3457899999998887533210 0  000113467799999999999999999999  455444

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

Probab=97.22  E-value=0.0012  Score=74.68  Aligned_cols=50  Identities=28%  Similarity=0.465  Sum_probs=38.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|.+.-+++|.++|......    ......++.++|++|+||||+++.++.
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~----~~~~g~~i~l~GppG~GKTtl~~~ia~  371 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRV----NKIKGPILCLVGPPGVGKTSLGQSIAK  371 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhc----ccCCCceEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999888732210    012456899999999999999999987

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.21  E-value=0.0024  Score=61.33  Aligned_cols=39  Identities=26%  Similarity=0.313  Sum_probs=31.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ...++.|+|++|+|||++|.+++..  ....-..++|++..
T Consensus        22 ~g~i~~i~G~~GsGKT~l~~~la~~--~~~~~~~v~yi~~e   60 (225)
T PRK09361         22 RGTITQIYGPPGSGKTNICLQLAVE--AAKNGKKVIYIDTE   60 (225)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEECC
Confidence            4679999999999999999999873  33334668899876

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

Probab=97.21  E-value=0.00082  Score=61.79  Aligned_cols=37  Identities=22%  Similarity=0.281  Sum_probs=25.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      ..-+.|+|++|+|||.||..+.+.  ...+=..+.|++.
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~--~~~~g~~v~f~~~   83 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANE--AIRKGYSVLFITA   83 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEEH
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHH--hccCCcceeEeec
Confidence            457999999999999999999884  3222233566653

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.

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=97.20  E-value=0.0011  Score=60.26  Aligned_cols=45  Identities=24%  Similarity=0.405  Sum_probs=34.5

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++|.+..+.++.+.+.....        ....|.|+|..|+||+.+|+.+++.
T Consensus         1 liG~s~~m~~~~~~~~~~a~--------~~~pVlI~GE~GtGK~~lA~~IH~~   45 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS--------SDLPVLITGETGTGKELLARAIHNN   45 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT--------STS-EEEECSTTSSHHHHHHHHHHC
T ss_pred             CEeCCHHHHHHHHHHHHHhC--------CCCCEEEEcCCCCcHHHHHHHHHHh
Confidence            47888888888888876553        3367789999999999999999884

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

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

Probab=97.18  E-value=0.0034  Score=64.00  Aligned_cols=129  Identities=15%  Similarity=0.143  Sum_probs=74.2

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-------------------cC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-------------------NF  227 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-------------------~F  227 (597)
                      .++|-+....++..+......        ....+.++|++|+||||+|..+.+...-..                   .+
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~--------~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~   73 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGR--------LPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNH   73 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCC--------CCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCC
Confidence            356777778888888874332        233599999999999999999987421111                   11


Q ss_pred             CeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCc
Q 041007          228 DKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYP  307 (597)
Q Consensus       228 ~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~  307 (597)
                      +.+..+..+.....-             -..+..+.+.+......                ..++.-+++||++...+ .
T Consensus        74 ~d~lel~~s~~~~~~-------------i~~~~vr~~~~~~~~~~----------------~~~~~kviiidead~mt-~  123 (325)
T COG0470          74 PDFLELNPSDLRKID-------------IIVEQVRELAEFLSESP----------------LEGGYKVVIIDEADKLT-E  123 (325)
T ss_pred             CceEEecccccCCCc-------------chHHHHHHHHHHhccCC----------------CCCCceEEEeCcHHHHh-H
Confidence            223333333222210             00122222222211110                02456799999997766 4


Q ss_pred             chHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          308 RYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       308 ~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      +.-..+...+......+.+|++|...
T Consensus       124 ~A~nallk~lEep~~~~~~il~~n~~  149 (325)
T COG0470         124 DAANALLKTLEEPPKNTRFILITNDP  149 (325)
T ss_pred             HHHHHHHHHhccCCCCeEEEEEcCCh
Confidence            45566666666777788888888744

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

Probab=97.18  E-value=0.0017  Score=72.78  Aligned_cols=137  Identities=15%  Similarity=0.234  Sum_probs=74.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.++.++.|...+......-. .++.....+.++|++|+|||.||+.++..  ...   ..+.++++.....    
T Consensus       458 ~~ViGQ~~ai~~l~~~i~~~~~gl~-~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~--l~~---~~i~id~se~~~~----  527 (758)
T PRK11034        458 MLVFGQDKAIEALTEAIKMSRAGLG-HEHKPVGSFLFAGPTGVGKTEVTVQLSKA--LGI---ELLRFDMSEYMER----  527 (758)
T ss_pred             ceEeCcHHHHHHHHHHHHHHhcccc-CCCCCcceEEEECCCCCCHHHHHHHHHHH--hCC---CcEEeechhhccc----
Confidence            3478999999988888873211000 01223457899999999999999999873  322   2233444322111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcC-ceEEEEEecccCCCCcchHHHHHHhhcCCC---
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQG-KKVLLVLDDLWWNAYPRYWEQLMYSLKSGS---  321 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~-kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~---  321 (597)
                                  .    .+ ..+.+..+.....+ ....+.+.+.. ...+|+||++...+ .+.++.+...+..+.   
T Consensus       528 ------------~----~~-~~LiG~~~gyvg~~-~~g~L~~~v~~~p~sVlllDEieka~-~~v~~~LLq~ld~G~ltd  588 (758)
T PRK11034        528 ------------H----TV-SRLIGAPPGYVGFD-QGGLLTDAVIKHPHAVLLLDEIEKAH-PDVFNLLLQVMDNGTLTD  588 (758)
T ss_pred             ------------c----cH-HHHcCCCCCccccc-ccchHHHHHHhCCCcEEEeccHhhhh-HHHHHHHHHHHhcCeeec
Confidence                        0    11 11211111110000 01122223333 34699999998776 667777777765321   


Q ss_pred             --------CCcEEEEEcc
Q 041007          322 --------EGSRILVTRS  331 (597)
Q Consensus       322 --------~gs~IIvTtR  331 (597)
                              .++-||+||-
T Consensus       589 ~~g~~vd~rn~iiI~TsN  606 (758)
T PRK11034        589 NNGRKADFRNVVLVMTTN  606 (758)
T ss_pred             CCCceecCCCcEEEEeCC
Confidence                    2445777774

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

Probab=97.17  E-value=0.0021  Score=62.68  Aligned_cols=38  Identities=24%  Similarity=0.301  Sum_probs=28.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      +..-+.++|++|+|||.||.++.+.  ....--.+.++++
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~--l~~~g~sv~f~~~  141 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNE--LLKAGISVLFITA  141 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHH--HHHcCCeEEEEEH
Confidence            3568999999999999999999995  4332233555554

>CHL00095 clpC Clp protease ATP binding subunit

Probab=97.17  E-value=0.0014  Score=75.07  Aligned_cols=142  Identities=15%  Similarity=0.217  Sum_probs=77.0

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.+..++.+...+......-. .++....++.++|++|+|||+||+.+.+.  .-+.-...+-++++.....    
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~-~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~--l~~~~~~~~~~d~s~~~~~----  581 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLK-NPNRPIASFLFSGPTGVGKTELTKALASY--FFGSEDAMIRLDMSEYMEK----  581 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhccc-CCCCCceEEEEECCCCCcHHHHHHHHHHH--hcCCccceEEEEchhcccc----
Confidence            5678999999999888763221000 01223346789999999999999998762  2111122333333322111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCce-EEEEEecccCCCCcchHHHHHHhhcCC----
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKK-VLLVLDDLWWNAYPRYWEQLMYSLKSG----  320 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr-~LLVLDdv~~~~~~~~~~~l~~~l~~~----  320 (597)
                                  ..    +...++.+ +.....++ ...+.+.++.++ .+++||++...+ ...++.+...+..+    
T Consensus       582 ------------~~----~~~l~g~~-~gyvg~~~-~~~l~~~~~~~p~~VvllDeieka~-~~v~~~Llq~le~g~~~d  642 (821)
T CHL00095        582 ------------HT----VSKLIGSP-PGYVGYNE-GGQLTEAVRKKPYTVVLFDEIEKAH-PDIFNLLLQILDDGRLTD  642 (821)
T ss_pred             ------------cc----HHHhcCCC-CcccCcCc-cchHHHHHHhCCCeEEEECChhhCC-HHHHHHHHHHhccCceec
Confidence                        00    01111111 11000000 112333444444 588999998776 77788888777643    


Q ss_pred             -------CCCcEEEEEccCC
Q 041007          321 -------SEGSRILVTRSGG  333 (597)
Q Consensus       321 -------~~gs~IIvTtR~~  333 (597)
                             ..++.+|+||...
T Consensus       643 ~~g~~v~~~~~i~I~Tsn~g  662 (821)
T CHL00095        643 SKGRTIDFKNTLIIMTSNLG  662 (821)
T ss_pred             CCCcEEecCceEEEEeCCcc
Confidence                   2456677777644

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.16  E-value=0.006  Score=69.29  Aligned_cols=55  Identities=22%  Similarity=0.256  Sum_probs=36.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCC---cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDE---ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~---~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.|.+..+++|.+.+...-...   ..-+-..++-|.++|++|+|||+||+.+++.
T Consensus       453 ~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e  510 (733)
T TIGR01243       453 SDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATE  510 (733)
T ss_pred             hhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHh
Confidence            456788888887777664211100   0000123456899999999999999999983

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.

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=97.15  E-value=0.0057  Score=69.50  Aligned_cols=54  Identities=26%  Similarity=0.312  Sum_probs=37.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+.|.+..+++|.+++...-.. +  ..-+-...+.|.|+|++|+|||+||+.+++
T Consensus       178 ~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~  234 (733)
T TIGR01243       178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVAN  234 (733)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHH
Confidence            45789999999998877422110 0  000012346789999999999999999988

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.

>PRK12608 transcription termination factor Rho; Provisional

Probab=97.14  E-value=0.0027  Score=64.38  Aligned_cols=101  Identities=20%  Similarity=0.220  Sum_probs=61.9

Q ss_pred             HHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC-Ce-eEEEEecCCCchhhhhhhhhhhc
Q 041007          175 KQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF-DK-RIWVSASYPRDEIRVARDEISVA  252 (597)
Q Consensus       175 ~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F-~~-~~wv~~~~~~~~~~~~~~~~~~~  252 (597)
                      ..++++.+..-.         ....+.|+|++|+|||||++.+++.  +.... +. ++|+.+.+....           
T Consensus       120 ~~RvID~l~PiG---------kGQR~LIvG~pGtGKTTLl~~la~~--i~~~~~dv~~vv~lIgER~~E-----------  177 (380)
T PRK12608        120 SMRVVDLVAPIG---------KGQRGLIVAPPRAGKTVLLQQIAAA--VAANHPEVHLMVLLIDERPEE-----------  177 (380)
T ss_pred             hHhhhhheeecC---------CCceEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEEecCCCCC-----------
Confidence            345777776433         3457799999999999999998883  33322 33 467666665443           


Q ss_pred             ccchHHHHHHHHHHhccCCCCc--hhh---HHHHHHHHHHHh--cCceEEEEEecc
Q 041007          253 RDRDEIRVAKAILESLKGSVSS--QVE---METVLQYINEFV--QGKKVLLVLDDL  301 (597)
Q Consensus       253 ~~~~~~~~~~~il~~l~~~~~~--~~~---~~~~~~~l~~~L--~~kr~LLVLDdv  301 (597)
                          ..++++.+...+.....+  ...   .......+.+++  .+++++||+|++
T Consensus       178 ----V~df~~~i~~~Vvast~de~~~~~~~v~~~~~~~Ae~f~~~GkdVVLvlDsl  229 (380)
T PRK12608        178 ----VTDMRRSVKGEVYASTFDRPPDEHIRVAELVLERAKRLVEQGKDVVILLDSL  229 (380)
T ss_pred             ----HHHHHHHHhhhEEeecCCCCHHHHHHHHHHHHHHHHHHHHcCCCEEEEEeCc
Confidence                156666666666553321  111   111222222333  388999999999

>PRK08118 topology modulation protein; Reviewed

Probab=97.12  E-value=0.00068  Score=61.68  Aligned_cols=35  Identities=31%  Similarity=0.618  Sum_probs=27.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhh-ccCCeeEE
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVK-ANFDKRIW  232 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~-~~F~~~~w  232 (597)
                      +.|.|+|++|+||||||+.+++..... -+|+..+|
T Consensus         2 ~rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~   37 (167)
T PRK08118          2 KKIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFW   37 (167)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCceecchhhc
Confidence            358999999999999999999853333 34666665

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.12  E-value=0.0018  Score=58.41  Aligned_cols=40  Identities=28%  Similarity=0.384  Sum_probs=29.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          199 VIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ++.|+|++|+|||+++..++..  ....-..++|++......
T Consensus         1 ~~~i~G~~G~GKT~l~~~i~~~--~~~~~~~v~~~~~e~~~~   40 (165)
T cd01120           1 LILVFGPTGSGKTTLALQLALN--IATKGGKVVYVDIEEEIE   40 (165)
T ss_pred             CeeEeCCCCCCHHHHHHHHHHH--HHhcCCEEEEEECCcchH
Confidence            3689999999999999999873  333345677887665443

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=97.10  E-value=0.0035  Score=66.73  Aligned_cols=55  Identities=20%  Similarity=0.248  Sum_probs=33.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .++.|.+..++.+.............-+-..++-|.++|++|+|||.+|+.+++.
T Consensus       228 ~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e  282 (489)
T CHL00195        228 SDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIAND  282 (489)
T ss_pred             HHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH
Confidence            3466776666555543211100000000124577999999999999999999883

>PHA00729 NTP-binding motif containing protein

Probab=97.07  E-value=0.0034  Score=59.27  Aligned_cols=25  Identities=36%  Similarity=0.464  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|.|+|.+|+||||||..+.+.
T Consensus        16 ~f~nIlItG~pGvGKT~LA~aLa~~   40 (226)
T PHA00729         16 GFVSAVIFGKQGSGKTTYALKVARD   40 (226)
T ss_pred             CeEEEEEECCCCCCHHHHHHHHHHH
Confidence            4467999999999999999999883

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

Probab=97.03  E-value=0.0055  Score=65.99  Aligned_cols=165  Identities=19%  Similarity=0.262  Sum_probs=92.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+-+|-++-.++|++.|.-....    ..-..++++++||+|||||+|++.++.  .....|   +-+++++..+.    
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~----~~~kGpILcLVGPPGVGKTSLgkSIA~--al~Rkf---vR~sLGGvrDE----  389 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLT----KKLKGPILCLVGPPGVGKTSLGKSIAK--ALGRKF---VRISLGGVRDE----  389 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHh----ccCCCcEEEEECCCCCCchhHHHHHHH--HhCCCE---EEEecCccccH----
Confidence            45679999999999998522110    023458999999999999999999998  555555   22444444443    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCc--hhhHHHHHHHHHHHhcCceEEEEEecccCCCCc---chHHHHHHhhcCC
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSS--QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYP---RYWEQLMYSLKSG  320 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~--~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~---~~~~~l~~~l~~~  320 (597)
                                  .+        +.+....  ..-...+++.+++. +.++-|++||.++.+...   +--..++..|.+.
T Consensus       390 ------------AE--------IRGHRRTYIGamPGrIiQ~mkka-~~~NPv~LLDEIDKm~ss~rGDPaSALLEVLDPE  448 (782)
T COG0466         390 ------------AE--------IRGHRRTYIGAMPGKIIQGMKKA-GVKNPVFLLDEIDKMGSSFRGDPASALLEVLDPE  448 (782)
T ss_pred             ------------HH--------hccccccccccCChHHHHHHHHh-CCcCCeEEeechhhccCCCCCChHHHHHhhcCHh
Confidence                        11        1111100  00112233333333 446678889998654311   1122344444321


Q ss_pred             CC--------------CcEEEEEccCCCC-CCCcccccccccCccccce-eecCCCChHHHHHHHHHHh
Q 041007          321 SE--------------GSRILVTRSGGKN-GTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       321 ~~--------------gs~IIvTtR~~~~-~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~  373 (597)
                      .+              ...+.|||-+... .+.         .....+. |++.+.+++|=.++-.+++
T Consensus       449 QN~~F~DhYLev~yDLS~VmFiaTANsl~tIP~---------PLlDRMEiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         449 QNNTFSDHYLEVPYDLSKVMFIATANSLDTIPA---------PLLDRMEVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             hcCchhhccccCccchhheEEEeecCccccCCh---------HHhcceeeeeecCCChHHHHHHHHHhc
Confidence            11              1234566655521 111         1222333 9999999999888777665

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

Probab=97.02  E-value=0.025  Score=59.85  Aligned_cols=55  Identities=20%  Similarity=0.235  Sum_probs=40.0

Q ss_pred             CccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+=|-+..+.+|.+++..-...+  ..-+-..++=|.++||+|+|||.||+.+++.
T Consensus       190 ~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAge  246 (802)
T KOG0733|consen  190 SDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGE  246 (802)
T ss_pred             hhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhh
Confidence            456689999999988886533211  0011234667899999999999999999994

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

Probab=97.01  E-value=0.0025  Score=53.23  Aligned_cols=21  Identities=52%  Similarity=1.037  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |.|+|++|+|||+||..++.+
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~   21 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKD   21 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            568999999999999998874

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>PTZ00494 tuzin-like protein; Provisional

Probab=97.01  E-value=0.059  Score=55.25  Aligned_cols=170  Identities=11%  Similarity=0.024  Sum_probs=101.3

Q ss_pred             ccCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          162 VIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       162 ~~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ...+..+|.|+.|-..+.+.|...+.       ..+++++++|.-|.||++|.+.....+     --..++|.+...   
T Consensus       367 ~a~~~~~V~R~~eE~~vRqvL~qld~-------aHPRIvV~TG~~GcGKSslcRsAvrkE-----~~paV~VDVRg~---  431 (664)
T PTZ00494        367 AAAEAFEVRREDEEALVRSVLTQMAP-------SHPRIVALAGGSGGGRCVPCRRAVRVE-----GVALVHVDVGGT---  431 (664)
T ss_pred             ccccccccchhhHHHHHHHHHhhccC-------CCCcEEEEecCCCCCchHHHHHHHHHc-----CCCeEEEEecCC---
Confidence            55678899999999999998886653       578999999999999999999886632     234567777655   


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCc--hhhHHHHHHHHHH---HhcCceEEEEEecccCCCCcchHHHHH--
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSS--QVEMETVLQYINE---FVQGKKVLLVLDDLWWNAYPRYWEQLM--  314 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~--~~~~~~~~~~l~~---~L~~kr~LLVLDdv~~~~~~~~~~~l~--  314 (597)
                                      ++.++.+.+.++.+.-+  .+-++-+.+....   ...++.-+||+-=- ..+   ++..+.  
T Consensus       432 ----------------EDtLrsVVKALgV~nve~CGDlLdFI~ea~~~A~~~~~g~~P~lVlkLR-EGs---sL~RVYnE  491 (664)
T PTZ00494        432 ----------------EDTLRSVVRALGVSNVEVCGDLLGFVEEAMRGATVKASDGVPFLVMRLR-EGS---DLGRVYGE  491 (664)
T ss_pred             ----------------cchHHHHHHHhCCCChhhhccHHHHHHHHHHHHHHhcCCCCCEEEEEec-cCC---cHHHHHHH
Confidence                            55677888888876533  1222333333332   23355555554311 111   222211  


Q ss_pred             -HhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHh
Q 041007          315 -YSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       315 -~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~  373 (597)
                       ..|.....-|+|++----+  ...+....++..+.     |.+.+|+.++|.++-.+..
T Consensus       492 ~vaLacDrRlCHvv~EVplE--SLT~~n~~LPRLDF-----y~VPnFSr~QAf~YtqH~l  544 (664)
T PTZ00494        492 VVSLVSDCQACHIVLAVPMK--ALTPLNVSSRRLDF-----YCIPPFSRRQAFAYAEHTL  544 (664)
T ss_pred             HHHHHccchhheeeeechHh--hhchhhccCcccee-----EecCCcCHHHHHHHHhccc
Confidence             1233445556777643222  11111111111111     8899999999988776654

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=97.01  E-value=0.0045  Score=56.66  Aligned_cols=127  Identities=17%  Similarity=0.162  Sum_probs=61.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch-hhhhhhhhhh-cccchHHHHHHHHHHhccCCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE-IRVARDEISV-ARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      ...+++|.|+.|.|||||.+.++.-.   ....+.+++.-...... .......... .+.....  ...+.+.+     
T Consensus        27 ~G~~~~l~G~nGsGKstLl~~i~G~~---~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~~~~~~~--~~t~~e~l-----   96 (171)
T cd03228          27 PGEKVAIVGPSGSGKSTLLKLLLRLY---DPTSGEILIDGVDLRDLDLESLRKNIAYVPQDPFLF--SGTIRENI-----   96 (171)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCC---CCCCCEEEECCEEhhhcCHHHHHhhEEEEcCCchhc--cchHHHHh-----
Confidence            34699999999999999999998731   22334343321100000 0000000000 0000000  00111111     


Q ss_pred             chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          274 SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                       ...-+...-.+...+..++-+|+||+-...-+......+...+.....+..||++|.+.
T Consensus        97 -LS~G~~~rl~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~sh~~  155 (171)
T cd03228          97 -LSGGQRQRIAIARALLRDPPILILDEATSALDPETEALILEALRALAKGKTVIVIAHRL  155 (171)
T ss_pred             -hCHHHHHHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEecCH
Confidence             01111222235555666788999999755444555555555554433457788888765

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.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.00  E-value=0.0076  Score=58.25  Aligned_cols=43  Identities=23%  Similarity=0.301  Sum_probs=32.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      +...++.|+|++|+|||+|+.++...  ....=..++|++.....
T Consensus        23 ~~g~~~~i~G~~GsGKt~l~~~~~~~--~~~~g~~~~y~~~e~~~   65 (234)
T PRK06067         23 PFPSLILIEGDHGTGKSVLSQQFVYG--ALKQGKKVYVITTENTS   65 (234)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHH--HHhCCCEEEEEEcCCCH
Confidence            45789999999999999999999653  22233467888886554

>cd01394 radB RadB

Probab=96.99  E-value=0.0062  Score=58.16  Aligned_cols=42  Identities=21%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      ...++.|+|++|+|||+++.+++..  ....-..++|++....+
T Consensus        18 ~g~i~~i~G~~GsGKT~l~~~~a~~--~~~~g~~v~yi~~e~~~   59 (218)
T cd01394          18 RGTVTQVYGPPGTGKTNIAIQLAVE--TAGQGKKVAYIDTEGLS   59 (218)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCCCC
Confidence            5679999999999999999999873  33333456788755443

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

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

Probab=96.99  E-value=0.027  Score=56.77  Aligned_cols=26  Identities=27%  Similarity=0.399  Sum_probs=23.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++.++|+|++|+|||.+|+.+++.
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~e  171 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKK  171 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHH
Confidence            35789999999999999999999994

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

Probab=96.99  E-value=0.006  Score=58.60  Aligned_cols=44  Identities=23%  Similarity=0.197  Sum_probs=32.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccC------CeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANF------DKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F------~~~~wv~~~~~~~~  241 (597)
                      ...++.|+|++|+|||+|+.+++..  .....      ..++|++....++.
T Consensus        18 ~g~v~~I~G~~GsGKT~l~~~ia~~--~~~~~~~~g~~~~v~yi~~e~~~~~   67 (226)
T cd01393          18 TGRITEIFGEFGSGKTQLCLQLAVE--AQLPGELGGLEGKVVYIDTEGAFRP   67 (226)
T ss_pred             CCcEEEEeCCCCCChhHHHHHHHHH--hhcccccCCCcceEEEEecCCCCCH
Confidence            5679999999999999999998763  22222      45788887665543

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.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=96.96  E-value=0.0092  Score=53.25  Aligned_cols=52  Identities=17%  Similarity=0.227  Sum_probs=34.9

Q ss_pred             HHHHHHHhcC-ceEEEEEecccCCC--CcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          282 LQYINEFVQG-KKVLLVLDDLWWNA--YPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~-kr~LLVLDdv~~~~--~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+..++.+.. +-=|||||++-..-  ..-..+.+...+.....+..||+|.|+.
T Consensus        84 ~~~a~~~~~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~  138 (159)
T cd00561          84 WAFAKEAIASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNA  138 (159)
T ss_pred             HHHHHHHHhcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCC
Confidence            3334444443 44599999984321  1225567777787788889999999987

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.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=96.96  E-value=0.0086  Score=60.58  Aligned_cols=72  Identities=13%  Similarity=0.046  Sum_probs=44.9

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|+|++...+ ...-..+...+.....++.+|++|.+......         .+...+. +.+.+++.+++.+.+
T Consensus       112 ~~~kV~iiEp~~~Ld-~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~---------ti~SRc~~~~~~~~~~~~~~~~L  181 (325)
T PRK08699        112 GGLRVILIHPAESMN-LQAANSLLKVLEEPPPQVVFLLVSHAADKVLP---------TIKSRCRKMVLPAPSHEEALAYL  181 (325)
T ss_pred             CCceEEEEechhhCC-HHHHHHHHHHHHhCcCCCEEEEEeCChHhChH---------HHHHHhhhhcCCCCCHHHHHHHH
Confidence            344455678887766 55666677777655556777777776521110         1111122 899999999998888


Q ss_pred             HHH
Q 041007          370 RQI  372 (597)
Q Consensus       370 ~~~  372 (597)
                      ...
T Consensus       182 ~~~  184 (325)
T PRK08699        182 RER  184 (325)
T ss_pred             Hhc
Confidence            653

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=96.94  E-value=0.00076  Score=59.30  Aligned_cols=108  Identities=19%  Similarity=0.265  Sum_probs=62.9

Q ss_pred             ccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhh-hccCCeeEEEEecCCCchhhhhhh
Q 041007          169 HGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV-KANFDKRIWVSASYPRDEIRVARD  247 (597)
Q Consensus       169 vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~F~~~~wv~~~~~~~~~~~~~~  247 (597)
                      ||+...++++.+.+.....        ....|.|+|..|+||+++|+.+++.... ...|..   +.+..   .      
T Consensus         1 vG~S~~~~~l~~~l~~~a~--------~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~---~~~~~---~------   60 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAK--------SSSPVLITGEPGTGKSLLARALHRYSGRANGPFIV---IDCAS---L------   60 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHC--------SSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCC---CCHHC---T------
T ss_pred             CCCCHHHHHHHHHHHHHhC--------CCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEE---echhh---C------
Confidence            5777778888777765443        3467899999999999999988774221 111111   00000   0      


Q ss_pred             hhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEE
Q 041007          248 EISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRI  326 (597)
Q Consensus       248 ~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~I  326 (597)
                                                   +    .+.+..   -+.-.|+|+|+...+ ......+...+.. ...+.++
T Consensus        61 -----------------------------~----~~~l~~---a~~gtL~l~~i~~L~-~~~Q~~L~~~l~~~~~~~~Rl  103 (138)
T PF14532_consen   61 -----------------------------P----AELLEQ---AKGGTLYLKNIDRLS-PEAQRRLLDLLKRQERSNVRL  103 (138)
T ss_dssp             -----------------------------C----HHHHHH---CTTSEEEEECGCCS--HHHHHHHHHHHHHCTTTTSEE
T ss_pred             -----------------------------c----HHHHHH---cCCCEEEECChHHCC-HHHHHHHHHHHHhcCCCCeEE
Confidence                                         0    111111   144567899997766 4455556666653 3677899


Q ss_pred             EEEccCC
Q 041007          327 LVTRSGG  333 (597)
Q Consensus       327 IvTtR~~  333 (597)
                      |.||..+
T Consensus       104 I~ss~~~  110 (138)
T PF14532_consen  104 IASSSQD  110 (138)
T ss_dssp             EEEECC-
T ss_pred             EEEeCCC
Confidence            9999876

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=96.94  E-value=0.0086  Score=58.79  Aligned_cols=176  Identities=22%  Similarity=0.228  Sum_probs=92.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC-hhhhccCCeeEEEEecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD-SDVKANFDKRIWVSASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~-~~~~~~F~~~~wv~~~~~~~~~~~  244 (597)
                      ..++|-.++...+..++....-      -+....|.|+||.|.|||+|......+ .++.++   .+-|...+.....  
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~------~gEsnsviiigprgsgkT~li~~~Ls~~q~~~E~---~l~v~Lng~~~~d--   92 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTIL------HGESNSVIIIGPRGSGKTILIDTRLSDIQENGEN---FLLVRLNGELQTD--   92 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHH------hcCCCceEEEccCCCCceEeeHHHHhhHHhcCCe---EEEEEECccchhh--
Confidence            3588999999999988874432      134567899999999999998887775 122223   3334444433220  


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhcc----CCCCc----hhhHHHHHHHHHHHhc--CceEEEEEecccCCCCcchHHHHH
Q 041007          245 ARDEISVARDRDEIRVAKAILESLK----GSVSS----QVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAYPRYWEQLM  314 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~----~~~~~----~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~~~~~~~l~  314 (597)
                                   .-.++.|.+++.    .....    ..+...+...+..--+  +.+++.|+|.++-.- ...-..+.
T Consensus        93 -------------k~al~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~-~h~rQtll  158 (408)
T KOG2228|consen   93 -------------KIALKGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFA-PHSRQTLL  158 (408)
T ss_pred             -------------HHHHHHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccc-cchhhHHH
Confidence                         223344444432    22111    2233333333332111  235788888774222 11222222


Q ss_pred             -Hhhc----CCCCCcEEEEEccCCCCCCCcccccccccCccccce----eecCCCChHHHHHHHHHHh
Q 041007          315 -YSLK----SGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME----IGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       315 -~~l~----~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~----~~l~~Ls~~es~~Lf~~~~  373 (597)
                       ..|.    ...+-+.|-+|||-..       ..+....|.....    +-+++++-++...+++...
T Consensus       159 YnlfDisqs~r~Piciig~Ttrld~-------lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  159 YNLFDISQSARAPICIIGVTTRLDI-------LELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             HHHHHHHhhcCCCeEEEEeeccccH-------HHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHh
Confidence             2222    2344566778888651       1111111211111    5566677788888888766

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=96.93  E-value=0.006  Score=59.00  Aligned_cols=47  Identities=21%  Similarity=0.220  Sum_probs=34.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhcc----CCeeEEEEecCCCch
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKAN----FDKRIWVSASYPRDE  241 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~  241 (597)
                      +...++.|+|++|+|||+|+.+++-.......    -..++|++....+..
T Consensus        17 ~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~~~~~   67 (235)
T cd01123          17 ETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEGTFRP   67 (235)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCCCcCH
Confidence            35679999999999999999999743122221    357899988775543

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 .

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=96.92  E-value=0.0004  Score=61.15  Aligned_cols=20  Identities=40%  Similarity=0.718  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      |.|+|++|+|||+||+.+++
T Consensus         2 vlL~G~~G~GKt~l~~~la~   21 (139)
T PF07728_consen    2 VLLVGPPGTGKTTLARELAA   21 (139)
T ss_dssp             EEEEESSSSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            68999999999999999988

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.91  E-value=0.0025  Score=57.94  Aligned_cols=37  Identities=16%  Similarity=0.264  Sum_probs=26.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          199 VIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ++.|.|.+|+|||++|.++...     ....++++.-...++
T Consensus         1 ~~li~G~~~sGKS~~a~~~~~~-----~~~~~~y~at~~~~d   37 (169)
T cd00544           1 IILVTGGARSGKSRFAERLAAE-----LGGPVTYIATAEAFD   37 (169)
T ss_pred             CEEEECCCCCCHHHHHHHHHHh-----cCCCeEEEEccCcCC
Confidence            3679999999999999999762     223566666555554

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.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.91  E-value=0.0048  Score=56.85  Aligned_cols=127  Identities=15%  Similarity=0.054  Sum_probs=62.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhh-cccc--hHHHHHHHHHHhccCCCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISV-ARDR--DEIRVAKAILESLKGSVS  273 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~-~~~~--~~~~~~~~il~~l~~~~~  273 (597)
                      ..+++|.|+.|+|||||++.++...   ....+.+++.-................ .+..  ....+...+.       .
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~-------~   97 (178)
T cd03247          28 GEKIALLGRSGSGKSTLLQLLTGDL---KPQQGEITLDGVPVSDLEKALSSLISVLNQRPYLFDTTLRNNLG-------R   97 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhccC---CCCCCEEEECCEEHHHHHHHHHhhEEEEccCCeeecccHHHhhc-------c
Confidence            4689999999999999999998732   122333433211000000000000000 0000  0011111110       0


Q ss_pred             chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          274 SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      ....-+...-.+...+-.++-+++||+....-+....+.+...+.....+..||++|.+.
T Consensus        98 ~LS~G~~qrv~laral~~~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~  157 (178)
T cd03247          98 RFSGGERQRLALARILLQDAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWITHHL  157 (178)
T ss_pred             cCCHHHHHHHHHHHHHhcCCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEecCH
Confidence            111112223335555667788999999765444555555555554433467788888765

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.

>smart00763 AAA_PrkA PrkA AAA domain

Probab=96.91  E-value=0.00099  Score=67.19  Aligned_cols=50  Identities=18%  Similarity=0.400  Sum_probs=41.3

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .++|-++.++++++++......    .....+++.|+|++|+||||||..+.+.
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g----~~~~r~il~L~GPPGsGKStla~~La~~  101 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQG----LEERKQILYLLGPVGGGKSSLVECLKRG  101 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhc----CCCCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            6999999999999999754421    1234689999999999999999999884

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

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

Probab=96.89  E-value=0.024  Score=59.97  Aligned_cols=134  Identities=19%  Similarity=0.258  Sum_probs=72.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      +.=|.++||+|+|||-||++|+|  +..-+|     +++.+                    .+++.....          
T Consensus       545 PsGvLL~GPPGCGKTLlAKAVAN--Eag~NF-----isVKG--------------------PELlNkYVG----------  587 (802)
T KOG0733|consen  545 PSGVLLCGPPGCGKTLLAKAVAN--EAGANF-----ISVKG--------------------PELLNKYVG----------  587 (802)
T ss_pred             CCceEEeCCCCccHHHHHHHHhh--hccCce-----EeecC--------------------HHHHHHHhh----------
Confidence            45688999999999999999999  455555     44433                    222222111          


Q ss_pred             hHHHHH-HHHHHHhcCceEEEEEecccCCC----C------cchHHHHHHhhcC--CCCCcEEEEEccCCCCCCCccccc
Q 041007          277 EMETVL-QYINEFVQGKKVLLVLDDLWWNA----Y------PRYWEQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIG  343 (597)
Q Consensus       277 ~~~~~~-~~l~~~L~~kr~LLVLDdv~~~~----~------~~~~~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~  343 (597)
                      +.+..+ ..+++.-...+++|+||.++..-    +      .....+++..+..  ...|.-||-.|-.+    ++++-.
T Consensus       588 ESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~gV~viaATNRP----DiIDpA  663 (802)
T KOG0733|consen  588 ESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRGVYVIAATNRP----DIIDPA  663 (802)
T ss_pred             hHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccceEEEeecCCC----cccchh
Confidence            112222 22333334679999999985321    1      1123444444543  24455566555433    111111


Q ss_pred             ccccCccccce--eecCCCChHHHHHHHHHHhc
Q 041007          344 LGEKNGTNMME--IGLGELSEEECRSLFRQIAF  374 (597)
Q Consensus       344 ~~~~~~~~~~~--~~l~~Ls~~es~~Lf~~~~~  374 (597)
                      +..   .+...  +-++.-+.+|=.++++...-
T Consensus       664 iLR---PGRlDk~LyV~lPn~~eR~~ILK~~tk  693 (802)
T KOG0733|consen  664 ILR---PGRLDKLLYVGLPNAEERVAILKTITK  693 (802)
T ss_pred             hcC---CCccCceeeecCCCHHHHHHHHHHHhc
Confidence            110   01111  55666777888888887764

>PRK07261 topology modulation protein; Provisional

Probab=96.86  E-value=0.0025  Score=58.30  Aligned_cols=22  Identities=41%  Similarity=0.614  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|.|+|++|+||||||+.+...
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~   23 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQH   23 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHH
Confidence            4899999999999999998763

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

Probab=96.85  E-value=0.0078  Score=58.82  Aligned_cols=48  Identities=23%  Similarity=0.221  Sum_probs=34.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc----cCCeeEEEEecCCCchhh
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA----NFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~~~  243 (597)
                      ...+.=|+|++|+|||.|+.+++-......    .=..++|++-...+...+
T Consensus        37 ~g~itEi~G~~gsGKTql~l~l~~~~~l~~~~~g~~~~vvyidTe~~f~~~R   88 (256)
T PF08423_consen   37 TGSITEIVGESGSGKTQLCLQLAVNVQLPEEIGGLGGKVVYIDTEGTFSPER   88 (256)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSGGCTTSSSSEEEEEESSSSS-HHH
T ss_pred             CCcEEEEEEecccccchHHHHHHHHhhcccccccCCCceEEEeCCCCCCHHH
Confidence            457999999999999999988764322221    123589999888887633

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 ....

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=96.84  E-value=0.0013  Score=59.83  Aligned_cols=21  Identities=24%  Similarity=0.434  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++.|.|.+|+|||++|..+..
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~   23 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAA   23 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHH
Confidence            689999999999999999876

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.84  E-value=0.013  Score=54.07  Aligned_cols=124  Identities=16%  Similarity=0.094  Sum_probs=65.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC--CCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC--
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY--PRDEIRVARDEISVARDRDEIRVAKAILESLKGSV--  272 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~--  272 (597)
                      ..+++|.|+.|.|||||++.++..  . ....+.+++.-..  ..+.. .....         .....++++.++...  
T Consensus        25 G~~~~l~G~nGsGKStLl~~i~G~--~-~~~~G~v~~~g~~~~~~~~~-~~~~~---------i~~~~q~l~~~gl~~~~   91 (180)
T cd03214          25 GEIVGILGPNGAGKSTLLKTLAGL--L-KPSSGEILLDGKDLASLSPK-ELARK---------IAYVPQALELLGLAHLA   91 (180)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--C-CCCCcEEEECCEECCcCCHH-HHHHH---------HhHHHHHHHHcCCHhHh
Confidence            469999999999999999999873  1 2233444432111  00110 00000         111111344433211  


Q ss_pred             ----CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CC-CcEEEEEccCC
Q 041007          273 ----SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SE-GSRILVTRSGG  333 (597)
Q Consensus       273 ----~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~-gs~IIvTtR~~  333 (597)
                          .....-+...-.+...+...+-++++|+--..-+....+.+...+... .. +..||++|.+.
T Consensus        92 ~~~~~~LS~G~~qrl~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tiii~sh~~  158 (180)
T cd03214          92 DRPFNELSGGERQRVLLARALAQEPPILLLDEPTSHLDIAHQIELLELLRRLARERGKTVVMVLHDL  158 (180)
T ss_pred             cCCcccCCHHHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence                111112222334555666788899999975444355556666655442 22 66788887765

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.

>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=96.83  E-value=0.0051  Score=57.09  Aligned_cols=39  Identities=23%  Similarity=0.245  Sum_probs=28.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          199 VIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      ++.|.|++|+|||+|+.++...  ....=..++|++.....
T Consensus         1 ~~li~G~~G~GKT~l~~~~~~~--~~~~g~~v~~~s~e~~~   39 (187)
T cd01124           1 STLLSGGPGTGKTTFALQFLYA--GLARGEPGLYVTLEESP   39 (187)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH--HHHCCCcEEEEECCCCH
Confidence            3689999999999999998774  22222457788776543

A related protein is found in archaea.

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

Probab=96.82  E-value=0.0038  Score=67.09  Aligned_cols=88  Identities=20%  Similarity=0.339  Sum_probs=55.1

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC
Q 041007          194 KPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       194 ~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      ++.-++..++|++|.||||||+-+++..    .| .++=|++|.....                ..+-..|...+...  
T Consensus       323 RP~kKilLL~GppGlGKTTLAHViAkqa----GY-sVvEINASDeRt~----------------~~v~~kI~~avq~~--  379 (877)
T KOG1969|consen  323 RPPKKILLLCGPPGLGKTTLAHVIAKQA----GY-SVVEINASDERTA----------------PMVKEKIENAVQNH--  379 (877)
T ss_pred             CCccceEEeecCCCCChhHHHHHHHHhc----Cc-eEEEecccccccH----------------HHHHHHHHHHHhhc--
Confidence            5677899999999999999999998842    22 2445666665554                33333333322211  


Q ss_pred             chhhHHHHHHHHHHHh--cCceEEEEEecccCCCCcchHHHHHHhhc
Q 041007          274 SQVEMETVLQYINEFV--QGKKVLLVLDDLWWNAYPRYWEQLMYSLK  318 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L--~~kr~LLVLDdv~~~~~~~~~~~l~~~l~  318 (597)
                                   ..+  .+++..||+|.++-.. ....+.+...+.
T Consensus       380 -------------s~l~adsrP~CLViDEIDGa~-~~~Vdvilslv~  412 (877)
T KOG1969|consen  380 -------------SVLDADSRPVCLVIDEIDGAP-RAAVDVILSLVK  412 (877)
T ss_pred             -------------cccccCCCcceEEEecccCCc-HHHHHHHHHHHH
Confidence                         112  2678899999996544 344555555553

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.82  E-value=0.0099  Score=60.82  Aligned_cols=105  Identities=13%  Similarity=0.109  Sum_probs=54.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      ...+++++|+.|+||||++..+......+.....+..++.... ..              +..+.+....+.++.+....
T Consensus       136 ~g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~-R~--------------ga~EqL~~~a~~~gv~~~~~  200 (374)
T PRK14722        136 RGGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSY-RI--------------GGHEQLRIFGKILGVPVHAV  200 (374)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccc-cc--------------cHHHHHHHHHHHcCCceEec
Confidence            3579999999999999999999873222222234555553221 11              01444555555555443222


Q ss_pred             hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhh
Q 041007          276 VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSL  317 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l  317 (597)
                      .+...+...+.+ +.++ -++++|..-.......+......+
T Consensus       201 ~~~~~l~~~l~~-l~~~-DlVLIDTaG~~~~d~~l~e~La~L  240 (374)
T PRK14722        201 KDGGDLQLALAE-LRNK-HMVLIDTIGMSQRDRTVSDQIAML  240 (374)
T ss_pred             CCcccHHHHHHH-hcCC-CEEEEcCCCCCcccHHHHHHHHHH
Confidence            222223333332 3444 566699885443222333344444

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

Probab=96.80  E-value=0.013  Score=63.03  Aligned_cols=67  Identities=19%  Similarity=0.313  Sum_probs=46.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ..-+|.++-++++.+.+.-..-.    ++.+.++++.+||+|||||++|+.++.  .....|   +-+++++-.+.
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLr----gs~qGkIlCf~GPPGVGKTSI~kSIA~--ALnRkF---fRfSvGG~tDv  477 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLR----GSVQGKILCFVGPPGVGKTSIAKSIAR--ALNRKF---FRFSVGGMTDV  477 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhc----ccCCCcEEEEeCCCCCCcccHHHHHHH--HhCCce---EEEeccccccH
Confidence            45679999999999988522110    134678999999999999999999988  444444   22444444443

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=96.79  E-value=0.056  Score=55.06  Aligned_cols=42  Identities=19%  Similarity=0.300  Sum_probs=32.4

Q ss_pred             hhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          172 NAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       172 ~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.-.+.|.+.+.....       ..+.+|+|.|.=|+|||++.+.+.+.
T Consensus         2 ~~~a~~la~~I~~~~~-------~~~~~IgL~G~WGsGKSs~l~~l~~~   43 (325)
T PF07693_consen    2 KPYAKALAEIIKNPDS-------DDPFVIGLYGEWGSGKSSFLNMLKEE   43 (325)
T ss_pred             hHHHHHHHHHHhccCC-------CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3445667777775431       35789999999999999999999874

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A

Probab=96.79  E-value=0.001  Score=56.97  Aligned_cols=21  Identities=43%  Similarity=0.673  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|+|.|++|+||||+|+.+..
T Consensus         1 vI~I~G~~gsGKST~a~~La~   21 (121)
T PF13207_consen    1 VIIISGPPGSGKSTLAKELAE   21 (121)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

...

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=96.78  E-value=0.007  Score=57.71  Aligned_cols=223  Identities=13%  Similarity=0.128  Sum_probs=116.6

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChh----hhccCCeeEEEEecCCCchhh
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSD----VKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~----~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      ..++++....|.....          ....+-..++||+|.||-|.+..+.+..-    .+-.-+..-|.+-+...-...
T Consensus        15 l~~~~e~~~~Lksl~~----------~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklEis   84 (351)
T KOG2035|consen   15 LIYHEELANLLKSLSS----------TGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLEIS   84 (351)
T ss_pred             cccHHHHHHHHHHhcc----------cCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEEEE
Confidence            5566666666666554          23578899999999999998877766411    111233445554443310000


Q ss_pred             h----hhhhhhhcc-cchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceE-EEEEecccCCCCcchHHHHHHhh
Q 041007          244 V----ARDEISVAR-DRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKV-LLVLDDLWWNAYPRYWEQLMYSL  317 (597)
Q Consensus       244 ~----~~~~~~~~~-~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~-LLVLDdv~~~~~~~~~~~l~~~l  317 (597)
                      .    +.-++..+. .....-+.++++.++....+-..            -..+.| ++|+-.++... .+.-..+....
T Consensus        85 tvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~------------~~qr~fKvvvi~ead~LT-~dAQ~aLRRTM  151 (351)
T KOG2035|consen   85 TVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIET------------QGQRPFKVVVINEADELT-RDAQHALRRTM  151 (351)
T ss_pred             EecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhh------------ccccceEEEEEechHhhh-HHHHHHHHHHH
Confidence            0    000000000 00113444555554433211100            012344 55666664433 44445566666


Q ss_pred             cCCCCCcEEEEEccCCCCCCCcccccccccCccccce--eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          318 KSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME--IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       318 ~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~--~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      ..-.+.+|+|+..-+..+.-          ..-+..+  +.+...+++|....++..+-..+-..  +  .+++.+|+++
T Consensus       152 EkYs~~~RlIl~cns~SriI----------epIrSRCl~iRvpaps~eeI~~vl~~v~~kE~l~l--p--~~~l~rIa~k  217 (351)
T KOG2035|consen  152 EKYSSNCRLILVCNSTSRII----------EPIRSRCLFIRVPAPSDEEITSVLSKVLKKEGLQL--P--KELLKRIAEK  217 (351)
T ss_pred             HHHhcCceEEEEecCcccch----------hHHhhheeEEeCCCCCHHHHHHHHHHHHHHhcccC--c--HHHHHHHHHH
Confidence            55567788877543321000          1111122  89999999999999998875443322  1  6789999999


Q ss_pred             cCCchHHHHHHHhhhccC---------C-CHHHHHHHHhhhc
Q 041007          396 CKGLPFAVKILGSLLRFK---------T-SIKEWQSVLDSEI  427 (597)
Q Consensus       396 ~~GlPLai~~~~~~l~~~---------~-~~~~w~~~l~~~~  427 (597)
                      ++|+---.-.+-..++-+         . ..-+|.-.+.+..
T Consensus       218 S~~nLRrAllmlE~~~~~n~~~~a~~~~i~~~dWe~~i~e~a  259 (351)
T KOG2035|consen  218 SNRNLRRALLMLEAVRVNNEPFTANSQVIPKPDWEIYIQEIA  259 (351)
T ss_pred             hcccHHHHHHHHHHHHhccccccccCCCCCCccHHHHHHHHH
Confidence            998654333332222211         0 1346877776543

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.77  E-value=0.017  Score=55.94  Aligned_cols=43  Identities=21%  Similarity=0.275  Sum_probs=32.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      +...++.|.|++|+|||++|.++...  .-..-..++|++.....
T Consensus        19 ~~gs~~lI~G~pGsGKT~la~~~l~~--~~~~ge~~lyvs~ee~~   61 (237)
T TIGR03877        19 PERNVVLLSGGPGTGKSIFSQQFLWN--GLQMGEPGIYVALEEHP   61 (237)
T ss_pred             cCCeEEEEEcCCCCCHHHHHHHHHHH--HHHcCCcEEEEEeeCCH
Confidence            35689999999999999999998663  22334567888876544

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.

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

Probab=96.76  E-value=0.0082  Score=58.53  Aligned_cols=44  Identities=18%  Similarity=0.339  Sum_probs=32.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCe-eEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDK-RIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+|++.+++  ..+.+|.. ++++-+.+....
T Consensus        68 ~GQr~~If~~~G~GKTtLa~~i~~--~i~~~~~~~~V~~~iGer~~E  112 (274)
T cd01133          68 KGGKIGLFGGAGVGKTVLIMELIN--NIAKAHGGYSVFAGVGERTRE  112 (274)
T ss_pred             cCCEEEEecCCCCChhHHHHHHHH--HHHhcCCCEEEEEEeccCcHH
Confidence            456899999999999999999999  45555644 555555555443

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.

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.76  E-value=0.005  Score=56.45  Aligned_cols=125  Identities=18%  Similarity=0.147  Sum_probs=63.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhh-hcccc---hHHHHHHHHHHhccCCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEIS-VARDR---DEIRVAKAILESLKGSV  272 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~-~~~~~---~~~~~~~~il~~l~~~~  272 (597)
                      ..+++|.|+.|.|||||++.++...   ....+.+++.-.............+. +.+..   ....+...+.       
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~~tv~~~~~-------   95 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLL---KPDSGEIKVLGKDIKKEPEEVKRRIGYLPEEPSLYENLTVRENLK-------   95 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC---CCCCeEEEECCEEcccchHhhhccEEEEecCCccccCCcHHHHhh-------
Confidence            4689999999999999999998732   12234444321100000000000000 00000   0001111111       


Q ss_pred             CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          273 SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       273 ~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                        ...-+...-.+...+..++-++++|+--..-+......+...+... ..|..||++|.+.
T Consensus        96 --LS~G~~qrv~laral~~~p~illlDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~th~~  155 (173)
T cd03230          96 --LSGGMKQRLALAQALLHDPELLILDEPTSGLDPESRREFWELLRELKKEGKTILLSSHIL  155 (173)
T ss_pred             --cCHHHHHHHHHHHHHHcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHCCCEEEEECCCH
Confidence              1111222334566667788899999975544455555565555442 2367788888765

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.

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=96.75  E-value=0.0053  Score=56.25  Aligned_cols=126  Identities=17%  Similarity=0.134  Sum_probs=60.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch-hhhhhhhhh-hcccchHHHHHHHHHHhccCCCCc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE-IRVARDEIS-VARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ..+++|.|+.|.|||||.+.++.-.   ....+.+++.-...... .......+. +.+.....  ...+.+.+      
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~q~~~~~--~~tv~~~l------   96 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGLL---RPTSGRVRLDGADISQWDPNELGDHVGYLPQDDELF--SGSIAENI------   96 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcc---CCCCCeEEECCEEcccCCHHHHHhheEEECCCCccc--cCcHHHHC------
Confidence            4699999999999999999998731   22233333321100000 000000000 00000000  00111111      


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      ...-+...-.+...+..++-+++||+--..-+......+...+... ..|..||++|.+.
T Consensus        97 LS~G~~qrv~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~  156 (173)
T cd03246          97 LSGGQRQRLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAALKAAGATRIVIAHRP  156 (173)
T ss_pred             cCHHHHHHHHHHHHHhcCCCEEEEECCccccCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            1111222233455555677799999975544444555555555432 3467788887765

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

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.75  E-value=0.0054  Score=62.37  Aligned_cols=46  Identities=17%  Similarity=0.263  Sum_probs=38.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|+...+.++.+.+.....        ...-|.|+|..|+||+++|+.++.
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~--------~~~pVlI~GE~GtGK~~lA~~iH~   51 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAP--------LDKPVLIIGERGTGKELIASRLHY   51 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhC--------CCCCEEEECCCCCcHHHHHHHHHH
Confidence            4589999999999988876553        345788999999999999999976

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=96.74  E-value=0.0044  Score=58.00  Aligned_cols=23  Identities=30%  Similarity=0.398  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -+++.|.|++|+|||+++..+..
T Consensus        18 ~~~~~l~G~aGtGKT~~l~~~~~   40 (196)
T PF13604_consen   18 DRVSVLQGPAGTGKTTLLKALAE   40 (196)
T ss_dssp             CSEEEEEESTTSTHHHHHHHHHH
T ss_pred             CeEEEEEECCCCCHHHHHHHHHH
Confidence            36899999999999999999876

>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=96.73  E-value=0.021  Score=51.97  Aligned_cols=116  Identities=15%  Similarity=-0.003  Sum_probs=60.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE-------ecCCCchhhhhhhhhhhcccchHHHHHHHHHHhc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS-------ASYPRDEIRVARDEISVARDRDEIRVAKAILESL  268 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l  268 (597)
                      ...+++|.|+.|.|||||++.++.-..   ...+.+++.       +.+....           ..   ..+...+.-. 
T Consensus        26 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~---~~~G~i~~~~~~~i~~~~q~~~~-----------~~---~tv~~nl~~~-   87 (166)
T cd03223          26 PGDRLLITGPSGTGKSSLFRALAGLWP---WGSGRIGMPEGEDLLFLPQRPYL-----------PL---GTLREQLIYP-   87 (166)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCC---CCCceEEECCCceEEEECCCCcc-----------cc---ccHHHHhhcc-
Confidence            346999999999999999999987421   112222221       1111110           00   1222222110 


Q ss_pred             cCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          269 KGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       269 ~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                        .......-+...-.+...+-.++-++++|+--..-+......+...+...  +..||++|.+.
T Consensus        88 --~~~~LS~G~~~rv~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~--~~tiiivsh~~  148 (166)
T cd03223          88 --WDDVLSGGEQQRLAFARLLLHKPKFVFLDEATSALDEESEDRLYQLLKEL--GITVISVGHRP  148 (166)
T ss_pred             --CCCCCCHHHHHHHHHHHHHHcCCCEEEEECCccccCHHHHHHHHHHHHHh--CCEEEEEeCCh
Confidence              11111222223334555556677888999865443344555555555443  35677777665

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

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

Probab=96.72  E-value=0.012  Score=61.21  Aligned_cols=53  Identities=26%  Similarity=0.372  Sum_probs=36.4

Q ss_pred             ccccch---hhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRN---AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~---~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.-|-|   .|++++++.|..... -..-+..-++-|.++|++|.|||-||++++-.
T Consensus       305 dVkG~DEAK~ELeEiVefLkdP~k-ftrLGGKLPKGVLLvGPPGTGKTlLARAvAGE  360 (752)
T KOG0734|consen  305 DVKGVDEAKQELEEIVEFLKDPTK-FTRLGGKLPKGVLLVGPPGTGKTLLARAVAGE  360 (752)
T ss_pred             cccChHHHHHHHHHHHHHhcCcHH-hhhccCcCCCceEEeCCCCCchhHHHHHhhcc
Confidence            345665   466777788874431 11111234677999999999999999999884

>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1)

Probab=96.72  E-value=0.028  Score=53.17  Aligned_cols=50  Identities=14%  Similarity=0.025  Sum_probs=32.2

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+-...-+....+.+...+.....+..+|++|.+.
T Consensus       135 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~th~~  184 (207)
T cd03369         135 CLARALLKRPRVLVLDEATASIDYATDALIQKTIREEFTNSTILTIAHRL  184 (207)
T ss_pred             HHHHHHhhCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEeCCH
Confidence            34555556778899999765544555666666665433467777777665

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=96.72  E-value=0.0053  Score=61.51  Aligned_cols=85  Identities=24%  Similarity=0.296  Sum_probs=52.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC--
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSV--  272 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~--  272 (597)
                      +..+++.|+|++|+||||||.+++..  ....-..++|++....++..                     .++.++...  
T Consensus        53 p~G~iteI~G~~GsGKTtLaL~~~~~--~~~~g~~v~yId~E~~~~~~---------------------~a~~lGvd~~~  109 (321)
T TIGR02012        53 PRGRIIEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPV---------------------YARKLGVDIDN  109 (321)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEcccchhHHH---------------------HHHHcCCCHHH
Confidence            35679999999999999999998773  33334557788776554431                     122222211  


Q ss_pred             ---CchhhHHHHHHHHHHHhc-CceEEEEEeccc
Q 041007          273 ---SSQVEMETVLQYINEFVQ-GKKVLLVLDDLW  302 (597)
Q Consensus       273 ---~~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~  302 (597)
                         ..+.+.++....+....+ +..-++|+|.+-
T Consensus       110 l~v~~p~~~eq~l~~~~~li~~~~~~lIVIDSv~  143 (321)
T TIGR02012       110 LLVSQPDTGEQALEIAETLVRSGAVDIIVVDSVA  143 (321)
T ss_pred             eEEecCCCHHHHHHHHHHHhhccCCcEEEEcchh
Confidence               112234445555555443 456799999974

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.

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

Probab=96.71  E-value=0.014  Score=57.91  Aligned_cols=41  Identities=34%  Similarity=0.413  Sum_probs=32.1

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHh
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      +-+|..+..--.++|..          +....|.+.|.+|.|||.||....
T Consensus       226 i~prn~eQ~~ALdlLld----------~dI~lV~L~G~AGtGKTlLALaAg  266 (436)
T COG1875         226 IRPRNAEQRVALDLLLD----------DDIDLVSLGGKAGTGKTLLALAAG  266 (436)
T ss_pred             cCcccHHHHHHHHHhcC----------CCCCeEEeeccCCccHhHHHHHHH
Confidence            44677777767777773          357899999999999999987654

>PRK06696 uridine kinase; Validated

Probab=96.71  E-value=0.0027  Score=60.85  Aligned_cols=44  Identities=16%  Similarity=0.148  Sum_probs=35.4

Q ss_pred             cchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       170 GR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|.+-+++|.+.+....       .+.+.+|+|.|.+|+||||||+.+...
T Consensus         2 ~~~~~~~~la~~~~~~~-------~~~~~iI~I~G~sgsGKSTlA~~L~~~   45 (223)
T PRK06696          2 SRKQLIKELAEHILTLN-------LTRPLRVAIDGITASGKTTFADELAEE   45 (223)
T ss_pred             cHHHHHHHHHHHHHHhC-------CCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            36777888888886533       236789999999999999999999873

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=96.71  E-value=0.0087  Score=67.49  Aligned_cols=47  Identities=26%  Similarity=0.386  Sum_probs=38.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|+...+.++.+.+.....        ....|.|+|..|+|||++|+.+++.
T Consensus       376 ~~liG~S~~~~~~~~~~~~~a~--------~~~pVLI~GE~GTGK~~lA~~ih~~  422 (686)
T PRK15429        376 GEIIGRSEAMYSVLKQVEMVAQ--------SDSTVLILGETGTGKELIARAIHNL  422 (686)
T ss_pred             cceeecCHHHHHHHHHHHHHhC--------CCCCEEEECCCCcCHHHHHHHHHHh
Confidence            3589999999998877775443        3457899999999999999999874

>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=96.71  E-value=0.011  Score=52.38  Aligned_cols=102  Identities=15%  Similarity=0.086  Sum_probs=57.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ..+++|.|+.|.|||||++.+....   ....+.+|+.-......         .      .+               ..
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~---~~~~G~i~~~~~~~i~~---------~------~~---------------lS   72 (144)
T cd03221          26 GDRIGLVGRNGAGKSTLLKLIAGEL---EPDEGIVTWGSTVKIGY---------F------EQ---------------LS   72 (144)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCCC---CCCceEEEECCeEEEEE---------E------cc---------------CC
Confidence            4699999999999999999998742   22334444421100000         0      00               00


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .-+...-.+...+..++-++++|+--..-+......+...+...  +..||++|.+.
T Consensus        73 ~G~~~rv~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~--~~til~~th~~  127 (144)
T cd03221          73 GGEKMRLALAKLLLENPNLLLLDEPTNHLDLESIEALEEALKEY--PGTVILVSHDR  127 (144)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHc--CCEEEEEECCH
Confidence            11111223445555677899999975444455556665555443  24677777654

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.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.71  E-value=0.0066  Score=61.71  Aligned_cols=45  Identities=18%  Similarity=0.262  Sum_probs=36.1

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++|+...++++.+.+.....        ....|.|+|..|+||+++|+.+++.
T Consensus         1 liG~S~~m~~~~~~~~~~a~--------~~~pVLI~GE~GtGK~~lAr~iH~~   45 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAP--------LDRPVLIIGERGTGKELIAARLHYL   45 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhC--------CCCCEEEECCCCChHHHHHHHHHHh
Confidence            46888888888888776543        3456899999999999999999763

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

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

Probab=96.69  E-value=0.019  Score=61.68  Aligned_cols=42  Identities=31%  Similarity=0.272  Sum_probs=31.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      .....|.|.|+.|+|||+||+++++... +.....+..++++.
T Consensus       429 ~~~~~Ill~G~~GsGKT~L~kal~~~~~-k~~~~hv~~v~Cs~  470 (952)
T KOG0735|consen  429 FRHGNILLNGPKGSGKTNLVKALFDYYS-KDLIAHVEIVSCST  470 (952)
T ss_pred             cccccEEEeCCCCCCHhHHHHHHHHHhc-cccceEEEEEechh
Confidence            3567899999999999999999998533 44445566676654

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=96.67  E-value=0.021  Score=53.95  Aligned_cols=76  Identities=14%  Similarity=0.090  Sum_probs=43.7

Q ss_pred             HHHHHHHHHhccCCC------C-chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEE
Q 041007          258 IRVAKAILESLKGSV------S-SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILV  328 (597)
Q Consensus       258 ~~~~~~il~~l~~~~------~-~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIv  328 (597)
                      ......+++.++...      + ....-++-.-.+.+.|...+-+|+.|+---.-+...-+.+...+...  ..|..||+
T Consensus       119 ~~~~~~l~~~lgl~~~~~~~~p~eLSGGqqQRVAIARAL~~~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~  198 (226)
T COG1136         119 KRAAEELLEVLGLEDRLLKKKPSELSGGQQQRVAIARALINNPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIM  198 (226)
T ss_pred             HHHHHHHHHhcCChhhhccCCchhcCHHHHHHHHHHHHHhcCCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEE
Confidence            445555666655431      1 12222344446777788889999999742111133444555555442  45778888


Q ss_pred             EccCC
Q 041007          329 TRSGG  333 (597)
Q Consensus       329 TtR~~  333 (597)
                      .|.+.
T Consensus       199 VTHd~  203 (226)
T COG1136         199 VTHDP  203 (226)
T ss_pred             EcCCH
Confidence            88887

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

Probab=96.67  E-value=0.029  Score=53.11  Aligned_cols=181  Identities=15%  Similarity=0.151  Sum_probs=93.9

Q ss_pred             CccccchhhHH---HHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQ---KILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~---~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ++.||.++...   -|.+.|.....    =+.-.++.|..+|++|.|||.+|+.+.+.  .+..|     +.+..     
T Consensus       121 ddViGqEeAK~kcrli~~yLenPe~----Fg~WAPknVLFyGppGTGKTm~Akalane--~kvp~-----l~vka-----  184 (368)
T COG1223         121 DDVIGQEEAKRKCRLIMEYLENPER----FGDWAPKNVLFYGPPGTGKTMMAKALANE--AKVPL-----LLVKA-----  184 (368)
T ss_pred             hhhhchHHHHHHHHHHHHHhhChHH----hcccCcceeEEECCCCccHHHHHHHHhcc--cCCce-----EEech-----
Confidence            45789887765   34566653321    01235789999999999999999999994  33222     21110     


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCC-----------CCcchHH
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWN-----------AYPRYWE  311 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~-----------~~~~~~~  311 (597)
                                     .++.   -+.+|.      ...++.+.....-+..+|+++||.+.-.           +..+..+
T Consensus       185 ---------------t~li---GehVGd------gar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVN  240 (368)
T COG1223         185 ---------------TELI---GEHVGD------GARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVN  240 (368)
T ss_pred             ---------------HHHH---HHHhhh------HHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHH
Confidence                           1111   111111      1122222223333456899999987421           1112333


Q ss_pred             HHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCccccce--eecCCCChHHHHHHHHHHhccCCCCCCccchHH
Q 041007          312 QLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME--IGLGELSEEECRSLFRQIAFHGRSSDYREKFEP  387 (597)
Q Consensus       312 ~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~--~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~  387 (597)
                      .++..+..  .+.|...|-.|... ...+.        .+.+...  |+..--+++|-.+++...+-.-.-+     +..
T Consensus       241 ALLTelDgi~eneGVvtIaaTN~p-~~LD~--------aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plp-----v~~  306 (368)
T COG1223         241 ALLTELDGIKENEGVVTIAATNRP-ELLDP--------AIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLP-----VDA  306 (368)
T ss_pred             HHHHhccCcccCCceEEEeecCCh-hhcCH--------HHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCc-----ccc
Confidence            34444433  23454444444433 11110        1111111  7777888888888888877422211     111


Q ss_pred             HHHHHHHhcCCch
Q 041007          388 IGRRVVGKCKGLP  400 (597)
Q Consensus       388 ~~~~I~~~~~GlP  400 (597)
                      -.+.++++++|..
T Consensus       307 ~~~~~~~~t~g~S  319 (368)
T COG1223         307 DLRYLAAKTKGMS  319 (368)
T ss_pred             CHHHHHHHhCCCC
Confidence            2466777777653

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=96.65  E-value=0.011  Score=59.33  Aligned_cols=46  Identities=13%  Similarity=0.201  Sum_probs=33.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhh----ccCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVK----ANFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~----~~F~~~~wv~~~~~~~~  241 (597)
                      ...++-|+|++|+|||+|+.+++-.....    ..=..++|++....+..
T Consensus        95 ~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~~f~~  144 (313)
T TIGR02238        95 SMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRP  144 (313)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCCCCCH
Confidence            56789999999999999999876421221    11236899998887765

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=96.65  E-value=0.0098  Score=65.05  Aligned_cols=49  Identities=12%  Similarity=0.243  Sum_probs=40.4

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|....++++.+.+.....        ....|.|+|..|+|||++|+.+++.
T Consensus       194 ~~~~liG~s~~~~~~~~~~~~~a~--------~~~pvli~Ge~GtGK~~lA~~ih~~  242 (534)
T TIGR01817       194 KEDGIIGKSPAMRQVVDQARVVAR--------SNSTVLLRGESGTGKELIAKAIHYL  242 (534)
T ss_pred             ccCceEECCHHHHHHHHHHHHHhC--------cCCCEEEECCCCccHHHHHHHHHHh
Confidence            345789999999999988875543        3456789999999999999999874

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.64  E-value=0.022  Score=58.12  Aligned_cols=25  Identities=24%  Similarity=0.389  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+++|+|+|++|+||||++..++..
T Consensus       240 ~~~vI~LVGptGvGKTTTiaKLA~~  264 (436)
T PRK11889        240 EVQTIALIGPTGVGKTTTLAKMAWQ  264 (436)
T ss_pred             CCcEEEEECCCCCcHHHHHHHHHHH
Confidence            4589999999999999999999863

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=96.64  E-value=0.014  Score=56.05  Aligned_cols=40  Identities=23%  Similarity=0.280  Sum_probs=27.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ...++.|.|++|+||||||.+++.. -.+.. ..+++++...
T Consensus        23 ~g~~~~i~G~~G~GKTtl~~~~~~~-~~~~g-~~~~yi~~e~   62 (230)
T PRK08533         23 AGSLILIEGDESTGKSILSQRLAYG-FLQNG-YSVSYVSTQL   62 (230)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH-HHhCC-CcEEEEeCCC
Confidence            4569999999999999998777653 22222 3456666433

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

Probab=96.64  E-value=0.0086  Score=54.26  Aligned_cols=116  Identities=16%  Similarity=0.094  Sum_probs=61.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ..+++|.|+.|.|||||.+.++..   .....+.+++.-......              +......   ..++.. .+..
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~i~G~---~~~~~G~v~~~g~~~~~~--------------~~~~~~~---~~i~~~-~qLS   84 (163)
T cd03216          26 GEVHALLGENGAGKSTLMKILSGL---YKPDSGEILVDGKEVSFA--------------SPRDARR---AGIAMV-YQLS   84 (163)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC---CCCCCeEEEECCEECCcC--------------CHHHHHh---cCeEEE-EecC
Confidence            469999999999999999999873   123344444432110000              0000000   001100 0011


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .-+...-.+...+-.++-++++|+--+.-+......+...+... ..+..||++|.+.
T Consensus        85 ~G~~qrl~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~  142 (163)
T cd03216          85 VGERQMVEIARALARNARLLILDEPTAALTPAEVERLFKVIRRLRAQGVAVIFISHRL  142 (163)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            11222333555556678899999975544455556666655432 3466788887765

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.

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

Probab=96.63  E-value=0.0059  Score=61.18  Aligned_cols=45  Identities=27%  Similarity=0.292  Sum_probs=34.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      +..+++-|+|++|+||||||.+++..  ....-..++|++....++.
T Consensus        53 p~G~iteI~Gp~GsGKTtLal~~~~~--~~~~g~~~vyId~E~~~~~   97 (325)
T cd00983          53 PKGRIIEIYGPESSGKTTLALHAIAE--AQKLGGTVAFIDAEHALDP   97 (325)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCCEEEECccccHHH
Confidence            35679999999999999999998763  3334456788887665554

RecA couples ATP hydrolysis to DNA strand exchange.

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

Probab=96.63  E-value=0.015  Score=58.86  Aligned_cols=84  Identities=25%  Similarity=0.304  Sum_probs=54.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC--
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS--  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~--  273 (597)
                      ...+|.|-|.+|||||||..+++.  +....- .+++|+-.+.                   ....+--.+.|+....  
T Consensus        92 ~Gs~iLIgGdPGIGKSTLLLQva~--~lA~~~-~vLYVsGEES-------------------~~QiklRA~RL~~~~~~l  149 (456)
T COG1066          92 PGSVILIGGDPGIGKSTLLLQVAA--RLAKRG-KVLYVSGEES-------------------LQQIKLRADRLGLPTNNL  149 (456)
T ss_pred             cccEEEEccCCCCCHHHHHHHHHH--HHHhcC-cEEEEeCCcC-------------------HHHHHHHHHHhCCCccce
Confidence            457999999999999999999988  444333 6777765433                   2223333445554322  


Q ss_pred             ---chhhHHHHHHHHHHHhcCceEEEEEecccCC
Q 041007          274 ---SQVEMETVLQYINEFVQGKKVLLVLDDLWWN  304 (597)
Q Consensus       274 ---~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~  304 (597)
                         ...+.+.+...+.+   .++-++|+|-++..
T Consensus       150 ~l~aEt~~e~I~~~l~~---~~p~lvVIDSIQT~  180 (456)
T COG1066         150 YLLAETNLEDIIAELEQ---EKPDLVVIDSIQTL  180 (456)
T ss_pred             EEehhcCHHHHHHHHHh---cCCCEEEEecccee
Confidence               13455555555554   67899999998643

>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=96.62  E-value=0.01  Score=55.38  Aligned_cols=39  Identities=28%  Similarity=0.320  Sum_probs=26.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      +++|.++|+.|+||||.+..++..  .+.+-..+..++...
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~--~~~~~~~v~lis~D~   39 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAAR--LKLKGKKVALISADT   39 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHH--HHHTT--EEEEEEST
T ss_pred             CEEEEEECCCCCchHhHHHHHHHH--HhhccccceeecCCC
Confidence            368999999999999888777763  333333466666543

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 ....

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=96.62  E-value=0.031  Score=53.67  Aligned_cols=137  Identities=15%  Similarity=0.141  Sum_probs=75.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChh-hhc----------cC---CeeEEEEecC--CCchhhhhhhhhhhcc-------
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSD-VKA----------NF---DKRIWVSASY--PRDEIRVARDEISVAR-------  253 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~-~~~----------~F---~~~~wv~~~~--~~~~~~~~~~~~~~~~-------  253 (597)
                      ...++|+||.|.|||||.+.+.--.. .++          .+   ..+.||+=..  +.+......+.+....       
T Consensus        30 G~~~~iiGPNGaGKSTLlK~iLGll~p~~G~i~~~g~~~~~~~~~~~IgYVPQ~~~~d~~fP~tV~d~V~~g~~~~~g~~  109 (254)
T COG1121          30 GEITALIGPNGAGKSTLLKAILGLLKPSSGEIKIFGKPVRKRRKRLRIGYVPQKSSVDRSFPITVKDVVLLGRYGKKGWF  109 (254)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCcCCcceEEEccccccccccCCeEEEcCcccccCCCCCcCHHHHHHccCccccccc
Confidence            47999999999999999999976211 000          01   2355554211  2222222222222211       


Q ss_pred             ---cchHHHHHHHHHHhccCCC------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCC
Q 041007          254 ---DRDEIRVAKAILESLKGSV------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEG  323 (597)
Q Consensus       254 ---~~~~~~~~~~il~~l~~~~------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~g  323 (597)
                         .....+...+.++.++...      .....-+.-.-.|.+.|..++=||+||.--..-+...-..+...+.. ...|
T Consensus       110 ~~~~~~d~~~v~~aL~~Vgm~~~~~r~i~~LSGGQ~QRV~lARAL~~~p~lllLDEP~~gvD~~~~~~i~~lL~~l~~eg  189 (254)
T COG1121         110 RRLNKKDKEKVDEALERVGMEDLRDRQIGELSGGQKQRVLLARALAQNPDLLLLDEPFTGVDVAGQKEIYDLLKELRQEG  189 (254)
T ss_pred             ccccHHHHHHHHHHHHHcCchhhhCCcccccCcHHHHHHHHHHHhccCCCEEEecCCcccCCHHHHHHHHHHHHHHHHCC
Confidence               0111355566666665421      11122233344577888899999999985433334444445555543 2338


Q ss_pred             cEEEEEccCC
Q 041007          324 SRILVTRSGG  333 (597)
Q Consensus       324 s~IIvTtR~~  333 (597)
                      ..||++|.+-
T Consensus       190 ~tIl~vtHDL  199 (254)
T COG1121         190 KTVLMVTHDL  199 (254)
T ss_pred             CEEEEEeCCc
Confidence            8999998876

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.62  E-value=0.02  Score=52.44  Aligned_cols=120  Identities=15%  Similarity=0.062  Sum_probs=59.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC---
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSV---  272 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~---  272 (597)
                      ...+++|.|+.|+|||||.+.+..+   .+   .+.|......+...    .....      .+  .+.+..++...   
T Consensus        20 ~G~~~~l~G~nG~GKSTLl~~il~~---~G---~v~~~~~~~~~~~~----~~~~~------~q--~~~l~~~~L~~~~~   81 (176)
T cd03238          20 LNVLVVVTGVSGSGKSTLVNEGLYA---SG---KARLISFLPKFSRN----KLIFI------DQ--LQFLIDVGLGYLTL   81 (176)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhhc---CC---cEEECCcccccccc----cEEEE------hH--HHHHHHcCCCcccc
Confidence            3569999999999999999988632   00   01111000000000    00000      00  23444444321   


Q ss_pred             ----CchhhHHHHHHHHHHHhcCc--eEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          273 ----SSQVEMETVLQYINEFVQGK--KVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       273 ----~~~~~~~~~~~~l~~~L~~k--r~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                          .....-+...-.+...+..+  +-+++||+--..-+....+.+...+... ..|..||++|.+.
T Consensus        82 ~~~~~~LSgGq~qrl~laral~~~~~p~llLlDEPt~~LD~~~~~~l~~~l~~~~~~g~tvIivSH~~  149 (176)
T cd03238          82 GQKLSTLSGGELQRVKLASELFSEPPGTLFILDEPSTGLHQQDINQLLEVIKGLIDLGNTVILIEHNL  149 (176)
T ss_pred             CCCcCcCCHHHHHHHHHHHHHhhCCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence                01111122223344455556  7788899875444344555555555432 2467788887765

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.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=96.58  E-value=0.0076  Score=59.87  Aligned_cols=25  Identities=28%  Similarity=0.373  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++++|+|++|+||||++..++..
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~  217 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAAR  217 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999998774

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

Probab=96.54  E-value=0.013  Score=57.28  Aligned_cols=92  Identities=23%  Similarity=0.236  Sum_probs=56.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCC-CC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGS-VS  273 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~-~~  273 (597)
                      +..+++=|+|+.|+||||||.+++-.  .+..-..++|++..+.++..+.             ..+....+..+... ..
T Consensus        58 ~~g~ItEiyG~~gsGKT~lal~~~~~--aq~~g~~a~fIDtE~~l~p~r~-------------~~l~~~~~d~l~v~~~~  122 (279)
T COG0468          58 PRGRITEIYGPESSGKTTLALQLVAN--AQKPGGKAAFIDTEHALDPERA-------------KQLGVDLLDNLLVSQPD  122 (279)
T ss_pred             ccceEEEEecCCCcchhhHHHHHHHH--hhcCCCeEEEEeCCCCCCHHHH-------------HHHHHhhhcceeEecCC
Confidence            46789999999999999999998763  4444447899998888876332             22222212222211 12


Q ss_pred             chhhHHHHHHHHHHHhcCceEEEEEecc
Q 041007          274 SQVEMETVLQYINEFVQGKKVLLVLDDL  301 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L~~kr~LLVLDdv  301 (597)
                      .......++..+......+--|+|+|.+
T Consensus       123 ~~e~q~~i~~~~~~~~~~~i~LvVVDSv  150 (279)
T COG0468         123 TGEQQLEIAEKLARSGAEKIDLLVVDSV  150 (279)
T ss_pred             CHHHHHHHHHHHHHhccCCCCEEEEecC
Confidence            2233334444444444444679999987

>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C

Probab=96.54  E-value=0.049  Score=52.04  Aligned_cols=50  Identities=14%  Similarity=0.121  Sum_probs=31.8

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+....-+......+...+.....+..||++|.+.
T Consensus       149 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~  198 (221)
T cd03244         149 CLARALLRKSKILVLDEATASVDPETDALIQKTIREAFKDCTVLTIAHRL  198 (221)
T ss_pred             HHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEeCCH
Confidence            34555556778999999765544555566666665433456777777665

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.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.53  E-value=0.011  Score=64.13  Aligned_cols=48  Identities=23%  Similarity=0.353  Sum_probs=40.7

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...++|+...++++.+.+.....        ....|.|+|..|+|||++|+.+++.
T Consensus       186 ~~~iig~s~~~~~~~~~i~~~a~--------~~~pVlI~Ge~GtGK~~~A~~ih~~  233 (509)
T PRK05022        186 EGEMIGQSPAMQQLKKEIEVVAA--------SDLNVLILGETGVGKELVARAIHAA  233 (509)
T ss_pred             CCceeecCHHHHHHHHHHHHHhC--------CCCcEEEECCCCccHHHHHHHHHHh
Confidence            45689999999999998886653        4567899999999999999999874

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

Probab=96.53  E-value=0.024  Score=60.60  Aligned_cols=59  Identities=20%  Similarity=0.264  Sum_probs=37.4

Q ss_pred             ccccchhhHHHHHHHhhCCCCCC---cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDE---ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF  227 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~---~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F  227 (597)
                      .+=|-++-+.+|.+.+.-...+-   ..=+-..++-|.++||||+|||++|+.+++  ....+|
T Consensus       435 dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAn--e~~~nF  496 (693)
T KOG0730|consen  435 DIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALAN--EAGMNF  496 (693)
T ss_pred             hccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhh--hhcCCe
Confidence            34457766667665554221100   000013567899999999999999999999  455555

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=96.52  E-value=0.027  Score=53.37  Aligned_cols=50  Identities=18%  Similarity=0.159  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-++++|+--+.-+......+...+... ..+..||++|.+.
T Consensus       138 ~la~al~~~p~~lllDEP~~~LD~~~~~~~~~~l~~~~~~~~tii~~sH~~  188 (210)
T cd03269         138 QFIAAVIHDPELLILDEPFSGLDPVNVELLKDVIRELARAGKTVILSTHQM  188 (210)
T ss_pred             HHHHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEECCCH
Confidence            3555556677899999975544455555555555432 3467788888765

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.

>PRK05973 replicative DNA helicase; Provisional

Probab=96.52  E-value=0.013  Score=56.16  Aligned_cols=42  Identities=14%  Similarity=0.201  Sum_probs=30.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      ...++.|.|.+|+|||+++.++...  ....-..+++++.....
T Consensus        63 ~Gsl~LIaG~PG~GKT~lalqfa~~--~a~~Ge~vlyfSlEes~  104 (237)
T PRK05973         63 PGDLVLLGARPGHGKTLLGLELAVE--AMKSGRTGVFFTLEYTE  104 (237)
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEEEeCCH
Confidence            4569999999999999999998764  22223456677766543

>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=96.50  E-value=0.0069  Score=55.81  Aligned_cols=50  Identities=16%  Similarity=0.090  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CC-CcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SE-GSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~-gs~IIvTtR~~  333 (597)
                      .+...+..++=++++|+--..-+......+...+... .. +..||++|.+.
T Consensus       110 ~la~al~~~p~llilDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~  161 (178)
T cd03229         110 ALARALAMDPDVLLLDEPTSALDPITRREVRALLKSLQAQLGITVVLVTHDL  161 (178)
T ss_pred             HHHHHHHCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3555566678899999875444455556666555442 22 56777777665

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.

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.50  E-value=0.0036  Score=59.38  Aligned_cols=23  Identities=26%  Similarity=0.316  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+++.|+|+.|.|||||.+.+..
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            47899999999999999999874

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

>PRK09354 recA recombinase A; Provisional

Probab=96.50  E-value=0.0093  Score=60.28  Aligned_cols=85  Identities=24%  Similarity=0.305  Sum_probs=53.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC--
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSV--  272 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~--  272 (597)
                      +..+++-|+|++|+|||||+.+++..  ....-..++|++....++..                     .++.++.+.  
T Consensus        58 p~G~IteI~G~~GsGKTtLal~~~~~--~~~~G~~~~yId~E~s~~~~---------------------~a~~lGvdld~  114 (349)
T PRK09354         58 PRGRIVEIYGPESSGKTTLALHAIAE--AQKAGGTAAFIDAEHALDPV---------------------YAKKLGVDIDN  114 (349)
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEECCccchHHH---------------------HHHHcCCCHHH
Confidence            35679999999999999999998873  33344567899877665541                     122222210  


Q ss_pred             ---CchhhHHHHHHHHHHHhc-CceEEEEEeccc
Q 041007          273 ---SSQVEMETVLQYINEFVQ-GKKVLLVLDDLW  302 (597)
Q Consensus       273 ---~~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~  302 (597)
                         ..+.+.++....+...++ +..-+||+|.+-
T Consensus       115 lli~qp~~~Eq~l~i~~~li~s~~~~lIVIDSva  148 (349)
T PRK09354        115 LLVSQPDTGEQALEIADTLVRSGAVDLIVVDSVA  148 (349)
T ss_pred             eEEecCCCHHHHHHHHHHHhhcCCCCEEEEeChh
Confidence               112234444555555544 456799999974

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.50  E-value=0.0054  Score=57.54  Aligned_cols=108  Identities=9%  Similarity=0.151  Sum_probs=55.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhh
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVE  277 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~  277 (597)
                      .+|.|+|+.|+||||++..+...  ...+....++.- ..+....  .            .. ...++.+-..    ..+
T Consensus         2 GlilI~GptGSGKTTll~~ll~~--~~~~~~~~i~t~-e~~~E~~--~------------~~-~~~~i~q~~v----g~~   59 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDY--INKNKTHHILTI-EDPIEFV--H------------ES-KRSLINQREV----GLD   59 (198)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--hhhcCCcEEEEE-cCCcccc--c------------cC-ccceeeeccc----CCC
Confidence            47999999999999999987763  333333344332 2211110  0            00 0001100000    001


Q ss_pred             HHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          278 METVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       278 ~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .....+.++..+...+=++++|++.+..   ........   ...|..++.|+...
T Consensus        60 ~~~~~~~i~~aLr~~pd~ii~gEird~e---~~~~~l~~---a~~G~~v~~t~Ha~  109 (198)
T cd01131          60 TLSFENALKAALRQDPDVILVGEMRDLE---TIRLALTA---AETGHLVMSTLHTN  109 (198)
T ss_pred             ccCHHHHHHHHhcCCcCEEEEcCCCCHH---HHHHHHHH---HHcCCEEEEEecCC
Confidence            1234556777777778899999994332   33333322   23455677776544

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.

>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds

Probab=96.49  E-value=0.029  Score=53.59  Aligned_cols=50  Identities=16%  Similarity=0.127  Sum_probs=32.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+.-..-+......+...+.....+..||++|.+.
T Consensus       143 ~la~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~  192 (220)
T cd03263         143 SLAIALIGGPSVLLLDEPTSGLDPASRRAIWDLILEVRKGRSIILTTHSM  192 (220)
T ss_pred             HHHHHHhcCCCEEEECCCCCCCCHHHHHHHHHHHHHHhcCCEEEEEcCCH
Confidence            35555667888999999755444555566666555433346788888765

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.

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

Probab=96.48  E-value=0.0022  Score=63.08  Aligned_cols=45  Identities=29%  Similarity=0.367  Sum_probs=37.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      +..+++.|+|.+|+|||+++.++..  ........++||+.......
T Consensus        21 p~g~~~lI~G~pGsGKT~f~~qfl~--~~~~~ge~vlyvs~~e~~~~   65 (260)
T COG0467          21 PRGSVVLITGPPGTGKTIFALQFLY--EGAREGEPVLYVSTEESPEE   65 (260)
T ss_pred             cCCcEEEEEcCCCCcHHHHHHHHHH--HHHhcCCcEEEEEecCCHHH
Confidence            4568999999999999999999988  55566888999998876544

>PHA02244 ATPase-like protein

Probab=96.46  E-value=0.013  Score=59.40  Aligned_cols=22  Identities=27%  Similarity=0.548  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..|.|+|++|+|||+||+.+++
T Consensus       120 ~PVLL~GppGtGKTtLA~aLA~  141 (383)
T PHA02244        120 IPVFLKGGAGSGKNHIAEQIAE  141 (383)
T ss_pred             CCEEEECCCCCCHHHHHHHHHH
Confidence            3578899999999999999988

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=96.46  E-value=0.0075  Score=55.29  Aligned_cols=23  Identities=35%  Similarity=0.423  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||++.+..
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~G   47 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAG   47 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            46999999999999999999987

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.

>PRK13538 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.44  E-value=0.034  Score=52.44  Aligned_cols=50  Identities=14%  Similarity=0.146  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-++++|+--..-+......+...+... ..+..||++|.+.
T Consensus       139 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~  189 (204)
T PRK13538        139 ALARLWLTRAPLWILDEPFTAIDKQGVARLEALLAQHAEQGGMVILTTHQD  189 (204)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecCh
Confidence            4555566778899999975444355555565555432 3356788887766

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.44  E-value=0.037  Score=51.99  Aligned_cols=51  Identities=14%  Similarity=0.135  Sum_probs=32.4

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      -.+...+..++-+|++|+--..-+...-+.+...+... ..|..||++|.+.
T Consensus       136 v~laral~~~p~~lilDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~  187 (200)
T PRK13540        136 VALLRLWMSKAKLWLLDEPLVALDELSLLTIITKIQEHRAKGGAVLLTSHQD  187 (200)
T ss_pred             HHHHHHHhcCCCEEEEeCCCcccCHHHHHHHHHHHHHHHHcCCEEEEEeCCc
Confidence            34555566678899999975443344445555555432 3467888888876

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

Probab=96.43  E-value=0.036  Score=57.58  Aligned_cols=23  Identities=35%  Similarity=0.507  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...++|.|++|+||||||+.+.-
T Consensus       362 G~~lgIIGPSgSGKSTLaR~lvG  384 (580)
T COG4618         362 GEALGIIGPSGSGKSTLARLLVG  384 (580)
T ss_pred             CceEEEECCCCccHHHHHHHHHc
Confidence            45899999999999999999854

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.43  E-value=0.02  Score=58.07  Aligned_cols=46  Identities=17%  Similarity=0.120  Sum_probs=33.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh---hcc-CCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV---KAN-FDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~---~~~-F~~~~wv~~~~~~~~  241 (597)
                      ...++-|+|++|+|||+|+.+++-....   .+. -..++|++....|..
T Consensus       125 ~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~tF~p  174 (344)
T PLN03187        125 TRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRP  174 (344)
T ss_pred             CCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCCCCCH
Confidence            5678889999999999999998642222   111 246899998887776

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=96.42  E-value=0.037  Score=50.09  Aligned_cols=55  Identities=15%  Similarity=0.090  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHhcCceEEEEEecc-cCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          279 ETVLQYINEFVQGKKVLLVLDDL-WWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       279 ~~~~~~l~~~L~~kr~LLVLDdv-~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      ++-.-.|.+.+-+++-+|+-|.- -+.|...+|+-+.-.-.-+..|+.||++|.+.
T Consensus       142 EQQRvaIARAiV~~P~vLlADEPTGNLDp~~s~~im~lfeeinr~GtTVl~ATHd~  197 (223)
T COG2884         142 EQQRVAIARAIVNQPAVLLADEPTGNLDPDLSWEIMRLFEEINRLGTTVLMATHDL  197 (223)
T ss_pred             HHHHHHHHHHHccCCCeEeecCCCCCCChHHHHHHHHHHHHHhhcCcEEEEEeccH
Confidence            33344566777788999999963 22243336655544334467899999999887

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=96.39  E-value=0.0023  Score=56.83  Aligned_cols=36  Identities=36%  Similarity=0.362  Sum_probs=27.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS  234 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~  234 (597)
                      ..+|.|+|.+|+||||||+.+.+  +....-..+.++.
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~--~L~~~g~~~~~LD   37 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALER--RLFARGIKVYLLD   37 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHH--HHHHTTS-EEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH--HHHHcCCcEEEec
Confidence            46899999999999999999998  5555545555554

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=96.38  E-value=0.033  Score=59.87  Aligned_cols=61  Identities=16%  Similarity=0.326  Sum_probs=43.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      .+++--...++++..||...-.     +....+++.++||+|+||||.++.+++.    -.|+..-|.+-
T Consensus        19 ~eLavhkkKv~eV~~wl~~~~~-----~~~~~~iLlLtGP~G~GKtttv~~La~e----lg~~v~Ew~np   79 (519)
T PF03215_consen   19 DELAVHKKKVEEVRSWLEEMFS-----GSSPKRILLLTGPSGCGKTTTVKVLAKE----LGFEVQEWINP   79 (519)
T ss_pred             HHhhccHHHHHHHHHHHHHHhc-----cCCCcceEEEECCCCCCHHHHHHHHHHH----hCCeeEEecCC
Confidence            3445556778899999975432     1234579999999999999999999873    24666678643

>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional

Probab=96.38  E-value=0.045  Score=53.60  Aligned_cols=137  Identities=12%  Similarity=0.017  Sum_probs=65.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hcc--CC---------eeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHH
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KAN--FD---------KRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAI  264 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~--F~---------~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i  264 (597)
                      ..+++|.|+.|+|||||++.+..-... .+.  |+         .+.|+.-.............+..............+
T Consensus        38 Ge~~~I~G~NGsGKSTLlk~l~Gl~~p~~G~i~~~g~~~~~~~~~i~~v~q~~~l~~~~tv~enl~~~~~~~~~~~~~~~  117 (257)
T PRK11247         38 GQFVAVVGRSGCGKSTLLRLLAGLETPSAGELLAGTAPLAEAREDTRLMFQDARLLPWKKVIDNVGLGLKGQWRDAALQA  117 (257)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCCeEEEECCEEHHHhhCceEEEecCccCCCCCcHHHHHHhcccchHHHHHHHH
Confidence            469999999999999999999763111 110  11         122322111110000111111111001112234455


Q ss_pred             HHhccCCCC------chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          265 LESLKGSVS------SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       265 l~~l~~~~~------~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      ++.++....      ....-+.-.-.|...+..++-+|+||+--+.-+......+...+...  ..+..||++|.+.
T Consensus       118 l~~~gl~~~~~~~~~~LSgGqkqrl~laraL~~~p~lllLDEPt~~LD~~~~~~l~~~L~~~~~~~~~tviivsHd~  194 (257)
T PRK11247        118 LAAVGLADRANEWPAALSGGQKQRVALARALIHRPGLLLLDEPLGALDALTRIEMQDLIESLWQQHGFTVLLVTHDV  194 (257)
T ss_pred             HHHcCChhHhcCChhhCCHHHHHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            555544210      11111222233445555677899999875444344555555555432  2356778887765

>PRK08233 hypothetical protein; Provisional

Probab=96.38  E-value=0.012  Score=54.20  Aligned_cols=24  Identities=29%  Similarity=0.349  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+|+|.|++|+||||||..+...
T Consensus         3 ~~iI~I~G~~GsGKtTla~~L~~~   26 (182)
T PRK08233          3 TKIITIAAVSGGGKTTLTERLTHK   26 (182)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhh
Confidence            479999999999999999999873

>PRK13695 putative NTPase; Provisional

Probab=96.36  E-value=0.013  Score=53.63  Aligned_cols=22  Identities=36%  Similarity=0.481  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|+|+|++|+|||||++.+++.
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~   23 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAEL   23 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999998874

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=96.35  E-value=0.039  Score=52.36  Aligned_cols=51  Identities=14%  Similarity=0.076  Sum_probs=31.6

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.+...+..++-+|+||+--..-+...-..+...+.....+..||++|.+.
T Consensus       139 v~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~vsH~~  189 (211)
T cd03264         139 VGIAQALVGDPSILIVDEPTAGLDPEERIRFRNLLSELGEDRIVILSTHIV  189 (211)
T ss_pred             HHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            345556667888999998644433445555555554432346788887765

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.

>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter

Probab=96.34  E-value=0.041  Score=51.79  Aligned_cols=135  Identities=11%  Similarity=0.057  Sum_probs=67.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE-----------------ecCCCch--hhhhhhhhhhcccch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS-----------------ASYPRDE--IRVARDEISVARDRD  256 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~-----------------~~~~~~~--~~~~~~~~~~~~~~~  256 (597)
                      ...+++|.|+.|.|||||.+.+..-..   ...+.+++.                 +.+....  .......+.......
T Consensus        25 ~Ge~~~i~G~nGsGKSTLl~~l~G~~~---~~~G~i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~~tv~e~l~~~~~~~  101 (201)
T cd03231          25 AGEALQVTGPNGSGKTTLLRILAGLSP---PLAGRVLLNGGPLDFQRDSIARGLLYLGHAPGIKTTLSVLENLRFWHADH  101 (201)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCC---CCCcEEEECCEecccccHHhhhheEEeccccccCCCcCHHHHHHhhcccc
Confidence            346999999999999999999876311   111112211                 0011000  001111111110111


Q ss_pred             HHHHHHHHHHhccCCCC------chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEE
Q 041007          257 EIRVAKAILESLKGSVS------SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVT  329 (597)
Q Consensus       257 ~~~~~~~il~~l~~~~~------~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvT  329 (597)
                      .......+++.++....      ....-+...-.+...+..++=+|++|+--..-+......+...+.. ...|..||++
T Consensus       102 ~~~~~~~~l~~~~l~~~~~~~~~~LS~G~~qrl~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~g~tiii~  181 (201)
T cd03231         102 SDEQVEEALARVGLNGFEDRPVAQLSAGQQRRVALARLLLSGRPLWILDEPTTALDKAGVARFAEAMAGHCARGGMVVLT  181 (201)
T ss_pred             cHHHHHHHHHHcCChhhhcCchhhCCHHHHHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHhCCCEEEEE
Confidence            12334455555543210      0111122233355556667779999997544445555666665543 2346678888


Q ss_pred             ccCC
Q 041007          330 RSGG  333 (597)
Q Consensus       330 tR~~  333 (597)
                      |.+.
T Consensus       182 sH~~  185 (201)
T cd03231         182 THQD  185 (201)
T ss_pred             ecCc
Confidence            8765

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.

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=96.34  E-value=0.0054  Score=55.92  Aligned_cols=39  Identities=23%  Similarity=0.264  Sum_probs=28.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhh-ccCCeeEEEEecC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVK-ANFDKRIWVSASY  237 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~-~~F~~~~wv~~~~  237 (597)
                      ..++.+.||.|+|||.||+.+..  ... +.....+-++++.
T Consensus         3 ~~~~ll~GpsGvGKT~la~~la~--~l~~~~~~~~~~~d~s~   42 (171)
T PF07724_consen    3 KSNFLLAGPSGVGKTELAKALAE--LLFVGSERPLIRIDMSE   42 (171)
T ss_dssp             SEEEEEESSTTSSHHHHHHHHHH--HHT-SSCCEEEEEEGGG
T ss_pred             EEEEEEECCCCCCHHHHHHHHHH--HhccCCccchHHHhhhc
Confidence            46889999999999999999988  344 3444555555543

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>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=96.32  E-value=0.012  Score=58.89  Aligned_cols=85  Identities=24%  Similarity=0.268  Sum_probs=51.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC-
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS-  273 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~-  273 (597)
                      +..+++-|+|+.|+||||||..+..  .....-..++|+.....++.                     ..++.++.+.+ 
T Consensus        51 p~G~ivEi~G~~ssGKttLaL~~ia--~~q~~g~~~a~ID~e~~ld~---------------------~~a~~lGvdl~r  107 (322)
T PF00154_consen   51 PRGRIVEIYGPESSGKTTLALHAIA--EAQKQGGICAFIDAEHALDP---------------------EYAESLGVDLDR  107 (322)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHH--HHHHTT-EEEEEESSS---H---------------------HHHHHTT--GGG
T ss_pred             ccCceEEEeCCCCCchhhhHHHHHH--hhhcccceeEEecCcccchh---------------------hHHHhcCccccc
Confidence            4568999999999999999999887  44445566899998766554                     22333433221 


Q ss_pred             ----chhhHHHHHHHHHHHhc-CceEEEEEeccc
Q 041007          274 ----SQVEMETVLQYINEFVQ-GKKVLLVLDDLW  302 (597)
Q Consensus       274 ----~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~  302 (597)
                          .+...++....+..+++ +.--++|+|.|-
T Consensus       108 llv~~P~~~E~al~~~e~lirsg~~~lVVvDSv~  141 (322)
T PF00154_consen  108 LLVVQPDTGEQALWIAEQLIRSGAVDLVVVDSVA  141 (322)
T ss_dssp             EEEEE-SSHHHHHHHHHHHHHTTSESEEEEE-CT
T ss_pred             eEEecCCcHHHHHHHHHHHhhcccccEEEEecCc
Confidence                12233445555555555 344588999873

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 ....

>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein

Probab=96.32  E-value=0.037  Score=53.23  Aligned_cols=52  Identities=15%  Similarity=0.073  Sum_probs=33.3

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .-.|...+..++-+|+||+-...-+....+.+...+.....+..||++|.+.
T Consensus       147 rv~la~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~  198 (229)
T cd03254         147 LLAIARAMLRDPKILILDEATSNIDTETEKLIQEALEKLMKGRTSIIIAHRL  198 (229)
T ss_pred             HHHHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEecCH
Confidence            3345556667788999999754444555555555554433467788887765

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.

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.32  E-value=0.029  Score=56.87  Aligned_cols=46  Identities=17%  Similarity=0.226  Sum_probs=34.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhcc----CCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKAN----FDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~  241 (597)
                      ...++-|+|++|+|||+++.+++-.......    =..++|++....++.
T Consensus       101 ~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~  150 (317)
T PRK04301        101 TQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRP  150 (317)
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCH
Confidence            5679999999999999999998754222111    136899998876665

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

Probab=96.31  E-value=0.021  Score=54.90  Aligned_cols=124  Identities=15%  Similarity=0.089  Sum_probs=69.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC--
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS--  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~--  273 (597)
                      ...+++|+|.+|+|||||++.+..   ....-.+.++..-.+-...           ......+...++++.++....  
T Consensus        38 ~ge~~glVGESG~GKSTlgr~i~~---L~~pt~G~i~f~g~~i~~~-----------~~~~~~~~v~elL~~Vgl~~~~~  103 (268)
T COG4608          38 EGETLGLVGESGCGKSTLGRLILG---LEEPTSGEILFEGKDITKL-----------SKEERRERVLELLEKVGLPEEFL  103 (268)
T ss_pred             CCCEEEEEecCCCCHHHHHHHHHc---CcCCCCceEEEcCcchhhc-----------chhHHHHHHHHHHHHhCCCHHHh
Confidence            356999999999999999999988   2232333333332111000           011114455666666664321  


Q ss_pred             ----chhhHHH-HHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--CCCCcEEEEEccCC
Q 041007          274 ----SQVEMET-VLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--GSEGSRILVTRSGG  333 (597)
Q Consensus       274 ----~~~~~~~-~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~~~gs~IIvTtR~~  333 (597)
                          ...+-.+ -.-.+.+.|.-++-++|.|..-++-+...-.++...+..  ...|...+..|.+-
T Consensus       104 ~ryPhelSGGQrQRi~IARALal~P~liV~DEpvSaLDvSiqaqIlnLL~dlq~~~~lt~lFIsHDL  170 (268)
T COG4608         104 YRYPHELSGGQRQRIGIARALALNPKLIVADEPVSALDVSVQAQILNLLKDLQEELGLTYLFISHDL  170 (268)
T ss_pred             hcCCcccCchhhhhHHHHHHHhhCCcEEEecCchhhcchhHHHHHHHHHHHHHHHhCCeEEEEEEEH
Confidence                1111112 222466777889999999997655544444555555543  23455566666554

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.30  E-value=0.022  Score=58.82  Aligned_cols=25  Identities=24%  Similarity=0.416  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...++.|+|++|+||||++..++..
T Consensus       222 ~~~vi~lvGptGvGKTTtaaKLA~~  246 (432)
T PRK12724        222 QRKVVFFVGPTGSGKTTSIAKLAAK  246 (432)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999863

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.30  E-value=0.035  Score=52.47  Aligned_cols=50  Identities=6%  Similarity=0.052  Sum_probs=32.4

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--..-+......+...+.. ...|..||++|.+.
T Consensus       137 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~  187 (207)
T PRK13539        137 ALARLLVSNRPIWILDEPTAALDAAAVALFAELIRAHLAQGGIVIAATHIP  187 (207)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCc
Confidence            345555667889999997544445555666665543 23467788888776

>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=96.29  E-value=0.04  Score=53.13  Aligned_cols=50  Identities=14%  Similarity=0.082  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+++||+--..-+...-..+...+...  ..|..||++|.+.
T Consensus       150 ~la~al~~~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~~~tvii~sH~~  201 (233)
T cd03258         150 GIARALANNPKVLLCDEATSALDPETTQSILALLRDINRELGLTIVLITHEM  201 (233)
T ss_pred             HHHHHHhcCCCEEEecCCCCcCCHHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            3445555677899999975444344555565555442  2367788888765

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.

>PRK14974 cell division protein FtsY; Provisional

Probab=96.28  E-value=0.036  Score=56.15  Aligned_cols=24  Identities=29%  Similarity=0.325  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++.+|.++|++|+||||++..++.
T Consensus       139 ~~~vi~~~G~~GvGKTTtiakLA~  162 (336)
T PRK14974        139 KPVVIVFVGVNGTGKTTTIAKLAY  162 (336)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHH
Confidence            468999999999999998888876

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=96.28  E-value=0.056  Score=59.20  Aligned_cols=25  Identities=28%  Similarity=0.248  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|+|+.|+|||||++.+..-
T Consensus       360 ~G~~vaIvG~SGsGKSTLl~lL~g~  384 (529)
T TIGR02868       360 PGERVAILGPSGSGKSTLLMLLTGL  384 (529)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4579999999999999999999763

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.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.27  E-value=0.028  Score=56.87  Aligned_cols=46  Identities=17%  Similarity=0.236  Sum_probs=34.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc----cCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA----NFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~  241 (597)
                      ...++-|+|++|+|||+++.+++.......    .-..++|++....+..
T Consensus        94 ~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~  143 (310)
T TIGR02236        94 TQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRP  143 (310)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCH
Confidence            467899999999999999999876422211    1126899998877665

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.

>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=96.27  E-value=0.037  Score=52.63  Aligned_cols=23  Identities=35%  Similarity=0.443  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+++|.|+.|+|||||++.+..-
T Consensus        24 e~~~i~G~nGsGKSTLl~~l~G~   46 (214)
T cd03297          24 EVTGIFGASGAGKSTLLRCIAGL   46 (214)
T ss_pred             eeEEEECCCCCCHHHHHHHHhCC
Confidence            79999999999999999999763

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters

Probab=96.27  E-value=0.075  Score=50.46  Aligned_cols=50  Identities=24%  Similarity=0.262  Sum_probs=31.2

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--+.-+......+...+... ..|..||++|.+.
T Consensus       142 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tvi~~sH~~  192 (213)
T cd03235         142 LLARALVQDPDLLLLDEPFAGVDPKTQEDIYELLRELRREGMTILVVTHDL  192 (213)
T ss_pred             HHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3555566778899999975444355555555555432 2466777777665

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.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.27  E-value=0.041  Score=56.82  Aligned_cols=107  Identities=10%  Similarity=0.042  Sum_probs=58.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc--cCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA--NFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~--~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~  273 (597)
                      .+++|.++|+.|+||||.+..++.......  +-..+..+++... ..              +....+....+.++.+..
T Consensus       173 ~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~-R~--------------aa~eQL~~~a~~lgvpv~  237 (388)
T PRK12723        173 KKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNY-RI--------------GAKKQIQTYGDIMGIPVK  237 (388)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCc-cH--------------HHHHHHHHHhhcCCcceE
Confidence            357999999999999999988876322211  1123444554422 11              003335555555655433


Q ss_pred             chhhHHHHHHHHHHHhcCceEEEEEecccCCCC-cchHHHHHHhhcC
Q 041007          274 SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY-PRYWEQLMYSLKS  319 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~-~~~~~~l~~~l~~  319 (597)
                      .....+.+...+.+.  .+.-++++|....... ...+..+...+..
T Consensus       238 ~~~~~~~l~~~L~~~--~~~DlVLIDTaGr~~~~~~~l~el~~~l~~  282 (388)
T PRK12723        238 AIESFKDLKEEITQS--KDFDLVLVDTIGKSPKDFMKLAEMKELLNA  282 (388)
T ss_pred             eeCcHHHHHHHHHHh--CCCCEEEEcCCCCCccCHHHHHHHHHHHHh
Confidence            333444454444443  3456888998855431 1133445444443

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=96.26  E-value=0.044  Score=53.19  Aligned_cols=50  Identities=12%  Similarity=0.076  Sum_probs=32.0

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+.-+.-+......+...+... ..|..||++|.+.
T Consensus       151 ~laral~~~p~llilDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~  201 (242)
T PRK11124        151 AIARALMMEPQVLLFDEPTAALDPEITAQIVSIIRELAETGITQVIVTHEV  201 (242)
T ss_pred             HHHHHHhcCCCEEEEcCCCCcCCHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            3555555677899999975554455666666655432 2366777777765

>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export

Probab=96.26  E-value=0.06  Score=51.57  Aligned_cols=24  Identities=29%  Similarity=0.361  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.+...
T Consensus        48 Ge~~~i~G~nGsGKSTLl~~l~G~   71 (224)
T cd03220          48 GERIGLIGRNGAGKSTLLRLLAGI   71 (224)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999874

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.

>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters

Probab=96.25  E-value=0.045  Score=52.24  Aligned_cols=50  Identities=12%  Similarity=0.038  Sum_probs=31.2

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--+.-+......+...+.....+..||++|.+.
T Consensus       150 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~  199 (220)
T cd03245         150 ALARALLNDPPILLLDEPTSAMDMNSEERLKERLRQLLGDKTLIIITHRP  199 (220)
T ss_pred             HHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEeCCH
Confidence            34445556678999999754443555566666665433346788888765

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.

>PRK07667 uridine kinase; Provisional

Probab=96.25  E-value=0.0086  Score=55.94  Aligned_cols=37  Identities=16%  Similarity=0.269  Sum_probs=28.7

Q ss_pred             HHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          175 KQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       175 ~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.|.+.+....        +...+|+|.|.+|+||||+|..+..
T Consensus         3 ~~~~~~~~~~~~--------~~~~iIgI~G~~gsGKStla~~L~~   39 (193)
T PRK07667          3 TNELINIMKKHK--------ENRFILGIDGLSRSGKTTFVANLKE   39 (193)
T ss_pred             HHHHHHHHHhcC--------CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            455666665433        3458999999999999999999987

>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=96.25  E-value=0.05  Score=51.97  Aligned_cols=135  Identities=16%  Similarity=0.105  Sum_probs=66.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hcc--C---------CeeEEEEecCCCchh--hhhhhhhhhc----c--cch
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KAN--F---------DKRIWVSASYPRDEI--RVARDEISVA----R--DRD  256 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~--F---------~~~~wv~~~~~~~~~--~~~~~~~~~~----~--~~~  256 (597)
                      ..+++|.|+.|+|||||++.++.-... .+.  |         ..+.++.  +.....  ......+...    .  ...
T Consensus        30 G~~~~i~G~nGsGKSTLl~~l~Gl~~~~~G~i~~~g~~~~~~~~~i~~v~--q~~~~~~~~tv~e~l~~~~~~~~~~~~~  107 (220)
T cd03293          30 GEFVALVGPSGCGKSTLLRIIAGLERPTSGEVLVDGEPVTGPGPDRGYVF--QQDALLPWLTVLDNVALGLELQGVPKAE  107 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCCCCCceEEEECCEECccccCcEEEEe--cccccccCCCHHHHHHHHHHHcCCCHHH
Confidence            468999999999999999999764211 110  1         1122222  111110  0111111100    0  011


Q ss_pred             HHHHHHHHHHhccCCC------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEE
Q 041007          257 EIRVAKAILESLKGSV------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILV  328 (597)
Q Consensus       257 ~~~~~~~il~~l~~~~------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIv  328 (597)
                      .......+++.++...      .....-+...-.+...+..++-+++||+--..-+...-..+...+...  ..+..||+
T Consensus       108 ~~~~~~~~l~~~~l~~~~~~~~~~LSgG~~qrl~la~al~~~p~lllLDEPt~~LD~~~~~~~~~~l~~~~~~~~~tiii  187 (220)
T cd03293         108 ARERAEELLELVGLSGFENAYPHQLSGGMRQRVALARALAVDPDVLLLDEPFSALDALTREQLQEELLDIWRETGKTVLL  187 (220)
T ss_pred             HHHHHHHHHHHcCChhhhhCCcccCCHHHHHHHHHHHHHHcCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHHcCCEEEE
Confidence            1233445555554321      111112222334555566678899999975444344555555555432  23567777


Q ss_pred             EccCC
Q 041007          329 TRSGG  333 (597)
Q Consensus       329 TtR~~  333 (597)
                      +|.+.
T Consensus       188 ~sH~~  192 (220)
T cd03293         188 VTHDI  192 (220)
T ss_pred             EecCH
Confidence            77665

ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=96.25  E-value=0.056  Score=51.40  Aligned_cols=137  Identities=15%  Similarity=0.085  Sum_probs=66.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hcc--CC-----------eeEEEEecCCCchhhhhhhhhhh---cccchHHH
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KAN--FD-----------KRIWVSASYPRDEIRVARDEISV---ARDRDEIR  259 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~--F~-----------~~~wv~~~~~~~~~~~~~~~~~~---~~~~~~~~  259 (597)
                      ..+++|.|+.|.|||||++.++..... .+.  |+           .+.++.-.............+..   ........
T Consensus        37 Ge~~~i~G~nGsGKSTLl~~i~G~~~~~~G~i~~~g~~i~~~~~~~~i~~~~q~~~~~~~~t~~e~l~~~~~~~~~~~~~  116 (214)
T PRK13543         37 GEALLVQGDNGAGKTTLLRVLAGLLHVESGQIQIDGKTATRGDRSRFMAYLGHLPGLKADLSTLENLHFLCGLHGRRAKQ  116 (214)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCCCCCCCeeEEECCEEccchhhhhceEEeecCcccccCCcHHHHHHHHHHhcCCcHHH
Confidence            468999999999999999999864211 110  11           12233211100000011111100   00111123


Q ss_pred             HHHHHHHhccCCCC------chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccC
Q 041007          260 VAKAILESLKGSVS------SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSG  332 (597)
Q Consensus       260 ~~~~il~~l~~~~~------~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~  332 (597)
                      ....++..++....      ....-+...-.+...+-.++-+++||+--+.-+......+...+.. ...|..||++|.+
T Consensus       117 ~~~~~l~~~~l~~~~~~~~~~LS~G~~qrv~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~  196 (214)
T PRK13543        117 MPGSALAIVGLAGYEDTLVRQLSAGQKKRLALARLWLSPAPLWLLDEPYANLDLEGITLVNRMISAHLRGGGAALVTTHG  196 (214)
T ss_pred             HHHHHHHHcCChhhccCChhhCCHHHHHHHHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEecC
Confidence            33455555543210      1111122333344555566779999987544434455555555542 2345678888876


Q ss_pred             C
Q 041007          333 G  333 (597)
Q Consensus       333 ~  333 (597)
                      .
T Consensus       197 ~  197 (214)
T PRK13543        197 A  197 (214)
T ss_pred             h
Confidence            6

>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=96.24  E-value=0.044  Score=52.24  Aligned_cols=50  Identities=16%  Similarity=0.137  Sum_probs=31.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-C-CCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-S-EGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~-~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--..-+......+...+... . .|..||++|.+.
T Consensus       150 ~la~al~~~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~~~tii~~sH~~  201 (218)
T cd03255         150 AIARALANDPKIILADEPTGNLDSETGKEVMELLRELNKEAGTTIVVVTHDP  201 (218)
T ss_pred             HHHHHHccCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHhcCCeEEEEECCH
Confidence            3555666778899999975444355555565555442 2 366788887765

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.

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

Probab=96.24  E-value=0.06  Score=50.84  Aligned_cols=24  Identities=33%  Similarity=0.459  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|++|+|||||++.+.-
T Consensus        32 ~Ge~lgivGeSGsGKSTL~r~l~G   55 (252)
T COG1124          32 RGETLGIVGESGSGKSTLARLLAG   55 (252)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhc
Confidence            346999999999999999999864

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.24  E-value=0.086  Score=53.08  Aligned_cols=49  Identities=29%  Similarity=0.280  Sum_probs=33.6

Q ss_pred             eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHH
Q 041007          354 EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAV  403 (597)
Q Consensus       354 ~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai  403 (597)
                      .+++.+++.+|+..++.-..-.+-... ....+...+++.-..+|+|--+
T Consensus       258 ~i~v~~~s~~E~~~ll~yy~~~~~l~~-~~~~~~~~e~~~~~s~GNp~el  306 (309)
T PF10236_consen  258 PIEVPRLSKEEARSLLEYYADSGWLRS-RVDEELVLEKLFLSSNGNPREL  306 (309)
T ss_pred             eEEeCCCCHHHHHHHHHHHHHCCcccc-CCCCHHHHHHHHHhcCCCHHHh
Confidence            489999999999999988764332211 1223445667777789999644

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

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

Probab=96.24  E-value=0.015  Score=54.21  Aligned_cols=43  Identities=26%  Similarity=0.305  Sum_probs=29.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccC--------CeeEEEEecCCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANF--------DKRIWVSASYPR  239 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F--------~~~~wv~~~~~~  239 (597)
                      ..++.|.|++|+|||+++.++....-....|        ..++|++.....
T Consensus        32 g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~~   82 (193)
T PF13481_consen   32 GELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLEDSE   82 (193)
T ss_dssp             TSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESSS-H
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEeccCCH
Confidence            4589999999999999999987643222222        358888877664

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

Probab=96.23  E-value=0.053  Score=52.37  Aligned_cols=54  Identities=20%  Similarity=0.282  Sum_probs=35.1

Q ss_pred             ccccchhhHHHHHHHhhCCCC--CCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRNAEKQKILQLLKGESS--DEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~--~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+-|-+...+.|.+.+.-.-.  +-=.+.....+-|.++|++|.||+-||++|+..
T Consensus       134 DVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATE  189 (439)
T KOG0739|consen  134 DVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATE  189 (439)
T ss_pred             hhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhh
Confidence            345677777776665432110  000111335678999999999999999999984

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.22  E-value=0.054  Score=52.10  Aligned_cols=42  Identities=21%  Similarity=0.191  Sum_probs=31.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      ...++.|.|++|+|||+|+.++...  ....-..++|++.....
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~--~~~~g~~~~~is~e~~~   60 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYK--GLRDGDPVIYVTTEESR   60 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHH--HHhcCCeEEEEEccCCH
Confidence            4679999999999999999987653  22233467888875443

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.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=96.22  E-value=0.025  Score=57.04  Aligned_cols=46  Identities=17%  Similarity=0.190  Sum_probs=32.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh---hc-cCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV---KA-NFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~---~~-~F~~~~wv~~~~~~~~  241 (597)
                      ...++.|+|++|+|||+|+..++.....   .+ .-..++|++....+..
T Consensus        95 ~g~i~~i~G~~g~GKT~l~~~~~~~~~~~~~~Gg~~~~vvyIdtE~~f~~  144 (316)
T TIGR02239        95 TGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALYIDTEGTFRP  144 (316)
T ss_pred             CCeEEEEECCCCCCcCHHHHHHHHHHhhhhhcCCCCceEEEEECCCCCCH
Confidence            5679999999999999999988752111   11 1135789988776555

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).

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.21  E-value=0.099  Score=53.31  Aligned_cols=92  Identities=11%  Similarity=0.102  Sum_probs=52.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      +.++++|+|+.|+||||++..++..  ....-..+.++++......               ....++...+.++.+....
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~--l~~~g~~V~lItaDtyR~g---------------AveQLk~yae~lgvpv~~~  267 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQ--LLKQNRTVGFITTDTFRSG---------------AVEQFQGYADKLDVELIVA  267 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEeCCccCcc---------------HHHHHHHHhhcCCCCEEec
Confidence            4689999999999999999998863  2222234556665432211               0334444555555432222


Q ss_pred             hhHHHHHHHHHHHhc-CceEEEEEecccCC
Q 041007          276 VEMETVLQYINEFVQ-GKKVLLVLDDLWWN  304 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~-~kr~LLVLDdv~~~  304 (597)
                      .+...+...+...-. +..=+|++|-....
T Consensus       268 ~dp~dL~~al~~l~~~~~~D~VLIDTAGr~  297 (407)
T PRK12726        268 TSPAELEEAVQYMTYVNCVDHILIDTVGRN  297 (407)
T ss_pred             CCHHHHHHHHHHHHhcCCCCEEEEECCCCC
Confidence            344445554443321 34467888987553

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.21  E-value=0.031  Score=51.62  Aligned_cols=50  Identities=12%  Similarity=0.132  Sum_probs=32.3

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|+||+--..-+......+...+... ..+..||++|.+.
T Consensus       114 ~la~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~  164 (182)
T cd03215         114 VLARWLARDPRVLILDEPTRGVDVGAKAEIYRLIRELADAGKAVLLISSEL  164 (182)
T ss_pred             HHHHHHccCCCEEEECCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            3555666778899999975444455555665555432 3467788888765

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.

>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup

Probab=96.21  E-value=0.036  Score=52.62  Aligned_cols=50  Identities=18%  Similarity=0.139  Sum_probs=31.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       140 ~la~al~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~sH~~  191 (213)
T cd03259         140 ALARALAREPSLLLLDEPLSALDAKLREELREELKELQRELGITTIYVTHDQ  191 (213)
T ss_pred             HHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEEecCH
Confidence            3555566778899999975444344555555555442  2366788887765

This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional

Probab=96.21  E-value=0.057  Score=52.90  Aligned_cols=50  Identities=20%  Similarity=0.135  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       138 ~laral~~~p~lllLDEPt~~LD~~~~~~l~~~L~~~~~~~g~tviivsH~~  189 (255)
T PRK11248        138 GIARALAANPQLLLLDEPFGALDAFTREQMQTLLLKLWQETGKQVLLITHDI  189 (255)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3455556678899999975443344555555555432  2367788888765

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

Probab=96.19  E-value=0.0046  Score=68.29  Aligned_cols=44  Identities=27%  Similarity=0.505  Sum_probs=35.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+||++|++++++.|.....        +.+  .++|.+|||||+++.-++.
T Consensus       170 DPvIGRd~EI~r~iqIL~RR~K--------NNP--vLiGEpGVGKTAIvEGLA~  213 (786)
T COG0542         170 DPVIGRDEEIRRTIQILSRRTK--------NNP--VLVGEPGVGKTAIVEGLAQ  213 (786)
T ss_pred             CCCcChHHHHHHHHHHHhccCC--------CCC--eEecCCCCCHHHHHHHHHH
Confidence            4589999999999999986543        222  4689999999999887776

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=96.18  E-value=0.033  Score=62.08  Aligned_cols=54  Identities=19%  Similarity=0.279  Sum_probs=32.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.|-+...+++.+.+.......  ..-...-.+-|.|+|++|+|||++|+.++.
T Consensus       152 ~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~  207 (644)
T PRK10733        152 ADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG  207 (644)
T ss_pred             HHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHH
Confidence            346677766666655443211100  000001234599999999999999999987

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.17  E-value=0.027  Score=59.78  Aligned_cols=24  Identities=29%  Similarity=0.358  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|++|+||||++..+..
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa  372 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQ  372 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999988876

>TIGR01166 cbiO cobalt transport protein ATP-binding subunit

Probab=96.17  E-value=0.083  Score=49.15  Aligned_cols=50  Identities=22%  Similarity=0.204  Sum_probs=31.1

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+-..+-+|+||+--..-+......+...+... ..|..||++|.+.
T Consensus       137 ~laral~~~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~tili~sH~~  187 (190)
T TIGR01166       137 AIAGAVAMRPDVLLLDEPTAGLDPAGREQMLAILRRLRAEGMTVVISTHDV  187 (190)
T ss_pred             HHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHcCCEEEEEeecc
Confidence            3555566677899999975444344555555555432 3467788887654

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.

>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=96.17  E-value=0.075  Score=50.37  Aligned_cols=50  Identities=22%  Similarity=0.187  Sum_probs=31.3

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--+.-+......+...+... ..|..||++|.+.
T Consensus       144 ~laral~~~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~tvi~~sH~~  194 (211)
T cd03225         144 AIAGVLAMDPDILLLDEPTAGLDPAGRRELLELLKKLKAEGKTIIIVTHDL  194 (211)
T ss_pred             HHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            3455555677899999975544455555555555432 2367788888765

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.

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=96.17  E-value=0.06  Score=54.17  Aligned_cols=50  Identities=12%  Similarity=0.080  Sum_probs=32.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|+||+--+.-+......+...+.....+..||+||...
T Consensus       143 ~la~al~~~p~lliLDEPt~gLD~~~~~~l~~~l~~~~~~~tiii~sH~l  192 (301)
T TIGR03522       143 GLAQALIHDPKVLILDEPTTGLDPNQLVEIRNVIKNIGKDKTIILSTHIM  192 (301)
T ss_pred             HHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCH
Confidence            35556667888999999754443445555555554433467889998766

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.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=96.15  E-value=0.0051  Score=53.91  Aligned_cols=24  Identities=33%  Similarity=0.576  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|.|+|++|+|||||++.+.+.
T Consensus         5 ~mki~ITG~PGvGKtTl~~ki~e~   28 (179)
T COG1618           5 AMKIFITGRPGVGKTTLVLKIAEK   28 (179)
T ss_pred             ceEEEEeCCCCccHHHHHHHHHHH
Confidence            356899999999999999999874

>PF00485 PRK: Phosphoribulokinase / Uridine kinase family; InterPro: IPR006083 Phosphoribulokinase (PRK) 2

Probab=96.15  E-value=0.022  Score=53.26  Aligned_cols=21  Identities=43%  Similarity=0.643  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|+|.|++|+||||+|+.+..
T Consensus         1 IIgI~G~sgSGKTTla~~L~~   21 (194)
T PF00485_consen    1 IIGIAGPSGSGKTTLAKRLAQ   21 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            699999999999999999987

7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms []. In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups. Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction: ATP + Uridine = ADP + UMP Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2ZSE_A 2ZS7_A 3AF0_A 3AVP_A 2ZS9_A 2ZS8_A 3AEZ_A 2ZSB_A 2ZSD_A 2GEV_A ....

>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein

Probab=96.14  E-value=0.057  Score=51.41  Aligned_cols=50  Identities=22%  Similarity=0.191  Sum_probs=31.4

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--+.-+......+...+... ..|..||++|.+.
T Consensus       148 ~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~vsH~~  198 (216)
T TIGR00960       148 AIARAIVHKPPLLLADEPTGNLDPELSRDIMRLFEEFNRRGTTVLVATHDI  198 (216)
T ss_pred             HHHHHHhcCCCEEEEeCCCCcCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            4555666778899999975444344555555555432 2366788887765

>PRK14247 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.12  E-value=0.079  Score=51.71  Aligned_cols=50  Identities=12%  Similarity=-0.009  Sum_probs=31.6

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+--+.-+......+...+.....+..||++|.+.
T Consensus       156 ~laral~~~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sH~~  205 (250)
T PRK14247        156 CIARALAFQPEVLLADEPTANLDPENTAKIESLFLELKKDMTIVLVTHFP  205 (250)
T ss_pred             HHHHHHhcCCCEEEEcCCCccCCHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            34455556788999999755444555555555554433356788887765

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.11  E-value=0.021  Score=52.38  Aligned_cols=25  Identities=32%  Similarity=0.607  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|+|+|++|+||||+|+.+...
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~   27 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEK   27 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4569999999999999999999883

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.11  E-value=0.052  Score=48.29  Aligned_cols=22  Identities=41%  Similarity=0.824  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +|.|+|.+|+||||||+.+...
T Consensus         1 ~i~i~G~~GsGKSTla~~L~~~   22 (149)
T cd02027           1 VIWLTGLSGSGKSTIARALEEK   22 (149)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            5789999999999999999873

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=96.10  E-value=0.0058  Score=65.03  Aligned_cols=49  Identities=22%  Similarity=0.437  Sum_probs=39.2

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +++|.++.+++|++.|......-    ....+++.++||+|+||||||+.+.+
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl----~~~~~IL~LvGPpG~GKSsLa~~la~  125 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGL----EEKKQILYLLGPVGGGKSSLAERLKS  125 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhc----CCCCceEEEecCCCCCchHHHHHHHH
Confidence            58899999999999994322100    22457999999999999999999987

>PRK14269 phosphate ABC transporter ATP-binding protein; Provisional

Probab=96.10  E-value=0.071  Score=51.92  Aligned_cols=53  Identities=19%  Similarity=0.019  Sum_probs=32.8

Q ss_pred             HHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          281 VLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       281 ~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      ..-.+...+..++-+++||+.-..-+...-..+...+.....+..||++|.+.
T Consensus       149 qrv~laral~~~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~tH~~  201 (246)
T PRK14269        149 QRLCIARALAIKPKLLLLDEPTSALDPISSGVIEELLKELSHNLSMIMVTHNM  201 (246)
T ss_pred             HHHHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHhCCCEEEEEecCH
Confidence            33445666667788999999754433444455555554433366778777765

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=96.10  E-value=0.056  Score=52.40  Aligned_cols=24  Identities=33%  Similarity=0.412  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl   51 (239)
T cd03296          28 GELVALLGPSGSGKTTLLRLIAGL   51 (239)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999764

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.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.10  E-value=0.011  Score=55.67  Aligned_cols=23  Identities=22%  Similarity=0.147  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+++.|+|+.|.||||+.+.+..
T Consensus        29 ~~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          29 SRFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            47899999999999999998865

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

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.10  E-value=0.072  Score=49.38  Aligned_cols=134  Identities=16%  Similarity=0.165  Sum_probs=70.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc--hhhhhhhh-------hhh---------------
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD--EIRVARDE-------ISV---------------  251 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~--~~~~~~~~-------~~~---------------  251 (597)
                      ...+++|.|++|+|||||.+.+..   ....-.+.+|+.-.....  ....++..       +..               
T Consensus        27 ~Gevv~iiGpSGSGKSTlLRclN~---LE~~~~G~I~i~g~~~~~~~~~~~~R~~vGmVFQ~fnLFPHlTvleNv~lap~  103 (240)
T COG1126          27 KGEVVVIIGPSGSGKSTLLRCLNG---LEEPDSGSITVDGEDVGDKKDILKLRRKVGMVFQQFNLFPHLTVLENVTLAPV  103 (240)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHC---CcCCCCceEEECCEeccchhhHHHHHHhcCeecccccccccchHHHHHHhhhH
Confidence            346999999999999999999866   223334556664311110  00000000       000               


Q ss_pred             ----cccchHHHHHHHHHHhccCCCC------chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-C
Q 041007          252 ----ARDRDEIRVAKAILESLKGSVS------SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-G  320 (597)
Q Consensus       252 ----~~~~~~~~~~~~il~~l~~~~~------~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~  320 (597)
                          .....-.+....+++.++....      ....-++-.-.|.+.|.=++-++.+|..-+.-+++....+...+.. .
T Consensus       104 ~v~~~~k~eA~~~A~~lL~~VGL~~ka~~yP~qLSGGQqQRVAIARALaM~P~vmLFDEPTSALDPElv~EVL~vm~~LA  183 (240)
T COG1126         104 KVKKLSKAEAREKALELLEKVGLADKADAYPAQLSGGQQQRVAIARALAMDPKVMLFDEPTSALDPELVGEVLDVMKDLA  183 (240)
T ss_pred             HHcCCCHHHHHHHHHHHHHHcCchhhhhhCccccCcHHHHHHHHHHHHcCCCCEEeecCCcccCCHHHHHHHHHHHHHHH
Confidence                0111223344444555444221      1112233344577778888889999998666556665555555543 3


Q ss_pred             CCCcEEEEEccC
Q 041007          321 SEGSRILVTRSG  332 (597)
Q Consensus       321 ~~gs~IIvTtR~  332 (597)
                      ..|-..|+.|..
T Consensus       184 ~eGmTMivVTHE  195 (240)
T COG1126         184 EEGMTMIIVTHE  195 (240)
T ss_pred             HcCCeEEEEech
Confidence            455555555443

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.09  E-value=0.024  Score=58.39  Aligned_cols=40  Identities=35%  Similarity=0.375  Sum_probs=30.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ...++.|.|.+|+|||||+.+++..  ....-..++|++...
T Consensus        81 ~GslvLI~G~pG~GKStLllq~a~~--~a~~g~~VlYvs~EE  120 (372)
T cd01121          81 PGSVILIGGDPGIGKSTLLLQVAAR--LAKRGGKVLYVSGEE  120 (372)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEECCc
Confidence            4569999999999999999999873  333334577777543

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.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=96.09  E-value=0.028  Score=61.05  Aligned_cols=46  Identities=15%  Similarity=0.183  Sum_probs=36.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|....+.++.+.+.....        ....|.|+|..|+||+.+|+.+++
T Consensus       204 ~~~ig~s~~~~~~~~~~~~~A~--------~~~pvlI~GE~GtGK~~lA~aiH~  249 (520)
T PRK10820        204 SQIVAVSPKMRQVVEQARKLAM--------LDAPLLITGDTGTGKDLLAYACHL  249 (520)
T ss_pred             cceeECCHHHHHHHHHHHHHhC--------CCCCEEEECCCCccHHHHHHHHHH
Confidence            4689999988888887764432        234588999999999999999865

>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=96.08  E-value=0.056  Score=51.53  Aligned_cols=24  Identities=33%  Similarity=0.318  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        31 Ge~~~i~G~nGsGKSTLl~~l~Gl   54 (218)
T cd03266          31 GEVTGLLGPNGAGKTTTLRMLAGL   54 (218)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999763

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.

>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=96.08  E-value=0.056  Score=52.14  Aligned_cols=51  Identities=14%  Similarity=0.097  Sum_probs=33.4

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      -.+...+..++=+++||+.-..-+......+...+...  ..|..||++|.+.
T Consensus       139 l~laral~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~~~tiii~sh~~  191 (232)
T cd03300         139 VAIARALVNEPKVLLLDEPLGALDLKLRKDMQLELKRLQKELGITFVFVTHDQ  191 (232)
T ss_pred             HHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            34555566778899999976555455666666666542  2367788887765

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.

>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=96.08  E-value=0.082  Score=51.11  Aligned_cols=49  Identities=10%  Similarity=0.076  Sum_probs=32.1

Q ss_pred             HHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          285 INEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       285 l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      +...+-.++-+|+||+-...-+......+...+.....|..||++|.+.
T Consensus       149 laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sH~~  197 (237)
T cd03252         149 IARALIHNPRILIFDEATSALDYESEHAIMRNMHDICAGRTVIIIAHRL  197 (237)
T ss_pred             HHHHHhhCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEeCCH
Confidence            4445556778999999755544555666666555433467788888766

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.

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

Probab=96.07  E-value=0.068  Score=52.88  Aligned_cols=42  Identities=21%  Similarity=0.196  Sum_probs=30.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ...++.|.|++|+|||+++.+++... ...+-..++|+++...
T Consensus        29 ~g~~~~i~g~~G~GKT~l~~~~~~~~-~~~~g~~vl~iS~E~~   70 (271)
T cd01122          29 KGELIILTAGTGVGKTTFLREYALDL-ITQHGVRVGTISLEEP   70 (271)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHH-HHhcCceEEEEEcccC
Confidence            35689999999999999999987742 1222345788887654

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

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=96.07  E-value=0.031  Score=62.36  Aligned_cols=50  Identities=14%  Similarity=0.101  Sum_probs=33.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      .|.+.+-.++-+|+||..-+.-+...-..+...+.. ....+.|+||-|..
T Consensus       619 alARaLl~~P~ILlLDEaTSaLD~~sE~~I~~~L~~~~~~~T~I~IaHRl~  669 (709)
T COG2274         619 ALARALLSKPKILLLDEATSALDPETEAIILQNLLQILQGRTVIIIAHRLS  669 (709)
T ss_pred             HHHHHhccCCCEEEEeCcccccCHhHHHHHHHHHHHHhcCCeEEEEEccch
Confidence            466667788999999997554434455556666654 34466777777765

>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein

Probab=96.06  E-value=0.077  Score=50.40  Aligned_cols=50  Identities=14%  Similarity=0.161  Sum_probs=32.1

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-++++|+.-..-+......+...+...  ..+..||++|.+.
T Consensus       138 ~laral~~~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~~tii~vsh~~  189 (213)
T TIGR01277       138 ALARCLVRPNPILLLDEPFSALDPLLREEMLALVKQLCSERQRTLLMVTHHL  189 (213)
T ss_pred             HHHHHHhcCCCEEEEcCCCccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3445555678899999975544455556666655542  2367788887765

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.

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=96.05  E-value=0.053  Score=55.30  Aligned_cols=107  Identities=15%  Similarity=0.132  Sum_probs=57.1

Q ss_pred             CccEEEEEcCCCCcHH-HHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          196 TLPVIWILGNEGIGKT-ALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKT-tLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      +.++|+++||.||||| |||+..++-. ....=..+..++...-. .              +-...++...+-++.+...
T Consensus       202 ~~~vi~LVGPTGVGKTTTlAKLAar~~-~~~~~~kVaiITtDtYR-I--------------GA~EQLk~Ya~im~vp~~v  265 (407)
T COG1419         202 QKRVIALVGPTGVGKTTTLAKLAARYV-MLKKKKKVAIITTDTYR-I--------------GAVEQLKTYADIMGVPLEV  265 (407)
T ss_pred             cCcEEEEECCCCCcHHHHHHHHHHHHH-hhccCcceEEEEeccch-h--------------hHHHHHHHHHHHhCCceEE
Confidence            3789999999999999 5666665521 12222345556543211 1              1145555566666666544


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCC-CcchHHHHHHhhcCC
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNA-YPRYWEQLMYSLKSG  320 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~-~~~~~~~l~~~l~~~  320 (597)
                      ..+..++...+... ++. =+|.+|-+.... +......+...+...
T Consensus       266 v~~~~el~~ai~~l-~~~-d~ILVDTaGrs~~D~~~i~el~~~~~~~  310 (407)
T COG1419         266 VYSPKELAEAIEAL-RDC-DVILVDTAGRSQYDKEKIEELKELIDVS  310 (407)
T ss_pred             ecCHHHHHHHHHHh-hcC-CEEEEeCCCCCccCHHHHHHHHHHHhcc
Confidence            44444444444332 333 466678775433 123444555555443

>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed

Probab=96.05  E-value=0.068  Score=52.20  Aligned_cols=137  Identities=15%  Similarity=0.080  Sum_probs=65.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh-hcc--CC---eeEEEEecCCCch-h-hhhhhhhhhcccchHHHHHHHHHHh
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV-KAN--FD---KRIWVSASYPRDE-I-RVARDEISVARDRDEIRVAKAILES  267 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~--F~---~~~wv~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~il~~  267 (597)
                      ...+++|.|+.|.|||||++.++.-... .+.  ++   .+.++.-...... . .............. ......+++.
T Consensus        29 ~Ge~~~I~G~NGsGKSTLl~~i~Gl~~p~~G~i~~~~~~~i~~v~q~~~~~~~l~~~~~~~~~~~~~~~-~~~~~~~l~~  107 (251)
T PRK09544         29 PGKILTLLGPNGAGKSTLVRVVLGLVAPDEGVIKRNGKLRIGYVPQKLYLDTTLPLTVNRFLRLRPGTK-KEDILPALKR  107 (251)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCCCCCCceEEEECCccCEEEeccccccccccChhHHHHHhcccccc-HHHHHHHHHH
Confidence            3468999999999999999999864211 111  11   1222221111100 0 00111100000001 1223445555


Q ss_pred             ccCCC------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          268 LKGSV------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       268 l~~~~------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      ++...      .....-+...-.+...+..++-+|+||+--+.-+......+...+...  ..|..||++|.+.
T Consensus       108 ~gl~~~~~~~~~~LSgGq~qrv~laral~~~p~lllLDEPt~~LD~~~~~~l~~~L~~~~~~~g~tiiivsH~~  181 (251)
T PRK09544        108 VQAGHLIDAPMQKLSGGETQRVLLARALLNRPQLLVLDEPTQGVDVNGQVALYDLIDQLRRELDCAVLMVSHDL  181 (251)
T ss_pred             cCChHHHhCChhhCCHHHHHHHHHHHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            44321      011111222333555566678899999975544344555555555432  2266777777765

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=96.05  E-value=0.046  Score=51.68  Aligned_cols=50  Identities=22%  Similarity=0.122  Sum_probs=32.0

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+--..-+......+...+... ..+..||++|.+.
T Consensus       136 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~tH~~  186 (208)
T cd03268         136 GIALALLGNPDLLILDEPTNGLDPDGIKELRELILSLRDQGITVLISSHLL  186 (208)
T ss_pred             HHHHHHhcCCCEEEECCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEcCCH
Confidence            3455556677899999975544455555565555432 2467788888765

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.

>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=96.05  E-value=0.094  Score=49.68  Aligned_cols=50  Identities=12%  Similarity=0.143  Sum_probs=32.3

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+--..-+......+...+...  ..+..||++|.+.
T Consensus       138 ~ia~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~~tii~~sH~~  189 (211)
T cd03298         138 ALARVLVRDKPVLLLDEPFAALDPALRAEMLDLVLDLHAETKMTVLMVTHQP  189 (211)
T ss_pred             HHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            4555556678899999975544455666666666542  2367788877665

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.

>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=96.04  E-value=0.061  Score=51.98  Aligned_cols=50  Identities=12%  Similarity=-0.045  Sum_probs=31.8

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-C-CCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-S-EGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~-~gs~IIvTtR~~  333 (597)
                      .|...+..++-+|+||+--..-+......+...+... . .|..||++|.+.
T Consensus       146 ~ia~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tvi~vsH~~  197 (235)
T cd03261         146 ALARALALDPELLLYDEPTAGLDPIASGVIDDLIRSLKKELGLTSIMVTHDL  197 (235)
T ss_pred             HHHHHHhcCCCEEEecCCcccCCHHHHHHHHHHHHHHHHhcCcEEEEEecCH
Confidence            4555566678899999975544455555565555442 2 366788887665

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.

>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=96.04  E-value=0.053  Score=49.59  Aligned_cols=22  Identities=36%  Similarity=0.514  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++.++|++|+||||++..+...
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~   23 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALY   23 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            6789999999999999998873

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.

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=96.04  E-value=0.059  Score=52.10  Aligned_cols=50  Identities=16%  Similarity=0.131  Sum_probs=32.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+--..-+......+...+...  ..|..||++|.+.
T Consensus       142 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiii~sH~~  193 (236)
T TIGR03864       142 EIARALLHRPALLLLDEPTVGLDPASRAAIVAHVRALCRDQGLSVLWATHLV  193 (236)
T ss_pred             HHHHHHhcCCCEEEEcCCccCCCHHHHHHHHHHHHHHHHhCCCEEEEEecCh
Confidence            4555666778899999975544455556666655542  2466788887766

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.

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=96.04  E-value=0.067  Score=50.47  Aligned_cols=51  Identities=14%  Similarity=0.165  Sum_probs=33.3

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      -.+...+..++-+|+||+--..-+....+.+...+... ..|..||++|.+.
T Consensus       143 ~~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sh~~  194 (206)
T TIGR03608       143 VALARAILKDPPLILADEPTGSLDPKNRDEVLDLLLELNDEGKTIIIVTHDP  194 (206)
T ss_pred             HHHHHHHHcCCCEEEEeCCcCCCCHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            34556666788899999975544455556666555432 2367788887765

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.

>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria

Probab=96.03  E-value=0.055  Score=52.27  Aligned_cols=51  Identities=16%  Similarity=0.095  Sum_probs=33.8

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.+...|..++-+|+||+-...-+......+...+.....|..||++|.+.
T Consensus       146 l~la~aL~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sh~~  196 (236)
T cd03253         146 VAIARAILKNPPILLLDEATSALDTHTEREIQAALRDVSKGRTTIVIAHRL  196 (236)
T ss_pred             HHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEcCCH
Confidence            345566667888999999765444555566666665433367788888765

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.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=96.03  E-value=0.091  Score=49.56  Aligned_cols=137  Identities=17%  Similarity=0.113  Sum_probs=66.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hcc--CC-----------eeEEEEecCCCch-hhhhhhhhhhcc--cchHHH
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KAN--FD-----------KRIWVSASYPRDE-IRVARDEISVAR--DRDEIR  259 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~--F~-----------~~~wv~~~~~~~~-~~~~~~~~~~~~--~~~~~~  259 (597)
                      ..+++|.|+.|+|||||.+.++.-..- .+.  ++           .+.++.-...... .......+....  ......
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~~~~~~~~~~i~~~~q~~~~~~~~~tv~e~l~~~~~~~~~~~~  105 (205)
T cd03226          26 GEIIALTGKNGAGKTTLAKILAGLIKESSGSILLNGKPIKAKERRKSIGYVMQDVDYQLFTDSVREELLLGLKELDAGNE  105 (205)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCceEEEECCEEhhhHHhhcceEEEecChhhhhhhccHHHHHhhhhhhcCccHH
Confidence            469999999999999999999763110 110  10           1122221110000 011111111100  001112


Q ss_pred             HHHHHHHhccCCCC------chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccC
Q 041007          260 VAKAILESLKGSVS------SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSG  332 (597)
Q Consensus       260 ~~~~il~~l~~~~~------~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~  332 (597)
                      ...++++.++....      ....-+.-.-.+...+..++-+|+||+--..-+......+...+... ..|..||++|.+
T Consensus       106 ~~~~~l~~~~l~~~~~~~~~~LS~G~~qrv~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sH~  185 (205)
T cd03226         106 QAETVLKDLDLYALKERHPLSLSGGQKQRLAIAAALLSGKDLLIFDEPTSGLDYKNMERVGELIRELAAQGKAVIVITHD  185 (205)
T ss_pred             HHHHHHHHcCCchhcCCCchhCCHHHHHHHHHHHHHHhCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEeCC
Confidence            34555665544211      11111222233455556678899999975444455555555555432 346678888776


Q ss_pred             C
Q 041007          333 G  333 (597)
Q Consensus       333 ~  333 (597)
                      .
T Consensus       186 ~  186 (205)
T cd03226         186 Y  186 (205)
T ss_pred             H
Confidence            5

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.

>TIGR02673 FtsE cell division ATP-binding protein FtsE

Probab=96.02  E-value=0.065  Score=50.92  Aligned_cols=24  Identities=25%  Similarity=0.533  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.+..-
T Consensus        28 G~~~~l~G~nGsGKSTLl~~i~Gl   51 (214)
T TIGR02673        28 GEFLFLTGPSGAGKTTLLKLLYGA   51 (214)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999763

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.

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.02  E-value=0.019  Score=56.40  Aligned_cols=23  Identities=30%  Similarity=0.377  Sum_probs=18.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.|.|+|.||+||||+|+++...
T Consensus         2 pLiil~G~P~SGKTt~a~~L~~~   24 (270)
T PF08433_consen    2 PLIILCGLPCSGKTTRAKELKKY   24 (270)
T ss_dssp             -EEEEE--TTSSHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCcHHHHHHHHHHH
Confidence            47899999999999999999873

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.02  E-value=0.043  Score=55.75  Aligned_cols=46  Identities=17%  Similarity=0.184  Sum_probs=33.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh---hc-cCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV---KA-NFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~---~~-~F~~~~wv~~~~~~~~  241 (597)
                      ...++-|+|++|+|||+|+..++-....   .+ .-..++|++....+..
T Consensus       122 ~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~~f~~  171 (342)
T PLN03186        122 TGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRP  171 (342)
T ss_pred             CceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCCCccH
Confidence            4678999999999999999988743111   11 1136899998887765

>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=96.01  E-value=0.069  Score=51.62  Aligned_cols=24  Identities=25%  Similarity=0.268  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~Gl   49 (236)
T cd03219          26 GEIHGLIGPNGAGKTTLFNLISGF   49 (236)
T ss_pred             CcEEEEECCCCCCHHHHHHHHcCC
Confidence            468999999999999999999763

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).

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=96.01  E-value=0.07  Score=50.63  Aligned_cols=24  Identities=29%  Similarity=0.347  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++..
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~   49 (213)
T cd03301          26 GEFVVLLGPSGCGKTTTLRMIAGL   49 (213)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999864

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.

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=96.01  E-value=0.054  Score=51.87  Aligned_cols=50  Identities=18%  Similarity=0.084  Sum_probs=32.4

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+-..+-+++||+--+.-+....+.+...+... ..|..||++|.+.
T Consensus       134 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~L~~~~~~~~tiii~sH~~  184 (223)
T TIGR03740       134 GIAIALLNHPKLLILDEPTNGLDPIGIQELRELIRSFPEQGITVILSSHIL  184 (223)
T ss_pred             HHHHHHhcCCCEEEECCCccCCCHHHHHHHHHHHHHHHHCCCEEEEEcCCH
Confidence            3455556678899999975544455555665555432 3466788888776

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=96.00  E-value=0.0069  Score=63.55  Aligned_cols=43  Identities=21%  Similarity=0.246  Sum_probs=36.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||++.++.+...+...            ..|.|.|++|+|||+||+.+...
T Consensus        20 ~~i~gre~vI~lll~aalag------------~hVLL~GpPGTGKT~LAraLa~~   62 (498)
T PRK13531         20 KGLYERSHAIRLCLLAALSG------------ESVFLLGPPGIAKSLIARRLKFA   62 (498)
T ss_pred             hhccCcHHHHHHHHHHHccC------------CCEEEECCCChhHHHHHHHHHHH
Confidence            34899999999998888733            46899999999999999999873

>PRK04328 hypothetical protein; Provisional

Probab=96.00  E-value=0.038  Score=53.91  Aligned_cols=43  Identities=16%  Similarity=0.187  Sum_probs=32.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ...++.|.|++|+|||+|+.++...  ....-..++|++......
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~--~~~~ge~~lyis~ee~~~   64 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWN--GLQMGEPGVYVALEEHPV   64 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH--HHhcCCcEEEEEeeCCHH
Confidence            5679999999999999999998763  222345678888766443

>PTZ00035 Rad51 protein; Provisional

Probab=95.99  E-value=0.057  Score=54.97  Aligned_cols=46  Identities=15%  Similarity=0.182  Sum_probs=32.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh---hc-cCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV---KA-NFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~---~~-~F~~~~wv~~~~~~~~  241 (597)
                      ...++.|+|++|+|||+|+..++-....   .+ .-..++|++....+..
T Consensus       117 ~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~~f~~  166 (337)
T PTZ00035        117 TGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRP  166 (337)
T ss_pred             CCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccCCCCH
Confidence            5679999999999999999988743221   11 1234678887766554

>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway

Probab=95.99  E-value=0.027  Score=53.71  Aligned_cols=21  Identities=33%  Similarity=0.480  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|+|.|++|+||||||+.+..
T Consensus         1 IigI~G~sGSGKTTla~~L~~   21 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQA   21 (220)
T ss_pred             CEEeeCCCCCCHHHHHHHHHH
Confidence            589999999999999999987

The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=95.99  E-value=0.005  Score=53.03  Aligned_cols=21  Identities=38%  Similarity=0.547  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |.|.|++|+||||+|+++...
T Consensus         1 I~i~G~~GsGKtTia~~L~~~   21 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAER   21 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHH
Confidence            689999999999999999873

...

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

Probab=95.99  E-value=0.49  Score=44.71  Aligned_cols=63  Identities=21%  Similarity=0.250  Sum_probs=42.1

Q ss_pred             ccc-chhhHHHHHHHhhCCCCCC---cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          168 FHG-RNAEKQKILQLLKGESSDE---ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       168 ~vG-R~~e~~~l~~~L~~~~~~~---~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      .+| -+..+++|.+.+.-...+-   +.-+-.+++-|.++|++|.|||-||+.|+++       ..+-|+.+|.
T Consensus       148 MiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahh-------t~c~firvsg  214 (404)
T KOG0728|consen  148 MIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHH-------TDCTFIRVSG  214 (404)
T ss_pred             HhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhh-------cceEEEEech
Confidence            454 5788888877765332210   1111346778999999999999999999984       2344566664

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

Probab=95.99  E-value=0.14  Score=55.97  Aligned_cols=55  Identities=27%  Similarity=0.290  Sum_probs=36.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCc-CCCC-CCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEE-SGSK-PTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~-~~~~-~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +++=|-++-+.+|.+-+.-.-.+-+ -+++ ....=|.++|++|.|||-||++|+..
T Consensus       672 dDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATE  728 (953)
T KOG0736|consen  672 DDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATE  728 (953)
T ss_pred             hcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhh
Confidence            3455788888888887754211000 0001 12456889999999999999999983

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=95.98  E-value=0.084  Score=49.37  Aligned_cols=24  Identities=29%  Similarity=0.493  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|.|||||++.++..
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~G~   49 (195)
T PRK13541         26 SAITYIKGANGCGKSSLLRMIAGI   49 (195)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhcC
Confidence            459999999999999999999874

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.98  E-value=0.056  Score=52.40  Aligned_cols=21  Identities=24%  Similarity=0.230  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +..|+|++|+|||+|+..++-
T Consensus         3 ~~ll~g~~G~GKS~lal~la~   23 (239)
T cd01125           3 VSALVAPGGTGKSSLLLVLAL   23 (239)
T ss_pred             eeEEEcCCCCCHHHHHHHHHH
Confidence            567899999999999999875

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.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=95.98  E-value=0.04  Score=51.50  Aligned_cols=50  Identities=20%  Similarity=0.071  Sum_probs=32.3

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-++++|+.-+.-+......+...+... ..+..||++|.+.
T Consensus       121 ~laral~~~p~illlDEP~~~LD~~~~~~l~~~l~~~~~~~~tiii~sh~~  171 (194)
T cd03213         121 SIALELVSNPSLLFLDEPTSGLDSSSALQVMSLLRRLADTGRTIICSIHQP  171 (194)
T ss_pred             HHHHHHHcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEecCc
Confidence            4555566677899999975544455556666555432 3477788888765

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.

>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=95.98  E-value=0.076  Score=50.71  Aligned_cols=24  Identities=25%  Similarity=0.314  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||.+.++..
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~i~G~   49 (220)
T cd03265          26 GEIFGLLGPNGAGKTTTIKMLTTL   49 (220)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999763

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.

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

Probab=95.97  E-value=0.12  Score=56.01  Aligned_cols=136  Identities=16%  Similarity=0.162  Sum_probs=72.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      ..+.+.++|++|.|||.||+.+++  ....+|     +.+... +....                      .+      .
T Consensus       275 ~~~giLl~GpPGtGKT~lAkava~--~~~~~f-----i~v~~~-~l~sk----------------------~v------G  318 (494)
T COG0464         275 PPKGVLLYGPPGTGKTLLAKAVAL--ESRSRF-----ISVKGS-ELLSK----------------------WV------G  318 (494)
T ss_pred             CCCeeEEECCCCCCHHHHHHHHHh--hCCCeE-----EEeeCH-HHhcc----------------------cc------c
Confidence            456899999999999999999999  344444     332222 11000                      00      0


Q ss_pred             hhHHHHHHHHHHHhcCceEEEEEecccCC-----CC-c----chHHHHHHhhcCC--CCCcEEEEEccCCCCCCCccccc
Q 041007          276 VEMETVLQYINEFVQGKKVLLVLDDLWWN-----AY-P----RYWEQLMYSLKSG--SEGSRILVTRSGGKNGTNMTEIG  343 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~~kr~LLVLDdv~~~-----~~-~----~~~~~l~~~l~~~--~~gs~IIvTtR~~~~~~~~~~~~  343 (597)
                      .....+...+....+..+++|++|++...     +. .    ....++...+...  ..+..||-||-.. ...+..   
T Consensus       319 esek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v~vi~aTN~p-~~ld~a---  394 (494)
T COG0464         319 ESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRP-DDLDPA---  394 (494)
T ss_pred             hHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCceEEEecCCCc-cccCHh---
Confidence            11122333344444578999999998432     10 1    2333444444332  2333334444333 111100   


Q ss_pred             ccccCccccce--eecCCCChHHHHHHHHHHhc
Q 041007          344 LGEKNGTNMME--IGLGELSEEECRSLFRQIAF  374 (597)
Q Consensus       344 ~~~~~~~~~~~--~~l~~Ls~~es~~Lf~~~~~  374 (597)
                      +   .......  +.+.+-+.++..+.|..+..
T Consensus       395 ~---lR~gRfd~~i~v~~pd~~~r~~i~~~~~~  424 (494)
T COG0464         395 L---LRPGRFDRLIYVPLPDLEERLEIFKIHLR  424 (494)
T ss_pred             h---cccCccceEeecCCCCHHHHHHHHHHHhc
Confidence            0   0000111  88888899999999999874

>TIGR03005 ectoine_ehuA ectoine/hydroxyectoine ABC transporter, ATP-binding protein

Probab=95.97  E-value=0.071  Score=52.13  Aligned_cols=50  Identities=8%  Similarity=0.109  Sum_probs=31.3

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|+||+.-..-+......+...+...  ..|..||++|.+.
T Consensus       156 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~  207 (252)
T TIGR03005       156 AIARALAMRPKVMLFDEVTSALDPELVGEVLNVIRRLASEHDLTMLLVTHEM  207 (252)
T ss_pred             HHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCcEEEEEeCCH
Confidence            4555556677899999975444344555555555432  2367788887765

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.

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

Probab=95.97  E-value=0.25  Score=54.60  Aligned_cols=192  Identities=13%  Similarity=0.103  Sum_probs=98.3

Q ss_pred             Cccccchh---hHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNA---EKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~---e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      .++.|-++   |+.++++.|..+.. -..-+-.-++=+.|+||+|+|||-||++++-..  .     +-|++++..--+ 
T Consensus       311 kDVAG~deAK~El~E~V~fLKNP~~-Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA--g-----VPF~svSGSEFv-  381 (774)
T KOG0731|consen  311 KDVAGVDEAKEELMEFVKFLKNPEQ-YQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA--G-----VPFFSVSGSEFV-  381 (774)
T ss_pred             ccccCcHHHHHHHHHHHHHhcCHHH-HHHcCCcCcCceEEECCCCCcHHHHHHHHhccc--C-----CceeeechHHHH-
Confidence            35667765   44555666654321 000011346678999999999999999999842  2     334555532111 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC--------------cc
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY--------------PR  308 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~--------------~~  308 (597)
                                             +.+.+..     ...+.+.+...=...++++.+|++.....              ..
T Consensus       382 -----------------------E~~~g~~-----asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~  433 (774)
T KOG0731|consen  382 -----------------------EMFVGVG-----ASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQ  433 (774)
T ss_pred             -----------------------HHhcccc-----hHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHH
Confidence                                   1111110     01112222222235688999988743210              11


Q ss_pred             hHHHHHHhhcCCCC-CcEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          309 YWEQLMYSLKSGSE-GSRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       309 ~~~~l~~~l~~~~~-gs~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      .++++...+..... +..|++.+.+++...+..-.     ...+ ...+.+..-+...-.++|.-++..-..   ..+..
T Consensus       434 tlnQll~emDgf~~~~~vi~~a~tnr~d~ld~all-----rpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~---~~e~~  505 (774)
T KOG0731|consen  434 TLNQLLVEMDGFETSKGVIVLAATNRPDILDPALL-----RPGRFDRQIQIDLPDVKGRASILKVHLRKKKL---DDEDV  505 (774)
T ss_pred             HHHHHHHHhcCCcCCCcEEEEeccCCccccCHHhc-----CCCccccceeccCCchhhhHHHHHHHhhccCC---Ccchh
Confidence            33444444443332 33455555444322211100     0001 111777777778888888888743222   13344


Q ss_pred             HHHHHHHHhcCCchHHH
Q 041007          387 PIGRRVVGKCKGLPFAV  403 (597)
Q Consensus       387 ~~~~~I~~~~~GlPLai  403 (597)
                      ++.+ |+..+-|.+=|.
T Consensus       506 dl~~-~a~~t~gf~gad  521 (774)
T KOG0731|consen  506 DLSK-LASLTPGFSGAD  521 (774)
T ss_pred             hHHH-HHhcCCCCcHHH
Confidence            5555 888888887554

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.97  E-value=0.11  Score=47.14  Aligned_cols=53  Identities=19%  Similarity=0.218  Sum_probs=34.9

Q ss_pred             HHHHHHHHhcCc-eEEEEEecccCCC--CcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          281 VLQYINEFVQGK-KVLLVLDDLWWNA--YPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       281 ~~~~l~~~L~~k-r~LLVLDdv~~~~--~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .....++.+... -=|||||.+-..-  ..-..+.+...+...+.+..||+|.|+.
T Consensus        85 ~~~~a~~~l~~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~  140 (173)
T TIGR00708        85 AWQHAKEMLADPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGC  140 (173)
T ss_pred             HHHHHHHHHhcCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCC
Confidence            344445555444 4599999973211  0124556777777778889999999987

Alternate name: corrinoid adenosyltransferase.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=95.97  E-value=0.092  Score=55.22  Aligned_cols=25  Identities=28%  Similarity=0.356  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.+|.++|++|+||||++..++..
T Consensus        94 ~p~vI~lvG~~GsGKTTtaakLA~~  118 (437)
T PRK00771         94 KPQTIMLVGLQGSGKTTTAAKLARY  118 (437)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH
Confidence            5689999999999999999999874

>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=95.96  E-value=0.069  Score=51.87  Aligned_cols=24  Identities=21%  Similarity=0.279  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|.|||||++.++..
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~G~   50 (242)
T cd03295          27 GEFLVLIGPSGSGKTTTMKMINRL   50 (242)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            468999999999999999999763

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.

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=95.96  E-value=0.072  Score=51.11  Aligned_cols=50  Identities=10%  Similarity=-0.034  Sum_probs=32.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .|...+..++-+++||+--..-+......+...+...  ..|..||++|.+.
T Consensus       147 ~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tvii~sh~~  198 (225)
T PRK10247        147 SLIRNLQFMPKVLLLDEITSALDESNKHNVNEIIHRYVREQNIAVLWVTHDK  198 (225)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEECCh
Confidence            4555666778899999975444355556666665542  2367788888765

>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=95.95  E-value=0.084  Score=50.14  Aligned_cols=50  Identities=20%  Similarity=0.194  Sum_probs=30.9

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+++||+--..-+......+...+... ..|..||++|.+.
T Consensus       146 ~laral~~~p~llllDEPt~~LD~~~~~~~~~~l~~~~~~~~tiiivtH~~  196 (214)
T cd03292         146 AIARAIVNSPTILIADEPTGNLDPDTTWEIMNLLKKINKAGTTVVVATHAK  196 (214)
T ss_pred             HHHHHHHcCCCEEEEeCCCCcCCHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            3455555677899999975444344555555555432 3466777777665

The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=95.95  E-value=0.11  Score=50.22  Aligned_cols=50  Identities=18%  Similarity=0.104  Sum_probs=32.2

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       155 ~la~al~~~p~lllLDEPt~~LD~~~~~~l~~~l~~~~~~~g~tvii~sH~~  206 (233)
T PRK11629        155 AIARALVNNPRLVLADEPTGNLDARNADSIFQLLGELNRLQGTAFLVVTHDL  206 (233)
T ss_pred             HHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            3555566678899999975444455555566555542  2467788887765

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=95.95  E-value=0.017  Score=52.77  Aligned_cols=23  Identities=35%  Similarity=0.681  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.|.++|.+|+||||+|+++.+.
T Consensus         2 pLiIlTGyPgsGKTtfakeLak~   24 (261)
T COG4088           2 PLIILTGYPGSGKTTFAKELAKE   24 (261)
T ss_pred             ceEEEecCCCCCchHHHHHHHHH
Confidence            57889999999999999999883

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=95.94  E-value=0.028  Score=50.48  Aligned_cols=115  Identities=15%  Similarity=0.105  Sum_probs=59.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ..+++|.|+.|.|||||++.+...  . ......+++.-........              ..    ....++-... ..
T Consensus        25 g~~~~i~G~nGsGKStll~~l~g~--~-~~~~G~i~~~~~~~~~~~~--------------~~----~~~~i~~~~q-lS   82 (157)
T cd00267          25 GEIVALVGPNGSGKSTLLRAIAGL--L-KPTSGEILIDGKDIAKLPL--------------EE----LRRRIGYVPQ-LS   82 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC--C-CCCccEEEECCEEcccCCH--------------HH----HHhceEEEee-CC
Confidence            369999999999999999999873  2 2234444443211110000              00    0011110000 11


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .-+...-.+...+...+-++++|+.-..-+......+...+... ..+..+|++|.+.
T Consensus        83 ~G~~~r~~l~~~l~~~~~i~ilDEp~~~lD~~~~~~l~~~l~~~~~~~~tii~~sh~~  140 (157)
T cd00267          83 GGQRQRVALARALLLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDP  140 (157)
T ss_pred             HHHHHHHHHHHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            11222223445555667899999985544444555555555432 2256778877655

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.

>TIGR01188 drrA daunorubicin resistance ABC transporter ATP-binding subunit

Probab=95.93  E-value=0.085  Score=53.10  Aligned_cols=50  Identities=22%  Similarity=0.163  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|+||+--+.-+...-..+...+.. ...|..||++|.+.
T Consensus       134 ~la~al~~~p~lllLDEPt~gLD~~~~~~l~~~l~~~~~~g~tvi~~sH~~  184 (302)
T TIGR01188       134 DIAASLIHQPDVLFLDEPTTGLDPRTRRAIWDYIRALKEEGVTILLTTHYM  184 (302)
T ss_pred             HHHHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEECCCH
Confidence            455566678889999996544334444444444433 23477899998876

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.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=95.92  E-value=0.076  Score=50.41  Aligned_cols=50  Identities=14%  Similarity=0.133  Sum_probs=31.3

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++=+|+||+--..-+......+...+... ..|..||++|.+.
T Consensus       145 ~la~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~~tvi~~sh~~  195 (213)
T cd03262         145 AIARALAMNPKVMLFDEPTSALDPELVGEVLDVMKDLAEEGMTMVVVTHEM  195 (213)
T ss_pred             HHHHHHhcCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            3455556677899999975444455555565555432 2466788887665

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

>PTZ00301 uridine kinase; Provisional

Probab=95.92  E-value=0.0092  Score=56.31  Aligned_cols=23  Identities=35%  Similarity=0.535  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|++|+||||||+.+..
T Consensus         3 ~~iIgIaG~SgSGKTTla~~l~~   25 (210)
T PTZ00301          3 CTVIGISGASGSGKSSLSTNIVS   25 (210)
T ss_pred             CEEEEEECCCcCCHHHHHHHHHH
Confidence            46999999999999999998876

>TIGR03873 F420-0_ABC_ATP proposed F420-0 ABC transporter, ATP-binding protein

Probab=95.91  E-value=0.094  Score=51.39  Aligned_cols=51  Identities=12%  Similarity=0.038  Sum_probs=32.8

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      -.+...+..++-+++||+.-..-+......+...+... ..|..||++|.+.
T Consensus       146 l~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~  197 (256)
T TIGR03873       146 VHVARALAQEPKLLLLDEPTNHLDVRAQLETLALVRELAATGVTVVAALHDL  197 (256)
T ss_pred             HHHHHHHhcCCCEEEEcCccccCCHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            34555666778899999975544455555665555432 2366788888765

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.

>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA

Probab=95.91  E-value=0.082  Score=49.55  Aligned_cols=50  Identities=16%  Similarity=0.076  Sum_probs=31.1

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|++|+.-+.-+......+...+.. ...|..||++|.+.
T Consensus       137 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tii~~sH~~  187 (198)
T TIGR01189       137 ALARLWLSRAPLWILDEPTTALDKAGVALLAGLLRAHLARGGIVLLTTHQD  187 (198)
T ss_pred             HHHHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEEccc
Confidence            355556677889999997544434455555555543 23456777777765

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.

>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein

Probab=95.90  E-value=0.09  Score=50.22  Aligned_cols=24  Identities=25%  Similarity=0.313  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||.+.++..
T Consensus        31 G~~~~i~G~nGsGKSTLl~~i~G~   54 (221)
T TIGR02211        31 GEIVAIVGSSGSGKSTLLHLLGGL   54 (221)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999763

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.

>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=95.90  E-value=0.078  Score=50.68  Aligned_cols=50  Identities=22%  Similarity=0.313  Sum_probs=31.1

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|++|+--..-+......+...+... ..+..||++|.+.
T Consensus       142 ~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~tiii~sH~~  192 (222)
T cd03224         142 AIARALMSRPKLLLLDEPSEGLAPKIVEEIFEAIRELRDEGVTILLVEQNA  192 (222)
T ss_pred             HHHHHHhcCCCEEEECCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            3445555677899999975443344555555555432 2467888888765

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.

>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=95.90  E-value=0.1  Score=50.42  Aligned_cols=50  Identities=20%  Similarity=0.077  Sum_probs=33.1

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+.-..-+......+...+...  ..+..||++|.+.
T Consensus       163 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tiiivsH~~  214 (236)
T cd03267         163 EIAAALLHEPEILFLDEPTIGLDVVAQENIRNFLKEYNRERGTTVLLTSHYM  214 (236)
T ss_pred             HHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHHHHHHHhcCCCEEEEEecCH
Confidence            4555666778899999975554455556666665542  2366788888766

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.

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

Probab=95.89  E-value=0.012  Score=56.46  Aligned_cols=44  Identities=36%  Similarity=0.437  Sum_probs=30.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      +...++.|.|++|+|||+|+.++... ..+..=..++|++...+.
T Consensus        17 p~gs~~li~G~~GsGKT~l~~q~l~~-~~~~~ge~vlyvs~ee~~   60 (226)
T PF06745_consen   17 PKGSVVLISGPPGSGKTTLALQFLYN-GLKNFGEKVLYVSFEEPP   60 (226)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHH-HHHHHT--EEEEESSS-H
T ss_pred             CCCcEEEEEeCCCCCcHHHHHHHHHH-hhhhcCCcEEEEEecCCH
Confidence            45689999999999999999998763 122213457788876554

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 ....

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=95.88  E-value=0.08  Score=51.50  Aligned_cols=138  Identities=15%  Similarity=0.043  Sum_probs=66.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh-hc--cCCe--eEEEEecCCCchhhhhhhhhhhc-c-cchHHHHHHHHHHhc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV-KA--NFDK--RIWVSASYPRDEIRVARDEISVA-R-DRDEIRVAKAILESL  268 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~--~F~~--~~wv~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~il~~l  268 (597)
                      ...+++|.|+.|+|||||++.+.....- .+  .++.  +.++.-.............+... . ..........+++.+
T Consensus        24 ~Ge~~~i~G~NGsGKSTLlk~L~G~~~p~~G~i~~~g~~i~~~~q~~~~~~~~tv~e~l~~~~~~~~~~~~~~~~~l~~l  103 (246)
T cd03237          24 ESEVIGILGPNGIGKTTFIKMLAGVLKPDEGDIEIELDTVSYKPQYIKADYEGTVRDLLSSITKDFYTHPYFKTEIAKPL  103 (246)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCcCCCCeEEECCceEEEecccccCCCCCCHHHHHHHHhhhccccHHHHHHHHHHc
Confidence            3469999999999999999999874211 11  1111  22221110000000111111100 0 000012234455554


Q ss_pred             cCCC------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          269 KGSV------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       269 ~~~~------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      +...      .....-+...-.|...|..++-+++||+--..-+......+...+...  ..+..||++|.+.
T Consensus       104 ~l~~~~~~~~~~LSgGe~qrv~iaraL~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tiiivsHd~  176 (246)
T cd03237         104 QIEQILDREVPELSGGELQRVAIAACLSKDADIYLLDEPSAYLDVEQRLMASKVIRRFAENNEKTAFVVEHDI  176 (246)
T ss_pred             CCHHHhhCChhhCCHHHHHHHHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            4321      111111222334556667788899999975443344445555555432  2366788887765

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.

>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD

Probab=95.87  E-value=0.1  Score=50.61  Aligned_cols=51  Identities=20%  Similarity=0.063  Sum_probs=32.1

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.+...+-.++-+|+||+.-+.-+......+...+.....+..||++|.+.
T Consensus       152 v~laral~~~p~~lllDEPt~~LD~~~~~~l~~~l~~~~~~~tii~~sH~~  202 (242)
T TIGR03411       152 LEIGMLLMQDPKLLLLDEPVAGMTDEETEKTAELLKSLAGKHSVVVVEHDM  202 (242)
T ss_pred             HHHHHHHhcCCCEEEecCCccCCCHHHHHHHHHHHHHHhcCCEEEEEECCH
Confidence            345555666778999999755444555555655554433356788887765

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.

>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]

Probab=95.87  E-value=0.016  Score=54.05  Aligned_cols=24  Identities=33%  Similarity=0.562  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.+|+|.|.+|+||||+|+.++.
T Consensus         7 ~~iiIgIaG~SgSGKTTva~~l~~   30 (218)
T COG0572           7 KVIIIGIAGGSGSGKTTVAKELSE   30 (218)
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHH
Confidence            568999999999999999999988

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=95.86  E-value=0.084  Score=51.16  Aligned_cols=24  Identities=33%  Similarity=0.418  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.+...
T Consensus        27 Ge~~~l~G~nGsGKSTLl~~l~G~   50 (240)
T PRK09493         27 GEVVVIIGPSGSGKSTLLRCINKL   50 (240)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999763

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=95.85  E-value=0.061  Score=50.41  Aligned_cols=22  Identities=27%  Similarity=0.264  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++++|+|+.|.|||||.+.+.-
T Consensus        26 ~~~~ltGpNg~GKSTllr~i~~   47 (199)
T cd03283          26 NGILITGSNMSGKSTFLRTIGV   47 (199)
T ss_pred             cEEEEECCCCCChHHHHHHHHH
Confidence            7999999999999999998865

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

>PRK10418 nikD nickel transporter ATP-binding protein NikD; Provisional

Probab=95.84  E-value=0.12  Score=50.53  Aligned_cols=24  Identities=21%  Similarity=0.291  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++-.
T Consensus        29 Ge~~~l~G~nGsGKSTLl~~l~Gl   52 (254)
T PRK10418         29 GRVLALVGGSGSGKSLTCAAALGI   52 (254)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999763

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=95.84  E-value=0.079  Score=59.68  Aligned_cols=122  Identities=16%  Similarity=0.201  Sum_probs=69.9

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCC-CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSK-PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~-~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .++|.++.+..|.+.+......-   .+ .....+.+.|+.|+|||-||+++..  .+-+..+..+-++++.        
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl---~~~~~~awflflGpdgvGKt~lAkaLA~--~~Fgse~~~IriDmse--------  629 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAGL---KDPNPDAWFLFLGPDGVGKTELAKALAE--YVFGSEENFIRLDMSE--------  629 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhccc---CCCCCCeEEEEECCCchhHHHHHHHHHH--HHcCCccceEEechhh--------
Confidence            45677777777777776444211   11 2466788999999999999999877  3333333344444332        


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceE-EEEEecccCCCCcchHHHHHHhhcC
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKV-LLVLDDLWWNAYPRYWEQLMYSLKS  319 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~-LLVLDdv~~~~~~~~~~~l~~~l~~  319 (597)
                                    ... +.+.++.+. .-.. .+....|.+.++.++| +|+||||...+ ......+...+..
T Consensus       630 --------------~~e-vskligsp~-gyvG-~e~gg~LteavrrrP~sVVLfdeIEkAh-~~v~n~llq~lD~  686 (898)
T KOG1051|consen  630 --------------FQE-VSKLIGSPP-GYVG-KEEGGQLTEAVKRRPYSVVLFEEIEKAH-PDVLNILLQLLDR  686 (898)
T ss_pred             --------------hhh-hhhccCCCc-cccc-chhHHHHHHHHhcCCceEEEEechhhcC-HHHHHHHHHHHhc
Confidence                          111 222223322 1110 1123356666777775 66699997766 5555655566543

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=95.83  E-value=0.007  Score=53.36  Aligned_cols=21  Identities=33%  Similarity=0.600  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|.+.|++|+||||+|+.+..
T Consensus         1 lii~~G~pgsGKSt~a~~l~~   21 (143)
T PF13671_consen    1 LIILCGPPGSGKSTLAKRLAK   21 (143)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999975

...

>PRK05439 pantothenate kinase; Provisional

Probab=95.83  E-value=0.048  Score=54.48  Aligned_cols=25  Identities=28%  Similarity=0.313  Sum_probs=22.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+-+|+|.|.+|+||||+|+.+..
T Consensus        84 ~~~~iIgIaG~~gsGKSTla~~L~~  108 (311)
T PRK05439         84 KVPFIIGIAGSVAVGKSTTARLLQA  108 (311)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4678999999999999999998876

>PRK10867 signal recognition particle protein; Provisional

Probab=95.83  E-value=0.063  Score=56.28  Aligned_cols=24  Identities=33%  Similarity=0.476  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.+|.++|++|+||||.+..++.
T Consensus        99 ~p~vI~~vG~~GsGKTTtaakLA~  122 (433)
T PRK10867         99 PPTVIMMVGLQGAGKTTTAGKLAK  122 (433)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHH
Confidence            468999999999999998888776

>cd03294 ABC_Pro_Gly_Bertaine This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea

Probab=95.82  E-value=0.12  Score=51.13  Aligned_cols=50  Identities=10%  Similarity=0.030  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .|...+-.++-+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       170 ~lAral~~~p~illLDEPt~~LD~~~~~~l~~~l~~~~~~~g~tiii~tH~~  221 (269)
T cd03294         170 GLARALAVDPDILLMDEAFSALDPLIRREMQDELLRLQAELQKTIVFITHDL  221 (269)
T ss_pred             HHHHHHhcCCCEEEEcCCCccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3555666778899999975444344555555555432  2367788887765

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.

>PRK10908 cell division protein FtsE; Provisional

Probab=95.82  E-value=0.12  Score=49.45  Aligned_cols=25  Identities=20%  Similarity=0.392  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|.|+.|+|||||++.++.-
T Consensus        27 ~Ge~~~i~G~nGsGKSTLl~~l~G~   51 (222)
T PRK10908         27 PGEMAFLTGHSGAGKSTLLKLICGI   51 (222)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3469999999999999999999763

>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=95.82  E-value=0.1  Score=50.45  Aligned_cols=50  Identities=14%  Similarity=0.055  Sum_probs=32.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+....-+......+...+.....|..||++|.+.
T Consensus       149 ~la~al~~~p~llllDEP~~gLD~~~~~~l~~~l~~~~~g~~vi~~sh~~  198 (238)
T cd03249         149 AIARALLRNPKILLLDEATSALDAESEKLVQEALDRAMKGRTTIVIAHRL  198 (238)
T ss_pred             HHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEeCCH
Confidence            35555566777999999765544555566666664433567788888765

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.

>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional

Probab=95.81  E-value=0.11  Score=50.71  Aligned_cols=50  Identities=8%  Similarity=0.119  Sum_probs=30.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .|...+..++-+|+||+--+.-+......+...+... ..|..||++|.+.
T Consensus       154 ~la~al~~~p~lllLDEPt~~LD~~~~~~l~~~l~~~~~~~~tvi~~tH~~  204 (250)
T PRK11264        154 AIARALAMRPEVILFDEPTSALDPELVGEVLNTIRQLAQEKRTMVIVTHEM  204 (250)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3455556677899999975444344555555554432 2366777777765

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=95.81  E-value=0.22  Score=46.89  Aligned_cols=53  Identities=8%  Similarity=-0.040  Sum_probs=32.4

Q ss_pred             HHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHh-hcC-CCCCcEEEEEccCC
Q 041007          281 VLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYS-LKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       281 ~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~-l~~-~~~gs~IIvTtR~~  333 (597)
                      ..-.+...+..++-++++|+--..-+....+.+... +.. ...|..||++|.+.
T Consensus       134 qrv~laral~~~p~llllDEP~~~LD~~~~~~l~~~ll~~~~~~~~tvi~~sh~~  188 (204)
T cd03250         134 QRISLARAVYSDADIYLLDDPLSAVDAHVGRHIFENCILGLLLNNKTRILVTHQL  188 (204)
T ss_pred             HHHHHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHHhccCCCEEEEEeCCH
Confidence            334466667778899999996544334455555543 332 23467777777665

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.

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=95.80  E-value=0.11  Score=51.08  Aligned_cols=52  Identities=13%  Similarity=0.113  Sum_probs=32.7

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .-.|...+-.++-+++||+--..-+......+...+... ..|..||++|.+.
T Consensus       160 rv~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~l~~~g~tiiivsH~~  212 (257)
T PRK10619        160 RVSIARALAMEPEVLLFDEPTSALDPELVGEVLRIMQQLAEEGKTMVVVTHEM  212 (257)
T ss_pred             HHHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            334555666677899999875444455555565555432 2467778777765

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=95.80  E-value=0.047  Score=51.28  Aligned_cols=50  Identities=14%  Similarity=0.020  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-++++|+--+.-+......+...+... ..+..||++|.+.
T Consensus       114 ~laral~~~p~illlDEPt~~LD~~~~~~l~~~L~~~~~~~~tiii~sh~~  164 (200)
T cd03217         114 EILQLLLLEPDLAILDEPDSGLDIDALRLVAEVINKLREEGKSVLIITHYQ  164 (200)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHCCCEEEEEecCH
Confidence            4555566778899999975444344555555555432 2366788887765

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.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=95.80  E-value=0.053  Score=53.47  Aligned_cols=39  Identities=21%  Similarity=0.329  Sum_probs=27.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ..+++.++|++|+||||++..++..  ....-..+.++++.
T Consensus        71 ~~~vi~l~G~~G~GKTTt~akLA~~--l~~~g~~V~li~~D  109 (272)
T TIGR00064        71 KPNVILFVGVNGVGKTTTIAKLANK--LKKQGKSVLLAAGD  109 (272)
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHH--HHhcCCEEEEEeCC
Confidence            4689999999999999999888763  33332345555543

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.

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=95.79  E-value=0.059  Score=50.25  Aligned_cols=23  Identities=26%  Similarity=0.377  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|.|||||++.++.
T Consensus        33 Ge~~~l~G~nGsGKSTLl~~l~G   55 (192)
T cd03232          33 GTLTALMGESGAGKTTLLDVLAG   55 (192)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            46999999999999999999986

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.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=95.78  E-value=0.0063  Score=46.17  Aligned_cols=22  Identities=32%  Similarity=0.631  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +|+|.|.+|+||||+++.+.+.
T Consensus         1 ~i~i~G~~gsGKst~~~~l~~~   22 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQ   22 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999873

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.78  E-value=0.11  Score=47.74  Aligned_cols=53  Identities=17%  Similarity=0.186  Sum_probs=35.5

Q ss_pred             HHHHHHHHhcC-ceEEEEEecccCCC--CcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          281 VLQYINEFVQG-KKVLLVLDDLWWNA--YPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       281 ~~~~l~~~L~~-kr~LLVLDdv~~~~--~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .....++.+.. +-=|||||.+-..-  ..-..+.+...+...+.+..||+|-|..
T Consensus       103 ~~~~a~~~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~  158 (191)
T PRK05986        103 GWEEAKRMLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGA  158 (191)
T ss_pred             HHHHHHHHHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCC
Confidence            34445555544 44599999973221  0224567777887778889999999977

>TIGR00235 udk uridine kinase

Probab=95.78  E-value=0.0076  Score=57.05  Aligned_cols=25  Identities=40%  Similarity=0.662  Sum_probs=22.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +...+|+|+|++|+|||||++.+..
T Consensus         4 ~~g~vi~I~G~sGsGKSTl~~~l~~   28 (207)
T TIGR00235         4 PKGIIIGIGGGSGSGKTTVARKIYE   28 (207)
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHHH
Confidence            3568999999999999999999986

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.77  E-value=0.054  Score=57.01  Aligned_cols=39  Identities=18%  Similarity=0.198  Sum_probs=26.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      .++++++|++|+||||++..++........-..+..++.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~  259 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITL  259 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEEC
Confidence            469999999999999998887763221122234555654

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.76  E-value=0.13  Score=49.95  Aligned_cols=50  Identities=12%  Similarity=-0.012  Sum_probs=31.6

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|+||+.-+.-+......+...+...  ..|..||++|.+.
T Consensus       141 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~g~tii~~sH~~  192 (241)
T PRK14250        141 SIARTLANNPEVLLLDEPTSALDPTSTEIIEELIVKLKNKMNLTVIWITHNM  192 (241)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhCCCEEEEEeccH
Confidence            3555555677899999975544455555565555542  2366788877765

>TIGR00968 3a0106s01 sulfate ABC transporter, ATP-binding protein

Probab=95.75  E-value=0.085  Score=51.02  Aligned_cols=50  Identities=10%  Similarity=0.044  Sum_probs=32.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+.-..-+....+.+...+...  ..+..||++|.+.
T Consensus       140 ~laral~~~p~llllDEP~~~LD~~~~~~~~~~l~~~~~~~~~tvli~sH~~  191 (237)
T TIGR00968       140 ALARALAVEPQVLLLDEPFGALDAKVRKELRSWLRKLHDEVHVTTVFVTHDQ  191 (237)
T ss_pred             HHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3455556677899999975554455666666666542  2266788887765

>PRK14256 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.75  E-value=0.14  Score=50.03  Aligned_cols=23  Identities=30%  Similarity=0.463  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||++.++.
T Consensus        30 Ge~~~i~G~nGsGKSTLl~~l~G   52 (252)
T PRK14256         30 NSVTAIIGPSGCGKSTVLRSINR   52 (252)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999999976

>TIGR00554 panK_bact pantothenate kinase, bacterial type

Probab=95.75  E-value=0.047  Score=54.08  Aligned_cols=24  Identities=29%  Similarity=0.342  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.+|+|.|+.|+||||+|+.+..
T Consensus        61 ~p~IIGIaG~~GSGKSTlar~L~~   84 (290)
T TIGR00554        61 IPYIISIAGSVAVGKSTTARILQA   84 (290)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            568999999999999999987754

Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model.

>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins

Probab=95.75  E-value=0.12  Score=49.78  Aligned_cols=51  Identities=12%  Similarity=-0.029  Sum_probs=32.9

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.+...+..++-+++||+.-+.-+....+.+...+.....+..||++|.+.
T Consensus       147 v~la~al~~~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~sh~~  197 (234)
T cd03251         147 IAIARALLKDPPILILDEATSALDTESERLVQAALERLMKNRTTFVIAHRL  197 (234)
T ss_pred             HHHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEecCH
Confidence            345555666777999999755444555666666665433466788888765

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.

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=95.74  E-value=0.12  Score=50.99  Aligned_cols=52  Identities=12%  Similarity=0.013  Sum_probs=32.4

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .-.+...+..++-+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       155 rv~laral~~~p~lllLDEPt~~LD~~~~~~~~~~l~~l~~~~~~tiii~sH~~  208 (265)
T PRK10575        155 RAWIAMLVAQDSRCLLLDEPTSALDIAHQVDVLALVHRLSQERGLTVIAVLHDI  208 (265)
T ss_pred             HHHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            334556666788899999975443344555555555432  2366788887765

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=95.74  E-value=0.1  Score=50.61  Aligned_cols=50  Identities=22%  Similarity=0.155  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .|...+...+-+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       154 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~tH~~  205 (241)
T cd03256         154 AIARALMQQPKLILADEPVASLDPASSRQVMDLLKRINREEGITVIVSLHQV  205 (241)
T ss_pred             HHHHHHhcCCCEEEEeCccccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3455556677899999975544455555565555442  2366778777765

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.

>PRK10771 thiQ thiamine transporter ATP-binding subunit; Provisional

Probab=95.74  E-value=0.14  Score=49.36  Aligned_cols=50  Identities=10%  Similarity=0.164  Sum_probs=31.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+--..-+......+...+...  ..|..||++|.+.
T Consensus       139 ~laral~~~p~lllLDEP~~gLD~~~~~~~~~~l~~~~~~~~~tiii~sH~~  190 (232)
T PRK10771        139 ALARCLVREQPILLLDEPFSALDPALRQEMLTLVSQVCQERQLTLLMVSHSL  190 (232)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEECCH
Confidence            3445556677899999875444455555565555432  2366788888766

>cd03299 ABC_ModC_like Archeal protein closely related to ModC

Probab=95.73  E-value=0.11  Score=50.29  Aligned_cols=24  Identities=29%  Similarity=0.301  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++..
T Consensus        25 Ge~~~i~G~nG~GKStLl~~l~G~   48 (235)
T cd03299          25 GDYFVILGPTGSGKSVLLETIAGF   48 (235)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999764

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.

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=95.73  E-value=0.02  Score=56.15  Aligned_cols=43  Identities=23%  Similarity=0.318  Sum_probs=31.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      +...++.|.|++|+|||+++.+++..  ....=..+++++...+.
T Consensus        34 p~gs~~lI~G~pGtGKT~l~~qf~~~--~a~~Ge~vlyis~Ee~~   76 (259)
T TIGR03878        34 PAYSVINITGVSDTGKSLMVEQFAVT--QASRGNPVLFVTVESPA   76 (259)
T ss_pred             ECCcEEEEEcCCCCCHHHHHHHHHHH--HHhCCCcEEEEEecCCc
Confidence            45679999999999999999998663  22223457778876433

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

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=95.73  E-value=0.029  Score=53.75  Aligned_cols=43  Identities=26%  Similarity=0.320  Sum_probs=31.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ...++.|.|.+|+|||+++.+++..  ....=..++|++.....+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~--~~~~g~~~~y~s~e~~~~   57 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQ--GLKNGEKAMYISLEEREE   57 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCCCHH
Confidence            4679999999999999999998763  222234577888766543

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.

>PRK14267 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.73  E-value=0.12  Score=50.54  Aligned_cols=50  Identities=16%  Similarity=0.041  Sum_probs=30.8

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .|...+..++-+|+||+--+.-+......+...+.....+..||++|.+.
T Consensus       159 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sH~~  208 (253)
T PRK14267        159 VIARALAMKPKILLMDEPTANIDPVGTAKIEELLFELKKEYTIVLVTHSP  208 (253)
T ss_pred             HHHHHHhcCCCEEEEcCCCccCCHHHHHHHHHHHHHHhhCCEEEEEECCH
Confidence            34555566788999999754433445555555554433346777777765

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=95.73  E-value=0.12  Score=49.58  Aligned_cols=50  Identities=14%  Similarity=0.088  Sum_probs=31.8

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+...+=+|+||+--..-+....+.+...+...  ..|..||++|.+.
T Consensus       156 ~la~al~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~~~tii~~sH~~  207 (228)
T PRK10584        156 ALARAFNGRPDVLFADEPTGNLDRQTGDKIADLLFSLNREHGTTLILVTHDL  207 (228)
T ss_pred             HHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            3455555677799999975544455556666655432  2366788888765

>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein

Probab=95.73  E-value=0.095  Score=50.88  Aligned_cols=24  Identities=29%  Similarity=0.361  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|+.|+|||||++.++.-
T Consensus        28 Ge~~~l~G~nGsGKSTLl~~l~Gl   51 (243)
T TIGR02315        28 GEFVAIIGPSGAGKSTLLRCINRL   51 (243)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999998753

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.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=95.72  E-value=0.0087  Score=56.74  Aligned_cols=25  Identities=32%  Similarity=0.582  Sum_probs=22.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +..+|+|.|++|+|||||++.+...
T Consensus         5 ~~~iI~I~G~sGsGKTTl~~~l~~~   29 (209)
T PRK05480          5 KPIIIGIAGGSGSGKTTVASTIYEE   29 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            5679999999999999999999873

>TIGR00959 ffh signal recognition particle protein

Probab=95.71  E-value=0.084  Score=55.33  Aligned_cols=25  Identities=28%  Similarity=0.341  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.++.++|++|+||||.+..++..
T Consensus        98 ~p~vi~~vG~~GsGKTTtaakLA~~  122 (428)
T TIGR00959        98 PPTVILMVGLQGSGKTTTCGKLAYY  122 (428)
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHH
Confidence            4679999999999999998888773

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.

>TIGR01184 ntrCD nitrate transport ATP-binding subunits C and D

Probab=95.71  E-value=0.094  Score=50.47  Aligned_cols=50  Identities=14%  Similarity=0.044  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+...+..++=+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       124 ~la~al~~~p~lllLDEPt~gLD~~~~~~l~~~l~~~~~~~~~tii~~sH~~  175 (230)
T TIGR01184       124 AIARALSIRPKVLLLDEPFGALDALTRGNLQEELMQIWEEHRVTVLMVTHDV  175 (230)
T ss_pred             HHHHHHHcCCCEEEEcCCCcCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            3555566677899999975444455555666555432  2366788887765

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.

>PRK03846 adenylylsulfate kinase; Provisional

Probab=95.71  E-value=0.037  Score=51.91  Aligned_cols=25  Identities=28%  Similarity=0.494  Sum_probs=22.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +...+|+|+|++|+||||||+.+..
T Consensus        22 ~~~~~i~i~G~~GsGKSTla~~l~~   46 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEE   46 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999999987

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.70  E-value=0.064  Score=56.94  Aligned_cols=40  Identities=35%  Similarity=0.386  Sum_probs=30.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ...++.|.|++|+|||||+.+++..  ....-..++|++...
T Consensus        79 ~Gs~~lI~G~pG~GKTtL~lq~a~~--~a~~g~~vlYvs~Ee  118 (446)
T PRK11823         79 PGSVVLIGGDPGIGKSTLLLQVAAR--LAAAGGKVLYVSGEE  118 (446)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEccc
Confidence            4569999999999999999999874  322223567887654

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.69  E-value=0.089  Score=48.67  Aligned_cols=25  Identities=32%  Similarity=0.477  Sum_probs=21.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +...|.++.||+|+||||+.+.+-+
T Consensus        31 ~~~~VTAlIGPSGcGKST~LR~lNR   55 (253)
T COG1117          31 PKNKVTALIGPSGCGKSTLLRCLNR   55 (253)
T ss_pred             cCCceEEEECCCCcCHHHHHHHHHh
Confidence            3568999999999999999998854

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=95.69  E-value=0.03  Score=57.38  Aligned_cols=26  Identities=27%  Similarity=0.414  Sum_probs=23.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCCh
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDS  221 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~  221 (597)
                      .++=+-|||..|.|||.|+-.+|+..
T Consensus        61 ~~~GlYl~G~vG~GKT~Lmd~f~~~l   86 (362)
T PF03969_consen   61 PPKGLYLWGPVGRGKTMLMDLFYDSL   86 (362)
T ss_pred             CCceEEEECCCCCchhHHHHHHHHhC
Confidence            56789999999999999999999863

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=95.67  E-value=0.091  Score=52.51  Aligned_cols=134  Identities=18%  Similarity=0.093  Sum_probs=68.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeE-------------------EEEecCCCchhhhhhh---hhhhccc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRI-------------------WVSASYPRDEIRVARD---EISVARD  254 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~-------------------wv~~~~~~~~~~~~~~---~~~~~~~  254 (597)
                      ..++++.|+.|+|||||.+.+..-.  +. ..+.+                   ++.-...+........   .+.....
T Consensus        31 Gei~gllG~NGAGKTTllk~l~gl~--~p-~~G~i~i~G~~~~~~~~~~~~~igy~~~~~~~~~~lT~~e~l~~~~~l~~  107 (293)
T COG1131          31 GEIFGLLGPNGAGKTTLLKILAGLL--KP-TSGEILVLGYDVVKEPAKVRRRIGYVPQEPSLYPELTVRENLEFFARLYG  107 (293)
T ss_pred             CeEEEEECCCCCCHHHHHHHHhCCc--CC-CceEEEEcCEeCccCHHHHHhheEEEccCCCCCccccHHHHHHHHHHHhC
Confidence            4699999999999999999998732  11 22222                   2221111111111111   1111111


Q ss_pred             ---chHHHHHHHHHHhccCCCCch------hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCC-
Q 041007          255 ---RDEIRVAKAILESLKGSVSSQ------VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEG-  323 (597)
Q Consensus       255 ---~~~~~~~~~il~~l~~~~~~~------~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~g-  323 (597)
                         .........+++.++......      ..-..-.-.+...|-.++=+++||+--+.-++..-..+...+... ..| 
T Consensus       108 ~~~~~~~~~~~~~l~~~~L~~~~~~~~~~lS~G~kqrl~ia~aL~~~P~lliLDEPt~GLDp~~~~~~~~~l~~l~~~g~  187 (293)
T COG1131         108 LSKEEAEERIEELLELFGLEDKANKKVRTLSGGMKQRLSIALALLHDPELLILDEPTSGLDPESRREIWELLRELAKEGG  187 (293)
T ss_pred             CChhHHHHHHHHHHHHcCCchhhCcchhhcCHHHHHHHHHHHHHhcCCCEEEECCCCcCCCHHHHHHHHHHHHHHHhCCC
Confidence               112345666777766553111      111112223445566788999999864443344444455555432 233 


Q ss_pred             cEEEEEccCC
Q 041007          324 SRILVTRSGG  333 (597)
Q Consensus       324 s~IIvTtR~~  333 (597)
                      ..||+||...
T Consensus       188 ~tvlissH~l  197 (293)
T COG1131         188 VTILLSTHIL  197 (293)
T ss_pred             cEEEEeCCcH
Confidence            6888888765

>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=95.66  E-value=0.1  Score=51.81  Aligned_cols=52  Identities=13%  Similarity=0.032  Sum_probs=34.2

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .-.|...+..++-+|+||+.-..-+......+...+...  ..|..||++|.+.
T Consensus       148 rv~lAral~~~p~lLlLDEPt~~LD~~~~~~l~~~l~~l~~~~g~tilivtH~~  201 (279)
T PRK13650        148 RVAIAGAVAMRPKIIILDEATSMLDPEGRLELIKTIKGIRDDYQMTVISITHDL  201 (279)
T ss_pred             HHHHHHHHHcCCCEEEEECCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            334566666788899999976554455556666655442  2377888887765

>PRK11144 modC molybdate transporter ATP-binding protein; Provisional

Probab=95.65  E-value=0.098  Score=53.84  Aligned_cols=24  Identities=29%  Similarity=0.386  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        24 Ge~~~l~G~nGsGKSTLl~~iaGl   47 (352)
T PRK11144         24 QGITAIFGRSGAGKTSLINAISGL   47 (352)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999763

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=95.65  E-value=0.03  Score=54.66  Aligned_cols=22  Identities=23%  Similarity=0.579  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|.++|++|+||||+|+.+...
T Consensus         1 LIvl~G~pGSGKST~a~~La~~   22 (249)
T TIGR03574         1 LIILTGLPGVGKSTFSKELAKK   22 (249)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHH
Confidence            3789999999999999999873

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>cd03290 ABCC_SUR1_N The SUR domain 1

Probab=95.65  E-value=0.23  Score=47.26  Aligned_cols=24  Identities=25%  Similarity=0.459  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|.|||||.+.++..
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~i~G~   50 (218)
T cd03290          27 GQLTMIVGQVGCGKSSLLLAILGE   50 (218)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            469999999999999999999864

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.

>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2

Probab=95.64  E-value=0.18  Score=49.97  Aligned_cols=49  Identities=16%  Similarity=0.196  Sum_probs=30.7

Q ss_pred             HHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          285 INEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       285 l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      +.+.+-.++=+|++|+....-+......+...+.....++.||++|.+.
T Consensus       149 LaRall~~p~illlDEpts~LD~~~~~~l~~~l~~~~~~~tii~isH~~  197 (275)
T cd03289         149 LARSVLSKAKILLLDEPSAHLDPITYQVIRKTLKQAFADCTVILSEHRI  197 (275)
T ss_pred             HHHHHhcCCCEEEEECccccCCHHHHHHHHHHHHHhcCCCEEEEEECCH
Confidence            4445556678999999765544555566666665434466677766554

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.

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=95.63  E-value=0.05  Score=58.60  Aligned_cols=43  Identities=26%  Similarity=0.332  Sum_probs=31.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      +...++.|.|++|+|||||+.+++..  ...+-..+++++..+..
T Consensus       261 ~~gs~~li~G~~G~GKt~l~~~f~~~--~~~~ge~~~y~s~eEs~  303 (484)
T TIGR02655       261 FKDSIILATGATGTGKTLLVSKFLEN--ACANKERAILFAYEESR  303 (484)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEEeeCCH
Confidence            35689999999999999999999874  32333456777765543

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.

>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains

Probab=95.63  E-value=0.061  Score=50.66  Aligned_cols=50  Identities=16%  Similarity=0.105  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHH-HHHHhhcCCC-C-CcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWE-QLMYSLKSGS-E-GSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~-~l~~~l~~~~-~-gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+.-..-+..... .+...+.... . +..||++|.+.
T Consensus       131 ala~al~~~p~illlDEP~~~LD~~~~~~~l~~~l~~~~~~~~~~iiiitH~~  183 (204)
T cd03240         131 ALAETFGSNCGILALDEPTTNLDEENIEESLAEIIEERKSQKNFQLIVITHDE  183 (204)
T ss_pred             HHHHHhccCCCEEEEcCCccccCHHHHHHHHHHHHHHHHhccCCEEEEEEecH
Confidence            3455666788999999985544344555 5555554432 2 56677777765

The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=95.63  E-value=0.14  Score=51.53  Aligned_cols=50  Identities=22%  Similarity=0.154  Sum_probs=31.8

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      .|...+-.++=+|+||+--..-+...-..+...+.. ...|..||+||...
T Consensus       148 ~la~aL~~~P~lllLDEPt~gLD~~~~~~l~~~l~~l~~~g~till~sH~l  198 (306)
T PRK13537        148 TLARALVNDPDVLVLDEPTTGLDPQARHLMWERLRSLLARGKTILLTTHFM  198 (306)
T ss_pred             HHHHHHhCCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEECCCH
Confidence            355666678899999986444334444444444433 23478899999776

>PTZ00088 adenylate kinase 1; Provisional

Probab=95.62  E-value=0.039  Score=52.86  Aligned_cols=21  Identities=29%  Similarity=0.504  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|.|.|++|+||||+|+.+..
T Consensus         8 rIvl~G~PGsGK~T~a~~La~   28 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSK   28 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            489999999999999999977

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

Probab=95.62  E-value=0.084  Score=49.74  Aligned_cols=53  Identities=25%  Similarity=0.353  Sum_probs=36.0

Q ss_pred             ccccchhhHHHHHHHhhCCCCCC----cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDE----ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~----~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+-|-+-..+++.+...-.-.+.    ..+ -..++-|.++|++|.|||.||+.|+++
T Consensus       156 diggld~qkqeireavelplt~~~ly~qig-idpprgvllygppg~gktml~kava~~  212 (408)
T KOG0727|consen  156 DIGGLDVQKQEIREAVELPLTHADLYKQIG-IDPPRGVLLYGPPGTGKTMLAKAVANH  212 (408)
T ss_pred             ccccchhhHHHHHHHHhccchHHHHHHHhC-CCCCcceEEeCCCCCcHHHHHHHHhhc
Confidence            34577777777777664321100    000 124677889999999999999999995

>PRK14272 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.61  E-value=0.17  Score=49.35  Aligned_cols=50  Identities=10%  Similarity=0.052  Sum_probs=31.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+.-+.-+......+...+.....+..||++|.+.
T Consensus       158 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~sH~~  207 (252)
T PRK14272        158 CIARALAVEPEILLMDEPTSALDPASTARIEDLMTDLKKVTTIIIVTHNM  207 (252)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            34555566778999999755443455555655554433456778887765

>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=95.61  E-value=0.12  Score=49.59  Aligned_cols=23  Identities=26%  Similarity=0.395  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||++.++.
T Consensus        26 Ge~~~i~G~nGsGKSTLl~~i~G   48 (227)
T cd03260          26 GEITALIGPSGCGKSTLLRLLNR   48 (227)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46999999999999999999875

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).

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

Probab=95.61  E-value=0.052  Score=54.43  Aligned_cols=35  Identities=14%  Similarity=0.090  Sum_probs=28.5

Q ss_pred             HHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHhc
Q 041007           20 QMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEK   54 (597)
Q Consensus        20 ~~~~~~~~~~~~~~~~~~l~~~l~~i~~~l~~a~~   54 (597)
                      ....++.+++.+..-.-.++.-|..|+..+..+..
T Consensus        11 k~ar~~al~G~~d~~~~~~~g~~~~~~r~l~s~~d   45 (491)
T KOG0738|consen   11 KLAREYALLGNYDSAGIYYRGLLYLMNRYLVSTGD   45 (491)
T ss_pred             HHHHHHHHhcCcchhHHHHHhHHHHHHHHHhccCC
Confidence            46678888899988888999999999888876553

>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional

Probab=95.61  E-value=0.19  Score=49.40  Aligned_cols=24  Identities=29%  Similarity=0.367  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|.|||||++.++..
T Consensus        50 Ge~~~liG~NGsGKSTLlk~L~Gl   73 (264)
T PRK13546         50 GDVIGLVGINGSGKSTLSNIIGGS   73 (264)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999874

>PRK14261 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.60  E-value=0.17  Score=49.50  Aligned_cols=50  Identities=6%  Similarity=0.033  Sum_probs=30.6

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+...+-+++||+.-..-+......+...+.....+..||++|.+.
T Consensus       159 ~laral~~~p~lllLDEP~~gLD~~~~~~l~~~l~~~~~~~tvii~sh~~  208 (253)
T PRK14261        159 CIARTLAVNPEVILMDEPCSALDPIATAKIEDLIEDLKKEYTVIIVTHNM  208 (253)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHhhCceEEEEEcCH
Confidence            45555566788999999755444445555555554332345777777665

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=95.59  E-value=0.033  Score=60.15  Aligned_cols=47  Identities=21%  Similarity=0.343  Sum_probs=38.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|....++++.+.+.....        ....|.|.|..|+||+.+|+.+++.
T Consensus       212 ~~iiG~S~~m~~~~~~i~~~A~--------~~~pVLI~GE~GTGKe~lA~~IH~~  258 (526)
T TIGR02329       212 DDLLGASAPMEQVRALVRLYAR--------SDATVLILGESGTGKELVAQAIHQL  258 (526)
T ss_pred             hheeeCCHHHHHHHHHHHHHhC--------CCCcEEEECCCCcCHHHHHHHHHHh
Confidence            3589999999999888865443        3467899999999999999999874

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]

Probab=95.59  E-value=0.016  Score=56.19  Aligned_cols=47  Identities=23%  Similarity=0.183  Sum_probs=36.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ++..+|+|+|.||+|||||.-.+......+++--.++-|+-|.++.-
T Consensus        49 G~a~viGITG~PGaGKSTli~~L~~~l~~~G~rVaVlAVDPSSp~TG   95 (323)
T COG1703          49 GNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTG   95 (323)
T ss_pred             CCCcEEEecCCCCCchHHHHHHHHHHHHHCCcEEEEEEECCCCCCCC
Confidence            46789999999999999999998876545555555677777777665

>TIGR03771 anch_rpt_ABC anchored repeat-type ABC transporter, ATP-binding subunit

Probab=95.58  E-value=0.19  Score=48.02  Aligned_cols=51  Identities=18%  Similarity=0.119  Sum_probs=33.3

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      -.+...+-.++-++++|+--..-+......+...+... ..|..||++|.+.
T Consensus       122 v~laral~~~p~llilDEP~~~LD~~~~~~l~~~l~~~~~~~~tvii~sH~~  173 (223)
T TIGR03771       122 VLVARALATRPSVLLLDEPFTGLDMPTQELLTELFIELAGAGTAILMTTHDL  173 (223)
T ss_pred             HHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHcCCEEEEEeCCH
Confidence            34556666788899999975444355555565555432 3477788888765

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.

>PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional

Probab=95.57  E-value=0.12  Score=50.15  Aligned_cols=24  Identities=29%  Similarity=0.318  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.+...
T Consensus        29 Ge~~~l~G~nGsGKSTLl~~l~G~   52 (241)
T PRK10895         29 GEIVGLLGPNGAGKTTTFYMVVGI   52 (241)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999764

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=95.56  E-value=0.12  Score=58.73  Aligned_cols=24  Identities=29%  Similarity=0.385  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....++|+|+.|+|||||++.+..
T Consensus       499 ~G~~vaIvG~SGsGKSTLlklL~g  522 (708)
T TIGR01193       499 MNSKTTIVGMSGSGKSTLAKLLVG  522 (708)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            356899999999999999999965

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.

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=95.56  E-value=0.26  Score=51.91  Aligned_cols=44  Identities=20%  Similarity=0.330  Sum_probs=32.4

Q ss_pred             hhhHHHHHHHhh--CCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          172 NAEKQKILQLLK--GESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       172 ~~e~~~l~~~L~--~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+.++..||.  ....     ++.+.+++.|+||+|+||||.++.++..
T Consensus        88 kkKI~eVk~WL~~~~~~~-----~~l~~~iLLltGPsGcGKSTtvkvLske  133 (634)
T KOG1970|consen   88 KKKISEVKQWLKQVAEFT-----PKLGSRILLLTGPSGCGKSTTVKVLSKE  133 (634)
T ss_pred             HHhHHHHHHHHHHHHHhc-----cCCCceEEEEeCCCCCCchhHHHHHHHh
Confidence            355678888887  1111     1235679999999999999999998773

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.56  E-value=0.16  Score=56.69  Aligned_cols=40  Identities=18%  Similarity=0.281  Sum_probs=27.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ..+++++|+.|+||||.+..++...........+..++..
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~D  224 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTD  224 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCc
Confidence            4799999999999999998888742222222344555443

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=95.56  E-value=0.018  Score=49.80  Aligned_cols=25  Identities=28%  Similarity=0.456  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|.+.|.-|+||||+++.+++.
T Consensus        21 ~~~~i~l~G~lGaGKTtl~~~l~~~   45 (133)
T TIGR00150        21 FGTVVLLKGDLGAGKTTLVQGLLQG   45 (133)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            3469999999999999999999885

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>PRK10744 pstB phosphate transporter ATP-binding protein; Provisional

Probab=95.56  E-value=0.16  Score=49.81  Aligned_cols=51  Identities=10%  Similarity=0.022  Sum_probs=30.9

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.|...+..++-+|+||+.-+.-+......+...+.....+..||++|.+.
T Consensus       165 v~laral~~~p~lllLDEPt~~LD~~~~~~l~~~L~~~~~~~tiii~sH~~  215 (260)
T PRK10744        165 LCIARGIAIRPEVLLLDEPCSALDPISTGRIEELITELKQDYTVVIVTHNM  215 (260)
T ss_pred             HHHHHHHHCCCCEEEEcCCCccCCHHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            345556667788999999754433444555555554333355677777655

>PRK06762 hypothetical protein; Provisional

Probab=95.56  E-value=0.0087  Score=54.39  Aligned_cols=22  Identities=45%  Similarity=0.708  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|.|+|++|+||||+|+.+.+
T Consensus         3 ~li~i~G~~GsGKST~A~~L~~   24 (166)
T PRK06762          3 TLIIIRGNSGSGKTTIAKQLQE   24 (166)
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            6899999999999999999987

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=95.55  E-value=0.081  Score=56.96  Aligned_cols=47  Identities=19%  Similarity=0.328  Sum_probs=37.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|+...+.++...+.....        ....|.|+|.+|+|||++|+.+++.
T Consensus       138 ~~lig~s~~~~~l~~~~~~~~~--------~~~~vli~Ge~GtGK~~lA~~ih~~  184 (469)
T PRK10923        138 TDIIGEAPAMQDVFRIIGRLSR--------SSISVLINGESGTGKELVAHALHRH  184 (469)
T ss_pred             ccceecCHHHHHHHHHHHHHhc--------cCCeEEEEeCCCCcHHHHHHHHHhc
Confidence            3588998888888777764432        3456889999999999999999874

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=95.55  E-value=0.093  Score=49.89  Aligned_cols=24  Identities=33%  Similarity=0.458  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..-.|+|.|++|+|||||.+.+.-
T Consensus        28 ~GEfvsilGpSGcGKSTLLriiAG   51 (248)
T COG1116          28 KGEFVAILGPSGCGKSTLLRLIAG   51 (248)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            346999999999999999999964

>PRK14235 phosphate transporter ATP-binding protein; Provisional

Probab=95.54  E-value=0.16  Score=50.20  Aligned_cols=50  Identities=8%  Similarity=0.032  Sum_probs=31.4

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .|...+-.++-+|+||+--..-+......+...+.....+..||++|.+.
T Consensus       173 ~laral~~~p~lllLDEPt~~LD~~~~~~l~~~L~~l~~~~tiiivtH~~  222 (267)
T PRK14235        173 CIARAIAVSPEVILMDEPCSALDPIATAKVEELIDELRQNYTIVIVTHSM  222 (267)
T ss_pred             HHHHHHHcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHhcCCeEEEEEcCH
Confidence            45555666788999999755444555555655554433355677777664

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=95.53  E-value=0.2  Score=53.61  Aligned_cols=134  Identities=12%  Similarity=0.062  Sum_probs=65.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE-------ecCCCchhhhhhhhhhh------cccchHHHHHHH
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS-------ASYPRDEIRVARDEISV------ARDRDEIRVAKA  263 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~-------~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~  263 (597)
                      ..+++|.|+.|+|||||++.++....   ...+.+++.       ..............+..      ............
T Consensus        50 GEivgIiGpNGSGKSTLLkiLaGLl~---P~sGeI~I~G~~~~i~~~~~l~~~lTV~EnL~l~~~~~~~~~~e~~e~i~e  126 (549)
T PRK13545         50 GEIVGIIGLNGSGKSTLSNLIAGVTM---PNKGTVDIKGSAALIAISSGLNGQLTGIENIELKGLMMGLTKEKIKEIIPE  126 (549)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCCCC---CCceEEEECCEeeeEEeccccCCCCcHHHHHHhhhhhcCCCHHHHHHHHHH
Confidence            46999999999999999999987421   112222221       11000000011111100      000111122334


Q ss_pred             HHHhccCCC------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          264 ILESLKGSV------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       264 il~~l~~~~------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      +++.++...      .....-+...-.|...+...+-+|+||+--..-+......+...+.. ...|..||++|.+.
T Consensus       127 lLe~lgL~~~ld~~~~~LSGGQrQRVaLArAL~~~P~LLLLDEPTsgLD~~sr~~LlelL~el~~~G~TIIIVSHdl  203 (549)
T PRK13545        127 IIEFADIGKFIYQPVKTYSSGMKSRLGFAISVHINPDILVIDEALSVGDQTFTKKCLDKMNEFKEQGKTIFFISHSL  203 (549)
T ss_pred             HHHHcCChhHhhCCcccCCHHHHHHHHHHHHHHhCCCEEEEECCcccCCHHHHHHHHHHHHHHHhCCCEEEEEECCH
Confidence            444443321      11111122233455566677889999997544334444455555433 23466788888765

>KOG1532 consensus GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair]

Probab=95.51  E-value=0.066  Score=51.14  Aligned_cols=27  Identities=22%  Similarity=0.380  Sum_probs=23.4

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCCh
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDS  221 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~  221 (597)
                      .++.+|.++||+|+||||..+.++.+.
T Consensus        17 ~~p~~ilVvGMAGSGKTTF~QrL~~hl   43 (366)
T KOG1532|consen   17 QRPVIILVVGMAGSGKTTFMQRLNSHL   43 (366)
T ss_pred             cCCcEEEEEecCCCCchhHHHHHHHHH
Confidence            457788999999999999999998753

>PF03308 ArgK: ArgK protein; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components

Probab=95.51  E-value=0.017  Score=55.27  Aligned_cols=60  Identities=23%  Similarity=0.254  Sum_probs=35.9

Q ss_pred             hHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          174 EKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       174 e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      +..++++.+....        ++..+|+|+|+||+|||||...+....+.+++--.++-|+-+.+++-
T Consensus        14 ~~~~ll~~l~~~~--------g~a~~iGiTG~PGaGKSTli~~l~~~~~~~g~~VaVlAVDPSSp~tG   73 (266)
T PF03308_consen   14 EARELLKRLYPHT--------GRAHVIGITGPPGAGKSTLIDALIRELRERGKRVAVLAVDPSSPFTG   73 (266)
T ss_dssp             HHHHHHHHHGGGT--------T-SEEEEEEE-TTSSHHHHHHHHHHHHHHTT--EEEEEE-GGGGCC-
T ss_pred             HHHHHHHHHHhhc--------CCceEEEeeCCCCCcHHHHHHHHHHHHhhcCCceEEEEECCCCCCCC
Confidence            4455555555332        35679999999999999999998874333333334555655555543

In Escherichia coli, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK [] resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 3MD0_A 3P32_A 2QM7_A 2QM8_A 2WWW_D 2P67_A 3NXS_A.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=95.50  E-value=0.055  Score=60.66  Aligned_cols=47  Identities=15%  Similarity=0.368  Sum_probs=37.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.++|....+.++.+.+.....        ....|.|+|..|+||+++|+.+++.
T Consensus       325 ~~l~g~s~~~~~~~~~~~~~a~--------~~~pvli~Ge~GtGK~~~A~~ih~~  371 (638)
T PRK11388        325 DHMPQDSPQMRRLIHFGRQAAK--------SSFPVLLCGEEGVGKALLAQAIHNE  371 (638)
T ss_pred             cceEECCHHHHHHHHHHHHHhC--------cCCCEEEECCCCcCHHHHHHHHHHh
Confidence            4578999889888888875543        2345889999999999999999874

>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE

Probab=95.48  E-value=0.13  Score=49.50  Aligned_cols=25  Identities=32%  Similarity=0.527  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|.|+.|.|||||++.++.-
T Consensus        25 ~Ge~~~l~G~nGsGKSTLl~~l~G~   49 (230)
T TIGR03410        25 KGEVTCVLGRNGVGKTTLLKTLMGL   49 (230)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3469999999999999999999763

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.

>PRK14268 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.48  E-value=0.16  Score=49.81  Aligned_cols=50  Identities=10%  Similarity=0.028  Sum_probs=30.9

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+++||+--+.-+......+...+.....+..||++|.+.
T Consensus       164 ~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~l~~~~tiiivsH~~  213 (258)
T PRK14268        164 CIARTLAVKPKIILFDEPTSALDPISTARIEDLIMNLKKDYTIVIVTHNM  213 (258)
T ss_pred             HHHHHHHcCCCEEEEeCCCcccCHHHHHHHHHHHHHHhhCCEEEEEECCH
Confidence            34555556778999999754433555555555554333356777777765

>cd03291 ABCC_CFTR1 The CFTR subfamily domain 1

Probab=95.48  E-value=0.2  Score=49.80  Aligned_cols=25  Identities=28%  Similarity=0.424  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|.|+.|+|||||++.++..
T Consensus        62 ~Ge~~~liG~NGsGKSTLl~~I~Gl   86 (282)
T cd03291          62 KGEMLAITGSTGSGKTSLLMLILGE   86 (282)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3469999999999999999999874

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.

>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=95.47  E-value=0.15  Score=49.09  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        26 Ge~~~l~G~nGsGKSTLl~~l~Gl   49 (232)
T cd03218          26 GEIVGLLGPNGAGKTTTFYMIVGL   49 (232)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999763

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.

>PRK14246 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.47  E-value=0.21  Score=48.90  Aligned_cols=52  Identities=10%  Similarity=-0.063  Sum_probs=32.8

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .-.|...+-.++-+++||+--..-+......+...+.....+..||++|.+.
T Consensus       161 rl~laral~~~P~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tiilvsh~~  212 (257)
T PRK14246        161 RLTIARALALKPKVLLMDEPTSMIDIVNSQAIEKLITELKNEIAIVIVSHNP  212 (257)
T ss_pred             HHHHHHHHHcCCCEEEEcCCCccCCHHHHHHHHHHHHHHhcCcEEEEEECCH
Confidence            3345555666788999998654433455556666654433357788888765

>PRK14257 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.45  E-value=0.18  Score=51.40  Aligned_cols=24  Identities=25%  Similarity=0.342  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|+.|.|||||++.++..
T Consensus       108 Ge~v~IvG~~GsGKSTLl~~L~g~  131 (329)
T PRK14257        108 NKVTAFIGPSGCGKSTFLRNLNQL  131 (329)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            468999999999999999999864

>TIGR00416 sms DNA repair protein RadA

Probab=95.44  E-value=0.08  Score=56.24  Aligned_cols=40  Identities=35%  Similarity=0.373  Sum_probs=29.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ...++.|.|.+|+|||||+.++...  ....-..++|++...
T Consensus        93 ~GsvilI~G~pGsGKTTL~lq~a~~--~a~~g~kvlYvs~EE  132 (454)
T TIGR00416        93 PGSLILIGGDPGIGKSTLLLQVACQ--LAKNQMKVLYVSGEE  132 (454)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH--HHhcCCcEEEEECcC
Confidence            4579999999999999999998764  222223577887543

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)).

>TIGR02770 nickel_nikD nickel import ATP-binding protein NikD

Probab=95.44  E-value=0.18  Score=48.53  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|.|+.|+|||||++.++.-
T Consensus        11 ~Ge~~~i~G~nGsGKSTLl~~l~Gl   35 (230)
T TIGR02770        11 RGEVLALVGESGSGKSLTCLAILGL   35 (230)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3469999999999999999999874

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.

>PRK11153 metN DL-methionine transporter ATP-binding subunit; Provisional

Probab=95.44  E-value=0.14  Score=52.46  Aligned_cols=50  Identities=16%  Similarity=0.079  Sum_probs=32.3

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .|...|..++-+|+||+--..-+......+...+...  ..|..||++|.+.
T Consensus       150 ~lAraL~~~p~iLlLDEPts~LD~~~~~~l~~~L~~l~~~~g~tiilvtH~~  201 (343)
T PRK11153        150 AIARALASNPKVLLCDEATSALDPATTRSILELLKDINRELGLTIVLITHEM  201 (343)
T ss_pred             HHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            4555566778899999975444455555666655542  2367788888765

>PRK14271 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.43  E-value=0.18  Score=49.99  Aligned_cols=25  Identities=28%  Similarity=0.375  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|+|+.|.|||||++.++--
T Consensus        46 ~Ge~~~I~G~nGsGKSTLl~~l~Gl   70 (276)
T PRK14271         46 ARAVTSLMGPTGSGKTTFLRTLNRM   70 (276)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhcc
Confidence            3468999999999999999999763

>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=95.43  E-value=0.12  Score=57.08  Aligned_cols=25  Identities=24%  Similarity=0.351  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|+|+.|.|||||++.+...
T Consensus       365 ~G~~~aivG~sGsGKSTL~~ll~g~  389 (574)
T PRK11160        365 AGEKVALLGRTGCGKSTLLQLLTRA  389 (574)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4569999999999999999999764

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=95.42  E-value=0.03  Score=51.37  Aligned_cols=22  Identities=41%  Similarity=0.656  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|.|.|++|+||||+|+.+.+.
T Consensus         2 riiilG~pGaGK~T~A~~La~~   23 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK   23 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            4789999999999999999884

>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional

Probab=95.42  E-value=0.16  Score=50.17  Aligned_cols=50  Identities=12%  Similarity=0.088  Sum_probs=30.9

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .|...+-.++-+|+||+--+.-+......+...+...  ..|..||++|.+.
T Consensus       153 ~laral~~~p~lllLDEPt~~LD~~~~~~l~~~l~~~~~~~g~tiiivsH~~  204 (269)
T PRK11831        153 ALARAIALEPDLIMFDEPFVGQDPITMGVLVKLISELNSALGVTCVVVSHDV  204 (269)
T ss_pred             HHHHHHhcCCCEEEEcCCCccCCHHHHHHHHHHHHHHHHhcCcEEEEEecCH
Confidence            3455555677899999965443344555555555442  2366788887764

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=95.41  E-value=0.1  Score=49.08  Aligned_cols=24  Identities=21%  Similarity=0.418  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.+...
T Consensus        33 Ge~~~i~G~nGsGKSTLl~~l~G~   56 (202)
T cd03233          33 GEMVLVLGRPGSGCSTLLKALANR   56 (202)
T ss_pred             CcEEEEECCCCCCHHHHHHHhccc
Confidence            469999999999999999999874

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.

>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=95.40  E-value=0.15  Score=50.39  Aligned_cols=24  Identities=25%  Similarity=0.380  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||.+.++.-
T Consensus        35 Ge~~~l~G~nGsGKSTLl~~l~Gl   58 (271)
T PRK13632         35 GEYVAILGHNGSGKSTISKILTGL   58 (271)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            469999999999999999998764

>PRK06547 hypothetical protein; Provisional

Probab=95.38  E-value=0.014  Score=53.20  Aligned_cols=25  Identities=32%  Similarity=0.407  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|+|.|++|+||||+|..+...
T Consensus        14 ~~~~i~i~G~~GsGKTt~a~~l~~~   38 (172)
T PRK06547         14 GMITVLIDGRSGSGKTTLAGALAAR   38 (172)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
Confidence            5689999999999999999999873

>PRK14244 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.38  E-value=0.17  Score=49.45  Aligned_cols=50  Identities=14%  Similarity=0.092  Sum_probs=30.6

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--..-+......+...+.....+..||++|.+.
T Consensus       159 ~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tiiiisH~~  208 (251)
T PRK14244        159 CIARAIAVKPTMLLMDEPCSALDPVATNVIENLIQELKKNFTIIVVTHSM  208 (251)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            34455556778999999744333445555555554333466777777765

>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=95.36  E-value=0.16  Score=50.19  Aligned_cols=24  Identities=25%  Similarity=0.353  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|.|||||.+.++.-
T Consensus        35 Ge~~~I~G~nGsGKSTLl~~i~Gl   58 (269)
T PRK13648         35 GQWTSIVGHNGSGKSTIAKLMIGI   58 (269)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            469999999999999999999763

>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein

Probab=95.36  E-value=0.24  Score=48.25  Aligned_cols=24  Identities=29%  Similarity=0.433  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|.|+.|+|||||++.+.-
T Consensus        26 ~Ge~~~i~G~nGsGKSTLl~~l~G   49 (247)
T TIGR00972        26 KNQVTALIGPSGCGKSTLLRSLNR   49 (247)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346999999999999999999975

This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters.

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=95.36  E-value=0.78  Score=45.80  Aligned_cols=96  Identities=8%  Similarity=0.069  Sum_probs=60.0

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|+|++.... ......+...+...+.++.+|++|.+......         -+...+. +++.++++++..+.+
T Consensus        89 ~~~KvvII~~~e~m~-~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~---------TI~SRc~~~~f~~l~~~~l~~~l  158 (299)
T PRK07132         89 SQKKILIIKNIEKTS-NSLLNALLKTIEEPPKDTYFLLTTKNINKVLP---------TIVSRCQVFNVKEPDQQKILAKL  158 (299)
T ss_pred             CCceEEEEecccccC-HHHHHHHHHHhhCCCCCeEEEEEeCChHhChH---------HHHhCeEEEECCCCCHHHHHHHH
Confidence            467788999987665 55667788888777778888776654311000         1111122 999999999998777


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      ....    . .     .+.+..++...+|.=-|+..+
T Consensus       159 ~~~~----~-~-----~~~a~~~a~~~~~~~~a~~~~  185 (299)
T PRK07132        159 LSKN----K-E-----KEYNWFYAYIFSNFEQAEKYI  185 (299)
T ss_pred             HHcC----C-C-----hhHHHHHHHHcCCHHHHHHHH
Confidence            6531    1 1     234566666777633455553

>PRK14262 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.35  E-value=0.18  Score=49.17  Aligned_cols=51  Identities=16%  Similarity=0.067  Sum_probs=31.1

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.+...+-.++-+|+||+.-..-+......+...+.....+..||++|.+.
T Consensus       155 ~~la~al~~~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tili~sH~~  205 (250)
T PRK14262        155 LCIARALAVEPEVILLDEPTSALDPIATQRIEKLLEELSENYTIVIVTHNI  205 (250)
T ss_pred             HHHHHHHhCCCCEEEEeCCccccCHHHHHHHHHHHHHHhcCcEEEEEeCCH
Confidence            344555566788999999754433445555555554333356777777765

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=95.35  E-value=0.23  Score=56.60  Aligned_cols=25  Identities=24%  Similarity=0.335  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|+.|+|||||++.+..-
T Consensus       504 ~Ge~vaIvG~sGsGKSTLlklL~gl  528 (710)
T TIGR03796       504 PGQRVALVGGSGSGKSTIAKLVAGL  528 (710)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999999653

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.

>TIGR01288 nodI ATP-binding ABC transporter family nodulation protein NodI

Probab=95.33  E-value=0.22  Score=50.22  Aligned_cols=50  Identities=22%  Similarity=0.167  Sum_probs=31.0

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      .|...+..++-+|+||+--+.-+...-..+...+.. ...|..||++|.+.
T Consensus       145 ~la~al~~~p~lllLDEPt~gLD~~~~~~l~~~l~~~~~~g~til~~sH~~  195 (303)
T TIGR01288       145 TLARALINDPQLLILDEPTTGLDPHARHLIWERLRSLLARGKTILLTTHFM  195 (303)
T ss_pred             HHHHHHhcCCCEEEEeCCCcCCCHHHHHHHHHHHHHHHhCCCEEEEECCCH
Confidence            355556678889999986444334444444444433 13477888888765

This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=95.33  E-value=0.014  Score=54.09  Aligned_cols=24  Identities=25%  Similarity=0.581  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|+|.|++|+||||+++.+..
T Consensus         2 ~~~ii~i~G~~GsGKsTl~~~l~~   25 (188)
T TIGR01360         2 KCKIIFIVGGPGSGKGTQCEKIVE   25 (188)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999986

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>PRK14259 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.32  E-value=0.23  Score=49.10  Aligned_cols=25  Identities=24%  Similarity=0.319  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|.|+.|+|||||++.++..
T Consensus        38 ~Ge~~~l~G~nGsGKSTLl~~l~Gl   62 (269)
T PRK14259         38 RGKVTALIGPSGCGKSTVLRSLNRM   62 (269)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcc
Confidence            3469999999999999999999763

>PRK11231 fecE iron-dicitrate transporter ATP-binding subunit; Provisional

Probab=95.31  E-value=0.21  Score=48.84  Aligned_cols=50  Identities=10%  Similarity=0.092  Sum_probs=31.6

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--+.-+......+...+... ..|..||++|.+.
T Consensus       148 ~laral~~~p~llllDEP~~~LD~~~~~~l~~~l~~l~~~~~tiii~tH~~  198 (255)
T PRK11231        148 FLAMVLAQDTPVVLLDEPTTYLDINHQVELMRLMRELNTQGKTVVTVLHDL  198 (255)
T ss_pred             HHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEECCH
Confidence            3555566678899999975544455555565555432 2366788887765

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=95.30  E-value=0.086  Score=57.33  Aligned_cols=118  Identities=16%  Similarity=0.131  Sum_probs=0.0

Q ss_pred             CCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccC
Q 041007          192 GSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN-FDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKG  270 (597)
Q Consensus       192 ~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~  270 (597)
                      ++=+...++.|.|.+|+|||+|+.++..  ....+ -..++|++....                   .+-+..-+..++-
T Consensus        26 GG~p~Gs~~li~G~pGsGKT~l~~qf~~--~~~~~~ge~~lyis~ee~-------------------~~~i~~~~~~~g~   84 (509)
T PRK09302         26 GGLPKGRPTLVSGTAGTGKTLFALQFLV--NGIKRFDEPGVFVTFEES-------------------PEDIIRNVASFGW   84 (509)
T ss_pred             CCCCCCcEEEEEeCCCCCHHHHHHHHHH--HHHHhcCCCEEEEEccCC-------------------HHHHHHHHHHcCC


Q ss_pred             CCCchh-----------------------hHHHHHHHHHHHhc-CceEEEEEecccC----CCCcchHHHHHHhhcC--C
Q 041007          271 SVSSQV-----------------------EMETVLQYINEFVQ-GKKVLLVLDDLWW----NAYPRYWEQLMYSLKS--G  320 (597)
Q Consensus       271 ~~~~~~-----------------------~~~~~~~~l~~~L~-~kr~LLVLDdv~~----~~~~~~~~~l~~~l~~--~  320 (597)
                      ......                       +.+.+...+.+... .+.-.+|+|.+..    .+...........+..  .
T Consensus        85 d~~~~~~~g~l~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~i~~~~~~~vVIDSls~l~~~~d~~~~~r~~l~~L~~~Lk  164 (509)
T PRK09302         85 DLQKLIDEGKLFILDASPDPSEQEEAGEYDLEALFIRIEYAIDKIGAKRVVLDSIEALFSGFSNEAVVRRELRRLFAWLK  164 (509)
T ss_pred             CHHHHhhCCeEEEEecCcccccccccccccHHHHHHHHHHHHHhhCCCEEEECCHHHHHhhccCHHHHHHHHHHHHHHHH


Q ss_pred             CCCcEEEEEc
Q 041007          321 SEGSRILVTR  330 (597)
Q Consensus       321 ~~gs~IIvTt  330 (597)
                      ..|..+|+|+
T Consensus       165 ~~g~TvLlt~  174 (509)
T PRK09302        165 QKGVTAVITG  174 (509)
T ss_pred             hCCCEEEEEE

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=95.30  E-value=0.036  Score=56.77  Aligned_cols=108  Identities=11%  Similarity=0.156  Sum_probs=57.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ...|.|.|+.|+||||++..+.+  .+..+....++. +.++....  .            .. ...+..+-..    ..
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~--~i~~~~~~~i~t-iEdp~E~~--~------------~~-~~~~i~q~ev----g~  179 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMID--YINKNAAGHIIT-IEDPIEYV--H------------RN-KRSLINQREV----GL  179 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH--hhCcCCCCEEEE-EcCChhhh--c------------cC-ccceEEcccc----CC
Confidence            36899999999999999999877  344344444443 22221110  0            00 0000000000    01


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccC
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSG  332 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~  332 (597)
                      ........++..|+..+=+|++|.+.+.   ..+.....   ....|..++.|...
T Consensus       180 ~~~~~~~~l~~~lr~~pd~i~vgEird~---~~~~~~l~---aa~tGh~v~~T~Ha  229 (343)
T TIGR01420       180 DTLSFANALRAALREDPDVILIGEMRDL---ETVELALT---AAETGHLVFGTLHT  229 (343)
T ss_pred             CCcCHHHHHHHhhccCCCEEEEeCCCCH---HHHHHHHH---HHHcCCcEEEEEcC
Confidence            1123455677778888999999999533   34443332   23345556666543

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK14258 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.30  E-value=0.26  Score=48.40  Aligned_cols=52  Identities=12%  Similarity=0.055  Sum_probs=32.6

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--CCCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--GSEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~~~gs~IIvTtR~~  333 (597)
                      .-.+...+..++-+|+||+.-..-+......+...+..  ...+..||++|.+.
T Consensus       158 rv~laral~~~p~vllLDEP~~~LD~~~~~~l~~~l~~l~~~~~~tiiivsH~~  211 (261)
T PRK14258        158 RLCIARALAVKPKVLLMDEPCFGLDPIASMKVESLIQSLRLRSELTMVIVSHNL  211 (261)
T ss_pred             HHHHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHHHhCCCEEEEEECCH
Confidence            33455555667889999997554445556666665554  22366777777665

>TIGR02314 ABC_MetN D-methionine ABC transporter, ATP-binding protein

Probab=95.29  E-value=0.15  Score=52.18  Aligned_cols=51  Identities=18%  Similarity=0.086  Sum_probs=32.9

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      -.|...|..++-+|++|+.-+.-+...-..+...+...  ..|..||++|.+.
T Consensus       149 V~IARAL~~~P~iLLlDEPts~LD~~t~~~i~~lL~~l~~~~g~tiiliTH~~  201 (343)
T TIGR02314       149 VAIARALASNPKVLLCDEATSALDPATTQSILELLKEINRRLGLTILLITHEM  201 (343)
T ss_pred             HHHHHHHHhCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            34566677788899999975544454555555555442  2367788877765

Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria.

>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=95.29  E-value=0.24  Score=48.92  Aligned_cols=50  Identities=14%  Similarity=0.137  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .|...+..++-+|+||+--..-+......+...+... ..|..||++|.+.
T Consensus       146 ~laraL~~~p~lllLDEPt~~LD~~~~~~l~~~l~~~~~~g~tii~vtH~~  196 (271)
T PRK13638        146 AIAGALVLQARYLLLDEPTAGLDPAGRTQMIAIIRRIVAQGNHVIISSHDI  196 (271)
T ss_pred             HHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            4555666778899999975444344555555555432 2366788887765

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=95.29  E-value=0.012  Score=55.46  Aligned_cols=21  Identities=29%  Similarity=0.275  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHh
Q 041007          198 PVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      ++++|+|+.|.|||||.+.+.
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            689999999999999999987

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

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=95.28  E-value=0.18  Score=49.36  Aligned_cols=52  Identities=13%  Similarity=0.061  Sum_probs=32.6

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .-.|...+..++-+|+||+.-+.-+...-..+...+...  ..|..||++|.+.
T Consensus       161 rv~la~al~~~p~llllDEPt~~LD~~~~~~l~~~L~~~~~~~~~tii~~sH~~  214 (255)
T PRK11300        161 RLEIARCMVTQPEILMLDEPAAGLNPKETKELDELIAELRNEHNVTVLLIEHDM  214 (255)
T ss_pred             HHHHHHHHhcCCCEEEEcCCccCCCHHHHHHHHHHHHHHHhhcCCEEEEEeCCH
Confidence            334555666788899999975544344555555555432  2367788887765

>PRK13647 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=95.28  E-value=0.21  Score=49.51  Aligned_cols=52  Identities=23%  Similarity=0.179  Sum_probs=33.6

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .-.|...|..++-+|+||+.-..-+......+...+... ..|..||++|.+.
T Consensus       146 rv~laraL~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~g~tili~tH~~  198 (274)
T PRK13647        146 RVAIAGVLAMDPDVIVLDEPMAYLDPRGQETLMEILDRLHNQGKTVIVATHDV  198 (274)
T ss_pred             HHHHHHHHHcCCCEEEEECCCcCCCHHHHHHHHHHHHHHHHCCCEEEEEeCCH
Confidence            334556667788899999976554455555555555432 2367788887765

>PRK06002 fliI flagellum-specific ATP synthase; Validated

Probab=95.27  E-value=0.068  Score=55.93  Aligned_cols=24  Identities=25%  Similarity=0.322  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....++|+|+.|+|||||++.+..
T Consensus       164 ~Gqri~I~G~SGsGKTTLL~~Ia~  187 (450)
T PRK06002        164 AGQRIGIFAGSGVGKSTLLAMLAR  187 (450)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            356899999999999999998876

>PRK14265 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.27  E-value=0.23  Score=49.21  Aligned_cols=50  Identities=16%  Similarity=0.022  Sum_probs=32.2

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .|...+..++=+|+||+--..-+....+.+...+.....+..||++|.+.
T Consensus       171 ~LAraL~~~p~lllLDEPt~~LD~~~~~~l~~~L~~~~~~~tiii~sH~~  220 (274)
T PRK14265        171 CIARAIAMKPDVLLMDEPCSALDPISTRQVEELCLELKEQYTIIMVTHNM  220 (274)
T ss_pred             HHHHHHhhCCCEEEEeCCcccCCHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            45555667788999999754444555555665555433356788888766

>PRK14245 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.26  E-value=0.21  Score=48.70  Aligned_cols=50  Identities=10%  Similarity=0.018  Sum_probs=31.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+++||+.-..-+......+...+.....+..||++|.+.
T Consensus       156 ~laral~~~p~lllLDEPt~~LD~~~~~~l~~~l~~~~~~~tiiivtH~~  205 (250)
T PRK14245        156 CIARAMAVSPSVLLMDEPASALDPISTAKVEELIHELKKDYTIVIVTHNM  205 (250)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            45555666778999999755444555566665554433456677777665

>PRK14236 phosphate transporter ATP-binding protein; Provisional

Probab=95.26  E-value=0.23  Score=49.18  Aligned_cols=51  Identities=12%  Similarity=-0.014  Sum_probs=31.2

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.|...+-.++-+|+||+--..-+......+...+.....+..||++|.+.
T Consensus       177 v~laral~~~p~lllLDEPt~gLD~~~~~~l~~~L~~~~~~~tiiivtH~~  227 (272)
T PRK14236        177 LVIARAIAIEPEVLLLDEPTSALDPISTLKIEELITELKSKYTIVIVTHNM  227 (272)
T ss_pred             HHHHHHHHCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCeEEEEeCCH
Confidence            345555666788999999754433445555555554432345677777765

>TIGR00958 3a01208 Conjugate Transporter-2 (CT2) Family protein

Probab=95.26  E-value=0.19  Score=57.04  Aligned_cols=25  Identities=24%  Similarity=0.331  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|+|+.|.|||||++.+..-
T Consensus       506 ~Ge~vaIvG~SGsGKSTLl~lL~gl  530 (711)
T TIGR00958       506 PGEVVALVGPSGSGKSTVAALLQNL  530 (711)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhc
Confidence            4579999999999999999999764

>PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed

Probab=95.26  E-value=0.095  Score=50.40  Aligned_cols=25  Identities=28%  Similarity=0.364  Sum_probs=22.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +...+|+|.|+.|+|||||++.+..
T Consensus        31 ~~~~iigi~G~~GsGKTTl~~~L~~   55 (229)
T PRK09270         31 QRRTIVGIAGPPGAGKSTLAEFLEA   55 (229)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4578999999999999999999987

>PRK14249 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.25  E-value=0.3  Score=47.67  Aligned_cols=50  Identities=8%  Similarity=0.026  Sum_probs=30.6

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+-.++-+|+||+--..-+......+...+.....+..||++|.+.
T Consensus       157 ~laral~~~p~lllLDEPt~~LD~~~~~~l~~~l~~~~~~~tilivsh~~  206 (251)
T PRK14249        157 CIARVLAIEPEVILMDEPCSALDPVSTMRIEELMQELKQNYTIAIVTHNM  206 (251)
T ss_pred             HHHHHHhcCCCEEEEeCCCccCCHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            44555566788999999754433445555555544333466777777655

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.24  E-value=0.033  Score=51.30  Aligned_cols=22  Identities=36%  Similarity=0.600  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +|+|.|.+|+||||||..+...
T Consensus         1 ii~i~G~sgsGKttla~~l~~~   22 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQ   22 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999999873

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=95.24  E-value=0.059  Score=48.20  Aligned_cols=25  Identities=32%  Similarity=0.590  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +..+|.++|.+|+||||+|..+...
T Consensus        22 ~~~viW~TGLSGsGKSTiA~ale~~   46 (197)
T COG0529          22 KGAVIWFTGLSGSGKSTIANALEEK   46 (197)
T ss_pred             CCeEEEeecCCCCCHHHHHHHHHHH
Confidence            4679999999999999999999883

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=95.24  E-value=0.086  Score=51.12  Aligned_cols=43  Identities=21%  Similarity=0.261  Sum_probs=31.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPR  239 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~  239 (597)
                      ...++.|.|++|+|||+++.+++.+. ...+=..++|++...+.
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~-~~~~g~~vly~s~E~~~   54 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENI-AKKQGKPVLFFSLEMSK   54 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH-HHhCCCceEEEeCCCCH
Confidence            45699999999999999999987642 22213456777766544

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.

>PRK14242 phosphate transporter ATP-binding protein; Provisional

Probab=95.24  E-value=0.26  Score=48.16  Aligned_cols=50  Identities=10%  Similarity=0.028  Sum_probs=30.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .+...+..++-+|+||+--..-+......+...+.....+..||++|.+.
T Consensus       159 ~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tvii~tH~~  208 (253)
T PRK14242        159 CIARALAVEPEVLLMDEPASALDPIATQKIEELIHELKARYTIIIVTHNM  208 (253)
T ss_pred             HHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHhcCCeEEEEEecH
Confidence            35555666788999999754433445555555554433356677777655

>PRK13548 hmuV hemin importer ATP-binding subunit; Provisional

Probab=95.22  E-value=0.25  Score=48.43  Aligned_cols=24  Identities=38%  Similarity=0.548  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~i~G~   51 (258)
T PRK13548         28 GEVVAILGPNGAGKSTLLRALSGE   51 (258)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            468999999999999999999764

>PF00625 Guanylate_kin: Guanylate kinase; InterPro: IPR008144 Guanylate kinase (2

Probab=95.21  E-value=0.019  Score=53.08  Aligned_cols=37  Identities=22%  Similarity=0.437  Sum_probs=29.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      .++|.|+|+.|+|||||+..+..  .....|...++.+-
T Consensus         2 ~r~ivl~Gpsg~GK~~l~~~L~~--~~~~~~~~~v~~TT   38 (183)
T PF00625_consen    2 RRPIVLVGPSGSGKSTLAKRLIQ--EFPDKFGRVVSHTT   38 (183)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHH--HSTTTEEEEEEEES
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH--hcccccccceeecc
Confidence            47899999999999999999988  45566755555443

7.4.8 from EC) (GK) [] catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown [, , ] to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus. Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) [], and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55kDa erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; GO: 0005515 protein binding; PDB: 3UAT_A 3KFV_A 2ANC_F 2F3T_E 2ANB_A 2AN9_A 1S96_A 2F3R_B 3TR0_A 1LVG_A ....

>PRK09580 sufC cysteine desulfurase ATPase component; Reviewed

Probab=95.19  E-value=0.28  Score=47.78  Aligned_cols=24  Identities=29%  Similarity=0.371  Sum_probs=21.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|.|||||++.++..
T Consensus        27 Ge~~~i~G~nGsGKSTLl~~l~Gl   50 (248)
T PRK09580         27 GEVHAIMGPNGSGKSTLSATLAGR   50 (248)
T ss_pred             CCEEEEECCCCCCHHHHHHHHcCC
Confidence            469999999999999999999874

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=95.18  E-value=0.16  Score=49.00  Aligned_cols=138  Identities=16%  Similarity=0.104  Sum_probs=68.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc---c-------------C-CeeEEEEecCCCchhhhhhhhhhhcc-----
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA---N-------------F-DKRIWVSASYPRDEIRVARDEISVAR-----  253 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~---~-------------F-~~~~wv~~~~~~~~~~~~~~~~~~~~-----  253 (597)
                      ...+++|.|+.|+|||||.+.++.-.....   .             + ....+++=+..........+.+...+     
T Consensus        27 ~G~i~~iiGpNG~GKSTLLk~l~g~l~p~~G~V~l~g~~i~~~~~kelAk~ia~vpQ~~~~~~~~tV~d~V~~GR~p~~~  106 (258)
T COG1120          27 KGEITGILGPNGSGKSTLLKCLAGLLKPKSGEVLLDGKDIASLSPKELAKKLAYVPQSPSAPFGLTVYELVLLGRYPHLG  106 (258)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCCCCCCEEEECCCchhhcCHHHHhhhEEEeccCCCCCCCcEEeehHhhcCCcccc
Confidence            457999999999999999999977321100   0             0 11334432221111111111111100     


Q ss_pred             -----cchHHHHHHHHHHhccCCC------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--C
Q 041007          254 -----DRDEIRVAKAILESLKGSV------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--G  320 (597)
Q Consensus       254 -----~~~~~~~~~~il~~l~~~~------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~  320 (597)
                           .....+.....++.++...      .....-+.-.-.+...|..+.=+|+||+--+.-+...--.+...+..  .
T Consensus       107 ~~~~~~~~D~~~v~~aL~~~~~~~la~r~~~~LSGGerQrv~iArALaQ~~~iLLLDEPTs~LDi~~Q~evl~ll~~l~~  186 (258)
T COG1120         107 LFGRPSKEDEEIVEEALELLGLEHLADRPVDELSGGERQRVLIARALAQETPILLLDEPTSHLDIAHQIEVLELLRDLNR  186 (258)
T ss_pred             cccCCCHhHHHHHHHHHHHhCcHHHhcCcccccChhHHHHHHHHHHHhcCCCEEEeCCCccccCHHHHHHHHHHHHHHHH
Confidence                 0111234444555554321      12222344455677788888889999984221111122223333332  2


Q ss_pred             CCCcEEEEEccCC
Q 041007          321 SEGSRILVTRSGG  333 (597)
Q Consensus       321 ~~gs~IIvTtR~~  333 (597)
                      ..|..||+++.+-
T Consensus       187 ~~~~tvv~vlHDl  199 (258)
T COG1120         187 EKGLTVVMVLHDL  199 (258)
T ss_pred             hcCCEEEEEecCH
Confidence            4577888888776

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=95.18  E-value=0.18  Score=49.55  Aligned_cols=25  Identities=24%  Similarity=0.218  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|.|+.|+|||||.+.+...
T Consensus       110 ~~~~~~i~g~~g~GKttl~~~l~~~  134 (270)
T TIGR02858       110 RVLNTLIISPPQCGKTTLLRDLARI  134 (270)
T ss_pred             CeeEEEEEcCCCCCHHHHHHHHhCc
Confidence            3578999999999999999999883

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.

>TIGR02142 modC_ABC molybdenum ABC transporter, ATP-binding protein

Probab=95.18  E-value=0.23  Score=51.25  Aligned_cols=24  Identities=38%  Similarity=0.418  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++.-
T Consensus        23 Gei~~l~G~nGsGKSTLl~~iaGl   46 (354)
T TIGR02142        23 QGVTAIFGRSGSGKTTLIRLIAGL   46 (354)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            469999999999999999999764

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.

>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor

Probab=95.15  E-value=0.25  Score=48.35  Aligned_cols=25  Identities=24%  Similarity=0.397  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|+|+.|.|||||.+.++.-
T Consensus        25 ~Ge~~~IvG~nGsGKSTLlk~l~Gl   49 (255)
T cd03236          25 EGQVLGLVGPNGIGKSTALKILAGK   49 (255)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3469999999999999999999763

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.

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=95.15  E-value=0.0089  Score=50.78  Aligned_cols=27  Identities=30%  Similarity=0.561  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHhCChhhhccCC
Q 041007          200 IWILGNEGIGKTALARQVFDDSDVKANFD  228 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~~~~~~~F~  228 (597)
                      |.|+|.+|+|||++|+.++.  .....|.
T Consensus         2 vLleg~PG~GKT~la~~lA~--~~~~~f~   28 (131)
T PF07726_consen    2 VLLEGVPGVGKTTLAKALAR--SLGLSFK   28 (131)
T ss_dssp             EEEES---HHHHHHHHHHHH--HTT--EE
T ss_pred             EeeECCCccHHHHHHHHHHH--HcCCcee
Confidence            67999999999999999988  4555553

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PRK15112 antimicrobial peptide ABC system ATP-binding protein SapF; Provisional

Probab=95.15  E-value=0.22  Score=49.08  Aligned_cols=24  Identities=29%  Similarity=0.434  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|+.|+|||||.+.++.-
T Consensus        39 Ge~~~i~G~NGsGKSTLl~~l~Gl   62 (267)
T PRK15112         39 GQTLAIIGENGSGKSTLAKMLAGM   62 (267)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHhCC
Confidence            468999999999999999999764

>PRK14274 phosphate ABC transporter ATP-binding protein; Provisional

Probab=95.15  E-value=0.22  Score=48.92  Aligned_cols=51  Identities=12%  Similarity=0.018  Sum_probs=30.9

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.|...+..++-+++||+--..-+......+...+.....+..||++|.+.
T Consensus       164 v~laral~~~p~llllDEPt~~LD~~~~~~l~~~l~~~~~~~tiiivtH~~  214 (259)
T PRK14274        164 LCIARALATNPDVLLMDEPTSALDPVSTRKIEELILKLKEKYTIVIVTHNM  214 (259)
T ss_pred             HHHHHHHhcCCCEEEEcCCcccCCHHHHHHHHHHHHHHhcCCEEEEEEcCH
Confidence            345555666778999999755444555555555554433345666666654

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=95.14  E-value=0.25  Score=50.55  Aligned_cols=50  Identities=22%  Similarity=0.167  Sum_probs=31.5

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~IIvTtR~~  333 (597)
                      .|...|..++-+|+||+--+.-+...-..+...+.. ...|..||++|.+.
T Consensus       182 ~lA~aL~~~P~lLiLDEPt~gLD~~~r~~l~~~l~~l~~~g~tilisSH~l  232 (340)
T PRK13536        182 TLARALINDPQLLILDEPTTGLDPHARHLIWERLRSLLARGKTILLTTHFM  232 (340)
T ss_pred             HHHHHHhcCCCEEEEECCCCCCCHHHHHHHHHHHHHHHhCCCEEEEECCCH
Confidence            455566678889999987544334444444444433 22477899998766

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=95.14  E-value=0.059  Score=58.23  Aligned_cols=47  Identities=17%  Similarity=0.302  Sum_probs=38.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|....++++.+.+.....        ....|.|+|..|+||+.+|+.+++.
T Consensus       219 ~~iiG~S~~m~~~~~~i~~~A~--------s~~pVLI~GE~GTGKe~~A~~IH~~  265 (538)
T PRK15424        219 GDLLGQSPQMEQVRQTILLYAR--------SSAAVLIQGETGTGKELAAQAIHRE  265 (538)
T ss_pred             hheeeCCHHHHHHHHHHHHHhC--------CCCcEEEECCCCCCHHHHHHHHHHh
Confidence            4589999999999888865443        3467899999999999999999874

>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis

Probab=95.13  E-value=0.036  Score=49.53  Aligned_cols=35  Identities=26%  Similarity=0.506  Sum_probs=30.2

Q ss_pred             hhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          173 AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       173 ~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.+++|.++|.            + +++++.|+.|+|||||...+...
T Consensus        24 ~g~~~l~~~l~------------~-k~~vl~G~SGvGKSSLiN~L~~~   58 (161)
T PF03193_consen   24 EGIEELKELLK------------G-KTSVLLGQSGVGKSSLINALLPE   58 (161)
T ss_dssp             TTHHHHHHHHT------------T-SEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCHHHHHHHhc------------C-CEEEEECCCCCCHHHHHHHHHhh
Confidence            46778888886            2 79999999999999999999885

RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=95.13  E-value=0.25  Score=51.64  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++++|+.|+||||++..+..
T Consensus       190 ~g~vi~lvGpnG~GKTTtlakLA~  213 (420)
T PRK14721        190 QGGVYALIGPTGVGKTTTTAKLAA  213 (420)
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999987765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	597
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	8e-84
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	3e-82
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-43
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	3e-19
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	1e-08
2fna_A	357	Conserved hypothetical protein; structural genomic	5e-05
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	2e-04

>2a5y_B CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis elegans} SCOP: a.4.5.80 a.77.1.3 c.37.1.20 PDB: 3lqq_A* 3lqr_A* Length = 549

 Score =  271 bits (694), Expect = 8e-84
 Identities = 79/552 (14%), Positives = 162/552 (29%), Gaps = 66/552 (11%)

Query: 42  LEAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDH 101
            E     L  A  R + D +     D L  L       +D  +  +    +L        
Sbjct: 3   CEIECRALSTAHTRLIHDFE---PRDALTYLEGKNIFTEDHSELISKMSTRLERIANFLR 59

Query: 102 KASKVRSFTCHLRIALRFDIGCKLKN-LSRRVDAIAGKKDGFVIKLMSGSGEGGIMTT-- 158
              +  S    L     ++    L + L   +D    + D     +++      ++    
Sbjct: 60  IYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQMLDRKL 119

Query: 159 -SSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQV 217
               V   +  + R     ++++ L      +          +++ G  G GK+ +A Q 
Sbjct: 120 LLGNVPKQMTCYIREYHVDRVIKKLDEMCDLDSF-------FLFLHGRAGSGKSVIASQA 172

Query: 218 FDDSD--VKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESL-----KG 270
              SD  +  N+D  +W+  S             +     D       +L+S        
Sbjct: 173 LSKSDQLIGINYDSIVWLKDS-----------GTAPKSTFDLFTDILLMLKSEDDLLNFP 221

Query: 271 SVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVT- 329
           SV     +       N  +     L V DD+      R+ ++L           R LVT 
Sbjct: 222 SVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQEL---------RLRCLVTT 272

Query: 330 RSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIG 389
           R           + +          I +  L  +EC                 EK E + 
Sbjct: 273 RD----------VEISNAASQTCEFIEVTSLEIDECYDFLEAYGM---PMPVGEKEEDVL 319

Query: 390 RRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSP-L 448
            + +    G P  + +       KT  ++   + +         +       Y+ L+  L
Sbjct: 320 NKTIELSSGNPATLMMFFKSCEPKTF-EKMAQLNNKLESRGLVGVECITPYSYKSLAMAL 378

Query: 449 LLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGN 508
                 LS   +    +  + P   +I       +        S E + ++    +    
Sbjct: 379 QRCVEVLSDEDRSALAFAVVMPPGVDIPVKLWSCVIPVDIC--SNEEEQLDDEVADRLKR 436

Query: 509 LSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKS---HNFNAEVKGSDQECQSKSS 565
           LS R      +       ++  ++  I+H F + +  +    N  + ++    E  + + 
Sbjct: 437 LSKRGALLSGK----RMPVLTFKIDHIIHMFLKHVVDAQTIANGISILEQRLLEIGNNNV 492

Query: 566 HEKFRHLMIMFE 577
               RH+   F+
Sbjct: 493 SVPERHIPSHFQ 504

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens} Length = 591

 Score =  268 bits (687), Expect = 3e-82
 Identities = 85/570 (14%), Positives = 171/570 (30%), Gaps = 85/570 (14%)

Query: 43  EAIREVLDDAEKRQVKDVKDKAVEDWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHK 102
              R  L    +   KD+K   + D +        + ++ +    T  Q+   A      
Sbjct: 3   AKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRA--AMLIKMI 60

Query: 103 ASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGSGEGGIMT---TS 159
             K          AL   +    K+L+  +            K         + T     
Sbjct: 61  LKKDNDSYVSFYNAL---LHEGYKDLAALLHDGIPVVSSSSGKDSVSGITSYVRTVLCEG 117

Query: 160 SAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD 219
                P+ F  R      I Q L     +           + I G  G GK+ LA +   
Sbjct: 118 GVPQRPVVFVTRKKLVNAIQQKLSKLKGE--------PGWVTIHGMAGCGKSVLAAEAVR 169

Query: 220 DSDVKANF--DKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVE 277
           D  +          WVS         + +             +   + +    S    + 
Sbjct: 170 DHSLLEGCFPGGVHWVSVGKQDKSGLLMKL----------QNLCTRLDQDESFSQRLPLN 219

Query: 278 METVLQYINEFV--QGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKN 335
           +E     +   +  +  + LL+LDD+W               K+     +IL+T      
Sbjct: 220 IEEAKDRLRILMLRKHPRSLLILDDVW---DSWVL-------KAFDSQCQILLT------ 263

Query: 336 GTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK 395
            T    +         ++ +    L +E+   +        ++             ++ +
Sbjct: 264 -TRDKSVTDSVMGPKYVVPV-ESSLGKEKGLEILSLFVNMKKAD-----LPEQAHSIIKE 316

Query: 396 CKGLPFAVKILGSLLRFKTSI-KEWQSVLDSEIWNLDSEICKRAGVGYECLSP-LLLSYF 453
           CKG P  V ++G+LLR   +  + +   L ++ +     I K +   YE L   + +S  
Sbjct: 317 CKGSPLVVSLIGALLRDFPNRWEYYLKQLQNKQF---KRIRKSSSYDYEALDEAMSISVE 373

Query: 454 DLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRS 513
            L   +K  +   SI  K+ ++    L  LW  +               E+      ++S
Sbjct: 374 MLREDIKDYYTDLSILQKDVKVPTKVLCILWDMETE-----------EVEDILQEFVNKS 422

Query: 514 LFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKSHNFNAEVKGSDQEC-QSKSSHEKFRHL 572
           L       + +G+  R  +H +  +F           ++++   ++       + +   L
Sbjct: 423 LLF----CDRNGKSFRYYLHDLQVDFLT-----EKNCSQLQDLHKKIITQFQRYHQPHTL 473

Query: 573 MIMFETDHGAFPNSVY------NQKKLRSL 596
               E     +    Y        K+L +L
Sbjct: 474 SPDQEDCMYWYNFLAYHMASAKMHKELCAL 503

>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 =  165 bits (418), Expect = 4e-43
 Identities = 87/591 (14%), Positives = 180/591 (30%), Gaps = 120/591 (20%)

Query: 33  TDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVEDWLRE-LTDTCYAVDDALDEWNTAIQ 91
            +  + +   + I  V +DA      D KD  V+D  +  L+     +D  +   +    
Sbjct: 9   FETGEHQYQYKDILSVFEDAFVDNF-DCKD--VQDMPKSILSKE--EIDHIIMSKDAVSG 63

Query: 92  -KLLLANETDHKASKVRSFTCHLRIALRFDIGCKLKNLSRRVDAIAGKKDGFVIKLMSGS 150
              L       +   V+ F   +   LR +    +  +       +     ++ +     
Sbjct: 64  TLRLFWTLLSKQEEMVQKF---VEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQR---- 116

Query: 151 GEGGIMTTSSAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWIL--GNEGI 208
                +   + V        R    Q  L+L +              P   +L  G  G 
Sbjct: 117 ---DRLYNDNQVFAKY-NVSR---LQPYLKLRQALLELR--------PAKNVLIDGVLGS 161

Query: 209 GKTALARQVFDDSDVKANFDKRI-WVSASYPRDEIRVARDEISVARDRDEIRVAKAILES 267
           GKT +A  V     V+   D +I W++            + +     +   ++       
Sbjct: 162 GKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP-----ETVLEMLQKLLYQIDPNWTSR 216

Query: 268 LKGSVSSQVEMETVLQYINEFVQGK---KVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGS 324
              S + ++ + ++   +   ++ K     LLVL ++      + W    ++L       
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ---NAKAWN--AFNL-----SC 266

Query: 325 RILV-TRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYRE 383
           +IL+ TR        +T+           ++     L+ +E +SL  +     R  D   
Sbjct: 267 KILLTTRF-----KQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYL-DCRPQDLPR 320

Query: 384 KFEPIGRRVVGKCKGLPFAVKILGSLLR-FKTSIKEWQSVLDSEIWNLDSEICKRAGVGY 442
           +               P  + I+   +R    +   W+ V       L + I        
Sbjct: 321 E----------VLTTNPRRLSIIAESIRDGLATWDNWKHV---NCDKLTTII----ESSL 363

Query: 443 ECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVG 502
             L P            +K F   S+FP +  I    L  +W     +   +   M +V 
Sbjct: 364 NVLEPAEY---------RKMFDRLSVFPPSAHIPTILLSLIW---FDVIKSD--VMVVVN 409

Query: 503 EEYFGNLSSRSLFQDFQKSEFDGRI--------IRCQ------MHPIVHEFAQLLSKSHN 548
           +     L   SL    +K   +  I        ++ +      +H  + +   +     +
Sbjct: 410 K-----LHKYSL---VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDS 461

Query: 549 FNAEVKGSDQECQSKSSHEKFRHLMIMFETDHGAFPNSVY-N----QKKLR 594
            +      DQ   S   H    HL  +   +       V+ +    ++K+R
Sbjct: 462 DDLIPPYLDQYFYSHIGH----HLKNIEHPERMTLFRMVFLDFRFLEQKIR 508

>3sfz_A APAF-1, apoptotic peptidase activating factor 1; apoptosis, caspase activation, cytochrome C, procaspase-9, A nucleotide, cytosol; HET: ADP; 3.00A {Mus musculus} PDB: 3shf_A* 3iyt_A* 3iza_A* Length = 1249

 Score = 91.4 bits (227), Expect = 3e-19
 Identities = 75/397 (18%), Positives = 137/397 (34%), Gaps = 66/397 (16%)

Query: 165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQ-VFDDSDV 223
           P+ F  R      I Q L   + +           + I G  G GK+ LA + V D S +
Sbjct: 123 PVIFVTRKKLVHAIQQKLWKLNGEP--------GWVTIYGMAGCGKSVLAAEAVRDHSLL 174

Query: 224 KANF-DKRIWVS-ASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETV 281
           +  F     WVS     +  + +    + +  D++E     +  + L  ++    +   V
Sbjct: 175 EGCFSGGVHWVSIGKQDKSGLLMKLQNLCMRLDQEE-----SFSQRLPLNIEEAKDRLRV 229

Query: 282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTE 341
           L       +  + LL+LDD+W    P         LK+     +IL+T       T    
Sbjct: 230 LM----LRKHPRSLLILDDVW---DPWV-------LKAFDNQCQILLT-------TRDKS 268

Query: 342 IGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPF 401
           +        +++ +    L  E+   +        +     E        ++ +CKG P 
Sbjct: 269 VTDSVMGPKHVVPV-ESGLGREKGLEILSLFVNMKKEDLPAEA-----HSIIKECKGSPL 322

Query: 402 AVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFD-LSPALK 460
            V ++G+LLR       W   L          I K +   YE L   +    + L   +K
Sbjct: 323 VVSLIGALLR--DFPNRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIK 380

Query: 461 KCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQK 520
             +   SI  K+ ++    L  LW         E++++E + +E      ++SL      
Sbjct: 381 DYYTDLSILQKDVKVPTKVLCVLW-------DLETEEVEDILQE----FVNKSLLF---- 425

Query: 521 SEFDGRIIRCQMHPIVHEFA-----QLLSKSHNFNAE 552
              +G+     +H +  +F        L   H     
Sbjct: 426 CNRNGKSFCYYLHDLQVDFLTEKNRSQLQDLHRKMVT 462

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare} Length = 115

 Score = 52.1 bits (125), Expect = 1e-08
 Identities = 20/125 (16%), Positives = 47/125 (37%), Gaps = 16/125 (12%)

Query: 7   VSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKRQVKDVKDKAVE 66
           +S ++ +L  +  +    +L   GV  ++E L   LE++   L    +   +   D   +
Sbjct: 3   ISNLIPKLGELLTE--EFKLH-KGVKKNIEDLGKELESMNAALIKIGEVPREQ-LDSQDK 58

Query: 67  DWLRELTDTCYAVDDALDEWNTAIQKLLLANETDHKASKVRSFTCHLRIALRFDIGCKLK 126
            W  E+ +  Y ++D +D++       L+  +          F   ++          LK
Sbjct: 59  LWADEVRELSYVIEDVVDKF-------LVQVDGIKSDDNNNKFKGLMK-----RTTELLK 106

Query: 127 NLSRR 131
            +  +
Sbjct: 107 KVKHK 111

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20 Length = 357

 Score = 45.1 bits (106), Expect = 5e-05
 Identities = 48/356 (13%), Positives = 107/356 (30%), Gaps = 50/356 (14%)

Query: 164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV 223
           +  +F  R  E +K+  L                P+  +LG    GK+++ +   ++ ++
Sbjct: 11  NRKDFFDREKEIEKLKGLRA--------------PITLVLGLRRTGKSSIIKIGINELNL 56

Query: 224 K--------------ANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLK 269
                           ++   +          ++     +   ++   I +    ++   
Sbjct: 57  PYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIK-FN 115

Query: 270 GSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVT 329
            +   ++    +L+   +      V++VLD+       R    L     +     RI   
Sbjct: 116 WNRKDRLSFANLLESFEQ-ASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFI 174

Query: 330 RSGGKNGTNMTEIGLGEKNGTNMM------EIGLGELSEEECRSLFRQIAFHGRSSDYRE 383
            SG + G  +    L  ++  + +       + L   S EE     R+  F     D+++
Sbjct: 175 MSGSEMG--LLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRG-FQEADIDFKD 231

Query: 384 KFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEW-QSVLDSEIWNLDSEICKRAGVGY 442
                   V  K  G+P  +   G +     ++       L+     +  E         
Sbjct: 232 YEV-----VYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLILKEFENF----L 282

Query: 443 ECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDM 498
                    Y ++   L KC  + S   +  E+E+   I       YL        
Sbjct: 283 HGREIARKRYLNIMRTLSKCGKW-SDVKRALELEEGIEISDSEIYNYLTQLTKHSW 337

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae} Length = 318

 Score = 43.0 bits (100), Expect = 2e-04
 Identities = 16/174 (9%), Positives = 52/174 (29%), Gaps = 26/174 (14%)

Query: 160 SAVIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD 219
            ++        +  +  +I   +       ++         +I   +   K  L   V D
Sbjct: 14  ESLQKRELLKSQVEDFTRIFLPIYDSLMSSQNKL------FYITNADDSTKFQLVNDVMD 67

Query: 220 DSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKG-SVSSQVEM 278
           +    +   +       +           I          + + I  ++   ++   + +
Sbjct: 68  ELITSSARKELPIFDYIH-----------IDALELAGMDALYEKIWFAISKENLCGDISL 116

Query: 279 ETVLQYINEFV--QGKKVLLVLDDLWWNAYPRYWEQLMYSL--KSGSEGSRILV 328
           E +  YI      + +K L+++ +          E+++        S+ S++ +
Sbjct: 117 EALNFYITNVPKAKKRKTLILIQNPENLLS----EKILQYFEKWISSKNSKLSI 166

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	597
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	100.0
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	100.0
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	100.0
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	100.0
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.75
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.74
2fna_A	357	Conserved hypothetical protein; structural genomic	99.72
3qfl_A	115	MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-	99.67
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.57
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.56
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.54
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.47
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.4
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.34
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.25
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.17
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.03
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.01
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	98.89
2chq_A	319	Replication factor C small subunit; DNA-binding pr	98.8
3bos_A	242	Putative DNA replication factor; P-loop containing	98.71
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.7
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.67
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	98.65
3pvs_A	447	Replication-associated recombination protein A; ma	98.52
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	98.52
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.51
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.51
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.48
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.42
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	98.41
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.4
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	98.39
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	98.39
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.37
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	98.36
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.34
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	98.31
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.31
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.28
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.28
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.25
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.23
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.19
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.17
3co5_A	143	Putative two-component system transcriptional RES	98.1
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.08
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.01
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	98.0
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	97.99
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	97.99
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	97.98
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	97.97
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.97
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	97.97
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	97.97
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	97.92
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	97.92
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	97.9
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.9
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	97.86
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	97.81
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.79
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	97.78
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	97.76
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	97.73
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	97.72
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.7
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	97.63
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.61
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	97.58
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	97.51
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.47
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.45
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.42
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	97.31
2r44_A	331	Uncharacterized protein; putative ATPase, structur	97.31
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	97.28
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	97.27
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	97.23
2qgz_A	308	Helicase loader, putative primosome component; str	97.17
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.11
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.1
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.09
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	97.06
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.99
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.98
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	96.95
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.94
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	96.86
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	96.84
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.78
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	96.75
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	96.73
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.64
3io5_A	333	Recombination and repair protein; storage dimer, i	96.59
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	96.49
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	96.48
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	96.45
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	96.44
2z43_A	324	DNA repair and recombination protein RADA; archaea	96.39
1sgw_A	214	Putative ABC transporter; structural genomics, P p	96.37
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.34
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.33
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.32
1ji0_A	240	ABC transporter; ATP binding protein, structural g	96.29
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.29
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.25
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	96.25
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	96.24
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	96.23
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	96.22
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	96.21
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	96.15
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.14
2ghi_A	260	Transport protein; multidrug resistance protein, M	96.14
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	96.12
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.1
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.06
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	96.06
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.02
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	96.01
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	95.99
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	95.97
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.97
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	95.96
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.83
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	95.81
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.67
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.65
3ice_A	422	Transcription termination factor RHO; transcriptio	95.61
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	95.61
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	95.61
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	95.58
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.58
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.52
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	95.51
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.47
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.46
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.44
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.43
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	95.38
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	95.37
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.3
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	95.27
3b5x_A	582	Lipid A export ATP-binding/permease protein MSBA;	95.25
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	95.23
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.22
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.21
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.19
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.14
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.14
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	95.12
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	95.09
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.07
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.06
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	95.05
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	95.03
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.03
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.03
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	95.0
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	94.99
3b60_A	582	Lipid A export ATP-binding/permease protein MSBA;	94.99
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	94.97
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	94.95
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.95
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	94.92
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	94.92
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.92
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	94.91
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	94.91
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	94.9
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	94.9
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	94.89
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	94.87
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.87
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.82
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	94.82
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	94.79
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	94.77
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.75
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.72
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.72
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	94.71
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	94.7
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	94.69
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	94.65
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	94.64
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	94.64
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	94.62
1fx0_B	498	ATP synthase beta chain; latent ATPase, thermal st	94.61
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	94.61
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	94.57
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.56
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.56
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	94.53
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	94.52
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	94.51
1via_A	175	Shikimate kinase; structural genomics, transferase	94.51
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.47
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	94.47
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	94.45
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.43
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.41
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	94.39
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	94.37
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	94.36
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	94.35
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	94.35
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.34
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	94.33
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	94.32
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	94.3
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	94.29
2vli_A	183	Antibiotic resistance protein; transferase, tunica	94.26
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	94.26
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.25
2r6a_A	454	DNAB helicase, replicative helicase; replication,	94.24
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	94.23
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	94.23
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.23
3l0o_A	427	Transcription termination factor RHO; helicase, RH	94.23
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	94.22
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	94.22
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	94.19
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	94.19
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	94.18
1tue_A	212	Replication protein E1; helicase, replication, E1E	94.18
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	94.18
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.16
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	94.15
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	94.13
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	94.11
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	94.1
3hjn_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.08
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	94.07
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	94.04
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	94.02
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.02
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	93.96
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.94
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	93.94
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	93.93
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	93.93
3qf4_A	587	ABC transporter, ATP-binding protein; multidrug tr	93.91
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	93.87
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	93.86
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	93.83
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	93.81
2yl4_A	595	ATP-binding cassette SUB-family B member 10, mitoc	93.77
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	93.76
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	93.75
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	93.74
2ck3_D	482	ATP synthase subunit beta\, mitochondrial; hydrola	93.72
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	93.67
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	93.59
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.57
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	93.56
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	93.53
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	93.52
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	93.52
3fwy_A	314	Light-independent protochlorophyllide reductase I	93.52
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	93.49
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	93.48
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.46
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	93.46
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	93.42
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	93.39
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	93.39
2xxa_A	433	Signal recognition particle protein; protein trans	93.37
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.37
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.36
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	93.36
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	93.27
1yqt_A	538	RNAse L inhibitor; ATP-binding cassette, ribosome	93.26
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.25
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	93.21
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.2
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	93.17
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	93.17
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.16
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	93.15
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.12
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	93.12
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	93.12
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	93.12
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	93.1
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	93.09
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.08
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	93.07
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.04
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.0
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	92.97
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	92.97
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	92.96
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.92
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	92.91
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	92.9
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	92.89
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	92.88
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	92.87
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	92.87
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	92.86
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	92.86
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	92.83
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	92.82
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	92.79
3j16_B	608	RLI1P; ribosome recycling, translation, eukarya, r	92.73
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	92.72
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	92.66
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	92.65
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	92.62
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.6
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	92.6
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	92.59
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	92.58
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	92.57
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	92.56
3vr4_D	465	V-type sodium ATPase subunit D; V-ATPase, rotary m	92.56
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	92.53
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.51
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	92.51
2eyu_A	261	Twitching motility protein PILT; pilus retraction	92.49
2wji_A	165	Ferrous iron transport protein B homolog; membrane	92.47
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	92.4
1g6h_A	257	High-affinity branched-chain amino acid transport	92.37
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	92.36
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	92.29
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	92.27
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	92.21
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	92.2
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	92.15
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	92.15
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	92.13
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	92.13
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	92.11
2og2_A	359	Putative signal recognition particle receptor; nuc	92.09
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	92.07
3oaa_A	513	ATP synthase subunit alpha; rossmann fold, hydrola	92.07
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	92.05
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	92.04
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	92.04
4bas_A	199	ADP-ribosylation factor, putative (small GTPase, p	92.04
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	92.03
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	92.01
2r9v_A	515	ATP synthase subunit alpha; TM1612, structural gen	91.88
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	91.85
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.82
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	91.81
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	91.78
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	91.7
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	91.69
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	91.56
3vr4_A	600	V-type sodium ATPase catalytic subunit A; V-ATPase	91.52
3end_A	307	Light-independent protochlorophyllide reductase ir	91.49
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	91.48
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	91.46
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	91.39
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	91.38
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	91.34
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	91.33
2qe7_A	502	ATP synthase subunit alpha; blockage of ATP hydrol	91.32
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	91.27
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	91.25
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	91.19
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	91.19
1nrj_B	218	SR-beta, signal recognition particle receptor beta	91.18
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	91.16
3kta_A	182	Chromosome segregation protein SMC; structural mai	91.16
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	91.15
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	91.12
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	91.11
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	91.1
3iev_A	308	GTP-binding protein ERA; ERA, GTPase, KH domain, a	91.07
3gqb_B	464	V-type ATP synthase beta chain; A3B3, V-ATPase, AT	91.02
3cbq_A	195	GTP-binding protein REM 2; FLJ38964A, structural g	90.99
3mfy_A	588	V-type ATP synthase alpha chain; A-type ATP syntha	90.82
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	90.73
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	90.7
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	90.7
1fx0_A	507	ATP synthase alpha chain; latent ATPase, thermal s	90.7
1nij_A	318	Hypothetical protein YJIA; structural genomics, P-	90.67
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	90.66
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	90.65
2qu8_A	228	Putative nucleolar GTP-binding protein 1; GTPase,	90.64
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	90.6
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	90.57
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	90.56
2ck3_A	510	ATP synthase subunit alpha\, mitochondrial; hydrol	90.55
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	90.54
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	90.52
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	90.43
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	90.42
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	90.4
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	90.39
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	90.39
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	90.33
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	90.32
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	90.3
2c61_A	469	A-type ATP synthase non-catalytic subunit B; hydro	90.3
3llu_A	196	RAS-related GTP-binding protein C; structural geno	90.29
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	90.25
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	90.22
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	90.19
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	90.19
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	90.17
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	90.14
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	90.13
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	90.1
1cp2_A	269	CP2, nitrogenase iron protein; oxidoreductase; 1.9	90.03
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	89.96
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	89.95
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	89.94
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	89.94
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	89.88
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	89.87
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	89.85
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	89.76
3b6e_A	216	Interferon-induced helicase C domain-containing P;	89.74
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	89.73
2ewv_A	372	Twitching motility protein PILT; pilus retraction	89.65
2g3y_A	211	GTP-binding protein GEM; small GTPase, GDP, inacti	89.64
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	89.62
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	89.61
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	89.6
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	89.59
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	89.57
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	89.57
4dkx_A	216	RAS-related protein RAB-6A; GTP binding fold, memb	89.53
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	89.53
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	89.53
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	89.51
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	89.51
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	89.51
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	89.5
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	89.49
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	89.48
4dhe_A	223	Probable GTP-binding protein ENGB; melioidosis, RA	89.48
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	89.47
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	89.46
2fh5_B	214	SR-beta, signal recognition particle receptor beta	89.45
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	89.39
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	89.32
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	89.31
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	89.3
3g5u_A	1284	MCG1178, multidrug resistance protein 1A; P-glycop	89.28
2afh_E	289	Nitrogenase iron protein 1; nitrogen fixation, iro	89.28
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	89.27
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	89.26
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	89.22
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	89.21
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	89.17
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	89.16
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	89.16
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	89.14
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	89.09
2qnr_A	301	Septin-2, protein NEDD5; structural genomics conso	89.08
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	89.07
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	89.03
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	89.0
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	88.99
2aka_B	299	Dynamin-1; fusion protein, GTPase domain, myosin,	88.98
2j1l_A	214	RHO-related GTP-binding protein RHOD; GTPase, memb	88.98
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	88.96
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	88.91
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	88.86
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	88.8
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	88.8
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	88.77
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	88.73
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	88.73
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	88.69
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	88.67
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	88.66
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	88.65
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	88.62
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	88.58
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	88.56
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	88.54
1ega_A	301	Protein (GTP-binding protein ERA); GTPase, RNA-bin	88.54
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	88.53
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	88.5
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	88.48
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	88.45
2xtp_A	260	GTPase IMAP family member 2; immune system, G prot	88.44
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	88.35
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	88.34
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	88.31
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	88.3
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	88.3
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	88.2
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	88.17
3io3_A	348	DEHA2D07832P; chaperone, membrane traffic, ATPase;	88.17
1p9r_A	418	General secretion pathway protein E; bacterial typ	88.16
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	88.12
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	88.11
3iqw_A	334	Tail-anchored protein targeting factor GET3; ATPas	88.07
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	88.07
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	88.04
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	88.01

>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=100.00  E-value=3.5e-49  Score=429.50  Aligned_cols=312  Identities=20%  Similarity=0.262  Sum_probs=248.2

Q ss_pred             ccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC--ChhhhccCCeeEEEEecCCC--chhhh
Q 041007          169 HGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD--DSDVKANFDKRIWVSASYPR--DEIRV  244 (597)
Q Consensus       169 vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~--~~~~~~~F~~~~wv~~~~~~--~~~~~  244 (597)
                      |||+.++++|.++|....       ....++|+|+||||+||||||+++|+  +.+++.+|+.++||++++..  +.   
T Consensus       131 ~GR~~~~~~l~~~L~~~~-------~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~---  200 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMC-------DLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKST---  200 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHT-------TSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHH---
T ss_pred             CCchHHHHHHHHHHhccc-------CCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCH---
Confidence            599999999999997542       13579999999999999999999997  56889999999999999875  55   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccCCCC-------chhhHHHHHHHHHHHhcCc-eEEEEEecccCCCCcchHHHHHHh
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKGSVS-------SQVEMETVLQYINEFVQGK-KVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~~~~-------~~~~~~~~~~~l~~~L~~k-r~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                   ..++..|+.+++....       ...+.+.+...+++.|.++ ||||||||||+.+.. .|..    
T Consensus       201 -------------~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~~-~~~~----  262 (549)
T 2a5y_B          201 -------------FDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEETI-RWAQ----  262 (549)
T ss_dssp             -------------HHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHHH-HHHH----
T ss_pred             -------------HHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchhh-cccc----
Confidence                         8889999999876521       1234567788999999996 999999999975511 2321    


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-----eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHH
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-----EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRR  391 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-----~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~  391 (597)
                          .+||+||||||+.              .++..+     .|+|++|+.++|++||.+.++...   .++.+.+++.+
T Consensus       263 ----~~gs~ilvTTR~~--------------~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~---~~~~~~~~~~~  321 (549)
T 2a5y_B          263 ----ELRLRCLVTTRDV--------------EISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMP---VGEKEEDVLNK  321 (549)
T ss_dssp             ----HTTCEEEEEESBG--------------GGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC-----CHHHHHHHH
T ss_pred             ----cCCCEEEEEcCCH--------------HHHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCC---CchhHHHHHHH
Confidence                2799999999998              554433     299999999999999999987542   24677889999


Q ss_pred             HHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHH-------
Q 041007          392 VVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFL-------  464 (597)
Q Consensus       392 I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~-------  464 (597)
                      |+++|+|+||||+++|+.++.+ + .+|...+.+..+..         ...++..+|.+||++||+++|.||+       
T Consensus       322 I~~~c~GlPLAl~~~g~~l~~~-~-w~~~~~l~~~l~~~---------~~~~i~~~l~~Sy~~L~~~lk~~f~~Ls~~er  390 (549)
T 2a5y_B          322 TIELSSGNPATLMMFFKSCEPK-T-FEKMAQLNNKLESR---------GLVGVECITPYSYKSLAMALQRCVEVLSDEDR  390 (549)
T ss_dssp             HHHHHTTCHHHHHHHHTTCCSS-S-HHHHHHHHHHHHHH---------CSSTTCCCSSSSSSSHHHHHHHHHHTSCHHHH
T ss_pred             HHHHhCCChHHHHHHHHHhccc-h-HHHHHHhHHHhhcc---------cHHHHHHHHhcccccccHHHHHHHhccchhhh
Confidence            9999999999999999999765 3 23434444332221         1456899999999999999999999       


Q ss_pred             ----HhhcCCCCcccChhHHHHHHHHc--CCcccCC-CCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEEeChHHH
Q 041007          465 ----YCSIFPKNYEIEKDRLIKLWMAQ--GYLKSQE-SKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVH  537 (597)
Q Consensus       465 ----~ls~Fp~~~~i~~~~Li~~W~ae--g~i~~~~-~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~mH~lv~  537 (597)
                          |||+||+++.|+    +++|+|+  ||+.... ..+.+++++ ||++|+++|||++...+    ...+|+|||+||
T Consensus       391 ~l~~~ls~fp~~~~i~----i~~w~a~~~G~i~~~~~~~~~~~~~~-~l~~L~~rsLl~~~~~~----~~~~~~mHdlv~  461 (549)
T 2a5y_B          391 SALAFAVVMPPGVDIP----VKLWSCVIPVDICSNEEEQLDDEVAD-RLKRLSKRGALLSGKRM----PVLTFKIDHIIH  461 (549)
T ss_dssp             HHTTGGGSSCTTCCEE----HHHHHHHSCC-------CCCTHHHHH-HHHHTTTBSSCSEEECS----SSCEEECCHHHH
T ss_pred             hHhhheeeeCCCCeee----eeeeeeeccceeccCCCCCCHHHHHH-HHHHHHHcCCeeEecCC----CceEEEeChHHH
Confidence                999999999999    8999999  9998755 667788887 99999999999987543    134699999999


Q ss_pred             HHHHHhhccccE
Q 041007          538 EFAQLLSKSHNF  549 (597)
Q Consensus       538 ~~a~~~~~~~~~  549 (597)
                      +||++++.++++
T Consensus       462 ~~a~~~~~~~~~  473 (549)
T 2a5y_B          462 MFLKHVVDAQTI  473 (549)
T ss_dssp             HHHHTTSCTHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999999887765

>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=100.00  E-value=2.1e-39  Score=387.72  Aligned_cols=318  Identities=20%  Similarity=0.238  Sum_probs=242.2

Q ss_pred             ccCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhh-hccC-CeeEEEEecCCC
Q 041007          162 VIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV-KANF-DKRIWVSASYPR  239 (597)
Q Consensus       162 ~~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~F-~~~~wv~~~~~~  239 (597)
                      +..+..||||++++++|.++|....        ...++|+|+||||+||||||++++++.+. ..+| +.++|++++...
T Consensus       120 p~~~~~~vgR~~~~~~l~~~l~~~~--------~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~~~~~  191 (1249)
T 3sfz_A          120 PQRPVIFVTRKKLVHAIQQKLWKLN--------GEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSIGKQD  191 (1249)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHHTTT--------TSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEECCSCC
T ss_pred             CCCCceeccHHHHHHHHHHHHhhcc--------CCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEECCcC
Confidence            3456779999999999999997543        25789999999999999999999997543 4445 567799998754


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccCCC----CchhhHHHHHHHHHHHhcCc--eEEEEEecccCCCCcchHHHH
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKGSV----SSQVEMETVLQYINEFVQGK--KVLLVLDDLWWNAYPRYWEQL  313 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~----~~~~~~~~~~~~l~~~L~~k--r~LLVLDdv~~~~~~~~~~~l  313 (597)
                      ..              .....+..++..+....    ....+.+.+...++..+.++  |+||||||+|+..   .|   
T Consensus       192 ~~--------------~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~---~~---  251 (1249)
T 3sfz_A          192 KS--------------GLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPW---VL---  251 (1249)
T ss_dssp             HH--------------HHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHH---HH---
T ss_pred             ch--------------HHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHH---HH---
Confidence            32              11444556666665432    22456788889999999877  9999999998543   22   


Q ss_pred             HHhhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-----ceeecCC-CChHHHHHHHHHHhccCCCCCCccchHH
Q 041007          314 MYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-----MEIGLGE-LSEEECRSLFRQIAFHGRSSDYREKFEP  387 (597)
Q Consensus       314 ~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-----~~~~l~~-Ls~~es~~Lf~~~~~~~~~~~~~~~~~~  387 (597)
                          ....+|++||||||++              .++..     ..+++.+ |+.+++++||...++..     .+.+.+
T Consensus       252 ----~~~~~~~~ilvTtR~~--------------~~~~~~~~~~~~~~~~~~l~~~~a~~l~~~~~~~~-----~~~~~~  308 (1249)
T 3sfz_A          252 ----KAFDNQCQILLTTRDK--------------SVTDSVMGPKHVVPVESGLGREKGLEILSLFVNMK-----KEDLPA  308 (1249)
T ss_dssp             ----TTTCSSCEEEEEESST--------------TTTTTCCSCBCCEECCSSCCHHHHHHHHHHHHTSC-----STTCCT
T ss_pred             ----HhhcCCCEEEEEcCCH--------------HHHHhhcCCceEEEecCCCCHHHHHHHHHHhhCCC-----hhhCcH
Confidence                2336899999999998              44422     2288886 99999999999988432     233456


Q ss_pred             HHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhh-cCCCCCcccchhccccCCChhHhHHHHHh
Q 041007          388 IGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKR-AGVGYECLSPLLLSYFDLSPALKKCFLYC  466 (597)
Q Consensus       388 ~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~-~~~~~~~~~~l~~sy~~L~~~~k~cf~~l  466 (597)
                      .+.+|+++|+|+||||+++|++|+.++  ..|...+..+........... ......+..+|.+||+.||+++|.||+||
T Consensus       309 ~~~~i~~~~~glPLal~~~~~~l~~~~--~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~l~~s~~~L~~~~~~~~~~l  386 (1249)
T 3sfz_A          309 EAHSIIKECKGSPLVVSLIGALLRDFP--NRWAYYLRQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDL  386 (1249)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHHHHHHSS--SCHHHHHHHHHSCCCCCSSCTTCTTHHHHHHHHHHHHHTSCTTTHHHHHHG
T ss_pred             HHHHHHHHhCCCHHHHHHHHHHhhcCh--hHHHHHHHHHhhhhhhhcccccccchHHHHHHHHHHHHhCCHHHHHHHHHh
Confidence            789999999999999999999998765  346666654433221111000 00013578899999999999999999999


Q ss_pred             hcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEEeChHHHHHHHHhhcc
Q 041007          467 SIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLSKS  546 (597)
Q Consensus       467 s~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~mH~lv~~~a~~~~~~  546 (597)
                      |+||+++.|+++.++.+|.++           ++.++.+|++|+++|||+....+    +..+|+||++||+|++..+.+
T Consensus       387 ~~f~~~~~i~~~~~~~~~~~~-----------~~~~~~~l~~L~~~sl~~~~~~~----~~~~~~~h~l~~~~~~~~~~~  451 (1249)
T 3sfz_A          387 SILQKDVKVPTKVLCVLWDLE-----------TEEVEDILQEFVNKSLLFCNRNG----KSFCYYLHDLQVDFLTEKNRS  451 (1249)
T ss_dssp             GGSCTTCCEEHHHHHHHHTCC-----------HHHHHHHHHHHHHTTSCEEEESS----SSEEEECCHHHHHHHHHHTGG
T ss_pred             CccCCCCeeCHHHHHHHhCCC-----------HHHHHHHHHHHHhccceEEecCC----CceEEEecHHHHHHHHhhhhH
Confidence            999999999999999999664           35789999999999999865422    245799999999999999776


Q ss_pred             c
Q 041007          547 H  547 (597)
Q Consensus       547 ~  547 (597)
                      +
T Consensus       452 ~  452 (1249)
T 3sfz_A          452 Q  452 (1249)
T ss_dssp             G
T ss_pred             H
Confidence            5

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=100.00  E-value=1.2e-39  Score=359.22  Aligned_cols=280  Identities=20%  Similarity=0.199  Sum_probs=218.6

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCe-eEEEEecCCCchhhhhh
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDK-RIWVSASYPRDEIRVAR  246 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~~~~~  246 (597)
                      .|||+.++++|.++|....         ..++|+|+||||+||||||++++++.+++.+|+. ++|+++++.++.     
T Consensus       130 ~VGRe~eLeeL~elL~~~d---------~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~~~d~-----  195 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELR---------PAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSP-----  195 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCC---------SSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCCSSSH-----
T ss_pred             CCCcHHHHHHHHHHHhccC---------CCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCCCCCH-----
Confidence            4999999999999998432         3689999999999999999999987678899987 999999988776     


Q ss_pred             hhhhhcccchHHHHHHHHHHhccC---C----C----CchhhHHHHHHHHHHHh---cCceEEEEEecccCCCCcchHHH
Q 041007          247 DEISVARDRDEIRVAKAILESLKG---S----V----SSQVEMETVLQYINEFV---QGKKVLLVLDDLWWNAYPRYWEQ  312 (597)
Q Consensus       247 ~~~~~~~~~~~~~~~~~il~~l~~---~----~----~~~~~~~~~~~~l~~~L---~~kr~LLVLDdv~~~~~~~~~~~  312 (597)
                                 ..++..++..++.   .    .    ....+.+.+...+++.|   .++|+||||||+|+..   .|+.
T Consensus       196 -----------~~IL~~Ll~lL~~i~~~~~~~~d~~~~ip~~leeL~e~Lr~lL~~l~~KRvLLVLDDVwd~e---qLe~  261 (1221)
T 1vt4_I          196 -----------ETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAK---AWNA  261 (1221)
T ss_dssp             -----------HHHHHHHHHHHHHHCSSSTTTSCCCSSHHHHHHHHHHHHHHHHHHSTTSSCEEEEESCCCHH---HHHH
T ss_pred             -----------HHHHHHHHHHHhhcCcccccccccccCCCCCHHHHHHHHHHHHHhhcCCCEEEEEeCcChHH---HHHh
Confidence                       5555555553221   1    0    11234566677777766   6899999999998744   5654


Q ss_pred             HHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc----eeecC------CCChHHHHHHHHHHhccCCCCCCc
Q 041007          313 LMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM----EIGLG------ELSEEECRSLFRQIAFHGRSSDYR  382 (597)
Q Consensus       313 l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~----~~~l~------~Ls~~es~~Lf~~~~~~~~~~~~~  382 (597)
                      +    +   +||+||||||+.              .++..+    .+.++      +|+.+||++||.+.... .    .
T Consensus       262 f----~---pGSRILVTTRd~--------------~Va~~l~g~~vy~LeL~d~dL~LS~eEA~eLF~~~~g~-~----~  315 (1221)
T 1vt4_I          262 F----N---LSCKILLTTRFK--------------QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDC-R----P  315 (1221)
T ss_dssp             H----H---SSCCEEEECSCS--------------HHHHHHHHHSSCEEEECSSSSCCCHHHHHHHHHHHHCC-C----T
T ss_pred             h----C---CCeEEEEeccCh--------------HHHHhcCCCeEEEecCccccCCcCHHHHHHHHHHHcCC-C----H
Confidence            3    2   789999999998              544211    25566      99999999999998421 1    1


Q ss_pred             cchHHHHHHHHHhcCCchHHHHHHHhhhccCC-CHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhH-h
Q 041007          383 EKFEPIGRRVVGKCKGLPFAVKILGSLLRFKT-SIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPAL-K  460 (597)
Q Consensus       383 ~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~~-~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~-k  460 (597)
                         .++..+|   |+|+||||+++|+.|+.+. +.+.|...          .       ...+..+|.+||+.||+++ |
T Consensus       316 ---eeL~~eI---CgGLPLALkLaGs~Lr~k~~s~eeW~~~----------~-------~~~I~aaLelSYd~Lp~eelK  372 (1221)
T 1vt4_I          316 ---QDLPREV---LTTNPRRLSIIAESIRDGLATWDNWKHV----------N-------CDKLTTIIESSLNVLEPAEYR  372 (1221)
T ss_dssp             ---TTHHHHH---CCCCHHHHHHHHHHHHHSCSSHHHHHHC----------S-------CHHHHHHHHHHHHHSCTTHHH
T ss_pred             ---HHHHHHH---hCCCHHHHHHHHHHHhCCCCCHHHHhcC----------C-------hhHHHHHHHHHHHhCCHHHHH
Confidence               2233344   9999999999999998774 67788652          0       3457789999999999999 9


Q ss_pred             HHHHHhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEEeChHHHHHH
Q 041007          461 KCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFA  540 (597)
Q Consensus       461 ~cf~~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~mH~lv~~~a  540 (597)
                      .||+|||+||+++.|+.+.++.+|+++|          ++.++.+|++|+++|||+...  .    ..+|+|||++++++
T Consensus       373 ~cFL~LAIFPed~~I~~elLa~LW~aeG----------eedAe~~L~eLvdRSLLq~d~--~----~~rYrMHDLllELr  436 (1221)
T 1vt4_I          373 KMFDRLSVFPPSAHIPTILLSLIWFDVI----------KSDVMVVVNKLHKYSLVEKQP--K----ESTISIPSIYLELK  436 (1221)
T ss_dssp             HHHHHTTSSCTTSCEEHHHHHHHHCSSC----------SHHHHHHHHHHHTSSSSSBCS--S----SSEEBCCCHHHHHH
T ss_pred             HHHHHHhCCCCCCCCCHHHHHHHhcCCC----------HHHHHHHHHHHHhhCCEEEeC--C----CCEEEehHHHHHHh
Confidence            9999999999999999999999999987          136889999999999998731  1    23599999999965

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=100.00  E-value=5.2e-37  Score=338.31  Aligned_cols=313  Identities=20%  Similarity=0.248  Sum_probs=228.8

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhh-hccCC-eeEEEEecCCCch
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV-KANFD-KRIWVSASYPRDE  241 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~F~-~~~wv~~~~~~~~  241 (597)
                      .+..||||+.++++|.++|....        +..++|+|+||||+||||||.+++++.++ +.+|+ .++|++++.....
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~~--------~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~~~~~~  193 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKLK--------GEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVGKQDKS  193 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTST--------TSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEESCCHH
T ss_pred             CCCeecccHHHHHHHHHHHhccc--------CCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECCCCchH
Confidence            45679999999999999997532        25689999999999999999999997665 78894 7999998765321


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCC----CCchhhHHHHHHHHHHHhcC--ceEEEEEecccCCCCcchHHHHHH
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGS----VSSQVEMETVLQYINEFVQG--KKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~----~~~~~~~~~~~~~l~~~L~~--kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                                    .....+..++..++..    .....+.+.+...+...+.+  +++||||||+|+..   .   +  
T Consensus       194 --------------~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~---~---l--  251 (591)
T 1z6t_A          194 --------------GLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSW---V---L--  251 (591)
T ss_dssp             --------------HHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHH---H---H--
T ss_pred             --------------HHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHH---H---H--
Confidence                          0022223334444421    12234566777788888875  78999999997532   2   2  


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc---ceeec---CCCChHHHHHHHHHHhccCCCCCCccchHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM---MEIGL---GELSEEECRSLFRQIAFHGRSSDYREKFEPIG  389 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~---~~~~l---~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~  389 (597)
                        ....++++||||||+.              .+...   ..+++   .+|+.+|+++||...++..     .....+.+
T Consensus       252 --~~l~~~~~ilvTsR~~--------------~~~~~~~~~~~~v~~l~~L~~~ea~~L~~~~~~~~-----~~~~~~~~  310 (591)
T 1z6t_A          252 --KAFDSQCQILLTTRDK--------------SVTDSVMGPKYVVPVESSLGKEKGLEILSLFVNMK-----KADLPEQA  310 (591)
T ss_dssp             --HTTCSSCEEEEEESCG--------------GGGTTCCSCEEEEECCSSCCHHHHHHHHHHHHTSC-----GGGSCTHH
T ss_pred             --HHhcCCCeEEEECCCc--------------HHHHhcCCCceEeecCCCCCHHHHHHHHHHHhCCC-----cccccHHH
Confidence              1236789999999988              33222   11333   6999999999999988531     12234568


Q ss_pred             HHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhh-hcCCCCCcccchhccccCCChhHhHHHHHhhc
Q 041007          390 RRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICK-RAGVGYECLSPLLLSYFDLSPALKKCFLYCSI  468 (597)
Q Consensus       390 ~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~-~~~~~~~~~~~l~~sy~~L~~~~k~cf~~ls~  468 (597)
                      .+|+++|+|+||||+++|+.++...  ..|...+..+.......... .......+..++.+||+.||++.|.||++||+
T Consensus       311 ~~i~~~~~G~PLal~~~a~~l~~~~--~~w~~~l~~l~~~~~~~~~~~~~~~~~~l~~~l~~s~~~L~~~~~~~l~~la~  388 (591)
T 1z6t_A          311 HSIIKECKGSPLVVSLIGALLRDFP--NRWEYYLKQLQNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSI  388 (591)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHST--TCHHHHHHHHHSCCCCCSSCCCSSCCHHHHHHHHHHHHTSCTTTHHHHHHGGG
T ss_pred             HHHHHHhCCCcHHHHHHHHHHhcCc--hhHHHHHHHHHHhHHHHhhhccccchHHHHHHHHHHHHhCCHHHHHHHHHccc
Confidence            9999999999999999999998764  35776666543322111000 00112357788999999999999999999999


Q ss_pred             CCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEEeChHHHHHHHHhh
Q 041007          469 FPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQMHPIVHEFAQLLS  544 (597)
Q Consensus       469 Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~mH~lv~~~a~~~~  544 (597)
                      ||+++.|+.+.++.+|.++           .+.+..++++|+++|||+....+    ...+|+||+++|+|++...
T Consensus       389 f~~~~~i~~~~l~~l~~~~-----------~~~~~~~l~~L~~~~Ll~~~~~~----~~~~~~~H~lv~~~~~~~~  449 (591)
T 1z6t_A          389 LQKDVKVPTKVLCILWDME-----------TEEVEDILQEFVNKSLLFCDRNG----KSFRYYLHDLQVDFLTEKN  449 (591)
T ss_dssp             CCTTCCEEHHHHHHHHTCC-----------HHHHHHHHHHHHHTTSSEEEEET----TEEEEECCHHHHHHHHHHT
T ss_pred             cCCCCccCHHHHHHHhccC-----------HHHHHHHHHHHHhCcCeEEecCC----CccEEEEcHHHHHHHHhhh
Confidence            9999999999999999653           24678899999999999854322    1457999999999999873

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.75  E-value=3.3e-17  Score=167.72  Aligned_cols=311  Identities=12%  Similarity=0.115  Sum_probs=177.1

Q ss_pred             ccCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          162 VIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       162 ~~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ...+..|+||+.++++|.+++..            .+++.|+|++|+|||||++++++.  .    . .+|+++......
T Consensus         8 ~~~~~~~~gR~~el~~L~~~l~~------------~~~v~i~G~~G~GKT~Ll~~~~~~--~----~-~~~~~~~~~~~~   68 (350)
T 2qen_A            8 KTRREDIFDREEESRKLEESLEN------------YPLTLLLGIRRVGKSSLLRAFLNE--R----P-GILIDCRELYAE   68 (350)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHH------------CSEEEEECCTTSSHHHHHHHHHHH--S----S-EEEEEHHHHHHT
T ss_pred             CCChHhcCChHHHHHHHHHHHhc------------CCeEEEECCCcCCHHHHHHHHHHH--c----C-cEEEEeeccccc
Confidence            44567899999999999999872            169999999999999999999873  2    1 677765432100


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccC-----------------CCC-chhhHHHHHHHHHHHhcC-ceEEEEEeccc
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKG-----------------SVS-SQVEMETVLQYINEFVQG-KKVLLVLDDLW  302 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~-----------------~~~-~~~~~~~~~~~l~~~L~~-kr~LLVLDdv~  302 (597)
                                ....+...++..+...+..                 ..+ ...+...+...+.+.... ++++|||||++
T Consensus        69 ----------~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~  138 (350)
T 2qen_A           69 ----------RGHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQ  138 (350)
T ss_dssp             ----------TTCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGG
T ss_pred             ----------ccCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHH
Confidence                      0000002333333333321                 000 123455666666666543 38999999998


Q ss_pred             CCCC------cchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCcc-cc-ceeecCCCChHHHHHHHHHHhc
Q 041007          303 WNAY------PRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGT-NM-MEIGLGELSEEECRSLFRQIAF  374 (597)
Q Consensus       303 ~~~~------~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~-~~-~~~~l~~Ls~~es~~Lf~~~~~  374 (597)
                      +.+.      ...+..+...+.. ..+..+|+|++................... .. ..+.+.||+.+|+.+++.....
T Consensus       139 ~~~~~~~~~~~~~~~~L~~~~~~-~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~  217 (350)
T 2qen_A          139 YLRFYGSRGGKELLALFAYAYDS-LPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFR  217 (350)
T ss_dssp             GGGGBTTTTTHHHHHHHHHHHHH-CTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHH
T ss_pred             HHhccCccchhhHHHHHHHHHHh-cCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHH
Confidence            8652      1223333333222 257888998765310000000000000111 11 2499999999999999987653


Q ss_pred             cCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccC
Q 041007          375 HGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFD  454 (597)
Q Consensus       375 ~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~  454 (597)
                      ..+..    -..+.+..|++.|+|+|+++..++..+....+...+...+..   ..              ...+.-.+..
T Consensus       218 ~~~~~----~~~~~~~~i~~~tgG~P~~l~~~~~~~~~~~~~~~~~~~~~~---~~--------------~~~~~~~l~~  276 (350)
T 2qen_A          218 EVNLD----VPENEIEEAVELLDGIPGWLVVFGVEYLRNGDFGRAMKRTLE---VA--------------KGLIMGELEE  276 (350)
T ss_dssp             TTTCC----CCHHHHHHHHHHHTTCHHHHHHHHHHHHHHCCHHHHHHHHHH---HH--------------HHHHHHHHHH
T ss_pred             HcCCC----CCHHHHHHHHHHhCCCHHHHHHHHHHHhccccHhHHHHHHHH---HH--------------HHHHHHHHHH
Confidence            22111    114567899999999999999998764322222222211110   00              0001111112


Q ss_pred             C---ChhHhHHHHHhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcccccccCCCCeeeEEE
Q 041007          455 L---SPALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKSEFDGRIIRCQ  531 (597)
Q Consensus       455 L---~~~~k~cf~~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~~~~~~~~~~~  531 (597)
                      +   ++..+..+..+|.  ..  ++...+.....+. .    .+.+ ......+++.|++.+||....     +   .|.
T Consensus       277 l~~~~~~~~~~l~~la~--g~--~~~~~l~~~~~~~-~----~~~~-~~~~~~~l~~L~~~gli~~~~-----~---~y~  338 (350)
T 2qen_A          277 LRRRSPRYVDILRAIAL--GY--NRWSLIRDYLAVK-G----TKIP-EPRLYALLENLKKMNWIVEED-----N---TYK  338 (350)
T ss_dssp             HHHHCHHHHHHHHHHHT--TC--CSHHHHHHHHHHT-T----CCCC-HHHHHHHHHHHHHTTSEEEET-----T---EEE
T ss_pred             HHhCChhHHHHHHHHHh--CC--CCHHHHHHHHHHH-h----CCCC-HHHHHHHHHHHHhCCCEEecC-----C---EEE
Confidence            2   7889999999998  22  3445555443221 1    0112 245678999999999997641     1   255


Q ss_pred             e-ChHHHHHHH
Q 041007          532 M-HPIVHEFAQ  541 (597)
Q Consensus       532 m-H~lv~~~a~  541 (597)
                      + |++++++.+
T Consensus       339 ~~~p~~~~~~~  349 (350)
T 2qen_A          339 IADPVVATVLR  349 (350)
T ss_dssp             ESSHHHHHHHT
T ss_pred             EecHHHHHHHc
Confidence            5 788888764

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=99.74  E-value=3.7e-17  Score=171.43  Aligned_cols=310  Identities=13%  Similarity=0.038  Sum_probs=180.0

Q ss_pred             CCCccccchhhHHHHHHHh-hCCCCCCcCCCCCCccEEEE--EcCCCCcHHHHHHHHhCChhhhc-----cCC-eeEEEE
Q 041007          164 DPLEFHGRNAEKQKILQLL-KGESSDEESGSKPTLPVIWI--LGNEGIGKTALARQVFDDSDVKA-----NFD-KRIWVS  234 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L-~~~~~~~~~~~~~~~~vv~I--~G~gGiGKTtLA~~v~~~~~~~~-----~F~-~~~wv~  234 (597)
                      .+..|+||+.++++|..+| ......    .....+.+.|  +|++|+|||+|++.+++.  ...     .|. .++|++
T Consensus        20 ~p~~l~gR~~el~~l~~~l~~~~~~~----~~~~~~~~li~i~G~~G~GKT~L~~~~~~~--~~~~~~~~~~~~~~~~~~   93 (412)
T 1w5s_A           20 IPPELRVRRGEAEALARIYLNRLLSG----AGLSDVNMIYGSIGRVGIGKTTLAKFTVKR--VSEAAAKEGLTVKQAYVN   93 (412)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTS----SCBCCEEEEEECTTCCSSSHHHHHHHHHHH--HHHHHHHTTCCEEEEEEE
T ss_pred             CCCCCCChHHHHHHHHHHHhHHHhcC----CCCCCCEEEEeCcCcCCCCHHHHHHHHHHH--HHHHHhccCCceeEEEEE
Confidence            3467999999999999998 532110    0013457777  999999999999999984  332     122 357777


Q ss_pred             ecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHHhc--CceEEEEEecccCCCC-----
Q 041007          235 ASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAY-----  306 (597)
Q Consensus       235 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~-----  306 (597)
                      +......                ..++..++..++...+. ..+...+...+.+.+.  +++++|||||+|+...     
T Consensus        94 ~~~~~~~----------------~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~  157 (412)
T 1w5s_A           94 AFNAPNL----------------YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIA  157 (412)
T ss_dssp             GGGCCSH----------------HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSC
T ss_pred             CCCCCCH----------------HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcc
Confidence            6555444                77888888888654322 2234455566666654  6799999999987542     


Q ss_pred             cchHHHHHHhhcCC---C--CCcEEEEEccCCCCCCCccc---ccccccCccccceeecCCCChHHHHHHHHHHhccCCC
Q 041007          307 PRYWEQLMYSLKSG---S--EGSRILVTRSGGKNGTNMTE---IGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRS  378 (597)
Q Consensus       307 ~~~~~~l~~~l~~~---~--~gs~IIvTtR~~~~~~~~~~---~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~  378 (597)
                      ...+..+...+...   .  .+..+|+||+..... ....   ..... .. .. .+.+.||+.++++++|...+.....
T Consensus       158 ~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~-~~l~~~~~~~~~-~~-~~-~i~l~~l~~~e~~~ll~~~~~~~~~  233 (412)
T 1w5s_A          158 AEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRAL-SYMREKIPQVES-QI-GF-KLHLPAYKSRELYTILEQRAELGLR  233 (412)
T ss_dssp             HHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHH-HHHHHHCHHHHT-TC-SE-EEECCCCCHHHHHHHHHHHHHHHBC
T ss_pred             hHHHHHHHHHHHhcccCCCCceEEEEEEeccccHH-HHHhhhcchhhh-hc-CC-eeeeCCCCHHHHHHHHHHHHHhcCC
Confidence            13344444443322   2  445578788654100 0000   00000 01 11 1899999999999999876431111


Q ss_pred             CCCccchHHHHHHHHHhcC------CchHHHHHHHhhh---c---cC--CCHHHHHHHHhhhcccCChhhhhhcCCCCCc
Q 041007          379 SDYREKFEPIGRRVVGKCK------GLPFAVKILGSLL---R---FK--TSIKEWQSVLDSEIWNLDSEICKRAGVGYEC  444 (597)
Q Consensus       379 ~~~~~~~~~~~~~I~~~~~------GlPLai~~~~~~l---~---~~--~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~  444 (597)
                      .  ..-..+....|++.|+      |+|..+..+....   .   ..  -+.+.+...+....               . 
T Consensus       234 ~--~~~~~~~~~~i~~~~~~~~~~~G~p~~~~~l~~~a~~~a~~~~~~~i~~~~v~~~~~~~~---------------~-  295 (412)
T 1w5s_A          234 D--TVWEPRHLELISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENE---------------A-  295 (412)
T ss_dssp             T--TSCCHHHHHHHHHHHCGGGTSCCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHC------------------
T ss_pred             C--CCCChHHHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh---------------c-
Confidence            0  1112456788999999      9997655544321   1   11  12333333332210               0 


Q ss_pred             ccchhccccCCChhHhHHHHHhhcCC--CCcccChhHHHHHHHHcC--CcccCCCCCHHHHHHHHHHHHhhCCCccccc
Q 041007          445 LSPLLLSYFDLSPALKKCFLYCSIFP--KNYEIEKDRLIKLWMAQG--YLKSQESKDMELVGEEYFGNLSSRSLFQDFQ  519 (597)
Q Consensus       445 ~~~l~~sy~~L~~~~k~cf~~ls~Fp--~~~~i~~~~Li~~W~aeg--~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~  519 (597)
                      ...+.-++..||++.+.++..++.+.  .+..++...+...+....  ... .+.. .......+++.|+..+||....
T Consensus       296 ~~~~~~~l~~l~~~~~~~l~aia~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~l~~L~~~gli~~~~  372 (412)
T 1w5s_A          296 ASIQTHELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYN-VKPR-GYTQYHIYLKHLTSLGLVDAKP  372 (412)
T ss_dssp             ----CCSSSSSCHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHHHHHSC-CCCC-CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             cchHHHHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhhcC-CCCC-CHHHHHHHHHHHHhCCCEEeec
Confidence            22345577899999999999888754  233466655555442210  000 0111 1345678999999999997654

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=99.72  E-value=1.7e-16  Score=162.80  Aligned_cols=305  Identities=12%  Similarity=0.060  Sum_probs=171.1

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC----
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP----  238 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~----  238 (597)
                      ..+..|+||+.++++|.+ +.            . +++.|+|++|+|||+|++++++.  ...   ..+|+++...    
T Consensus        10 ~~~~~~~gR~~el~~L~~-l~------------~-~~v~i~G~~G~GKT~L~~~~~~~--~~~---~~~~~~~~~~~~~~   70 (357)
T 2fna_A           10 DNRKDFFDREKEIEKLKG-LR------------A-PITLVLGLRRTGKSSIIKIGINE--LNL---PYIYLDLRKFEERN   70 (357)
T ss_dssp             CSGGGSCCCHHHHHHHHH-TC------------S-SEEEEEESTTSSHHHHHHHHHHH--HTC---CEEEEEGGGGTTCS
T ss_pred             CCHHHhcChHHHHHHHHH-hc------------C-CcEEEECCCCCCHHHHHHHHHHh--cCC---CEEEEEchhhcccc
Confidence            456789999999999999 75            1 59999999999999999999873  322   2578877642    


Q ss_pred             -CchhhhhhhhhhhcccchHHHHHHHHHHhc--------------cC------CC-C--------chhhHHHHHHHHHHH
Q 041007          239 -RDEIRVARDEISVARDRDEIRVAKAILESL--------------KG------SV-S--------SQVEMETVLQYINEF  288 (597)
Q Consensus       239 -~~~~~~~~~~~~~~~~~~~~~~~~~il~~l--------------~~------~~-~--------~~~~~~~~~~~l~~~  288 (597)
                       .+.                ...+..+.+.+              ..      +. .        .......+...+.+.
T Consensus        71 ~~~~----------------~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~  134 (357)
T 2fna_A           71 YISY----------------KDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQA  134 (357)
T ss_dssp             CCCH----------------HHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHT
T ss_pred             CCCH----------------HHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhc
Confidence             111                11111111111              00      00 0        112345555555544


Q ss_pred             hcCceEEEEEecccCCCC---cchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccc--cceeecCCCChH
Q 041007          289 VQGKKVLLVLDDLWWNAY---PRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN--MMEIGLGELSEE  363 (597)
Q Consensus       289 L~~kr~LLVLDdv~~~~~---~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~--~~~~~l~~Ls~~  363 (597)
                      .. ++++|||||+++.+.   ...+..+. .+.....+..+|+|++....................  ...+.+.||+.+
T Consensus       135 ~~-~~~vlvlDe~~~~~~~~~~~~~~~l~-~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~  212 (357)
T 2fna_A          135 SK-DNVIIVLDEAQELVKLRGVNLLPALA-YAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSRE  212 (357)
T ss_dssp             CS-SCEEEEEETGGGGGGCTTCCCHHHHH-HHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHH
T ss_pred             CC-CCeEEEEECHHHhhccCchhHHHHHH-HHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHH
Confidence            33 499999999988642   22333333 332223467899998864100000000000001111  124899999999


Q ss_pred             HHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHH-hhhcccCChhhhhhcCCCC
Q 041007          364 ECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVL-DSEIWNLDSEICKRAGVGY  442 (597)
Q Consensus       364 es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l-~~~~~~~~~~~~~~~~~~~  442 (597)
                      |+.+++...+...+.  ....    ...|++.|+|+|+++..++..+....+...|...+ +.....+          ..
T Consensus       213 e~~~~l~~~~~~~~~--~~~~----~~~i~~~t~G~P~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~  276 (357)
T 2fna_A          213 EAIEFLRRGFQEADI--DFKD----YEVVYEKIGGIPGWLTYFGFIYLDNKNLDFAINQTLEYAKKLI----------LK  276 (357)
T ss_dssp             HHHHHHHHHHHHHTC--CCCC----HHHHHHHHCSCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH----------HH
T ss_pred             HHHHHHHHHHHHcCC--CCCc----HHHHHHHhCCCHHHHHHHHHHHccccchHHHHHHHHHHHHHHH----------HH
Confidence            999999876531111  1111    17899999999999999987764333333342211 1100000          00


Q ss_pred             CcccchhccccCCChhHhHHHHHhhcCCCCcccChhHHHHHHH-HcCCcccCCCCCHHHHHHHHHHHHhhCCCccccccc
Q 041007          443 ECLSPLLLSYFDLSPALKKCFLYCSIFPKNYEIEKDRLIKLWM-AQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQKS  521 (597)
Q Consensus       443 ~~~~~l~~sy~~L~~~~k~cf~~ls~Fp~~~~i~~~~Li~~W~-aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~~  521 (597)
                      .+...+. .-..|++..+..+..+|+   +.  +...|..... ..|.     .. .......+++.|++.+||....  
T Consensus       277 ~l~~~~~-~~~~l~~~~~~~l~~la~---g~--~~~~l~~~~~~~~g~-----~~-~~~~~~~~L~~L~~~gli~~~~--  342 (357)
T 2fna_A          277 EFENFLH-GREIARKRYLNIMRTLSK---CG--KWSDVKRALELEEGI-----EI-SDSEIYNYLTQLTKHSWIIKEG--  342 (357)
T ss_dssp             HHHHHHT-TCGGGHHHHHHHHHHHTT---CB--CHHHHHHHHHHHHCS-----CC-CHHHHHHHHHHHHHTTSEEESS--
T ss_pred             HHHHHhh-ccccccHHHHHHHHHHHc---CC--CHHHHHHHHHHhcCC-----CC-CHHHHHHHHHHHHhCCCEEecC--
Confidence            0111110 001688899999999998   21  3444433211 1121     01 1235678999999999997542  


Q ss_pred             CCCCeeeEEEe-ChHHHHHH
Q 041007          522 EFDGRIIRCQM-HPIVHEFA  540 (597)
Q Consensus       522 ~~~~~~~~~~m-H~lv~~~a  540 (597)
                        +    .|++ |++++++.
T Consensus       343 --~----~y~f~~~~~~~~l  356 (357)
T 2fna_A          343 --E----KYCPSEPLISLAF  356 (357)
T ss_dssp             --S----CEEESSHHHHHHT
T ss_pred             --C----EEEecCHHHHHhh
Confidence              1    2664 78888764

>3qfl_A MLA10; coiled-coil, (CC) domain, NLRS, nucleotide-binding domain, L rich repeat containing receptors, protein binding; 2.00A {Hordeum vulgare}

Probab=99.67  E-value=2e-17  Score=138.68  Aligned_cols=80  Identities=20%  Similarity=0.399  Sum_probs=74.1

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHhcc--ccccCCcHHHHHHHHHHHhhhhhhhhHH
Q 041007            6 TVSTVLDQLSSITQQMNGARLLVGGVVTDVEKLRSHLEAIREVLDDAEKR--QVKDVKDKAVEDWLRELTDTCYAVDDAL   83 (597)
Q Consensus         6 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~i~~~l~~a~~~--~~~~~~~~~~~~Wl~~l~~~ayd~ed~l   83 (597)
                      +++++++||.++   +.+|+.++.||++++++|+++|++|+++|.+++.+  +.   .++.++.|+++||+++||+|||+
T Consensus         2 ~v~~ll~KL~~l---l~~E~~l~~gv~~~i~~Lk~eL~~m~a~L~da~~~~~~~---~d~~vk~W~~~vrdlaYD~ED~i   75 (115)
T 3qfl_A            2 AISNLIPKLGEL---LTEEFKLHKGVKKNIEDLGKELESMNAALIKIGEVPREQ---LDSQDKLWADEVRELSYVIEDVV   75 (115)
T ss_dssp             TTCSHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCGGG---CCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHH---HHHHHHHHhchHHHHHHHHHHHHHHHHHHHHHHHhcccc---CCHHHHHHHHHHHHHHHHHHHHH
Confidence            678899999998   78999999999999999999999999999999987  44   78999999999999999999999


Q ss_pred             HHHHHHHH
Q 041007           84 DEWNTAIQ   91 (597)
Q Consensus        84 d~~~~~~~   91 (597)
                      |+|.++..
T Consensus        76 D~f~~~~~   83 (115)
T 3qfl_A           76 DKFLVQVD   83 (115)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhc
Confidence            99998764

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.57  E-value=6.4e-13  Score=137.69  Aligned_cols=304  Identities=15%  Similarity=0.073  Sum_probs=177.9

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc------CCeeEEEEecC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN------FDKRIWVSASY  237 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~------F~~~~wv~~~~  237 (597)
                      .|..|+||+.+++++..++.....      ....+.+.|+|++|+|||+||+.+++.  ....      -...+|+++..
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~~------~~~~~~vll~G~~G~GKT~l~~~~~~~--~~~~~~~~~~~~~~~~i~~~~   88 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPALR------GEKPSNALLYGLTGTGKTAVARLVLRR--LEARASSLGVLVKPIYVNARH   88 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGTS------SCCCCCEEECBCTTSSHHHHHHHHHHH--HHHHHHHHTCCEEEEEEETTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHc------CCCCCcEEEECCCCCCHHHHHHHHHHH--HHHHHhccCCCeEEEEEECCc
Confidence            347799999999999999964321      124578999999999999999999984  3221      12356777766


Q ss_pred             CCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHHhc--CceEEEEEecccCCCCcc-hHHHH
Q 041007          238 PRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAYPR-YWEQL  313 (597)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~~~-~~~~l  313 (597)
                      ..+.                ..++..++..++...+. ......+...+...+.  +++.+||||+++...... ..+.+
T Consensus        89 ~~~~----------------~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l  152 (387)
T 2v1u_A           89 RETP----------------YRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLL  152 (387)
T ss_dssp             SCSH----------------HHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHH
T ss_pred             CCCH----------------HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHH
Confidence            5555                77788888888654322 2234455556666663  568999999997553110 22233


Q ss_pred             HHhhc---CC--CCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccC-CCCCCccchHH
Q 041007          314 MYSLK---SG--SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHG-RSSDYREKFEP  387 (597)
Q Consensus       314 ~~~l~---~~--~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~-~~~~~~~~~~~  387 (597)
                      ...+.   ..  ..+..+|.||+......... ..+.  .-.....+.+.|++.++..+++...+... ......   .+
T Consensus       153 ~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~-~~l~--~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~---~~  226 (387)
T 2v1u_A          153 YRITRINQELGDRVWVSLVGITNSLGFVENLE-PRVK--SSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLD---PD  226 (387)
T ss_dssp             HHHHHGGGCC-----CEEEEECSCSTTSSSSC-HHHH--TTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBC---SS
T ss_pred             HhHhhchhhcCCCceEEEEEEECCCchHhhhC-HHHH--hcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCC---HH
Confidence            33232   11  45667788877652111110 0000  00111238999999999999999875320 111112   23


Q ss_pred             HHHHHHHhcC---CchH-HHHHHHhhh---c--cC--CCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCC
Q 041007          388 IGRRVVGKCK---GLPF-AVKILGSLL---R--FK--TSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLS  456 (597)
Q Consensus       388 ~~~~I~~~~~---GlPL-ai~~~~~~l---~--~~--~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~  456 (597)
                      ..+.|++.++   |.|- ++..+..+.   .  ..  -+.+.+...+.....                 ..+.-++..|+
T Consensus       227 ~~~~l~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~a~~~~~~-----------------~~~~~~~~~l~  289 (387)
T 2v1u_A          227 VVPLCAALAAREHGDARRALDLLRVAGEIAERRREERVRREHVYSARAEIER-----------------DRVSEVVRTLP  289 (387)
T ss_dssp             HHHHHHHHHHSSSCCHHHHHHHHHHHHHHHHHTTCSCBCHHHHHHHHHHHHH-----------------HHHHHHHHSSC
T ss_pred             HHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHhh-----------------chHHHHHHcCC
Confidence            4567777777   9994 333332221   1  11  145666665554211                 12444678899


Q ss_pred             hhHhHHHHHhh-cCCCCcccChhHHHHHHHH----cCCcccCCCCCHHHHHHHHHHHHhhCCCccccc
Q 041007          457 PALKKCFLYCS-IFPKNYEIEKDRLIKLWMA----QGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQ  519 (597)
Q Consensus       457 ~~~k~cf~~ls-~Fp~~~~i~~~~Li~~W~a----eg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~  519 (597)
                      ++.+..+..++ ++.....+....+.+....    .| +.    .-....+..+++.|...|++....
T Consensus       290 ~~~~~~l~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~----~~~~~~~~~~l~~L~~~gli~~~~  352 (387)
T 2v1u_A          290 LHAKLVLLSIMMLEDGGRPASTGEIYERYKELTSTLG-LE----HVTLRRVSGIISELDMLGIVKSRV  352 (387)
T ss_dssp             HHHHHHHHHHHHHSSSSCCEEHHHHHHHHHHHHHHTT-CC----CCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhcC-CC----CCCHHHHHHHHHHHHhCCCeEEEe
Confidence            98888777666 4432234555544443222    22 11    112356788999999999998754

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=99.56  E-value=5.9e-13  Score=138.12  Aligned_cols=303  Identities=14%  Similarity=0.097  Sum_probs=181.9

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC-CeeEEEEecCCCchhh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF-DKRIWVSASYPRDEIR  243 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F-~~~~wv~~~~~~~~~~  243 (597)
                      |..++||+.++++|..++......    ..+..+.+.|+|++|+|||||++.+++  ...... ...+|+++....+.  
T Consensus        16 p~~l~gr~~~~~~l~~~l~~~~~~----~~~~~~~~li~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~i~~~~~~~~--   87 (389)
T 1fnn_A           16 PKRLPHREQQLQQLDILLGNWLRN----PGHHYPRATLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYINGFIYRNF--   87 (389)
T ss_dssp             CSCCTTCHHHHHHHHHHHHHHHHS----TTSSCCEEEEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEETTTCCSH--
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcC----CCCCCCeEEEECCCCCCHHHHHHHHHH--HHhhhcCeeEEEEeCccCCCH--
Confidence            467999999999999998753110    012334899999999999999999987  333331 34667776665555  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHHhc--CceEEEEEecccCCCCcchHHHHHHhhcCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAYPRYWEQLMYSLKSG  320 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~  320 (597)
                                    ..++..++..++...+. ......+...+...+.  +++.+||||++++.+ ......+...+...
T Consensus        88 --------------~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~-~~~~~~L~~~~~~~  152 (389)
T 1fnn_A           88 --------------TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLA-PDILSTFIRLGQEA  152 (389)
T ss_dssp             --------------HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSC-HHHHHHHHHHTTCH
T ss_pred             --------------HHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccc-hHHHHHHHHHHHhC
Confidence                          67777888877654321 2234445555555554  568999999998874 45555665555332


Q ss_pred             C----CCcEEEEEccCCCCCCCcccccccccCcc---ccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          321 S----EGSRILVTRSGGKNGTNMTEIGLGEKNGT---NMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       321 ~----~gs~IIvTtR~~~~~~~~~~~~~~~~~~~---~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      .    .+..||++|+.........      ..+.   ....+.+.|++.++..+++...+......  ..-..+....|+
T Consensus       153 ~~~~~~~~~iI~~~~~~~~~~~l~------~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~--~~~~~~~~~~l~  224 (389)
T 1fnn_A          153 DKLGAFRIALVIVGHNDAVLNNLD------PSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAE--GSYSEDILQMIA  224 (389)
T ss_dssp             HHHSSCCEEEEEEESSTHHHHTSC------HHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCT--TSSCHHHHHHHH
T ss_pred             CCCCcCCEEEEEEECCchHHHHhC------HHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCC--CCCCHHHHHHHH
Confidence            2    4677888776541000000      0110   11138999999999999998876421100  111245678889


Q ss_pred             Hhc---------CCchHHHHHHHhhh-c-----cC--CCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCC
Q 041007          394 GKC---------KGLPFAVKILGSLL-R-----FK--TSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLS  456 (597)
Q Consensus       394 ~~~---------~GlPLai~~~~~~l-~-----~~--~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~  456 (597)
                      +.+         +|.|..+..+.... .     ..  -+.+.....+....                 ...+.-.+..|+
T Consensus       225 ~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a~~~~~~~i~~~~v~~~~~~~~-----------------~~~~~~~l~~l~  287 (389)
T 1fnn_A          225 DITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPEDVRKSSKEVL-----------------FGISEEVLIGLP  287 (389)
T ss_dssp             HHHSBSSTTCTTSCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHS-----------------CCCCHHHHHHSC
T ss_pred             HHHhhcccCCCCCCcHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHh-----------------hhhHHHHHHcCC
Confidence            988         78875544333221 1     11  12333333332211                 122334567889


Q ss_pred             hhHhHHHHHhhcCC---CCcccChhHHHHHHHH----cCCcccCCCCCHHHHHHHHHHHHhhCCCcccccc
Q 041007          457 PALKKCFLYCSIFP---KNYEIEKDRLIKLWMA----QGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQK  520 (597)
Q Consensus       457 ~~~k~cf~~ls~Fp---~~~~i~~~~Li~~W~a----eg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~  520 (597)
                      ++.+.++..++.+.   .+-.+....+...+-.    .|.    ...+ ......+++.|...++|.....
T Consensus       288 ~~~~~~L~~l~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~----~~~~-~~~~~~~l~~L~~~gli~~~~~  353 (389)
T 1fnn_A          288 LHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGE----RPRV-HSQLWSYLNDLREKGIVETRQN  353 (389)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTTC----CCCC-HHHHHHHHHHHHHTTSSEEEEC
T ss_pred             HHHHHHHHHHHHHHhhccCCCccHHHHHHHHHHHHHHcCC----CCCC-HHHHHHHHHHHHhCCCeEEeee
Confidence            99998888887654   2214555666555443    121    1111 2456789999999999987543

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.54  E-value=6.6e-13  Score=137.55  Aligned_cols=302  Identities=12%  Similarity=0.017  Sum_probs=176.8

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh----cc--CCeeEEEEecCC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK----AN--FDKRIWVSASYP  238 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~----~~--F~~~~wv~~~~~  238 (597)
                      |..|+||+.+++++..++.....      ....+.+.|+|++|+|||+||+.+++.....    ..  ....+|+++...
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~------~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~   92 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVK------NEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREV   92 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHT------TCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHc------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccC
Confidence            47799999999999988864221      1245699999999999999999999842111    11  234677776544


Q ss_pred             C-chhhhhhhhhhhcccchHHHHHHHHHHhccCCCC--chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHH
Q 041007          239 R-DEIRVARDEISVARDRDEIRVAKAILESLKGSVS--SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMY  315 (597)
Q Consensus       239 ~-~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~--~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~  315 (597)
                      . +.                ..++..++..+.+...  .......+...+.+.+..++.+|||||+++.......+.+..
T Consensus        93 ~~~~----------------~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~~~~~l~  156 (384)
T 2qby_B           93 GGTP----------------QAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRGGDIVLY  156 (384)
T ss_dssp             CSCH----------------HHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTTSHHHHH
T ss_pred             CCCH----------------HHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCCCceeHH
Confidence            3 43                6677777777733211  122234556677777776666999999976531111222022


Q ss_pred             hhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc--ceeecCCCChHHHHHHHHHHhccC-CCCCCccchHHHHHHH
Q 041007          316 SLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM--MEIGLGELSEEECRSLFRQIAFHG-RSSDYREKFEPIGRRV  392 (597)
Q Consensus       316 ~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~--~~~~l~~Ls~~es~~Lf~~~~~~~-~~~~~~~~~~~~~~~I  392 (597)
                      .+.....+..||+||+..........      .+...  ..+.+.|++.++..++|...+... ......   .+..+.|
T Consensus       157 ~l~~~~~~~~iI~~t~~~~~~~~l~~------~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~---~~~~~~i  227 (384)
T 2qby_B          157 QLLRSDANISVIMISNDINVRDYMEP------RVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYD---DEILSYI  227 (384)
T ss_dssp             HHHTSSSCEEEEEECSSTTTTTTSCH------HHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCC---SHHHHHH
T ss_pred             HHhcCCcceEEEEEECCCchHhhhCH------HHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcC---HHHHHHH
Confidence            33222267888888886521110000      11111  149999999999999999886421 111111   3456677


Q ss_pred             HHhcC---CchH-HHHHHHhhh--c-c--CCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHH
Q 041007          393 VGKCK---GLPF-AVKILGSLL--R-F--KTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCF  463 (597)
Q Consensus       393 ~~~~~---GlPL-ai~~~~~~l--~-~--~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf  463 (597)
                      ++.|+   |.|. ++..+-...  . .  .-+.+.+...+.....                 ..+..++..|+++.+..+
T Consensus       228 ~~~~~~~~G~~r~a~~~l~~a~~~a~~~~~i~~~~v~~~~~~~~~-----------------~~~~~~~~~l~~~~~~~l  290 (384)
T 2qby_B          228 AAISAKEHGDARKAVNLLFRAAQLASGGGIIRKEHVDKAIVDYEQ-----------------ERLIEAVKALPFHYKLAL  290 (384)
T ss_dssp             HHHHHTTCCCHHHHHHHHHHHHHHTTSSSCCCHHHHHHHHHHHHH-----------------HHHHHHHHSSCHHHHHHH
T ss_pred             HHHHHhccCCHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHhc-----------------chHHHHHHcCCHHHHHHH
Confidence            77887   8887 444333222  1 1  1256777666654211                 235556788999888888


Q ss_pred             HHhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHHHHhhCCCcccccc
Q 041007          464 LYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFGNLSSRSLFQDFQK  520 (597)
Q Consensus       464 ~~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~~~  520 (597)
                      ..++....+-.+. .......-..| +.    .........+++.|...|++.....
T Consensus       291 ~al~~~~~~~~~~-~~~~~~~~~~g-~~----~~~~~~~~~~l~~L~~~gli~~~~~  341 (384)
T 2qby_B          291 RSLIESEDVMSAH-KMYTDLCNKFK-QK----PLSYRRFSDIISELDMFGIVKIRII  341 (384)
T ss_dssp             HHHHTCCBHHHHH-HHHHHHHHHTT-CC----CCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHhcccChHH-HHHHHHHHHcC-CC----CCCHHHHHHHHHHHHhCCCEEEEec
Confidence            7777611101111 11112111222 11    1123466789999999999986543

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=99.47  E-value=1.5e-12  Score=134.88  Aligned_cols=304  Identities=14%  Similarity=0.089  Sum_probs=171.7

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC---CeeEEEEecCCCc
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF---DKRIWVSASYPRD  240 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F---~~~~wv~~~~~~~  240 (597)
                      .|..|+||+.+++.|.+++.....      ......+.|+|++|+|||||++.+++  .....+   ...+|+++.....
T Consensus        18 ~p~~~~gr~~e~~~l~~~l~~~~~------~~~~~~vli~G~~G~GKTtl~~~l~~--~~~~~~~~~~~~~~i~~~~~~~   89 (386)
T 2qby_A           18 IPDELPHREDQIRKIASILAPLYR------EEKPNNIFIYGLTGTGKTAVVKFVLS--KLHKKFLGKFKHVYINTRQIDT   89 (386)
T ss_dssp             CCSCCTTCHHHHHHHHHSSGGGGG------TCCCCCEEEEECTTSSHHHHHHHHHH--HHHHHTCSSCEEEEEEHHHHCS
T ss_pred             CCCCCCChHHHHHHHHHHHHHHHc------CCCCCeEEEECCCCCCHHHHHHHHHH--HHHHHhcCCceEEEEECCCCCC
Confidence            357799999999999999874311      12457899999999999999999998  344432   2466777654433


Q ss_pred             hhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHHhc--CceEEEEEecccCCCC---cchHHHHH
Q 041007          241 EIRVARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAY---PRYWEQLM  314 (597)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~---~~~~~~l~  314 (597)
                      .                ..++..++..++...+. ..+...+...+.+.+.  +++.+||||++++...   ...+..+.
T Consensus        90 ~----------------~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~~~l~~l~  153 (386)
T 2qby_A           90 P----------------YRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDDILYKLS  153 (386)
T ss_dssp             H----------------HHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCSTHHHHHH
T ss_pred             H----------------HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcCHHHHHHh
Confidence            3                56666776666543221 1223444555555554  4589999999976421   22344444


Q ss_pred             HhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHH
Q 041007          315 YSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVV  393 (597)
Q Consensus       315 ~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~  393 (597)
                      ..+.. ...+..+|+||+......... ..+.  .......+.+.|++.++..+++...+.....  ...-..+....|+
T Consensus       154 ~~~~~~~~~~~~~I~~~~~~~~~~~~~-~~~~--~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~--~~~~~~~~~~~l~  228 (386)
T 2qby_A          154 RINSEVNKSKISFIGITNDVKFVDLLD-PRVK--SSLSEEEIIFPPYNAEELEDILTKRAQMAFK--PGVLPDNVIKLCA  228 (386)
T ss_dssp             HHHHSCCC--EEEEEEESCGGGGGGCT-THHH--HTTTTEEEEECCCCHHHHHHHHHHHHHHHBC--SSCSCHHHHHHHH
T ss_pred             hchhhcCCCeEEEEEEECCCChHhhhC-HHHh--ccCCCeeEEeCCCCHHHHHHHHHHHHHhhcc--CCCCCHHHHHHHH
Confidence            44432 234566777776541000000 0000  0001124999999999999999986531110  0111245567777


Q ss_pred             HhcC---CchHHH-HHHHhhhc-----c--CCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHH
Q 041007          394 GKCK---GLPFAV-KILGSLLR-----F--KTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKC  462 (597)
Q Consensus       394 ~~~~---GlPLai-~~~~~~l~-----~--~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~c  462 (597)
                      +.++   |.|..+ .++.....     .  .-+.+.+..++....                 ...+.-++..||++.+..
T Consensus       229 ~~~~~~~G~~r~~~~ll~~a~~~a~~~~~~~i~~~~v~~a~~~~~-----------------~~~~~~~~~~l~~~~~~i  291 (386)
T 2qby_A          229 ALAAREHGDARRALDLLRVSGEIAERMKDTKVKEEYVYMAKEEIE-----------------RDRVRDIILTLPFHSKLV  291 (386)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHHHHHHTTCSSCCHHHHHHHHHHHH-----------------HHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHhcCCHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHHHHh-----------------hchHHHHHHcCCHHHHHH
Confidence            7777   999844 33322211     1  114555555554321                 113445667888888887


Q ss_pred             HHHhhcCCC-C-cccChhHHHHHHH--H--cCCcccCCCCCHHHHHHHHHHHHhhCCCcccc
Q 041007          463 FLYCSIFPK-N-YEIEKDRLIKLWM--A--QGYLKSQESKDMELVGEEYFGNLSSRSLFQDF  518 (597)
Q Consensus       463 f~~ls~Fp~-~-~~i~~~~Li~~W~--a--eg~i~~~~~~~~e~~~~~~l~~Lv~rsli~~~  518 (597)
                      +..++.+.+ + ..+....+.+...  +  .|. .    .-.......+++.|...++|...
T Consensus       292 l~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~g~-~----~~~~~~~~~~l~~L~~~gli~~~  348 (386)
T 2qby_A          292 LMAVVSISSEENVVSTTGAVYETYLNICKKLGV-E----AVTQRRVSDIINELDMVGILTAK  348 (386)
T ss_dssp             HHHHHHHC-----CEEHHHHHHHHHHHHHHHTC-C----CCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHhcCCCceeHHHHHHHHHHHHHhcCC-C----CCCHHHHHHHHHHHHhCCCEEEE
Confidence            777764321 2 1233433322211  1  121 1    11123567799999999999764

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=99.40  E-value=1.1e-11  Score=119.24  Aligned_cols=200  Identities=13%  Similarity=0.135  Sum_probs=119.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..|+||+..++.|..++....         ....+.|+|++|+||||||+.+++.  ....+.... ..+..   .    
T Consensus        23 ~~~~g~~~~~~~l~~~l~~~~---------~~~~~ll~G~~G~GKT~l~~~~~~~--~~~~~~~~~-~~~~~---~----   83 (250)
T 1njg_A           23 ADVVGQEHVLTALANGLSLGR---------IHHAYLFSGTRGVGKTSIARLLAKG--LNCETGITA-TPCGV---C----   83 (250)
T ss_dssp             GGCCSCHHHHHHHHHHHHHTC---------CCSEEEEECSTTSCHHHHHHHHHHH--HHCTTCSCS-SCCSC---S----
T ss_pred             HHHhCcHHHHHHHHHHHHcCC---------CCeEEEEECCCCCCHHHHHHHHHHH--hcCCCCCCC-CCCcc---c----
Confidence            468999999999999997432         2458999999999999999999873  322211100 00000   0    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhc-----cCCCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESL-----KGSVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l-----~~~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  .. ...+....     ..........+.+...+...    ..+++.+|||||+++.+ ...++.+...
T Consensus        84 ------------~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~-~~~~~~l~~~  149 (250)
T 1njg_A           84 ------------DN-CREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS-RHSFNALLKT  149 (250)
T ss_dssp             ------------HH-HHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC-HHHHHHHHHH
T ss_pred             ------------HH-HHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECccccc-HHHHHHHHHH
Confidence                        00 00000000     00000011111122222211    13567999999998765 5567777777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhc
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKC  396 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~  396 (597)
                      +.....+..+|+||+........        -......+.+.+++.++..+++...+...+..    -..+....|++.|
T Consensus       150 l~~~~~~~~~i~~t~~~~~~~~~--------l~~r~~~i~l~~l~~~e~~~~l~~~~~~~~~~----~~~~~~~~l~~~~  217 (250)
T 1njg_A          150 LEEPPEHVKFLLATTDPQKLPVT--------ILSRCLQFHLKALDVEQIRHQLEHILNEEHIA----HEPRALQLLARAA  217 (250)
T ss_dssp             HHSCCTTEEEEEEESCGGGSCHH--------HHTTSEEEECCCCCHHHHHHHHHHHHHHTTCC----BCHHHHHHHHHHH
T ss_pred             HhcCCCceEEEEEeCChHhCCHH--------HHHHhhhccCCCCCHHHHHHHHHHHHHhcCCC----CCHHHHHHHHHHc
Confidence            76666778888888764211000        00112239999999999999999887542211    1245678999999


Q ss_pred             CCchHHHHHHHhhh
Q 041007          397 KGLPFAVKILGSLL  410 (597)
Q Consensus       397 ~GlPLai~~~~~~l  410 (597)
                      +|+|..+..+...+
T Consensus       218 ~G~~~~~~~~~~~~  231 (250)
T 1njg_A          218 EGSLRDALSLTDQA  231 (250)
T ss_dssp             TTCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999988775543

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=99.34  E-value=1.9e-11  Score=115.89  Aligned_cols=185  Identities=14%  Similarity=0.044  Sum_probs=114.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CC-eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN-FD-KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~-~~~wv~~~~~~~~~~  243 (597)
                      ..++||+..++.+.+++...          ..+.+.|+|++|+|||+||+.+++.  .... +. ..+.+..+.....  
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~----------~~~~~ll~G~~G~GKT~l~~~l~~~--~~~~~~~~~~~~~~~~~~~~~--   82 (226)
T 2chg_A           17 DEVVGQDEVIQRLKGYVERK----------NIPHLLFSGPPGTGKTATAIALARD--LFGENWRDNFIEMNASDERGI--   82 (226)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT----------CCCCEEEECSTTSSHHHHHHHHHHH--HHGGGGGGGEEEEETTCTTCH--
T ss_pred             HHHcCcHHHHHHHHHHHhCC----------CCCeEEEECCCCCCHHHHHHHHHHH--HhccccccceEEeccccccCh--
Confidence            46899999999999999743          2334999999999999999999873  3222 21 2233333222211  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                    .. ....+.......              ....+++.+|||||++... ....+.+...+.....+
T Consensus        83 --------------~~-~~~~~~~~~~~~--------------~~~~~~~~vliiDe~~~l~-~~~~~~l~~~l~~~~~~  132 (226)
T 2chg_A           83 --------------DV-VRHKIKEFARTA--------------PIGGAPFKIIFLDEADALT-ADAQAALRRTMEMYSKS  132 (226)
T ss_dssp             --------------HH-HHHHHHHHHTSC--------------CSTTCSCEEEEEETGGGSC-HHHHHHHHHHHHHTTTT
T ss_pred             --------------HH-HHHHHHHHhccc--------------CCCccCceEEEEeChhhcC-HHHHHHHHHHHHhcCCC
Confidence                          11 111111110000              0012578999999998765 44566666666666677


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                      ..+|+||+.......         .+.. ...+.+.+++.++..+++.+.+...+..    -..+....|++.++|.|..
T Consensus       133 ~~~i~~~~~~~~~~~---------~l~~r~~~i~~~~~~~~~~~~~l~~~~~~~~~~----~~~~~~~~l~~~~~g~~r~  199 (226)
T 2chg_A          133 CRFILSCNYVSRIIE---------PIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK----ITEDGLEALIYISGGDFRK  199 (226)
T ss_dssp             EEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC----BCHHHHHHHHHHHTTCHHH
T ss_pred             CeEEEEeCChhhcCH---------HHHHhCceeecCCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHcCCCHHH
Confidence            888888875411100         1111 1138999999999999999877432211    1145678899999999996


Q ss_pred             HHHHH
Q 041007          403 VKILG  407 (597)
Q Consensus       403 i~~~~  407 (597)
                      +..+.
T Consensus       200 l~~~l  204 (226)
T 2chg_A          200 AINAL  204 (226)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55443

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=99.25  E-value=1.3e-10  Score=117.16  Aligned_cols=268  Identities=16%  Similarity=0.091  Sum_probs=146.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..|+|++..++.+..++......     ......+.|+|++|+|||+||+.+++.  ....   .++++++.....    
T Consensus        12 ~~~ig~~~~~~~l~~~l~~~~~~-----~~~~~~vll~G~~GtGKT~la~~i~~~--~~~~---~~~~~~~~~~~~----   77 (324)
T 1hqc_A           12 DEYIGQERLKQKLRVYLEAAKAR-----KEPLEHLLLFGPPGLGKTTLAHVIAHE--LGVN---LRVTSGPAIEKP----   77 (324)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHH-----CSCCCCCEEECCTTCCCHHHHHHHHHH--HTCC---EEEECTTTCCSH----
T ss_pred             HHhhCHHHHHHHHHHHHHHHHcc-----CCCCCcEEEECCCCCCHHHHHHHHHHH--hCCC---EEEEeccccCCh----
Confidence            56999999999998888632100     013467889999999999999999873  3222   233433221111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCC----
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS----  321 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~----  321 (597)
                                  ..                     +...+...+ .++.+|+||+++... ......+...+....    
T Consensus        78 ------------~~---------------------l~~~l~~~~-~~~~~l~lDEi~~l~-~~~~~~L~~~l~~~~~~~v  122 (324)
T 1hqc_A           78 ------------GD---------------------LAAILANSL-EEGDILFIDEIHRLS-RQAEEHLYPAMEDFVMDIV  122 (324)
T ss_dssp             ------------HH---------------------HHHHHTTTC-CTTCEEEETTTTSCC-HHHHHHHHHHHHHSEEEEC
T ss_pred             ------------HH---------------------HHHHHHHhc-cCCCEEEEECCcccc-cchHHHHHHHHHhhhhHHh
Confidence                        11                     111111111 346799999997765 334444544443211    


Q ss_pred             --------------CCcEEEEEccCCCCCCCcccccccccCcccc--ceeecCCCChHHHHHHHHHHhccCCCCCCccch
Q 041007          322 --------------EGSRILVTRSGGKNGTNMTEIGLGEKNGTNM--MEIGLGELSEEECRSLFRQIAFHGRSSDYREKF  385 (597)
Q Consensus       322 --------------~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~--~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~  385 (597)
                                    .+..+|.||........         .....  ..+.+.+++.++..+++...+...+..    -.
T Consensus       123 ~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~---------~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~----~~  189 (324)
T 1hqc_A          123 IGQGPAARTIRLELPRFTLIGATTRPGLITA---------PLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVR----IT  189 (324)
T ss_dssp             CSSSSSCCCEEEECCCCEEEEEESCCSSCSC---------STTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCC----CC
T ss_pred             ccccccccccccCCCCEEEEEeCCCcccCCH---------HHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCC----CC
Confidence                          23566666654421110         11222  238999999999999998877532221    12


Q ss_pred             HHHHHHHHHhcCCchHHHHHHHhhhcc------C--CCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCCh
Q 041007          386 EPIGRRVVGKCKGLPFAVKILGSLLRF------K--TSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSP  457 (597)
Q Consensus       386 ~~~~~~I~~~~~GlPLai~~~~~~l~~------~--~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~  457 (597)
                      .+....|++.|+|+|-.+..+...+..      .  -+.+.....+..                      +..++..|+.
T Consensus       190 ~~~~~~l~~~~~G~~r~l~~~l~~~~~~a~~~~~~~i~~~~~~~~~~~----------------------~~~~~~~l~~  247 (324)
T 1hqc_A          190 EEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEALAA----------------------LGLDELGLEK  247 (324)
T ss_dssp             HHHHHHHHHHSCSCHHHHHHHHHHHTTTSTTTSCSCCCHHHHHHHHHH----------------------HTCCTTCCCH
T ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHH----------------------hcccccCCCH
Confidence            456788999999999887766544321      1  123333333322                      1122344555


Q ss_pred             hHhHHHHHhh-cCCCC----------cccChhHHHH----HHHHcCCccc-CCCCCHHHHHHHHHH-HHhhCCCccc
Q 041007          458 ALKKCFLYCS-IFPKN----------YEIEKDRLIK----LWMAQGYLKS-QESKDMELVGEEYFG-NLSSRSLFQD  517 (597)
Q Consensus       458 ~~k~cf~~ls-~Fp~~----------~~i~~~~Li~----~W~aeg~i~~-~~~~~~e~~~~~~l~-~Lv~rsli~~  517 (597)
                      ..+..+..+. .|..+          ..+++..+.+    +-+..|++.. ..+....+.|.+||+ ++.+|+||||
T Consensus       248 ~e~~~i~~~~~~~~g~~~~~~~~a~~lgi~~~tl~~~l~~~~i~~~li~~~~~g~~~~~~~~~~~~~~~~~~~~~~~  324 (324)
T 1hqc_A          248 RDREILEVLILRFGGGPVGLATLATALSEDPGTLEEVHEPYLIRQGLLKRTPRGRVPTELAYRHLGYPPPVGPLLEP  324 (324)
T ss_dssp             HHHHHHHHHHHHSCSSCCCHHHHHHHTTSCHHHHHHHTHHHHHHTTSEEEETTEEEECHHHHHHTTCCCCC------
T ss_pred             HHHHHHHHHHHHhcCCCchHHHHHHHhCCCHHHHHHHHhHHHHHhcchhcCCccceecHHHHHHHhcCCCCCCCCCC
Confidence            5555555433 33222          1134444433    2455778765 334556678888887 8888888875

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.17  E-value=1.7e-10  Score=116.21  Aligned_cols=186  Identities=17%  Similarity=0.168  Sum_probs=112.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CC-eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN-FD-KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~-~~~wv~~~~~~~~~~  243 (597)
                      ..++|++..++.|..++...          ..+.+.|+|++|+|||++|+.+++.  .... +. ..++++.+....   
T Consensus        21 ~~~~g~~~~~~~l~~~l~~~----------~~~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~~~~---   85 (323)
T 1sxj_B           21 SDIVGNKETIDRLQQIAKDG----------NMPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRG---   85 (323)
T ss_dssp             GGCCSCTHHHHHHHHHHHSC----------CCCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCS---
T ss_pred             HHHHCCHHHHHHHHHHHHcC----------CCCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCCEEEecCccccC---
Confidence            56899999999999999743          2334899999999999999999883  3221 11 133333222111   


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHh-cCceEEEEEecccCCCCcchHHHHHHhhcCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFV-QGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSE  322 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L-~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~  322 (597)
                                    ......++..+...              ...+ .+++.+|||||++... ...++.+...+.....
T Consensus        86 --------------~~~i~~~~~~~~~~--------------~~~~~~~~~~viiiDe~~~l~-~~~~~~L~~~le~~~~  136 (323)
T 1sxj_B           86 --------------IDVVRNQIKHFAQK--------------KLHLPPGKHKIVILDEADSMT-AGAQQALRRTMELYSN  136 (323)
T ss_dssp             --------------HHHHHTHHHHHHHB--------------CCCCCTTCCEEEEEESGGGSC-HHHHHTTHHHHHHTTT
T ss_pred             --------------hHHHHHHHHHHHhc--------------cccCCCCCceEEEEECcccCC-HHHHHHHHHHHhccCC
Confidence                          11111111111100              0011 3458899999998765 3455556666655566


Q ss_pred             CcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchH
Q 041007          323 GSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       323 gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPL  401 (597)
                      ++.+|+||........         .+...+ .+.+.+++.++..+++...+...+..    -..+....|++.|+|.|.
T Consensus       137 ~~~~il~~~~~~~l~~---------~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~----~~~~~~~~l~~~~~G~~r  203 (323)
T 1sxj_B          137 STRFAFACNQSNKIIE---------PLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVK----YTNDGLEAIIFTAEGDMR  203 (323)
T ss_dssp             TEEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC----BCHHHHHHHHHHHTTCHH
T ss_pred             CceEEEEeCChhhchh---------HHHhhceEEeecCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHcCCCHH
Confidence            7888888865411000         111111 39999999999999999876422211    114567889999999995


Q ss_pred             -HHHHHHh
Q 041007          402 -AVKILGS  408 (597)
Q Consensus       402 -ai~~~~~  408 (597)
                       ++..+..
T Consensus       204 ~a~~~l~~  211 (323)
T 1sxj_B          204 QAINNLQS  211 (323)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence             4554433

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=99.03  E-value=2.4e-09  Score=107.97  Aligned_cols=186  Identities=14%  Similarity=0.091  Sum_probs=113.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC-C-eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF-D-KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F-~-~~~wv~~~~~~~~~~  243 (597)
                      ..++|++..++.|..++...          ..+.+.|+|++|+|||++|+.+++.  ..... . ..+.+..+....   
T Consensus        25 ~~~~g~~~~~~~l~~~l~~~----------~~~~~ll~G~~G~GKT~la~~l~~~--l~~~~~~~~~~~~~~~~~~~---   89 (327)
T 1iqp_A           25 DDIVGQEHIVKRLKHYVKTG----------SMPHLLFAGPPGVGKTTAALALARE--LFGENWRHNFLELNASDERG---   89 (327)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT----------CCCEEEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETTCHHH---
T ss_pred             HHhhCCHHHHHHHHHHHHcC----------CCCeEEEECcCCCCHHHHHHHHHHH--hcCCcccCceEEeeccccCc---
Confidence            45899999999999999743          3345999999999999999999883  32211 1 122333221100   


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                    .......+......              .....+++.+||+||++... ...++.+...+.....+
T Consensus        90 --------------~~~~~~~~~~~~~~--------------~~~~~~~~~vliiDe~~~l~-~~~~~~L~~~le~~~~~  140 (327)
T 1iqp_A           90 --------------INVIREKVKEFART--------------KPIGGASFKIIFLDEADALT-QDAQQALRRTMEMFSSN  140 (327)
T ss_dssp             --------------HHTTHHHHHHHHHS--------------CCGGGCSCEEEEEETGGGSC-HHHHHHHHHHHHHTTTT
T ss_pred             --------------hHHHHHHHHHHHhh--------------CCcCCCCCeEEEEeCCCcCC-HHHHHHHHHHHHhcCCC
Confidence                          00000001000000              00112568899999998775 45666677777666677


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                      +++|+||........         .+...+ .+.+.|++.++..+++...+...+..    -..+....|++.++|.|..
T Consensus       141 ~~~i~~~~~~~~l~~---------~l~sr~~~~~~~~l~~~~~~~~l~~~~~~~~~~----~~~~~~~~l~~~~~g~~r~  207 (327)
T 1iqp_A          141 VRFILSCNYSSKIIE---------PIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE----LTEEGLQAILYIAEGDMRR  207 (327)
T ss_dssp             EEEEEEESCGGGSCH---------HHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE----ECHHHHHHHHHHHTTCHHH
T ss_pred             CeEEEEeCCccccCH---------HHHhhCcEEEecCCCHHHHHHHHHHHHHhcCCC----CCHHHHHHHHHHCCCCHHH
Confidence            888888765411000         111111 38999999999999998876432211    1245678899999999986


Q ss_pred             HHHHHh
Q 041007          403 VKILGS  408 (597)
Q Consensus       403 i~~~~~  408 (597)
                      +..+..
T Consensus       208 ~~~~l~  213 (327)
T 1iqp_A          208 AINILQ  213 (327)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            654433

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.01  E-value=5.9e-09  Score=103.32  Aligned_cols=178  Identities=13%  Similarity=0.099  Sum_probs=103.7

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc---cCC--eeEEEEecCCCch
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA---NFD--KRIWVSASYPRDE  241 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~---~F~--~~~wv~~~~~~~~  241 (597)
                      .+.||++|+++|...|...-.      .+..+.+.|+|++|+|||++++.+++......   ...  ..+.+++....+.
T Consensus        21 ~L~~Re~E~~~i~~~L~~~i~------~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~   94 (318)
T 3te6_A           21 LLKSQVEDFTRIFLPIYDSLM------SSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGM   94 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH------TTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--
T ss_pred             ccCCHHHHHHHHHHHHHHHhc------CCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCH
Confidence            378999999999988875432      23578999999999999999999998432111   111  2455665555555


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHH--hcCceEEEEEecccCCCCcchHHHHHHhhc
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEF--VQGKKVLLVLDDLWWNAYPRYWEQLMYSLK  318 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~--L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~  318 (597)
                                      ..++..|.+++.+.... ....+.+...+...  -.+++++++||+++...   .-+.+...+.
T Consensus        95 ----------------~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~---~q~~L~~l~~  155 (318)
T 3te6_A           95 ----------------DALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL---SEKILQYFEK  155 (318)
T ss_dssp             ----------------HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC---CTHHHHHHHH
T ss_pred             ----------------HHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh---cchHHHHHHh
Confidence                            77888888888654321 11223333333322  24678999999997654   2233333332


Q ss_pred             --CC-CCCcEEEEEccCCCCCCCcccccccccCccccc---eeecCCCChHHHHHHHHHHhc
Q 041007          319 --SG-SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM---EIGLGELSEEECRSLFRQIAF  374 (597)
Q Consensus       319 --~~-~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~---~~~l~~Ls~~es~~Lf~~~~~  374 (597)
                        .. .....||.++... ..+.   ..+. ..+...+   .+.+.|++.+|..+++.+++.
T Consensus       156 ~~~~~~s~~~vI~i~n~~-d~~~---~~L~-~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~  212 (318)
T 3te6_A          156 WISSKNSKLSIICVGGHN-VTIR---EQIN-IMPSLKAHFTEIKLNKVDKNELQQMIITRLK  212 (318)
T ss_dssp             HHHCSSCCEEEEEECCSS-CCCH---HHHH-TCHHHHTTEEEEECCCCCHHHHHHHHHHHHH
T ss_pred             cccccCCcEEEEEEecCc-ccch---hhcc-hhhhccCCceEEEeCCCCHHHHHHHHHHHHH
Confidence              11 1222333334332 0100   0000 0111121   289999999999999998874

>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=98.89  E-value=3.1e-08  Score=101.79  Aligned_cols=196  Identities=12%  Similarity=0.136  Sum_probs=113.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|++..++.|...+....         ....+.|+|++|+||||+|+.+++.  ....... ....+...       
T Consensus        16 ~~~vg~~~~~~~L~~~l~~~~---------~~~~~ll~G~~G~GKT~la~~la~~--l~~~~~~-~~~~~~~~-------   76 (373)
T 1jr3_A           16 ADVVGQEHVLTALANGLSLGR---------IHHAYLFSGTRGVGKTSIARLLAKG--LNCETGI-TATPCGVC-------   76 (373)
T ss_dssp             TTSCSCHHHHHHHHHHHHHTC---------CCSEEEEESCTTSSHHHHHHHHHHH--HSCTTCS-CSSCCSSS-------
T ss_pred             hhccCcHHHHHHHHHHHHhCC---------CCeEEEEECCCCCCHHHHHHHHHHH--hCCCCCC-CCCCCccc-------
Confidence            458999999999999997432         2457899999999999999999773  2211100 00000000       


Q ss_pred             hhhhhhcccchHHHHHHHHHHh-------ccCCC-CchhhHHHHHHHHHHH-hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILES-------LKGSV-SSQVEMETVLQYINEF-VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~-------l~~~~-~~~~~~~~~~~~l~~~-L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                   .....+...       +.... ........+...+... ..+++.+||+||++..+ ....+.+...
T Consensus        77 -------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~-~~~~~~Ll~~  142 (373)
T 1jr3_A           77 -------------DNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS-RHSFNALLKT  142 (373)
T ss_dssp             -------------HHHHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSC-HHHHHHHHHH
T ss_pred             -------------HHHHHHhccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhc-HHHHHHHHHH
Confidence                         000000000       00000 0111222222222111 13567899999998776 5566777777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCcc-ccceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGT-NMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~-~~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +.....+..+|++|........         .+. ....+.+.+++.++..+++...+...+..    -..+....|++.
T Consensus       143 le~~~~~~~~Il~~~~~~~l~~---------~l~sr~~~i~~~~l~~~~~~~~l~~~~~~~~~~----~~~~a~~~l~~~  209 (373)
T 1jr3_A          143 LEEPPEHVKFLLATTDPQKLPV---------TILSRCLQFHLKALDVEQIRHQLEHILNEEHIA----HEPRALQLLARA  209 (373)
T ss_dssp             HHSCCSSEEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCC----BCHHHHHHHHHH
T ss_pred             HhcCCCceEEEEEeCChHhCcH---------HHHhheeEeeCCCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHH
Confidence            7666667777777764411000         111 11238999999999999998776322211    114567889999


Q ss_pred             cCCchHHHHHHH
Q 041007          396 CKGLPFAVKILG  407 (597)
Q Consensus       396 ~~GlPLai~~~~  407 (597)
                      ++|.|..+..+.
T Consensus       210 ~~G~~r~~~~~l  221 (373)
T 1jr3_A          210 AEGSLRDALSLT  221 (373)
T ss_dssp             SSSCHHHHHHHH
T ss_pred             CCCCHHHHHHHH
Confidence            999999876554

>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=98.80  E-value=2.1e-08  Score=100.56  Aligned_cols=183  Identities=15%  Similarity=0.063  Sum_probs=109.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-cCC-eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-NFD-KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-~F~-~~~wv~~~~~~~~~~  243 (597)
                      .+++|++..++.|..++...          ..+.+.|+|++|+|||++|+.+++.  ... .+. ..+.++.+..... .
T Consensus        17 ~~~~g~~~~~~~l~~~l~~~----------~~~~~ll~G~~G~GKt~la~~l~~~--l~~~~~~~~~~~~~~~~~~~~-~   83 (319)
T 2chq_A           17 DEVVGQDEVIQRLKGYVERK----------NIPHLLFSGPPGTGKTATAIALARD--LFGENWRDNFIEMNASDERGI-D   83 (319)
T ss_dssp             GGSCSCHHHHHHHHTTTTTT----------CCCCEEEESSSSSSHHHHHHHHHHH--HHTTCHHHHCEEEETTSTTCT-T
T ss_pred             HHHhCCHHHHHHHHHHHhCC----------CCCeEEEECcCCcCHHHHHHHHHHH--hcCCcccCCeEEEeCccccCh-H
Confidence            45899999999999988742          2334899999999999999999873  211 111 1223333321111 0


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHh-cCceEEEEEecccCCCCcchHHHHHHhhcCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFV-QGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSE  322 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L-~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~  322 (597)
                      .            .......+...                   ..+ .+++.++|+|+++... ....+.+...+.....
T Consensus        84 ~------------~~~~~~~~~~~-------------------~~~~~~~~~vliiDe~~~l~-~~~~~~L~~~le~~~~  131 (319)
T 2chq_A           84 V------------VRHKIKEFART-------------------APIGGAPFKIIFLDEADALT-ADAQAALRRTMEMYSK  131 (319)
T ss_dssp             T------------SSHHHHHHHHS-------------------CCSSSCCCEEEEEETGGGSC-HHHHHTTGGGTSSSSS
T ss_pred             H------------HHHHHHHHHhc-------------------CCCCCCCceEEEEeCCCcCC-HHHHHHHHHHHHhcCC
Confidence            0            01111111100                   001 2567899999997765 3344555555555556


Q ss_pred             CcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchH
Q 041007          323 GSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       323 gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPL  401 (597)
                      ++.+|+||........         .+... ..+.+.+++.++..+++...+...+..    -..+....|++.++|.+.
T Consensus       132 ~~~~i~~~~~~~~l~~---------~l~sr~~~i~~~~~~~~~~~~~l~~~~~~~~~~----i~~~~l~~l~~~~~G~~r  198 (319)
T 2chq_A          132 SCRFILSCNYVSRIIE---------PIQSRCAVFRFKPVPKEAMKKRLLEICEKEGVK----ITEDGLEALIYISGGDFR  198 (319)
T ss_dssp             SEEEEEEESCGGGSCH---------HHHTTCEEEECCCCCHHHHHHHHHHHHHTTCCC----BCHHHHHHHHHTTTTCHH
T ss_pred             CCeEEEEeCChhhcch---------HHHhhCeEEEecCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHcCCCHH
Confidence            7788888755410000         11111 139999999999999998877432221    124567889999999998


Q ss_pred             HHHHH
Q 041007          402 AVKIL  406 (597)
Q Consensus       402 ai~~~  406 (597)
                      .+...
T Consensus       199 ~~~~~  203 (319)
T 2chq_A          199 KAINA  203 (319)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            65444

>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=98.71  E-value=2.2e-07  Score=88.82  Aligned_cols=180  Identities=12%  Similarity=0.070  Sum_probs=103.0

Q ss_pred             Cccccch---hhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRN---AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~---~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..|+|++   ..++.+..++...          ..+.+.|+|++|+|||+||+.+++.  .......+.|++++......
T Consensus        28 ~~~~~~~~~~~~~~~l~~~~~~~----------~~~~~ll~G~~G~GKT~la~~l~~~--~~~~~~~~~~~~~~~~~~~~   95 (242)
T 3bos_A           28 TSYYPAAGNDELIGALKSAASGD----------GVQAIYLWGPVKSGRTHLIHAACAR--ANELERRSFYIPLGIHASIS   95 (242)
T ss_dssp             TTSCC--CCHHHHHHHHHHHHTC----------SCSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEGGGGGGSC
T ss_pred             hhccCCCCCHHHHHHHHHHHhCC----------CCCeEEEECCCCCCHHHHHHHHHHH--HHHcCCeEEEEEHHHHHHHH
Confidence            4577633   5556666666522          3578999999999999999999883  43333445666654321110


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcch-HHHHHHhhcCC-
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRY-WEQLMYSLKSG-  320 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~-~~~l~~~l~~~-  320 (597)
                                     .    .+                    + +.+ .++.+|||||++....... .+.+...+... 
T Consensus        96 ---------------~----~~--------------------~-~~~-~~~~vliiDe~~~~~~~~~~~~~l~~~l~~~~  134 (242)
T 3bos_A           96 ---------------T----AL--------------------L-EGL-EQFDLICIDDVDAVAGHPLWEEAIFDLYNRVA  134 (242)
T ss_dssp             ---------------G----GG--------------------G-TTG-GGSSEEEEETGGGGTTCHHHHHHHHHHHHHHH
T ss_pred             ---------------H----HH--------------------H-Hhc-cCCCEEEEeccccccCCHHHHHHHHHHHHHHH
Confidence                           0    00                    0 001 3467999999977652222 23344333221 


Q ss_pred             CCC-cEEEEEccCCCCCCCcccccccccCcccc----ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          321 SEG-SRILVTRSGGKNGTNMTEIGLGEKNGTNM----MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       321 ~~g-s~IIvTtR~~~~~~~~~~~~~~~~~~~~~----~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      ..+ ..+|+||+..........     ......    ..+.+.+++.++..+++...+...+..    -..+....|++.
T Consensus       135 ~~~~~~ii~~~~~~~~~~~~~~-----~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~----~~~~~~~~l~~~  205 (242)
T 3bos_A          135 EQKRGSLIVSASASPMEAGFVL-----PDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQ----LPEDVGRFLLNR  205 (242)
T ss_dssp             HHCSCEEEEEESSCTTTTTCCC-----HHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTCC----CCHHHHHHHHHH
T ss_pred             HcCCCeEEEEcCCCHHHHHHhh-----hhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHH
Confidence            122 247777765521111000     011111    238999999999999999877432211    124567889999


Q ss_pred             cCCchHHHHHHH
Q 041007          396 CKGLPFAVKILG  407 (597)
Q Consensus       396 ~~GlPLai~~~~  407 (597)
                      ++|.+-.+..+.
T Consensus       206 ~~g~~r~l~~~l  217 (242)
T 3bos_A          206 MARDLRTLFDVL  217 (242)
T ss_dssp             TTTCHHHHHHHH
T ss_pred             ccCCHHHHHHHH
Confidence            999887665443

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.70  E-value=7.9e-08  Score=88.33  Aligned_cols=45  Identities=27%  Similarity=0.414  Sum_probs=38.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++++.+.+...          ..+.+.|+|++|+|||+||+.+++.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~----------~~~~~ll~G~~G~GKT~l~~~~~~~   66 (195)
T 1jbk_A           22 DPVIGRDEEIRRTIQVLQRR----------TKNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS----------SSCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cccccchHHHHHHHHHHhcC----------CCCceEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999742          3467899999999999999999874

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.67  E-value=1.6e-06  Score=87.66  Aligned_cols=257  Identities=14%  Similarity=0.117  Sum_probs=140.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..|+|++..++++..++.....     .......|.|+|++|+|||+||+.+++  .....|   +.+++.....     
T Consensus        29 ~~iiG~~~~~~~l~~~l~~~~~-----~~~~~~~vll~G~~GtGKT~la~~ia~--~~~~~~---~~~~~~~~~~-----   93 (338)
T 3pfi_A           29 DGYIGQESIKKNLNVFIAAAKK-----RNECLDHILFSGPAGLGKTTLANIISY--EMSANI---KTTAAPMIEK-----   93 (338)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHH-----TTSCCCCEEEECSTTSSHHHHHHHHHH--HTTCCE---EEEEGGGCCS-----
T ss_pred             HHhCChHHHHHHHHHHHHHHHh-----cCCCCCeEEEECcCCCCHHHHHHHHHH--HhCCCe---EEecchhccc-----
Confidence            5689999999999998874311     012345789999999999999999977  332222   2233221110     


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCC----
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS----  321 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~----  321 (597)
                                  ..                    .+...+..  ..+..+|+||+++... ......+...+....    
T Consensus        94 ------------~~--------------------~~~~~~~~--~~~~~vl~lDEi~~l~-~~~~~~Ll~~l~~~~~~~~  138 (338)
T 3pfi_A           94 ------------SG--------------------DLAAILTN--LSEGDILFIDEIHRLS-PAIEEVLYPAMEDYRLDII  138 (338)
T ss_dssp             ------------HH--------------------HHHHHHHT--CCTTCEEEEETGGGCC-HHHHHHHHHHHHTSCC---
T ss_pred             ------------hh--------------------HHHHHHHh--ccCCCEEEEechhhcC-HHHHHHHHHHHHhccchhh
Confidence                        11                    11111111  2356799999997765 444455555554321    


Q ss_pred             --------------CCcEEEEEccCCCCCCCcccccccccCcccc--ceeecCCCChHHHHHHHHHHhccCCCCCCccch
Q 041007          322 --------------EGSRILVTRSGGKNGTNMTEIGLGEKNGTNM--MEIGLGELSEEECRSLFRQIAFHGRSSDYREKF  385 (597)
Q Consensus       322 --------------~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~--~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~  385 (597)
                                    ++..+|.||..... ..        ......  ..+.+.+++.++...++...+.....    .-.
T Consensus       139 ~~~~~~~~~~~~~~~~~~~i~atn~~~~-l~--------~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~----~~~  205 (338)
T 3pfi_A          139 IGSGPAAQTIKIDLPKFTLIGATTRAGM-LS--------NPLRDRFGMQFRLEFYKDSELALILQKAALKLNK----TCE  205 (338)
T ss_dssp             ------CCCCCCCCCCCEEEEEESCGGG-SC--------HHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTC----EEC
T ss_pred             cccCccccceecCCCCeEEEEeCCCccc-cC--------HHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCC----CCC
Confidence                          12455555544210 00        011111  23899999999999999887743221    122


Q ss_pred             HHHHHHHHHhcCCchHHHHHHHhhh------ccCC--CHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCCh
Q 041007          386 EPIGRRVVGKCKGLPFAVKILGSLL------RFKT--SIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSP  457 (597)
Q Consensus       386 ~~~~~~I~~~~~GlPLai~~~~~~l------~~~~--~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~  457 (597)
                      .+....|++.+.|.|-.+..+...+      ....  +.+.....+..                      +..+...++.
T Consensus       206 ~~~~~~l~~~~~G~~r~l~~~l~~~~~~a~~~~~~~i~~~~~~~~~~~----------------------~~~~~~~l~~  263 (338)
T 3pfi_A          206 EKAALEIAKRSRSTPRIALRLLKRVRDFADVNDEEIITEKRANEALNS----------------------LGVNELGFDA  263 (338)
T ss_dssp             HHHHHHHHHTTTTCHHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHH----------------------HTCCTTCCCH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHhhcCCccCHHHHHHHHHH----------------------hCCcccCCCH
Confidence            4567889999999996554433221      1111  22222222221                      2223334555


Q ss_pred             hHhHHHHHhhcCCCCcccChhHHHHHHHHcCCcccCCCCCHHHHHHHHHH-HHhhCCCccccc
Q 041007          458 ALKKCFLYCSIFPKNYEIEKDRLIKLWMAQGYLKSQESKDMELVGEEYFG-NLSSRSLFQDFQ  519 (597)
Q Consensus       458 ~~k~cf~~ls~Fp~~~~i~~~~Li~~W~aeg~i~~~~~~~~e~~~~~~l~-~Lv~rsli~~~~  519 (597)
                      ..+..+..++-. .+..+....+...   .|.       + .....++++ .|++.++|....
T Consensus       264 ~e~~~l~~l~~~-~~~~~~~~~~a~~---lg~-------~-~~tl~~~l~~~l~~~gli~~~~  314 (338)
T 3pfi_A          264 MDLRYLELLTAA-KQKPIGLASIAAA---LSE-------D-ENTIEDVIEPYLLANGYIERTA  314 (338)
T ss_dssp             HHHHHHHHHHHS-CSCCBCHHHHHHH---TTC-------C-HHHHHHTTHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHh-cCCCchHHHHHHH---hCC-------C-HHHHHHHHhHHHHHcCceecCC
Confidence            546666655555 4444555544332   222       1 224455566 888899997654

>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=98.65  E-value=3.6e-07  Score=93.00  Aligned_cols=195  Identities=13%  Similarity=0.086  Sum_probs=110.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCC-eeEEEEecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFD-KRIWVSASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~~~~~~~~~~~  244 (597)
                      ..++|++..++.|..++....          .+.+.|+|++|+||||+|+.+++.......+. ..+.++.+.....   
T Consensus        37 ~~i~g~~~~~~~l~~~l~~~~----------~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~---  103 (353)
T 1sxj_D           37 DEVTAQDHAVTVLKKTLKSAN----------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGI---  103 (353)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTT----------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCH---
T ss_pred             HHhhCCHHHHHHHHHHHhcCC----------CCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccccch---
Confidence            568999999999999987432          23489999999999999999988421111111 1223333221111   


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccC-CCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKG-SVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~-~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                    ......+..... ........     .....-.+++-+|++|+++... ......+...+......
T Consensus       104 --------------~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~vliiDE~~~l~-~~~~~~Ll~~le~~~~~  163 (353)
T 1sxj_D          104 --------------SIVREKVKNFARLTVSKPSKH-----DLENYPCPPYKIIILDEADSMT-ADAQSALRRTMETYSGV  163 (353)
T ss_dssp             --------------HHHTTHHHHHHHSCCCCCCTT-----HHHHSCCCSCEEEEETTGGGSC-HHHHHHHHHHHHHTTTT
T ss_pred             --------------HHHHHHHHHHhhhcccccchh-----hcccCCCCCceEEEEECCCccC-HHHHHHHHHHHHhcCCC
Confidence                          111111111100 00000000     0001112356799999997665 44456666666655566


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                      .++|++|........         .+...+ .+.+.+++.++....+...+...+...    ..+..+.|++.++|.|-.
T Consensus       164 ~~~il~~~~~~~l~~---------~l~sR~~~i~~~~~~~~~~~~~l~~~~~~~~~~i----~~~~l~~l~~~~~G~~r~  230 (353)
T 1sxj_D          164 TRFCLICNYVTRIID---------PLASQCSKFRFKALDASNAIDRLRFISEQENVKC----DDGVLERILDISAGDLRR  230 (353)
T ss_dssp             EEEEEEESCGGGSCH---------HHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCC----CHHHHHHHHHHTSSCHHH
T ss_pred             ceEEEEeCchhhCcc---------hhhccCceEEeCCCCHHHHHHHHHHHHHHhCCCC----CHHHHHHHHHHcCCCHHH
Confidence            777777644310000         111111 289999999999999988764322111    145678899999999986


Q ss_pred             HHHH
Q 041007          403 VKIL  406 (597)
Q Consensus       403 i~~~  406 (597)
                      +..+
T Consensus       231 ~~~~  234 (353)
T 1sxj_D          231 GITL  234 (353)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5433

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=98.52  E-value=2.1e-06  Score=89.81  Aligned_cols=180  Identities=13%  Similarity=0.120  Sum_probs=100.2

Q ss_pred             CccccchhhH---HHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEK---QKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~---~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..++|.+..+   ..|...+...          ....+.|+|++|+||||||+.+++  .....|     +.++..... 
T Consensus        26 ~~ivGq~~~~~~~~~L~~~i~~~----------~~~~vLL~GppGtGKTtlAr~ia~--~~~~~f-----~~l~a~~~~-   87 (447)
T 3pvs_A           26 AQYIGQQHLLAAGKPLPRAIEAG----------HLHSMILWGPPGTGKTTLAEVIAR--YANADV-----ERISAVTSG-   87 (447)
T ss_dssp             TTCCSCHHHHSTTSHHHHHHHHT----------CCCEEEEECSTTSSHHHHHHHHHH--HTTCEE-----EEEETTTCC-
T ss_pred             HHhCCcHHHHhchHHHHHHHHcC----------CCcEEEEECCCCCcHHHHHHHHHH--HhCCCe-----EEEEeccCC-
Confidence            5689998888   6777777632          357899999999999999999988  333222     222221111 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCC
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSE  322 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~  322 (597)
                                     ....+.++..                .......+++.+|+||+++... ....+.+...+..  .
T Consensus        88 ---------------~~~ir~~~~~----------------a~~~~~~~~~~iLfIDEI~~l~-~~~q~~LL~~le~--~  133 (447)
T 3pvs_A           88 ---------------VKEIREAIER----------------ARQNRNAGRRTILFVDEVHRFN-KSQQDAFLPHIED--G  133 (447)
T ss_dssp             ---------------HHHHHHHHHH----------------HHHHHHTTCCEEEEEETTTCC-------CCHHHHHT--T
T ss_pred             ---------------HHHHHHHHHH----------------HHHhhhcCCCcEEEEeChhhhC-HHHHHHHHHHHhc--C
Confidence                           1111111111                0011124678899999997665 3334444444443  2


Q ss_pred             CcEEEE-EccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCC---CCccchHHHHHHHHHhcC
Q 041007          323 GSRILV-TRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSS---DYREKFEPIGRRVVGKCK  397 (597)
Q Consensus       323 gs~IIv-TtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~---~~~~~~~~~~~~I~~~~~  397 (597)
                      ...+|. ||.+..  ..     +.. .+...+ .+.+.+++.++...++.+.+......   ....-..+..+.|++.++
T Consensus       134 ~v~lI~att~n~~--~~-----l~~-aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~  205 (447)
T 3pvs_A          134 TITFIGATTENPS--FE-----LNS-ALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVN  205 (447)
T ss_dssp             SCEEEEEESSCGG--GS-----SCH-HHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHC
T ss_pred             ceEEEecCCCCcc--cc-----cCH-HHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCC
Confidence            234444 443331  00     000 111111 28899999999999999887431110   111123556788888999


Q ss_pred             CchHHHHH
Q 041007          398 GLPFAVKI  405 (597)
Q Consensus       398 GlPLai~~  405 (597)
                      |.+-.+.-
T Consensus       206 Gd~R~lln  213 (447)
T 3pvs_A          206 GDARRALN  213 (447)
T ss_dssp             SCHHHHHH
T ss_pred             CCHHHHHH
Confidence            98875543

>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=98.52  E-value=7.2e-07  Score=90.81  Aligned_cols=104  Identities=10%  Similarity=0.021  Sum_probs=66.6

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|||++...+ ......+...+.....++.+|++|........         .+... ..+.+.+++.++..+.+
T Consensus       133 ~~~~vlilDE~~~L~-~~~~~~L~~~le~~~~~~~~Il~t~~~~~l~~---------~l~sR~~~~~~~~~~~~~~~~~l  202 (354)
T 1sxj_E          133 HRYKCVIINEANSLT-KDAQAALRRTMEKYSKNIRLIMVCDSMSPIIA---------PIKSQCLLIRCPAPSDSEISTIL  202 (354)
T ss_dssp             -CCEEEEEECTTSSC-HHHHHHHHHHHHHSTTTEEEEEEESCSCSSCH---------HHHTTSEEEECCCCCHHHHHHHH
T ss_pred             CCCeEEEEeCccccC-HHHHHHHHHHHHhhcCCCEEEEEeCCHHHHHH---------HHHhhceEEecCCcCHHHHHHHH
Confidence            467799999998765 55566677766655567788888765421110         11111 23999999999999999


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILG  407 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~  407 (597)
                      ...+...+....   ..+.+..|++.++|.+-.+..+.
T Consensus       203 ~~~~~~~~~~~~---~~~~l~~i~~~~~G~~r~a~~~l  237 (354)
T 1sxj_E          203 SDVVTNERIQLE---TKDILKRIAQASNGNLRVSLLML  237 (354)
T ss_dssp             HHHHHHHTCEEC---CSHHHHHHHHHHTTCHHHHHHHH
T ss_pred             HHHHHHcCCCCC---cHHHHHHHHHHcCCCHHHHHHHH
Confidence            887643221111   02456788999999887654443

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.51  E-value=1.3e-06  Score=85.93  Aligned_cols=196  Identities=15%  Similarity=0.076  Sum_probs=101.1

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ....++|.+..+++|...+...... +  ...+-...+.+.|+|++|+|||+||+.+++.  ....   .+.+..+....
T Consensus        15 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~--~~~~---~~~v~~~~~~~   89 (285)
T 3h4m_A           15 RYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATE--TNAT---FIRVVGSELVK   89 (285)
T ss_dssp             CGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHH--TTCE---EEEEEGGGGCC
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHH--hCCC---EEEEehHHHHH
Confidence            3456899999999998887532000 0  0000023567999999999999999999873  3222   22233221111


Q ss_pred             hhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCC----------CcchH
Q 041007          241 EIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNA----------YPRYW  310 (597)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~----------~~~~~  310 (597)
                      .                              . .......+...+......++.+|+||+++...          .....
T Consensus        90 ~------------------------------~-~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~  138 (285)
T 3h4m_A           90 K------------------------------F-IGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQ  138 (285)
T ss_dssp             C------------------------------S-TTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHH
T ss_pred             h------------------------------c-cchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHH
Confidence            0                              0 00011112222233334567899999995431          01112


Q ss_pred             HHHHHhh---c--CCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccc
Q 041007          311 EQLMYSL---K--SGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREK  384 (597)
Q Consensus       311 ~~l~~~l---~--~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~  384 (597)
                      ..+...+   .  ....+..||.||.....    .+..+..  .... ..+.+.+.+.++-.++|...+..... .....
T Consensus       139 ~~l~~ll~~~~~~~~~~~~~vI~ttn~~~~----l~~~l~~--~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~-~~~~~  211 (285)
T 3h4m_A          139 RTLMQLLAEMDGFDARGDVKIIGATNRPDI----LDPAILR--PGRFDRIIEVPAPDEKGRLEILKIHTRKMNL-AEDVN  211 (285)
T ss_dssp             HHHHHHHHHHHTTCSSSSEEEEEECSCGGG----BCHHHHS--TTSEEEEEECCCCCHHHHHHHHHHHHTTSCB-CTTCC
T ss_pred             HHHHHHHHHhhCCCCCCCEEEEEeCCCchh----cCHHHcC--CCcCCeEEEECCCCHHHHHHHHHHHHhcCCC-CCcCC
Confidence            2232222   2  12345667777754310    0000000  0011 12899999999999999888743221 11112


Q ss_pred             hHHHHHHHHHhcCC-chHHHHHH
Q 041007          385 FEPIGRRVVGKCKG-LPFAVKIL  406 (597)
Q Consensus       385 ~~~~~~~I~~~~~G-lPLai~~~  406 (597)
                          ...|++.+.| .|-.|..+
T Consensus       212 ----~~~l~~~~~g~~~~~i~~l  230 (285)
T 3h4m_A          212 ----LEEIAKMTEGCVGAELKAI  230 (285)
T ss_dssp             ----HHHHHHHCTTCCHHHHHHH
T ss_pred             ----HHHHHHHcCCCCHHHHHHH
Confidence                3667777777 45444433

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.51  E-value=3.3e-06  Score=86.34  Aligned_cols=106  Identities=10%  Similarity=0.008  Sum_probs=58.8

Q ss_pred             eEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCc---c-cccccccCccccce-eecCCCChHHHHH
Q 041007          293 KVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNM---T-EIGLGEKNGTNMME-IGLGELSEEECRS  367 (597)
Q Consensus       293 r~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~---~-~~~~~~~~~~~~~~-~~l~~Ls~~es~~  367 (597)
                      +.+|+||+++..+ ......+...+...... .++++|......-..   . ...+. ..+...+. +.+.+++.++..+
T Consensus       190 ~~vl~IDEi~~l~-~~~~~~L~~~le~~~~~-~~ii~t~~~~~~i~~t~~~~~~~l~-~~l~sR~~~i~~~~~~~~e~~~  266 (368)
T 3uk6_A          190 PGVLFIDEVHMLD-IESFSFLNRALESDMAP-VLIMATNRGITRIRGTSYQSPHGIP-IDLLDRLLIVSTTPYSEKDTKQ  266 (368)
T ss_dssp             BCEEEEESGGGSB-HHHHHHHHHHTTCTTCC-EEEEEESCSEEECBTSSCEEETTCC-HHHHTTEEEEEECCCCHHHHHH
T ss_pred             CceEEEhhccccC-hHHHHHHHHHhhCcCCC-eeeeecccceeeeeccCCCCcccCC-HHHHhhccEEEecCCCHHHHHH
Confidence            4599999998776 55556666666544433 344444321000000   0 00000 01111112 8999999999999


Q ss_pred             HHHHHhccCCCCCCccchHHHHHHHHHhcC-CchHHHHH
Q 041007          368 LFRQIAFHGRSSDYREKFEPIGRRVVGKCK-GLPFAVKI  405 (597)
Q Consensus       368 Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~-GlPLai~~  405 (597)
                      ++...+......    -..+....|++.+. |.|--+..
T Consensus       267 il~~~~~~~~~~----~~~~~l~~l~~~~~~G~~r~~~~  301 (368)
T 3uk6_A          267 ILRIRCEEEDVE----MSEDAYTVLTRIGLETSLRYAIQ  301 (368)
T ss_dssp             HHHHHHHHTTCC----BCHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHHHHHcCCC----CCHHHHHHHHHHhcCCCHHHHHH
Confidence            999877532221    12456788888887 77765543

>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=98.48  E-value=5.1e-06  Score=80.50  Aligned_cols=197  Identities=14%  Similarity=0.102  Sum_probs=98.6

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      -..++|.+..+++|.+++......+  ...+....+.+.|+|++|+|||+||+.+++  .....   .+.+.++......
T Consensus         5 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~--~~~~~---~~~~~~~~~~~~~   79 (262)
T 2qz4_A            5 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT--EAQVP---FLAMAGAEFVEVI   79 (262)
T ss_dssp             TTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHH--HHTCC---EEEEETTTTSSSS
T ss_pred             HHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHH--HhCCC---EEEechHHHHhhc
Confidence            3568999988887766553211000  000012356789999999999999999988  33222   2334433221110


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC--------------cc
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY--------------PR  308 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~--------------~~  308 (597)
                                                     .......+...+.......+.+|+||+++....              ..
T Consensus        80 -------------------------------~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~  128 (262)
T 2qz4_A           80 -------------------------------GGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQ  128 (262)
T ss_dssp             -------------------------------TTHHHHHHHHHHHHHHHTCSEEEEEECC-------------------CH
T ss_pred             -------------------------------cChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHH
Confidence                                           000111122223333345678999999975410              11


Q ss_pred             hHHHHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccch
Q 041007          309 YWEQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKF  385 (597)
Q Consensus       309 ~~~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~  385 (597)
                      ....+...+..  ...+..||.||.... .   .+..+.  ..... ..+.+.+.+.++-.+++...+.....   ....
T Consensus       129 ~l~~ll~~~~~~~~~~~~~vi~~tn~~~-~---ld~~l~--~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~---~~~~  199 (262)
T 2qz4_A          129 TLNQLLVEMDGMGTTDHVIVLASTNRAD-I---LDGALM--RPGRLDRHVFIDLPTLQERREIFEQHLKSLKL---TQSS  199 (262)
T ss_dssp             HHHHHHHHHHTCCTTCCEEEEEEESCGG-G---GGSGGG--STTSCCEEEECCSCCHHHHHHHHHHHHHHTTC---CBTH
T ss_pred             HHHHHHHHhhCcCCCCCEEEEecCCChh-h---cCHHHh--cCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCC---Ccch
Confidence            12233333332  223445555554331 0   000000  00011 22788999999999999887643221   1112


Q ss_pred             HHHHHHHHHhcCCchH-HHHHH
Q 041007          386 EPIGRRVVGKCKGLPF-AVKIL  406 (597)
Q Consensus       386 ~~~~~~I~~~~~GlPL-ai~~~  406 (597)
                      ......+++.+.|.+- .|..+
T Consensus       200 ~~~~~~l~~~~~g~~~~~l~~l  221 (262)
T 2qz4_A          200 TFYSQRLAELTPGFSGADIANI  221 (262)
T ss_dssp             HHHHHHHHHTCTTCCHHHHHHH
T ss_pred             hhHHHHHHHHCCCCCHHHHHHH
Confidence            2234778888888654 44433

>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=98.42  E-value=2.6e-06  Score=91.21  Aligned_cols=205  Identities=15%  Similarity=0.175  Sum_probs=107.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCC-----CcCC--CCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSD-----EESG--SKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~-----~~~~--~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      .+++|++..+++|..++......     ...+  +.+..+.+.|+|++|+|||++|+.+++.  .  .+ ..+.++++..
T Consensus        39 ~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~--l--~~-~~i~in~s~~  113 (516)
T 1sxj_A           39 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE--L--GY-DILEQNASDV  113 (516)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH--T--TC-EEEEECTTSC
T ss_pred             HHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHH--c--CC-CEEEEeCCCc
Confidence            56899999999999999751100     0000  0124579999999999999999999883  3  12 2333443332


Q ss_pred             CchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC--cchHHHHHHh
Q 041007          239 RDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY--PRYWEQLMYS  316 (597)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~--~~~~~~l~~~  316 (597)
                      ...                 ......+...........-......  .....+++.+|+||+++....  ...+..+...
T Consensus       114 ~~~-----------------~~~~~~i~~~~~~~~~~~~~~~~~~--~~~~~~~~~vliIDEid~l~~~~~~~l~~L~~~  174 (516)
T 1sxj_A          114 RSK-----------------TLLNAGVKNALDNMSVVGYFKHNEE--AQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQF  174 (516)
T ss_dssp             CCH-----------------HHHHHTGGGGTTBCCSTTTTTC------CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHH
T ss_pred             chH-----------------HHHHHHHHHHhccccHHHHHhhhhh--hhhccCCCeEEEEECCCccchhhHHHHHHHHHH
Confidence            221                 1222222211110000000000000  001235688999999976542  1223445444


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +...  +..||+++..... ....       .... ...+.+.+++.++..+++...+...+....    .+....|++.
T Consensus       175 l~~~--~~~iIli~~~~~~-~~l~-------~l~~r~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~----~~~l~~la~~  240 (516)
T 1sxj_A          175 CRKT--STPLILICNERNL-PKMR-------PFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLD----PNVIDRLIQT  240 (516)
T ss_dssp             HHHC--SSCEEEEESCTTS-STTG-------GGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC----TTHHHHHHHH
T ss_pred             HHhc--CCCEEEEEcCCCC-ccch-------hhHhceEEEEeCCCCHHHHHHHHHHHHHHcCCCCC----HHHHHHHHHH
Confidence            4332  2335544443210 0000       1111 123899999999999998877643222111    2346788999


Q ss_pred             cCC-chHHHHHHHh
Q 041007          396 CKG-LPFAVKILGS  408 (597)
Q Consensus       396 ~~G-lPLai~~~~~  408 (597)
                      ++| ++-++..+..
T Consensus       241 s~GdiR~~i~~L~~  254 (516)
T 1sxj_A          241 TRGDIRQVINLLST  254 (516)
T ss_dssp             TTTCHHHHHHHHTH
T ss_pred             cCCcHHHHHHHHHH
Confidence            999 5555655543

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=98.41  E-value=3.6e-06  Score=88.08  Aligned_cols=187  Identities=17%  Similarity=0.178  Sum_probs=105.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCC--eeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFD--KRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS  274 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~--~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~  274 (597)
                      ...+.|+|++|+||||||+.+++  .....++  .++++++                      ..+...+...+...   
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~--~l~~~~~~~~v~~v~~----------------------~~~~~~~~~~~~~~---  182 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGN--YVVQNEPDLRVMYITS----------------------EKFLNDLVDSMKEG---  182 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHH--HHHHHCCSSCEEEEEH----------------------HHHHHHHHHHHHTT---
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH--HHHHhCCCCeEEEeeH----------------------HHHHHHHHHHHHcc---
Confidence            56899999999999999999998  4444432  2345443                      22233333333221   


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCc-chHHHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccc
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYP-RYWEQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM  352 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~-~~~~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~  352 (597)
                        .    ...+...+..+.-+|+|||++..... ...+.+...+.. ...|..||+||...........     ..+...
T Consensus       183 --~----~~~~~~~~~~~~~vL~IDEi~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~-----~~L~sR  251 (440)
T 2z4s_A          183 --K----LNEFREKYRKKVDILLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQ-----DRLVSR  251 (440)
T ss_dssp             --C----HHHHHHHHTTTCSEEEEECGGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCC-----HHHHHH
T ss_pred             --c----HHHHHHHhcCCCCEEEEeCcccccCChHHHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHH-----HHHHhh
Confidence              0    11223333336779999999765522 233344444432 2456788888876521110000     011111


Q ss_pred             ----ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHHhhh------ccC-CCHHHHHH
Q 041007          353 ----MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILGSLL------RFK-TSIKEWQS  421 (597)
Q Consensus       353 ----~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l------~~~-~~~~~w~~  421 (597)
                          ..+.+.+++.++-.+++.+.+...+.. .+   .+....|++.++|.+--+.-+...+      ... -+.+.+..
T Consensus       252 ~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~-i~---~e~l~~la~~~~gn~R~l~~~L~~~~~~a~~~~~~It~~~~~~  327 (440)
T 2z4s_A          252 FQMGLVAKLEPPDEETRKSIARKMLEIEHGE-LP---EEVLNFVAENVDDNLRRLRGAIIKLLVYKETTGKEVDLKEAIL  327 (440)
T ss_dssp             HHSSBCCBCCCCCHHHHHHHHHHHHHHHTCC-CC---TTHHHHHHHHCCSCHHHHHHHHHHHHHHHHHSSSCCCHHHHHH
T ss_pred             ccCCeEEEeCCCCHHHHHHHHHHHHHHcCCC-CC---HHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence                238899999999999998877432211 12   2346788899999886554332211      122 25566666


Q ss_pred             HHhh
Q 041007          422 VLDS  425 (597)
Q Consensus       422 ~l~~  425 (597)
                      ++..
T Consensus       328 ~l~~  331 (440)
T 2z4s_A          328 LLKD  331 (440)
T ss_dssp             HTST
T ss_pred             HHHH
Confidence            6654

>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=98.40  E-value=9.3e-06  Score=81.34  Aligned_cols=193  Identities=16%  Similarity=0.094  Sum_probs=103.2

Q ss_pred             CCccccchhhHHHHHHHhhCCCC-CC-cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESS-DE-ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~-~~-~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      -..++|.+..+++|.+.+..... .+ -.......+.|.|+|++|+|||+||+.+++  .....|   +.++++      
T Consensus        17 ~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~--~~~~~~---~~v~~~------   85 (322)
T 3eie_A           17 WEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVAT--EANSTF---FSVSSS------   85 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHH--HHTCEE---EEEEHH------
T ss_pred             HHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHH--HHCCCE---EEEchH------
Confidence            35689999999999888731000 00 000012356799999999999999999988  333222   223221      


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHH-HHHHHHHHhcCceEEEEEecccCCCCc----------chHH
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMET-VLQYINEFVQGKKVLLVLDDLWWNAYP----------RYWE  311 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~-~~~~l~~~L~~kr~LLVLDdv~~~~~~----------~~~~  311 (597)
                                      .+..    ..      ....+. +...+...-..++.+|+||+++.....          ....
T Consensus        86 ----------------~l~~----~~------~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~  139 (322)
T 3eie_A           86 ----------------DLVS----KW------MGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKT  139 (322)
T ss_dssp             ----------------HHHT----TT------GGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHH
T ss_pred             ----------------HHhh----cc------cchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHH
Confidence                            1100    00      001111 112222223356789999999654210          1133


Q ss_pred             HHHHhhcC---CCCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          312 QLMYSLKS---GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       312 ~l~~~l~~---~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      .+...+..   ...+..||.||...... .   .     .+.+..  .+.+...+.++-.++|...+.......    ..
T Consensus       140 ~ll~~l~~~~~~~~~v~vi~atn~~~~l-d---~-----al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~----~~  206 (322)
T 3eie_A          140 ELLVQMNGVGNDSQGVLVLGATNIPWQL-D---S-----AIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVL----TK  206 (322)
T ss_dssp             HHHHHHGGGGTSCCCEEEEEEESCGGGS-C---H-----HHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCC----CH
T ss_pred             HHHHHhccccccCCceEEEEecCChhhC-C---H-----HHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCC----CH
Confidence            34444432   33455556566543100 0   0     111111  278888999999999998874322111    13


Q ss_pred             HHHHHHHHhcCC-chHHHHHHH
Q 041007          387 PIGRRVVGKCKG-LPFAVKILG  407 (597)
Q Consensus       387 ~~~~~I~~~~~G-lPLai~~~~  407 (597)
                      .....|++.+.| .+-.|..+.
T Consensus       207 ~~l~~la~~t~g~sg~di~~l~  228 (322)
T 3eie_A          207 EDYRTLGAMTEGYSGSDIAVVV  228 (322)
T ss_dssp             HHHHHHHHTTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHH
Confidence            456788899987 455555444

>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=98.39  E-value=7.9e-06  Score=82.32  Aligned_cols=98  Identities=10%  Similarity=-0.049  Sum_probs=66.3

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|+|+++... ....+.+...+.....++.+|++|.+......         .+...+ .+.+.+++.++..+.+
T Consensus       107 ~~~kvviIdead~l~-~~a~naLLk~lEep~~~~~~Il~t~~~~~l~~---------ti~SRc~~~~~~~~~~~~~~~~L  176 (334)
T 1a5t_A          107 GGAKVVWVTDAALLT-DAAANALLKTLEEPPAETWFFLATREPERLLA---------TLRSRCRLHYLAPPPEQYAVTWL  176 (334)
T ss_dssp             SSCEEEEESCGGGBC-HHHHHHHHHHHTSCCTTEEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHH
T ss_pred             CCcEEEEECchhhcC-HHHHHHHHHHhcCCCCCeEEEEEeCChHhCcH---------HHhhcceeeeCCCCCHHHHHHHH
Confidence            567899999998776 45566777777666667777777765411100         111122 2999999999999998


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKILG  407 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~~  407 (597)
                      ....   .  .    ..+.+..+++.++|.|..+..+.
T Consensus       177 ~~~~---~--~----~~~~~~~l~~~s~G~~r~a~~~l  205 (334)
T 1a5t_A          177 SREV---T--M----SQDALLAALRLSAGSPGAALALF  205 (334)
T ss_dssp             HHHC---C--C----CHHHHHHHHHHTTTCHHHHHHTT
T ss_pred             HHhc---C--C----CHHHHHHHHHHcCCCHHHHHHHh
Confidence            8775   1  1    13456789999999998665443

>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=98.39  E-value=4.2e-06  Score=84.01  Aligned_cols=177  Identities=16%  Similarity=0.144  Sum_probs=100.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.+..++.|..++....         ...++.+.|++|+|||++|+.+++.  ..   ...+.++.+...      
T Consensus        26 ~~ivg~~~~~~~l~~~l~~~~---------~~~~~L~~G~~G~GKT~la~~la~~--l~---~~~~~i~~~~~~------   85 (324)
T 3u61_B           26 DECILPAFDKETFKSITSKGK---------IPHIILHSPSPGTGKTTVAKALCHD--VN---ADMMFVNGSDCK------   85 (324)
T ss_dssp             TTSCCCHHHHHHHHHHHHTTC---------CCSEEEECSSTTSSHHHHHHHHHHH--TT---EEEEEEETTTCC------
T ss_pred             HHHhCcHHHHHHHHHHHHcCC---------CCeEEEeeCcCCCCHHHHHHHHHHH--hC---CCEEEEcccccC------
Confidence            568999999999999998432         3467888899999999999999873  32   123344433211      


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH--hcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEF--VQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~--L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                  .......+..                 ....  ..+++.+|+|||++........+.+...+.....+
T Consensus        86 ------------~~~i~~~~~~-----------------~~~~~~~~~~~~vliiDEi~~l~~~~~~~~L~~~le~~~~~  136 (324)
T 3u61_B           86 ------------IDFVRGPLTN-----------------FASAASFDGRQKVIVIDEFDRSGLAESQRHLRSFMEAYSSN  136 (324)
T ss_dssp             ------------HHHHHTHHHH-----------------HHHBCCCSSCEEEEEEESCCCGGGHHHHHHHHHHHHHHGGG
T ss_pred             ------------HHHHHHHHHH-----------------HHhhcccCCCCeEEEEECCcccCcHHHHHHHHHHHHhCCCC
Confidence                        1111111111                 0110  12468899999996553122444455555444456


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHH-------HHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSL-------FRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~L-------f~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      ..+|+||........         .+...+ .+.+.+++.++-.++       +...+...+... ++  .+....|++.
T Consensus       137 ~~iI~~~n~~~~l~~---------~l~sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~-~~--~~~~~~l~~~  204 (324)
T 3u61_B          137 CSIIITANNIDGIIK---------PLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAI-AD--MKVVAALVKK  204 (324)
T ss_dssp             CEEEEEESSGGGSCT---------THHHHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCB-SC--HHHHHHHHHH
T ss_pred             cEEEEEeCCccccCH---------HHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCC-Cc--HHHHHHHHHh
Confidence            788888765421000         111112 289999998874333       222222111111 11  2567788888


Q ss_pred             cCCchHHH
Q 041007          396 CKGLPFAV  403 (597)
Q Consensus       396 ~~GlPLai  403 (597)
                      ++|.+-.+
T Consensus       205 ~~gd~R~a  212 (324)
T 3u61_B          205 NFPDFRKT  212 (324)
T ss_dssp             TCSCTTHH
T ss_pred             CCCCHHHH
Confidence            88876543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.37  E-value=9.6e-07  Score=77.35  Aligned_cols=115  Identities=17%  Similarity=0.149  Sum_probs=71.1

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhh
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVAR  246 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~  246 (597)
                      .++|+...++++.+.+.....        ....|.|+|++|+|||++|+.+++... +...+. + ++++.....     
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~--------~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~-v-~~~~~~~~~-----   65 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSE--------TDIAVWLYGAPGTGRMTGARYLHQFGR-NAQGEF-V-YRELTPDNA-----   65 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTT--------CCSCEEEESSTTSSHHHHHHHHHHSST-TTTSCC-E-EEECCTTTS-----
T ss_pred             CceeCCHHHHHHHHHHHHHhC--------CCCCEEEECCCCCCHHHHHHHHHHhCC-ccCCCE-E-EECCCCCcc-----
Confidence            578999999999988864432        234678999999999999999987421 112222 3 555432211     


Q ss_pred             hhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEE
Q 041007          247 DEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRI  326 (597)
Q Consensus       247 ~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~I  326 (597)
                                                   ...   ...+...   +.-+|+||+++... ......+...+.......++
T Consensus        66 -----------------------------~~~---~~~~~~a---~~g~l~ldei~~l~-~~~q~~Ll~~l~~~~~~~~~  109 (145)
T 3n70_A           66 -----------------------------PQL---NDFIALA---QGGTLVLSHPEHLT-REQQYHLVQLQSQEHRPFRL  109 (145)
T ss_dssp             -----------------------------SCH---HHHHHHH---TTSCEEEECGGGSC-HHHHHHHHHHHHSSSCSSCE
T ss_pred             -----------------------------hhh---hcHHHHc---CCcEEEEcChHHCC-HHHHHHHHHHHhhcCCCEEE
Confidence                                         000   0111111   23478999998776 44555666666555666788


Q ss_pred             EEEccCC
Q 041007          327 LVTRSGG  333 (597)
Q Consensus       327 IvTtR~~  333 (597)
                      |.||...
T Consensus       110 I~~t~~~  116 (145)
T 3n70_A          110 IGIGDTS  116 (145)
T ss_dssp             EEEESSC
T ss_pred             EEECCcC
Confidence            8888654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=98.36  E-value=1.5e-06  Score=79.23  Aligned_cols=45  Identities=29%  Similarity=0.409  Sum_probs=38.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++.+.+.+...          ..+.+.|+|++|+|||+||+.+++.
T Consensus        22 ~~~~g~~~~~~~l~~~l~~~----------~~~~vll~G~~G~GKT~la~~~~~~   66 (187)
T 2p65_A           22 DPVIGRDTEIRRAIQILSRR----------TKNNPILLGDPGVGKTAIVEGLAIK   66 (187)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS----------SSCEEEEESCGGGCHHHHHHHHHHH
T ss_pred             chhhcchHHHHHHHHHHhCC----------CCCceEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999742          3467899999999999999999873

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.34  E-value=4.9e-06  Score=82.83  Aligned_cols=173  Identities=14%  Similarity=0.091  Sum_probs=90.2

Q ss_pred             ccccchhhHHHHHHHhhCCCCC-----CcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          167 EFHGRNAEKQKILQLLKGESSD-----EESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~-----~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      .++|.+..++.|.+++......     .+.........+.|+|++|+|||+||+.+++............++.++.. ..
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~-~l  110 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRD-DL  110 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGG-GT
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHH-Hh
Confidence            4789998888887766421000     00000124567999999999999999988873221111111122332210 00


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCC--------CcchHHHH
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNA--------YPRYWEQL  313 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~--------~~~~~~~l  313 (597)
                                                 ..... ......+...+...   +..+|+||+++...        .......+
T Consensus       111 ---------------------------~~~~~-g~~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~~~~~~~~~~~~L  159 (309)
T 3syl_A          111 ---------------------------VGQYI-GHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPDNERDYGQEAIEIL  159 (309)
T ss_dssp             ---------------------------CCSST-TCHHHHHHHHHHHH---TTSEEEEETGGGSCCCC---CCTHHHHHHH
T ss_pred             ---------------------------hhhcc-cccHHHHHHHHHhc---CCCEEEEEChhhhccCCCcccccHHHHHHH
Confidence                                       00000 00011111222221   34599999997441        13344566


Q ss_pred             HHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhcc
Q 041007          314 MYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFH  375 (597)
Q Consensus       314 ~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~  375 (597)
                      ...+.....+..||+||.....    .........+....  .+.+.+++.++..+++...+..
T Consensus       160 l~~l~~~~~~~~~i~~~~~~~~----~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~~  219 (309)
T 3syl_A          160 LQVMENNRDDLVVILAGYADRM----ENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDD  219 (309)
T ss_dssp             HHHHHHCTTTCEEEEEECHHHH----HHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCCCEEEEEeCChHHH----HHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHHH
Confidence            6666666667788888753200    00000000222222  2999999999999999887743

>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=98.31  E-value=1.7e-05  Score=79.48  Aligned_cols=162  Identities=15%  Similarity=0.135  Sum_probs=87.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      ....+.|+|++|+||||||+.+++.  ....-...+++++.                      .....+...+...    
T Consensus        36 ~~~~lll~G~~GtGKT~la~~i~~~--~~~~~~~~~~i~~~----------------------~~~~~~~~~~~~~----   87 (324)
T 1l8q_A           36 LYNPIFIYGSVGTGKTHLLQAAGNE--AKKRGYRVIYSSAD----------------------DFAQAMVEHLKKG----   87 (324)
T ss_dssp             SCSSEEEECSSSSSHHHHHHHHHHH--HHHTTCCEEEEEHH----------------------HHHHHHHHHHHHT----
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHH--HHHCCCEEEEEEHH----------------------HHHHHHHHHHHcC----
Confidence            3567999999999999999999983  32221223455432                      2222222222110    


Q ss_pred             hhHHHHHHHHHHHhcCceEEEEEecccCCCCc-chHHHHHHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCcccc-
Q 041007          276 VEMETVLQYINEFVQGKKVLLVLDDLWWNAYP-RYWEQLMYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-  352 (597)
Q Consensus       276 ~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~-~~~~~l~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-  352 (597)
                       ....    +...+. +..+|+|||++..... ...+.+...+.. ...+..||+|+...........-     ..... 
T Consensus        88 -~~~~----~~~~~~-~~~vL~iDEi~~l~~~~~~~~~l~~~l~~~~~~~~~iii~~~~~~~~l~~l~~-----~L~sR~  156 (324)
T 1l8q_A           88 -TINE----FRNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSD-----RLVSRF  156 (324)
T ss_dssp             -CHHH----HHHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCH-----HHHHHH
T ss_pred             -cHHH----HHHHhc-CCCEEEEcCcccccCChHHHHHHHHHHHHHHHCCCeEEEEecCChHHHHHhhh-----Hhhhcc
Confidence             1111    122222 3679999999765421 222334444322 23456788887654211000000     11111 


Q ss_pred             ---ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          353 ---MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       353 ---~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                         ..+.+.| +.++..+++...+...+.. .+   .+....|++.+ |..-.
T Consensus       157 ~~~~~i~l~~-~~~e~~~il~~~~~~~~~~-l~---~~~l~~l~~~~-g~~r~  203 (324)
T 1l8q_A          157 EGGILVEIEL-DNKTRFKIIKEKLKEFNLE-LR---KEVIDYLLENT-KNVRE  203 (324)
T ss_dssp             HTSEEEECCC-CHHHHHHHHHHHHHHTTCC-CC---HHHHHHHHHHC-SSHHH
T ss_pred             cCceEEEeCC-CHHHHHHHHHHHHHhcCCC-CC---HHHHHHHHHhC-CCHHH
Confidence               2388999 9999999999887532221 11   45567788888 76643

>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=98.31  E-value=9.4e-06  Score=82.54  Aligned_cols=194  Identities=11%  Similarity=0.066  Sum_probs=102.0

Q ss_pred             CccccchhhHHHHHHHhhCCCC-CC-cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESS-DE-ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~-~~-~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      ..++|.+..++.|.+.+...-. .+ -.......+.|.|+|++|+|||+||+.+++.  ....   .+.++++.....  
T Consensus        84 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~--~~~~---~~~i~~~~l~~~--  156 (357)
T 3d8b_A           84 EDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQ--SGAT---FFSISASSLTSK--  156 (357)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHH--TTCE---EEEEEGGGGCCS--
T ss_pred             HHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHH--cCCe---EEEEehHHhhcc--
Confidence            4689999999999888752100 00 0000124578999999999999999999873  3221   233443321111  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC----------cchHHHH
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY----------PRYWEQL  313 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~----------~~~~~~l  313 (597)
                                                  .. ......+...+...-..++.+|+||+++....          ......+
T Consensus       157 ----------------------------~~-g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l  207 (357)
T 3d8b_A          157 ----------------------------WV-GEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEF  207 (357)
T ss_dssp             ----------------------------ST-THHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHH
T ss_pred             ----------------------------cc-chHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHH
Confidence                                        00 00001111112222235678999999954310          0112334


Q ss_pred             HHhhcCC----CCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccchHH
Q 041007          314 MYSLKSG----SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEP  387 (597)
Q Consensus       314 ~~~l~~~----~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~  387 (597)
                      ...+...    ..+..||.||.....    .+.     .+....  .+.+...+.++-.+++...+......    -...
T Consensus       208 L~~l~~~~~~~~~~v~vI~atn~~~~----l~~-----~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~----l~~~  274 (357)
T 3d8b_A          208 LVQLDGATTSSEDRILVVGATNRPQE----IDE-----AARRRLVKRLYIPLPEASARKQIVINLMSKEQCC----LSEE  274 (357)
T ss_dssp             HHHHHC----CCCCEEEEEEESCGGG----BCH-----HHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBC----CCHH
T ss_pred             HHHHhcccccCCCCEEEEEecCChhh----CCH-----HHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCC----ccHH
Confidence            4444321    234455556543210    000     111111  27888889999888888776432211    1145


Q ss_pred             HHHHHHHhcCC-chHHHHHHHh
Q 041007          388 IGRRVVGKCKG-LPFAVKILGS  408 (597)
Q Consensus       388 ~~~~I~~~~~G-lPLai~~~~~  408 (597)
                      ....|++.+.| .+-.|..+..
T Consensus       275 ~l~~la~~t~G~s~~dl~~l~~  296 (357)
T 3d8b_A          275 EIEQIVQQSDAFSGADMTQLCR  296 (357)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHH
Confidence            67788999988 5666665544

>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=98.28  E-value=1.1e-05  Score=78.78  Aligned_cols=47  Identities=21%  Similarity=0.259  Sum_probs=33.9

Q ss_pred             CccccchhhHHHHHH-------HhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQ-------LLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~-------~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.+..++++..       .+....       ......+.|+|++|+|||+||+.+++
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~-------~~~~~~vLl~G~~GtGKT~la~~ia~   86 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSD-------RTPLVSVLLEGPPHSGKTALAAKIAE   86 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCS-------SCSEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccC-------CCCCeEEEEECCCCCcHHHHHHHHHH
Confidence            346777777666655       332111       13467899999999999999999988

>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=98.28  E-value=1e-05  Score=81.82  Aligned_cols=178  Identities=14%  Similarity=0.108  Sum_probs=102.7

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CC-eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN-FD-KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~-~~~wv~~~~~~~~~~  243 (597)
                      ..++|.+..++.|...+...          ..+.+.++|++|+||||+|+.+++.  .... +. ...-++.+.....  
T Consensus        25 ~~~~g~~~~~~~L~~~i~~g----------~~~~~ll~Gp~G~GKTtla~~la~~--l~~~~~~~~~~~~~~~~~~~~--   90 (340)
T 1sxj_C           25 DEVYGQNEVITTVRKFVDEG----------KLPHLLFYGPPGTGKTSTIVALARE--IYGKNYSNMVLELNASDDRGI--   90 (340)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT----------CCCCEEEECSSSSSHHHHHHHHHHH--HHTTSHHHHEEEECTTSCCSH--
T ss_pred             HHhcCcHHHHHHHHHHHhcC----------CCceEEEECCCCCCHHHHHHHHHHH--HcCCCccceEEEEcCcccccH--
Confidence            45789998899998888742          2334899999999999999999873  2211 11 0111211111000  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHH---hcCceEEEEEecccCCCCcchHHHHHHhhcCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEF---VQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG  320 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~---L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~  320 (597)
                                    .. .+.++.                 .+.+.   +.+.+-++|+|+++... ....+.+...+...
T Consensus        91 --------------~~-ir~~i~-----------------~~~~~~~~~~~~~~viiiDe~~~l~-~~~~~~L~~~le~~  137 (340)
T 1sxj_C           91 --------------DV-VRNQIK-----------------DFASTRQIFSKGFKLIILDEADAMT-NAAQNALRRVIERY  137 (340)
T ss_dssp             --------------HH-HHTHHH-----------------HHHHBCCSSSCSCEEEEETTGGGSC-HHHHHHHHHHHHHT
T ss_pred             --------------HH-HHHHHH-----------------HHHhhcccCCCCceEEEEeCCCCCC-HHHHHHHHHHHhcC
Confidence                          11 111111                 11100   12346789999997665 44556666666555


Q ss_pred             CCCcEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCc
Q 041007          321 SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGL  399 (597)
Q Consensus       321 ~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~Gl  399 (597)
                      ...+.+|++|........         .+...+ .+.+.+++.++..+.+...+.......    ..+..+.|++.++|.
T Consensus       138 ~~~~~~il~~n~~~~i~~---------~i~sR~~~~~~~~l~~~~~~~~l~~~~~~~~~~i----~~~~~~~i~~~s~G~  204 (340)
T 1sxj_C          138 TKNTRFCVLANYAHKLTP---------ALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKL----SPNAEKALIELSNGD  204 (340)
T ss_dssp             TTTEEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCB----CHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEEecCccccch---------hHHhhceeEeccCCCHHHHHHHHHHHHHHcCCCC----CHHHHHHHHHHcCCC
Confidence            566777777643310000         111112 288999999999988887663222111    144667889999998


Q ss_pred             hHHH
Q 041007          400 PFAV  403 (597)
Q Consensus       400 PLai  403 (597)
                      +--+
T Consensus       205 ~r~~  208 (340)
T 1sxj_C          205 MRRV  208 (340)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8644

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.25  E-value=3.4e-05  Score=76.24  Aligned_cols=193  Identities=15%  Similarity=0.121  Sum_probs=98.9

Q ss_pred             CccccchhhHHHHHHHhhCCCC-CC-cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESS-DE-ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~-~~-~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      ..++|.+..++.|.+++..... .+ -.+-....+.+.|+|++|+|||+||+.+++.  ....   .+.++++.....  
T Consensus        21 ~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~--~~~~---~~~i~~~~l~~~--   93 (297)
T 3b9p_A           21 TDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATE--CSAT---FLNISAASLTSK--   93 (297)
T ss_dssp             GGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHH--TTCE---EEEEESTTTSSS--
T ss_pred             HHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHH--hCCC---eEEeeHHHHhhc--
Confidence            5689999999999888742100 00 0000113568999999999999999999873  3222   233443322111  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCc----------chHHHH
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYP----------RYWEQL  313 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~----------~~~~~l  313 (597)
                                                  ... .........+......++.+|+||++......          .....+
T Consensus        94 ----------------------------~~~-~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l  144 (297)
T 3b9p_A           94 ----------------------------YVG-DGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEF  144 (297)
T ss_dssp             ----------------------------SCS-CHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHH
T ss_pred             ----------------------------ccc-hHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHH
Confidence                                        000 00111111122222356789999999654211          111123


Q ss_pred             HHhhcCC-----CCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          314 MYSLKSG-----SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       314 ~~~l~~~-----~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      ...+...     ..+..||.||....... .        .+....  .+.+...+.++-..++...+.......    ..
T Consensus       145 l~~l~~~~~~~~~~~v~vi~~tn~~~~l~-~--------~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~----~~  211 (297)
T 3b9p_A          145 LVEFDGLPGNPDGDRIVVLAATNRPQELD-E--------AALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSPL----DT  211 (297)
T ss_dssp             HHHHHHCC------CEEEEEEESCGGGBC-H--------HHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCCS----CH
T ss_pred             HHHHhcccccCCCCcEEEEeecCChhhCC-H--------HHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCCC----CH
Confidence            3222211     13345565665431000 0        111111  267777788888888877664322111    13


Q ss_pred             HHHHHHHHhcCCchH-HHHHHH
Q 041007          387 PIGRRVVGKCKGLPF-AVKILG  407 (597)
Q Consensus       387 ~~~~~I~~~~~GlPL-ai~~~~  407 (597)
                      .....|++.+.|.+- .+..+.
T Consensus       212 ~~~~~la~~~~g~~~~~l~~l~  233 (297)
T 3b9p_A          212 EALRRLAKITDGYSGSDLTALA  233 (297)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHH
Confidence            456788899998775 554443

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.23  E-value=5.1e-05  Score=75.87  Aligned_cols=196  Identities=14%  Similarity=0.083  Sum_probs=100.9

Q ss_pred             CCccccchhhHHHHHHHhhCCCC-CC-cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESS-DE-ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~-~~-~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      -..++|.+..++.|.+.+...-. .+ -.+.....+.|.|+|++|+|||+||+.+++.  ...  ...+.++.+.-... 
T Consensus        11 ~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~--~~~--~~~~~i~~~~l~~~-   85 (322)
T 1xwi_A           11 WSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATE--ANN--STFFSISSSDLVSK-   85 (322)
T ss_dssp             GGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHH--TTS--CEEEEEECCSSCCS-
T ss_pred             HHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHH--cCC--CcEEEEEhHHHHhh-
Confidence            35688999988888876631100 00 0000123578999999999999999999883  211  11223333221110 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC------cch----HHH
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY------PRY----WEQ  312 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~------~~~----~~~  312 (597)
                        +                      .+   .   ....+...+...-..++.+|+||+++....      ...    ...
T Consensus        86 --~----------------------~g---~---~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~  135 (322)
T 1xwi_A           86 --W----------------------LG---E---SEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTE  135 (322)
T ss_dssp             --S----------------------CC---S---CHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHH
T ss_pred             --h----------------------hh---H---HHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHH
Confidence              0                      00   0   011111112222235788999999965410      011    122


Q ss_pred             HHHhhcC---CCCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccchHH
Q 041007          313 LMYSLKS---GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEP  387 (597)
Q Consensus       313 l~~~l~~---~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~  387 (597)
                      +...+..   ...+..||.||.... ....        .+.+..  .+.+.+.+.++-.+++...+......    -...
T Consensus       136 ll~~ld~~~~~~~~v~vI~atn~~~-~ld~--------al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~----l~~~  202 (322)
T 1xwi_A          136 FLVQMQGVGVDNDGILVLGATNIPW-VLDS--------AIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNS----LTEA  202 (322)
T ss_dssp             HHHHHHCSSSCCTTEEEEEEESCTT-TSCH--------HHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBC----CCHH
T ss_pred             HHHHHhcccccCCCEEEEEecCCcc-cCCH--------HHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCC----CCHH
Confidence            3333332   233445555554331 1110        111111  27888888888889998876422211    1134


Q ss_pred             HHHHHHHhcCCc-hHHHHHHHh
Q 041007          388 IGRRVVGKCKGL-PFAVKILGS  408 (597)
Q Consensus       388 ~~~~I~~~~~Gl-PLai~~~~~  408 (597)
                      ....|++.+.|. +-.|..+..
T Consensus       203 ~l~~la~~t~G~sgadl~~l~~  224 (322)
T 1xwi_A          203 DFRELGRKTDGYSGADISIIVR  224 (322)
T ss_dssp             HHHHHHHTCTTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHH
Confidence            568899999986 544655543

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.19  E-value=3.2e-05  Score=79.59  Aligned_cols=194  Identities=14%  Similarity=0.112  Sum_probs=98.8

Q ss_pred             CCccccchhhHHHHHHHhhCCCCC-C-cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSD-E-ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~-~-~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      -..++|.+..++.|..++...... + -.......+.|.|+|++|+|||+||+.+++  +....   .+.++++..... 
T Consensus       114 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~--~~~~~---~~~v~~~~l~~~-  187 (389)
T 3vfd_A          114 FDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAA--ESNAT---FFNISAASLTSK-  187 (389)
T ss_dssp             GGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHH--HTTCE---EEEECSCCC----
T ss_pred             hHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHH--hhcCc---EEEeeHHHhhcc-
Confidence            356899999999999888321000 0 000011357899999999999999999977  32221   233333221110 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC----------cchHHH
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY----------PRYWEQ  312 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~----------~~~~~~  312 (597)
                                       .       .+      .....+...+...-...+.+|+||+++....          ......
T Consensus       188 -----------------~-------~g------~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~  237 (389)
T 3vfd_A          188 -----------------Y-------VG------EGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTE  237 (389)
T ss_dssp             ----------------------------------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHH
T ss_pred             -----------------c-------cc------hHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHH
Confidence                             0       00      0001111122222234568999999964310          011122


Q ss_pred             HHHhhcC----CCCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          313 LMYSLKS----GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       313 l~~~l~~----~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      +...+..    ......||.||.... ..   +.     .+...+  .+.+...+.++-.+++...+......    -..
T Consensus       238 ll~~l~~~~~~~~~~v~vI~atn~~~-~l---~~-----~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~----l~~  304 (389)
T 3vfd_A          238 FLIEFDGVQSAGDDRVLVMGATNRPQ-EL---DE-----AVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSP----LTQ  304 (389)
T ss_dssp             HHHHHHHHC-----CEEEEEEESCGG-GC---CH-----HHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCC----SCH
T ss_pred             HHHHhhcccccCCCCEEEEEecCCch-hc---CH-----HHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCC----CCH
Confidence            2222221    123345555554321 00   00     111112  27888899999999998877432211    123


Q ss_pred             HHHHHHHHhcCCchH-HHHHHH
Q 041007          387 PIGRRVVGKCKGLPF-AVKILG  407 (597)
Q Consensus       387 ~~~~~I~~~~~GlPL-ai~~~~  407 (597)
                      +....|++.+.|..- .|..+.
T Consensus       305 ~~~~~la~~~~g~~~~~l~~L~  326 (389)
T 3vfd_A          305 KELAQLARMTDGYSGSDLTALA  326 (389)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHH
Confidence            456788888988543 555543

>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=98.17  E-value=2.5e-05  Score=79.27  Aligned_cols=193  Identities=16%  Similarity=0.113  Sum_probs=99.5

Q ss_pred             CccccchhhHHHHHHHhhCCCC-CC-cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESS-DE-ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~-~~-~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      ..++|.+..++.|...+..... .+ -.......+.|.|+|++|+|||+||+.+++.  ....|   +.++++       
T Consensus        51 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~--~~~~~---~~v~~~-------  118 (355)
T 2qp9_X           51 EDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATE--ANSTF---FSVSSS-------  118 (355)
T ss_dssp             GGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHH--HTCEE---EEEEHH-------
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHH--hCCCE---EEeeHH-------
Confidence            4689999999999887731100 00 0000123456889999999999999999983  32222   222221       


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCc----------chHHHH
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYP----------RYWEQL  313 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~----------~~~~~l  313 (597)
                                     .+..    ...+     .....+...+......++.+|+||+++.....          .....+
T Consensus       119 ---------------~l~~----~~~g-----~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~l  174 (355)
T 2qp9_X          119 ---------------DLVS----KWMG-----ESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTEL  174 (355)
T ss_dssp             ---------------HHHS----CC--------CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHH
T ss_pred             ---------------HHhh----hhcc-----hHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHH
Confidence                           1110    0000     00111111222222357899999999754311          012333


Q ss_pred             HHhhcC---CCCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccchHHH
Q 041007          314 MYSLKS---GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPI  388 (597)
Q Consensus       314 ~~~l~~---~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~  388 (597)
                      ...+..   ...+..||.||..... .   +.     .+.+..  .+.+.+.+.++-.+++...+.......    ....
T Consensus       175 l~~l~~~~~~~~~v~vI~atn~~~~-l---d~-----al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~----~~~~  241 (355)
T 2qp9_X          175 LVQMNGVGNDSQGVLVLGATNIPWQ-L---DS-----AIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVL----TKED  241 (355)
T ss_dssp             HHHHHHCC---CCEEEEEEESCGGG-S---CH-----HHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCC----CHHH
T ss_pred             HHHhhcccccCCCeEEEeecCCccc-C---CH-----HHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCC----CHHH
Confidence            333322   2334555555543310 0   00     111111  277888899999999988774322111    1345


Q ss_pred             HHHHHHhcCC-chHHHHHHH
Q 041007          389 GRRVVGKCKG-LPFAVKILG  407 (597)
Q Consensus       389 ~~~I~~~~~G-lPLai~~~~  407 (597)
                      ...|++.+.| .+-.|..+.
T Consensus       242 l~~la~~t~G~sg~dl~~l~  261 (355)
T 2qp9_X          242 YRTLGAMTEGYSGSDIAVVV  261 (355)
T ss_dssp             HHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHH
Confidence            6788999988 454555543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.10  E-value=3.2e-06  Score=73.77  Aligned_cols=47  Identities=15%  Similarity=0.268  Sum_probs=35.0

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|++..++++.+.+.....        ....|.|+|++|+|||++|+.+++.
T Consensus         4 ~~~iG~s~~~~~l~~~~~~~~~--------~~~~vll~G~~GtGKt~lA~~i~~~   50 (143)
T 3co5_A            4 FDKLGNSAAIQEMNREVEAAAK--------RTSPVFLTGEAGSPFETVARYFHKN   50 (143)
T ss_dssp             ----CCCHHHHHHHHHHHHHHT--------CSSCEEEEEETTCCHHHHHGGGCCT
T ss_pred             cCceeCCHHHHHHHHHHHHHhC--------CCCcEEEECCCCccHHHHHHHHHHh
Confidence            3578999999999888764322        2345889999999999999999884

>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=98.08  E-value=1e-05  Score=73.57  Aligned_cols=43  Identities=21%  Similarity=0.245  Sum_probs=31.3

Q ss_pred             chhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          171 RNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       171 R~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++.+..++.....       .....+.|+|++|+|||||++.+++.
T Consensus        19 ~~~~~~~~~~~~~~~~~-------~~g~~~~l~G~~G~GKTtL~~~i~~~   61 (180)
T 3ec2_A           19 QNRALLTIRVFVHNFNP-------EEGKGLTFVGSPGVGKTHLAVATLKA   61 (180)
T ss_dssp             HHHHHHHHHHHHHSCCG-------GGCCEEEECCSSSSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccc-------cCCCEEEEECCCCCCHHHHHHHHHHH
Confidence            44555566666654332       23578999999999999999999884

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.01  E-value=1.2e-05  Score=74.50  Aligned_cols=55  Identities=13%  Similarity=0.172  Sum_probs=35.8

Q ss_pred             hhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          173 AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       173 ~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      ..++.+.+++.....      ....+.+.|+|++|+|||+||+.+++  ........++|+++
T Consensus        36 ~~~~~~~~~~~~~~~------~~~~~~~~l~G~~GtGKT~la~~i~~--~~~~~~~~~~~~~~   90 (202)
T 2w58_A           36 KAIRFAERFVAEYEP------GKKMKGLYLHGSFGVGKTYLLAAIAN--ELAKRNVSSLIVYV   90 (202)
T ss_dssp             HHHHHHHHHHHHCCS------SCCCCEEEEECSTTSSHHHHHHHHHH--HHHTTTCCEEEEEH
T ss_pred             HHHHHHHHHHHHhhh------ccCCCeEEEECCCCCCHHHHHHHHHH--HHHHcCCeEEEEEh
Confidence            344556666654321      11237899999999999999999998  34333344566653

>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=98.00  E-value=1.6e-05  Score=90.53  Aligned_cols=45  Identities=27%  Similarity=0.422  Sum_probs=38.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++++.+.|...          ....+.|+|++|+|||+||+.+++.
T Consensus       170 d~viGr~~~i~~l~~~l~~~----------~~~~vlL~G~pG~GKT~la~~la~~  214 (854)
T 1qvr_A          170 DPVIGRDEEIRRVIQILLRR----------TKNNPVLIGEPGVGKTAIVEGLAQR  214 (854)
T ss_dssp             CCCCSCHHHHHHHHHHHHCS----------SCCCCEEEECTTSCHHHHHHHHHHH
T ss_pred             cccCCcHHHHHHHHHHHhcC----------CCCceEEEcCCCCCHHHHHHHHHHH
Confidence            56899999999999999743          2345789999999999999999883

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.99  E-value=0.00019  Score=72.76  Aligned_cols=187  Identities=17%  Similarity=0.106  Sum_probs=95.3

Q ss_pred             CccccchhhHHHHHHHhhCCC-CCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQKILQLLKGES-SDE--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~-~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..+.|-++.+++|.+.+.-.- ..+  ..-+-..++-|.++||+|+|||.||+++++  .....|   +.++.+.-... 
T Consensus       148 ~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~--e~~~~f---~~v~~s~l~sk-  221 (405)
T 4b4t_J          148 DMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAH--HTDCKF---IRVSGAELVQK-  221 (405)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHH--HHTCEE---EEEEGGGGSCS-
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHH--hhCCCc---eEEEhHHhhcc-
Confidence            456789988888877664210 000  000012456789999999999999999998  444333   33433321111 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC-------c--c----h
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY-------P--R----Y  309 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~-------~--~----~  309 (597)
                                                   . .......+...+...-...+++|++|+++....       .  .    .
T Consensus       222 -----------------------------~-vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~  271 (405)
T 4b4t_J          222 -----------------------------Y-IGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRT  271 (405)
T ss_dssp             -----------------------------S-TTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHH
T ss_pred             -----------------------------c-cchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHH
Confidence                                         0 001111122222222346789999999864310       0  0    1


Q ss_pred             HHHHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcccc--ceeecCCCChHHHHHHHHHHhccCCCCCCccch
Q 041007          310 WEQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM--MEIGLGELSEEECRSLFRQIAFHGRSSDYREKF  385 (597)
Q Consensus       310 ~~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~--~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~  385 (597)
                      ...++..+..  ...+..||.||... ...+..   +.  . .+.  ..+.+...+.++-.++|..+...... ....+ 
T Consensus       272 l~~lL~~lDg~~~~~~V~vIaATNrp-d~LDpA---ll--R-pGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l-~~dvd-  342 (405)
T 4b4t_J          272 MLELLNQLDGFETSKNIKIIMATNRL-DILDPA---LL--R-PGRIDRKIEFPPPSVAARAEILRIHSRKMNL-TRGIN-  342 (405)
T ss_dssp             HHHHHHHHHTTTCCCCEEEEEEESCS-SSSCHH---HH--S-TTSSCCEEECCCCCHHHHHHHHHHHHTTSBC-CSSCC-
T ss_pred             HHHHHHhhhccCCCCCeEEEeccCCh-hhCCHh---Hc--C-CCcCceEEEcCCcCHHHHHHHHHHHhcCCCC-CccCC-
Confidence            2223333332  23344455565444 111100   00  0 011  12888888888888888877632211 11122 


Q ss_pred             HHHHHHHHHhcCCch
Q 041007          386 EPIGRRVVGKCKGLP  400 (597)
Q Consensus       386 ~~~~~~I~~~~~GlP  400 (597)
                         ...|++.|.|.-
T Consensus       343 ---l~~lA~~t~G~S  354 (405)
T 4b4t_J          343 ---LRKVAEKMNGCS  354 (405)
T ss_dssp             ---HHHHHHHCCSCC
T ss_pred             ---HHHHHHHCCCCC
Confidence               366778887754

>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=97.99  E-value=0.00011  Score=76.95  Aligned_cols=194  Identities=13%  Similarity=0.094  Sum_probs=99.5

Q ss_pred             CCccccchhhHHHHHHHhhCC---CCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          165 PLEFHGRNAEKQKILQLLKGE---SSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~---~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      -..++|.+..++.|...+...   ..-- .+.....+.|.|+|++|+|||+||+.+++.  ..    ...++.++...-.
T Consensus       133 ~~di~G~~~~k~~l~~~v~~p~~~~~~~-~~~~~~~~~vLL~GppGtGKT~lA~aia~~--~~----~~~~~~v~~~~l~  205 (444)
T 2zan_A          133 WSDVAGLEGAKEALKEAVILPIKFPHLF-TGKRTPWRGILLFGPPGTGKSYLAKAVATE--AN----NSTFFSISSSDLV  205 (444)
T ss_dssp             GGGSCSCHHHHHHHHHHHTHHHHCTTTT-SGGGCCCSEEEEECSTTSSHHHHHHHHHHH--CC----SSEEEEECCC---
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhhCHHHh-hccCCCCceEEEECCCCCCHHHHHHHHHHH--cC----CCCEEEEeHHHHH
Confidence            356899999999998877311   0000 000123578999999999999999999883  21    1123333321100


Q ss_pred             hhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC------cchH----H
Q 041007          242 IRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY------PRYW----E  311 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~------~~~~----~  311 (597)
                                          ...   .+..   ......+.   ...-..++.+|+||+++....      ....    .
T Consensus       206 --------------------~~~---~g~~---~~~~~~~f---~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~  256 (444)
T 2zan_A          206 --------------------SKW---LGES---EKLVKNLF---QLARENKPSIIFIDEIDSLCGSRSENESEAARRIKT  256 (444)
T ss_dssp             -----------------------------C---CCTHHHHH---HHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHH
T ss_pred             --------------------hhh---cchH---HHHHHHHH---HHHHHcCCeEEEEechHhhccCCCCccccHHHHHHH
Confidence                                000   0100   11111111   222235678999999975411      1111    2


Q ss_pred             HHHHhhcC---CCCCcEEEEEccCCCCCCCcccccccccCccccc--eeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          312 QLMYSLKS---GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       312 ~l~~~l~~---~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      .+...+..   ...+..||.||....    ..+.     .+.+..  .+.+...+.++-..+|...+.....    .-..
T Consensus       257 ~lL~~l~~~~~~~~~v~vI~atn~~~----~ld~-----al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~----~l~~  323 (444)
T 2zan_A          257 EFLVQMQGVGVDNDGILVLGATNIPW----VLDS-----AIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQN----SLTE  323 (444)
T ss_dssp             HHHTTTTCSSCCCSSCEEEEEESCGG----GSCH-----HHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCE----ECCH
T ss_pred             HHHHHHhCcccCCCCEEEEecCCCcc----ccCH-----HHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCC----CCCH
Confidence            23333322   134555666664331    0000     111112  2778888888888888887642211    1113


Q ss_pred             HHHHHHHHhcCC-chHHHHHHH
Q 041007          387 PIGRRVVGKCKG-LPFAVKILG  407 (597)
Q Consensus       387 ~~~~~I~~~~~G-lPLai~~~~  407 (597)
                      .....|++.+.| .+-.|..+.
T Consensus       324 ~~l~~la~~t~G~sgadl~~l~  345 (444)
T 2zan_A          324 ADFQELGRKTDGYSGADISIIV  345 (444)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHH
Confidence            456788999988 454555543

>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=97.98  E-value=0.00012  Score=72.42  Aligned_cols=190  Identities=14%  Similarity=0.113  Sum_probs=97.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..++|.+..+++|.+++...-.. +  ..-.-...+.|.|+|++|+|||+||+.+++.  ....     ++.+..     
T Consensus        15 ~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~--~~~~-----~i~v~~-----   82 (301)
T 3cf0_A           15 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE--CQAN-----FISIKG-----   82 (301)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHH--TTCE-----EEEECH-----
T ss_pred             HHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHH--hCCC-----EEEEEh-----
Confidence            46889999988888877531000 0  0000123568999999999999999999883  3222     122211     


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCC-------------Ccch
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNA-------------YPRY  309 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~-------------~~~~  309 (597)
                                     ..+.....   +..   ...   +...+.......+.+|+||++....             ....
T Consensus        83 ---------------~~l~~~~~---g~~---~~~---~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~  138 (301)
T 3cf0_A           83 ---------------PELLTMWF---GES---EAN---VREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRV  138 (301)
T ss_dssp             ---------------HHHHHHHH---TTC---TTH---HHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHH
T ss_pred             ---------------HHHHhhhc---Cch---HHH---HHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHH
Confidence                           22222111   111   111   1222333334568999999995311             0112


Q ss_pred             HHHHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          310 WEQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       310 ~~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      ...+...+..  ...+..||.||..... ..   ..+.  ..... ..+.+.+.+.++-.+++...+..... .....  
T Consensus       139 ~~~lL~~l~~~~~~~~v~vi~atn~~~~-ld---~al~--r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~-~~~~~--  209 (301)
T 3cf0_A          139 INQILTEMDGMSTKKNVFIIGATNRPDI-ID---PAIL--RPGRLDQLIYIPLPDEKSRVAILKANLRKSPV-AKDVD--  209 (301)
T ss_dssp             HHHHHHHHHSSCTTSSEEEEEEESCGGG-SC---GGGG--STTSSCEEEECCCCCHHHHHHHHHHHHTTSCB-CSSCC--
T ss_pred             HHHHHHHhhcccCCCCEEEEEecCCccc-cC---hHHh--cCCccceEEecCCcCHHHHHHHHHHHHccCCC-Cccch--
Confidence            3444444432  2334556666644310 00   0000  00011 12888999999888888877643221 11122  


Q ss_pred             HHHHHHHHhcCCchHH
Q 041007          387 PIGRRVVGKCKGLPFA  402 (597)
Q Consensus       387 ~~~~~I~~~~~GlPLa  402 (597)
                        ...+++.+.|.|-+
T Consensus       210 --~~~la~~~~g~sg~  223 (301)
T 3cf0_A          210 --LEFLAKMTNGFSGA  223 (301)
T ss_dssp             --HHHHHHTCSSCCHH
T ss_pred             --HHHHHHHcCCCCHH
Confidence              24566677777654

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.97  E-value=0.0003  Score=72.55  Aligned_cols=185  Identities=14%  Similarity=0.121  Sum_probs=96.0

Q ss_pred             CccccchhhHHHHHHHhhCCCC-CC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQKILQLLKGESS-DE--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~-~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..+.|-++.+++|.+.+.-.-. .+  ..-+-..++-|.++||+|+|||.||+.+++  .....|   +.++.+.-.+. 
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~--e~~~~~---~~v~~s~l~sk-  254 (437)
T 4b4t_L          181 DGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAA--TIGANF---IFSPASGIVDK-  254 (437)
T ss_dssp             GGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH--HHTCEE---EEEEGGGTCCS-
T ss_pred             hHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHH--HhCCCE---EEEehhhhccc-
Confidence            4567899888888776642100 00  000013467899999999999999999998  343332   33443322111 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC---------cc----h
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY---------PR----Y  309 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~---------~~----~  309 (597)
                                                   . .......+...+...-...+++|++|+++..-.         ..    .
T Consensus       255 -----------------------------~-~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~  304 (437)
T 4b4t_L          255 -----------------------------Y-IGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRT  304 (437)
T ss_dssp             -----------------------------S-SSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHH
T ss_pred             -----------------------------c-chHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHH
Confidence                                         0 000111112222222346789999999863210         01    1


Q ss_pred             HHHHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCccc--cc--eeecCCCChHHHHHHHHHHhccCCCCCCcc
Q 041007          310 WEQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN--MM--EIGLGELSEEECRSLFRQIAFHGRSSDYRE  383 (597)
Q Consensus       310 ~~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~--~~--~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~  383 (597)
                      ...++..+..  ...+..||.||..... .+.        .+.+  ..  .+.+...+.++-.++|..+...-.. ....
T Consensus       305 l~~lL~~lDg~~~~~~vivI~ATNrp~~-LDp--------AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~-~~d~  374 (437)
T 4b4t_L          305 LMELLTQMDGFDNLGQTKIIMATNRPDT-LDP--------ALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKK-TGEF  374 (437)
T ss_dssp             HHHHHHHHHSSSCTTSSEEEEEESSTTS-SCT--------TTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCB-CSCC
T ss_pred             HHHHHHHhhcccCCCCeEEEEecCCchh-hCH--------HHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCC-Cccc
Confidence            2233444432  2345566666654411 110        1111  11  1778777777777888776643221 1112


Q ss_pred             chHHHHHHHHHhcCCch
Q 041007          384 KFEPIGRRVVGKCKGLP  400 (597)
Q Consensus       384 ~~~~~~~~I~~~~~GlP  400 (597)
                      +    ...|++.+.|.-
T Consensus       375 d----l~~lA~~t~G~s  387 (437)
T 4b4t_L          375 D----FEAAVKMSDGFN  387 (437)
T ss_dssp             C----HHHHHHTCCSCC
T ss_pred             C----HHHHHHhCCCCC
Confidence            2    366778887754

>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=97.97  E-value=0.0012  Score=66.28  Aligned_cols=49  Identities=29%  Similarity=0.401  Sum_probs=36.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.+..++.+...+.....     +...+..+.|+|++|+||||||+.+++
T Consensus        25 ~~~~g~~~~~~~l~~~i~~~~~-----~~~~~~~~ll~Gp~G~GKTTLa~~ia~   73 (334)
T 1in4_A           25 DEFIGQENVKKKLSLALEAAKM-----RGEVLDHVLLAGPPGLGKTTLAHIIAS   73 (334)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHH-----HTCCCCCEEEESSTTSSHHHHHHHHHH
T ss_pred             HHccCcHHHHHHHHHHHHHHHh-----cCCCCCeEEEECCCCCcHHHHHHHHHH
Confidence            4578988888877766653200     011346799999999999999999988

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=97.97  E-value=2e-05  Score=83.07  Aligned_cols=44  Identities=30%  Similarity=0.449  Sum_probs=38.0

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++||+.+++++...|...          ....+.|+|++|+|||+||+.+++
T Consensus       180 d~iiGr~~~i~~l~~~l~r~----------~~~~~LL~G~pG~GKT~la~~la~  223 (468)
T 3pxg_A          180 DPVIGRSKEIQRVIEVLSRR----------TKNNPVLIGEPGVGKTAIAEGLAQ  223 (468)
T ss_dssp             CCCCCCHHHHHHHHHHHHCS----------SSCEEEEESCTTTTTHHHHHHHHH
T ss_pred             CCccCcHHHHHHHHHHHhcc----------CCCCeEEECCCCCCHHHHHHHHHH
Confidence            45899999999999999743          235678999999999999999987

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.97  E-value=0.00012  Score=75.22  Aligned_cols=54  Identities=22%  Similarity=0.267  Sum_probs=37.4

Q ss_pred             CccccchhhHHHHHHHhhCCCC-CC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESS-DE--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~-~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.|-++.+++|.+.+...-. .+  ..-+-..++-|.++||+|+|||+||+++++
T Consensus       172 ~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~  228 (428)
T 4b4t_K          172 ADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVAN  228 (428)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            4678999998888776642100 00  000012467799999999999999999998

>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=97.92  E-value=4.7e-05  Score=80.36  Aligned_cols=194  Identities=13%  Similarity=0.101  Sum_probs=100.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCc---CCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEE---SGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~---~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..++|.+..+++|.+++........   .-+....+-|.|+|++|+|||+||+.+++  .....   .+.++++.     
T Consensus       204 ~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~--~~~~~---fv~vn~~~-----  273 (489)
T 3hu3_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGAF---FFLINGPE-----  273 (489)
T ss_dssp             GGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHH--HCSSE---EEEEEHHH-----
T ss_pred             HHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHH--HhCCC---EEEEEchH-----
Confidence            4589999999999888763200000   00001346799999999999999999987  33222   23333211     


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC----------cchHHH
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY----------PRYWEQ  312 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~----------~~~~~~  312 (597)
                                       +.    ..+.     ......+...+.....+++.+|+||+++....          ......
T Consensus       274 -----------------l~----~~~~-----g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~  327 (489)
T 3hu3_A          274 -----------------IM----SKLA-----GESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQ  327 (489)
T ss_dssp             -----------------HH----TSCT-----THHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHH
T ss_pred             -----------------hh----hhhc-----chhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHH
Confidence                             11    0000     01112223334444456788999999943211          012233


Q ss_pred             HHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHH
Q 041007          313 LMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIG  389 (597)
Q Consensus       313 l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~  389 (597)
                      +...+..  ...+..||.||......    +..+.  ..... ..+.+.+.+.++-.++|...+..... .....    .
T Consensus       328 LL~~ld~~~~~~~v~vIaaTn~~~~L----d~al~--r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l-~~~~~----l  396 (489)
T 3hu3_A          328 LLTLMDGLKQRAHVIVMAATNRPNSI----DPALR--RFGRFDREVDIGIPDATGRLEILQIHTKNMKL-ADDVD----L  396 (489)
T ss_dssp             HHHHHHHSCTTSCEEEEEEESCGGGB----CGGGG--STTSSCEEEECCCCCHHHHHHHHHHHTTTSCB-CTTCC----H
T ss_pred             HHHHhhccccCCceEEEEecCCcccc----CHHHh--CCCcCceEEEeCCCCHHHHHHHHHHHHhcCCC-cchhh----H
Confidence            4444442  23344555555543110    00000  00011 12889999999999999887642221 11112    3


Q ss_pred             HHHHHhcCCc-hHHHHHH
Q 041007          390 RRVVGKCKGL-PFAVKIL  406 (597)
Q Consensus       390 ~~I~~~~~Gl-PLai~~~  406 (597)
                      .++++.+.|. +-.|..+
T Consensus       397 ~~la~~t~g~s~~dL~~L  414 (489)
T 3hu3_A          397 EQVANETHGHVGADLAAL  414 (489)
T ss_dssp             HHHHHTCTTCCHHHHHHH
T ss_pred             HHHHHHccCCcHHHHHHH
Confidence            5677777774 5445444

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=97.92  E-value=3.7e-05  Score=76.39  Aligned_cols=68  Identities=15%  Similarity=0.264  Sum_probs=43.3

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      .++|.+..++.+...+......- ..+......+.|+|++|+|||++|+.+++.  ....-...+.+.++.
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~-~~~~~~~~~~ll~G~~GtGKt~la~~la~~--~~~~~~~~~~~~~~~   85 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGL-KDPNRPIGSFLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTE   85 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTC-SCTTSCSEEEEEESCSSSSHHHHHHHHHHH--HHSCGGGEEEEEGGG
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCC-CCCCCCceEEEEECCCCcCHHHHHHHHHHH--HcCCCcceEEeeccc
Confidence            47899999888888876431100 001122357999999999999999999883  322222344555543

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=97.90  E-value=0.00019  Score=69.18  Aligned_cols=55  Identities=18%  Similarity=0.251  Sum_probs=35.0

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -..++|.+..++++.+.+......+  ..-+....+-+.|+|++|+||||||+.+++
T Consensus        11 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   67 (257)
T 1lv7_A           11 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG   67 (257)
T ss_dssp             GGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             HHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHH
Confidence            3568899888877765543210000  000001234689999999999999999987

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=97.90  E-value=6.1e-05  Score=74.43  Aligned_cols=151  Identities=10%  Similarity=0.015  Sum_probs=89.8

Q ss_pred             cchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChh-hhccCCeeEEEEecCCCchhhhhhhh
Q 041007          170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSD-VKANFDKRIWVSASYPRDEIRVARDE  248 (597)
Q Consensus       170 GR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~-~~~~F~~~~wv~~~~~~~~~~~~~~~  248 (597)
                      |-++.++.|...+...          ..+...++|++|+|||++|..+.+... ....+....++..+.....       
T Consensus         1 g~~~~~~~L~~~i~~~----------~~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~-------   63 (305)
T 2gno_A            1 GAKDQLETLKRIIEKS----------EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIG-------   63 (305)
T ss_dssp             ---CHHHHHHHHHHTC----------SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBC-------
T ss_pred             ChHHHHHHHHHHHHCC----------CCcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCC-------
Confidence            3455667777777632          357899999999999999999976310 1111222344433211111       


Q ss_pred             hhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEE
Q 041007          249 ISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILV  328 (597)
Q Consensus       249 ~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIv  328 (597)
                               .+..+.+.+.+....                ..+++-++|+|+++... ....+.+...+...++.+.+|+
T Consensus        64 ---------id~ir~li~~~~~~p----------------~~~~~kvviIdead~lt-~~a~naLLk~LEep~~~t~fIl  117 (305)
T 2gno_A           64 ---------IDDIRTIKDFLNYSP----------------ELYTRKYVIVHDCERMT-QQAANAFLKALEEPPEYAVIVL  117 (305)
T ss_dssp             ---------HHHHHHHHHHHTSCC----------------SSSSSEEEEETTGGGBC-HHHHHHTHHHHHSCCTTEEEEE
T ss_pred             ---------HHHHHHHHHHHhhcc----------------ccCCceEEEeccHHHhC-HHHHHHHHHHHhCCCCCeEEEE
Confidence                     122222333222110                12456799999998776 5567778877877777888888


Q ss_pred             EccCCCCCCCcccccccccCccccceeecCCCChHHHHHHHHHHh
Q 041007          329 TRSGGKNGTNMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       329 TtR~~~~~~~~~~~~~~~~~~~~~~~~~l~~Ls~~es~~Lf~~~~  373 (597)
                      +|.+......         .+... .+++.++++++..+.+.+.+
T Consensus       118 ~t~~~~kl~~---------tI~SR-~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          118 NTRRWHYLLP---------TIKSR-VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             EESCGGGSCH---------HHHTT-SEEEECCCCHHHHHHHHHHH
T ss_pred             EECChHhChH---------HHHce-eEeCCCCCHHHHHHHHHHHh
Confidence            7754411110         11122 58999999999999998876

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.86  E-value=0.00046  Score=71.07  Aligned_cols=54  Identities=24%  Similarity=0.246  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHhhCCC-CCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGES-SDE--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~-~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.|-++.+++|.+.+.-.- ..+  ..-+-..++-|.++|++|+|||.||+.+++
T Consensus       209 ~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~  265 (467)
T 4b4t_H          209 SDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVAN  265 (467)
T ss_dssp             SSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHh
Confidence            357789988888877653100 000  000013567899999999999999999998

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.81  E-value=0.00035  Score=71.91  Aligned_cols=54  Identities=17%  Similarity=0.198  Sum_probs=37.4

Q ss_pred             CccccchhhHHHHHHHhhCCC-CCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGES-SDE--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~-~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.|-++.+++|.+.+...- ..+  ..-+-+.++-|.++||+|+|||.||+++++
T Consensus       181 ~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~  237 (434)
T 4b4t_M          181 SDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAA  237 (434)
T ss_dssp             GGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHH
T ss_pred             HhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHH
Confidence            457899999988877653210 000  000013467899999999999999999998

>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=97.79  E-value=0.00028  Score=79.32  Aligned_cols=45  Identities=27%  Similarity=0.347  Sum_probs=38.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++++.+.|...          ....+.|+|++|+|||++|+.+++.
T Consensus       186 d~~iGr~~~i~~l~~~l~~~----------~~~~vlL~G~~GtGKT~la~~la~~  230 (758)
T 1r6b_X          186 DPLIGREKELERAIQVLCRR----------RKNNPLLVGESGVGKTAIAEGLAWR  230 (758)
T ss_dssp             CCCCSCHHHHHHHHHHHTSS----------SSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCccCCHHHHHHHHHHHhcc----------CCCCeEEEcCCCCCHHHHHHHHHHH
Confidence            46899999999999999743          3456789999999999999999873

>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=97.78  E-value=0.00056  Score=71.57  Aligned_cols=188  Identities=13%  Similarity=0.100  Sum_probs=94.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      ..++|.++.++++.+.+.......  ..-+-..++-|.|+|++|+|||+||+.+++  +....|   +.++++.....  
T Consensus        16 ~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~--~~~~~f---~~is~~~~~~~--   88 (476)
T 2ce7_A           16 KDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAG--EANVPF---FHISGSDFVEL--   88 (476)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHH--HHTCCE---EEEEGGGTTTC--
T ss_pred             HHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHH--HcCCCe---eeCCHHHHHHH--
Confidence            458899988777766553211000  000001234588999999999999999988  332222   23333321111  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCc-------------chH
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYP-------------RYW  310 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~-------------~~~  310 (597)
                       +                            .......+...+.......+.+|+||+++.....             ...
T Consensus        89 -~----------------------------~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l  139 (476)
T 2ce7_A           89 -F----------------------------VGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTL  139 (476)
T ss_dssp             -C----------------------------TTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHH
T ss_pred             -H----------------------------hcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHH
Confidence             0                            0001112223344444567899999999653210             122


Q ss_pred             HHHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHH
Q 041007          311 EQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEP  387 (597)
Q Consensus       311 ~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~  387 (597)
                      ..+...+..  ...+..||.||..... ..   ..+..  ..+. ..+.+.+.+.++-.+++..++..... .....   
T Consensus       140 ~~LL~~ld~~~~~~~viVIaaTn~~~~-Ld---~allR--~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l-~~~v~---  209 (476)
T 2ce7_A          140 NQLLVEMDGFDSKEGIIVMAATNRPDI-LD---PALLR--PGRFDKKIVVDPPDMLGRKKILEIHTRNKPL-AEDVN---  209 (476)
T ss_dssp             HHHHHHHHHSCGGGTEEEEEEESCGGG-SC---GGGGS--TTSSCEEEECCCCCHHHHHHHHHHHHTTSCB-CTTCC---
T ss_pred             HHHHHHHhccCCCCCEEEEEecCChhh-hc---hhhcc--cCcceeEeecCCCCHHHHHHHHHHHHHhCCC-cchhh---
Confidence            333333322  1234556666554311 00   00000  0011 12778888888777888776632211 11111   


Q ss_pred             HHHHHHHhcCCch
Q 041007          388 IGRRVVGKCKGLP  400 (597)
Q Consensus       388 ~~~~I~~~~~GlP  400 (597)
                       ...|++.+.|..
T Consensus       210 -l~~la~~t~G~s  221 (476)
T 2ce7_A          210 -LEIIAKRTPGFV  221 (476)
T ss_dssp             -HHHHHHTCTTCC
T ss_pred             -HHHHHHhcCCCc
Confidence             345788888877

>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=97.76  E-value=5.9e-05  Score=73.12  Aligned_cols=47  Identities=17%  Similarity=0.226  Sum_probs=34.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|++..+.++.+.+.....        ....|.|+|++|+|||+||+.+++.
T Consensus         6 ~~~ig~~~~~~~~~~~~~~~~~--------~~~~vll~G~~GtGKt~la~~i~~~   52 (265)
T 2bjv_A            6 DNLLGEANSFLEVLEQVSHLAP--------LDKPVLIIGERGTGKELIASRLHYL   52 (265)
T ss_dssp             ----CCCHHHHHHHHHHHHHTT--------SCSCEEEECCTTSCHHHHHHHHHHT
T ss_pred             ccceeCCHHHHHHHHHHHHHhC--------CCCCEEEECCCCCcHHHHHHHHHHh
Confidence            4588999999988877764332        2356889999999999999999874

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.73  E-value=0.00097  Score=67.96  Aligned_cols=54  Identities=24%  Similarity=0.257  Sum_probs=37.0

Q ss_pred             CccccchhhHHHHHHHhhCCC-CCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGES-SDE--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~-~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.|-++.+++|.+.+...- ..+  ..-+-+.++-|.++||+|+|||.||+++++
T Consensus       182 ~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~  238 (437)
T 4b4t_I          182 SDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVAN  238 (437)
T ss_dssp             GGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHH
T ss_pred             eecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHH
Confidence            456789988888877664210 000  000013467899999999999999999998

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=97.72  E-value=0.00043  Score=68.46  Aligned_cols=54  Identities=24%  Similarity=0.367  Sum_probs=37.2

Q ss_pred             CccccchhhHHHHHHHhhCC--CC--CCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGE--SS--DEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~--~~--~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|++..++.+...+...  ..  ............+.|+|++|+|||++|+.+++
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   72 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   72 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHH
Confidence            45889999999998877531  00  00000001345788999999999999999987

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.70  E-value=0.00082  Score=70.55  Aligned_cols=101  Identities=11%  Similarity=-0.000  Sum_probs=58.9

Q ss_pred             EEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEc---------cCCCCCCCcccccccccCccccce-eecCCCChH
Q 041007          294 VLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTR---------SGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEE  363 (597)
Q Consensus       294 ~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTt---------R~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~  363 (597)
                      -++++|+++..+ ....+.+...+...... .+|+.|         .+....+.    .++. .+...+. +.+.+++.+
T Consensus       297 ~VliIDEa~~l~-~~a~~aLlk~lEe~~~~-~~il~tn~~~~~i~~~~~~~~~~----~l~~-~i~sR~~~~~~~~~~~~  369 (456)
T 2c9o_A          297 GVLFVDEVHMLD-IECFTYLHRALESSIAP-IVIFASNRGNCVIRGTEDITSPH----GIPL-DLLDRVMIIRTMLYTPQ  369 (456)
T ss_dssp             CEEEEESGGGCB-HHHHHHHHHHTTSTTCC-EEEEEECCSEEECBTTSSCEEET----TCCH-HHHTTEEEEECCCCCHH
T ss_pred             eEEEEechhhcC-HHHHHHHHHHhhccCCC-EEEEecCCccccccccccccccc----cCCh-hHHhhcceeeCCCCCHH
Confidence            399999998876 66777777777655545 344344         11000000    0000 1112222 899999999


Q ss_pred             HHHHHHHHHhccCCCCCCccchHHHHHHHHHhc-CCchHHHHH
Q 041007          364 ECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKC-KGLPFAVKI  405 (597)
Q Consensus       364 es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~-~GlPLai~~  405 (597)
                      +..+++...+......    -..+....|++.+ .|.|.....
T Consensus       370 e~~~iL~~~~~~~~~~----~~~~~~~~i~~~a~~g~~r~a~~  408 (456)
T 2c9o_A          370 EMKQIIKIRAQTEGIN----ISEEALNHLGEIGTKTTLRYSVQ  408 (456)
T ss_dssp             HHHHHHHHHHHHHTCC----BCHHHHHHHHHHHHHSCHHHHHH
T ss_pred             HHHHHHHHHHHHhCCC----CCHHHHHHHHHHccCCCHHHHHH
Confidence            9999998876321111    1144567788888 787765443

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=97.63  E-value=5.5e-05  Score=74.93  Aligned_cols=46  Identities=22%  Similarity=0.337  Sum_probs=37.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|+...+.++.+.+.....        ....|.|+|++|+|||++|+.+++
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~--------~~~~vLi~Ge~GtGKt~lAr~i~~   47 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAP--------SDATVLIHGDSGTGKELVARALHA   47 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCS--------TTSCEEEESCTTSCHHHHHHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHhC--------CCCcEEEECCCCchHHHHHHHHHH
Confidence            3588999999999888875432        345688999999999999999987

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.61  E-value=0.00013  Score=81.94  Aligned_cols=45  Identities=29%  Similarity=0.446  Sum_probs=38.5

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++||+.+++++...|...          ...-+.|+|++|+|||++|+.+++.
T Consensus       180 d~iiG~~~~i~~l~~~l~~~----------~~~~vLL~G~pGtGKT~la~~la~~  224 (758)
T 3pxi_A          180 DPVIGRSKEIQRVIEVLSRR----------TKNNPVLIGEPGVGKTAIAEGLAQQ  224 (758)
T ss_dssp             CCCCCCHHHHHHHHHHHHCS----------SSCEEEEESCTTTTTHHHHHHHHHH
T ss_pred             CCccCchHHHHHHHHHHhCC----------CCCCeEEECCCCCCHHHHHHHHHHH
Confidence            46899999999999999743          2356889999999999999999873

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=97.58  E-value=0.00023  Score=79.90  Aligned_cols=168  Identities=14%  Similarity=0.212  Sum_probs=89.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      ..++|.+..++.+...+........ .++.....+.++|++|+|||+||+.+++.  ....-...+.++++........ 
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~-~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~--l~~~~~~~i~i~~s~~~~~~~~-  566 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLK-DPKRPIGSFIFLGPTGVGKTELARALAES--IFGDEESMIRIDMSEYMEKHST-  566 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCS-CTTSCSEEEEEESCTTSSHHHHHHHHHHH--HHSCTTCEEEEEGGGGCSSCCC-
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccC-CCCCCceEEEEECCCCCCHHHHHHHHHHH--hcCCCcceEEEechhccccccc-
Confidence            4588999999988888874332110 01122337999999999999999999883  3222233455555433222000 


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-----
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-----  320 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-----  320 (597)
                                  .                   ...+...++   .....+|+||++.... ......+...+..+     
T Consensus       567 ------------~-------------------~~~l~~~~~---~~~~~vl~lDEi~~~~-~~~~~~Ll~~le~g~~~~~  611 (758)
T 3pxi_A          567 ------------S-------------------GGQLTEKVR---RKPYSVVLLDAIEKAH-PDVFNILLQVLEDGRLTDS  611 (758)
T ss_dssp             ------------C----------------------CHHHHH---HCSSSEEEEECGGGSC-HHHHHHHHHHHHHSBCC--
T ss_pred             ------------c-------------------cchhhHHHH---hCCCeEEEEeCccccC-HHHHHHHHHHhccCeEEcC
Confidence                        0                   001111111   1234599999997765 55666666666432     


Q ss_pred             ------CCCcEEEEEccCCCCCCCcc----cccccccCccccc--eeecCCCChHHHHHHHHHHh
Q 041007          321 ------SEGSRILVTRSGGKNGTNMT----EIGLGEKNGTNMM--EIGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       321 ------~~gs~IIvTtR~~~~~~~~~----~~~~~~~~~~~~~--~~~l~~Ls~~es~~Lf~~~~  373 (597)
                            ..+..||+||..........    ...+ .....+..  .+.+.|++.++..+++...+
T Consensus       612 ~g~~~~~~~~~iI~ttn~~~~~~~~~~~~~~~~f-~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l  675 (758)
T 3pxi_A          612 KGRTVDFRNTILIMTSNVGASEKDKVMGELKRAF-RPEFINRIDEIIVFHSLEKKHLTEIVSLMS  675 (758)
T ss_dssp             ---CCBCTTCEEEEEESSSTTCCHHHHHHHHHHS-CHHHHTTSSEEEECC--CHHHHHHHHHHHH
T ss_pred             CCCEeccCCeEEEEeCCCChhhHHHHHHHHHhhC-CHHHHhhCCeEEecCCCCHHHHHHHHHHHH
Confidence                  23568888887432110000    0000 00111111  27888888888777766544

>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=97.51  E-value=3.1e-05  Score=75.23  Aligned_cols=55  Identities=20%  Similarity=0.276  Sum_probs=36.0

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCc--CCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEE--SGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~--~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -..++|.+..++.|.+.+......+.  .-.....+.+.|+|++|+|||+||+.+++
T Consensus        10 ~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~   66 (268)
T 2r62_A           10 FKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAG   66 (268)
T ss_dssp             STTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHH
Confidence            35689999888888776642100000  00001234478999999999999999988

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.47  E-value=0.00067  Score=63.34  Aligned_cols=98  Identities=18%  Similarity=0.065  Sum_probs=52.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCC-CCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGS-VSS  274 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~-~~~  274 (597)
                      ...++.|.|++|+|||||+..++.     ..-..++|++........... ...... .....    .++..+... ...
T Consensus        19 ~G~~~~i~G~~GsGKTtl~~~l~~-----~~~~~v~~i~~~~~~~~~~~~-~~~~~~-~~~~~----~~~~~~~~~~~~~   87 (220)
T 2cvh_A           19 PGVLTQVYGPYASGKTTLALQTGL-----LSGKKVAYVDTEGGFSPERLV-QMAETR-GLNPE----EALSRFILFTPSD   87 (220)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHH-----HHCSEEEEEESSCCCCHHHHH-HHHHTT-TCCHH----HHHHHEEEECCTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH-----HcCCcEEEEECCCCCCHHHHH-HHHHhc-CCChH----HHhhcEEEEecCC
Confidence            456999999999999999999976     112457788766533331110 000000 00001    122222211 112


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCC
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWN  304 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~  304 (597)
                      ..+.......+...+..+.-+||||.+...
T Consensus        88 ~~~~~~~~~~~~~l~~~~~~lliiD~~~~~  117 (220)
T 2cvh_A           88 FKEQRRVIGSLKKTVDSNFALVVVDSITAH  117 (220)
T ss_dssp             TSHHHHHHHHHHHHCCTTEEEEEEECCCCC
T ss_pred             HHHHHHHHHHHHHHhhcCCCEEEEcCcHHH
Confidence            222334455555555445789999998544

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.45  E-value=0.00011  Score=64.22  Aligned_cols=24  Identities=29%  Similarity=0.495  Sum_probs=21.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+.|+|+.|+|||||++.++..
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~   59 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQ   59 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999999884

>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=97.42  E-value=0.0013  Score=72.92  Aligned_cols=185  Identities=12%  Similarity=0.082  Sum_probs=95.7

Q ss_pred             CccccchhhHHHHHHHhhC---CCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQKILQLLKG---ESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~---~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..+.|-++.+++|.+++.-   ...--..-+-..++-|.++|++|+|||+||+.+++.  ...+|   +.++.+.     
T Consensus       204 ~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~e--lg~~~---~~v~~~~-----  273 (806)
T 3cf2_A          204 DDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE--TGAFF---FLINGPE-----  273 (806)
T ss_dssp             GGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTT--TTCEE---EEEEHHH-----
T ss_pred             hhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHH--hCCeE---EEEEhHH-----
Confidence            4467888888888776531   110000001234678999999999999999999994  33332   3333211     


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC------cc----hHHH
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY------PR----YWEQ  312 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~------~~----~~~~  312 (597)
                                       +.        .. ........+...+.......+.+|+||+++..-.      ..    ....
T Consensus       274 -----------------l~--------sk-~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~  327 (806)
T 3cf2_A          274 -----------------IM--------SK-LAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQ  327 (806)
T ss_dssp             -----------------HH--------SS-CTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHH
T ss_pred             -----------------hh--------cc-cchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHH
Confidence                             00        00 0111222333344444457799999999864310      11    1222


Q ss_pred             HHHhhcCC--CCCcEEEEEccCCCCCCCcccccccccCccc--c--ceeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          313 LMYSLKSG--SEGSRILVTRSGGKNGTNMTEIGLGEKNGTN--M--MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       313 l~~~l~~~--~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~--~--~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      +...+...  ..+..||.||........         .+.+  .  ..+++...+.++=.++|..+...... ....+  
T Consensus       328 LL~~mdg~~~~~~V~VIaaTN~~d~LD~---------ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~-~~dvd--  395 (806)
T 3cf2_A          328 LLTLMDGLKQRAHVIVMAATNRPNSIDP---------ALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKL-ADDVD--  395 (806)
T ss_dssp             HHTHHHHCCGGGCEEEEEECSSTTTSCT---------TTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEE-CTTCC--
T ss_pred             HHHHHhcccccCCEEEEEecCChhhcCH---------HHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCC-CcccC--
Confidence            33333221  223445555544311110         1111  1  12888888888888888766532111 11122  


Q ss_pred             HHHHHHHHhcCCch
Q 041007          387 PIGRRVVGKCKGLP  400 (597)
Q Consensus       387 ~~~~~I~~~~~GlP  400 (597)
                        ...|++++.|.-
T Consensus       396 --l~~lA~~T~Gfs  407 (806)
T 3cf2_A          396 --LEQVANETHGHV  407 (806)
T ss_dssp             --HHHHHHHCCSCC
T ss_pred             --HHHHHHhcCCCC
Confidence              356788888764

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=97.31  E-value=0.00043  Score=68.05  Aligned_cols=24  Identities=29%  Similarity=0.422  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++.+.|+|++|+|||+||+.+++
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~   58 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFR   58 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457889999999999999999998

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=97.31  E-value=0.00052  Score=68.78  Aligned_cols=42  Identities=17%  Similarity=0.093  Sum_probs=35.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|++..++.+...+..            ...+.|+|++|+|||+||+.+.+
T Consensus        27 ~~i~g~~~~~~~l~~~l~~------------~~~vll~G~pGtGKT~la~~la~   68 (331)
T 2r44_A           27 KVVVGQKYMINRLLIGICT------------GGHILLEGVPGLAKTLSVNTLAK   68 (331)
T ss_dssp             TTCCSCHHHHHHHHHHHHH------------TCCEEEESCCCHHHHHHHHHHHH
T ss_pred             cceeCcHHHHHHHHHHHHc------------CCeEEEECCCCCcHHHHHHHHHH
Confidence            3578999999998888863            23688999999999999999987

>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=97.28  E-value=0.00058  Score=77.62  Aligned_cols=53  Identities=17%  Similarity=0.342  Sum_probs=37.8

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .++|.+..++.+...+......- ..++.....+.|+|++|+|||++|+.+++.
T Consensus       559 ~viG~~~a~~~l~~~i~~~~~g~-~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~  611 (854)
T 1qvr_A          559 RVVGQDEAIRAVADAIRRARAGL-KDPNRPIGSFLFLGPTGVGKTELAKTLAAT  611 (854)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGC-SCSSSCSEEEEEBSCSSSSHHHHHHHHHHH
T ss_pred             ccCCcHHHHHHHHHHHHHHhccc-CCCCCCceEEEEECCCCCCHHHHHHHHHHH
Confidence            57899999998888876432100 001123358999999999999999999873

>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=97.27  E-value=0.00053  Score=77.04  Aligned_cols=53  Identities=15%  Similarity=0.257  Sum_probs=37.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.+..++.+...+......- ..++.....+.++|++|+|||++|+.+++
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~-~~~~~p~~~~ll~G~~GtGKT~la~~la~  510 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGL-GHEHKPVGSFLFAGPTGVGKTEVTVQLSK  510 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTC-SCTTSCSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             hhccCHHHHHHHHHHHHHHHhccc-CCCCCCceEEEEECCCCCcHHHHHHHHHH
Confidence            457899999888877775322100 00112334799999999999999999987

>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=97.23  E-value=0.0016  Score=62.42  Aligned_cols=54  Identities=24%  Similarity=0.347  Sum_probs=33.3

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCC---cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDE---ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~---~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -.+++|.+..+.++.+....-....   .-+ -.-.+-+.|+|++|+|||||++.++.
T Consensus        15 ~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~-~~~~~g~ll~G~~G~GKTtl~~~i~~   71 (254)
T 1ixz_A           15 FKDVAGAEEAKEELKEIVEFLKNPSRFHEMG-ARIPKGVLLVGPPGVGKTHLARAVAG   71 (254)
T ss_dssp             GGGCCSCHHHHHHHHHHHHHHHCHHHHHHTT-CCCCSEEEEECCTTSSHHHHHHHHHH
T ss_pred             HHHhCCcHHHHHHHHHHHHHHHCHHHHHHcC-CCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            3568888877666655443111000   000 00122389999999999999999987

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.17  E-value=0.00027  Score=69.97  Aligned_cols=43  Identities=23%  Similarity=0.366  Sum_probs=30.5

Q ss_pred             chhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          171 RNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       171 R~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +...+..+.+++.....       .....+.|+|++|+|||+||..+++.
T Consensus       133 ~~~~~~~~~~~i~~~~~-------~~~~~lll~G~~GtGKT~La~aia~~  175 (308)
T 2qgz_A          133 RMEAFSAILDFVEQYPS-------AEQKGLYLYGDMGIGKSYLLAAMAHE  175 (308)
T ss_dssp             HHHHHHHHHHHHHHCSC-------SSCCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccc-------cCCceEEEECCCCCCHHHHHHHHHHH
Confidence            33444556666664321       12468999999999999999999984

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.11  E-value=0.0021  Score=62.56  Aligned_cols=56  Identities=23%  Similarity=0.353  Sum_probs=34.9

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCC---cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDE---ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~---~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .....++|.+..+.++.+....-....   .-+ -.-.+-+.|+|++|+|||||++.++.
T Consensus        37 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~-~~~~~gvll~Gp~GtGKTtl~~~i~~   95 (278)
T 1iy2_A           37 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMG-ARIPKGVLLVGPPGVGKTHLARAVAG   95 (278)
T ss_dssp             CCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTT-CCCCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcC-CCCCCeEEEECCCcChHHHHHHHHHH
Confidence            334568898877776665543211000   000 00112389999999999999999987

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.09  E-value=0.0016  Score=61.24  Aligned_cols=38  Identities=24%  Similarity=0.251  Sum_probs=27.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ..+++|.|++|+|||||+..++..  ....-..++|+...
T Consensus        23 G~~~~i~G~~GsGKTtl~~~l~~~--~~~~~~~v~~~~~~   60 (235)
T 2w0m_A           23 GFFIALTGEPGTGKTIFSLHFIAK--GLRDGDPCIYVTTE   60 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHH--HHHHTCCEEEEESS
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHH--HHHCCCeEEEEEcc
Confidence            469999999999999999999863  22222346666643

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=97.06  E-value=0.0039  Score=65.58  Aligned_cols=56  Identities=20%  Similarity=0.268  Sum_probs=35.3

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .-..++|.++.+.++.+....-....  ..-+-.-.+-|.|+|++|+|||+||+.++.
T Consensus        29 ~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~   86 (499)
T 2dhr_A           29 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAG   86 (499)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHH
Confidence            34568899887777665543211100  000001123489999999999999999987

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.99  E-value=0.00073  Score=63.12  Aligned_cols=113  Identities=16%  Similarity=0.113  Sum_probs=61.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC--
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS--  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~--  273 (597)
                      ...++.|+|+.|+||||++..+.++  ...+-..++.+.........                   ..++..++....  
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r--~~~~g~kVli~~~~~d~r~~-------------------~~i~srlG~~~~~~   69 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHR--LEYADVKYLVFKPKIDTRSI-------------------RNIQSRTGTSLPSV   69 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHH--HHHTTCCEEEEEECCCGGGC-------------------SSCCCCCCCSSCCE
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHH--HHhcCCEEEEEEeccCchHH-------------------HHHHHhcCCCcccc
Confidence            3478999999999999999998874  33332233334322211110                   011112221111  


Q ss_pred             chhhHHHHHHHHHHHhcCc-eEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          274 SQVEMETVLQYINEFVQGK-KVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       274 ~~~~~~~~~~~l~~~L~~k-r~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .......+...+.+.+.+. .-+||+|.++..+ .+..+.+.. +..  .+..||+|.+..
T Consensus        70 ~~~~~~~i~~~i~~~~~~~~~dvViIDEaQ~l~-~~~ve~l~~-L~~--~gi~Vil~Gl~~  126 (223)
T 2b8t_A           70 EVESAPEILNYIMSNSFNDETKVIGIDEVQFFD-DRICEVANI-LAE--NGFVVIISGLDK  126 (223)
T ss_dssp             EESSTHHHHHHHHSTTSCTTCCEEEECSGGGSC-THHHHHHHH-HHH--TTCEEEEECCSB
T ss_pred             ccCCHHHHHHHHHHHhhCCCCCEEEEecCccCc-HHHHHHHHH-HHh--CCCeEEEEeccc
Confidence            1122234555555544444 4599999997654 234344433 322  278899998865

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=96.98  E-value=0.0025  Score=60.41  Aligned_cols=44  Identities=14%  Similarity=0.156  Sum_probs=31.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc----cCCeeEEEEecCCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA----NFDKRIWVSASYPR  239 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~  239 (597)
                      ...++.|.|++|+|||||+..++.......    .-..++|++....+
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~~~   70 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEGTF   70 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCCCc
Confidence            457999999999999999999876211111    13467888766543

>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=96.95  E-value=0.0013  Score=70.43  Aligned_cols=50  Identities=30%  Similarity=0.491  Sum_probs=33.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|-+.-...+.+.+.-..-.    .......+.|+|++|+||||||+.++.
T Consensus        81 ~di~G~~~vk~~i~~~~~l~~~~----~~~~g~~vll~Gp~GtGKTtlar~ia~  130 (543)
T 3m6a_A           81 EEHHGLEKVKERILEYLAVQKLT----KSLKGPILCLAGPPGVGKTSLAKSIAK  130 (543)
T ss_dssp             HHCSSCHHHHHHHHHHHHHHHHS----SSCCSCEEEEESSSSSSHHHHHHHHHH
T ss_pred             HHhccHHHHHHHHHHHHHHHHhc----ccCCCCEEEEECCCCCCHHHHHHHHHH
Confidence            34678777777665443211000    012456899999999999999999987

>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=96.94  E-value=0.00031  Score=68.86  Aligned_cols=34  Identities=18%  Similarity=0.215  Sum_probs=25.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      .+++.|+|++|+|||+||.+++..   .  -..++|++.
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~---~--G~~VlyIs~  156 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA---L--GGKDKYATV  156 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH---H--HTTSCCEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh---C--CCCEEEEEe
Confidence            467889999999999999999873   1  123456666

>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=96.86  E-value=0.0072  Score=57.14  Aligned_cols=50  Identities=6%  Similarity=0.006  Sum_probs=31.8

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhc---CCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLK---SGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~---~~~~gs~IIvTtR~~  333 (597)
                      .+...|-.++-+|+||+--..-+......+...+.   ....|..||++|.+.
T Consensus       137 ~lAraL~~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~~~~tviivtH~~  189 (237)
T 2cbz_A          137 SLARAVYSNADIYLFDDPLSAVDAHVGKHIFENVIGPKGMLKNKTRILVTHSM  189 (237)
T ss_dssp             HHHHHHHHCCSEEEEESTTTTSCHHHHHHHHHHTTSTTSTTTTSEEEEECSCS
T ss_pred             HHHHHHhcCCCEEEEeCcccccCHHHHHHHHHHHHHHHhhcCCCEEEEEecCh
Confidence            34455556777899999755444555566666663   223477788888765

>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=96.84  E-value=0.0049  Score=62.80  Aligned_cols=23  Identities=30%  Similarity=0.482  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+.|+|++|+|||++|+.+++
T Consensus        72 ~~~ill~Gp~GtGKT~la~~la~   94 (376)
T 1um8_A           72 KSNILLIGPTGSGKTLMAQTLAK   94 (376)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCHHHHHHHHHH
Confidence            45789999999999999999987

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.78  E-value=0.0032  Score=57.07  Aligned_cols=52  Identities=19%  Similarity=0.238  Sum_probs=35.1

Q ss_pred             HHHHHHHHhcCce-EEEEEecccCC---CCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          281 VLQYINEFVQGKK-VLLVLDDLWWN---AYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       281 ~~~~l~~~L~~kr-~LLVLDdv~~~---~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      .....++.+.+.+ =|||||++-..   . .-..+.+...+........||+|+|..
T Consensus       108 ~l~~a~~~l~~~~yDlvILDEi~~al~~g-~l~~~ev~~~l~~Rp~~~~vIlTGr~a  163 (196)
T 1g5t_A          108 VWQHGKRMLADPLLDMVVLDELTYMVAYD-YLPLEEVISALNARPGHQTVIITGRGC  163 (196)
T ss_dssp             HHHHHHHHTTCTTCSEEEEETHHHHHHTT-SSCHHHHHHHHHTSCTTCEEEEECSSC
T ss_pred             HHHHHHHHHhcCCCCEEEEeCCCccccCC-CCCHHHHHHHHHhCcCCCEEEEECCCC
Confidence            4445555565444 49999998321   1 224566777777777889999999987

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=96.75  E-value=0.017  Score=55.91  Aligned_cols=20  Identities=40%  Similarity=0.634  Sum_probs=19.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|+|++|+||||||+.++.
T Consensus        47 vlL~Gp~GtGKTtLakala~   66 (274)
T 2x8a_A           47 VLLAGPPGCGKTLLAKAVAN   66 (274)
T ss_dssp             EEEESSTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            99999999999999999987

>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=96.73  E-value=0.014  Score=54.83  Aligned_cols=50  Identities=12%  Similarity=-0.065  Sum_probs=31.9

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhh-cCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSL-KSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l-~~~~~gs~IIvTtR~~  333 (597)
                      .+...|-.++-+|+||+--..-+......+...+ .....+..||++|.+.
T Consensus       140 ~lAral~~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~~tvi~vtH~~  190 (229)
T 2pze_A          140 SLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKM  190 (229)
T ss_dssp             HHHHHHHSCCSEEEEESTTTTSCHHHHHHHHHHCCCCCTTTSEEEEECCCH
T ss_pred             HHHHHHhcCCCEEEEECcccCCCHHHHHHHHHHHHHHhhCCCEEEEEcCCh
Confidence            4555566778899999975544455556666543 3333467788888764

>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=96.64  E-value=0.0034  Score=62.92  Aligned_cols=85  Identities=24%  Similarity=0.286  Sum_probs=52.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC---
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSV---  272 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~---  272 (597)
                      ...++.|.|++|+|||||+.+++..  ....-..++|++....++.                .     .++.++...   
T Consensus        60 ~G~i~~I~GppGsGKSTLal~la~~--~~~~gg~VlyId~E~s~~~----------------~-----ra~rlgv~~~~l  116 (356)
T 3hr8_A           60 RGRIVEIFGQESSGKTTLALHAIAE--AQKMGGVAAFIDAEHALDP----------------V-----YAKNLGVDLKSL  116 (356)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCH----------------H-----HHHHHTCCGGGC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEecccccch----------------H-----HHHHcCCchhhh
Confidence            4579999999999999999999873  3222234678876655543                1     122222211   


Q ss_pred             --CchhhHHHHHHHHHHHhc-CceEEEEEecccC
Q 041007          273 --SSQVEMETVLQYINEFVQ-GKKVLLVLDDLWW  303 (597)
Q Consensus       273 --~~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~~  303 (597)
                        ....+.++....+...++ .+.-++|+|.+..
T Consensus       117 ~i~~~~~~e~~l~~~~~l~~~~~~dlvVIDSi~~  150 (356)
T 3hr8_A          117 LISQPDHGEQALEIVDELVRSGVVDLIVVDSVAA  150 (356)
T ss_dssp             EEECCSSHHHHHHHHHHHHHTSCCSEEEEECTTT
T ss_pred             hhhhccCHHHHHHHHHHHhhhcCCCeEEehHhhh
Confidence              112334555555555444 4566899998743

>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=96.59  E-value=0.0059  Score=59.61  Aligned_cols=83  Identities=13%  Similarity=0.213  Sum_probs=51.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCChhhhcc--CCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC---
Q 041007          199 VIWILGNEGIGKTALARQVFDDSDVKAN--FDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS---  273 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~~~~~~~--F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~---  273 (597)
                      ++.|.|++|+|||||+.+++..  ....  =..++|++....++.                .     .++.++....   
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~--~~~~g~g~~vlyId~E~s~~~----------------~-----ra~~lGvd~d~ll   86 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSS--YMRQYPDAVCLFYDSEFGITP----------------A-----YLRSMGVDPERVI   86 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHH--HHHHCTTCEEEEEESSCCCCH----------------H-----HHHHTTCCGGGEE
T ss_pred             eEEEECCCCCCHHHHHHHHHHH--HHhcCCCceEEEEeccchhhH----------------H-----HHHHhCCCHHHeE
Confidence            7899999999999999998774  3332  245789987766654                1     1344443321   


Q ss_pred             --chhhHHHH-HHHHHHH--h-cCceEEEEEecccCC
Q 041007          274 --SQVEMETV-LQYINEF--V-QGKKVLLVLDDLWWN  304 (597)
Q Consensus       274 --~~~~~~~~-~~~l~~~--L-~~kr~LLVLDdv~~~  304 (597)
                        .+.+.+++ ...+...  + .++.-|||+|-+...
T Consensus        87 v~~~~~~E~~~l~i~~~l~~i~~~~~~lvVIDSI~aL  123 (333)
T 3io5_A           87 HTPVQSLEQLRIDMVNQLDAIERGEKVVVFIDSLGNL  123 (333)
T ss_dssp             EEECSBHHHHHHHHHHHHHTCCTTCCEEEEEECSTTC
T ss_pred             EEcCCCHHHHHHHHHHHHHHhhccCceEEEEeccccc
Confidence              12234444 3333222  2 356889999998544

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=96.49  E-value=0.011  Score=56.35  Aligned_cols=137  Identities=15%  Similarity=0.137  Sum_probs=68.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hcc---CCeeEEEEecCCCchhhhhhhhhhhcc----------cchHHHHHH
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KAN---FDKRIWVSASYPRDEIRVARDEISVAR----------DRDEIRVAK  262 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~---F~~~~wv~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~  262 (597)
                      ..+++|.|+.|+|||||.+.++.-..- .+.   ...+.++.-.............+....          .........
T Consensus        31 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~I~~~~~i~~v~q~~~~~~~~tv~enl~~~~~~~~~~~~~~~~~~~~~~~  110 (253)
T 2nq2_C           31 GDILAVLGQNGCGKSTLLDLLLGIHRPIQGKIEVYQSIGFVPQFFSSPFAYSVLDIVLMGRSTHINTFAKPKSHDYQVAM  110 (253)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHTTSSCCSEEEEEECSCEEEECSCCCCSSCCBHHHHHHGGGGGGSCTTCCCCHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCCCcEEEEeccEEEEcCCCccCCCCCHHHHHHHhhhhhcccccCCCHHHHHHHH
Confidence            458999999999999999999863111 111   112333321111110011111111100          111133455


Q ss_pred             HHHHhccCCC---Cc---hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          263 AILESLKGSV---SS---QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       263 ~il~~l~~~~---~~---~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .+++.++...   ..   ...-+.-.-.|...|..++-+|+||+--..-+...-..+...+...  ..|..||++|.+.
T Consensus       111 ~~l~~~~l~~~~~~~~~~LSgGq~qrv~lAraL~~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~~g~tvi~vtHd~  189 (253)
T 2nq2_C          111 QALDYLNLTHLAKREFTSLSGGQRQLILIARAIASECKLILLDEPTSALDLANQDIVLSLLIDLAQSQNMTVVFTTHQP  189 (253)
T ss_dssp             HHHHHTTCGGGTTSBGGGSCHHHHHHHHHHHHHHTTCSEEEESSSSTTSCHHHHHHHHHHHHHHHHTSCCEEEEEESCH
T ss_pred             HHHHHcCChHHhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEecCH
Confidence            6677665421   11   1112222334555666778899999975443344555555555432  2266788887654

>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=96.48  E-value=0.015  Score=55.23  Aligned_cols=51  Identities=10%  Similarity=0.060  Sum_probs=31.4

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      -.|...|-.++-+|+||+--..-+......+...+.....|..||++|.+.
T Consensus       154 v~iAraL~~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~g~tviivtH~~  204 (247)
T 2ff7_A          154 IAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRL  204 (247)
T ss_dssp             HHHHHHHTTCCSEEEECCCCSCCCHHHHHHHHHHHHHHHTTSEEEEECSSG
T ss_pred             HHHHHHHhcCCCEEEEeCCcccCCHHHHHHHHHHHHHHcCCCEEEEEeCCH
Confidence            345556667788999999755443444444544443322467788888765

>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=96.45  E-value=0.0086  Score=58.18  Aligned_cols=131  Identities=17%  Similarity=0.164  Sum_probs=64.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhcc----------CCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHH
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKAN----------FDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAIL  265 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----------F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il  265 (597)
                      ...++.|.|++|+|||||+..++..  ....          -..+++++..............+..  ..+ ......++
T Consensus        29 ~G~i~~i~G~~GsGKTtl~~~l~~~--~~~g~~~~g~~~~~~~~v~~~~~e~~~~~~~~r~~~~g~--~~~-~~~~~~~~  103 (279)
T 1nlf_A           29 AGTVGALVSPGGAGKSMLALQLAAQ--IAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGA--HLS-AEERQAVA  103 (279)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH--HHTCCCTTCCCCCCCCCEEEEESSSCHHHHHHHHHHHHT--TSC-HHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHH--HhcCCCcCCCccCCCccEEEEECCCCHHHHHHHHHHHHh--hcC-hhhhhhcc
Confidence            3579999999999999999998752  2221          1235666655443221111111110  000 11123334


Q ss_pred             HhccCCC-----CchhhHHHHHHHHHHHhcCceEEEEEecccC--CCCc---chHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          266 ESLKGSV-----SSQVEMETVLQYINEFVQGKKVLLVLDDLWW--NAYP---RYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       266 ~~l~~~~-----~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~--~~~~---~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      +.+....     ....+... ...+..... +.-+||||.+-.  ..+.   .....+...|...  ..|+.||+++...
T Consensus       104 ~~l~l~~~~~~~~~~ls~g~-~~~i~~l~~-~~~livlDe~~~~~~~d~~~~~~~~~~~~~L~~l~~~~g~tvi~i~H~~  181 (279)
T 1nlf_A          104 DGLLIQPLIGSLPNIMAPEW-FDGLKRAAE-GRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHAS  181 (279)
T ss_dssp             HHEEECCCTTSCCCTTSHHH-HHHHHHHHT-TCSEEEEECGGGGCCSCTTCHHHHHHHHHHHHHHHHHHCCEEEEEEEC-
T ss_pred             CceEEeecCCCCcccCCHHH-HHHHHHhcC-CCCEEEECCHHHhcCCCcCchHHHHHHHHHHHHHHHHcCCEEEEEecCC
Confidence            4443211     11111122 334444444 467999999865  2111   1224444444332  3477888887655

>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=96.44  E-value=0.013  Score=58.76  Aligned_cols=46  Identities=15%  Similarity=0.198  Sum_probs=33.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc----cCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA----NFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~----~F~~~~wv~~~~~~~~  241 (597)
                      ...++.|+|++|+|||+||.+++.......    .-..++|++....++.
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~~~~~  170 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRP  170 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCH
Confidence            457999999999999999999876311111    1246889988776554

>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=96.39  E-value=0.01  Score=59.00  Aligned_cols=46  Identities=20%  Similarity=0.211  Sum_probs=32.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhcc----CCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKAN----FDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~  241 (597)
                      ...++.|+|++|+|||+||.+++........    -..++|++....++.
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~~~~~  155 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEGTFRW  155 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSSCCCH
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCCCCCH
Confidence            4579999999999999999998763111110    246789988776544

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=96.37  E-value=0.021  Score=52.84  Aligned_cols=136  Identities=15%  Similarity=0.070  Sum_probs=67.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hc--cC---------CeeEEEEecCCCchhhhhhhhhhhc----c-cchHHH
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KA--NF---------DKRIWVSASYPRDEIRVARDEISVA----R-DRDEIR  259 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~--~F---------~~~~wv~~~~~~~~~~~~~~~~~~~----~-~~~~~~  259 (597)
                      ..+++|+|+.|+|||||.+.++.-... .+  .|         ..+.++.-.............+...    . ... ..
T Consensus        35 Ge~~~iiG~NGsGKSTLlk~l~Gl~~p~~G~I~~~g~~~~~~~~~i~~v~q~~~~~~~~tv~enl~~~~~~~~~~~~-~~  113 (214)
T 1sgw_A           35 GNVVNFHGPNGIGKTTLLKTISTYLKPLKGEIIYNGVPITKVKGKIFFLPEEIIVPRKISVEDYLKAVASLYGVKVN-KN  113 (214)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTSSCCSEEEEEETTEEGGGGGGGEEEECSSCCCCTTSBHHHHHHHHHHHTTCCCC-HH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCCeEEEECCEEhhhhcCcEEEEeCCCcCCCCCCHHHHHHHHHHhcCCchH-HH
Confidence            358999999999999999999763110 00  01         1122332111110000111111100    0 111 33


Q ss_pred             HHHHHHHhccCCCC--ch---hhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          260 VAKAILESLKGSVS--SQ---VEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       260 ~~~~il~~l~~~~~--~~---~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      ....+++.++....  ..   ..-+.-.-.+...|..++-+|+||+--..-+......+...+... ..|..||++|.+.
T Consensus       114 ~~~~~l~~~gl~~~~~~~~~LSgGqkqrv~laraL~~~p~lllLDEPts~LD~~~~~~l~~~l~~~~~~g~tiiivtHd~  193 (214)
T 1sgw_A          114 EIMDALESVEVLDLKKKLGELSQGTIRRVQLASTLLVNAEIYVLDDPVVAIDEDSKHKVLKSILEILKEKGIVIISSREE  193 (214)
T ss_dssp             HHHHHHHHTTCCCTTSBGGGSCHHHHHHHHHHHHTTSCCSEEEEESTTTTSCTTTHHHHHHHHHHHHHHHSEEEEEESSC
T ss_pred             HHHHHHHHcCCCcCCCChhhCCHHHHHHHHHHHHHHhCCCEEEEECCCcCCCHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            45566776654321  11   111222334556667788899999865443344555555444332 2356777777765

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.34  E-value=0.011  Score=55.97  Aligned_cols=41  Identities=22%  Similarity=0.241  Sum_probs=29.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ...++.|.|++|+|||||+.+++..  ....-..++|++....
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~--~~~~~~~v~~~~~e~~   62 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWN--GLKMGEPGIYVALEEH   62 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEESSSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HHhcCCeEEEEEccCC
Confidence            3469999999999999999888763  2222245777775543

>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=96.32  E-value=0.0084  Score=60.20  Aligned_cols=86  Identities=22%  Similarity=0.189  Sum_probs=52.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC--
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS--  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~--  273 (597)
                      ...++.|.|++|+||||||.+++..  ....=..++|++....++..                     ..+.++....  
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~--~~~~g~~vlyi~~E~~~~~~---------------------~a~~lG~~~~~l  116 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVAN--AQAAGGIAAFIDAEHALDPE---------------------YAKKLGVDTDSL  116 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHH---------------------HHHHTTCCGGGC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHhCCCeEEEEECCCCcCHH---------------------HHHHcCCCHHHe
Confidence            4579999999999999999999863  32222457888877655431                     1222222110  


Q ss_pred             ---chhhHHHHHHHHHHHhc-CceEEEEEecccCC
Q 041007          274 ---SQVEMETVLQYINEFVQ-GKKVLLVLDDLWWN  304 (597)
Q Consensus       274 ---~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~~~  304 (597)
                         ...+.++....+..... .+.-+||+|.+...
T Consensus       117 ~i~~~~~~e~~l~~~~~l~~~~~~~lIVIDsl~~l  151 (349)
T 2zr9_A          117 LVSQPDTGEQALEIADMLVRSGALDIIVIDSVAAL  151 (349)
T ss_dssp             EEECCSSHHHHHHHHHHHHTTTCCSEEEEECGGGC
T ss_pred             EEecCCCHHHHHHHHHHHHhcCCCCEEEEcChHhh
Confidence               11234455555554443 45679999998543

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=96.29  E-value=0.033  Score=52.59  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        32 Ge~~~l~G~nGsGKSTLl~~l~G   54 (240)
T 1ji0_A           32 GQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46999999999999999999975

>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=96.29  E-value=0.0091  Score=60.25  Aligned_cols=86  Identities=21%  Similarity=0.185  Sum_probs=53.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC---
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSV---  272 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~---  272 (597)
                      ...++.|.|++|+||||||.+++..  ....-..++|++....++...                     +..++...   
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~--~~~~g~~vlyi~~E~s~~~~~---------------------a~~~g~d~~~l  129 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQ--AQKAGGTCAFIDAEHALDPVY---------------------ARALGVNTDEL  129 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCHHH---------------------HHHTTCCGGGC
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHH--HHHCCCeEEEEECCCChhHHH---------------------HHHcCCCHHHc
Confidence            4568999999999999999998773  322224688998876655411                     22222211   


Q ss_pred             --CchhhHHHHHHHHHHHhc-CceEEEEEecccCC
Q 041007          273 --SSQVEMETVLQYINEFVQ-GKKVLLVLDDLWWN  304 (597)
Q Consensus       273 --~~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~~~  304 (597)
                        ....+.+++...+....+ ...-+||+|.+...
T Consensus       130 ~i~~~~~~e~~l~~l~~l~~~~~~~lVVIDsl~~l  164 (366)
T 1xp8_A          130 LVSQPDNGEQALEIMELLVRSGAIDVVVVDSVAAL  164 (366)
T ss_dssp             EEECCSSHHHHHHHHHHHHTTTCCSEEEEECTTTC
T ss_pred             eeecCCcHHHHHHHHHHHHhcCCCCEEEEeChHHh
Confidence              012244555666665554 34569999998543

>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=96.25  E-value=0.0098  Score=59.12  Aligned_cols=46  Identities=17%  Similarity=0.133  Sum_probs=32.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc---------cC-----CeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA---------NF-----DKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~---------~F-----~~~~wv~~~~~~~~  241 (597)
                      ...++.|.|++|+|||+||.+++.......         ..     ..++|++....++.
T Consensus        97 ~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~  156 (322)
T 2i1q_A           97 SQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRP  156 (322)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCCCCCH
Confidence            457999999999999999999875311111         11     36788888776544

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=96.25  E-value=0.019  Score=55.00  Aligned_cols=131  Identities=15%  Similarity=0.113  Sum_probs=65.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE----------------ecCCCchhhhhhhhhhhccc--chHH
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS----------------ASYPRDEIRVARDEISVARD--RDEI  258 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~----------------~~~~~~~~~~~~~~~~~~~~--~~~~  258 (597)
                      ..+++|.|+.|+|||||.+.++.-  .  ...+.+++.                +.+...........+.....  ....
T Consensus        30 Ge~~~i~G~NGsGKSTLlk~l~Gl--~--p~~G~I~~~g~~~~~~~~~~~i~~~v~Q~~~l~~tv~enl~~~~~~~~~~~  105 (263)
T 2pjz_A           30 GEKVIILGPNGSGKTTLLRAISGL--L--PYSGNIFINGMEVRKIRNYIRYSTNLPEAYEIGVTVNDIVYLYEELKGLDR  105 (263)
T ss_dssp             SSEEEEECCTTSSHHHHHHHHTTS--S--CCEEEEEETTEEGGGCSCCTTEEECCGGGSCTTSBHHHHHHHHHHHTCCCH
T ss_pred             CEEEEEECCCCCCHHHHHHHHhCC--C--CCCcEEEECCEECcchHHhhheEEEeCCCCccCCcHHHHHHHhhhhcchHH
Confidence            358999999999999999999863  1  222333321                11111100000111100000  0012


Q ss_pred             HHHHHHHHhccCC-CC---c---hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEcc
Q 041007          259 RVAKAILESLKGS-VS---S---QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRS  331 (597)
Q Consensus       259 ~~~~~il~~l~~~-~~---~---~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR  331 (597)
                      ....++++.++.. ..   .   ...-+.-.-.+...|..++-+|+||+--..-+...-..+...+.....  .||++|.
T Consensus       106 ~~~~~~l~~~gl~~~~~~~~~~~LSgGqkqRv~lAraL~~~p~lllLDEPts~LD~~~~~~l~~~L~~~~~--tviivtH  183 (263)
T 2pjz_A          106 DLFLEMLKALKLGEEILRRKLYKLSAGQSVLVRTSLALASQPEIVGLDEPFENVDAARRHVISRYIKEYGK--EGILVTH  183 (263)
T ss_dssp             HHHHHHHHHTTCCGGGGGSBGGGSCHHHHHHHHHHHHHHTCCSEEEEECTTTTCCHHHHHHHHHHHHHSCS--EEEEEES
T ss_pred             HHHHHHHHHcCCChhHhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEECCccccCHHHHHHHHHHHHHhcC--cEEEEEc
Confidence            3345566666543 11   1   111122233455566677889999997544435555556555554333  6777776


Q ss_pred             CC
Q 041007          332 GG  333 (597)
Q Consensus       332 ~~  333 (597)
                      +.
T Consensus       184 d~  185 (263)
T 2pjz_A          184 EL  185 (263)
T ss_dssp             CG
T ss_pred             CH
Confidence            54

>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=96.24  E-value=0.036  Score=53.25  Aligned_cols=23  Identities=30%  Similarity=0.478  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||++.+..
T Consensus        37 Ge~~~liG~nGsGKSTLl~~l~G   59 (266)
T 4g1u_C           37 GEMVAIIGPNGAGKSTLLRLLTG   59 (266)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            46999999999999999999976

>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=96.23  E-value=0.018  Score=54.66  Aligned_cols=23  Identities=22%  Similarity=0.247  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~G   50 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLER   50 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            46999999999999999999975

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=96.22  E-value=0.083  Score=52.75  Aligned_cols=163  Identities=10%  Similarity=-0.042  Sum_probs=96.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQ  275 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~  275 (597)
                      -.++..++|+.|.||++.+..+.+.. ....|+....+......+                                   
T Consensus        17 ~~~~yl~~G~e~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~~-----------------------------------   60 (343)
T 1jr3_D           17 LRAAYLLLGNDPLLLQESQDAVRQVA-AAQGFEEHHTFSIDPNTD-----------------------------------   60 (343)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHH-HHHTCCEEEEEECCTTCC-----------------------------------
T ss_pred             CCcEEEEECCcHHHHHHHHHHHHHHH-HhCCCCeeEEEEecCCCC-----------------------------------
Confidence            35799999999999999999987731 122343221122221111                                   


Q ss_pred             hhHHHHHHHHHH-HhcCceEEEEEecccC-CCCcchHHHHHHhhcCCCCCcEEEEEccCCCC-C-CCcccccccccCccc
Q 041007          276 VEMETVLQYINE-FVQGKKVLLVLDDLWW-NAYPRYWEQLMYSLKSGSEGSRILVTRSGGKN-G-TNMTEIGLGEKNGTN  351 (597)
Q Consensus       276 ~~~~~~~~~l~~-~L~~kr~LLVLDdv~~-~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~-~-~~~~~~~~~~~~~~~  351 (597)
                        ..++.+.+.. -+-+++-++|+|+++. .. ...++.+...+...++++.+|+++..... . ......     .+..
T Consensus        61 --~~~l~~~~~~~plf~~~kvvii~~~~~kl~-~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~-----~i~s  132 (343)
T 1jr3_D           61 --WNAIFSLCQAMSLFASRQTLLLLLPENGPN-AAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFT-----ALAN  132 (343)
T ss_dssp             --HHHHHHHHHHHHHCCSCEEEEEECCSSCCC-TTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHH-----HHTT
T ss_pred             --HHHHHHHhcCcCCccCCeEEEEECCCCCCC-hHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHH-----HHHh
Confidence              1222222221 1335677889999976 43 45778888888766677777776643200 0 000000     0111


Q ss_pred             cc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHHHHHH
Q 041007          352 MM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAVKIL  406 (597)
Q Consensus       352 ~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai~~~  406 (597)
                      .+ .++..+++.++....+...+...+..    -..+.+..|++.++|.+..+...
T Consensus       133 r~~~~~~~~l~~~~l~~~l~~~~~~~g~~----i~~~a~~~l~~~~~gdl~~~~~e  184 (343)
T 1jr3_D          133 RSVQVTCQTPEQAQLPRWVAARAKQLNLE----LDDAANQVLCYCYEGNLLALAQA  184 (343)
T ss_dssp             TCEEEEECCCCTTHHHHHHHHHHHHTTCE----ECHHHHHHHHHSSTTCHHHHHHH
T ss_pred             CceEEEeeCCCHHHHHHHHHHHHHHcCCC----CCHHHHHHHHHHhchHHHHHHHH
Confidence            11 28899999999998888776432211    12456788999999988877543

>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=96.21  E-value=0.0094  Score=58.43  Aligned_cols=39  Identities=21%  Similarity=0.163  Sum_probs=28.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCC-eeEEEEec
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFD-KRIWVSAS  236 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~-~~~wv~~~  236 (597)
                      ...+++|.|++|+|||||+..++..  ...... .++|++..
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~ia~~--~~~~~G~~v~~~~~e   73 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQQALQ--WGTAMGKKVGLAMLE   73 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHHH--HHHTSCCCEEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH--HHHHcCCeEEEEeCc
Confidence            3469999999999999999998873  222222 45666654

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=96.15  E-value=0.047  Score=52.61  Aligned_cols=50  Identities=14%  Similarity=0.030  Sum_probs=32.7

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCC--CCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGS--EGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~--~gs~IIvTtR~~  333 (597)
                      .|...|-.++-+|+||+--..-+...-..+...+....  .|..||++|.+.
T Consensus       166 ~lAraL~~~p~lllLDEPts~LD~~~~~~i~~~l~~~~~~~g~tviivtHd~  217 (271)
T 2ixe_A          166 ALARALIRKPRLLILDNATSALDAGNQLRVQRLLYESPEWASRTVLLITQQL  217 (271)
T ss_dssp             HHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHHCTTTTTSEEEEECSCH
T ss_pred             HHHHHHhcCCCEEEEECCccCCCHHHHHHHHHHHHHHHhhcCCEEEEEeCCH
Confidence            45566667788999999755444555555666665432  377788888764

>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=96.14  E-value=0.011  Score=59.49  Aligned_cols=44  Identities=25%  Similarity=0.259  Sum_probs=33.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ...++.|.|++|+||||||.+++..  ....-..++|++....++.
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~--~~~~g~~vlyid~E~s~~~  105 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDP  105 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEeCCCCccH
Confidence            4579999999999999999998873  3222236888988766554

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=96.14  E-value=0.026  Score=54.07  Aligned_cols=24  Identities=21%  Similarity=0.396  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|+.|+|||||++.++.-
T Consensus        46 Ge~~~i~G~nGsGKSTLl~~l~Gl   69 (260)
T 2ghi_A           46 GTTCALVGHTGSGKSTIAKLLYRF   69 (260)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcc
Confidence            469999999999999999999763

>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=96.12  E-value=0.042  Score=52.42  Aligned_cols=51  Identities=22%  Similarity=0.102  Sum_probs=31.2

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      -.|...|..++-+|+||+--..-+......+...+... ..|..||++|.+.
T Consensus       155 v~lAraL~~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~tiiivtHd~  206 (256)
T 1vpl_A          155 LLIARALMVNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTILVSSHNM  206 (256)
T ss_dssp             HHHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEEECCH
T ss_pred             HHHHHHHHcCCCEEEEeCCccccCHHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            34556667788899999865443344444444444321 2367788887764

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.10  E-value=0.0055  Score=56.32  Aligned_cols=43  Identities=21%  Similarity=0.105  Sum_probs=33.5

Q ss_pred             cchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       170 GR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+..++.|.+.+....       .....+|+|.|+.|+|||||++.+..
T Consensus         2 ~~~~~~~~l~~~~~~~~-------~~~~~~i~i~G~~GsGKstl~~~l~~   44 (201)
T 1rz3_A            2 ELRDRIDFLCKTILAIK-------TAGRLVLGIDGLSRSGKTTLANQLSQ   44 (201)
T ss_dssp             CHHHHHHHHHHHHHTSC-------CSSSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHhc-------cCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            35667778888776432       13467999999999999999999876

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.06  E-value=0.023  Score=51.29  Aligned_cols=23  Identities=22%  Similarity=0.069  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .++.|+|+.|+||||++..++++
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~   26 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEI   26 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHH
Confidence            58899999999999999777663

>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=96.06  E-value=0.041  Score=53.51  Aligned_cols=50  Identities=12%  Similarity=-0.065  Sum_probs=31.8

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhh-cCCCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSL-KSGSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l-~~~~~gs~IIvTtR~~  333 (597)
                      .|...|..++-+|+||+--..-+...-..+...+ .....|..||++|.+.
T Consensus       169 ~lAraL~~~p~lllLDEPts~LD~~~~~~i~~~ll~~~~~~~tviivtHd~  219 (290)
T 2bbs_A          169 SLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKM  219 (290)
T ss_dssp             HHHHHHHSCCSEEEEESTTTTCCHHHHHHHHHHCCCCCTTTSEEEEECCCH
T ss_pred             HHHHHHHCCCCEEEEECCcccCCHHHHHHHHHHHHHHhhCCCEEEEEecCH
Confidence            4555566778899999975544455555566543 2333467788888764

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=96.02  E-value=0.02  Score=58.37  Aligned_cols=45  Identities=13%  Similarity=0.160  Sum_probs=30.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh----hccCCeeEEEEecCCCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV----KANFDKRIWVSASYPRD  240 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~----~~~F~~~~wv~~~~~~~  240 (597)
                      ...++.|.|++|+|||||+..++-....    ...-..++|++....+.
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~~~~  225 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFR  225 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSSCCC
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCCccC
Confidence            4579999999999999999976521111    11234578887665443

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=96.01  E-value=0.059  Score=50.27  Aligned_cols=52  Identities=15%  Similarity=0.086  Sum_probs=32.1

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .-.+...|..++-+|+||+--..-+...-..+...+... ..|..||++|.+.
T Consensus       148 rv~laral~~~p~lllLDEPt~~LD~~~~~~~~~~l~~l~~~g~tvi~vtHd~  200 (224)
T 2pcj_A          148 RVAIARALANEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHER  200 (224)
T ss_dssp             HHHHHHHTTTCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             HHHHHHHHHcCCCEEEEeCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEcCCH
Confidence            334566677788899999865443344444455444332 2367888888764

>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=95.99  E-value=0.057  Score=51.72  Aligned_cols=50  Identities=14%  Similarity=0.149  Sum_probs=31.0

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~IIvTtR~~  333 (597)
                      .|...|..++-+|+||+--..-+...-..+...+... ..|..||++|.+.
T Consensus       169 ~lAraL~~~p~lllLDEPts~LD~~~~~~~~~~l~~l~~~g~tvi~vtHd~  219 (263)
T 2olj_A          169 AIARALAMEPKIMLFDEPTSALDPEMVGEVLSVMKQLANEGMTMVVVTHEM  219 (263)
T ss_dssp             HHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             HHHHHHHCCCCEEEEeCCcccCCHHHHHHHHHHHHHHHhCCCEEEEEcCCH
Confidence            4556667778899999965443344444444444331 2367888888764

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=95.97  E-value=0.056  Score=51.90  Aligned_cols=135  Identities=17%  Similarity=0.131  Sum_probs=67.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hc--cCC-----------eeEEEEecCCCc-h--hhhhhhhhhhc-----cc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KA--NFD-----------KRIWVSASYPRD-E--IRVARDEISVA-----RD  254 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~--~F~-----------~~~wv~~~~~~~-~--~~~~~~~~~~~-----~~  254 (597)
                      ..+++|+|+.|+|||||.+.++.-... .+  .++           .+.++.  +... .  .......+...     ..
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl~~p~~G~I~~~g~~~~~~~~~~~i~~v~--q~~~~~~~~~tv~enl~~~~~~~~~~  110 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGLIEPTSGDVLYDGERKKGYEIRRNIGIAF--QYPEDQFFAERVFDEVAFAVKNFYPD  110 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCSEEEEEETTEECCHHHHGGGEEEEC--SSGGGGCCCSSHHHHHHHTTTTTCTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCCCCCcEEEECCEECchHHhhhhEEEEe--ccchhhcCCCcHHHHHHHHHHhcCCH
Confidence            469999999999999999999763110 00  000           122222  2110 0  00111111110     01


Q ss_pred             chHHHHHHHHHHhccCC--C---Cc---hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC-CCCcE
Q 041007          255 RDEIRVAKAILESLKGS--V---SS---QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG-SEGSR  325 (597)
Q Consensus       255 ~~~~~~~~~il~~l~~~--~---~~---~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~-~~gs~  325 (597)
                      .........+++.++..  .   ..   ...-+.-.-.|...|..++-+|+||.--..-+...-..+...+... ..|..
T Consensus       111 ~~~~~~~~~~l~~~gl~~~~~~~~~~~~LSgGq~qRv~lAraL~~~p~lllLDEPts~LD~~~~~~l~~~l~~l~~~g~t  190 (266)
T 2yz2_A          111 RDPVPLVKKAMEFVGLDFDSFKDRVPFFLSGGEKRRVAIASVIVHEPDILILDEPLVGLDREGKTDLLRIVEKWKTLGKT  190 (266)
T ss_dssp             SCSHHHHHHHHHHTTCCHHHHTTCCGGGSCHHHHHHHHHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCE
T ss_pred             HHHHHHHHHHHHHcCcCCcccccCChhhCCHHHHHHHHHHHHHHcCCCEEEEcCccccCCHHHHHHHHHHHHHHHHcCCE
Confidence            11123345566665543  1   11   1111222334556667788899999975444344555555555432 23677


Q ss_pred             EEEEccCC
Q 041007          326 ILVTRSGG  333 (597)
Q Consensus       326 IIvTtR~~  333 (597)
                      ||++|.+.
T Consensus       191 ii~vtHd~  198 (266)
T 2yz2_A          191 VILISHDI  198 (266)
T ss_dssp             EEEECSCC
T ss_pred             EEEEeCCH
Confidence            88888775

>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=95.97  E-value=0.024  Score=56.93  Aligned_cols=43  Identities=23%  Similarity=0.398  Sum_probs=29.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhh---ccCC-eeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVK---ANFD-KRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~---~~F~-~~~wv~~~~~  238 (597)
                      ...++.|+|++|+|||||+..++......   +... .++|++....
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~~  176 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENT  176 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCCC
Confidence            45799999999999999999987631111   1112 3488876554

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=95.96  E-value=0.026  Score=53.34  Aligned_cols=133  Identities=15%  Similarity=0.031  Sum_probs=65.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE----------------ecCCCchh--hhhhhhhhhc-c---cc
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS----------------ASYPRDEI--RVARDEISVA-R---DR  255 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~----------------~~~~~~~~--~~~~~~~~~~-~---~~  255 (597)
                      .+++|.|+.|+|||||.+.++.-..   ...+.+++.                +.+.....  ......+... .   ..
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~~---p~~G~i~~~g~~~~~~~~~~~~i~~v~q~~~l~~~ltv~enl~~~~~~~~~~  101 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIVK---PDRGEVRLNGADITPLPPERRGIGFVPQDYALFPHLSVYRNIAYGLRNVERV  101 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSC---CSEEEEEETTEECTTSCTTTSCCBCCCSSCCCCTTSCHHHHHHTTCTTSCHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCCC---CCceEEEECCEECCcCchhhCcEEEEcCCCccCCCCcHHHHHHHHHHHcCCc
Confidence            7999999999999999999976311   111222221                01111000  0011111110 0   01


Q ss_pred             hHHHHHHHHHHhccCCCC---c---hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEE
Q 041007          256 DEIRVAKAILESLKGSVS---S---QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRIL  327 (597)
Q Consensus       256 ~~~~~~~~il~~l~~~~~---~---~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~II  327 (597)
                      .......++++.++....   .   ...-+.-.-.+...|..++-+|+||+--..-+...-..+...+...  ..|..||
T Consensus       102 ~~~~~~~~~l~~~~l~~~~~~~~~~LSgGqkqRv~lAral~~~p~lllLDEPts~LD~~~~~~~~~~l~~l~~~~g~tvi  181 (240)
T 2onk_A          102 ERDRRVREMAEKLGIAHLLDRKPARLSGGERQRVALARALVIQPRLLLLDEPLSAVDLKTKGVLMEELRFVQREFDVPIL  181 (240)
T ss_dssp             HHHHHHHHHHHTTTCTTTTTCCGGGSCHHHHHHHHHHHHHTTCCSSBEEESTTSSCCHHHHHHHHHHHHHHHHHHTCCEE
T ss_pred             hHHHHHHHHHHHcCCHHHhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhcCCEEE
Confidence            113344566676654321   1   1111222334566667788899999864443344444455544432  2256677


Q ss_pred             EEccCC
Q 041007          328 VTRSGG  333 (597)
Q Consensus       328 vTtR~~  333 (597)
                      ++|.+.
T Consensus       182 ~vtHd~  187 (240)
T 2onk_A          182 HVTHDL  187 (240)
T ss_dssp             EEESCH
T ss_pred             EEeCCH
Confidence            777654

>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=95.83  E-value=0.021  Score=55.85  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|++|+||||++..++.
T Consensus       104 ~g~vi~lvG~~GsGKTTl~~~LA~  127 (296)
T 2px0_A          104 HSKYIVLFGSTGAGKTTTLAKLAA  127 (296)
T ss_dssp             CSSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999876

>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=95.81  E-value=0.027  Score=55.24  Aligned_cols=24  Identities=25%  Similarity=0.502  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||++.+..
T Consensus        79 ~Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           79 PGQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             TTCEEEEESSSCHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCchHHHHHHHHHc
Confidence            346999999999999999999976

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.67  E-value=0.023  Score=56.18  Aligned_cols=41  Identities=20%  Similarity=0.117  Sum_probs=30.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ...++.|.|.+|+||||||.+++.+...++  ..++|++....
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~~g--~~vl~~slE~s  107 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSDND--DVVNLHSLEMG  107 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHTTT--CEEEEEESSSC
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHcC--CeEEEEECCCC
Confidence            356999999999999999999876422222  56788876543

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.65  E-value=0.0088  Score=55.25  Aligned_cols=24  Identities=21%  Similarity=0.354  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|+.|+|||||++.+..
T Consensus        21 ~g~~v~I~G~sGsGKSTl~~~l~~   44 (208)
T 3c8u_A           21 GRQLVALSGAPGSGKSTLSNPLAA   44 (208)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999877

>3ice_A Transcription termination factor RHO; transcription, ATPase, hexamer, helicase, RNA, RECA, OB fold ATP-binding, hydrolase; HET: MSE ADP SPD; 2.80A {Escherichia coli k-12} PDB: 1pv4_A 1pvo_A* 1xpo_A* 1xpr_A* 1xpu_A* 2ht1_A

Probab=95.61  E-value=0.01  Score=59.51  Aligned_cols=43  Identities=14%  Similarity=0.040  Sum_probs=29.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc-cCCe-eEEEEecCCCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA-NFDK-RIWVSASYPRD  240 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-~F~~-~~wv~~~~~~~  240 (597)
                      ....++|+|++|+|||||++.+.+.  +.. +-+. ++++-+.+...
T Consensus       173 rGQr~~IvG~sG~GKTtLl~~Iar~--i~~~~~~v~~I~~lIGER~~  217 (422)
T 3ice_A          173 RGQRGLIVAPPKAGKTMLLQNIAQS--IAYNHPDCVLMVLLIDERPE  217 (422)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHHHHH--HHHHCTTSEEEEEEESSCHH
T ss_pred             CCcEEEEecCCCCChhHHHHHHHHH--HhhcCCCeeEEEEEecCChH
Confidence            4569999999999999999998773  322 2222 34566665443

>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=95.61  E-value=0.0088  Score=60.57  Aligned_cols=53  Identities=21%  Similarity=0.297  Sum_probs=35.8

Q ss_pred             ccccchhhHHHHHHHhhCC----CCCC-cCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLKGE----SSDE-ESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~----~~~~-~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|.+..++.+...+...    .... ..........|.|+|++|+|||++|+.+++
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~   73 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLAR   73 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHH
Confidence            3689999888888877200    0000 000012356789999999999999999987

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=95.61  E-value=0.007  Score=63.72  Aligned_cols=42  Identities=21%  Similarity=0.240  Sum_probs=35.8

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .++|++..++.+...+..            ...|.|+|++|+|||+||+.+++.
T Consensus        23 ~ivGq~~~i~~l~~al~~------------~~~VLL~GpPGtGKT~LAraLa~~   64 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALS------------GESVFLLGPPGIAKSLIARRLKFA   64 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHH------------TCEEEEECCSSSSHHHHHHHGGGG
T ss_pred             hhHHHHHHHHHHHHHHhc------------CCeeEeecCchHHHHHHHHHHHHH
Confidence            478999999988887763            247899999999999999999883

>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=95.58  E-value=0.0066  Score=54.38  Aligned_cols=22  Identities=23%  Similarity=0.398  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|.|+|++|+||||+|+.+..
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~   25 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999977

>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=95.58  E-value=0.044  Score=51.03  Aligned_cols=42  Identities=24%  Similarity=0.337  Sum_probs=28.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh---hc-cCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV---KA-NFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~---~~-~F~~~~wv~~~~  237 (597)
                      ...+++|+|++|+|||||++.++.....   .. .-...+|+....
T Consensus        24 ~G~~~~l~G~nGsGKSTll~~l~g~~~~~~~~g~~~~~~i~~~~~~   69 (231)
T 4a74_A           24 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN   69 (231)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCEEEEEECCC
Confidence            4579999999999999999998642111   11 123477776544

>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=95.52  E-value=0.0068  Score=53.92  Aligned_cols=20  Identities=40%  Similarity=0.602  Sum_probs=18.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHH
Q 041007          198 PVIWILGNEGIGKTALARQV  217 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v  217 (597)
                      .+|+|.|++|+||||+|+.+
T Consensus         2 ~~I~l~G~~GsGKsT~a~~L   21 (179)
T 3lw7_A            2 KVILITGMPGSGKSEFAKLL   21 (179)
T ss_dssp             CEEEEECCTTSCHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHH
Confidence            47999999999999999999

>1sky_E F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alpha3BETA3 SUBC F1-ATPase, hydrolase; 3.20A {Bacillus SP} SCOP: a.69.1.1 b.49.1.1 c.37.1.11

Probab=95.51  E-value=0.062  Score=55.49  Aligned_cols=41  Identities=17%  Similarity=0.351  Sum_probs=28.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccC-CeeEEEEecCCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANF-DKRIWVSASYPR  239 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F-~~~~wv~~~~~~  239 (597)
                      ...++|+|++|+|||||+..+..+  ....+ ..++++.+....
T Consensus       151 Gq~~~i~G~sGvGKTtL~~~l~~~--~~~~~~~i~V~~~iGert  192 (473)
T 1sky_E          151 GGKIGLFGGAGVGKTVLIQELIHN--IAQEHGGISVFAGVGERT  192 (473)
T ss_dssp             TCEEEEECCSSSCHHHHHHHHHHH--HHHHTCCCEEEEEESSCH
T ss_pred             CCEEEEECCCCCCccHHHHHHHhh--hhhccCcEEEEeeeccCc
Confidence            357899999999999999999874  33222 345556555443

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.47  E-value=0.0085  Score=53.95  Aligned_cols=23  Identities=17%  Similarity=0.499  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|++|+|||||++.+..
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~   27 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLIT   27 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46999999999999999999876

>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=95.46  E-value=0.06  Score=53.93  Aligned_cols=52  Identities=17%  Similarity=0.052  Sum_probs=33.3

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .-.|...|..++-+|++|.--..-+...-..+...+...  ..|..||++|.+-
T Consensus       171 RVaIArAL~~~P~lLLlDEPTs~LD~~~~~~i~~lL~~l~~~~g~Tii~vTHdl  224 (366)
T 3tui_C          171 RVAIARALASNPKVLLCDQATSALDPATTRSILELLKDINRRLGLTILLITHEM  224 (366)
T ss_dssp             HHHHHHHTTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCH
T ss_pred             HHHHHHHHhcCCCEEEEECCCccCCHHHHHHHHHHHHHHHHhCCCEEEEEecCH
Confidence            445667778888999999975443344445555555432  3367788777764

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.44  E-value=0.034  Score=55.22  Aligned_cols=40  Identities=15%  Similarity=0.026  Sum_probs=29.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ...++.|.|.+|+||||||..++.+...  .=..++|++...
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~ia~~~a~--~g~~Vl~fSlEm   84 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMNMVLSALN--DDRGVAVFSLEM   84 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHH--TTCEEEEEESSS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHH--cCCeEEEEeCCC
Confidence            3469999999999999999999874222  223567776543

>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=95.43  E-value=0.0084  Score=54.38  Aligned_cols=25  Identities=20%  Similarity=0.356  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|.|++|+|||||++.+...
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3468999999999999999999873

>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=95.38  E-value=0.0081  Score=53.32  Aligned_cols=22  Identities=18%  Similarity=0.215  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|.|++|+||||+++.+..
T Consensus         2 ~~i~l~G~~GsGKsT~~~~L~~   23 (173)
T 3kb2_A            2 TLIILEGPDCCFKSTVAAKLSK   23 (173)
T ss_dssp             CEEEEECSSSSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>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=95.37  E-value=0.091  Score=53.28  Aligned_cols=24  Identities=25%  Similarity=0.378  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|.|+.|+|||||.+.++.
T Consensus        46 ~Ge~~~llGpsGsGKSTLLr~iaG   69 (390)
T 3gd7_A           46 PGQRVGLLGRTGSGKSTLLSAFLR   69 (390)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhC
Confidence            346999999999999999999976

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.30  E-value=0.0088  Score=53.55  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|.|.|++|+||||+|+.+..
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            5799999999999999999976

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=95.27  E-value=0.01  Score=54.41  Aligned_cols=23  Identities=30%  Similarity=0.501  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|+|++|+||||+++.+..
T Consensus        25 ~~~i~l~G~~GsGKsTl~~~La~   47 (199)
T 3vaa_A           25 MVRIFLTGYMGAGKTTLGKAFAR   47 (199)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999986

>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=95.25  E-value=0.11  Score=56.15  Aligned_cols=24  Identities=21%  Similarity=0.340  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||++.+..
T Consensus       368 ~G~~~~ivG~sGsGKSTll~~l~g  391 (582)
T 3b5x_A          368 QGKTVALVGRSGSGKSTIANLFTR  391 (582)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346999999999999999999875

>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=95.23  E-value=0.11  Score=51.76  Aligned_cols=133  Identities=16%  Similarity=0.042  Sum_probs=66.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE----------------ecCCCchhh--hhhhhhhh----ccc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS----------------ASYPRDEIR--VARDEISV----ARD  254 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~----------------~~~~~~~~~--~~~~~~~~----~~~  254 (597)
                      ..+++|.|+.|+|||||.+.++--..   ...+.+++.                +.+.+....  .....+..    ...
T Consensus        26 Ge~~~llGpnGsGKSTLLr~iaGl~~---p~~G~I~~~g~~i~~~~~~~r~ig~v~Q~~~l~~~ltv~enl~~~~~~~~~  102 (348)
T 3d31_A           26 GEYFVILGPTGAGKTLFLELIAGFHV---PDSGRILLDGKDVTDLSPEKHDIAFVYQNYSLFPHMNVKKNLEFGMRMKKI  102 (348)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSSC---CSEEEEEETTEECTTSCHHHHTCEEECTTCCCCTTSCHHHHHHHHHHHHCC
T ss_pred             CCEEEEECCCCccHHHHHHHHHcCCC---CCCcEEEECCEECCCCchhhCcEEEEecCcccCCCCCHHHHHHHHHHHcCC
Confidence            46999999999999999999976311   111222221                111111100  00000000    000


Q ss_pred             chHHHHHHHHHHhccCCCC-----c-hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEE
Q 041007          255 RDEIRVAKAILESLKGSVS-----S-QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRI  326 (597)
Q Consensus       255 ~~~~~~~~~il~~l~~~~~-----~-~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~I  326 (597)
                      .. .....++++.++....     . ...-+.-.-.|...|-.++-+|+||+--..-+...-..+...+...  ..|..|
T Consensus       103 ~~-~~~v~~~l~~~~L~~~~~~~~~~LSgGq~QRvalAraL~~~P~lLLLDEP~s~LD~~~~~~l~~~l~~l~~~~g~ti  181 (348)
T 3d31_A          103 KD-PKRVLDTARDLKIEHLLDRNPLTLSGGEQQRVALARALVTNPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTV  181 (348)
T ss_dssp             CC-HHHHHHHHHHTTCTTTTTSCGGGSCHHHHHHHHHHHHTTSCCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEE
T ss_pred             CH-HHHHHHHHHHcCCchHhcCChhhCCHHHHHHHHHHHHHHcCCCEEEEECccccCCHHHHHHHHHHHHHHHHhcCCEE
Confidence            01 1344556666654321     1 1112233335666777788899999864433344444444444332  236677


Q ss_pred             EEEccCC
Q 041007          327 LVTRSGG  333 (597)
Q Consensus       327 IvTtR~~  333 (597)
                      |++|.+.
T Consensus       182 i~vTHd~  188 (348)
T 3d31_A          182 LHITHDQ  188 (348)
T ss_dssp             EEEESCH
T ss_pred             EEEeCCH
Confidence            7777654

>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=95.22  E-value=0.011  Score=54.59  Aligned_cols=25  Identities=32%  Similarity=0.519  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|+|+|+.|+|||||++.+...
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~   31 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKD   31 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHS
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhh
Confidence            3579999999999999999999763

>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=95.21  E-value=0.27  Score=50.55  Aligned_cols=24  Identities=21%  Similarity=0.411  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.+|.++|++|+||||++..++.
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~  122 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLAR  122 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHH
Confidence            468999999999999999988876

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.19  E-value=0.017  Score=56.97  Aligned_cols=46  Identities=17%  Similarity=0.205  Sum_probs=32.2

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|-...+..+...+.....      ...+.+|+|.|+.|+|||||++.+..
T Consensus        69 ~~~~~~~l~~~~~~~l~~~~------~~~p~iigI~GpsGSGKSTl~~~L~~  114 (321)
T 3tqc_A           69 YVTARQTLQQATYQFLGKPE------PKVPYIIGIAGSVAVGKSTTSRVLKA  114 (321)
T ss_dssp             HHHHHHHHHHHHHHHHTCCC------CCCCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             hhcchHHHHHHHHHHhccCC------CCCCEEEEEECCCCCCHHHHHHHHHH
Confidence            34555555555555543322      23567999999999999999998865

>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=95.14  E-value=0.012  Score=53.99  Aligned_cols=25  Identities=36%  Similarity=0.496  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|+|.|++|+|||||++.+...
T Consensus        24 ~g~~i~l~G~sGsGKSTl~~~La~~   48 (200)
T 3uie_A           24 KGCVIWVTGLSGSGKSTLACALNQM   48 (200)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999999873

>1vma_A Cell division protein FTSY; TM0570, structural genomics, JCS protein structure initiative, PSI, joint center for structu genomics; HET: CIT; 1.60A {Thermotoga maritima} SCOP: a.24.13.1 c.37.1.10

Probab=95.14  E-value=0.09  Score=51.50  Aligned_cols=38  Identities=21%  Similarity=0.211  Sum_probs=27.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEe
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSA  235 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~  235 (597)
                      ...+|+|+|++|+||||++..++..  ....-..+.++..
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~--l~~~g~kV~lv~~  140 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKM--FVDEGKSVVLAAA  140 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHH--HHHTTCCEEEEEE
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHH--HHhcCCEEEEEcc
Confidence            4579999999999999999998873  3322223445543

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=95.12  E-value=0.0096  Score=52.98  Aligned_cols=22  Identities=32%  Similarity=0.631  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|+|++|+|||||++.+..
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~   26 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQ   26 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999976

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=95.09  E-value=0.081  Score=53.09  Aligned_cols=23  Identities=26%  Similarity=0.369  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.++-
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (362)
T 2it1_A           29 GEFMALLGPSGSGKSTLLYTIAG   51 (362)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            46999999999999999999975

>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=95.07  E-value=0.014  Score=52.07  Aligned_cols=24  Identities=29%  Similarity=0.455  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|++|+||||+++.+..
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~   30 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAH   30 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            356899999999999999999876

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.06  E-value=0.013  Score=53.78  Aligned_cols=24  Identities=33%  Similarity=0.490  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|+.|+|||||++.+..
T Consensus        28 ~g~~i~l~G~~GsGKSTl~~~L~~   51 (200)
T 4eun_A           28 PTRHVVVMGVSGSGKTTIAHGVAD   51 (200)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999976

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=95.05  E-value=0.012  Score=52.97  Aligned_cols=23  Identities=35%  Similarity=0.598  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.|.|+|++|+||||+|+.+..
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~   27 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAK   27 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>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=95.03  E-value=0.0087  Score=60.09  Aligned_cols=44  Identities=18%  Similarity=0.300  Sum_probs=32.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.+..++.+...+...          ...-|.|+|++|+|||+||+.+++
T Consensus        24 ~~i~G~~~~~~~l~~~~~~~----------~~~~vLl~G~~GtGKT~la~~la~   67 (350)
T 1g8p_A           24 SAIVGQEDMKLALLLTAVDP----------GIGGVLVFGDRGTGKSTAVRALAA   67 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHCG----------GGCCEEEECCGGGCTTHHHHHHHH
T ss_pred             hhccChHHHHHHHHHHhhCC----------CCceEEEECCCCccHHHHHHHHHH
Confidence            45899988666654444321          123489999999999999999987

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.03  E-value=0.014  Score=53.60  Aligned_cols=23  Identities=30%  Similarity=0.447  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||++.+..
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~   29 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVK   29 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECcCCCCHHHHHHHHHh
Confidence            46899999999999999999876

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.03  E-value=0.019  Score=55.88  Aligned_cols=24  Identities=29%  Similarity=0.541  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.+|.|.|++|+||||+|+.+..
T Consensus        32 ~~~livl~G~sGsGKSTla~~L~~   55 (287)
T 1gvn_B           32 SPTAFLLGGQPGSGKTSLRSAIFE   55 (287)
T ss_dssp             SCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467899999999999999999976

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=95.00  E-value=0.09  Score=52.54  Aligned_cols=23  Identities=30%  Similarity=0.462  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.++-
T Consensus        41 Ge~~~llGpnGsGKSTLLr~iaG   63 (355)
T 1z47_A           41 GEMVGLLGPSGSGKTTILRLIAG   63 (355)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46999999999999999999975

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=94.99  E-value=0.013  Score=53.73  Aligned_cols=23  Identities=22%  Similarity=0.439  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|++|+||||+|+.+..
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~   40 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAE   40 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>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=94.99  E-value=0.11  Score=55.90  Aligned_cols=25  Identities=20%  Similarity=0.308  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|+|+.|+|||||++.+..-
T Consensus       368 ~G~~~~ivG~sGsGKSTLl~~l~g~  392 (582)
T 3b60_A          368 AGKTVALVGRSGSGKSTIASLITRF  392 (582)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhhc
Confidence            3468999999999999999999763

>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=94.97  E-value=0.013  Score=53.03  Aligned_cols=24  Identities=29%  Similarity=0.450  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|.|.|++|+||||+++.+..
T Consensus         4 ~~~~I~l~G~~GsGKST~~~~L~~   27 (193)
T 2rhm_A            4 TPALIIVTGHPATGKTTLSQALAT   27 (193)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999999976

>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=94.95  E-value=0.015  Score=52.16  Aligned_cols=24  Identities=38%  Similarity=0.708  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.|+|++|+||||+++.+..
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l~~   33 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKELAS   33 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHH
Confidence            346899999999999999999976

>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=94.92  E-value=0.012  Score=53.20  Aligned_cols=22  Identities=36%  Similarity=0.605  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      |.|+|+||+|+|||||++.+..
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~   23 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            4588999999999999999875

>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=94.92  E-value=0.017  Score=52.10  Aligned_cols=24  Identities=33%  Similarity=0.390  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....|+|+|++|+||||+++.+..
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~   32 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAA   32 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999876

>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=94.92  E-value=0.016  Score=52.74  Aligned_cols=24  Identities=13%  Similarity=0.486  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|+|+|+.|+|||||++.+..
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~   41 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLS   41 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHh
Confidence            457999999999999999999875

>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=94.91  E-value=0.074  Score=53.64  Aligned_cols=23  Identities=26%  Similarity=0.424  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.+.-
T Consensus        29 Ge~~~llGpsGsGKSTLLr~iaG   51 (381)
T 3rlf_A           29 GEFVVFVGPSGCGKSTLLRMIAG   51 (381)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHHc
Confidence            46999999999999999999976

>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=94.91  E-value=0.11  Score=52.01  Aligned_cols=23  Identities=35%  Similarity=0.595  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.++-
T Consensus        30 Ge~~~llGpsGsGKSTLLr~iaG   52 (359)
T 3fvq_A           30 GEILFIIGASGCGKTTLLRCLAG   52 (359)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCchHHHHHHHHhc
Confidence            46999999999999999999976

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=94.90  E-value=0.013  Score=53.79  Aligned_cols=24  Identities=29%  Similarity=0.672  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|++|+|||||++.+..
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~   34 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLS   34 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999976

>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=94.90  E-value=0.15  Score=50.38  Aligned_cols=24  Identities=29%  Similarity=0.369  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+||||++..++.
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag  151 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLAN  151 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            568999999999999999999887

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=94.89  E-value=0.012  Score=52.38  Aligned_cols=24  Identities=29%  Similarity=0.704  Sum_probs=20.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||++.++.
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~~~~   31 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKKHFK   31 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHSC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHcc
Confidence            346999999999999999998664

>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=94.87  E-value=0.13  Score=51.41  Aligned_cols=75  Identities=15%  Similarity=0.094  Sum_probs=40.6

Q ss_pred             HHHHHHHHhccCCC-----Cc-hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEc
Q 041007          259 RVAKAILESLKGSV-----SS-QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTR  330 (597)
Q Consensus       259 ~~~~~il~~l~~~~-----~~-~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTt  330 (597)
                      ....++++.++...     .. ...-+.-.-.|...|..++-+|+||+--..-+...-..+...+...  ..|..||++|
T Consensus       119 ~~v~~~l~~~~L~~~~~~~~~~LSGGq~QRvalAraL~~~P~lLLLDEP~s~LD~~~r~~l~~~l~~l~~~~g~tvi~vT  198 (353)
T 1oxx_K          119 KRVEEVAKILDIHHVLNHFPRELSGAQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVS  198 (353)
T ss_dssp             HHHHHHHHHTTCGGGTTSCGGGSCHHHHHHHHHHHHHTTCCSEEEEESTTTTSCGGGHHHHHHHHHHHHHHHCCEEEEEE
T ss_pred             HHHHHHHHHcCCchHhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEECCcccCCHHHHHHHHHHHHHHHHhcCCEEEEEe
Confidence            34556666665421     11 1112223335666777788899999864433344445555544332  2256777777


Q ss_pred             cCC
Q 041007          331 SGG  333 (597)
Q Consensus       331 R~~  333 (597)
                      .+.
T Consensus       199 Hd~  201 (353)
T 1oxx_K          199 HDP  201 (353)
T ss_dssp             SCH
T ss_pred             CCH
Confidence            654

>3jvv_A Twitching mobility protein; hexameric P-loop ATPase, secretion ATPase, ATP-binding, FIMB nucleotide-binding, transport; HET: ACP CIT; 2.60A {Pseudomonas aeruginosa} PDB: 3jvu_A*

Probab=94.87  E-value=0.032  Score=56.06  Aligned_cols=108  Identities=8%  Similarity=0.122  Sum_probs=57.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhh
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVE  277 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~  277 (597)
                      .+++|+|+.|+|||||.+.+..  .........+ +.+.++.....  .....             ++.+.... ...  
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g--~~~~~~~~~i-~t~ed~~e~~~--~~~~~-------------~v~q~~~~-~~~--  182 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLD--YLNNTKYHHI-LTIEDPIEFVH--ESKKC-------------LVNQREVH-RDT--  182 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHH--HHHHHCCCEE-EEEESSCCSCC--CCSSS-------------EEEEEEBT-TTB--
T ss_pred             CEEEEECCCCCCHHHHHHHHHh--cccCCCCcEE-EEccCcHHhhh--hcccc-------------ceeeeeec-ccc--
Confidence            5999999999999999999876  2322222222 22222211100  00000             00000000 000  


Q ss_pred             HHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          278 METVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       278 ~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                       ......+...|...+=+|++|+..+   ...++.+....   ..|..||+|+...
T Consensus       183 -~~~~~~La~aL~~~PdvillDEp~d---~e~~~~~~~~~---~~G~~vl~t~H~~  231 (356)
T 3jvv_A          183 -LGFSEALRSALREDPDIILVGEMRD---LETIRLALTAA---ETGHLVFGTLHTT  231 (356)
T ss_dssp             -SCHHHHHHHHTTSCCSEEEESCCCS---HHHHHHHHHHH---HTTCEEEEEESCS
T ss_pred             -CCHHHHHHHHhhhCcCEEecCCCCC---HHHHHHHHHHH---hcCCEEEEEEccC
Confidence             1233477888888899999999952   33455444432   2366788888765

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.82  E-value=0.017  Score=53.04  Aligned_cols=23  Identities=26%  Similarity=0.585  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|+|++|+|||||++.+..
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~   28 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFE   28 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999876

>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=94.82  E-value=0.028  Score=54.80  Aligned_cols=26  Identities=23%  Similarity=0.424  Sum_probs=22.7

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.+|+|.|+.|+||||||+.+...
T Consensus        29 ~~~~ii~I~G~sGsGKSTla~~L~~~   54 (290)
T 1odf_A           29 KCPLFIFFSGPQGSGKSFTSIQIYNH   54 (290)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHH
Confidence            35679999999999999999988773

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=94.79  E-value=0.016  Score=52.42  Aligned_cols=22  Identities=27%  Similarity=0.513  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|.|++|+||||+++.+..
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~   25 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMD   25 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999987

>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=94.77  E-value=0.019  Score=52.77  Aligned_cols=24  Identities=33%  Similarity=0.353  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|++|+|||||++.+..
T Consensus        20 ~~~~i~i~G~~GsGKSTl~~~L~~   43 (207)
T 2qt1_A           20 KTFIIGISGVTNSGKTTLAKNLQK   43 (207)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999987

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.75  E-value=0.016  Score=53.52  Aligned_cols=24  Identities=38%  Similarity=0.357  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|+.|+|||||++.+..
T Consensus         5 ~~~~i~i~G~~GsGKSTl~~~l~~   28 (211)
T 3asz_A            5 KPFVIGIAGGTASGKTTLAQALAR   28 (211)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999876

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.72  E-value=0.014  Score=53.44  Aligned_cols=23  Identities=26%  Similarity=0.530  Sum_probs=20.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.++|+|+.|+|||||++.+..
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~   26 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQ   26 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            36899999999999999999876

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=94.72  E-value=0.33  Score=49.86  Aligned_cols=25  Identities=28%  Similarity=0.280  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.+|.++|++|+||||++..++..
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~  120 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYF  120 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999998863

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=94.71  E-value=0.015  Score=52.59  Aligned_cols=22  Identities=23%  Similarity=0.413  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|.|++|+||||+++.+..
T Consensus         2 ~~I~i~G~~GsGKsT~~~~L~~   23 (194)
T 1nks_A            2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            4789999999999999999987

>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=94.70  E-value=0.066  Score=55.92  Aligned_cols=23  Identities=26%  Similarity=0.432  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.+.|.|++|+|||+++..+...
T Consensus        46 ~~~li~G~aGTGKT~ll~~~~~~   68 (459)
T 3upu_A           46 HHVTINGPAGTGATTLTKFIIEA   68 (459)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHH
Confidence            38999999999999999998874

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=94.69  E-value=0.019  Score=52.56  Aligned_cols=24  Identities=29%  Similarity=0.627  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|++|+||||+++.+..
T Consensus        14 ~~~~I~l~G~~GsGKsT~~~~L~~   37 (203)
T 1ukz_A           14 QVSVIFVLGGPGAGKGTQCEKLVK   37 (203)
T ss_dssp             TCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999976

>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=94.65  E-value=0.079  Score=56.88  Aligned_cols=22  Identities=27%  Similarity=0.530  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +++.|+|++|+||||++..+..
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~  226 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVAD  226 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            6899999999999999999876

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=94.64  E-value=0.049  Score=65.92  Aligned_cols=84  Identities=23%  Similarity=0.250  Sum_probs=52.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC---
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSV---  272 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~---  272 (597)
                      ..+.|.|+|++|+|||+||.++...  ....=..++|+++...++.+.                     ++.++.+.   
T Consensus      1426 ~g~~vll~GppGtGKT~LA~ala~e--a~~~G~~v~Fi~~e~~~~~l~---------------------a~~~G~dl~~l 1482 (2050)
T 3cmu_A         1426 MGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY---------------------ARKLGVDIDNL 1482 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH--HHTTTCCEEEECTTSCCCHHH---------------------HHHTTCCTTTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH--HHHcCCcEEEEEcccccCHHH---------------------HHHcCCCchhc
Confidence            5679999999999999999999873  333323567787776655421                     22333111   


Q ss_pred             --CchhhHHHHHHHHHHHhc-CceEEEEEeccc
Q 041007          273 --SSQVEMETVLQYINEFVQ-GKKVLLVLDDLW  302 (597)
Q Consensus       273 --~~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~  302 (597)
                        ....+.++....+....+ .+.-+||+|.+.
T Consensus      1483 ~v~~~~~~E~~l~~~~~lvr~~~~~lVVIDsi~ 1515 (2050)
T 3cmu_A         1483 LCSQPDTGEQALEICDALARSGAVDVIVVDSVA 1515 (2050)
T ss_dssp             EEECCSSHHHHHHHHHHHHHHTCCSEEEESCGG
T ss_pred             eeecCChHHHHHHHHHHHHhcCCCCEEEEcChh
Confidence              011223445555554443 567899999984

>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=94.64  E-value=0.021  Score=52.18  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|++|+||||+|+.+..
T Consensus        19 ~~~~I~l~G~~GsGKST~a~~La~   42 (201)
T 2cdn_A           19 SHMRVLLLGPPGAGKGTQAVKLAE   42 (201)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            446899999999999999999976

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=94.62  E-value=0.02  Score=52.04  Aligned_cols=23  Identities=22%  Similarity=0.564  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|++|+||||+|+.+..
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~La~   31 (196)
T 2c95_A            9 TNIIFVVGGPGSGKGTQCEKIVQ   31 (196)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>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=94.61  E-value=0.1  Score=54.02  Aligned_cols=45  Identities=22%  Similarity=0.285  Sum_probs=34.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+|+..+.++. .+.+-+.++++-+.+....
T Consensus       164 kGqr~gIfgg~GvGKT~L~~~l~~~~-a~~~~~v~V~~~iGER~rE  208 (498)
T 1fx0_B          164 RGGKIGLFGGAGVGKTVLIMELINNI-AKAHGGVSVFGGVGERTRE  208 (498)
T ss_dssp             TTCCEEEEECSSSSHHHHHHHHHHHT-TTTCSSCEEEEEESCCSHH
T ss_pred             cCCeEEeecCCCCCchHHHHHHHHHH-HhhCCCEEEEEEcccCcHH
Confidence            45679999999999999999988731 2234567888888776654

>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=94.61  E-value=0.085  Score=55.84  Aligned_cols=41  Identities=15%  Similarity=-0.033  Sum_probs=30.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKAN-FDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~~~~wv~~~~~  238 (597)
                      ...++.|.|.+|+||||||.+++.+  .... =..++|++....
T Consensus       241 ~G~l~li~G~pG~GKT~lal~~a~~--~a~~~g~~vl~~s~E~s  282 (503)
T 1q57_A          241 GGEVIMVTSGSGMVMSTFVRQQALQ--WGTAMGKKVGLAMLEES  282 (503)
T ss_dssp             TTCEEEEEESSCHHHHHHHHHHHHH--HTTTSCCCEEEEESSSC
T ss_pred             CCeEEEEeecCCCCchHHHHHHHHH--HHHhcCCcEEEEeccCC
Confidence            4579999999999999999998874  2222 235777776543

>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=94.57  E-value=0.092  Score=52.89  Aligned_cols=23  Identities=30%  Similarity=0.416  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.++-
T Consensus        37 Ge~~~llGpnGsGKSTLLr~iaG   59 (372)
T 1v43_A           37 GEFLVLLGPSGCGKTTTLRMIAG   59 (372)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCChHHHHHHHHHc
Confidence            46999999999999999999975

>1rj9_A FTSY, signal recognition protein; SRP-GTPase domain, heterodimer, nucleotide twinning, protein complex, protein transport; HET: GCP; 1.90A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 2q9c_A* 2q9b_A* 2q9a_A* 1okk_D* 2xkv_D 2iyl_D* 2cnw_D* 2j7p_D*

Probab=94.56  E-value=0.025  Score=55.54  Aligned_cols=24  Identities=25%  Similarity=0.397  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|++|+|||||+..++.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lag  124 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGR  124 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHH
Confidence            467999999999999999999876

>1ye8_A Protein THEP1, hypothetical UPF0334 kinase-like protein AQ_1292; mixed alpha-beta protein, rossman fold, signaling protein, transferase; 1.40A {Aquifex aeolicus} SCOP: c.37.1.11

Probab=94.56  E-value=0.019  Score=51.51  Aligned_cols=22  Identities=36%  Similarity=0.708  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .++|+|+.|+|||||++.++..
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~   23 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            5899999999999999998763

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=94.53  E-value=0.02  Score=50.72  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=20.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|++|+||||+++.+..
T Consensus         6 ~~~~i~l~G~~GsGKSTva~~La~   29 (168)
T 1zuh_A            6 HMQHLVLIGFMGSGKSSLAQELGL   29 (168)
T ss_dssp             --CEEEEESCTTSSHHHHHHHHHH
T ss_pred             ccceEEEECCCCCCHHHHHHHHHH
Confidence            567999999999999999999976

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=94.52  E-value=0.017  Score=55.08  Aligned_cols=22  Identities=32%  Similarity=0.329  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|.|++|+||||||+.++.
T Consensus         2 ~li~I~G~~GSGKSTla~~La~   23 (253)
T 2ze6_A            2 LLHLIYGPTCSGKTDMAIQIAQ   23 (253)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHh
Confidence            4789999999999999999976

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=94.51  E-value=0.033  Score=55.39  Aligned_cols=44  Identities=20%  Similarity=0.372  Sum_probs=30.2

Q ss_pred             cchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          170 GRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       170 GR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +-+.-.+++.+.+...-.      .+....|.|+|++|+||||+++.++.
T Consensus         3 ~~~~L~~~il~~l~~~i~------~g~~~~i~l~G~~G~GKTTl~~~la~   46 (359)
T 2ga8_A            3 DTHKLADDVLQLLDNRIE------DNYRVCVILVGSPGSGKSTIAEELCQ   46 (359)
T ss_dssp             CHHHHHHHHHHHHHHTTT------TCSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHhc------cCCeeEEEEECCCCCcHHHHHHHHHH
Confidence            334445556665543221      23456799999999999999999877

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=94.51  E-value=0.017  Score=51.52  Aligned_cols=22  Identities=36%  Similarity=0.478  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|.|.|++|+||||+|+.+..
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~   26 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAK   26 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHH
Confidence            3689999999999999999976

>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=94.47  E-value=0.019  Score=51.93  Aligned_cols=22  Identities=23%  Similarity=0.475  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+++|.|+.|+|||||++.+..
T Consensus         3 ~ii~l~G~~GaGKSTl~~~L~~   24 (189)
T 2bdt_A            3 KLYIITGPAGVGKSTTCKRLAA   24 (189)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHhc
Confidence            4789999999999999999964

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=94.47  E-value=0.02  Score=51.93  Aligned_cols=23  Identities=26%  Similarity=0.579  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+|+|.|++|+||||+|+.+..
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~   25 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVE   25 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999876

>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=94.45  E-value=0.018  Score=51.87  Aligned_cols=22  Identities=27%  Similarity=0.552  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|+|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAK   24 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4699999999999999999976

>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=94.43  E-value=0.022  Score=52.96  Aligned_cols=24  Identities=17%  Similarity=0.318  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g   38 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLK   38 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhc
Confidence            457999999999999999999876

>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=94.41  E-value=0.022  Score=52.02  Aligned_cols=24  Identities=33%  Similarity=0.364  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|+.|+||||+++.+..
T Consensus         7 ~~~~I~i~G~~GsGKST~~~~La~   30 (203)
T 1uf9_A            7 HPIIIGITGNIGSGKSTVAALLRS   30 (203)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            567999999999999999999977

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=94.39  E-value=0.032  Score=53.23  Aligned_cols=25  Identities=28%  Similarity=0.315  Sum_probs=22.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.+|.|.|++|+||||+|+.+..
T Consensus        30 ~~~~~i~l~G~~GsGKSTla~~L~~   54 (253)
T 2p5t_B           30 KQPIAILLGGQSGAGKTTIHRIKQK   54 (253)
T ss_dssp             SSCEEEEEESCGGGTTHHHHHHHHH
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3467899999999999999999976

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=94.37  E-value=0.027  Score=51.89  Aligned_cols=24  Identities=17%  Similarity=0.216  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|+.|+||||+++.+..
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~   32 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVE   32 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHH
Confidence            357899999999999999999987

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=94.36  E-value=0.042  Score=51.91  Aligned_cols=42  Identities=19%  Similarity=0.270  Sum_probs=29.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ...++.|.|.+|+|||+||.+++.+. ....-..+++++....
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~-~~~~~~~v~~~s~E~~   70 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKG-AEEYGEPGVFVTLEER   70 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHH-HHHHCCCEEEEESSSC
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH-HHhcCCCceeecccCC
Confidence            45699999999999999999976531 2222345666665543

>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=94.35  E-value=0.022  Score=53.11  Aligned_cols=22  Identities=41%  Similarity=0.629  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|+|++|+||||+++.+..
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~   27 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAE   27 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999976

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=94.35  E-value=0.026  Score=50.85  Aligned_cols=25  Identities=36%  Similarity=0.571  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|.|.|++|+||||+++.+...
T Consensus        12 ~~~~i~l~G~~GsGKsT~~~~L~~~   36 (186)
T 2yvu_A           12 KGIVVWLTGLPGSGKTTIATRLADL   36 (186)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHH
Confidence            4578999999999999999999873

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.34  E-value=0.12  Score=53.79  Aligned_cols=41  Identities=20%  Similarity=0.078  Sum_probs=29.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ...++.|.|.+|+|||+||..++.+.... .=..++|++...
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~ia~~~a~~-~g~~vl~~slE~  239 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALTIAQNAALK-EGVGVGIYSLEM  239 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHHHHHHHHHT-TCCCEEEEESSS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHh-CCCeEEEEECCC
Confidence            34699999999999999999998742221 123577777653

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=94.33  E-value=0.023  Score=51.74  Aligned_cols=23  Identities=26%  Similarity=0.600  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|++|+||||+|+.+..
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~   34 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVE   34 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999977

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=94.32  E-value=0.027  Score=52.17  Aligned_cols=25  Identities=28%  Similarity=0.546  Sum_probs=22.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...++|.|.|++|+||||.|+.+..
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~   51 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQ   51 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999999877

>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=94.30  E-value=0.022  Score=54.54  Aligned_cols=23  Identities=22%  Similarity=0.538  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|.|.|++|+||||+|+.+..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~   26 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAK   26 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>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=94.29  E-value=0.024  Score=53.77  Aligned_cols=23  Identities=30%  Similarity=0.445  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+|+|.|++|+|||||++.+..
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~   49 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQ   49 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999984

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=94.26  E-value=0.017  Score=51.91  Aligned_cols=24  Identities=42%  Similarity=0.787  Sum_probs=17.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|.|.|++|+||||+|+.+..
T Consensus         4 ~~~~I~l~G~~GsGKST~a~~La~   27 (183)
T 2vli_A            4 RSPIIWINGPFGVGKTHTAHTLHE   27 (183)
T ss_dssp             -CCEEEEECCC----CHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999999975

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=94.26  E-value=0.022  Score=52.97  Aligned_cols=24  Identities=25%  Similarity=0.548  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||++.+..
T Consensus        22 ~G~~~~lvGpsGsGKSTLl~~L~g   45 (218)
T 1z6g_A           22 NIYPLVICGPSGVGKGTLIKKLLN   45 (218)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            346899999999999999999876

>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=94.25  E-value=0.026  Score=51.97  Aligned_cols=24  Identities=21%  Similarity=0.365  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|.|+.|+|||||++.+..
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~g   42 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRE   42 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            356999999999999999999876

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=94.24  E-value=0.1  Score=54.45  Aligned_cols=41  Identities=20%  Similarity=0.225  Sum_probs=29.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ...++.|.|.+|+|||||+..++.+.... .-..++|++...
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~-~g~~Vl~~s~E~  242 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATK-TNENVAIFSLEM  242 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHH-SSCCEEEEESSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHh-CCCcEEEEECCC
Confidence            34699999999999999999998742222 122577777554

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=94.23  E-value=0.024  Score=51.78  Aligned_cols=21  Identities=29%  Similarity=0.531  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|+.|+||||+++.+..
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~   22 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISK   22 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHH
Confidence            689999999999999999987

>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=94.23  E-value=0.021  Score=50.63  Aligned_cols=22  Identities=27%  Similarity=0.576  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~   24 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELAR   24 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>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=94.23  E-value=0.024  Score=51.99  Aligned_cols=22  Identities=32%  Similarity=0.442  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|+|+.|+||||+++.+..
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999999976

>3l0o_A Transcription termination factor RHO; helicase, RHO factor, RNA capture mechanism, ATP-binding, hydrolase, nucleotide-binding, RN binding; 2.35A {Thermotoga maritima}

Probab=94.23  E-value=0.14  Score=51.17  Aligned_cols=55  Identities=16%  Similarity=0.225  Sum_probs=36.8

Q ss_pred             HHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-cCCe-eEEEEecCCCch
Q 041007          176 QKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-NFDK-RIWVSASYPRDE  241 (597)
Q Consensus       176 ~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-~F~~-~~wv~~~~~~~~  241 (597)
                      -+.++.|..-.         ....++|.|.+|+|||+|+..+.+.  +.. +-+. ++++-+.+....
T Consensus       163 iraID~l~Pig---------rGQR~lIfg~~g~GKT~Ll~~Ia~~--i~~~~~dv~~V~~lIGER~~E  219 (427)
T 3l0o_A          163 TRLIDLFAPIG---------KGQRGMIVAPPKAGKTTILKEIANG--IAENHPDTIRIILLIDERPEE  219 (427)
T ss_dssp             HHHHHHHSCCB---------TTCEEEEEECTTCCHHHHHHHHHHH--HHHHCTTSEEEEEECSCCHHH
T ss_pred             chhhhhccccc---------CCceEEEecCCCCChhHHHHHHHHH--HhhcCCCeEEEEEEeccCcch
Confidence            35667776433         4568999999999999999998883  322 2232 345666665444

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=94.22  E-value=0.025  Score=52.08  Aligned_cols=23  Identities=30%  Similarity=0.281  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+|+|.|++|+||||+|+.+...
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~   27 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDW   27 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH
Confidence            58999999999999999999873

>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=94.22  E-value=0.037  Score=50.99  Aligned_cols=23  Identities=22%  Similarity=0.387  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~   31 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVE   31 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999987

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=94.19  E-value=0.43  Score=46.98  Aligned_cols=25  Identities=24%  Similarity=0.441  Sum_probs=22.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....+|+|+|++|+||||++..++.
T Consensus       103 ~~~~vI~ivG~~G~GKTT~~~~LA~  127 (320)
T 1zu4_A          103 NRLNIFMLVGVNGTGKTTSLAKMAN  127 (320)
T ss_dssp             TSCEEEEEESSTTSSHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999999877

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=94.19  E-value=0.024  Score=51.01  Aligned_cols=23  Identities=26%  Similarity=0.358  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...|+|.|++|+||||+++.+..
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~   26 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQ   26 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999976

>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=94.18  E-value=0.024  Score=51.88  Aligned_cols=22  Identities=32%  Similarity=0.430  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|+|+.|+||||+++.+..
T Consensus         2 ~~i~i~G~~GsGKSTl~~~L~~   23 (204)
T 2if2_A            2 KRIGLTGNIGCGKSTVAQMFRE   23 (204)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCcCHHHHHHHHHH
Confidence            3799999999999999999876

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=94.18  E-value=0.027  Score=51.24  Aligned_cols=36  Identities=19%  Similarity=0.322  Sum_probs=27.2

Q ss_pred             HHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          175 KQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       175 ~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +..+..++...         +....+.|+|++|+|||++|..+++
T Consensus        45 ~~~l~~~~~~i---------Pkkn~ili~GPPGtGKTt~a~ala~   80 (212)
T 1tue_A           45 LGALKSFLKGT---------PKKNCLVFCGPANTGKSYFGMSFIH   80 (212)
T ss_dssp             HHHHHHHHHTC---------TTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHhcC---------CcccEEEEECCCCCCHHHHHHHHHH
Confidence            45566666521         2345799999999999999998887

>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=94.18  E-value=0.2  Score=50.40  Aligned_cols=23  Identities=30%  Similarity=0.423  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.++-
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (372)
T 1g29_1           29 GEFMILLGPSGCGKTTTLRMIAG   51 (372)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCcHHHHHHHHHHc
Confidence            46899999999999999999975

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=94.16  E-value=0.028  Score=49.76  Aligned_cols=25  Identities=24%  Similarity=0.328  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++.|.|+.|+|||||+..+...
T Consensus         3 ~~~~i~i~G~sGsGKTTl~~~L~~~   27 (169)
T 1xjc_A            3 AMNVWQVVGYKHSGKTTLMEKWVAA   27 (169)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHh
Confidence            4679999999999999999999873

>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=94.15  E-value=0.03  Score=50.53  Aligned_cols=23  Identities=26%  Similarity=0.530  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|++|+||||+|+.+..
T Consensus         6 ~~~I~l~G~~GsGKsT~~~~L~~   28 (194)
T 1qf9_A            6 PNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>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=94.13  E-value=0.058  Score=59.82  Aligned_cols=57  Identities=18%  Similarity=0.216  Sum_probs=38.6

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCC-C--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSD-E--ESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~-~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-..+.|-++.+++|.+.+...-.. +  ...+...++-|.++|++|.|||.||+.+++.
T Consensus       475 ~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e  534 (806)
T 3cf2_A          475 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE  534 (806)
T ss_dssp             CSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHT
T ss_pred             CHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHH
Confidence            3355678888888887776533210 0  0111234556889999999999999999984

>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=94.11  E-value=0.22  Score=46.64  Aligned_cols=21  Identities=38%  Similarity=0.523  Sum_probs=17.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHh
Q 041007          198 PVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      +.+.|.|+.|+||||+...+.
T Consensus        77 ~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           77 SVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             SEEEEECCTTSSHHHHHHHHH
T ss_pred             CEEEEEeCCCCCcHHhHHHHH
Confidence            689999999999998766554

>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=94.10  E-value=0.026  Score=53.73  Aligned_cols=24  Identities=17%  Similarity=0.306  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|++|+||||+|+.+..
T Consensus        21 ~~~iI~I~G~~GSGKST~a~~L~~   44 (252)
T 1uj2_A           21 EPFLIGVSGGTASGKSSVCAKIVQ   44 (252)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CcEEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999876

>3hjn_A DTMP kinase, thymidylate kinase; ATP-binding, nucleotide biosynth nucleotide-binding, transferase, structural genomics; HET: ADP TYD; 2.10A {Thermotoga maritima}

Probab=94.08  E-value=0.16  Score=46.27  Aligned_cols=22  Identities=23%  Similarity=0.261  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|+|-|.-|+||||.++.+.+.
T Consensus         2 fI~~EG~DGsGKsTq~~~L~~~   23 (197)
T 3hjn_A            2 FITFEGIDGSGKSTQIQLLAQY   23 (197)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            4788999999999999999883

>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=94.07  E-value=0.035  Score=52.57  Aligned_cols=24  Identities=21%  Similarity=0.167  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+..|+|.|++|+||||+|+.+..
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~   51 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKK   51 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            457899999999999999999976

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=94.04  E-value=0.029  Score=53.17  Aligned_cols=24  Identities=17%  Similarity=0.357  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|+.|+|||||++.+..
T Consensus        24 ~g~iigI~G~~GsGKSTl~k~L~~   47 (245)
T 2jeo_A           24 RPFLIGVSGGTASGKSTVCEKIME   47 (245)
T ss_dssp             CSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999998866

>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=94.02  E-value=0.03  Score=52.03  Aligned_cols=23  Identities=22%  Similarity=0.315  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...|+|.|++|+||||+|+.+..
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~   26 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQE   26 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>3aez_A Pantothenate kinase; transferase, homodimer, COA biosynthesis, nucleotide binding binding, cytoplasm, nucleotide-binding; HET: GDP PAZ; 2.20A {Mycobacterium tuberculosis} PDB: 2ges_A* 2geu_A* 2gev_A* 2zs7_A* 2zs8_A* 2zs9_A* 2zsa_A* 2zsb_A* 2zsd_A* 2zse_A* 2zsf_A* 2get_A* 3af0_A* 3af1_A* 3af2_A* 3af3_A* 3af4_A* 3avp_A* 3avo_A* 3avq_A*

Probab=94.02  E-value=0.029  Score=55.31  Aligned_cols=24  Identities=25%  Similarity=0.324  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|+.|+|||||++.+..
T Consensus        89 ~g~ivgI~G~sGsGKSTL~~~L~g  112 (312)
T 3aez_A           89 VPFIIGVAGSVAVGKSTTARVLQA  112 (312)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCCCchHHHHHHHHHh
Confidence            457999999999999999999876

>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=93.96  E-value=0.031  Score=50.02  Aligned_cols=24  Identities=25%  Similarity=0.490  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|+.|+||||+++.+..
T Consensus         4 ~g~~i~l~G~~GsGKST~~~~L~~   27 (179)
T 2pez_A            4 RGCTVWLTGLSGAGKTTVSMALEE   27 (179)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            356899999999999999999977

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.94  E-value=0.04  Score=51.27  Aligned_cols=25  Identities=28%  Similarity=0.440  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||+..+...
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~   61 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDN   61 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4678999999999999999999873

>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=93.94  E-value=0.033  Score=48.80  Aligned_cols=24  Identities=29%  Similarity=0.589  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|.|+.|+|||||++.++.
T Consensus        32 ~Ge~v~L~G~nGaGKTTLlr~l~g   55 (158)
T 1htw_A           32 KAIMVYLNGDLGAGKTTLTRGMLQ   55 (158)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            346999999999999999999876

>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=93.93  E-value=0.2  Score=54.03  Aligned_cols=137  Identities=14%  Similarity=0.046  Sum_probs=68.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hcc--CC-eeEEEEecCCCchhhhhhhhhhhc--ccchHHHHHHHHHHhccC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KAN--FD-KRIWVSASYPRDEIRVARDEISVA--RDRDEIRVAKAILESLKG  270 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~--F~-~~~wv~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~il~~l~~  270 (597)
                      ..+++|.|+.|+|||||++.++.-..- .+.  +. .+.++.-.............+...  ...........+++.++.
T Consensus       382 Gei~~i~G~NGsGKSTLlk~l~Gl~~p~~G~I~~~~~i~~v~Q~~~~~~~~tv~e~~~~~~~~~~~~~~~~~~~l~~~~l  461 (607)
T 3bk7_A          382 GEVIGIVGPNGIGKTTFVKMLAGVEEPTEGKVEWDLTVAYKPQYIKAEYEGTVYELLSKIDSSKLNSNFYKTELLKPLGI  461 (607)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCCSBSCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHHCHHHHHHTHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCCceEEEEeeEEEEEecCccCCCCCcHHHHHHhhhccCCCHHHHHHHHHHHcCC
Confidence            458999999999999999999864211 111  11 233332211110000111111100  000012334556666654


Q ss_pred             CCC---c---hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          271 SVS---S---QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       271 ~~~---~---~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      ...   .   ...-+.-.-.|...|..++-+|+||+--+.-+...-..+...+...  ..|..||++|.+.
T Consensus       462 ~~~~~~~~~~LSGGe~QRv~iAraL~~~p~lLlLDEPt~~LD~~~~~~l~~~l~~l~~~~g~tvi~vsHd~  532 (607)
T 3bk7_A          462 IDLYDRNVEDLSGGELQRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDV  532 (607)
T ss_dssp             TTTTTSBGGGCCHHHHHHHHHHHHHTSCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHTTCEEEEECSCH
T ss_pred             chHhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEeCCccCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            321   1   1112333335666777788899999864433344444455444432  2466777777764

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=93.93  E-value=0.11  Score=56.12  Aligned_cols=24  Identities=21%  Similarity=0.238  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....++|+|+.|+|||||++.+..
T Consensus       366 ~G~~~~ivG~sGsGKSTll~~l~g  389 (578)
T 4a82_A          366 KGETVAFVGMSGGGKSTLINLIPR  389 (578)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhc
Confidence            356999999999999999998865

>3qf4_A ABC transporter, ATP-binding protein; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=93.91  E-value=0.26  Score=53.13  Aligned_cols=24  Identities=25%  Similarity=0.412  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....++|+|+.|+|||||++.+..
T Consensus       368 ~Ge~~~ivG~sGsGKSTll~~l~g  391 (587)
T 3qf4_A          368 PGSLVAVLGETGSGKSTLMNLIPR  391 (587)
T ss_dssp             TTCEEEEECSSSSSHHHHHHTTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhC
Confidence            346999999999999999999876

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=93.87  E-value=0.031  Score=49.27  Aligned_cols=21  Identities=19%  Similarity=0.327  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSR   22 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999977

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=93.86  E-value=0.031  Score=52.21  Aligned_cols=24  Identities=25%  Similarity=0.389  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....|+|.|++|+||||+|+.+..
T Consensus         6 ~~~~I~l~G~~GsGKsT~a~~La~   29 (227)
T 1zd8_A            6 RLLRAVIMGAPGSGKGTVSSRITT   29 (227)
T ss_dssp             -CCEEEEEECTTSSHHHHHHHHHH
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999999976

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=93.83  E-value=0.035  Score=52.91  Aligned_cols=23  Identities=35%  Similarity=0.575  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|+.|+|||||++.+..
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~   49 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAE   49 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            46999999999999999999985

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=93.81  E-value=0.032  Score=51.97  Aligned_cols=24  Identities=17%  Similarity=0.127  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....|.|.|++|+||||+++.+..
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~   27 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKT   27 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999999976

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=93.76  E-value=0.033  Score=50.36  Aligned_cols=21  Identities=33%  Similarity=0.623  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|+|.|+.|+||||+++.+..
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~   22 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYE   22 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999987

>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=93.75  E-value=0.035  Score=53.84  Aligned_cols=23  Identities=30%  Similarity=0.442  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHh
Q 041007          196 TLPVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      ...+|+|+|+.|+||||+|+.+.
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La   96 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK   96 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            45789999999999999999997

>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=93.74  E-value=0.037  Score=50.55  Aligned_cols=24  Identities=21%  Similarity=0.271  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|.|+.|+||||+++.+...
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~   27 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMES   27 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHT
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHH
Confidence            368999999999999999999873

>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=93.72  E-value=0.17  Score=52.11  Aligned_cols=45  Identities=22%  Similarity=0.316  Sum_probs=32.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+|+..+.++. .+.+-+.++++-+.+....
T Consensus       152 kGQr~~Ifgg~G~GKT~L~~~i~~~~-~~~~~~v~V~~~iGER~rE  196 (482)
T 2ck3_D          152 KGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTRE  196 (482)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHT-TTTCSSEEEEEEESCCHHH
T ss_pred             cCCeeeeecCCCCChHHHHHHHHHhh-HhhCCCEEEEEECCCcchH
Confidence            45689999999999999999987731 2233456777777765543

>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=93.67  E-value=0.067  Score=52.60  Aligned_cols=24  Identities=29%  Similarity=0.347  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|+.|+|||||++.+..
T Consensus        79 ~g~iigI~G~~GsGKSTl~~~L~~  102 (308)
T 1sq5_A           79 IPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999876

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=93.59  E-value=0.036  Score=51.24  Aligned_cols=21  Identities=33%  Similarity=0.536  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999976

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.57  E-value=0.33  Score=50.26  Aligned_cols=41  Identities=20%  Similarity=0.083  Sum_probs=29.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ...++.|.|.+|+||||||.+++.+...+  =..++|++....
T Consensus       196 ~G~liiIaG~pG~GKTtlal~ia~~~a~~--g~~vl~fSlEms  236 (444)
T 3bgw_A          196 RRNFVLIAARPSMGKTAFALKQAKNMSDN--DDVVNLHSLEMG  236 (444)
T ss_dssp             SSCEEEEEECSSSSHHHHHHHHHHHHHHT--TCEEEEECSSSC
T ss_pred             CCcEEEEEeCCCCChHHHHHHHHHHHHHc--CCEEEEEECCCC
Confidence            35699999999999999999998753222  235677765543

>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=93.56  E-value=0.3  Score=45.00  Aligned_cols=24  Identities=21%  Similarity=0.228  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|.|+.|+||||+++.+...
T Consensus         6 g~~i~~eG~~gsGKsT~~~~l~~~   29 (213)
T 4edh_A            6 GLFVTLEGPEGAGKSTNRDYLAER   29 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHH
Confidence            468999999999999999999873

>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=93.53  E-value=0.04  Score=50.04  Aligned_cols=25  Identities=24%  Similarity=0.316  Sum_probs=22.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....+|+|+|+.|+||||+++.+..
T Consensus        10 ~~~~iIgltG~~GSGKSTva~~L~~   34 (192)
T 2grj_A           10 HHHMVIGVTGKIGTGKSTVCEILKN   34 (192)
T ss_dssp             CCEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccceEEEEECCCCCCHHHHHHHHHH
Confidence            3567999999999999999999876

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=93.52  E-value=0.034  Score=51.56  Aligned_cols=24  Identities=17%  Similarity=0.255  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....|+|.|++|+||||+|+.+..
T Consensus         4 ~~~~I~l~G~~GsGKsT~a~~La~   27 (217)
T 3be4_A            4 KKHNLILIGAPGSGKGTQCEFIKK   27 (217)
T ss_dssp             GCCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            346799999999999999999977

>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=93.52  E-value=0.038  Score=54.44  Aligned_cols=41  Identities=15%  Similarity=0.182  Sum_probs=28.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      +.++|+|.|-|||||||.+..+.--  ....=..+.-+.+...
T Consensus        47 ~aKVIAIaGKGGVGKTTtavNLA~a--LA~~GkkVllID~Dpq   87 (314)
T 3fwy_A           47 GAKVFAVYGKGGIGKSTTSSNLSAA--FSILGKRVLQIGCDPK   87 (314)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEEESSS
T ss_pred             CceEEEEECCCccCHHHHHHHHHHH--HHHCCCeEEEEecCCC
Confidence            5689999999999999998877652  2222223555666543

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=93.49  E-value=0.043  Score=54.18  Aligned_cols=24  Identities=21%  Similarity=0.422  Sum_probs=21.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .++|+|+|+.|+|||||+..++..
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~   63 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAH   63 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CceEEEECCCCCCHHHHHHHHHHH
Confidence            469999999999999999999883

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=93.48  E-value=0.029  Score=52.62  Aligned_cols=23  Identities=22%  Similarity=0.381  Sum_probs=16.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHh-C
Q 041007          197 LPVIWILGNEGIGKTALARQVF-D  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~-~  219 (597)
                      ..+++|+|+.|+|||||++.+. .
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~   50 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEK   50 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC-
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            4689999999999999999998 5

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=93.46  E-value=0.21  Score=51.21  Aligned_cols=24  Identities=25%  Similarity=0.318  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|++|+||||++..++..
T Consensus        98 ~~vi~i~G~~GsGKTT~~~~LA~~  121 (425)
T 2ffh_A           98 RNLWFLVGLQGSGKTTTAAKLALY  121 (425)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999998873

>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=93.46  E-value=0.039  Score=51.02  Aligned_cols=21  Identities=19%  Similarity=0.453  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVE   22 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999865

>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=93.42  E-value=0.043  Score=50.60  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|.|.|+.|+||||+++.+...
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~   48 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQ   48 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHH
Confidence            3478999999999999999999873

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=93.39  E-value=0.054  Score=58.78  Aligned_cols=43  Identities=16%  Similarity=0.248  Sum_probs=36.1

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|.+..++.+...+..            ...+.|+|++|+||||||+.++..
T Consensus        41 ~~i~G~~~~l~~l~~~i~~------------g~~vll~Gp~GtGKTtlar~ia~~   83 (604)
T 3k1j_A           41 DQVIGQEHAVEVIKTAANQ------------KRHVLLIGEPGTGKSMLGQAMAEL   83 (604)
T ss_dssp             HHCCSCHHHHHHHHHHHHT------------TCCEEEECCTTSSHHHHHHHHHHT
T ss_pred             ceEECchhhHhhccccccC------------CCEEEEEeCCCCCHHHHHHHHhcc
Confidence            4579999888888887762            258999999999999999999873

>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=93.39  E-value=0.048  Score=51.33  Aligned_cols=23  Identities=22%  Similarity=0.278  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||.+.+..
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~G   53 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGC   53 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhc
Confidence            46999999999999999999976

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.37  E-value=0.24  Score=50.96  Aligned_cols=25  Identities=24%  Similarity=0.272  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+++|.|+|.+|+||||++..++..
T Consensus        99 ~~~vI~ivG~~GvGKTT~a~~LA~~  123 (433)
T 2xxa_A           99 PPAVVLMAGLQGAGKTTSVGKLGKF  123 (433)
T ss_dssp             SSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4689999999999999999998873

>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=93.37  E-value=0.18  Score=49.18  Aligned_cols=24  Identities=25%  Similarity=0.318  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|.+|+||||++..++..
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~  121 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALY  121 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH
Confidence            468999999999999999999873

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.36  E-value=0.048  Score=50.51  Aligned_cols=25  Identities=28%  Similarity=0.404  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++|+|+|.+|+|||||+..+...
T Consensus        29 ~~~~i~i~G~~g~GKTTl~~~l~~~   53 (221)
T 2wsm_A           29 GTVAVNIMGAIGSGKTLLIERTIER   53 (221)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHH
Confidence            4679999999999999999998773

>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=93.36  E-value=0.024  Score=52.30  Aligned_cols=21  Identities=33%  Similarity=0.502  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|+|.|+.|+||||+++.+..
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~   22 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSG   22 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHH
Confidence            789999999999999999977

>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=93.27  E-value=0.042  Score=56.60  Aligned_cols=54  Identities=24%  Similarity=0.365  Sum_probs=35.5

Q ss_pred             CccccchhhHHHHHHHhhCC----CCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGE----SSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~----~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.++.++.|...+...    ............+-|.++|++|+|||++|+.++.
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~   72 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   72 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHH
Confidence            35789888888887666321    0000000011345699999999999999999987

>1yqt_A RNAse L inhibitor; ATP-binding cassette, ribosome biogenesis, hydrolyase/translation complex; HET: ADP; 1.90A {Pyrococcus furiosus}

Probab=93.26  E-value=0.14  Score=54.54  Aligned_cols=137  Identities=15%  Similarity=0.053  Sum_probs=66.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhh-hcc--CC-eeEEEEecCCCchhhhhhhhhhhc--ccchHHHHHHHHHHhccC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDV-KAN--FD-KRIWVSASYPRDEIRVARDEISVA--RDRDEIRVAKAILESLKG  270 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~-~~~--F~-~~~wv~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~il~~l~~  270 (597)
                      ..+++|+|+.|+|||||++.++.-... .+.  +. .+.++.-.............+...  ...........+++.++.
T Consensus       312 Ge~~~i~G~NGsGKSTLlk~l~Gl~~p~~G~i~~~~~i~~v~Q~~~~~~~~tv~~~~~~~~~~~~~~~~~~~~~l~~~~l  391 (538)
T 1yqt_A          312 GEVIGIVGPNGIGKTTFVKMLAGVEEPTEGKIEWDLTVAYKPQYIKADYEGTVYELLSKIDASKLNSNFYKTELLKPLGI  391 (538)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTSSCCSBCCCCCCCCEEEECSSCCCCCSSBHHHHHHHHHHHHHTCHHHHHHTTTTTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECceEEEEecCCcCCCCCcHHHHHHhhhccCCCHHHHHHHHHHHcCC
Confidence            468999999999999999999874211 111  11 133332111110000111111000  000001223334444433


Q ss_pred             CC---Cc---hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          271 SV---SS---QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       271 ~~---~~---~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      ..   ..   ...-+.-.-.|...|..++-+|+||+--+.-+...-..+...+...  ..|..||++|.+.
T Consensus       392 ~~~~~~~~~~LSGGe~qrv~lAraL~~~p~lLlLDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vsHd~  462 (538)
T 1yqt_A          392 IDLYDREVNELSGGELQRVAIAATLLRDADIYLLDEPSAYLDVEQRLAVSRAIRHLMEKNEKTALVVEHDV  462 (538)
T ss_dssp             GGGTTSBGGGCCHHHHHHHHHHHHHTSCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHHTCEEEEECSCH
T ss_pred             hhhhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEeCCcccCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            21   01   1112333445667777888899999864443344555555555432  2356777777764

>1j8m_F SRP54, signal recognition 54 kDa protein; signaling protein; 2.00A {Acidianus ambivalens} SCOP: a.24.13.1 c.37.1.10 PDB: 1j8y_F

Probab=93.25  E-value=0.23  Score=48.44  Aligned_cols=38  Identities=32%  Similarity=0.176  Sum_probs=26.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ..+++++|++|+||||++..++..  ....-..+.++...
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~--~~~~g~~v~l~~~D  135 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYF--YKKKGFKVGLVGAD  135 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHH--HHHCCCeEEEEecC
Confidence            579999999999999999998863  32222235555543

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=93.21  E-value=0.091  Score=56.85  Aligned_cols=24  Identities=21%  Similarity=0.361  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||++.+..
T Consensus       380 ~G~~~~ivG~sGsGKSTll~~l~g  403 (598)
T 3qf4_B          380 PGQKVALVGPTGSGKTTIVNLLMR  403 (598)
T ss_dssp             TTCEEEEECCTTSSTTHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            456999999999999999999976

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.20  E-value=0.05  Score=49.05  Aligned_cols=25  Identities=36%  Similarity=0.438  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~   71 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTD   71 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4568999999999999999998764

>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=93.17  E-value=0.052  Score=48.38  Aligned_cols=25  Identities=24%  Similarity=0.473  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++++|+|+.|+|||||+..+...
T Consensus         5 ~~~~i~i~G~sGsGKTTl~~~l~~~   29 (174)
T 1np6_A            5 MIPLLAFAAWSGTGKTTLLKKLIPA   29 (174)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCHHHHHHHHHHh
Confidence            3679999999999999999998873

>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=93.17  E-value=0.053  Score=52.78  Aligned_cols=24  Identities=33%  Similarity=0.458  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|+|.|+.|+||||||..++.
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~   32 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRK   32 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEECCCccCHHHHHHHHHH
Confidence            457899999999999999999987

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.16  E-value=0.031  Score=49.71  Aligned_cols=23  Identities=26%  Similarity=0.404  Sum_probs=20.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++++|+|+.|+|||||+..+..-
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~   25 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPI   25 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            58999999999999999998773

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=93.15  E-value=0.14  Score=62.11  Aligned_cols=86  Identities=21%  Similarity=0.212  Sum_probs=55.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC--
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS--  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~--  273 (597)
                      ...++.|.|++|+||||||.+++..  ....-..++|++.....+...                     ++.++.+..  
T Consensus       382 ~G~lilI~G~pGsGKTtLaLqia~~--~a~~G~~vlyis~E~s~~~~~---------------------a~~lGvd~~~L  438 (2050)
T 3cmu_A          382 MGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY---------------------ARKLGVDIDNL  438 (2050)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH--HHTTTCCEEEECTTSCCCHHH---------------------HHHTTCCTTTC
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHH--HHhcCCeEEEEEcCCCHHHHH---------------------HHHcCCCHHHe
Confidence            4679999999999999999999874  332224678888776655411                     233333211  


Q ss_pred             ---chhhHHHHHHHHHHHhc-CceEEEEEecccCC
Q 041007          274 ---SQVEMETVLQYINEFVQ-GKKVLLVLDDLWWN  304 (597)
Q Consensus       274 ---~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~~~  304 (597)
                         ...+.+++...+....+ .+.-+||+|.+...
T Consensus       439 ~I~~~~~~e~il~~~~~lv~~~~~~lIVIDSL~al  473 (2050)
T 3cmu_A          439 LCSQPDTGEQALEICDALARSGAVDVIVVDSVAAL  473 (2050)
T ss_dssp             EEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGC
T ss_pred             EEeCCCCHHHHHHHHHHHHHhcCCcEEEECCHHHh
Confidence               12345556665554443 45679999998644

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.12  E-value=0.063  Score=48.06  Aligned_cols=25  Identities=20%  Similarity=0.365  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus         6 ~~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            6 KSYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3467999999999999999999874

>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=93.12  E-value=0.049  Score=49.83  Aligned_cols=21  Identities=33%  Similarity=0.491  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|+|.|+.|+||||+++.+..
T Consensus         4 ~i~i~G~~GsGKst~~~~la~   24 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAA   24 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            899999999999999999976

>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=93.12  E-value=0.05  Score=50.39  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|+.|+||||+++.+..
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~   26 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD   26 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999864

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=93.12  E-value=0.29  Score=49.73  Aligned_cols=45  Identities=27%  Similarity=0.417  Sum_probs=32.6

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|....++++.+.+.....       .. ..|.|.|.+|+|||++|+.+..
T Consensus       138 ~~ig~s~~m~~l~~~i~~~a~-------~~-~~vli~Ge~GtGK~~lAr~ih~  182 (387)
T 1ny5_A          138 EYVFESPKMKEILEKIKKISC-------AE-CPVLITGESGVGKEVVARLIHK  182 (387)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTT-------CC-SCEEEECSTTSSHHHHHHHHHH
T ss_pred             hhhhccHHhhHHHHHHHHhcC-------CC-CCeEEecCCCcCHHHHHHHHHH
Confidence            356666677777776664332       12 3458999999999999998876

>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=93.10  E-value=0.12  Score=61.89  Aligned_cols=87  Identities=22%  Similarity=0.218  Sum_probs=54.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCC---
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSV---  272 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~---  272 (597)
                      ..+++.|.|++|+||||||.+++..  ....=..++|++.....+...                     ++.++.+.   
T Consensus       382 ~G~lilI~G~pGsGKTtLaLq~a~~--~~~~G~~vlyis~E~s~~~~~---------------------a~~lGvd~~~L  438 (1706)
T 3cmw_A          382 MGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDPIY---------------------ARKLGVDIDNL  438 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEECTTSCCCHHH---------------------HHHTTCCGGGC
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHH--HHHhCCCeEEEEccCchHHHH---------------------HHHcCCCHHHe
Confidence            4679999999999999999999874  333334688888776665421                     22232211   


Q ss_pred             --CchhhHHHHHHHHHHHhc-CceEEEEEecccCCC
Q 041007          273 --SSQVEMETVLQYINEFVQ-GKKVLLVLDDLWWNA  305 (597)
Q Consensus       273 --~~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~~~~  305 (597)
                        ....+.+++...+....+ .+.-+||+|.+....
T Consensus       439 ~i~~~~~~e~~l~~l~~lv~~~~~~lVVIDSL~al~  474 (1706)
T 3cmw_A          439 LCSQPDTGEQALEICDALARSGAVDVIVVDSVAALT  474 (1706)
T ss_dssp             EEECCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCC
T ss_pred             EEcCCCCHHHHHHHHHHHHHhcCCCEEEECCHHHhh
Confidence              012234555555554443 456799999986543

>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=93.09  E-value=0.05  Score=53.03  Aligned_cols=23  Identities=22%  Similarity=0.314  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|+|.|+.|+||||||..++.
T Consensus         3 ~~~i~i~GptgsGKt~la~~La~   25 (322)
T 3exa_A            3 EKLVAIVGPTAVGKTKTSVMLAK   25 (322)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CcEEEEECCCcCCHHHHHHHHHH
Confidence            35899999999999999999987

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.08  E-value=0.045  Score=49.58  Aligned_cols=23  Identities=26%  Similarity=0.515  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+++|+|+.|+|||||++.++..
T Consensus         2 ~~i~i~G~nG~GKTTll~~l~g~   24 (189)
T 2i3b_A            2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             CEEEEECCCCChHHHHHHHHHhh
Confidence            37899999999999999998764

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=93.07  E-value=0.27  Score=45.62  Aligned_cols=25  Identities=24%  Similarity=0.206  Sum_probs=22.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|.|+.|+||||+++.+.+.
T Consensus        20 ~~~~i~~~G~~g~GKst~~~~l~~~   44 (223)
T 3ld9_A           20 GSMFITFEGIDGSGKTTQSHLLAEY   44 (223)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4678999999999999999999884

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.04  E-value=0.17  Score=47.08  Aligned_cols=25  Identities=28%  Similarity=0.244  Sum_probs=19.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|.|+.|+||||+++.+.+.
T Consensus        24 ~g~~I~~eG~~GsGKsT~~~~l~~~   48 (227)
T 3v9p_A           24 RGKFITFEGIDGAGKTTHLQWFCDR   48 (227)
T ss_dssp             CCCEEEEECCC---CHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            3568999999999999999999874

>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=93.00  E-value=0.15  Score=46.81  Aligned_cols=110  Identities=11%  Similarity=0.056  Sum_probs=53.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc-
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS-  274 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-  274 (597)
                      ...+..++|+-|.||||.+....++... ......++ ....+  .                ..-...+...++..... 
T Consensus        27 ~G~l~vitG~MgsGKTT~lL~~a~r~~~-~g~kVli~-k~~~d--~----------------R~ge~~i~s~~g~~~~a~   86 (214)
T 2j9r_A           27 NGWIEVICGSMFSGKSEELIRRVRRTQF-AKQHAIVF-KPCID--N----------------RYSEEDVVSHNGLKVKAV   86 (214)
T ss_dssp             SCEEEEEECSTTSCHHHHHHHHHHHHHH-TTCCEEEE-ECC-----------------------------------CCEE
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHHHH-CCCEEEEE-EeccC--C----------------cchHHHHHhhcCCeeEEe
Confidence            3468899999999999999888774322 22333333 21111  1                11111233333221110 


Q ss_pred             -hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          275 -QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       275 -~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                       ..+..    .+.+.+.++--+|++|.++..+ .+.++.+....+   .|..||+|.++.
T Consensus        87 ~~~~~~----~~~~~~~~~~dvViIDEaQF~~-~~~V~~l~~l~~---~~~~Vi~~Gl~~  138 (214)
T 2j9r_A           87 PVSASK----DIFKHITEEMDVIAIDEVQFFD-GDIVEVVQVLAN---RGYRVIVAGLDQ  138 (214)
T ss_dssp             ECSSGG----GGGGGCCSSCCEEEECCGGGSC-TTHHHHHHHHHH---TTCEEEEEECSB
T ss_pred             ecCCHH----HHHHHHhcCCCEEEEECcccCC-HHHHHHHHHHhh---CCCEEEEEeccc
Confidence             00111    1222223333499999997754 334544433222   377999998865

>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=92.97  E-value=0.055  Score=50.64  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|.|++|+||||+++.+..
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~   31 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLAR   31 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999999976

>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=92.97  E-value=0.054  Score=49.01  Aligned_cols=24  Identities=25%  Similarity=0.393  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.|.|.|++|+||||||.++...
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~   57 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQR   57 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHh
Confidence            357899999999999999999874

>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=92.96  E-value=0.087  Score=52.95  Aligned_cols=24  Identities=21%  Similarity=0.214  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|.+|+|||||+..+..
T Consensus        78 ~~~~I~i~G~~G~GKSTl~~~L~~  101 (355)
T 3p32_A           78 NAHRVGITGVPGVGKSTAIEALGM  101 (355)
T ss_dssp             CSEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            568999999999999999999875

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.92  E-value=0.06  Score=51.55  Aligned_cols=24  Identities=33%  Similarity=0.409  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||.+.++.
T Consensus        31 ~Ge~~~liG~nGsGKSTLlk~l~G   54 (262)
T 1b0u_A           31 AGDVISIIGSSGSGKSTFLRCINF   54 (262)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            346999999999999999999976

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=92.91  E-value=0.9  Score=45.49  Aligned_cols=25  Identities=24%  Similarity=0.577  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.|+|+|..|+|||||...+...
T Consensus        33 ~lp~I~vvG~~~sGKSSLln~l~g~   57 (360)
T 3t34_A           33 SLPAIAVVGGQSSGKSSVLESIVGK   57 (360)
T ss_dssp             CCCEEEEECBTTSSHHHHHHHHHTS
T ss_pred             cCCEEEEECCCCCcHHHHHHHHhCC
Confidence            5679999999999999999999874

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=92.90  E-value=0.051  Score=51.57  Aligned_cols=23  Identities=22%  Similarity=0.394  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|+|+.|+||||+++.+..
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~   70 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMAR   70 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999977

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=92.89  E-value=0.051  Score=53.84  Aligned_cols=22  Identities=36%  Similarity=0.422  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|.|+.|+||||||..++.
T Consensus         8 ~lI~I~GptgSGKTtla~~La~   29 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAK   29 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEECCCcCcHHHHHHHHHH
Confidence            5899999999999999999877

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=92.88  E-value=0.091  Score=55.90  Aligned_cols=25  Identities=28%  Similarity=0.462  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|.|++|+|||||++.++..
T Consensus       280 ~G~i~~i~G~~GsGKSTLl~~l~g~  304 (525)
T 1tf7_A          280 KDSIILATGATGTGKTLLVSRFVEN  304 (525)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            4569999999999999999999863

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=92.87  E-value=0.033  Score=54.33  Aligned_cols=24  Identities=21%  Similarity=0.448  Sum_probs=18.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +..+|+|.|+.|+||||+|+.+..
T Consensus         4 ~~~iIgItG~sGSGKSTva~~L~~   27 (290)
T 1a7j_A            4 KHPIISVTGSSGAGTSTVKHTFDQ   27 (290)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            456899999999999999999876

>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=92.87  E-value=0.064  Score=55.22  Aligned_cols=26  Identities=23%  Similarity=0.423  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +...+|.|+|++|+||||+|+.+...
T Consensus       256 ~~~~lIil~G~pGSGKSTla~~L~~~  281 (416)
T 3zvl_A          256 PNPEVVVAVGFPGAGKSTFIQEHLVS  281 (416)
T ss_dssp             SSCCEEEEESCTTSSHHHHHHHHTGG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHh
Confidence            35689999999999999999999873

>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=92.86  E-value=0.054  Score=48.53  Aligned_cols=22  Identities=41%  Similarity=0.679  Sum_probs=20.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+...
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5889999999999999999873

>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=92.86  E-value=0.085  Score=50.81  Aligned_cols=52  Identities=17%  Similarity=0.072  Sum_probs=31.8

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .-.|...|..++-+|+||+--..-+...-..+...+...  ..|..||++|.+.
T Consensus       151 Rv~iAraL~~~P~lLlLDEPts~LD~~~~~~i~~~l~~l~~~~g~tvi~vtHdl  204 (275)
T 3gfo_A          151 RVAIAGVLVMEPKVLILDEPTAGLDPMGVSEIMKLLVEMQKELGITIIIATHDI  204 (275)
T ss_dssp             HHHHHHHHTTCCSEEEEECTTTTCCHHHHHHHHHHHHHHHHHHCCEEEEEESCC
T ss_pred             HHHHHHHHHcCCCEEEEECccccCCHHHHHHHHHHHHHHHhhCCCEEEEEecCH
Confidence            334666677788899999864443344444455444332  2367777777765

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=92.83  E-value=0.057  Score=52.89  Aligned_cols=24  Identities=33%  Similarity=0.386  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+||||++..++.
T Consensus        99 ~g~vi~lvG~nGsGKTTll~~Lag  122 (302)
T 3b9q_A           99 KPAVIMIVGVNGGGKTTSLGKLAH  122 (302)
T ss_dssp             SCEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHH
Confidence            357999999999999999999987

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=92.82  E-value=1.1  Score=41.74  Aligned_cols=36  Identities=22%  Similarity=0.243  Sum_probs=26.1

Q ss_pred             chhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          171 RNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       171 R~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      |+...+.+..++..             .-+.|+|+.|.|||.+|..+..
T Consensus        95 ~~~Q~~ai~~~~~~-------------~~~ll~~~tG~GKT~~a~~~~~  130 (237)
T 2fz4_A           95 RDYQEKALERWLVD-------------KRGCIVLPTGSGKTHVAMAAIN  130 (237)
T ss_dssp             CHHHHHHHHHHTTT-------------SEEEEEESSSTTHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhC-------------CCEEEEeCCCCCHHHHHHHHHH
Confidence            55555666655531             2378899999999999988765

>1ak2_A Adenylate kinase isoenzyme-2; nucleoside monophosphate kinase, phosphotransferase; 1.92A {Bos taurus} SCOP: c.37.1.1 g.41.2.1 PDB: 2ak2_A 2c9y_A*

Probab=92.79  E-value=0.065  Score=50.24  Aligned_cols=24  Identities=25%  Similarity=0.238  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....|.|.|++|+||||+|+.+..
T Consensus        15 ~~~~I~l~G~~GsGKsT~a~~La~   38 (233)
T 1ak2_A           15 KGVRAVLLGPPGAGKGTQAPKLAK   38 (233)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999999987

>3j16_B RLI1P; ribosome recycling, translation, eukarya, ribosome; HET: ATP; 7.20A {Saccharomyces cerevisiae}

Probab=92.73  E-value=0.35  Score=52.05  Aligned_cols=136  Identities=8%  Similarity=-0.033  Sum_probs=65.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhh-cc-C-C-eeEEEEecCCCchhhhhhhhhh-h-cccchHHHHHHHHHHhccCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVK-AN-F-D-KRIWVSASYPRDEIRVARDEIS-V-ARDRDEIRVAKAILESLKGS  271 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~-~~-F-~-~~~wv~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~il~~l~~~  271 (597)
                      .+++|.|+.|+|||||++.++--..-. +. . . .+.++.-.............+. . ............+++.++..
T Consensus       379 Eiv~iiG~NGsGKSTLlk~l~Gl~~p~~G~~~~~~~i~~~~q~~~~~~~~tv~e~~~~~~~~~~~~~~~~~~~l~~l~l~  458 (608)
T 3j16_B          379 EILVMMGENGTGKTTLIKLLAGALKPDEGQDIPKLNVSMKPQKIAPKFPGTVRQLFFKKIRGQFLNPQFQTDVVKPLRID  458 (608)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHTSSCCSBCCCCCSCCEEEECSSCCCCCCSBHHHHHHHHCSSTTTSHHHHHHTHHHHTST
T ss_pred             eEEEEECCCCCcHHHHHHHHhcCCCCCCCcCccCCcEEEecccccccCCccHHHHHHHHhhcccccHHHHHHHHHHcCCh
Confidence            579999999999999999997632111 11 0 0 1222221100000000001000 0 00001123344556655532


Q ss_pred             C------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          272 V------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       272 ~------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .      .....-+.-.-.|...|..++=+|+||.--..-+...-..+...+...  ..|..||++|.+.
T Consensus       459 ~~~~~~~~~LSGGqkQRv~iAraL~~~p~lLlLDEPT~gLD~~~~~~i~~ll~~l~~~~g~tviivtHdl  528 (608)
T 3j16_B          459 DIIDQEVQHLSGGELQRVAIVLALGIPADIYLIDEPSAYLDSEQRIICSKVIRRFILHNKKTAFIVEHDF  528 (608)
T ss_dssp             TTSSSBSSSCCHHHHHHHHHHHHTTSCCSEEEECCTTTTCCHHHHHHHHHHHHHHHHHHTCEEEEECSCH
T ss_pred             hhhcCChhhCCHHHHHHHHHHHHHHhCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            1      111222333445677788889999999864333233334444444331  2366777777654

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=92.72  E-value=0.56  Score=55.60  Aligned_cols=24  Identities=17%  Similarity=0.278  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....|+|+|+.|+|||||++.+++
T Consensus      1104 ~Ge~vaIVG~SGsGKSTL~~lL~r 1127 (1321)
T 4f4c_A         1104 PGQTLALVGPSGCGKSTVVALLER 1127 (1321)
T ss_dssp             TTCEEEEECSTTSSTTSHHHHHTT
T ss_pred             CCCEEEEECCCCChHHHHHHHHhc
Confidence            346899999999999999999976

>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=92.66  E-value=0.067  Score=52.28  Aligned_cols=24  Identities=17%  Similarity=0.333  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||++.+..
T Consensus       125 ~Ge~vaIvGpsGsGKSTLl~lL~g  148 (305)
T 2v9p_A          125 KKNCLAFIGPPNTGKSMLCNSLIH  148 (305)
T ss_dssp             TCSEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhh
Confidence            457999999999999999999887

>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=92.65  E-value=0.062  Score=49.35  Aligned_cols=21  Identities=29%  Similarity=0.534  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|.|.|++|+||||.|+.+..
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~   22 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAK   22 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            578999999999999999987

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=92.62  E-value=0.29  Score=49.36  Aligned_cols=46  Identities=26%  Similarity=0.445  Sum_probs=33.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|....+.++...+.....        ....|.|+|.+|+||+++|+.+.+
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~a~--------~~~~vli~GesGtGKe~lAr~ih~  174 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKIAK--------SKAPVLITGESGTGKEIVARLIHR  174 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHHT--------SCSCEEEECCTTSSHHHHHHHHHH
T ss_pred             ccccccchHHHHHHhhhhhhhc--------cchhheEEeCCCchHHHHHHHHHH
Confidence            3477887777776666543322        223577999999999999999876

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.60  E-value=0.47  Score=48.63  Aligned_cols=25  Identities=24%  Similarity=0.282  Sum_probs=22.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...++..|.|.+|.||||+..+.++
T Consensus       159 ~~~~v~~I~G~aGsGKTt~I~~~~~  183 (446)
T 3vkw_A          159 SSAKVVLVDGVPGCGKTKEILSRVN  183 (446)
T ss_dssp             CCSEEEEEEECTTSCHHHHHHHHCC
T ss_pred             ccccEEEEEcCCCCCHHHHHHHHhc
Confidence            4678999999999999999999886

>3lv8_A DTMP kinase, thymidylate kinase; structural genomics, in diseases, center for structural genomics of infectious DISE ATP-binding; HET: ADP TMP TYD; 1.80A {Vibrio cholerae o1 biovar eltor} PDB: 3n2i_A*

Probab=92.60  E-value=0.44  Score=44.62  Aligned_cols=36  Identities=25%  Similarity=0.299  Sum_probs=26.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEE
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWV  233 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  233 (597)
                      ...|+|.|+.|+||||+++.+..... ..++..+...
T Consensus        27 ~~~i~~eG~~GsGKsT~~~~l~~~l~-~~~~~~~~~~   62 (236)
T 3lv8_A           27 AKFIVIEGLEGAGKSTAIQVVVETLQ-QNGIDHITRT   62 (236)
T ss_dssp             CCEEEEEESTTSCHHHHHHHHHHHHH-HTTCCCEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH-hcCCCeeeee
Confidence            46899999999999999999987422 2345534433

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=92.59  E-value=0.43  Score=50.00  Aligned_cols=24  Identities=29%  Similarity=0.376  Sum_probs=20.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|+|+|.+|+||||++..+..
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~  123 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAY  123 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            467999999999999999999886

>1e4v_A Adenylate kinase; transferase(phosphotransferase); HET: AP5; 1.85A {Escherichia coli} SCOP: c.37.1.1 g.41.2.1 PDB: 1e4y_A* 1ake_A* 1ank_A* 2eck_A* 3hpq_A* 4ake_A 3hpr_A*

Probab=92.58  E-value=0.062  Score=49.62  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|++|+||||+|+.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~   22 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIME   22 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            478999999999999999976

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=92.57  E-value=0.059  Score=52.98  Aligned_cols=22  Identities=41%  Similarity=0.711  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|+|+|+.|+||||||..++.
T Consensus         6 ~~i~i~GptGsGKTtla~~La~   27 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALAD   27 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999987

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=92.56  E-value=0.063  Score=49.99  Aligned_cols=21  Identities=38%  Similarity=0.480  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|++|+||||+++.+..
T Consensus         2 ~I~l~G~~GsGKsT~a~~La~   22 (223)
T 2xb4_A            2 NILIFGPNGSGKGTQGNLVKD   22 (223)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            588999999999999999976

>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=92.56  E-value=0.14  Score=52.54  Aligned_cols=43  Identities=12%  Similarity=0.133  Sum_probs=29.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCC----eeEEEEecCCCch
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFD----KRIWVSASYPRDE  241 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~----~~~wv~~~~~~~~  241 (597)
                      ...++|.|.+|+|||+|+.++.+.  ...+-+    .++++-+.+....
T Consensus       151 GQr~~Ifgg~G~GKt~L~~~Ia~~--~~~~~d~~~~~~V~~~iGeR~~E  197 (465)
T 3vr4_D          151 GQKLPVFSGSGLPHKELAAQIARQ--ATVLDSSDDFAVVFAAIGITFEE  197 (465)
T ss_dssp             TCBCCEEECTTSCHHHHHHHHHHH--CBCSSCSSCEEEEEEEEEECHHH
T ss_pred             CCEEEEeCCCCcChHHHHHHHHHH--HHhccCCCceEEEEEEecCCcHH
Confidence            456789999999999999998874  222223    4566666655433

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=92.53  E-value=0.049  Score=50.14  Aligned_cols=23  Identities=35%  Similarity=0.358  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||++.++.
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~G   44 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAV   44 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhc
Confidence            35899999999999999999875

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.51  E-value=0.48  Score=43.59  Aligned_cols=23  Identities=39%  Similarity=0.436  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..|+|.|+.|+||||+++.+...
T Consensus         4 ~~i~~eG~~gsGKsT~~~~l~~~   26 (213)
T 4tmk_A            4 KYIVIEGLEGAGKTTARNVVVET   26 (213)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            68999999999999999999874

>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=92.51  E-value=0.16  Score=60.79  Aligned_cols=85  Identities=22%  Similarity=0.274  Sum_probs=58.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC-
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS-  273 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~-  273 (597)
                      +..++|-|+|+.|+||||||.++..  .....=...+|+.+....+.                .     .++.++.+.. 
T Consensus      1429 prg~~iei~g~~~sGkttl~~~~~a--~~~~~g~~~~~i~~e~~~~~----------------~-----~~~~~Gv~~~~ 1485 (1706)
T 3cmw_A         1429 PMGRIVEIYGPESSGKTTLTLQVIA--AAQREGKTCAFIDAEHALDP----------------I-----YARKLGVDIDN 1485 (1706)
T ss_dssp             ETTSEEEEECSTTSSHHHHHHHHHH--HHHHTTCCEEEECTTSCCCH----------------H-----HHHHTTCCGGG
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHH--HHHhcCCeEEEEecCCCCCH----------------H-----HHHHcCCCHHH
Confidence            5678999999999999999999987  44445566788887766655                1     1455554422 


Q ss_pred             ----chhhHHHHHHHHHHHhc-CceEEEEEeccc
Q 041007          274 ----SQVEMETVLQYINEFVQ-GKKVLLVLDDLW  302 (597)
Q Consensus       274 ----~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~  302 (597)
                          .++..++....+...++ +..-+||+|-|-
T Consensus      1486 l~~~~p~~~e~~l~~~~~~~~s~~~~~vvvDsv~ 1519 (1706)
T 3cmw_A         1486 LLCSQPDTGEQALEICDALARSGAVDVIVVDSVA 1519 (1706)
T ss_dssp             CEEECCSSHHHHHHHHHHHHHHTCCSEEEESCST
T ss_pred             eEEeCCCcHHHHHHHHHHHHHcCCCCEEEEccHH
Confidence                23333555555666665 566799999873

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=92.49  E-value=0.07  Score=51.05  Aligned_cols=23  Identities=26%  Similarity=0.511  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||++.+..
T Consensus        25 g~~v~i~Gp~GsGKSTll~~l~g   47 (261)
T 2eyu_A           25 MGLILVTGPTGSGKSTTIASMID   47 (261)
T ss_dssp             SEEEEEECSTTCSHHHHHHHHHH
T ss_pred             CCEEEEECCCCccHHHHHHHHHH
Confidence            46999999999999999999877

>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=92.47  E-value=0.073  Score=46.68  Aligned_cols=23  Identities=22%  Similarity=0.426  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..|+|+|.+|+|||||...+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999874

>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=92.40  E-value=0.077  Score=50.95  Aligned_cols=23  Identities=30%  Similarity=0.391  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||++.++.
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~G   68 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAG   68 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46999999999999999999987

>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=92.37  E-value=0.075  Score=50.70  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        33 Ge~~~liG~nGsGKSTLlk~l~G   55 (257)
T 1g6h_A           33 GDVTLIIGPNGSGKSTLINVITG   55 (257)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46999999999999999999975

>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=92.36  E-value=0.066  Score=52.34  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|.|.|++|+||||+|+.+..
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~   24 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIA   24 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999876

>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=92.29  E-value=0.072  Score=48.14  Aligned_cols=24  Identities=25%  Similarity=0.531  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-.|+|+|++|+|||||.+.+...
T Consensus        29 ~~kv~lvG~~g~GKSTLl~~l~~~   52 (191)
T 1oix_A           29 LFKVVLIGDSGVGKSNLLSRFTRN   52 (191)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            357899999999999999998764

>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=92.27  E-value=0.079  Score=50.33  Aligned_cols=23  Identities=26%  Similarity=0.400  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.++.
T Consensus        29 Ge~~~l~G~nGsGKSTLlk~l~G   51 (250)
T 2d2e_A           29 GEVHALMGPNGAGKSTLGKILAG   51 (250)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            46999999999999999999987

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=92.21  E-value=0.2  Score=59.43  Aligned_cols=25  Identities=16%  Similarity=0.349  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|+|+.|+|||||++.+...
T Consensus       443 ~G~~vaivG~sGsGKSTll~ll~~~  467 (1321)
T 4f4c_A          443 AGQTVALVGSSGCGKSTIISLLLRY  467 (1321)
T ss_dssp             TTCEEEEEECSSSCHHHHHHHHTTS
T ss_pred             CCcEEEEEecCCCcHHHHHHHhccc
Confidence            4568999999999999999999774

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=92.20  E-value=0.98  Score=56.81  Aligned_cols=22  Identities=27%  Similarity=0.392  Sum_probs=19.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +-|.++|++|+|||++|+.+..
T Consensus      1268 ~~vLL~GPpGtGKT~la~~~l~ 1289 (2695)
T 4akg_A         1268 RGIILCGPPGSGKTMIMNNALR 1289 (2695)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHh
Confidence            6788999999999999977765

>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=92.15  E-value=0.13  Score=48.98  Aligned_cols=36  Identities=22%  Similarity=0.362  Sum_probs=27.5

Q ss_pred             HHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          176 QKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       176 ~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+..||....        +....|.|+|++|+|||.+|..+++
T Consensus        91 ~~l~~~l~~~~--------~~~n~~~l~GppgtGKt~~a~ala~  126 (267)
T 1u0j_A           91 SVFLGWATKKF--------GKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             HHHHHHHTTCS--------TTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             HHHHHHHhCCC--------CCCcEEEEECCCCCCHHHHHHHHHh
Confidence            44667776321        2345799999999999999999987

>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=92.15  E-value=0.083  Score=53.35  Aligned_cols=24  Identities=25%  Similarity=0.261  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|++|+|||||++.+..
T Consensus       168 ~~~~i~l~G~~GsGKSTl~~~l~~  191 (377)
T 1svm_A          168 KKRYWLFKGPIDSGKTTLAAALLE  191 (377)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHh
Confidence            457999999999999999999986

>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=92.13  E-value=0.07  Score=48.32  Aligned_cols=24  Identities=21%  Similarity=-0.036  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+..++|+.|.||||.+....++
T Consensus         8 g~i~v~~G~mgsGKTT~ll~~a~r   31 (191)
T 1xx6_A            8 GWVEVIVGPMYSGKSEELIRRIRR   31 (191)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHH
Confidence            479999999999999999888774

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=92.13  E-value=0.11  Score=46.88  Aligned_cols=25  Identities=24%  Similarity=0.534  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4578999999999999999999875

>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=92.11  E-value=0.58  Score=52.96  Aligned_cols=132  Identities=16%  Similarity=0.031  Sum_probs=66.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCC---eeEEEEecCCC---chhhhhhhhhhhcccchHHHHHHHHHHhccC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFD---KRIWVSASYPR---DEIRVARDEISVARDRDEIRVAKAILESLKG  270 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~---~~~wv~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~  270 (597)
                      ..+++|+|+.|+|||||.+.+..- .+. .++   ..-.+.+.+..   .........+.. ...+.......+++.++.
T Consensus       461 Ge~v~LiGpNGsGKSTLLk~LagG-~i~-g~~~~~~~~~~~v~q~~~~~~~~ltv~e~l~~-~~~~~~~~v~~~L~~lgL  537 (986)
T 2iw3_A          461 ARRYGICGPNGCGKSTLMRAIANG-QVD-GFPTQEECRTVYVEHDIDGTHSDTSVLDFVFE-SGVGTKEAIKDKLIEFGF  537 (986)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHT-CST-TCCCTTTSCEEETTCCCCCCCTTSBHHHHHHT-TCSSCHHHHHHHHHHTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC-CcC-CCccccceeEEEEcccccccccCCcHHHHHHH-hhcCHHHHHHHHHHHcCC
Confidence            458999999999999999999731 111 111   00012222211   000000111100 000003334556666654


Q ss_pred             CC-------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          271 SV-------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       271 ~~-------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      ..       .....-+...-.|...+..++-+|+||.--+.-+...-..+...+..  .|..||++|.+.
T Consensus       538 ~~~~~~~~~~~LSGGqkQRvaLArAL~~~P~lLLLDEPTs~LD~~~~~~l~~~L~~--~g~tvIivSHdl  605 (986)
T 2iw3_A          538 TDEMIAMPISALSGGWKMKLALARAVLRNADILLLDEPTNHLDTVNVAWLVNYLNT--CGITSITISHDS  605 (986)
T ss_dssp             CHHHHHSBGGGCCHHHHHHHHHHHHHHTTCSEEEEESTTTTCCHHHHHHHHHHHHH--SCSEEEEECSCH
T ss_pred             ChhhhcCCcccCCHHHHHHHHHHHHHhcCCCEEEEECCccCCCHHHHHHHHHHHHh--CCCEEEEEECCH
Confidence            21       01111222333455566677889999986544335555556666655  467788887764

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=92.09  E-value=0.079  Score=53.08  Aligned_cols=24  Identities=33%  Similarity=0.386  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+||||++..++.
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag  179 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAH  179 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHh
Confidence            457999999999999999999987

>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=92.07  E-value=0.087  Score=49.97  Aligned_cols=23  Identities=22%  Similarity=0.468  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        26 Ge~~~liG~NGsGKSTLlk~l~G   48 (249)
T 2qi9_C           26 GEILHLVGPNGAGKSTLLARMAG   48 (249)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            45899999999999999999976

>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=92.07  E-value=0.45  Score=49.21  Aligned_cols=42  Identities=26%  Similarity=0.332  Sum_probs=29.3

Q ss_pred             CccEEEEEcCCCCcHHHHH-HHHhCChhhhccCC-eeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALA-RQVFDDSDVKANFD-KRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA-~~v~~~~~~~~~F~-~~~wv~~~~~~~~  241 (597)
                      ....++|.|..|+|||+|+ ..+.+.    .+-+ .++++-+.+....
T Consensus       161 rGQR~~Ifg~~g~GKT~l~l~~I~n~----~~~dv~~V~~~IGeR~~e  204 (513)
T 3oaa_A          161 RGQRELIIGDRQTGKTALAIDAIINQ----RDSGIKCIYVAIGQKAST  204 (513)
T ss_dssp             TTCBCEEEESSSSSHHHHHHHHHHTT----SSSSCEEEEEEESCCHHH
T ss_pred             cCCEEEeecCCCCCcchHHHHHHHhh----ccCCceEEEEEecCChHH
Confidence            3467899999999999996 466662    2233 3567777766544

>1yrb_A ATP(GTP)binding protein; GTPase, P-loop, rossman fold, GDP, HYDR; HET: GDP; 1.75A {Pyrococcus abyssi} SCOP: c.37.1.10 PDB: 1yr6_A* 1yr8_A* 1yr9_A* 1yra_A* 1yr7_A* 2oxr_A*

Probab=92.05  E-value=0.082  Score=50.40  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...++.+.|.||+||||++..+..
T Consensus        13 ~~~i~~~~GkgGvGKTTl~~~La~   36 (262)
T 1yrb_A           13 ASMIVVFVGTAGSGKTTLTGEFGR   36 (262)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCCHHHHHHHHHH
Confidence            457889999999999999999975

>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=92.04  E-value=0.075  Score=48.27  Aligned_cols=24  Identities=25%  Similarity=0.531  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|+|++|+|||||.+.+...
T Consensus         5 ~~kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            5 LFKVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECcCCCCHHHHHHHHhcC
Confidence            356899999999999999999764

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=92.04  E-value=0.13  Score=45.47  Aligned_cols=25  Identities=32%  Similarity=0.464  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus         7 ~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            7 RPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            5678999999999999999999764

>4bas_A ADP-ribosylation factor, putative (small GTPase, putative); hydrolase; HET: GNP; 2.00A {Trypanosoma brucei TREU927}

Probab=92.04  E-value=0.085  Score=47.65  Aligned_cols=26  Identities=27%  Similarity=0.250  Sum_probs=22.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .....|+|+|.+|+|||||...+...
T Consensus        15 ~~~~ki~v~G~~~~GKSsl~~~l~~~   40 (199)
T 4bas_A           15 KTKLQVVMCGLDNSGKTTIINQVKPA   40 (199)
T ss_dssp             -CEEEEEEECCTTSCHHHHHHHHSCC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhcC
Confidence            45678999999999999999999875

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=92.03  E-value=0.11  Score=46.59  Aligned_cols=25  Identities=20%  Similarity=0.428  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           22 LKGEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             TTCEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHcC
Confidence            4567899999999999999999875

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=92.01  E-value=0.074  Score=49.76  Aligned_cols=24  Identities=29%  Similarity=0.278  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|.|+.|+|||||++.+..
T Consensus        19 ~g~~i~i~G~~GsGKSTl~~~L~~   42 (230)
T 2vp4_A           19 QPFTVLIEGNIGSGKTTYLNHFEK   42 (230)
T ss_dssp             CCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHh
Confidence            457999999999999999999877

>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=91.88  E-value=0.33  Score=50.34  Aligned_cols=42  Identities=21%  Similarity=0.305  Sum_probs=29.4

Q ss_pred             CccEEEEEcCCCCcHHHHH-HHHhCChhhhccCCe-eEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALA-RQVFDDSDVKANFDK-RIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA-~~v~~~~~~~~~F~~-~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+|| ..+.+..    .-+. ++++-+.+....
T Consensus       174 rGQR~~I~g~~g~GKT~Lal~~I~~~~----~~dv~~V~~~IGeR~~E  217 (515)
T 2r9v_A          174 RGQRELIIGDRQTGKTAIAIDTIINQK----GQGVYCIYVAIGQKKSA  217 (515)
T ss_dssp             TTCBEEEEEETTSSHHHHHHHHHHTTT----TTTEEEEEEEESCCHHH
T ss_pred             cCCEEEEEcCCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCcHH
Confidence            3567899999999999996 4677732    2453 466777765543

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=91.85  E-value=0.092  Score=45.45  Aligned_cols=23  Identities=22%  Similarity=0.495  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +-|+|.|.+|+|||||...+...
T Consensus         2 ~ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            2 HKVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999998764

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.82  E-value=0.094  Score=50.65  Aligned_cols=23  Identities=26%  Similarity=0.222  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||.+.++.
T Consensus        47 Ge~~~liG~NGsGKSTLlk~l~G   69 (279)
T 2ihy_A           47 GDKWILYGLNGAGKTTLLNILNA   69 (279)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46899999999999999999976

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=91.81  E-value=0.1  Score=48.98  Aligned_cols=25  Identities=24%  Similarity=0.205  Sum_probs=22.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....+|+|.|+.|+||||+++.+..
T Consensus        14 ~~~~~i~i~G~~gsGKst~~~~l~~   38 (236)
T 1q3t_A           14 MKTIQIAIDGPASSGKSTVAKIIAK   38 (236)
T ss_dssp             CCCCEEEEECSSCSSHHHHHHHHHH
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3567899999999999999999876

>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=91.78  E-value=0.31  Score=55.10  Aligned_cols=22  Identities=27%  Similarity=0.184  Sum_probs=20.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHH
Q 041007          196 TLPVIWILGNEGIGKTALARQV  217 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v  217 (597)
                      ...+++|+|+.|.||||+.+.+
T Consensus       661 ~g~i~~ItGpNGsGKSTlLr~i  682 (934)
T 3thx_A          661 KQMFHIITGPNMGGKSTYIRQT  682 (934)
T ss_dssp             TBCEEEEECCTTSSHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHH
Confidence            3579999999999999999988

>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=91.70  E-value=0.11  Score=48.51  Aligned_cols=25  Identities=32%  Similarity=0.468  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|.|++|+||||+++.+...
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~   49 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHR   49 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHH
Confidence            4578999999999999999999873

>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=91.69  E-value=0.093  Score=46.16  Aligned_cols=24  Identities=38%  Similarity=0.564  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            356899999999999999999875

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=91.56  E-value=0.07  Score=57.60  Aligned_cols=22  Identities=23%  Similarity=0.380  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|.++|++|+|||+||+.+++.
T Consensus       329 ~vLL~GppGtGKT~LAr~la~~  350 (595)
T 3f9v_A          329 HILIIGDPGTAKSQMLQFISRV  350 (595)
T ss_dssp             CEEEEESSCCTHHHHHHSSSTT
T ss_pred             ceEEECCCchHHHHHHHHHHHh
Confidence            6899999999999999999884

>3vr4_A V-type sodium ATPase catalytic subunit A; V-ATPase, rotary motor, P-loop, hydrolas ATPase, ATP binding; HET: MSE B3P; 2.17A {Enterococcus hirae} PDB: 3vr3_A* 3vr2_A* 3vr5_A 3vr6_A*

Probab=91.52  E-value=0.41  Score=50.31  Aligned_cols=51  Identities=16%  Similarity=0.198  Sum_probs=36.7

Q ss_pred             HHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          177 KILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       177 ~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      +.++.|..-.         ....++|.|..|+|||+|+.++.+.    .+-+.++++-+.+...
T Consensus       221 rvID~l~Pig---------rGqr~~Ifgg~g~GKT~L~~~ia~~----~~~~v~V~~~iGER~~  271 (600)
T 3vr4_A          221 RVIDTFFPVT---------KGGAAAVPGPFGAGKTVVQHQIAKW----SDVDLVVYVGCGERGN  271 (600)
T ss_dssp             HHHHHHSCCB---------TTCEEEEECCTTSCHHHHHHHHHHH----SSCSEEEEEEEEECHH
T ss_pred             hhhhccCCcc---------CCCEEeeecCCCccHHHHHHHHHhc----cCCCEEEEEEecccHH
Confidence            4566666433         4578999999999999999998773    2335677777776543

>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=91.48  E-value=0.51  Score=43.13  Aligned_cols=30  Identities=30%  Similarity=0.531  Sum_probs=23.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCe
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDK  229 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~  229 (597)
                      +.|+|-|..|+||||+++.+..  .....++.
T Consensus         3 kFI~~EG~dGsGKsTq~~~L~~--~L~~~~~v   32 (205)
T 4hlc_A            3 AFITFEGPEGSGKTTVINEVYH--RLVKDYDV   32 (205)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH--HHTTTSCE
T ss_pred             CEEEEECCCCCcHHHHHHHHHH--HHHCCCCE
Confidence            4789999999999999999887  34444443

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=91.46  E-value=0.099  Score=45.56  Aligned_cols=22  Identities=41%  Similarity=0.576  Sum_probs=19.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+.+.
T Consensus         4 ki~~vG~~~~GKSsli~~l~~~   25 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGGV   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCc
Confidence            5789999999999999999764

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=91.39  E-value=0.17  Score=46.76  Aligned_cols=23  Identities=22%  Similarity=0.250  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -.|.+.|.||+||||+|..+...
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~   29 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHA   29 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHH
T ss_pred             EEEEEECCCCCcHHHHHHHHHHH
Confidence            34888999999999999888874

>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=91.38  E-value=0.1  Score=52.82  Aligned_cols=22  Identities=41%  Similarity=0.616  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|+|.|+.|+||||||..++.
T Consensus         3 ~~i~i~GptgsGKttla~~La~   24 (409)
T 3eph_A            3 KVIVIAGTTGVGKSQLSIQLAQ   24 (409)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHH
T ss_pred             cEEEEECcchhhHHHHHHHHHH
Confidence            5899999999999999999986

>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=91.34  E-value=0.11  Score=54.14  Aligned_cols=24  Identities=29%  Similarity=0.432  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||++.++.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAg  315 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLAR  315 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHH
Confidence            457999999999999999999887

>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=91.33  E-value=0.1  Score=45.23  Aligned_cols=22  Identities=32%  Similarity=0.653  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|.|.+|+|||||+..+...
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5889999999999999999754

>2qe7_A ATP synthase subunit alpha; blockage of ATP hydrolysis, F1-ATPase, single analysis, thermoalkaliphilic, hydrolase; 3.06A {Bacillus SP} PDB: 1sky_B

Probab=91.32  E-value=0.32  Score=50.37  Aligned_cols=42  Identities=21%  Similarity=0.286  Sum_probs=29.1

Q ss_pred             CccEEEEEcCCCCcHHHHHH-HHhCChhhhccCCe-eEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALAR-QVFDDSDVKANFDK-RIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~-~v~~~~~~~~~F~~-~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+||. .+.+.  .  +-+. ++++-+.+....
T Consensus       161 rGQR~~Ifg~~g~GKT~Lal~~I~~~--~--~~dv~~V~~~iGeR~~E  204 (502)
T 2qe7_A          161 RGQRELIIGDRQTGKTTIAIDTIINQ--K--GQDVICIYVAIGQKQST  204 (502)
T ss_dssp             TTCBCEEEECSSSCHHHHHHHHHHGG--G--SCSEEEEEEEESCCHHH
T ss_pred             cCCEEEEECCCCCCchHHHHHHHHHh--h--cCCcEEEEEECCCcchH
Confidence            45678999999999999964 66663  2  3443 466777765443

>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=91.27  E-value=0.11  Score=45.39  Aligned_cols=21  Identities=29%  Similarity=0.552  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -|+|+|.+|+|||||...+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            588999999999999999875

>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=91.25  E-value=0.11  Score=45.37  Aligned_cols=24  Identities=17%  Similarity=0.398  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            346889999999999999998764

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=91.19  E-value=0.11  Score=50.06  Aligned_cols=21  Identities=33%  Similarity=0.765  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|+|+.|+|||||.+.++.
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g   24 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFK   24 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            589999999999999999875

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=91.19  E-value=0.14  Score=45.67  Aligned_cols=25  Identities=32%  Similarity=0.444  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        15 ~~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           15 QEVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhcC
Confidence            3467899999999999999999875

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.18  E-value=0.13  Score=47.28  Aligned_cols=25  Identities=36%  Similarity=0.438  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|++|+|||||...+...
T Consensus        11 ~~~~i~~~G~~g~GKTsl~~~l~~~   35 (218)
T 1nrj_B           11 YQPSIIIAGPQNSGKTSLLTLLTTD   35 (218)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            4678999999999999999998764

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=91.16  E-value=0.11  Score=45.34  Aligned_cols=23  Identities=22%  Similarity=0.455  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            45889999999999999999864

>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=91.16  E-value=0.13  Score=45.94  Aligned_cols=22  Identities=23%  Similarity=0.403  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+.+|+|+.|+|||||+..++-
T Consensus        27 g~~~i~G~NGsGKStll~ai~~   48 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILF   48 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            4899999999999999998854

>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=91.15  E-value=0.11  Score=45.90  Aligned_cols=23  Identities=22%  Similarity=0.288  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..|+|+|.+|+|||||...+...
T Consensus         5 ~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            5 MKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46889999999999999999874

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=91.12  E-value=0.13  Score=45.30  Aligned_cols=25  Identities=28%  Similarity=0.351  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..--|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            5 RQLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             ceEEEEEECcCCCCHHHHHHHHHhC
Confidence            3456889999999999999999764

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=91.11  E-value=0.12  Score=48.74  Aligned_cols=23  Identities=22%  Similarity=0.320  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +..|+|.|..|+||||+++.+..
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~   24 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHH
Confidence            36899999999999999999987

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=91.10  E-value=0.13  Score=45.32  Aligned_cols=25  Identities=28%  Similarity=0.506  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus         8 ~~~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A            8 ETHKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             CEEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            4567899999999999999998764

>3iev_A GTP-binding protein ERA; ERA, GTPase, KH domain, anti-SD, 16S rRNA, 30S ribosome ASSE GTP-binding, nucleotide-binding; HET: GNP; 1.90A {Aquifex aeolicus} PDB: 3r9w_A* 3r9x_A*

Probab=91.07  E-value=0.11  Score=51.14  Aligned_cols=27  Identities=19%  Similarity=0.405  Sum_probs=23.8

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          194 KPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       194 ~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++....|+|+|.+|+|||||...+...
T Consensus         7 ~~~~g~v~ivG~~nvGKSTLin~l~g~   33 (308)
T 3iev_A            7 HMKVGYVAIVGKPNVGKSTLLNNLLGT   33 (308)
T ss_dssp             CCEEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            456789999999999999999999764

>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=91.02  E-value=0.25  Score=50.63  Aligned_cols=25  Identities=16%  Similarity=0.201  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|.|.+|+|||+|+.++++.
T Consensus       146 rGQr~~Ifgg~G~GKt~L~~~Ia~~  170 (464)
T 3gqb_B          146 RGQKLPIFSGSGLPANEIAAQIARQ  170 (464)
T ss_dssp             TTCBCCEEEETTSCHHHHHHHHHHH
T ss_pred             cCCEEEEecCCCCCchHHHHHHHHH
Confidence            3457789999999999999998874

>3cbq_A GTP-binding protein REM 2; FLJ38964A, structural genomics consortium, SGC, GDP, membrane, nucleotide-binding, nucleotide binding protein; HET: GDP; 1.82A {Homo sapiens}

Probab=90.99  E-value=0.1  Score=47.25  Aligned_cols=24  Identities=25%  Similarity=0.454  Sum_probs=20.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...-|+|+|.+|+|||||...+..
T Consensus        22 ~~~ki~vvG~~~vGKSsLi~~l~~   45 (195)
T 3cbq_A           22 GIFKVMLVGESGVGKSTLAGTFGG   45 (195)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHTCC
T ss_pred             cEEEEEEECCCCCCHHHHHHHHHh
Confidence            345789999999999999999864

>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=90.82  E-value=0.33  Score=50.77  Aligned_cols=42  Identities=21%  Similarity=0.183  Sum_probs=32.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~  241 (597)
                      ....++|.|..|+|||+|+.++.+.    .+-+.++++-+.+....
T Consensus       226 kGqr~~I~g~~g~GKT~L~~~ia~~----~~~~~~V~~~iGER~~E  267 (588)
T 3mfy_A          226 KGGTAAIPGPAGSGKTVTQHQLAKW----SDAQVVIYIGCGERGNE  267 (588)
T ss_dssp             TTCEEEECSCCSHHHHHHHHHHHHH----SSCSEEEEEECCSSSSH
T ss_pred             cCCeEEeecCCCCCHHHHHHHHHhc----cCCCEEEEEEecccHHH
Confidence            4568999999999999999998662    23356788888877665

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=90.73  E-value=0.12  Score=46.20  Aligned_cols=23  Identities=30%  Similarity=0.580  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||+..+...
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999999764

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=90.70  E-value=0.13  Score=45.38  Aligned_cols=25  Identities=32%  Similarity=0.601  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcC
Confidence            3457899999999999999999875

>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=90.70  E-value=0.13  Score=44.71  Aligned_cols=23  Identities=35%  Similarity=0.603  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-|+|.|.+|+|||||...+...
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999998754

>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=90.70  E-value=0.3  Score=50.65  Aligned_cols=42  Identities=19%  Similarity=0.287  Sum_probs=29.0

Q ss_pred             CccEEEEEcCCCCcHHHHH-HHHhCChhhhccCC-eeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALA-RQVFDDSDVKANFD-KRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA-~~v~~~~~~~~~F~-~~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+|| ..+.+..    .-+ .++++-+.+....
T Consensus       162 rGQR~~Ifg~~g~GKT~Lal~~I~~~~----~~dv~~V~~~iGeR~~E  205 (507)
T 1fx0_A          162 RGQRELIIGDRQTGKTAVATDTILNQQ----GQNVICVYVAIGQKASS  205 (507)
T ss_dssp             TTCBCBEEESSSSSHHHHHHHHHHTCC----TTTCEEEEEEESCCHHH
T ss_pred             cCCEEEEecCCCCCccHHHHHHHHHhh----cCCcEEEEEEcCCCchH
Confidence            4567899999999999996 4677742    234 3466777665443

>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=90.67  E-value=0.11  Score=51.38  Aligned_cols=24  Identities=33%  Similarity=0.587  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++++|+|+.|+|||||.+.+..
T Consensus         3 ~i~v~~i~G~~GaGKTTll~~l~~   26 (318)
T 1nij_A            3 PIAVTLLTGFLGAGKTTLLRHILN   26 (318)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHH
T ss_pred             cccEEEEEecCCCCHHHHHHHHHh
Confidence            467999999999999999999985

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=90.66  E-value=0.12  Score=47.04  Aligned_cols=23  Identities=35%  Similarity=0.450  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-|+|+|.+|+|||||...+...
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~~~   48 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLKDD   48 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhcC
Confidence            46889999999999999999874

>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=90.65  E-value=0.096  Score=54.00  Aligned_cols=25  Identities=32%  Similarity=0.408  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.+|+|+|++|+||||++..+...
T Consensus        98 ~~~vI~ivG~~GvGKTTla~~La~~  122 (432)
T 2v3c_C           98 KQNVILLVGIQGSGKTTTAAKLARY  122 (432)
T ss_dssp             SCCCEEEECCSSSSTTHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHH
Confidence            4579999999999999999998774

>2qu8_A Putative nucleolar GTP-binding protein 1; GTPase, malaria, structural genomics, structural genomics consortium, SGC, unknown function; HET: GDP; 2.01A {Plasmodium falciparum}

Probab=90.64  E-value=0.18  Score=46.84  Aligned_cols=25  Identities=20%  Similarity=0.286  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        28 ~~~kI~vvG~~~vGKSsLin~l~~~   52 (228)
T 2qu8_A           28 HKKTIILSGAPNVGKSSFMNIVSRA   52 (228)
T ss_dssp             TSEEEEEECSTTSSHHHHHHHHTTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4568999999999999999999875

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=90.60  E-value=0.13  Score=45.97  Aligned_cols=22  Identities=23%  Similarity=0.419  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+...
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            5789999999999999999875

>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=90.57  E-value=0.73  Score=51.97  Aligned_cols=23  Identities=30%  Similarity=0.310  Sum_probs=20.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHh
Q 041007          196 TLPVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      ...+++|+|+.|.|||||.+.+.
T Consensus       672 ~g~i~~ItGPNGaGKSTlLr~i~  694 (918)
T 3thx_B          672 SERVMIITGPNMGGKSSYIKQVA  694 (918)
T ss_dssp             SCCEEEEESCCCHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCchHHHHHHHH
Confidence            45799999999999999999875

>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=90.56  E-value=0.13  Score=44.54  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999998754

>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=90.55  E-value=0.71  Score=47.92  Aligned_cols=46  Identities=20%  Similarity=0.283  Sum_probs=29.8

Q ss_pred             CccEEEEEcCCCCcHHHHH-HHHhCChhh----hccCC-eeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALA-RQVFDDSDV----KANFD-KRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA-~~v~~~~~~----~~~F~-~~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+|| ..+.+....    ..+-+ .++++-+.+....
T Consensus       161 rGQR~~I~g~~g~GKT~Lal~~I~~q~~~~~~~~~~~d~~~V~~~IGeR~~E  212 (510)
T 2ck3_A          161 RGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRST  212 (510)
T ss_dssp             TTCBCEEEESTTSSHHHHHHHHHHHTHHHHTSCCTTTCCEEEEEEESCCHHH
T ss_pred             cCCEEEEecCCCCCchHHHHHHHHHHHhhccccccCCCeEEEEEECCCCcHH
Confidence            4567899999999999995 456663221    01234 3667777765544

>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=90.54  E-value=0.14  Score=44.60  Aligned_cols=22  Identities=36%  Similarity=0.640  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5789999999999999998754

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=90.52  E-value=0.17  Score=44.99  Aligned_cols=25  Identities=32%  Similarity=0.586  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..--|+|+|.+|+|||||...+.+.
T Consensus        17 ~~~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           17 PTYKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhC
Confidence            3456899999999999999998754

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=90.43  E-value=0.15  Score=51.10  Aligned_cols=24  Identities=17%  Similarity=0.137  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|++|+|||||...+..
T Consensus        73 ~~~~v~lvG~pgaGKSTLln~L~~   96 (349)
T 2www_A           73 LAFRVGLSGPPGAGKSTFIEYFGK   96 (349)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHH
Confidence            467999999999999999999876

>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=90.42  E-value=0.14  Score=44.42  Aligned_cols=21  Identities=24%  Similarity=0.324  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -|+|+|.+|+|||||...+..
T Consensus         2 ki~~~G~~~~GKssl~~~l~~   22 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKL   22 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            378999999999999999865

>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=90.40  E-value=0.16  Score=50.84  Aligned_cols=23  Identities=26%  Similarity=0.287  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|+|||||.+.++-
T Consensus        29 Ge~~~llGpnGsGKSTLLr~iaG   51 (359)
T 2yyz_A           29 GEFVALLGPSGCGKTTTLLMLAG   51 (359)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHT
T ss_pred             CCEEEEEcCCCchHHHHHHHHHC
Confidence            46999999999999999999975

>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=90.39  E-value=0.22  Score=48.69  Aligned_cols=21  Identities=19%  Similarity=0.453  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHh
Q 041007          198 PVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      .+++|.|+.|+|||||.+.+.
T Consensus       166 ~i~~l~G~sG~GKSTLln~l~  186 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSRLT  186 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHH
Confidence            589999999999999999997

>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=90.39  E-value=0.86  Score=50.72  Aligned_cols=21  Identities=29%  Similarity=0.482  Sum_probs=17.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHh
Q 041007          198 PVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      .++.|+|+.|.||||++..+.
T Consensus       110 ~~vii~gpTGSGKTtllp~ll  130 (773)
T 2xau_A          110 QIMVFVGETGSGKTTQIPQFV  130 (773)
T ss_dssp             SEEEEECCTTSSHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHH
Confidence            589999999999999766554

>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=90.33  E-value=0.14  Score=44.53  Aligned_cols=22  Identities=18%  Similarity=0.514  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+...
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5789999999999999998754

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=90.32  E-value=0.14  Score=45.79  Aligned_cols=24  Identities=29%  Similarity=0.351  Sum_probs=20.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           20 ELKVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            346889999999999999887654

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=90.30  E-value=0.14  Score=46.17  Aligned_cols=23  Identities=26%  Similarity=0.501  Sum_probs=19.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .--|+|+|.+|+|||||...+..
T Consensus         6 ~~kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            6 YYRVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEEECCCCCCHHHHHHHHhc
Confidence            34689999999999999999863

>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=90.30  E-value=0.24  Score=50.99  Aligned_cols=46  Identities=13%  Similarity=0.174  Sum_probs=30.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhcc--CCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKAN--FDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~--F~~~~wv~~~~~~~~  241 (597)
                      ....++|.|.+|+|||+|+..++++......  =+.++++-+.+....
T Consensus       151 rGQr~~Ifgg~G~GKt~Ll~~Ia~~~~~n~~~~~~~~V~~~iGER~~E  198 (469)
T 2c61_A          151 RGQKLPIFSASGLPHNEIALQIARQASVPGSESAFAVVFAAMGITNEE  198 (469)
T ss_dssp             TTCBCCEEECTTSCHHHHHHHHHHHCBCTTCSSCEEEEEEEEEECHHH
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHHHhhccCCCCcEEEEEEccCCcHH
Confidence            3457788999999999999999875332211  134566666655433

>3llu_A RAS-related GTP-binding protein C; structural genomics consortium, SGC, cytoplasm, nucleotide-binding, nucleus, phosphoprotein; HET: GNP; 1.40A {Homo sapiens} PDB: 2q3f_A*

Probab=90.29  E-value=0.17  Score=45.77  Aligned_cols=25  Identities=28%  Similarity=0.569  Sum_probs=20.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..--|+|+|.+|+|||||...+.+.
T Consensus        19 ~~~ki~~vG~~~vGKTsLi~~l~~~   43 (196)
T 3llu_A           19 SKPRILLMGLRRSGKSSIQKVVFHK   43 (196)
T ss_dssp             -CCEEEEEESTTSSHHHHHHHHHSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHHhc
Confidence            3457899999999999999987764

>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=90.25  E-value=0.1  Score=47.75  Aligned_cols=25  Identities=16%  Similarity=0.170  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        25 ~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           25 TGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999998764

>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=90.22  E-value=0.093  Score=50.19  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +...|+|.|..|+||||+++.+..
T Consensus        23 ~~~~I~ieG~~GsGKST~~~~L~~   46 (263)
T 1p5z_B           23 RIKKISIEGNIAAGKSTFVNILKQ   46 (263)
T ss_dssp             CCEEEEEECSTTSSHHHHHTTTGG
T ss_pred             CceEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999998877

>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=90.19  E-value=0.15  Score=44.51  Aligned_cols=23  Identities=30%  Similarity=0.655  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            46889999999999999998753

>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=90.19  E-value=0.15  Score=45.10  Aligned_cols=25  Identities=36%  Similarity=0.694  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus         7 ~~~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            7 NILKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            4567899999999999999998764

>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=90.17  E-value=0.15  Score=44.45  Aligned_cols=23  Identities=26%  Similarity=0.657  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+...
T Consensus         7 ~~i~v~G~~~~GKSsli~~l~~~   29 (170)
T 1z0j_A            7 LKVCLLGDTGVGKSSIMWRFVED   29 (170)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            46889999999999999998764

>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=90.14  E-value=0.15  Score=44.89  Aligned_cols=25  Identities=28%  Similarity=0.594  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus         6 ~~~~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            6 SLFKVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceeEEEEECCCCCCHHHHHHHHHcC
Confidence            3457899999999999999998753

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=90.13  E-value=0.17  Score=50.44  Aligned_cols=24  Identities=21%  Similarity=0.221  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|++|+|||||...+..
T Consensus        54 ~g~~v~i~G~~GaGKSTLl~~l~g   77 (337)
T 2qm8_A           54 RAIRVGITGVPGVGKSTTIDALGS   77 (337)
T ss_dssp             CSEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            457999999999999999999875

>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=90.10  E-value=0.14  Score=44.63  Aligned_cols=24  Identities=25%  Similarity=0.380  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            456899999999999999998754

>1cp2_A CP2, nitrogenase iron protein; oxidoreductase; 1.93A {Clostridium pasteurianum} SCOP: c.37.1.10

Probab=90.03  E-value=0.27  Score=46.92  Aligned_cols=41  Identities=22%  Similarity=0.267  Sum_probs=28.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ++|+|.|-||+||||+|..+...  ....=..++-+++....+
T Consensus         2 ~vI~vs~KGGvGKTT~a~nLA~~--la~~G~~VlliD~D~q~~   42 (269)
T 1cp2_A            2 RQVAIYGKGGIGKSTTTQNLTSG--LHAMGKTIMVVGCDPKAD   42 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEEECTTSC
T ss_pred             cEEEEecCCCCcHHHHHHHHHHH--HHHCCCcEEEEcCCCCCC
Confidence            47888999999999999888763  322222456666654443

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=89.96  E-value=0.16  Score=44.66  Aligned_cols=23  Identities=30%  Similarity=0.446  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..-|.|.|++|+||||||.++..
T Consensus        16 G~gvli~G~SGaGKStlal~L~~   38 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALID   38 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            35789999999999999999876

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=89.95  E-value=0.17  Score=45.18  Aligned_cols=25  Identities=32%  Similarity=0.347  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..--|+|+|.+|+|||||...+...
T Consensus         6 ~~~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            6 VKCKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEEEECCCCCCHHHHHHHHhcC
Confidence            3456889999999999999998764

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=89.94  E-value=0.16  Score=44.18  Aligned_cols=24  Identities=21%  Similarity=0.387  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            6 QFKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999998753

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=89.94  E-value=0.16  Score=45.55  Aligned_cols=24  Identities=33%  Similarity=0.472  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        21 ~~ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           21 EVNLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCcHHHHHHHHHhC
Confidence            346889999999999999988764

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=89.88  E-value=0.16  Score=45.70  Aligned_cols=24  Identities=29%  Similarity=0.397  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           23 HGKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             -CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            347899999999999999998763

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=89.87  E-value=0.16  Score=46.91  Aligned_cols=22  Identities=27%  Similarity=0.345  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|+|+.|+||||+++.+..
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~   25 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVAS   25 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999999866

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=89.85  E-value=0.22  Score=52.34  Aligned_cols=45  Identities=4%  Similarity=-0.057  Sum_probs=30.8

Q ss_pred             cccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          168 FHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       168 ~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.|.+-.+.+.+.....        ..+..+|.+.|++|+||||+|+.+...
T Consensus       374 ~f~rpeV~~vLr~~~~~~--------~~~~~~I~l~GlsGsGKSTIa~~La~~  418 (511)
T 1g8f_A          374 WFSYPEVVKILRESNPPR--------PKQGFSIVLGNSLTVSREQLSIALLST  418 (511)
T ss_dssp             TTSCHHHHHHHHHHSCCG--------GGCCEEEEECTTCCSCHHHHHHHHHHH
T ss_pred             cccChhhHHHHHHhcccc--------cccceEEEecccCCCCHHHHHHHHHHH
Confidence            345555555555544211        124578999999999999999999883

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=89.76  E-value=0.18  Score=44.86  Aligned_cols=26  Identities=19%  Similarity=0.337  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCCh
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDS  221 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~  221 (597)
                      ....|+|.|.+|+|||||...+.+..
T Consensus        17 ~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           17 RELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            34678999999999999999998753

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=89.74  E-value=0.35  Score=44.18  Aligned_cols=22  Identities=32%  Similarity=0.226  Sum_probs=18.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+.|.++.|.|||.++.....
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~   70 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAK   70 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHH
Confidence            3578899999999998877654

>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=89.73  E-value=0.14  Score=52.20  Aligned_cols=24  Identities=17%  Similarity=0.347  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|+|+.|+|||||.+.+..
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~G   91 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRG   91 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhC
Confidence            346999999999999999999987

>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=89.65  E-value=0.18  Score=50.93  Aligned_cols=23  Identities=26%  Similarity=0.511  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||++.+..
T Consensus       136 g~~i~ivG~~GsGKTTll~~l~~  158 (372)
T 2ewv_A          136 MGLILVTGPTGSGKSTTIASMID  158 (372)
T ss_dssp             SEEEEEECSSSSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999999877

>2g3y_A GTP-binding protein GEM; small GTPase, GDP, inactive state, RGK family, structur genomics, structural genomics consortium, SGC, signaling PR; HET: GDP; 2.40A {Homo sapiens} SCOP: c.37.1.8

Probab=89.64  E-value=0.18  Score=46.43  Aligned_cols=23  Identities=26%  Similarity=0.501  Sum_probs=20.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..-|+|+|.+|+|||||...+..
T Consensus        37 ~~kVvlvG~~~vGKSSLl~r~~~   59 (211)
T 2g3y_A           37 YYRVVLIGEQGVGKSTLANIFAG   59 (211)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHh
Confidence            34689999999999999999874

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=89.62  E-value=0.18  Score=44.43  Aligned_cols=24  Identities=29%  Similarity=0.516  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999998764

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=89.61  E-value=0.15  Score=45.17  Aligned_cols=25  Identities=32%  Similarity=0.444  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~ki~~~G~~~~GKSsli~~l~~~   29 (181)
T 3t5g_A            5 KSRKIAILGYRSVGKSSLTIQFVEG   29 (181)
T ss_dssp             EEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECcCCCCHHHHHHHHHcC
Confidence            3467899999999999999998743

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=89.60  E-value=0.18  Score=44.84  Aligned_cols=24  Identities=25%  Similarity=0.270  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|+|.+|+|||||...+...
T Consensus        21 ~~~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           21 EHKVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999999874

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=89.59  E-value=0.14  Score=45.41  Aligned_cols=25  Identities=32%  Similarity=0.349  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~~   41 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQIG   41 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCCS
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            3467899999999999999999864

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=89.57  E-value=0.18  Score=45.51  Aligned_cols=24  Identities=21%  Similarity=0.229  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~~   52 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKLG   52 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCSS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhC
Confidence            456899999999999999999764

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=89.57  E-value=0.18  Score=44.44  Aligned_cols=23  Identities=30%  Similarity=0.492  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+...
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~   37 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYD   37 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46889999999999999998753

>4dkx_A RAS-related protein RAB-6A; GTP binding fold, membrane trafficking, GTP, cytosol, protei transport; HET: GDP; 1.90A {Homo sapiens} PDB: 3bbp_A*

Probab=89.53  E-value=0.15  Score=47.11  Aligned_cols=22  Identities=32%  Similarity=0.572  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|+..+.++
T Consensus        15 KivlvGd~~VGKTsLi~r~~~~   36 (216)
T 4dkx_A           15 KLVFLGEQSVGKTSLITRFMYD   36 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCcCHHHHHHHHHhC
Confidence            4788999999999999998754

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=89.53  E-value=0.17  Score=50.86  Aligned_cols=24  Identities=33%  Similarity=0.569  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|+.|+|||||++.+..-
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~~  198 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQE  198 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhc
Confidence            358999999999999999999873

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=89.53  E-value=0.18  Score=45.08  Aligned_cols=24  Identities=38%  Similarity=0.533  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        11 ~~ki~v~G~~~~GKSsli~~l~~~   34 (195)
T 3bc1_A           11 LIKFLALGDSGVGKTSVLYQYTDG   34 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999999754

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=89.51  E-value=0.37  Score=56.98  Aligned_cols=25  Identities=20%  Similarity=0.300  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|+|+.|+|||||++.+..-
T Consensus       415 ~G~~~~ivG~sGsGKSTl~~ll~g~  439 (1284)
T 3g5u_A          415 SGQTVALVGNSGCGKSTTVQLMQRL  439 (1284)
T ss_dssp             TTCEEEEECCSSSSHHHHHHHTTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3468999999999999999998763

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=89.51  E-value=0.19  Score=45.61  Aligned_cols=24  Identities=38%  Similarity=0.556  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            8 MFKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456899999999999999999875

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=89.51  E-value=0.14  Score=45.32  Aligned_cols=23  Identities=22%  Similarity=0.400  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+.+.
T Consensus         8 ~ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            8 LRLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEEECCGGGCHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999998764

>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=89.50  E-value=0.28  Score=48.91  Aligned_cols=24  Identities=17%  Similarity=0.178  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|.+|+|||||+..+..
T Consensus        55 ~~~~i~i~G~~g~GKSTl~~~l~~   78 (341)
T 2p67_A           55 NTLRLGVTGTPGAGKSTFLEAFGM   78 (341)
T ss_dssp             CSEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHH
Confidence            568999999999999999999875

>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=89.49  E-value=0.18  Score=44.89  Aligned_cols=23  Identities=30%  Similarity=0.631  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+.+.
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            46889999999999999999764

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=89.48  E-value=0.19  Score=45.22  Aligned_cols=23  Identities=39%  Similarity=0.693  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-|+|+|.+|+|||||...+...
T Consensus        27 ~ki~vvG~~~~GKSsLi~~l~~~   49 (192)
T 2il1_A           27 LQVIIIGSRGVGKTSLMERFTDD   49 (192)
T ss_dssp             EEEEEECSTTSSHHHHHHHHCC-
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            46889999999999999999875

>4dhe_A Probable GTP-binding protein ENGB; melioidosis, RAS-like GTPase, cell division, cell cycle, SEP GTP-binding; 2.20A {Burkholderia thailandensis}

Probab=89.48  E-value=0.16  Score=46.80  Aligned_cols=25  Identities=20%  Similarity=0.319  Sum_probs=22.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        28 ~~~~i~v~G~~~~GKSslin~l~~~   52 (223)
T 4dhe_A           28 VQPEIAFAGRSNAGKSTAINVLCNQ   52 (223)
T ss_dssp             CSCEEEEEESCHHHHHHHHHHHTTC
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHhCC
Confidence            4578899999999999999999875

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=89.47  E-value=0.24  Score=43.20  Aligned_cols=24  Identities=33%  Similarity=0.374  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|+|.+|+|||||...+...
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~~   30 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQVG   30 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999999653

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=89.46  E-value=0.22  Score=52.96  Aligned_cols=24  Identities=29%  Similarity=0.415  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|+.|+|||||++.+..
T Consensus       368 ~G~iI~LiG~sGSGKSTLar~La~  391 (552)
T 3cr8_A          368 QGFTVFFTGLSGAGKSTLARALAA  391 (552)
T ss_dssp             SCEEEEEEESSCHHHHHHHHHHHH
T ss_pred             cceEEEEECCCCChHHHHHHHHHH
Confidence            346899999999999999999987

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=89.45  E-value=0.2  Score=45.87  Aligned_cols=25  Identities=20%  Similarity=0.260  Sum_probs=20.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus         6 ~~~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            6 SQRAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             --CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4567899999999999999999764

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=89.39  E-value=0.18  Score=44.78  Aligned_cols=24  Identities=33%  Similarity=0.602  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+.+.
T Consensus        10 ~~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           10 LFKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcC
Confidence            457889999999999999998754

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=89.32  E-value=0.2  Score=45.35  Aligned_cols=24  Identities=21%  Similarity=0.268  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+.+.
T Consensus        20 ~~ki~~~G~~~~GKssl~~~l~~~   43 (201)
T 2q3h_A           20 GVKCVLVGDGAVGKTSLVVSYTTN   43 (201)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999999875

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=89.31  E-value=0.19  Score=45.13  Aligned_cols=24  Identities=25%  Similarity=0.497  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           25 VFKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            456899999999999999998764

>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=89.30  E-value=0.19  Score=44.57  Aligned_cols=24  Identities=38%  Similarity=0.634  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhC
Confidence            356899999999999999998754

>3g5u_A MCG1178, multidrug resistance protein 1A; P-glycoprotein, PGP, cyclic peptide, membrane protein; 3.80A {Mus musculus} PDB: 3g61_A* 3g60_A*

Probab=89.28  E-value=1  Score=53.29  Aligned_cols=25  Identities=16%  Similarity=0.259  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|+|+.|+|||||++.++.-
T Consensus      1058 ~Ge~v~ivG~sGsGKSTl~~~l~g~ 1082 (1284)
T 3g5u_A         1058 KGQTLALVGSSGCGKSTVVQLLERF 1082 (1284)
T ss_dssp             SSSEEEEECSSSTTHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcC
Confidence            3468999999999999999999763

>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=89.28  E-value=0.34  Score=46.86  Aligned_cols=41  Identities=22%  Similarity=0.249  Sum_probs=28.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ++|+|.|-||+||||+|..+...  ....=..++-|++....+
T Consensus         3 kvIavs~KGGvGKTT~a~nLA~~--La~~G~rVlliD~D~q~~   43 (289)
T 2afh_E            3 RQCAIYGKGGIGKSTTTQNLVAA--LAEMGKKVMIVGCDPKAD   43 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEEECSSSC
T ss_pred             eEEEEeCCCcCcHHHHHHHHHHH--HHHCCCeEEEEecCCCCC
Confidence            67888999999999999988773  322212355666654433

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=89.27  E-value=0.19  Score=44.39  Aligned_cols=24  Identities=21%  Similarity=0.274  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            8 FIKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999998764

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=89.26  E-value=0.19  Score=44.54  Aligned_cols=24  Identities=21%  Similarity=0.274  Sum_probs=20.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+.+.
T Consensus         5 ~~~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            5 AIKCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999998754

>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=89.22  E-value=0.19  Score=45.03  Aligned_cols=23  Identities=22%  Similarity=0.122  Sum_probs=19.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .--|+|+|.+|+|||||.+.+..
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~   36 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYS   36 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            34688999999999999976654

>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=89.21  E-value=0.31  Score=47.59  Aligned_cols=23  Identities=22%  Similarity=0.388  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+++|.|++|+|||||.+.+...
T Consensus       170 eiv~l~G~sG~GKSTll~~l~g~  192 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAINPG  192 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTT
T ss_pred             CeEEEECCCCCcHHHHHHHhccc
Confidence            58999999999999999999873

>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=89.17  E-value=0.18  Score=50.77  Aligned_cols=23  Identities=30%  Similarity=0.456  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...++|+|+.|+|||||++.+..
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~g  192 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAA  192 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHH
T ss_pred             hCeEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999998865

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=89.16  E-value=0.2  Score=45.39  Aligned_cols=24  Identities=29%  Similarity=0.585  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~   48 (200)
T 2o52_A           25 LFKFLVIGSAGTGKSCLLHQFIEN   48 (200)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHC-
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            456889999999999999999864

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=89.16  E-value=0.21  Score=46.85  Aligned_cols=25  Identities=24%  Similarity=0.441  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        28 ~~~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           28 SQLRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHcCC
Confidence            4567999999999999999999875

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=89.14  E-value=0.24  Score=44.52  Aligned_cols=25  Identities=20%  Similarity=0.385  Sum_probs=21.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..--|+|+|.+|+|||||...+...
T Consensus         7 ~~~ki~vvG~~~~GKSsli~~l~~~   31 (199)
T 2gf0_A            7 NDYRVVVFGAGGVGKSSLVLRFVKG   31 (199)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHS
T ss_pred             CeeEEEEECCCCCcHHHHHHHHHcC
Confidence            3457899999999999999998753

>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=89.09  E-value=0.19  Score=44.42  Aligned_cols=24  Identities=29%  Similarity=0.508  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            346899999999999999998754

>2qnr_A Septin-2, protein NEDD5; structural genomics consortium, SGC, mitosis, GDP, C cycle, cell division, GTP-binding, nucleotide-binding; HET: GDP; 2.60A {Homo sapiens} PDB: 2qa5_A* 3ftq_A*

Probab=89.08  E-value=0.17  Score=49.48  Aligned_cols=21  Identities=29%  Similarity=0.702  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -|+|+|+.|+|||||...++.
T Consensus        20 ~I~lvG~nG~GKSTLl~~L~g   40 (301)
T 2qnr_A           20 TLMVVGESGLGKSTLINSLFL   40 (301)
T ss_dssp             EEEEEEETTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            459999999999999999765

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=89.07  E-value=0.2  Score=45.16  Aligned_cols=24  Identities=29%  Similarity=0.493  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            356889999999999999998764

>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=89.03  E-value=0.24  Score=44.89  Aligned_cols=25  Identities=36%  Similarity=0.616  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus        13 ~~~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           13 ALHKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEEECCCCCCHHHHHHHHHhC
Confidence            3457899999999999999998754

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=89.00  E-value=0.2  Score=45.59  Aligned_cols=24  Identities=42%  Similarity=0.661  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        26 ~~ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           26 LFKIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            457899999999999999998754

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=88.99  E-value=0.21  Score=44.08  Aligned_cols=24  Identities=29%  Similarity=0.493  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        10 ~~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           10 AFKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHhC
Confidence            346899999999999999998754

>2aka_B Dynamin-1; fusion protein, GTPase domain, myosin, contractIle protein; 1.90A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 3l43_A*

Probab=88.98  E-value=0.49  Score=45.88  Aligned_cols=25  Identities=24%  Similarity=0.505  Sum_probs=22.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        25 ~~~~i~vvG~~~~GKSSLln~l~g~   49 (299)
T 2aka_B           25 DLPQIAVVGGQSAGKSSVLENFVGR   49 (299)
T ss_dssp             CCCEEEEEEBTTSCHHHHHHHHHTS
T ss_pred             CCCeEEEEeCCCCCHHHHHHHHHCC
Confidence            5678999999999999999999874

>2j1l_A RHO-related GTP-binding protein RHOD; GTPase, membrane, prenylation, hydrolase, nucleotide-binding, methylation, lipoprotein, endosome DYNA; HET: GDP; 2.5A {Homo sapiens}

Probab=88.98  E-value=0.21  Score=45.90  Aligned_cols=24  Identities=29%  Similarity=0.399  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        34 ~~ki~vvG~~~vGKSsli~~l~~~   57 (214)
T 2j1l_A           34 SVKVVLVGDGGCGKTSLLMVFADG   57 (214)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHC-
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcC
Confidence            356889999999999999999874

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=88.96  E-value=0.2  Score=45.72  Aligned_cols=24  Identities=33%  Similarity=0.361  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||+..+...
T Consensus        28 ~~ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           28 KCKIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999999764

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=88.91  E-value=0.21  Score=44.84  Aligned_cols=24  Identities=33%  Similarity=0.540  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        23 ~~ki~v~G~~~~GKSsli~~l~~~   46 (191)
T 3dz8_A           23 MFKLLIIGNSSVGKTSFLFRYADD   46 (191)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCcCHHHHHHHHhcC
Confidence            346889999999999999998763

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=88.86  E-value=0.21  Score=45.34  Aligned_cols=25  Identities=40%  Similarity=0.659  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus         7 ~~~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            7 VLLKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             cceEEEEECcCCCCHHHHHHHHHcC
Confidence            3467899999999999999998764

>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=88.80  E-value=0.22  Score=44.60  Aligned_cols=24  Identities=17%  Similarity=0.162  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        22 ~~ki~v~G~~~~GKSsli~~l~~~   45 (188)
T 1zd9_A           22 EMELTLVGLQYSGKTTFVNVIASG   45 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHcC
Confidence            346889999999999999999754

>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=88.80  E-value=0.26  Score=52.75  Aligned_cols=25  Identities=28%  Similarity=0.280  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+|.|.|++|+||||+|+.+...
T Consensus       395 ~~~~I~l~GlsGSGKSTiA~~La~~  419 (573)
T 1m8p_A          395 QGFTIFLTGYMNSGKDAIARALQVT  419 (573)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             cceEEEeecCCCCCHHHHHHHHHHH
Confidence            4568999999999999999999873

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=88.77  E-value=0.21  Score=45.22  Aligned_cols=25  Identities=36%  Similarity=0.514  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus        23 ~~~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           23 RYRKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHS
T ss_pred             CcEEEEEECCCCcCHHHHHHHHHhC
Confidence            3457899999999999999998764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=88.73  E-value=0.22  Score=44.90  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus         7 ~~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            7 SYKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456889999999999999999764

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=88.73  E-value=0.28  Score=43.76  Aligned_cols=25  Identities=24%  Similarity=0.259  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        15 ~~~~i~v~G~~~~GKssl~~~l~~~   39 (187)
T 1zj6_A           15 QEHKVIIVGLDNAGKTTILYQFSMN   39 (187)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            3467899999999999999999864

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=88.69  E-value=0.22  Score=44.78  Aligned_cols=24  Identities=25%  Similarity=0.569  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+...
T Consensus        23 ~~ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           23 ELKVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            346899999999999999998754

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=88.67  E-value=0.22  Score=44.48  Aligned_cols=24  Identities=29%  Similarity=0.523  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcC
Confidence            357899999999999999998764

>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=88.66  E-value=1.1  Score=41.35  Aligned_cols=106  Identities=12%  Similarity=0.062  Sum_probs=53.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc--
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSS--  274 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~--  274 (597)
                      ..+..++|+-|.||||.+....++.. .......++-..-+. ..                  - ..+...++.....  
T Consensus        19 g~l~v~~G~MgsGKTT~lL~~~~r~~-~~g~kvli~kp~~D~-Ry------------------g-~~i~sr~G~~~~a~~   77 (234)
T 2orv_A           19 GQIQVILGPMFSGKSTELMRRVRRFQ-IAQYKCLVIKYAKDT-RY------------------S-SSFCTHDRNTMEALP   77 (234)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHH-TTTCCEEEEEETTCC-CC------------------------------CEEEE
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHH-HCCCeEEEEeecCCc-cc------------------h-HHHHhhcCCeeEEEe
Confidence            46889999999999988877766322 223333333322211 10                  0 1222222221100  


Q ss_pred             hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCC
Q 041007          275 QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGG  333 (597)
Q Consensus       275 ~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~  333 (597)
                      ..+..++...+     ++--+|++|.++-..   ...++...+..  .|..||+|.++.
T Consensus        78 i~~~~di~~~~-----~~~dvViIDEaQF~~---~v~el~~~l~~--~gi~VI~~GL~~  126 (234)
T 2orv_A           78 ACLLRDVAQEA-----LGVAVIGIDEGQFFP---DIVEFCEAMAN--AGKTVIVAALDG  126 (234)
T ss_dssp             ESSGGGGHHHH-----TTCSEEEESSGGGCT---THHHHHHHHHH--TTCEEEEECCSB
T ss_pred             cCCHHHHHHHh-----ccCCEEEEEchhhhh---hHHHHHHHHHh--CCCEEEEEeccc
Confidence            00111122221     233499999997765   24445545544  677999999884

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=88.62  E-value=0.23  Score=44.68  Aligned_cols=24  Identities=25%  Similarity=0.332  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+.+.
T Consensus        23 ~~ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           23 ALKIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eeEEEEECcCCCCHHHHHHHHhcC
Confidence            356889999999999999999764

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=88.58  E-value=0.23  Score=44.55  Aligned_cols=24  Identities=38%  Similarity=0.548  Sum_probs=20.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .--|+|+|.+|+|||||...+.+.
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           21 LFKYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcC
Confidence            346889999999999999998754

>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=88.56  E-value=0.19  Score=44.96  Aligned_cols=24  Identities=21%  Similarity=0.260  Sum_probs=21.3

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-.|+|+|.+|+|||||...+...
T Consensus        21 ~~ki~v~G~~~~GKSsli~~l~~~   44 (190)
T 2h57_A           21 EVHVLCLGLDNSGKTTIINKLKPS   44 (190)
T ss_dssp             CEEEEEEECTTSSHHHHHHHTSCG
T ss_pred             ccEEEEECCCCCCHHHHHHHHhcC
Confidence            356889999999999999999875

>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=88.54  E-value=0.24  Score=52.41  Aligned_cols=24  Identities=25%  Similarity=0.378  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|.++|++|+||||+|+.+..
T Consensus        34 ~~~lIvlvGlpGSGKSTia~~La~   57 (520)
T 2axn_A           34 SPTVIVMVGLPARGKTYISKKLTR   57 (520)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            346899999999999999999976

>1ega_A Protein (GTP-binding protein ERA); GTPase, RNA-binding, RAS-like, hydrolase; 2.40A {Escherichia coli} SCOP: c.37.1.8 d.52.3.1 PDB: 1x1l_X 3ieu_A* 1x18_X

Probab=88.54  E-value=0.23  Score=48.49  Aligned_cols=25  Identities=24%  Similarity=0.434  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus         7 r~~~VaIvG~~nvGKSTLln~L~g~   31 (301)
T 1ega_A            7 YCGFIAIVGRPNVGKSTLLNKLLGQ   31 (301)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHCC
Confidence            3468999999999999999999864

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=88.53  E-value=0.24  Score=44.23  Aligned_cols=24  Identities=25%  Similarity=0.475  Sum_probs=20.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        20 ~~ki~v~G~~~~GKSsli~~l~~~   43 (189)
T 1z06_A           20 IFKIIVIGDSNVGKTCLTYRFCAG   43 (189)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            457899999999999999998753

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=88.50  E-value=0.23  Score=44.53  Aligned_cols=24  Identities=33%  Similarity=0.639  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        16 ~~ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           16 LFKLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcC
Confidence            456899999999999999998764

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=88.48  E-value=0.21  Score=45.57  Aligned_cols=22  Identities=23%  Similarity=0.243  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+|+|.|+.|+||||+++.+..
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~   28 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAE   28 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEeCCCCCCHHHHHHHHHH
Confidence            5999999999999999999987

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=88.45  E-value=0.24  Score=46.11  Aligned_cols=24  Identities=25%  Similarity=0.322  Sum_probs=20.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..-.++|.|++|+||||+|+.+..
T Consensus         7 ~~~~~~~~G~pGsGKsT~a~~L~~   30 (230)
T 3gmt_A            7 HHMRLILLGAPGAGKGTQANFIKE   30 (230)
T ss_dssp             --CEEEEECCTTSCHHHHHHHHHH
T ss_pred             cccceeeECCCCCCHHHHHHHHHH
Confidence            345789999999999999999876

>2xtp_A GTPase IMAP family member 2; immune system, G protein; HET: MSE; 1.50A {Homo sapiens} PDB: 2xto_A* 2xtm_A* 2xtn_A* 3p1j_A

Probab=88.44  E-value=0.26  Score=46.82  Aligned_cols=25  Identities=24%  Similarity=0.445  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|+|.+|+|||||...+...
T Consensus        21 ~~~~I~lvG~~g~GKStl~n~l~~~   45 (260)
T 2xtp_A           21 SELRIILVGKTGTGKSAAGNSILRK   45 (260)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHTS
T ss_pred             CceEEEEECCCCCCHHHHHHHHhCC
Confidence            4567999999999999999999764

>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=88.35  E-value=0.24  Score=44.12  Aligned_cols=21  Identities=29%  Similarity=0.450  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.|+|.+|+|||++|.++...
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~   22 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD   22 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            689999999999999999873

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=88.34  E-value=0.24  Score=44.77  Aligned_cols=25  Identities=16%  Similarity=0.351  Sum_probs=21.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...-|+|+|.+|+|||||...+...
T Consensus        27 ~~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           27 KAYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             -CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHhC
Confidence            3467899999999999999998754

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=88.31  E-value=0.26  Score=44.92  Aligned_cols=24  Identities=29%  Similarity=0.667  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        20 ~~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           20 IMKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            457899999999999999998753

>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=88.30  E-value=0.2  Score=49.72  Aligned_cols=22  Identities=23%  Similarity=0.519  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+++|+|+.|+|||||++.+..
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g  193 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIME  193 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGG
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            5899999999999999999987

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=88.30  E-value=0.26  Score=47.22  Aligned_cols=24  Identities=25%  Similarity=0.419  Sum_probs=21.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|+|.+|+|||||...+...
T Consensus         3 ~~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            3 LKTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eeEEEEECCCCCCHHHHHHHHhCC
Confidence            357899999999999999999764

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=88.20  E-value=0.16  Score=45.15  Aligned_cols=24  Identities=29%  Similarity=0.574  Sum_probs=10.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+.+.
T Consensus         8 ~~ki~v~G~~~~GKssl~~~l~~~   31 (183)
T 2fu5_C            8 LFKLLLIGDSGVGKTCVLFRFSED   31 (183)
T ss_dssp             EEEEEEECCCCC------------
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            456899999999999999998764

>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=88.17  E-value=0.26  Score=49.19  Aligned_cols=23  Identities=22%  Similarity=0.447  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+++|+|++|+|||||...+...
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~  238 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGL  238 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CEEEEECCCCccHHHHHHHHhcc
Confidence            58999999999999999999873

>3io3_A DEHA2D07832P; chaperone, membrane traffic, ATPase; HET: ADP; 1.80A {Debaryomyces hansenii}

Probab=88.17  E-value=0.6  Score=46.53  Aligned_cols=39  Identities=23%  Similarity=0.372  Sum_probs=27.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhh--ccCCeeEEEEec
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVK--ANFDKRIWVSAS  236 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~--~~F~~~~wv~~~  236 (597)
                      ..+++.+.|.||+||||+|..++..  ..  ..=..++-++..
T Consensus        17 ~~~i~~~~gkGGvGKTt~a~~lA~~--la~~~~g~~vllid~D   57 (348)
T 3io3_A           17 SLKWIFVGGKGGVGKTTTSSSVAVQ--LALAQPNEQFLLISTD   57 (348)
T ss_dssp             TCSEEEEECSTTSSHHHHHHHHHHH--HHHHCTTSCEEEEECC
T ss_pred             CcEEEEEeCCCCCcHHHHHHHHHHH--HHHhcCCCeEEEEECC
Confidence            4689999999999999999888763  33  222235556654

>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=88.16  E-value=0.45  Score=48.71  Aligned_cols=23  Identities=22%  Similarity=0.322  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|+|+.|+|||||.+.+..
T Consensus       167 ggii~I~GpnGSGKTTlL~allg  189 (418)
T 1p9r_A          167 HGIILVTGPTGSGKSTTLYAGLQ  189 (418)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHh
Confidence            46999999999999999999876

>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=88.12  E-value=0.28  Score=52.72  Aligned_cols=24  Identities=25%  Similarity=0.490  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|.|.|++|+||||+|+.+..
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~   74 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEE   74 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHH
Confidence            457899999999999999999977

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=88.11  E-value=0.35  Score=43.86  Aligned_cols=24  Identities=17%  Similarity=0.206  Sum_probs=21.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|+|+|++|+||+++|..+.+
T Consensus        10 ~~~II~itGk~~SGKd~va~~l~~   33 (202)
T 3ch4_B           10 PRLVLLFSGKRKSGKDFVTEALQS   33 (202)
T ss_dssp             CSEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCChHHHHHHHHH
Confidence            457999999999999999988754

>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=88.07  E-value=0.62  Score=46.13  Aligned_cols=41  Identities=20%  Similarity=0.243  Sum_probs=28.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ..+++.+.|-||+||||+|..++..  ....=..++-+++...
T Consensus        15 ~~~i~~~sgkGGvGKTt~a~~lA~~--la~~g~~vllid~D~~   55 (334)
T 3iqw_A           15 SLRWIFVGGKGGVGKTTTSCSLAIQ--LAKVRRSVLLLSTDPA   55 (334)
T ss_dssp             TCCEEEEECSTTSSHHHHHHHHHHH--HTTSSSCEEEEECCSS
T ss_pred             CeEEEEEeCCCCccHHHHHHHHHHH--HHhCCCcEEEEECCCC
Confidence            4678899999999999999888762  2222233555665533

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=88.07  E-value=0.25  Score=44.87  Aligned_cols=24  Identities=38%  Similarity=0.655  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus         8 ~~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            8 LFKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            457899999999999999998754

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=88.04  E-value=0.26  Score=44.12  Aligned_cols=23  Identities=39%  Similarity=0.657  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+.+.
T Consensus        16 ~~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           16 LKILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46899999999999999999764

>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=88.01  E-value=0.32  Score=41.94  Aligned_cols=23  Identities=26%  Similarity=0.463  Sum_probs=19.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.+|+|+.|.|||||...++-
T Consensus        23 ~g~~~I~G~NGsGKStil~Ai~~   45 (149)
T 1f2t_A           23 EGINLIIGQNGSGKSSLLDAILV   45 (149)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHH
Confidence            35889999999999999888753

---

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	597
d2a5yb3	277	c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenor	6e-33
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	0.003

>d2a5yb3 c.37.1.20 (B:109-385) CED-4, NB-ARC domain {Caenorhabditis elegans [TaxId: 6239]} Length = 277

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: CED-4, NB-ARC domain
species: Caenorhabditis elegans [TaxId: 6239]

 Score =  125 bits (315), Expect = 6e-33
 Identities = 47/306 (15%), Positives = 94/306 (30%), Gaps = 51/306 (16%)

Query: 162 VIDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDS 221
           V   +  + R     ++++ L      +          +++ G  G GK+ +A Q    S
Sbjct: 16  VPKQMTCYIREYHVDRVIKKLDEMCDLD-------SFFLFLHGRAGSGKSVIASQALSKS 68

Query: 222 D--VKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEME 279
           D  +  N+D  +W+  S    +                I +     + L    S +    
Sbjct: 69  DQLIGINYDSIVWLKDSGTAPKSTFDLFTD--------ILLMLKSEDDLLNFPSVEHVTS 120

Query: 280 TVL--QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGT 337
            VL     N  +     L V DD+      R+ ++L           R LVT    +   
Sbjct: 121 VVLKRMICNALIDRPNTLFVFDDVVQEETIRWAQEL---------RLRCLVTTRDVEISN 171

Query: 338 NMTEIGLGEKNGTNMMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCK 397
             ++             I +  L  +EC              +   K E +  + +    
Sbjct: 172 AASQ---------TCEFIEVTSLEIDECYDFLEAYGMPMPVGE---KEEDVLNKTIELSS 219

Query: 398 GLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSP 457
           G P  + +       KT  ++   + + ++ +      +              SY  L+ 
Sbjct: 220 GNPATLMMFFKSCEPKT-FEKMAQLNN-KLESRGLVGVECI---------TPYSYKSLAM 268

Query: 458 ALKKCF 463
           AL++C 
Sbjct: 269 ALQRCV 274

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

 Score = 37.4 bits (85), Expect = 0.003
 Identities = 30/272 (11%), Positives = 80/272 (29%), Gaps = 36/272 (13%)

Query: 164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDV 223
           +  +F  R  E +K+  L                P+  +LG    GK+++ +   ++ ++
Sbjct: 10  NRKDFFDREKEIEKLKGLRA--------------PITLVLGLRRTGKSSIIKIGINELNL 55

Query: 224 K------ANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVE 277
                    F++R ++S      E++   +++          +       + G+      
Sbjct: 56  PYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNW 115

Query: 278 METVLQYINEFVQGKKVLLVLDDLWWNAYPRYW-----EQLMYSLKSGSEGSRILVTRSG 332
                      ++  +     + +      +         L+ +L    +  + +     
Sbjct: 116 NRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMS 175

Query: 333 GKNGTNMTEIGLGEKNGTNMM-----EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEP 387
           G     + +    E   + +       + L   S EE     R+        +    F+ 
Sbjct: 176 GSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRR-----GFQEADIDFKD 230

Query: 388 IGRRVVGKCKGLPFAVKILGSLLRFKTSIKEW 419
               V  K  G+P  +   G +     ++   
Sbjct: 231 Y-EVVYEKIGGIPGWLTYFGFIYLDNKNLDFA 261

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	597
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	100.0
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.33
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.93
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.82
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.8
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.79
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.78
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.72
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	98.68
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.67
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	98.54
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.5
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	98.49
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.45
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	98.4
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.37
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.24
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.24
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	98.22
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.2
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.16
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	97.89
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	97.88
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	97.51
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	97.18
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.15
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.92
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	96.84
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.69
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.65
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	96.63
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	96.62
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	96.61
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.57
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.56
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.56
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.56
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	96.54
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.51
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.5
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	96.49
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.48
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.44
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.44
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	96.38
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.37
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	96.37
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	96.36
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	96.35
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	96.33
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.3
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	96.23
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.22
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.22
d1okkd2	207	GTPase domain of the signal recognition particle r	96.21
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.18
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.17
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.16
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.15
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.13
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	96.1
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	96.08
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.07
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	96.05
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	96.03
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	96.02
d1g2912	240	Maltose transport protein MalK, N-terminal domain	95.99
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	95.97
d1j8yf2	211	GTPase domain of the signal sequence recognition p	95.96
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.96
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	95.92
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.88
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	95.88
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	95.87
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	95.77
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	95.69
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	95.68
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.66
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	95.64
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.63
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	95.62
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.62
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	95.5
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	95.47
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.47
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	95.46
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.41
d1xpua3	289	Transcription termination factor Rho, ATPase domai	95.35
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	95.31
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	95.21
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.1
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	95.09
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	95.02
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	95.01
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	94.99
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	94.99
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.98
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	94.92
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.88
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.85
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.84
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	94.81
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	94.77
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	94.59
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.56
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	94.54
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	94.53
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.5
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	94.48
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	94.44
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	94.4
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.4
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	94.37
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	94.31
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	94.3
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.29
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.26
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	94.2
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	94.14
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	94.08
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	94.01
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	93.95
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	93.88
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	93.73
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	93.66
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	93.52
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	93.5
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	93.32
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	93.29
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.22
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.05
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.96
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	92.93
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	92.91
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.78
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	92.69
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.69
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.66
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	92.54
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	92.54
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	92.45
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	92.45
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	92.44
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	92.41
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	92.37
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	92.32
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	92.29
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	92.23
d2jdia3	285	Central domain of alpha subunit of F1 ATP synthase	92.2
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	92.15
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	92.14
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	92.11
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	92.11
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	91.98
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	91.94
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	91.91
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	91.9
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	91.89
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	91.87
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	91.84
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	91.84
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	91.77
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.75
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	91.72
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	91.69
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	91.62
d1nrjb_	209	Signal recognition particle receptor beta-subunit	91.59
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.57
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	91.56
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	91.55
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.54
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	91.48
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	91.45
d2fh5b1	207	Signal recognition particle receptor beta-subunit	91.39
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	91.38
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	91.32
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.25
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	91.24
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	91.12
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	91.11
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	91.1
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	91.07
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	91.03
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	90.98
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	90.82
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	90.77
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	90.75
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	90.7
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	90.7
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	90.65
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.59
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	90.56
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	90.56
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	90.46
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	90.35
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	90.33
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	90.31
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	90.3
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	90.27
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	90.22
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	90.16
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	90.14
d1g3qa_	237	Cell division regulator MinD {Archaeon Pyrococcus	90.09
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	90.09
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	90.08
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	89.96
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	89.93
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	89.86
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	89.83
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.77
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	89.72
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	89.72
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	89.6
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	89.6
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	89.59
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	89.54
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	89.19
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	89.08
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	88.81
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	88.71
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	87.48
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	87.41
d1f5na2	277	Interferon-induced guanylate-binding protein 1 (GB	87.03
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	86.81
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	86.79
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	86.03
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	85.3
d1tuea_	205	Replication protein E1 helicase domain {Human papi	84.85
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	84.75
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	84.64
d2bv3a2	276	Elongation factor G (EF-G), N-terminal (G) domain	84.6
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	84.58
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	84.23
d1g7sa4	227	Initiation factor IF2/eIF5b, N-terminal (G) domain	82.54
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	82.37
d1e2ka_	329	Thymidine kinase {Herpes simplex virus type 1, dif	82.03
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	80.23
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	80.08
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	80.03

>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=100.00  E-value=2.2e-38  Score=310.92  Aligned_cols=243  Identities=17%  Similarity=0.162  Sum_probs=185.1

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChh--hhccCCeeEEEEecCCCch
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSD--VKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~--~~~~F~~~~wv~~~~~~~~  241 (597)
                      ..+.++||+.++++|+++|....+       ...++|+|+||||+||||||+++|++..  ...+|++++|+++++.++.
T Consensus        18 ~~~~~~gR~~~~~~i~~~L~~~~~-------~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~   90 (277)
T d2a5yb3          18 KQMTCYIREYHVDRVIKKLDEMCD-------LDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPK   90 (277)
T ss_dssp             CCCCSCCCHHHHHHHHHHHHHHTT-------SSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTT
T ss_pred             CCCceeCcHHHHHHHHHHHHhccC-------CCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCH
Confidence            445688999999999999975432       3568999999999999999999997533  6778999999999988776


Q ss_pred             hhhhhhhhhhcccchHHHHHHH---HHHhccCCC-------CchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHH
Q 041007          242 IRVARDEISVARDRDEIRVAKA---ILESLKGSV-------SSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWE  311 (597)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~---il~~l~~~~-------~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~  311 (597)
                                      ..+...   ++..++...       ............+.+.+.++++|+||||+|+..   .|.
T Consensus        91 ----------------~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~---~~~  151 (277)
T d2a5yb3          91 ----------------STFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEE---TIR  151 (277)
T ss_dssp             ----------------HHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHH---HHH
T ss_pred             ----------------HHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHh---hhh
Confidence                            333333   333333221       112233444556788899999999999999765   555


Q ss_pred             HHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCccccc-----eeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          312 QLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMM-----EIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       312 ~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-----~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                      .+.      ..||+||||||+.              .++..+     .|+|++|+.+||++||...++...   ..+..+
T Consensus       152 ~~~------~~~srilvTTR~~--------------~v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~~~~~~---~~~~~~  208 (277)
T d2a5yb3         152 WAQ------ELRLRCLVTTRDV--------------EISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMP---VGEKEE  208 (277)
T ss_dssp             HHH------HTTCEEEEEESBG--------------GGGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC-----CHHH
T ss_pred             hhc------ccCceEEEEeehH--------------HHHHhcCCCCceEECCCCCHHHHHHHHHHHhCCcc---CchhhH
Confidence            433      2478999999998              555432     289999999999999999887433   234557


Q ss_pred             HHHHHHHHhcCCchHHHHHHHhhhccCCCHHHHHHHHhhhcccCChhhhhhcCCCCCcccchhccccCCChhHhHHHHHh
Q 041007          387 PIGRRVVGKCKGLPFAVKILGSLLRFKTSIKEWQSVLDSEIWNLDSEICKRAGVGYECLSPLLLSYFDLSPALKKCFLYC  466 (597)
Q Consensus       387 ~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~~w~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~sy~~L~~~~k~cf~~l  466 (597)
                      +++++|+++|+|+||||+++|+.++.+ +.+.|....+.+....          ..++..++.+||++||+++|.||.++
T Consensus       209 ~~~~~iv~~c~GlPLAl~~ig~~l~~k-~~~~~~~~~~~L~~~~----------~~~v~~il~~sY~~L~~~lk~c~~~l  277 (277)
T d2a5yb3         209 DVLNKTIELSSGNPATLMMFFKSCEPK-TFEKMAQLNNKLESRG----------LVGVECITPYSYKSLAMALQRCVEVL  277 (277)
T ss_dssp             HHHHHHHHHHTTCHHHHHHHHTTCCSS-SHHHHHHHHHHHHHHC----------SSTTCCCSSSSSSSHHHHHHHHHHTS
T ss_pred             HHHHHHHHHhCCCHHHHHHHHHHhccC-CHHHHHHHHHHHhcCc----------HHHHHHHHHHHHhcccHHHHHHHHhC
Confidence            889999999999999999999999754 6788887666543211          46789999999999999999999874

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Archaeal ATPase SSO1545
species: Sulfolobus solfataricus [TaxId: 2287]

Probab=99.33  E-value=1.7e-12  Score=125.58  Aligned_cols=227  Identities=15%  Similarity=0.164  Sum_probs=114.7

Q ss_pred             cCCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          163 IDPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       163 ~~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..+..||||++++++|.+.              ..++|.|+|++|+|||+|++++.+  ....   ...|+.+.......
T Consensus         9 ~~~~~f~GR~~el~~l~~~--------------~~~~i~i~G~~G~GKTsLl~~~~~--~~~~---~~~~i~~~~~~~~~   69 (283)
T d2fnaa2           9 DNRKDFFDREKEIEKLKGL--------------RAPITLVLGLRRTGKSSIIKIGIN--ELNL---PYIYLDLRKFEERN   69 (283)
T ss_dssp             CSGGGSCCCHHHHHHHHHT--------------CSSEEEEEESTTSSHHHHHHHHHH--HHTC---CEEEEEGGGGTTCS
T ss_pred             CChhhCCChHHHHHHHHhc--------------cCCEEEEEcCCCCcHHHHHHHHHH--HCCC---CeEEEEeccccccc
Confidence            4568899999999998763              136899999999999999999987  3332   23455543222111


Q ss_pred             hh----hhhhhhhcccchHHHHHHHHHHhccCC---------------CCchhhHHHHHHHHHHHhcCceEEEEEecccC
Q 041007          243 RV----ARDEISVARDRDEIRVAKAILESLKGS---------------VSSQVEMETVLQYINEFVQGKKVLLVLDDLWW  303 (597)
Q Consensus       243 ~~----~~~~~~~~~~~~~~~~~~~il~~l~~~---------------~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~  303 (597)
                      ..    +...+.. ...........+...+...               .........+...+.+ ..++++++|+|++.+
T Consensus        70 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~-~~~~~~~i~id~~~~  147 (283)
T d2fnaa2          70 YISYKDFLLELQK-EINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQ-ASKDNVIIVLDEAQE  147 (283)
T ss_dssp             CCCHHHHHHHHHH-HHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHH-TCSSCEEEEEETGGG
T ss_pred             cccHHHHHHHHHH-HhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHh-hcccccccccchhhh
Confidence            11    0000000 0000001111111111110               0011223333333322 346889999999854


Q ss_pred             CCC---cchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccc-cccccCcc-ccceeecCCCChHHHHHHHHHHhccCCC
Q 041007          304 NAY---PRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEI-GLGEKNGT-NMMEIGLGELSEEECRSLFRQIAFHGRS  378 (597)
Q Consensus       304 ~~~---~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~-~~~~~~~~-~~~~~~l~~Ls~~es~~Lf~~~~~~~~~  378 (597)
                      ...   ...+..+..... .......+++++........... ........ ....+.|.||+.+++.+++.+.+.....
T Consensus       148 ~~~~~~~~~~~~l~~~~~-~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~~~  226 (283)
T d2fnaa2         148 LVKLRGVNLLPALAYAYD-NLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEADI  226 (283)
T ss_dssp             GGGCTTCCCHHHHHHHHH-HCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHHTC
T ss_pred             hcccchHHHHHHHHHHHH-hhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhcCC
Confidence            211   112233333322 22344444443322000000000 00000001 1123899999999999999876532221


Q ss_pred             CCCccchHHHHHHHHHhcCCchHHHHHHHhhhccCCCHH
Q 041007          379 SDYREKFEPIGRRVVGKCKGLPFAVKILGSLLRFKTSIK  417 (597)
Q Consensus       379 ~~~~~~~~~~~~~I~~~~~GlPLai~~~~~~l~~~~~~~  417 (597)
                        ..+.    .++|++.++|+|..+..++..+....+.+
T Consensus       227 --~~~~----~~~i~~~~~G~P~~L~~~~~~~~~~~~~~  259 (283)
T d2fnaa2         227 --DFKD----YEVVYEKIGGIPGWLTYFGFIYLDNKNLD  259 (283)
T ss_dssp             --CCCC----HHHHHHHHCSCHHHHHHHHHHHHHHCCHH
T ss_pred             --CHHH----HHHHHHHhCCCHHHHHHHHHHHHhcccHH
Confidence              1112    46899999999999999988775544443

>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=98.93  E-value=6.2e-08  Score=92.29  Aligned_cols=181  Identities=17%  Similarity=0.204  Sum_probs=104.6

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCe-eEEEEecCCCchh
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDK-RIWVSASYPRDEI  242 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~-~~wv~~~~~~~~~  242 (597)
                      -|..++||+.++++|.++|...-..    +...++.+.|+|++|+|||++|+.+++  ........ .+|+.+...... 
T Consensus        14 ~p~~l~~Re~ei~~l~~~l~~~l~~----~~~~~~~lll~GppGtGKT~l~~~l~~--~l~~~~~~~~~~~~~~~~~~~-   86 (276)
T d1fnna2          14 VPKRLPHREQQLQQLDILLGNWLRN----PGHHYPRATLLGRPGTGKTVTLRKLWE--LYKDKTTARFVYINGFIYRNF-   86 (276)
T ss_dssp             CCSCCTTCHHHHHHHHHHHHHHHHS----TTSSCCEEEEECCTTSSHHHHHHHHHH--HHTTSCCCEEEEEETTTCCSH-
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHhC----CCCCCCceEEECCCCCCHHHHHHHHHH--HHhcccCCcEEEecchhhhhh-
Confidence            3456899999999999998642100    023567899999999999999999998  44443332 455665555555 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHHhc--CceEEEEEecccCCCCcchHHHHHHhhc-
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEFVQ--GKKVLLVLDDLWWNAYPRYWEQLMYSLK-  318 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~L~--~kr~LLVLDdv~~~~~~~~~~~l~~~l~-  318 (597)
                                     ......+....+..... ......+...+.+.+.  ....++++|+++... ......+...+. 
T Consensus        87 ---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~-~~~~~~~~~~~~~  150 (276)
T d1fnna2          87 ---------------TAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLA-PDILSTFIRLGQE  150 (276)
T ss_dssp             ---------------HHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSC-HHHHHHHHHHTTC
T ss_pred             ---------------hhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhh-hhhhhhHHHHHhc
Confidence                           66677777776654322 2233444444444443  356777888886554 222222222221 


Q ss_pred             --C-CCCCcEEEEEccCCCCCCCcccccccccCccc---cceeecCCCChHHHHHHHHHHh
Q 041007          319 --S-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN---MMEIGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       319 --~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~---~~~~~l~~Ls~~es~~Lf~~~~  373 (597)
                        . ......+|.++.... ......     ..+..   ...+.+.+++.++.++++.+++
T Consensus       151 ~~~~~~~~~~~i~~~~~~~-~~~~~~-----~~~~~r~~~~~i~~~~~~~~e~~~il~~r~  205 (276)
T d1fnna2         151 ADKLGAFRIALVIVGHNDA-VLNNLD-----PSTRGIMGKYVIRFSPYTKDQIFDILLDRA  205 (276)
T ss_dssp             HHHHSSCCEEEEEEESSTH-HHHTSC-----HHHHHHHTTCEEECCCCBHHHHHHHHHHHH
T ss_pred             cccccccceEEeecCCchh-hhhhcc-----hhhhhhhcchhccccchhHHHHHHHHHHHH
Confidence              1 122334444444320 000000     00111   1128899999999999998765

>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=98.82  E-value=9.7e-09  Score=95.24  Aligned_cols=181  Identities=16%  Similarity=0.111  Sum_probs=107.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC-C-eeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF-D-KRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F-~-~~~wv~~~~~~~~~~  243 (597)
                      .+++|.++.++.|..|+...          ..+.+.++|++|+||||+|+.+++.  ....+ . .++-+..+.....  
T Consensus        15 ~d~ig~~~~~~~L~~~~~~~----------~~~~~ll~Gp~G~GKTt~a~~la~~--l~~~~~~~~~~~~n~~~~~~~--   80 (224)
T d1sxjb2          15 SDIVGNKETIDRLQQIAKDG----------NMPHMIISGMPGIGKTTSVHCLAHE--LLGRSYADGVLELNASDDRGI--   80 (224)
T ss_dssp             GGCCSCTHHHHHHHHHHHSC----------CCCCEEEECSTTSSHHHHHHHHHHH--HHGGGHHHHEEEECTTSCCSH--
T ss_pred             HHhcCCHHHHHHHHHHHHcC----------CCCeEEEECCCCCCchhhHHHHHHH--HhccccccccccccccccCCc--
Confidence            56899999999999999843          3455789999999999999998873  32221 1 1222333322221  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                    ..+...+........              ....++.-++|+|+++... ......+...+......
T Consensus        81 --------------~~i~~~~~~~~~~~~--------------~~~~~~~kviiiDe~d~~~-~~~~~~ll~~~e~~~~~  131 (224)
T d1sxjb2          81 --------------DVVRNQIKHFAQKKL--------------HLPPGKHKIVILDEADSMT-AGAQQALRRTMELYSNS  131 (224)
T ss_dssp             --------------HHHHTHHHHHHHBCC--------------CCCTTCCEEEEEESGGGSC-HHHHHTTHHHHHHTTTT
T ss_pred             --------------eehhhHHHHHHHhhc--------------cCCCcceEEEEEecccccc-hhHHHHHhhhccccccc
Confidence                          111111111100000              0012355688999997665 33444455555556667


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchHH
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFA  402 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLa  402 (597)
                      +++++++........         .+...+ .+.+.+++.++...++...+...+...    ..+....|++.|+|.+--
T Consensus       132 ~~~i~~~~~~~~i~~---------~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e~~~i----~~~~l~~I~~~s~Gd~R~  198 (224)
T d1sxjb2         132 TRFAFACNQSNKIIE---------PLQSQCAILRYSKLSDEDVLKRLLQIIKLEDVKY----TNDGLEAIIFTAEGDMRQ  198 (224)
T ss_dssp             EEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB----CHHHHHHHHHHHTTCHHH
T ss_pred             eeeeeccCchhhhhh---------HHHHHHHHhhhcccchhhhHHHHHHHHHhcccCC----CHHHHHHHHHHcCCcHHH
Confidence            777777665421110         111112 299999999999999988774332211    145678999999998753

>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=98.80  E-value=1.9e-08  Score=93.34  Aligned_cols=178  Identities=14%  Similarity=0.142  Sum_probs=106.8

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhcc-CCe-eEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKAN-FDK-RIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~-F~~-~~wv~~~~~~~~~~  243 (597)
                      .++||.++.++.|..|+...          ..+.+.++|++|+||||+|+.+++.  .... +.. ..-.+.+.....  
T Consensus        14 ~divg~~~~~~~L~~~i~~~----------~~~~lLl~Gp~G~GKttl~~~la~~--l~~~~~~~~~~e~~~~~~~~~--   79 (227)
T d1sxjc2          14 DEVYGQNEVITTVRKFVDEG----------KLPHLLFYGPPGTGKTSTIVALARE--IYGKNYSNMVLELNASDDRGI--   79 (227)
T ss_dssp             GGCCSCHHHHHHHHHHHHTT----------CCCCEEEECSSSSSHHHHHHHHHHH--HHTTSHHHHEEEECTTSCCSH--
T ss_pred             HHccCcHHHHHHHHHHHHcC----------CCCeEEEECCCCCChhHHHHHHHHH--hhcCCCcceeEEecccccCCe--
Confidence            56999999999999999743          3445779999999999999999883  2211 111 111222211111  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                     ...........              .......++.-++|+|++.... ...-..+...+......
T Consensus        80 ---------------~~~~~~~~~~~--------------~~~~~~~~~~kiiiiDe~d~~~-~~~~~~Ll~~le~~~~~  129 (227)
T d1sxjc2          80 ---------------DVVRNQIKDFA--------------STRQIFSKGFKLIILDEADAMT-NAAQNALRRVIERYTKN  129 (227)
T ss_dssp             ---------------HHHHTHHHHHH--------------HBCCSSSCSCEEEEETTGGGSC-HHHHHHHHHHHHHTTTT
T ss_pred             ---------------eeeecchhhcc--------------ccccccCCCeEEEEEeccccch-hhHHHHHHHHhhhcccc
Confidence                           11111111000              0000112345689999997665 44455566666666778


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccccc-eeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCch
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTNMM-EIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLP  400 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~~~-~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlP  400 (597)
                      +.++++|........         .....+ .+.+.+++.++...++.+.+...+...    ..+..+.|++.++|..
T Consensus       130 ~~~~~~~~~~~~i~~---------~i~sr~~~i~~~~~~~~~i~~~l~~I~~~e~i~i----~~~~l~~i~~~s~Gd~  194 (227)
T d1sxjc2         130 TRFCVLANYAHKLTP---------ALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKL----SPNAEKALIELSNGDM  194 (227)
T ss_dssp             EEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHTTTCCB----CHHHHHHHHHHHTTCH
T ss_pred             eeeccccCcHHHhHH---------HHHHHHhhhccccccccccccccccccccccccC----CHHHHHHHHHHcCCcH
Confidence            888888765421110         111112 289999999999999988775433221    1456788999999864

>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=98.79  E-value=2.7e-08  Score=92.93  Aligned_cols=195  Identities=14%  Similarity=0.062  Sum_probs=112.3

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-cCCeeEEEEecCCCchhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-NFDKRIWVSASYPRDEIRV  244 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-~F~~~~wv~~~~~~~~~~~  244 (597)
                      .+++|.++.++.|..++...          ..+.+.++|++|+||||+|+.+++...... .......+..+........
T Consensus        12 ~diig~~~~~~~l~~~i~~~----------~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~   81 (237)
T d1sxjd2          12 DEVTAQDHAVTVLKKTLKSA----------NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGISIV   81 (237)
T ss_dssp             TTCCSCCTTHHHHHHHTTCT----------TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHHHH
T ss_pred             HHccCcHHHHHHHHHHHHcC----------CCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccchHH
Confidence            56899999999999999743          345588999999999999999988421111 1122333333333222000


Q ss_pred             hhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCc
Q 041007          245 ARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGS  324 (597)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs  324 (597)
                                   ............ ......       .+......+.-++|+|++.... ...+..+...+.......
T Consensus        82 -------------~~~~~~~~~~~~-~~~~~~-------~~~~~~~~~~~viiiDe~d~l~-~~~~~~l~~~~~~~~~~~  139 (237)
T d1sxjd2          82 -------------REKVKNFARLTV-SKPSKH-------DLENYPCPPYKIIILDEADSMT-ADAQSALRRTMETYSGVT  139 (237)
T ss_dssp             -------------TTHHHHHHHSCC-CCCCTT-------HHHHSCCCSCEEEEETTGGGSC-HHHHHHHHHHHHHTTTTE
T ss_pred             -------------HHHHHHHhhhhh-hhhhHH-------HHhhccccCceEEEEecccccC-HHHHHHHhhccccccccc
Confidence                         011111111111 111111       1122223445579999997765 445556666565566677


Q ss_pred             EEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCch-HH
Q 041007          325 RILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLP-FA  402 (597)
Q Consensus       325 ~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlP-La  402 (597)
                      .+|+|+........         .+... ..+.+.+++.++...++...+...+...    ..+..+.|++.++|.+ -|
T Consensus       140 ~~i~~~~~~~~~~~---------~l~sr~~~i~f~~~~~~~~~~~L~~i~~~e~i~i----~~~~l~~ia~~s~gd~R~a  206 (237)
T d1sxjd2         140 RFCLICNYVTRIID---------PLASQCSKFRFKALDASNAIDRLRFISEQENVKC----DDGVLERILDISAGDLRRG  206 (237)
T ss_dssp             EEEEEESCGGGSCH---------HHHHHSEEEECCCCCHHHHHHHHHHHHHTTTCCC----CHHHHHHHHHHTSSCHHHH
T ss_pred             cccccccccccccc---------cccchhhhhccccccccccchhhhhhhhhhcCcC----CHHHHHHHHHHcCCCHHHH
Confidence            77777655411110         11111 2299999999999999988875433221    1456788999998854 44


Q ss_pred             HHH
Q 041007          403 VKI  405 (597)
Q Consensus       403 i~~  405 (597)
                      +..
T Consensus       207 i~~  209 (237)
T d1sxjd2         207 ITL  209 (237)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            443

>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=98.78  E-value=1.6e-07  Score=87.69  Aligned_cols=195  Identities=13%  Similarity=0.158  Sum_probs=112.2

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|.++.++.|..++....         -+..+.|+|++|+||||+|+.+++.  ......    .. ......    
T Consensus        12 ~dlig~~~~~~~L~~~i~~~~---------~~~~~Ll~Gp~G~GKtt~a~~~~~~--l~~~~~----~~-~~~~~~----   71 (239)
T d1njfa_          12 ADVVGQEHVLTALANGLSLGR---------IHHAYLFSGTRGVGKTSIARLLAKG--LNCETG----IT-ATPCGV----   71 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHTTC---------CCSEEEEECSTTSSHHHHHHHHHHH--HHCTTC----SC-SSCCSC----
T ss_pred             HHccChHHHHHHHHHHHHcCC---------CCeeEEEECCCCCcHHHHHHHHHHH--hcCccc----cc-cCcccc----
Confidence            468999999999999997432         2456889999999999999998763  211110    00 000000    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccC-----CCCchhhHHHHHHHHHHH----hcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          246 RDEISVARDRDEIRVAKAILESLKG-----SVSSQVEMETVLQYINEF----VQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~-----~~~~~~~~~~~~~~l~~~----L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                                  ......+...-..     ........+.+...+...    ..++.-++|||+++... ...-..+...
T Consensus        72 ------------~~~~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~-~~~q~~Llk~  138 (239)
T d1njfa_          72 ------------CDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS-RHSFNALLKT  138 (239)
T ss_dssp             ------------SHHHHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC-HHHHHHHHHH
T ss_pred             ------------chHHHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCC-HHHHHHHHHH
Confidence                        0011111111000     000111122222222111    12455689999998775 4455567777


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +...+.++.+|++|.+......         .+...+. +.+.+++.++....+...+.......    ..+.+..|++.
T Consensus       139 lE~~~~~~~~il~tn~~~~i~~---------~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e~~~~----~~~~l~~i~~~  205 (239)
T d1njfa_         139 LEEPPEHVKFLLATTDPQKLPV---------TILSRCLQFHLKALDVEQIRHQLEHILNEEHIAH----EPRALQLLARA  205 (239)
T ss_dssp             HHSCCTTEEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCCB----CHHHHHHHHHH
T ss_pred             HhcCCCCeEEEEEcCCccccCh---------hHhhhhcccccccCcHHHhhhHHHHHHhhhccCC----CHHHHHHHHHH
Confidence            7666777888888765411100         1111222 99999999999998888764333221    24567889999


Q ss_pred             cCCchH-HHHHH
Q 041007          396 CKGLPF-AVKIL  406 (597)
Q Consensus       396 ~~GlPL-ai~~~  406 (597)
                      ++|.+- |+..+
T Consensus       206 s~Gd~R~ain~l  217 (239)
T d1njfa_         206 AEGSLRDALSLT  217 (239)
T ss_dssp             TTTCHHHHHHHH
T ss_pred             cCCCHHHHHHHH
Confidence            999885 55544

>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=98.72  E-value=2.8e-08  Score=93.80  Aligned_cols=209  Identities=13%  Similarity=0.123  Sum_probs=102.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChh----hhccCCeeEEEEecCCCch
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSD----VKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~----~~~~F~~~~wv~~~~~~~~  241 (597)
                      .+++|+++..+.|..++....         ..+.+.|+|++|+||||+|+.+++...    ....++...|.........
T Consensus        11 ~diig~~~~~~~L~~~~~~~~---------~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~~   81 (252)
T d1sxje2          11 NALSHNEELTNFLKSLSDQPR---------DLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKLE   81 (252)
T ss_dssp             GGCCSCHHHHHHHHTTTTCTT---------CCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-----------------
T ss_pred             HHccCcHHHHHHHHHHHHcCC---------CCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchhh
Confidence            468999998888888876432         344578999999999999999987311    0111122222211111100


Q ss_pred             hhhhhhhhhh-----cccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHh
Q 041007          242 IRVARDEISV-----ARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYS  316 (597)
Q Consensus       242 ~~~~~~~~~~-----~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~  316 (597)
                      ..........     .........................      ..-.....++.-++|||+++... ...+..+...
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~iiiide~d~l~-~~~~~~l~~~  154 (252)
T d1sxje2          82 LNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDF------QDSKDGLAHRYKCVIINEANSLT-KDAQAALRRT  154 (252)
T ss_dssp             -CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------------CCEEEEEECTTSSC-HHHHHHHHHH
T ss_pred             hhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhh------hhcccccCCCceEEEeccccccc-cccchhhhcc
Confidence            0000000000     0000001111111111111000000      00001112344588999997765 4556666666


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      +......+++|+||.+......         .+... ..+++.+++.++..+++...+-..+...   ...+..+.|++.
T Consensus       155 ~e~~~~~~~~Il~tn~~~~i~~---------~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e~~~~---~~~~~l~~i~~~  222 (252)
T d1sxje2         155 MEKYSKNIRLIMVCDSMSPIIA---------PIKSQCLLIRCPAPSDSEISTILSDVVTNERIQL---ETKDILKRIAQA  222 (252)
T ss_dssp             HHHSTTTEEEEEEESCSCSSCH---------HHHTTSEEEECCCCCHHHHHHHHHHHHHHHTCEE---CCSHHHHHHHHH
T ss_pred             cccccccccceeeeccccchhh---------hhhcchheeeecccchhhHHHHHHHHHHHcCCCC---CcHHHHHHHHHH
Confidence            6666677787877765521110         01111 2288999999999999877653222111   113566889999


Q ss_pred             cCCchHH
Q 041007          396 CKGLPFA  402 (597)
Q Consensus       396 ~~GlPLa  402 (597)
                      +.|.+-.
T Consensus       223 s~Gd~R~  229 (252)
T d1sxje2         223 SNGNLRV  229 (252)
T ss_dssp             HTTCHHH
T ss_pred             cCCcHHH
Confidence            9998643

>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=98.68  E-value=1e-07  Score=89.37  Aligned_cols=161  Identities=18%  Similarity=0.181  Sum_probs=90.3

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-----c-CCeeEEE-EecCCC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-----N-FDKRIWV-SASYPR  239 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-----~-F~~~~wv-~~~~~~  239 (597)
                      ..+||++|++++...|....          -..+.++|++|+|||+|+..+++.  +..     . ....+|. +++.- 
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~----------k~n~lLVG~~GvGKTalv~~la~r--i~~~~vp~~l~~~~i~~l~~~~l-   85 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRR----------KNNPLLVGESGVGKTAIAEGLAWR--IVQGDVPEVMADCTIYSLDIGSL-   85 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSS----------SCEEEEECCTTSSHHHHHHHHHHH--HHHTCSCGGGTTCEEEECCCC---
T ss_pred             cccChHHHHHHHHHHHhcCc----------cCCcEEECCCCCcHHHHHHHHHHH--HHhCCcccccccceeEEeeechH-
Confidence            47899999999999998443          357789999999999999998873  221     1 1234443 22110 


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHh-cCceEEEEEecccCCCC----cchHHHHH
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFV-QGKKVLLVLDDLWWNAY----PRYWEQLM  314 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L-~~kr~LLVLDdv~~~~~----~~~~~~l~  314 (597)
                                                  +.+ .....+.+.....+.+.+ +.++.+|++|+++..-.    ...-..+.
T Consensus        86 ----------------------------iag-~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a  136 (268)
T d1r6bx2          86 ----------------------------LAG-TKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAA  136 (268)
T ss_dssp             -----------------------------CC-CCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHH
T ss_pred             ----------------------------hcc-CccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHH
Confidence                                        000 111223333344444444 45679999999865421    11112233


Q ss_pred             Hhhc-CC-CCCcEEEEEccCCCCCCCcccccccccCccccce-eecCCCChHHHHHHHHHHh
Q 041007          315 YSLK-SG-SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME-IGLGELSEEECRSLFRQIA  373 (597)
Q Consensus       315 ~~l~-~~-~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~-~~l~~Ls~~es~~Lf~~~~  373 (597)
                      ..|. .. ...-++|.||....    .....-......+... +.+.+++.+++.+++....
T Consensus       137 ~~Lkp~L~rg~i~vIgatT~ee----y~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         137 NLIKPLLSSGKIRVIGSTTYQE----FSNIFEKDRALARRFQKIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             HHHSSCSSSCCCEEEEEECHHH----HHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHH
T ss_pred             HHhhHHHhCCCCeEEEeCCHHH----HHHHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhh
Confidence            3332 22 33567777776540    0000000001222222 9999999999999987644

>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=98.67  E-value=6.5e-08  Score=89.91  Aligned_cols=179  Identities=15%  Similarity=0.100  Sum_probs=106.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-cCCe-eEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKA-NFDK-RIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-~F~~-~~wv~~~~~~~~~~  243 (597)
                      .+++|.+..++.|..++...          ..+.+.|+|++|+||||+|+.+++.  ... .+.. .+-++++.....  
T Consensus        24 ~diig~~~~~~~l~~~i~~~----------~~~~lll~Gp~G~GKTtla~~iak~--l~~~~~~~~~~e~n~s~~~~~--   89 (231)
T d1iqpa2          24 DDIVGQEHIVKRLKHYVKTG----------SMPHLLFAGPPGVGKTTAALALARE--LFGENWRHNFLELNASDERGI--   89 (231)
T ss_dssp             TTCCSCHHHHHHHHHHHHHT----------CCCEEEEESCTTSSHHHHHHHHHHH--HHGGGHHHHEEEEETTCHHHH--
T ss_pred             HHccCcHHHHHHHHHHHHcC----------CCCeEEEECCCCCcHHHHHHHHHHH--HHhcccCCCeeEEecCcccch--
Confidence            56999999999999999843          3567889999999999999999883  322 1111 122222211100  


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCC
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEG  323 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~g  323 (597)
                                    ..+...+.....               .......++.++++|++.... ...+..+...+......
T Consensus        90 --------------~~~~~~~~~~~~---------------~~~~~~~~~~iilide~d~~~-~~~~~~ll~~l~~~~~~  139 (231)
T d1iqpa2          90 --------------NVIREKVKEFAR---------------TKPIGGASFKIIFLDEADALT-QDAQQALRRTMEMFSSN  139 (231)
T ss_dssp             --------------HTTHHHHHHHHH---------------SCCGGGCSCEEEEEETGGGSC-HHHHHHHHHHHHHTTTT
T ss_pred             --------------hHHHHHHHHHHh---------------hhhccCCCceEEeehhhhhcc-hhHHHHHhhhcccCCcc
Confidence                          000000000000               000112467899999997665 45566666666655556


Q ss_pred             cEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcCCchH
Q 041007          324 SRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       324 s~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPL  401 (597)
                      ..+|.||........         .... ...+.+.+.+..+....+...+......    -..+..+.|++.|+|..-
T Consensus       140 ~~~i~~~n~~~~i~~---------~l~sR~~~i~~~~~~~~~~~~~l~~~~~~e~i~----i~~~~l~~I~~~~~gdiR  205 (231)
T d1iqpa2         140 VRFILSCNYSSKIIE---------PIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLE----LTEEGLQAILYIAEGDMR  205 (231)
T ss_dssp             EEEEEEESCGGGSCH---------HHHHTEEEEECCCCCHHHHHHHHHHHHHTTTCE----ECHHHHHHHHHHHTTCHH
T ss_pred             eEEEeccCChhhchH---------hHhCccccccccccchhhHHHHHHHHHHHhCCC----CCHHHHHHHHHHcCCCHH
Confidence            666666654411000         1111 1229999999999999998887533221    124567889999998653

>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=98.54  E-value=1.7e-07  Score=82.99  Aligned_cols=44  Identities=25%  Similarity=0.446  Sum_probs=37.8

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+||++|++++...|....          -.-+.++|++|+|||+++..+++.
T Consensus        23 ~~igRd~Ei~~l~~iL~r~~----------k~n~lLvG~pGVGKTalv~~LA~r   66 (195)
T d1jbka_          23 PVIGRDEEIRRTIQVLQRRT----------KNNPVLIGEPGVGKTAIVEGLAQR   66 (195)
T ss_dssp             CCCSCHHHHHHHHHHHTSSS----------SCEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCcCcHHHHHHHHHHHhccC----------CCCeEEEecCCcccHHHHHHHHHH
Confidence            47899999999999998543          356789999999999999998873

>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=98.50  E-value=4.6e-07  Score=86.56  Aligned_cols=122  Identities=17%  Similarity=0.208  Sum_probs=70.1

Q ss_pred             CCCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhh---cc-CCeeEEEEecCCC
Q 041007          164 DPLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVK---AN-FDKRIWVSASYPR  239 (597)
Q Consensus       164 ~~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~---~~-F~~~~wv~~~~~~  239 (597)
                      .|..++||+.++++|.+.+....... .++.....++.|+|++|+|||++++.+++.....   .. .....++.+....
T Consensus        14 ~P~~~~~Re~e~~~l~~~l~~~~~~~-~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   92 (287)
T d1w5sa2          14 IPPELRVRRGEAEALARIYLNRLLSG-AGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNAP   92 (287)
T ss_dssp             CCSSCSSSCHHHHHHHHHHHHHHHTS-SCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGCC
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHcC-CCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeecccccc
Confidence            46789999999999988764211100 0001123356678999999999999999842111   11 1234556555544


Q ss_pred             chhhhhhhhhhhcccchHHHHHHHHHHhccCCCCc-hhhHHHHHHHHHHHhc--CceEEEEEeccc
Q 041007          240 DEIRVARDEISVARDRDEIRVAKAILESLKGSVSS-QVEMETVLQYINEFVQ--GKKVLLVLDDLW  302 (597)
Q Consensus       240 ~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~-~~~~~~~~~~l~~~L~--~kr~LLVLDdv~  302 (597)
                      ..                ......+...++..... ..........+.+...  +...++++|.+.
T Consensus        93 ~~----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d  142 (287)
T d1w5sa2          93 NL----------------YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQ  142 (287)
T ss_dssp             SH----------------HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTH
T ss_pred             ch----------------hhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEE
Confidence            44                55666666665543322 2233334444444442  567788888764

>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=98.49  E-value=1.9e-06  Score=78.12  Aligned_cols=94  Identities=10%  Similarity=-0.036  Sum_probs=66.4

Q ss_pred             CceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHH
Q 041007          291 GKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLF  369 (597)
Q Consensus       291 ~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf  369 (597)
                      +++-++|+|+++... ......++..+.....++.+|+||.+......         .+... ..+.+.+++.++....+
T Consensus       107 ~~~kviIide~d~l~-~~a~n~Llk~lEep~~~~~fIl~t~~~~~ll~---------tI~SRc~~i~~~~~~~~~~~~~L  176 (207)
T d1a5ta2         107 GGAKVVWVTDAALLT-DAAANALLKTLEEPPAETWFFLATREPERLLA---------TLRSRCRLHYLAPPPEQYAVTWL  176 (207)
T ss_dssp             SSCEEEEESCGGGBC-HHHHHHHHHHHTSCCTTEEEEEEESCGGGSCH---------HHHTTSEEEECCCCCHHHHHHHH
T ss_pred             CccceEEechhhhhh-hhhhHHHHHHHHhhcccceeeeeecChhhhhh---------hhcceeEEEecCCCCHHHHHHHH
Confidence            456799999998876 66677788888777888998888876521110         11112 22999999999999988


Q ss_pred             HHHhccCCCCCCccchHHHHHHHHHhcCCchHHH
Q 041007          370 RQIAFHGRSSDYREKFEPIGRRVVGKCKGLPFAV  403 (597)
Q Consensus       370 ~~~~~~~~~~~~~~~~~~~~~~I~~~~~GlPLai  403 (597)
                      .....      .   ..+.+..|++.++|.|-.+
T Consensus       177 ~~~~~------~---~~~~~~~i~~~s~Gs~r~a  201 (207)
T d1a5ta2         177 SREVT------M---SQDALLAALRLSAGSPGAA  201 (207)
T ss_dssp             HHHCC------C---CHHHHHHHHHHTTTCHHHH
T ss_pred             HHcCC------C---CHHHHHHHHHHcCCCHHHH
Confidence            76531      1   1456788999999988544

>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=98.45  E-value=1.4e-06  Score=81.69  Aligned_cols=202  Identities=15%  Similarity=0.112  Sum_probs=105.0

Q ss_pred             CccccchhhHHHHHHHhhCCC-------CCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          166 LEFHGRNAEKQKILQLLKGES-------SDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~-------~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      .+++|.+..+++|..+|..-.       ...+..+.+..+.+.++||+|+||||+|+.+++.  ..   ...++++.+..
T Consensus        14 ~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~--~~---~~~~~~~~~~~   88 (253)
T d1sxja2          14 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE--LG---YDILEQNASDV   88 (253)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHH--TT---CEEEEECTTSC
T ss_pred             HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHH--HH---hhhhccccccc
Confidence            578999999999999985310       0000111345678999999999999999999883  22   22445555443


Q ss_pred             CchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC--cchHHHHHHh
Q 041007          239 RDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY--PRYWEQLMYS  316 (597)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~--~~~~~~l~~~  316 (597)
                      ...                 .....................  .........++..++++|++.....  ...+..+...
T Consensus        89 ~~~-----------------~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~~~~~~  149 (253)
T d1sxja2          89 RSK-----------------TLLNAGVKNALDNMSVVGYFK--HNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVGQLAQF  149 (253)
T ss_dssp             CCH-----------------HHHHHTGGGGTTBCCSTTTTT--C----CCSSTTSEEEEECSGGGCCTTSTTHHHHHHHH
T ss_pred             hhh-----------------HHHHHHHHHHhhcchhhhhhh--hhhhcccccccceEEEeeeccccccchhhhhHHHhhh
Confidence            332                 122222221111110000000  0001112335678899999865431  2234444433


Q ss_pred             hcCCCCCcEEEEEccCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHh
Q 041007          317 LKSGSEGSRILVTRSGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGK  395 (597)
Q Consensus       317 l~~~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~  395 (597)
                      ..... ...+++++........         .... ...+.+.+++.++....+...+...+....    .+..++|++.
T Consensus       150 ~~~~~-~~ii~i~~~~~~~~~~---------~l~~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~----~~~l~~i~~~  215 (253)
T d1sxja2         150 CRKTS-TPLILICNERNLPKMR---------PFDRVCLDIQFRRPDANSIKSRLMTIAIREKFKLD----PNVIDRLIQT  215 (253)
T ss_dssp             HHHCS-SCEEEEESCTTSSTTG---------GGTTTSEEEECCCCCHHHHHHHHHHHHHHHTCCCC----TTHHHHHHHH
T ss_pred             hcccc-cccccccccccccccc---------cccceeeeeeccccchhHHHHHHHHHHHHhCCCCC----HHHHHHHHHh
Confidence            32222 2233333322211000         1111 123999999999999888876643222221    1346889999


Q ss_pred             cCCch-HHHHH
Q 041007          396 CKGLP-FAVKI  405 (597)
Q Consensus       396 ~~GlP-Lai~~  405 (597)
                      ++|.. -||..
T Consensus       216 s~GDiR~ai~~  226 (253)
T d1sxja2         216 TRGDIRQVINL  226 (253)
T ss_dssp             TTTCHHHHHHH
T ss_pred             CCCcHHHHHHH
Confidence            99966 44443

>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=98.40  E-value=2e-06  Score=78.14  Aligned_cols=161  Identities=17%  Similarity=0.142  Sum_probs=88.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCCchh
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVSSQV  276 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~  276 (597)
                      ...+.|+|++|+|||.|++.+++  ........+++++.                      ......+...+...     
T Consensus        36 ~n~l~l~G~~G~GKTHLl~A~~~--~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~-----   86 (213)
T d1l8qa2          36 YNPIFIYGSVGTGKTHLLQAAGN--EAKKRGYRVIYSSA----------------------DDFAQAMVEHLKKG-----   86 (213)
T ss_dssp             CSSEEEECSSSSSHHHHHHHHHH--HHHHTTCCEEEEEH----------------------HHHHHHHHHHHHHT-----
T ss_pred             CCcEEEECCCCCcHHHHHHHHHH--HhccCccceEEech----------------------HHHHHHHHHHHHcc-----
Confidence            34588999999999999999999  45555556667654                      33333333333211     


Q ss_pred             hHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHH-HHhhcC-CCCCcEEEEEccCCCCCCCcccccccccCccccce
Q 041007          277 EMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQL-MYSLKS-GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNMME  354 (597)
Q Consensus       277 ~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l-~~~l~~-~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~~~  354 (597)
                      .....    .+.+. .--+|+|||++.......|+.. ...+.. ...|..||+|++..+........++.+ .......
T Consensus        87 ~~~~~----~~~~~-~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p~~l~~~~~dL~S-RL~~g~~  160 (213)
T d1l8qa2          87 TINEF----RNMYK-SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHPQKLDGVSDRLVS-RFEGGIL  160 (213)
T ss_dssp             CHHHH----HHHHH-TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCGGGCTTSCHHHHH-HHHTSEE
T ss_pred             chhhH----HHHHh-hccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcchhccccchHHHH-HhhCceE
Confidence            11111    12222 3458999999766545566653 333332 356788999998873222110000000 0011112


Q ss_pred             eecCCCChHHHHHHHHHHhccCCCCCCccchHHHHHHHHHhcC
Q 041007          355 IGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIGRRVVGKCK  397 (597)
Q Consensus       355 ~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~~~I~~~~~  397 (597)
                      +.+. +++++-.+++.+.+...+-. .+   .+++.-|++++.
T Consensus       161 ~~i~-p~d~~~~~iL~~~a~~rgl~-l~---~~v~~yl~~~~~  198 (213)
T d1l8qa2         161 VEIE-LDNKTRFKIIKEKLKEFNLE-LR---KEVIDYLLENTK  198 (213)
T ss_dssp             EECC-CCHHHHHHHHHHHHHHTTCC-CC---HHHHHHHHHHCS
T ss_pred             EEEC-CCcHHHHHHHHHHHHHcCCC-CC---HHHHHHHHHhcC
Confidence            7775 47777778888777433322 11   345566666653

>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=98.37  E-value=6.9e-06  Score=76.15  Aligned_cols=177  Identities=16%  Similarity=0.116  Sum_probs=97.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      +++||-++-+++|..++......     ...++.+.++||+|+||||+|+.+++.  ...+   ..+++.+.....    
T Consensus         9 ddivGq~~~~~~L~~~i~~~~~~-----~~~~~~~Ll~GPpG~GKTtla~~la~~--~~~~---~~~~~~~~~~~~----   74 (239)
T d1ixsb2           9 DEYIGQERLKQKLRVYLEAAKAR-----KEPLEHLLLFGPPGLGKTTLAHVIAHE--LGVN---LRVTSGPAIEKP----   74 (239)
T ss_dssp             GGSCSCHHHHHHHHHHHHHHTTS-----SSCCCCEEEECCTTSCHHHHHHHHHHH--HTCC---EEEEETTTCCSH----
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhc-----CCCCCeEEEECCCCCCHHHHHHHHHHH--hCCC---eEeccCCccccc----
Confidence            46899999999998888643221     124567889999999999999999873  2222   233333222111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC------
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS------  319 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~------  319 (597)
                                                       ......+...+ +.+.++++|+++... ...-+.+...+..      
T Consensus        75 ---------------------------------~~~~~~~~~~~-~~~~i~~iDe~~~~~-~~~~~~l~~~~e~~~~~~~  119 (239)
T d1ixsb2          75 ---------------------------------GDLAAILANSL-EEGDILFIDEIHRLS-RQAEEHLYPAMEDFVMDIV  119 (239)
T ss_dssp             ---------------------------------HHHHHHHHTTC-CTTCEEEEETGGGCC-HHHHHHHHHHHHHSEEEEE
T ss_pred             ---------------------------------hhhHHHHHhhc-cCCCeeeeecccccc-hhHHHhhhhhhhhhhhhhh
Confidence                                             11111222222 234466778886554 2222222222210      


Q ss_pred             ------------CCCCcEEEEEc-cCCCCCCCcccccccccCccc-cceeecCCCChHHHHHHHHHHhccCCCCCCccch
Q 041007          320 ------------GSEGSRILVTR-SGGKNGTNMTEIGLGEKNGTN-MMEIGLGELSEEECRSLFRQIAFHGRSSDYREKF  385 (597)
Q Consensus       320 ------------~~~gs~IIvTt-R~~~~~~~~~~~~~~~~~~~~-~~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~  385 (597)
                                  ..+...++.+| +.......         .... ...+.+.+.+.++...++...+.....    ...
T Consensus       120 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~---------~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i----~~~  186 (239)
T d1ixsb2         120 IGQGPAARTIRLELPRFTLIGATTRPGLITAP---------LLSRFGIVEHLEYYTPEELAQGVMRDARLLGV----RIT  186 (239)
T ss_dssp             CSCTTCCCEEEEECCCCEEEEEESCCSSCSCG---------GGGGCSEEEECCCCCHHHHHHHHHHHHGGGCC----CBC
T ss_pred             hccchhhhhcccCCCCEEEEeeccCcccccch---------hhcccceeeEeeccChhhhhHHHHHHHHHhCC----ccc
Confidence                        11223344443 33211100         1111 122888999999999888877643322    122


Q ss_pred             HHHHHHHHHhcCCchHHHH
Q 041007          386 EPIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       386 ~~~~~~I~~~~~GlPLai~  404 (597)
                      .+....|++.++|.+-.+.
T Consensus       187 ~~~l~~ia~~s~gd~R~a~  205 (239)
T d1ixsb2         187 EEAALEIGRRSRGTMRVAK  205 (239)
T ss_dssp             HHHHHHHHHHTTSSHHHHH
T ss_pred             hHHHHHHHHHcCCCHHHHH
Confidence            5678899999999875543

>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=98.24  E-value=8.2e-06  Score=76.10  Aligned_cols=185  Identities=12%  Similarity=0.111  Sum_probs=96.3

Q ss_pred             CccccchhhHHHHHHHh---hCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQKILQLL---KGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L---~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      .+++|-++.+++|.+.+   ..... -..-+...++.+.++|++|+|||+||+.+++  ....+   .+-++.+.-.+. 
T Consensus        12 ~Di~Gl~~~k~~l~e~v~~~~~~~~-~~~~g~~~~~~iLL~GppGtGKT~la~~iA~--~~~~~---~~~i~~~~l~~~-   84 (256)
T d1lv7a_          12 ADVAGCDEAKEEVAELVEYLREPSR-FQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG--EAKVP---FFTISGSDFVEM-   84 (256)
T ss_dssp             GGSCSCHHHHHHTHHHHHHHHCGGG-C-----CCCCEEEEECCTTSCHHHHHHHHHH--HHTCC---EEEECSCSSTTS-
T ss_pred             HHHhchHHHHHHHHHHHHHHHCHHH-HHHcCCCCCCeEEeeCCCCCCccHHHHHHHH--HcCCC---EEEEEhHHhhhc-
Confidence            46889988888776543   21110 0000012357789999999999999999997  33322   122322221110 


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCC---------Ccch----
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNA---------YPRY----  309 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~---------~~~~----  309 (597)
                                                   . .......+...+...-+..+++|+|||++...         ....    
T Consensus        85 -----------------------------~-~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~  134 (256)
T d1lv7a_          85 -----------------------------F-VGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQT  134 (256)
T ss_dssp             -----------------------------C-CCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHH
T ss_pred             -----------------------------c-hhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHH
Confidence                                         0 00111222333333335678999999985310         0012    


Q ss_pred             HHHHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcc---cc-ceeecCCCChHHHHHHHHHHhccCCCCCCcc
Q 041007          310 WEQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGT---NM-MEIGLGELSEEECRSLFRQIAFHGRSSDYRE  383 (597)
Q Consensus       310 ~~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~---~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~  383 (597)
                      ...+...+..  ...+.-||.||........         .+.   +. ..+.+.+.+.++-.++|......... ....
T Consensus       135 ~~~ll~~~d~~~~~~~v~vIatTn~~~~ld~---------al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~-~~~~  204 (256)
T d1lv7a_         135 LNQMLVEMDGFEGNEGIIVIAATNRPDVLDP---------ALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPL-APDI  204 (256)
T ss_dssp             HHHHHHHHHTCCSSSCEEEEEEESCTTTSCG---------GGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCB-CTTC
T ss_pred             HHHHHHHhhCCCCCCCEEEEEeCCCcccCCH---------hHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCc-Cccc
Confidence            2233333332  2334455556665421110         111   11 12889999999989999887643221 1122


Q ss_pred             chHHHHHHHHHhcCCchH
Q 041007          384 KFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       384 ~~~~~~~~I~~~~~GlPL  401 (597)
                      +    ...+++.+.|..-
T Consensus       205 ~----~~~la~~t~G~s~  218 (256)
T d1lv7a_         205 D----AAIIARGTPGFSG  218 (256)
T ss_dssp             C----HHHHHHTCTTCCH
T ss_pred             C----HHHHHHhCCCCCH
Confidence            2    3567788888643

>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=98.24  E-value=7.5e-06  Score=75.81  Aligned_cols=177  Identities=16%  Similarity=0.164  Sum_probs=97.6

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVA  245 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~  245 (597)
                      .+++|-++.+++|..++......     ....+.+.++||+|+||||+|+.+++  .....|   ..++.+.....    
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~-----~~~~~~~L~~GPpGtGKT~lA~~la~--~~~~~~---~~~~~~~~~~~----   74 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMR-----GEVLDHVLLAGPPGLGKTTLAHIIAS--ELQTNI---HVTSGPVLVKQ----   74 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHH-----TCCCCCEEEESSTTSSHHHHHHHHHH--HHTCCE---EEEETTTCCSH----
T ss_pred             HHcCChHHHHHHHHHHHHHHHhc-----CCCCCeEEEECCCCCcHHHHHHHHHh--ccCCCc---ccccCcccccH----
Confidence            56899999999999888532110     12345688999999999999999987  333222   22332221111    


Q ss_pred             hhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC------
Q 041007          246 RDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS------  319 (597)
Q Consensus       246 ~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~------  319 (597)
                                  . ....++                    .  ...++..+++|++...+ ...-+.+......      
T Consensus        75 ------------~-~~~~~~--------------------~--~~~~~~~~~ide~~~~~-~~~~~~l~~~~~~~~~~~~  118 (238)
T d1in4a2          75 ------------G-DMAAIL--------------------T--SLERGDVLFIDEIHRLN-KAVEELLYSAIEDFQIDIM  118 (238)
T ss_dssp             ------------H-HHHHHH--------------------H--HCCTTCEEEEETGGGCC-HHHHHHHHHHHHTSCCCC-
T ss_pred             ------------H-HHHHHH--------------------H--hhccCCchHHHHHHHhh-hHHHhhcccceeeeeeeee
Confidence                        1 111111                    1  12345677788875543 2111222222211      


Q ss_pred             ------------CCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchH
Q 041007          320 ------------GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFE  386 (597)
Q Consensus       320 ------------~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~  386 (597)
                                  ..++..+|.+|.........        ..... ..+.+.+.+.++...++...+......    ...
T Consensus       119 ~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~~--------~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~----~~~  186 (238)
T d1in4a2         119 IGKGPSAKSIRIDIQPFTLVGATTRSGLLSSP--------LRSRFGIILELDFYTVKELKEIIKRAASLMDVE----IED  186 (238)
T ss_dssp             --------------CCCEEEEEESCGGGSCHH--------HHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCC----BCH
T ss_pred             ecCcccccccccCCCCeEEEEecCCCcccccc--------ceeeeeEEEEecCCCHHHHHHHHHHhhhhccch----hhH
Confidence                        12244555555544110000        00011 117899999999999998877543322    224


Q ss_pred             HHHHHHHHhcCCchHHHH
Q 041007          387 PIGRRVVGKCKGLPFAVK  404 (597)
Q Consensus       387 ~~~~~I~~~~~GlPLai~  404 (597)
                      +....|++.++|.+-.+.
T Consensus       187 ~~l~~i~~~s~gd~R~ai  204 (238)
T d1in4a2         187 AAAEMIAKRSRGTPRIAI  204 (238)
T ss_dssp             HHHHHHHHTSTTCHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHH
Confidence            567899999999866553

>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=98.22  E-value=4.1e-06  Score=82.81  Aligned_cols=43  Identities=26%  Similarity=0.484  Sum_probs=35.5

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++||+.++++++..|.....          ..+.++|++|||||+|+..+++
T Consensus        23 ~~~gr~~ei~~~~~~L~r~~k----------~n~llvG~~GvGKtaiv~~la~   65 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLRRTK----------NNPVLIGEPGVGKTAIVEGLAQ   65 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHCSSC----------CCCEEEECTTSCHHHHHHHHHH
T ss_pred             CCcCcHHHHHHHHHHHhcCCC----------CCCeEECCCCCCHHHHHHHHHH
Confidence            478999999999999985432          3457789999999999987776

>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=98.20  E-value=1.1e-05  Score=75.71  Aligned_cols=187  Identities=13%  Similarity=0.102  Sum_probs=97.0

Q ss_pred             ccccchhhHHHHHHHhh----CCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          167 EFHGRNAEKQKILQLLK----GESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~----~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      .++|-+..+++|.+.+.    .... -...+-..++-|.++|++|+|||++|+.+++  ....+|   +.++.+.     
T Consensus         5 dv~G~~~~k~~l~~~i~~~l~~~~~-~~~~g~~~~~giLL~GppGtGKT~l~~ala~--~~~~~~---~~i~~~~-----   73 (258)
T d1e32a2           5 DVGGCRKQLAQIKEMVELPLRHPAL-FKAIGVKPPRGILLYGPPGTGKTLIARAVAN--ETGAFF---FLINGPE-----   73 (258)
T ss_dssp             GCCSCSHHHHHHHHHHHHHHHCHHH-HHHCCCCCCCEEEEECCTTSSHHHHHHHHHH--HTTCEE---EEECHHH-----
T ss_pred             hhccHHHHHHHHHHHHHHHhcCHHH-HHhCCCCCCceeEEecCCCCCchHHHHHHHH--HhCCeE---EEEEchh-----
Confidence            47899999888887642    1100 0000012456799999999999999999988  332222   2222111     


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCC------cchHH----H
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAY------PRYWE----Q  312 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~------~~~~~----~  312 (597)
                                               +.... .......+...+...-..++++|+|||+.....      .....    .
T Consensus        74 -------------------------l~~~~-~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~  127 (258)
T d1e32a2          74 -------------------------IMSKL-AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQ  127 (258)
T ss_dssp             -------------------------HTTSC-TTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHH
T ss_pred             -------------------------hcccc-cccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHH
Confidence                                     00000 011122223333333457899999999964321      11122    2


Q ss_pred             HHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHHHH
Q 041007          313 LMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEPIG  389 (597)
Q Consensus       313 l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~~~  389 (597)
                      +...+..  ...+.-||.||........    .+.  ...+. ..+.+...+.++-.++|......... ....+    .
T Consensus       128 ~~~~~~~~~~~~~vlvi~tTn~~~~ld~----al~--r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~-~~~~~----~  196 (258)
T d1e32a2         128 LLTLMDGLKQRAHVIVMAATNRPNSIDP----ALR--RFGRFDREVDIGIPDATGRLEILQIHTKNMKL-ADDVD----L  196 (258)
T ss_dssp             HHHHHHTCCCSSCEEEEEEESCGGGSCG----GGT--STTSSCEEEECCCCCHHHHHHHHHHTTTTSCB-CTTCC----H
T ss_pred             hccccccccccCCccEEEeCCCccccch----hhh--hcccccceeECCCCCHHHHHHHhhhhccCccc-ccccc----h
Confidence            2222222  2334455557765411110    000  00011 12899999999999999877632211 11112    3


Q ss_pred             HHHHHhcCCchH
Q 041007          390 RRVVGKCKGLPF  401 (597)
Q Consensus       390 ~~I~~~~~GlPL  401 (597)
                      ..|++.+.|.--
T Consensus       197 ~~la~~t~G~s~  208 (258)
T d1e32a2         197 EQVANETHGHVG  208 (258)
T ss_dssp             HHHHHHCTTCCH
T ss_pred             hhhhhcccCCCH
Confidence            678899988543

>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=98.16  E-value=9.3e-06  Score=75.37  Aligned_cols=189  Identities=13%  Similarity=0.090  Sum_probs=93.9

Q ss_pred             CccccchhhHHHHHHHhhCCCCCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhh
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDE--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIR  243 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~  243 (597)
                      ..++|-++.+++|.+.+......+  ...+...++-|.++|++|+|||+||+.+++  ....+   .+.++.+       
T Consensus         9 ~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~--~~~~~---~~~i~~~-------   76 (247)
T d1ixza_           9 KDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAG--EARVP---FITASGS-------   76 (247)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHH--HTTCC---EEEEEHH-------
T ss_pred             HHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHH--HcCCC---EEEEEhH-------
Confidence            468899888777665432100000  000012356799999999999999999997  33222   2223221       


Q ss_pred             hhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCC-------C--cc----hH
Q 041007          244 VARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNA-------Y--PR----YW  310 (597)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~-------~--~~----~~  310 (597)
                                     .+..    .    . .......+...+...-...+++|+|||++...       .  ..    ..
T Consensus        77 ---------------~l~~----~----~-~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~  132 (247)
T d1ixza_          77 ---------------DFVE----M----F-VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTL  132 (247)
T ss_dssp             ---------------HHHH----S----C-TTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHH
T ss_pred             ---------------Hhhh----c----c-ccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHH
Confidence                           1110    0    0 00111222233333334678999999985210       0  00    12


Q ss_pred             HHHHHhhcCC--CCCcEEEEEccCCCCCCCcccccccccCcccc-ceeecCCCChHHHHHHHHHHhccCCCCCCccchHH
Q 041007          311 EQLMYSLKSG--SEGSRILVTRSGGKNGTNMTEIGLGEKNGTNM-MEIGLGELSEEECRSLFRQIAFHGRSSDYREKFEP  387 (597)
Q Consensus       311 ~~l~~~l~~~--~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~~~-~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~~~~~  387 (597)
                      ..+...+...  ..+.-||.||......    +..+.+  ..+. ..+.+.+.+.++-.++|......... .....   
T Consensus       133 ~~ll~~~d~~~~~~~vivi~tTn~~~~l----d~al~R--~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~-~~~~~---  202 (247)
T d1ixza_         133 NQLLVEMDGFEKDTAIVVMAATNRPDIL----DPALLR--PGRFDRQIAIDAPDVKGREQILRIHARGKPL-AEDVD---  202 (247)
T ss_dssp             HHHHHHHHTCCTTCCEEEEEEESCGGGS----CGGGGS--TTSSCEEEECCSCCHHHHHHHHHHHHTTSCB-CTTCC---
T ss_pred             HHHHHHhhCCCCCCCEEEEEeCCCcccc----CHhHcC--CCCCcEEEEECCcCHHHHHHHHHHHhcccCC-ccccC---
Confidence            2233333322  2233333455443111    000000  0011 12899999999999999988743222 11222   


Q ss_pred             HHHHHHHhcCCchH
Q 041007          388 IGRRVVGKCKGLPF  401 (597)
Q Consensus       388 ~~~~I~~~~~GlPL  401 (597)
                       ...+++.|.|..-
T Consensus       203 -~~~la~~t~g~s~  215 (247)
T d1ixza_         203 -LALLAKRTPGFVG  215 (247)
T ss_dssp             -HHHHHHTCTTCCH
T ss_pred             -HHHHHHHCCCCCH
Confidence             3577788887543

>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=97.89  E-value=3.7e-05  Score=71.20  Aligned_cols=54  Identities=17%  Similarity=0.147  Sum_probs=34.4

Q ss_pred             CccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          166 LEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|..++++.+.+.+......-..+....++.|.++|++|+|||++|+.+++
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~   62 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAE   62 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHH
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhh
Confidence            347887777766655443110000000022456799999999999999999988

>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=97.88  E-value=3.3e-05  Score=72.50  Aligned_cols=186  Identities=13%  Similarity=0.057  Sum_probs=94.1

Q ss_pred             CccccchhhHHHHHHHhhCCC-CCC--cCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchh
Q 041007          166 LEFHGRNAEKQKILQLLKGES-SDE--ESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEI  242 (597)
Q Consensus       166 ~~~vGR~~e~~~l~~~L~~~~-~~~--~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~  242 (597)
                      ..++|-++.+++|.+.+...- ..+  ...+-+..+.|.++|++|+|||+||+.+++  ....+|     +.++.     
T Consensus         7 ~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~--~~~~~~-----~~~~~-----   74 (265)
T d1r7ra3           7 EDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIAN--ECQANF-----ISIKG-----   74 (265)
T ss_dssp             SSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHH--HTTCEE-----EEECH-----
T ss_pred             HHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHH--HhCCcE-----EEEEH-----
Confidence            346787777777766553100 000  000023456799999999999999999988  333322     22210     


Q ss_pred             hhhhhhhhhcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCc---------ch----
Q 041007          243 RVARDEISVARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYP---------RY----  309 (597)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~---------~~----  309 (597)
                                     ..+.        ... .......+...+...-...+++|+|||++.....         ..    
T Consensus        75 ---------------~~l~--------~~~-~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~  130 (265)
T d1r7ra3          75 ---------------PELL--------TMW-FGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRV  130 (265)
T ss_dssp             ---------------HHHH--------TSC-TTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHH
T ss_pred             ---------------HHhh--------hcc-ccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHH
Confidence                           1110        000 1111222333343444467899999999643210         11    


Q ss_pred             HHHHHHhhcC--CCCCcEEEEEccCCCCCCCcccccccccCcc--cc--ceeecCCCChHHHHHHHHHHhccCCCCCCcc
Q 041007          310 WEQLMYSLKS--GSEGSRILVTRSGGKNGTNMTEIGLGEKNGT--NM--MEIGLGELSEEECRSLFRQIAFHGRSSDYRE  383 (597)
Q Consensus       310 ~~~l~~~l~~--~~~gs~IIvTtR~~~~~~~~~~~~~~~~~~~--~~--~~~~l~~Ls~~es~~Lf~~~~~~~~~~~~~~  383 (597)
                      ...+...+..  ...+.-||.||........         .+.  ..  ..+++.+.+.++-.++|...+..... ....
T Consensus       131 ~~~ll~~l~~~~~~~~v~vi~ttn~~~~ld~---------al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~-~~~~  200 (265)
T d1r7ra3         131 INQILTEMDGMSTKKNVFIIGATNRPDIIDP---------AILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPV-AKDV  200 (265)
T ss_dssp             HHHHHHTCC------CCEEEECCBSCTTTSC---------GGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC-----CC
T ss_pred             HHHHHHHhhCcCCCCCEEEEEeCCCchhCCH---------HHhCCCCccEEEEecchHHHHHHHHHHHHhccCCc-hhhh
Confidence            1223333322  2334556666665521111         111  11  12999999999999999876532111 1112


Q ss_pred             chHHHHHHHHHhcCCchH
Q 041007          384 KFEPIGRRVVGKCKGLPF  401 (597)
Q Consensus       384 ~~~~~~~~I~~~~~GlPL  401 (597)
                      +    ...|++++.|...
T Consensus       201 ~----l~~la~~t~g~s~  214 (265)
T d1r7ra3         201 D----LEFLAKMTNGFSG  214 (265)
T ss_dssp             C----CHHHHHHHCSSCC
T ss_pred             h----HHHHHhcCCCCCH
Confidence            2    2567778887653

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=97.51  E-value=0.0003  Score=62.45  Aligned_cols=115  Identities=10%  Similarity=0.014  Sum_probs=70.6

Q ss_pred             hHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccC---CeeEEEEecCCCchhhhhhhhhh
Q 041007          174 EKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANF---DKRIWVSASYPRDEIRVARDEIS  250 (597)
Q Consensus       174 e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F---~~~~wv~~~~~~~~~~~~~~~~~  250 (597)
                      +++-|..++..          .....+.++|++|+|||++|..+.+.  +...+   +-.+++......-.         
T Consensus         2 ~~~~l~~~i~~----------~~~~~~l~~G~~g~gk~~~a~~l~~~--i~~~~~~h~D~~~i~~~~~~I~---------   60 (198)
T d2gnoa2           2 QLETLKRIIEK----------SEGISILINGEDLSYPREVSLELPEY--VEKFPPKASDVLEIDPEGENIG---------   60 (198)
T ss_dssp             HHHHHHHHHHT----------CSSEEEEEECSSSSHHHHHHHHHHHH--HHTSCCCTTTEEEECCSSSCBC---------
T ss_pred             HHHHHHHHHhc----------CCCceEEEECCCCCCHHHHHHHHHHH--HhccccCCCCEEEEeCCcCCCC---------
Confidence            34555666652          35689999999999999999998863  32211   22444432211100         


Q ss_pred             hcccchHHHHHHHHHHhccCCCCchhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCCCCCcEEEEEc
Q 041007          251 VARDRDEIRVAKAILESLKGSVSSQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSGSEGSRILVTR  330 (597)
Q Consensus       251 ~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~~~gs~IIvTt  330 (597)
                             .+..+++...+....                ..+++-++|+|+++... ...+..++..+..-+.++.+|++|
T Consensus        61 -------Id~IR~i~~~~~~~~----------------~~~~~KviIId~ad~l~-~~aqNaLLK~LEEPp~~t~fiLit  116 (198)
T d2gnoa2          61 -------IDDIRTIKDFLNYSP----------------ELYTRKYVIVHDCERMT-QQAANAFLKALEEPPEYAVIVLNT  116 (198)
T ss_dssp             -------HHHHHHHHHHHTSCC----------------SSSSSEEEEETTGGGBC-HHHHHHTHHHHHSCCTTEEEEEEE
T ss_pred             -------HHHHHHHHHHHhhCc----------------ccCCCEEEEEeCccccc-hhhhhHHHHHHhCCCCCceeeecc
Confidence                   112222322222111                12455699999998887 777888888888777888888877


Q ss_pred             cCC
Q 041007          331 SGG  333 (597)
Q Consensus       331 R~~  333 (597)
                      .+.
T Consensus       117 ~~~  119 (198)
T d2gnoa2         117 RRW  119 (198)
T ss_dssp             SCG
T ss_pred             CCh
Confidence            665

>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=97.18  E-value=0.00029  Score=67.41  Aligned_cols=125  Identities=14%  Similarity=0.232  Sum_probs=63.9

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhh
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVAR  246 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~  246 (597)
                      .++|.++.++.+...+......- ..++....++.++|+.|+|||.||+.+...  .-+.-...+-++++...+. ..  
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~l-~~~~kp~~~~lf~Gp~G~GKt~lak~la~~--l~~~~~~~~~~~~~~~~~~-~~--   97 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAGL-KDPNRPIGSFLFLGPTGVGKTELAKTLAAT--LFDTEEAMIRIDMTEYMEK-HA--   97 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGGC-SCSSSCSEEEEEBSCSSSSHHHHHHHHHHH--HHSSGGGEEEECTTTCCSS-GG--
T ss_pred             eEeCHHHHHHHHHHHHHHHhcCC-CCCCCCceEEEEECCCcchHHHHHHHHHHH--hcCCCcceEEEeccccccc-hh--
Confidence            36788888887766554221000 001223447889999999999999998772  3111122233333332221 00  


Q ss_pred             hhhhhcccchHHHHHHHHHHhccCCCCc---hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC
Q 041007          247 DEISVARDRDEIRVAKAILESLKGSVSS---QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS  319 (597)
Q Consensus       247 ~~~~~~~~~~~~~~~~~il~~l~~~~~~---~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~  319 (597)
                                        ...+.+..+.   ......+.+.++   +....+++||++...+ ...++.+...+..
T Consensus        98 ------------------~~~L~g~~~gyvG~~~~~~l~~~~~---~~p~~Vvl~DEieK~~-~~v~~~ll~~l~~  151 (315)
T d1qvra3          98 ------------------VSRLIGAPPGYVGYEEGGQLTEAVR---RRPYSVILFDEIEKAH-PDVFNILLQILDD  151 (315)
T ss_dssp             ------------------GGGC--------------CHHHHHH---HCSSEEEEESSGGGSC-HHHHHHHHHHHTT
T ss_pred             ------------------hhhhcCCCCCCcCcccCChHHHHHH---hCCCcEEEEehHhhcC-HHHHHHHHHHhcc
Confidence                              0011111110   001112233333   2456899999998776 6677777777643

>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=97.15  E-value=0.00042  Score=66.34  Aligned_cols=136  Identities=15%  Similarity=0.225  Sum_probs=74.0

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhh
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVAR  246 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~  246 (597)
                      .++|-++.++.+...+......- ..++....++.++||+|+|||.||+.++.  ..   +...+-++++.-.+.     
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l-~~~~~p~~~~lf~Gp~GvGKT~lak~la~--~l---~~~~i~~d~s~~~~~-----   91 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGL-GHEHKPVGSFLFAGPTGVGKTEVTVQLSK--AL---GIELLRFDMSEYMER-----   91 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTC-SCTTSCSEEEEEECSTTSSHHHHHHHHHH--HH---TCEEEEEEGGGCSSS-----
T ss_pred             eecChHHHHHHHHHHHHHHHccC-CCCCCCceEEEEECCCcchhHHHHHHHHh--hc---cCCeeEeccccccch-----
Confidence            46899988888877664111000 00122345788999999999999999987  22   223344444432221     


Q ss_pred             hhhhhcccchHHHHHHHHHHhccCCCCchh--hH-HHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC---
Q 041007          247 DEISVARDRDEIRVAKAILESLKGSVSSQV--EM-ETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG---  320 (597)
Q Consensus       247 ~~~~~~~~~~~~~~~~~il~~l~~~~~~~~--~~-~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~---  320 (597)
                                 ..     ...+-+..+...  +. ..+...+   .+....+++||++...+ .+.|+.+...+..+   
T Consensus        92 -----------~~-----~~~l~g~~~gy~g~~~~~~l~~~~---~~~~~~vvl~DeieKa~-~~V~~~lLqild~G~lt  151 (315)
T d1r6bx3          92 -----------HT-----VSRLIGAPPGYVGFDQGGLLTDAV---IKHPHAVLLLDEIEKAH-PDVFNILLQVMDNGTLT  151 (315)
T ss_dssp             -----------SC-----CSSSCCCCSCSHHHHHTTHHHHHH---HHCSSEEEEEETGGGSC-HHHHHHHHHHHHHSEEE
T ss_pred             -----------hh-----hhhhcccCCCccccccCChhhHHH---HhCccchhhhccccccc-chHhhhhHHhhccceec
Confidence                       00     011111111111  11 1112222   13556789999998876 77888887777421   


Q ss_pred             --------CCCcEEEEEccCC
Q 041007          321 --------SEGSRILVTRSGG  333 (597)
Q Consensus       321 --------~~gs~IIvTtR~~  333 (597)
                              ..++-+|.||...
T Consensus       152 d~~Gr~vdf~n~iiI~Tsnig  172 (315)
T d1r6bx3         152 DNNGRKADFRNVVLVMTTNAG  172 (315)
T ss_dssp             ETTTEEEECTTEEEEEEECSS
T ss_pred             CCCCCccCccceEEEeccchh
Confidence                    2345566776543

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.92  E-value=0.00019  Score=62.48  Aligned_cols=38  Identities=18%  Similarity=0.136  Sum_probs=28.6

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHhCChhhhc-cCCeeEEE
Q 041007          194 KPTLPVIWILGNEGIGKTALARQVFDDSDVKA-NFDKRIWV  233 (597)
Q Consensus       194 ~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~-~F~~~~wv  233 (597)
                      ..+..+|.|+|++|+||||+|+.+..  +... .++...++
T Consensus         3 ~~~g~~I~l~G~~GsGKTTia~~La~--~L~~~~~~~~~~~   41 (183)
T d1m8pa3           3 ATQGFTIFLTGYMNSGKDAIARALQV--TLNQQGGRSVSLL   41 (183)
T ss_dssp             TTCCEEEEEECSTTSSHHHHHHHHHH--HHHHHCSSCEEEE
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHH--HHhhcCCCchhhh
Confidence            34567999999999999999999988  4433 34444444

>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=96.84  E-value=0.0013  Score=60.44  Aligned_cols=45  Identities=27%  Similarity=0.399  Sum_probs=37.0

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +|||....++++.+.+.....        ...-|.|+|+.|+|||++|+.++.
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~--------~~~pvlI~Ge~GtGK~~~A~~ih~   45 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISC--------AECPVLITGESGVGKEVVARLIHK   45 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTT--------CCSCEEEECSTTSSHHHHHHHHHH
T ss_pred             CeEecCHHHHHHHHHHHHHhC--------CCCCEEEECCCCcCHHHHHHHHHH
Confidence            489999999999888876543        234578999999999999999975

>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=96.69  E-value=0.0028  Score=58.55  Aligned_cols=85  Identities=22%  Similarity=0.235  Sum_probs=57.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC-
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS-  273 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~-  273 (597)
                      +..+++-|.|++|+|||+||.+++..  .+..-..++|++....++.                ..     ++.++.+.+ 
T Consensus        58 ~~g~i~e~~G~~~~GKT~l~l~~~~~--~q~~g~~~vyIDtE~~~~~----------------e~-----a~~~GvD~d~  114 (269)
T d1mo6a1          58 PRGRVIEIYGPESSGKTTVALHAVAN--AQAAGGVAAFIDAEHALDP----------------DY-----AKKLGVDTDS  114 (269)
T ss_dssp             CSSSEEEEECSSSSSHHHHHHHHHHH--HHHTTCEEEEEESSCCCCH----------------HH-----HHHHTCCGGG
T ss_pred             ccceeEEEecCCCcHHHHHHHHHHHH--HhcCCCEEEEEECCccCCH----------------HH-----HHHhCCCHHH
Confidence            46789999999999999999888873  3333456899998887765                21     233343321 


Q ss_pred             ----chhhHHHHHHHHHHHhc-CceEEEEEeccc
Q 041007          274 ----SQVEMETVLQYINEFVQ-GKKVLLVLDDLW  302 (597)
Q Consensus       274 ----~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~  302 (597)
                          .....++..+.+..... ++.-|||+|.+-
T Consensus       115 il~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~  148 (269)
T d1mo6a1         115 LLVSQPDTGEQALEIADMLIRSGALDIVVIDSVA  148 (269)
T ss_dssp             CEEECCSSHHHHHHHHHHHHHTTCEEEEEEECST
T ss_pred             eEEecCCCHHHHHHHHHHHHhcCCCCEEEEeccc
Confidence                12345555555555554 457799999984

>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=96.65  E-value=0.0011  Score=58.23  Aligned_cols=37  Identities=24%  Similarity=0.095  Sum_probs=27.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS  234 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~  234 (597)
                      ++-+|+|.|++|+||||||+.+..  ...........++
T Consensus        21 ~~~iIgI~G~~GSGKSTla~~L~~--~l~~~~~~~~~~~   57 (198)
T d1rz3a_          21 GRLVLGIDGLSRSGKTTLANQLSQ--TLREQGISVCVFH   57 (198)
T ss_dssp             SSEEEEEEECTTSSHHHHHHHHHH--HHHHTTCCEEEEE
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHH--Hhccccccceecc
Confidence            566899999999999999999987  3444443333333

>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=96.63  E-value=0.00048  Score=59.93  Aligned_cols=23  Identities=26%  Similarity=0.515  Sum_probs=21.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.|.|+|++|+|||||+++++..
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~   24 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEV   24 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHH
Confidence            57999999999999999999874

>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=96.62  E-value=0.00042  Score=60.44  Aligned_cols=24  Identities=29%  Similarity=0.407  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -.+.|+|.|++|+||||||+.+..
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~   29 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAA   29 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999999987

>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=96.61  E-value=0.0004  Score=59.18  Aligned_cols=22  Identities=32%  Similarity=0.631  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|.|+|++|+||||+|+.+..
T Consensus         3 k~I~l~G~~GsGKSTvak~La~   24 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQ   24 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            4688999999999999999987

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.57  E-value=0.0005  Score=57.94  Aligned_cols=22  Identities=32%  Similarity=0.575  Sum_probs=19.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|.|+|++|+||||||+++..
T Consensus         3 klIii~G~pGsGKTTla~~L~~   24 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIA   24 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4788999999999999998754

>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=96.56  E-value=0.0024  Score=58.91  Aligned_cols=84  Identities=21%  Similarity=0.247  Sum_probs=54.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC--
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS--  273 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~--  273 (597)
                      ..+++-|+|++|+|||||+.+++..  ....=..++|++....++.                .     .++.++.+.+  
T Consensus        53 ~g~itei~G~~gsGKTtl~l~~~~~--~q~~g~~~vyidtE~~~~~----------------~-----~a~~~Gvd~d~v  109 (263)
T d1u94a1          53 MGRIVEIYGPESSGKTTLTLQVIAA--AQREGKTCAFIDAEHALDP----------------I-----YARKLGVDIDNL  109 (263)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCH----------------H-----HHHHTTCCGGGC
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHH--HHcCCCEEEEEccccccCH----------------H-----HHHHhCCCHHHE
Confidence            5679999999999999999999884  3333345789988877665                1     1333333211  


Q ss_pred             ---chhhHHHHHHHHHHHhc-CceEEEEEeccc
Q 041007          274 ---SQVEMETVLQYINEFVQ-GKKVLLVLDDLW  302 (597)
Q Consensus       274 ---~~~~~~~~~~~l~~~L~-~kr~LLVLDdv~  302 (597)
                         ...+.++..+.+....+ +..-|+|+|.+-
T Consensus       110 ~~~~~~~~E~~~~~i~~l~~~~~~~liViDSi~  142 (263)
T d1u94a1         110 LCSQPDTGEQALEICDALARSGAVDVIVVDSVA  142 (263)
T ss_dssp             EEECCSSHHHHHHHHHHHHHHTCCSEEEEECGG
T ss_pred             EEecCCCHHHHHHHHHHHHhcCCCCEEEEECcc
Confidence               12234445555555444 445688999884

>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=96.56  E-value=0.00054  Score=60.36  Aligned_cols=36  Identities=17%  Similarity=0.187  Sum_probs=27.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEE
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWV  233 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  233 (597)
                      ...+|.|+|++|+||||+|+.+..  +....+....++
T Consensus        18 ~g~vI~L~G~pGSGKTTiAk~La~--~l~~~~~~~~~~   53 (195)
T d1x6va3          18 RGCTVWLTGLSGAGKTTVSMALEE--YLVCHGIPCYTL   53 (195)
T ss_dssp             CCEEEEEESSCHHHHHHHHHHHHH--HHHHTTCCEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH--HHHhcCCCccch
Confidence            457889999999999999999987  455545444444

>d1np6a_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Escherichia coli [TaxId: 562]

Probab=96.56  E-value=0.00054  Score=58.78  Aligned_cols=23  Identities=26%  Similarity=0.527  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++++|+|++|+|||||+..+.+
T Consensus         2 ~Pvi~itG~~GSGKTTL~~~L~~   24 (170)
T d1np6a_           2 IPLLAFAAWSGTGKTTLLKKLIP   24 (170)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            36999999999999999999987

>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=96.54  E-value=0.0028  Score=58.61  Aligned_cols=85  Identities=20%  Similarity=0.216  Sum_probs=57.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCchhhhhhhhhhhcccchHHHHHHHHHHhccCCCC-
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRDEIRVARDEISVARDRDEIRVAKAILESLKGSVS-  273 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~il~~l~~~~~-  273 (597)
                      +..+++-|+|++|+|||+||.+++..  ....=..++|++....++.                .     +++.++.+.+ 
T Consensus        55 p~g~itei~G~~~sGKT~l~l~~~~~--aqk~g~~v~yiDtE~~~~~----------------~-----~a~~~Gvd~d~  111 (268)
T d1xp8a1          55 PRGRITEIYGPESGGKTTLALAIVAQ--AQKAGGTCAFIDAEHALDP----------------V-----YARALGVNTDE  111 (268)
T ss_dssp             ETTSEEEEEESTTSSHHHHHHHHHHH--HHHTTCCEEEEESSCCCCH----------------H-----HHHHTTCCGGG
T ss_pred             cCceEEEEecCCccchHHHHHHHHHH--HHhCCCEEEEEECCccCCH----------------H-----HHHHhCCCchh
Confidence            35679999999999999999998874  3322245889998877765                2     3445554322 


Q ss_pred             ----chhhHHHHHHHHHHHhcC-ceEEEEEeccc
Q 041007          274 ----SQVEMETVLQYINEFVQG-KKVLLVLDDLW  302 (597)
Q Consensus       274 ----~~~~~~~~~~~l~~~L~~-kr~LLVLDdv~  302 (597)
                          .+.+.++..+.+....+. ..-|+|+|-+-
T Consensus       112 i~~~~~~~~E~~~~~~~~l~~~~~~~liIiDSi~  145 (268)
T d1xp8a1         112 LLVSQPDNGEQALEIMELLVRSGAIDVVVVDSVA  145 (268)
T ss_dssp             CEEECCSSHHHHHHHHHHHHTTTCCSEEEEECTT
T ss_pred             EEEEcCCCHHHHHHHHHHHHhcCCCcEEEEeccc
Confidence                123455566666665553 46689999883

>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=96.51  E-value=0.00055  Score=58.85  Aligned_cols=22  Identities=23%  Similarity=0.475  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|.|+|++|+||||+|+.+..
T Consensus         3 klI~i~G~~GsGKTTva~~L~~   24 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAA   24 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999999875

>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=96.50  E-value=0.0011  Score=60.62  Aligned_cols=41  Identities=24%  Similarity=0.325  Sum_probs=33.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ...++.|+|++|+|||+||.+++.  ....+...++|++....
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~--~~~~~~~~~~~is~e~~   65 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVE--NACANKERAILFAYEES   65 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHH--HHHTTTCCEEEEESSSC
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHH--HHHHhccccceeeccCC
Confidence            567999999999999999999988  45556667888886543

>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=96.49  E-value=0.00094  Score=62.20  Aligned_cols=25  Identities=28%  Similarity=0.513  Sum_probs=22.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++.|.++|++|+||||||+.+++
T Consensus        30 ~~P~~ilL~GpPGtGKT~la~~la~   54 (273)
T d1gvnb_          30 ESPTAFLLGGQPGSGKTSLRSAIFE   54 (273)
T ss_dssp             SSCEEEEEECCTTSCTHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3567899999999999999999988

>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=96.48  E-value=0.005  Score=54.42  Aligned_cols=25  Identities=28%  Similarity=0.406  Sum_probs=20.8

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.+|.++|+.|+||||.+..++.
T Consensus         7 ~~p~vi~lvGptGvGKTTTiAKLA~   31 (211)
T d2qy9a2           7 KAPFVILMVGVNGVGKTTTIGKLAR   31 (211)
T ss_dssp             CTTEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999987766665

>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=96.44  E-value=0.00086  Score=57.59  Aligned_cols=26  Identities=27%  Similarity=0.417  Sum_probs=23.5

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          194 KPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       194 ~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +...+++.|.|++|+||||+|+.+..
T Consensus         3 ~~~~~iivl~G~~GsGKsT~a~~La~   28 (171)
T d1knqa_           3 NHDHHIYVLMGVSGSGKSAVASEVAH   28 (171)
T ss_dssp             CTTSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHH
Confidence            45678999999999999999999987

>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=96.44  E-value=0.006  Score=55.27  Aligned_cols=23  Identities=35%  Similarity=0.494  Sum_probs=21.1

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...++|+|+.|+|||||++.+..
T Consensus        29 Ge~vaIvG~sGsGKSTLl~ll~g   51 (241)
T d2pmka1          29 GEVIGIVGRSGSGKSTLTKLIQR   51 (241)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHh
Confidence            46899999999999999999976

>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=96.38  E-value=0.0054  Score=56.14  Aligned_cols=23  Identities=22%  Similarity=0.391  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...++|+|+.|+|||||++.+..
T Consensus        41 Ge~iaivG~sGsGKSTLl~ll~g   63 (253)
T d3b60a1          41 GKTVALVGRSGSGKSTIASLITR   63 (253)
T ss_dssp             TCEEEEEECTTSSHHHHHHHHTT
T ss_pred             CCEEEEECCCCChHHHHHHHHhc
Confidence            46899999999999999999965

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.37  E-value=0.001  Score=57.46  Aligned_cols=25  Identities=24%  Similarity=0.433  Sum_probs=22.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+.+|.++|++|+||||+|+.++.
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~   36 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLV   36 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTG
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHH
Confidence            4678999999999999999999876

>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=96.37  E-value=0.00072  Score=58.10  Aligned_cols=22  Identities=36%  Similarity=0.732  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|+|+|++|+||||+|+.+..
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~   26 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELAS   26 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            5678999999999999999976

>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=96.36  E-value=0.0036  Score=56.47  Aligned_cols=133  Identities=14%  Similarity=0.009  Sum_probs=68.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE---e-------------cCCCchhh--hhhhh----hhhcccc
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS---A-------------SYPRDEIR--VARDE----ISVARDR  255 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~---~-------------~~~~~~~~--~~~~~----~~~~~~~  255 (597)
                      .+++|.|+.|+|||||.+.++.-.   ..-.+.+|+.   +             .+.+....  .....    +......
T Consensus        25 e~~~liGpnGaGKSTll~~i~Gl~---~p~~G~I~~~G~~i~~~~~~~r~ig~v~Q~~~l~~~ltV~enl~~~l~~~~~~  101 (240)
T d2onka1          25 DYCVLLGPTGAGKSVFLELIAGIV---KPDRGEVRLNGADITPLPPERRGIGFVPQDYALFPHLSVYRNIAYGLRNVERV  101 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSS---CCSEEEEEETTEECTTSCTTTSCCBCCCSSCCCCTTSCHHHHHHTTCTTSCHH
T ss_pred             EEEEEECCCCChHHHHHHHHHcCC---CCCceEEEECCEECCcCCHHHcCceeeccchhhcccchhhHhhhhhhcccCHH
Confidence            488899999999999999997631   1122233331   0             11111100  00000    0011112


Q ss_pred             hHHHHHHHHHHhccCCCCc------hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--CCCCcEEE
Q 041007          256 DEIRVAKAILESLKGSVSS------QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--GSEGSRIL  327 (597)
Q Consensus       256 ~~~~~~~~il~~l~~~~~~------~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~~~gs~II  327 (597)
                      ...+...++++.++.....      ...-+.-.-.|.+.+..++-+|+||+--..-+...-..+...+..  ...|..||
T Consensus       102 ~~~~~v~~~l~~~gl~~~~~~~~~~LSGG~kQRvaiAral~~~P~illlDEPts~LD~~~~~~i~~~i~~l~~~~g~tvi  181 (240)
T d2onka1         102 ERDRRVREMAEKLGIAHLLDRKPARLSGGERQRVALARALVIQPRLLLLDEPLSAVDLKTKGVLMEELRFVQREFDVPIL  181 (240)
T ss_dssp             HHHHHHHHHHHTTTCTTTTTCCGGGSCHHHHHHHHHHHHHTTCCSSBEEESTTSSCCHHHHHHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHHHHHHHHhcCcHhhhhCChhhCCHHHHHHHHHHHHHhccCCceEecCccccCCHHHHHHHHHHHHHHHHhcCCeEE
Confidence            2234456666666553211      111223334566777888999999986443334444444444433  22356677


Q ss_pred             EEccCC
Q 041007          328 VTRSGG  333 (597)
Q Consensus       328 vTtR~~  333 (597)
                      ++|.+.
T Consensus       182 ~vtHd~  187 (240)
T d2onka1         182 HVTHDL  187 (240)
T ss_dssp             EEESCH
T ss_pred             EEeCCH
Confidence            777654

>d1sgwa_ c.37.1.12 (A:) Putative ABC transporter PF0895 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative ABC transporter PF0895
species: Pyrococcus furiosus [TaxId: 2261]

Probab=96.35  E-value=0.0069  Score=53.31  Aligned_cols=24  Identities=33%  Similarity=0.415  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|+|+.|+|||||.+.++.-
T Consensus        27 Gei~~l~G~NGsGKSTLl~~i~gl   50 (200)
T d1sgwa_          27 GNVVNFHGPNGIGKTTLLKTISTY   50 (200)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCChHHHHHHHHhcc
Confidence            468999999999999999999763

>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=96.33  E-value=0.0075  Score=54.55  Aligned_cols=138  Identities=13%  Similarity=0.007  Sum_probs=68.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhc------------c----CCeeEEEEecCCCchhhhhhhh------hhhcc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKA------------N----FDKRIWVSASYPRDEIRVARDE------ISVAR  253 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~------------~----F~~~~wv~~~~~~~~~~~~~~~------~~~~~  253 (597)
                      ...+++|.|+.|+|||||.+.+..-..-..            .    -..+.+++-.............      +....
T Consensus        27 ~Gei~glvG~nGaGKSTLl~~l~G~~~p~~G~i~i~G~~i~~~~~~~~~~i~~vpq~~~~~~~ltv~e~l~~~~~~~~~~  106 (238)
T d1vpla_          27 EGEIFGLIGPNGAGKTTTLRIISTLIKPSSGIVTVFGKNVVEEPHEVRKLISYLPEEAGAYRNMQGIEYLRFVAGFYASS  106 (238)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTSSCCSEEEEEETTEETTTCHHHHHTTEEEECTTCCCCTTSBHHHHHHHHHHHHCCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCCCCCCCEEEECcEecccChHHHHhhEeEeeeccccCCCccHHHHHHHHHHhcCCC
Confidence            346999999999999999999965311000            0    0113333221111000000000      00111


Q ss_pred             cchHHHHHHHHHHhccCCCC------chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC-CCCCcEE
Q 041007          254 DRDEIRVAKAILESLKGSVS------SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS-GSEGSRI  326 (597)
Q Consensus       254 ~~~~~~~~~~il~~l~~~~~------~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~-~~~gs~I  326 (597)
                      ..........+++.++....      ....-+.-.-.+...|..++=+|+||+--..-++.....+...+.. ...|..|
T Consensus       107 ~~~~~~~~~~~l~~~~l~~~~~~~~~~lSgG~~qrv~iA~al~~~p~illLDEPt~gLD~~~~~~i~~~i~~~~~~g~ti  186 (238)
T d1vpla_         107 SSEIEEMVERATEIAGLGEKIKDRVSTYSKGMVRKLLIARALMVNPRLAILDEPTSGLDVLNAREVRKILKQASQEGLTI  186 (238)
T ss_dssp             HHHHHHHHHHHHHHHCCGGGGGSBGGGCCHHHHHHHHHHHHHTTCCSEEEEESTTTTCCHHHHHHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHHHHHhCCCHHHHhhhhhhCCHHHHHHHHHHHHHhcCCCEEEecCCCCCCCHHHHHHHHHHHHHHHhcCCEE
Confidence            12223334444444432211      1111222333566777788889999986444334444555444433 2347788


Q ss_pred             EEEccCC
Q 041007          327 LVTRSGG  333 (597)
Q Consensus       327 IvTtR~~  333 (597)
                      |+||.+-
T Consensus       187 i~~tH~l  193 (238)
T d1vpla_         187 LVSSHNM  193 (238)
T ss_dssp             EEEECCH
T ss_pred             EEEeCCH
Confidence            8888765

>d2awna2 c.37.1.12 (A:4-235) Maltose transport protein MalK, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.30  E-value=0.0088  Score=53.65  Aligned_cols=50  Identities=12%  Similarity=0.125  Sum_probs=31.1

Q ss_pred             HHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--CCCCcEEEEEccCC
Q 041007          284 YINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--GSEGSRILVTRSGG  333 (597)
Q Consensus       284 ~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~~~gs~IIvTtR~~  333 (597)
                      .|...|..++-+|++|.--..-+...-..+...+..  ...|..||++|.+-
T Consensus       140 aiAraL~~~P~illlDEPts~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~  191 (232)
T d2awna2         140 AIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQ  191 (232)
T ss_dssp             CHHHHHHTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHSCCEEEEEESCH
T ss_pred             HHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCH
Confidence            355566678889999986444334444445544443  23477888888765

>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=96.23  E-value=0.0013  Score=56.57  Aligned_cols=25  Identities=36%  Similarity=0.476  Sum_probs=22.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      |..-.|.|.|++|+||||+|+.+..
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~   27 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAA   27 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHH
Confidence            4567899999999999999999976

>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=96.22  E-value=0.0012  Score=56.90  Aligned_cols=23  Identities=22%  Similarity=0.362  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|.|.|++|+||||+|+.+.+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~   25 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQS   25 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            47999999999999999999987

>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=96.22  E-value=0.0013  Score=58.02  Aligned_cols=25  Identities=24%  Similarity=0.494  Sum_probs=22.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.+|.|.|++|+||||+|+.++.
T Consensus         4 ~kp~iI~i~G~pGSGKsT~a~~La~   28 (194)
T d1qf9a_           4 SKPNVVFVLGGPGSGKGTQCANIVR   28 (194)
T ss_dssp             CCCEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            3568999999999999999999987

>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=96.21  E-value=0.0041  Score=54.92  Aligned_cols=41  Identities=20%  Similarity=0.272  Sum_probs=28.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ++.++|.++|+.|+||||.+..++..  .+.+=..+..+++..
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~--~~~~g~kV~lit~Dt   44 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRY--YQNLGKKVMFCAGDT   44 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHH--HHTTTCCEEEECCCC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEEecc
Confidence            46789999999999999877766653  322223466666543

>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=96.18  E-value=0.0012  Score=56.80  Aligned_cols=24  Identities=21%  Similarity=0.426  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.++|.|.|++|+||||+|+.+..
T Consensus         3 ~g~iI~l~G~~GsGKSTia~~La~   26 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIAEALAN   26 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            357999999999999999999977

>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=96.17  E-value=0.017  Score=51.58  Aligned_cols=53  Identities=15%  Similarity=0.112  Sum_probs=34.9

Q ss_pred             HHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--CCCCcEEEEEccCC
Q 041007          281 VLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--GSEGSRILVTRSGG  333 (597)
Q Consensus       281 ~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~~~gs~IIvTtR~~  333 (597)
                      -.-.|...|..++-+|++|.--..-+...-..+...+..  ...|..||++|.+.
T Consensus       152 QRvaIAraL~~~P~lLllDEPTs~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~  206 (230)
T d1l2ta_         152 QRVAIARALANNPPIILADQPTGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDI  206 (230)
T ss_dssp             HHHHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHTTCCEEEEECSCH
T ss_pred             HHHHHHhhhhcCCCEEEecCCccccCHHHHHHHHHHHHHHHHhhCCEEEEECCCH
Confidence            344567777888999999996443334444555555544  24578888888765

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.16  E-value=0.019  Score=50.58  Aligned_cols=39  Identities=23%  Similarity=0.275  Sum_probs=26.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      +.+++.++|+.|+||||.+..++..  .+.+-..+..+++.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~--~~~~g~kV~lit~D   47 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALY--YKGKGRRPLLVAAD   47 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEecc
Confidence            4678999999999999877777653  33332335555543

>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=96.15  E-value=0.041  Score=50.83  Aligned_cols=25  Identities=28%  Similarity=0.424  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...+++|+|+.|+|||||++.++.-
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl   85 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGE   85 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCC
Confidence            3468999999999999999999763

>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=96.13  E-value=0.0015  Score=57.67  Aligned_cols=25  Identities=28%  Similarity=0.593  Sum_probs=23.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +..++|+|.|++|+||||+|+.++.
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~   30 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVK   30 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4688999999999999999999977

>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=96.10  E-value=0.00091  Score=63.81  Aligned_cols=53  Identities=25%  Similarity=0.358  Sum_probs=34.8

Q ss_pred             ccccchhhHHHHHHHhh----CCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLK----GESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~----~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|.++.++.+...+.    ...-.....++..++.+.++||+|+|||.||+.+++
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~   71 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAK   71 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhh
Confidence            46798888888876551    111000000011346788999999999999999987

>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=96.08  E-value=0.0059  Score=55.85  Aligned_cols=24  Identities=21%  Similarity=0.238  Sum_probs=20.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....++|+|+.|+|||||++.+..
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~g   66 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPR   66 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHh
Confidence            346899999999999999998854

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.07  E-value=0.0062  Score=55.65  Aligned_cols=24  Identities=25%  Similarity=0.358  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....++|+|+.|+|||||++.+..
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~g   62 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQN   62 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhc
Confidence            346999999999999999999975

>d1mv5a_ c.37.1.12 (A:) Multidrug resistance ABC transporter LmrA, C-terminal domain {Lactococcus lactis [TaxId: 1358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter LmrA, C-terminal domain
species: Lactococcus lactis [TaxId: 1358]

Probab=96.05  E-value=0.0072  Score=54.84  Aligned_cols=24  Identities=21%  Similarity=0.238  Sum_probs=21.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....++|+|+.|+|||||++.+..
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~g   50 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLER   50 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHH
Confidence            346999999999999999999965

>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=96.03  E-value=0.0092  Score=53.72  Aligned_cols=51  Identities=8%  Similarity=-0.001  Sum_probs=32.4

Q ss_pred             HHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          283 QYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       283 ~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      -.|...|..++-+|+||.--..-++..-..+...+...  ..|..||++|.+-
T Consensus       145 vaiAraL~~~P~iLllDEPts~LD~~~~~~i~~ll~~l~~~~g~tii~vTHd~  197 (239)
T d1v43a3         145 VAVARAIVVEPDVLLMDEPLSNLDAKLRVAMRAEIKKLQQKLKVTTIYVTHDQ  197 (239)
T ss_dssp             HHHHHHHTTCCSEEEEESTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             HHHHhhhccCCCceeecCCcccCCHHHHHHHHHHHHHHHHhcCCeEEEEeCCH
Confidence            34666777889999999864443344444454444432  2377788888765

>d2iyva1 c.37.1.2 (A:2-166) Shikimate kinase (AroK) {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=96.02  E-value=0.0011  Score=56.86  Aligned_cols=20  Identities=25%  Similarity=0.509  Sum_probs=17.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      |++.|++|+||||+++.++.
T Consensus         4 IvliG~~G~GKSTig~~La~   23 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAK   23 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            44559999999999999987

>d1g2912 c.37.1.12 (1:1-240) Maltose transport protein MalK, N-terminal domain {Archaeon Thermococcus litoralis [TaxId: 2265]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Maltose transport protein MalK, N-terminal domain
species: Archaeon Thermococcus litoralis [TaxId: 2265]

Probab=95.99  E-value=0.0077  Score=54.31  Aligned_cols=52  Identities=12%  Similarity=0.079  Sum_probs=33.4

Q ss_pred             HHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEEccCC
Q 041007          282 LQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVTRSGG  333 (597)
Q Consensus       282 ~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvTtR~~  333 (597)
                      .-.|.+.|..++-+|++|+--..-+...-..+...+...  ..|..||++|.+-
T Consensus       147 Rv~IAraL~~~P~iLllDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~vTHd~  200 (240)
T d1g2912         147 RVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTHDQ  200 (240)
T ss_dssp             HHHHHHHHHTCCSEEEEECTTTTSCHHHHHHHHHHHHHHHHHHTCEEEEEESCH
T ss_pred             HHHHHHHHhcCCCEEEecCCCcccCHHHHHHHHHHHHHHHhccCCEEEEEcCCH
Confidence            345677778889999999864433344444455555432  2377888888765

>d1b0ua_ c.37.1.12 (A:) ATP-binding subunit of the histidine permease {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: ATP-binding subunit of the histidine permease
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.97  E-value=0.016  Score=52.96  Aligned_cols=24  Identities=33%  Similarity=0.409  Sum_probs=21.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|.|+.|+|||||++.+.-
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~G   50 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINF   50 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHc
Confidence            346999999999999999999975

>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=95.96  E-value=0.015  Score=51.38  Aligned_cols=40  Identities=30%  Similarity=0.275  Sum_probs=23.3

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ..+.+|.++|+.|+||||.+..++.... .... .+..+++.
T Consensus        10 k~p~vi~lvGptGvGKTTTiAKLA~~~~-~~g~-kV~lit~D   49 (211)
T d1j8yf2          10 KIPYVIMLVGVQGTGKATTAGKLAYFYK-KKGF-KVGLVGAD   49 (211)
T ss_dssp             SSSEEEEEECSCCC----HHHHHHHHHH-HTTC-CEEEEECC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHH-HCCC-ceEEEEee
Confidence            4678999999999999977666665322 2222 35666654

>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=95.96  E-value=0.0017  Score=56.39  Aligned_cols=22  Identities=27%  Similarity=0.513  Sum_probs=20.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|+|.|++|+||||+++.+..
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~   23 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMD   23 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHH
Confidence            6999999999999999999987

>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=95.92  E-value=0.016  Score=52.07  Aligned_cols=76  Identities=14%  Similarity=0.033  Sum_probs=43.2

Q ss_pred             HHHHHHHHHhccCCCC------chhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--CCCCcEEEEE
Q 041007          258 IRVAKAILESLKGSVS------SQVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--GSEGSRILVT  329 (597)
Q Consensus       258 ~~~~~~il~~l~~~~~------~~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~~~gs~IIvT  329 (597)
                      .+...++++.++....      ....-+.-.-.|...|..++-+|++|.--..-+...-..+...+..  ...|..||++
T Consensus       118 ~~~v~~~L~~vgL~~~~~~~~~~LSGG~~QRvaiAraL~~~P~lLllDEPt~~LD~~~~~~i~~~l~~l~~~~g~tvi~v  197 (240)
T d3dhwc1         118 KRRVTELLSLVGLGDKHDSYPSNLSGGQKQRVAIARALASNPKVLLCDEATSALDPATTRSILELLKDINRRLGLTILLI  197 (240)
T ss_dssp             HHHHHHHHHHHSTTTTTSSCBSCCCHHHHHHHHHHHHHHTCCSEEEEESGGGSSCHHHHHHHHHHHHHHHHHHCCEEEEE
T ss_pred             HHHHHHHHHHcCCchhhhCChhhCCHHHHHHHHHhhhhccCCCeEEeccccccCCHHHhhHHHHHHHHHHhccCCEEEEE
Confidence            3445566666654321      1111222333566777788999999986443334444455555543  2237788888


Q ss_pred             ccCC
Q 041007          330 RSGG  333 (597)
Q Consensus       330 tR~~  333 (597)
                      |.+-
T Consensus       198 THdl  201 (240)
T d3dhwc1         198 THEM  201 (240)
T ss_dssp             BSCH
T ss_pred             cCCH
Confidence            8765

>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=95.88  E-value=0.015  Score=51.29  Aligned_cols=41  Identities=20%  Similarity=0.180  Sum_probs=28.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ..+.+|.++|+.|+||||.+..++..  ...+-..+..+++..
T Consensus         9 ~~p~vi~lvGptGvGKTTTiAKLAa~--~~~~~~kV~lit~Dt   49 (213)
T d1vmaa2           9 EPPFVIMVVGVNGTGKTTSCGKLAKM--FVDEGKSVVLAAADT   49 (213)
T ss_dssp             SSCEEEEEECCTTSSHHHHHHHHHHH--HHHTTCCEEEEEECT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCceEEEeecc
Confidence            35679999999999999876666653  232224466666543

>d1ye8a1 c.37.1.11 (A:1-178) Hypothetical kinase-like protein Aq_1292 {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hypothetical kinase-like protein Aq 1292
species: Aquifex aeolicus [TaxId: 63363]

Probab=95.88  E-value=0.0017  Score=55.99  Aligned_cols=21  Identities=38%  Similarity=0.768  Sum_probs=19.4

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|++|+|||||++.+...
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~   23 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVER   23 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCcHHHHHHHHHHhc
Confidence            789999999999999999873

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: NTPase P4
species: Bacteriophage phi-12 [TaxId: 161736]

Probab=95.87  E-value=0.0065  Score=57.35  Aligned_cols=27  Identities=19%  Similarity=0.327  Sum_probs=21.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhcc
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKAN  226 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~  226 (597)
                      .++.++|++|+|||.||+.++.  +...+
T Consensus       124 g~~l~~G~pG~GKT~la~ala~--~~~~~  150 (321)
T d1w44a_         124 GMVIVTGKGNSGKTPLVHALGE--ALGGK  150 (321)
T ss_dssp             EEEEEECSSSSCHHHHHHHHHH--HHHTT
T ss_pred             ceEEEECCCCccHHHHHHHHHH--HhcCC
Confidence            4566689999999999999998  44433

>d1bifa1 c.37.1.7 (A:37-249) 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
domain: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase, kinase domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.77  E-value=0.0021  Score=57.11  Aligned_cols=23  Identities=22%  Similarity=0.349  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+|.++|.+|+||||||+++++
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~   24 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTR   24 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            35899999999999999999987

>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=95.69  E-value=0.0017  Score=55.27  Aligned_cols=20  Identities=40%  Similarity=0.572  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      |.|.|++|+||||+++.++.
T Consensus         3 I~liG~~GsGKsTi~k~La~   22 (161)
T d1viaa_           3 IVFIGFMGSGKSTLARALAK   22 (161)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            77889999999999999988

>d1szpa2 c.37.1.11 (A:145-395) DNA repair protein Rad51, catalytic domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: DNA repair protein Rad51, catalytic domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.68  E-value=0.018  Score=51.98  Aligned_cols=46  Identities=13%  Similarity=0.157  Sum_probs=33.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhcc----CCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKAN----FDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~----F~~~~wv~~~~~~~~  241 (597)
                      ..+++.|.|++|+|||+|+.++.........    -...+|++....+..
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~~~   82 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTFRP   82 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCCCG
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchHHH
Confidence            5679999999999999999999775322222    235778877666554

>d1xjca_ c.37.1.10 (A:) Molybdopterin-guanine dinucleotide biosynthesis protein MobB {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Molybdopterin-guanine dinucleotide biosynthesis protein MobB
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.66  E-value=0.0035  Score=53.42  Aligned_cols=23  Identities=26%  Similarity=0.307  Sum_probs=21.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++++|+|..|+|||||+..+...
T Consensus         2 kii~I~G~~gSGKTTli~~l~~~   24 (165)
T d1xjca_           2 NVWQVVGYKHSGKTTLMEKWVAA   24 (165)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHH
Confidence            68999999999999999999883

>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=95.64  E-value=0.0025  Score=54.73  Aligned_cols=21  Identities=29%  Similarity=0.612  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|.|+|++|+||||+|+.++.
T Consensus         4 ~Iil~G~~GsGKSTia~~LA~   24 (170)
T d1e6ca_           4 PIFMVGARGCGMTTVGRELAR   24 (170)
T ss_dssp             CEEEESCTTSSHHHHHHHHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHH
Confidence            467889999999999999987

>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=95.63  E-value=0.0037  Score=54.35  Aligned_cols=22  Identities=23%  Similarity=0.413  Sum_probs=20.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|.|.|++|+||||+++.+..
T Consensus         2 kiivi~G~~GsGKTT~~~~La~   23 (194)
T d1nksa_           2 KIGIVTGIPGVGKSTVLAKVKE   23 (194)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH
Confidence            5889999999999999999987

>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=95.62  E-value=0.0093  Score=53.74  Aligned_cols=76  Identities=14%  Similarity=0.076  Sum_probs=43.4

Q ss_pred             HHHHHHHHHhccCCCC-----c-hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcCC--CCCcEEEEE
Q 041007          258 IRVAKAILESLKGSVS-----S-QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKSG--SEGSRILVT  329 (597)
Q Consensus       258 ~~~~~~il~~l~~~~~-----~-~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~~--~~gs~IIvT  329 (597)
                      .+...++++.++....     . ...-+.-.-.|.+.|..++-+|++|+--..-+...-..+...+...  ..|..||++
T Consensus       118 ~~~v~~~l~~~gL~~~~~~~p~~LSGGqkQRvaiARaL~~~P~llllDEPt~~LD~~~~~~i~~~i~~l~~~~g~tvi~v  197 (242)
T d1oxxk2         118 RKRVEEVAKILDIHHVLNHFPRELSGAQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVV  197 (242)
T ss_dssp             HHHHHHHHHHTTCGGGTTSCGGGSCHHHHHHHHHHHHHTTCCSEEEEESTTTTSCGGGHHHHHHHHHHHHHHHCCEEEEE
T ss_pred             HHHHHHHHhhcChHhhhhCChhhCCHHHHhHHHHHhHHhhcccceeecCCccCCCHHHHHHHHHHHHHHHhccCCEEEEE
Confidence            3445566666654311     1 1112333345777788899999999864443344545555555432  236778888


Q ss_pred             ccCC
Q 041007          330 RSGG  333 (597)
Q Consensus       330 tR~~  333 (597)
                      |.+.
T Consensus       198 THd~  201 (242)
T d1oxxk2         198 SHDP  201 (242)
T ss_dssp             ESCH
T ss_pred             ECCH
Confidence            8764

>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=95.62  E-value=0.016  Score=54.28  Aligned_cols=25  Identities=28%  Similarity=0.321  Sum_probs=22.6

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+-+|+|.|.+|+||||+|+.+..
T Consensus        78 k~P~iIGIaG~sgSGKSTla~~L~~  102 (308)
T d1sq5a_          78 RIPYIISIAGSVAVGKSTTARVLQA  102 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCCCCCcHHHHHHHH
Confidence            4678999999999999999999876

>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=95.50  E-value=0.0032  Score=55.25  Aligned_cols=23  Identities=26%  Similarity=0.579  Sum_probs=21.0

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.+|.|.|++|+||||+|+.++.
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~   23 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVE   23 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHH
Confidence            36899999999999999999987

>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=95.47  E-value=0.015  Score=52.61  Aligned_cols=24  Identities=21%  Similarity=0.382  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+++|.|+.|.|||||.+.+.-
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~G   54 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAG   54 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            346999999999999999999965

>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=95.47  E-value=0.0034  Score=56.25  Aligned_cols=23  Identities=39%  Similarity=0.585  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|+|.||+|+||||+|+.+.+
T Consensus         3 ~piI~I~GppGSGKgT~ak~La~   25 (225)
T d1ckea_           3 APVITIDGPSGAGKGTLCKAMAE   25 (225)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHH
Confidence            36999999999999999999988

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=95.46  E-value=0.017  Score=52.90  Aligned_cols=44  Identities=20%  Similarity=0.296  Sum_probs=32.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ....++|.|.+|+|||+|+..+.++. .+.+=+.++++-+.+...
T Consensus        67 kGQr~~If~~~g~GKt~l~~~i~~~~-~~~~~~v~V~~~iGer~~  110 (276)
T d2jdid3          67 KGGKIGLFGGAGVGKTVLIMELINNV-AKAHGGYSVFAGVGERTR  110 (276)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHH-TTTCSSEEEEEEESCCHH
T ss_pred             CCCEEEeeCCCCCCHHHHHHHHHHHH-HhhCCCeEEEEEeccChH
Confidence            34579999999999999999998731 233445677887776543

>d1uj2a_ c.37.1.6 (A:) Uridine-cytidine kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Uridine-cytidine kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.41  E-value=0.0037  Score=55.75  Aligned_cols=23  Identities=17%  Similarity=0.320  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +-+|+|.|+.|+||||||+.+..
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~   24 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQ   24 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            46899999999999999998876

>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=95.35  E-value=0.02  Score=52.81  Aligned_cols=47  Identities=19%  Similarity=0.126  Sum_probs=33.4

Q ss_pred             HHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEE
Q 041007          177 KILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWV  233 (597)
Q Consensus       177 ~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv  233 (597)
                      ++++.|..-.         ....++|.|.+|+|||+|+..+.+... ..+-.+++.+
T Consensus        32 r~ID~l~Pig---------rGQr~~I~g~~g~GKT~l~~~i~~~~~-~~~~~~v~~~   78 (289)
T d1xpua3          32 RVLDLASPIG---------RGQRGLIVAPPKAGKTMLLQNIAQSIA-YNHPDCVLMV   78 (289)
T ss_dssp             HHHHHHSCCB---------TTCEEEEEECSSSSHHHHHHHHHHHHH-HHCTTSEEEE
T ss_pred             eeeeeccccc---------CCCeeeEeCCCCCCHHHHHHHHHHHHh-hcCCCeEEEE
Confidence            5777777443         457899999999999999999988422 2333444444

>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=95.31  E-value=0.0045  Score=54.99  Aligned_cols=24  Identities=29%  Similarity=0.440  Sum_probs=22.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ...+|.++|++|+||||||+.+..
T Consensus        23 kg~vIwltGlsGsGKTTia~~L~~   46 (208)
T d1m7ga_          23 RGLTIWLTGLSASGKSTLAVELEH   46 (208)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            567999999999999999999987

>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=95.21  E-value=0.03  Score=49.87  Aligned_cols=133  Identities=16%  Similarity=0.037  Sum_probs=66.8

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEE---e-------------cCCCc------hhhhhhhhhhhccc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVS---A-------------SYPRD------EIRVARDEISVARD  254 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~---~-------------~~~~~------~~~~~~~~~~~~~~  254 (597)
                      ..+++|.|+.|+|||||.+.+.--.   ..-.+.+++.   +             .+.+.      +...+.........
T Consensus        26 Ge~~~liGpsGaGKSTll~~l~Gl~---~p~sG~I~~~G~~i~~~~~~~r~ig~v~Q~~~l~~~~tV~enl~~~~~~~~~  102 (229)
T d3d31a2          26 GEYFVILGPTGAGKTLFLELIAGFH---VPDSGRILLDGKDVTDLSPEKHDIAFVYQNYSLFPHMNVKKNLEFGMRMKKI  102 (229)
T ss_dssp             TCEEEEECCCTHHHHHHHHHHHTSS---CCSEEEEEETTEECTTSCHHHHTCEEECTTCCCCTTSCHHHHHHHHHHHHCC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCc---CCCCCEEEEccEeccccchhHhcceeeccccccCccccHHHHHHHHHhhccc
Confidence            4699999999999999999996531   1111122221   1             11111      10000000001111


Q ss_pred             chHHHHHHHHHHhccCCCCc------hhhHHHHHHHHHHHhcCceEEEEEecccCCCCcchHHHHHHhhcC--CCCCcEE
Q 041007          255 RDEIRVAKAILESLKGSVSS------QVEMETVLQYINEFVQGKKVLLVLDDLWWNAYPRYWEQLMYSLKS--GSEGSRI  326 (597)
Q Consensus       255 ~~~~~~~~~il~~l~~~~~~------~~~~~~~~~~l~~~L~~kr~LLVLDdv~~~~~~~~~~~l~~~l~~--~~~gs~I  326 (597)
                      .. .+...++++.++...-.      ...-+.-.-.|.+.|-.++=+|+||+--..-+...-..+...+..  ...|..|
T Consensus       103 ~~-~~~~~~~l~~~~l~~~~~~~~~~LSGG~~QRvaiAraL~~~P~iLllDEPts~LD~~~~~~i~~~l~~l~~~~g~ti  181 (229)
T d3d31a2         103 KD-PKRVLDTARDLKIEHLLDRNPLTLSGGEQQRVALARALVTNPKILLLDEPLSALDPRTQENAREMLSVLHKKNKLTV  181 (229)
T ss_dssp             CC-HHHHHHHHHHTTCTTTTTSCGGGSCHHHHHHHHHHHHTTSCCSEEEEESSSTTSCHHHHHHHHHHHHHHHHHTTCEE
T ss_pred             cH-HHHHHHHHHHhcchhhHhCChhhCCHHHhcchhhhhhhhccCCceeecCCCcCCCHHHHHHHHHHHHHHHhcCCcEE
Confidence            11 23345555655543211      111223334566777788999999986443334444444444433  2346778


Q ss_pred             EEEccCC
Q 041007          327 LVTRSGG  333 (597)
Q Consensus       327 IvTtR~~  333 (597)
                      |++|.+.
T Consensus       182 i~vtHd~  188 (229)
T d3d31a2         182 LHITHDQ  188 (229)
T ss_dssp             EEEESCH
T ss_pred             EEEcCCH
Confidence            8777765

>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=95.10  E-value=0.0038  Score=54.45  Aligned_cols=22  Identities=36%  Similarity=0.605  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|+|+|++|+|||||++.++.
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~   23 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFA   23 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHH
Confidence            3588999999999999999876

>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=95.09  E-value=0.0069  Score=52.87  Aligned_cols=24  Identities=25%  Similarity=0.382  Sum_probs=20.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.-.|.|.|++|+||||+|+.++.
T Consensus         5 r~mrIiliG~PGSGKtT~a~~La~   28 (189)
T d2ak3a1           5 RLLRAAIMGAPGSGKGTVSSRITK   28 (189)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHH
T ss_pred             cceeEEEECCCCCCHHHHHHHHHH
Confidence            445666789999999999999987

>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=95.02  E-value=0.0056  Score=53.39  Aligned_cols=23  Identities=17%  Similarity=0.133  Sum_probs=20.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +-.|.|.|++|+||||+|+.+.+
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~   25 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKT   25 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHH
Confidence            34688999999999999999876

>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=95.01  E-value=0.042  Score=50.01  Aligned_cols=24  Identities=29%  Similarity=0.357  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++|.|+.|+|||||++.++--
T Consensus        30 Gei~~liG~nGaGKSTLl~~i~Gl   53 (254)
T d1g6ha_          30 GDVTLIIGPNGSGKSTLINVITGF   53 (254)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCEEEEECCCCCcHHHHHHHHHCC
Confidence            469999999999999999999763

>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=94.99  E-value=0.0062  Score=53.34  Aligned_cols=24  Identities=21%  Similarity=0.535  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|.|.|++|+||||+|+.+..
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~   30 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQ   30 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHH
Confidence            468999999999999999999977

>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=94.99  E-value=0.0051  Score=53.78  Aligned_cols=21  Identities=29%  Similarity=0.631  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|+||+|+|||||++.+..
T Consensus         2 pIvl~GPsGsGK~tl~~~L~~   22 (190)
T d1lvga_           2 PVVLSGPSGAGKSTLLKKLFQ   22 (190)
T ss_dssp             CEEEECCTTSSHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHH
Confidence            477999999999999999876

>d2qm8a1 c.37.1.10 (A:5-327) Metallochaperone MeaB {Methylobacterium extorquens [TaxId: 408]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Metallochaperone MeaB
species: Methylobacterium extorquens [TaxId: 408]

Probab=94.98  E-value=0.0089  Score=56.77  Aligned_cols=26  Identities=19%  Similarity=0.133  Sum_probs=23.1

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++..+|+|+|++|+|||||...+...
T Consensus        49 ~~~~~igitG~pGaGKSTli~~l~~~   74 (323)
T d2qm8a1          49 GRAIRVGITGVPGVGKSTTIDALGSL   74 (323)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCceEEeeeCCCCCCHHHHHHHHHHH
Confidence            36789999999999999999998863

>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=94.92  E-value=0.0059  Score=54.66  Aligned_cols=23  Identities=30%  Similarity=0.342  Sum_probs=20.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -+|+|.|++|+||||+|+.+..+
T Consensus         4 i~IaIdGp~GsGKgT~ak~La~~   26 (223)
T d1q3ta_           4 IQIAIDGPASSGKSTVAKIIAKD   26 (223)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            36889999999999999999873

>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=94.88  E-value=0.01  Score=56.45  Aligned_cols=26  Identities=15%  Similarity=0.093  Sum_probs=23.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ++..+|+|+|++|+|||||...+...
T Consensus        52 ~~~~~IgitG~pGaGKSTLi~~l~~~   77 (327)
T d2p67a1          52 GNTLRLGVTGTPGAGKSTFLEAFGML   77 (327)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHH
T ss_pred             CCceEEEeeCCCCCCHHHHHHHHHHH
Confidence            36789999999999999999998764

>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=94.85  E-value=0.026  Score=52.19  Aligned_cols=25  Identities=24%  Similarity=0.436  Sum_probs=22.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+-+|+|.|..|+|||||+..+..
T Consensus        25 ~~P~iIGi~G~qGSGKSTl~~~l~~   49 (286)
T d1odfa_          25 KCPLFIFFSGPQGSGKSFTSIQIYN   49 (286)
T ss_dssp             CSCEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCCEEEEeECCCCCCHHHHHHHHHH
Confidence            3566999999999999999998876

>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=94.84  E-value=0.0069  Score=52.41  Aligned_cols=22  Identities=23%  Similarity=0.465  Sum_probs=20.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|+|+||+|+|||||++.+..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~   24 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRE   24 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            6899999999999999998865

>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=94.81  E-value=0.015  Score=53.86  Aligned_cols=52  Identities=13%  Similarity=0.171  Sum_probs=33.6

Q ss_pred             hHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecC
Q 041007          174 EKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASY  237 (597)
Q Consensus       174 e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~  237 (597)
                      ++..+.+.+.          ++..++|.++|-||+||||++..+...  ....-..++-|.+..
T Consensus         7 ~~~~~~~~~~----------~~~~~iii~sGKGGVGKTT~a~nLA~~--lA~~G~rVllvD~Dp   58 (279)
T d1ihua2           7 SLSALVDDIA----------RNEHGLIMLMGKGGVGKTTMAAAIAVR--LADMGFDVHLTTSDP   58 (279)
T ss_dssp             CHHHHHHHHH----------TTSCEEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEESCC
T ss_pred             cHHHHHHHhh----------cCCCEEEEEECCCCCCHHHHHHHHHHH--HHHCCCcEEEEeCCC
Confidence            3555666665          245799999999999999988777653  222212355555543

>d1zina1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.77  E-value=0.0066  Score=52.38  Aligned_cols=20  Identities=25%  Similarity=0.494  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      |.|.|++|+||||+|+.++.
T Consensus         3 I~i~G~pGSGKsT~a~~La~   22 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVA   22 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            77999999999999999877

>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=94.59  E-value=0.053  Score=47.75  Aligned_cols=24  Identities=21%  Similarity=0.367  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|+|.|+.|+||||+++.+.+.
T Consensus         3 G~lI~ieG~dGsGKsT~~~~L~~~   26 (209)
T d1nn5a_           3 GALIVLEGVDRAGKSTQSRKLVEA   26 (209)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eeEEEEECCCCCCHHHHHHHHHHH
Confidence            368999999999999999999883

>d1kgda_ c.37.1.1 (A:) Guanylate kinase-like domain of Cask {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase-like domain of Cask
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.56  E-value=0.007  Score=52.23  Aligned_cols=22  Identities=18%  Similarity=0.555  Sum_probs=20.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|+|+||+|+|||||++.+..
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~   25 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLIT   25 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHH
Confidence            5799999999999999998875

>d2cdna1 c.37.1.1 (A:1-181) Adenylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.54  E-value=0.008  Score=51.88  Aligned_cols=21  Identities=29%  Similarity=0.477  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|++|+||||+|+.++.
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~   22 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAE   22 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            378889999999999999987

>d1ak2a1 c.37.1.1 (A:14-146,A:177-233) Adenylate kinase {Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Cow (Bos taurus), mitochondrial izozyme-2 [TaxId: 9913]

Probab=94.53  E-value=0.01  Score=51.62  Aligned_cols=23  Identities=26%  Similarity=0.458  Sum_probs=19.5

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.++| |.|++|+||||+|+.++.
T Consensus         3 ~~rii-l~G~pGSGKsT~a~~La~   25 (190)
T d1ak2a1           3 GVRAV-LLGPPGAGKGTQAPKLAK   25 (190)
T ss_dssp             CCEEE-EECCTTSSHHHHHHHHHH
T ss_pred             ccEEE-EECCCCCCHHHHHHHHHH
Confidence            45555 789999999999999986

>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=94.50  E-value=0.0096  Score=51.85  Aligned_cols=23  Identities=35%  Similarity=0.372  Sum_probs=20.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHh
Q 041007          196 TLPVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      .+-+|+|+|+.|+||||+|..+-
T Consensus         2 ~p~IIgitG~~gSGKstva~~l~   24 (191)
T d1uf9a_           2 HPIIIGITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH
Confidence            35689999999999999998773

>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=94.48  E-value=0.019  Score=51.54  Aligned_cols=42  Identities=17%  Similarity=0.192  Sum_probs=28.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ...++.|.|++|+|||+||.+++... ....-..++|++....
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~~-~~~~~~~~~~~s~e~~   66 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYNG-IIEFDEPGVFVTFEET   66 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHH-HHHHCCCEEEEESSSC
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHH-HHhcCCCcccccccCC
Confidence            46799999999999999998865431 2222234566665543

>d1fx0a3 c.37.1.11 (A:97-372) Central domain of alpha subunit of F1 ATP synthase {Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Spinach (Spinacia oleracea), chloroplast [TaxId: 3562]

Probab=94.44  E-value=0.05  Score=49.86  Aligned_cols=42  Identities=19%  Similarity=0.184  Sum_probs=29.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      ...++|.|.+|+|||+|+......  ...+-..++++-+.....
T Consensus        67 GQr~~Ifg~~g~GKt~l~~~~~~~--~~~~~~v~V~~~iGer~~  108 (276)
T d1fx0a3          67 GQRELIIGDRQTGKTAVATDTILN--QQGQNVICVYVAIGQKAS  108 (276)
T ss_dssp             TCBCBEEESSSSSHHHHHHHHHHT--CCTTTCEEEEEEESCCHH
T ss_pred             CceEeeccCCCCChHHHHHHHHhh--hcccCceeeeeeecchhH
Confidence            456889999999999999876442  233445667777766543

>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=94.40  E-value=0.095  Score=46.86  Aligned_cols=25  Identities=24%  Similarity=0.126  Sum_probs=21.4

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+++.|+|+.+.||||+.+.+.-.
T Consensus        40 ~~~~~iiTGpN~~GKSt~lk~i~l~   64 (234)
T d1wb9a2          40 QRRMLIITGPNMGGKSTYMRQTALI   64 (234)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CceEEEEeccCchhhHHHHHHHHHH
Confidence            3478999999999999999998543

>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=94.40  E-value=0.17  Score=45.34  Aligned_cols=47  Identities=15%  Similarity=0.123  Sum_probs=33.5

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhCCh----hhhccCCeeEEEEecCCCch
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFDDS----DVKANFDKRIWVSASYPRDE  241 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~~~----~~~~~F~~~~wv~~~~~~~~  241 (597)
                      +...++.|+|++|+|||++|.+++.+.    .....+..+.|+.....+..
T Consensus        35 p~G~~~~i~G~~GsGKT~lalq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (258)
T d1v5wa_          35 ESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTENTFRP   85 (258)
T ss_dssp             CSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSSCCCH
T ss_pred             cCCEEEEEECCCCCCHHHHHHHHHHHHHhhhhcccccceEEEechHHHHHH
Confidence            456799999999999999999987531    12233456778876655543

>d1s3ga1 c.37.1.1 (A:1-125,A:161-217) Adenylate kinase {Bacillus globisporus [TaxId: 1459]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Bacillus globisporus [TaxId: 1459]

Probab=94.37  E-value=0.0093  Score=51.51  Aligned_cols=21  Identities=29%  Similarity=0.491  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|.|.|++|+||||+|+.++.
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~   22 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVE   22 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            377899999999999999987

>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=94.31  E-value=0.011  Score=54.63  Aligned_cols=24  Identities=21%  Similarity=0.448  Sum_probs=18.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++|+|.|.+|+||||+++.+.+
T Consensus         3 k~pIIgIaG~SGSGKTTva~~l~~   26 (288)
T d1a7ja_           3 KHPIISVTGSSGAGTSTVKHTFDQ   26 (288)
T ss_dssp             TSCEEEEESCC---CCTHHHHHHH
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHH
Confidence            457999999999999999998876

>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=94.30  E-value=0.017  Score=53.25  Aligned_cols=39  Identities=21%  Similarity=0.245  Sum_probs=27.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      +.|+|+|-||+||||+|..+..-  ....-..++-|++...
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~--LA~~G~rVllID~D~q   40 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSG--LHAMGKTIMVVGCDPK   40 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHTTTCCEEEEEECTT
T ss_pred             CEEEEECCCcCCHHHHHHHHHHH--HHhCCCcEEEEecCCC
Confidence            67999999999999999888773  3222224556666543

>d2vp4a1 c.37.1.1 (A:12-208) Deoxyribonucleoside kinase {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyribonucleoside kinase
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=94.29  E-value=0.0092  Score=52.22  Aligned_cols=25  Identities=28%  Similarity=0.268  Sum_probs=22.2

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+-+|+|-|..|+||||+++.+.+
T Consensus         7 ~kp~~I~ieG~~GsGKTTl~~~L~~   31 (197)
T d2vp4a1           7 TQPFTVLIEGNIGSGKTTYLNHFEK   31 (197)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHH
Confidence            4566999999999999999999876

>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=94.26  E-value=0.012  Score=51.89  Aligned_cols=23  Identities=17%  Similarity=0.332  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+|+|+||+|+|||||.+.+..
T Consensus         2 G~livi~GPSG~GK~tl~~~L~~   24 (205)
T d1s96a_           2 GTLYIVSAPSGAGKSSLIQALLK   24 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHh
Confidence            36899999999999999998876

>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=94.20  E-value=0.062  Score=51.58  Aligned_cols=41  Identities=22%  Similarity=0.244  Sum_probs=25.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCCh-hhhccCCeeEEEEecC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDS-DVKANFDKRIWVSASY  237 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~-~~~~~F~~~~wv~~~~  237 (597)
                      .+++.|+|++|.||||++..+.... +....-...+.+....
T Consensus       163 ~~~~vI~G~pGTGKTt~i~~~l~~l~~~~~~~~~~I~l~ApT  204 (359)
T d1w36d1         163 RRISVISGGPGTGKTTTVAKLLAALIQMADGERCRIRLAAPT  204 (359)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHHTCSSCCCCEEEEBSS
T ss_pred             CCeEEEEcCCCCCceehHHHHHHHHHHHHhccCCeEEEecCc
Confidence            3699999999999999886654311 1111123356666554

>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=94.14  E-value=0.01  Score=56.81  Aligned_cols=44  Identities=18%  Similarity=0.274  Sum_probs=31.7

Q ss_pred             CCccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHh
Q 041007          165 PLEFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       165 ~~~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      -+.++|.+.-+..|.-.+...          +..-|.|.|++|+|||+||+.+.
T Consensus         6 f~~I~Gq~~~kral~laa~~~----------~~h~vLl~G~pG~GKT~lar~~~   49 (333)
T d1g8pa_           6 FSAIVGQEDMKLALLLTAVDP----------GIGGVLVFGDRGTGKSTAVRALA   49 (333)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCG----------GGCCEEEECCGGGCTTHHHHHHH
T ss_pred             hhhccCcHHHHHHHHHHHhcc----------CCCeEEEECCCCccHHHHHHHHH
Confidence            356799987777654333211          22458999999999999999885

>d1akya1 c.37.1.1 (A:3-130,A:169-220) Adenylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=94.08  E-value=0.012  Score=50.81  Aligned_cols=20  Identities=25%  Similarity=0.473  Sum_probs=17.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      |.|.|++|+||||+|+.++.
T Consensus         5 Ivl~G~pGSGKtT~a~~La~   24 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQE   24 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45779999999999999977

>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=94.01  E-value=0.017  Score=50.38  Aligned_cols=27  Identities=22%  Similarity=0.490  Sum_probs=23.3

Q ss_pred             CCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          194 KPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       194 ~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.+.|+|+|.+|+|||||...+.+.
T Consensus        20 ~~~~~~I~lvG~~n~GKSTLin~L~g~   46 (195)
T d1svia_          20 EGGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CSCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHhcCC
Confidence            345678999999999999999999863

>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=93.95  E-value=0.013  Score=50.45  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=18.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|.|.|++|+||||+|+.++.
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~   22 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIME   22 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            367899999999999999986

>d1ihua1 c.37.1.10 (A:1-296) Arsenite-translocating ATPase ArsA {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Arsenite-translocating ATPase ArsA
species: Escherichia coli [TaxId: 562]

Probab=93.88  E-value=0.027  Score=52.49  Aligned_cols=41  Identities=20%  Similarity=0.315  Sum_probs=28.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      .+++|.++|-||+||||+|..++..  ....=..++-|++...
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~--lA~~G~rVLlvD~Dp~   47 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIR--LAEQGKRVLLVSTDPA   47 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHH--HHHTTCCEEEEECCTT
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHH--HHHCCCCEEEEeCCCC
Confidence            4789999999999999998887763  3222223566665543

>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=93.73  E-value=0.041  Score=50.58  Aligned_cols=22  Identities=32%  Similarity=0.323  Sum_probs=19.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+..|+|++|+|||||+.+++-
T Consensus        30 ~~~~i~G~~G~GKS~l~l~la~   51 (274)
T d1nlfa_          30 TVGALVSPGGAGKSMLALQLAA   51 (274)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHH
Confidence            5888999999999999988765

>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=93.66  E-value=0.016  Score=52.39  Aligned_cols=21  Identities=29%  Similarity=0.495  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ||+|+|+.|+|||||...+.+
T Consensus         2 vi~v~G~~GsGKTTLl~~ll~   22 (244)
T d1yrba1           2 IVVFVGTAGSGKTTLTGEFGR   22 (244)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEcCCCCcHHHHHHHHHH
Confidence            789999999999999999875

>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=93.52  E-value=0.023  Score=54.74  Aligned_cols=25  Identities=28%  Similarity=0.352  Sum_probs=22.9

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +..+.+.++||+|+|||++|..+++
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~  176 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLE  176 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHH
Confidence            4567999999999999999999988

>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=93.50  E-value=0.058  Score=48.69  Aligned_cols=46  Identities=22%  Similarity=0.263  Sum_probs=32.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCChhh----hccCCeeEEEEecCCCch
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDDSDV----KANFDKRIWVSASYPRDE  241 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~~~~----~~~F~~~~wv~~~~~~~~  241 (597)
                      ...++.|.|++|+|||++|.+++.+...    .......+|+........
T Consensus        35 ~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (254)
T d1pzna2          35 TQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRP   84 (254)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCH
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHH
Confidence            5679999999999999999998753211    122345777776655543

>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=93.32  E-value=0.096  Score=46.17  Aligned_cols=24  Identities=25%  Similarity=0.326  Sum_probs=21.7

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+.|+|-|+-|+||||+++.+..
T Consensus         2 kGk~I~iEG~DGsGKST~~~~L~~   25 (214)
T d1tmka_           2 RGKLILIEGLDRTGKTTQCNILYK   25 (214)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHH
T ss_pred             CeEEEEEECCCCCcHHHHHHHHHH
Confidence            457899999999999999999876

>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=93.29  E-value=0.02  Score=50.65  Aligned_cols=25  Identities=20%  Similarity=0.213  Sum_probs=22.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...++.|.|++|+|||+||.+++.+
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~   46 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVT   46 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHH
Confidence            4579999999999999999998754

>d4tmka_ c.37.1.1 (A:) Thymidylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Escherichia coli [TaxId: 562]

Probab=93.22  E-value=0.13  Score=44.92  Aligned_cols=34  Identities=26%  Similarity=0.388  Sum_probs=25.2

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhc-cCCeeEEE
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKA-NFDKRIWV  233 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~-~F~~~~wv  233 (597)
                      +.|+|-|+.|+||||++..+..  .... .+..+.+.
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~--~L~~~g~~~~~~~   37 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVE--TLEQLGIRDMVFT   37 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHH--HHHHTTCCCEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHH--HHHhCCCCeEEEe
Confidence            5799999999999999999987  3332 34444443

>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=93.05  E-value=0.023  Score=47.33  Aligned_cols=21  Identities=24%  Similarity=0.357  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |.|+|.+|+|||||...+..+
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            679999999999999998754

>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=92.96  E-value=0.025  Score=48.21  Aligned_cols=23  Identities=30%  Similarity=0.570  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||+|...+.++
T Consensus         7 ~Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           7 HKLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            35779999999999999998754

>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=92.93  E-value=0.32  Score=44.27  Aligned_cols=39  Identities=21%  Similarity=0.125  Sum_probs=26.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          197 LPVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ..++.|.|.+|+|||+++.+++.+.-....+ .+++++..
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~-~v~~~s~E   73 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWGTAMGK-KVGLAMLE   73 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHHHTSCC-CEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhhhhccc-ceeEeeec
Confidence            3589999999999999999987632222333 34555543

>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=92.91  E-value=0.039  Score=51.35  Aligned_cols=41  Identities=22%  Similarity=0.249  Sum_probs=28.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCCCc
Q 041007          198 PVIWILGNEGIGKTALARQVFDDSDVKANFDKRIWVSASYPRD  240 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~~~  240 (597)
                      +.|+|+|-||+||||+|..+...  ....=..++-|++....+
T Consensus         3 r~IaisgKGGVGKTT~a~NLA~~--LA~~G~rVLlID~DpQ~~   43 (289)
T d2afhe1           3 RQCAIYGKGGIGKSTTTQNLVAA--LAEMGKKVMIVGCDPKAD   43 (289)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHH--HHHTTCCEEEEEECSSSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHH--HHHCCCCEEEEecCCCCC
Confidence            57889999999999999887663  222222366677654433

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.78  E-value=0.027  Score=50.81  Aligned_cols=23  Identities=22%  Similarity=0.320  Sum_probs=21.4

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++.|+|-|+-|+||||+++.+..
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~   24 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTK   24 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHH
Confidence            57999999999999999999976

>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=92.69  E-value=0.0097  Score=50.07  Aligned_cols=22  Identities=23%  Similarity=0.338  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||..++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4779999999999999998753

>d1upta_ c.37.1.8 (A:) ADP-ribosylation factor {Human (Homo sapiens), ARL1 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: ADP-ribosylation factor
species: Human (Homo sapiens), ARL1 [TaxId: 9606]

Probab=92.69  E-value=0.023  Score=47.67  Aligned_cols=22  Identities=36%  Similarity=0.486  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+..+
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999998765

>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=92.66  E-value=0.03  Score=47.50  Aligned_cols=21  Identities=24%  Similarity=0.578  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||||...+.++
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            678999999999999998875

>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=92.54  E-value=0.025  Score=47.76  Aligned_cols=22  Identities=32%  Similarity=0.578  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|+..+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           6 KYIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3778999999999999998754

>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=92.54  E-value=0.025  Score=48.17  Aligned_cols=21  Identities=38%  Similarity=0.650  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|+..+.++
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            678999999999999998764

>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=92.45  E-value=0.25  Score=39.57  Aligned_cols=24  Identities=17%  Similarity=0.335  Sum_probs=20.2

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..++..|+++.|.|||+++..++.
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~   30 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYA   30 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHH
Confidence            568899999999999998876654

>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=92.45  E-value=0.033  Score=46.80  Aligned_cols=22  Identities=23%  Similarity=0.471  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+...
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            3679999999999999998764

>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=92.44  E-value=0.2  Score=44.32  Aligned_cols=22  Identities=27%  Similarity=0.342  Sum_probs=19.5

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +++.|+|+...||||+.+.+.-
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l   57 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTAL   57 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHH
T ss_pred             cEEEEECCCccccchhhhhhHH
Confidence            4789999999999999998854

>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=92.41  E-value=0.051  Score=48.45  Aligned_cols=39  Identities=21%  Similarity=0.170  Sum_probs=28.9

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHhCChhhhccCCeeEEEEecCC
Q 041007          198 PVIWIL-GNEGIGKTALARQVFDDSDVKANFDKRIWVSASYP  238 (597)
Q Consensus       198 ~vv~I~-G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~~~  238 (597)
                      ++|+|+ |-||+||||+|..++..  ....-..++.|.+...
T Consensus         2 kvIav~s~KGGvGKTtia~nlA~~--la~~g~~VlliD~D~~   41 (232)
T d1hyqa_           2 RTITVASGKGGTGKTTITANLGVA--LAQLGHDVTIVDADIT   41 (232)
T ss_dssp             EEEEEEESSSCSCHHHHHHHHHHH--HHHTTCCEEEEECCCS
T ss_pred             EEEEEECCCCCChHHHHHHHHHHH--HHhCCCCEEEEeCCCC
Confidence            577777 88999999999998873  4444345778876543

>d1z06a1 c.37.1.8 (A:32-196) Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Rab-33b
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.37  E-value=0.027  Score=47.41  Aligned_cols=21  Identities=29%  Similarity=0.585  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |.|.|.+|+|||||+..+.++
T Consensus         5 v~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999998764

>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=92.32  E-value=0.035  Score=47.82  Aligned_cols=22  Identities=32%  Similarity=0.596  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||+..+.+.
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~~   28 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTDN   28 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECCCCcCHHHHHHHHhcC
Confidence            3778999999999999999874

>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=92.29  E-value=0.034  Score=49.03  Aligned_cols=20  Identities=25%  Similarity=0.454  Sum_probs=18.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHh
Q 041007          199 VIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~  218 (597)
                      +|+|+|+.|+||||+|..+-
T Consensus         5 iIgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH
T ss_pred             EEEEECCCcCCHHHHHHHHH
Confidence            89999999999999998763

>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=92.23  E-value=0.034  Score=46.79  Aligned_cols=21  Identities=19%  Similarity=0.542  Sum_probs=18.6

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+++|.+|+|||||+..+.+.
T Consensus         5 v~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            679999999999999988754

>d2jdia3 c.37.1.11 (A:95-379) Central domain of alpha subunit of F1 ATP synthase {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of alpha subunit of F1 ATP synthase
species: Cow (Bos taurus) [TaxId: 9913]

Probab=92.20  E-value=0.19  Score=46.00  Aligned_cols=25  Identities=24%  Similarity=0.278  Sum_probs=20.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....++|.|.+|+|||+|+..+...
T Consensus        67 ~GQr~~If~~~g~GKt~ll~~~~~~   91 (285)
T d2jdia3          67 RGQRELIIGDRQTGKTSIAIDTIIN   91 (285)
T ss_dssp             TTCBCEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCEEEeecCCCCChHHHHHHHHHh
Confidence            3467899999999999999887653

>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=92.15  E-value=0.036  Score=48.68  Aligned_cols=22  Identities=32%  Similarity=0.442  Sum_probs=19.1

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -+|+|+|..|+||||+|+.+-.
T Consensus         3 ~iIgITG~igSGKStv~~~l~~   24 (205)
T d1jjva_           3 YIVGLTGGIGSGKTTIANLFTD   24 (205)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            4799999999999999987743

>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=92.14  E-value=0.036  Score=46.84  Aligned_cols=21  Identities=43%  Similarity=0.631  Sum_probs=19.0

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|+..+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            678999999999999998764

>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=92.11  E-value=0.033  Score=47.53  Aligned_cols=24  Identities=33%  Similarity=0.414  Sum_probs=20.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..-|+|+|.+|+|||||...+...
T Consensus        13 ~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          13 TGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             CEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            345779999999999999999775

>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=92.11  E-value=0.03  Score=47.24  Aligned_cols=22  Identities=36%  Similarity=0.631  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|...+.++
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3778999999999999998764

>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=91.98  E-value=0.032  Score=47.21  Aligned_cols=21  Identities=33%  Similarity=0.662  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|...+.++
T Consensus         5 i~lvG~~~vGKTsli~r~~~~   25 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLTK   25 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            578999999999999999865

>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=91.94  E-value=0.032  Score=47.08  Aligned_cols=22  Identities=27%  Similarity=0.504  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|+..+.++
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3689999999999999998754

>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=91.91  E-value=0.033  Score=46.83  Aligned_cols=21  Identities=33%  Similarity=0.626  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|+..+.++
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998754

>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=91.90  E-value=0.068  Score=47.25  Aligned_cols=34  Identities=21%  Similarity=0.314  Sum_probs=27.5

Q ss_pred             hHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          174 EKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       174 e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -++.|.++|.             .+..++.|.+|+|||||...+..+
T Consensus        85 g~~~L~~~l~-------------~kt~~~~G~SGVGKSTLiN~L~~~  118 (225)
T d1u0la2          85 GIEELKEYLK-------------GKISTMAGLSGVGKSSLLNAINPG  118 (225)
T ss_dssp             THHHHHHHHS-------------SSEEEEECSTTSSHHHHHHHHSTT
T ss_pred             hHhhHHHHhc-------------CCeEEEECCCCCCHHHHHHhhcch
Confidence            3567777774             257889999999999999999764

>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=91.89  E-value=0.044  Score=46.38  Aligned_cols=22  Identities=23%  Similarity=0.552  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|+|.|.+|+|||||...+...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            6899999999999999999763

>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=91.87  E-value=0.034  Score=47.09  Aligned_cols=22  Identities=41%  Similarity=0.622  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+++|.+|+|||||...+.++
T Consensus         7 Ki~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           7 KILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999988654

>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=91.84  E-value=0.033  Score=47.20  Aligned_cols=22  Identities=41%  Similarity=0.718  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+.++
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999998764

>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=91.84  E-value=0.025  Score=50.95  Aligned_cols=24  Identities=25%  Similarity=0.246  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.|+|-|+.|+||||+++.+...
T Consensus         2 ~k~I~ieG~dGsGKST~~~~L~~~   25 (241)
T d1p5zb_           2 IKKISIEGNIAAGKSTFVNILKQL   25 (241)
T ss_dssp             CEEEEEECSTTSSHHHHHTTTGGG
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
Confidence            478999999999999999998774

>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=91.77  E-value=0.035  Score=46.86  Aligned_cols=21  Identities=29%  Similarity=0.782  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||||...+.++
T Consensus         7 i~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999998764

>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=91.75  E-value=0.06  Score=45.63  Aligned_cols=23  Identities=35%  Similarity=0.523  Sum_probs=20.3

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+...
T Consensus        17 ~kI~vvG~~~vGKSsLi~~l~~~   39 (176)
T d1fzqa_          17 VRILLLGLDNAGKTTLLKQLASE   39 (176)
T ss_dssp             EEEEEEESTTSSHHHHHHHHCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            45789999999999999999774

>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=91.72  E-value=0.074  Score=51.10  Aligned_cols=24  Identities=29%  Similarity=0.483  Sum_probs=20.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ....+...||.|+|||.||+.++.
T Consensus        67 p~~niLfiGPTGvGKTElAk~LA~   90 (364)
T d1um8a_          67 SKSNILLIGPTGSGKTLMAQTLAK   90 (364)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             CCcceeeeCCCCccHHHHHHHHHh
Confidence            456788999999999999999875

>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=91.69  E-value=0.036  Score=46.92  Aligned_cols=22  Identities=23%  Similarity=0.504  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~   29 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3688999999999999998754

>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=91.62  E-value=0.037  Score=47.04  Aligned_cols=22  Identities=41%  Similarity=0.773  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+.++
T Consensus         4 Ki~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           4 KVIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHcC
Confidence            3789999999999999998753

>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=91.59  E-value=0.047  Score=47.76  Aligned_cols=23  Identities=39%  Similarity=0.527  Sum_probs=20.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.|+|+|.+|+|||||...+.+.
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            58899999999999999999754

>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=91.57  E-value=0.063  Score=46.92  Aligned_cols=21  Identities=33%  Similarity=0.502  Sum_probs=19.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|+|.|.-|+||||+++.+..
T Consensus         2 lI~ieG~dGsGKST~~~~L~~   22 (208)
T d1gsia_           2 LIAIEGVDGAGKRTLVEKLSG   22 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            589999999999999999987

>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=91.56  E-value=0.041  Score=49.56  Aligned_cols=25  Identities=28%  Similarity=0.254  Sum_probs=22.1

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...++.|.|++|+|||++|.+++.+
T Consensus        33 ~G~l~~i~G~~G~GKT~~~l~~a~~   57 (258)
T d2i1qa2          33 SQSVTEFAGVFGSGKTQIMHQSCVN   57 (258)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            4579999999999999999999754

>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=91.55  E-value=0.037  Score=46.62  Aligned_cols=23  Identities=35%  Similarity=0.511  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-|+|.|.+|+|||+|...+.++
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            45788999999999999998654

>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=91.54  E-value=0.037  Score=46.87  Aligned_cols=22  Identities=32%  Similarity=0.608  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|...+..+
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3789999999999999988764

>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=91.48  E-value=0.039  Score=46.53  Aligned_cols=21  Identities=38%  Similarity=0.697  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|...+..+
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHcC
Confidence            678999999999999998754

>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=91.45  E-value=0.039  Score=46.48  Aligned_cols=22  Identities=32%  Similarity=0.721  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+.+.
T Consensus         4 Ki~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           4 KILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998764

>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=91.39  E-value=0.051  Score=47.62  Aligned_cols=23  Identities=22%  Similarity=0.284  Sum_probs=20.4

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +.|+|+|.+|+|||||...+...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            46899999999999999998764

>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=91.38  E-value=0.04  Score=46.42  Aligned_cols=21  Identities=33%  Similarity=0.711  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|...+.++
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            788999999999999998764

>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=91.32  E-value=0.041  Score=46.93  Aligned_cols=22  Identities=32%  Similarity=0.359  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|...+.++
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678899999999999998764

>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=91.25  E-value=0.053  Score=45.96  Aligned_cols=23  Identities=26%  Similarity=0.322  Sum_probs=19.8

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|.|+|.+|+|||||...+..+
T Consensus        16 ~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          16 HKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35779999999999999998764

>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=91.24  E-value=0.043  Score=46.71  Aligned_cols=22  Identities=23%  Similarity=0.576  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|..|+|||||+..+.++
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998664

>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=91.12  E-value=0.05  Score=46.13  Aligned_cols=22  Identities=32%  Similarity=0.653  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||+..+..+
T Consensus         7 KI~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           7 KFLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999998653

>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=91.11  E-value=0.052  Score=45.04  Aligned_cols=22  Identities=32%  Similarity=0.486  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||...+...
T Consensus         2 KI~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           2 KLLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999998764

>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=91.10  E-value=0.055  Score=45.87  Aligned_cols=21  Identities=29%  Similarity=0.597  Sum_probs=18.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -|.++|.+|+|||+|+..+..
T Consensus         5 Kv~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           5 RVVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            377999999999999999865

>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=91.07  E-value=0.046  Score=46.21  Aligned_cols=22  Identities=18%  Similarity=0.514  Sum_probs=18.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|...+.+.
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3678999999999999998754

>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=91.03  E-value=0.052  Score=46.74  Aligned_cols=21  Identities=24%  Similarity=0.395  Sum_probs=18.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -|.+.|.+|+|||+|..++..
T Consensus         4 KivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           4 KLLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhh
Confidence            367999999999999998754

>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=90.98  E-value=0.059  Score=45.86  Aligned_cols=25  Identities=20%  Similarity=0.360  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.|+|+|.+|+|||||...++..
T Consensus         4 ~~~~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           4 YSGFVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             cCcEEEEECCCCCCHHHHHHHHhCC
Confidence            3458999999999999999999864

>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=90.82  E-value=0.1  Score=51.45  Aligned_cols=49  Identities=27%  Similarity=0.422  Sum_probs=33.9

Q ss_pred             ccccchhhHHHHHHHhh--------CCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLK--------GESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~--------~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..||.++.++.|.-.+.        .....+    .-..+-|.+.||+|+|||-||+.++.
T Consensus        15 yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~----ei~ksNILliGPTGvGKTlLAr~LAk   71 (443)
T d1g41a_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRH----EVTPKNILMIGPTGVGKTEIARRLAK   71 (443)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHSCTTTTT----TCCCCCEEEECCTTSSHHHHHHHHHH
T ss_pred             cccCcHHHHHHHHHHHHHHHHHhhccccccc----ccccccEEEECCCCCCHHHHHHHHHH
Confidence            46788888777755442        111100    12356799999999999999999987

>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=90.77  E-value=0.039  Score=46.75  Aligned_cols=21  Identities=24%  Similarity=0.605  Sum_probs=17.5

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|...+.++
T Consensus         6 i~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC--
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999988764

>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=90.75  E-value=0.049  Score=48.48  Aligned_cols=25  Identities=32%  Similarity=0.599  Sum_probs=22.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..++..|+|.-|+|||||.+.+.+.
T Consensus         2 ~iPv~iitGFLGaGKTTll~~lL~~   26 (222)
T d1nija1           2 PIAVTLLTGFLGAGKTTLLRHILNE   26 (222)
T ss_dssp             CEEEEEEEESSSSSCHHHHHHHHHS
T ss_pred             CCCEEEEeeCCCCCHHHHHHHHHhc
Confidence            4689999999999999999998763

>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=90.70  E-value=0.058  Score=46.75  Aligned_cols=19  Identities=32%  Similarity=0.545  Sum_probs=17.4

Q ss_pred             EEEEEcCCCCcHHHHHHHH
Q 041007          199 VIWILGNEGIGKTALARQV  217 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v  217 (597)
                      -|.|.|.+|+|||||...+
T Consensus         4 KivllG~~~vGKTsll~r~   22 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQM   22 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            4679999999999999998

>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=90.70  E-value=0.042  Score=47.31  Aligned_cols=22  Identities=27%  Similarity=0.436  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|.|+|.+|+|||+|...+.++
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~   32 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYAND   32 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhhC
Confidence            4889999999999999998764

>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=90.65  E-value=0.06  Score=45.42  Aligned_cols=22  Identities=32%  Similarity=0.613  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||+|+..+.+.
T Consensus         8 Ki~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           8 KVMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999988654

>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=90.59  E-value=0.062  Score=45.03  Aligned_cols=22  Identities=18%  Similarity=0.255  Sum_probs=18.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|.|.+|+|||||...+...
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~   25 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            3668899999999999988654

>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=90.56  E-value=0.051  Score=46.06  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=20.3

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+ |.|+|.+|+|||||...+.+.
T Consensus        12 ~~k-IvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          12 EMR-ILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             CEE-EEEEEETTSSHHHHHHHTTCC
T ss_pred             eEE-EEEECCCCCCHHHHHHHHhcC
Confidence            345 668999999999999999865

>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=90.56  E-value=0.054  Score=45.69  Aligned_cols=22  Identities=36%  Similarity=0.647  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||+..+.++
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4779999999999999998654

>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=90.46  E-value=0.063  Score=46.52  Aligned_cols=22  Identities=36%  Similarity=0.711  Sum_probs=19.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|+|.+|+|||||+..+.++
T Consensus         8 KivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           8 KLLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhhC
Confidence            3789999999999999998754

>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=90.35  E-value=0.069  Score=45.31  Aligned_cols=25  Identities=24%  Similarity=0.434  Sum_probs=21.9

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ....|+|.|.+|+|||||...+.+.
T Consensus         4 ~~~~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           4 YCGFIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEEEEECSSSSSHHHHHHHHHTC
T ss_pred             cccEEEEECCCCCCHHHHHHHHhCC
Confidence            3567999999999999999999864

>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=90.33  E-value=0.051  Score=46.40  Aligned_cols=21  Identities=19%  Similarity=0.338  Sum_probs=19.2

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||||...+...
T Consensus         4 VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999753

>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=90.31  E-value=0.074  Score=45.07  Aligned_cols=22  Identities=27%  Similarity=0.492  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .-|.|.|++|+||||||..+..
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHH
Confidence            5688999999999999999876

>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=90.30  E-value=0.058  Score=45.73  Aligned_cols=21  Identities=29%  Similarity=0.707  Sum_probs=18.7

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||||+..+.++
T Consensus         9 I~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999888654

>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=90.27  E-value=0.067  Score=45.61  Aligned_cols=22  Identities=23%  Similarity=0.419  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .|+|+|.+|+|||||...+.+.
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999864

>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=90.22  E-value=0.059  Score=46.04  Aligned_cols=21  Identities=38%  Similarity=0.521  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |++.|..|+|||+|+..+.+.
T Consensus         5 ivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678999999999999998764

>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=90.16  E-value=0.057  Score=46.26  Aligned_cols=21  Identities=43%  Similarity=0.784  Sum_probs=18.9

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||||+..+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            779999999999999998754

>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=90.14  E-value=0.063  Score=45.93  Aligned_cols=23  Identities=22%  Similarity=0.303  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||+|...+..+
T Consensus         6 iKivviG~~~vGKTsli~~~~~~   28 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTN   28 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35889999999999999998764

>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=90.09  E-value=0.098  Score=46.57  Aligned_cols=37  Identities=24%  Similarity=0.299  Sum_probs=27.2

Q ss_pred             cEEEEE-cCCCCcHHHHHHHHhCChhhhccCCeeEEEEec
Q 041007          198 PVIWIL-GNEGIGKTALARQVFDDSDVKANFDKRIWVSAS  236 (597)
Q Consensus       198 ~vv~I~-G~gGiGKTtLA~~v~~~~~~~~~F~~~~wv~~~  236 (597)
                      ++|+|+ +-||+||||+|..++..  ....-..++-+++.
T Consensus         3 ~vIav~~~kGGvGKTtia~nLA~~--la~~g~~VlliD~D   40 (237)
T d1g3qa_           3 RIISIVSGKGGTGKTTVTANLSVA--LGDRGRKVLAVDGD   40 (237)
T ss_dssp             EEEEEECSSTTSSHHHHHHHHHHH--HHHTTCCEEEEECC
T ss_pred             eEEEEECCCCCCcHHHHHHHHHHH--HHhCCCCEEEEeCC
Confidence            688888 77999999999998873  33333346667654

>d2ngra_ c.37.1.8 (A:) CDC42 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: CDC42
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.09  E-value=0.061  Score=46.46  Aligned_cols=21  Identities=24%  Similarity=0.400  Sum_probs=18.5

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|...+.++
T Consensus         6 vvllG~~~vGKTSli~r~~~~   26 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTTN   26 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            678899999999999988754

>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=90.08  E-value=0.058  Score=46.12  Aligned_cols=23  Identities=35%  Similarity=0.419  Sum_probs=19.7

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|+|.+|+|||||...+.+.
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~~~   40 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQIG   40 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            34669999999999999998765

>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=89.96  E-value=0.065  Score=45.23  Aligned_cols=21  Identities=38%  Similarity=0.792  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |.++|.+|+|||+|...+.++
T Consensus         7 i~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            567899999999999998764

>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=89.93  E-value=0.057  Score=46.04  Aligned_cols=25  Identities=16%  Similarity=0.170  Sum_probs=21.8

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +...|+|+|.+++|||||...+...
T Consensus        15 ~~~~I~lvG~~NvGKSSL~n~L~~~   39 (188)
T d1puia_          15 TGIEVAFAGRSNAGKSSALNTLTNQ   39 (188)
T ss_dssp             CSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHhCC
Confidence            4678999999999999999988664

>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=89.86  E-value=0.087  Score=43.66  Aligned_cols=24  Identities=29%  Similarity=0.589  Sum_probs=21.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .-+|.+.|.=|+||||+++.+++.
T Consensus        33 g~ii~L~G~LGaGKTtfvr~~~~~   56 (158)
T d1htwa_          33 AIMVYLNGDLGAGKTTLTRGMLQG   56 (158)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CeEEEEecCCCccHHHHHHHHHhh
Confidence            458999999999999999999875

>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=89.83  E-value=0.081  Score=44.80  Aligned_cols=23  Identities=26%  Similarity=0.414  Sum_probs=20.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..-|.|.|.+|+||||||.++..
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHH
Confidence            35789999999999999999765

>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=89.77  E-value=0.076  Score=45.83  Aligned_cols=20  Identities=25%  Similarity=0.429  Sum_probs=18.1

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      |.|.|.+|+|||+|...+..
T Consensus         5 iv~lG~~~vGKTsll~r~~~   24 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRI   24 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            67999999999999999855

>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=89.72  E-value=0.08  Score=44.98  Aligned_cols=21  Identities=43%  Similarity=0.782  Sum_probs=18.8

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||+|...+.++
T Consensus        10 i~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988654

>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=89.72  E-value=0.053  Score=46.48  Aligned_cols=21  Identities=24%  Similarity=0.341  Sum_probs=19.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHhC
Q 041007          199 VIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -|+|+|.+|+|||||...+.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999865

>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=89.60  E-value=0.22  Score=48.34  Aligned_cols=40  Identities=20%  Similarity=0.313  Sum_probs=29.4

Q ss_pred             ccch-hhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          169 HGRN-AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       169 vGR~-~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .|-. ...+.+..++..           ....|.|+|+.|+||||....+.+
T Consensus       140 LG~~~~~~~~l~~l~~~-----------~~GliLvtGpTGSGKSTTl~~~l~  180 (401)
T d1p9ra_         140 LGMTAHNHDNFRRLIKR-----------PHGIILVTGPTGSGKSTTLYAGLQ  180 (401)
T ss_dssp             SCCCHHHHHHHHHHHTS-----------SSEEEEEECSTTSCHHHHHHHHHH
T ss_pred             hcccHHHHHHHHHHHhh-----------hhceEEEEcCCCCCccHHHHHHhh
Confidence            3543 445556665542           347999999999999999988877

>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=89.60  E-value=0.082  Score=47.46  Aligned_cols=22  Identities=23%  Similarity=0.397  Sum_probs=19.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ++|+|+|..|+||||+|..+..
T Consensus         2 ~iIgiTG~igSGKsTva~~l~e   23 (241)
T d1deka_           2 KLIFLSGVKRSGKDTTADFIMS   23 (241)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHH
Confidence            5899999999999999998854

>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=89.59  E-value=0.072  Score=45.31  Aligned_cols=22  Identities=23%  Similarity=0.453  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHhCC
Q 041007          199 VIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      -|+|.|.+|+|||+|...+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4789999999999999988764

>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=89.54  E-value=0.062  Score=48.04  Aligned_cols=23  Identities=22%  Similarity=0.468  Sum_probs=20.9

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..+++|.|+.|.|||||.+.+..
T Consensus        25 Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          25 GEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCEEEEECCCCCcHHHHHHHHhC
Confidence            46999999999999999998876

>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=89.19  E-value=0.058  Score=45.72  Aligned_cols=21  Identities=29%  Similarity=0.680  Sum_probs=8.3

Q ss_pred             EEEEcCCCCcHHHHHHHHhCC
Q 041007          200 IWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~~  220 (597)
                      |+|+|.+|+|||||...+.++
T Consensus         9 i~vvG~~~vGKTsLi~~l~~~   29 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSED   29 (173)
T ss_dssp             EEEECCCCC------------
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            778899999999999988764

>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=89.08  E-value=0.098  Score=43.98  Aligned_cols=23  Identities=30%  Similarity=0.442  Sum_probs=20.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      ..-|.|.|.+|+||||||.++..
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~   37 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIK   37 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHH
Confidence            35789999999999999988866

>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=88.81  E-value=0.099  Score=46.31  Aligned_cols=22  Identities=23%  Similarity=0.358  Sum_probs=18.9

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .-|.|.|.+|+|||||..++..
T Consensus         7 ~KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           7 HRLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhc
Confidence            3578999999999999999854

>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=88.71  E-value=0.11  Score=44.34  Aligned_cols=23  Identities=22%  Similarity=0.470  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      --|+|.|.+|+|||||...+...
T Consensus         9 ~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           9 IKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
Confidence            35789999999999999998764

>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=87.48  E-value=0.14  Score=44.89  Aligned_cols=23  Identities=17%  Similarity=0.414  Sum_probs=20.1

Q ss_pred             cEEEEEcCC-CCcHHHHHHHHhCC
Q 041007          198 PVIWILGNE-GIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~g-GiGKTtLA~~v~~~  220 (597)
                      +.+.|+|-| ||||||++..++.-
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~a   25 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQA   25 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHH
T ss_pred             ceEEEEECCCCccHHHHHHHHHHH
Confidence            468899998 99999999888873

>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=87.41  E-value=0.26  Score=44.62  Aligned_cols=40  Identities=23%  Similarity=0.431  Sum_probs=29.1

Q ss_pred             hhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          173 AEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       173 ~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ..+.++...+.....        ..-.|+|+|.+|+|||||...++..
T Consensus        16 ~~l~e~~~~l~~~~~--------~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          16 TKLLELLGNLKQEDV--------NSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             HHHHHHHHHHHHTTC--------CEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             HHHHHHHHHHhhcCC--------CCcEEEEECCCCCcHHHHHHHHhCC
Confidence            445566666654332        3457889999999999999999864

>d1f5na2 c.37.1.8 (A:7-283) Interferon-induced guanylate-binding protein 1 (GBP1), 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: G proteins
domain: Interferon-induced guanylate-binding protein 1 (GBP1), N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.03  E-value=0.57  Score=42.64  Aligned_cols=25  Identities=24%  Similarity=0.313  Sum_probs=23.0

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      .+.||+|+|+-+.|||+|+..++..
T Consensus        31 ~v~vvsi~G~~~sGKS~llN~l~~~   55 (277)
T d1f5na2          31 PMVVVAIVGLYRTGKSYLMNKLAGK   55 (277)
T ss_dssp             BEEEEEEEEBTTSSHHHHHHHHTTC
T ss_pred             CEEEEEEECCCCCCHHHHHHHHcCC
Confidence            5889999999999999999999874

>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=86.81  E-value=0.19  Score=47.16  Aligned_cols=22  Identities=23%  Similarity=0.519  Sum_probs=20.0

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhC
Q 041007          198 PVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|.|+|+.|+||||+...++.
T Consensus       167 ~nili~G~tgSGKTT~l~al~~  188 (323)
T d1g6oa_         167 KNVIVCGGTGSGKTTYIKSIME  188 (323)
T ss_dssp             CCEEEEESTTSSHHHHHHHHGG
T ss_pred             CCEEEEeeccccchHHHHHHhh
Confidence            4589999999999999999987

>d2p6ra3 c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=86.79  E-value=1.2  Score=38.03  Aligned_cols=18  Identities=28%  Similarity=0.254  Sum_probs=15.0

Q ss_pred             EEEEEcCCCCcHHHHHHH
Q 041007          199 VIWILGNEGIGKTALARQ  216 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~  216 (597)
                      .+.|.++.|.|||+.|..
T Consensus        42 ~~il~apTGsGKT~~a~l   59 (202)
T d2p6ra3          42 NLLLAMPTAAGKTLLAEM   59 (202)
T ss_dssp             CEEEECSSHHHHHHHHHH
T ss_pred             CEEEEcCCCCchhHHHHH
Confidence            467999999999988744

>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=86.03  E-value=1.4  Score=37.46  Aligned_cols=19  Identities=32%  Similarity=0.394  Sum_probs=14.7

Q ss_pred             EEEEcCCCCcHHHHHHHHh
Q 041007          200 IWILGNEGIGKTALARQVF  218 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~  218 (597)
                      +.|+++.|.|||.++..+.
T Consensus        26 ~lv~~pTGsGKT~i~~~~~   44 (200)
T d1wp9a1          26 CLIVLPTGLGKTLIAMMIA   44 (200)
T ss_dssp             EEEECCTTSCHHHHHHHHH
T ss_pred             eEEEeCCCCcHHHHHHHHH
Confidence            4578999999998666554

>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=85.30  E-value=0.37  Score=45.18  Aligned_cols=24  Identities=29%  Similarity=0.445  Sum_probs=21.5

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +-.|.|-|+-|+||||+++.+.+.
T Consensus         6 ~~rI~iEG~iGsGKSTl~~~L~~~   29 (333)
T d1p6xa_           6 IVRIYLDGVYGIGKSTTGRVMASA   29 (333)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHSG
T ss_pred             eEEEEEECCccCCHHHHHHHHHHH
Confidence            557889999999999999999984

>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=84.85  E-value=0.32  Score=41.69  Aligned_cols=37  Identities=19%  Similarity=0.280  Sum_probs=29.0

Q ss_pred             hHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          174 EKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       174 e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      -+..+..+|..         .+.-..+.|+|+++.|||.+|..+.+
T Consensus        39 Fl~~l~~~l~~---------~PKkn~i~~~GP~~TGKS~f~~sl~~   75 (205)
T d1tuea_          39 FLGALKSFLKG---------TPKKNCLVFCGPANTGKSYFGMSFIH   75 (205)
T ss_dssp             HHHHHHHHHHT---------CTTCSEEEEESCGGGCHHHHHHHHHH
T ss_pred             HHHHHHHHHcC---------CCCceEEEEECCCCccHHHHHHHHHH
Confidence            34566667753         24568999999999999999988876

>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=84.75  E-value=6.4  Score=33.33  Aligned_cols=40  Identities=23%  Similarity=0.219  Sum_probs=28.6

Q ss_pred             ccccchhhHHHHHHHhhCCCCCCcCCCCCCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          167 EFHGRNAEKQKILQLLKGESSDEESGSKPTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       167 ~~vGR~~e~~~l~~~L~~~~~~~~~~~~~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .+-=|+...+.+..++..             ....|.++.|.|||.+|..+..
T Consensus        68 ~~~Lr~yQ~eav~~~~~~-------------~~~ll~~~tG~GKT~~a~~~~~  107 (206)
T d2fz4a1          68 EISLRDYQEKALERWLVD-------------KRGCIVLPTGSGKTHVAMAAIN  107 (206)
T ss_dssp             CCCCCHHHHHHHHHHTTT-------------SEEEEEESSSTTHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHHHHhC-------------CCcEEEeCCCCCceehHHhHHH
Confidence            344577787777776641             2335778999999998887765

>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=84.60  E-value=0.21  Score=45.54  Aligned_cols=24  Identities=25%  Similarity=0.254  Sum_probs=21.6

Q ss_pred             CccEEEEEcCCCCcHHHHHHHHhC
Q 041007          196 TLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       196 ~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +.|-|+|+|.+|.|||||+..+..
T Consensus         5 ~iRni~i~gh~~~GKTtL~e~ll~   28 (276)
T d2bv3a2           5 RLRNIGIAAHIDAGKTTTTERILY   28 (276)
T ss_dssp             GEEEEEEEECTTSCHHHHHHHHHH
T ss_pred             hceEEEEEeCCCCCHHHHHHHHHH
Confidence            578899999999999999998864

>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=84.58  E-value=0.08  Score=43.93  Aligned_cols=20  Identities=25%  Similarity=0.644  Sum_probs=18.4

Q ss_pred             EEEEcCCCCcHHHHHHHHhC
Q 041007          200 IWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       200 v~I~G~gGiGKTtLA~~v~~  219 (597)
                      |+|.|.+|+|||||...+..
T Consensus         3 I~liG~~n~GKSSLin~l~g   22 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLN   22 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999864

>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=84.23  E-value=0.15  Score=45.10  Aligned_cols=23  Identities=22%  Similarity=0.447  Sum_probs=19.6

Q ss_pred             cEEEEEcCCCCcHHHHHHHHhCC
Q 041007          198 PVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       198 ~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      +..++.|.+|+|||||...+..+
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-
T ss_pred             ceEEEECCCCccHHHHHHhhccH
Confidence            46678999999999999999874

>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=82.54  E-value=0.38  Score=42.48  Aligned_cols=23  Identities=30%  Similarity=0.521  Sum_probs=20.2

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhC
Q 041007          197 LPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      .++|+|.|-+++|||||+..+..
T Consensus         5 ~p~IaIiGh~d~GKSTL~~~L~~   27 (227)
T d1g7sa4           5 SPIVSVLGHVDHGKTTLLDHIRG   27 (227)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccHHHHHHHHHh
Confidence            36799999999999999988854

>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=82.37  E-value=0.32  Score=44.14  Aligned_cols=22  Identities=27%  Similarity=0.608  Sum_probs=19.7

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHh
Q 041007          197 LPVIWILGNEGIGKTALARQVF  218 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~  218 (597)
                      .|.|+|.|..|.|||||+..+.
T Consensus         2 iRNv~iiGh~~~GKTtL~e~ll   23 (267)
T d2dy1a2           2 IRTVALVGHAGSGKTTLTEALL   23 (267)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHH
T ss_pred             eeEEEEEcCCCCcHHHHHHHHH
Confidence            3689999999999999999874

>d1e2ka_ c.37.1.1 (A:) Thymidine kinase {Herpes simplex virus type 1, different strains [TaxId: 10298]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Herpes simplex virus type 1, different strains [TaxId: 10298]

Probab=82.03  E-value=0.27  Score=46.03  Aligned_cols=24  Identities=29%  Similarity=0.443  Sum_probs=20.6

Q ss_pred             ccEEEEEcCCCCcHHHHHHHHhCC
Q 041007          197 LPVIWILGNEGIGKTALARQVFDD  220 (597)
Q Consensus       197 ~~vv~I~G~gGiGKTtLA~~v~~~  220 (597)
                      ...|.|-|.-|+||||+++.+.+.
T Consensus         4 ~lrI~IEG~iGsGKTTl~~~La~~   27 (329)
T d1e2ka_           4 LLRVYIDGPHGMGKTTTTQLLVAL   27 (329)
T ss_dssp             EEEEEECSCTTSSHHHHHHHHTC-
T ss_pred             ceEEEEECCcCCCHHHHHHHHHHH
Confidence            456899999999999999999873

>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=80.23  E-value=0.92  Score=40.95  Aligned_cols=25  Identities=28%  Similarity=0.547  Sum_probs=22.0

Q ss_pred             CCccEEEEEcCCCCcHHHHHHHHhC
Q 041007          195 PTLPVIWILGNEGIGKTALARQVFD  219 (597)
Q Consensus       195 ~~~~vv~I~G~gGiGKTtLA~~v~~  219 (597)
                      +....+.++|+|+.|||+++..+.+
T Consensus       102 ~k~n~~~l~G~~~tGKS~f~~~i~~  126 (267)
T d1u0ja_         102 GKRNTIWLFGPATTGKTNIAEAIAH  126 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHH
T ss_pred             CccEEEEEEcCCCCCHHHHHHHHHH
Confidence            3567999999999999999988876

>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=80.08  E-value=0.36  Score=44.51  Aligned_cols=17  Identities=29%  Similarity=0.427  Sum_probs=13.8

Q ss_pred             EEEEEcCCCCcHHHHHH
Q 041007          199 VIWILGNEGIGKTALAR  215 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~  215 (597)
                      .+.|.|.+|+||||.+.
T Consensus        16 ~~lI~g~aGTGKTt~l~   32 (306)
T d1uaaa1          16 PCLVLAGAGSGKTRVIT   32 (306)
T ss_dssp             EEEECCCTTSCHHHHHH
T ss_pred             CEEEEeeCCccHHHHHH
Confidence            46788999999997643

>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=80.03  E-value=0.38  Score=44.72  Aligned_cols=18  Identities=28%  Similarity=0.484  Sum_probs=14.3

Q ss_pred             EEEEEcCCCCcHHHHHHH
Q 041007          199 VIWILGNEGIGKTALARQ  216 (597)
Q Consensus       199 vv~I~G~gGiGKTtLA~~  216 (597)
                      .+.|.|.+|+||||.+.+
T Consensus        26 ~~lV~g~aGSGKTt~l~~   43 (318)
T d1pjra1          26 PLLIMAGAGSGKTRVLTH   43 (318)
T ss_dssp             CEEEEECTTSCHHHHHHH
T ss_pred             CEEEEecCCccHHHHHHH
Confidence            367889999999976543